twisted amides: not your typical amide bond
TRANSCRIPT
Twisted Amides: Not Your Typical Amide Bond
Sarah E. MarshallMichigan State UniversitySeptember 10, 2008
Two important questions:
What makes an amide bond so stable?
• If amide bonds are so stable, then how do peptidases cleave them?
Radzicka, A.; Wolfenden, R. J. Am. Chem. Soc. 1996, 118, 6106-6109.
Hydrolysis of Amide Bonds
If carboxypeptidase B is added to the solution at 23˚C, the t1/2 = 2.91 ms for the hydrolysis of acetylglycilglycine
H3C NH
HN OH
O
O
O
H3C NH
H2N OH
O
O
OOHt1/2 = 500 years
pH = 6.8, 25˚C
Ishida, H. Z. Naturforsh. 2000, 55a, 769-771. D.R. Lide, Editor, CRC Handbook of Chemistry and Physics (3rd electronic ed.), CRC Press, Boca Raton, FL (2000).
Stability of Amide Bonds
Comparison of Bond Lengths
R2NR3
O
R1 R2NR3
O
R1
H3CH2C NH2
1.470 ÅH3C
O
NH2
1.380 Å
O
CH3H3C
1.213 Å1.220 Å
O
R1
R2
R3NnN π∗COC O C
R1
R2
R3N
Eliel E.L. and Wilen, S.H. In Stereochemistry of Carbon Compounds, Wiley-Interscience, New York, 2000.Kirby, A.J.; Komarov, I.R.; Feeder, N. J. Chem. Soc., Perkin Trans. 2, 2001, 522-529.
Twist-angle distribution of tertiary amides in the Cambridge
Crystallographic Database (CCDB) on 20th September
2000. Data for 9098 groups from 5641 accurate structures.
Twist angle (τ):
Planarity of Amide Bonds
(ωC4-C3-N-C2 + ωO-C3-N-C1)2
τ =
1CN
2C
3CO
4C 2C
1C
3C
O
4C
Fundamentals of Twisted Amides
Cos, J.D.; Pilcher, G. Thermohemistry of Organic and Organometallic Compounds; Academic Press: New York, 1970.The Amide Linkage Selected Structural Aspects in Chemistry Biochemistry, and Materials Science (Eds.: Greenberg, A.; Breneman, C.M.; Liebman, J.F), Wiley Interscience, 2000, 215-217.
∆G = 19.1 to 21.5 kcal/mol for E/Z isomerization (180˚ twisting)
120˚ Bond Angles,Planar
τ = +/- 90˚R3N
R2
O
R1R3N
R2
O
R1 N R3R2
O
R1
Intramolecular Steric Repulsion
Intramolecular Steric Restriction
Intermolecular Interaction
R1 N R3
R2
O
N R3R2
O
R1N
O
p
q
r
Bredtʼs Rule-in a bicyclic system, it is not possible to have a double bond at the bridgehead carbon unless the alkene
is part of a large ring
1* 2* 3*Represent forbidden isomers of norbornene
Fundamental Principle of Twisted Amides - Bredtʼs Rule
J. Bredt, H. Thouet and J. Schnitz Liebigs Ann. 1924, 437, 1.
It is possible to generate a twisted amide by
placing a nitrogen at the bridgehead of a bicyclic
system.
These molecules are known as anti-Bredt
molecules.
Fundamental Principle of Twisted Amides - Bredtʼs Rule
N
NH
O
O
NH
O
N
N
O
O
N
O
H
Hybridization of Nitrogen in Twisted Amides
NO
N
O
sp3
sp3sp2
sp2
NO
N
O
Examples of Twisted Amides
Sheehan, K.R. and Henery-Logan, K.R. J. Am. Chem. Soc. 1959, 81, 3089-3094.Kirby, A.J.; Komarov, I.R.; Feeder, N. J. Chem. Soc., Perkin Trans. 2, 2001, 522-529.Tani, K. and Stoltz, B.M. Nature, 2006, 441, 731-734.Somayaji, V.; Brown, R.S. J. Org. Chem. 1986, 51, 2676.Blackburn, G.M.; Skaife, C.J.; Kay, I.T. J. Chem. Res. 1980, 3650-3669.Bashore, C.G.; Samardjiev, I.J.; Bordern, J.; Coe, J.W. J. Am Chem. Soc. 2003 125, 3268-3272.
Penicillin 2-Quinuclidone 1-Aza-2-Adamantanone
NMeMe O N O
N
MeMeMe
O
N
S
OCO2H
NO
HNR
O
N OBenzo-1-Aza-Adamantane 2,2-dimethylquinuclidin-7-one Benzoquinuclidin-2-one
What is penicillin?
Antibiotic effective against bacterial infections,usually gram-positive bacteria
Discovered by Sir Alexander Fleming in 1928
Harold Raistrick tried to isolate penicillin but found it to be quite unstable
In 1939, Robert Florey, Ernst Chain, and Sir William Dunn turned to penicillin research as a laboratory curiosity
In the early 1940ʼs, penicillin production started in the U.S.
In June of 1942, there was only enough penicillin in the United States to treat 10 patients
http://www.biology.ed.ac.uk/research/groups/jdeacon/microbes/penicill.htmThe Chemistry of Penicillin (Eds.: H.T. Clark, J.R. Johnson, R. Robinson), Princeton University Press, Princeton, 1949, 440.The Amide Linkage Selected Structural Aspects in Chemistry Biochemistry, and Materials Science (Eds.: Greenberg, A.; Breneman, C.M.; Liebman, J.F), Wiley Interscience, 2000, 157-162.
Penicillin-A Turning Point in the History of Twisted Amides
Side Products and Proposed Structures for Penicillin
The Chemistry of Penicillin (Eds.: H.T. Clark, J.R. Johnson, R. Robinson), Princeton University Press, Princeton, 1949, 1-5.
N
O NH
S
O
R
CO2H
CH3CH3
N
S
O
CH3
CH3
CO2H
HNR
O
ThiazolidineoxazoloneRobert Robinson
β-Lactam StructureRobert Woodward
Penicillamine Penillic AcidPenicilloic Acid
NH
S
O
CH3CH3
CO2H
NHR
O
OHN
S CH3CH3
CO2H
HO O
HN
R
HSH3C
CH3 O
OHNH2
O
OHNH
O
O
H
N-(2-oxoethyl)-2-phenylacetamide 2-phenylacetic acid
Crystal Structure of PenicillinThe crystal structure of penicillin was obtained in 1945 by Dorothy Hodgekin.
CP, p 7.
Degradation of Penicillin to Penicilloic Acid
Penicilloic Acid
The Chemistry of Penicillin (Eds.: H.T. Clark, J.R. Johnson, R. Robinson), Princeton University Press, Princeton, 1949, 445.
N
S
OCO2H
HNR
O
H2O
NH
S
OCO2H
HNR
O
OH
NH
S
HO CO2H
HNR
OO
NH
S
CO2H
NHR
OO
OH
Degradation of Penicillin to Penillic Acid
N
S
CO2H
O
O
NH
RN
S
CO2H
HOO
HN
R
NH
S
CO2H
O
NH
O
RN
S
CO2H
O
O
NH
R H
-H
Penillic Acid
The Chemistry of Penicillin (Eds.: H.T. Clark, J.R. Johnson, R. Robinson), Princeton University Press, Princeton, 1949, 445.
N
S
OCO2H
HNR
OH2O
N
S
OCO2H
HNR
OH
O
HN
NH
S
CO2HO
R
Hydrolysis and Administration of Penicillin
Benedict, R.G.; Schmidt, W.H.; Coghill, R.D.; Oleson, A.P. J. Bacteriol., 1945, 49, 85-95.Golden, M.J.; Neumeier, F.M. Science, 1946, 104, 102-104.
t1/2=240 hrs
pH=7, 24˚CN
S
OCO2H
HNR
ONo Antibiotic Reactivity
Facts about administration of penicillin:Must be stored in the refrigeratorUsually given as an intravenous or intramuscular injectionOral administration of penicillin is acceptable if it is given with antacids or buffers
Mode of Action of Penicillin
The Amide Linkage Selected Structural Aspects in Chemistry Biochemistry, and Materials Science (Eds.: Greenberg, A.; Breneman, C.M.; Liebman, J.F), Wiley Interscience, 2000, 340-341.
Peptidoglycan is a polymer which forms a mesh-like layer on the plasma membrane of eubacteria.
Penicillin binding proteins or transpeptidases form the oligopeptide bonds which cross link the peptidoglycans.
Penicillin inhibits cell wall synthesis by preventing the cross linking of the sugar polymers, which leads to lysing of the cell.
N-acetyl muramic acid (MurNAc)
N-acetylglucosamine (GlcNAc)
Peptide cross-links
Mechanism of Cross-linked Peptidoglycan Formation
Erlanger, B.F.; Goode, L. Nature, 1967, 213, 183-184.
O
B
ONH2
H3CO
OH
O
B H
ONH
H3CO
OH
O
B
ONH2
H3CO
OH
NH2H3C
OOH
O
B
O
O
NH2H3C
O
B
O
O
HNH3C
O
O
HNH3C
O
B
Transpeptidase Peptidoglycan A
Peptidoglycan B
Cross-linked Peptidoglycan
O
B
ONH2
H3CO
OH
Structural Resemblance of D-alanyl-D-alanine to Penicillin
NHPeptidoglycan
O
HN
O HCO2HHH3C
CH3
NHR
ON
O
S
H
CH3CH3
CO2H
Erlanger, B.F.; Goode, L. Nature, 1967, 213, 183-184.
Mode of Action of Penicillin
NH
S
OCO2H
NHR
OO
B
HNS
O
HO2C
NHR
O
O
B
Transpeptidase
HNS
O
HO2C
NHR
OO
B
Erlanger, B.F.; Goode, L. Nature, 1967, 213, 183-184.
Sheehan, K.R. and Henery-Logan, K.R. J. Am. Chem. Soc. 1959, 81, 3089-3094.
The First Synthesis of Penicillin
N
O
OO
OO
AcONaHS
NH2•HCl
O
OHN
O
OO
O
HNS
HO2C
EtOH (aq) 24%
1. N2H4
2. aq. HCl82%
NH2•HCl
O
O
HNS
HO2C
Et3N, 70%
OPhO
ClHN
O
O
HNS
HO2C
O
OPh
Sheehan, K.R. and Henery-Logan, K.R. J. Am. Chem. Soc. 1959, 81, 3089-3094.
