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MCAT Organic Equation Sheet

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MOLECULAR STRUCTURE

Hybridization:
an atom is SP
3
hybridized if it contains only single bonds (tetrahedral
geometry) 109.5
o
an atom is SP
2
hybridized if it contains 1 double bond (trigonal geometry) 120
o
an atom is SP hybridized if it contains 2 double bonds or 1 triple bond (linear,
180
o
)
***NOTE*** this only works for neutral atoms a carbocation is sp
2
hybridized

Determining formal charge: # of electrons an atom wants (4 for C, 5 or N, 6
for O) (# of bonds and each electron in a lone pair)
a single bond has 1 o bond
a double bond has 1 o bond and 1 t bond
a triple bond has 1 o bond and 2 t bonds

Resonance:
- occurs when theres o,|-unsaturation next to an atom with a charge or an
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
negative charge)

CH
3
H
H H
+
H CH
3
H H
+
O
O
. .
. .
. .
. .
.
.
. .
.
.
-
-
OH
R
R
+
+ O
R
R
H


Naming alkenes: E or Z
When an alkene is tri- or tetra- substituted, E/Z nomenclature is used. To do
this, each substituent across the double bond is assigned a priority according
to the Cahn-Ingold-Prelog rules:
(i) Rank according to atomic number of attached atom (Br>Cl>O>N>C>H)
(ii) If the above rule does not solve the ranking, look at 2
nd
, 3
rd
, 4
th
, atoms away
to try and find a difference in atomic number
(iii) Multiple-bonded atoms are equivalent to the same number of single-
bonded
atoms


High
Low
High
Low
Low
High
High
Low
Z- on the same side E- on opposite sides


Assigning stereochemistry to chiral centers:
substituents are ranked according to the Cahn-Ingold-Prelog rules (E/Z
alkenes)
Once substituents have been ranked, the lowest ranked is aimed away
from the viewer (i.e. into the page).
- If the remaining 1
st
, 2
nd
and 3
rd
ranked substituents are arranged:
(i) Clockwise: R Stereochemistry
(ii) Counter-clockwise S Stereochemistry

Racemic mixtures:
equal (50:50) mixtures of two enantiomers; often denoted by (+/-)
Enantiomers have identical physical properties but diastereomers do not.

Meso compounds- molecules that have at least 2 stereocentres BUT are
achiral
because they have a plane of symmetry.

Fischer Projections:
A
C
B D
A
C
D B =

- most highly oxidized group at the top (position A)
- longest carbon chain is vertical (A to C)
- Can rotate 180 but not 90 or 270
- Can hold one substituent in place then rotate others either clockwise or
counter-c.w.

isomers
(have the same molecular formula)
structural isomers
(also known as constitutional isomers)
- have a different bonding arrangement of atoms
ex.
H
3
C
C
H
2
H
2
C
CH
3
H
3
C
CH
CH
3
CH
3
sterioisomers
(have the same bonding arrangement of atoms
but a different 3-D arrangement of atoms)
geometric
(also know as cis/trans)
or Z / E
Cis/Z Trans/E
***NOTE*** a conformation is a rotation of a bond
or a flip of the chair in cyclohexane
- double bonds in a ring can't
have cis/trans isomers
- double bonds with 2 of the
same substituents on the
same carbon can't have
cis/trans isomers
ex.
can't have cis/trans isomers
chiral centers
(also known as steriocenters
or stereogenic centers)
- occurs at an sp3 hybridized
carbon with 4 different
substituents
Cl
H
F
CH
3
Cl
H
F
H
3
C
R S
enantiomers
- C=O's don't have
cis/trans isomers
definitions:
- enantiomers are
sterioisomers which are
mirror images
- diasteriomers are
sterioisomers which aren't
mirror images
- meso compounds have 2
or more chiral centers and
a plane of symmetry making
them achiral
ex. if you have a molecule
with 2 chiral centers which
are R,R
- it's enantiomer would be S,S
- it's diasteriomers would be
R,S or S,R
total stereoisomers = 2
n
(where n equals the number of chiral centers and double
bonds which can have cis/trans isomers)


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Important functional groups:
R OH R
O
R
R H
2
N
R
H
N
R
R
N R
R
R H
O
R
O
R
R
O
OH
R
O
O
R
R
O
NH
2
alkane
alkene
alkyne
alcohol ether amine
aldehyde ketone
carboxylic acid
ester amide


