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Chem 215-216 HH W11 Notes – Dr. Masato Koreeda - Page 1 of 14. Date: April 14, 2011
Chapter 16-2: Acidity and Basicity of Polyfunctional Compounds I. Polyprotic acids Diprotic acid
O O H
O
O
H
oxalic acid(found in spinach)
pKa1 1.27; pKa2 4.27
O O H
O
O
O OO
OH
inductively electrons are pushed toward
the C(=O)OH?
stabilized by an intra-molecular H-bonding
less acidic than thefirst C(=O)OH
also,
considerably more acidicthan usual R-C(=O)OH
H O O H
O
Osuccinic acid
(found in amber, fossil, and fungi)
pKa1 4.21; pKa2 5.64 O O HH OH
HO
O
OHH(+)-tartaric acid(a byproduct inwine making)
pKa1 2.93; pKa2 4.23
O OH O
HO
O
OHH
H
low pKa1 due to the H-bonding of theconjugate base?
Acidity Constant (pKa)
AH + H2O A- + H3O+Ke
€
Ke =(aA−)(aH3O+)(aAH)(aH2O)
(aX) : activity of each species; Ke : equilibrium constant
At low concentrations, (aH2O) ≈ constant.
Therefore, Ka’ = Ke• (aH2O) =
€
(aA−)(aH3O +)(aAH)
=
€
[A−][H3O+][AH] where Ka
’ : (thermodynamic) acidity constant
[X] : concentration of each species; f : activity coefficient, i.e., (aX) = fX • [X] This equation can be approximated as follows in a dilute solution:
Ka’ ≈
€
[A−][H3O+][AH]
= Ka Ka = acidity constant
pKa = - log Ka thus, smaller pKa → stronger acid
pH vs. pKa
Since pH = - log [H+] = log
€
1[H+]
, note: [H+] = [H3O +]
Ka =
€
[A−][H3O+][AH]
can be transformed into pKa = log
€
[AH][A−]
+ pH
Note: The pH of a solution can be adjusted by adding an acid or base.
Chem 215-216 HH W11 Notes – Dr. Masato Koreeda - Page 2 of 14. Date: April 14, 2011
16.2: pKa (cont’d)
succinic aicd
H O O H
O
O
HO
OO
OO OO
O
OH OH
H3O H3O
diacid - at low pHs mono anion(mono carboxylate)at intermediate pHs
dianion (dicarboxylate)at high pHspH << 4.21
~ pH 4.8 pH >> 5.64
16.2; 23.3 Amino Acids and Isoelectric Point (pI)
H3N O H
H R
Oα H3N O
H R
Oα H2N O
H R
OαOH
H3O
OH
H3O
pKa ~1.8-2.6
pKa 8.8-10.3
stronger acid than normal R-C(=O)OHdue to the presence
of the α-NH3+
at verylow pHs
net charge: +1 net charge: 0 net charge: -1
at very high pHsdipolar ionor Zwitter ion
Chem 215-216 HH W11 Notes – Dr. Masato Koreeda - Page 3 of 14. Date: April 14, 2011
(2) Alternatively, a titration curve may be used to determine the pI
[taken from Wade, L. G., Jr. “Organic Chemistry” 5th edition, Prentice Hall, 2003]
(3) Lysine
Chem 215-216 HH W11 Notes – Dr. Masato Koreeda - Page 4 of 14. Date: April 14, 2011
15.8, 23.6: Chemical Synthesis of Peptides Peptides: Any polymer of amino acids linked by amide bonds between the amino group of each amino acid and the carbonyl group of the neighboring amino acid.
Polypeptide: A peptide containing many amino acid residues, but usually having a molecular weight of less than about 5,000. Proteins: Mw 6,000-40,000,000 Oligopeptides: Peptides containg about 4 – 10 amino acid residues.
OO
H3CNH3H
OO
HNH3H
alanine glycine
H3N NH
O
H CH3
O H H
O
H3N NH
O
H H
O CH3H
O
amide group
S
S
S
alanylglycine
glycylalanine
amide group
+peptide linkage
?
