MCAT Organic Chemistry

IUPAC Naming Steps

Alkane

Hydrocarbon with only single bonds -ane

Alkene

Hydrocarbon with double bond -ene

Alkyne

Hydrocarbon with triple bond -yne

Alcohol

-OH with -ol suffix and hydroxy- prefix

Diol

Contains 2 hydroxyl groups.

Geminal: If on same carbon

Vicinal: If on adjacent carbons

Carbonyl

C=O

Aldehyde

Carbonyl group on the end of carbon chain

Ketone

Carbonyl group in the middle of carbon chain

1,2,3, Alcohols

1,2,3, Amide

Carboxylic Acid

Highest priority functional group since it contains 3 bonds to oxygen. -oic

Ester

Derivative of carboxylic acid with -OH replaced with -O-

Amide

Replace -OH in carboxylic acid with an amino group

Chiral center

4 different groups attached to a central carbon

2ⁿ rule

n = number of chiral centers # of stereoisomers = 2^n

Types of isomers

Cyclohexane substituents

Equatorial: In the plane of the molecule.

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

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 2 enantiomers. Not optically active

Meso compounds

Have an internal plane of symmetry, will also be optically inactive because the two sides of the molecule cancel each other out.

Diasteromers

Not mirror image but are stereoisomers

Cis-Trans

A subtype of diastereomers. They differ at some, but not all, chiral centers. Different chemical and physical properties.

Relative configuration

Gives stereochemistry of a compound in comparison to another

Absolute configuration

Gives the stereochemistry of a compound without having to compare to other compounds

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

ZE for akenes

Z is highest on same while E is highest on opposite

RS for stereoisomers

R is clockwise and S is counterclockwise

Fisher projection

Alternating 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

Bonding orbitals

Created by head-to-head or tail-to-tail overlap of atomic orbitals of the same sign. Lower energy more ­stable

Antibonding orbitals

Created by head-to-head or tail-to-tail overlap of atomic orbitals of opposite signs. ­More energy less stable

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

Alpha-carbon

Carbon adjacent to a carbonyl

Alpha-hydrogen

Hydrogen connected to an alpha carbon

Nucleophiles

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

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 = 𝑘 [substrate]

Sn2

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 = 𝑘 [nucleophile] [substrate]

Polar protic

Acetic Acid, H2O, ROH, NH3

Polar aprotic

DMF, DMSO, Acetone, Ethyl Acetate

Leaving groups chart

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 and types

Benzene ring with –OH groups attached. Named for the relative position of the –OH groups

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

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

Primary Alcohol

Can be oxidized to aldehydes only by PCC; oxidized all the way to carboxylic acids by any stronger oxidizing agents

Secondary Alcohol

Can be oxidized to ketones by any common oxidizing agent

Mesylates

Contains -SO3CH3

Tosylates

Contains -SO3C6H4CH3

Acetal

Primary carbon with -OR and H atom

Ketal

Secondary carbon with 2 -OR groups

Deprotection

Acetal or ketal back to a carbonyl by acid

Oxydation in aldehydes and ketones

Are produced in primary and secondary alcoholds. PCC must be used for aldehydes or it will end up being a carboxylic acid

Keto/enol

Aldehydes and ketones exist in both keto and enol form

Tautomers

Isomers that can be interconverted by moving a hydrogen and a double bond

Michael Addition

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 fast, reversible reactions at HIGH TEMP with weaker, smaller bases

Enamines

Tautomers of imines. Less common

Aldol

Contains aldehyde and alcohol

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,bunsaturated carbonyl.

Retro-Aldol Reactions

Reverse of aldol reactions. Catalyzed by heat and base. Bond between a- and b-carbon is cleaved.

Carboxylic acid nomenclature

Suffix –oic acid. Salts are named with the suffix –oate, and dicarboxylic acids are –dioic acids

Carboxylic acid properties

Carboxylic acids are polar and hydrogen bond well, resulting in high BP. They often exist as dimers in solution.

Carboxylic acid 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

Beta-dicarboxylic acids

Like other 1,3-dicarbonyl compounds, they have an ahydrogen that is also highly acidic

Reactions of carboxylic acids

Anhydrides

-O- connecting 2 carbonyls. 5 or 6 membered rings are stable

Steric hinderance

When a reaction cannot proceed because of crowding

Induction

Uneven distribution of charge across a sigma bond due to differences in electronegativity. More electronegativity = greater reactivity

Conjugation

Alternating single and multiple bonds, which create delocalized pi electron clouds. More reactive

Ring strain

More reactive. Torsional strain from eclipsing interactions and angle strain from compression bond angles below 109.5

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.

Amino acid structure

Aliphatic

Non-aromatic. Side chains contains only C and H

Peptide bonds

C-N bond and formed by condensation reactions. Need strong acid/base to cleave peptide bond

Polypeptides

Made up of multiple amino acids linked by peptide bonds. Proteins are large, folded, functional polypeptides.

Strecker Synthesis

Generates an amino acid from an aldehyde

Gabriel synthesis

Generates an amino acid from potassium phthalimide, diethyl bromomalonate, and an alkyl halide.

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

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.

Organic phosphates

Carbon containing compounds that also have phosphate groups. The most notable examples are nucleotide triphosphates (such as ATP or GTP) and DNA.

Important peaks for IR

UV spec

Good for double bonds or heteroions.

HOMO and 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.

TMS

NMR spectra are calibrated using tetramethylsilane (TMS), which has a chemical shift of 0 ppm

Integration

Area under the curve that is proportional to the number of protons 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 and deshielded

Upfield

Right and more shielded