HASPI Medical Chemistry Lab 2a

Modeling Molecules:
A 3D look at what youre made of
Teacher Information
Lab Overview
In this lab students will learn to draw Lewis structures using their knowledge of the
periodic table and valence electrons, then create physical models of specific molecules
using VSEPR (Valence Shell Electron Pair Repulsion). The background information links
the 3D structure of molecules to the interaction between biological receptors and
medications or other ligands that can bind.
Next Generation Science Standards
NGSS/Common Core State Standards
Students who demonstrate understanding can:

HS-PS1-1: Use the periodic table as a model to predict the relative properties of elements
based on the energy level of atoms.
HS-PS1-3: Plan and conduct an investigation to compare the structure of substances at
the bulk scale to infer the strength of electrical forces between particles.
Medical Application: Students study the connection between molecular shape and biological
receptor-ligand interactions.
Science and Engineering
Disciplinary Core Ideas
Crosscutting Concepts
Practices
PS1.A: Structure and Properties Patterns
Developing and Using Models
of Matter
Develop a model based on
Different patterns may be observed
Each atom has a charged
evidence to illustrate the
at each of the scales at which a
relationships between systems or substructure consisting of a
system is studied and can provide
between components of a system. nucleus, which is made of protons evidence for causality in
and neutrons, surrounded by
explanations of phenomena.
Planning and Carrying Out
electrons.
Investigations
Plan and conduct an investigation The periodic table orders elements
individually and collaboratively to horizontally by the number of
produce data to serve as the basis protons in the atoms nucleus and
places those with similar chemical
for evidence, and in the design:
properties in columns. The
decide on types, how much, and
accuracy of data needed to produce repeating patterns of this table
reflect patterns of outer electron
reliable measurements and
states.
consider limitations on the
precision of the data (e.g., number The structure and interactions of
of trials, cost, risk, time), and refine matter at the bulk scale are
determined by electrical forces
the design accordingly.
within and between atoms.
Connections to other DCIs in this grade-band:

HS.ESS2.C;HS.LS1.C
Articulation of DCIs across grade-bands:

MS.PS1.A;MS.PS1.B;MS.PS2.B

Common Core State Standards Connections:ELA/Literacy

RST.9-10.7
Translate quantitative or technical information expressed in words in a text into visual form (e.g.,
a table or chart) and translate information expressed visually or mathematically (e.g., in an
equation) into words. (HS-PS1-1)
RST.11Cite specific textual evidence to support analysis of science and technical texts, attending to important dis
12.1
any gaps or inconsistencies in the account. (HS-PS1-3)

HASPI Medical Chemistry Unit 2: Electrons & The Periodic TablePage 1

WHST.912.7

Conduct short as well as more sustained research projects to answer a question (including a self-generated
narrow or broaden the inquiry when appropriate; synthesize multiple sources on the subject, demonstrating
under investigation. (HS-PS1-3)

WHST.1112.8

Gather relevant information from multiple authoritative print and digital sources, using advanced searches
and limitations of each source in terms of the specific task, purpose, and audience; integrate information in
the flow of ideas, avoiding plagiarism and overreliance on any one source and following a standard format
Draw evidence from informational texts to support analysis, reflection, and research. (HS-PS1-3)

WHST.912.9
Common Core State Standards Connections: Mathematics HSN-Q.A.1
Use units as a way to understand problems and to guide the solution of multi-step problems; choose and in
formulas; choose and interpret the scale and the origin in graphs and data displays. (HS-PS1-3)
HSN-Q.A.3
Choose a level of accuracy appropriate to limitations on measurement when reporting quantities. (HS-PS1-

Objectives
By the end of this activity students will be able to:
Draw a Lewis structure for any covalent compound
Create a 3D model of any small molecule with one central atom following VSEPR
and identify the shape
Explain octet rule and its implications in bonding, including the determination of
double and triple bonds
Time

Estimated Time
Setup: 5 minutes

Actual Time (please make note below)

Background and review

questions: 10-20 minutes
Lab 02: 45 - 50 minutes
Materials
Supplies needed for 5
sections

