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Chemical

Thinking
Volume I

University of Arizona
Chemical Thinking

Preface
The chemical thinking curriculum introduces an alternative way of conceptualizing the introduc-
tory chemistry curriculum for science and engineering majors. The curriculum has been designed
with the following goals in mind:

• Present chemistry as a powerful way of thinking rather than as a static body of knowledge
• Use essential questions in the discipline to guide the presentation and discussion of relevant
content
• Emphasize conceptual understanding of core concepts and ideas in chemistry
• Build student understanding through carefully designed learning progressions based on exist-
ing research in chemistry education
• Offer many opportunities for students to engage with core concepts and ideas through activi-
ties that ask them to analyze data, model chemical systems, and generate evidence-based
explanations
• Create opportunities for students to demonstrate and self-assess their understanding via the
application of their knowledge and skills in solving relevant integrated problems
• Engage students in thinking about important issues in four critical areas of interest for the
science and technology of the 21st century: energy sources, environmental issues, life and
medicine, and materials by design
• Take advantage of diverse educational tools that allow students to explore chemical ideas and
phenomena in interactive ways

The chemical thinking curriculum has been developed, tested, and implemented at the University
of Arizona. We thank all the students, instructors, and educational staff that had made it possible.
The project was initially funded by the National Science Foundation (DUE-0736844).

Vicente Talanquer
John Pollard
Chemical Thinking I

Contents
U1. How do we distinguish substances? 2
M1. Searching for differences................................................................4
M2. Modeling matter...........................................................................18
M3. Analyzing particles........................................................................36
M4. Determining composition.............................................................58

U2. How do we determine structure? 82


M1. Analyzing light-matter interactions..............................................84
M2. Looking for patterns....................................................................100
M3. Predicting geometry...................................................................124
M4. Inferring charge distribution......................................................144

U3. How do we predict properties? 166


M1. Analyzing molecular structure...................................................168
M2. Considering different scales.......................................................190
M3. Characterizing ionic networks....................................................202

U4. How do we characterize chemical processes? 228


M1. Modeling chemical reactions.....................................................230
M2. Understanding proportions........................................................246
M3. Tracking energy...........................................................................260

1
UNIT 1
How do we
distinguish
substances?
Our world is characterized by its diversity at all levels,
from the wide variety of living organisms to the multi-
tude of materials present in everything that surrounds
us. Understanding the diversity of the material world
has been particularly important for the survival of hu-
mans on Earth. The ability to detect, identify, separate,
and quantify different types of substances has allowed
us to take advantage of the many natural resources that
our planet has to offer. These same abilities are also
likely to help us save Earth from the environmental
consequences of our decisions and actions.

The central goal of this Unit is to help you under-


stand and apply basic ideas and ways of thinking
to distinguish the different substances present in a
variety of systems of interest. Although the ideas and
models that we will discuss are useful in many relevant
contexts, to illustrate their power we will analyze many
examples related to our Earth’s atmosphere, trying to
answer questions such as:

What is it made of?


How do we separate its components?
How do we identify them?
How do we explain their properties? Blue Marble
How do we model their behavior? NASA

2
Chemical Thinking

UNIT 1 MODULES

M1. Searching for Differences


Identifying differences that allow us to
separate components.
M2. Modeling Matter
Using the particulate model of matter to
explain differences.
M3. Analyzing Particles
Analyzing differences in particle compo-
sition and mass.
M4. Determining Composition
Characterizing differences in particle
composition.

3
4

Searching for
Differences
Most things in our surroundings are complex systems composed of many sub-
U1: MODULE 1
stances in different states of matter. For example, the air we breathe contains at
least a dozen different substances, from oxygen gas to microscopic water droplets
to solid sodium chloride particles. This chemical complexity may be a blessing or
a curse. On the one hand, this diversity of substances and phases has allowed the
emergence of life on Earth and the development of the rich
natural resources that sustain it. On the other hand, the
large number of substances found in a single breath
makes it difficult to detect, identify, and isolate the
things that can threaten that same life.
The large number of substances present in our
own bodies, and in most of the systems with which
we interact on a daily basis, poses a constant chal-
lenge to many professionals. How do we detect the
presence of cholesterol in a complex mixture, such as
Earth’s
blood? How do we identify the pollutants that may be Atmosphere
present in drinking water? How do we know what substances are NASA
in the soil or in the minerals that are extracted from the ground? The answers to
these questions require some “chemical thinking,” as illustrated in the following
challenge.

THE CHALLENGE Extracting Oxygen


Imagine that you were interested in separating pure oxygen from the atmo-
sphere for commercial purposes. You may want to sell it to hospitals for using
in the treatment of pneumonia, emphysema, and other respiratory diseases.

• How would you separate oxygen from other air components?


• What properties of this substance would help you separate it?

Make a list of potential strategies that you would follow to solve this problem.
Then, share and discuss your ideas with one of your classmates.

Module 1 will help you develop the type of chemical reasoning that is used to
answer questions similar to those posed in the challenge. In particular, the central
goal of Module 1 is to help you recognize distinctive properties of chemical sub-
stances that can be used to identify and separate them.
Chemical Thinking U1 How do we distinguish substances? 5

Differentiating Characteristics
In modern times, many people are interested in finding out the chemical composi-
tion of a variety of things in their surroundings. Everybody now expects food labels

http://www.chem.arizona.edu/tpp/chemthink/resources/U1_M1/Ozone.html
Total Ozone
to list the contents of what they eat. Many cities around the world monitor the
presence of well known atmospheric pollutants on a regular basis. Artificial satel- Low High
lites detect and quantify the amounts of important
substances in our atmosphere, such as ozone (see
Figure 1.1) and carbon dioxide, every day. The abil-
ity to detect or identify all the substances present
in a given system is an extraordinary achievement

CLICK TO PLAY
of human kind. Most of the systems we encounter,
natural or artificial, are mixtures of many different
substances. Many of these mixtures are homoge-
neous: combinations of substances that have uni-
form composition and properties and may look like
single substances, such as clean air and drinking wa-
ter. Other mixtures are heterogeneous and they are
composed of visibly different substances that can be
in the same or in different phases (e.g., solid, liquid, or gas), as is the case of many Figure 1.1 NASA has developed
and launched in space instruments
minerals on Earth and our own body. The composition and properties of some sys- that allow constant monitoring of
the amount of ozone in the strato-
tems remain constant for long periods of time, but in other situations they change sphere. Click on the image to see
how ozone amounts vary during
on a regular basis. Given the diversity of the materials in our world, how can we the year over Antarctica.
determine their chemical composition?
The chemical analysis of the substances present in any given system is
based on a simple assumption made by chemists about the nature of the world:
Each substance, no matter how simple or complex, has at least one differentiating
characteristic that makes it unique. If we find this differentiating property and are
able to measure it, we will be in a good position to detect, identify, separate, and
quantify the amount of that substance in a variety of places and circumstances.

Choosing Properties LET’S THINK

Air is a mixture of many substances, including nitrogen, oxygen, carbon diox-


ide, argon, and water. Which of the following properties of substances would
be good “differentiating characteristics” to separate each component?

Temperature Mass Viscosity


Boiling Point Density Volume
Pressure Solubility Concentration

Share your ideas with one or more classmates. Make sure to:
• Identify the basic features that you think a good differentiating charac-
teristic should have.
• Discuss why some properties in this list are not good differentiating
characteristics.
6 MODULE 1 Searching for Differences

Good differentiating characteristics are properties that do not depend on the


amount of substance that we have (intensive properties). These are properties
such as melting point, density, and conductivity. Properties that depend on the
amount of substance (extensive properties), such as mass and volume, are not
differentiating characteristics because they can take many values for the same sub-
stance or similar values for different ones. Being an intensive property, however,
is not good enough for purposes of identification. Temperature and pressure are
intensive properties of a system, but they cannot be used as differentiating charac-
teristics for any substance because they are properties of the entire system, and not
of its individual components. Good differentiating characteristics are properties
with unique values for each substance, that do not vary with the size of the sample,
and that can be selectively measured.
For example, the boiling points of the different components
of the air in the atmosphere are very useful differentiating char-
Table 1.1 Air Main Components
acteristics to separate them. The boiling point is the temperature
Boiling Temperatures ( 1 atm) at which a substance transforms from liquid to gas at a given
Substance pressure and, in general, takes values that vary from substance
o
C K
to substance. The boiling temperature also corresponds to the
Water 100 373.15
temperature at which the gas turns into a liquid. As a result, if
Oxygen -182.9 90.20 we were to cool down an air sample at sea level, we would see
Argon -189.3 87.36 the different air components condensing at the temperatures
Nitrogen -195.8 77.36 shown in Table 1.1, which are the boiling temperatures at at-
mospheric pressure at sea level (normal boiling points). This
information can be used to identify the substance that is condensing and separate
it from the mixture.

USEFUL TOOLS transformed into degrees Kelvin using the


following relationship:
The differentiating characteristics of chemi-
cal substances are conventionally mea- [K] = [oC] + 273.15
sured at constant atmospheric tempera-
ture and pressure. These quantities can Thus, for example, the boiling point of wa-
be expressed in a variety of units that you ter (= 100 oC) corresponds to
must recognize and be able to manipulate.
[K] = 100 oC + 273.15 = 373.15 K
Units of Temperature. In the International
System of Units (SI), temperature is mea- Units of Pressure. In the SI, pressure is mea-
sured using the Kelvin scale. This is an ab- sured using units called Pascals (Pa). One
solute temperature scale in which the zero pascal is equivalent to a pressure of one
of the scale (0 K) corresponds to the low- newton per square meter (1 N/m2). In sci-
est temperature that can be theoretically ence and engineering it is also common to
achieved. Increments in temperature are use the standard atmosphere (atm) as unit
measured in Kelvins (K). of pressure, where 1 atm is approximately
Another temperature scale used in sci- equal to the average atmospheric pressure
ence and engineering is the Celsius scale. In at sea level in our planet. Another common
this system, the zero of the scale is defined unit is “millimeters of mercury” (mm Hg or
as the freezing point of water (0 oC) and Torr). Conversions between these different
100 oC corresponds to the boiling tempera- units can be performed using the following
ture of the same substance. A temperature conversion factors:
measurement in degrees Celsius can be
1 atm = 101, 325 Pa = 760 mm Hg
Chemical Thinking U1 How do we distinguish substances? 7

Phase Transitions

The transformation of a pure substance from one phase to another at constant


pressure occurs at a well defined temperature that can be used as differentiating
characteristic. During this phase transition, or phase change, the chemical nature
of the substance is preserved and the transition temperature can be measured with
great accuracy and precision using digital devices. Understanding phase behavior
is crucial for designing successful strategies to identify and separate many sub-
stances of interest. For example, extracting oxygen from air, caffeine from coffee
beans, and medicines from plants.

Changing Phases LET’S THINK

It is almost certain that you have seen ice melting and liquid water boiling. Imag-
ine that you had a sample of solid water at -20 oC at atmospheric pressure and
you heated it up supplying energy at a constant rate until the temperature reached
120 oC. If during the experiment you were to measure the temperature (T) of the
sample as a function of time (t), as well as the amount of energy absorbed by the
system during the heating process (DE), what would you expect to see if you were
to plot the data using the following types of graphs?

T(oC) DE

100

By Mysid (Own work) [CCA: Public domain] via Wikimedia Commons


0

t 0 100 T(oC)
Based on your prior knowledge and experience:

• Predict how temperature will change as a function of time. Keep in mind


that solid water turns into a liquid at 0 oC and that the liquid becomes a gas
at 100 oC.
• Predict how the total amount of energy absorbed by the system (DE) will
change as the temperature (T) of the system increases. Consider whether How does the temperature of
the system change as
more, or less, energy will be required to change the sample from solid to water ice melts?
liquid than from liquid to gas (HINT: DE = 0 at the t = 0; DE > 0 when the
system absorbs energy; DE < 0 when the system releases energy).
• Compare your predictions with those of another classmate. Discuss how
your predictions would change if you were cooling down a gas sample or
you were working with a different substance.

Share your ideas with a classmate and clearly justify your reasoning.
8 MODULE 1 Searching for Differences

Phase transitions between two different states of matter share many similari-
T(oC)
ties independently of the chemical nature of the system of interest. For example,
Vapor cools
during a change of state at constant pressure the temperature of the system re-
mains constant until one of the phases has been fully transformed into the other.
and condenses
Tb The transition points define the range of temperatures within which each phase is
Liquid cools
stable at any given pressure. In the case of water, the liquid phase is stable between
0 oC (solid-liquid) and 100 oC (liquid-gas) at 1 atm of pressure. Within these two
and solidifies points, adding energy to the system will result in increasing temperature; remov-
Tm
Solid cools
ing energy from the system will cause the temperature to decrease. However, at the
phase transition, the energy added or removed induces a change of state without
t altering the actual temperature of the system as shown in Figure 1.2.
Some changes of state require the addi-
Figure 1.2 Cooling curve for a Common
generic substance that under- tion of energy, as is the case of the transitions Phase

By Flanker, penubag (Own work) [CCA: Public domain]


goes two phase transitions, from from solid to liquid (melting), liquid to gas Changes
gas to liquid at Tb and from liquid
to solid at Tm. (boiling), and from solid to gas (sublima-

via Wikimedia Commons


tion). The reverse processes (solidification,
condensation, and deposition, respectively)
release energy that needs to be removed
from the system if we want the phase transi-
tion to occur. As shown in Figure 1.3, these
Tm Tb T(oC) energy changes occur at constant tempera-
G ture and the amount of energy absorbed or
released varies from substance to substance.
In fact, the energy per unit of mass exchanged during a phase transition is also a
L differentiating characteristic of the material. In general, the larger the change in
density induced by the phase transition, the larger the energy transfer.
During a phase transition many of the physical properties of the substance
S
DE change. Some of these changes can be quite large, as illustrated by the drastic
decrease in density in the transition from liquid to gas. A phase transition is a pro-
Figure 1.3 Amount of energy totypical example of a physical change in which the transformation does not alter
released (DE) as a function of the chemical nature of the substance involved. In some cases, adding or removing
temperature (T) during cooling of
a generic substance that under- energy from the system could cause the substance to chemically decompose or to
goes two phase transitions, from
gas to liquid at Tb and from liquid react with other substances before the phase change occurs. In these cases, it is not
to solid at Tm. possible to use phase behavior as a differentiating characteristic for the substance
of interest.

USEFUL TOOLS gy invested in applying a force of one new-


ton (1 N) through a distance of one meter
Adding energy to a system or removing (1 m).
energy from it are common strategies to
change its properties. Being able to mea- Another commonly used unit of energy is
sure or indirectly determine the amount of the calorie (cal). One calorie (1 cal) is ap-
energy that is exchanged is critical to con- proximately equal to the amount of energy
trol the change. In science and engineering, needed to increase the temperature of one
energy is commonly measured using the gram (1 g) of water by 1 oC. Energy mea-
following units: sured in calories can be transformed into
joules using the following conversion factor:
Units of Energy. In the International System
of Units (SI), energy is measured in joules 1 cal = 4.184 J
(J). One joule (1 J) is equivalent to the ener-
Chemical Thinking U1 How do we distinguish substances? 9

Phase Diagrams

The temperatures at which a substance undergoes a phase transition depend on the


value of the external pressure. This means that the range
of temperatures in which each phase is stable changes
with pressure. For example, liquid water is stable between
0 oC and 100 oC at 1 atm of pressure but if the pressure is
increased to 50 atm, melting will now occur at -0.37 oC
while boiling will take place at 262.5 oC. In this case, in-
creasing the pressure widens the range of temperatures in
which liquid water is stable. By carefully measuring the
temperatures at which a phase transition occurs at dif-
ferent pressures one can build a graphical representation
that depicts the zones of stability for each phase and their
Figure 1.4 Phase diagram for
corresponding boundaries (the temperatures and pressures at which a transition a generic substance. The letters
to another phase will occur). These graphical representations of phase change and show the phase that is stable at
that particular temperature (T)
stability are called phase diagrams (see Figure 1.4) and each substance will have a and pressure (P): Gas (G), liquid
(L), or solid(L). The solid lines
characteristic phase diagram. show the T and P values at which
a phase transition will occur.

The Case of Water LET’S THINK

The following tables include experimental information about the tempera-


tures at which water undergoes a phase transition at different pressures.

Liquid-Gas Liquid-Solid Solid-Gas


T P T P T P
(K) (mm Hg) (K) (mm Hg) (K) (mm Hg)
273.16 4.58 273.16 4.58 248.15 0.475
324.77 100 273.16 100 253.15 0.774
339.65 200 273.15 200 258.15 1.24

http://www.chem.arizona.edu/tpp/chemthink/resources/U1_M1/graph.html
356.15 400 273.15 400 263.15 1.95
366.68 600 273.15 600 268.15 3.01
374.58 800 273.15 800 273.16 4.58

• Each of these tables includes data that can be used to build the three
main boundaries in the phase diagram for water. Click
CLICK TO PLAY

on the image to launch a graphing tool and use it to


build the phase diagram in the range from 240 K to
380 K and from 0 to 800 mm Hg.
• Show on the diagram the areas in which the solid, liq-
uid, and gas phases are stable.
• Estimate the boiling point of water in Tucson, Arizona where the atmo-
spheric pressure is close to 700 mm Hg.
• Discuss with one of your classmates whether any of the phase transi-
tions in the diagram may be induced by changing the pressure at con-
stant temperature.
10 MODULE 1 Searching for Differences

In a pressure-temperature phase diagram like that shown in Figure 1.5, the


transition lines do not only define the specific temperature (T) and pressure (P) at
which a phase change occurs but they also specify the conditions under which the
two phases can simultaneously exist as stable phases.
Supercritical
Fluid
It is common to say that the two phases coexist or are
Liquid in equilibrium with each other under such conditions.
Solid Consequently, three different phases can coexist with
PRESSURE

Critical
Point each other at the temperature and pressure that cor-
responds to the point in which two phase transition
lines intersect. This particular state is called a triple
Gas
point. For water, for example, the solid-liquid-gas
Triple triple point occurs at 0.01 oC and 4.58 mm Hg. The
Point temperature and pressure at the triple point have spe-
cific values for every substance and thus they can be
used as differentiating characteristics.
TEMPERATURE
The phase transition between the solid and the liq-
uid phase, or between the solid and the gas phase of a pure substance always leads
Figure 1.5 Pressure-tempera-
ture phase diagram for a generic to an abrupt density change as the phase change occurs. However, the transition
substance showing the location between the liquid and gas phases exhibits a different behavior. The liquid and the
of the different phase transi-
tions, the triple point, and the gas have sharply different densities at low temperatures and pressures but the two
critical point.
phases become more alike as temperature and pressure increase. At certain values
of T and P, characteristic for every substance, both phases become identical and
the possibility of observing an actual phase change disappears beyond this critical
point (see Fig. 1.5). At temperatures and pressures higher than the critical point,
the gas and liquid phases are indistinguishable from each other and the substance
is said to exist as a supercritical fluid.

LET’S THINK Comparing Phase Behavior



Consider the pressure-temperature phase diagrams for water and carbon dioxide:

218
73
Water
Liquid Liquid
P (atm)

P (atm)

10 Solid
Solid Gas
1.0 5.2

0.00603 Gas 5
1.0
Carbon
Dioxide

0.01 100 374 -78 -57 0 31


T (oC) T (oC)

• Identify the stable phase of each substance at 1 atm and 40 oC.


• List the phase changes that this stable phase may undergo by increasing or decreasing
a) the temperature and b) the pressure. Estimate the temperatures and pressures at which
these phase changes will take place.
• Analyze what particular features of each of the phase diagram are responsible for such differ-
ent phase behaviors.
Chemical Thinking U1 How do we distinguish substances? 11

The liquid-gas transition line in a pressure-temperature phase diagram is also


called the vapor pressure curve. At any given temperature, a liquid enclosed in a
sealed container evaporates to a certain extent producing vapor that 1000
exerts pressure on its surroundings. The higher the temperature, the
higher the rate of evaporation and the larger the pressure exerted by A B C
800
the vapor (or vapor pressure). Boiling occurs when the vapor pres-
sure of a liquid becomes equal to the external pressure acting on the

P (mm Hg)
fluid as the gas can then freely escape. The liquid-gas transition line 600
thus traces the value of the vapor pressure of the liquid at different
temperatures. Liquids that are more volatile (evaporate more eas-
400
ily) have higher vapor pressures than less volatile fluids at any given
temperature (see Figure 1.6). Consequently, volatile liquids have
lower boiling points as their vapor pressures become equal to the 200
external pressure at lower temperatures. The comparison of vapor
pressure curves for different substances is very useful in the process 280 300 320 340 360 380
of separating mixtures in gaseous or liquid states as it helps predict T (K)
the order in which different substances will separate.
Figure 1.6 Vapor pressure
curves for A) Methanol B) Etha-
Separations nol, and C) Water. A is more
volatile than B; B is more volatile
than C.
Now that we have a better understanding of the general phase behavior of pure
substances, we can use our knowledge to analyze and discuss how important sepa-
ration techniques are used in chemical analysis. Not all separation techniques rely
on phase properties or phase behavior to separate substances, but some of the most
commonly used strategies do. Among them we find: Filtration, crystallization,
and distillation.

Filtration: This technique is based on the mechanical separa-


tion of substances in the solid state from substances in a fluid

By Ahanix1989 (Own work) [CCA: Public


phase (liquid or gas) by using a physical barrier which only the

domain] via Wikimedia Commons


fluid can pass. The separation of the two types of phases is never
complete as some solid will pass through the filter and some
fluid will be attached to the solid material. The efficiency of the
separation will largely depend on the filter’s thickness and pore
size. Air filters are commonly used to improve air quality in
house, building, and car engine and ventilation systems.
Car Air Filter

Crystallization: In this strategy, the formation of a solid phase is induced


by changing the temperature or the concentration of the com-
ponents in a fluid (liquid or gas) mixture, or by adding other
substances. In a mixture of substances, these changes affect the
solubility of one substance in the other and the components are
likely to separate. The solid phase that is formed tends to be a
pure crystalline material. Crystallization is commonly used in
processes such as the extraction of common salt from sea wa-
ter and the production of pure silicon for computer chips and
Insulin Crystals, by NASA/Marshall other electronic devices.
12 MODULE 1 Searching for Differences

Distillation: This technique is used to separate substances in a liquid mixture tak-


ing advantage of differences in the boiling points of the various components. The
method involves a phase change from liquid to gas and subsequent reconversion
of the separated substances to the liquid phase. In a simple distillation,
By John Kershaw (Derivative: Thresa Knott) [CCA: Share Alike 3.0] via Wikimedia Commons

the liquid mixture is heated up in a flask. When the boiling point of


the most volatile component is approached, the mixture boils and
the temperature remains relatively constant until most of the volatile
substance becomes a vapor. The vapor produced can be directed to
a condenser where it cools down and transforms back into a liquid
that can be collected. By continuously heating the liquid mixture, the
same process can be repeated until all components are separated.
Separation by distillation is never perfect and it is common to
redistill the different portions or fractions of liquid that are collected.
To improve the separation, particularly for substances with similar
boiling points, one may use fractional distillation (see Figure 1.7). In
this case, the evaporating fluid passes through a vertical column with
trays or plates placed at different heights. The temperature decreases
gradually from the bottom to the top of the column and substances
condense on different plates depending on their boiling points: the
Figure 1.7 Main components of most volatile substances will condense at lower temperatures and will
a fractional distillation apparatus. be found towards the top of the column; the least volatile substances will condense
on the bottom plates.

LET’S THINK Distilled Spirits

Hard liquors or spirits, such as brandy, whisky, and tequila, are commonly
produced by fermentation of carbohydrate-rich natural products. In the pro-
cess, a mixture containing water (C), ethanol (B), methanol (A), and many
other components is generated. Methanol needs to be removed because of its
toxic properties; water is extracted to produce beverages with various concen-
trations of ethanol.

• What would you expect


1000
to happen as you heat up
the alcoholic mixture?
In which order will the A B C
800
three main substances
separate? At which
P (mm Hg)

600
temperatures will each
fraction distill?
400
• Based on the vapor
pressure curves, would
you see any advantage in 200
changing the pressure at
which the distillation is 280 300 320 340 360 380
T (K)
performed? Why?
Chemical Thinking U1 How do we distinguish substances? 13

FACING THE CHALLENGE condense. The liquefied air is then heated up and
distilled in one or two different distillation col-
umns, depending on the desired products.
Separating Air More than half of the oxygen extracted from
air by cryogenic distillation is used to produce steel.
The concepts, ideas, and ways of thinking intro- The rest is consumed for
duced in this module can be applied to the chemi-

By Deglr6328 (Own Work) [CCA: Share Alike 3.0]


medical applications,
cal analysis of a variety of systems, from the atmo- water treatment, and to
sphere in our planet to the oil spilled in the Gulf

via Wikimedia Commons


power rocket fuels. On
of Mexico in 2010. For example, let us go back to the other hand, the ar-
our original challenge: the separation of substances gon that is produced in
present in the air we breathe. the process is used to fill
The separation of air components can be use- incandescent lights, cre-
ful for a variety of reasons. We may want, for ex- ate inert atmospheres
ample, to know the proportion in which different to avoid undesirable
substances are present in the air. Or we may be in- chemical reactions, and Solid Argon Melting
terested in eliminating atmospheric pollutants. We in cryosurgery (application of extreme cold to
could also be interested in “mining” air; this means eliminate diseased tissue) to destroy cancer cells.
to extract from air substances that have commer- Nitrogen also has important industrial appli-
cial value. In fact, air is the main source of nitro- cations, such as in the creation of safe atmospheres
gen, oxygen, and inert gases such as argon used in fuel systems in military aircraft or on top of liq-
for industrial or medical purposes. These three uid explosives. The gas is also used to create modi-
substances are the main components of Earth’s at- fied atmospheres to preserve packaged food. One
mosphere: of the main uses of the nitrogen extracted from air
is in the synthesis of ammonia, one of the most
Air Components highly-produced substances in the world because
Substance % Volume Tb (oC) of its central role in the production of fertilizers
and explosives.
Nitrogen 78.084 -195.79
Liquid nitrogen is also widely used in cryogen-
Oxygen 20.957 -182.95 ics, the study and production of very low tempera-
Argon 0.934 -185.85 tures (lower than -150 oC) and the investigation of
the properties of materials under such conditions.
These air components are actually separated Some substances acquire surprising properties at
using a technique called cryogenic air distillation. very low temperatures, such as losing all electrical
How does this work? Well, the first step is to fil- resistivity and becoming superconducting materi-
ter the air to eliminate solid als. Superconductors are
particles and then compress used to produce magnets
it to pressures between 5 to that generate strong mag-
10 atm. The mixture is then netic fields, such as those
passed through another fil- required for Magnetic Res-
tering system that allows the onance Imaging (MRI).
removal of water and car- This noninvasive medical
bon dioxide. The processed imaging technique allows
air is then cooled down to doctors to visualize inter-
temperatures as low as -200 nal structures and func-
o
C (73 K), conditions under tions in our bodies.
which all main components Air Distillation Column
By photographer- Company (Own Work) [CCA: Share Alike 3.0] via Wikimedia Commons
14 MODULE 1 Searching for Differences

Let’s Apply
Investigating Other Planets
The analysis of the atmosphere of other planets in our Solar System is of central importance for
understanding not only how our planet originated but for exploring the possibility of life beyond
Earth. The table below summarizes relevant information for the atmospheres of Venus, Earth, and
Mars:
ASSESS WHAT YOU KNOW

Venus Earth Mars


Distance from Sun in
0.723 1.00 1.50
Astronomical Units (AU)
Average Surface 460 oC (day) 20 oC (day) -5 oC (day)
Temperature 460 oC (night) 10 oC(night) -85 oC(night)
500 oC (highest ) 58 oC (highest) 27 oC (highest)
Extreme Temperatures
400 oC (lowest) -88 oC (lowest) -143 oC (lowest)
Air Density at
65 kg/m3 1.2 kg/m3 ~0.020 kg/m3
ground level
Atmospheric pressure
92 atm 1.0 atm 0.0059 atm
at ground level
78% Nitrogen 95.3% Carbon Dioxide
Atmosphere 96.5% Carbon Dioxide
21% Oxygen 2.7% Nitrogen
composition 3.5% Nitrogen
~1% Water 0.13% Oxygen
(Main components) 0.002% Water
0.035% Carbon Dioxide 0.03% Water

As you can see, the at-


mospheric conditions in
104
these three planets are very
different. Consequently, 103
the same substances may
exist in different states of 102
Pressure (atm)

matter from one planet to


another. The phase behav- 101
ior of every substance in a
given planet can be pre- 1.0
dicted using the respective CARBON
10-1
phase diagrams. In partic- DIOXIDE
ular, we include the phase 10-2
diagrams of water and car-
bon dioxide. Notice, that 10-3
-120 -80 -40 0 40 80
pressure in these diagrams
is represented using a loga- Temperature (oC)
rithmic scale.
Chemical Thinking U1 How do we distinguish substances? 15

1 MPa
WATER
Pressure 1 KPa

1 Pa

0 100 200 300 400 500 600 700 800 900 1000

ASSESS WHAT YOU KNOW


Temperature (K)

Your Predictions

Answer the following questions based


on the information provided and
your own knowledge of the phase
behavior of chemical substances.
Earth You may also need to do some ba-
NASA
sic research to find relevant phase
behavior data for other substances present Venus
in these planets. NASA

• What is the state of matter of water and carbon dioxide at day


and night in each of these three planets? Justify your answer by
showing on the phase diagrams the states of matter of the differ-
ent substances in each of the planets.
• Would it be possible to find solid carbon dioxide (dry ice) in
any of these three planets? Justify your answer.
• Would it be possible to find liquid nitrogen in any of these
planets? Justify your answer.
• The United States and Soviet Union have sent many spacecraft
to Venus. Some flew by the planet, some orbited around it, and
some descended through the atmosphere. Imagine that you
were able to get a sample of Venus’ atmosphere, how would you
propose to separate its main components? In which order would
Mars you be able to separate them? Write a detailed description of
NASA what you propose to do and what you would expect to happen
at each step of the separation process.
• Would it be possible to find a planet in which both water and
carbon dioxide exist in liquid form? If yes, what average tem-
perature and pressure would this planet have?
16 MODULE 1 Searching for Differences

Let’s Apply
Refining Petroleum
Crude oil or petroleum is a mixture of hundreds of substances, most of them made of hydrogen
and carbon (hydrocarbons). The mixture is a thick black liquid in
which different substances that are solid, liquid, and gases at room

By Luigi Chiesa (Own work) [CCA: 3.0 Generic] via Wikimedia Commons
temperature are present. In an oil refinery, crude oil is separated into
ASSESS WHAT YOU KNOW

“fractions” (mixtures that consist of compounds with similar boiling


points) by fractional distillation.
During the distillation process, crude oil is injected into a boiler
and heated. The vapor passes into a distillation column with a tem-
perature gradient, coolest at the top, hottest at the bottom. There are
plates or trays across the column with holes through which the rising
vapor passes through. Different substances condense in trays at differ-
ent temperatures according to their boiling points.
Imagine that you have to separate the components of different
samples of crude oil extracted from the ground. What strategies
would you follow? Let’s explore how well you can apply the concepts,
ideas, and ways of thinking introduced in this module.

Problem Mixture 1

A rich fuel mixture containing the 10.0


following hydrocarbons has been ex-
tracted from underground:
A B
Vapor Pressure (atm) [Log Scale]

A. Propane
B. Butane
C. Neo-Pentane C
D. 2-Heptene 1.0

The mixture is at an initial tempera-


ture of 5 oC. Based on the data pro- D
vided:

• Identify a differentiating char-


acteristic that you could use to 0.1
-30 -10 10 30 50 70
separate each of the components. Temperature (oC)
• Design a procedure to separate
each component. Describe the steps that you would follow and
the outcome of each step in the separation process.
Chemical Thinking U1 How do we distinguish substances? 17

Problem Mixture 2

The second mixture you have to separate contains the following components listed in order of
increasing melting (Tm) and boiling temperatures (Tb) at atmospheric pressure:

Substance Tm(oC) Tb (oC) Substance Tm(oC) Tb (oC)


Methane -182 -164 Pentadecane 10 271
Propane -188 -42 Hexadecane 18 287
Butane -138 -0.5 Heptadecane 21 302
Hexane -95 69 Nonadecane 33 330

ASSESS WHAT YOU KNOW


Heptane -91 98 Tricosane 49 380
Octane -57 126 Tetracosane 52 391
Nonane -53 151 Pentacosane 54 402
Dodecane -10 216 Tetracontane 81 524

Your task is to design a fractional distillation column to separate the following five fractions:

1. Liquid fuels less volatile than water that can be used to power vehicles at all temperatures
between the lowest (5 oC) and the highest (38 oC) By Tysto (Own work) [CCA: Public domain] via Wikimedia Commons
average temperatures in Tucson, Arizona (the fuel
should remain liquid in that range of tempera-
tures).
2. Gaseous fuels that can be used for cooking and
heating houses in Tucson.
3. Liquids with a higher volatility than water that
can be used as solvents in industries and labs.
4. Dense oils that can be used as lubricants in cars
and machinery (these substances may be solid or
liquid depending on the temperature in Tucson). Gasoline and diesel are most often produced by
fractional distillation
5. Solid paraffin waxes that can be used to make
candles in Tucson.
15 oC
Assume that the temperatures at the top and bottom of your column
are 15 oC and 360 oC, respectively.

• What is the minimum number of distillation plates or trays,


beyond the top and bottom exhausts, that are needed to complete
the separation?
• At what temperatures should each of these trays be placed to
ensure that the desired fractions separate?
• What substances will be mixed in each of the fractions extracted
from the column?
360 oC
18

Modeling
Matter
The assumption that every single substance in our surroundings has at least one
U1: MODULE 2
differentiating characteristic that makes it unique is at the base of chemical analy-
sis. What causes these differences? Why does water boil at 100 oC while oxygen
boils at -183 oC? Why is carbon dioxide a gas at room tem- Why are

Materialscientist(talk)) [CCA: Share Alike 3.0]


diamond and
perature while pure carbon is a solid under the same condi- graphite so
tions? To explain these differences, humans through history different if

By UIser:Itub (Derivative:
via Wikimedia Commons
both are made
have developed “models” of matter. In general, models are of carbon?
simplified representations of objects or processes built to
better describe, explain, predict, and even control their
properties and behavior. Some of these models may be
concrete, as the model of a bridge used by an engineer
to understand how the system responds to stress. Some models are
abstract, including entities that may be treated as tangible objects (e.g.,
force, energy) but actually represent abstract concepts or ideas that help us make
sense of properties and events.
Modeling substances and processes is at the core of chemical thinking. It is
through modeling that chemists have been able not only to analyze and explain
the diversity of the material word, but to design strategies to create new materials.
Many of the models used in chemistry are abstract and refer to entities that cannot
be seen by the naked eye. That sometimes makes chemical thinking challenging.
However, the explanatory and predictive power of those models is extraordinary.

THE CHALLENGE Clouds


The formation of clouds in the atmosphere is of critical importance to sustain
life on Earth. Clouds are necessary for precipitation to occur and help regulate
the energy absorbed and reflected by the planet. By Axel Rouvin (Own work)
via Wikimedia Commons

• How do you think clouds form?


[CCA: Public domain]

• Based on what you know, how would you “model”


the process of cloud formation in the atmosphere?

Share and discuss your ideas with one of your classmates.

Module 2 will help you develop the type of chemical reasoning that is used to
answer questions similar to those posed in the challenge. In particular, the central
goal of Module 2 is to help you understand and apply the particulate model of
matter to explain differences in the phase behavior and related physical prop-
erties of diverse substances in our world.
Chemical Thinking U1 How do we distinguish substances? 19

Particulate Model of Matter


The tasks of analyzing and synthesizing substances has been greatly simplified by
the development of models of their internal composition and structure. Since

By Heron (Own work) [CCA: Public domain]


ancient times, humans have proposed different models to explain and predict
the properties of matter. Aristotelians, for example, thought of all substances

via Wikimedia Commons


as composed of four elementary principles: water, fire, air, and earth
(Figure 1.8). It was thought that these “elements” gave a substance its
characteristic properties depending on the proportion in which they
were present. Other greek philosophers, like Leucippus and Democritus
thought of matter as made up of small indivisible particles called “atoms” mov-
ing around in empty space. In this model, differences in substance properties were
attributed to the existence of atoms with an infinite number of different shapes
and sizes that could move and arrange in diverse ways. Although our theories and
Figure 1.8 The four Aristotelian
models of matter have evolved considerably over the years, some core assumptions elements and their associated es-
sential properties.
about the composition and structure of the substances in our world are similar to
those of the ancient Greeks. For example, we still consider the existence of atoms
as essential components of matter although we model them in different ways.
During the 18h and 19th centuries, chemists and physicists accumulated
enough experimental evidence to support a model of matter that proposes that
all substances are composed of small particles in constant movement. This par-

http://www.cbc.arizona.edu/tpp/chemthink/resources/U1_M2/powersoften.html
ticulate model of matter has become one of the most powerful ideas of modern
science as it can be used to explain and predict the physical properties of many
materials. This model is based on the following fundamental assumptions:

Assumption 1. Any macroscopic sample of a substance is composed of an ex-


tremely large number of very small identical particles.
CLICK TO PLAY
In a first approximation, these “particles” may be thought of as very small
rigid objects. However, as discussed in the second part of this module, we
will need to assume that these particles have internal structure if we want
to better explain the physical and chemical properties of matter. The size of
the particles is assumed to be pretty small, of the order of one billionth of a
meter, or one nanometer (1 nm = 1 x 10-9 m), although the actual value will
vary from substance to substance. Thus, a macroscopic sample of any sub-
stance will be composed of trillions of billions of the same type of particles.
For example, one milliliter (1 mL) of liquid water contains approximately
3.35 x 1022 water particles. This number is similar to the estimated number
of stars in the entire Universe! Imagining the world at this small scale can be
difficult, but chemists have devised ways to simplify the challenge.

Relative Size LET’S THINK


Click on the image on this page to open an interactive image that illustrates the relative sizes of
different components of the human body, from a hand to a cell to a DNA molecule.

• Estimate how many times smaller is an atom in a DNA molecule than a human cell.
20 MODULE 2 Modeling Matter

The particles of matter are expected to be so small that they cannot be seen
by the naked eye or even using an optical microscope. That is why it is common
http://www.cbc.arizona.edu/tpp/chemthink/resources/U1_M2/partmodel1.html

CLICK TO PLAY to make references to the “submicroscopic world” when describing matter at the
particulate level or scale. Experimental results suggest that these particles also have
very small masses. For example, a single particle of the oxygen we breathe has a
mass close to 5.3 x 10-23 g. This is a billion billion times less massive than a tiny
speck of dust!

Assumption 2. Particles of matter are constantly moving in random directions


through empty space.

The particulate model of matter is also based on the ideas that the particles
that make up a substance are in constant random motion through void space (see
Figure 1.9 Representation of a Figure 1.9). It is this motion which allows us to explain, for example, why gases
gas using the particulate model
of matter. The sides of this square and liquids exert pressure on the walls of their containers. This pressure can be
should be assumed to be only a
few nanometers long. Click on seen as the result of the force per unit area exerted by particles of the fluid that
the image to open an animated
simulation collide with the particles of the container. The pressure depends on the number of
particles contained in a given volume; the larger the number of particles and the
smaller the volume, the grater the pressure. The pressure also depends on how fast
the particles are moving; the faster the particles move, the larger the pressure they
create. However, what determines the speed at which the particles are moving? In
the next activity you will explore the answer to this question.

USEFUL TOOLS Numbers larger than one can be written in sci-


The study of the properties of chemical sub- entific notation by increasing the exponent by
stances often requires the measurement of one for each place the decimal point is moved
quantities that can be very large or very small. to the left. For numbers smaller than one, the
To simplify the representation and manipula- exponent is decreased by one for each place
tion of these amounts it is common to use sci- the decimal point is moved to the right.
entific notation and multiple or submultiples of
standard measurement units. Multiples/Submultiples: In the International
System of Units (SI) prefixes are added to pro-
Scientific Notation: In this notation, numbers duce a multiple or a submultiple of the original
are represented as the product of a real num-
unit. All multiples and submultiples represent a
ber A and a power of ten:
power of ten. The following table summarizes
some of the most common prefixes used to ex-
A x 10n
press units in chemistry:
where the coefficient A is a number greater
than or equal to 1 and less than 10, and the Name hecto- kilo- mega- giga-
exponent n is an integer. Numbers greater than Larger Symbol h K M G
one have positive exponents; numbers smaller
than one have negative exponents. For exam- Factor 10 2
10 3
10 6
109
ple, the number 54000 is expressed in the fol-
lowing way: Name centi- milli- micro- nano-
Smaller Symbol c m m n
54000 = 5.4 x 10000 = 5.4 x 104
Factor 10 -2
10 -3
10 -6
10-9
The number 0.00054 is written as:
For example, the size of a water particle,
0.00054 = 5.4 x 0.0001 = 5.4 x 10 -4 0.00000000028 m, can be expressed as
0.28 nm (nanometer) using the nano prefix.
Chemical Thinking U1 How do we distinguish substances? 21

Particle’s speed LET’S THINK


Imagine that you had a sample of pure liquid water, water vapor, and water ice at this substance’s
triple point (273.16 K, 4.58 mm Hg). If you could measure the speed of the water particles at the
submicroscopic level:

• In which state of matter would you expect particles to have the lowest average speed? In
which phase would the average speed be greatest?
• Would you expect all of the particles in a given phase to be moving at the same speed?
• How would you expect the average speed of particles in the different phases to change when
the temperature is increased or decreased?

Share and discuss your ideas with one of your classmates, and clearly justify your predictions.

One of the most common difficulties in applying the particulate model of


matter to describe, explain, or predict the properties and behavior of a substance is
that we often project the macroscopic properties that we observe or measure to the
submicroscopic level. Thus, for example, people may think that particles in a solid
are moving at lower speeds than particles in a fluid because solids seem more static; T1
others may consider that particles in a solid only move when the actual object is T2

Fraction of Particles
T3
moving. We need to be careful with this type of thinking because the properties
that we measure in a macroscopic sample are often quite different from the proper-
ties of the individual particles that make up the system. T1< T2< T3
In the particulate model of matter, the average speed of particles depends on
two main variables: the temperature of the system (T) and the mass of the indi-
vidual particles (m). In particular, temperature is seen as a measure of the average
kinetic energy per particle (< Ek >) given by 0 250 500 1000 1250
v (m/s)

(1.1) < Ek > = 1/2 m < v >2 Figure 1.10 Distribution of par-
ticle speeds for the same sub-
stance at different temperatures.
where < v > represents the average particle speed. The higher the temperature,
the greater the average kinetic energy per particle in the system and the faster the
particles will move. Consequently, particles of the same substance in two different
coexisting phases at a certain temperature will have the same average kinetic en-
0.4

m1
ergy, and thus the same average particle speed independently of the state of matter
of the material.
Fraction of Particles
0.3

At any given temperature, individual particles that make up a substance move m1> m2> m3> m4
m2
at different speeds. Some particles move faster than others; many of them move at
0.2

speeds close to the average value. This is illustrated in Figure 1.10 where we show m3
the typical shape of the distribution of speeds for a generic gaseous substance at
0.1

m4
three different temperatures. As shown in this figure, as the temperature increases
the fraction of particles with low speeds decreases while the fraction of those with
high speeds increases. Substances made up of particles of different masses will v (m/s)
have different speed distributions at any given temperature (see Figure 1.11), but Figure 1.11 Distribution of parti-
their average kinetic energy will be the same. According to equation (1.1), lighter cle speeds for different substanc-
es at the same temperature.
particles should then have higher average speeds than heavier particles at any given
temperature.
22 MODULE 2 Modeling Matter

Assumption 3. Particles interact with each other and the strength of these
interactions depends on distance.

