Organic

IUPAC Naming Conventions

Step 1: Find the parent chain, the longest carbon chain that

contains the highest-priority functional group.

Step 2: Number the chain in such a way that the highest-priority

functional group receives the lowest possible number.

Step 3: Name the substituents with a prefix. Multiples of the same

type receive (di-, tri-, tetra-, etc.).

Step 4: Assign a number to each substituent depending on the

carbon to which it is bonded.

Step 5: Alphabetize substituents and separate numbers from each

other by commas and from words by hyphens.

Alkane: Hydrocarbon with no double or triple bonds.

Alkane = C)H(,)-,)

Naming: Alkanes are named according to the number of carbons

present followed by the suffix –ane.

Alkene: Contains a double bond. Use suffix -ene.

Alkyne: Contains a triple bond. Use suffix –yne.

Alcohol: Contains a –OH group. Use suffix –ol or prefix hydroxy-.

Alcohols have higher priority than double or triple bonds.

Diol: Contains 2 hydroxyl groups.

Geminal: If on same carbon

Vicinal: If on adjacent carbons

Hydrocarbons and Alcohols

Aldehyde Ketone

Carbonyl Group: C=O. Aldehydes and ketones both have a carbonyl

group.

Aldehyde: Carbonyl group on terminal C.

Ketone: Carbonyl group on nonterminal C.

Aldehydes and Ketones

Carboxylic Acid

Carboxylic Acid: The highest priority functional group because it

contains 3 bonds to oxygen.

Naming: Suffix –oic acid.

Ester Amide

Ester: Carboxylic Acid derivative where –OH is replaced

with -OR.

Amide: Replace the –OH group of a carboxylic acid with

an amino group that may or may not be

substituted.

Carboxylic Acids & Derivatives

1° 2° 3°

Alcohols:

Amines:

Primary, Secondary, and Tertiary

Organic Chemistry 2: Isomers

14

• Share only a molecular formula.

• Have different physical and chemical properties.

Structural Isomers

Chiral Center: Four different groups attached to a central carbon.

2n Rule: � = # of chiral centers # of stereoisomers = 23

Conformational Isomers

Anti Gauche Eclipsed

Differ by rotation around a single (s) bond

Cyclohexane

Substituents:

Equatorial: In the plane of the molecule.

Axial: Sticking up/down from the molecule’s plane.

Configurational Isomers

Enantiomers

Enantiomers: Nonsuperimposable mirror images. Opposite

stereochemistry at every chiral carbon. Same

chemical and physical properties, except for

rotation of plane polarized light.

Optical Activity: The ability of a molecule to rotate plane-polarized

light: d- or (+) = RIGHT, l- or (-) = LEFT.

Racemic Mixture: 50:50 mixture of two enantiomers. Not optically

active because the rotations cancel out.

Meso Compounds: Have an internal plane of symmetry, will also be

optically inactive because the two sides of the

molecule cancel each other out.

Diastereomers

Diastereomers: Stereoisomers that are NOT mirror image.

Cis-Trans: A subtype of diastereomers. They differ at some,

but not all, chiral centers. Different chemical and

physical properties.

Stereoisomers

Relative Configuration: Gives the stereochemistry of a compound in

comparison to another compound. E.g. D and L.

Absolute Configuration: Gives the stereochemistry of a compound

without having to compare to other compounds.

E.g. S and R.

Cahn-Ingold-Prelog

Priority Rules:

Priority is given by looking at atoms connected to

the chiral carbon or double-bonded carbons;

whichever has the highest atomic # gets highest

priority.

(Z) and (E) for Alkenes: (Z): Highest priority on same side.

(E): Highest priority on opposite sides.

(R) and (S) for

Stereocenters:

A stereocenter’s configuration is determined by

putting the lowest priority group in the back and

drawing a circle from group 1-2-3.

(R): Clockwise

(S): Counterclockwise

Fischer Projection: Vertical lines go to back of page (dashes);

horizontal lines come out of the page (wedges).

Altering Fischer

Projection:

Switching 1 pair of substituents inverts the

stereochemistry; switching 2 pairs retains

stereochemistry. Rotating entire diagram 90°

inverts the stereochemistry; rotating 180°

retains stereochemistry.

Relative & Absolute Configuration

Compounds with atoms connected in the

same order but differing in 3D orientation.

Organic Chemistry 3: Bonding

15

Quantum Numbers: Describe the size, shape, orientation, and number

of atomic orbitals in an element

Atomic Orbitals & Quantum Numbers

Bonding Orbitals: Created by head-to-head or tail-to-tail overlap of

atomic orbitals of the same sign. ̄energy ­stable

Antibonding Orbitals: Created by head-to-head or tail-to-tail overlap of

atomic orbitals of opposite signs. ­energy ̄stable

Single Bonds: 1 s bond, contains 2 electrons

Double Bonds: 1 s + 1 p

Pi bonds are created by sharing of electrons

between two unhybridized p-orbitals that align

side-by-side

Triple Bonds: 1 s + 2 p

Multiple bonds are less flexible than single bonds because rotation is not

permitted in the presence of a p bond. Multiple bonds are shorter and

stronger than single bonds, although individual p are weaker than s bonds

Molecular Orbitals

sp3: 25% s character and 75% p character

Tetrahedral geometry with 109.5° bond angles

sp2: 33% s character and 67% p character

Trigonal planar geometry with 120° bond angles

sp: 50% s character and 50% p character

Linear geometry with 180° bond angles

Resonance: Describes the delocalization of electrons in

molecules that have conjugated bonds

Conjugation: Occurs when single and multiple bonds alternate,

creating a system of unhybridized p orbitals down

the backbone of the molecule through which p

electrons can delocalize

Hybridization

Quantum

Number Name What it Labels Possible

Values Notes

n Principal e- energy level or

shell number

1, 2, 3, ... Except for d-orbitals, the shell

# matches the row of the

periodic table

l Azimuthal 3D shape of orbital 0, 1, 2, ..., n-1 0 = s orbital

1 = p orbital

2 = d orbital

3 = f orbital

4 = g orbital

ml Magnetic Orbital sub-type Integers

–l ® +l

ms Spin Electron spin + "

# , − "

#

Maximum e- in terms of n = 2n2

Maximum e- in subshell = 4l + 2

Organic Chemistry 4: Analyzing Organic Reactions

16

Lewis Acid: e- acceptor. Has vacant orbitals or + polarized atoms.

Lewis Base: e- donor. Has a lone pair of e-

, are often anions.

Brønsted-Lowry Acid: Proton donor

Brønsted-Lowry Base: Proton acceptor

Amphoteric

Molecules:

Can act as either acids or bases, depending on

reaction conditions.

Ka: Acid dissociation constant. A measure of acidity. It is

the equilibrium constant corresponding to the

dissociation of an acid, HA, into a proton and its

conjugate base.

pKa: An indicator of acid strength. pKa decreases down the

periodic table and increases with EN.

p�# = −log (�#)

a-carbon: A carbon adjacent to a carbonyl.

a-hydrogen: Hydrogen connected to an a-carbon.

Acids and Bases

Oxidation Number: The charge an atom would have if all its bonds were

completely ionic.

Oxidation: Raises oxidation state. Assisted by oxidizing agents.

Oxidizing Agent: Accepts electrons and is reduced in the process.

Reduction: Lowers oxidation state. Assisted by reducing agents.

Reducing Agent: Donates electrons and is oxidized in the process.

REDOX Reactions

Nucleophiles: “Nucleus-loving”. Contain lone pairs or p bonds. They have

­EN and often carry a NEG charge. Amino groups are

common organic nucleophiles.

Nucleophilicity: A kinetic property. The nucleophile’s strength. Factors that

affect nucleophilicity include charge, EN, steric hindrance,

and the solvent.

Electrophiles: “Electron-loving”. Contain a + charge or are positively

polarized. More positive compounds are more electrophilic.