?
(1) Introduction
N-terminus C-terminus
Synthesis of peptides:
i. Formation of amide bonds between the amino group of one amino acid (A.A.) and the COOH group of another AA. ii. Has to be achieved in a specific order of A.A.s Normal amide synthesis methods such as
OH
O
Cl
O
HN
OSOCl2H2N2
do not work well for peptide synthesis since acid chlorides react with amines and others randomly. In addition, acid halides are too reactive and unstable.
Problems/solutions: i. Need to protect an amino group until it is ready to react. ii. Need to activate a carboxyl group. iii. Need to selectively deprotect (protected) amino groups in ways that do not affect peptide linkages. i.e., hydrolysis of peptide bonds has to be avoided. iv. Need to avoid racemization (at each of α-amino attached carbon centers).
OHO
H3CN-PG1
H
O-PG2O
HNH2
H
S
H
Want the reaction only between these two groups!
The only nucleophile in this AA.
PG1-N NH
O-PG2
H CH3
O H H
OS
H
PG1-N NH
OH
H CH3
O H H
OS
H
O-PG2O
HNH2
H
PG1-N NH
HN
H CH3
O H H
OS
H
O-PG2H H
O
coupling
coupling
deprotection of PG2
peptide linkage formed
peptide linkage formed
Chem 215-216 HH W11 Notes – Dr. Masato Koreeda - Page 5 of 14. Date: April 14, 2011 (2) Protection of α-Amino groups
protecting groups: Have to be readily removable later in the synthesis without cleaving peptide bonds. Therefore, amides would not be suitable as protecting groups. (a) Carbamates: Can be deprotected under anhydrous acidic conditions without affecting peptide bonds.
RHN O
R'O
i. Benzyl carbamate RHN O
CH2O
Formation
OO
H3CNH3
H
alanine (Ala or A)
SCl
OO
benzyl chloroformate*
(CH3CH2)3Ntriethylamine
OHO
H3CNH
HO
O
* ClCO2BnBn = CH2Ph
(CH3CH2)3N•HCl+
(>95%)
N-Cbz-Alaor N-benzyloxycarbonylalanineor N-carbobenzoylalanine
Formation: Mechanism
OO
H3CNH
alanine (Ala or A)
ClO
Ph
O
(CH3CH2)3NH
HH
OO
H3CNH
H H
ClO
Ph
O
OO
H3CNH
H H
O
Ph
O
OO
H3CNH
H H
O
Ph
O
OHO
H3CNH
H
proton transfers
More acidic than the COOH!
OHO
H3CNH
HO
O
N-Cbz-Ala
Deprotection of the N-Cbz group• Catalytic hydrogenolysis
OHO
H3CNH
HOH
H3CO
toluene
H2, Pd/CCH3OH
+
Not isolable!
OO
H3CN
H
HH
H
+ CO2
OHO
H3CNH
O
O
H :BH
H B
** **
R OCH2
O
H Hcatalyst surface
*
*
The group here has to be either a phenyl orCH=CH2 for the hydrogenolysis to occur.
The Ph group is likely to interact with Pd metal.
Chem 215-216 HH W11 Notes – Dr. Masato Koreeda - Page 6 of 14. Date: April 14, 2011
Deprotection of the N-Cbz group (continued)• Hydrogen bromide (HBr; gaseous) in trifluoroacetic acid (CF3COOH)
OHO
H3CNH
HO
O
N-Cbz-Ala
H Br OHO
H3CNH
HO
O H
Br
SN2! OHO
H3CNH
O
O
HH
OHO
H3CN
H
H HH
O CF3
O
or H B
OHO
H3CN
H
H HH
Ala-H+
CO2
ii. tert-Butyl carbamate RHN O C
O
Formation
CH3CH3
CH3 RHN Boc
Boc = tert-butyloxycarbonyl
Cl O C
O
CH3CH3
CH3
•tert-Butyl chloroformate: not very stable and, thus, not usually used for the N-Boc formation.
Boc group: one of the most frequently used amino protecting groups; Inert towards catalytic hydrogenolysis and extremely resistent towards basic and nucleophilic reagents; an ideal orthogonalN-protecting group to benzyl esters and benzyl carbamates.
• Commonly used reagents:(a) tert-butyl azidoformate
N O CCH3
OCH3
CH3
NN(explosive; needs to be made in situ from Boc-hydrazide with nitrous acid and used without purification)
(b) tert-butyl pyrocarbonateor Boc anhydride or di-tert-butyl dicarbonate
H3CC O O O C
CH3
O O CH3CH3
CH3H3C Boc2O
H3CC OH
CH3H3C
+ + CO2
S
HN OH
O Boc2O ( 1.0 mol equiv)
N (1.1 mol equiv)
H3CCN (solvent)rt, 2 days
H3O+ (to pH 1 - 2)
S
N OH
OBoc
~100%
Chem 215-216 HH W11 Notes – Dr. Masato Koreeda - Page 7 of 14. Date: April 14, 2011 N-Boc formation with Boc2O (continued) Mechansim:
H3CC O O O C
CH3
O O CH3CH3
CH3H3C
R-NH2
H3CC O
O O CCH3
O O CH3CH3
CH3H3C
R-NH2H3C
CO
O CCH3
O
CH3CH3
CH3H3C
NH
R H
+ CO2
+H3CC
O
OCH3H3C
NR
HHO C
CH3
CH3CH3
+
Boc-NHR
Boc2O
(c) "BOC-ON"= 2-(tert-butoxycarbonyloxyimino)-2-phenylacetonitrile
H3CC
O ON
OCH3H3C BOC-ON
O
ONH3
N(CH2CH3)3 (1.0 mol equiv)H2O-dioxane (solvent)rt, 3 h
BOC-ON (1.0 mol equiv)O
OHHN
Boc
H3O+ (to pH 1 - 2)
C CN
Ph
Mechanism of the N-Boc formation:
H3CC
O ON
OCH3H3C C C
N
Ph
R NH2H3C
CO O
NOCH3
H3CC C
N
Ph
R NH H
H3CC
O C
ON
OCH3H3C
C CN
PhH
NR
H
H3CC
O C
OCH3H3C
RN
HO
N C C N
PhH
RNH-Boc
+
+
phenylalanine (Phe or F)> 95% N-Boc-Phe
Deprotection of the N-Boc group:
With dry trifluoroacetic acid; usually within 5-10 min at room temperature; often trifluoroacetic acid as a solvent.
O
OHHN
N-Boc-Phe
F3C OH
O
O
OHNH3
Phe-H+
+ CO2 + C CH2
H3C
H3Cisobutylene
O C CH3
O CH3CH3
Chem 215-216 HH W11 Notes – Dr. Masato Koreeda - Page 8 of 14. Date: April 14, 2011
Deptrotection of the N-Boc group - Mechanism:
O
OHHN
N-Boc-Phe
F3C O
OO
OHNH2
Phe-H+
+ CO2
C CH2
H3C
H3Cisobutylene
O C CH3
O CH3CH3
H
pKa 0.50
O
OHHN O C CH3
O CH3CH3
HF3C O
O
+
O
OHHN O
CCH3
O
H3C C
H
H H
H
A
+
O
OHNH3
H-A(or A )(or H-A)
A
A H
H-A A+
A HA
(4) Fmoc [(9-fluoromethyl)methoxycarbonyl] group The Fmoc group is exceptionally stable towards acid. Therefore, carboxylic acids can be converted to acid chlorides with thionyl chloride or tert-butyl esters using sulfuric acid and isobutylene. Formation: (9-fluoromethyl)methoxycarbonyl chloride
O CH2O
HCl Fmoc-Cl
NH3
O
O
Na2CO3 (1.5 mol equiv)H2O-dioxane (solvent)
FmocCl (1.0 mol equiv)
0 C° - rt, 8 hHN
O
OHO C
H2O
H
N-Fmoc-Phe
Example:
Phe
Deprotection: Treatment with a mild base such as piperidine.