The existence of phase transitions between different states of matter can be ex-
plained if we assume that particles attract each other at relative long distances but
repel each other when they come into close proximity (Figure 1.12). Without
these interactions all substances would always exist in a single phase.

http://www.cbc.arizona.edu/tpp/chemthink/resources/U1_M2/partmodel2.html
LET’S THINK Phase Changes

The core assumptions of the particulate model of matter, together


with basic physics principles to predict the dynamic effects of
the interaction between particles, can be used to build computer
simulations to analyze the predictions of the model under differ-

CLICK TO PLAY
ent conditions:

• Use this simulation to analyze the effect of changing tem-


perature on the speed and spatial distribution of particles in
a simple substance. Study the behavior of the system in the
presence and in the absence of interactions between particles.
Share and discuss your findings with one of your classmates.

Note: Repulsion between particles at short distances is modeled by assuming that particles behave
like hard billiard balls (they strongly repel each other at distances smaller than their own diameter).

According to the particulate model of matter, a solid phase forms as a result


of the attractive interactions between particles. These interactions keep particles
together at low temperatures when their average kinetic energy is relatively low.
Attractive and repulsive interactions constrain the movement of
Distance particles that cannot freely move from one place to another. As
the temperature increases, the average speed of the particles in-
creases and they gain some freedom to move around each other,
Interaction Force (N)

which explains the fluidity of the liquid phase. At higher tem-


peratures, when the liquid transforms into a gas, most particles
acquire enough kinetic energy to move across the entire system
barely influenced by their interactions. The stronger the attractive
interactions between particles, the more energy will be needed to
separate them and induce a phase transition from solid to liquid
Repulsion Attraction or from liquid to gas. Within this model, differences in melting
and boiling points are attributed to differences in the strength of
the interactions between particles at the submicroscopic level. As
Distance (m)
we will discuss in more detail in Unit 3, making sense of these
Figure 1.12 Representa- differences in terms of the specific composition and structure of the particles of
tion of the interaction force
between two particles of ar- matter is critical to explain the diverse properties of the substances in our world.
gon as a function of distance
between any two particles. The particulate model of matter can be used to explain and predict the proper-
By convention, repulsive
forces are assigned positive ties and behavior of a variety of systems and phenomena. To illustrate it, in follow-
values and attractive forces ing sections we will apply the model to the analysis and understanding of a) the
negative values.
properties of gases and b) the nature of phase transitions.
Chemical Thinking U1 How do we distinguish substances? 23

Modeling Gases
Substances that exist in the gas phase at room temperature play a central role in
our lives. We breathe in air containing gaseous substances such as oxyge, and we
breathe out air richer in other gases such as carbon dioxide. This gas is also one
of the main products of the combustion of the fossil fuels that we use to generate
electricity and power our cars. The rapid increase of the concentration of carbon
dioxide in the atmosphere in the last two hundred years is thought to be the main
cause of global warming. Understanding gas properties and behavior is thus of
central relevance in modern times.
The study of the properties of gases was of central importance in the develop-
ment of modern chemistry. Through the study of the properties of the different
gaseous substances chemists were able to build many of the models and theories
that guide chemical thinking nowadays. Although the gas phase is perhaps the
simplest in structure at the particulate level, many people struggle to understand
its properties because most gases cannot be seen or felt. So, it is not uncommon to
think that gases have no weight or that the particles of matter become smaller or
lose mass when a substance turns into a gas. Modeling and analyzing the gas phase
at the submicroscopic scale may help us dispel some of these misconceptions.
Most substances become gases at high temperatures and low pressures. Under
those conditions, we can imagine the particles that make up the system to be far
apart from each other and rarely crossing paths. So, in a first approximation, the In which ways
particulate model of a gas could be simplified by assuming that particles do not are these types
of particulate
interact with each other at all; the only interactions that they experience are with representations of
solids, liquids, and
the walls of their container. This is a reasonable hypothesis if the average distance gases limited or
between particles is much larger than their own size. What can this simple model inaccurate?

predict about the properties and behavior of gases? Let’s explore it.

Ideal Gases LET’S THINK

http://www.cbc.arizona.edu/tpp/chemthink/resources/U1_M2/partmodel3.html
The simulation included in this activity is based on a model that neglects all interactions between
particles and treats their interactions with the walls of the container as perfectly elastic collisions
(no kinetic energy is lost during the collision). Use this simulation to analyze the effect on the
pressure (P) exerted by the particles on the walls of the container by:

a) Changing the temperature (T) at constant volume (V) and number of particles (N);
b) Changing V at constant T and N;
CLICK TO PLAY
c) Changing N at constant T and V.

The simulation will allow you to collect the value of the average pressure in
the system as a function of different variables. Use the load button to collect
data making sure that the pressure is stabilized before registering its value.

• Use your data to sketch three graphs that show how P changes with increasing T, V, or N
when the other variables are held constant.
• Share your results and ideas with one of your classmates. Discuss what types of mathemati-
cal equations could best describe the relationships between P and T, P and V, and P and N
predicted by this model of gases.
24 MODULE 2 Modeling Matter

Our simplified particulate model of gaseous substances predicts that the pres-
sure (P) of a gas is directly proportional to both the absolute temperature (T,
measured in kelvin) and the number of particles (N) in the system, and inversely
proportional to the volume (V). This behavior is actually observed in many gases
at high temperatures and low pressures; when this happens it is said that the sub-
stance behaves as an “ideal gas.” The quantitative relationship between pressure,
temperature, volume, and number of particles in the ideal gas model can be ex-
pressed in mathematical terms as:

(1.2) P = kB ( N T / V )

where the proportionality constant kB = 1.380 x 10-23 J/K is known as Boltzmann


constant. One of the most interesting features of this relationship, also called the
ideal gas law or ideal gas equation of state, is that none of the quantities in equa-
tion (1.2) depends on the chemical composition of the actual system. The ideal gas
model predicts that all substances, independently of their chemical structure and
composition, will behave identically under conditions of temperature and pressure
where the interactions between their particles can be neglected. This prediction of
universal behavior has been confirmed experimentally and it is one of the greatest
accomplishments of the model.
The ideal gas model works well when describing and predicting the behavior
of gases at high temperatures and low pressures. However, problems arise when
the effects of interactions between particles cannot be neglected. In the absence of
particle interactions a gas would never turn into a liquid or a solid. Consequently,
the closer we get to the conditions under which a gaseous substance will undergo
a phase change, the worse the predictions of the ideal gas model will be. To predict
the behavior of “real” gases we need to understand how particle interactions affect
the behavior of these systems.

LET’S THINK Real Gases

http://www.cbc.arizona.edu/tpp/chemthink/resources/U1_M2/partmodel4.html
The simulation in this activity allows you to turn on or off particle interactions in the particulate
model of a simple substance, as well as to change the strength of the attractive forces. Use the
simulation to investigate the effect of particle interactions on the pressure of a gas.

• Analyze how the average pressure changes as you turn on


the repulsive interactions but not the attractive interactions.
CLICK TO PLAY

Repulsions between particles are modeled by assuming that


the particles behave like hard billiard balls. Investigate how
the magnitude of the effect of the repulsive interactions de-
pends on the temperature, volume, and number of particles
in the system.
• Analyze how the average pressure changes as you increase the strength of the attractive
interactions keeping repulsive interactions on. Investigate how the magnitude of this effect
depends on the temperature, volume, and number of particles in the system.

Discuss your results with one of your classmates and suggest possible explanations for what you
observe in each case.
Chemical Thinking U1 How do we distinguish substances? 25

Particle interactions affect gas properties because they alter particle movement.
For example, given that particles repel each other at close distances, there is less
effective space for particles to move. Their movements are more constrained; it is
as if the particles were in a container with a smaller effective volume. The larger
the particles, the smaller the free available space and the more frequently these
particles will collide with the walls of the container. This in turn should result in
higher pressures than those predicted by the ideal gas model.
Attractive interactions will also constrain particle movement as forces will
change particles’ velocity, both speed and direction. On average one can expect
particles that are attracted to each other to spend more time close together and
to interact less frequently with the walls of the container; this will result in lower
pressures than those associated with ideal gas behavior.
The net outcome of these competing effects on gas properties will depend on
factors such as the size of the container, the external temperature, the number and
size of the particles present in the system, as well as on the strength of the attrac-
tive interactions between them.

Modeling Phase Transitions


We have seen how the particulate model of matter can be used to describe, explain,
and predict the properties of substances in the gas phase. As we will discuss in the
following paragraphs, the same model can be applied to analyze the properties
and behavior of materials in the liquid and the solid phases, as well as to study the
transition between different states of matter.
A phase change is a very interesting event given that two or more phases with
rather different properties can coexist during the transition. Understanding this

By Markus Schweiss (Own Work) [CCA: Share Alike 3.0]


phenomenon has not been easy. For many years natural philosophers and scientists
thought that the chemical nature of substances actually changed during a change

via Wikimedia Commons


of state. The observable properties of, for example, liquid water and water vapor
are so different that is not surprising that people had problems thinking of them
as the same substance (Figure 1.13). However, chemical analysis revealed that no
chemical change occurred during a phase change and the particulate model of
matter helped make sense of the results.
One of the most fundamental ideas to understand when using the particulate
model of matter is the concept of emergence. The particulate model relies on
the assumption that many macroscopic properties of a substance that are observ- Figure 1.13 It is common
to think that the bubbles in
able or measurable in our laboratories may not be the same as the properties of boiling water are made of
the individual particles that compose the system. Many macroscopic properties oxygen and hydrogen par-
ticles, instead of water par-
“emerge” from the spatial distribution, movement, and interactions between the ticles. What do you think?
many of particles present in a macroscopic sample of the material. So, for example,
a solid is more rigid than a fluid because the strong interactions between particles
in close proximity in the solid phase make it difficult for them to move around
and separate. An alternative explanation would be to think that particles in the
solid state are hard and become softer as we increase the temperature. However,
experiments suggest that hardness is not a property of each individual particle but
rather a property that emerges from the interactions between the many particles in
a system. Emergent properties and behaviors are common in our surroundings. A
traffic jam, an ant colony, and even the movement of people in a busy intersection
emerge from the interaction between multiple components.
26 MODULE 2 Modeling Matter

LET’S THINK Emergent Properties

Consider the following intensive properties of a substance:

Density Viscosity Color Boiling Temperature Malleability



• Which of these properties are emergent properties of the substance and which of them are
properties of the individual particles that compose the system?
• How would you expect the value of each of these properties to differ for samples of the sub-
stance that have 10, 102, 1012, and 1023 particles?
• Which other emergent properties of a substance can you identify?

Share and discuss your ideas with a classmate, and clearly justify your reasoning.

The temperatures at which phase transitions occur are in fact emergent proper-
ties of substances. According to the particulate model of matter, individual particles
do not melt or boil with changing temperature or pressure; they do not become
smaller or larger, or softer or harder, during a phase change. The overall strength of
the interaction forces between particles does not change with tem-
perature and pressure either. The only thing that changes during
By Nandiyanto (Own work) [CCA: Public domain]

the phase transition is how particles are distributed in space and


the amount of energy that they have. Because the temperature at
via Wikimedia Commons

which a substance boils is an emergent property of a system with


many particles, we cannot expect a nanoscopic droplet of water
comprised of 20 particles to boil at the same temperature as a mac-
roscopic droplet of the same substance with 1022 particles (Figure
1.14). In fact, it is likely that the nanoscopic droplet would gradu-
ally evaporate and never actually boil because each of its particles is
not subject to the attractive force of many others. The particulate
model of matter can still be applied to explain and predict the be-
havior of systems made up of a few particles, but predicted proper-
ties will be different from those of macroscopic samples.
Figure 1.14 Electron micros- We have seen that to induce a phase transition in a macroscopic sample of a
copy images of silica nanoclu-
sters of different sizes. The material we need to provide or extract energy from the system. However, once the
properties of nanoaggregates transition point is reached, the temperature remains constant until the transforma-
tend to vary dramatically with
their size and shape. tion is complete. Why does this happen? How can the temperature stay constant
when energy is being added to or removed from the system? Let us analyze this
phenomenon using the particulate model of matter.
In a dynamic system of interacting particles, energy can be present in two main
forms, kinetic energy (Ek) due to particle motion (Equation (1.1)) and potential
energy (Ep) due to particle interactions. The potential energy can be conceived as
energy stored in the system of interacting particles and its value changes as particles
approach or move way from each other. The potential energy always decreases as
particles move in the same direction as the forces between them. If the particles at-
tract each other, Ep decreases as the particles get closer together; if the particles repel
each other, Ep decreases as the particles move away from each other. The reduction
in potential energy due to the action of internal forces results in a gain in kinetic
Chemical Thinking U1 How do we distinguish substances? 27

energy. In general, the change in the value of the potential energy, DEp, is a measure
Figure 1.15 The potential
of the energy that needs to be invested (DEp > 0) or removed (DEp < 0) from a sys- energy (Ep) of a pair of par-
ticles that attract each other
tem of particles to change their relative positions. decreases as the distance (r)
By convention, the value of potential energy is set to zero when the interacting between them decreases. By
convention, the maximum
particles are at an infinite distance from each other (i.e., when the interaction force potential energy is set to be
zero when the distance (r) be-
between them is zero). As a result, the potential energy of particles that attract tween the particles is infinite.
each other always has a negative value (Ep decreases as the particles move towards
each other), and this value
becomes more negative as
the particles get closer to-
gether (Figure 1.15). A pair
of particles that move under
the influence of their attrac- Attractive Force
tive force will gain kinetic
energy as particles approach
each other and will lose po- Potential
tential energy in the process. Energy
The stronger the attractive Decreases
force between the particles,
the greater the decrease in
the potential energy of the system when the particles get closer together (and the
greater the increase in their kinetic energy).
In situations when particles repel each other, their potential energy increases
(becomes more positive) as the particles get closer together. This increase in po-
tential energy is accompanied by a decrease in the kinetic energy of the particles
(particles slow down as they get closer due to the repulsive forces between them).
Particles that move away from each other under the action of their repulsive force,
lose potential energy but gain kinetic energy as they separate.

Potential Energy Plot LET’S THINK


The following graph shows the calculated potential energy for the interaction of two argon par-
ticles as a function of distance.

• Identify on the graph the range of distances


where the particles attract each other and
the range of distances where they repel each
other (Hint: Analyze how Ep is changing
Potential Energy (J)

with increasing distance). Is there a distance


where the force between them is zero?
• Describe what would happen to the poten- Distance
tial energy and to the kinetic energy of two
argon particles initially separated by a large
distance if they were to move freely under
the influence of their interaction force. Distance (m)

Share and discuss your ideas with a classmate, and clearly justify your reasoning.
28 MODULE 2 Modeling Matter

For substances in the solid or liquid phase, attractive and repulsive


interactions between particles tend to keep them at distances where the
E Liquid Gas average force is close to zero and the potential energy is at a minimum.
Particles of substances in these states of matter have much lower potential
energy (more negative) than the same particles in the gas phase, where
the potential energy due to particle interaction is almost zero. To induce a
phase transition from liquid to gas energy needs to be provided to separate
the particles and increase their potential energy (Figure 1.16). During a
Kinetic Energy liquid to gas phase transition the temperature remains constant because
Potential Energy the energy provided through heating is transformed into potential energy
and not into kinetic energy of the particles (remember that temperature
is a measure of the average kinetic energy per particle). In the reverse process, the
Figure 1.16 During the phase tran- change from gas to liquid, particles lose potential energy and gain kinetic energy as
sition from liquid to gas, the total
kinetic energy of the particles in the they get closer together. As particles in the system collide with the container they
system remains constant while the
total potential energy increases, go- transfer their excess kinetic energy to the surroundings. We then say that energy is
ing from a negative value to almost
zero for particles in the gas phase. released in the form of heat. In a similar fashion, energy will be needed to separate
particles in the melting of a solid and energy will be released in the solidification of
a liquid. The energy released or absorbed during a phase transition due to changes
in the potential energy of the system is often called latent heat.

A Central Idea
One central idea in chemical thinking is that many of the changes that we ob-
serve in our surroundings, from phase transitions, to the mixing of substances, to
chemical reactions, can be seen as the result of two competing phenomena. On
the one hand, the particles that make up a system are constantly moving in ran-
dom directions and with random speeds. Random movement and collisions tend
to lead to states in which particles are homogeneously distributed in the available
space. On the other hand, attractive interactions between particles may lead to the
formation of small clusters or large conglomerates of particles. The outcome of the
competition between random motion and attractive interactions will depend on
the strength of such interactions and on factors such as temperature and pressure.
Predicting the changes that a system may undergo can be simplified by analyz-
Liquid-Like Configurations
ing two critical elements:
a. The potential energy of the different states available to the system;
b. The number of configurations that particles can take in each of those states.
Derivative from image by Mark Bishop

Comparing the potential energy of two different states allows us to evaluate the
energy cost associated with a change. If changing from one state to another re-
quires a high energy input, the change will be less likely to occur, particularly at
low temperatures. On the other hand, comparing the number of configurations
that the particles can take in each state allows us to assess how easily they may
rearrange. If particles can be in many different configurations in a given state, the
probability for them to move away from that state will be low.
Gas-Like Configurations Consider, for example, the liquid and gas states. Particles are closer and attract
each other more strongly in the liquid phase than in the gas phase. Thus, the po-
Figure 1.17 Particles can
tential energy of the liquid is lower than that of the gas. From this perspective, the
adopt many more configura- liquid phase is more “energetically” favored than the gas phase (as it takes energy
tions in the gas phase than in
the liquid or solid phases. to change from liquid to gas). However, there are many more configurations that
particles can take in the gas phase than in the liquid phase (Figure 1.17) because
Chemical Thinking U1 How do we distinguish substances? 29

gaseous particles may occupy the entire volume of the container. Consequently, Figure 1.18 Placing the different
states of a system in a Potential Ener-
random motion is more likely to induce a change to the gas phase. Which of these gy-Configuration diagram can be use-
effects is dominant depends on factors such as temperature. At low temperatures, ful to predict which state is more like-
ly to exist under different conditions.
where little energy is available, escaping the lower energy state is more difficult and The likelihood of different states may
be influenced by changing tempera-
the liquid state is more likely to form. At high temperatures, random motions will ture (T) and pressure (P).
likely take the system to the gas phase.
The construction of potential energy-configuration (PEC) Favored at Low P
diagrams like the one shown in Figure 1.18 can help us analyze
and predict the likely changes that a system may undergo given Favored at High P
some basic knowledge about the properties of available states. In
Ep Gas
general, a system is likely to evolve to those states that have the
larger number of configurations and the lower potential energy.
This happens because once particles randomly adopt those types

Favored at Low T
Favored at High T
of states, the probability of them changing to other states will be
pretty low. States that have low potential energy and a low num- Liquid
ber of configurations are likely to be adopted only at low temper-
atures, when the energy available is not enough to overcome at-
tractive interactions between particles in the system. States with
high potential energies and a large number of configurations will
become more favored at high temperatures, while those states
with high potential energy and a low number of configurations
will be the least favored under most normal conditions.
# Configurations

PEC Diagrams LET’S THINK


The potential energy-configuration (PEC) diagram to the
Ep
right shows the liquid and gas states for nitrogen (represent-
ed as blue circles) and oxygen (represented as red circles).
The gaseous states for both substances are represented as
overlapping because they have similar potential energies and
number of possible configurations.

• Use the PEC diagram to predict which substance, nitro-


gen or oxygen, is likely to have a higher boiling point?
Clearly justify your reasoning. # Configurations

Liquid crystals are substances that can exist in states


of matter with properties intermediate between
those of liquids and crystalline solids.

• Build a PEC diagram to represent these three SMECTIC


phases of a liquid crystal and discuss the phase
changes that will take place when changing ISOTROPIC NEMATIC
temperature.

Share and discuss your ideas with a classmate, and


clearly justify your reasoning.
30 MODULE 2 Modeling Matter

Analyzing Changes LET’S THINK


A critical skill in chemical thinking is to be able to describe, explain, and predict the changes in diverse
types of systems based on the analysis of the properties of available states under particular conditions. Let us
explore how well you can do it.

Evaporation

By Jarombouts (Own Work)


via Wikimedia Commons
[CCA: Share Alike 3.0]
Even when the temperature of a small pond of water never reaches
100 oC, the water evaporates and the pond disappears.

• How could you explain this phenomenon based on the ideas


discussed in this module?

Sweating
By Kullez (Own Work)

via Flickr Commons

Our body uses “sweating” as a cooling mechanism.


[Generic 2.0]

• How does this work?


• How would you explain it based on the particulate model of matter?

Solid Transformations Ep Diamond


Analyze the potential energy-configuration diagram for diamond

Materialscientist(talk)) [CCA: Share


Alike 3.0] via Wikimedia Commons

By UIser:Itub (Derivative:
and graphite, two different forms of carbon.

• Which of these phases of carbon is the most favored based on


potential energy and number of configurations?
• What changes would you expect to see when the temperature
is increased? Graphite
• What would you expect to see when the pressure increases?
# Configurations

Degassing
By en:User:Spiff (Own Work)

via Wikimedia Commons


[CCA: Public domain]

Oxygen dissolved in water escapes when water is heated up.

• Build a potential energy-configuration diagram to explain this phe-


nomenon.
Chemical Thinking U1 How do we distinguish substances? 31

FACING THE CHALLENGE water crystals. Solid carbon dioxide (dry ice), can
also be used as this material reduces the tempera-
ture to such low values that ice crystals form spon-
From Clouds to Proteins taneously from the vapor phase.
How can everything that we have discussed in this Most clouds in our planet form in the lowest
module be used to understand the formation of region of the atmosphere, called the troposphere.
clouds in our planet? Clouds are large atmospheric Higher layers of the atmosphere tend to be too dry
objects made up of small liquid droplets or tiny for the nucleation process to occur. However, some
crystals of water and other minor components. clouds that form in the winter polar stratosphere,
Clouds form as hot air raises in between 15,000 to 25,000 m
the atmosphere and rapidly ex- above sea level, play a crucial
pands due to reduced atmospheric role in our planet. Nucleation in

By Axel Rouvin (Own work) [CCA: Public domain]


pressures at higher altitudes. In or- these clouds occurs at tempera-
der for the gas to expand, particles tures close to -80 oC. The clusters

via Wikimedia Commons


in the ascending air need to push that form at these temperatures
particles in their surroundings and are mixtures of water with other
transfer part of their kinetic ener- substances such as nitric acid and
gy. The average kinetic energy of sulfuric acid. These droplets and
the particles in the raising air de- crystals trap pollutants and ac-
creases, and thus the system cools celerate chemical processes that
down. At this lower temperatures, consume ozone particles in the
the attractive forces between water stratosphere. The phenomenon
particles cause them to aggregate of ozone depletion in our plan-
into clusters or nuclei that may grow into larger et is thus strongly associated to the formation of
droplets by the addition of more water particles. these types of clouds.
In order for nuclei to grow, the rate at which Nucleation is not only important in the for-
water particles escape from the cluster should be mation of clouds. Most phase transitions in our
smaller than the rate at which other water particles surroundings are initiated via the nucleation of na-
deposit onto it. For this to happen, clusters have noscopic droplets, bubbles, or crystals. Inducing
to reach a critical size in which there are enough and controlling the formation of these nuclei are
particles in the system to hold it together through ways we have to influence the properties of the new
attractive interactions. The formation of nuclei, or phase that emerges from the process. The develop-
the nucleation process, is facilitated by the pres- ment of new materials via nanotechnology relies to
ence of other substances that attract water particles a great extent on the ability to stop the nucleation
and act like centers on which the water nuclei can process when clusters of particles reach the proper
form. Typical nucleation centers include dust and size. In biochemistry, the nucleation of protein
sodium chloride crystals. Liquid droplets tend to crystals is a necessary step to determine the struc-
form at low altitudes, but ice crystals are prevalent ture of enzymes and other important components By Mathias Klode (Own Work) [CCA: Share Alike 3.0]

at higher elevations. of our cells. However,


Humans have developed strategies to “seed producing good crys-
via Wikimedia Commons

clouds,” this is to artificially induce the formation tals for analysis can
of nuclei in regions where the concentration of wa- be extremely challeng-
ter particles is not enough for them to aggregate ing. In all these cases,
spontaneously. Cloud seeding often requires the understanding phase
dispersion in the atmosphere of solid substances transitions at the par-
with a crystalline structure similar to ice, such as ticulate level is an in-
silver chloride, which induces the nucleation of valuable asset. Protein Crystal
32 MODULE 2 Modeling Matter

Let’s Apply
Up and Down our Planet
The properties of gases change when you move up and down in Earth’s atmosphere or underwa-
ter. This table lists temperature and pressure data gathered at various altitudes in the atmosphere
and various depths in the ocean:
ASSESS WHAT YOU KNOW

Atmosphere Hydrosphere (middle latitudes)


Altitude Temperature Pressure Depth Temperature Pressure
(km) (K) (atm) (km) (K) (atm)
0 293 1.0 0 293 1.0
1 287 0.883 0.1 290 11
2 280 0.779 0.2 279 21
3 273 0.687 0.3 278 31
4 267 0.607 0.4 277.4 41

LET’S THINK Your Lungs

Imagine that you model your lungs as a 5 L sealed balloon filled with an ideal
gas at sea level:

• How will the volume of your lungs change as you climb up to the top of a
mountain at 5 km above the sea level? Estimate the volume of your lungs at
the top of the mountain.
• How will the volume of your lungs change as you dive down into the ocean
to 100 m below sea level? Estimate the volume of your lungs at the bottom
of your dive.
• Why would you need pressurized tanks for scuba diving? Why

By Soljaguar (Own Work)


via Wikimedia Commons
[CCA: Share Alike 3.0]
would it be necessary to exhale and rise slowly when ascending
from the ocean depths?
• How do the problems that you might have in scuba diving com-
pare with those of a pilot climbing to a higher altitude in a pres-
surized plane?
• Build a particulate representation of the air inside your lungs (the balloon)
as you move from 5 km above sea level to 100 m below the ocean surface.
How would the following properties change as you descend a) Average
speed of the particles; b) Mass of a single particle; b) Volume of a single
particle; d) Distribution of the particles inside the balloon.

Share and discuss your ideas with a classmate, and clearly justify your reasoning.
Chemical Thinking U1 How do we distinguish substances? 33

Cooking

By US Department of Agriculture
Recipes for cooking with boiling water need to be modified based on the altitude

via Wikimedia Commons


[CCA: Public domain]
of the place where you cook.

• Why is that? How would you explain it?


• How does a change in pressure affect the potential energy and the number
of configurations available to a system in liquid or gas state?

ASSESS WHAT YOU KNOW


In the Beach

Sodas contain pressurized carbon dioxide at a pressure close to 2 atm.


Imagine that you were to take a soda can out of a cooler and open it
http://www.cbc.arizona.edu/tpp/chemthink/resources/U1_M2/submicro.html

on the beach in a warm day at 300 K.

• How would the average kinetic energy of the carbon dioxide


particles in the system change when the can is opened?
CLICK TO PLAY
• How would the average potential energy of the carbon dioxide
particles in the system change?
• Use the interactive tool to build a particulate representation of
a nanoscopic portion of the can at the moment it is opened.
• Build a potential energy-configuration (PEC) diagram showing
the state of the can before and after it is opened.

Share and discuss your ideas with one of your classmates, and clearly
justify your reasoning.

Forming Clouds

When cold pressurized beverages such as this are opened, it


is common to observe the formation of small “cloud” around
the opening (see image). A similar phenomenon is respon-
sible for the formation of clouds when air ascends in the at-
mosphere and quickly expands.

• How would you explain this phenomenon using the


particulate model of matter?

Share and discuss your ideas and justify your reasoning.


34 MODULE 2 Modeling Matter

Let’s Apply
Fighting Intuition
The properties and behavior of matter at the submicroscopic level sometimes defies our intuition.
We are not used to building explanations about the things that we observe in our daily lives based
on the movement and interactions of myriads of submicroscopic particles that we cannot see with
ASSESS WHAT YOU KNOW

our eyes. Testing and recognizing the limits of our intuitive ways of describing and explaining the
world is crucial in the process of becoming a better chemical thinker. Thus, in these pages we pose
a few challenges to test your reasoning.

• Evaluate the answer given by some students to the following questions. Share and discuss
your ideas with a classmate. Discuss what misunderstandings or intuitive ideas may lead
students to make mistakes and select incorrect answers.

Cooling

A cook takes a hot iron frying pan off the stove to cool. What happens as the iron pan cools?

a. The mass of the iron particles increases, so the pan gets a tiny bit heavier.
b. The mass of the iron particles does not change, so the pan remains the same.
c. The distance between the iron particles decreases, so the pan gets a tiny bit smaller.
d. The distance between the iron particles does not change, so the pan remains the same.

Several students selected answer A as correct. What do you think?

The following diagram represents a magnified view of a small portion


of a steel tank filled with helium gas at 20 °C and 3 atm pressure. The
dots represent the distribution of helium atoms. Which of the follow-
ing diagrams best illustrates the distribution of helium atoms in the
steel tank if the temperature is lowered to –100 °C (helium is still a
gas at this temperature)?
a. b. c. d.

A chemistry student chose representation a. What do you think?


Chemical Thinking U1 How do we distinguish substances? 35

Substance Properties

Why does solid water (ice) float in liquid water?

a. The particles of liquid water are heavier than the particles of ice.
b. The particles of ice have a smaller volume than the particles of liquid water.
c. The particles of ice are farther apart than the particles of liquid water.
d. The particles of liquid water are more rigid than the particles of ice.

A chemistry student thinks that options a and c are correct. What do you think?

ASSESS WHAT YOU KNOW


Why does liquid candle wax flow but solid candle wax does not?

a. Because the particles of liquid candle wax are softer than the particles of solid candle wax
b. Because the particles of liquid candle wax weigh less than the particles of solid candle wax
c. Because the particles of liquid candle wax are moving but the particles of solid candle wax
are not
d. Because the particles of liquid candle wax can easily move past one another but the particles
of solid candle wax cannot

A chemistry student thinks that options d in the only one correct. What do you think?

Particle Properties

Following is a list of properties of a sample of solid sulfur:


i. Brittle, crystalline solid. ii. Melting point of 113 oC.
iii. Density of 2.1 g/cm .
3
iv. Reacts with oxygen to form sulfur dioxide.

Which, if any, of these properties would be the same for one single particle of sulfur obtained
from the sample?

A chemistry student thinks that all these properties of solid sulfur would be the same for
one single particle of sulfur. What do you think?

Which of the following processes will make the particles that make up a substance larger?

a. Freezing b. Boiling c. Condensing d. None of them

A chemistry student selected a (freezing). What do you think?

Solid, liquid, and gaseous water coexist at the triple point (0.01 oC and 0.006 atm). In which of
these phases do water particles have the lowest average speed at 0.01 oC and 0.006 atm?
a. Gas b. Liquid
c. Solid d. The average speed is the same in the three phases

A chemistry student selected d (the average speed is the same in the three phases). What
do you think?
36

Analyzing
Particles
The particulate model of matter can be used to explain why different substances
U1: MODULE 3
have different properties. These differences are due to the presence of interaction
forces between particles that vary in type and strength. Why are the interaction
forces different? To answer this question, we need to zoom into the submicrosco-
pic world to better understand the structure of matter. Chemists have shown that
if we know the specific nature of the particles that compose a substance,
we can predict its properties. How can we determine the
specific characteristics of nanoscopic particles that we
cannot see or isolate in a conventional chemistry lab?
The characterization of the particles that make up a
chemical substance is one of the major goals and chal-
lenges in chemistry. The task is accomplished in a vari- What is the mass of
ety of clever and creative ways that generate information a single molecule of
butane?
about the mass, chemical composition, and structure of these
particles. In this module, we will introduce the models used to describe the differ-
ent composition and structure of the particles that make up the diverse substances
in our world. Then, we will analyze the type of thinking that is used to determine
the mass of these particles and the number of particles present in a given amount
of substance. This information is critical for many important tasks, from deter-
mining the concentration of pollutants in the air we breathe to measuring the
concentration of diverse metabolites in our blood.

THE CHALLENGE Air Pollution


Modern technology allows us to quantify the concentration of different types
of pollutants in the atmosphere.

• If someone told you that the concentration of ozone in the place you
live is 2 x 10-4 mg/L, what would you need to know to determine how
many particles of ozone you breathe per liter of air that you take in?
• Why would these numbers be important to know?

Share and discuss your ideas with one of your classmates.

Module 3 will help you develop the type of chemical thinking that is needed
to solve problems similar to the one presented in this challenge. In particular, the
central goal of Module 3 is to introduce the atomic model of substances and
discuss how to use information about atomic and molecular masses to calculate
the number of particles of different types present in a system of interest.
Chemical Thinking U1 How do we distinguish substances? 37

Atomic Model of Substances


Helium Atom
It is a fundamental assumption in modern chemical thinking that substances in
our world have different properties because they are made of particles with different Hydrogen
compositions and structures. In particular, in the atomic model of substances it is Molecule
proposed that the particles that compose the substances in our surroundings have
internal structure. They are made up of smaller units called atoms which are held
together by strong attractive forces called chemical bonds. These internal forces
are much stronger than the forces acting between different particles in the system.
There are only a few substances composed of particles that are single atoms; argon
Water
and helium are two examples. Most substances have a more complex submicrosco-
Molecule
pic structure. For example, many of them are made up of particles where two or
more atoms of the same or different types are bonded together. These composite Figure 1.19 Particles of he-
particles are called molecules (Figure 1.19). All of the molecules of a given sub- lium are made of single at-
oms; particles of hydrogen
stance are assumed to be identical to each other but different from the molecules are made up of molecules
with two identical atoms;
of a different substance. Differences between molecules result from differences in particles of water are made
the types of atoms present in them, differences in the way these atoms are arranged up of molecules with three
atoms, two hydrogen atoms
in space, or both. A molecule’s composition and structure determines how the and one oxygen atom.
molecule will interact with other particles of similar or different type.

Particles in the Atmosphere LET’S THINK


The image in this activity shows a particulate representation of a nanoscopic section of the air in
our atmosphere.

• How many different substances are present in this


system?
• Which substances in air are made up of particles that
are single atoms and which are made up of molecules?
• Air is a mixture of substances. How is a mixture dif-
ferent from a single substance at the particulate level?

Share and discuss your ideas with a classmate, and clearly


justify your reasoning.

Note: The following color code is commonly used to represent atoms of different types:
Argon Hydrogen
Oxygen
Carbon Nitrogen

The atomic model of substances allows us to make sense of many observations


and experimental results about the properties of substances and their mixtures.
For example, if we assume that air is a gaseous mixture of several substances each
of them characterized by a particular type of particle, then that explains why the
different components can be separated by simply cooling down the mixture. The
strength of the interaction between different types of particles can be expected to
be different and substances will condense at different temperatures. But how do
we know how particles differ from each other? How do we know that molecules
38 MODULE 3 Analyzing Particles

By Dnn87 (Own Work)


[CCA: Share Alike 3.0]
of carbon dioxide are made up of two oxygen atoms and one carbon atom, or that
via Wikimedia Commons
nitrogen molecules have two atoms of the same type? Although we will take some
Sodium time to build the answers to these questions through the following units, we can
present some experimental evidence that supports this model.
Through experimentation, chemists have identified two major types of sub-
stances. There are some substances that cannot be decomposed into simpler stable
substances by any physical or chemical procedures. There is no known experimen-
tal technique that allows us to take a sample of these substances and split it into two
or more different stable substances. We call these types of substances elementary
substances (Figure 1.20). They include, for example, the oxygen, nitrogen, and
argon that we separate from air in the atmosphere. There are, however, substances
By Enricoros (Own Work)
[CCA: Public domain]
that we can split into two or more simpler stable substances by inducing a
via Wikimedia Commons chemical reaction. We call these types of substances chemical compounds;
water and carbon dioxide are two typical substances in this group. Water
can be separated into the elementary substances hydrogen and oxy-
gen, while carbon dioxide can be decomposed into carbon, another
Silicon elementary substance, and oxygen. Whenever a chemical compound
undergoes this decomposition, the proportion of elementary substances
that are recovered is always the same. For example, during the decomposition of
water we always produce twice the volume of hydrogen gas than oxygen gas.
The atomic model of substances allows us to explain the above macro-
scopic differences in the behavior of elementary substances and chemi-
Sulfur cal compounds in the following way. Elementary substances cannot be
decomposed into two or more stable substances because they are made
up of particles, atoms or molecules, that contain one single type of atom.
Chemical compounds can be decomposed into other substances because
their particles contain two or more different types of atoms that can rear-
Figure 1.20 Samples of dif- range to produce elementary substances. When this happens, the relative
ferent elementary substances,
together with a particulate rep- amount of the elementary substances that are produced is determined by the
resentation at the nanoscale. ratio of the different types of atoms that make up the particles of the compound.

LET’S THINK What are they?


Analyze the following particulate representation of nanoscopic samples of elementary substances,
chemical compounds, and mixtures

• Classify each of the images as a repre-


sentation of an elementary substance, a
compound, or a mixture of substances.
• In the case of mixtures, identify what
types of substances, elementary or
compound, are present in them.
• Identify the state of matter in which
each of the substances or mixtures is
represented to be.

Share and discuss your ideas with a classmate, and clearly justify your reasoning.
Chemical Thinking U1 How do we distinguish substances? 39

From the perspective of the atomic model of matter, elementary substances


are the most simple stable substances that we know. They are composed of identi-
cal particles made up of free or bonded atoms of the same type. The isolation and
identification of the various elementary substances in Nature has allowed chem-
ists to identify all of the different types of atoms that make up the particles of all
substances, natural and synthetic, in our world. Up to this day, over a hundred
different types of atoms have been identified. Each of these species of atoms is
recognized as a different chemical element. The list of these elements is presented
in the following “Periodic Table of the Chemical Elements” (Figure 1.21). Each
type of atom or element in this table is assigned a symbol that, as we will see later,
greatly simplifies its representation. Atoms or elements in a given column in the
Periodic Table are said to be in the same “group,” while those in the same row be-
long to the same “period.” The location of an element in the Periodic Table is not
arbitrary and provides information about its chemical reactivity.
http://www.cbc.arizona.edu/tpp/chemthink/resources/U1_M2/pt.html

Figure 1.21 Periodic Table

CLICK TO PLAY
of the Chemical Elements
displaying the symbols com-
monly used to represent
each type of atom. Click on
the image to display an inter-
active Periodic Table.

Each of the atoms or elements listed in this table has the same name as the
elementary substance whose particles are made up by that type of atom. However,
it is important to recognize that the properties of the atoms included in the Peri-
odic Table are not necessarily the same as the properties of the particles that make
up the elementary substance nor the properties of the actual chemical substance.
For example, the oxygen that we found in the atmosphere is made up of molecules
composed of two atoms of oxygen each. The structure and properties of these
molecules are different from those of a single oxygen atom. Similarly, a sample of
copper is made up of many copper atoms bonded together in a metallic network; By de:user:Tomihahndorf (Own Work)

this sample conducts electricity. Electrical conductivity is a property of a large col-


via Wikimedia Commons
[CCA: Public domain]

lection of atoms and cannot be defined for a single atom.


Elementary substances are traditionally subdivided into three main groups:
Metals, metalloids or semimetals, and nonmetals, based on similarities in physical
and chemical properties. Metals are usually solids at room temperature and con-
duct heat and electricity remarkably well; most nonmetals, in the other hand, are
gases under the same conditions and are poor conductors of heat and electricity.
Metalloids share some properties of metals and nonmetals. The symbols of the Iodine
Nonmetallic
atoms that make up the particles of these different types of substances are com- Elementary Substance
monly displayed with different colors on the Periodic Table (Figure 1.21). It is
also common to refer to the types of atoms that make up these different groups of
substances as metallic, metalloid (or semimetal), and nonmetallic elements.
40 MODULE 3 Analyzing Particles

Chemists have developed a variety of ways to represent the composition, struc-


ture, and properties of the actual chemical substances in our surroundings and of
the models used to describe, explain and predict their behavior (see Figure 1.22).
At the macroscopic level we can use actual images of the substances or descriptions
of their measured properties. At the submicroscopic level, we can create drawings or
create dynamic animations and simulations to try to represent different types of
particles. Additionally, chemists have developed a sophisticated symbolic language
to represent the composition and structure of chemical substances. A chemical
formula, for example, is a symbol that conveys information about the atomic
Figure 1.22 Different ways composition of a given substance. Thus, the chemical formula for oxygen gas is
of representing elementary
substances. The labels (g), O2(g), where the subindex is used to show that every single molecule of this sub-
(l), (s), indicate the state of
matter of the substance.
stance is made of two oxygen (O) atoms and the label within parenthesis indicates
the state of matter (g, gas; l, liquid; s, solid) of a macroscopic sample.
Macroscopic Submicroscopic Symbolic
Ar
Atomic
Elementary
Substance
Argon
Gas Ar(g)
N2
By Cory Doctorow
(Own Work) [CCA:
Share Alike 2.0], via
Wikimedia Commons
Molecular
Liquid
Nitrogen N2(l)
Elementary
Substance P4
By Tomihahndorf Solid
(Own Work) [CCA:
Public domain], via
Wikimedia Commons
Red
Phosphorus
P4(s)
Most substances in Nature are not elementary substances but chemical com-
pounds. As mentioned before, chemical compounds are substances whose parti-
cles are made up of bonded atoms of two or more different types. Chemists classify
chemical compounds into two major groups: Ionic and molecular (or covalent)
compounds, based on their physical and chemical properties. Ionic compounds
tend to be solids with high meting points that conduct electricity when dissolved
Caffeine in water or in the liquid state (molten). Molecular compounds exist in different
Molecule states of matter and, in general, are not good electrical conductors in any phase.
C8H10N4O2 Differences in properties can also be explained based on the composition and
structure of these substances at the submicroscopic level.
Molecular compounds often result from the chemical combination of nonme-
Cholesterol tallic elements (see Figure 1.21). When these types of atoms combine they tend to
Molecule form molecules, this is, independent particles composed of two or more bonded
C27H46O atoms of different types. For example, water is a molecular compound in
which each of its molecules contains two hydrogen atoms and one oxygen
atom. The chemical formula of liquid water is thus H2O(l). Numerical sub-
indexes after an atomic symbol are used in chemical formulas to show the
number of atoms of a given type in the particles of the compound (see Figure
1.23). From the perspective of the atomic model, the wide number and diver-
sity of molecular compounds in our world is due to the possibility of having many
different types of molecules that differ in composition, size, and structure.
Chemical Thinking U1 How do we distinguish substances? 41

Color Code Macroscopic Submicroscopic Symbolic

CO2
Solid
C
Carbon
Dioxide
CO2(s)
H

N NH3
O
Ammonia
Gas NH3(g)
Ionic compounds result from the combination of metallic and nonmetallic Figure 1.23 Different
ways of representing
elements. Their particular properties can be explained by assuming that their sub- molecular compounds.
microscopic structure is different from that of molecular compounds. In particu-
lar, ionic compounds are not seen as composed of individual molecules but of
electrically charged particles arranged in crystalline networks (Figure 1.24). These
charged particles are called ions and they can be atoms or molecules with a net
electrical charge. An ionic network is made up of positively charged ions (cations)
and negatively charged ions (anions) attracted to each other by electrostatic forces.
The ratio of anions to cations in any sample of this type of substances is such that
the material has no net electrical charge. These different ions gain mobility when
the solid compound is molten or dissolved in water and that explains why ionic
compounds conduct electricity under such conditions. Typical examples of ionic
compounds include sodium chloride, the major component in common salt, and
calcium carbonate, the main component in limestone.

Color Code Macroscopic Submicroscopic Symbolic

Na+
By Choba Poncho Solid
Cl
NaCl(s)
(Own Work) [CCA:
Public domain], via
Wikimedia Commons
Sodium
Chloride
H
Cl–
N NH4+
By Walkerma (Own Solid
Work) [CCA: Public
domain], via Wikime-
dia Commons
Na Ammonium
Chloride
NH4Cl(s)
Given that ionic compounds are not made up of molecules, their chemical Figure 1.24 Different
ways of representing
formula conveys different information than that of a molecular compound. The ionic compounds.
chemical formula of an ionic compound, or its formula unit, simply establishes
the lowest ratio of cations to anions in the system. For example, the formula unit
of sodium chloride is NaCl, which indicates that the ionic network of this chemi-
cal compound is composed of sodium cations (Na+) and chloride anions (Cl–) in a
ratio of one to one (1:1). The formula unit of calcium fluoride is CaF2, which tells
us that calcium cations (Ca2+) and fluoride anions (F–) are present in a 1:2 ratio.
42 MODULE 3 Analyzing Particles

LET’S THINK Submicro and Symbolic

The ability to translate from submicroscopic (particulate) representations


of matter to symbolic language and vice versa is a critical skill in chemical
thinking. The following images show submicroscopic representations of sev-
eral pollutants in our atmosphere in different states of matter.

• Write the chemical formulas of each of theses substances.

http://www.cbc.arizona.edu/tpp/chemthink/resources/U1_M2/submicro.html
Cl

O
• Create submicroscopic representations of the
following substances. Use the interactive tool
on this page to make your drawings.

CH4(g) KCl(s)
NO(g) Cl2(l)

Share and discuss your ideas with one of your classmates. CLICK TO PLAY

Throughout this book we will use a variety of visual representations of chemi-


cal compounds at the submicroscopic level using drawings and symbols of differ-

Methane ent types. These diverse representations are intended to emphasize different char-
acteristics or properties of the represented atoms, molecules, or ionic networks.

CH4
For example, the so-called space-filling representations are typically used to em-
phasize the relative size of the atoms that compose a system. On the other hand,
ball-and-stick representations highlight the connectivity between different atoms
in a molecule or ionic network. In both cases, the representations allows us to de-
Molecule velop a better sense of the three dimensional geometry of the objects of interest.
In general, modern computational technology has helped us generate many types
of static and dynamic images to better visual-
ize the modeled submicroscopic world. All these
representations have limitations that may create
misconceptions. For example, chemical bonds
in ball-and-stick representations are depicted
as solid rods connecting two atoms. However,
these bonds are not physical objects but only
Space-Filling strong interaction forces between atoms.
Representation Ball-and-Stick Representation
CLICK TO PLAY
http://www.cbc.arizona.edu/tpp/chemthink/resources/U1_M2/ch4.html
Chemical Thinking U1 How do we distinguish substances? 43

Phases and Components LET’S THINK


The image below is a representation of a nanoscopic portion of the surface of a soft drink can:

• How many different phase are present in this system? Which phases
are these? How many substances are present in each phase?
• How many of the substances in this system are a) elementary sub-
stances; b) chemical compounds? Write their chemical formulas.
• In which of the different phases present in the system: a) Are the
attractive forces between particles the strongest? b) Is the average
potential energy per particle the lowest (most negative)? c) Is the
average particle speed the highest? d) Is the average kinetic energy
per particle the lowest? Justify your answers.
• Which of the components seems to have the lowest vapor pressure?

USEFUL TOOLS The name of a binary ionic compound includes


Chemists have not only created useful ways of the name of the cation followed by the name of
representing chemical substances at the macro- the anion. For example, NaCl is named sodium
scopic, submicroscopic, and symbolic levels, but chloride while Al2O3 is called aluminum oxide.
they have also developed a systematic language Notice that the number of each type of ion
to name each chemical element and compound present in the formula unit is not included in the
in our world. Understanding this “chemical no- name of the compound.
menclature” greatly simplifies chemical thinking
and communication. Let us explore how to name Molecular Compounds: The name of a binary
molecular and ionic compounds made up of two molecular compound is also derived from the
different types of atoms, or binary compounds:
atoms that made up their molecules. In this
case, the name of the atom farthest to the left in
Ionic Compounds: The name of binary ionic
the Periodic Table (Figure 1.21) goes first. If both
compounds results from the combination of the
types of atoms are in the same group, the atom
names of the positive ions (cations) and negative
farthest down in the table is named first. So, for
ions (anions) present in the system.
example the name of the compound CO2 begins
with “carbon”, and that of SO2 with “sulfur.”
The cations have the same name as the atom
from which they derive. These are atoms of
The name of the second component of the
metallic elements that acquired a positive
molecular compound is built by adding the suffix
charge. For example, Na+ is the sodium ion while
-ide to the root the atom’s name. Greek numeral
Al3+ is the aluminum ion. Some atoms can form
prefixes are used to indicate the number of at-
more than one type of positive ion and a Roman
oms of each type (mono- for one; di- for two; tri-
numeral in parenthesis is used to distinguish one
three). However, this numeral is not added if the
cation from another. For example, Cu+ is named
molecule only has one atom of the element that
the copper(I) ion, while Cu2+ is the copper(II) ion.
is named first. The following examples illustrate
the application of these rules:
The name of the anions is built by adding the
suffix -ide to the root of the name of the atom
CO Carbon monoxide
from which the ion is derived. These are atoms
CS2 Carbon disulfide
of nonmetallic elements. Thus, Cl– is the chloride
N2O Dinitrogen monoxide
ion while O2– is the oxide ion.
PCl3 Phosphorus trichloride
44 MODULE 3 Analyzing Particles

Relative Masses
Atoms, molecules, and ions have masses and sizes so small that they cannot be
measured directly with a balance or similar instruments. It is thus necessary to
rely on indirect measurement techniques to accomplish the task. In particular, the
problem has been solved by comparing the masses of macroscopic samples of dif-
ferent substances containing the same number of particles. For example, imagine
that you had two tanks of gas containing the same number of particles but two dif-
ferent substances such as helium and argon. If you measured the mass of the gas in
each tank you would find out that the argon gas sample is ten times heavier than
the helium gas sample with the same number of particles. What does this mean
from the perspective of the atomic model of substances? Given that argon and he-
lium are elementary substances made up of single atoms, it implies that each atom
of argon (Ar) should be ten times more massive than each atom of helium (He). If
we knew the mass of a helium atom, we could calculate the mass of an argon atom
Figure 1.25 If these gas tanks or vice versa. If we could measure or calculate the number of atoms in any of the
contain the same number of
particles of each substance, how samples, we could also calculate the mass of the individual atoms.
many times heavier is an oxygen
atom than a hydrogen atom? The problem of determining atomic or molecular masses is intimately con-
nected to the challenge of figuring out how to collect samples of different sub-
stances with the same number of particles, and how to determine the actual num-
ber of particles in these samples. The application of the particulate model of matter
provides a nice solution to these challenges. Let’s investigate how.

LET’S THINK Mass Effect?

http://www.cbc.arizona.edu/tpp/chemthink/resources/U1_M3/partmodel5.html
We can use a simulation of an ideal gas to explore the effect of changing the mass of the particles
on the pressure of the system at any given temperature and volume. In this computer simulation,
particles with different masses can be used to model different chemical substances. Click on the im-
age to launch the simulation of an ideal gas and begin your analysis.
CLICK TO PLAY
• Explore the effect of the mass of the particles on the average pressure of
an ideal gas at constant temperature, volume, and number of particles.
Remember to wait until fluctuations in the value of the average pres-
sure are minimal before collecting any data.
• Use the results of your investigation to propose a strategy to experi-
mentally prepare two samples of different gases with the same number of particles.

Share and discuss your ideas with a classmate, and clearly justify your reasoning.

The results of our exploration suggest that under the conditions in which
the ideal gas model provides a good description of the behavior of gaseous sub-
stances, equal volumes of two different gases at the same temperature and pressure
will contain the same number of particles. In fact, we could have predicted this
outcome by simply analyzing equation (1.2) for the ideal gas law, which can be
re-expressed as:

(1.3) N = P V / ( kB T ).
Chemical Thinking U1 How do we distinguish substances? 45

This model predicts that the number of particles for an ideal gas is solely deter-
mined by the values of P, V, and T independently of the mass of the particles;
equal volumes of two different gases at the same T and P should then have the
same number of particles. By simply comparing the masses of equal volumes of
gas at the same temperature and pressure, we can determine the relative masses of
the particles that make up each gas; this should work as long as the gases behave
ideally. This approach to determining the relative masses of particles was first pro-
posed by Amadeo Avogadro in 1811, who was also the first to suggest based on
experimental data that equal volumes of different gases at the same temperature
and pressure would have the same number of particles (Avogadro’s Hypothesis).

Unknown Masses LET’S THINK


Imagine that the mass of three identical tanks separately containing hydrogen gas [H2(g)] and
two unknown elementary substances were measured at the same temperature and pressure:

• How many times more massive is an A atom than a H atom?


• How many times more massive is a B atom than a H atom?
• If you were to assign a mass of “1.0” to a hydrogen atom in an
arbitrary unit, what would the relative masses of the A and B
atoms be when expressed in that unit?
• How would the relative masses change if you decided to arbi-
trarily assign a relative mass of “2.0” to an A atom?
• Is one of the scales of relative masses that you generated better than the other? If yes, how?

Share and discuss your ideas and results with one of your classmates.

Using methods similar to the ones you applied in the last activity, together
with careful measurements of the proportions in which different types of atoms
chemically react with each other, chemists have been able to determine the “aver- Figure 1.26 Click on the image
to display a Periodic Table of the

http://www.cbc.arizona.edu/tpp/chemthink/resources/U1_M3/ptm.html
age relative atomic mass” of all the known atoms. These values are expressed in Chemical Elements listing the aver-
age relative mass of each atom.
so-called “atomic mass units” (amu) and are listed in the Periodic Table of the
Chemical Elements displayed by clicking on Figure 1.26. These numbers are de- CLICK TO PLAY
termined by choosing one type of atom as a reference (as you did it in the last ac-
tivity) and they allow us to calculate
how many times more massive one
atom is with respect to another. For
example, given that the relative mass
of one atom of sulfur (S) is close to
32 amu and that of an oxygen atoms
(O) is 16 amu, we can infer that a
sulfur atom is, on average, twice as
massive as an oxygen atom. In Mod-
ule 4 of Unit 1 we will analyze in
more detail how the relative atomic
masses have been determined using
modern analytical techniques.
46 MODULE 3 Analyzing Particles

LET’S THINK Number of Atoms

The list of average relative atomic masses is very useful in chemistry and many other disciplines in
which it is important to figure out the relative number of particles of different species in a system.
To understand it, imagine that you were in the business of buying and selling precious metals and
had the following samples: 107.9 g of Ag(s), 197.0 g of Au(s), and 195.1 g of Pt(s).

• Which of the three samples has more atoms? Why?


• How many grams of palladium metal, Pd(s), would you need to weigh to have as many atoms
as in 107.9 g of Ag(s)?
• How many grams of copper metal, Cu(s), would you have to weigh to have half the number of
atoms that you have in 197.0 g of Au(s)?
• Based on these results, why do you think it is useful to know the relative masses of the differ-
ent atoms in the periodic table?

Share and discuss your ideas with one of your classmates., and clearly justify your answers.

Number of Particles
One can think of the relative masses of the different atoms in the Periodic Table
Figure 1.27 Click on the image in Figure 1.26 as indicative of how much more massive each type of atom is than
to display a sequence of repre-
http://www.cbc.arizona.edu/tpp/chemthink/resources/U1_M3/avogadro.html

sentations based on number of a reference atom with an assigned mass of 1 amu (one atomic mass unit). For
pennies that may help you grasp
how large Avogadro’s Number is. example, helium atoms (He), with a relative mass of 4.003 amu are, on average,
four times more massive than the reference atoms while argon atoms (Ar), with
a relative mass of 39.95 amu, are close to forty times heavier than the
reference particles. This implies that if we were to weigh 1.000 g of the
reference atoms and 4.003 g of He atoms, both samples should have
the same number of atoms. In fact, a sample of 39.95 g of Ar atoms
should also be composed of the same number of atoms. So, whenever
we weigh masses of different types of atoms and these masses are equal
in magnitude to each atom’s average relative atomic mass, we should
have samples with the same number of atoms. This fact is very useful
as it allows us to use the mass of our samples, a quantity that we can
measure, to compare number of particles without having to know how
many of them are present in each system. In this way, based on the data
listed in the Periodic Table we can predict that 20.0 mg of calcium, with
a relative atomic mass of 40.08 amu, will have approximately half the number of
CLICK TO PLAY
atoms present in 9.0 mg of beryllium, with a relative atomic mass of 9.012 amu.
Although comparing number of particles using relative masses is useful,
it would be easier if we could just measure or calculate the actual number of
particles in any given sample. Fortunately, chemists have devised approaches to
do so. In particular, they have experimentally determined the number of atoms
in samples of substances with a mass equal in magnitude to their average rel-
ative mass expressed in grams. For example, the number of particles in 4.003
g of helium, 9.012 g of beryllium, or 40.08 g of calcium. This number, called
Avogadro’s Number NA, is very large (see Figure 1.27) and has a constant value
equal to 6.022 x 1023 particles.
Chemical Thinking U1 How do we distinguish substances? 47

Molecular Species LET’S THINK

Some elementary substances are made up of molecules rather than single at-
oms. That is the case for hydrogen, H2, nitrogen, N2, oxygen, O2, fluorine, F2,
phosphorus, P4, sulfur, S8, chlorine, Cl2, bromine, Br2, and iodine, I2. We need
consider this fact when trying to figure out the relative mass of their particles
or the number of molecules in a given sample.

• If the average relative atomic mass of oxygen atoms is 16.00, what is the
average relative mass of oxygen molecules O2?
• How many grams of phosphorus should you weigh to have 6.022 x 1023
molecules of this substance?
• How many molecules should we expect to have in 35.45 g of chlorine
gas?

Share and discuss your ideas and results with one of your classmates.

From the chemical point of view, having information about the number of
particles in a sample of a given substance is frequently more relevant than knowing
its mass. Thus, it is convenient to define a unit of measurement that can be used
to simplify the quantification of the number of particles in a system of interest.
Avogadro’s Number, NA = 6.022 x 1023, has been chosen as the base to build such
unit of measurement. In particular, the new unit measurement, called a mole
(1 mol), is defined as the amount of substance that contains one Avogadro’s Num-
ber of particles of such substance. Based on our previous discussion, together with
the information provided in the Periodic Table in Figure 1.26, we can say that
4.003 g of helium is 1 mol of helium atoms, 39.95 g of argon is 1 mol of argon
atoms, and 38.00 g of fluorine, made up of F2 molecules, is 1 mol of these mol-
ecules. One mole of any substance always contains 6.022 x 1023 particles.
Measuring the amount of substance using the mole as a unit is a way of ex-
pressing how many times, or what fraction of, an Avogadro’s Number of particles
of a given substance we have in our hands. For example, if someone says that they
have 3.0 mol of copper (Cu) atoms in a bag, we know the bag contains Figure 1.28 The dozen,
just as the mole, is a unit
of amount of substance.
It allows us to simplify the
3.0 x (6.022 x 1023) = 1.8 x 1024 Cu atoms. counting in systems com-
posed of discrete things.

On the other hand, if they have 0.10 mol of silver (Ag) atoms in the same bag,
there will be

0.10 x (6.022 x 1023) = 6.0 x 1022 Ag atoms

in the system. In general, if n is the amount of substance expressed in moles, the


number of atoms in the sample N can be calculated using the following relation-
ship:

(1.4) N = n x NA
48 MODULE 3 Analyzing Particles

LET’S THINK The Mole

To assess your understanding of the “mole”, evaluate the veracity of the following statements: a) The
mass of one mole of neon (Ne) atoms is 20.18 amu; b) The mass of one potassium atom is 39.10
g; c) The mass of 1.2 x 1023 aluminum (Al) atoms is 53.96 g; d) One mole of O2 molecules weighs
16.00 g; e) Three moles of palladium are made up of three atoms; f ) 106.4 g of Pd(s) have the same
number of atoms as one mole of He atoms.

If you judge that a statement is incorrect, rewrite it to make it true.

The mass of one mole of particles of any substance is called its molar mass M and
is equal to the mass of 6.022 x 1023 particles of the substance. M is traditionally
ONE MOLE
expressed using the units g/mol. The molar mass of elementary substances made
32.07 g S up of atoms has the same magnitude as their average relative atomic mass. Thus,
253.8 g I2
the molar mass of helium is 4.003 g/mol and that of calcium is 40.08 g/mol. These
are the masses of 6.022 x 1023 atoms of each of these substances. For molecular
elementary substances, such as hydrogen and oxygen, the molar mass is equal to
24.31 g Mg the mass of one mole of molecules and has to be calculated taking into account
63.55 g Cu the number of atoms present in each molecule:

MOLAR MASS M(H2) = 2 x M(H) = 2 x 1.008 = 2.016 g/mol

The same procedure can be applied to calculate the molar mass of any molecular
compound, using the chemical formula to determine the number of atoms of each
type in its molecules. For example, the molar mass of carbon dioxide is:

M(CO2) = M(C) + 2 x M(O) = 12.01 + 2 x 16.00 = 44.01 g/mol

The molar mass of an ionic compound, such as aluminum chloride AlCl3(s), rep-
resents the mass of 6.022 x 1023 formula units of this substance:

M(AlCl3) = M(Al) + 3 x M(Cl) = 26.98 + 3 x 35.45 = 133.33 g/mol


By Andrew Magill (Derivative from Original)
[CCA: 2.0 Generic] via Flickr Commons

The molar mass of a substance is a useful quantity as it can be used to calculate


the amount of substance n present in any sample; once n is calculated we can use
equation (1.4) to determine the number of particles in the system. The amount of
substance (in moles) n is a measure of how many times larger, or smaller, the mass
M(H2O) = of the sample m is compared to the molar mass of the substance M:
18.02 g/mol
(1.5) n=m/M

For example, if we know that a medium-size car releases around 400. g of CO2(g)
into the atmosphere per mile that it moves, we can calculate the amount of sub-
stance n and the number of particles N that it emits along that distance:

n = m / M = 400. / 44.01 = 9.08 moles of CO2(g)


N = n x NA = 9.08 x 6.022 x 1023 = 5.47 x 1024 CO2 molecules.
Chemical Thinking U1 How do we distinguish substances? 49

LET’S THINK Breathing AIr

As we move to higher altitudes, the concentration of oxygen gas in the atmosphere decreas-
es as shown in the following table. This reduces the likelihood of oxygen molecules, O2,
dissolving in our blood. As a result, we may suffer hypoxia (oxygen deprivation).

h (km) C (g/L) n (mol/L) N (molecules/L)


0 (Sea level) 0.283
0.7 (City of Tucson) 0.260
8.8 (Top of Mount Everest) 0.111
12 (Airplane cruising altitude) 0.065

• Use the information in the table to calculate the amount of substance n and the num-
ber of molecules N per liter of air at different altitudes. Analyze how many times fewer
molecules there are at the different altitudes compared with the number at sea level.

Share and discuss your ideas with a classmate.

USEFUL TOOLS tity is expressed. To do the conversion one


needs to:
One critical chemical thinking skill is the abili-
a) Identify the original and the new units of
ty to use experimental results for the mass or
the quantity to transform. For example, if we
volume of different substances and calculate
want to know how many atoms of carbon are
the number of particles in the system. One
present in 0.030 moles of this chemical ele-
can use equations (1.4) and (1.5) to accom-
ment, we can set the problem as:
plish the task, but sometimes it is easier to
rely on appropriate conversion factors. Let’s
0.030 mol (old unit) = ? atoms (new unit)
analyze how to do it.
b) Multiply the original quantity by the proper
Factor-Label Method. This problem-solving unit conversion factor that will replace the old
strategy is based on the fact that any number units by the new ones by cancellation:
can be multiplied by one without changing its
value. The challenge is to express the multi- 6.022 x 1023 C atoms
plicative “one” as a proper unit conversion 0.030 mol C(s) x
factor. 1 mol C(s)
Unit conversion factors can be built
from any two terms that describe equivalent c) Perform the mathematical operations indi-
amounts of a physical or chemical quantity. cated by the resulting expression:
For example, we can use the identity
0.030 x 6.022 x 1023 = 1.8 x 1022 C atoms
1 mol of atoms = 6.022 x 10 atoms
23

Using this approach we can directly transform


to build these two unit conversion factors: from mass to number of atoms, or vice versa,
using a single unit conversion factor:
1 mol of atoms 6.022 x 1023 atoms
or 12.01 g of C(s)
6.022 x 1023 atoms 1 mol of atoms 1.8 x 1022 C atoms x
6.022 x 1023 C atoms
These types of unit conversion factors can be
used to transform the units in which a quan- = 0.36 g of C(s).
50 MODULE 3 Analyzing Particles

Quantification
The ideas presented in the previous sections are useful for quantifying the number
of moles or particles of substances present in different states in diverse environ-
Figure 1.29 The transforma- ments. If the substance is in the solid state, for example, we can measure the mass
tion from mass (m) to number (m) of the sample using a balance and use the molar mass (M) of the substance to
of particles (N), or vice versa,
is facilitated by calculating the calculate the number of moles (n). These number of moles can then be converted
moles of substance using the
molar mass (M) and Avoga- into number of particles (N) using Avogadro’s Number (NA). Figure 1.29 sum-
dro’s Number (NA). marizes the relationships that can be used to accomplish these transformations:

AMOUNT
n=m/M OF N = n x NA
SUBSTANCE
m=nxM n n = N / NA
NUMBER OF
MASS PARTICLES
m NA = 6.022 x 1023 N
If the substance of interest is a liquid, we need information about the density
(d) of the fluid to calculate the number of particles present in the system. The mass
of a volume V of the sample will be given by: m = V x d. Once the mass is known,
the number of moles (n) and the number of particles (N) can be determined using
the relationships summarized in Figure 1.29.
In many situations, the substances of interest are dissolved in a liquid solvent
such as water. When working with an aqueous solution of a given substance A
(the solute), it is common to express the concentration of A in the mixture as the
ratio of the number of moles solute A, n(A), to the volume, V, of the solution:
[A] = n(A)/V. The quantity [A] is known as the “molar concentration” or the “mo-
larity” of solute A. Common units for the molar concentration are mol/L, also
expressed as “M” (molar).

LET’S THINK Molar Concentration


Many substances that we use or interact with in our daily lives are dissolved in water forming aqueous
solutions. In these cases, it is important to know how to quantify their amounts or concentrations.

• Commercial vinegar contains close to 5 g of acetic acid (CH3COOH) per 100 mL of solution.
What is the molarity of acetic acid in vinegar?
• Household bleach is approximately a 0.85 M solution of sodium hypochlorite (NaOCl). How
many grams of NaOCl are present in a cup (~250 mL) of bleach?
• The average molarity of citric acid (C6H8O7) in orange juice is close to 0.01 M. Imagine you
wanted to prepare a solid tablet containing as much citric acid as that present in 500 mL of
orange juice. What mass of citric acid would you need to measure?
• Aqueous solutions of sodium chloride (common salt) used for brining foods have concentra-
tions close to 3.5% in mass. What is the molarity of these solutions?

Share and discuss your ideas with a classmate, and clearly justify your ideas.
Chemical Thinking U1 How do we distinguish substances? 51

Many substances of interest in our surroundings are in the gas state. In these
cases, we can apply our knowledge about the macroscopic and submicroscopic
properties of gases to develop a strategy to estimate the number of moles or the
number of particles in a given sample. For example, if we assume that the gases
behave ideally, we can use equation (1.3) to determine the number of particles
N given information about the temperature T, pressure P, and volume V of the
system. Using the relationship between amount of substance n and number of par-
ticles as expressed by equation (1.4), we could also calculate the value of number
of moles (n) given by:

(1.6) n = N / NA = P V / ( NA kB T ) = P V / ( R T )

where the constant R = NA x kB is known as the universal gas constant (see Figure R values Units
1.30). This expression can also be used to make quick estimations about the vol- 8.314 J K–1 mol–1
ume or the pressure of certain mass m of a gaseous substance with a molar mass M
0.08206 L atm K–1 mol–1
at any temperature. For this purpose we can combine equations (1.5) and (1.6) to
generate the following expression for the equation of state of an ideal gas: 1.986 cal K–1 mol–1

Figure 1.30 The universal


(1.7) P V = n R T = m R T / M. gas constant R can be ex-
pressed in different units.

Using this relationship, we can estimate the volume in liters (L) occupied
by 1 mol of gas at certain pressure and temperature. In particular, let’s take T =
273.15 K (0 oC) and P = 1 atm (760 mmHg), which are traditionally identified
as standard conditions for temperature and pressure (STP) in experimental mea-
surements. Using equation (1.7), together with the value of R in proper units (see
Figure 1.30), we get:

nRT 1 x 0.08206 x 273.15


V= = = 22.41 L
P 1

If we assume that gases behave ideally, this volume will be the same independently
of the type of substance that we have. When T and P change, the volume of a gas
changes and so does the density or concentration of the gaseous substance.

Identification LET’S THINK


The equation of state of the ideal gas as expressed in equation (1.7) can also be used to find the iden-
tity of unknown gases by using their molar mass M as differentiating characteristic. Imagine that you
measured the volume occupied by 2.8 x 10-3 g of an unknown pollutant at standard temperature and
pressure. Your results show that the gas sample occupies a volume of 2.24 mL.

• What is the molar mass of the pollutant?


• If you knew that the pollutant is a chemical compound made of carbon and oxygen, could
you infer what its chemical formula is?

Share and discuss your ideas with a classmate, and clearly justify your ideas.
52 MODULE 3 Analyzing Particles

Gaseous substances in our environment are normally mixed with other com-
ponents forming homogeneous solutions, as is the case of the air that surrounds
us. Thus, it is common to use concentrations rather than total amounts when
quantifying their presence in any given system. The concentration give us infor-
mation about how much of a substance we have per unit volume of the mixture.
For example, we could indicate how many micrograms per cubic meter (mg/m3),
how many moles per liter (mol/L), or how many molecules per cubic centimeter
(molecules/cm3) of a certain substance we have. No matter what units we use, the
ideas discussed in this module can be applied to convert from one unit to another.

LET’S THINK Clean Air

The Environmental Protection Agency (EPA) has set National Ambient Air Quality Standards for
various pollutants. These standards set the maximum concentrations not to be exceeded in certain
average time (as measured at 25 oC and 1 atm):

Pollutant Max (mg/m3) Average Time mol/L # molecules/mL


CO(g) 1.03 x 101 8-hour
NO2(g) 9.97 x 10–2
Annual
SO2(g) 7.85 x 10–2
Annual

• Express the maximum concentrations for these different substances in moles/L and number
of molecules/mL? (1 m3 =1000 L; 1 L =1000 mL; 1 g = 1000 mg).
• How much would the concentration limits change if the temperature was 0 oC?

Share and discuss your ideas and calculations with a classmate.

LET’S THINK Harvesting Air

Most of the nitrogen and oxygen that we use for practical purposes are extracted from air. But
exactly how much of each of these chemical elements can we get from every liter of air?

• Based on what you have learned in this module, design and implement a strategy to calcu-
late the mass in grams of oxygen and nitrogen that can be extracted per liter of air at stan-
dard temperature and pressure.
• Analyze how your results would change at higher altitudes, where the pressure may decrease
to half its value at sea level and the absolute temperature may be lower by 10%.

The following information may be useful in completing this task:

a. The %volume of N2(g) and O2(g) in the atmosphere are


78.08% and 20.95%, respectively.
b. The volume of one mole of ideal gas at STP is 22.41 L.
c. For an ideal gas, V = nRT/P.

Discuss and share your ideas with one of your classmates.


Chemical Thinking U1 How do we distinguish substances? 53

FACING THE CHALLENGE [O3(g)], and sulfur dioxide [SO2(g)].


Carbon monoxide is a toxic substances that we
cannot detect with our senses. Once it enters into
Clean Air? the bloodstream, it disrupts the delivery of oxy-
Our ability to monitor the quality of the air we gen throughout the body. CO(g) is often produced
breathe strongly depends on the clever applica- when carbon-containing compounds are burned
tion of many of the ideas discussed in this module. in closed spaces with limited oxygen supply, such
Ambient monitoring, this is the determination of as in stoves or inside the combustion engines of
pollutant concentration in ambient air, can now our cars. Carbon monoxide poisoning is respon-

By Wurstsalat (Own work) [CCA: Sahre Alike 3.0], via Wikimedia Commons
be done in real-time us- sible for the death of millions
ing instruments that can of people every year in devel-
measure very small con- oping countries. Thus, moni-
centrations with very fast toring its concentration in
response times (seconds to local environments is of cen-
minutes). Many of these tral importance. In the US,
measurements are based emissions of CO(g) by cars
on the determination of dropped 60% from 1990 to
the amount of light ab- 2005 thanks to technological
sorbed by individual pol- advances in car manufactur-
lutants, absorption that is ing.
frequently proportional to the concentration of Ozone is a gas with a sharp odor, one that can
molecules of that substance in an air sample. In- be smelled around photocopier and electric mo-
formation about amount of substance (in moles) tors. It is a toxic substance that harms lung func-
or number of molecules can then be expressed in tion and irritates the respiratory system. O3(g) is
terms of mass per unit volume if we know the mo- produced through the interaction of other pollut-
lar mass of the pollutant and the temperature and ants with high-energy radiation from the Sun. This
pressure at which the measurements were taken. substance is one of the most closely monitored in
Most major cities and towns in the world are urban areas, and one of the main causes of envi-
equipped with air-quality monitoring stations that ronmental alerts in large cities.
track the concentration of pollutants, sometimes Nitrogen dioxide and sulfur dioxide are also
on an hourly basis. These concentrations are then toxic substances that cause irritation of the respira-
compared to the air-quality standards in force and tory system. One of the main sources of NO2(g) is
alerts, warnings or emergencies may be declared the burning of gasoline in car engines. The burning
if the air quality is not satisfactory. In the United of coal for the production of electric power is the
States, the Clean Air Act passed in major source of SO2(g) emissions.
1970 requires the Environmen- Regulations enacted through the
tal Protection Agency (EPA) to Clean Air Act have helped re-
set National Ambient Air Quality duce local average concentrations
Standards for pollutants consid- of NO2(g) by 46% and those of
ered harmful to public health and SO2(g) by 71% in the last thirty
the environment. These standards years in the US.
define maximum expected con- The concentrations of these
centrations of six major pollutants major pollutants in metropolitan
in clean outdoor air. These pol- areas are used to calculate the so-
lutants include four atmospheric called Air Quality Index (AQI)
gases: carbon monoxide [CO(g)], traditionally listed in the daily
nitrogen dioxide [NO2(g)], ozone forecast section of newspapers.
By EPA
54 MODULE 3 Analyzing Particles

Let’s Apply
Ozone Matters
Some chemical elements can exist in different forms, or allotropes. That is the case of oxygen,
which in its most stable form is made up of O2 molecules, but can also exist as ozone, a substance
composed of molecules with three oxygen atoms, O3. Ozone gas affects the respiratory system even
at very low concentrations and damages the leaves and needles of trees.
ASSESS WHAT YOU KNOW

O3(g) is called a secondary pollutant because it is not directly emitted into the atmosphere, but
produced from chemical reactions between O2(g) and other pollutants such as NO2(g), stimulated
by the presence of sunlight. Ozone concentrations are monitored regularly in major cities across
the world. In the US, the EPA has set the clean air quality standard for this substance at an average
of 0.16 mg/m3 at 25 oC and 1 atm over an 8-hour period.

Concentrations

The following map shows the evolution of O3(g) concentrations in Tucson, Arizona on No-
vember 6, 2013.

• Analyze the variations CLICK TO PLAY


in the concentrations mg/m3
of O3(g) along the +0.736

day. How would you 0.228 - 0.735

http://www.airinfonow.com/html/ozone.html
explain these changes? 0.208 - 0.227
• Estimate the lowest
0.188 - 0.207
and highest concen-
trations of ozone in 0.169 - 0.187

moles/L. 0.149 - 0.167

• Concentration of O3 0.133 - 0.148


above 0.17 mg/m3 are 0.116 - 0.132
considered harmful.
What is this limit in 0.0087 - 0.115

molecules/L? 0.0060 -0.0086

• What is this limit in 0.0030 - 0.0059


moles of O3 per mole 0 - 0.0029
of air at 25 oC? (Hint:
Calculate the volume in liters of 1 mole air at 25 oC?
• How would the lowest and the highest concentrations of O3(g) change if the temperature
decreased from 25 oC to 5 oC?

Share and discuss you ideas with a classmate, and clearly justify your reasoning.
Chemical Thinking U1 How do we distinguish substances? 55

Breathing

On average, people take 24,000 breaths each day.  One single breath has a volume
close to 0.5 L.

• Estimate the total number of particles in one single breath of air at STP condi-
tions.
• Estimate the total number of O3 molecules breathed by one person living in
Tucson on August 18, 2010 assuming an average concentration of 0.1 mg/m3
of O3 across the day.

ASSESS WHAT YOU KNOW


• Estimate the total number of O2 molecules breathed by the same person
during the day. What percentage of all the oxygen particles breathed by this
person were O3 molecules?

Share and discuss your ideas with one of your classmates, and clearly justify your
reasoning and procedures.

Good Ozone

The graph on this page (NASA source) shows the concentration of ozone as a
function of altitude in the atmosphere. The region with high ozone concen-
trations defines the so-called “ozone layer.” The concentration in this graph is
expressed in parts per million in volume (ppmv). One ppmv of O3 is equiva-
lent to 1 mole of O3 in one
100
million moles of air.
Thermosphere
80
• Estimate the volume
of one mole of air at
T = -40 oC
P = 2 x 10–3 atm
Altitude (km)

60
the temperature and Mesosphere
pressure where ozone
40
concentrations reach
their maximum.
20
• Use your result and the Stratosphere

data from the graph 0


Troposphere
to estimate the num- 0 3 6 9
Ozone (ppmv)
ber of moles, the mass
in grams, and the number of particles of O3 in one liter of air in the
ozone layer.

Discuss your ideas with a classmate, and clearly justify your reasoning and
procedures.
56 MODULE 3 Analyzing Particles

Let’s Apply
Greenhouse Gases
Some atmospheric gases, such as CO2(g) and CH4(g), absorb infrared radiation emitted by both the
Sun and our own planet, trapping thermal energy in the atmosphere. They are called greenhouse
gases and help sustain average global temperatures favorable to life on Earth. They are also thought
to be responsible for the current increase in average temperatures across the world (global warm-
ASSESS WHAT YOU KNOW

ing) due to their much higher concentration in the atmosphere compared to pre-industrial times.
The following table includes important information for the analysis of the properties and effects of
major greenhouse gases in our planet:

Substance Concentration* Concentration* Lifetime GWP


(Pre-1750) (Recent Times) (Years) (over 100 years)
CO2(g) 504 mg/m3 695 mg/m3 variable 1
CH4(g) 459 mg/m3 1224 mg/m3 12 25
N2O(g) 486 mg/m 3
581 mg/m 3
114 298
CCl2F2(g) 0 2.61 mg/m3 100 10,900
*At 25 C and 1 atm
o

The lifetime in this table is a measure of the average time it takes for the concentrations of
a given substance to return to its natural value following an increase in its concentration in the
atmosphere. The global warming potential (GWP) is a measure of the thermal energy trapped per
unit mass of the greenhouse gas relative to that of a reference gas (CO2(g)). The GWP is calculated
over a specific time interval as its value depends on the lifetime of each species.

Concentrations

Using the concentrations provided in the table for the different green-
house gases:

• Calculate the percent increase in the concentration of each gas in


the atmosphere from pre-industrial to present time. Investigate
what are the main sources of these four substances in modern so-
cieties, and propose an explanation for why some concentrations
have increased more than others.
• Express all the concentrations in the table in moles/L and in
number of molecules/mL.

Share and discuss you ideas and calculations with a classmate, and
clearly justify your reasoning and procedures.
Chemical Thinking U1 How do we distinguish substances? 57

GWP

The scale for the global warming potential (GWP) of a substance is set using CO2(g)
as a reference; in particular, the GWP for this gas is taken to be equal to one. Thus, if
the GWP for CH4(g) is 25, this implies that 1.0 g of methane traps the same amount
of thermal energy in the atmosphere as 25.0 g of CO2(g) do. Based on this informa-
tion:

• Estimate the number of molecules of CO2 needed to trap as much thermal


energy as:
a) 1 molecule of CH4;

ASSESS WHAT YOU KNOW


b) 1 molecule of N2O;
c) 1 molecule of CCl2F2;
• Which would be the advantages and disadvantages of expressing GWP as ther-
mal energy trapped per molecule rather than per gram of substance?

Share and discuss your ideas with one of your classmates, and clearly justify your
reasoning and procedures.

CFC’s

Chlorofluorocarbons (CFC’s), such as CCl2F2, are synthetic substances that were


used as refrigerants in cars and air conditioning systems but have been banned
due to their ability to react with ozone in the stratosphere and thus destroy the
ozone layer. Although present in very small concentration in the atmosphere,
CFC’s tend to have a very high GWP and are responsible for close to 10% of
atmospheric warming. CClF3

Although chlorofluorocarbons (CFC’s) were banned in 1996, there are still ap-
proximately 100 million functioning air conditioning units that use CCl2F2. If
each of these air conditioning units contains 1.1 kg of this compound and leaks CCl3F
25% a year:

• How many moles of CCl2F2 molecules are added to the atmosphere yearly?
• How many moles of CO2 molecules would have a warming effect equiva-
lent to that of the amount of CFC released every year?
• Americans produce close to 1.97 x 103 kg of CO2(g) per capita every year.
How many people would be needed to produce CO2(g) in amounts that
could have the same warming effect as the CFC released?
CHClF2
Share and discuss your ideas with one of your classmates, and clearly justify your
reasoning.
58

Determining
Composition
Most of our discussions about the properties of different substances have been
U1: MODULE 4
based on the assumption that we somehow know, or can know, the chemical
composition of the particles of matter. We say, for example, that
water molecules, H2O, are made of two hydrogen atoms and
one oxygen atom and can use this information to calculate
water’s molar mass. Even in dealing with more complex sub-
stances such as the most common form of hemoglobin in
human blood, we dare to claim that its chemical formula
is C2952H4664N812O832S8Fe4. How do we know? Our ability
to generate reliable information about the chemical com-
position of substances is based on the clever combination
of experimental evidence gathered using a variety of analytical Hemoglobin
techniques, together with theoretical principles and models of matter Molecule

at the submicroscopic level that guide the collection and interpretation of data.
The development of experimental strategies that can be used to derive the
chemical composition of substances relies to a great extent in models of the struc-
ture of matter at the “subatomic” level. This is, models devised to describe, explain,
and predict the internal structure of the atoms that make up molecules or ionic
networks. Thus, we need to zoom into an even smaller length scale to better un-
derstand what atoms are made of and what distinguishes one atom from another.

THE CHALLENGE Volatile Compounds

Many household products such as paints, varnishes, cosmetics, and adhesives


contain volatile substances that easily evaporate and pollute indoor air.

• How could you determine the chemical composition of these volatile


compounds?
• What would you measure to establish, for example, what percentage of
their mass is made of carbon or oxygen atoms?

Share and discuss your ideas with one of your classmates.

Module 4 is designed to help you develop the type of chemical thinking that is
needed to characterize the chemical composition of a substance of interest. In par-
ticular, the central goal of Module 4 is to discuss how to use experimental data
to determine the atomic composition of the particles that make up a chemical
compound.
Chemical Thinking U1 How do we distinguish substances? 59

Subatomic Model of Matter


According to the atomic model of matter, differences in properties between sub-
stances are the result of differences in the atomic composition of their particles.
But what makes an atom different from each other? For example, why do oxygen
atoms have a relative mass of 16.00 amu while the mass of argon atoms is close

By Zátonyi Sándora, (ifj.) (Own work)


to 40.00 amu? The answers to these types of questions are important if we want

via Wikimedia Commons


[CCA: Share Alike 3.0]
to devise strategies to identify the different types of atoms present in the particles
that make up a substance.
Experimental clues about the internal structure of atoms have been gathered
by many natural philosophers and scientists across centuries. Of particular rel-
evance were those experiments that revealed that matter had electrical properties.
For example, experiments showed that solid materials rubbed against each other Figure 1.31 The trajectory
could acquire electrical charge of opposite signs; that metallic substances allowed of electron beams (cathode
rays) is affected by the pres-
the movement of electric charge from one region to another; that metals could ence of a magnet. This indi-
cates that electrons have an
emit charged particles when heated up or when illuminated with certain types of electric charge.
light; and that some chemical elements, called radioactive elements, would trans-
form into other elements by emitting charged particles. All this evidence suggested
that atoms were made up of subatomic particles with electrical charge. The chal-
lenge was then to model how these particles were arranged inside an atom to best
explain the known properties of matter.

Comparing Models LET’S THINK


Positive
In 1904, Joseph J. Thomson proposed that atoms may be modeled as com- Charge
posed of tiny “corpuscles” with negative charge enclosed in a sphere of positive
charge that made the whole atom electrically neutral (plum pudding model of
the atom). In fact, Thomson discovered the existence of the negatively charged
particles, later called electrons, in an experiment in which electrons were
forced out of materials by applying a strong electric field (see Figure 1.31). Negative
Charge
Positive
Charge
In 1911, Ernest Rutherford proposed a different atomic model. In this case,
electrons were assumed to move through empty space, circling around a
nucleus composed of an equivalent number of positive charges due to the
attractive interactions between opposite charges. Positive particles in the
Negative
Charge nucleus were assumed to be much more massive than the electrons.

Imagine that you designed an experiment to test these two models in which a beam of positively
charged particles (similar in size and mass to an atomic nucleus in Rutherford’s model) were di-
rected at high speed at a thin piece of metal made of atoms arranged as shown in these images:

• What would each of the models predict will happen to the beam
of positively charged particles as it interacts with the atoms in the
system? Would the models predict particles to go through the thin
metal foil, bounce back, or at least deviate from their trajectory?

Share and discuss your ideas with a classmate, and clearly justify your reasoning.
60 MODULE 4 Determining Composition

Experiments such as the one described in the previous activity were conducted
by Hans Geiger and Ernest Marsden, under the direction of Ernest Rutherford,
CLICK TO PLAY in 1909. They observed that most positively charged particles in the beam passed
through the thin metal foil without much change, but a small fraction
of them suffered major deviations from their original trajectory. These
experimental results can be better explained by Rutherford’s planetary
model of the atom (see Figure 1.32) which proposes that most of the
mass of an atom is concentrated in a positively charged tiny nucle-
us while most of the atom’s volume, where electrons are in constant
movement, is empty space.
Many aspects of Rutherford’s model of the atom at the subatomic
level have been experimentally confirmed in the past hundred years.
So, the modern atomic model also conceives atoms as particles com-
posed of tiny nuclei but made up of two types of subatomic particles:
positively charged particles, called protons, together with particles
Figure 1.32 Rutherford’s with no net electrical charge, called neutrons. A single proton (p+) has a mass of
atomic model best explains
the results from Geiger-Mars- 1.673 x 10–27 kg and an electric charge of +1.602 x 10–19 Coulombs (C); a single
den’s experiment. Click the neutron (n0) is slightly more massive than a proton, with a mass of 1.675 x 10–27
image to play the animation.
kg. On the other hand, a single electron (e-) has a negative electric charge equal in
magnitude to that of a proton, –1.602 x 10–19 C, but its mass (me = 9.109 x 10–31
kg) is over 1800 times smaller than that of the nuclear particles. The radius of a
typical atomic nucleus is over ten thousand times smaller than the radius of the
actual atom. So, if the radius of an atom is a fraction of a nanometer, the radius of
the atomic nucleus is only a few femtometers (1 fm = 1 x 10–15 m; see Figure 1.33).
This is analogous to a pinhead in the middle of a football stadium.

~10–10 m ~10–14 m

neutron
Nucleus NUCLEUS
Figure 1.33 Representation electrons proton
of the subatomic model of the
atom. The yellowish volume
represents the space where
ATOM
electrons move.