Up to 20 lab groups per period

1 inch Styrofoam balls
Sewing pins with a colored ball at the
end
Sewing pins with no colored ball at the
end

Provided
(P) or
Needed (N)

Quantit
y

P
P
P

Company/
Item #

Approxima
te
Cost

20
80

JoAnn #5762828
JoAnn #7417744

$4
$4

40

JoAnn #1073600

$3.50

Company Contact Information

JoAnn fabric & craft
www.JoAnn.com
These can be found at many fabric & craft
stores

HASPI Medical Chemistry Unit 2: Electrons & The Periodic TablePage 2

Prerequisite Knowledge
Students should already know the following information:
Students can identify the number of valence electrons on any main group element
Students can draw Lewis dot structures on single main group elements
Atoms follow the octet rule, needing 8 valence electrons (except H and He follow
the duet rule)
Students are asked to name each of the molecules so they should be familiar with
naming covalent compounds
Lab Setup
There is minimal setup for this lab. You may want to create a baggie with the materials
each group will need.
Each group needs:
1 Styrofoam ball
4 pins with a ball on the end
1 pin with a ball on the end of a different color
2 pins with no ball on the end
Lab Notes & Common Misconceptions
The Background and Review questions are a perfect pre-lab assignment to send
home with students as homework before the lab.
Students have a hard time figuring out the tetrahedral shape they will often
create a molecule that is somewhat flat with the four outer atoms at right angles. I
try to show them the tetrahedral form using my arms and legs, so that my legs are
side to side (like a jumping jack) and my arms go forward and backwards. This
helps students to better understand the three dimensional nature of the
substances.
In this lab the pins with no head represent two electrons. This means they can act
as a lone pair of electrons, OR they can act as the two additional electrons in a
double bond.
Let us know how it went! Go to www.ClarkeChemistry.com/feedback or email
Jewyl@ClarkeChemistry.com
Here are pictures of each model for your reference:

CH4

H2O

CO2

PBr3

CF4

Connections & Application

Have students go to http://www.rcsb.org/pdb/101/structural_view_of_biology.do.
Find the pull down menu Jump to a Molecule and have them select any molecule
that is listed as a receptor. Click on Jmol1 to load the 3D model and drag the
mouse to move the molecules around.
HASPI Medical Chemistry Unit 2: Electrons & The Periodic TablePage 3

HCN

Assign students different drugs and have them research which of the receptors
each drug interacts with in the body, and what signal is started or stopped because
of this interaction.
Give students some polyatomic ions and have the students draw Lewis structures
of them.
Give students a molecule or polyatomic atom and see if they can find the
resonance structures of that substance.
Have students look at the electronegativities of the atoms to determine which of
the molecules are polar and which are non-polar.

Resources & References

http://www.kshitij-iitjee.com/Discrimination-of-Enantiomers-by-Biological-Molecules
http://www.rcsb.org/pdb/101/motm.do?momID=182
http://www.treccani.it/scuola/lezioni/scienze_naturali/forma_molecole.html
http://openi.nlm.nih.gov/detailedresult.php?img=2857793_keq059f1&req=4

HASPI Medical Chemistry Unit 2: Electrons & The Periodic TablePage 4

Name(s):

Period:

Date:

Modeling Molecules: A 3D look at molecular structures

HASPI Medical Chemistry Lab 2a

Background/Introduction
Molecular shape can have a significant effect on the
activity of a molecule. Inside of your body, ions or
molecules such as hormones, medications or
proteins connect to receptors for many different
reasons. The chemical that connects to the
receptor is called a ligand. When these ligands fit
http://www.kshitij-iitjee.com/Discrimination-of-Enantiomers-by-Biological-Molecules
into a receptor it can send a message, stop a message or activate an enzyme.

