Effect of hydrogen bonds on pK a values: Importance of networking

Journal of the American Chemical Society

Volumn 134, Issue 25, 2012, Pages 10646-10650

  Shokri, Alireza ^a   Abedin, Azardokht ^b   Fattahi, Alireza ^b   Kass, Steven R ^a  

^a University of Minnesota   (United States)

^b SHARIF UNIVERSITY OF TECHNOLOGY   (Iran)

Author keywords

[No Author keywords available]

Indexed keywords

ACID CATALYST; ACIDITY CONSTANTS; CHARGE DELOCALIZATION; EFFECT OF HYDROGEN; ELECTRON-WITHDRAWING SUBSTITUENTS; ENZYMATIC REACTION; GAS-PHASE ACIDITIES; HYDROXYL GROUPS; SOLVATION SHELL; TERT-BUTYL ALCOHOLS; TERTIARY ALCOHOLS;

ACETIC ACID; ALCOHOLS; STABILIZATION;

HYDROGEN BONDS;

ACETIC ACID; ALCOHOL; DIMETHYL SULFOXIDE; HYDROXYL GROUP; POLYOL;

ARTICLE; CHEMICAL STRUCTURE; ELECTRON; ENZYME MECHANISM; HYDROGEN BOND; PKA;

ACIDS; ACYLATION; ALKALIES; DIMETHYL SULFOXIDE; HYDROGEN BONDING; HYDROGEN-ION CONCENTRATION; MOLECULAR STRUCTURE; PHASE TRANSITION;

EID: 84863489479     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja3037349     Document Type: Article

References (80)