Leaving Group: Molecular fragments that retain the electrons after

heterolysis. The best LG can stabilize additional charge

through resonance or induction. Weak bases make good LG.

SN1 Reactions: Unimolecular nucleophilic substitution. 2 steps. In the 1st

step, the LG leaves, forming a carbocation. In the 2nd step,

the nucleophile attacks the planar carbocation from either

side, leading to a racemic mixture of products.

Rate = � [substrate]

SN2 Reactions: Bimolecular nucleophilic substitution. 1 concerted step. The

nucleophile attacks at the same time as the LG leaves. The

nucleophile must perform a backside attack, which leads to

inversion of stereochemistry. (R) and (S) is also changed if

the nucleophile and LG have the same priority level. SN2

prefers less-substituted carbons because steric hindrance

inhibits the nucleophile from accessing the electrophilic

substrate carbon.

Rate = � [nucleophile] [substrate]

Nucleophiles, Electrophiles and Leaving Groups

Both nucleophile-electrophile and REDOX reactions tend to

act at the highest-priority (most oxidized) functional group.

One can make use of steric hindrance properties to

selectively target functional groups that might not primarily

react, or to protect functional groups.

Chemoselectivity

Substrate Polar Protic

Solvent

Polar Aprotic

Solvent

Strong Small

Base

Strong Bulky

Base

Methyl

SN2 SN2 SN2 SN2

Primary

SN2 SN2 SN2 E2

Secondary

SN1 / E1 SN2 E2 E2

Tertiary

SN1 / E1 SN1 / E1 E2 E2

Solvents

Polar Protic Polar Aprotic

Polar Protic solvents

Acetic Acid, H2O,

ROH, NH3

Polar Aprotic solvents

DMF, DMSO,

Acetone, Ethyl Acetate

SN1 SN2 E1 E2

Organic Chemistry 5: Alcohols

17

Alcohols: Have the general form ROH and are named with the suffix –ol.

If they are NOT the highest priority, they are given the prefix

hydroxy-

Phenols: Benzene ring with –OH groups attached. Named for the relative

position of the –OH groups:

ortho meta

para

• Alcohols can hydrogen bond, raising their boiling and melting

points

• Phenols are more acidic than other alcohols because the

aromatic ring can delocalize the charge of the conjugate base

• Electron-donating groups like alkyl groups decrease acidity

because they destabilize negative charges. EWG, such as EN

atoms and aromatic rings, increase acidity because they stabilize

negative charges

Description & Properties

Quinones: Synthesized through oxidation of phenols. Quinones

are resonance-stabilized electrophiles. Vitamin K1

(phylloquinone) and Vitamin K2 (the menaquinones) are

examples of biochemically relevant quinones

Quinone

Hydroxyquinones: Produced by oxidation of quinones, adding a variable

number of hydroxyl gruops

Ubiquinone: Also called coenzyme Q. Another biologically active

quinone that acts as an electron acceptor in Complexes

I, II, and III of the electron transport chain. It is reduced

to ubiquinol

Reactions of Phenols

Primary

Alcohols:

Can be oxidized to aldehydes only by pyridinium

chlorochromate (PCC); they will be oxidized all the way to

carboxylic acids by any stronger oxidizing agents

Secondary

Alcohols:

Can be oxidized to ketones by any common oxidizing agent

Alcohols can be converted to mesylates or tosylates to make them better

leaving groups for nucleophilic substitution reactions

Mesylates: Contain the functional group –SO3CH3

Tosylates: Contain the functional group –SO3C6H4CH3

Mesylate Tosylate

Aldehydes or ketones can be protected by converting them into acetals or

ketals

Acetal: A 1° carbon with two –OR groups and an H atom

Ketal: A 2° carbon with two –OR groups

Acetal Ketal

Deprotection: The process of converting an acetal or ketal back to a

carbonyl by catalytic acid

Reactions of Alcohols

Organic Chemistry 6: Aldehydes and Ketones I: Electrophilicity and Oxidation-Reduction

18

Aldehydes: Are terminal functional groups containing a carbonyl bonded

to at least one hydrogen. Nomenclature: suffix –al. In rings,

they are indicated by the suffix –carbaldehyde.

