for the first time: carbon nucleophiles, leaving groups
breaking / forming carbon-carbon binds
E
O
O:
C
carbanion nucleophile
R C CR
3
R
R
C
+ :CR3
R
carbanion leaving group
intro
carbon Nu, LG in biological reactions are usually enolates:
O
R
O
CR2
R
O:
CR2
H
R
CR2
enolate ion
:B
sometimes, carbon nucleophiles are from alkenes
(electrophilic addition)
E
C C
Keto-enol tautomerization
tautomers: different consitutional isomers in rapid equilibrium
O
O
H3C
C
H3C
CH3
keto form of acetone
R
R H
keto
B
O
O:
R
R
CH2
enol form of acetone
H
O
C
H
:B
R
R
enolate
H
R
R
R
enol
13.1A
usually, keto form predominates, but there are exceptions:
H
O
O
keto form (24%)
O
O
enol form (76%)
13.1A
imine – enamine tautomerization
N H
N:
C
C
C
H
C
enamine
imine
eg: degration of serine:
NH2
O
H
A
NH2
O
CH3
CH2
O
enamine
O
imine
H2O
NH3
O
O
CH3
O
pyruvate
13.1B
Isomerization reactions
carbonyl isomerization: triose-phosphate isomerase
H A
:B
O
OH
PO
OH
HS
PO
3
2
HR
O
1
H
H
:B
DHAP
(ketone)
HO H
H A
ene-diol
PO
O
H
GAP
(aldehyde)
13.2A
OH
OP
OH
OH
O
OH
glucose-6-phosphate
OH
OP
OH
OH
OH
O
fructose-6-phosphate
13.2A
stereoisomerization: racemization
OH
PO
O
4 (R) 2
3
5
OH
OH
PO
HO H
xylulose-5-phosphate
ribulose-5-phosphate
Zn
PO
OH
(S)
1
HO H
OH
O
Zn
O
OH
OH
3
Zn
OH
O:
PO
OH
O
PO
OH
1
6
HO H
HO H
OH
O
H
O
Asp1
O
O
Asp2
13.2B
The aldol reaction
(carbon-carbon bond forming)
what happens to an enolate?
It can go to the enol (oxygen acts as base):
H
A
OH
O:
R
R
R
R
R
R
enolate
enol
13.3A
it can go back to the keto (carbon acts as base):
O:
O
H A
R
R
R
R
R
R
enolate
O
R
R
H R
keto
. . .or carbon can act as a nucleophile
O
O
O
R
C
R
R
R
R
C
R
C
H
A
OH
R
R
C R
O
R
R
C
R
O
=
R
R
R OH
C
C
R
R R
on the electrophilic side of the picture, this is just a carbonyl addition!
13.3A
the ‘classic’ aldol reaction: self-condensation of an aldehyde
A
H
O
H
O
H
R
H
R H
aldehyde
R
R H
O:
C
C
C
R
alcohol
O
R
H
H OH
C
R
C
R R H R
:B
13.3A
best-studied biochemical aldol reaction: fructose 1,6bisphosphate aldolase
new C-C bond
OH
OH
OH
OP
OH
OP
+
OP
GAP
O
O
DHAP
OP
OH
O
fructose-1,6-bisphosphate
13.3B
‘class II’ aldolase: enolate stabilized by Zn2+
H OH
OH
OP
OP
H
H
B:
O
O:
Zn
Zn
new stereocenter
OH
OP
OH
OH
OP
H
OH
O:
H
Zn
OP
OH
O
Zn
OP
O
H A
13.3B
‘Class I aldolase: enamine intermediate rather than enolate
first, Schiff base (imine) forms with enzyme lysine:
OH
OP
H2O
O
NH3
enz
OH
OP
N
enz
13.3B
H
OH
OH
OP
H
H
B:
OP
H A
N
enz
NH
enz
enamine
13.3B
OH
OP
OH
OH
OP
H2O
OH
OH
OP
NH
H
OP
OH
OP
OH
OP
NH
OH
O
NH3
enz
O
enz
enz
H A
13.3B
eg: methanotrophs incorporating (toxic) formaldehyde:
OH
O
PO
OH
O
PO
OH
+
H
OH
H
HO H
HO H
ribulose-5-phosphate
O
formaldehyde
OH
hexulose-6-phosphate
draw the key enamine intermediate!
