Eliminations (to form double bond)
Addition (to double bond)
O


Nu O
addition
elimination


H
Also in this chapter: the electron-sink
coenzymes thiamine and pyridoxal
intro
We’re used to seeing a nucleophile attack a carbonyl carbon:
H A
O
R
C
OH
R
R
:Nu
C
R
Nu
. . .but the -carbon of - unsaturated
carbonyl is also an electrophile
 carbon is electrophilic
carbonyl carbon is
electrophilic
R 

O
O
O
R
R 

R
R 

R
14.1A
Michael (conjugated) addition:
Nu:
O
R 
Nu
1
R

R 
O
Nu
R

2
O

R 
H A
R
H
The reverse: E1cb elimination
Nu
R

O

Nu
R
R

O

O
R
R


R
H
:B
14.1A
E1 and E2 mechanisms:
:B
X H
H
C C
C C
C C
E1 elimination
(see section 14.3)
:B
X H
C C
C C
E2 elimination
. . But most biological eliminations are E1cb, not E1 or E2!
HO CO2
O
oxidation
B:
1
H
OP
HO CO2
O
O
2

H
OH
HO CO2
OH

OH
OP
OH
O
O
OP
3
carbonyl
hydroxyl
HO CO2
HO CO2
O
reduction
O
4
H2C
OH
OH
hydroxyl
H2C
OH
O
carbonyl
14.1A
Note: next chapter, we’ll study electrophilic additions:
H A
C C
Nu:
H
Nu H
C C
C C
electrophilic addition to an alkene
(see section 15.2)
14.1A
Stereochemistry of alkene addition:
Nu
C C
anti addition
H
C C
Nu
H
C C
syn addition
(review:
hydroboration-oxidation
catalytic hydrogenation
addition of Br2)
A syn addition:
H
:B
H O
R
H
C C
H
HO
H
O
SCoA
R C C
H
A
HO
H
O
SCoA
HR
HS
C
C
R
O
H
SCoA
14.1B
R
H
C C
H
O
SCoA
D2O
HO
(R)
D
H
R C(S) C
O
H
SCoA
actual enzymatic product
R
(S)
H O
H C C
(R)
HO
D
SCoA
DO
(S)
H O
R C C
(S)
H
D
SCoA
D
(R)
R
H
H C(R) C
O
DO
SCoA
other possible hydration products
14.1B
Eliminations are also syn or anti:
dehydration
anti elimination
(fatty acid synthesis)
R
HR
H C C HS
(R)
O
HO
SACP
HO
HR
(S)
HS
R C C
O
H
SCoA
H
O
H
R
anti
H
C C
H
O
SACP
H
syn
O
H
R
H
C C
H
O
hydration
syn addition
(fatty acid degradation)
SCoA
Differences between synthetic and
degradative directions - common theme!
Important for regulation
14.1B
skip 14.1C
E1cb can occur with enamine intermediate:
A H
B:
HO CO2
H2O
HR
HO CO2
HO CO2
HR
H
HS
HS
O
HN
OH
OH
Lys
Lys
H 2O
H
OH
OH
OH
HN
OH
OH
CO2
CO2
O
OH
H
HN
Lys
OH
OH
14.1D
Pro-chiral ‘arms’ on citrate
CO2
HO CO2
O2C
3
2
pro-R
O2C
CO2
2
4
pro-S
3
CO2
4
OH
(2R,3S)-isocitrate
citrate
How does this happen?
HO CO2
O2C
2
3
H CO2
CO2
CO2
O2C
Hs H
R
O2C
2
3
CO2
OH
H
citrate
CO2
3
2
same proton ends up
in back!
A
(2R,3S)-isocitrate
proton is in front
14.1D
Answer: molecule flips in the active site!
H
(in front)
HO CO2
O2C
CO2
3
2
pro-R
A
4
pro-S
O2C
dehydration
2
CO2
CO2
3
4
citrate
180o flip
O2C H
O2C
4
3
H
CO2
A
(still in front)
2
OH
(2R,3S)-isocitrate
hydration
(water comes from behind)
O2C
4
CO2
CO2
3
2
14.1D
Laboratory aldol reactions often are followed by
dehydration (E1cb)
O
O
CH3
+
O
H
OH
aldol
(E1cb dehydration)
H2O
O
Robinson annulation:
Michael addition, ring-forming aldol, dehydration)
1
7
2
3
+
1
O
CH3
6
H
7
5
O
4
OH
2
6
O 5
3
4
14.1D
Double bond isomerization via Michael addition
CO2 O
O
O
CO2
cis
O
CO2
O2C
trans
14.2A
NH3
H
N
O2C
Reaction requires glutathione
O
N
O
CO2
H
SH
glutathione
(GSH)
H A
CO2

