MCAT MilesDown Organic Chemistry

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 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 subsituent depending on the carbon to which it is bonded

step 5: Alphabetize substituents and separate numbers from each other by commas and form words by hyphens

alkane

hydrocarbon with no double or triple bonds

alkane = CnH(2n+2)

naming alkanes

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

-uses 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 it is on the same carbon

-vicinal: if on adjacent carbons

aldehyde

carbonyl group on terminal C

ketone

carbonyl group on nonterminal C

carbonyl group

C=O

-aldehydes and ketones both have a carbonyl group

primary, secondary, and tertiary alcohols

primary, secondary, and tertiary amines

methane

CH4

ethane

C2H6

propane

C3H8

butane

C4H10

pentane

C5H12

hexane

C6H14

heptane

C7H16

octane

C8H18

nonane

C9H20

decane

C10H22

undecane

C11H24

dodecane

C12H26

tridecane

C13H28

icosane

C20H42

triacontane

C30H62

carboxylic acid

the highest priority functional group because it contains 3 bonds to oxygen

naming carboxylic acid derivatives

suffix -oic acid

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

structural isomers

- share only a molecular formula

- have different physical and chemical properties

stereoisomers

compounds with atoms connected in the same order but differing in 3D orientation

chiral center

four different groups attached to a central carbon

2^n rule

n= number of chiral centers

# of stereoisomers = 2^n

conformational isomers

differ by rotation around a single sigma bond

cyclohexane substituents

equatorial: in the plane of the molecule

axial: sticking up/down from the molecule's plane

configurational isomers

enantiomers, diastereomers, and meso compounds

enantiomers

-non superimposable mirror images

-opposite stereochemistry at every chiral carbon

-same chemical and physical properties, except for rotation of plane polarized light

optical activity

the ability fo a molecule to rotate plane-polarized light: d- or (+) = RIGHT, I- 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

stereoisomers that are not mirror images

cis-trans

-a subtype of diastereomers

-they differ at some, but not all chiral centers

-different chemical and physical properties

relative configuration

gives the stereochemistry of a compound in comparison to another compound

ex: D and L

absolute configuration

gives the stereochemistry of a compound without having to compare to other molecules

ex: 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 number gets the 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 the back of the page (dashes)

-horizontal lines come out of the page (wedges)

alternating fischer projection

-switching one pair of substituents inverts the stereochemistry

-switching 2 pairs retains stereochemistry

-rotating entire diagram 90 degrees inverts the stereochemistry

-rotating 180 degrees retains stereochemistry `

compounds chart

same molecular formula?

yes: isomers

no: different compounds

isomers

same connectivity of atoms?

yes: stereoisomers

no: constitutional isomers

stereoisomers:

interconversion requires breaking bonds?

yes: configurational isomers

no: conformers

configurational isomers:

non-superimposable mirror images?

yes: enantiomers

no: diastereomers

bonding orbitals

created by head-to-head or tail-to-tail overlap of atomic orbitals of the same sign

-lower energy

-higher stable

antibonding orbitals

created by head-to-head or tail-to-tail overlap of atomic orbitals of opposite signs

-higher energy

-lower stable

single bond

1 sigma bond, contains 2 electrons

double bonds

1 sigma bond and 1 pi bond

pi bonds are created by sharing of electrons between two unhybridized p-orbitals that align side-by-side

triple bonds

1 sigma bond and 2 pi bonds

-multiple bonds are less flexible than single bonds because rotation is not permitted in the presence of a pi bond

-multiple bonds are shorter and stronger than single bonds, although individual pi are weaker than sigma bonds

sp3

25% s character and 75% p character

-tetrahedral geometry with 109.5 degree bond angles

sp2

33% s character and 67% p character

-trigonal planar geometry with 120 degree bond angles

sp

50% s character and 50% p character

-linear geometry with 180 degree bond angels

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 backbond of the molecule through which pi electrons can delocalize

-refers to the presence of alternating single and multiple bonds, which creates delocalized pi electron clouds above and below the plane of the molecule

-electrons experience resonance through unhybridized p-orbitals, increasing stability

-conjugated carbonyl containing compounds are more reactive because they stabilize their transition states

chemoselectivity

-both nucleophile-electrophile and REDOX reactions tend to act at the highest-priority (most oxidized) functional group

-one can make use of steric hinderance to selectively target functional groups that might not primarily react, or to protect functional groups

nucleophiles

-"nucleus-loving"

-contains lone pairs or pi bonds

-they have higher electronegativity 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 positive charge or are positively polarized

-more positive compounds are more electrophilic

leaving groups

-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

-unipolar nucleophilic substitution

-2 steps

-1st step: LG leaves forming a carbocation

-2nd step: the nucleophile attacks the planar carbocation from either side, leading to a racemic mixture of products

-rate = k[substrate]

SN2 reactions

-bimolecular nucleophilic substitution

-1 concerted step

-the nucleophile attacks at the same time as the LG leaves which leads to inversion of stereochemistry

-R and S is also changed if the nucleophile and LG have the same priority level

-SN2 prefers the less substituted carbons because steric hindrance inhibits the nucelophile from accessing the electrophilic substrate carbon

-rate= k[nucleophile][substrate]

polar protic solvents

-acetic acid

-H2O

-ROH

-NH3

polar aprotic solvents

-DMF

-DMSO

-acetone

-ethyl acetate

substrate: methyl

-polar protic solvent: SN2

-polar aprotic solvent: SN2

-strong small base: SN2

-strong bulky base: SN2

primary substrate

-polar protic solvent: SN2

-polar aprotic solvent: SN2

-strong small base: SN2

-strong bulky base: E2

secondary substrate

-polar protic solvent: SN1/E1

-polar aprotic solvent: SN2

-strong small base: E2

-strong bulky base: E2

tertiary substrate

-polar protic solvent: SN1/E1

-polar aprotic solvent: SN1/E1

-strong small base: E2

-strong bulky base: E2

E1 reaction

a multistep elimination where the leaving group is lost in a slow ionization then a proton is lost in a second step. Zaitsev orientation is generally preferred.

E2 reaction

a concerted elimination reaction involving a transition state where the base is abstracting a proton at the same time that the leaving group is leaving. The anti-coplanar transition state is generally preferred. Zaitsev orientation is usually preferred unless the base or the leaving group is unusually bulky.

alcohols definition

have the general form ROH and are named with suffix -ol

-if they are NOT the highest priority, they are given the prefix hydroxy-

phenols

benzene rings 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

quinones

-synthesized through oxidation of phenols

-quinones are resonance-stabilized electrophiles

-vitamin K1 (phylloquinone) and vitamin K2 (the menaquinones)

hydroxyquinones

produced by oxidation of quinones, adding a variable number of hydroxyl groups

ubiquinone

also called coenzyme Q

-another biologically active quinone that acts as an electron acceptor in complexes I, II, and III of the ETC

-it is reduced to ubiquinol

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 agents

alcohols can be converted to mesylates or tosylates to make them better leaving groups for

nucleophilic substitutions

mesylates

contain the functional group -SO3CH3

tosylates

contain the functional group -SO3C6H4CH3

aldehydes or ketones can be protected by

converting them into acetals or ketals

acetals

a primary carbon with two -O2 groups and an H atom

ketal

a secondary carbon with two -OR groups

deprotection

the process of converting an acetal or ketal back to a carbonyl by catalytic acid

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 positive charge so it is electrophilic

-carbonyl containing compounds have a higher boiling point than equivalent alkanes due to dipole interactions

-alcohols have higher boiling point than carbonyls due to hydrogen bonding