1. Jencks, W. P. Adv. Enzymol. Relat. Areas Mol. Biol. 1975, 43, 219-410
2. Jencks, W. P. Acc. Chem. Res. 1976, 9, 425-432
3. Jencks, W. P. Catalysis in Chemistry and Enzymology; Dover: New York, 1987; p 864.
4. Fersht, A. Structure and Mechanism in Protein Science; Freeman: New York, 1998; p 650.
5. Guthrie, J. P. Chem. Biol. 1996, 3, 163-170
6. Cleland, W. W. Biochemistry 1992, 31, 317-319
7. Gerlt, J. A.; Gassman, P. G. Biochemistry 1993, 32, 11943-11952
8. Gerlt, J. A.; Gassman, P. G. J. Am. Chem. Soc. 1993, 115, 11552-11568
9. Cleland, W. W.; Kreevoy, M. M. Science 1994, 264, 1887-1890
10. Frey, P. A.; Whitt, S. A.; Tobin, J. B. Science 1994, 264, 1927-1930
11. Cleland, W. W.; Frey, P. A.; Gerlt, J. A. J. Biol. Chem. 1998, 273, 25529-25532
12. Cleland, W. W. Adv. Phys. Org. Chem. 2010, 44, 1-17
13. Frey, P. A. In Isotope Effects in Chemistry and Biology; Kohen, A.; Limbach, H. H., Eds.; CRC Press: Boca Raton, FL, 2006; Chapter 40, pp 975-993.
14. Frey, P. A. Encyl. Biol. Chem. 2004, 2, 594-598
15. Northrop, D. B. Acc. Chem. Res. 2001, 34, 790-797
16. Perrin, C. L. Acc. Chem. Res. 2010, 43, 1550-1557
17. Warshel, A.; Sharma, P. K.; Kato, M.; Xiang, Y.; Liu, H.; Olsson, M. H. M. Chem. Rev. 2006, 106, 3210-3235
18. Schutz, C. N.; Warshel, A. Proteins: Struct., Funct., Bioinf. 2004, 55, 711-723
19. Shan, S. O.; Herschlag, D. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 14474-14479
20. Shan, S. O.; Herschlag, D. J. Am. Chem. Soc. 1996, 118, 5515-5518
21. Shan, S. O.; Loh, S.; Herschlag, D. Science 1996, 272, 97-101
22. Shan, S. O.; Herschlag, D. Methods Enzymol. 1999, 308, 246-276
23. Tian, Z.; Fattahi, A.; Lis, L.; Kass, S. R. J. Am. Chem. Soc. 2009, 131, 16984-16988
24. For the gas-phase acidities, see the following reference unless otherwise noted: Ervin, K. M.; DeTuri, V. F. J. Phys. Chem. A 2002, 106, 9947-9956
25. a values, see: Bordwell, F. G. Acc. Chem. Res. 1988, 21, 456-463
26. Thorson, J. S.; Chapman, E.; Murphy, E. C.; Schultz, P. G. J. Am. Chem. Soc. 1995, 117, 1157-1158
27. Kuliopulos, A.; Mildvan, A. S.; Shortle, D.; Talalay, P. Biochemistry 1989, 28, 149-159
28. Kraut, D. A.; Sigala, P. A.; Fenn, T. D.; Herschlag, D. Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 1960-1965
29. Horovitz, A. Fold Des. 1996, 1, R121-R126
30. - were reported in the following reference: Shokri, A.; Schmidt, J.; Wang, X. B.; Kass, S. R. J. Am. Chem. Soc. 2012, 134, 2094-2099
31. Chu, Y.; Deng, H.; Cheng, J. P. J. Org. Chem. 2007, 72, 7790-7793
32. 9-Carboxymethylfluorene was prepared as previously described. See: Matthews, W. S.; Bares, J. E.; Bartmess, J. E.; Bordwell, F. G.; Cornforth, F. J.; Drucker, G. E.; Margolin, Z.; McCallum, R. J.; McCollum, G. J.; Vanier, N. R. J. Am. Chem. Soc. 1975, 97, 7006-7014
33. Spartan '08 for Macintosh; Wavefunction, Inc.: Irvine, CA.
34. Becke, A. D. J. Chem. Phys. 1993, 98, 5648-5652
35. Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. B 1988, 37, 785-789
36. Zhao, Y.; Truhlar, D. G. J. Phys. Chem. A 2008, 112, 1095-1099
37. Zhao, Y.; Truhlar, D. G. Theor. Chem. Acc. 2008, 120, 215-241
38. Zhao, Y.; Truhlar, D. G. Acc. Chem. Res. 2008, 41, 157-167
39. Papajak, E.; Truhlar, D. G. J. Chem. Theory Comput. 2010, 6, 597-601
40. Frisch, M. J.; Gaussian 09; Gaussian, Inc.: Pittsburgh, PA, 2009.
41. Guthrie, J. P. J. Phys. Chem. A 2001, 105, 8495-8499
42. Barone, V.; Cossi, M.; Tomasi, J. J. Chem. Phys. 1997, 107, 3210-3221
43. Cammi, R.; Mennucci, B.; Tomasi, J. J. Phys. Chem. A 1998, 102, 870-875
44. Cammi, R.; Mennucci, B.; Tomasi, J. J. Phys. Chem. A 2000, 104, 4690-4698
45. Cossi, M.; Rega, N.; Scalmani, G.; Barone, V. J. Comput. Chem. 2003, 24, 669-681
46. Silva, C. O.; Silva, M. A.; Nascimento, M. A. C. J. Phys. Chem. A 1999, 103, 11194-11199
47. Toth, A. M.; Liptak, M. D.; Phillips, D. L.; Shields, G. C. J. Chem. Phys. 2001, 114, 4595-4606
48. Liptak, M. D.; Shields, G. C. J. Am. Chem. Soc. 2001, 123, 7314-7319
49. Liptak, M. D.; Gross, K. C.; Seybold, P. G.; Feldgus, S.; Shields, G. C. J. Am. Chem. Soc. 2002, 124, 6421-6429
50. Richard, J. P. Biochemistry 1998, 37, 4305-4309
51. Kirby, A. J. Acc. Chem. Res. 1997, 30, 290-296
52. Fafarman, A. T.; Sigala, P. A.; Schwans, J. P.; Fenn, T. D.; Herschlag, D.; Boxer, S. G. Proc. Natl. Acad. Sci. U.S.A. 2012, 109, E299-E308
53. Dong, J.; Zhuang, Z.; Song, F.; Dunaway-Mariano, D.; Carey, P. R. J. Raman Spectrosc. 2012, 43, 65-71
54. Chenprakhon, P.; Panijpan, B.; Chaiyen, P. J. Chem. Educ. 2012, 89, 791-795
55. Childs, W.; Boxer, S. G. Biochemistry 2010, 49, 2725-2731
56. Zhao, G.; Jorns, M. S. Biochemistry 2005, 44, 16866-16874
57. Liang, T. C.; Abeles, R. H. Biochemistry 1987, 26, 7603-7608
58. Ding, F.; Smith, J. M.; Wang, H. J. Org. Chem. 2009, 74, 2679-2691
59. Fu, Y.; Liu, L.; Li, R. Q.; Liu, R.; Guo, Q. X. J. Am. Chem. Soc. 2004, 126, 814-822
60. Namazian, M.; Heidary, H. THEOCHEM 2003, 620, 257-263
61. Saracino, G. A. A.; Improta, R.; Barone, V. Chem. Phys. Lett. 2003, 373, 411-415
62. Cramer, C. J.; Truhlar, D. G. Chem. Rev. 1999, 99, 2161-2200
63. Angel, L. A.; Ervin, K. M. J. Phys. Chem. A 2006, 110, 10392-10403
64. Wang, X. B.; Vorpagel, E. R.; Yang, X.; Wang, L. S. J. Phys. Chem. A 2001, 105, 10468-10474
65. Bartmess, J. E. In NIST Chemistry WebBook, NIST Standard Reference Database Number 6; Mallard, W. G., Linstrom, P. J., Eds.; National Institute of Standards and Technology: Gaithersburg, MD, http://webbook.nist.gov.
66. n, where n = 1-6, and the second solvation shell (n = 4-6) is worth 36% of the inner one (n = 1-3). See: Meot-Ner (Mautner), M. J. Phys. Chem. 1986, 90, 6616-6624
67. Chen, J.; McAllister, M. A.; Lee, J. K.; Houk, K. N. J. Org. Chem. 1998, 63, 4611-4619
68. Pan, Y.; McAllister, M. A. J. Am. Chem. Soc. 1998, 120, 166-169
69. Rueping, M.; Kuenkel, A.; Atodiresei., I. Chem. Soc. Rev. 2011, 40, 4539-4549
70. Akiyama, T. Chem. Rev. 2007, 107, 5744-5758
71. Akiyama, T.; Itoh, J.; Fuchibe, K. Adv. Synth. Catal. 2006, 348, 999-1010
72. Duhamel, L.; Duhamel, P.; Plaquevent, J. C. Tetrahedron: Asymmetry 2004, 15, 3653-3691
73. Eames, J.; Weerasooriya, N. Tetrahedron: Asymmetry 2001, 12, 1-24
74. Fehr, C. Angew. Chem., lnt. Ed. Engl. 1996, 35, 2566-2587
75. Van Arnam, E. B.; Lester, H. A.; Dougherty, D. A. ACS Chem. Biol. 2011, 6, 1063-1068
76. Kohrer, C.; RajBhandary, U. L. Nucleic Acids Mol. Biol. 2009, 22, 205-229
77. England, P. M. Biochemistry 2004, 43, 11623-11629
78. Beene, D. L.; Dougherty, D. A.; Lester, H. A. