Concept Summary 1

When naming organic compounds:

Find longest chain of carbonsthat contains the highest priority group; make
sure multiple bonds are on the chain whenever possible
Number the carbon chainso that substituents get the lowest numbers possible
Name the substituents as prefixes (the beginning of the name)
Put the whole name together, and remember to alphabetize the substituents
More complicated compounds
Priority in nomenclature is determined by oxidation state; the more oxidized the
higher the priority
The highest priority group takes the suffix (the end of the name), all other groups
are named in the prefix
Multiple Bonds
Alkyl chains with double bonds are called alkenes and end with ene
Alkyl chains with triple bonds are called alkynes and end with yne
Substituted Alkanes
Haloalkanes, ethers, and ketones are often given common names (e.g., methyl
chloride, ethyl methyl ether, diethyl ketone)
Aldehydes and carboxylic acids are terminal functional groups; if present, they
define C 1 of the carbon chain and do not need to be numbered in the name
When naming substituents on a nitrogen atom, precede the substituents with
N
Concept Summary 2
Structural Isomers
Share only a molecular formula
Have different physical and chemical properties
Stereoisomers
Share the same molecular formula and atomic connectivity
Differ in their three-dimensional shape
Geometric Isomers
Differ in positioning around a double bond
Differ in many chemical and physical properties.
Chiral Center
Has four different groups attached to the central carbon
Is given the absolute configuration of either R or S
o Note that a lone pair may also be considered as one of the four different
groups
Enantiomers
Have the same chemical and physical properties in an achiral environment
Differ only in the way they rotate plane-polarized light and how they react in chiral
environments
Diastereomers
Non-mirror-image stereoisomers
Differ at some but not all chiral centers
Have different chemical and physical properties
Constitute cis-trans isomers as well
Meso
Compounds
Have an internal plane of symmetry and are not optically active
Conformational Isomers
Are the same compound at different points in rotation around a single bond
Chair conformation is the most favored position for cyclohexane
o In ring structures, big bulky groups prefer to be in the equatorial position
Concept Summary 3
Atomic Orbitals
The principal quantum number, n, indicates distance from nucleus and energy
level; possible values are integers greater than or equal to 1
The azimuthal quantum number, l, determines the shape of the orbital; possible
values are 0 to n 1 (corresponding to s-, p-, d-, and f-orbitals)
Molecular Orbitals
Bonding orbitals share the same sign and are energetically favorable
Antibonding orbitals have opposite signs and are energetically unfavorable
Hybridization
Single bond = one sigma bond, sp
3
hybridized, 109.5 bond angles; examples:
C C, C H
Double bond = one sigma bond + one pi bond, sp
2
hybridized, 120 bond
angles; examples: C=C, C=O
Triple bond = one sigma bond + two pi bonds, sp hybridized, 180 bond angles;
examples: C C, C N
Concept Summary 4
Physical Properties of Alkanes
chain length, boiling point, melting point, density
branching, boiling point, density
Reactions
Combustion: Alkane + O
2
CO
2
+ H
2
O + heat
Free radical halogenation : initiation, propagation, termination
Pyrolysis
Nucleophiles
Nucleophiles = electron rich; electrophiles = electron deficient
Solvents affect nucleophilicity
Leaving Groups
Weak bases make good leaving groups
S
N
1 versus S
N
2
Steps: S
N
1: two steps; S
N
2: one step
Solvent: S
N
1: favored in protic solvents; S
N
2: favored in aprotic solvents.
Substrate: S
N
1: 3 > 2 >> 1 ; S
N
2: 1 > 2 >>>3
Rate: S
N
1: rate = k[RX]; S
N
2: rate = k[Nu][RX]
Stereochemistry: S
N
1: racemic products; S
N
2: inverted product
Nucleophile: S
N
1: doesn't matter, but favored with bulky nucleophile; S
N
2: strong
nucleophile
Concept Summary 5
Alkenes
Have carbon-carbon double bonds (sp
2
hybridization) and end in the suffix
ene
Physical Properties
o Cis-isomers = more polar = increased intermolecular forces = higher
boiling point; worse at stacking = lower melting point
o Trans-isomers = less polar = decreased intermolecular forces = lower
boiling point; better at stacking = higher melting point
Synthesis
o S
N
2 and E2 occur under different reaction conditions, so it is easier to