By convention, it is common to express atomic charges using the charge of


a proton as the unit of measurement. Thus, in these elementary charge units the
charge of a proton is equal to +1 and that of an electron is equal to –1. Atoms are
neutral entities with no net electric charge. This implies that a neutral atom has the
same number of protons and electrons. To explain the existence of ions, the model
assumes that atoms can lose or gain electrons. For example, if a particle loses one
electron its net charge will be +1, given that there will be one more proton than
electrons. If the particle gains one electron, its net charge will be –1 as now there
will be more electrons than protons. Given that the mass of an electron is very
small compared to that of other subatomic particles, losing or gaining a few elec-
trons does not significantly change the atomic mass.
Chemical Thinking U1 How do we distinguish substances? 61

One of the most fundamental assumptions of the subatomic model of matter


is that the identity of an atom is determined by the number of protons in its nucleus,
also called its atomic number Z. Thus, while all hydrogen atoms have only one
proton in their nuclei (Z = 1), the nuclei of all carbon atoms have six protons
(Z = 6) and those of uranium atoms have ninety two of these subatomic particles
(Z = 92). The atomic number is in fact the property that is used to sequentially
arrange the different types of chemical elements in the Periodic Table. Thus, when
an atom loses or gains electrons and becomes an ion, its chemical identity is pre-
served because its atomic number has not changed. This does not imply, however,
that the physical and chemical properties of the ions will be the same as that of

http://www.cbc.arizona.edu/tpp/chemthink/resources/U1_M4/ms.html
their parent atoms; in fact, they usually are quite different. Figure 1.34 Click on the im-
age to open an animation of
The subatomic model of matter has guided the development of experimental the internal processes in a
techniques that are very useful in the task of determining the composition and mass spectrometer.

structure of the particles that make up a substance. Such is the case of


a powerful analytical technique known as Mass Spectrometry (MS). In
this technique, a sample of the substance to be analyzed is ionized by pro-
viding enough energy to free some electrons from nuclear attraction and
to break molecules apart (see Figure 1.34). The fragments that are formed
tend to be cations with a +1 electric charge and they can thus be acceler-
ated and separated using a combination of electric and magnetic fields.
Ions with different mass-to-charge ratios (called m/q or m/z ratios) follow
different trajectories in a magnetic field and thus reach different areas in
a detector. A mass spectrometer provides information about the relative
mass of each of the different types of ions that are generated and about the relative CLICK TO PLAY
proportion in which the ions are produced. As we will see later in this module, this
information is very valuable in the process of characterizing chemical substances.

Neon’s Case LET’S THINK


Imagine that you take a sample of natural neon gas, Ne(g), and run it through a mass spectrom-
eter. The image in this activity sketches the mass spectrum that you would get. The horizontal axis
establishes the value of the m/q ratio for the ions that
will be generated; this quantity can be seen as a direct
measure of the relative mass of the different ions. The 90.48%
vertical axis provides information about the percent
abundance of the ions produced during the analysis.
% Abundance

• Given that neon is an atomic elementary sub-


stance, how do you explain that the experiment 0.27%
produced three peaks with distinctive relative
masses instead of one?
9.25%
• What do these results tell you about the atomic
composition of natural Ne(g)?
18 19 20 21 22 23
m/q
Share and discuss your ideas with a classmate. Build a
model about the atomic composition of Ne(g) that may explain these experimental results.
62 MODULE 4 Determining Composition

Atomic Diversity
If all the atoms in a pure sample of an atomic elementary substance were identi-
cal, the mass spectrum of the substance should produce a single peak given that
all the atoms should have the same relative mass. The fact that this is not the case
for many of them, as we saw for the case of Ne(g) in the past activity, suggests that
there are different types of atoms in a natural sample of these elementary substanc-
es. But how is this possible if we already established that elementary substances are
made up of atoms of the same type? Given that the mass of an atom is essentially
determined by the sum of the masses of protons and neutrons in their nuclei, this
experimental puzzle has been solved by proposing that atoms of the same chemi-
cal element have the same number of protons (same atomic number Z), but may
differ in the number of neutrons that they have. If we define the mass number
A of an atom as the sum of the number of protons and neutrons in its nucleus,

Figure 1.35 Mass spectrum for (1.8) A = # p+ + # n0,


boron (B). For purposes of repre-
sentation, it is common to scale
all results so that the maximum we can say that there are atoms of a given chemical element that have the same
relative abundance is at 100. The
actual %Abundance of each iso- atomic number Z but different mass number A. These atoms are said to be iso-
tope is shown.
topes.
Stable isotopes of a chemical element exist with different percent abun-
Relative Abundance

80.1%
dance (%Abundance) in Nature. This information can be derived from the
mass spectrum of the chemical substance. For example, boron (Z = 5) has
two stable isotopes that can be represented using the following symbolism:
19.9% A 10 11
Z 5B 5 B
m/q As indicated by the mass spectrum in Figure 1.35, the percent abundance
of the isotope with 5 neutrons in the nucleus (boron-10, A = 10) is 19.9%, while
that for the isotope with 6 neutrons per atom (boron-11, A = 11) is 80.1%. This
information can be used to calculate the average relative atomic mass (r.a.m.) of
this chemical element, defined as the weighted mean mass of all of the isotopes
http://www.cbc.arizona.edu/tpp/chemthink/resources/U1_M4/ptis.html

in a natural sample of the substance. To do this calculation we need to know the


relative atomic mass of each of the isotopes as well as their percent abundance,
information that can be derived from the mass spectrum:

(1.9) r.a.m. =
S(Relative mass isotope x %Abundance)
Figure 1.36 Click on the im- 100
age to display a Periodic Table
of the chemical atoms that in-
cludes information about most 10.01 amu x 19.9 + 11.01 amu x 80.1
abundant isotopes. r.a.m = = 10.8 amu
100

This is actually the procedure used to calculate the average atomic mass of the
elemental atoms listed in the periodic table in Figure 1.36, where we also include
information about the three most abundant isotopes for each of the different types
of atoms. As shown in this table, there are elements, such as fluorine (F) and phos-
phorus (P), that only have one stable isotope, while most heavy atoms do not have
CLICK TO PLAY any stable isotopes as they tend to be radioactive.
Chemical Thinking U1 How do we distinguish substances? 63

By convention, the scale of relative atomic masses for different isotopes in Na-
ture has been set by assigning a value of exactly 12.00 amu to the relative atomic
mass of the isotope of carbon with a mass number A =12 (carbon-12). This is the
standard used to define the scale for the m/q-axis of mass spectrometers and to
precisely define the mole and Avogadro’s number. Based on this standard, a mole
of a substance is defined as the amount of substance that contains as many par-
ticles as there are atoms in 12.00 g of the isotope carbon-12; this is one Avogadro’s
Number (6.022 x 1023) of particles.

MS Identification LET’S THINK


Mass spectrometry is commonly used to identify chemical substances. Imagine, for example, that
you were assigned to find the identity of a toxic gas emanating from local sewage. You suspect the
substance is a molecular elementary substance with the generic chemical formula X2. The mass
spectrum of this substance is shown on this page.

• How many stable isotopes should atom X have to explain the observed number of peaks in
this mass spectrum?
100
• Use the spectrum to estimate the
relative atomic mass of each of 75.76% 57.40%
80
Relative Abundance

the stable isotopes;


36.73%
• What is the composition of the 60
particles responsible for each of
the peaks in this spectrum? 40
24.24%
• What is the average relative
atomic mass of atom X? The 20
5.87%
%Abundance of each species is
shown on the spectrum. 0
30 40 50 60 70 80
• Which chemical element is this? m/q

Share and discuss your ideas with a classmate, and clearly justify your reasoning and procedures.

Mass spectrometry is particularly useful in the determination of the relative


mass and molecular structure of chemical compounds. Take for example, the case Figure 1.37 Mass spectrum of
of water that produces a mass spectrum like that shown in Figure 1.37. The rela- water, H2O.
tive mass of the water molecule, 18 amu, can be inferred from 100
the location on the m/q-axis of the peak for the heaviest ion,
which corresponds to the molecular ion H2O+. The other ma- 80
H2O+
Relative Abundance

jor peak, with a relative mass of 17 amu, reveals the formation


of a molecular fragment in which one hydrogen atom has been 60
lost, the ion OH+. Additionally, there is a very small peak at 16
40
amu, corresponding to the ion O+, which does not form in great OH+
quantities during the experiment. The analysis of the potential O+
20
composition of the different fragments generated by MS is a use-
ful aid in the process of establishing the molecular structure of 0
15 16 17 18 19 20 21
chemical compounds. m/q
64 MODULE 4 Determining Composition

Often, but not always, the peak with the highest m/q value in the mass spec-
Figure 1.38 Mass spectrum of trum results from the detection of the molecular ion M+ (the ion of the intact
methane CH4. molecule), while peaks at lower m/q correspond to molecular fragments. How-
100 ever, the determination of the relative mass of the molecular
compound from its mass spectrum should be done taking into
CH4+
Relative Abundance

80 account that a fraction of the molecules in the sample will be


60
CH3+ made up of different isotopes. Thus, we may see small second-
ary peaks corresponding to molecular ions composed of the less
40 abundant isotopes. For example, the mass spectrum for meth-
CH2+ ? ane (CH4) in Figure 1.38 has a large peak corresponding to
20 CH+
C+ molecular ions CH4+ with a relative mass of 16 amu. These
0 ions are made up of the most stable isotopes of carbon and
11 12 13 14 15 16 17 18 hydrogen, carbon-12 and hydrogen-1. However, the spectrum
m/q
reveals the existence of a small fraction of CH4+ ions composed
of carbon-13 atoms with a relative mass of 17 amu. The actual average molecular
mass of this compound should thus be calculated taking into account the relative
mass and abundance of the different isotopic species. Although the mass spectrum
of large molecules can be quite complex, the determination of the molecular mass
of the substance and the analysis of the fragmentation pattern provide invaluable
clues about the composition and molecular structure of the chemical compound.

LET’S THINK MS Analysis



Methanol (CH4O) is a volatile chemical compound used extensively in the synthesis
of important products, such as plastics and gasoline additives. This substance is ranked
among the top five chemicals released into the atmosphere in the US. It is considered
a toxic substance that causes eye and respiratory track irritation. Consider the mass
spectrum for this substance:

• Identify the peak that


100
likely corresponds
to the molecular ion
80
Relative Abundance

CH4O+ and estimate its


relative molecular mass; 60
• Based on the chemical
formula of methanol 40
and data from the spec-
20
trum, infer the chemi-
cal composition of the
0
different ions that led 0 10 20 30 40
to all the visible peaks m/q
in this spectrum.
• Try to identify those peaks in the mass spectrum that may correspond to ions
made up of less abundant isotopes of carbon, hydrogen, or oxygen.

Share and discuss your ideas with a classmate, and clearly justify your reasoning and
procedures.
Chemical Thinking U1 How do we distinguish substances? 65

Combustion Analysis
In general, mass spectrometry provides qualitative information about the types
of atoms that are present in a chemical compound; in particular, we can use their
relative masses to identify them. However, MS does not necessarily tell us the
number of atoms of each type that make up a molecule, or the percentage of the
mass of a compound that corresponds to atoms of a given element. To generate
this information we need to use other methods, such as combustion analysis.
As its names indicates, combustion analysis is based on burning a known
amount of the substance of interest in the presence of oxygen gas O2(g). During
this process, chemical compounds of well known composition, such as H2O(g)
Figure 1.39 Typical experi-
and CO2(g), are formed and collected, weighing their masses with precision (see mental setup for combustion
Figure 1.39). This information is then used to determine the mass percentages of analysis. Modern instruments
perform this analysis in an au-
the different chemical elements present in the sample. tomated manner.

Combustion analysis generates elemental composition in mass percentage that


can be used to determine the chemical formula of the compound. To better un-
derstand how the method works, let us discuss a specific example step by step.
Recently, the analysis of some cosmetics has revealed the presence of a potentially
toxic substance. Combustion analysis of this molecular compound indicates the
following chemical composition in percent mass: 54.53% carbon (C), 9.152%
hydrogen (H), and 36.32% oxygen (O). To determine the chemical formula of
this compound we can follow a systematic procedure:

1. Assume that you have a 100.0 g of the substance and calculate the total mass of
each type of atom or element present in the system. In this case we get:

m(C) = 100.0 x 0.5453 = 54.53 g m(H) = 100.0 x 0.09152 = 9.152 g

m(O) = 100.0 x 0.3632 = 36.32 g

2. Calculate the number of moles (n = m/M) of each type of atom present in the
sample. The molar masses of the elemental atoms are needed to complete this
calculation:
1.000 mol C
n(C) = 54.53 g C x = 4.540 mol C
12.01 g C
1.000 mol H
n(H) = 9.152 g H x = 9.079 mol H
1.008 g H
1.000 mol O
n(O) = 36.32 g O x = 2.270 mol O
16.00 g O
66 MODULE 4 Determining Composition

3. Compare the amounts of the different atoms that make up the substance by
taking mole ratios with respect to the type of atom present in the lowest amount:

ratio(C/O) = 4.540 mol C / 2.270 mol O = 2.000 C to 1.000 O

ratio(H/O) = 9.079 mol H / 2.270 mol O = 4.000 H to 1.000 O

These mole ratios state the proportion in which different types of atoms are pres-
ent in the system. In our specific example, these ratios indicate that we have twice
the number of carbon atoms and four times the number of hydrogen atoms per
atom of oxygen in each of the molecules that make up the substance. We can
use this information to establish the so-called empirical formula of the chemical
compound. The empirical formula states the simplest whole number ratio of the
atoms or ions present in a molecule or formula unit of a chemical compound. In
Figure 1.40 Mass spectrum of our example, the empirical formula is C2H4O.
the potentially toxic substance
found in cosmetics.
4. Calculate the relative mass (or the molar mass) of an
100
empirical formula of the compound and compare it to the
relative mass (or the molar mass) of the actual compound as
Relative Abundance

80
determined by, for example, mass spectrometry. In our case
60 M+ we have:

40 M(C2H4O) = 2 x 12.01 + 4 x 1.008 + 16.00 = 44.05 g/mol
20
The molar mass of the unknown compound X, as de-
0 termined from the mass spectrum in Figure 1.40, is
0 20 40 60 80 100 88.10 g/mol. Taking the ratio of these two values we get
m/q
M(X) / M(C2H4O) = 88.10 / 44.05 = 2.000. The ratio of
masses suggests that the molecules of the compound contain two times the number
of each type of atom as present in the empirical formula. Thus, we can conclude
that the actual chemical formula of the unknown substance should be C4H8O2.
This is, in fact, the chemical formula of dioxane, a probable human carcinogen.

The determination of the chemical formula of a chemical compound using this


procedure is usually straightforward. However, complications may arise in estab-
lishing the empirical formula, particularly in those cases where the mole ratios as
calculated in step 3 are not whole numbers. In these situations, all the mole ratios
need to be multiplied by a common factor that transforms them into the lowest
whole numbers that maintain the same proportions. For example, imagine that
Dioxane you obtain the following mole ratios in the analysis of a molecular compound
Molecule made up of carbon, hydrogen, and oxygen atoms:

ratio(C/O) = 2.000 C to 1.000 O ratio(H/O) = 3.333 H to 1.000 O

To transform these mole ratios into the smallest whole numbers without changing
the actual proportions, we should multiply both of them by 3. This leads to a 6 to
3 proportion for C to O atoms, and a 10 to 3 proportion for H to O atoms. The
empirical formula of this compound results then to be C6H10O3.
Chemical Thinking U1 How do we distinguish substances? 67

Chemical Formulas LET’S THINK


Consider these two problems related to the analysis of pollutants in the air we breathe:

The analysis of the exhaust gases from


motor traffic reveals the presence of a 100
carcinogenic substance. Combustion
analysis reveals that the substance 80 M+

Relative Abundance
contains 92.26% C and 7.74% H.
The mass spectrum of the substance 60
is shown.
40
• Estimate the molar mass of this
molecular compound; 20
• What is the empirical formula of
this compound? 0
0 15 30 45 60 75 90
• What is the molecular formula m/q
of this compound?

The analysis of indoor air in some Tuc-


100
son homes treated for termites reveals
the presence of a harmful substance
80 that affects the nervous system. Com-
Relative Abundance

bustion analysis provides the follow-


60 ing percent composition: 29.31% C,
1.476% H, and 69.22% Cl.
40
• Estimate the molar mass of this
M+ molecular compound;
20
• What is the empirical formula of
0 this compound?
0 100 200 300 400 500
m/q • What is the molecular formula
of this compound?

Share and discuss your ideas with a classmate, and clearly justify your procedures.

Combine and Conquer


We started Unit 1 by discussing the importance of separation techniques based
on specific differentiating characteristics in the process of analyzing chemical sub-
stances. Our work in this module has shown us how we can use methods of ele-
mental analysis, such as mass spectrometry and combustion analysis, to determine
the chemical composition of the particles that make up elements and compounds.
To finish Unit 1 it seems appropriate to describe how these different analytical
techniques can be combined to answer the central question of the Unit: How do
we distinguish substances? In particular, we will focus on the combination of two
powerful strategies, chromatography and mass spectrometry.
68 MODULE 4 Determining Composition

One of the most powerful set of separations techniques currently used in in-
dustrial, medical, and scientific research labs around the world receives the name
of chromatography. These separations strategies are based on the recognition that
the strength of the interaction forces between different substances will depend
on the chemical composition and structure of their atoms, ions, or molecules.
In general, chromatographic techniques involve the passing of a mix-
Standard B ture in liquid or gas phase (mobile phase) through a stationary phase,
A
typically a liquid or a solid deposited on a plate or enclosed in a chro-
matographic column. Components of the mixture in the mobile phase
that are strongly attracted to the stationary phase will take more time
to pass through the system and will exit at later times than those that
Unknown A B exhibit weaker interactions. Modern chromatographs include detectors
that register the time at which each substance exits the plate or column
(retention time), and the amount of substance that passes through it.
Thus, chromatography can be used to separate the components of the
mixture and to quantify the relative amounts in which they are present
in a sample (see Figure 1.41).
Figure 1.41 Typical chromatograph The combination of gas chromatography (GC) with mass spectrometry (MS)
showing the separation of chemical
compounds with retention times tR. in a combined technique known as GC/MS is perhaps one of the most powerful
The area under each peak is propor-
tional to the amount of substance. identification methods used nowadays in diverse fields, from forensic investiga-
Retention times can be used to iden-
tify substances in a mixture by com-
tions to environmental analysis. A GC/MS system is composed of a gas chromato-
parison to standards graph in which the evaporated mixture is carried by an inert gas through a capil-
lary column covered with a microscopic layer of liquid that serves as a stationary
phase. At the end of the chromatograph, a mass spectrometer takes the place of the
detector, analyzing each substance as it exits from the chromatographic column.
The combination of information about retention times and fragmentation pat-
terns provides solid evidence about the identity of each substance in the mixture.

LET’S THINK Modeling Separations

http://www.cbc.arizona.edu/tpp/chemthink/resources/U1_M4/chroma.html
Modeling the separation of substances in a chromatographic column can help us not only
better understand how the process occurs, but also identify the best conditions for separat-
ing a mixture if we have information about the properties of its components.

The simulation included in this activity allows you to investigate the effect of changing the
relative strength of the interactions between two substance and the stationary phase in a gas
chromatograph, as well as the flow rate at which the mixture is passed through the column.

• Use the simulation to determine the minimum


ratio of interaction strengths for substances B
CLICK TO PLAY

and R that allows you to fully separate the two


components at a given flow rate.
• Investigate how the flow rate affects substance
separation at constant interaction strength.

Share and discuss your ideas with a classmate.


Chemical Thinking U1 How do we distinguish substances? 69

FACING THE CHALLENGE in less than five


minutes and detect
Portable GC/MS

VOCs in concentra-
Indoor Air tions of a few ppbv.
Have you ever wondered about the quality of the A sample of in-

By Inficon
air you breathe inside your home or at your dorm? door air may have
Indoor air quality may be affected by the presence from 50 to hundreds
of a wide variety of gaseous substances released by, of different VOCs.
among other sources, household products, build- Among the most
ing materials, furnishings, and heating systems. common substances in this group we found form-
In particular, many household products are made aldehyde (CH2O), dichloromethane (CH2Cl2),
with volatile substances that although not highly and benzene (C6H6), a well known human carcin-
toxic may have chronic effects. Paints, varnishes, ogen. At home, the most common source of form-
and waxes, as well as cleaning, disinfecting, and aldehyde are pressed wood products made of wood
cosmetic products typically contain solvents that particles and wood fibers mixed with adhesives
readily evaporate at room temperature. The mol- that contain urea-formaldehyde resins. CH2Cl2
ecules of these solvents tend to have a backbone of is a chemical compound found in products such
carbon and hydrogen atoms, and thus are gener- as paint strippers, adhesive removers, and aerosol
ally classified as organic compounds. spray paints. Among the main indoor sources of
Volatile organic compounds, or VOCs, can benzene we have stored fuels and paint supplies,
potentially induce a variety of health problems together with car engine emissions in garages.
such as eye and respiratory track irritation, head- However, about 50% of the human exposure to
aches, and nausea. Some of them are known to benzene in the US results from smoking tobacco
cause cancer in animals and, probably, in humans. or from inhaling tobacco smoke.
The extent and nature of the health effects depends VOCs such as benzene and toluene (C7H8)
on factors such as level of exposure and length of are also important pollutants in outdoor air. These

By Tom Murphy VII (Own work) [CCA: Public domain] via Wikimedia Commons
time exposed. However, little is known about the chemical compounds are common constituents of
health effects from expo- lead-free gasoline and
sure to VOCs at the con- evaporate directly to the
centrations usually found atmosphere. Once in
in homes, which have the air, they react with
been shown to be 2 to 5 oxygen and nitrogen
times higher than those compounds to produce
detected in outdoor air. other pollutants that we
As you can imagine, identify as smog.
fast and easily portable Volatile organic
instruments to detect and compounds are not only
identify VOCs in differ- generated by human
ent indoor environments are highly valued. GC/ products and activities. In fact, over 80% of all
MS is the most common analytical technique used VOCs released into the atmosphere have a natural
for this purpose. In many cases, the indoor air source. The aroma of pine or sandalwood is caused
samples are collected in canisters or sorbent tubes by the evaporation of a group of VOCs called ter-
(containers filled with a solid adsorbent material) penes from their leaves. Our own body produces
and subsequently analyzed in an environmental hundreds of VOCs that can be detected in our
lab. This procedure may take from a few hours to breath. Abnormal concentrations of these sub-
several days. However, portable GC/MS systems stances in our blood have been used as evidence in
have been developed that can analyze air samples the diagnosis of lung disease.
70 MODULE 4 Determining Composition

Let’s Apply
Organobromines
Organobromines are organic compounds made up of molecules in which carbon atoms are bonded
to bromine (Br) atoms. For many years, these substances were used for a variety of purposes,
from gasoline additives, to fire extinguishers, to pesticides. However, their use has been banned
or discouraged because of the damage that gaseous bromine compounds can cause to the ozone
ASSESS WHAT YOU KNOW

layer. Volatile organobromine compounds can survive in the atmosphere long enough to reach the
stratosphere where Br atoms are 50 times more damaging to ozone than Cl atoms from CFCs.
Some of these bromine compounds may also affect human health. Thus, monitoring their presence
in the environment has become increasingly important.

Natural Compounds

Some organobromines are produced naturally by marine organisms in large amounts. Com-
bustion analysis of the most common natural organobromine, which is also widely used as a
pesticide, reveals the following chemical composition: 12.65% C, 3.18% H, and 84.17% Br.

• What is the empirical formula of this chemical compound?

MS analysis of this compound produced the mass spectrum shown on this page. Given that
bromine is known to have two
stable isotopes with the follow- 100
ing %Abundance: Bromine-79,
50.69%; Bromine-81, 49.31%: 80
Relative Abundance

• Would you expect the chemi- 60


cal formula to be different
from the empirical formula? 40
• Which peaks in this spec-
trum are associated with the 20
main two molecular ions M+
for the compound? What iso- 0
0 20 40 60 80 100
topes of each element should
m/q
be present in these ions?
• Estimate the relative mass of the main two molecular species and their %Abundance.
Use this information to calculate the average relative mass of the compound.
• Infer the chemical composition of the ions associated with the three most abundant
peaks in the spectrum.

Share and discuss your ideas with a classmate.


Chemical Thinking U1 How do we distinguish substances? 71

Gasoline Additive

One of the most toxic organobromines, once an important constituent of antiknock


mixtures for leaded gasoline, has the following elemental composition: 12.79% C,
2.14% H, and 85.07% Br. The mass spectrum for this substance is shown below.

• What is the empirical formu- 100


la of this compound?
• What is its molecular for- 80

Relative Abundance
mula?
60

ASSESS WHAT YOU KNOW


Share and discuss your ideas with
40
a classmate, and clearly justify
your ideas and procedures. M+
20

0
0 40 80 120 160 200
m/q

Atmospheric Species

Once in the stratosphere, high energy radiation from the Sun can brake the bonds
between bromine atoms and carbon atoms in organobromines compounds. Free
bromine atoms then react with themselves or other species, generating things such
as HBr, BrO, HOBr, and Br2. The detection of these types of species has been used
to follow the temporal evolution of ozone depletion in the stratosphere.

Imagine that you wanted to use some form of mass spectrometry to detect these
four species in the atmosphere. To do so, it would be useful to predict how their
mass spectra would look like.

• Using information about


100
the atomic structure, relative
mass, and percent abundance
of the main isotopes of the 80
Relative Abundance

atoms present in these spe-


cies (see Figure 1.36), sketch 60
the mass spectrum that each
of them could be expected to
40
generate.

Compare your sketches with those 20


of another classmate. Explain your
ideas and resolve any differences in 0
your predictions. m/q
72 MODULE 4 Determining Composition

Let’s Apply
VOCs in Ground Water VOC Pollution in US Aquifers

In 2006, the US Geological Survey (USGS)


published the results of a major research study
on the presence of VOCs in ground water in
the United States. As part of the National Wa-
ASSESS WHAT YOU KNOW

ter Quality Assessment Program, the occur-


rence of 55 well known VOCs was analyzed in
about 2,400 domestic wells and about 1,100
public wells across the country. The project re- Total concentration, mg/L
No detection or less than 0.02
0.02 to less than 0.2
lied on the application of analytical techniques 0.2 to less than 1
1 to less than 10
10 or greater
similar to those described in this module.
The results of this study indicated that many of the Nation’s aquifers are vulnerable to low-level
(< 1 mg/L) VOC contamination, showing the need to more closely monitor the presence of these
compounds in the environment.

100 Major Pollutants


80
A
The USGS ground water study
Relative Abundance

10.06% C
revealed that 15 different VOCs
60 0.85% H
account for most of the pollu-
89.09% Cl
tion in domestic and public
40
wells. Relevant information to
20 derive the chemical formulas of
two of the most common pol-
0 lutants found in ground wa-
0 40 80 120 160 ter is shown on this page. The
m/q source of pollutant A, the most
frequently detected compound,
100 is attributed, in part, to the re-
cycling of chlorinated waters to
80 B aquifers. Pollutant B is a solvent
Relative Abundance

14.49% C used in dry cleaning.


60 85.51% Cl
• Identify the molecular ion
40 peak on each mass spec-
trum.
20
• What are the chemical
0 formulas of these two com-
0 40 80 120 160 200 pounds?
m/q
Chemical Thinking U1 How do we distinguish substances? 73

Where From?
Where To? By Martina Rathgens
(Own Work)
[CCA: 2.0 Generic],
via Flickr Commons

The central goal of this Unit was to help you


understand and apply basic ideas and ways of ZOOMING IN
thinking that can be used to distinguish the dif-
ferent substances present in
a variety of systems of
interest, such as the
atmosphere in our
planet. In this pro-
cess, we have dis-
cussed how mod-
els of matter at the The determination of the mass and chemical
particulate, atomic, composition of the particles of matter is certainly
Earth and subatomic scale very useful in the characterization of chemical
NASA
are useful intellectual tools substances. However, the experimental evidence
in the design of experimental strategies that al- gathered by chemists over the past two hundred
lows us to separate, detect, identify, and quantify years suggests that the true identity of a chemical
the wide variety of chemical elements and com- substance relies on its molecular or ionic struc-
pounds in our world. These models also guide us ture. This is, the specific way in which atoms or
in the interpretation of experimental results and ions are bonded to each other and arranged in
in the generation of explanations and predictions space. Thus, our goal in the next Unit is to help
about the properties and behavior of matter. you develop ways of thinking that can be used
Our analysis started at the macroscopic level, to predict the atomic and molecular structure of
recognizing the types of properties that can serve substances. To do so, we will have to discuss how
as differentiating characteristics in the separa- the analysis of the interaction of light with mat-
tion and identification of chemical substances. ter has been crucial in the development of the
Then, we recognized the need to zoom into the experimental techniques
particulate scale to understand how phase behav- and theoretical models
ior, and many other physical properties of matter, that are currently used to
seem to emerge from the dynamic interactions of determine the geometry
From Microsoft Office

myriads of tiny particles. But to truly understand of molecules in molecular


the diversity of the material world, we needed to compounds and the ar-
explore the composition of matter at the single rangement of ions in three
particle level, analyzing the particle’s mass and dimensional networks
atomic composition. This task demanded that in ionic compounds.
we zoomed even deeper into the atoms, trying But before we move
to uncover their inner structure. In this journey on, let us explore if
from the macroscopic to the subatomic scales, we “YOU ARE READY” by assessing your ability to
gathered powerful tools for exploring and think- apply what you have learned in this Unit to the
ing about the world that surrounds us. analysis of some interesting problems.
74 Are You Ready?

Are You Ready? Titan


NASA

Titan is the largest moon of Saturn. It has a dense atmosphere and there is data that suggests that stable
bodies of liquid are present on its surface. The Cassini-Huygens robotic spacecraft mission arrived in Sat-
urn in 2004 and is currently studying the chemical composition of the planet and its moons, including
Titan. The following table and graphs summarize important information about Titan:

TITAN Additional Information

This temperature does not vary much during the


Average surface tempera-
93.7 K day or the seasons
ture
(min ~90 K; max 94 K)

The atmospheric pressure on Earth


Average surface pressure 1.47 atm
is close to 1 atm.

Air density at ground level 5 kg/m3 The air density on Earth is 1.2 kg/m3

Atmosphere composition 80-85% N2; Compared to 78% N2; 21% O2


(% in Volume) 5-25% Ar; 3-6% CH4 in our planet

Hydrosphere composition 72% C2H6; Compared to ~100% H2O


(% in Mass) 22.4% CH4; 5.6% N2 in our planet

The central goal of this activity is that you demonstrate that you can apply
chemical thinking to explain and predict the properties and behavior of the
substances present in a real system, such as Titan.
Chemical Thinking U1 How do we distinguish substances? 75

Exploring Titan
Methane

The figure depicts the phase diagram of methane


(CH4), one of the main components of the atmo-
sphere and hydrosphere in Titan.

• Label on the diagram the stable phase in


each of the three major regions.
• What is the stable phase of CH4 on the
surface of Titan? Justify your answer using
the diagram.
• Can we expect to see CH4 in gaseous form
anywhere in this moon? If yes, at what alti-
tudes? Justify your answer in one sentence.

CH4 C2H6 The Liposphere

The graph depicts the vapor pressure graphs


for methane (CH4) and ethane (C2H6), the
major components in Titan’s hydrosphere
(also called the liposphere).

• Estimate the temperatures at which each


of these substances boils on the surface
of Titan.
• Propose a strategy to separate these two
components from a sample of Titan’s
liposphere.

Relative Numbers
If you separated 10.0 g of a hydrosphere sample,

• How many times more molecules of ethane (C2H6) than of methane (CH4) would you find in that
sample? (Check the available data for information about the % of mass of each of these compo-
nents in Titan’s hydrosphere).
76 Are You Ready?

Exploring Titan Huygens on Titan


NASA

Lakes in Titan
A scientist has proposed that if the lakes of Titan were
made of pure methane (CH4) they would freeze when
the wind blows and the lakes evaporate, even if the
temperature of the atmosphere is slightly above the
freezing point for CH4.

• Use the particulate model of matter to explain


why this is a reasonable hypothesis.

Ocean’s Bottom
A sample of the bottom of Titan’s ocean (bottom of the liposphere) shows that one of
the main components is a solid hydrocarbon. The analysis of this substance by mass
spectrometry leads to the spectrum that is shown. Elemental analysis reveals the follow-
ing compositions: 92.26% C and 7.74% H.

• What is the empirical formula of 100


this substance?
80
Relative Abundance

Based on the mass spectrum for this sub-


stance, shown on this page: 60

• What is the molecular formula of 40


this substance? Justify your answer.
20

0
8 12 16 20 24 28 32
m/q

Probing
Imagine that an elastic balloon carrying analytical equipment is used as a probe to explore Titan’s
atmosphere.

• Would the volume of the balloon increase or decrease as it descends through the atmosphere?
Justify your reasoning using the particulate model of matter.
Chemical Thinking U1 How do we distinguish substances? 77

Are You Ready?


Titan’s Haze
Titan’s atmosphere has a characteristic haze that seems to absorb
high energy radiation from the Sun, in a similar way as the ozone
layer in our planet. The space filling representations of the mol-
ecules that seem to be present in this haze are shown on this page.

• What is the chemical formula of each of these substances?

The concentration of one of the most abundant species in this


haze, HCN, is estimated to be close to 0.1 ppmv (part per million
in volume).

• What is the %mol of this substance in Titan’s haze?

Representations
Based on your work on this activity, togeth-
er with the information provided, build a
particulate representation of a cross sec-
tion of Titan. Provide the information that
is requested for each region of the planet:

Atmosphere
Number of elements
Number of compounds
Number of pure substances

Liposphere
Number of elements
Number of compounds
Number of pure substances

Bottom of Liposphere
Number of elements
Number of compounds
Number of pure substances

CLICK TO PLAY
78 Are You Ready?

Are You Ready?


Bombardier beetles have an amazing defense mechanism. They produce a mixture of chemical compounds
that can undergo a violent chemical reaction. When they are threatened, they squirt the mixture into a
reaction chamber where proteins accelerate the chemical process. The reaction releases oxygen gas, O2(g),
and generates enough heat to bring the mixture to the boiling point and vaporize a fraction of it.

Two Phases

The mixture produced by the beetle is a heterogeneous system composed of two liquid
phases. One of the phases is rich in water, H2O(l), hydrogen peroxide, H2O2(l), and
several other chemical compounds. The other phase is mostly a mixture of hydrocar-
bons (water and hydrocarbons do not dissolve much into each other). To analyze the
hydrocarbon-rich phase, we need to separate it from the water-rich phase.

• Design an experimental strategy to achieve this separation.

Separation and Elemental Analysis

Analysis of the hydrocarbon-rich mixture using gras


chromatography (GC) reveals the pres-
ence of more than 25 different com-
pounds. The most important component
in this mixture is the substance that reacts
with H2O2(l) to produce O2(g) and large Chromatograph
amounts of energy. Information about

By Patrick Coin (Own work) [CCA: Share Alike 2.5] via Wikimedia Commons
the elemental composition of this chemi-
cal compound X are shown on this page.

• What is the molar mass of 100


this chemical compound?
80 X
Relative Abundance

• What is the empirical for- 65.45% C


mula of the compound? 60 5.49% H
• What is the molecular for- 29.06% O
mula of the compound? 40

Share and discuss your ideas 20


with a classmate.
0
0 20 40 60 80 100 120
m/q
Chemical Thinking U1 How do we distinguish substances? 79

Bombardier Beetle
Other Components

GC analysis of the hydrocarbon-rich phase reveals that the major com-


ponent in this mixture has the molecular structure shown to the side.

• What is the chemical formula of this compound?


PENTADECANE
• What is its molar mass?

Phase Behavior

The analysis of the phase behavior of compound X


produces the phase diagram shown to the side:

• What is the stable phase of this substance at


room temperature (20 oC)?
• What are the normal melting and boiling
points of this substance?

Share and discuss your ideas with a classmate.

Relative Amounts

Quantitative measurements indicate that the concentration of H2O2(l) in the water-rich phase is close to
0.25 g/mL, while that of compound X is about 0.1 g/mL. If the density of liquid water, H2O(l), is close
to 1.0 g/mL:

• How many molecules of H2O are there per molecule of compound X?


• How many molecules of H2O2 are there per molecule of compound X?
• If the density of pentadecane is close to 0.77 g/mL, compare the number of molecules in 1 mL of
the hydrocarbon compared to the number of molecules in 1 mL of H2O.

Share and discuss your ideas with a classmate, and clearly justify your ideas and procedures.
80 Are You Ready?

Bombardier Beetle
Submicroscopic Representation
CLICK TO PLAY
• Use all of the information that you
have gathered to create a sub-
microscopic representation of a
nanoscopic sample of the mixture
produced by the beetle. Your repre-
sentation should include molecules
of the four major components in
the proportion in which they are
actually present in the mixture. The
interactive tool included in this
page may facilitate your work.
By Thomas Eisner et al.(2000) The Journal of Experimental Biology, 203, 1265-1275

Modeling the Process

The chemical reaction inside the beetle produces O2(g) and enough energy to
increase the temperature of the mixture to values as high as 100 oC. Under
those conditions, close to one fifth of the liquid mixture is vaporized. We
could try to model the system by imagining a closed container with two main
components, one in gas phase and the other in liquid phase.

• Use the simulation that you CLICK TO PLAY


can access in this page to
identify the right balance
of attractive interactions
between different particles
in the system to generate a
mixture in which one com-
ponent is a liquid and the
other is a gas at a particular
temperature.
• Use this particulate model
of the system to predict what would happen if you were to open a small
hole in the container.

Share your ideas with a classmate. Discuss how this simple particulate model
of the reaction chamber inside a bombardier beetle can be used to explain
how its defense mechanism works.
Chemical Thinking U1 How do we distinguish substances? 81

Unit 1: Image Attributions


Module 1
P2 & P3: Background “Blue Marble” by NASA; P4: “Earth’s Atmosphere” by NASA; P5: Fig. 1.1 Derivative from video by NASA; P7: “Melting
icecubes” by Mysid (Own work) [Public domain] http://commons.wikimedia.org/wiki/File:Melting_icecubes.gif; P8: Center right derived from
“Phase change - en” by Flanker, penubag (Own work) [Public domain] http://commons.wikimedia.org/wikiFile:Phase_change_-_en.svg; P11:
Center right «Dirty-air-filter» by Ahanix1989 (Own work) [Public domain] http://commons.wikimedia.org/wiki/File:Dirty-air-filter.jpg, bottom
left “Insulin Crystals” by NASA/Marshall; P12: Fig. 1.7 “Fractional distillation lab apparatus” by John Kershaw (Derivative: Theresa knott) [Share
Alike 3.0] http://commons.wikimedia.org/wiki/File:Fractional_distillation_lab_apparatus.svg, bottom right Own work; P13: Top right “Argon
ice 1” by Deglr6328 (Own work) [Share Alike 3.0] http://commons.wikimedia.org/wiki/File:Argon_ice_1.jpg, bottom center “Coldbox” by pho-
tographer - Company.(Own work) [Share Alike 3.0] http://commons.wikimedia.org/wiki/File:Coldbox.JPG; P15: Center left “Blue Marble” by
NASA, center right “Venus” by NASA, bottom left “Mars” by NASA; P16: top right “Colonne distillazione” by User:Luigi Chiesa (Own work)
[3.0 Generic] http://commons.wikimedia.org/wiki/File:Colonne_distillazione.jpg, bottom right Own work; P17: Center right “Gas-pump-Indi-
ana-USA”by Tysto (Own work) [Public domain] http://commons.wikimedia.org/wiki/File:Gas-pump-Indiana-USA.jpg.

Module 2
P18: Top right Derivative of “Diamond and graphite2” by User:Itub (Derivative: Materialscientist (talk)) [Alike 3.0] http://commons.wikimedia.
org/wiki/File:Diamond_and_graphite2.jpg, Bottom right “Clouds” by Axel Rouvin (Own Work) [Public domain] http://commons.wikimedia.
org/wiki/File:Clouds.JPG; P19: Fig. 1.8 “Four elements representation” by en:User:Heron (Own Work) [Public domain] http://commons.wiki-
media.org/wiki/File:Four_elements_representation.svg; P19: Bottom right Derivative from the video “Powers of ten” by Charle & Ray Eames -
http://www.powersof10.com/film; P26: Center right Own work; P25: Fig. 1.13 “Kochendes wasser02” by Markus Schweiss (Own work) [Share
Alike 3.0] http://commons.wikimedia.org/wiki/File:Kochendes_wasser02.jpg; P26: Fig. 1.14: “Mesoporous Silica Nanoparticle” by Nandiyanto
(Own work) [Public domain] http://commons.wikimedia.org/wiki/File:Mesoporous_Silica_Nanoparticle.jpg, P28: Bottom right derivative from
image by Mark Bishop; P30: Top right “Watervapor cup”by Jarombout (Own work) [Share Alike 3.0] http://commons.wikimedia.org/wiki/
File:Watervapor_cup.jpg, Center left “Sweat or rain” by Kullez (Own work) [Generic 2.0] https://www.flickr.com/photos/kullez/5598159209/,
Center right Derivative of “Diamond and graphite2” by User:Itub (Derivative: Materialscientist (talk)) [Alike 3.0] http://commons.wikimedia.
org/wiki/File:Diamond_and_graphite2.jpg, Bottom left “Soda bubbles macro” by en:User:Spiff (Own work) [Public domain] http://commons.
wikimedia.org/wiki/File:Soda_bubbles_macro.jpg; P31: Center “Clouds” by Axel Rouvin (Own Work) [Public domain] http://commons.wiki-
media.org/wiki/File:Clouds.JPGBottom right “Lysozyme crystal1” by Mathias Klode (Own work) [Share Alike 3.0] http://commons.wikime-
dia.org/wiki/File:Lysozyme_crystal1.JPG; P32: Bottom left “Buzo” by Soljaguar (Own work) [Share Alike 3.0] http://commons.wikimedia.org/
wiki/File:Buzo.jpg; P33: Upper left “Starchy-foods.” by US Department of Agriculture [Public domain] http://commons.wikimedia.org/wiki/
File:Starchy-foods..jpg

Module 3
P38: Fig. 1.20 Top left “Na (Sodium)” by Dnn87 (Own work) [Share Alike 3.0] http://commons.wikimedia.org/wiki/File:Na_(Sodium).jpg,
Center left “SiliconCroda” by Enricoros (Own work) [Public domain] http://commons.wikimedia.org/wiki/File:SiliconCroda.jpg; P34: Top right
Own work, Fig. 1.20 Own work; P39: Bottom right “Iod kristall” by de:user:Tomihahndorf (Own work) [Public domain] http://commons.wi-
kimedia.org/wiki/File:Iod_kristall.jpg: P40: Fig. 1.22 Center left “Liquidnitrogen” by Cory Doctorow (Own work) [Share Alike 2.0] http://com-
mons.wikimedia.org/wiki/File:Liquidnitrogen.jpg., Bottom left “Phosphor rot” by Tomihahndorf -(Own work) [Public domain] http://commons.
wikimedia.org/wiki/File:Phosphor_rot.jpg; P41: Fig. 1.24 Center left “Sodiumchloride crystal 01” by Choba Poncho (Own work) http://com-
mons.wikimedia.org/wiki/File:Sodiumchloride_crystal_01.jpg, Bottom left “Ammonium chloride” by Walkerma (Own work) [Public domain] via
Wikimedia Commons - http://commons.wikimedia.org/wiki/File:Ammonium_chloride.jpg; P53: Center “Santiago30std” by Wurstsalat (Own
work) [Share Alike 3.0] http://commons.wikimedia.org/wiki/Fitxer:Santiago30std.jpg, Bottom center by EPA; P54: Own work derived from
information at http://www.airinfonow.com/html/ozone.html; P55: Bottom right by NASA.

Module 4
P59: Fig. 1.31 “Katódsugarak mágneses mezőben(3)” by Zátonyi Sándor, (ifj.) (Own work.) [Share Alike 3.0] http://commons.wikimedia.org/
wiki/File:Kat%C3%B3dsugarak_m%C3%A1gneses_mez%C5%91ben(3).jpg; P69: Top right “Hapsite” by Inficon, Bottom center “EWM paint
2007” by Tom Murphy VII (Own work) [Public domain] http://commons.wikimedia.org/wiki/File:EWM_paint_2007.jpg; P72: Top right by
US Geological Survey, Center & Bottom left Own work; P73: Top right “Blue drop” by Martina Rathgens (Own work) [2.0 Generic] https://
www.flickr.com/photos/riviera2008/2970609301/, Own Work, Center left “Blue Marble” by NASA, Bottom right Derivative from Microsoft
Office Image; P74 & P75: Background “Titan” by NASA, Own Work; P76 & P77: Background “Huygens on Titan” by NASA; P78 &
P79: Background “Brachinus spPCCA20060328-2821B” by Patrick Coin (Own work) [Share Alike 2.5] http://commons.wikimedia.org/wiki/
File:Brachinus_spPCCA20060328-2821B.jpg, Own work; P80: Left Source: Thomas Eisner et al.(2000) The Journal of Experimental Biology,
203, 1265-1275.