Acidity Summary:
HI HBr HCl
O
OH R
OH
R H > >
> >
> > > >
O
H R
> >
H
H
RNH
2
RCH
2
ROH
H
2
O
CH
3
R
O
>
pka less than 1 5 10 15 20 25 30 35 35 50
Poorer leaving groups
Better leaving groups
Strongest acids Weakest acids
Strongest conjugate bases Weakest conjugate bases

HYDROCARBONS, ALCOHOLS, AND
SUBSTITUTIONS\ELIMINATIONS

Cyclohexane:
C
A (axial)
B
D
B
C
D
A (equatori al)
Ring-flip in cyclohexane

1,3-Diaxial interactions (occur between A-C, C-D and A-D, on the left above)
- Result from steric strain between axial substituents 3 carbons
apart on a ring
- Equatorial position generally preferred to avoid 1,3-diaxial
interactions

Radical Reactions:
Homolytic bond breaking
An example of a radical reaction mechanism
Cl Cl +
Cl
hv
H CH
3 Cl H
+ CH
3
CH
3
Cl Cl CH
3
Step 1: Initiation
Step 2: Propagation
Step 3: Termination
Cl Cl


Alkenes
Alkenes may be synthesized via alcohol dehydration

OH
major minor
+
Zaitsev's Rule:
form most substituted double bond
E
1
H
2
SO
4
or
H
3
PO
4

or dehydrohalogenation (similar mechanism).

Addition reactions:
H a l o h y d r i n
R
R H
H
B r
2
B r
H O
H
2
O
A n t i a n d
M a r k o v n i k o v
R
R
H
H

R
R H
H
H O H
2
H
2
S O
4
M a r k o v n i k o v
H y d r a t i o n : I n d u s t r i a l
H
H O
R
R
H
H

H g ( O A c )
2
R
R H
H
H
2
O ,
t h e n N a B H
4
H
H
R
R
H
H O
M a r k o v n i k o v
H y d r a t i o n : O x y m e r c u r a t i o n

R
R
H
H
2 . H
2
O
2
/ N a O H
H
H
O H
R
R
H
1 . B H
3
/ T H F
n o t e : s y n a d d i t i o n
A n t i - M a r k o v n i k o v
H y d r a t i o n : H y d r o b o r a t i o n

R H
H R
(i) O
3
/-78
R R H H
O O
R H
R R
KMnO
4
/H
+
R R
O
P e r m a n g a n a t e C l e a v a g e
( i i ) Z n / H
+
+
+
O z o n o l y s i s
R OH
O


Substitution/Elimination Summary:
SN
2
1
o
> benzylic/allylic > 2
o
> (3
o
does not work)
Needs a stong nucleophile
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SN
1
3
o
> benzylic/allylic > 2
o
> (1
o
does not work)
Weak nucleophiles will do since any nucleophile will attack a
carbocation
E
2
Doesnt matter what the carbon with the nucleophile is since youre
pulling an H
Need a strong base
E
1
3
o
> benzylic/allylic > 2
o
> (1
o
does not work)
Weak bases will do since any base will attack a carbocation
C Br
H
3
C
H
OH
C
H
3
C
H
Br HO
C
CH
3
H
HO
(R)-confuguration
(S)-configuration
optically
pure
optically
pure
SN
2
SN
1
E
1
C Br
C
H
2
O H
2
O
C OH
C HO +
H
2
O
ethanol
nucleophilecan
attack fromeither
face
(R)-configuration
50%(R) 50%(S)
racemic
optically
pure
H
+
loss
slow fast
E
2
H
I
CH
3
H
H
3
C
O
H
3
C CH
3
H
anti-periplanar
relationship of H and X
(E)-alkene
only
C Br
C
C
H
CH
3
OH
+ CH
3
OH
2
+
slow
fast


Carbocation Stability: 3
o
> benzylic/allylic > 2
o
> 1
o
> methyl
Lv CH
3
H
benzylic carbon
benzylic leaving group
CH
3
Lv
allylic leaving group
allylic carbon


When the atom with the lone pair can act as a base or nucleophile:
SN
2
and E
2
will compete and SN
1
and E
1
will compete.