Ketones: Internal functional groups containing a carbonyl bonded to

two alkyl chains. In nomenclature, they use the suffix –one

and the prefix oxo- or keto-.

Carbonyl: A carbon-oxygen double bond. The reactivity of a carbonyl is

dictated by the polarity of the double bond. The carbon has a

d+ so it is electrophilic. Carbonyl containing compounds have a

­BP than equivalent alkanes due to dipole interactions.

Alcohols have ­BP than carbonyls due to hydrogen bonding.

Oxidation: Aldehydes and ketones are commonly produced by oxidation

of primary and secondary alcohols, respectively. Weaker,

anhydrous oxidizing agents like pyridinium chlorochromate

(PCC) must be used for synthesizing aldehydes, or the reaction

will continue oxidizing to a carboxylic acid.

1° Alcohol Aldehyde

Description and Properties

When a nucleophile attacks and forms a bond with a carbonyl carbon,

electrons in the p bond are pushed to the oxygen atom. If there is no good

leaving group (aldehydes and ketones), the carbonyl will remain open and

is protonated to form an alcohol. If there is a good leaving group

(carboxylic acid and derivatives), the carbonyl will reform and kick off the

leaving group.

Hydration Rxns: Water adds to a carbonyl, forming a geminal diol.

Aldehyde or Gem-diol

Ketone

Aldehyde + Alcohol: When one equivalent of alcohol reacts with an

aldehyde, a hemiacetal is formed. When the same

rxn occurs with a ketone, a hemiketal is formed.

When another equivalent of alcohol reacts with a

hemiacetal (via nucleophilic substitution), an acetal

is formed. When the same reaction occurs with a

hemiketal, a ketal is formed.

Nitrogen + Carbonyl: Nitrogen and nitrogen derivatives react with

carbonyls to form imines, oximes, hydrazones, and

semicarbazones. Imines can tautomerize to form

enamines.

1° Amine Aldehyde or Imine

Ketone

Imine Enamine

HCN + Carbonyl: Hydrogen cyanide reacts with carbonyls to form

cyanohydrins.

Nucleophilic Addition Reactions

Aldehydes: Aldehydes can be oxidized to carboxylic acids using an

oxidizing agent like KMnO4, CrO3, Ag2O, or H2O2. They can be

reduced to primary alcohols via hydride reagents (LiAlH4,

NaBH4).

Ketones: Ketones cannot be further oxidized, but can be reduced to

secondary alcohols using the same hydride reagents.

Oxidation-Reduction Reactions

Oxidizing Agent Reactant Product

PCC 1° alcohol

Aldehyde

2° alcohol Ketone

KMnO4 or H2Cr2O4 1° alcohol

Carboxylic Acid

2° alcohol Ketone

Reducing Agent Reactant Product

NaBH4

Aldehydes / Ketones 1° alcohol 2° alcohol

LiAlH4 (LAH)

Aldehydes Ketones

Carboxylic Acid Ester

1° alcohol 2° alcohol

1° alcohol 2° alcohol

Common Oxidizing / Reducing Agents

Organic Chemistry 7: Aldehydes and Ketones II: Enolates

19

a-carbon: The carbon adjacent to the carbonyl is the a-carbon. The

hydrogens attached to the a-carbon are the a-hydrogens.

a-hydrogens: Relatively acidic and can be removed by a strong base.

The e- withdrawing O of the carbonyl weakens the C-H

bonds on a-hydrogens. The enolate resulting from

deprotonation can be stabilized by resonance with the

carbonyl.

Ketones: Ketones are less reactive toward nucleophiles because of

steric hindrance and a-carbanion de-stabilization. The

presence of an additional alkyl group crowds the transition

step and increases energy. The alkyl group also donates e-

density to the carbanion, making it less stable.