control which occurs; strong bulky base favors E2
o S
N
1 and E1 occur under the same reaction conditions, so they happen
simultaneously and competitively
Reactions
o Reduction = adding hydrogen atoms; if we use a metal
catalyst, syn addition occurs
o Oxidation = adding oxygen atoms; compound with many oxygen atoms =
oxidizing agent
Nonterminal alkenes and alkynes can be oxidatively cleaved with
hot, basic KMnO
4
(followed by acidification) to form carboxylic
acids
Cold, dilute KMnO
4
turns double bonds into vicinal alcohols
o Electrophilic addition follows Markovnikov s rule (adding to the most
substituted carbon) except with hydroboration-oxidation
o Radical addition follows anti-Markovnikov addition (adding to the least
substituted carbon)
Alkynes
Have carbon-carbon triple bonds (sp hybridization) and end in the suffix yne
Alkynes have similar physical properties and reactivates as alkenes
Terminal (end-of-carbon chain) alkynes have slightly acidic protons; this means
they can be deprotonated and used as nucleophiles
Concept Summary 7
Nomenclature
Alcohols = ROH
Ethers = ROR
Physical Properties
Alcohols can hydrogen bond, leading to relatively high boiling points
Ethers cannot hydrogen bond, leading to relatively low boiling points
Alkyl groups stabilize positive charges and destabilize negative charges
Synthesis
Alcohols can be synthesized by nucleophilic substitution, electrophilic addition to
a double bond, or nucleophilic addition to a carbonyl
Reactions
The oxygen atoms of alcohols or ethers can be protonated to make them into
better leaving groups
If a reactant has a lot of oxygen atoms, it's an oxidizing agent; if it has a lot of
hydrogen atoms, it's a reducing agent
Terminal alcohols are oxidized to carboxylic acids, secondary alcohols are
oxidized to ketones, and tertiary alcohols cannot be oxidized
PCC only oxidizes terminal (primary) alcohols to aldehydes
Cleavage of straight-chain ethers is acid catalyzed; cleavage of cyclic ethers
(epoxides) can be carried out with an acid or base
Base-induced epoxide cleavage is S
N
2 in character; acid-catalyzed cleavage is
S
N
1 and S
N
2 in character
Concept Summary 8
Nomenclature
Aldehydes are terminal functional groups
Ketones are midchain functional groups
Physical Properties
In a carbonyl , the carbon is partially positive and the oxygen is partially negative
Many nucleophiles will add to the electropositive carbonyl carbon
Synthesis
Aldehydes can be synthesized from primary alcohols with PCC
Reactions
The enol form is significant because it can act as a nucleophile, but it is not
prevalent in solution
Ammonia derivatives often add in condensation reactions, removing water and
forming a C=N bond
The Wittig reaction swaps out a carbonyl (C=O) for an alkene (C=C)
Aldehydes can be oxidized to carboxylic acids or reduced to primary alcohols
Ketones cannot be further oxidized, but they can be reduced to secondary
alcohols
The Wolff-Kishner reduction and the Clemmensen reduction completely remove
the carbonyl from ketones and aldehydes, reducing them to alkanes
Concept Summary 9
Nomenclature
Carboxylic acids have the highest priority
Physical Properties
Carboxylic acids hydrogen bond better than alcohols and, as a result, have
higher boiling and melting points
The acidity of a carboxylic acid is enhanced by resonance between its oxygen
atoms
Acidity can be further enhanced by substituents that delocalize the negative
charge through resonance or by electron-withdrawing groups, such as halides
Synthesis
Primary alcohols or aldehydes can be oxidized to carboxylic acids
Carboxylic acids can also be synthesized from the carbonation of organometallic
reagents or by hydrolyzing nitriles
Reactions
Carboxylic acids with long chains form soaps when neutralized with NaOH or
KOH
Carboxylic acids can be reduced to primary alcohols with a hydride reagent
Carboxylic acids readily undergo nucleophilic acyl substitution
1,3-Dicarboxylic acids and other -keto acids may spontaneously
undergo decarboxylationwhen heated, producing a ketone (or a monocarboxylic
acid in the case of the dicarboxylic acid) and carbon dioxide
Concept Summary 10
The most important derivatives of carboxylic acids are acyl halides, anhydrides, esters,
and amides. We decided to organize these derivatives from most reactive (least stable) to
least reactive (most stable).
Acyl halides
Can be formed by adding RCOOH + SOCl
2
, PCl
3
or PCl
5
, or PBr
3

Undergo many different nucleophilic substitutions; H
2
O yields carboxylic acid,
ROH yields an ester, and NH
3
yields an amide
Can participate in Friedel-Crafts acylation to form an alkyl aryl ketone
Can be reduced to alcohols or, selectively, to aldehydes
Anhydrides
Can be formed by RCOOH + RCOOH (condensation) or RCOO

+ RCOCl
(substitution)
Undergo many nucleophilic substitution reactions, forming products that include
carboxylic acids, amides, and esters
Can participate in Friedel-Crafts acylation
Esters
Formed by RCOOH + ROH or, even more easily, by acid chlorides or anhydrides
+ ROH
Hydrolyze to yield acids + alcohols; adding ammonia yields an amide
Reaction with Grignard reagent (2 moles) produces a tertiary alcohol
In the Claisen condensation, analogous to the aldol condensation, the ester
acts both as nucleophile and electrophile but note the product difference
Are very important in biological processes, particularly phosphate esters, which
can be found in membranes, nucleic acids, and metabolic reactions
Amides
Can be formed by acid chlorides + amines or acid anhydrides + ammonia
Hydrolysis yields carboxylic acids or carboxylate anions
Can be transformed to primary amines via Hofmann rearrangement or
reduction
Concept Summary 13
Infrared spectroscopy
Is used to find functional groups
o Carbonyls = sharp peak at 1,700 cm
1

o Hydroxides = broad peak at 3,300 cm
1

o Amines = sharper peaks at 3,300 3,400 cm
1

Nuclear Magnetic Resonance
N
1
H-NMR is useful in finding the structure of a compound, including functional
groups
In
1
H-NMR, protons three bonds apart experience coupling/splitting. If there is
one proton three bonds away, it is a doublet; if there are two, it is a triplet; three,
a quartet.

13
C-NMR is similar to
1
H-NMR, but = 0 210 ppm
Ultraviolet Spectroscopy
Is useful for conjugated compounds
Mass Spectroscopy
Is used to find the mass of the compound
Concept Summary 11
Nomenclature
The suffix amine is used when the amine has the highest priority
The prefix amino is used when the amine does not have the highest priority
Remember the nitrogen-containing functional groups: amides; carbamates =
urethanes; isocyanates; enamines; imines; nitriles = cyanides; nitro; diazo; azide;
carbene; nitrene
Properties
The boiling point of amines is between that of alcohols and alkanes
Certain amines can be optically active if inversion is inhibited by sterics
Amines have lone pairs, so they are bases/nucleophiles
A nitrogen double-bonded to carbon (imine) acts like an oxygen double-bonded
to carbon (carbonyl)
Synthesis
Addition of ammonia to an alkyl halide and the Gabriel synthesis are both S
N
2
reactions
Many nitrogen-containing functional groups are easily reduced to amines
Reactions
Exhaustive methylation = Hofmann elimination; in this reaction, the nitrogen of an
amine is released as trimethylamine, and the substituent is converted into the
least substituted alkene
Concept Summary 12
Basic Techniques
Extraction: Using the concept of like dissolves like to separate compounds
based on their differences in polarity
Filtration: Separating out a liquid from a solid
o Gravity filtration is used when the solvent is the desired product
o Vacuum filtration is used when the solid is the desired product
Recrystallization: Once the desired solid product is separated from the solvent,
it can be dissolved in a hot solvent to further purify it; when the solvent cools, the
product will precipitate out, while impurities stay in solution
Sublimation: Purifying a substance by exposing it to low temperatures and
pressures, then collecting the condensate on a cold finger
Centrifugation: Spinning a mixture very quickly to separate particles based on
relative densities
Distillation
Separating liquids according to differences in their boiling points (BP); the liquid
with the lowest boiling point vaporizes first and is collected as the distillate
Simple Distillation: lowest BP < 125 C; and BPs are > 25 apart
Vacuum distillation: lowest BP > 125 C
Fractional Distillation: BPs are < 25 apart
Chromatography
Separating or identifying different compounds based on their physical or chemical
properties; all forms of chromatography use two phases, a mobile phase and a
stationary phase: whichever phase is more similar to the sample will retain the
sample longer
Thin-Layer Chromatography (TLC): Used to identify a sample; stationary
phase = silica or alumina (polar), mobile phase = nonpolar
Column Chromatography: Utilizes several techniques to separate compounds
based on their physical or chemical properties (e.g., ion exchange, size-
exclusion, and affinity chromatographies)
Gas Chromatography (GC): Similar to other forms of chromatography, except
the sample must be vaporizable and a computer does all the analysis
High Pressure/Performance Liquid Chromatography (HPLC): Similar to
column but sample is forced though with high pressures; used if the sample size
is small or forces such as capillary action will affect results, and data is
interpreted, as in GC, by a computer
Electrophoresis
Uses an electrolytic cell to separate macromolecules based on their size and net
charge
Agarose Gel: Standard electrophoresis used for DNA
SDS-PAGE: Used for proteins; denatures and negatively charges proteins to
separate according to mass
Isoelectric Focusing: Uses a gel with a pH gradient to separate proteins based
on their pI
Concept Summary 14
Carbohydrates
Have the general formula C
n
(H
2
O)
n