In this molecule the medicinal activity can be improved by adding electron withdrawing groups (EWG) at R2 or altering th
http://thalesnano.com/publication

The interaction between a receptor and a ligand are based on the three dimensional
shape of the molecule as it relates to the receptor site. Two molecules can even have
the same formula, but if they do not have the same shape they will not interact with the
same receptor. This is why many drug molecules may have similar elements and
formulas, but may have very different medicinal properties. The study of these types of
interactions is called Structure-Activity Relationship or SAR, and it is a key part of what
scientists study when they are working on drug development. Although many molecules
may fit in one reactors binding site, the strength of the binding is called affinity, and it
can alter the action of the receptor depending on the strength of the binding.
HASPI Medical Chemistry Unit 2: Electrons & The Periodic TablePage 5

Most of the molecules that act in this way

are large molecules with 10 to 1000 atoms
or more. The receptor has a pocket that
the ligand is able to fit in, activating the
receptor to send the message. Aspirin and
ibuprofen can both fit in the Cox-1 site on
a platelet. This keeps the platelet from
being able to make a clot. If you take
http://openi.nlm.nih.gov/detailedresult.php?img=2857793_keq059f1&req=4
Aspirin, it will actually covalently bind to
the receptor to stop the clotting signal from attaching, which is why aspirin is commonly
used in patients who are at risk of forming dangerous clots. Clots are the cause of
strokes and many heart attacks, so small daily doses of aspirin keep people alive!

Pre Lab
1. Go to http://www.rcsb.org/pdb/101/motm.do?momID=182 and look at the insulin
receptor. Scroll down until you see the picture with a tab above it that says Jmol1.
Click on Jmol1 and once it loads click on the picture and drag to see the molecule
move around to see how insulin fits right in the pocket of the receptor. The pink
molecule within the receptor is the insulin.
What would happen to the 3Dshape if there was a mutation changing the structure
of insulin?
2. Many people explain receptors and ligands using the term lock and key.
Describe the interaction of receptors and ligands using this simile.
3. Look up the term chiral and explain why two molecules that are mirror images of
each other would not fit in the same receptor.

HASPI Medical Chemistry Unit 2: Electrons & The Periodic TablePage 6

Name(s):

Period:

Date:

Modeling Molecules
HASPI Medical Chemistry Lab 2a

Scenario
Today you will draw Lewis structures
and build molecules to get a better
feel for their three dimensional
shape.

Lewis Structures
A Lewis structure is a diagram that
shows the bonding between atoms
and the lone pairs that exist on
atoms. Bonds within a Lewis
structure are a line that represents 2
electrons within the bond. Electron
pairs are represented by two dots. In
a final Lewis structure you should not
see any unpaired electrons, as
unpaired electrons take part in
bonding.

VSEPR Modeling
Atoms are covered with electrons,
which are all negative. Since they all
have such a negative outer layer they
actually repel each other within a
molecule. This means that when you
determine the structure of an atom,
the atoms and electron pairs that are
on the central atom will work to be as
far apart from one another as
possible.
This is called VSEPR, or Valence Shell
Electron Pair Repulsion. Each pair of
electrons will repel any nearby atoms
as part of the shape of the molecule.
When you draw your Lewis structure,
the bonded atoms and the electron
pairs around the element are all
important parts of the way the
molecule will be shaped.

http://www.treccani.it/scuola/lezioni/scienze_naturali/forma_molecole.html

Dot Structure Practice

HASPI Medical Chemistry Unit 2: Electrons & The Periodic TablePage 7

Before you begin your Lewis structures, take a moment to draw the correct dot
structures representing the valence electrons around the following atoms:

Br

HASPI Medical Chemistry Unit 2: Electrons & The Periodic TablePage 8

Part 1: Drawing Lewis Dot Structures

Step 1
Step 2
Step 3
Step 4
Examine the
chemical formula
and name the
molecule

Find the number of

valence electrons
for each atom then
add them up

Put the atom with the

most unpaired
electrons in the
middle, placing dots
around it
representing
electrons. Surround
this with the dot
structure of the outer
atoms, placing
unpaired electrons
closest to the central
atom.

Draw a bond
between the
unpaired electrons on
the central atom and
the unpaired
electrons on any
surrounding atoms.

