MCAT Organic Equation Sheet

equal (50:50) mixtures of two enantiomers; often denoted by (+/-)

MOLECULAR STRUCTURE
Enantiomers have identical physical properties but diastereomers do not.
Hybridization:
an atom is SP3 hybridized if it contains only single bonds (tetrahedral Meso compounds- molecules that have at least 2 stereocentres BUT are
geometry) 109.5o achiral
an atom is SP2 hybridized if it contains 1 double bond (trigonal geometry) 120o because they have a plane of symmetry.
an atom is SP hybridized if it contains 2 double bonds or 1 triple bond (linear,
180o) Fischer Projections:
***NOTE*** this only works for neutral atoms a carbocation is sp2 hybridized A A

Determining formal charge: # of electrons an atom wants (4 for C, 5 or N, 6 B D = B D

for O) – (# of bonds and each electron in a lone pair)
a single bond has 1 σ bond
C C
a double bond has 1 σ bond and 1 π bond
- most highly oxidized group at the top (position A)
a triple bond has 1 σ bond and 2 π bonds
- longest carbon chain is vertical (A to C)
- Can rotate 180° but not 90 or 270°
Resonance:
- Can hold one substituent in place then rotate others either clockwise or
- occurs when there’s α,β-unsaturation next to an atom with a charge or an
counter-c.w.
atom with a lone pair next to a carbocation
- to draw the resonance contributor always move electrons (ie. Either the
double bond in the case of a cation and lone pair of electrons in the case of a isomers
negative charge) (have the same molecular formula)

H CH 3 H CH 3
+ +

H H H H
.O. - O structural isomers sterioisomers
..
..

(also known as constitutional isomers) (have the same bonding arrangement of atoms
.. but a different 3-D arrangement of atoms)
- - have a different bonding arrangement of atoms
ex.
R geometric chiral centers
R CH3
.. H2 (also know as cis/trans) (also known as steriocenters
+ OH
.O. + H3C C or Z / E or stereogenic centers)
.. H C CH3 CH
R R
H2 - occurs at an sp3 hybridized
H3C CH3
carbon with 4 different
Naming alkenes: E or Z substituents
When an alkene is tri- or tetra- substituted, E/Z nomenclature is used. To do Cl Cl
this, each substituent across the double bond is assigned a priority according enantiomers
Cis/Z Trans/E
to the Cahn-Ingold-Prelog rules: - double bonds in a ring can't F F
(i) Rank according to atomic number of attached atom (Br>Cl>O>N>C>H) have cis/trans isomers H H
CH3 H3C
(ii) If the above rule does not solve the ranking, look at 2nd, 3rd, 4th, atoms away - double bonds with 2 of the R S
to try and find a difference in atomic number same substituents on the definitions:
(iii) Multiple-bonded atoms are equivalent to the same number of single- same carbon can't have - enantiomers are
bonded cis/trans isomers sterioisomers which are
atoms ex. mirror images
- diasteriomers are
High High High Low sterioisomers which aren't
mirror images
- meso compounds have 2
can't have cis/trans isomers or more chiral centers and
- C=O's don't have a plane of symmetry making
Low Low Low High cis/trans isomers them achiral
ex. if you have a molecule
with 2 chiral centers which
Z- on the same side E- on opposite sides are R,R
- it's enantiomer would be S,S
Assigning stereochemistry to chiral centers: - it's diasteriomers would be
Æ substituents are ranked according to the Cahn-Ingold-Prelog rules (E/Z R,S or S,R
alkenes) ***NOTE*** a conformation is a rotation of a bond
Once substituents have been ranked, the lowest ranked is aimed away or a flip of the chair in cyclohexane
from the viewer (i.e. into the page). total stereoisomers = 2n (where n equals the number of chiral centers and double
- If the remaining 1st, 2nd and 3rd ranked substituents are arranged: bonds which can have cis/trans isomers)
(i) Clockwise: R Stereochemistry
(ii) Counter-clockwise S Stereochemistry

Racemic mixtures:

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Important functional groups: hv

Step 1: Initiation Cl Cl Cl + Cl

alkene alkyne Cl H CH3 Cl H + CH3

alkane Step 2: Propagation
R
O H
R H2N N R N
R OH R R
R R
alcohol ether amine R
Step 3: Termination
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Cl CH3 Cl CH3

O O
O Alkenes
Alkenes may be synthesized via alcohol dehydration
R R R OH
R H
H2SO4 or
OH
aldehyde ketone carboxylic acid H3PO4 Zaitsev's Rule:
+ E1 form most substituted double bond

O major minor
O

R or dehydrohalogenation (similar mechanism).