13.3B
thioesters, esters can also be the nucleophilic half of an aldol reaction:
:A
H A
B:
H
O
H
C
O2C
O
SCoA
H2C
H H
O2C
SCoA
SCoA
O
OH O
H A
CO2
CO2
(but electrophilic half must be aldehyde-ketone – if it’s a thioester or ester, something else happens!
13.3B
aldol reactions are reversable: retro-aldol
fructose 1,6,-bisphosphate in reverse (sugar-breaking) direction:
OH
OH
OP
OH
OH
OP
+
OP
OH
O
OP
fructose-1,6-bisphosphate
OH
OH
O
DHAP
GAP
OH
OP
O
H A
OP
OH
OH
OP
+
OP
O
O
H
Zn
OP
O
O:
O
Zn
B:
13.3C
recognizing a potential retro-aldol:
look for alcohol b to carbonyl (or imine)
:B
O
R
H
???
R
no retro-aldol possible! Leaving
group is unstabilized carbanion.
O
X
+
R
R
13.3C
here, OH is b to imine:
:B
H
H
A
N
H
(enamine)
(
t
r
y
p
t
OH
OP
OH
O
H
tautomerization
OP
OH
N
H
(imine)
H
O
OP
+
N
H
OH
13.2C
transaldol reactions: retro followed by forward
OH
OH
O
O
HO
O
+
OH
OH
OH
OH
OP
OP
fructose-6phosphate
erythrose-4phosphate
HO
O
OH
+
OP
glyceraldehyde3-phosphate
OH
OH
OH
OP
sedoheptulose-7phosphate
13.3D
imine link to
active site lysine
OH
N
OH
N
Lys H A
HO
Lys
H
HO
retroaldol
O H
OH
:B
OP
fructose-6-phosphate
O
OH
OP
glyceraldehyde3-phosphate
released from
active site
OH
N
HO
Lys
N
H
aldol
O
enters active site
OH
OH
H
OH
OH
OP
erythrose4-phosphate
A
HO
H
O
Lys H2O
HO
OH
OH
OH
OH
OH
OH
OP
OP
sedoheptulose-7phosphate
13.3D
Claisen reaction
enolate nucleophile, carboxylic acid derivative as electrophile
O
O:
R
R
O
X
R
R O:
X
O
R
O
R
new carboncarbon bond
from the electrophile side, this is an acyl transfer reaction!
13.4
eg. early cholesterol biosynthesis:
condensation of two acetyl CoA units
O
HSCoA
O
SCoA
O:
O
Cys
1
SCoA
S
SH
SCoA
2
H
B:
Cys
3
O:
O
O
SCoA
S
4
O
SCoA
Cys
13.4A
Claisens can also go backward (retro-Claisen)
key to recognition: look for b-keto (thio)ester!
eg. fatty acid degradation: first, b-keto group is introduced:
O
R
b

O
3 steps
SCoA
R
b
O

SCoA
fatty acyl CoA
(we’ll see these reactions later)
13.4B
O
O
R
SCoA
H
B:
O
R
O
O
SCoA
S
R
O:
S
SCoA
Cys
Cys
H
A
S
HSCoA
Cys
fatty acid has lost two
carbons
O
O
R
SCoA
SCoA
acetyl CoA
. . .just an acyl substitution reaction with a carbanion (enolate) LG!