Step 5
Check that all atoms
follow the octet rule
(except H=duet).
You may have
double or triple
bonds at times.

Step 6
Draw your final
Lewis structure
here.

CH4

H2O

CO2

PBr3

CF4

HCN

HASPI Medical Chemistry Unit 2: Electrons & The Periodic TablePage 9

BF3
Boron will not
have an octet in
this molecule. It
will have only 6
valence electrons

Part 2: VSEPR Modeling

Step 7
Step 8
Examine the
chemical formula
and name the
molecule

CH4

Draw the Lewis

structure and draw a
triangle around any
lone pairs

Identify the number

of bonded electron
groups and the
number of lone pairs.
Identify the
molecular shape

Step 9

Step 10

What is the bond

angle (or angles) for
this shape?

Create your 3D
molecule
Styrofoam ball =
central atom
Pin with ball tops =
bond with outer atom
Pin with flat tops =
electron pair or
double/triple bond
Draw a 3D diagram
of what this molecule
would look like

Initials
Have your
teacher initial or
stamp each
model you make

Bonded groups:
Lone Pairs:
Shape:

H2O

Bonded groups:
Lone Pairs:
Shape:

CO2

Bonded groups:
Lone Pairs:
Shape:

PBr3

Use an electron pair

pin next to your bond
to represent a double
bond

Bonded groups:
Lone Pairs:
Shape:

CF4

Bonded groups:
Lone Pairs:
Shape:

HCN

Bonded groups:
Lone Pairs:

Use two electron pair

pins next to your
bond to represent a
triple bond

Shape:

HASPI Medical Chemistry Unit 2: Electrons & The Periodic TablePage 10

Bonded groups:

BF3

Lone Pairs:
Shape:

Application Questions
Answer these questions on a separate sheet of paper
1. What is the octet rule?
2. How does the octet rule help to determine the number of bonds between two
atoms?
3. How many electrons are represented in a single bond?
4. How many times does each of the following atoms bond?
a. Oxygen
b. Carbon
c. Nitrogen
d. Hydrogen
e. Bromine
5. Explain why hydrogen and bromine can both bond only once
6. Draw the Lewis structure for the following diatomic molecules:
a. O2
b. N2
c. F2
7. Why does water have a bent shape?

Practice
Draw Lewis structures for each of the following molecules and write the 3D shape they
will take.
CCl4
H2S
OCl2
PH3
Lewis
Structur
e

Shape

Career Spotlight Crystallographer

A crystallographer uses x-rays, neutron and electron diffraction techniques in order to
discover the structure of a molecule. Scientists can then create a 3d digital model of the
drug to see the shape, confirm the structure and see how it will interact with other
HASPI Medical Chemistry Unit 2: Electrons & The Periodic TablePage 11

molecules. This is especially important in the drug discovery process, as making a

digital model of the new drug can help to determine if it will fit in the correct receptor in
the patient. The most famous crystallographer, Rosalind Franklin, was the first person to
image the crystalline structure of DNA and her images were used to determine DNAs
structure.
Annual Salary: $35,000-$85,000 per year with a bachelors degree, $65,000-$140,000
with a graduate degree (2010 data)
Education Requirements: An entry-level position as a laboratory technician requires a
bachelors degree in chemistry, biology, physics or a related field. Research positions
require advanced degrees.
More information:
http://www.inchemistrydigital.org/inchemistry/september_october_2014#pg21
http://www.acs.org/content/acs/en/careers/college-to-career/chemistrycareers/cystallography.html
http://www.amercrystalassn.org/content/pages/main-education-careers

Resources & References

http://www.kshitij-iitjee.com/Discrimination-of-Enantiomers-by-Biological-Molecules
http://www.rcsb.org/pdb/101/motm.do?momID=182
http://www.treccani.it/scuola/lezioni/scienze_naturali/forma_molecole.html
http://openi.nlm.nih.gov/detailedresult.php?img=2857793_keq059f1&req=4
http://thalesnano.com/publication

HASPI Medical Chemistry Unit 2: Electrons & The Periodic TablePage 12