The First Synthesis of Penicillin
Penicillin
HN
O
O
HNS
HO2C
O
OPh
2. C5H5NAcetone/H2OQuantitative
1. KOH (1 eq.)1. aq. HCl
2. DCC10-12%
HN
HO
O
HNS
HO2C
O
OPh
HNO
NSHO2C
O
OPh
Conclusions - Penicillin
N
S
OCO2H
HNR
O
Penicillin
The crystal structure revealed the fused β-lactam ring structure
The increased reactivity of β-lactams, and twisted amides in general, was recognized in deriving the structure of penicillin
Kirbyʼs Most Twisted Amide
1-aza-2-adamantanone
Kirby, A.J.; Komarov, I.R.; Feeder, N. J. Chem. Soc., Perkin Trans. 2, 2001, 522-529.
H3CH3C
CH3
N O
=
Structural Characteristics of Kirbyʼs Most Twisted Amide
(ωC4-C3-N-C2 + ωO-C3-N-C1)2
τ =
1CN
2C
3CO
4C 2C
1C
3C
O
4C
90.52.5Twist Angle τ (in ˚)
Kirby, A.J.; Komarov, I.V.; Feeder, Neil. J. Chem. Soc., Perkin Trans. 2, 2001, 522-529.Kirby, A.J.; Komarov, I.V.; Kowski, K. Rademacher, P. J. Chem. Soc., Perin Trans. 2, 1999, 1313.
H3CH3C
CH3
N ON OCH3
Structural Characteristics of Kirbyʼs Most Twisted Amide
The sum of the bond angles at the carbonyl carbon are used as a control
Sum of bond angles at the carbonyl carbon (in ˚)
359.9359.9
O
NN R3O
R3R1
R2R2R1
Kirby, A.J.; Komarov, I.V.; Feeder, Neil. J. Chem. Soc., Perkin Trans. 2, 2001, 522-529.Kirby, A.J.; Komarov, I.V.; Kowski, K. Rademacher, P. J. Chem. Soc., Perin Trans. 2, 1999, 1313.
H3CH3C
CH3
N ON OCH3
Structural Characteristics of Kirbyʼs Most Twisted Amide
Sum of bond angles at N (in ˚) 325.7358.9
The sum of the bond angles at nitrogen refers to its degree of pyramidalization
R4
R1
R3R2
R1R2R3
109.5˚120˚
Kirby, A.J.; Komarov, I.V.; Feeder, Neil. J. Chem. Soc., Perkin Trans. 2, 2001, 522-529.Kirby, A.J.; Komarov, I.V.; Kowski, K. Rademacher, P. J. Chem. Soc., Perin Trans. 2, 1999, 1313.
H3CH3C
CH3
N ON OCH3
Structural Characteristics of Kirbyʼs Most Twisted Amide
The sum of the bond angles at the carbonyl carbon are used as a control
Sum of bond angles at the carbonyl carbon (in ˚)
359.9359.9
O
NN R3O
R3R1
R2R2R1
Kirby, A.J.; Komarov, I.V.; Feeder, Neil. J. Chem. Soc., Perkin Trans. 2, 2001, 522-529.Kirby, A.J.; Komarov, I.V.; Kowski, K. Rademacher, P. J. Chem. Soc., Perin Trans. 2, 1999, 1313.
H3CH3C
CH3
N ON OCH3
Structural Characteristics of Kirbyʼs Most Twisted Amide
Bond Length C-N (in Å) 1.4751.325
Bond Length C-O(in Å) 1.1961.233
O
NN R3O
R3R1
R2R2R1
Kirby, A.J.; Komarov, I.V.; Feeder, Neil. J. Chem. Soc., Perkin Trans. 2, 2001, 522-529.Kirby, A.J.; Komarov, I.V.; Kowski, K. Rademacher, P. J. Chem. Soc., Perin Trans. 2, 1999, 1313.
H3CH3C
CH3
N ON OCH3
Structural Characteristics of Twisted Amides
Sum of bond angles at N (in ˚)
Twist Angle τ (in ˚)
325.7358.9
Sum of bond angles at C=O (in ˚) 359.9359.9
90.52.5
Bond Length C-N (in Å) 1.4751.325
Bond Length C-O(in Å) 1.1961.233
A B
Kirby, A.J.; Komarov, I.V.; Feeder, Neil. J. Chem. Soc., Perkin Trans. 2, 2001, 522-529.Kirby, A.J.; Komarov, I.V.; Kowski, K. Rademacher, P. J. Chem. Soc., Perin Trans. 2, 1999, 1313.
H3CH3C
CH3
N ON OCH3
IR Stretching Frequency of the Carbonyl in Kirbyʼs Most Twisted Amide
O O O
R EW R R R ED
*R = alkyl, EW = electron withdrawing, ED = electron donating
Higher υ υ ~ 1715 cm-1 Lower υ
N
CH3H3CH3C
ON OCH3 O
1732 cm-11653 cm-1 1720 cm-1
Kirby, A.J.; Komarov, I.V.; Feeder, Neil. J. Chem. Soc., Perkin Trans. 2, 2001, 522-529.Kirby, A.J.; Komarov, I.V.; Kowski, K. Rademacher, P. J. Chem. Soc., Perin Trans. 2, 1999, 1313.
13C NMR Chemical Shifts of Kirbyʼs Most Twisted Amide
Local diamagnetic shielding - this shielding is contributed to the isotropic circulation of electrons around the nucleus
200 ppm
165 ppm
218 ppm
13C NMR of C=O
Kirby, A.J.; Komarov, I.V.; Feeder, Neil. J. Chem. Soc., Perkin Trans. 2, 2001, 522-529.Kirby, A.J.; Komarov, I.V.; Kowski, K. Rademacher, P. J. Chem. Soc., Perin Trans. 2, 1999, 1313.
N
CH3H3CH3C
O
N OCH3
N OCH3
O
N
CH3H3CH3C
O
O
Ionization Potential of Kirbyʼs Most Twisted Amide
Ionization Potential - the amount of energy required to remove an electron from an isolated molecule or ion
8.30 eV n(N)9.36 eV n(O) 7.57 eV
NN
CH3H3CH3C
ON OCH3
* 1 eV = 1.602 x 10-19 J
Kirby, A.J.; Komarov, I.V.; Feeder, Neil. J. Chem. Soc., Perkin Trans. 2, 2001, 522-529.Kirby, A.J.; Komarov, I.V.; Kowski, K. Rademacher, P. J. Chem. Soc., Perin Trans. 2, 1999, 1313.
IR υC=O (cm-1) 17321653
δ 13C C=O (ppm) 200165
Kirby, J.A.; Komarov, I.V.; Feeder, Neil. J. Chem. Soc., Perkin Trans. 2, 2001, 522-529.
First IP (eV) 8.30n (N)9.36 n (O)
Spectral Characteristics of Kirbyʼs Most Twisted Amide
A B
N
CH3H3CH3C
ON OCH3
Kirby, J.A.; Komarov, I.V.; Feeder, Neil. J. Chem. Soc., Perkin Trans. 2, 2001, 522-529.
Unique Reactivity of Kirbyʼs Most Twisted Amide
Most Reactive
X = Cl, Br
Least Reactive
HO(CH2)3OH
benzene, TsOHreflux, 48 h 55.9%
H3CH3C
CH3
N OO
O
R X
O
R O
O
R OR'O
RO
R OH
O
R NH2
O
R R
O
R H> > > > >
H3CH3C
CH3
N O
Kirby, J.A.; Komarov, I.V.; Feeder, Neil. J. Chem. Soc., Perkin Trans. 2, 2001, 522-529.
Unique Reactivity of Kirbyʼs Most Twisted Amide
Most Reactive
X = Cl, Br
Least Reactive
H3CH3C
CH3
NPh3P=CH2
Et2Oreflux, 8 h64.3%
H3CH3C
CH3
N O
O
R X
O
R O
O
R OR'O
RO
R OH
O
R NH2
O
R R
O
R H> > > > >
Kirby, J.A.; Komarov, I.V.; Feeder, Neil. J. Chem. Soc., Perkin Trans. 2, 2001, 522-529.
Unique Reactivity of Kirbyʼs Most Twisted Amide
Most Reactive
X = Cl, Br
Least Reactive
CH2Cl2 quantitative
H3CH3C
CH3
N OCH3BF4
(CH3)3O BF4
O
R X
O
R O
O
R OR'O
RO
R OH
O
R NH2
O
R R
O
R H> > > > >
H3CH3C
CH3
N O
Kirby, J.A.; Komarov, I.V.; Feeder, Neil. J. Chem. Soc., Perkin Trans. 2, 2001, 522-529.
Unique Reactivity of Kirbyʼs Most Twisted Amide
Most Reactive
X = Cl, Br
Least Reactive
TsOH in dry
CD3CN H3CH3C
CH3
HN OTsO
H3CH3C
CH3
N O
O
R X
O
R O
O
R OR'O
RO
R OH
O
R NH2
O
R R
O
R H> > > > >
pKa of Kirbyʼs Most Twisted Amide
*Calculated using Advanced Chemistry Development (ACD/Labs) Software V8.14 for Solaris (c. 1994-2008 ACD/Labs)Kirby, A.J.; Komarov, I.V.; Feeder, Neil. J. Chem. Soc., Perkin Trans. 2, 2001, 522-529.Kirby, A.J.; Komarov, I.V.; Kowski, K.; Radeacher, P. J. Am. Chem. Soc., 1998, 120, 7101.Greenberg, A.; Moore, D.T.; DuBois, T.D. J. Am. Chem. Soc. 1996, 8658-8668.
5.23 10.38
O
NH2HH O
NH2H
pKa= 0.12
H3CH3C
CH3
N O H
H3CH3C
CH3
N OH
pKa= 4.8
H
-2.92 (+/- 0.20)*
NHNCH3H
HNCF3
pKa Values for Various Amines
Kirby, A.J.; Komarov, I.R.; Feeder, N. J. Chem. Soc., Perkin Trans. 2, 2001, 522-529.
Synthesis of Kirbyʼs Most Twisted Amide
H2O, acetone30 min, 86.3%
KMnO4
H3C
H3C
CH3
CO2HNAc
1.5 M HCl
reflux 24 hr 84.6% H3C
H3C
CH3
CO2
NH2 Sublimation
80˚C, 0.01 mmHg100%
H3C
H3C
CH3
N O
H3C
H3C
CH3
HO2CCO2H
CO2H
2) SOCl2, then MeOHH3C
H3C
CH3
CO2MeNHO
O LiAlH4 in Et2O,
H3C
H3C
CH3
NH OH
reflux, 24 hr 81.6 % since SM
2) CrO3•2PyCH2Cl2, 30 min74.3%
H3C
H3C
CH3
CHONAc
1) NH3, DMAP (cat.)reflux, 24 hr
1) Ac2O, MeOH 8 hr, 82%
H3C
H3C
CH3
N O H2O
H3C
H3C
CH3
CO2NH2 H+
H3C
H3C
CH3
HN OH
OH
<30s
21 3
42 3
Kirby, J.A.; Komarov, I.V.; Feeder, Neil. J. Am. Chem. Soc. 1998, 120, 7101-7102.