General Principles

Starts with an aldol addition to create an aldol and create a new C-C bond

Then it undergoes a dehydration to give a conjugated enone (α,β-

unsaturated carbonyl)

Aldol: Contains both aldehyde and an alcohol. “Ald – ol”

Aldol

Nucleophile:

The nucleophile is the enolate formed from the

deprotonation of the a-carbon.

Aldol

Electrophile:

The electrophile is the aldehyde or ketone in the form

of the keto tautomer.

Dehydration: After the aldol is formed, a dehydration reaction (loss

of water molecule) occurs. This results in an a,b-

unsaturated carbonyl.

Retro-Aldol

Reactions:

Reverse of aldol reactions. Catalyzed by heat and base.

Bond between a- and b-carbon is cleaved.

Aldol Condensation

Keto / Enol: Aldehydes and ketones exist in both keto form (more

common) and enol form (less common).

Tautomers: Isomers that can be interconverted by moving a

hydrogen and a double bond. Keto / Enol are

tautomers.

Michael Addition: An enolate attacks an a,b-unsaturated carbonyl,

creating a bond.

Kinetic Enolate: Favored by fast, irreversible reactions at LOW TEMP,

with strong, sterically hindered bases.

Thermodynamic

Enolate:

Favored by slower, reversible reactions at HIGH TEMP

with weaker, smaller bases.

Enamines: Tautomers of imines. Like enols, enamines are the less

common tautomer.

Enolate Chemistry

Organic Chemistry 8: Carboxylic Acids

20

Amide Synthesis

Carboxylic acids contain a carbonyl and a hydroxyl group connected to the

same carbon. They are always terminal groups.

Nomenclature: Suffix –oic acid. Salts are named with the suffix –oate,

and dicarboxylic acids are –dioic acids

Physical

Properties:

Carboxylic acids are polar and hydrogen bond well,

resulting in high BP. They often exist as dimers in solution.

Acidity: The acidity of a carb acid is enhanced by the resonance

between its oxygen atoms. The acidity can be further

enhanced by substituents that are electron-withdrawing,

and decreased by substituents that are electron-donating

b-dicarboxylic

Acids:

Like other 1,3-dicarbonyl compounds, they have an a-

hydrogen that is also highly acidic

a-proton is the most acidic due to resonance

Description and Properties

Oxidation: Carboxylic acids can be made by the oxidation of 1°

alcohols or aldehydes or the oxidation of 1° or 2° alkyl

groups using an oxidizing agent like KMnO4, Na2Cr2O7,

K2Cr2O7, or CrO3.

Nucleophilic Acyl

Substitution:

A common reaction in carboxylic acids. Nucleophile

attacks the electrophilic carbonyl carbon, opening the

carbonyl and forming a tetrahedral intermediate. The

carbonyl reforms, kicking off the L.G.

Nucleophiles: Ammonia / Amine: Forms an amide. Amides are given

the suffix –amide. Cyclic amides are called lactams.

Alcohol: Forms an ester. Esters are given the suffix –

oate. Cyclic esters are called lactones.

Carboxylic Acid: Forms an anhydride. Both linear and

cyclic anhydrides are given the suffix anyhydride.

Reduction: Carboxylic acids can be reduced to a 1° alcohol with a

strong reducing agent like LiAlH4. Aldehyde

intermediates are formed, but are also reduced to 1°

alcohols. NaBH4 is not strong enough to reduce a

carboxylic acid

Decarboxylation: b-dicarboxylic acids and other b-keto acids can

undergo spontaneous decarboxylation when heated,

losing a carbon as CO2. This reaction proceeds via a

six-membered cyclic intermediate

Saponification: Mixing long-chain carboxylic acids (fatty acids) with a

strong base results in the formation of a salt we call

soap. Soaps contain a hydrophilic carboxylate head

and hydrophobic alkyl chain tail. They organize in

hydrophilic environments to form micelles. A micelle

dissolves nonpolar organic molecules in its interior,

and can be solvated with water due to its exterior shell

of hydrophilic groups.