HN
O
OO
CH2O H N
HNH2
O
O
CH2
+ CO2+
HN
OO
O CH2O
N-Fmoc-Phepiperidine
piperidine
highly acidic H!
14 π aromatic systemnote: Alternatively, this could be an E2 process without involving a discrete carbanion.
Chem 215-216 HH W11 Notes – Dr. Masato Koreeda - Page 9 of 14. Date: April 14, 2011 (3) Protection of Carboxylic Acid Groups Usually as methyl, ethyl, tert-butyl, or benzyl esters.
Formation:With an alcohol (CH3OH, C2H5OH, or PhCH2OH) and an acid catalyst (H2SO4 or p-TsOH)
O
O
H3NH
O
O
H3NHp-TsOH
PhCH2OH (excess)
Δquantitative
With an alkyl iodide or benzyl bromide and Cs2CO3 (base).
With an alcohol and DCC (to be discussed later).
With isobutylene and H2SO4.
OH3N
O
O
O
OH2N
O
O
O
CCH3CH3
CH3
H3CC
H3CCH2isobutylene
H2SO4 (0.2 mol equiv)
(excess)
CH2Cl2, rt, 48 h
1.
2. NaHCO3 92%
OTs
Deprotection:Methyl, ethyl, and benzyl esters: easily hydrolyzable with H2O/HO-.Benzyl esters: hydrogenolysis with H2, Pd-C; deprotected with HBr in CH3COOH.
O
O
H2NH
OH
O
H2NH
O
O
H3NH
H2, Pd-C
tolueneNo decarboxylation here!
tert-Butyl esters: Readily deprotected in trifluoroacetic acid (neat or in CH2Cl2 solution) at room temperature with loss of isobutylene (essentially the reverse of the acid-catalyzed method of preparation).
R O CCH3
O CH3CH3
F3C OH
O
R OH
OC CH2
H3C
H3C+
R OC
CH3
O CH3CH3
H
H3C+
Chem 215-216 HH W11 Notes – Dr. Masato Koreeda - Page 10 of 14. Date: April 14, 2011 (4) Activation of the Carboxylic Acid Group and Formation of Peptide Bonds
Need to convertR O H
Oto a good leaving group.
R O H
OR'NH2
N C N
DCC
Use of Dicyclohexylcarbodiimide (DCC).
R NH
R'O H
NHN
O+ +DCC
A unit of H2O added to DCC.
Mechanism for the reaction with DCC
Note: Shown below is somewhat different from the mechanism given in the textbook (p. 634).
+
N C N
R O H
ON C N
R O
O
H
N CN
RO
O
H
R'NH2
N CN
RO
O
H
NR'H H
N CNH
O
R'NH2
R' NHHH
R'NH H
NC
NH
O
O
R
H
R NH
R'O
amide N,N'-dicyclohexylurea
a large leaving group!
Note: The ester formation can also be realized from a carboxylic acid and an alcohol using DCC. The reaction proceeds through a similar mechanism as shown above. But, the first step in this case will be the protonation of DCC by the carboxylic acid.
Chem 215-216 HH W11 Notes – Dr. Masato Koreeda - Page 11 of 14. Date: April 14, 2011 (5) Application to the synthesis of the tripeptide Ala-Gly-Gly
H3NHN N
HO
H3C
O
O
O
H
H
HH
H
Ala Gly Gly
N-terminus C-terminus
1. Protection of the NH2 group of alanine:
H3N
H3C
O
HO N
H
H3C
O
HOHBocBoc2O
N(CH2CH3)3
2. Protection of the COOH group of glycine:
H3N
H
O
HO H2N
H
O
HO
1. PhCH2OHp-TsOH
2. NaHCO3Ph
3. Amide bond formation with DCC:
+NH
H3C
O
HOHBoc
H2N
H
O
HO Ph DCC
NH
HN O
H3C
O
OH
HHPhBoc
carboxy-protectedamino acid
N-protectedamino acid
4. Removal of the carboxy-protecting group:
NH
HN O
H3C
O
OH
HHPhBoc
NH
HN OH
H3C
O
OH
HH
BocH2/Pd-C
5. Tripeptide synthesis with DCC and subsequent deprotection of both protecting groups:
+NH
HN OH
H3C
O
OH
HH
BocH2N
H
O
HO Ph
NH
HN N
HO
H3C
O
O
O
H
H
HH
H
Boc PhDCC
H3NHN N
HO
H3C
O
O
O
H
H
HH
H
1. HBrH3CCO2H 2. adjust pH to ca. 6
removal of both protecting groups
N-protected dipeptide carboxy-protectedamino acid
Chem 215-216 HH W11 Notes – Dr. Masato Koreeda - Page 12 of 14. Date: April 14, 2011
(5) Solid-Phase Peptide Synthesis (Chapter 21.8, pp 900-906)
Merrifield Method:
Developed by Bruce Merrifield (Nobel prize in chemistry in 1984) in 1969; has been automated. A large number of polypeptides have been prepared by the use of automated peptide synthesizers.
The most significant difference between solution-phase and solid-phase peptide synthesis lies in the fact that the solid-phase synthesis of peptides is carried out in the opposite direction, starting with the C-terminus attached to the solid support and proceed toward the N-terminus, i.e., from right to left as the peptide chain is drawn.
Synthesis of Val-Ala-Gly as an example: After each reaction step, the product attached to the polymer bead is collected by filtration and all reagents, etc. dissolved in the solvent are thus removed. The product attached to the bead is then exposed to the new reagents dissolved in the solvent for the next reaction step.
styrene
polystyrene(polymer; solid support)
polymerization
H2C H2C ClCl
ClCH2OCH3SnCl4CHCl3
(solvent)
Comments:1. Heterogenous reaction2. Friedel-Crafts alkylation involving +CH2OCH3 (or CH2=O+-CH3).3. Extent of chloromethylation can be controlled by adjusting the amounts of reagents used. O
HN
OH
O
OCH3C
CH3H3C
Boc
:N(CH2CH3)3CH2Cl2 (solvent)
CH2O
HNBoc
O
This becomes the C-terminus AAof the peptide.
Attached to the polymer as a benzyl ester.
N-protected AA
solid polymer bead
CH2OH2N
O
F3C OH
O1.
Deprotection of the Boc group.
2. :N(CH2CH3)3CH2Cl2 (solvent)
CH2Cl2(solvent)
This is to convert NH3
+ to NH2.
Chem 215-216 HH W11 Notes – Dr. Masato Koreeda - Page 13 of 14. Date: April 14, 2011
(5) Solid-Phase Peptide Synthesis: Synthesis of Val-Ala-Gly as an example (cont’d)
+
CH2O
HN
O
NH O
CH3H
DCC
N-protected AA
CH2O
HN
O
HNO
CH3H
Ala Gly
CH2Cl2(solvent)
HN OH
O
Boc
HNBoc
O
H
Hnew peptide bond
OHHN
O
NH O
CH3HH3N
O
H
HBr (gas) F3C OH
O (solvent)
H2CBrVal Ala Gly
pKa ~2.35
pKa ~9.72
pI ~ 6.0
OHN
O
NH O
CH3HH3N
O
Hadjust pHto around 6
Val-Ala-Gly
CH2OH2N
O DCC
ONH
Boc
O
CH3HH
N-protected AA
CH2Cl2 (solvent)CH2
OHN
O
NH
Boc
O
CH3H
peptide bond formed
F3C OHO
1.2. :N(CH2CH3)3
CH2Cl2CH2Cl2(solvent)
(solvent)
CH2O
HN
O
O
HBr
CH2O
HN
O
O
H
Br H2CBr
Mechanism for the release of the polymer support:
Chem 215-216 HH W11 Notes – Dr. Masato Koreeda - Page 14 of 14. Date: April 14, 2011 (5) Solid-Phase Peptide Synthesis (Chapter 21.8, pp 900-906) (continued)
Solid State Peptide Synthesis with Fmoc-protected amino acids and Wang resin
The repetitive cleavage of Boc groups by anhydrous CF3C(=O)OH and the final release of polypeptides from the benzyl-based resin under strongly acidic conditions [anhydrous HBr-CF3C(=O)OH]: deleterious in the synthesis of large polypeptides.