Hydrolysis of Kirbyʼs Most Twisted Amide
H3C
H3C
CH3
CO2NH2
H3C
H3C
CH3
HN OH
OH
H3C
H3C
CH3
N OOH
H
+ H
- H
Methyl Effects on Hydrolysis Rates
Kirby, J.A.; Komarov, I.V.; Feeder, Neil. J. Am. Chem. Soc. 1998, 120, 7101-7102.
H3C
H3C
CH3
NOH
H3C
H3C
CH3
CO2NH2 OH
O
CH3H3C
H3C
NH
OH
H
H
CH3
CO2NH2 OH
O
CH3H
H
NH
H
H
CH3
NOH
OH
Methyl Effects on Hydrolysis Rates
Kirby, J.A.; Komarov, I.V.; Feeder, Neil. J. Am. Chem. Soc. 1998, 120, 7101-7102.
H3C
H3C
CH3
NOH
H3C
H3C
CH3
CO2NH2 OH
O
CH3H3C
H3C
NH
OH
Radzicka, A.; Wolfenden, R. J. Am. Chem. Soc. 1996, 118, 6106-6109.Kirby, J.A.; Komarov, I.V.; Feeder, Neil. J. Chem. Soc., Perkin Trans. 2, 2001, 522-529.
Hydrolysis of Kirbyʼs Twisted Amide
Hydrolysis of peptide bonds:
Hydrolysis of peptide bonds using carboxypeptidase B:
Hydrolysis of 1-aza-2-adamantanone:
H3C NH
HN OH
O
O
O
H3C NH
H2N OH
O
O
OOHt1/2 = 2.91 ms
pH = 8, 23˚Ck = 238 s-1
H3C NH
HN OH
O
O
O
H3C NH
H2N OH
O
O
OOHt1/2 = 500 years
pH = 6.8, 25˚Ck = 4.4 x 10-11
H3CH3C
CH3
N O
H3CH3C
CH3
CO2NH2
t1/2 = 2.48 ms
pH = 7, 60˚Ck = 280 s-1
Conclusions - Kirbyʼs Most Twisted Amide
1-aza-2-adamantanone
Structural and spectroscopic properties are uniqueReactivity resembles an amino ketone
The nitrogen in the twisted amide is more basic than the oxygenThe buttressing methyl effects make the amide artificially stabilized
Hydrolysis rates of the twisted amide resemble the hydrolysis rates of enzymatic peptide bond cleavage
H3CH3C
CH3
N O
2-quinuclidone
The Legendary Twisted Amide - 2-Quinuclidone
1938 - Lukeš designs 2-quinuclidone
1941 - Robert Woodward gives the synthesis of 2-quinuclidone to Harry Wasserman
1957 - Yakhontov publishes the first synthesis of 2-quinuclidone
1965 - Pracejus attempts to use Yakhontovʼs method to synthesize 2-quinuclidone and fails to isolate the product, calling the first synthesis into question
Late 1990s - Stoltz first learns of 2-quinuclidone
2006 - Tani and Stoltz publish the first synthesis of 2-quinuclidone as its tetrafluoroborate salt
Wasserman, H.W. Nature. 2006, 441, 699.
NO
Yakhontov, L.N.; Rubsitov, M.V. J. Gen Chem. USSR, 1957, 27, 83-87.
The First Published Synthesis of 2-Quinuclidone
30 min, 50-55˚C
SOCl2
N
O OH
N
O Cl•HClCH2N2
Et2O48 hr, r.t
N
O CH2N2 Ag2O, EtOH
1.5 hr, 65˚C37% over 3 steps
NH
O
OEt
NH•HCl
O
OH
HCl (aq)93.7%
N
O
OEt
Pt, H2
EtOH24 hr100%
NH
O
Cl
NO
SOCl260˚C, 4 hr
K2CO3
CHCl3
Pracejusʼs Findings
NH•HCl
O
OH
NH
O
Cl
NO
SOCl260˚C, 4 hr
K2CO3
CHCl3
Unable to isolate the pure product
Pracejus, H.; Kehlen, M.; Kehlen, H.; Matschiner, H. Tetrahedron, 1965, 21, 2257-2270.
NO
H3C
CH3
H H
NO
H3C
CH3
H CH3
NO
H3C
CH3
H3C H
NO
H3C
CH3
H3C CH3
Pracejusʼs Findings
Not IsolatedPracejus, H.; Kehlen, M.; Kehlen, H.; Matschiner, H. Tetrahedron, 1965, 21, 2257-2270.
HN HNR3
R3
R3
R3O2C
CO2
R2
HR1
R1R2
NO
H3C
CH3
H H
NO
H3C
CH3
H CH3
NO
H3C
CH3
H3C H
NO
H3C
CH3
H3C CH3
NO
H
H
H H
Tani, K. and Stoltz, B.M. Nature, 2006, 441, 731-734.
Synthesis of 2-Quinuclidonium Tetrafluoroborate
NO
NOHN2
O
N3
Schmidt-Aubé
Reaction
Tani, K. and Stoltz, B.M. Nature, 2006, 441, 731-734.