Micelle: Polar heads, non-polar tails. The non-polar tails

dissolve non-polar molecules such as grease

Reactions of Carboxylic Acids

Nucleophilic Acyl Substitution

Ester Synthesis

Anhydride Synthesis

Carboxylic Acid Synthesis via Oxidation

Reduction of Carboxylic Acid Yields a 1° Alcohol

Acid Halide Synthesis

Organic Chemistry 9: Carboxylic Acid Derivatives

21

Amides: The condensation product of carboxylic acid and ammonia or

an amine. Amides are given the suffix –amide. The alkyl

groups on a substituted amide are written at the beginning of

the name with the prefix N-. Cyclic amides are called

lactams, named with the Greek letter of the carbon forming

the bond with the N.

N,N-Dimethylpropanamide b-Lactam

Esters: The condensation products of carboxylic acids with alcohols,

i.e., a Fischer Esterification. Esters are given the suffix –oate.

The esterifying group is written as a substituent, without a

number. Cyclic esters are called lactones, named by the

number of carbons in the ring and the Greek letter of the

carbon forming the bond with the oxygen. Triacylglycerols

include three ester bonds between glycerol and fatty acids.

Isopropyl butanoate b-Propiolactone

Anhydrides: The condensation dimers of carboxylic acids. Symmetric

anhydrides are named for the parent carb acid, followed by

anhydride. Asymmetric anhydrides are named by listing the

parent carb acids alphabetically, followed by anhydride.

Some cyclic anhydrides can be synthesized by heating dioic

acids. Five- or six-membered rings are generally stable.

Ethanoic Ethanoic anhydride Succinic anhydride

propanoic anhydride

Amides, Esters, and Anhydrides

In Nu- substitution reactions, reactivity is:

acid chloride > anhydrides > esters > amides > carboxylate

Steric Hindrance: Describes when a reaction cannot proceed (or

significantly slows) because substituents crowd the

reactive site. Protecting groups, such as acetals, can be

used to increase steric hindrance or otherwise

decrease the reactivity of a particular portion of a

molecule

Induction: Refers to uneven distribution of charge across a s bond

because of differences in EN. The more EN groups in a

carbonyl-containing compound, the greater its

reactivity

Conjugation: Refers to the presence of alternating single and

multiple bonds, which creates delocalized p electron

clouds above and below the plane of the molecule.

Electrons experience resonance through the

unhybridized p-orbitals, increasing stability.

Conjugated carbonyl-containing compounds are more

reactive because they can stabilize their transition

states.

Conjugation in Benzene

Ring Strain: Increased strain in a molecule can make it more

reactive. b-lactams are prone to hydrolysis because

they have significant ring strain. Ring strain is due to

torsional strain from eclipsing interactions and angle

strain from compression bond angles below 109.5°

Reactivity Principles

All carboxylic acid derivatives can undergo nucleophilic substitution

reactions. The rates at which they do so is determined by their relative

reactivities.

Cleavage: Anhydrides can be cleaved by the addition of a

nucleophile. Addition of ammonia or an amine results

in an amide and a carboxylic acid. Addition of an

alcohol results in an ester and a carboxylic acid.

Addition of water results in two carboxylic acids.

Transesterification: The exchange of one esterifying group for another on

an ester. The attacking nucleophile is an alcohol.

Amides: Can be hydrolyzed to carboxylic acids under strongly

acidic or basic conditions. The attacking nucleophile

is water or the hydroxide anion.

Fischer Esterification Nucleophilic Acyl Substitution Reactions

Synthesis of an Anhydride via Carboxylic Acid Condensation

Organic Chemistry 10: Nitrogen- and Phosphorus-Containing Compounds

22

Amino Acid: The a-carbon of an amino acid is attached to four groups:

an amino group, a carboxyl group, a hydrogen atom, and

an R group. It is chiral in all amino acids except glycine.

All amino acids in eukaryotes are L-amino acids. They all

have (S) stereochemistry except cysteine, which is (R).

Amphoteric: Amino acids are amphoteric, meaning they can act as acids

or bases. Amino acids get their acidic characteristics from

carboxylic acids and their basic characteristics from amino

groups. In neutral solution, amino acids tend to exist as

zwitterions (dipolar ions).