O
CO2
addition

GS H
:B
R
O

GS

SG
180o rotation
R
O
O2C
R
elimination
this bond is now free to rotate
O
O2C
R
14.2A
skip next fig (organometalic Michael additions)
go to 14.2B
Nucleophilic aromatic substitution
O
R
O
O
R
A H
H
X
X
Nu
X
R
X
Nu
aromaticity is lost!
:Nu
O
R
O
X
Nu
R
Nu
14.2B
Can also occur para to EWG
O
Nu:
R
X
O
R
Nu X
O
R
Nu
14.2B
Example: ‘tagging’ the N-terminus of proteins/peptides
R
R
O
+
F
N
H2N
O
N
O2N
O
O
H
NO2
NO2
Biosynthesis of purines DNA/RNA bases
O
N
HN
Cys
S
O
H2O
R
N
HN
HO
N
O
N
O
R
N
HN
N
H
R
14.2B
E2 and E1 eliminations
X R
concerted (E2) elimination
R C
R
R
C R
H
C C
R
R
C
R
C R
H
R
:B
X R
carbocation (E1) elimination
R
R
R
C C R
R
H
:B
14.3
Competition between SN and E
H Br H
H H H
H C C C H
H C C C H
H H H
O CH2CH3
H O H
H Br H
H
H C C
H H
C H
H
CH2CH3
H
H C C C H
H H
O CH2CH3
14.3A
Primary electrophile - SN
H H
Br
H C C C H
H H H
H H H
Br
H C C C OCH2CH3
H H H
O CH2CH3
mainly SN2 product
14.3A
2o electrophile – SN vs E competition
Weak base, more likely to act as nucleophile
H Br H
H H H
H C C C H
H C C C H
H H H
H O H
O
C
CH3
O
C
CH3
O
Strong, hindered base favors elimination
H Br H
H
H C C C H
H
H C C C H
H H H
(no SN2 product)
H H
CH3
O C CH3
CH3
(recall – Williamson ether synthesis)
14.3A
Solvolysis of tertiary electrophile leads to mix of SN and E products
H2C H
H2C H
H3C C Cl
H 3C C
CH3
CH3
SN1
H2C H
H3C C OH
CH3
SN1
H2O
HO CH2CH3
E1
H2C H
H3C C O CH2CH3
CH3
CH2
H3C C
CH3
14.3A
Regiochemistry, stereochemistry of eliminations
:B
H H H
H3C
H3C C C C H
H Cl H
H3C
H
C C
H
C C
+
H
CH3
CH3
H
(Z)-2-butene
(E)-2-butene
:B
H
H H H
H3C C C C H
H Cl H
trans> cis
H
H3C C
H
C C
H
H
1-butene
more substituted > less substituted
14.3A
skip Hoffman, Cope reactions
go to 14.3B (p. 541 middle)
In reality, E reactions can be hybrid between E1 and E2
X
 X

R
R C C R
R H
E1 intermediate
X
R
R
R C C R
R C C R
R H
R H
:B
'hybrid' E1/E2
transition state
:B
E2 transition state
14.3B
Biochemical E1/E2 reactions - notice, not adjacent to EWG
CO2
CO2
Pi
PO CO2
O C