Much milder conditions using Wang resin (4-benzyloxybenzyl alcohol resin) and Fmoc-protected amino acids.
CH2O
ONH
Fmoc
O
HH
HO
Wang resin
ONH
Fmoc
O
OH2N
O
NH(piperidine)
N H
O
(DMF; solvent)
ONH
Fmoc
O
PhHH
ONH O
HN
O
H
ONH
Fmoc
ONH
Fmoc
O
ONH O
NN
Fmoc-glycine linked to the resin by ester bond
DMF (solvent)
HN
Fmoc
O
H
DMF (solvent)
HBTU (coupling agent)
NH DMF (solvent)1.
2.
N
DMF (solvent)
HBTU (coupling agent)
N
NH
Fmoc
O
PhH
NH DMF (solvent)1.
ONH O
HN
O
HH3N
O
PhH2. aq F3C OH
O3. adjust pH 6-7
Phe-Val-Gly
The 20 naturally occurring amino acids
H2N OHH CH3
O
H2N OHH
O
H2N OHH H
O
ONH2
H2N OHH
O
H2N OHH
O
SH
O NH2
H2N OHH
O
H
H2N OHH
O
H2N OHH
O
SCH3
HN
OH
O
H
H2N OHH
O
OH
H2N OHH
O
HHO
H2N OHH
O
NH
H2N OHH
O
OH
H2N OHH
O
H2N OHH
O
Alanine
Asparagine
Cysteine
Glutamine
Glycine
Isoleucine
Leucine
Methionine
Phenylalanine
Proline
Serine
Threonine
Tryptophan
Tyrosine
Valine
Ala A
Asn N
Cys C
Gln Q
Gly G
Ile I
Leu L
Met M
Phe F
Pro P
Ser S
Thr T
Trp W
Tyr Y
Val V
Acidic amino acids Basic amino acids
name/structure abbreviations name/structure abbreviations name/structure abbreviations
name/structure abbreviations name/structure abbreviations
Neutral amino acids
H2N OHH
O
OOH
Aspartic acid
Asp D
H2N OHH
O
O OHGlutamic acid
Glu E
H2N OHH
O
NHArginine
Arg R
H2N OHH
O
Histidine
His H
H2N OHH
O
Lysine
Lys K
NH2
NH
NH2
HN N
name/structure abbreviations
pKa Values for the Ionizable Functional Groups of an α-Amino Acid
Amino acid α-COOH α-NH3+ Side chain pI
Alanine 2.35 9.87 - 6.1
Arginine 2.01 9.04 12.48 10.76
Asparagine 2.02 8.80 - 5.41
Aspartic acid 2.10 9.82 3.86 2.98
Cysteine 2.05 10.25 8.00 5.02
Glutamic acid 2.10 9.47 4.07 3.08
Glutamine 2.17 9.13 - 5.65
Glycine 2.35 9.78 - 6.06
Histidine 1.77 9.18 6.10 7.64
Isoleucine 2.32 9.76 - 6.04
Leucine 2.33 9.74 - 6.04
Lysine 2.18 8.95 10.53 9.74
Methionine 2.28 9.21 - 5.74
Phenylalanine 2.58 9.24 - 5.91
Proline 2.00 10.60 - 6.30
Serine 2.21 9.15 - 5.68
Threonine 2.09 9.10 - 5.60
Tryprophan 2.38 9.39 - 5.88
Tyrosine 2.20 9.11 10.07 5.63
Valine 2.29 9.72 - 6.00
_____________________________________________________________________