R NH2
R O

ester amide Addition reactions:

H a lo h y d rin
R H R R Br
Acidity Summary: B r2
Strongest acids Weakest acids
H 2O
Better leaving groups Poorer leaving groups R H
H
HO H
Weakest conjugate bases Strongest conjugate bases A n ti a n d
M a r k o v n ik o v
OH
O H H y d ra tio n : I n d u s tr ia l
O O
HI > HBr > HCl > > > ROH > > R H > > > RNH2 > RCH2
H2O R R H
R OH R H H R H H O H
R CH3 2

pka less than 1 5 10 15 20 25 30 35 35 50

H 2 S O 4 H
R H H O H
HYDROCARBONS, ALCOHOLS, AND M a rk o v n ik o v

SUBSTITUTIONS\ELIMINATIONS H y d ra tio n : O x y m e rc u ra tio n

Cyclohexane: R H R R H
H g (O A c )2
R in g -flip in c y c lo h e x a n e
D H 2 O , H
A (a x ia l) R H HO
D th e n N a B H H
C 4
M a rk o v n ik o v
B H y d ra tio n : H y d ro b o ra tio n
A (e q u a to ria l) H O H
C R H
1. B H 3 /T H F
B 2. H O /N a O H R H
2 2
R H R H
n o t e : s y n a d d it io n
1,3-Diaxial interactions (occur between A-C, C-D and A-D, on the left above) A n t i- M a r k o v n ik o v
- Result from steric strain between axial substituents 3 carbons O z o n o ly s is
apart on a ring R H
O O
- Equatorial position generally preferred to avoid 1,3-diaxial (i) O 3 /-78
+
+
interactions R H ( ii) Z n / H
R R H H

Radical Reactions:
Æ Homolytic bond breaking
An example of a radical reaction mechanism P e rm a n g a n a te C le a v a g e
O O
R H +
KMnO 4 /H
+
R R R OH
R R

Substitution/Elimination Summary:
SN2 1o > benzylic/allylic > 2o > (3o does not work)
Needs a stong nucleophile

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SN1 3o > benzylic/allylic > 2o > (1o does not work) - Look at degree of substitution of the halide, the more substituted, the greater
Weak nucleophiles will do since any nucleophile will attack a the chance
carbocation that it will undergo an SN1 or an E1
E2 Doesn’t matter what the carbon with the nucleophile is since you’re - Look at what the halide is reacting with:
pulling an H - a Nucleophile (SN2 or SN1)
Need a strong base - a Base (E2 or E1)
E1 3o > benzylic/allylic > 2o > (1o does not work) - If you have a molecule which can act as a base or a nucleophile look at the
Weak bases will do since any base will attack a carbocation double bond
that would be formed in the elimination mechanism. If it is conjugated or
H CH3
OH
H3C H
C Br
H3C H
HO C
highly
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substituted elimination will be favoured over substitution.
HO C Br
SN2 • Nucleophiles: are atoms with a lone pair of electrons. In nucleophilic
substitution they donate the pair of electrons to form a new covalent
(R)-confuguration bond.
(S)-configuration (factors listed from most important to least important)
optically
pure
optically I->Br->Cl->F-
pure CN->OH->F-
H2S>H2O
- the best nucleophiles are negatively charged (ie. OH- > H2O)
- the larger the atom the better the nucleophile (ie. I- > Br- > Cl- > F-)
SN1 H2O
ethanol H+ loss - smaller molecules are better nucleophiles than larger ones
C fast C OH + HO C CH3
C Br slow CH3

OH
-> OCH3 - > -O -
> O CH3
H2O H2O
50% (R) 50% (S)
(R)-configuration CH3 CH3
nucleophile can
optically attack from either racemic - the lower electronegativity of the atom with the lone pair, the stronger
pure face the Nu (ie. CN->OH->F)