General
Activity icons: Clip art from Microsoft Office; Molecular structures: Derived from online public software (Chemical Education Digital Library,
Jmol) and via Wikimedia Commons (Public domain images).
UNIT 2
How do we
determine
structure?
The identity of a chemical substance is determined by its structure at
the submicroscopic level. The way in which electrons are arranged in
atoms or molecules, the manner in which atoms or ions are bonded to
each other in molecules or ionic networks, the specific distribution of
these particles in three dimensional space - all of these factors make a
given substance unique and determine its physical and chemical prop-
erties. The quest for uncovering identities in chemistry is thus tightly
linked to the search for models and experimental methodologies that
allow us to gather evidence about structure at the nano scale.

The central goal of Unit 2 is to help you develop ways of thinking


that can be used to uncover and predict the atomic and molecular
structure of substances. Although the ideas, models and experimental
techniques that we will discuss can be applied in a wide variety of con-
texts, to illustrate their power we will pay particular attention to the
analysis of molecular substances that sustain, support or threaten life in
our planet. In particular, we will try to address questions such as:

How do we explore their electronic structure?


How do we investigate their molecular structure?
How can we predict their molecular structure?
How can we predict electron distribution in these molecules?

From Microsoft Office

82
Chemical Thinking

UNIT 2 MODULES

M1. Analyzing Light-Matter Interactions


Using spectroscopy to obtain information about the
structure of matter.
M2. Looking for Patterns
Using experiments and models to infer and predict
atom connectivity in molecules.
M3. Predicting Geometry
Predicting the three dimensional geometry of mol-
ecules.
M4. Inferring Charge Distribution
Analyzing the distribution of electrons in molecules.

From Microsoft Office

83
84

Analyzing
Light-Matter
Interactions
One of the most important applications of chemical thinking in various fields,
U2: MODULE 1

from forensic analysis to drug design, involves the determination of the structure
of the particles that make up a substance. We may want to determine the geom-
etry of the molecules of cocaine to better understand how this drug interferes with
brain activity. We may be interested in characterizing the three dimensional struc-
ture of a protein to design a chemical substance that can inhibit its action inside
the cells of a pathogen we want to eliminate. For this purpose, chemical scientists
have developed a set of powerful intellectual and practical tools that help them
explore or predict how atoms or ions are bonded to each other in

[NoDerivs 2.0 Generic] via Flickr Commons


the particles of a given substance (connectivity) and how they

By William Chien (Own work)


are arranged in space (geometry). Many of these tools rely on
experimental information derived from the analysis of the
interaction of the substance of interest with some form of
electromagnetic radiation. It is through the analysis of the
electromagnetic radiation absorbed or emitted by a substance
that we can reveal its internal structure. This information has
also been used by chemical and physical scientists to build theoreti- Different atoms
emit light of char-
cal models to explain and predict the properties of matter. acteristic colors.

THE CHALLENGE In our Blood


The presence of some metals, such as lead, arsenic, and mercury in human
blood can lead to serious diseases. However, some other metals such as iron
and copper are essential to health in very small amounts. Metal compounds
are known to emit light of different colors when heated.

• How would you detect the presence of these metals in blood?

Design a potential strategy that could help solve this problem.

This module will help you develop the type of chemical thinking that is used
to answer questions similar to those posed in the challenge. In particular, the cen-
tral goal of Module 1 is to help you understand how to use experimental data
on the light emitted or absorbed by chemical substances to derive information
and build models about atomic and molecular structure.
Chemical Thinking U2 How do we determine structure? 85

Spectroscopy
One of the central questions that we want to investigate in this unit is how we can
use visible light, or any other form of electromagnetic (EM) radiation, to derive
information about the structural properties of chemical substances. In particular,
we would like to use results from the analysis of light-matter interactions to de-
termine atom connectivity and geometry in molecules and ionic networks, as well
as to detect, identify, and quantify the amount of different substances present in a
system. We would also be interested in using such experimental evidence to gener-
ate models about atomic and molecular structure that could help us explain and
predict the properties of materials. We will be able to face this challenge through
information derived using a set of experimental techniques generically known as
spectroscopy. These analytical methods are based on the analysis of different types
of EM radiation absorbed or emitted by chemical substances. However, to better
understand how this works, we need to discuss some basic properties of EM radia-
tion.
EM radiation is a form of energy that can be generated by accelerating par- Figure 2.1 Representation of
an EM wave showing its basic
ticles that have an electric charge. This radiation takes the form of self-propagating components: Electric field (E);
waves that travel through matter or through vacuum at a characteristic speed (v) magnetic field (B), propagation
direction (k). This wave is charac-
that depends on the nature of the medium. EM waves are comprised of electric terized by its wavelength l.

Alike 3.0] via Wikimedia Commons


By SuperManu (Own work) [Share
and magnetic fields that oscillate in phase per-
pendicular to each other and perpendicular to E
the direction in which the wave propagates (see
Figure 2.1). Different types of EM radiation can k
be characterized by either wavelength (l) or fre- B
quency (n). The wavelength l is a measure of the
distance over which the shape of the wave is repeated; the frequency n indicates
the number of repeating waves that cross a certain point of space per unit time.
These two quantities are not independent from each other and their relationship
depends on the speed at which the waves travel through a certain medium.

LET’S THINK

http://www.chem.arizona.edu/tpp/chemthink/resources/U1_M1/graph.html
http://www.chem.arizona.edu/tpp/chemthink/resources/U2_M1/Wave.html
Wave Properties
You can use the simulation included on this page to determine the relationship between wave-
length (l), frequency (n), and speed of propagation (v) for EM waves
traveling through water. You can change the value of l (measured in
meters, m) and observe the corresponding changes in n (measured in
s-1, also called Hertz, Hz).
CLICK TO PLAY

• How does n change with increasing l? Build graphs of a) n


as a function of l and b) n as a function of 1/l (you may use the
graphing tool also included on this page). Use this information to
derive a mathematical relationship between these two variables.
• Based on your data, what is the actual average speed (v) of EM
waves in water.

Share and discuss your results and ideas with a classmate.


86 MODULE 1 Analyzing Light-Matter Interactions

The wavelength l, frequency n, and speed of propagation v of a wave are re-


lated to each other through the following mathematical relationship:

(2.1) l x n = v.

In the particular case of EM waves traveling through vacuum the speed of propa-
gation has the constant value v = c = 3.00 x 108 m/s. This value is the same no
matter what the wavelength or frequency of the radiation is. This is not necessarily
the case for EM radiation traveling through a material medium, such as glass or
water, where wave speed depends somewhat on wavelength.
Depending on its wavelength or frequency, EM radiation is classified as be-
longing to different types as illustrated in Figure 2.2. The different EM radiation
types span the so-called electromagnetic spectrum and they include X-rays, ul-
Figure 2.2 Electromagnetic traviolet (UV) radiation, infrared (IR) radiation, and radio waves, as well as EM
spectrum. The visible region radiation that is visible to the human eye (visible light). The visible part of the
of the spectrum has been
re-scaled to show the range spectrum includes radiation with l values that range from approximately 400 nm
of wavelengths characteris-
tic of different light colors. (violet region of the spectrum) to 700 nm (red region of the spectrum).

Increasing Frequency (n)

By Philip Ronan, Gringer (Own work) [Share Alike 3.0] via Wikimedia Commons
Increasing Wavelength (l)
Visible Spectrum

Increasing Wavelength (l) in nm

Detector
The distinction between different types of EM radiation is relevant in chem-
istry because chemical substances interact in distinctive manners with different
types of radiation. The type of EM radiation absorbed or emitted by a chemical
l
By ADInstruments (Derivative)

Sample
Spectrum
substance is, in fact, a differentiating characteristic of the material. Additionally,
we can obtain different types of structural information by analyzing the EM ra-
diation emitted or absorbed by a substance in the IR region of the EM spectrum
or, for example, the UV region. That is why there are a variety of spectroscopic
EM Radiation techniques, such as IR spectroscopy, UV-visible spectroscopy, and microwave
Source
spectroscopy. In all of these different techniques, the actual instruments include
Prism
detectors that measure the intensity of the EM radiation that passes through a
sample or that is emitted by a substance when heated or stimulated in some other
Figure 2.3 A typical absorp-
tion spectrometer includes a way (such as using other types of EM radiation). The detection is done at different
EM radiation source, a device wavelengths which allows us to build a spectrum that shows the intensity of the
to split the radiation into specif-
ic wavelengths, and a detector. radiation absorbed or transmitted as a function of l or n (see Figure 2.3).
Chemical Thinking U2 How do we determine structure? 87

Absorption Spectra LET’S THINK


When a chemical substance is analyzed using absorption 1.0
spectroscopy, the spectrometer generates a spectrum that
provides information about either the fraction of EM 0.9
radiation of a specific wavelength that was absorbed by the

Transmittance
substance (Absorbance) or the fraction of that EM radia- 0.8 CO2(g)
tion that went through the sample without being absorbed
0.7
(Transmittance). Consider, for example, the following
spectra for O2(g) and CO2(g), two vital substances in our
0.6
planet: 4.20 4.30 4.40
Wavelength (mm)
• What types of EM radiation were used to generate
each of these spectra? 1.5

• How would you interpret the information provided O2(g)


by each of these spectra? What information do the 1.0
peaks at different wavelengths or frequencies convey?

Absorbance
• What do you think these spectra tell us about how
0.5
chemical substances interact with EM radiation?

Share and discuss your results and ideas with a classmate, 0


50 55 60 65 70
and clearly justify your reasoning. Frequency (GHz)

Quantization
Based on the subatomic model of matter discussed in Unit 1, one could expect
atoms and molecules to interact with EM radiation because they are made up of
charged particles (electrons and protons) that are constantly moving. Electrons
and protons could either be affected by the oscillating electric and magnetic fields
of an EM wave, or they could generate EM radiation as they accelerate. In either
case, these phenomena lead to a transfer of energy between the charged particles
and their surroundings. The charged particles either absorb energy when interact-
ing with incoming EM radiation or release energy when generating EM radiation.
But, how much energy is actually transferred?
An answer to this question was proposed by Max Planck in 1900 while trying
to generate a model to describe, explain, and predict how the intensity of the EM
radiation generated by an object depends on the frequency of the radiation and the
temperature of the object. In order to explain existing experimental results Planck
had to assume two basic things:

a. The energy transferred (E) through light-matter interactions is proportional


to the frequency (n) of the EM radiation according to this expression:

(2.2) E=hxn

where h = 6.626 x 10–34 J s is a constant known a Planck’s constant.


88 MODULE 1 Analyzing Light-Matter Interactions

b. Energy transfer during light-matter interactions only occurs in integer mul-


tiples of the elementary unit of energy E = h n.

This last assumption implies that whenever matter interacts with EM radiation of
certain frequency n, the total energy transferred is always an integer multiple of
hn; this is, there is no way to transfer energy in amounts such as 1/2 hn or 3/4 hn,
or 200.5 hn using radiation with frequency n. The second of Planck’s postulates
indicates that energy transfer in light-matter interactions is quantized: it can only
take a set of discrete values instead of any possible value. This idea was unexpected at
Figure 2.4 In a photoelectric de-
vice, light with a frequency higher Planck’s time, to the point that even he doubted its validity. However, the concept
than a threshold value ejects elec-
trons from a solid surface. Elec- of “energy quantization” became one of the most powerful and revolutionary
tron emission is detected by the ideas of modern science.
presence of an electric current.
The suggestion that energy was quantized in light-matter interactions opened
the door to new ways of thinking about both the actual nature of EM ra-
diation and the internal structure of atoms and molecules. Albert Einstein,
for example, relied on this idea to propose a new model to conceptualize
light. At the beginning of the twentieth century scientists were puzzled
By PhET (Screenshot)

by the fact that when the surface of a solid is exposed to EM radiation


e-
with a frequency above certain threshold value, radiation is absorbed and
electrons are emitted with a kinetic energy proportional to the frequency
of the incident radiation (photoelectric effect; see Figure 2.4). Classical
views of this phenomenon suggested that the kinetic energy should be pro-
portional to the intensity of the EM radiation instead. Based on Planck’s
ideas, in 1905 Einstein solved the puzzle by proposing that EM radiation was
composed of discrete “quanta” of energy, called photons, rather than as continu-
ous waves. The energy of each of these photons depends on the frequency of the
radiation as stated in Planck’s relation in Equation (2.2). According to this mod-
el, electrons are ejected by direct interaction with those photons with an energy
E = hn above the threshold value, and the larger the frequency of the photon, the
larger the amount of energy transmitted to the charged particles. This new way of

http://www.chem.arizona.edu/tpp/chemthink/resources/U2_M1/spectraline.html
conceptualizing EM radiation implies that not only are light-matter interactions
quantized, but that quantization is an intrinsic property of light.

LET’S THINK Emission Spectra

The idea of energy quantization also allowed scientists to make sense of the nature of the absorp-
tion and emission spectra of different chemical substances. In particular, the analysis of the EM
radiation emitted by elemental atoms when heated, or absorbed when
they were exposed to a light source, led to the proposal of new sub-
atomic models of the atom. Consider the emission spectra of different
types of atoms included in the interactive tool in this activity:
CLICK TO PLAY
• In which ways are the spectra of different atoms similar or different?
• How would you use the idea of quantization of energy to explain the nature of these spectra?
• What do these experimental results suggests about the internal structure of atoms?

Share and discuss your results and ideas with a classmate, and clearly justify your reasoning.
Chemical Thinking U2 How do we determine structure? 89

The discrete line structure of the emission spectra of the atoms of different
elements, as seen in the previous activity, indicates that these particles
emit EM radiation with specific frequencies. These frequencies hap- Emission

pen to correspond to those of the light absorbed by these same atoms Hydrogen Line Spectrum
when exposed to a source of EM radiation (see Figure 2.5). This phe- Absorption
nomenon has been explained by assuming that electrons in atoms can (visible light background)

only exist in certain energy levels; this is, their energy is also quantized. 400 nm 500 nm 600 nm 700 nm

In order for an electron to change its energy level, it needs to absorb or release Figure 2.5 Emission and absorp-
a photon with an energy equal to the difference between two existing energy lev- tion spectra for hydrogen in the
visible range. Emission and ab-
els (see Figure 2.6). Thus, the location of the absorption or emission lines of the sorption lines have the same l.
spectra in the wavelength or frequency scales give use direct information about the
allowed energy levels for electrons in atoms.

Absorption Emission

Energy Ground State Excited State


n=4
n=3

n=2
DE
n=1
Figure 2.6 Different lines in the
If we assign a different label n = 1, 2,... to each allowed energy level for elec- absorption or emission spectra
trons in an atom as shown in Figure 2.6, the energy of each level can be represent- of atoms correspond to electron
transitions between different en-
ed as Ei. According to the model just described, the absolute value of the energy ergy levels.
difference between any two levels DE = Ej - Ei should then satisfy the relationship

(2.3) |DE| = h x n

where n is the frequency of a single photon absorbed or emitted by an electron


moving between those two energy levels; DE is thus energy per photon absorbed
or emitted (J/photon). Given that a macroscopic sample of any substance contains
myriads of atoms, the actual energy absorbed or emitted by all the atoms in the
sample that undergo this transition will be an integer multiple of this number. For
example, if one mole of atoms absorb or emit a photon with energy hn, the total
energy absorbed or released ET will be ET = NAhn, where NA is Avogadro’s number.
The electrons in most atoms or molecules of a given substance at standard
conditions of temperature and pressure tend to occupy the lowest energy levels
that are available in the system. We say that they tend to exist in their ground state.
When the substance is heated or exposed to EM radiation of the proper frequen-
cies, electrons may absorb energy and move to higher energy levels. We say then
that they are in an excited state. Changes in the energy level of an electron should
be associated with changes in both its speed and its average position with respect
to the nucleus of the atom. A variety of atomic models have been developed to
describe and predict these changes. Let us explore some of them.
90 MODULE 1 Analyzing Light-Matter Interactions

LET’S THINK Atomic Models

The results from emission and absorption spectroscopy experiments were of central importance in
the process of testing and developing subatomic models of
the atom at the beginning of the twentieth century. The in-

CLICK TO PLAY
teractive simulation that you can access in this activity shows
the typical results of an experiment designed to generate the
absorption spectrum for hydrogen atoms (Experiment sec-
tion). Open the simulation, click to show the spectrometer,
and turn on the light source (gun) to generate white light
(stream of photons with multiple frequencies):
http://www.cbc.arizona.edu/tpp/chemthink/sim/atom.jnlp

• Carefully analyze what happens in the system as the white light interacts with the hydrogen
gas in the box. Make sure that you understand the relationship between what you observe and
the data registered by the spectrometer.
• Turn on the source of monochromatic light (EM radiation of a specific wavelength or fre-
quency). Reset the experiment and change the wavelength of the incident light to identify the
specific values for different absorption lines in the spectrum. You can control light intensity
(number of photons per second) by changing the speed of the simulation.

The simulation also allows you to explore the predictions of different atomic models about the results
of the interaction between light and the hydrogen atoms (Prediction section):

• The Billiard Ball Model (by Dalton), the Plum Pudding Model (by Thomson), and the Clas-
sical Solar System Model (by Rutherford), failed to explain the results of light absorption
experiments. Analyze why these models were unable to reproduce the experimental data.

Bohr’s Atomic Model was the first to qualitatively explain the quantized nature of light absorption
by matter and to quantitatively predict the actual wavelength of the absorption lines. Bohr proposed
that the energy of electrons in atoms was quantized: it could only take certain specific values deter-
mined by the number of protons in the atomic nucleus.

• Analyze the predictions of Bohr’s atomic model. Show the electron energy level diagram and
analyze the relationship between an electron’s energy level and its location in space. Also ana-
lyze the relationship between energy level and kinetic energy (as determined by the electron’s
speed) and potential energy (as determined by its distance from the nucleus).
• Determine the wavelength needed to induce an electron transition from n=1 to n=3 and calcu-
late the energy difference DE between these two energy levels.

de Broglie’s and Schrödinger Atomic Models are based on the assumption that electrons in atoms
are better conceptualized as waves rather than as discrete particles. This behavior limits our ability
to predict the actual position of electrons at any given time. In particular Schrödinger’s model, the
current scientific view of an atom, establishes that we can only predict the probability of finding
electrons in certain regions of space.

• Use the simulation to analyze how these two models conceptualize the relationship between
energy transitions and changes in an electron’s distribution in space.
Chemical Thinking U2 How do we determine structure? 91

According to the current model of the atom, also known as the quantum me-
chanical model, atoms can exist in different electronic energy states depending on
how their electrons are distributed among various energy levels. The absorption or
emission of energy by an atom is associated with electron transitions between dif-
ferent energy levels. The energy difference between these energy levels can be de-
duced from spectroscopic data. For example, based on the simulation used in the
last activity the absorption of light with l = 122 nm induces an electron transition
from the ground state with n =1 to the excited state with n = 2 in the hydrogen
atom. Thus, using equations (2.1) and (2.3), we have:

hc 6.626 x 10–34 x 3.00 x 108


DE = h n = = = 1.63 x 10-18 J
l 122 x 10–9

This is the energy needed to promote a single electron from n = 1 to n = 2 in a

http://www.chem.arizona.edu/tpp/chemthink/resources/U2_M1/vibmodes.html
hydrogen atom. The total energy ET required to induce this change in a mole of
hydrogen atoms is then given by: CLICK TO PLAY

ET = NADE = 6.022 x 1023 x 1.63 x 10-18 = 9.82 x 105 J/mol = 982 kJ/mol

Electron transitions in atoms typically involve absorption or emission of en-


ergy from a few hundred to a few thousand kJ/mol. The type of EM radiation that
provides this amount of energy is typically in the visible and the ultraviolet regions
of the EM spectrum. The energy absorbed by electrons can be large enough to pro-
mote them to states in which they actually detach from the atom. Thus absorption
of high energy EM radiation, particularly in the ultraviolet, X-ray, and gamma ray
regions of the EM spectrum can result in the formation of ions.
Spectroscopic data strongly suggests that electron energy levels in atoms are
quantized. How do we explain it? In the quantum mechanical model of the atom,
energy quantization is seen as a direct result of the intrinsic properties of sub-
atomic particles. Based on ideas originally proposed by Louis de Broglie in 1924, Figure 2.7 A two-dimensional
the modern model of the atom assumes that electrons in confined systems, such surface, like that of a drum, can
only vibrate in certain modes.
as atoms or molecules, behave like standing or stationary waves. Such waves, like
the ones that can be established on a guitar string or a drum’s surface, occur only
in a discrete set of wavelengths or frequencies (see Figure 2.7). In musical instru-
ments this results in discrete sets of possible harmonics or overtones. In atoms, the
consequence is the existence of discrete electronic states.
If energy is associated with the frequency of each allowed standing wave, as is
the case for photons (E = hn), then quantization of energy is a natural consequence 10 nm By Stroscio et al. (Own work) [Public
domain] via Wikimedia Commons

of the wave-like behavior of electrons. While the allowed frequencies in musical


instruments such as pianos and guitars depend on the mass, length, and tension
of their strings, the quantized states in an atom are determined by the mass and
number of electrons in the system, together with the strength of the interactions
between electrons and protons in the atom. The wave-like behavior of electrons
has been experimentally confirmed in a variety of ways. For example, in 1993 a
group of scientists were able to confine electrons on the surface of metals inside Figure 2.8 Quantum corral:
Scanning Tunneling Microscope
nanoscopic rings made with other types of atoms. The electrons trapped in these image of individual cobalt at-
oms arranged in a circular ring
“quantum corrals” generate a wave pattern similar to that created by standing on a copper surface exposing
quantum electron waves.
waves on the surface of a drum (compare Figure 2.7 and Figure 2.8).
92 MODULE 1 Analyzing Light-Matter Interactions

The wave-like properties of matter at the submicroscopic level impose im-


portant limitations on what we can know about the behavior of particles at this
r scale. For example, it is impossible to simultaneously measure both the position
and momentum (i.e., mass times velocity) of a particle with unlimited precision;
x this restriction is known as Heisenberg’s Uncertainty Principle. Thus, we cannot
y determine the trajectories followed by electrons in atoms because that would re-
quire precise knowledge about their position and velocity as a function of time.
CLICK TO PLAY The most that we can predict or determine experimentally is the probability of
http://www.chem.arizona.edu/tpp/chemthink/resources/U2_M1/deloc.html

finding electrons in certain region of the space at a given time. For that reason,
modern descriptions of the internal structure of atoms refer to electron densities
rather than to electron trajectories. These electron densities are a measure of the
probability of electrons being present in specific locations.
In the quantum model of the atom, different electron states are character-
ized by different mathematical functions that describe the corresponding electron
waves. These wave functions are mathematical tools that can be used to calculate
the electron probability densities. Electrons with different energies are described
by different wave functions. In particular, their kinetic energy is directly related to
the wavelength of their associated wave function. As is the case for photons, the
shorter the associated wavelength the higher the kinetic energy of the electrons.
This relationship has important consequences in chemistry because an electron’s
wavelength is determined by the size of the space in which it can move around.
The smaller the volume, the shorter the electron’s wavelength and the higher its
kinetic energy. Thus, for example, electrons forced to move close to the nucleus in
an atom will have higher kinetic energies than those electrons that are farther away
Figure 2.9 Probability densi-
ties r of an electron confined and can move through a larger volume. The kinetic energy of some of these elec-
inside a flat surface . The more
“localized” an electron is, the trons can further decrease when atoms bond to other atoms and form molecules;
larger its kinetic energy. Thus
delocalization, or redistribution
bonding increases the space in which electrons can “delocalize” (Figure 2.9). But
of electrons in a larger space, before we talk more about chemical bonding, let us analyze what spectroscopic
reduces their kinetic energy.
measurements can tell us about molecular properties.

http://www.chem.arizona.edu/tpp/chemthink/resources/U2_M1/molspec.html
LET’S THINK Molecular Spectroscopy

Molecules absorb and emit EM radiation of different types. The changes induced by these pro-
cesses depend on the wavelength of the radiation. Consider the interactive tool included on this
page that simulates the interaction of a water molecule with EM radiation of different types:

• What types of changes are induced by the different types of EM radiation that interact with
the molecule?
• Which of these changes requires more or less energy to
occur? Roughly estimate the amount of energy, in kJ/
mol, that is necessary to induce each type of transition.
• Would you expect all types of molecules to absorb the
same types of radiation? What factors may influence
how different molecules interact with EM radiation?

Share and discuss your results and ideas with a classmate. CLICK TO PLAY
Chemical Thinking U2 How do we determine structure? 93

Molecular Transitions
Just like atoms, molecules also exist in quantized energy states. However, they not
only exhibit quantized electronic states, but also vibrational and rotational energy
states. By using different types of EM radiation, one can explore transitions be-
tween these different types of energy states and derive valuable information about
electronic and molecular structure. For example, radiation in the UV and visible
regions of the EM spectrum tends to induce electron excitations. Given that elec-
trons play a central role in keeping atoms together in a molecule, these changes
may result in bond breaking and atom separation. The energy required for these
Figure 2.10 Energy scale for
changes to occur ranges from a few hundreds to over a thousand kilojoules per different types of molecular
transitions.
mole. This suggests that energy differences between electronic levels in molecules
are of the order of 102 to 103 kJ/mol.
EM radiation of lower frequency, and thus lower energy, E (kJ/mol)
in the IR range stimulates transitions between different vibra-
tional states. Quantization of molecular vibrations implies that
Electron Excitation
103
molecules can only exist in a discrete set of vibrational levels. Bond Breaking
DE UV-visible
Energy differences between these different levels is of the order 102
of 10-1 to 102 kJ/mol. On the other hand, microwave radia-
tion induces molecular transitions between different rotational
states. The energy needed for these changes to happen is of the 101
Change in
order of thousandths to tenths of kilojoules per mole (10-3 to Vibrational State DE Infrared
10-1 kJ/mol). Common sources of energy, such a gas flame, an 1
incandescent bulb, or our own body emit most of their energy
in the form of IR radiation. Thus, they tend to stimulate vi- 10–1
brational transitions in the molecules that surround them. In
Change in
general, knowing how much energy is needed to induce differ- Rotational State 10–2 DE Microwave
ent molecular transitions is useful in predicting the changes that
substances may undergo when exposed to different energy sources.

http://www.chem.arizona.edu/tpp/chemthink/resources/U2_M1/infspec.html
CO2 vibrations LET’S THINK
The spectra of chemical substances in different regions of the EM spectrum are like fingerprints
that can be used as differentiating characteristics to detect or identify them. Consider the IR ab-
sorption spectrum of CO2(g) as represented in the interactive tool on this page. In this spectrum,
radiation transmittance is shown as a function of “wavenumber,” a quantity commonly used to
represent data in IR spectroscopy and defined as the inverse of the wavelength 1/l.

• What types of vibrational states are accessible to the


CLICK TO PLAY

CO2 molecule according with this simulation?


• Estimate the amount of energy, in kJ/mol, that is nec-
essary to induce each type of vibrational transition.
• What does the simulation tell you about how excited
molecules relax back to their ground state?

Share and discuss your results and ideas with a classmate, and justify your reasoning and numerical
procedures.
94 MODULE 1 Analyzing Light-Matter Interactions

As you may have noticed in the last activity, IR spectra are characterized by the
presence of absorption bands of different widths. This may seem surprising given
that we stated that vibrational energy states are quantized. If that is the case, why
do we observe absorption over a range of frequencies rather than at very
0 well defined values (single peaks or lines)? The existence of broad absorption
bands in molecular compounds is due to the multiple interactions between
0.1
atoms in the same molecule and between different molecules in the system.
Transmittance

Molecules are dynamic entities that are constantly undergoing small rear-
0.2 CO2(g)
rangements. The mere presence of other particles in their vicinity may alter
0.3 the distribution of electric charge in the molecule, introducing tiny changes
in the vibrational and rotational energy levels that are allowed. From this
0.4 perspective not allthe molecules of the same substance are identical to each
1.600 1.610 1.620
Wavelength (mm) other and thus absorb EM radiation of slightly different frequencies. Given
that common spectrometers cannot detect these small variations in absorp-
Figure 2.11 High Resolution tion frequencies, these instruments register absorption over a continuous frequen-
IR spectrum of CO2(g).
cy range. However, there are high resolution spectrometers that clearly reveal the
quantized nature of the transitions (see Figure 2.11).
Molecular spectroscopy is a powerful analytical tool that has greatly simpli-
fied the detection and identification of chemical substances in complex chemical
environments, some of which may not be directly accessible. For example, in 2004
NASA launched the Aura spacecraft designed to study Earth’s air quality
and climate. Aura is equipped with four main analytical instruments that
use UV, visible, IR, and microwave radiation to scan the atmosphere and
study its chemistry and dynamics. The spacecraft repeats its journey around
the globe every 16 days to provide atmospheric measurement over virtually
every point on Earth in a repeatable pattern (see Figure 2.12 and Figure
2.13). This permits us to follow the evolution of over 20 different chemical
substances over time across the planet. The detection and quantification of
these substances are based on available information about their emission
and absorption spectra over a wide range of frequencies. The Aura mission
Figure 2.12 Aura Mission is just one of many examples in which molecular spectroscopy is the tool of choice
(NASA): NO2 concentration
over the US from September for chemical analysis.
to November 2004.

Emission UV IR MW
h (km)
50

18
Troposhere
0
Figure 2.13 Aura Mission: Different types
of spectroscopic measurements permit
detection of several chemical species at
different altitudes (h) in the atmosphere.
O3 H2O CO HNO3 NO2 HCl ClO
Chemical Thinking U2 How do we determine structure? 95

FACING THE CHALLENGE vided is enough to break chemical bonds within


the sample and produce free ground-state atoms
or ions. The instrument also has a radiation source
Detecting Metals containing the same metal we are looking to de-
Chemical compounds of metallic elements are tect. The metal is excited to generate EM radiation
pretty common in our planet. These substances characteristic of its emission spectrum, which is
tend to be ionic compounds made up of ions ar- passed through the vaporized sample. If the metal
ranged in crystalline networks. Most minerals be- of interest is present in the mixture it will absorb
long to this group of substances and erosive pro- the incoming EM radiation. The amount of radia-
cesses dissolve them in water. Thus, both seawater tion absorbed will be proportional to the metal’s
and freshwater contain relatively high concentra- concentration. Comparative measurements of
tions of metal ions such as Na+, K+, Mg2+, and light intensity with and without the sample can
Ca2+, together with traces of many other heavier then be used to quantify the metal’s concentration.
ions such as Ba2+, Sr2+, Cu2+, and Fe3+. Consider- AAS can be used to determine the concen-
ing that water is the major component of most life tration of close to 70 different metals in solution
forms, metal ions are also present in living organ- down to parts per billion (mg/L). In environmental
isms. In humans, Na+ and K+ play a central role and food analysis, AAS is the preferred method for
in cell transport; Ca2+ facilitate cell communica- monitoring the concentration of toxic metals in
tion processes while Mg2+ helps maintain normal air, drinking water, and drinks such as wine, beer
muscle and nerve function. Other metals found in and fruit juices. During the production of pharma-
trace amounts in our bodies are also vital, such as ceutical products it is common to use metal com-
iron for oxygen transport in blood and copper for pounds to facilitate the synthesis of drugs; AAS is
the activation of important cellular processes. used to monitor the concentration of metals in the
Given the importance of metal ions in the final products. At the industrial level many raw
anatomy and physiology of life, their detection materials are examined using AAS to ensure that
and quantification in our surroundings or inside the concentration of toxic impurities, such as lead,
our bodies are frequent practices in environmental meet official standards. The technique is also em-
or clinical analysis. In either case, atomic absorp- ployed by the mining industry to determine the
tion spectroscopy (AAS) is one of the most com- concentration of metals in ores and decide wheth-
mon analytical methods used to accomplish the er it is worth investing in their extraction.
task, particularly in those situations in which met- Many pathological conditions in humans re-
al ions are expected to be present in trace amounts. sults in changes in the concentration of metal ions
The technique developed in the extracellular fluid.
by A. Walsh in 1955 is Total lead in gasoline
Changes in these compo-
based on the fundamen- 100 (thousand of tons) 160 nents are often lethal and
tal principles of energy Lead concentration
in blood (ppm)
thus rapid procedures are
quantization discussed in 140 required for the analy-
this module. 80 sis of body fluids (e.g.,
An atomic absorp- blood, saliva, sweating).
120
tion spectrometer in- 60 Instrumental techniques
cludes a device to va- such as AAS, or emission
porize and atomize the 100 spectroscopy, are thus
sample. This can be done 40 used routinely in clinical
using a flame or a graph- laboratories for the rapid
1976 1977 1978 1979 1980
ite furnace that can reach diagnostic and manage-
YEAR
temperatures as high as ment of diseases.
The detection of lead in human blood using AAS
3000 oC. The energy pro- has led to the banning of lead from consumer
products, such as gasoline (Source: NIEHS)
96 MODULE 1 Analyzing Light-Matter Interactions

Let’s Apply

Alike 3.0] via Wikimedia Commons


By ESA/Hubble (Own work) [Share
What is in a Star?
Astronomers use diverse spectroscopic techniques to investigate
the composition of stars and other celestial objects, such as gal-
axies and nebulae. Spectroscopic data provide information not
ASSESS WHAT YOU KNOW

only about the chemical composition of these objects, but also about their temperature, density,
distance, and even their motion. Let us explore how this can be done.

http://www.chem.arizona.edu/tpp/chemthink/resources/U2_M1/blackbody.html
Blackbody Radiation

Stars, as many hot solids, emit EM radiation in a continuous range of wavelengths


(l). However, the intensity of the radiation at each specific l is a function of tem-
perature (T). The EM spectrum of stars can
be modeled by assuming that they behave
as perfect radiation emitters or absorbers
(blackbody objects). The interactive tool
that can be accessed in this page simulates
the intensity of the EM radiation emitted
by a black body as a function of wavelength
at different temperatures.

• Set the temperature in the simulation


to that of a light bulb. What type of CLICK TO PLAY
EM radiation is mostly produced by this object?
• How does the nature of the EM radiation produced by a hot object changes
when a) increasing its temperature and b) decreasing its temperature?
• How will the color of a hot object change as its temperature increases?
• How would the change in the EM radiation produced with increasing tempera-
ture affect the elements and compounds in the object’s surroundings?
• The area under the intensity vs. wavelength curve is a measure of the total ener-
gy produced by the object. Estimate the fraction of the total
energy emitted by the Sun that is in the form of visible light.

Share and discuss your ideas with a classmate, and clearly jus-
tify your reasoning.
TRIFID NEBULA
NASA
Chemical Thinking U2 How do we determine structure? 97

Solar Spectrum

Our sun’s EM spectrum as measured 2.5


UV Visible Infrared
from Earth is similar to that of a
black body object with a surface tem- 2.0 Sunlight at Top of Atmosphere
perature close to 5500 oC. However,
its fine structure varies depending on 1.5

Intensity
5500 oC Blackbody Spectrum
the altitude where it is measured (see
1.0
the figure).
0.5
Radiation at Sea Level
• How would you explain the

ASSESS WHAT YOU KNOW


presence of absorption “dips”in 0
the solar spectrum measured at 250 750 1250 1750 2250
Wavelength (nm)
the top of the atmosphere?
• How would you explain the presence of deeper and wider absorption dips in the solar
spectrum measured at sea level?

Share and discuss your ideas with a classmate, and clearly justify your reasoning.

Stellar Spectra

Chemical elements in a star’s photosphere absorb specific radiation. The “dips” in their spec-
tra as measured at the top of our planet’s atmo-
sphere can then be used to detect their presence
in the star. Additionally, the shape of the spectra
is indicative of the star’s temperature. Consider
the spectra from two different stars.

• Use the blackbody radiation simulation


from the previous page to try to reproduce
the basic shape of each of these spectra and
estimate the temperature of each star.
• The following table lists the wavelengths
associated with major absorption lines for different types of atoms and ions. Use this
information to speculate about the chemical composition of each star.

Atom/Ion l (nm) Atom/Ion l (nm)


Ca+ 393.5, 396.8 Li 670.8
He+ 420, 541.2 Mg 518.3
H 410.2, 434.0, 486.1, 656.3 Na 588.9
Fe 425, 527 Ne 439, 618

Share and discuss your ideas with a classmate, and clearly justify your reasoning.
98 MODULE 1 Analyzing Light-Matter Interactions

Let’s Apply
The Water Case
Water (H2O) is certainly one of the most important chemical compounds for life in our planet. Its
physical and chemical properties have a crucial influence on environmental phenomena, as well
as in the anatomy and physiology of living organisms. In particular, the manner in which water
ASSESS WHAT YOU KNOW

molecules interact with EM radiation influences from our planet’s temperature to our ability to see
the world. Consider the following spectrum of liquid water in a wide range of wavelengths.

106
Absorbance (1/cm)

104

102

100

10–2
UV IR MW
10–4

10 102 103 104 105 106 107 108 109


Wavelength(nm)

EM Absorption

Analyze the absorption spectrum for water:

• What type of EM radiations are mostly absorbed by water molecules? What types of
radiations go through this liquid without much being absorbed?
• How would you explain that the spectrum shows such wide absorption bands?
• How would you use the data to explain why water is a clear liquid with a bluish tint?
• How would our ability to do observations of celestial objects be affected if water were to
strongly absorb EM radiation at all wavelengths?
• How might the nature of the EM radiation absorbed and not absorbed by water have
influenced the evolution of organs to detect light (e.g., eyes) in living organisms?

Share and discuss your ideas with a classmate, and clearly justify your reasoning.
Chemical Thinking U2 How do we determine structure? 99

Greenhouse Gas
CLICK TO PLAY

http://www.chem.arizona.edu/tpp/chemthink/resources/U2_M1/blackbody.html
http://www.chem.arizona.edu/tpp/chemthink/resources/U2_M1/vibrations.html
Most of the sunlight that reaches Earth’s tropo-
Bending Vibration Stretching Vibration
sphere is in the form of IR radiation and visible
light. The surface of the planet absorbs part of this
radiation, heats up, and re-emits radiation at dif-
ferent wavelengths. Water in the atmosphere ab-
sorbs IR radiation, mostly at wavenumbers corre-
sponding to the bending and stretching vibrational 1595 cm-1 3756 cm-1
transitions shown on the image.

ASSESS WHAT YOU KNOW


• Use the interactive simulation for blackbody radiation (click on the image
to the right), together with all of the information provided so far, to deter-
mine whether water molecules will absorb more (or less) radiation coming
from the Sun than radiation re-emitted by the surface of our planet.
• Calculate the energy (in kJ/mol) needed to induce the bending and stretching transi-
tions shown on the image.
• If water molecules in the atmosphere absorb incoming and outgoing IR radiation, where
does that energy go? How should that affect the temperature of the atmosphere?

Share and discuss your ideas with a classmate, and clearly justify your reasoning.

Microwave Oven

A microwave oven works by generating EM radiation with


a wavelength close to 12 cm in a closed cavity that reflects
that type of radiation.

• Locate this type of radiation on the EM spectrum of


water on the previous page. Determine whether EM
absorption for this l is low or high relative to the absorption at other wavelengths.
• Calculate the amount of energy (in kJ/mol) of this radiation. What type of molecular
transition would be induced if water molecules were to absorb this energy?

In the liquid phase, interactions between water molecules strongly affect each other’s proper-
ties and behavior, thus, absorption of microwave radiation occurs over a range of wavelengths
rather than at specific values. Once a water molecule interacts with MW radiation, the effect
propagates to neighboring molecules via interparticle interactions.

• How would you explain that food with a high water content heats up when exposed to
microwave radiation?
• Would you expect this effect to be stronger or weaker in frozen food?

Share and discuss your ideas with a classmate, and clearly justify your reasoning.
100

Looking for
Patterns
Experiments based on the analysis of light-matter interactions such as those de-
U2: MODULE 2
scribed in Module 1 of Unit 2 have facilitated the determination of the composi-
tion and structure of the particles of matter. This knowledge is of central impor-
tance in understanding the physical and chemical properties of substances in our
world. In particular, how atoms are bonded to each other in molecules, or how
ions are arranged around each other in ionic networks, will affect the distribution
of electric charge in each particular system. Charge distribution in turn influences
the nature and strength of the interactions among molecules or ions in the system
and with other particles in their surroundings. Thus, the determination or predic-
tion of atom connectivity in the particles of matter is a cru-
cial step in the process of inferring a substance’s properties.
Chemical scientists have developed a variety of strate-
gies, experimental and theoretical, to determine atom or ion
connectivity in molecular and ionic compounds. Spectro-
scopic techniques have been an invaluable analytical tool in
completing this task. However, the analysis of experimental Why do carbon atoms
form FOUR bonds?
data is greatly simplified by using atomic and molecular models
of matter that help us predict many aspects of atom connectivity. Some of these
models have been derived from the recognition of regularities in the bonding be-
havior of different types of atoms and from patterns in the distribution of their
electrons in different energy states. Knowing how to apply this information in
predicting atom connectivity is a critical skill in chemical thinking.

THE CHALLENGE Amazing Carbon


Carbon-based compounds are among the most abundant and diverse in our
world. Most molecules in our body are made of these types of atoms.

• Carbon atoms have the capacity to form four bonds with other atoms of
the same or a different type. What determines the bonding capacity of
carbon atoms? Why is this capacity different for other types of atoms?

Share and discuss your ideas with one of your classmates.

This module will help you develop the type of chemical thinking that is used
to answer questions similar to those posed in the challenge. In particular, the
central goal of Module 2 is to help you understand how to use experimental
spectroscopic data, together with information about atomic composition and
electron configurations, to infer atom connectivity in molecular compounds.
Chemical Thinking U2 How do we determine structure? 101

Covalent Bonding
Molecular compounds are chemical substances made up of independent particles
called molecules. The idea that molecules are in turn comprised of atoms con-
nected to each other and arranged in particular geometries in space has been very
useful in explaining and predicting the physical and chemical properties of chemi- Figure 2.14 The bond length is
cal substances. But, what holds atoms together in a molecule? Let us analyze it. defined as the distance at which
the average electron-electron
A useful way of modeling bonding between atoms in molecular systems is and proton-proton repulsive
forces (red arrows) are balanced
based on the analysis of the electrostatic interactions between electrons and pro- by the average electron-proton
attractive forces (black arrows).
tons of the atoms that form the “bond” (electrostatic model). As shown in Figure
2.14 the basic idea is that when two atoms get in close proximity of each
other, the electrostatic attraction between electrons located between the BOND LENGTH
atoms and the protons in each of the atomic nuclei leads to a net at-
tractive force between the two atoms. As the atoms get closer together,
the strength of the attractive interaction increases until reaching a point
in which repulsive interactions between charges of the same type be-
gin to dominate. There is an equilibrium distance at which attractive
forces between electrons and protons are balanced by proton-proton
and electron-electron repulsive forces. This equilibrium distance be-
BOND LENGTH
tween the nuclei of the interacting atoms is conventionally defined as
the “bond length” and the energy needed to separate the atoms from this position
to an infinite distance is taken as a measure of the “bond strength” (also called
bond dissociation energy). The bond between two neutral atoms that results from
this dynamic interaction between electrons and protons in the system receives the
name of covalent bond.

Hydrogen Molecule LET’S THINK


In this activity you can find two simulations based on an electrostatic model of bonding between
two hydrogen (H) atoms. In the first simulation, the interacting atoms form a H2 molecule that

http://www.chem.arizona.edu/tpp/chemthink/resources/U2_M2/bond2.html
http://www.chem.arizona.edu/tpp/chemthink/resources/U2_M2/bond1.html
can be dragged across the stage. In the second simulation, the total internal energy (ET) of the
interacting atoms is represented as a function of the distance (r) between them. ET is a measure of
the energy associated with the interaction and movement of the electrons in the system.