Synthesis of 2-Quinuclidonium Tetrafluoroborate
HO
OH
TsCl, Et3N
CH2Cl2, 20˚C74%
HO
OTsDMF, 70˚C92%
NaN3HO
N3
O m-CPBA, NaHCO3
CH2Cl2, 20˚C79%
O
O
LiAlH4
Et2O, 20˚C98%
Mechanism of the Schmidt-Aubé Reaction Used in the Synthesis of 2-Quinuclidonium Tetrafluoroborate
Tani, K. and Stoltz, B.M. Nature, 2006, 441, 731-734.
O
NNNH
O
NNN
H
N
HO
N N
NHO
N2
NOH
N2
H+ Transfer
H+ Transfer
NHO
NH
O
N
HO
N N
Synthesis of 2-Quinuclidonium Tetrafluoroborate
Tani, K. and Stoltz, B.M. Nature, 2006, 441, 731-734.
HO
N3
DMP
CH2Cl2, 20˚C93%
O
N3
TFA
60˚C3 hr
NH
NH
O O
MeOH
NH
CO2Me (Boc)2ONaHCO3
N
CO2Me
Boc
56%
N
CO2Me
Boc34%
CHCl3•H2ONH
CO2Me
TfO TfO
Tani, K. and Stoltz, B.M. Nature, 2006, 441, 731-734.
Optimization of Schmidt-Aubé Reaction
NH
NH
O O
MeOH
NH
CO2Me (Boc)2ONaHCO3
N
CO2Me
Boc56%
N
CO2Me
Boc34%
CHCl3•H2ONH
CO2Me
TfO TfO
O
N3
HBF4
Et2O, 20˚CNH
NH
O O
76% Yield 24% Yield
Recrystallization from CH3CN-Et2O38% Yield N
HOBF4
BF4 BF4
O
N3
TFA
60˚C3 hr
Attempts to Generate the Free-Base of 2-Quinuclidonium Tetrafluoroborate
Attempts to observe the free base of 2-quinuclidonium tetrafluoroborate salt resulted in the formation of polymeric
materialTani, K. and Stoltz, B.M. Nature, 2006, 441, 731-734.
n
N O
OH
H
NO
NH
OBF4
NH
OBF4
Structural Characteristics of 2-Quinuclidonium Tetrafluoroborate
Sum of bond angles at N (in ˚)
Twist Angle τ (in ˚)
325.7358.9
Sum of bond angles at C=O (in ˚) 359.9359.9
90.52.5
Bond Length C-N (in Å) 1.4751.325
Bond Length C-O(in Å) 1.1961.233
Kirby, J.A.; Komarov, I.V.; Feeder, Neil. J. Chem. Soc., Perkin Trans. 2, 2001, 522-529.Tani, K. and Stoltz, B.M. Nature, 2006, 441, 731-734.
A B C
90.9
328.4
360.0
1.526
1.192
N
CH3H3CH3C
ON OCH3
NH
OBF4
17321653
δ 13C C=O (ppm) 200165 175.9
1822
Kirby, J.A.; Komarov, I.V.; Feeder, Neil. J. Chem. Soc., Perkin Trans. 2, 2001, 522-529.Ali, M.H.; Syn. Commun. 2006, 36, 1761-1767.
Spectral Characteristics of 2-Quinuclidonium Tetrafluoroborate
A B C
IR υC=O (cm-1)
N
CH3H3CH3C
ON OCH3
NH
OBF4
Hydrolysis of 2-Quinuclidonium Tetrafluoroborate
Kirby, J.A.; Komarov, I.V.; Feeder, Neil. J. Chem. Soc., Perkin Trans. 2, 2001, 522-529.Tani, K. and Stoltz, B.M. Nature, 2006, 441, 731-734.
H3CH3C
CH3
N O
H3CH3C
CH3
CO2NH2
t1/2 = 2.48 ms
pH = 7, 60˚Ck = 280 s-1
NH
OBF4
t1/2 <15 s
pH = 7, rtNH2
CO2H
HBF4
Conclusions - 2-Quinuclidonium Tetrafluoroborate Salt
The carbonyl of 2-quinuclidonium tetrafluoroborate salt has a partial triple bond character
2-quinuclidone as the free-base may be too reactive to be isolated as pure compound
More precise hydrolysis rates should be determined
Tani, K. and Stoltz, B.M. Nature, 2006, 441, 731-734.
NH
OBF4
NH
OBF4 δ
δNO
Theoretical Study for Basicity of Twisted Amides
Violates Bredtʼs RuleIsolable Compound
Greenberg, A.; Moore, D.T.; DuBois, T.D. J. Am. Chem. Soc. 1996, 118, 8658-8668.
2.2.2 System3.3.1 System
N NOO
Sum of bond angles at N (in ˚)
Twist Angle τ (in ˚)
327.1340.1
Sum of bond angles at C=O (in ˚)
360.0359.8
90.012.1
Bond Length C-N (in Å)
1.4331.386
Bond Length C-O (in Å)
1.1831.196
Greenberg, A.; Moore, D.T.; DuBois, T.D. J. Am. Chem. Soc. 1996, 118, 8658-8668.Kirby, A.J.; Komarov, I.V.; Kowski, K. Rademacher, P. J. Chem. Soc., Perin Trans. 2, 1999, 1313.
Theoretical Study for Basicity of Twisted Amides
*All values were calculated using HF/6-31G* calculations
CB
358.9
359.9
2.5
1.325
1.233
N OCH3
A
N NOO
NO
NO
Total Energies (au) Calculated for Optimized Structures
NO
NO
Resonance Energy (RE)
RE = -11.8 kcal/mol
=
Greenberg, A.; Moore, D.T.; DuBois, T.D. J. Am. Chem. Soc. 1996, 118, 8658-8668.