CH3
• Leaving Groups: groups that best stabilize a negative charge (tosylate,
O
E2 H
H
iodide, bromide, chloride, acetate)
(factors listed from most important to least important)
H3C H3C CH3 - good leaving groups leave neutral
I
H - good leaving groups are stable anions (resonance stablilized)
- larger the atom bearing the negative charge the better the Lv group
(E)-alkene (I- > Br- > Cl- > F-)
anti-periplanar - more electronegative the atom bearing the negative charge the better
only
relationship of H and X
the leaving
group (F- > O- > N- > C-)
O O O

slow fast
S O R S O R S O
C C + CH3OH2+
C Br
E1 O O O

H Tosyl groups are very stable as they delocalize the negative charge
R over 3 different oxygens
CH3OH Note: halogens are good leaving groups too as they are very
electronegative, but they don’t have resonance stabilization like tosyl groups

• Bases: Are atoms with a lone pair of electrons. An atom with a lone pair
of electons can be a base or a nucleophile. By definition if an atom with a
lone pair attacks at the carbon it is a nucleophile. If it pulls a proton it is
Carbocation Stability: 3o > benzylic/allylic > 2o > 1o > methyl a base.
H - good bases are negatively charged
benzylic leaving group Lv CH 3 allylic carbon - the bigger the molecule with the lone pair the better the base and
poorer the Nu
benzylic carbon
CH 3
Nucleophile
s m a ll Nu
allylic leaving group la rg e b ase
Lv
n e g a tiv e stro n g
n e u tra l w eak

When the atom with the lone pair can act as a base or nucleophile: Grignards:
SN2 and E2 will compete and SN1 and E1 will compete.
RX + Mg RMgBr = R -
To determine the mechanism:

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A Grignard will act as a base 1st if there’s an acidic proton around (ROH, SH,
RCO2H) otherwise it acts as a Nucleophile. P C C = C rO 3 + H C l + N (w e a k o x id iz e r)
O
OH C h r o m ic A c id = H 2 C r O 4 /a c e to n e
1. R R o r K 2 C r 2 O 7 /H 2 S O 4 /a c e to n e ( s tr o n g o x id iz e rs )
R3C Mg X
R
acting as a nucleophile o r C r O 3 /H 2 S O 4 /a c e to n e
R3C
2. H3O+ R
P C C or
OH
o c h ro m ic a c id
RCO 2 H + RMgX RCO 2 -
+ RH + MgX acting as a base + 3 n o re a c tio n
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P C C or
OH
Is it an Oxidation or Reduction? 2o c h ro m ic a c id O

- oxidation is a gain of oxygen or loss of hydrogen

- reduction is gain of hydrogen or loss of oxygen
***NOTE*** treat S, I, Br, Cl and OH groups as oxygen PCC O
1o RCH 2 OH
***NOTE*** addition of HI, HBr, HCl or H-OH is not an oxidation or reduction H
since c h ro m ic a c id O
you’re adding an O and an H 1 o
RCH 2 OH
OH
Alcohols
Alkyl Halides from Alcohols Reductions:
OH Cl NaBH 4 or
S O C l2 O LiAlH 4 OH NaBH 4 and LiAlH 4 = H - (reducing agents)
P y r id in e mild strong
H H R R R R
OH Br O LiAlH 4
P B r3 RCH 2OH NaBH 4 not strong enough to do this
E th e r
R OR
H H
O LiAlH 4
RCH 2 OH NaBH 4 not strong enough to do this
Pinacol rearrangement
R OH
O
R R' O LiAlH 4
RCH 2NR NaBH 4 not strong enough to do this
H + R'
R NR
H
heat
HO OH
R CARBONYLS AND AMINES
Tosylation
CH3 CH3 CH3
pyr Nu- Carbonyl reactions:
Sn2
R OH Tos Cl Nucleophilic addition reactions
R OTos Nu R

δ−
O
Epoxide Formation δ+

R R' nucleophiles
O
RCO3H react here
These reactions produce an alcohol. Nucleophiles include H2O, CN- or RMgX

H H Wittig Reaction
H H R R' R
- + Ph
O CH 2 P R
Alkyl halide formation from ether Ph Ph

O Conjugate addition
+ HBr ROH + RBr H
O
N
R R' O

e th a n o l N
Oxidations:
O
O ) Cu Li
( 2

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The aldol condensation between two aldehydes to give a β-hydoxy aldehyde Amines
Basicity Review
OH O OH O
A base is an atom with a lone pair of electrons. The best bases are
mild base negatively charged.
NH2
O
H R H R H _ _ _ N
RCH2 > R2N +
H > OH > R3N > RNH2 > > > > ROH > NR4
R NR2