C H

H H
PO
OH
PO
O P O

 
O
RO
O2C H H
CH2
EPSP
O
H
O C
OH
O
O
CO2

O
P
O
H
RO
O2C H H
RO
H
O2C
H
14.3B
Conjugated E1-like elimination
CO2
PO
HR
HS
CO2
CO2
O C
OH
EPSP
:B
HR
HS
CO2
H
CO2
CO2
O C
CH2
OH
O C
CH2
OH
CH2
chorismate
14.3B
Combination decarboxylation / elimination
O
X
C O
R C C R
R
C C
R
R R
R
R
OP
PPO
PPO
O
O
O
O
CO2
CO2
HO
O
O
A H
14.3B
‘Electron sink’ coenzymes
14.4
PLP-dependent reactions common in amino acid metabolism Schiff base linkages
14.4A
PLP-dependent a.a. racemization
R
H R
H3N
R H
O
O
H3N
O
L-amino acid
H3N
O
O
D-amino acid
O
R
O
H3N
O
14.4B
Notice: PLP plays role of ‘electron sink’
14.4B
14.4B
PLP-dependent decarboxylation
amino acids can racemize without PLP –
can they decarboxylate without PLP?
14.4C
PLP-dependent retro-aldol
OH

H3N

serine
CO2
O
H H
H CH2
+
H3N
CO2
glycine
H
C
H
formaldehyde
14.4D
Transaminase reactions:
as part ammonia elimination, N atoms from amino acids are transferred to Glu
CO2
CO2
H R
H3N
CO2
amino acid
H
R
+
O
CO2
-ketoglutarate
O
CO2
-ketoacid
+
H3N
CO2
glutamate
NH3 eliminated
14.4E
part 1: ammonia transferred to coenzyme
14.4E
next, ammonia is transferred to a-ketoglutarate
(exact reverse of the previous step)
(you draw the mechanism in E14.5)
14.4E
Beta elimination:
H


H3N
CO2
serine
CH3
CH2
OH
H3N
CO2
O
CO2
pyruvate
(degradation of serine)
14.4F
14.4F
B-substitution: elim followed by addition
Elimination
B:
X
H
PLP
CH2
X
N
CO2
PLP N
CO2
PLP
N
CO2
H
Nu
Addition
:Nu
A H
CH2
PLP N
CO2
PLP N
Nu
CO2
PLP
N
CO2
14.4F
synthesis of cysteine from serine is a good example
– first, make the OH a better LG:
O
OH
H
HSCoA
O
+
H3N
CO2
serine
H3C
C
O
C
CH3
H
SCoA
H3N
CO2
14.4F
elimination:
addition:
14.4F
gamma-eliminations/substitutions:
X
H 
H3N
S
H
H3N



CO2
cystathionine





H3N
CO2
CO2
CO2


NH3
H3N

+
CO2
2-aminocrotonate
HS
CO2
NH3
cysteine
14.4G
14.4G
gamma substitution
X

N

N
CO2
addition
CO2
N
PLP
PLP

H

elimination
Nu



H
-substitution
(PLP-dependent)