439.836323 366.117251 423.841924 350.141642
*All values were calculated using HF/6-31G* calculations
*1 au = 627.5 kcal/mol
Resonance Energy of the 3.3.1 System
Total Energies (au) Calculated for Optimized Structures
Resonance Energy (RE) =
RE = -0.9 kcal/mol
Greenberg, A.; Moore, D.T.; DuBois, T.D. J. Am. Chem. Soc. 1996, 118, 8658-8668.
*All values were calculated using HF/6-31G* calculations
400.782023 327.078799 384.805384 311.103598
Resonance Energy of the 2.2.2 System
*1 au = 627.5 kcal/mol
NO
NO
NO
NO
0.342227
Relative Energy Differences (au) Calculated for Optimized Structures
0.000000 0.0000000.363951 0.3805890.359971
238.8228.4 214.7226.5
Greenberg, A.; Moore, D.T.; DuBois, T.D. J. Am. Chem. Soc. 1996, 118, 8658-8668.
Proton Affinity Values (kcal/mol)
Proton Affinity Values
*All values were calculated using HF/6-31G* calculations
Proton Affinity: the measure of a moleculeʼs gas phase basicity
*1 au = 627.5 kcal/mol
NH
O
NO H
NH
O
NO
H
NO
NO
NH
O
NO H
NH
O
NO
H
Various Proton Affinity Values
Greenberg, A.; Moore, D.T.; DuBois, T.D. J. Am. Chem. Soc. 1996, 118, 8658-8668.Hunter, E.P.; Lias, S.G. J. Phys. Chem. Ref. Data, 1998, 27, 3, 413-656. DePuy, C.H.; Gronert, S.; Barlow, S.E.; Bierbaum, V.M.; Damrauer, R., J. Am. Chem. Soc., 1989, 111, 1968.
227.6
238.8 kcal/mol228.4 kcal/mol 214.7 kcal/mol226.5 kcal/mol
194.0 234.7
Proton Affinity Values (in kcal/mol)
196.5
NH
O
NO H
NH
O
NO
H
218.0
O
NH2HH3C N
H2CH3
HOH
NH3
HN CH3
H3C
CH3
H3C
Relative Energies of N vs. O protonated Amides
Greenberg, A.; Moore, D.T.; DuBois, T.D. J. Am. Chem. Soc. 1996, 118, 8658-8668.Kim, K.S.; et al. J. Org Chem. 1997, 62, 4068-4071.
H
O
NH3 H
O
NH2
H
-24.1 kcal/mol-1.9 kcal/mol
NH
O
NO H
NH
O
NO
H
Relative Energies of Protonated Planar Amides calculated using the 6-31G+** Basis Set (in kcal/mol)
0.016.0
238.8 kcal/mol228.4 kcal/mol 214.7 kcal/mol226.5 kcal/mol
Conclusions - N vs. O Protonation in Twisted Amides
Greenberg, A.; Moore, D.T.; DuBois, T.D. J. Am. Chem. Soc. 1996, 118, 8658-8668.
NO
NO
RE = -0.9 kcal/mol
NR1
R2
O
R3
RE = -20 kcal/molNR1
R2
O
R3 NR1
R2
OH
R3
HN
R1 R2
O
R3H
NOH
NOH
NO
NO
NOH
RE = -11.8 kcal/molN
OH
H
H
H
H
H
Applications of Twisted Amides
N
O
RLiAlH4
H
O
R
O
NH
HN
R1
R2
O
peptidaseNH
HN
R1
R2
O
OHN
R1 HO
N R2
OHN
R1 OH2N
R2
OH= Polypeptide
O
Synthesis of Aldehydes
O
R2DIBAL-H
R2R1O H
O
-78˚C
O
R4Reducing Agent
R4R3OR3 = H or alkyl
HOOxidizing Agent
H
O
R4
R1 = alkyl
Hydrolysis of 2-Quinuclidonium Tetrafluoroborate
R1 NR2
O
R3 R1 NR2
O
R3
R1NR2
O
R3LiAlH4 R1
NR2
R3
O
R5LiAlH4
R5R4OR4 = H or alkyl
HO
Most Reactive
X = Cl, Br
O
R X
O
R O
O
R OR'O
RO
R OH
O
R NH2
O
R R
O
R H> > > > >
Least Reactive
Hydrolysis of 2-Quinuclidonium Tetrafluoroborate
Mechanism:
Brown, H. C.; Tsukamoto, A. J. Am. Chem. Soc. 1961, 83, 4549-4552..
N
O
R3LiAlH4
N R3R1
R2R1
R2
N
O
R3R1
R2
HN
O
R3R1
R2H
AlH3
N R3R1
R2
HN R3R1
R2
Mechanism:
N
O
RLiAlH4
H
O
R
N
O
RH
N
O
RH
H2ON
O
RHH
O
H RNH
AlH3
How do peptidases cleave peptide bonds?
There are several biological processes that involve the cleavage of peptide bonds
Actual cleavage may go through a twisted amide transition state
Various publications have shown mixed results
Romanelli, A.; Shekhtman, A.; Cowburn, D.; Muir, T.W. Proc. Natl. Acad. Sci. 2004, 101, 6397-6402.