13.4B
another example: (degradation of Tyr/Phe)
:B
H
O
H
H
O2C
CO2
O
O
O2C
CO2
O
O
Mg2+
O
Mg 2+
O2C
O
CO2
+
O
O
13.4B
occasionally, enol/enolate can attack in SN2 fashion:
H
:B
O
O
H3C
CO2
H
N
H
CO2
R
C
S
H H
SAM
R
N
H
in lab synthesis, alkyl halide (eg. CH3I) is used – we’ll see this soon
13.4C
Carboxylation:
aldol, with CO2 as electrophile:
Rubisco (carbon fixation by plants, some bacteria):
Mg
OH
PO
O
4
OP
2
1
5
HO H
OH
step 1
:B
ribulose-1,5-bisphosphate
Mg
O
PO
OH
OP
step 2
OH
PO
O
OP
O
O
C
H
O
step 3
OP
OH
PO
OH
CO2
O
13.5B
. . .second part of Rubisco reaction:
OP
OH
H2O
OH
PO
OH
OH
PO
O
O
+ PO
O
step 4
O
O
O
O
phosphoglycerate
notice: retro-Claisen!
13.5B
Decarboxylation
O
b carbonyl group
O
O
O
+
R
O
R
C
CH2
H
O
A
O
R
OH
R
O
X
+
R
CH2
O
O
OH
O
CH3
C
R
O
O
O
no decarboxylation!
CO2 is NOT the leaving group!
13.5C
examples:
O
O
CO2
O2C
O2C
CO2
CO2
CO2
CO2
OH
OH
CO2
O
O
OH
OH
OH
OH
OP
OP
13.5C
decarboxylation of imine:
Lys
Lys
H2O
O
CO2
N
CO2
N
H2O
O
CO2
13.5C
variation: decarboxylation (to form enolate), followed by Claisen
O
S
ACP
CO2
O
O
O
O
S
ACP
(ACP = acyl carrier protein)
:O
S
ACP
S O
ACP
S
O
ACP
O
S
ACP
(fatty acid biosynthesis)
13.5C
what’s happening here?
CO2
CO2
CO2
CO2
O
O
HO
O
(biosynthesis of Tyrosine)
13.5C
Carbanion reactions the lab
acetoacetic acid synthesis:
O
O
O
1) NaOCH2CH3
3) NaOH (aq)
2) R Br
4) HCl (aq)
O
R
NaBr
+ CO2
2 EtOH
malonic ester synthesis:
O
EtO
O
O
OEt
1) NaOCH2CH3
3) NaOH (aq)
2) R Br
4) HCl (aq)
HO
NaBr
R + CO2
3 EtOH
you get to write out the mechanisms!
13.6A
skip to section 13.6C
more carbon nucleophiles in the lab
another way to make a carbon nucleophile: deprotonate a
terminal alkyne:
pKa ~ 19
Na
R
C C H
Na+ NH2:NH3 (l)
R
R C C CH2R
C C:
R
Na Br
H C Br
H
then, can make cis / trans alkenes:
R
H
C C
R
H
CH2R
R C C CH2R
H
C C
CH2R
H
13.6C
The Grignard reaction
H
C Br + Mg(0)
R
H
C
O
R2
C
O
R1
R3
MgBr
H
H
H
C MgBr +
reacts like R
R C MgBr
H
R1
H
H
C
R2
H+
R3
R1
OH
C
R2
(plus enantiomer)
R3
13.6B
OH
O
Br
MgBr
H3C
+ Mg(0)
C
CH3
H+
C
CH3
CH3
O
MgBr
CO2
H+
C
OH
13.6D
Grignard plus epoxide:
1)
MgBr
OH
O
CH3
+
2) H3O+
CH3
Grignards react twice with esters, acid chloride
O
H3C
C
O
MgBr
O
CH3
+2
H3C
C
+ CH3O
OH
H3C C
O
H3O+
H 3C C
question: what about Grignard plus carboxylic acid?
13.6B