Aldoses are sugars with aldehydes at the C 1 position; ketoses are sugars with
ketones at the C 2 position
L-sugars have the highest-numbered chiral hydroxyl group on the left side of the
sugar; D-sugars have the highest-numbered chiral hydroxyl group on the right (in
a Fischer projection)
D- and L-sugars of the same name are enantiomers (nonsuperimposable mirror
images)
Epimers are sugars that differ at only one chiral center.
Reactions
Sugars can undergo intramolecular reactions that form rings
o Pyranose rings are six-membered sugar rings
o Furanoserings are five-membered rings
o C 1 becomes chiral when a ring is formed; this newly chiral atom is
known as theanomeric carbon
o For glucose, the anomeric carbon can either be (axial) or (equatorial)
Mutarotation is the interconversion between the and anomers via ring
opening and reclosing
The key reactions of monosaccharides are ester formation, oxidation ,
and glycosidic reactions
Polysaccharides
o Cellulose is a chain of glucose with 1,4 - -glycosidic bonds
o Starch and glycogen have mostly 1,4 - -glycosidic bonds (with some
1,6 - -glycosidic bonds that form branches off the chain)
Concept Summary 15
Amino Acids
Contain a carboxyl group, an amino group, a hydrogen, and an R-group attached
to a central -carbon
There are 20 naturally occurring amino acids, all of which are L-isomers except
for glycine,which is achiral
o Nonpolar amino acids are hydrophobic, so they are often found buried
within protein molecules
o Polar, acidic, and basic amino acids are hydrophilic and are often
found on the surface of proteins
Amino acids are amphoteric species (they can function as acids or bases)
In a neutral solution, nonpolar and polar amino acids exist as zwitterions, acidic
amino acids exist as negatively charged ions, and basic amino acids exist as
positive ions.
All amino acids have at least two pK
a
, and the isoelectric point (pI) is between
the two pK
a
; for amino acids with three pK
a
, the pI is between the two lowest
pK
a
for acidic amino acids and between the two highest pK
a
for basic amino acids
Titration of Amino Acids
When pH = pK
a
, concentration of the protonated species is equal to that of the
deprotonated species; this region is known as the buffer zone, and pH changes
very little in this region (appears as a horizontal line on the titration curve)
During titration, when pH = pI, all of the species have been deprotonated, and pH
changes drastically (appears as a somewhat vertical line on the titration curve)
Peptides and Proteins
Primary structure is determined by the amino acid sequence from the N-
terminus to the C-terminus
Secondary structure is determined by local hydrogen bonding
Tertiary structure (the three-dimensional shape) is determined largely by
hydrophobic and hydrophilic interactions but also by disulfide bonds
Quaternary structure results from the aggregation of more than one polypeptide
subunit
Conjugated proteins derive part of their function from prostheticgroups , which
can be either organic molecules or metal ions.