Aliphatic: Non-aromatic. Side chain contains only C and H. Gly, Ala,

Val, Leu, Ile, Pro. Met can also be considered aliphatic.

Peptide Bonds: Form by condensation reactions and can be cleaved

hydrolytically. Resonance of peptide bonds restricts

motion about the C-N bond, which takes on partial double

bond character. A strong acid or base is needed to cleave

a peptide bond. Formed when the N-terminus of an AA

nucleophilically attacks the C-terminus of another AA.

Polypeptides: Made up of multiple amino acids linked by peptide bonds.

Proteins are large, folded, functional polypeptides.

Amino Acids, Peptides, and Proteins

Biologically, amino acids are synthesized in many ways. In the lab, certain

standardized mechanisms are used.

Strecker

Synthesis:

Generates an amino acid from an aldehyde. An

aldeyhyde is mixed with ammonium chloride (NH4Cl)

and potassium cyanide. The ammonia attacks the

carbonyl carbon, generating an imine. The imine is

then attacked by the cyanide, generating an

aminonitrile. The aminonitrile is hydrolyzed by two

equivalents of water, generating an amino acid.

Gabriel Synthesis: Generates an amino acid from potassium phthalimide,

diethyl bromomalonate, and an alkyl halide.

Phthalimide attacks the diethyl bromomalonate,

generating a phthalimidomalonic ester. The

phthalimidomalonic ester attacks an alkyl halide,

adding an alkyl group to the ester. The product is

hydrolyzed, creating phthalic acid (with two carboxyl

groups) and converting the esters into carboxylic acids.

One carboxylic acid of the resulting 1,3-dicarbonyl is

removed by decarboxylation.

Synthesis of a-Amino Acids

Phosphoric Acid: Sometimes referred to as a phosphate group or

inorganic phosphate, denoted Pi. At physiological pH,

inorganic phosphate includes molecules of both

hydrogen phosphate (HPO4

2-) and dihydrogen

phosphate (H2PO4

-

).

Phosphoric Acid

Structure:

Contains 3 hydrogens, each with a unique pKa. The

wide variety in pKa values allows phosphoric acid to act

as a buffer over a large range of pH values.

Phosphodiester

Bonds:

Phosphorus is found in the backbone of DNA, which

uses phosphodiester bonds. In forming these bonds, a

pyrophosphate (PPi, P2O7

4-) is released. Pyrophosphate

can then be hydrolyzed to two inorganic phosphates.

Phosphate bonds are high energy because of large

negative charges in adjacent phosphate groups and

resonance stabilization of phosphates.

Organic

Phosphates:

Carbon containing compounds that also have phosphate

groups. The most notable examples are nucleotide

triphosphates (such as ATP or GTP) and DNA.

Phosphorus-Containing Compounds

Gabriel Synthesis of an Amino Acid

Strecker Synthesis of an Amino Acid

Organic Chemistry 11: Spectroscopy

23

Measures absorption of infrared light, which causes molecular vibration

(stretching, bending, twisting, and folding). Plotted as % transmittance vs.

wavenumber (!

l

).

Peaks to Know

for MCAT:

Bond Range (cm-1) Peak Type

N-H 3300 Sharp

O-H 3000 - 3300 Broad

C O, C N 1900 – 2200 Medium

C=O 1750 Sharp

C=C 1600 – 1680 Weak

Infrared Spectroscopy

NMR spectroscopy measures alignment of nuclear spin with an applied

magnetic field, which depends on the magnetic environment of the

nucleus itself. It is useful for determining the structure (connectivity) of a

compound, including functional groups.

Generally plotted as frequency vs. absorption energy. They are

standardized by using chemical shift (d), measured in parts per million

(ppm) of spectrophotometer frequency.

TMS: NMR spectra are calibrated using tetramethylsilane (TMS),

which has a chemical shift of 0 ppm

Integration: Area under the curve. Proportional to the number of

protons contained under the peak.