To determine the mechanism:
- Look at degree of substitution of the halide, the more substituted, the greater
the chance
that it will undergo an S
N
1 or an E1
- Look at what the halide is reacting with:
- a Nucleophile (S
N
2 or S
N
1)
- a Base (E2 or E1)
- If you have a molecule which can act as a base or a nucleophile look at the
double bond
that would be formed in the elimination mechanism. If it is conjugated or
highly
substituted elimination will be favoured over substitution.

- Nucleophiles: are atoms with a lone pair of electrons. In nucleophilic
substitution they donate the pair of electrons to form a new covalent
bond.
(factors listed from most important to least important)
I
-
>Br
-
>Cl
-
>F
-

CN
-
>OH
-
>F
-

H
2
S>H
2
O
- the best nucleophiles are negatively charged (ie. OH
-
> H
2
O)
- the larger the atom the better the nucleophile (ie. I
-
> Br
-
> Cl
-
> F
-
)
- smaller molecules are better nucleophiles than larger ones

OH > OCH
3
O
CH
3
CH
3
-
- - -
> >
O
CH
3
CH
3
CH
3

- the lower electronegativity of the atom with the lone pair, the stronger
the Nu (ie. CN
-
>OH
-
>F)

- Leaving Groups: groups that best stabilize a negative charge (tosylate,
iodide, bromide, chloride, acetate)
(factors listed from most important to least important)
- good leaving groups leave neutral
- good leaving groups are stable anions (resonance stablilized)
- larger the atom bearing the negative charge the better the Lv group
(I
-
> Br
-
> Cl
-
> F
-
)
- more electronegative the atom bearing the negative charge the better
the leaving
group (F
-
> O
-
> N
-
> C
-
)
S
O
O
O S
O
O
O R
S
O
O
O R
R
Tosyl groups are very stable as they delocalize the negative charge
over 3 different oxygens

Note: halogens are good leaving groups too as they are very
electronegative, but they dont 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
a base.
- good bases are negatively charged
- the bigger the molecule with the lone pair the better the base and
poorer the Nu

Nucleophile

s m a l l N u
l a r g e b a s e
n e g a t i v e s t r o n g
n e u t r a l w e a k


Grignards:
RX + Mg RMgBr = R
-

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A Grignard will act as a base 1
st
if theres an acidic proton around (ROH, SH,
RCO
2
H) otherwise it acts as a Nucleophile.
R
O
R
R
3
C
OH
R
R
R
3
C Mg X

1.
2. H
3
O
+
acting as a nucleophile

RCO
2
H + RMgX RCO
2
-
+ RH + MgX
+
acting as a base


Is it an Oxidation or Reduction?
- 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
***NOTE*** addition of HI, HBr, HCl or H-OH is not an oxidation or reduction
since
youre adding an O and an H

Alcohols
Alkyl Halides from Alcohols
O H
H
O H
H
C l
H
B r
H
S O C l
2
P y r i d i n e
P B r
3
E t h e r


Pinacol rearrangement
R R'
HO OH
heat
O
H
R'
R
H
+

Tosylation
pyr
R OH
CH
3
Tos Cl
R OTos
CH
3
Nu
-
S
n
2
Nu R
CH
3


Epoxide Formation

H
R' R
H
R R'
O
H H
RCO
3
H


R
O
R'
+ HBr ROH + RBr
Alkyl halide formation from ether



Oxidations:
N
PCC = CrO
3
+ HCl +
or K
2
Cr
2
O
7
/H
2
SO
4
/acetone ( str ong oxidizers)
or Cr O
3
/H
2
SO
4
/acetone
Chr omic Acid = H
2
Cr O
4
/acetone
(weak oxidizer)
OH
OH
RCH
2
OH
O
RCH
2
OH
H
O
OH
O
PCC or
c hrom ic ac id
PCC or
c hrom ic ac id
3
o
2
o
1
o
no reac tion
1
o
chrom ic aci d
PCC

Reductions:
R NR
O
R OH
O
R OR
O LiAlH
4
LiAlH
4
LiAlH
4
RCH
2
OH
RCH
2
OH
RCH
2
NR
R R
OH
R R
O
NaBH
4
or
LiAlH
4
NaBH
4
and LiAlH
4
= H
-
mild strong
(reducing agents)
NaBH
4
not strong enough to do this
NaBH
4
not strong enough to do this
NaBH
4
not strong enough to do this