OH O O
Reductive Aminolysis www.prep101.com
aldol products can dehydrate under acidic
or basic conditions to give the conjugated product H+ (know this forward
R H R H O + H2NR N + H2O
O 1o amine and backwards)
O R
1 3
3 aldol reactions can occur intramoleuclarly to give an imine or Schiff base
H 3C 2 2
cyclic products (favouring 5 or 6 membered rings)
5 1
4
H
4 5
a s e c o n d a ry
O H a m in e H
HO N
O N
Claisen condensation is similar to the aldol reaction, with esters as the starting material
+
OH O O O H
mild base
a n e n a m in e
OEt R OEt R OEt

Hoffmann Elimination:
CH3I Ag2O
CH3(CH2)5NH2 CH3(CH2)5N(CH3)3I CH3(CH2)3CH CH2 + N(CH3)3
Michael Addition (excess) H2O, heat
O 1-Hexene (60%)
Hexylamine Hexyltrimethyl-
ammonium iodide
O O- O O- Li+
LDA
THF
Diazotization Reaction:
-78oC
N
NH2 N
H2O + HNO2 + H2SO4 HSO4 + 2 H2O

O O O
NH 2 NH 2
W o lff- K is c h n e r r e d u c tio n
O OH KOH

Carboxylic Acid Diazonium Coupling Reaction:

LiAlH 4 O O Y
R OH + H2O
alcohols CrO 3 H + /heat R O R N N HSO4 Y N (E)
O O anhydrides N
O
CrO 3 R'OH
H+
R H R OH R' + H 2O
R O where Y = OH or NR2 An azo compound
aldyhydes
R'NH 2 esters
+ carboxylic
H / H 2O acids H+ O
N
C
R R' +
H 2O
R N
nitriles H
SO Cl 2
am ides

O
O
Nu Nucleophilic acyl
substitutions
R Cl
R Nu
acid chlorides

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- Then look for the number of CH3 peaks there are (integrate for 3
BIOCHEMISTRY AND LAB TECHNIQUES protons)
- Then use all the data you’ve learned from the molecular formula,
Lipids: IR and NMR to draw possible structures. Then look at each
hydrolysis structure and compare them to the number of chemical shifts in the
O NMR and the splitting and integration observed in the NMR. The
O
structure should match the observed NMR data perfectly. If it
HO C R doesn’t it is not the correct structure. Eliminate it and look at the
O C R OH O next possible structure.
O -

O C
O
R1
1) OH in H 2 O , heat

2) H 3 O +
OH + HO C R1 www.prep101.com
O
O C R2 OH

Glycerol HO C R2
Fatty acids

Amino Acids:
O O
O

+ NH2 O HN
NH2
HO + H2O
HO NH2

R' HO R R'
R

amino acids dipeptide

Carbohydrates
H
HO
O
H H
H OH O
OH H
HO H H
OH OH
H OH
H OH
H OH

C H 2O H D -glucose

The human body can assimilate only D-fructose and D-glucose and cannot
assimilate L-fructose and L-glucose.

An Approach To Structure Determination:

1. Determine the units of unsaturation

2. Gather information from the IR spectrum
From an IR spectrum you should be able to tell if there is a C=O, O-H,
CO2H, N-H, nitrile, C=C or alkyne
- an IR is good for determining functional groups present when there
are heteroatoms in the molecular formula
- ex. If there is an O in the molecular formula the IR can tell you if it
is a ketone or aldehyde, carboxylic acid or alcohol. If none of these
peaks are observed then it is probably an ether
ex. If there is an N in the molecular formula the IR can tell
you if it is an N-H or nitrile. If neither of these peaks are
observed the N may be a tertiary amine or amide. If it
was an amide you would observe a C=O peak in the IR.

3. Gather information from the NMR spectrum

- Easy things to spot in the NMR are aromatic ring, aldehyde,
carboxylic acid and alkene.
- If there is 4 or more units of unsaturation immediately look to see if
there is an aromatic ring in the structure (peak in the NMR spectrum
between 6.8-8 ppm)

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