• Analyze the formation of a covalent bond between two hydro-


gen atoms using the first simulation. What happens when you
move the atoms close to each other? What happens if you try
to have the nuclei touch each other? How easy is to “break”
the bond?
CLICK TO PLAY

• Use the second simulation to analyze the changes in total


internal energy (ET) when the two atoms are brought closer
to each other. How would you explain the changes in energy
that you observe? How would you explain the dynamic be-
havior of the bond once it is formed? How would you use the
information from the graph to estimate the bond length and
the bond strength for the hydrogen molecule H2?

Share and discuss your ideas with a classmate.


102 MODULE 2 Looking for Patterns

In the electrostatic model of covalent bonding, the formation of a bond be-


tween two atoms involves a variety of processes that alter the energy of the system.
For example, as the atoms get closer to each other, interactions between electrons
in one atom and protons in another atom pull some electrons toward the region
between the atoms. As electrons in one atom get farther away from that atom’s
nucleus their potential energy increases but their kinetic energy decreases. Addi-
tionally, as some electrons move towards the region between the two atoms other
electrons in each atom can get closer to their nuclei, which reduces their potential
energy. All these changes in the distribution of electric charge in the pair of atoms
lead to a net decrease in the total energy of the system. At even closer distances, the
attractive interactions between electrons in one atom and protons in another atom
dominate and produce a drastic decrease in the total potential energy. However,
if the atoms get too close to each other, repulsion between electric charges of the
same sign confined into a smaller space cause both the kinetic energy of electrons
and the potential energy of all interacting particles to increase. Thus, from the
Figure 2.15 Electron
energetic point of view, there is an optimal distance (bond length) at which the
density map for the hy- energy of the system is a minimum.
drogen molecule (H2).
From the perspective of the quantum mechanical model of the atom, in which
the position and speed of electrons cannot be precisely defined at the
Derivative from Image by Jindrich Kolorenc

same time (Heisenberg’s Uncertainty Principle), covalent bonding may


be explained by looking at changes in the electron density of the partici-
pating atoms. The formation of the covalent bond allows some electrons
to occupy a larger region of the space, which as we have seen decreases
their average kinetic energy; this phenomenon is called electron “delo-
calization.” As some electrons delocalize into the bonding region, the
remaining electrons in each atom can get closer to their atomic nuclei
which lowers their potential energy. According to this model, covalent bonding is
Electron Density
driven by the delocalization of electronic motion between the two bonded atoms
Low High
which causes a redistribution of electron density in the entire system. As we will
see in other modules of this book, electron delocalization plays a central role in the
formation of stable chemical substances.

http://www.chem.arizona.edu/tpp/chemthink/resources/U2_M2/bond3.html
http://www.chem.arizona.edu/tpp/chemthink/resources/U2_M2/bond1.html
LET’S THINK Comparing Models

Consider the following simulations of covalent bond formation based on the electrostatic model
of covalent bonding and on the quantum mechanical model of the atom:

• Compare the two models of bond formation and identify


major differences and similarities in their predictions of
electron charge distribution both as the atoms get close
CLICK TO PLAY

to each other and once the bond is formed. Which of the


models predicts more electron delocalization?
• What limitations do you see in each of the two representa-
tions of bond formation between two hydrogen atoms?

Share and discuss your ideas with a classmate, and clearly justify
your reasoning.
Chemical Thinking U2 How do we determine structure? 103

Bonding Patterns
Chemical bonds are dynamic entities in which the atomic nuclei and electrons
involved are in constant movement. Atoms in a bond vibrate around their equi-
librium positions at frequencies determined by both their atomic masses and the
bond strength. The bond strength depends on electron distribution between the
bonded atoms. Thus, a molecule made up of more than two atoms will experience
a variety of vibrational motions with frequencies determined by the molecule’s
atomic composition and connectivity.
Given that vibrational states are quantized, different molecules will undergo
vibrational transitions at characteristic frequencies when interacting with EM ra-
diation. In particular, the analysis of infrared (IR) radiation absorption as a func-
tion of wavenumber can give us important information about atom connectivity
in molecular compounds. Let us consider, for example, the IR absorption spec- Figure 2.16 IR absorption
trum (see Figure 2.16) for formaldehyde (CH2O), a chemical compound naturally spectrum for formaldehyde
(CH2O). Click on the image
produced by many living organisms, including ourselves, but that may be highly to observe the different vi-
brational modes of the CH2
toxic when present in low concentrations in the atmosphere. group in this molecule.

http://www.chem.arizona.edu/tpp/chemthink/resources/U2_M2/irspec.html
100
2785 cm-1
1165 cm-1
CH2
CH2
Symmetric
Wagging
Stretching
% Transmittance

2850 cm-1
CH2
50 Asymmetric 1485 cm-1 1250 cm-1
Stretching CH2 CH2
Scissoring Rocking

2850 cm-1
CO
Stretching
CLICK TO PLAY
0
3000 2000 1000 500
Wavenumber (cm-1)
As shown in this spectrum, specific types of bonding arrangements, such as a
carbon atom bonded to two hydrogen atoms (CH2), exhibit characteristic vibra-
tions (e.g., stretching, bending) that can be excited at specific frequencies or wave-
numbers. Although the actual location of the absorption band may shift somewhat
from one molecule to another, experimental results indicate that the existence of
an absorption band in a certain range of wavenumbers, or the identification of a
set of bands in specific locations of the spectrum, can be used as reliable cues to
infer the presence of a particular bonding arrangement in a molecule. This infor-
mation, together with experimental data from other analytical techniques such
as combustion analysis and mass spectrometry, is in many cases enough to infer
the molecular structure of a chemical compound. However, to take full advantage
of this information we need to better understand the different types of covalent
bonding that can occur between atoms.
104 MODULE 2 Looking for Patterns

Multiple pieces of experimental evidence suggests that stable covalent bonds


Figure 2.17 Every covalent bond are formed when at least two electrons are delocalized between the bonded atoms.
involving the delocalization of
two electrons is commonly rep- The covalent bond induced by two electrons is often described as a “single bond.”
resented using a single line be-
tween the bonded atoms. Double However, experiments also suggest that covalent bonding between some atoms
and triple bonds are then repre- may involve more than two electrons. In particular, some atoms form bonds in
sented using two or three linking
lines, respectively. which four or six electrons are delocalized; these types of covalent bonds are la-
beled as double and triple bonds, respectively (see Figure 2.17). The presence of
C C C N multiple bonds explains measured differences in the length and strength of bonds
between the same types of atoms. Interestingly, covalent bonding often involves
C C C N pairs of electrons, a phenomenon that we will try to explain later.
The presence of single, double, or triple covalent bonds between a pair of
C C C N atoms in a molecule changes bond strength, thus affecting the energy of the vibra-
tional states that are allowed in the system. The existence of multiple bonds can
then be detected through the analysis of the IR absorption spectrum of the chem-
ical substance. For a given type of vibration, absorption bands associated with
triple bonds tend to appear at higher wavenumbers (higher radiation energy) than
those of double bonds, and these latter bands are located at higher wavenumbers
than those of single bonds. In general, more energy is normally needed to induce
equivalent vibrational transitions involving stronger bonds. However, the energy
required also depends on the mass of the atoms involved in the bond. More ener-
gies is required to induce vibrational transitions in bonds between lighter atoms
which vibrate at higher frequencies.
The analysis of thousands of IR absorption spectra for a variety of known mo-
lecular compounds has allowed chemical scientists to delimit ranges of wavenum-
bers where vibrational absorption bands corresponding to specific bonding ar-
rangements are likely to appear (see Figure 2.18). Although the presence of a given
absorption band does not tell us how many bonds of a specific type are present in
a molecule, IR spectroscopic data is very useful in inferring molecular structure.
Figure 2.18 In general, most rel- C O C O
O H C N C N CH2 C N
evant vibrations involve molecu-
lar stretching and bending. The N H C C C C CH3 C C
location of the corresponding ab- stretch stretch stretch stretch bend stretch
sorption bands in the IR spectrum
can be used to infer how atoms X-H (with X = O, N) C-H Triples Doubles Singles
are connected in a molecule. cm-1
4000 3000 2000 1000

0.8
CH
Transmittance

0.6 C-H bends


stretch

0.4 O-H
stretch

0.2 C-O
stretch

0
3000 2000 1000
Wavenumber (cm-1)
Chemical Thinking U2 How do we determine structure? 105

Structure Determination LET’S THINK


The combination of information from infrared absorption spectroscopy (IR), mass spectrometry
(MS), and combustion analysis is very useful in the determination of the molecular structure of
molecular compounds. To assess your ability to use these types of experimental data in chemical
analysis, consider the following problems:

• Combustion analysis of a poison that causes blindness in humans reveals the formula CH4O.
The MS and IR spectra for this substance are shown below. Use this information to propose a
molecular structure that is consistent with the evidence provided.

100

80 0.8
Relative Abundance

Transmittance
60
0.6 C-H
40 C-H bend
0.4 stretch
20 C-O
O-H stretch
0.2 stretch
0
0 10 20 30 40 3000 2000 1000
m/q Wavenumber (cm-1)

• IR/MS breath analysis can be used to explore fat metabolism for people on a diet. Fat me-
tabolism produces a volatile organic compound with the formula C3H6O. The concentration
of this compound in people’s breath is indicative of how much body fat is being consumed
as a result of dieting. The IR and MS spectra of this molecular compound are shown below.
Use this information to propose a molecular structure that is consistent with the evidence
provided.

100
0.8

80
Relative Abundance

0.6
Transmittance

60
0.4
40
C-H
stretch C-C
20
0.2
C=O stretch
stretch
0
10 20 30 40 50 60 3000 2000 1000
m/q Wavenumber (cm-1)

HINT: Remember that the MS spectra contains useful information about molecular structure if you
pay attention to the fragmentation pattern. The mass of the most abundant ions formed during frag-
mentation can be used to infer their composition, which combined with IR data can help you figure out
molecular structure.

Share and discuss your ideas with a classmate.


106 MODULE 2 Looking for Patterns

The analysis of experimental data about the submicroscopic structure of mo-


Figure 2.19 Atoms in molecu-
lar compounds exhibit regular lecular compounds collected by many different means, from combustion analysis
bonding patterns. to IR spectroscopy to mass spectrometry, reveals the existence of bonding patterns
in these types of chemical substances. This means,
certain types of atoms tend to form the same num-
ber of bonds when they combine with other atoms
and the nature of these bonds is similar among
different compounds. Consider, for example, the
set of molecules depicted on Figure 2.19. If you
analyze the bonding patterns of the atoms that
make up these molecules you will notice that, for
example, carbon atoms always form four chemical
bonds with other atoms while oxygen atoms form
only two bonds (where double and triple bonds
account for two or three of those bonds, respec-
tively). It is as if these atoms had a fixed “bonding
capacity” independent of the nature of the atoms
to which they are connected. They may form sin-
gle, double, or triple bonds with different atoms, but the total number of electrons

http://www.chem.arizona.edu/tpp/chemthink/resources/U1_M2/pt.html
that are delocalized during bonding is frequently the same.

LET’S THINK A Periodic Trend?

Consider the molecules depicted in Figure 2.19:

• Analyze the structure of these molecules and identify the apparent “bonding capacity” of each
of the different types of atoms that made up these molecules;
• Locate each of the different types of atoms in the Periodic Table.
Analyze whether there is any relationship between the position
of an atom in the Periodic Table and its bonding capacity. Do
you detect any particular trend?

Share and discuss your ideas with a classmate. CLICK TO DISPLAY

Molecular compounds result from the combination of atoms of nonmetallic


VALENCY elements. The bonding capacity of these types of atoms, also called its “valence,” is
4 3 2 1 0 highly correlated to their location in the Periodic Table (Figure 2.20). For example,
all atoms from the so-called halogen group or family (i.e., F, Cl, Br, I) commonly
have a valence equal to one: they form a single bond when they combine with
other atoms. This common valence for atoms in the same group (column) in the
Periodic Table could somehow be expected given that group arrangements in this
table are based on similarities in chemical reactivity. Simply put, atoms in a given
group tend to chemically combine in the same proportion with atoms in other
groups in the Periodic Table. Atomic properties that vary regularly across a group
(column) or a period (row) in the Periodic Table are called “periodic properties,”
and valence is thus an example of this type of regular behavior. The recognition of
Figure 2.20 Valence of non- periodic properties is of great value in chemical thinking, because they allow us to
metallic atoms. predict the physical and chemical properties of substances.
Chemical Thinking U2 How do we determine structure? 107

Atoms of nonmetallic elements tend to exhibit a fixed valence. However, there


are exceptions and we may find molecular compounds that deviate from the ex-
pected patterns. These deviations from the regular periodic trend are more com-
mon in atoms with larger number of electrons in any given group, for example
in sulfur (S) versus oxygen (O) atoms, or in phosphorus (P) versus nitrogen (N)
atoms. Despite the existence of exceptions, the recognition of bonding patterns
greatly simplifies the determination and prediction of the molecular structure of
chemical compounds.

Combining Information LET’S THINK


The recognition of common bonding patterns of the atoms of nonmetallic elements help
us reduce the number of possible options when trying to infer the molecular structure of
a chemical compound based on experimental data. Let us assess your ability to apply this
information in the characterization of the structure of a molecular compound produced by
our own body.

• The analysis of various human secretions reveals the presence of a chemical compound
that seems to have antimicrobial properties. The elemental composition of this com-
pound obtained by combustion analysis is 40.00% C, 6.71% H, and 53.29% O. What
is the empirical formula of this molecular compound?
• Use the information from the mass spectrum of this compound to derive its molecular
formula.
• Use the information from the MS and 100

IR absorption spectra of this com- 80


Relative Abundance

pound , together with your knowl-


edge about common bonding pat- 60
terns, to propose a likely molecular
40
structure for this substance.
• Clearly show how your proposed 20
structure justifies the presence of 0
major absorption bands in the IR 0 10 20 30 40 50 60 70
spectrum. m/q

• Based on your proposed molecular


structure, propose different structures
0.8
for the ions that led to the MS peaks
with more than 10% relative abun- C-H
Transmittance

0.6
dance. stretch
0.4
• Can you think of a different molecu- C-C
lar structure that may produce similar 0.2
O-H C=O C-O
experimental data? What would you stretch stretch stretch
do to decide what is the actual mo-
3000 2000 1000
lecular structure of this compound? Wavenumber (cm-1)

Share and discuss your results and ideas with a classmate.


108 MODULE 2 Looking for Patterns

Atomic Patterns
Covalent bonding is driven by the delocalization of some electrons within a bond
between two atoms. Thus, to understand why atoms tend to exhibit a fixed valence,
and why this bonding capacity is a periodic property, we need to explore electron
Diffracted
distributions within atoms. This is not an easy task as we cannot determine with
rays
exact precision where electrons are and how they are moving at any point of time
Derivative from Images from Life Sciences Foundation

inside an atom. Thus, we need to rely on indirect measurements that can help us
X-ray beam
infer electron configurations --this is, how electrons distribute in both space and
energy levels within atoms.
As a first step, we may want to pay attention to the size of different atoms. This
information may be useful in comparing the probability of finding electrons in
certain regions of the space in different atomic systems. According to our current
model of an atom, atomic size is not a well defined quantity because electrons are
constantly moving through empty space and we cannot determine with precision
where they are at all times. However, chemical scientists have devised strategies to
locate the average position of atomic nuclei in molecules and ionic networks (see
Diffraction Pattern
Figure 2.21); this information can then be used to quantify atomic sizes. For ex-
ample, if we define the bond length (d) as the distance between the atomic nuclei
of two bonded atoms, we can assume that this distance should have a value close
to the result of adding the atomic radius (r) of each of the atoms. Thus, by mea-
suring the length of bonds between similar and different types of atoms in many
molecules, we can start building a scale of atomic sizes based on average values.
The set of atomic radii determined following this procedure are called “covalent
d = 2 r(C) = 0.153 nm atomic radii” to distinguish them from values determined by other approaches.
Figure 2.22 includes the values of the covalent atomic radii for several atoms
Figure 2.21 X-ray crystallogra-
phy is commonly used to deter- as determined using X-ray crystallography. As you can see in this figure, atomic
mine bond lengths. Each crystal-
lized substance diffracts X-ray
size also exhibits a periodic trend: the size of the neutral atoms decreases as the
radiation in different ways. The atomic number Z increases within a period and it increases as the atomic number
analysis of the diffraction pat-
tern provides information about increases within a group. This periodic pattern is commonly summarized stating
distances between atoms.
that atomic size increases as we move from right to left across a period (row) and from
top to bottom within a group (column) in the Periodic Table.
Group 1A Group 2A Group 3A Group 6A Group 7A
(1) (2) (13) (16) (17)

Li Be B O F
128 96 84 66 57

Na Mg Al S Cl
166 141 121 105 102

Figure 2.22 Atomic covalent K Ca Ga Se Br


radii in picometers (pm). 203 176 122 120 120
1 pm = 1 x 10-12 m = 1 x 10-3 nm.
Chemical Thinking U2 How do we determine structure? 109

The periodic trend in atomic size can be seen more clearly in


Figure 2.23a where we plot the covalent atomic radii as a func- Rb
K
tion of the atomic number (Z) for atoms with up to 38 protons
in the atomic nucleus. This graph elicits a pretty regular pattern Na
in the evolution of the atomic radius as the number of protons Li
and electrons increases. The pattern repeats systematically at val-
Ar Kr
ues of Z where a new period starts. This periodicity suggests the
existence of distinctive regularities in the spatial distribution of Ne
electrons for atoms in the same group of the Periodic Table. He a)
A similar behavior is observed when analyzing the minimum
energy needed to remove an electron from the neutral atoms of
an element in gaseous state. This energy, often called first ioniza-
tion energy (EI) or first ionization potential, induces the follow- He b)
Ne
ing process in a given substance M:
Ar
Kr
M(g) M+(g) + e-

The energy required to ionize the atoms of a substance can be


measured by bombarding a gaseous sample with fast-moving Li Na K Rb
electrons of known kinetic energy and analyzing the amount of
energy that these electrons lose during the collision. These types
of experiments lead to results like those summarized in Figure
2.23b where we show the first ionization energy (in kJ/mol) as a
Figure 2.23 a) Covalent
function of atomic number for atoms with up to 38 protons in the atomic nucleus. atomic radii (in pm) as a func-
tion of atomic number (Z);
In this case, the first ionization energy increases as we move from bottom to top within b) First ionization energy EI
a group (column) and from left to right across a period (row) in the Periodic Table. The (in kJ/mol) as a function of Z.

periodicity of this property is also evident as the same pattern repeats at values of
Z where a new period starts.

Back to Modeling LET’S THINK


The experimental data for the atomic radii and the first ionization energies summarized in Figure
2.23 suggest the existence of some sort of pattern in the spatial and energetic distribution of
electrons within atoms as a function of atomic number. If you had to build a model to explain or
justify the periodic behavior of these two properties:

• How would you explain that atomic radii decreases as we move from left to right within a
period in the Periodic Table even when more electrons are present in the system?
• How would you explain the big jump in atomic radius as we reach values of Z where a new
period begins?
• How would you explain the increase in first ionization energy as the atomic number in-
creases within a period?
• How would you explain the drastic decrease in the first ionization energy as we reach values
of Z where a new period begins?

Share and discuss your results and ideas with a classmate. Build drawings to represent the type of
electron distribution in space and energy levels that would explain the observed behaviors.
110 MODULE 2 Looking for Patterns

At a first level of approximation, we can make sense of the experimental data


for atomic radii and first ionization energy by conceiving electrons as distributed
in “shells” within atoms. A shell defines both a region in space where it is most
likely to find an electron as well as the total energy that such an electron is likely
to have. Thus, for example, electrons with the lowest energy in an atom are likely
to be those that are moving close to the atomic nucleus, occupying the first shell.
Higher energy electrons are more likely to be found farther away from the nucleus,
moving across a volume that corresponds to an outer shell. According to this “shell
model of an atom,” different shells correspond to different quantized energy states
in which several electrons may exist (see Figure 2.24). To explain the observed
periodicity in the behavior of atomic radii and first ionization energy the model
assumes that there is a limit to the number of electrons that can be found in the
same quantum energy state (or the same shell).

ET
H He Li Ne Na
0
First Ionization
Energy

Figure 2.24 Distribution in To better understand the assumptions about atomic structure made in the
energy and space of electrons
in different quantum states ac- shell model, let’s use this model to try to explain the experimental data summa-
cording to the shell model of
the atom. The zero of energy rized in Figure 2.23. The simplest known atom, the hydrogen atom has one single
in this figure corresponds to electron that we can assume occupies the first atomic shell (n = 1). It is followed by
electrons detached from the
atom. the He atom that has one additional electron and proton. To explain the observed
increase in ionization energy EI and the decrease in atomic radius r as we move
from hydrogen to helium in the Periodic Table, we assume that both electrons
in the He atom also occupy its first atomic shell. However, the energy of this
quantized state in a He atom should be lower than in a H atom because a larger
nuclear charge will exert a stronger attractive force on each electron, keeping them
closer to the nucleus and lowering their potential energy. A stronger attractive
force on each electron will reduce the likelihood of these particles moving too far
away from the nucleus, reducing the average atomic size. It also implies that more
energy will be required to remove one of these electrons from the atom.
The sudden increase in atomic radius and decrease in first ionization energy
as we move from helium to lithium can be justified if we assume that only two
electrons can occupy the first atomic shell. Thus, the third electron in a Li atom
is forced to move in a region of the space farther away from the nucleus where its
total energy will be higher (second atomic shell, n = 2). In consequence the size of
the atom increases and the energy required to ionize it is lower. As we move across
Chemical Thinking U2 How do we determine structure? 111

a period in the Periodic Table, electrons occupy the second atomic shell until it is
full. Based on the experimental data that we have, that seems to occur when eight Atomic Maximum
electrons are in that state (the next drastic change in atomic size and first ioniza- Shell # of e-
tion energy occurs when Z =11, for the sodium atom). Addition of electrons to
n=1 2
the same shell does not result in a larger atomic size because the more positive
nuclear charge pulls those electrons towards the nucleus; this stronger attractive n=2 8
force is also responsible for the higher ionization energy values. Major changes n=3 8
in this pattern only occur when a shell is full and electrons are forced to occupy n=4 18
a higher energy shell. Thus, the maximum shell occupancy can be inferred from n=5 18
experimental data such as that shown in Figure 2.23. This analysis leads to the re-
sults summarized in the table shown to the right, where different shells have been
n=6 32
assigned the label n = 1, 2, 3,...
The shell model of the atom does a pretty good job at explaining the general
trends in several atomic properties, such as atomic size and first ioniza- Detector
tion energy. However, it provides limited explanation for anomalies or

By Bvcrist (Own work) [Public domain]


Ionization
deviations from the general pattern and fails to account for experimental Energy

via Wikimedia Commons


X-ray
results for other atomic properties, such as the energy needed to remove photons
EI = h n - Ek
not just one electron but many electrons from a single atom. This mth ion- E=hn Ejected
Electrons
ization energy, where m is the number of electrons that are ejected from E = Ek
an atom, can be measured using an analytical technique called photoelec-
tron spectroscopy (PES). This method relies on the use of several types
of EM radiation, particularly X-rays in those cases in which the goal is to
remove all electrons from an atom. The ionization energy is determined Figure 2.25 In PES, ioniza-
by bombarding atoms with photons of known energy hn and measuring the ki- tion energies are calculated by
taking the difference between
netic energy of the ejected electrons (Figure 2.25). The more weakly the electron the energy of incoming pho-
tons and ejected electrons .
is held to the atom, the more kinetic energy it will have when ejected. Inner shell
electrons (referred to as core electrons) are held much more tightly to the nucleus
so it usually takes high energy x-ray photons to remove them from an atom.

Adjusting the Model LET’S THINK

http://www.chem.arizona.edu/tpp/chemthink/resources/U2_M2/pes.html
X-ray PES can be used to determine how many electrons exist in a given energy state in an atom.
These electrons are expected to have similar ionization energies. A plot of number of electrons as
a function of ionization energy is then indicative of the number and distribution of atomic shells.

• Based on your understanding of the shell model of the atom, predict the structure of the
PES spectra for all of the atoms with an atomic number Z ≤ 11. Use the PES spectrum of
Li atoms shown on this page as a guide for your
predictions;
• The interactive tool associated with this activity
CLICK TO PLAY

displays the actual PES spectra for atoms with


Z ≤ 20. Use the tool to verify your predictions;
• Based on your analysis, discuss how you pro-
pose to change the shell model of the atom to
better explain these experimental results.

Share and discuss your ideas with a classmate.


112 MODULE 2 Looking for Patterns

As you have seen in the previous activity, the results from PES correlate well
with the predictions of the shell model of the atom for atoms with an atomic num-
ber Z up to four. However, for higher values of Z unexpected deviations occur.
Electrons in the second shell, which we assumed could be occupied by a maximum
of eight electrons, seem to be arranged into two “subshells:” one subshell that can
hold up to two electrons and another subshell with a maximum occupancy
Atomic Atomic Maximum of six electrons. This pattern repeats itself for atoms in the third period in the
Shell Subshell # of e- Periodic Table. PES analysis of atoms with a larger atomic number reveals
n=1 s 2 the existence of other subshells, some of them with a maximum capacity of
s 2 10 electrons and others that can be occupied by up to 14 electrons. Based
n=2 on these experimental results, the shell model of an atom can be modified
p 6
to allow for the existence of shells and subshells in which electrons can be
s 2 distributed as shown in the table to the left. In this table, the labels n=1, 2,
n=3 p 6 3,... are used to distinguish one shell from another, while the letters s, p, d,
d 10 and f are used to label subshells with a maximum occupancy of 2, 6, 10, and
s 2 14 electrons, respectively.
The existence of atomic subshells is predicted by the modern quantum
p 6
n=4 mechanical model of an atom. In fact, this model reveals an even more com-
d 10 plex distribution of electrons within atoms. According to this model, sub-
f 14 shells that can accommodate more than two electrons (subshells p, d, f ) are
actually composed by “sub-subshells” each of them with a maximum capacity
of two electrons. These sub-subshells are traditionally called “orbitals” and thus
we say that the s subshell is equivalent to one “s” orbital, the p subshell contains
three “p” orbitals, the d subshell contains five “d” orbitals, while the f subshell is
composed of seven “f ”orbitals. As it was the case for the terms shell and subshells
in the other models that we have discussed, orbitals should not be thought of
as containers where electrons are placed. Rather, orbitals define energy states in
which electrons can exist and the probability densities of finding these electrons in
certain regions of the space. For example, an electron in a 1s orbital is in the lowest
energy state of an atom and it is likely to be found in a spherical region close to the
atomic nucleus. On the other hand, an electron in a 2p orbital will have a higher
energy and will most likely be found farther away from the nucleus. Additionally,
our current model of the atom predicts that the distribution in space of electrons
in 2p states is not the same in all directions (see Figure 2.26).
E d
p
s
Derivative from image by Florian Marquardt (Own work) [Share Alike 3.0]

n=3 3px 3py 3pz


3dxy 3dxz 3dyz 3dx2-y2 3dz2
y x z y z
3s
x z y x y
via Wikimedia Commons

z y x z x
n=2
2px 2py 2pz
2s
x y z
Figure 2.26 Each of these images represents the probability den-
z x y sity for electrons in atomic orbitals at different energy levels. The
lighter the color in each of these images, the higher the probabil-
n=1 y z x ity of finding the electron in those regions of space. 3D axes are
shown to indicate the particular perspective from which each image
1s is drawn. Notice that probability densities associated with the same
y types of orbital (s, p, d) have similar symmetries.
x
z
Chemical Thinking U2 How do we determine structure? 113

Electrons in an atom in its ground state are expected to occupy the lower en-
ergy levels available in the system. For example, in a hydrogen atom the only elec-
tron will be in the 1s energy level. The ground state electron configuration of this
atom is then said to be 1s1, where the superscript is used to represent the number
of electrons in a particular energy level. The electron configurations of subsequent
atoms in the Periodic Table can then be expressed in the following way:

Electron Configuration
Atom
Spectroscopic Notation Noble Gas Notation
He (Z = 2) 1s 2
[He]
Li (Z = 3) 1s 2s
2 1
[He]2s1
Be (Z = 4) 1s22s2 [He]2s2
B (Z = 5) 1s22s22p1 [He]2s22p1
Ne (Z = 10) 1s22s22p6 [Ne]
Na (Z = 11) 1s 2s 2p 3s
2 2 6 1
[Ne]3s1

You may wonder how the relative energy of different atomic orbitals is deter-
mined. How do we know, for example, that the 2s orbitals are lower in
energy than the 2p and thus are filled up first? The answer is provided by 1s
the analysis of experimental data, such as ionization energies from PES, 2s 2p
together with the application of the quantum mechanical model of the 3s 3p
atom. This information leads to the orbital filling sequence summarized
4s 3d 4p
in Figure 2.27. You may have also noticed that electron configurations
in the so-called spectroscopic notation in the table above can be short- 5s 4d 5p
ened by using a noble gas notation. In this latter format, the bracketed 6s 4f 5d 6p
chemical symbol of the noble gas atom that precedes the atom of inter- 7s 5f 6d 7p
est in the Periodic Table is used to represent that part of the electron
configuration that is similar between the two atoms. This part of the electron con- Figure 2.27 Orbital filling se-
quence based on the relative
figuration happens to represent the distribution of electrons in those inner shells energies. Electrons always oc-
cupy the lowest energy levels
that are already full --it describes the distribution of the so-called “core” electrons available.
in an atom.

Patterns in Electron Configurations LET’S THINK


The analysis of the electron configuration of atoms in the same group in the Periodic Table leads
to the identification of interesting and useful patterns.

• Build the electron configurations, using both spectroscopic and noble gas notations, of the
following types of atoms: C, N, O, F, Mg, Al, Si, P, S, Cl, and Ar. You may use the filling
sequence summarized in Figure 2.27 to guide your work.
• Compare the electron configurations of atoms in the same group in the Periodic Table.
What similarities do you observe?
• Compare the electron configurations of atoms in the same period of the Periodic Table.
What similarities do you notice?

Share and discuss your ideas with a classmate.


114 MODULE 2 Looking for Patterns

Atoms in the same group of the Periodic Table have similar distributions of
electrons in their higher energy states. This can be seen by comparing electron
configurations in the noble gas notation. For example, for the Li atom we have:
[He]2s1 while for the Na atom we have: [Ne]3s1. The orbital occupation is identi-
cal for those energy levels outside the core of each atom. Electrons in these more
external and higher energy orbitals are called “valence” electrons. Thus, according
to our analysis, atoms in the same group of the Periodic Table have similar valence
electron configurations. These similarities are made explicit in Figure 2.27, where
we show the prototypical electron configuration of the valence electrons of atoms
in each of the different groups in the Periodic Table:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
s1 s2 s d s d s d s d s d s d s d s2d8 s2d9 s2d10 s2p1 s2p2 s2p3 s2p4 s2p5 s2p6
2 1 2 2 2 3 2 4 2 5 2 6 2 7

1
2 [Ar] 4s23d104p2
3
4

5
The periodicity in valence electron configurations greatly simplifies the con-
Figure 2.28 Valence elec-
tron configurations for the struction of full electron configurations for different atoms. Imagine that we want-
germanium atom (Ge) us-
ing noble gas notation.
ed to build the ground state electron configuration for a germanium (Ge, Z = 32)
atom. The first step is to localize the period (n = 4) and group (14) in which this
atom is in the Periodic Table. The second step is to identify the noble gas atom pre-
ceding Ge in the table, in this case argon (Ar, Z = 18), which we can assume will
have a similar electron configuration to that of the core electrons in Ge. The final
step is to add the electron configuration of the 14 remaining electrons, which can
be deduced from the valence electron configuration of the preceding atoms in the
same period as the Ge atom and from the general structure of the valence electron
configuration of those atoms in the same group (s2p2). Thus we have:

Ge : [Ar] 4s23d104p2

According to the information summarized in Figure 2.27, valence electrons oc-


cupy s and p orbitals in the shell with the same label as the period in which the
atom is located (period 4 in the case of the Ge atoms). However, d and f orbitals
from inner shells will be occupied before than the outer p orbitals.

LET’S THINK Predictions

The construction of electron configurations allows us to predict the properties of chemical substances:

• Build the electron configuration of a bromine atom and sketch its expected PES spectrum.

Share and discuss your ideas with a classmate, and justify your reasoning.
Chemical Thinking U2 How do we determine structure? 115

Understanding Bonding
Current chemical models of atomic structure allow us to make sense of the physi-
cal and chemical properties of substances. In particular, as we will see in the fol-
lowing paragraphs, they provide a basic explanation to the observed periodicity
in the bonding capacity (valence) of different types of atoms. Understanding how
atoms bond to each other is of central importance for predicting the three dimen-
sional structure of molecules and the nature of the interactions among them.
Explanations and predictions about chemical bonding can be greatly simpli-
fied if we assume that electrons in atoms can be divided into two major groups.
On the one hand we have core electrons that occupy the low energy, inner orbitals
in atoms. These types of electrons are most likely to be found in regions of space
close to the atomic nucleus and thus we can assume they are not significantly
perturbed by the presence of other atoms. On the other hand, we have valence
electrons which occupy the higher energy, outer orbitals and are significantly af-
fected by neighboring particles. A central idea in chemistry is that the formation of
different types of chemical bonds can be understood by paying attention to the properties
of valence electrons in atoms. To illustrate the power of this idea, let us reanalyze the
formation of covalent bonds between atoms of nonmetallic elements.
When two atoms get close to each other, electrostatic interactions between
protons in one atom and valence electrons in the other atom will attract electrons
to the space between the atoms. This electron delocalization changes the distribu-
tion of the valence electrons in each atom and lowers their average energy. Delocal-
ization favors the formation of chemical bonds because the energy of the bonded
particles tends to be lower than that of the isolated atoms. From this perspective,
the more valence electrons are delocalized through bond formation, the lower the Electron Density
energy of the molecule that may form. However, electron delocalization is con-
strained by the number of available unfilled valence orbitals that the delocalized Low High
electrons can occupy.
Electrons that get delocalized during bonding occupy valence
orbitals that are shared by the bonded atoms (bonding orbitals).
From this point of view, they can be thought as belonging to both
atoms. Therefore, for bonding to occur, atoms should have unfilled

By Dvaid Young & James F. Harrison


valence orbitals that can be occupied by the delocalized electrons.
Given that the formation of bonding orbitals lowers the energy of
the system, it is likely that atoms will form as many covalent bonds
as unfilled electron states are available in their valence shells. Let’s
consider, for example, the case of an oxygen atom with an electron
configuration [He]2s22p4. Given that the p subshell has a maxi-
mum occupancy of six electrons, we can expect an oxygen atom
to induce the delocalization of 6 - 4 = 2 electrons when bonding
with other atoms. Oxygen atoms are then likely to form two bonds
when interacting with atoms of other nonmetallic elements. On the other hand, a
Figure 2.29 Electron density
hydrogen atom with an electron configuration 1s1 will likely form one single bond map for the water molecule.
Bonding has a strong effect
because its valence shell (s orbital) can only hold a maximum of two electrons. on the distribution of valence
Therefore, the most stable molecule that can form during the interaction of one electrons in the system.

oxygen atom with hydrogen atoms is H2O, where one O atom is linked by a single
bond to two H atoms (Figure 2.29).
116 MODULE 2 Looking for Patterns

LET’S THINK Predicting Structural Formulas

Based on the electron configurations of these atoms: H, C, N, Cl, and S, predict the structural
formula of the molecules that will form when combining the following pairs of atoms: H and H,
H and C, H and N, C and Cl, S and Cl, and Cl with Cl.

Share and discuss your ideas with a classmate, and justify your reasoning.

The valence shell of nonmetallic atoms can be occupied by a maximum of two


electrons in the case of hydrogen and by 2 + 6 = 8 electrons for all the other atoms
of nonmetallic elements. According to our model, their bonding capac-
VALENCE ity (valence) will then be given by the numerical difference between the
4 3 2 1 0 maximum occupancy of their valence shell and the actual number of va-
s2p2 s2p3 s2p4 s2p5 sp
2 6 lence electrons in the isolated atom. As a result of covalent bonding, each
atom in a molecule can be thought of as having a full valence shell. Thus,
it is common to say that the most stable structures that are formed when
atoms bond to each other are those in which each atom has a full valence
electron shell. Given that for most nonmetallic atoms a full valence shell
corresponds to eight electrons, this statement is known as the octet rule.
The octet rule is a useful heuristic to predict the structure of molecular
compounds, but it must be applied and interpreted with caution. For ex-
ample, it is common to think that the octet rule implies that atoms bond
to each other because they “want” to get a full valence electron shell. It
is also common to assume that the octet rule is an unbreakable principle
that controls the behavior of all atoms. However, these simplifications and
over-generalizations often lead people astray in explaining or predicting
the properties of many chemical compounds. Atoms do not have wishes
Figure 2.30 The most com- or desires and their behavior is highly influenced by the forces acting on them.
mon valency of these set of
atoms is given by the numeri- Despite regularities in their properties, they may deviate from the regular patterns
cal difference between the
maximum occupancy of their depending on the nature of the particles with which they interact. Thus, rather
valence shell and the actual
number of valence electrons in than blindly applying a rule to solve any type of problem, it is more effective to pay
the isolated atom. attention to the main factors that control chemical bonding. These factors may be
summarized in the following form:

Factor 1. Bonding is a stabilizing process for atoms with unfilled valence or-
bitals because some electrons gain access to lower energy states. In general, the
more electrons occupy those states, the lower the energy of the system and the
greater its stability relative to that of the isolated atoms.

Factor 2. The number of electrons that gain access to lower energy states is con-
strained by the number of unfilled valence orbitals in the bonding atoms. Because
there is a limit to the number of electrons that can exist in a given energy state,
there will be a limit to the number of bonds that an atom can form. Therefore the
bonding capacity of an atom (its valence) will likely be determined by the number
of available unfilled valence orbitals.
Chemical Thinking U2 How do we determine structure? 117

If electron delocalization into bonding orbitals lowers the energy of atomic sys-
tems, one may wonder why more bonds are not formed by delocalizing electrons
in the unoccupied higher energy orbitals of the bonded atom. In general this does O
not happen because the energy increase required to place electrons in those states is
larger than the energy reduction coming from electron delocalization. However, in HO S OH
systems involving large nonmetallic atoms the energy cost of promoting electrons
to higher energy states is considerably lower; thus, it is not uncommon for these O
types of atoms to form molecules in which the number of bonds per atom deviates Figure 2.31 Sulfur atoms
from the common patterns. For example, phosphorus frequently exhibits a valence form 6 bonds in molecules
of sulfuric acid (H2SO4).
of 5 instead of 3, and sulfur forms important compounds in which these types of
atoms have a valence of 6 instead of 2 (Figure 2.31).

Breaking the Rules LET’S THINK


Several molecules that play an important role in the metabolism of living organisms exhibit
bonding patterns that deviate from those most commonly observed in chemical compounds.

• Based on your analysis of atomic electron configurations, which of the following stable mol-
ecules are likely to exhibit unusual bonding patterns: O2, N2, CO, CO2, NO, CH4, SO2?

Share and discuss your ideas with a classmate, and clearly justify your reasoning.

The formation of covalent bonds is driven by the delocalization of electrons


into lower energy bonding orbitals shared by the bonded atoms. As is the case
with all orbitals, a maximum of two electrons can occupy those energy states.
This is why a single covalent bond tends to involve the delocalization of only two
electrons. In general, the formation of a single bond leads to the delocalization of
one electron from each of the participating atoms. However, this does not need
to be the case in all situations and deviations from this behavior may also result in
unusual bonding patterns.

Electron Spin
The limit in electron occupancy of atomic and molecular orbitals has a large im-
pact on the molecular structure of chemical compounds. Experimental data sug-
gest that this phenomenon is due to an intrinsic property of electrons that con-
straints the number of these particles that can simultaneously occupy the N S
exact same region of space. This intrinsic property is called spin and can
be conceptualized as a measure of the rotational motion of an electron
on its own axis. Analyses of the behavior of electrons in the presence of
magnetic fields suggest that an electron spins at a fixed, invariant rate, and
that all electrons spin at the same rate. However, an electron may only
spin in one of two possible directions: it can rotate clockwise (denoted ↑
or with the value +1/2) or counterclockwise (denoted ↓ or with the value
S N
-1/2). This implies that an electron’s spin is a quantized property. Given
that an electron is a charged particle, its spin gives it magnetic properties. -1/2 +1/2
In fact, spinning electrons can be conceptualized as subatomic magnets that will Figure 2.32 Classical repre-
sentation of electron spin.
be subject to forces in the presence of a magnetic field (Figure 2.32).
118 MODULE 2 Looking for Patterns

Wolfang Pauli introduced the idea of electrons having a quantized spin to


make sense of the electron configurations and bonding capacities inferred from
the type of experimental data discussed in this module. In particular, he proposed
that no two electrons with the same properties could occupy the same orbital
simultaneously (The Pauli Exclusion Principle). The only way this could happen
was if each electron had a different spin. Given that electrons can only exist in two
possible spin states, no more than two electrons can simultaneously occupy the
same quantum state described by an orbital.
Pauli exclusion principle implies that electrons with the same spin in an atom
will be found occupying different regions of the space. This helps reduce the po-
tential energy of the system by keeping electrons far from each other and also al-
lowing them to get closer to the nucleus. From this perspective, pairing electrons
with opposite spin into the same orbital has an energy cost. Pauli’s principle also
requires that for two electrons to occupy the same bonding orbital they should
have opposite spins. This means that in order for a covalent bond to form, the
energy needed to pair up the electrons should be smaller than the energy gained
by delocalizing the electrons into the bonding orbital.
Given that delocalization of electrons into bonding orbitals lowers the aver-
Figure 2.33 The molecule of age energy of the interacting atoms, one can expect available bonding orbitals to
nitrogen monoxide is a radi- be filled with as many valence electrons as possible. However, there are situations
cal. Chemical bonds involving
less than two electrons are in which the number of valence electrons may be an odd, rather than an even,
commonly represented with
dashed lines. number and some bonding orbitals may be occupied by one single electron. These
types of chemical species are called radicals and tend to be extremely reactive; they
have unfilled valence orbitals that will induce the delocalization of electrons from
other species. Although radicals are not very stable particles, they play a central
role in the chemistry of the atmosphere and of our own bodies (Figure 2.33).

LET’S THINK Quantum Explanations

The formation of covalent bonds between atoms of nonmetallic elements is largely controlled by
“quantum” phenomena such as energy quantization, electron delocalization, and electron spin.

• Discuss what you understand by each of these concepts. What do they mean to you? How
would you explain each phenomenon in your own words?
• Discuss how each of these phenomena determines or affects the formation of covalent bonds
between atoms of nonmetallic elements.
• Self-assess the extent to which you can use arguments based on these three phenomena to
explain why:
a) It is necessary to invest energy to separate two bonded atoms;
b) Hydrogen gas is made up of H2 molecules while Helium gas is made up of single atoms;
c) It takes more energy to separate the two bonded atoms in a N2 molecule than in a O2
molecule;
d) A chemical compound such as SF6, used as a contrast agent for ultrasound imaging, can be
stable;
e) The chemical species OH formed in our atmosphere is highly reactive.

Share and discuss your ideas with a classmate.


Chemical Thinking U2 How do we determine structure? 119

FACING THE CHALLENGE with oxygen in compounds such as silica (SiO2).