Deshielding: Occurs when electron-withdrawing groups pull electron

density away from the proton’s nucleus, allowing it to be

more easily affected by the magnetic field. Deshielding

moves a peak further downfield

Downfield: LEFT. Deshielded by EWG or EN atom nearby.

Upfield: RIGHT. More shielded, by EDG or less EN atom nearby.

Spin-Spin

Coupling:

When hydrogens are on adjacent atoms, they interfere with

each other’s magnetic environment, causing spin-spin

coupling (splitting). A proton’s (or a group of protons’) peak

is split into n+ 1 subpeaks, where n is the number of protons

that are three bonds away from the proton of interest.

Splitting patterns include doublets, triplets, and multiplets.

Nuclear Magnetic Resonance Spectroscopy

UV spectroscopy is most useful for studying compounds containing double

bonds and/or heteroatoms with lone pairs that create conjugated systems.

Measures the absorption of UV light, which causes movement of electrons

between molecular orbitals. UV spectra are generally plotted as percent

transmittance or absorbance vs. Wavelength.

HOMO & LUMO: To appear on a UV spectrum, a molecule must have a

small enough energy difference between its HOMO and

LUMO to permit an electron to move from one orbital to

the other. The smaller the difference between HOMO

and LUMO, the longer the wavelengths a molecule can

absorb.

Ultraviolet Spectroscopy

1H-NMR Shifts to Know for the MCAT

IR Spectrum of Cyclohexylamine

IR Spectrum of Benzaldehyde

IR Spectrum of Cyclohexanol

Used to determine the molecular weight and aid in determining molecular

structure. The charged molecule collides with an electron, resulting in the

ejection of an electron from the molecule, making it a radical.

Base Peak: Tallest peak (not always the intact molecule)

Molecular Ion Peak: Peak that represents the molecule.

M+1 Peak: Relative abundance of 13C. Found in relative

abundance of 1.1%. So, if M+1 has an m/z value of

4.4, that means there are 4 carbons. 4.4/1.1 = 4.

M+2 Peak: Relative abundance of either 81Br or 37Cl.

Br has a 1:1 ratio relative to the M peak.

Cl has a 3:1 ratio relative to the M peak.

Mass Spectrometry

Mass Spec of Bromoethane. M+ has similar intensity as M+2.

Organic Chemistry 12: Separations and Purifications

24

Extraction: Combines two immiscible liquids, one of which easily

dissolves the compound of interest.

Nonpolar Layer: Organic layer, dissolves nonpolar

compounds.

Polar Layer: Aqueous (water) layer. Dissolves

compounds with hydrogen bonding or polarity.

Wash: The reverse of an extraction. A small amount of

solvent that dissolves impurities is run over the

compound of interest.

Filtration: Isolates a solid (residue) from a liquid (filtrate)

Gravity Filtration: Use when the product of interest is

in the filtrate. Hot solvent is used to maintain

solubility.

Vacuum Filtration: Used when the product of interest

is the solid. A vacuum is connected to the flask to pull

the solvent through more quickly.

Recrystallization: The product is dissolved in a minimum amount of hot

solvent. If the impurities are more soluble, the

crystals will reform while the flask cools, excluding the

impurities.

Solubility-Based Methods

Separates two or more molecules from a mixture. Includes liquid

chromatography, gas chromatography, size-exclusion chromatography,

ion-exchange chromatography, affinity chromatography, and thin-layer

chromatography.

Chromatography

Distillation: Separates liquids according to differences in their boiling

points. The liquid with the lowest BP vaporizes first and is

collected as the distillate.

Simple

Distillation:

Can be used if the boiling points are under 150°C and are at

least 25°C apart.

Vacuum

Distillation:

Should be used if the boiling points are over 150°C to

prevent degradation of the product. The vacuum lowers

the air pressure, which decreases the temp the liquid must

reach in order to boil.

Fractional

Distillation:

Should be used if the boiling points are less than 25°C apart

because it allows more refined separation of liquids by BP.

Distillation

Extraction: Polar solutes dissolve in the aqueous

layer. Non-polar solutes dissolve in the organic layer.