CARBONYLS AND AMINES

Carbonyl reactions:

Nucleophilic addition reactions

O
nucleophiles
react here
o
o+

These reactions produce an alcohol. Nucleophiles include H
2
O, CN
-
or RMgX

Wittig Reaction
+ -
O CH
2
P
Ph
Ph
Ph
R
R

Conjugate addition
O
H
N O
N e t h a n o l
O
O
Cu Li )
(
2

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R
O
H
OH
H
O OH
H
H
R
mild base
The aldol condensation between two aldehydes to give a |-hydoxy aldehyde
O
H R
O
H R
OH
aldol products can dehydrate under acidic
or basic conditions to give the conjugated product
O
H
O
H
3
C
O
HO
H
1
2
3
4
5 1
2
3
4 5
aldol reactions can occur intramoleuclarly to give
cyclic products (favouring 5 or 6 membered rings)
R
O
OEt
OH
OEt
O O
OEt R
mild base
Claisen condensation is similar to the aldol reaction, with esters as the starting material


Michael Addition
O
O
LDA
THF
-78
o
C
O
-
O
-
Li
+
O
H
2
O
OH
O
O
O


Carboxylic Acid
R
O
OH
R OH
R
O
R
C
N
H
CrO
3
CrO
3
H
+
/ H
2
O
LiAlH
4
R
O
O
R
O
O
R
O
N
H
R
O
R'
R'
H
+
/heat
R'OH
H
+
R'NH
2
H
+
H
2
O
H
2
O
H
2
O
+
+
+
alcohols
aldyhydes
nitriles
anhydrides
esters
amides
carboxylic
acids
R
O
Cl
SOCl
2
acid chlorides
R
O
Nu
Nu
Nucleophilic acyl
substitutions


Amines
Basicity Review
A base is an atom with a lone pair of electrons. The best bases are
negatively charged.
RCH
2
_
_
R
2
N > R
3
N > RNH
2
>
N
NH
2
> >
O
R NR
2
> ROH > NR
4
+
> OH >
_

O
H
+
N
R
Reductive Aminolysis
+ H
2
NR
1
o
amine
+ H
2
O
(know this forward
and backwards)
an imine or Schiff base


O
H
N
N
H
+
a s e c o n d a r y
a m i n e
a n e n a m i n e



Hoffmann Elimination:
CH
3
(CH
2
)
5
NH
2
CH
3
I
(excess)
CH
3
(CH
2
)
5
N(CH
3
)
3
I
Ag
2
O
H
2
O, heat
CH
3
(CH
2
)
3
CH CH
2
+ N(CH
3
)
3
1-Hexene (60%)
Hexyltrimethyl-
ammonium iodide
Hexylamine


Diazotization Reaction:
NH
2
+ HNO
2
+ H
2
SO
4
N
N
HSO
4
+ 2 H
2
O

O
NH
2
NH
2
KOH
W ol ff - Ki schner r educti on


Diazonium Coupling Reaction:
N N HSO
4
Y
N
An azo compound where Y = OH or NR
2
N
(E)
Y










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BIOCHEMISTRY AND LAB TECHNIQUES

Lipids:
hydrolysis
O
O
O
C
C
C
O
O
O
R
2
R
1
R
1) OH
-
in H
2
O, heat
2) H
3
O
+
OH
OH
OH
+
C
O
R HO
C
O
R
1
HO
C
O
R
2
HO Glycerol
Fatty acids


Amino Acids:
HO
O
NH
2
R
HO
O
NH
2
R'
HO
O HN
R
O
NH
2
R'
+
+ H
2
O
amino acids dipeptide


Carbohydrates
H
O
H OH
H HO
OH H
OH H
CH
2
OH
O
HO
H
H
OH
OH
H
H
OH
H
OH
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,
CO
2
H, 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)
- Then look for the number of CH
3
peaks there are (integrate for 3
protons)
- Then use all the data youve learned from the molecular formula,
IR and NMR to draw possible structures. Then look at each
structure and compare them to the number of chemical shifts in the
NMR and the splitting and integration observed in the NMR. The
structure should match the observed NMR data perfectly. If it
doesnt it is not the correct structure. Eliminate it and look at the
next possible structure.