H3C NH
HN OH
O
O
O
H3C NH
H2N OH
O
O
OOHt1/2 = 500 years
pH = 6.8, 25˚Ck = 4.4 x 10-11
O
NH
S
N'-Protein C'-Protein
H
O
SN'-Protein C'-Protein
NH2
t1/2 = 11.2 min
How do peptidases cleave peptide bonds?
Brown, H. C.; Tsukamoto, A. J. Am. Chem. Soc. 1961, 83, 4549-4552.Kirby, A.J.; Komarov, I.R.; Feeder, N. J. Chem. Soc., Perkin Trans. 2, 2001, 522-529.Radzicka, A.; Wolfenden, R. J. Am. Chem. Soc. 1996, 118, 6106-6109.
H3C NH
HN OH
O
O
O
H3C NH
H2N OH
O
O
OOHt1/2 = 2.91 ms
pH = 8, 23˚Ck = 238 s-1
H3CH3C
CH3
N O
H3CH3C
CH3
CO2NH2
t1/2 = 2.48 ms
pH = 7, 60˚Ck = 280 s-1
t1/2=240 hrs
pH=7, 24˚CN
S
OCO2H
HNR
ONo Antibiotic Reactivity
Hydrolysis of 2-aza-adamantanone:
Hydrolysis of Penicillin:
Hydrolysis of peptide bonds using carboxypeptidase B:
Mycobacterium xenopi DNA gyrase A
Romanelli, A.; Shekhtman, A.; Cowburn, D.; Muir, T.W. Proc. Natl. Acad. Sci. 2004, 101, 6397-6402.
Mycobacterium xenopi DNA gyrase A
N
HN
NH2
O
O
ON
H
SHR
HN
Protein
ProteinH
3.6
3.9
3.63.0
Asn74
His75
Thr72
Cys1
Romanelli, A.; Shekhtman, A.; Cowburn, D.; Muir, T.W. Proc. Natl. Acad. Sci. 2004, 101, 6397-6402.
General NMR ShiftsGeneral Effects of H-bonding on Amide N-H Chemical Shifts in H1 NMR:
O
R1 NR2H
O
R3
R4 O
R1 NR2H
O
R3
R4
General Effects of H-bonding on the Nitrogen Coupling Constants in 15N NMR:
Downfield shift of amide proton
Upfield shift of amide proton
O
R1 NR2H
O
R3
R4
Decreases the value of the
coupling constant
O
R1 NR2H
H O R3
Increases the value of the coupling
constant
Romanelli, A.; Shekhtman, A.; Cowburn, D.; Muir, T.W. Proc. Natl. Acad. Sci. 2004, 101, 6397-6402.
Evidence of a Twisted Transition State
ON
H
SHR
HN
Protein
Protein
Cys1H1 NMR Shift= 6.61 ppm
Cysteine amide hydrogen shifts in proteins are ~ 8.35 ppm
General effects of H-bonding on Chemical Shifts in 1H NMR:Short H-bonds result in downfield shifts of amide protonsLong H-bond lengths results in upfield shifts of amide protons
Romanelli, A.; Shekhtman, A.; Cowburn, D.; Muir, T.W. Proc. Natl. Acad. Sci. 2004, 101, 6397-6402.
Evidence of a Polarized Transition State
ON
H
SHR
HN
Protein
Protein
Cys11JNCʼ is 12.3 +/- 0.3 Hz
1JNCʼ for proteins are in the range of 13-17 Hz
General effects of H-bonding on Coupling Constants in 15N NMR:H-bonding to amide carbonyl increases the value of the coupling constantH-bonding to amide hydrogen decreases the value of the coupling constant
Romanelli, A.; Shekhtman, A.; Cowburn, D.; Muir, T.W. Proc. Natl. Acad. Sci. 2004, 101, 6397-6402.
Applying the NMR Data to a Proposed Transition State
Romanelli, A.; Shekhtman, A.; Cowburn, D.; Muir, T.W. Proc. Natl. Acad. Sci. 2004, 101, 6397-6402.
N
HN
NH2
O
O
ON
H
SHR
HN
Protein
ProteinH
3.6
3.9
3.63.0
Asn74
His75
Thr72
Cys1
N
HN
NH2
O
O
ON
H
SHR
HN
Protein
Protein
H
3.6
3.9
3.0
Asn74
His75
Thr72
Cys1
The synthesis of three twisted amides have been highlighted, as well as their structural and spectroscopic characteristics.
The nitrogen and carbonyl of twisted amides react as separate functional groups, having similar reactivity to an amino-ketone.
Utilizing the behavior of twisted amides can lead to synthetic applications which may include the development of new methodologies.
Twisted amides may have a bright future in biological research since twisted amide transition states have been observed in the cleavage of peptide bonds.
Twisted Amides - Conclusions
“These significantly different properties of twisted amides compared to planar ones suggest that the
highly twisted amides behave not like amides but like amino-ketones; therefore, it would be no exaggeration
to say that the twisted amide is a new functional group.”
The Amide Linkage Selected Structural Aspects in Chemistry Biochemistry, and Materials Science (Eds.: Greenberg, A.; Breneman, C.M.; Liebman, J.F), Wiley Interscience, 2000, 243.
Prof. Babak BorhanProf. Ned JacksonAman K., Arvind, Atefeh, Calvin, Carmin, Camille, Chrysoula, Dan, Marina, Mercy, Roozbeh, Sing, Stewart, Toyin, Wenjing, Xiaoyong, XiaofeiKarrie Manes
Acknowledgements