Therefore, although Si atoms have a high bond-
ing capacity, their reactivity with oxygen limits the
Amazing Carbon number of silicon compounds that are stable in
The number of known chemical substances, both contact with our planet’s atmosphere.
natural and synthetic, exceeds 50 million and A third important property of carbon atoms is
continues to grow exponentially. Many of these their ability to covalently bond to each other and
substances are molecular compounds made up of create linear chains or rings of different sizes. This
carbon atoms covalently bonded to other carbon property opens the door for the synthesis of myri-
atoms and to atoms of different nonmetallic ele- ads of different compounds made up of molecules
ments, such as hydrogen, nitrogen, and oxygen. that not only differ in their chemical composition
Among these substances we find the core compo- but in their three dimensional structure. Carbon
nents of living organisms, including atoms’ capacity to form chains partly
proteins and nuclei acids (DNA). depends on its high valence. How-
Why is carbon such a “prolific” ele- ever, atoms such as nitrogen, with
ment? Could it be possible for other a valence equal to three, and oxy-
types of chemical elements to serve gen, with a valence of two, could,
as the basis for life in other planets? in principle, also form chain-like
One of the properties that makes structures. Why does this not hap-
carbon atoms so special is their pen? The reason lies on the relative
bonding capacity. With a valency strength of multiple bonds between
equal to four, carbon atoms have the these different types of atoms.
highest bonding capacity among the Carbon atoms can form single,
atoms of nonmetallic elements. A double, or triple bonds among them-
high valence facilitates the synthesis selves. However, the delocalization
of a larger diversity of compounds in of electrons into single bonds among
which carbon bonds to different par- many C atoms leads to a larger de-
ticles. However, other types of atoms crease in energy than the formation
in the same group as carbon in the of double and triple bonds between
Periodic Table, such as silicon (Si), a few atoms. From this perspective,
have the same valence. Why is it then DNA
the synthesis of chain-like structures
that they do not react to produce as Molecule is energetically favored. On the con-
many different types of compounds trary, a double bond between two
as carbon does? The answer to this question has to oxygen atoms is more energetically favored than
do with the reactivity of carbon and oxygen atoms. the formation of two single bonds with other oxy-
Although carbon atoms react with oxygen at- gen atoms, and a triple bond between two nitrogen
oms to form relatively strong bonds, these bonds atoms leads to a larger energy reduction than the
are similar in strength to the bonds that carbon creation of three single bonds with other N atoms.
atoms form with atoms of other nonmetallic ele- Thus, rather than long chains or rings, oxygen and
ments. In a planet with a high concentration of nitrogen atoms are most stable as diatomic mol-
elemental oxygen in the atmosphere, this prop- ecules, O2 and N2, with double and triple bonds.
erty of the carbon atoms has been critical to the Carbon compounds have other distinctive
development of life. In particular, it has allowed properties that make them unique, particularly in
for the formation of many compounds of carbon the way in which they interact with water. How-
besides CO and CO2. Silicon atoms, on the other ever, to understand these phenomena we first need
hand, form such strong bonds with oxygen atoms to explore the three dimensional geometry of mol-
that most of the silicon in our planet is combined ecules, as discussed in the following module.
120 MODULE 2 Looking for Patterns

Let’s Apply
What is in your Breath?
Breath analysis of mouth air can serve many purposes, from detecting alcohol levels in blood to
monitoring body fat consumption as part of dieting. It is also useful in understanding and treating
mouth diseases, such as halitosis (bad breath). Let’s see what can you infer from experimental data
ASSESS WHAT YOU KNOW

for mouth air from a patient with this disease.

Potential Structures

Breath analysis of mouth air using GC/MS reveals the presence of three ma-
jor compounds assumed to be responsible for halitosis (bad breath). A compari-
son search in a MS database allows to identify the substances as 1) H2S, 2) CH4S, and
3) C2H6S.
1 1

• Propose a molecular structure for the first two com-


pounds. Justify your decisions based on the electron 2 2

configurations of each of the atoms involved.


3

Share and discuss your ideas with a classmate, and clearly 3

justify your reasoning.


Room Air Mouth Air Saliva

The Third Compound

Based on your previous analysis and the additional spectroscopic information shown below:

• Propose a molecular structure for the third compound, C2H6S.

100 1.0

80 0.8
Relative Abundance

Transmittance

60 0.6
C-H C-H
40 0.4 stretch
bend
20 0.2 C-S
stretch
0
10 20 30 40 50 60 70 3000 2000 1000
m/q Wavenumber (cm-1)

Share and discuss your ideas with a classmate, and clearly justify your reasoning.
Chemical Thinking U2 How do we determine structure? 121

Deathly Smells

Chemical compounds responsible for bad breath are the waste products of the anaerobic respi-
ration of tongue bacteria. These organisms not only produce volatile sulfur compounds such as
the three substances analyzed on the previous page, but also chemical compounds responsible
for the bad smell of dead animals. Combustion analysis of one of these substances reveals the
following chemical composition: 54.49% C, 13.72% H, 31.79% N. The MS and IR spectra
of this substance are shown below.

100 1.0

ASSESS WHAT YOU KNOW


80
NH2 C-H
Relative Abundance

0.8

Transmittance
60
bend bend
0.6
C-C
40 stretch
0.4
20 C-H C-N
0.2 stretch stretch
0
0 20 40 60 80 100 3000 2000 1000
m/q Wavenumber (cm-1)

• Determine the empirical and molecular formulas of this chemical compound;


• Assuming that all the atoms in this compound bond to each other according to com-
mon bonding patterns, propose one potential structure for this chemical substance.
Show how your proposed structure could lead to the MS fragmentation pattern and IR
absorption bands in the spectra above.
• Explore whether there are other molecular structures involving the same types and num-
ber of atoms that could generate similar MS and IR spectra.

Share and discuss your ideas with a classmate, and clearly justify your reasoning.

Mouth Wash

Mouth washes used to prevent bad breath often contain antibacterial agents
such as ClO2. This chemical substance is also used for bleaching wood pulp in
the paper industry and for disinfecting water.

• Based on the ground state electron configurations of the Cl and O atoms,


discuss whether a ClO2 molecule can be expected to exhibit common
bonding patterns. If it does, propose a potential molecular structure. If it
does not, explain how such a molecule may be stable.
• Discuss whether you would expect this chemical substance to be highly
reactive with other chemical species. How would low or high chemical
reactivity be useful for a substance used as an antibacterial agent?

Share and discuss your ideas with a classmate, and clearly justify your reasoning.
122 MODULE 2 Looking for Patterns

Let’s Apply
A Different Universe
Imagine that you were able to communicate with aliens from a parallel universe. Among the in-
formation that you manage to exchange and translate into our scientific language, there is a table
and some other data for atomic and molecular properties in their universe. Your task is to use the
available evidence to develop a chemical model of the atom in this parallel universe.
ASSESS WHAT YOU KNOW

Atomic First Ionization Atomic First Ionization


Symbol Z Symbol Z
Radius (pm) Energy (kJ/mol) Radius (pm) Energy (kJ/mol)
A 1 37 1312 W 23 174 509.8
B 2 32 2372.3 X 24 144 553.1
C 3 29 3200 Y 25 136 578.8
D 4 134 520.2 Z 26 127 579.9
E 5 90 700.5 AA 27 125 583.9
F 6 82 800.6 BB 28 124 637.3
G 7 77 1086.5 CC 29 123 665.5
H 8 75 1202.3 DD 30 122 680.4
I 9 73 1413.9 EE 31 121 697.1
J 10 71 1682 FF 32 119 720.2
K 11 69 2080.7 GG 33 118 735.3
L 12 65 2500 HH 34 117 750.2
M 13 154 495.8 II 35 116 759.6
N 14 130 520.7 JJ 36 115 764.3
O 15 118 577.5 KK 37 115 776.4
P 16 111 786.5 LL 38 114 850.2

http://www.chem.arizona.edu/tpp/chemthink/resources/U1_M1/graph.html
Q 17 106 870.8 MM 39 110 929.2
R 18 102 999.6 NN 40 109 1205
S 19 99 1251.2 OO 41 108 1451
T 20 ?? ?? PP 42 107 1502
U 21 95 1750 QQ 43 211 403.2
V 22 196 418.8 RR 44 199 475.8

Your Model

Based on the information provided in the table, build a model of the atom in this parallel uni-
verse that can explain the experimental data. CLICK TO USE

• Would a shell model allow you to explain the data?


How many shells would you propose? How would
electrons be distributed in the different shells?

Share and discuss your ideas with a classmate, and clearly


justify your reasoning.
Chemical Thinking U2 How do we determine structure? 123

Additional Cues

http://www.chem.arizona.edu/tpp/chemthink/resources/U2_M2/pesp.html
Among the data that you receive there are results of PES analysis of some of the chemical ele-
ments in the parallel universe. The information is summarized in the interactive tool associated
with this activity.

• Would you need to introduce the idea of subshells to


better explain this data? Why? How many subshells
would you have to assume in each major shell? How
many electrons would occupy each sub-shell?

ASSESS WHAT YOU KNOW


Share and discuss your ideas with a classmate, and clearly
justify your reasoning.
CLICK TO PLAY

Bonding Patterns

Atoms in the parallel universe form the following stable molecules: AB, JK, HJ, HK2, AK, JB,
HB2. Based on all of the information that you have:

• How many electrons would you suspect are shared during the formation of a single
covalent bond between two atoms in this Universe?
• Which atoms would you expect to have a similar valence? What would the value of the
bonding capacity be for different groups of atoms?
• What would the equivalent to the “octet rule” be in this other universe?

Share and discuss your ideas with a classmate, and clearly justify your reasoning.

Predictions

Chemical models allow us to predict the properties of chemical substances. According to your
atomic model:

• How would you organize the different atoms into a “Periodic Table”?
• What would the electron configuration of atom “T” be based on its location in the Peri-
odic Table? (Create your own notation to represent electron configurations).
• Estimate the atomic radius and the first ionization energy of this type of atom.
• What would you expect the valence of atom “T” to be?
• Would you expect element “T” to exist as single atoms or as diatomic molecules?
• Predict the molecular formulas of the compounds formed when element “T” reacts with
elements Q, R, and S.

Share and discuss your ideas with a classmate, and clearly justify your reasoning.
124

Predicting
Geometry
A central idea in chemistry is that the physical and chemical properties of molecu-
U2: MODULE 3
lar compounds are not only determined by the composition and connectivity be-
tween the atoms that make up their molecules, but also by the way in which these
atoms are distributed in space. Determining or predicting molecular geometry is
thus as important as establishing atomic composition and atom connectivity
in a molecular compound. Fortunately, these three molecular prop-
erties: composition, connectivity, and geometry are not
independent of each other and we can use infor-
mation about the chemical makeup and structure
of molecules to predict their geometry.
As we will discuss in this module, molecular
geometry is determined by the number and dis-
3D-Geometry
tribution of valence electrons in a molecule. Inter- Aspirin
actions between electrons influence how the atoms that Molecule
make up a molecule distribute relative to each other in
space. Therefore, the atomic and molecular models of matter that we have dis-
cussed in previous modules will become essential tools for prediction. Inferences
about molecular geometry are also greatly simplified by the identification of pat-
terns in the types of geometries that emerge from interactions between specific
numbers of valence electrons. The recognition of these patterns is particularly
useful in analyzing the geometry of large molecules with many different atomic
centers.

THE CHALLENGE Molecular Recognition


Many cellular processes in our body depend on the ability of some molecules
to “recognize” the molecular geometry of other molecules.

• How do you think molecular recognition works? How may it be impor-


tant in triggering or hindering important processes within cells?

Share and discuss your ideas with one of your classmates.

This module will help you develop the type of chemical thinking that can help
you explain phenomena similar to that described in the challenge. In particular,
the central goal of Module 3 is to help you understand how to predict molecu-
lar geometry based on the analysis of the number and types of valence electron
pairs surrounding different atomic centers in a molecule.
Chemical Thinking U2 How do we determine structure? 125

Lewis Structures
The task of predicting molecular geometries is greatly simplified by following a
systematic procedure to derive the molecular structure of any given chemical com-
pound. Such a procedure was first introduced in 1916 by Gilbert Lewis and it is
based on the creation of electron dot diagrams (also called Lewis dot structures).
These diagrams are schematic representations of how valence electrons are likely to
distribute among atoms in a molecule. To understand how to build these electron
dot diagrams, let us start by creating the simplest types of symbolic representations Figure 2.34 Typical steps in the
construction of the Lewis dot
corresponding to isolated atoms. The rules are straightforward: diagrams for isolated atoms.

H C F
1. The atomic nucleus and core electrons of an atom are represented by using the
chemical symbol of the atom, such as H for a hydrogen atom, C for a carbon
atom, or F for a fluorine atom (see Figure 2.34).
2. Each valence electron in a given atom is represented using a dot placed around
the chemical symbol. The dots are placed in specific regions chosen to represent
the different valence orbitals. In the case of a hydrogen atom, in which there

H C F
is only one valence orbital, the dot representing the single valence electron
can be drawn anywhere around the symbol. For other atoms of nonmetallic
elements, it is common to identify the regions on top, below, to the right, and
to the left of a chemical symbol as representations of the four valence orbitals
associated with these types of atoms.
3. Given that pairing electrons with different spins in a single orbital requires
energy, it is assumed that valence electrons will singly occupy empty orbitals
when available. Thus, dots representing valence electrons are drawn in differ-
ent regions around the chemical symbol until there is a need to pair them up
H C F
(for atoms with five or more valence electrons). No more than two electrons
should be drawn in any of the regions representing a single orbital.

Electron Dot Diagrams LET’S THINK


• Build the electron dot diagrams for the following atoms: He, O, N, P, S,
and Ne.

Share and discuss your ideas with a classmate.

Electron dot diagrams for atoms (Figure 2.34) explicitly show the number of
FF Lone
Electron
unfilled energy states available for bonding. Thus, these representations help us Pair

F F
predict the bonds that an atom will form with other atoms. For example, we
know that fluorine is a chemical element made up of diatomic molecules, F2. The
formation of this type of molecule results from the delocalization of the unpaired
electron in each participating fluorine atom into a bonding orbital shared by both
atoms. Using electron dot diagrams, the F2 molecule can be represented as shown Bonding
in Figure 2.35. The dot diagram is commonly modified to represent each bonding Electron Pair
electron pair as a solid line between the bonded atoms while other pairs of valence
electrons (lone electron pairs) are depicted as pairs of dots. This type of representa- Figure 2.35 Electron dot
diagram and Lewis structure
tion is known as the Lewis structure of the molecule. of the fluorine molecule, F2.
126 MODULE 3 Predicting Geometry

LET’S THINK Diatomic Molecules

As you know, the chemical elements oxygen and nitrogen also exists as homonuclear (composed
of the same type of atoms) diatomic molecules in nature.

• How would you explain the particular Lewis structure of the O2 molecule


shown to the side?
Build the Lewis structure of the N2 molecule based on the number of O O
unfilled valence energy states in the nitrogen atoms.

Share and discuss your ideas with a classmate, and clearly justify your reasoning.

When atoms of nonmetallic elements combine with each other, their valence
electrons are reorganized. The number of covalent bonds that are formed are de-
termined by the total number of electrons that can be delocalized in the available
unfilled orbitals. Once the molecule is formed, the number of valence electrons
around each atom tends to correspond to the number of electrons in the full
Figure 2.36 Construction valence shell of each atom (two electrons for hydrogen; eight electrons for other
of the Lewis structure of
the water molecule, H2O. atoms of nonmetallic elements). We can use these ideas to formulate a set of basic
steps to facilitate the construction of the Lewis structure of most common mol-

H2O
ecules. Let us illustrate their application in building the Lewis structure of the
water molecule, H2O (see Figure 2.36).

1. As a first step, we need to select a central atom from which the molecule will
be built. In general, the central atom tends to be the one with the highest
O bonding capacity (highest valence). If the atoms present in the system have the
same valence, the largest of these atoms will be central; this is the atom most
Central
Atom likely to form additional bonds by delocalizing electrons in higher energy or-
bitals. Small atoms with a valence equal to one, such as H and F, never play
the role of central atoms.
Total # of
valence e-
=2x1+6=8 2. Count the total number of valence electrons in the molecule. This number is
calculated by adding the valence electrons of each atom present in the system.
3. Use as many pairs of electrons as needed to form single bonds between the
H O H central atom and the other atoms in the molecule. Use a solid line to represent
each bonding electron pair.
4. Use the remaining lone electron pairs to fill the valence shell of each atom as
H O H needed. Start with the terminal or outside atoms; place any leftover valence
electrons on the central atom.

LET’S THINK Lewis Structures

• Build the Lewis structure of the following molecules: CH4, H2S, NH3, CCl4, HF.

Share and discuss your ideas with a classmate, and clearly justify your reasoning.
Chemical Thinking U2 How do we determine structure? 127

The outlined steps can be followed to build the Lewis structures of molecules
in which atoms are connected to each other by single bonds. However, in systems
where some atoms are bonded via double or triple bonds, and additional step
should be considered. Let us analyze the case of the molecule of carbon dioxide,
CO2
CO2, as an example:

1. Which is the central atom? Carbon, the atom with the highest valence. C Central Atom
2. How many valence electrons are in the molecule? We have four valence
electrons from carbon and six valence electrons from each oxygen, for a total Total # of
valence e-
= 4 +2 x 6 =16
of 16 valence electrons (or 8 electron pairs).
3. How many initial bonding electron pairs are required? Two pairs of elec-
trons are needed to connect the carbon atom to the two oxygen atoms.
O C O
4. How do we distribute the lone electron pairs left? There are six pairs of elec-
trons left, three of them can be distributed around each oxygen atom.
If we were to stop the construction of the Lewis structure here, the valence shell of
the carbon atom would not be full; there are only four valence electrons surround-
O C O
ing this atom. A more stable structure can be formed by assuming that one of the
lone electron pairs placed on each oxygen atom will be delocalicazed as additional
bonding pairs. Therefore, we need to add the following step to the construction of
the Lewis structure of molecular compounds:

5. If the valence shell of the central atom is not full, delocalize lone electron pairs
from the external atoms into the bonding region to form double or triple
O C O
bonds as needed.

The formation of double bonds between the carbon and the oxygen atoms leads to
maximum electron delocalization in the available valence orbitals. In general, the O C O
most stable structures are those in which each atom forms as many bonds as unfilled
electron states are available in their valence shells (e.g, 2 bonds for O, 4 bonds for C).

Multiple Bonds LET’S THINK


As discussed in the previous unit, many toxic substances contribute to
indoor air pollution. Among them we find, formaldehyde (CH2O), carbon
monoxide (CO), carbon disulfide (CS2), and hydrogen cyanide (HCN).

• Build the Lewis structure of the molecules of each of these compounds.

Share and discuss your ideas with a classmate.

All the molecules discussed so far contain only one central atom. What do we
do in those systems in which we have more than one atomic center? In these cases
we can apply the set of steps just described to build the structure of the molecule
but center by center. However, the task will require additional information about
the connectivity between different atoms in the system. Results from IR absorp-
tion spectroscopy, for example, are very useful in these situations.
128 MODULE 3 Predicting Geometry

For molecules composed of C, H, N, and O atoms, the task of build-


ing Lewis structures is simplified by recognizing common valence electron
H distributions around bonded atoms (see Figure 2.37). We know, for ex-
ample, that carbon atoms tend to form four bonds with atoms of the same
or different kind. This occurs in four main forms: a) four
C C C C single bonds, b) two single bonds and one double bond,
c) one single bond and one triple bond, and d) two double bonds.
Oxygen atoms are likely to have two lone electron pairs in their
N N N valence shell and to form either two single bonds or one double
bond with different types of atoms. Keeping these types of patterns
in mind is useful in building the molecular structures of complex
Figure 2.37 Common molecules, predicting the value of angles between different bonds
O O
distribution of elec-
tron pairs around H, C, in a molecule, and recognizing potential mistakes in the symbolic
N, and O atoms. representations of chemical substances.

LET’S THINK Larger Molecules

To simplify the identification and representation of more complex molecules, chemical scientists
often use semi-structural formulas that convey partial information about the distribution and
connectivity of atoms in molecules. Consider the following semi-structural formulas for ethanol
and other molecules produced during the metabolism of this substance in our body:

Ethanol - CH3CH2OH Acetaldehyde- CH3CHO Acetic Acid- CH3COOH

• Use these semi-structural formulas, together with the common distribution of valence elec-
trons around the involved atoms, to build the Lewis structures of these three molecules.

Share and discuss your ideas with a classmate, and clearly justify your reasoning.

Resonance
For some substances, the derivation of the Lewis structure may be not so straight-

O3
forward due to the existence of different ways of arranging valence electrons among
atoms in a molecule. To illustrate this phenomenon, let us consider the case of the
ozone molecule, O3.

1. Which is the central atom? Oxygen, the only option.


Total # of
valence e-
= 3 x 6 =18 2. How many valence electrons are in the molecule? 18 electrons (9 pairs).
3. How many initial bonding electron pairs are required? We need two pairs
of valence electrons to connect the atoms.

? 4. How do we distribute the lone electron pairs left? There are seven pairs of
electrons left. Three of them can be distributed around each of the external
oxygen atoms, while the last pair can be placed on the central atom.
O O O 5. Can multiple bonds be expected among atoms? If the valence shell of each
of the atoms is to be full, a double bond can be expected. But, between which
pair of atoms?
Chemical Thinking U2 How do we determine structure? 129

Given the symmetry of the molecule, we may think that it does not matter
which of the two double bonds actually forms. The outcome is the same in both
cases. However, the experimental analysis of the bond length in the O3 molecule
reveals that predictions based on the proposed Lewis structure (Figure 2.38) do
not match the data. In particular, the model predicts the existence of two types of
bonds, one single and one double, with different expected lengths (double bonds
tend to be shorter than single bonds between the same atoms because of a stron-
ger net attraction between bonding electrons and their atomic nuclei). The actual
O O O
experimental results indicate the presence of two identical bonds with a length in-
termediate between that of a single and a double bond between two oxygen atoms:

Bond Type
O-O
Bond Length (pm)
148
O O O
O3 128
Figure 2.38 Resonance
structures of the ozone
O=O 121 molecule.

These experimental data suggest that covalent bonds in the O3 molecule are
intermediate in length between single and double bonds. We may thus think that
rather than forming a double bond between one of the pairs of oxygen atoms, we
should delocalize one single electron in each of the two bonding regions. However,
theoretical calculations suggest that the electron configuration of this molecule is
actually more complex. The two electrons seem to be delocalized across the entire
molecule and cannot be assigned to any of the two bonding regions.
Molecules such as O3, in which some valence electrons are delocalized across
more than one covalent bond are said to exhibit resonance. When electrons get
delocalized their kinetic energy decreases as well as the potential energy of the re-
maining electrons in each atom that can get closer to their atomic nuclei. The net
decrease in total energy stabilizes the molecule. The larger the volume (or number
of bonds) in which electrons can be delocalized, the greater the stabilization.
Given the difficulties representing the actual structure of molecules that exhib- O O O
it resonance, it is common to build each of the Lewis structures that can be drawn
Figure 2.39 Alternate
for the molecule (see Figure 2.38), labeling each of them as a different “resonance representation of an
structure.” However, it should be made clear that none of these representations ozone molecule.

matches the actual molecular structure. Another common approach is to build the
backbone of the molecule and use dashed lines to show the presence of delocalized
electrons across multiple bonds (Figure 2.39).

Resonance Structures LET’S THINK


The combustion of sulfur and sulfur-containing compounds produces two major pollutants:
SO2(g) and SO3(g). Molecules of these compounds exhibit resonance.

• Draw all of the possible resonance structures for each of these molecules.
• Which of these molecules is likely to exhibit more resonance stabilization? Justify your rea-
soning.

NOTE: Sulfur atoms in these molecules exhibit a valence that deviates from common patterns.
130 MODULE 3 Predicting Geometry

Molecular Ions and Radicals


Many important molecular species in our surroundings and inside our own body
are either charged particles (ions) or have unpaired valence electrons (radicals).
In general, their Lewis structures can be built by following the same set of steps
described in the previous sections. We just need to properly count and distribute
the total number of valence electrons present in each system.
In the case of molecular ions, attention should be paid to the total number of
valence electrons when building their Lewis structure. If the species is positively
charged (cation), the total number of valence electrons will be smaller as a result
of the loss of electrons; if the species’ electrical charge is negative (anion), the pres-
ence of additional valence electrons should be taken into account. Consider, for
example, the cases of the H3O+ (hydronium) and the CO32- (carbonate) ions, two
species that play a central role in determining the acidity of aqueous solutions in
both living organisms and the environment. The total number of valence elec-
trons in each of these species can be calculated in the following way:

# valence e- (H3O+) = 3 x 1 + 6 - 1 = 8

# valence e- (CO32-) = 4 + 3 x 6 + 2 = 24

where one valence electron has been subtracted from the normal count in the case
of the H3O+ ion to account for its 1+ charge, while two electrons have been added
to the count for the CO32- ion to reflect the presence of a 2- charge. Using the
above numbers, the corresponding Lewis structures can be built using standard
procedures:

H
H O H
2 2 2
O O O
O C O O C O O C O
Notice the use of brackets to indicate the charge of the ions. As you can see, some
ions can also exhibit resonance structures and, thus, resonance stabilization.

LET’S THINK Other Ions

The following molecular ions, NO2- (nitrite ion) and NO3- (nitrate ion), also play a central role in
many environmental processes, from cloud formation to the destruction of the ozone layer.

• Build the Lewis structures of these ions and analyze whether they can exhibit resonance.

Share and discuss your ideas with a classmate, and clearly justify your reasoning.
Chemical Thinking U2 How do we determine structure? 131

Radical species, also called free radicals, have unpaired valence electrons and
can be neutral or charged particles. In general, they are easily recognizable because O H or OH
they have an odd, rather than an even, number of valence electrons. These chemi-
cal substances are highly reactive due to the presence of unfilled valence orbit-
als in their atoms or molecules. Radicals play an important role in combustion
processes, atmospheric chemistry, and biological processes such as cell signaling
N O
and immune defense. They are also believed to be involved in the development
or NO
of degenerative diseases, such as Parkinson’s and Alzheimer’s, as well as in cancer N O
development and progression.
The Lewis structure of some radicals is pretty simple, such as that of the hy-
droxyl radical OH (see top of Figure 2.40). This species has seven valence electrons O N O
and thus one of the valence orbitals associated with the oxygen atom is unfilled.
The OH radical is produced in the atmosphere through reactions involving water
and oxygen. It is a highly reactive chemical species that reacts with many pollut-
ants in the atmosphere. Inside our body, the hydroxyl radical can cause serious O N O
damage by reacting with nucleic acids and thus inducing mutations.
Another important radical species is nitrogen monoxide, NO, a particle with
11 valence electrons. In this case, the unpaired electron is delocalized in the bond- O N O
ing region between the two atoms (Figure 2.40). This radical is an important
molecule in our body, helping protect organs from damage and controlling vaso-
dilation. However, it is also associated with pathological processes such as multiple
sclerosis and arthritis. O N O
Radical species can also exhibit resonance stabilization. Such is the case of
nitrogen dioxide, NO2, a chemical species with 17 valence electrons which plays or NO2
a major role in urban pollution. This chemical compound is produced during the
combustion of fossil fuels in our cars and is responsible for the reddish-brown haze Figure 2.40 Lewis structures
characteristic of polluted cities. As shown in Figure 2.40, the NO2 molecule has and other common symbolic
representations of various
several resonance structures that represent the delocalization of multiple electrons radical species.
across the entire particle.

Radical Action LET’S THINK


Many free radicals in the atmosphere are produced through the interaction of gaseous
substances with solar UV radiation. UV photons have enough energy to break chemi-
cal bonds and generate radical species. Take, for example, the case of chlorofluoro-
carbon (CFC) molecules such as CCl2F2 which generate the radicals •CClF2 and •Cl
when reaching the stratosphere.

• Build the Lewis structures of the •CClF2 and •Cl radicals.

The •Cl radical in turns reacts with O3 molecules to generate O2 and •ClO particles.
This process is one of the major causes of ozone depletion on our planet.

• Build as many Lewis structures as you can of the •ClO radical in which at least
one of the atoms has a full valence shell. What does the existence of several poten-
tial structures tell you about the stability of this radical?

Share and discuss your results and ideas with a classmate.


132 MODULE 3 Predicting Geometry

Molecular Geometry
The Lewis structure of a molecule can be used to infer its three dimensional ge-
ometry by paying attention to the interactions between valence electrons in the
system. Electrons are charged particles that repel each other and repulsive forces
between them will keep them separated as far as possible. On the other hand,
attractive forces between electrons and protons will pull electrons towards the dif-
ferent atomic nuclei in the molecule. In general, we can expect valence electrons
to adopt spatial configurations in which electron-electron repulsions are minimal
and both electron-proton attractions and electron delocalization into bonding re-
gions are maximal. Given that covalent bonding involves the delocalization of one
or more pairs of valence electrons in the space between two atoms, the distribu-
tion of atoms around any atomic center in a molecule will be determined by the
repulsion between all the valence electrons associated with the central atom. The
previous ideas suggest that molecular geometry can be inferred from the Lewis
structure of a molecule by identifying two main things:
O
1. The number of regions, or domains, of high electron density around each
H C O H atomic center in a molecule (see Figure 2.41);
2. The geometrical arrangement in the three dimensional space that will keep
these “electron domains” as far apart as possible.
Figure 2.41 Each of the
encircled areas represents
a different electron do-
main in this Lewis struc- This suggestion is at the core of the so-called Valence Shell Electron Pair Repul-
ture of formic acid (CH2O2). sion (VSEPR) Theory of molecular shape. A central assumption in this theory is
that the most stable spatial distribution of electron domains in a molecule (electron
domain geometry) will determine how its several atomic nuclei arrange in space
(molecular geometry).

LET’S THINK From Structure to Geometry

Consider the following Lewis structures for a set of important molecules in Earth’s atmosphere:

F H
O C O Cl C Cl H C O
F
H
O S O H O H H N H

• How many regions of high electron density (electron domains) do you identify around each
central atom?
• How would you arrange the electron domains around each central atom to minimize re-
pulsions between electrons in different domains? Hint: It may help to think of the electron
domains as inflated balloons with their ends attached to the same point (central atom).

Share and discuss your ideas with a classmate, and clearly justify your reasoning.
Chemical Thinking U2 How do we determine structure? 133

It is important to point out that in the VSEPR theory, an electron domain

http://www.chem.arizona.edu/tpp/chemthink/resources/U2_M3/co2.html
represents a region in the space around each atom in a molecule where valence
electrons are likely to be found. This region may not need to correspond to an
orbital and may contain more than two electrons. For example, all the electron
pairs in the bonding region between two atoms, no matter whether they are part
of a single, a double or a triple bond, are thought to belong to the same electron O C O
domain. Although bonding electron pairs also repel each other, electron-proton
interactions will confine them in the region between the two atoms. Thus, they
will be associated with the same electron domain.
As you may have inferred in the previous activity, when an atomic center is
surrounded by two electron domains, such as in the molecule of CO2, the most CLICK TO PLAY
stable configuration is that in which each electron domain forms an angle of 180o
degrees with the other. The electron domain geometry is then said to be “linear.” As Figure 2.42 The mo-
lecular geometry of the
a result of this electron distribution, the nuclei of the three atoms in the CO2 mol- CO2 molecule is linear.
ecule are expected to be on a same line and the molecular geometry (the distribution
of atomic nuclei in space) will be linear as well (see Figure 2.42).
In the case of the molecule of formaldehyde (CH2O, Figure 2.43), the central
atom is surrounded by three electron domains. Electron repulsions are minimized
when the electron domains are in the same plane, close to 120o degrees from each
other. For these molecule we can expect the three angles not to be identical be-
O
cause the electron domain corresponding to the double bond has a higher electron
C
density than the others. Repulsions between electrons in the double bond region
and those in the single bonds are stronger than those between the single bonds
H H
themselves; as a result the angle between the single bonds is smaller. The geometry
of both of the electron domains and the actual molecule is “trigonal planar.”
A molecule such as ozone, O3, is also characterized by the presence of three 121o
electron domains around the central atom. We can thus infer that the electron
domain geometry around this atomic center will be trigonal planar too. However,
one of the electron domains in this case corresponds to a lone electron pair rather
than to a bonding region. Given that there is not an atom in the direction of this 118o
electron domain, the actual geometry of the molecule is different from the electron
Figure 2.43 The mo-
domain geometry. The three atomic nuclei in this system form what is called a

http://www.chem.arizona.edu/tpp/chemthink/resources/U2_M3/o3.html
lecular geometry of the
“bent” or “angular” structure. In general, lone electron pairs are less confined than CH2O molecule is trigo-
nal planar.
bonding electron pairs and tend to occupy a larger space. Therefore, the net repul-
sion force that they exert on other electron domains is larger. This effect, together
with the delocalization of additional electrons across the bonding regions in the
ozone molecules, explains the smaller angle (< 120o) in the ozone molecule (see
Figure 2.44).
Electron Domain Molecular
Geometry Geometry
CLICK TO PLAY

Figure 2.44 Electron

O
domain and molecu-
lar geometries of the

O O ozone, O3, molecule.

116.8o

Trigonal Planar Bent or Angular


134 MODULE 3 Predicting Geometry

LET’S THINK From Structure to Geometry

Based on the Lewis structure for the following molecules, ions, and radicals of importance in our
atmosphere: CS2, SO2, SO3 HCN, •NO2, N2O, NO2-, NO3-:

• Infer the electron domain geometry and the molecular geometry of each species;
• Discuss whether the different bond angles in these chemical species would be equal to,
smaller or larger than the bond angles expected for symmetrical molecules with a similar
electron domain geometry.
http://www.chem.arizona.edu/tpp/chemthink/resources/U1_M2/ch4.html

Share and discuss your ideas with a classmate. Clearly justify your reasoning.

For molecules with four equivalent electron domains around an atomic center,
CLICK TO PLAY such as the CH4 (methane) molecule, the most stable configurations corresponds
to a tetrahedral geometry in which electrons domains are 109.5o degrees apart
from each other (see Figure 2.45). As it is the case for all systems in which all of
the electron domains around the atomic center of interest correspond to bonding
electron pairs, the molecular geometry is the same as the electron pair geometry.
However, for chemical species in which one or two of the four electron domains
correspond to lone electron pairs, molecular geometry needs to be inferred from
the actual location of the atomic nuclei.
Figure 2.45 Molecular The ammonia molecule, NH3, is a typical example of a molecule with one
geometry of the meth-
ane, CH4, molecule. atomic center surrounded by four electrons domains, one of which corresponds
to a lone electron pair. As shown in Figure 2.46a, the electron pair geometry is
tetrahedral, but the geometrical shape defined by the atomic nuclei is called “tri-
gonal pyramidal.” The stronger repulsive force between lone and bonding electron
pairs leads to an effective bond angle of 107.8o versus 109.5o in the case of CH4.

http://www.chem.arizona.edu/tpp/chemthink/resources/U2_M3/nh3.html
http://www.chem.arizona.edu/tpp/chemthink/resources/U2_M3/h2o.html
For the water molecule, H2O, where two of the four electron domains around the
oxygen atom are associated with lone electron pairs (Figure 2.46b), the molecular
geometry is “bent” or “angular” with an even smaller bond angle (104.5o) due to
the larger net repulsive forces exerted by the two lone electron pairs.

a) b)
CLICK TO PLAY

Figure 2.46 Electron do-


main and molecular geom-
etries of the molecules of a)
ammonia, NH3; b) water, H2O.

There are molecules, ions, and radicals with more than four electron domains
around a central atom. In these cases, the most stable electron domain geometries
also correspond to those configurations in which repulsion forces are minimized
while bonding interactions are maximized. For example, for five electron domains
the geometry is “triangular bipyramidal” while for six electron domains the geom-
etry is “octahedral.” Differences between electron domain and molecular geom-
etries will also arise whenever one or more of the electron domains is associated
with lone electron pairs.
Chemical Thinking U2 How do we determine structure? 135

From Structure to Geometry LET’S THINK


Based on the Lewis structure for the following molecules, ions, and radicals of importance in our
planet: H2S, •CClF2, CCl3F, PO43-, H3O+, NH4+, SO42-.

• Infer the electron domain geometry and the molecular geometry of each species. Predict
expected deviations in the value of different bond angles.

Share and discuss your ideas with a classmate. Clearly justify your reasoning.

Figure 2.47 summarizes basic information about electron domain and mo-
lecular geometries for different types of chemical species:

# of Electron Lewis Structure Electron Domain Molecular


Domains (Example) Geometry Geometry

2 O C O
Linear Linear

O
H C H
Trigonal Planar Trigonal Planar
3

O O O Figure 2.47 Electron do-


main and molecular geom-
etries for chemical species
with different numbers of
Trigonal Planar Bent or Angular electron domains around a
central atom. Balloons are

H used to represent the vol-


ume where electrons are
more likely to be found in

H C H
the different domains.

H Tetrahedral Tetrahedral

H N H
4
H
Tetrahedral Trigonal Pyramidal

H O H
Tetrahedral Bent or Angular
136 MODULE 3 Predicting Geometry

The different molecules that we have used to illustrate how to infer electron
domain and molecular geometries from Lewis structures have a single central
atom. However, most molecules of interest have two or more atomic centers. In
these cases, identifying a particular geometrical shape to represent the entire mol-
ecule may not be easy. Moreover, molecules are dynamic systems in which the rela-
tive orientation of one atomic center with respect to another may change pretty
quickly. Therefore, for larger molecules it is common to build and describe their
molecular shape working on one atomic center at a time. This task is greatly sim-
plified by following a systematic procedure to identify molecular geometry and
Figure 2.48 Systematic
(Figure 2.48) and by recognizing the typical geometrical shapes associated with
procedure to infer the mo- common central atoms (e.g., C, O, and N; Figure 2.49).
lecular geometry around
any given atomic center. The following image illustrates a sequence of steps that facilitate the derivation
of the molecular geometry around any given atomic center “A”:
STEP 1 STEP 2 STEP 3 STEP 4

A A A A
Build Lewis structure and Count # Infer Electron Identify Molecular
identify central atom Electron Domains Domain Geometry Geometry

In this particular example, the molecular geometry around the atomic center “A”
is triangular pyramid with an expected bond angle slightly smaller than 109.5o
due to the presence of a lone electron pair. Notice that in this figure we have intro-
duced a new set of symbols to represent a three-dimensional structure in a plane,
the so called “wedge and dash projection.” This type of representation is based on
the use of three types of lines to convey perspective: a) solid lines represent bonds
which are in the plane of the paper, b) dashed wedges symbolize bonds that extend
away from the viewer, and c) bold wedges represent bonds that extend towards the
viewer. While Lewis structures (step 1 in Figure 2.48) explicitly convey informa-
tion about connectivity and number of electron domains, but not molecular ge-
ometry, wedge and dash projections are designed to more clearly represent three-
Figure 2.49 Common ge- dimensional shape (step 4 in Figure 2.48).
ometries around C, N, and Inferences about molecular geometry are also facilitated by recognizing the
O atoms in molecules of
organic compounds. following geometrical patterns in the bonding of C, N, and O atoms:

Carbon (C) Nitrogen (N) Oxygen (O)


~109o
C Tetrahedral N
~108 o
Trigonal Pyramidal
O
~120o
C Trigonal Planar ~105o

N Bent or Angular
C ~180o
C Linear
~118o
Bent or Angular
Chemical Thinking U2 How do we determine structure? 137

To illustrate the application of these ideas in the derivation of the molecular


geometry around various atomic centers, let us analyze the molecular geometry of
the simplest amino acid produced by our body, glycine (C2H5NO2 or NH2CH-
2
COOH). Based on its Lewis structure (see Figure 2.50), and applying the basic
ideas discussed on the previous page, we can see that this molecule has four atomic
centers with the following molecular geometries: 1) triangular pyramid; 2) tetra-
hedral, 3) trigonal planar, and 4) bent or angular. The identification of these basic
shapes helps us predict the angles between different bonds across the molecule.

H O ~122 o

Figure 2.50 Analysis of the


molecular geometry around
1 2 3 4
H N C C O H
different atomic centers in the
molecule of glycine. Compare
the Lewis structure with dy-
namic ball-stick representation
~105 o
of the molecule.
~108 H H
o
~109 o

Analyzing Geometries LET’S THINK


Psychoactive drugs are chemical substances that act primarily on our central nervous system,
affecting brain function. Analyze the molecular geometry of the psychoactive drugs most con-
sumed by humans:

• Identify the molecular geometry around each atomic center H H 1


4
in the molecule of ethanol. Predict the expected value of the
H C C O H
http://www.chem.arizona.edu/tpp/chemthink/resources/U2_M3/caffeine.html

bond angles marked on its Lewis structure. Make a sketch


of the three-dimensional structure of this molecule.
3 H H 2

CLICK TO PLAY
• Three-dimensional visualizations of molecules using ball-and-
stick or space-filling representations often do not show double
and triple bonds. Their presence has to be inferred from the typi-
cal valence and molecular geometry around each central atom.
Analyze the interactive representation of the molecule of caffeine
shown to the left. Identify the location of the missing double or
triple bonds. Build the Lewis structure of this molecule.

• The image to the right shows a representation of the molecule of


nicotine. In this case, carbon and hydrogen atoms are not explic-
4 1
itly represented. Carbon atoms are assumed to be located at the
junction between two lines or at the end of single lines. The pres-
2
ence of hydrogen atoms can be inferred from the typical valence of 3
each central atom. Identify the location of the missing hydrogens
and predict the value of the selected bond angles.

Share and discuss your ideas with a classmate.


138 MODULE 3 Predicting Geometry

Chemical scientists have devised multiple types of molecular representations


that help visualize different aspects of a molecule’s shape, composition, and con-
nectivity. Some of these representations have been designed to simplify the writing
or displaying of complex molecular structures. Such is the case of the so-called
“skeletal” or “bond-line” structures in which most or all the carbon and hydrogen
atoms in a molecule are not shown explicitly. This type of short-hand notation
is widely used to represent organic molecules. The basic idea is to use solid lines
to represent the “carbon skeleton” of a molecule, assuming that a carbon atom is
implicitly located at the junction of two lines or at the end of any line, unless a
different type of atom is explicitly represented in the structure. The number of
hydrogens bonded to each carbon atom may be inferred from its typical valence
Figure 2.51 Skeletal struc- (i.e., four bonds). Lines representing bonds are drawn at angles that try to capture
tures of different molecules. the basic geometry around different atomic centers in the molecule. To illustrate
Ball-and-stick representations
shown for comparison. these ideas, consider the skeletal structures of the following common molecules:

O
NH2
OH
H

Butane Butene Ethanol Acetaldehyde Aniline


Notice how hydrogens bonded to atoms different from carbon are explicitly
shown. In some other cases, such as for the molecule of acetaldehyde, one may
choose to highlight the presence of some hydrogens in certain parts of a molecule.