CO2
PLP
an example:
CO2
O
H
H3N
S
CO2
O
CO2
O-succinylhomoserine
cysteine
succinate
NH3
H
H3N
CO2
cystathionine
14.4G
changing a racemase to a (retro-)aldolase
H 3C H
H CH3
H3N
CO2
racemase
(wild-type)
HO
H3N
H3N
CO2
H H
CO2
retroaldolase
(mutant)
+
H3N
CO2
O
H
14.4H
His
racemase
(wild-type)
O
HN
N:
H
Tyr
H CH3
N
CO2
PLP
His
retroaldolase
(mutant)
HN
N:
H
H3C
O
Ala
N
CO2
PLP
14.4H
Thiamine
thiazole ring
H
S
NH2
N
N
PPO
CH3
N
CH3
thiamine diphosphate (TPP)
14.5
The benzoin condensation
O
O
C
NaOH, thiamine
H + H C
C
C
HO H
O
benzoin
2 benzaldyhyde
What is the nucleophile?
14.5A
O
C:
O
???
H
C
C
HO H
C
O
H A
???
not acidic!
O
C
O
C:
H
:B
X
14.5A
R
H3C
R
H3C
N
N
H
S
R
OH
R
S
thiazole ylide
HO H
R
O
C
H 3C
H
H3C
R
N
not acidic
H3C
O
C
1
R
N
R
H
R
S
acidic!
N
R
OH
O
C
2
H
H
S
Now this carbon is a
nucleophile!
S
R
H3C
N
H
O
C
R
S
14.5A
B:
R
H3C
N
R
H
H3C
O
C
R
R
H3C
O
C Ph
3
S
N
R
H
S H C Ph
N
4
S
R
OH
H
+
O
C
C Ph
O
H
A
H C Ph
OH
benzoin
14.5A
Transketolase - a TPP-dependent reaction
OH
O
OH
O
O
HO
OH
+
OH
OP
xylulose-5phosphate
HO
OH
OH
O
+
OH
OH
OP
OP
ribose-5phosphate
glyceraldehyde-3phosphate
OH
OH
OP
sedoheptulose-7phosphate
14.5B
O
OH
O
OH
B:
O
=
C
C
???
H H
+
H O
HO
O
OH
OH
OP
OP
hypothetical carbonyl-anion
intermediate
This is the same carbanion intermediate as in the benzoin condensation!
OH
OH
O
A H
O
HO
O
OH
OH
OH
OH
OH
OH
OP
OP
14.5B
R
H3C
R
B:
N
R
OH
S
H3C
HO
H
O
N
OP
O
1
OH
OP
S
R
OH OH
OH
H A
2
R
B:
R
CH3
H S
OH O
OH
R
OH
O
N
OH
OP
+
N
PO
OH
H3C
3
R
OH
OH
S
OH
OH
OH
PO
H
4
OH
OH
OH
O
H
O
A
PO
OH
OH
OH
14.5B
TPP-dependent decarboxylation
CO2
O
H3C
O
pyruvate
O
O
H3C
H
acetaldehyde
(you get to draw the mechanism as an exercise)
14.5C
A TPP mimic in the lab: dithianes
O
R
C
H
H
+ H C
I
H
R
R
H
+
R
C
C
CH3
O
O
O
C
O
R
R
C
C
OH
R R
O
R
C
not acidic
H
+
slightly acidic
H+
HS
SH
1,3-dithiol
S
S
C
R
H
1,3-dithiane
14.5D
H
A
O
S
S
S
strong base
C
R
H
1,3-dithiane
R
S
R
C
C
R
S
R
CH3
S
R
C
OH
CH3I H3O+
O
N R
C
C
R R
equivalent to carbonyl anion
intermediate in TPP reactions
R
S
R
C
C
OH
R R
14.5D
OTs
6
5
1
CH3
2
CH3
+
3
4
H3C C O
E2
1
4
CH3
2
3
CH3
CH3
OTs
6
5
CH3
+
CH3
+
H 3C C O
CH3
CH3
E2
X
(only)
CH3
(not observed)
14.6A
Stereochemical constraints
X
X

sp3 orbitals are coplanar
(plane of the page)
=

H
X
H


H
X:
:B
X

X
X

=

H
p orbitals in  bond are
always parallel
=

X
XH
H
=
 


H
anti elimination
syn elimination




14.6A
X
X

H

X
=
H
 
(no E2 possible from this conformation)


Br
H
H3C
H
H
H
H
H3C
H
H
14.6A
OTs
5
4
6
3
1
2
CH3
E2
CH3
H
OTs
CH3
E2
CH3
H
14.6A
CH3
H
H3C
4
H
6
5
2
3
H
OTs
1
XE2
X
CH3
C-H bonds are not
coplanar with C-OTs bond!
(no E2 possible)
OTs
6
1
2
Hb
1
6
(only one possible E2
E2
Ha
CH3
Hb product)
2
CH3
Ha (on C6) is coplanar to leaving group
Hb (on C2) is not coplanar to leaving group
14.6A
14.6B