LET’S THINK Skeletal Drawings

• Draw the skeletal structures of the following molecules of importance in our body:

Lactic Acid Methionine Adenine Glucose

• Derive the Lewis structure of these other physiologically important molecules:

Glutamic Acid Arachidonic Acid Adrenaline


Share and discuss your ideas with a classmate.
Chemical Thinking U2 How do we determine structure? 139

FACING THE CHALLENGE mimic those of biological molecules and thus can
trigger or hinder specific cellular processes.
Many biological processes that depend on
Molecular Recognition molecular recognition are commonly described
The existence of any living organism relies on the and explained by using some sort of “lock-and-
coordination of multiple physical and chemical key” model. The basic idea behind this model is
processes. This coordination is achieved at the that molecules that “recognize” each other possess
submicroscopic level, through the interactions of specific complementary geometric shapes that fit
molecules, ions, and free radicals inside, outside, exactly into one another, like a key into a lock.
and within the membranes of living cells. For ex- Although very useful in a first approximation, the
ample, the presence of molecules of one particular lock-and-key model fails to recognize the dynamic
compound, such as adrenaline, near a cell may af- nature of molecules. In particular, it can be ex-
fect the structure of some proteins embedded in its pected that interactions between molecules may
membrane. In turn, structural changes in the com- induce slight changes in their shapes. Therefore,
ponents of the cell membrane may trigger other more than acting as a rigid key in a hard lock, a
molecular processes inside the cell. For a mecha- better analogy would be to think of them as a hand
nism like this to work, it is fitting into an elastic glove.
crucial that the affected pro- Processes based on mo-
teins do not respond in the lecular recognition may
same way to the presence of involve more than two spe-
every molecule in their sur- cific types of molecules with
roundings. Somehow, the complementary shapes. For
interactions between adrena- example, current models
line and the target proteins developed to explain how
should be specific to this set different odors are detected
of substances. by humans propose that
The results of multiple molecules of a single smelly
experiments suggest that By Sarah Harris (Own work) [Generic 3.0] via Openstax substance may activate vari-
the specificity in the interactions between differ- ous types of protein receptors in our nose. Simi-
ent chemical species in biological systems is highly larly, these protein receptors may respond to the
dependant on molecular geometry and composi- presence of more than one type of odor molecule.
tion. This implies that a molecule such as adrena- How is then that “recognition” occurs? In these
line triggers structural changes in specific proteins types of systems, it is believed that every specific
because of its particular shape and composition; molecule will induce different degrees of changes
some characteristic features in its structure lead in a group of protein receptors. It is the specific
to distinctive interactions with the target protein pattern of change generated by a certain type of
molecules. This selective process of interaction be- molecule that results in an specific odor percep-
tween molecular species is often called “molecular tion.
recognition” and plays a central role in the biology Molecular recognition clearly depends on the
of living organisms, from controlling the speed of nature of the interactions between different mol-
chemical reactions within cells, to transferring ner- ecules. These interactions are in turn determined
vous stimuli, to detecting odors in the surround- by the atomic composition, connectivity, and ge-
ings. Understanding these types of processes has ometry of the molecules. As we will discuss it in
been critical in the development of pharmaceuti- the next module, these three factors influence how
cal drugs that mimic the properties and behavior electrons are distributed across a molecule, many
of biological molecules. The idea has been to syn- times creating uneven distributions of charge that
thesize molecules with structures that somehow affect how molecules interact with each other.
140 MODULE 3 Predicting Geometry

Let’s Apply
Functionality
A central idea in chemistry is that the chemical properties of
many molecules are determined by the presence of distinctive H H
arrangements of atoms that tend to behave as a single chemi-
H C C O H
ASSESS WHAT YOU KNOW

cal entity during a reaction. These distinctive groups of atoms


are called “functional groups” and their properties depend on
their atomic composition, connectivity and geometry. For ex-
ample, the molecules of all alcohols, such as ethanol, include H H Hydroxyl
the so-called “hydroxyl” functional group (-OH): Group

Main Functional Groups

The presence of a given functional group in the molecules that make up a substance is used to
classify it in particular groups. For example, all substances made up of molecules that include
the hydroxyl functional group are classified as “alcohols.” The following table lists other com-
mon functional groups together with the chemical classes of substances that they define. The
table includes the Lewis structure of the functional group, using the symbols “R, R1, R2,...” to
represent other parts of the molecule.

Chemical Functional Lewis Chemical Functional Lewis


Class Group Structure Class Group Structure

O
Ketone Ketone
R1 C R2
Ether Alkoxy R1 O R2

O Amine R1
Aldehyde Aldehyde Amine (R1 and R2 can
R1 C H be H atoms) R N R2
H H
Carboxylic O C C
Carboxyl Aromatic Phenyl R C C H
Acid R1 C O H C C
H H

• Determine the molecular geometry around the atomic centers in each functional group.
Estimate the values of the angles between different bonds in each functional group.

Share and discuss your ideas with a classmate, and clearly justify your reasoning.
Chemical Thinking U2 How do we determine structure? 141

Biological Molecules

Most biologically active molecules include different functional groups in their structure. This
feature enriches their physical and chemical properties.

• For example, this is the Lewis structure


of phenylalanine, an essential amino H 1 H
acid needed by our body to biochemi-
cally synthesize a wide variety of pro-
C C 2 H H O 3
teins. a) Identify the different functional H C C C C C O H
groups present in this molecule; b)

ASSESS WHAT YOU KNOW


Determine the chemical classes to which C C H N H 4
phenylalanine belongs; c) Estimate the H H H 5
values of the selected bond angles.

• Norepinephrine plays the role of hormone and neurotrans-


mitter in our body. The ball-and-stick representation of
a molecule of this substance is shown to the left. a) Iden-
tify the location of missing double or triple bonds in this
representation; b) Identify the different functional groups
present in this molecule; c) Write the Lewis structure of
this molecule; e) Describe the different molecular geom-
etries of the various atomic centers in this molecule.

• The Lewis structure of the oxaloacetate ion is


shown to the right. Oxaloacetate is produced 2-
during the combustion of glucose (cell respira- 1 O 2 H O
tion) in our body. a) Determine the molecular
geometry around each atomic center in this O C C C C O
molecular ion; b) Draw all possible resonance
forms of this ion; c) Estimate the values of the
4 O H 3
selected bond angles.

• Guaifenesin is a component of common


over-the-counter drugs used as expectorants.
1 A skeletal representation of a guaifenesin
2
molecule is shown to the left. a) Identify the
different functional groups in this molecule;
3 4 b) Describe the different molecular geometries
around central atoms in this molecule; c) Esti-
mate the value of the selected bond angles.

Share and discuss your ideas with a classmate, and clearly justify your reasoning.
142 MODULE 3 Predicting Geometry

Let’s Apply
Molecular Mimicking
The development of many pharmaceutical drugs focuses on the design of chemical substances that
somewhat resemble or mimic the size, shape, and atomic composition of natural substances used
by our body or by pathogen organisms that we want to eliminate from our system. The molecules
of these drugs can then effectively interact with protein receptors in the living organisms triggering
ASSESS WHAT YOU KNOW

or inhibiting their function.

Antibacterial Drugs

Sulfanilamide was one of the first commercially available synthetic antibacterial agents. This
chemical substance interferes with the production of folic acid in bacteria, a vital nutrient re-
quired by these organisms to grow. Bacteria produce folic acid using para-amino benzoic acid
(PABA) as the natural substrate. The skeletal structures of sulfanilamide and PABA are below:

• Identify common functional groups between PABA


the PABA and sulfanilamide molecules; Sulfanilamide

• Determine the basic molecular geometry of


these functional groups;
• Explain how you think sulfanilamide may
inhibit the synthesis of folic acid;
• Predict whether the third molecule shown in
the image could also work as an antibacterial

http://www.chem.arizona.edu/tpp/chemthink/resources/U2_M3/builder.html
agent. Justify your ideas based on structural
arguments.

Some antibacterials interact with proteins that speed up important chemical reactions in bac-
teria, like the synthesis of cell walls. Proteins are large molecules made by the chemical com-
bination of amino acids such a alanine, a molecular compound with the structural formula
CH3CH(NH2)COOH.

• Write the Lewis structure of alanine and identify its


major functional groups;
• Describe the molecular geometry around each of the
atomic centers in this molecule. Build a sketch of the
three-dimensional shape of this molecule. Use the
interactive tool associated with this activity to verify
your predictions.
CLICK TO PLAY
Share and discuss your ideas with a classmate, and clearly justify your reasoning.
Chemical Thinking U2 How do we determine structure? 143

During the synthesis of the cell walls in bacteria, the proteins that facilitate wall construction
bind to portions of the growing cell membrane made by a couple of bonded alanine mol-
ecules. The Lewis structure of the binding region is shown below, together with a representa-
tion of its molecular geometry using dashes and wedges to show perspective (the symbol R
represents the rest of the molecule):

O
R C
H
O H H O H H O N
C CH3 H

ASSESS WHAT YOU KNOW


R C N C C N C C O H H
C N C CH3
CH3 CH3 O
H C O
O H

• Analyze the molecular geometry around each atomic center in this binding region of the
bacterial cell membrane and verify that the dash and wedge projection is correct for each
center. If you find representational mistakes, indicate how they need to be corrected.

Two very important groups of antibacterial agents, penicillins and cephalosporins, inhibit the
action of the protein that speeds up the synthesis of the bacterial cell wall. The molecules of
these pharmaceutical drugs bind to the proteins and block their action. Consider the following
skeletal representations of two widely used types of penicillin and cephalosporin:

Penicillin G Cephalexin

• Compare the molecular structure and atomic composition of these two antibacterial
agents to that of the cell binding site (first image on this page) to which cell wall-synthe-
sizing proteins attach. Identify the structural features in these pharmaceutical drugs that
are similar to the binding site (this part of the drug its called the “pharmacophore”).
• Search for the chemical structures of other types of penicillins and cephalosporins
and verify that they have the same pharmacophore that you identified. If they do not,
reevaluate your answer.

Share and discuss your ideas with a classmate, and clearly justify your reasoning.
144

Inferring Charge
Distribution
The physical and chemical properties of materials, as well as the physical and
U2: MODULE 4
chemical changes that they undergo, are determined by the interactions among
the particles that make up the system at the submicroscopic level. The nature and
strength of these interactions depend, in turn, on the atomic composition and
connectivity of the interacting particles, as well as on their molecular geometry.
These three factors influence how electrons arrange within molecules and how
easily these electrons are affected by the presence of other molecules or
ions in their vicinity. Knowing how to infer charge distribution
in molecules from composition and structural cues is thus a
critical skill in chemical thinking.
The analysis of charge distribution in molecular
systems is of such importance that chemical scientists
have developed a variety of strategies to both qualita-
tively and quantitatively identify regions in a molecule Electrostatic Potential
of low and high electron density. In this module we will Map for N2O

discuss methods that are useful in the analysis of the physical properties of sub-
stances, such as the determination of bond and molecular polarity and the con-
struction of electrostatic potential maps such as that shown in the figure. We will
leave for subsequent course units the discussion of strategies that aid in the pre-
diction of the chemical reactivity of different types of compounds, such as the
identification of oxidation states.

THE CHALLENGE Greenhouse Gases


Gaseous substances that absorb and emit infrared (IR) radiation in a planet’s
atmosphere are called greenhouse gases. Substances such CO2(g) and N2O(g)
are greenhouse gases while N2(g) and O2(g) are not.

• What structural properties of the CO2 and N2O molecules, not present
in N2 and O2, may determine how they interact with IR radiation?

Share and discuss your ideas with one of your classmates.

This module will help you develop the type of chemical reasoning that can be
used to explain phenomena similar to that described in the challenge. In particu-
lar, the central goal of Module 4 is to help you understand how to infer charge
distribution in a molecule based on its atomic composition, connectivity, and
three dimensional geometry.
Chemical Thinking U2 How do we determine structure? 145

Contrasting Behaviors LET’S THINK


http://www.chem.arizona.edu/tpp/chemthink/resources/U2_M4/hexwat.html

Chemical substances interact with charged objects in different ways. Analyze, for example,
the following movies showing the interactions of liquid hexane C6H14(l) and liquid water
H2O(l) with objects that have been electrically charged by rubbing:
CLICK TO PLAY

CLICK TO PLAY
C6H14(l) H2O(l)

• How would you explain the different behaviors of these two substances?
• How could substances that do not have a net electric charge be attracted to an electri-
cally charged object? How may electric charge be distributed in the molecules of
these types of substances to explain their behavior?

Share and discuss your ideas with a classmate, and clearly justify your reasoning.

Partial Charges
Experimental results such as the ones illustrated in the previous activity suggest
that electric charge is not evenly distributed in all types of molecules. This allows
us to explain the attractive interaction between some chemical substances and d- d+
electrically charged objects. If we assume, for example, that valence electrons in a
water molecule spend more time in certain regions of the molecule than in others,
the electron density will vary from atom to atom. One average, some regions of
the molecule will have a higher electron density than others and exhibit a partial
negative charge (d-, measured in units of electron charge); other parts of the mol-
ecule where valence electrons spend a lesser amount of time will have a positive
partial charge (d+). Although the molecule as a whole will be neutral (the sum of
all partial charges will be zero), the uneven distribution of charge will affect how
the molecule interacts with other neutral or charged particles.
To illustrate these ideas, imagine that we modeled a water molecule as an el-
lipsoidal particle with positive and negative partial charges on opposite sides of the
+
particle (see Figure 2.52). These electrical charges would have to be identical in
magnitude but opposite in sign for the molecule to be neutral. When a stream of
these molecules passes nearby a positively charged object, we can expect the nega-
tive sides of the molecules to turn towards the object while their positive sides turn
away. Given that the negative sides of the molecules will be closer to the positively
charged object, they will be subject to an electrostatic force of attraction larger in
magnitude than the repulsion exerted on the farther side with the positive partial
charge. The end result will be a net force of attraction on the water molecules that Figure 2.52 Model of the
will deviate them from their initial trajectory (Figure 2.52). attraction between water
molecules and an electri-
cally charged object.
146 MODULE 4 Inferring Charge Distribution

The assumption that valence electrons are unevenly distributed across the mol-
ecules of some substances allow us to explain many of their physical and chemical
properties. But, what causes this unequal distribution of electrons? The answer lies
in the nature of the atoms that are present in the system. Some atoms seem to exert
stronger forces of attraction on electrons than others, increasing the likelihood of
valence electrons in a bond spending more time in the vicinity of those atoms than
in other regions of a molecule. These types of atoms tend to have valence energy
states that are lower in energy than equivalent states in other atoms. The relative
ability of atoms in a molecule to attract valence electrons in their vicinity can be
quantified by analyzing the relative average energy of their unfilled valence energy
states.

LET’S THINK Back to PES

Photoelectron spectroscopy (PES) data for isolated atoms provides informa- ET


tion about the energy needed to remove electrons from different atomic
states (mth ionization energy). The more energy is needed to eject an electron 0
from an atom, the lower the energy of the orbital it occupies. Thus PES data Ionization
Energy
can be used to estimate the average energy of the valence electrons.
Valence electrons in atoms of nonmetallic elements occupy s and p orbit-
als. In a first approximation, the average energy of these valence electrons (EAV) can be calculated
by first multiplying the number of electrons in each of these orbitals (nS and nP) by their associated

http://www.chem.arizona.edu/tpp/chemthink/resources/U2_M2/pes.html
ionization energy (IS and IP), and then dividing this result by the total number of valence electrons
(nS + nP) in the system:
nS x IS + nP x IP
EAV =
nS + nP
CLICK TO PLAY
• The interactive tool that you can launch by clicking on the image allows
you to display the PES spectra of different atoms. Using the “dual mode” in
this tool, visually compare the energies of the valence electrons for the fol-
lowing atoms: H, C, N, O, F, S, and Cl. Then, use the relationship shown
above to complete the following table of EAV values for each of these atoms.

Atom H C N O F S Cl
EAV (MJ/mol) 1.31 1.89 2.31 1.59

• What periodic trends do you observe in the previous data?


• When a covalent bond is formed, some valence electrons are delocalized into the bonding
region. If the bonded atoms are of different types, bonding electrons are likely to spend more
time moving in a volume closer to one of the atoms. Based on your previous results for EAV,
discuss which atom is likely to have a negative partial charge when the following covalent
bonds are formed: H-C, H-O, H-Cl, C-N, C-O, C-F, and C-Cl.
• Use all your data to identify a simple way to predict the sign of the partial charges on each of
the atoms in a covalent bond based on their relative positions on the periodic table.

Share and discuss your ideas with a classmate, and clearly justify your reasoning.
Chemical Thinking U2 How do we determine structure? 147

The average energy of the valence electrons in isolated atoms (EAV) as calcu-
lated in the previous activity can be used to predict which atom in a bond is likely
to have a negative or positive partial charge. Based on these types of analyses,
chemical scientists have defined a property of atoms in a bond that allows us to
predict charge distribution in molecules. This property, called electronegativity
(c), is a measure of the decrease in the total energy of an atomic system if a bond-
ing electron were to be localized in the vicinity of a given type of atom. The larger
this decrease in energy, the larger the electronegativity of that type of atom and the
larger the likelihood of finding bonding electrons closer to it. The electronegativity
of an atom can also be thought of as a measure of the probability of finding bond-
ing electrons localized in the vicinity of that atom.
Atomic electronegativities (c) have been estimated using different strategies,
from determining the average energy of valence electrons to calculating the force
between valence electrons and protons in atoms to analyzing the energy required
to break different types of bonds. Figure 2.53 shows electronegativity values com- Figure 2.53 Electronega-
tivities (c) of the different
monly used in predicting charge distribution in chemical systems: elemental atoms.

As you can see in this image, the electronegativity values for the elemental
atoms follow periodic trends: c increases as we move up a group (column) in the
periodic table and as we go from left to right across a period (row). This is the same
pattern followed by the first ionization energy of isolated atoms and opposite to
variations in the average energy of valence electrons (EAV) and in atomic size. Thus,
the most electronegative atoms tend to be those that are the smaller in size and
with the lower valence electron energy states.
The electronegativity of an atom not only provides information about the
likelihood of electrons in a bond to be more or less localized around certain atom.
This quantity also tells us how energetically costly it would be to displace elec-
trons away from that atom. As a consequence, when a chemical bond between
atoms A and B is formed, the partial electric charge that each of them acquires is
determined by both the difference in electronegativities Dc = cA - cB between the
bonded atoms and their average electronegativity cAV = (cA + cB)/2. The first of
these quantities Dc is a measure of the tendency of valence electrons to move to-
wards one of the atoms, while cAV quantifies the average “resistance” in the system
for this to happen. Thus, the partial charge on each atom in a diatomic molecule
can be estimated using the following relationship:
cA - cB Dc
(2.4) dA = = = - dB
cA + cB 2cAV
148 MODULE 4 Inferring Charge Distribution

Given that most atoms of nonmetallic elements have relatively high electro-
negativities, Dc < 2.0 and cAV > 2.0 for covalent bonds. Therefore, partial charges
on bonded atoms will have either small or middle-sized magnitudes (|d| < 0.35)
and bonding electrons will still be largely delocalized between the two atoms.

http://www.chem.arizona.edu/tpp/chemthink/resources/U2_M4/pten.html
LET’S THINK Partial Charges

Equation (2.4) can be used to generate a first estimate of the partial charges (d) on atoms linked by a
single bond. These numbers are useful in identifying regions in a molecule with high or low electron
density and in estimating the probabilities of finding bonding electrons in different locations.

• Estimate the partial charges on each of the atoms in the following


bonds: H-C, H-N, H-O, H-F, C-O, C-N, C-F. Atomic electronegativity
values are included in the interactive periodic table to the right.
• Consider a chemical bond between two atoms A-B with partial charges
dA = - dB = -0.2. What is the probability of finding the bonding elec-
CLICK TO PLAY
trons in the vicinity of atom A versus atom B? What partial charge
would atoms A and B have if the likelihood of finding bonding electrons localized around
atom A was four times higher than that of finding them around atom B?

Share and discuss your ideas with a classmate, and clearly justify your reasoning.

Bond and Molecular Polarity


Differences in electronegativity between bonded atoms lead to an unequal distri-
bution of electron charge density. The existence of positive (d+) and negative (d-)
partial charges separated by a certain distance creates an electric dipole in a bond.
The effect of this electric dipole on its surroundings is determined by the magni-

tude and direction of the associated electric dipole moment ( m ). The magnitude of
d- d+ this quantity results from the product of the magnitude of the partial charge (d) on
the bonded atoms times the distance (d, bond length) between them:

m (2.5) m = |d| x d.

By convention, chemical scientists assign the direction of the electric dipole mo-
ment on a bond from the positive to the negative poles (Figure 2.54) representing
the direction towards which electron density is shifted. The magnitude of a bond’s
dipole moment is said to be a measure of the polarity of the bond. Thus, the larger
the dipole moment the more polar the bond. For diatomic molecules (particles
Figure 2.54 Representa-
made up of only two atoms) the magnitude and direction of the bond dipole
tion of the electric dipole determine the strength of the molecules’ electrostatic interactions with charged
moment associated with a
polar chemical bond. particles and other electric dipoles in the surroundings.
The units of the dipole moment in the International System of Units are Cou-
lomb-meters (C-m). However, it is common to express dipole moments using
the Debye (1 D = 3.335 x 10-30 C-m) as the basic unit. In general, single covalent
bonds have dipole moments that do not exceed the 2 Debyes. For example, the
average dipole moment for a C-H bond is estimated to be close to 0.4 D (weakly
polar), while that for the H-F bond is close to 1.9 D (strongly polar).
Chemical Thinking U2 How do we determine structure? 149

Bond Dipoles LET’S THINK


The magnitude of a bond’s dipole moment (m) depends on the partial charge (d) on the bonded
atoms and the bond length (see Equation (2.5)). Based on Equation (2.4) we can thus expect
the value of m to be proportional to the difference in electronegativities Dc between the bonded
atoms. Consider the following molecules of importance in our planet’s atmosphere:

CF4 CO2 N2 CH4 H2O O2 SO2

• Arrange these molecules in order of increasing bond polarity;


• Draw the dipole moment vectors on each of the bonds of these molecules. Given that
dipole moments are vectorial quantities, discuss how you would add the individual bond
dipoles in each molecule to determine the net molecular dipole moment.

Share and discuss your ideas with a classmate, and clearly justify your reasoning.

The presence of polar bonds in a molecule does not necessarily imply that the
molecule has a net dipole moment itself. The electric dipole moment is a vectorial
quantity and the effects of bond dipoles directed in opposite directions will cancel
each other out. Thus, in analyzing the net polarity of a molecule it is not only im-
portant to analyze the relative magnitude of each bond dipole but to consider their
orientation in space. Molecular polarity strongly depends on molecular geometry.

USEFUL TOOLS magnitude or direction:

To determine the net dipole moment of a mol- R


ecule, the individual dipoles associated with R
each bond in the system need to be added. R
The graphical method is the simplest approach
to sum vectors. To illustrate the application of The vector sum R, or net dipole moment, cor-
this strategy for vector addition let us consider responds to the arrow that goes from the be-
a concrete example: ginning to the end point of the sequence of
added dipoles (black arrows above). As shown
Imagine that you wanted to add three bond in the image, the net result is independent of
dipoles m1, m2, and m3 with magnitudes of 0.5 the order in which the dipoles are sequenced.
D, 1.0 D, and 1.5 D, respectively, and directions
as shown in the image. To
find the vector sum, we This head-to-tail procedure to add vectors can
start by representing the m2 be used with as many bond dipoles as pres-
dipoles by arrows drawn m3 ent in a molecule. However, in many cases the
to scale based on each di- m1 addition has to be made in three dimensional
pole’s magnitude. Then, space. Although vector addition is more diffi-
we draw the arrows in sequence by placing the cult to visualize in these situations, the graphi-
beginning of one of the arrows at the end of cal method can still be applied to generate the
another (head-to-tail), without changing their vector sum.
150 MODULE 4 Inferring Charge Distribution

To illustrate how to qualitatively infer the net dipole moment of a molecule


with more than one bond, let us first consider the case of the CO2 molecule. Each
of the two double bonds in this particle are polar with associated dipole moments
equal in magnitude but with opposite directions:

d- d+ d- Vector Sum

m=0
m=0 As it can be inferred from the symmetry of this molecule, the individual bond
dipoles cancel each other out and the net dipole moment for the CO2 molecule is
equal to zero. The molecule is then said to be “nonpolar.” As this example shows,
the lack of net polarity in a molecular system does not imply that the electric
charge is equally distributed across the molecule; electron density around the car-
bon atom in CO2 is certainly lower than in the vicinity of the oxygen atoms. A
m=0
zero net dipole moment is also characteristic of systems in which charge distribu-
tion is fully symmetrical around an atomic center, such that the contributions of
individual bond dipoles cancel each other out. This is the case of other common
molecules such as SO3 and CH4 (see Figure 2.55). Interactions involving mole-
cules of this type are similar in nature to those of nonpolar particles with no partial
charge on any atom, such as N2 or O2.
The water molecule is a typical example of a “polar” molecule with a non-
Figure 2.55 Dipole mo- zero net dipole moment. In this case, bond dipoles do not cancel each other out
ment addition leads to a
zero net dipole moment because of the bent geometry of the molecule. Rather, they add up to produce a
for SO3 and CH4.
dipole moment with a magnitude close to 1.85 D:

d- Vector Sum

m = 1.85 D
d+ d+

The presence of this net dipole moment has a strong influence on the nature of
m = 0.53 D the interactions between water and other molecules or ions. In general, substances
made up of polar molecules are attracted to charged objects and measurements of
d+ the strength of these interactions can be used to determine their dipole moment.
Polar molecules are made up of atoms with higher electronegativity differences
Dc and tend to be asymmetrical. The presence of atomic centers with lone electron
pairs commonly leads to the existence of a net dipole moment because they create
regions with high electron density (see Figure 2.56). Thus, for example, in the wa-
d- d- ter molecule the presence of the two lone electron pairs associated with the oxygen
atom further increases the electron density around this atom, contributing to this
molecule’s high dipole moment.
Figure 2.56 Ozone (O3) is a
polar molecule despite being The determination of the polarity of molecules with more than one atomic
made up of the same types of center is simplified by analyzing the system center by center. For organic mol-
atoms. Lone pair electrons on
the external atoms of this non- ecules, it is useful to pay attention to the symmetry of the molecule and to the
linear molecule create regions
of high electron density. polarity of the functional groups present in the system. In general, the dipole mo-
ment associated with the C-H bond is so small (Dc~0.4) that hydrocarbon chains
are assumed to be nonpolar for all practical purposes.
Chemical Thinking U2 How do we determine structure? 151

Molecular Polarity LET’S THINK

http://www.chem.arizona.edu/tpp/chemthink/resources/U2_M4/dipole.html
Consider the following molecules: NO2, N2O, NH3, CH2O, CCl4, and CHCl3.

• Use the interactive tools that you can access on this page
to aid you in drawing and adding the bond dipoles on
each of these molecules; take into account the difference
in electronegativities between atoms to estimate the rela-
tive magnitude of the dipole moments.
• Add the bond dipoles using the graphical method to de-
termine each molecule’s net dipole moment.

NOTE: Bond dipole vectors can be drawn by clicking on the screen


of the interactive tools and dragging the mouse at the same time.
Click on and drag a vector’s arrow head to move it across the screen.
For non-planar molecules you need to carefully think about how to
add vectors in three dimensions.

Share and discuss your ideas with a classmate, and clearly justify
your reasoning.
CLICK TO PLAY

Electrostatic Potential Maps


The identification of areas in a molecule with different partial charges helps us
predict molecular polarity and the nature of the molecule’s interactions with other
particles. To simplify this task, chemical scientists have developed strategies to
visually represent charge distribution in molecules and ions. One useful approach
is to create the electrostatic potential map of the particles of interest. These types of
representations are built using a standard color scheme to depict areas in a mol-
ecule with different electrostatic potentials.
The electrostatic potential at any point is a measure of the energy required
to place a unit positive charge (e.g., a proton) at that particular point. The more
positively charged the region of the space, the more energy will be needed to add
another positive charge due to repulsive forces between equally charged particles. Figure 2.57 Electro-
static potential map for
Therefore, the electrostatic potential will be high, or very positive, at that loca- the water molecule.
tion. On the contrary, bringing a positive charge to a negatively charged region
of a system will cost little or even generate energy, and the electrostatic potential
will be low or negative. Thus, by calculating the electrostatic potential at differ-
ent points around a molecule we can map the distribution of charge in the
system.
To display electrostatic potential data for a molecule it is common to
use the following coloring conventions: dark blue areas identify regions
with the highest or most positive electrostatic potential (positive partial
charge) while dark red areas correspond to regions with the lowest or most
negative electrostatic potential (negative partial charge). Intermediate poten-
tials are assigned colors according to the standard color spectrum (Figure 2.57).
152 MODULE 4 Inferring Charge Distribution

Electrostatic potential maps allow us to make quick judgments about molecu-


lar polarity and charge distribution in molecules and ions. Compare, for example,
the electrostatic potential maps for the ammonia molecule NH3 and the ammo-
nium ion NH4+:

NH3 NH4+

These potential maps clearly show the uneven distribution of charge in the polar
NH3 molecule, with a negative partial charge in the vicinity of the nitrogen atom,
while the positive electric charge in the NH4+ ion appears to be equally distributed
across the system.
Electrostatic potential maps also help us identify those regions in a molecule
that will determine the nature and strength of its interactions with other particles.
In general, we may expect that positively charged regions (or areas with a high
electrostatic potential) in one particle will be attracted to negatively charged re-
gions (or areas with a low electrostatic potential) in another particle (Figure 2.58).

Figure 2.58 How would you


expect CO2 and H2O mole-
cules to interact among them-
selves and with each other?

LET’S THINK Larger Molecules

Electrostatic potential maps are particularly useful in analyzing the polarity of larger organic mol-
ecules with many atomic centers. Consider the following electrostatic potential maps for important
volatile organic compounds (VOCs) in our atmosphere:

Hexane Acetone Benzene Ethyl


Acetate

C6H14 C3H6O C6H6 C4H8O2

• Analyze the distribution of charge in each of these molecules and identify regions of positive
and negative partial charge. Discuss whether you would expect each of these molecules to be
polar or nonpolar.

Share and discuss your ideas with a classmate, and clearly justify your reasoning.
Chemical Thinking U2 How do we determine structure? 153

FACING THE CHALLENGE the greenhouse effect is smaller because it is pres-


ent in much smaller concentrations. The potential
of a substance to contribute to the greenhouse ef-
Greenhouse Gases fect also depends on its lifetime in the atmosphere.
Our planet receives energy from the Sun, most of This is, the average time it takes for its concentra-
it in the form of visible light. Earth’s surface ab- tions to return to its natural value following an in-
sorbs a large proportion of this energy and releases crease in its concentration in the atmosphere.
it back in the form of infrared radiation. A fraction Measured average temperatures of our plan-
of this IR radiation is in turn absorbed by some et in the past sixty years indicate the presence
gases in our atmosphere (greenhouse gases) and of a warming trend. The term “global warming”
re-emitted back to the surface. Earth’s atmosphere is currently used to refer to the measured in-
normally traps 84% of the solar energy re-emit- crease in the average temperature of the Earth’s
ted by the planet’s surface. near-surface air and oceans
This phenomenon is called since the mid 20th century,
the Greenhouse Effect and and its projected continua-
helps our planet sustain tion. Most experts in earth
an average temperature of and atmospheric sciences
15 C.
o
consider that the increasing
Greenhouse gases are concentrations of atmospher-
chemical substances that ab- ic greenhouse gases caused by
sorb and emit IR radiation. human activities are mostly
This property is determined responsible for this unprec-
by their molecular geometry edented rapid rise in global
and polarity. For a molecule temperatures in recent years.
to absorb IR radiation two Global warming is expected
By Barb Deluisi, NOAA
basic conditions must be to induce climate changes in
met: 1) At least one of the molecule’s modes of our planet with potentially harmful consequences
vibration must lead to changes (oscillations) in its for the environment and human health.
net dipole moment; 2) The energy of the IR pho- Since the beginning of the industrial revolu-
tons interacting with the molecule should match tion human activities have led to a significant
the energy difference between allowed vibrational increase in the concentration of atmospheric
states in the system. The change in the dipole mo- greenhouse gases. Some of these activities include:
ment of the molecule is required because it allows burning of fossil fuels and deforestation that result
the particle to interact with the oscillating electric in higher CO2(g) concentrations; use of CFCs in
field of the IR radiation wave. Therefore, fully refrigeration systems which are released into the
symmetrical molecules with no bond dipoles will environment; agricultural practices based on the
not absorb EM radiation in the IR range and thus use of fertilizers that generate gaseous nitrogen
will not act as greenhouse gases. compounds; livestock and manure management
The primary greenhouse gases in our planet’s that lead to higher methane atmospheric concen-
atmosphere are water vapor (H2O(g)), carbon trations. Overall, existing data reveal increases be-
dioxide (CO2(g)), methane (CH4(g)), and ozone tween 15% to 60% in the concentrations of dif-
(O3(g)). The contribution of a gaseous chemical ferent atmospheric greenhouse gases compared to
substance to the greenhouse effect depends on its pre-industrial values. A significant proportion of
chemical composition and structure, as well as on the current human-induced greenhouse gas emis-
its abundance. For example, although one gram of sions comes from industrialized countries. The
methane traps 25 times more thermal energy than US, for example, contributes with close to 16% of
one gram of carbon dioxide, its contribution to the total annual emissions in the world.
154 MODULE 4 Inferring Charge Distribution

Let’s Apply
Warming Substances
The relatively rapid increase of average near surface temperatures in the past 50 years in our planet
seems to be associated with the presence of greenhouse gases in our atmosphere that can absorb IR
radiation. Understanding the properties of these chemical substances is thus crucial to predict their
warming potential and to make decisions about how to best reduce or control their environmental
ASSESS WHAT YOU KNOW

effects.

Temperature Changes By Giorgiogp2 (Own work) [Share


Alike 3.0] via Wikimedia Commons

http://www.chem.arizona.edu/tpp/chemthink/resources/U2_M4/temp.html
The graph and movie associated with this ac-
tivity (from NOAA and NASA data sources)
summarize information about how average
global and local temperatures in our planet have Temperature Anomaly
changed in the past 120 years. The data shows
the 1880-2007 global mean surface tempera-
ture difference (temperature anomaly) relative
to the average value in the 1951–1980 period.

• What specific trends do you observe in the


average global temperature variations?
Year
• What specific trends do you observe in
average local temperature variations?
• How would you explain that average local tem-
perature changes are not the same across the globe?
CLICK TO PLAY
Share and discuss your ideas with a classmate.

Active Vibrations

Greenhouse gases are made up of molecules with at least one mode of vibration that leads to
temporal changes (oscillations) in its net dipole moment (IR active vibration modes).

• Which of the following vibration modes for the CO2 molecule are IR active?
CLICK TO PLAY

http://www.chem.arizona.edu/tpp/chemthink/resources/U2_M4/co2vib.html

Share and discuss your ideas with a classmate, and clearly justify your reasoning.
Chemical Thinking U2 How do we determine structure? 155

The Methane Case Source: Chemistry at Penn State University

Methane is an important greenhouse gas in our


planet.

• Which of the vibration modes represented


in the image are IR active?
• How would the net dipole moment of the
CH4 molecule change in each of the IR ac-
tive vibrations?

ASSESS WHAT YOU KNOW


Share and discuss your ideas with a classmate.
Clearly justify your reasoning.

Greenhouse Gases?

Many pollutants in our atmosphere can act as greenhouse gases.

• Analyze the polarity of these molecules and discuss whether they can absorb IR radiation.

Cl2 SO3 C2H6 SF6

N2O CH2Cl2

Share and discuss your ideas with a classmate. Clearly justify your reasoning.

Relative Contributions

The following image shows the IR 0.8


CO2
spectra of the main greenhouse gases
in our planet. Each spectrum is scaled H2O
Transmittance

0.6

considering the substance’s concen- N2O


0.4 CH4
tration and global warming potential
C3F8
(GWP). The image also shows Earth’s
0.2 CFCs
emission spectrum (black line).

3500 3000 2500 2000 1500 1000 500


• Analyze the IR spectrum of each
Wavenumber (cm-1)
of the different gases. Identify
which of them can be expected to absorb outgoing IR radiation emitted by our planet.
• Estimate the relative amount of Earth’s IR radiation absorbed by each of the different
gases and arrange them in order of decreasing contribution to the greenhouse effect.

Share and discuss your ideas with a classmate. Clearly justify your reasoning.
156 MODULE 4 Inferring Charge Distribution

Let’s Apply
More on Functional Groups
The nature and strength of the interactions between organic substances depend on the polarity of
the functional groups present in the interacting molecules.
ASSESS WHAT YOU KNOW

Functional Group Polarity

Consider the following functional groups:

Chemical Functional Lewis Chemical Functional Lewis


Class Group Structure Class Group Structure

O
Ketone Ketone
R1 C R2
Ether Alkoxy R1 O R2

Carboxylic O Amine R1
Carboxyl Amine (R1 and R2 can
Acid R1 C O H be H atoms) R N R2

• Assign partial charges to the visible C, H, O, and N atoms in these functional groups;
• Determine the relative magnitude and direction of relevant bond dipoles assuming that
R1 and R2 groups represent hydrocarbon chains;
• Determine the direction of the net dipole moment of each functional group.

Consider the electrostatic potential maps of molecules of medical relevance:

Amphetamine Glutamic Acid Tyrosine

• Based on the composition and structure of each molecule, explain the distribution of
charge as implied by the electrostatic potential maps.

Share and discuss your ideas with a classmate, and clearly justify your reasoning.
Chemical Thinking U2 How do we determine structure? 157

Where From?
restrict the possible states (orbitals) in which they
can exist; b) their spin, that constrains the num-
ber of electrons that can occupy the same orbital.

Where To? Zooming into the electronic structure of at-


oms allowed us to explain and predict the bonding
patterns between atoms of nonmetallic elements.
Our analysis showed that covalent bonding is
The central goal of this unit was to help you de- driven by the delocalization of valence electrons
velop ways of thinking that can be used to uncov- into the space between two atom, which lowers
er and predict the atomic and molecular structure the energy of the system. However, the number
of substances. In particular, we have discussed of bonds formed is constrained by the number of
how the careful analysis of the unfilled orbitals in the interacting atoms.
interactions between EM ra-
diation and matter allows us ZOOMING IN
From Microsoft Office

to derive information about ET


both atom connectivity in
1s22s22p4
molecules and electron distri-
bution in these particles. This
information can then be used
to build models to explain O
and predict molecular geometry and polarity. H H
Our analysis of light-matter interactions re-
vealed important properties of molecules, atoms,
and electrons. Of central importance is the fact ZOOMING OUT
that their energy is quantized, this is, it can only
take a set of discrete values that are characteristic How valence electrons distribute around
of each type of system. The quantization of ener- atomic centers in a molecule determines both
gy states in atoms and molecules is clearly mani- its three dimensional geometry and polarity. In
fested in the absorption and emission spectra of general, the most stable configurations are those
chemical substances. These spectra are unique in which electrostatic repulsions between valence
fingerprints that reveal the internal structure of electrons are minimized and attractions between
the particles that make up chemical elements and electrons and protons are maximized. This could
compounds. lead to an uneven distribution of bonding elec-
Experimental results from spectroscopic anal- trons between atoms in a molecule, creating cen-
ysis also show the existence of periodic patterns ters with positive and negative partial charge. As
for important atomic properties such as valence, we will see in the next Unit,
atomic size, and ionization energy. The analysis of the presence of polar bonds
Source: Bessonov & Harauz

these periodic trends has guided the development and of a net dipole mo-
of theoretical models of the electronic structure ment in molecules has
of atoms. In a first approximation, periodic prop- a strong influence on
erties can be explained assuming that electrons in the physical properties of
atoms are arranged in shells and subshells with chemical substances. But
a well defined occupancy. In the quantum me- before we move on, let us
chanical model of the atom, specific electron con- explore if “YOU ARE READY” by assessing your
figurations result from two fundamental proper- ability to apply what you have learned in this
ties of electrons: a) their wave-like properties, that Unit to the analysis of some interesting problems.
158 Are you Ready?

Are You Ready?


An odorant is a substance capable of triggering an olfactory response; odor is the sensation resulting from
stimulation of the olfactory organs. Odors play an important part in our everyday life, from appetite
stimulation to serving as warning signals for disease detection. Several theories of how molecules interact
with protein receptors in olfactory cells are currently under investigation. However, many of them suggest
a strong relationship between type of odor and molecular size, shape, and polarity. Let’s investigate this.

100
Orange Smell

Relative Abundance
80
Elemental analysis of one of the chemi-
cal substances that we associate with 60
the smell of fresh orange juice reveals 40
the following composition: 62.04% C,
10.41% H, 27.55% O. The mass and 20
IR spectra of the substance are shown
0
below. 0 20 40 60 80 100 120
m/q
• Determine the empirical and mo-
lecular formulas for this chemical
compound. 0.8
• Propose a structural formula this
C-H
Transmittance

compound (Hint: Your formula 0.6


should explain the presence of stretch C=O
stretch
peaks at m/q = 29, 43, and 71 in 0.4
C-H C-C
the mass spectrum). bendC-O
0.2
stretch
Share and discuss your results with a
3000 2000 1000
classmate. Clearly justify your reasoning.
Wavenumber (cm-1)

Bitter Poison

HCN is an extremely poisonous and highly volatile liquid with a faint, bitter, almond-like odor that some
people are unable to detect due to a genetic trait. This compound is obtainable from some fruits that have a pit,
such as cherries, apricots, apples, and bitter almonds, from which almond oil and flavoring are made.

• Draw the Lewis structure of HCN and determine its molecular geometry. Assign partial charges to each
atom in the system and sketch each bond dipole. Determine whether this molecule is polar or nonpolar.
• CH3CN is a solvent with a sweet odor that can be metabolized to form HCN when ingested. It is struc-
turally similar to HCN. Draw the Lewis structure of CH3CN and indicate the electron domain and mo-
lecular geometries around each C and N atoms. Analyze bond and molecular polarity for this molecule.
Chemical Thinking U2 How do we determine structure? 159

What’s that Smell?


Molecules Molecules Important Factors
with a smell with no smell
Based on the information provided in the table shown to the left:
NH3, H2S, N2, O2,
HBr, HCN CO2, CH4 • Suggest which of the following factors: i) bond polarity, ii) molecu-
lar polarity, or iii) molecular geometry, seems to affect whether a
small molecule will trigger an odor or not.

Share and discuss your ideas with a classmate, and justify your reasoning.

Important Factors
H
Citronellal is the main component in the mixture of chemical com-
pounds that give citronella oil its distinctive lemon scent. Its Lewis H C H
structure is represented to the right.
C C H3
• Indicate the molecular geometry of each of the encircled atomic
centers;
H C
• Estimate the value of the bond angles marked on the image; H C H
• Draw three dimensional structures of this molecule using:
a) wedge and dash projections; b) skeletal or bond-line structures.
H C H
• Identify and name the functional group that may be responsible H C C H3
for the characteristic odor produced by this substance.
H C H
Share and discuss your ideas with a classmate, and justify your thinking. H C O

Fruity Smell

All the molecules shown to the left have fruity smells.


By Johanna84 (Own Work) [Public domain] via Pixabay

• Compare the chemical composition, molecular ge-


ometry, and charge distribution of these molecules.
What structural factors do they have in common?
Which of these factors may be responsible for their
fruity smell?
160 Are you Ready?

What’s that Smell?


Nutty, Medicinal Smells

Although the relationship between odor and molecular structure is complex,


there is solid evidence that they are interrelated. For example, flat or planar
molecules tend to have nutty, medicinal smells.

• Which of these molecules are likely to be in this category?

H H H H H
N C H C C H C C
H H
H3C C C CH3 C C HO C C CH3
HO H
C N H C C H C C
H H H H H

Justify your answer based on the analysis of their molecular geometry.

Something Fishy

The three compounds that are shown below have a strong “fishy” odor, which is thought to be associated
with the presence of a particular functional group.

H H
H H H H CH3 C C

By Schwarzenarzisse (Own Work) [Public domain] via Pixabay


H C C N C H H3C N CH3 H C C NH2
H H H C C
H H
• Assume that in order to generate that odor, these molecules have to fit into a protein receptor with
the same molecular geometry as their active functional group. What would this geometry be?
• How is charge distributed in each of these molecules? Sketch the associated electrostatic maps.

Share and discuss your ideas with a classmate. Clearly justify your reasoning.

Your Design

• Based on what you have learned, design three molecules that you think will have a) a nutty, me-
dicinal smell, b) a fishy smell, and c) a fruity smell. Draw the Lewis structure of the molecules and
justify your choices based on the expected composition and geometry of the molecules.
Chemical Thinking U2 How do we determine structure? 161

Are You Ready?


The Role of Ions

Olfactory receptors are proteins that bridge through the cell membrane. It has been found that
the structure of these proteins changes dramatically when certain metal ions bind to them. The
charge of the relevant ions can be explored using photoelectron spectroscopy (PES). Imagine
that PES analysis reveals the presence of certain X2+ ions in some type of olfactory receptors. The
spectrum of these ions is shown below. Based on this information:

• What is the electron configuration of this ion?


• What is the identity of element X? (Remember this is the spectrum of the ion X2+, not of
the neutral atom X).

Absorption spectroscopy of the metal-protein system reveals a sharp absorption peak at 244 nm.

• What is the energy (in J) absorbed by each ion (1 photon per ion)?
• What is the energy absorbed by one mole of ions (in kJ/mol)?

Share and discuss your ideas with a classmate. Justify your reasoning and calculations.
162 Are you Ready?

Are You Ready?


The determination of a substance’s identity based on the analysis of its molecular structure is a fundamental
analytical tool in forensic science. Consider, for example, this case described in the San Francisco Chronicle
in May 13, 2001:

In the thick of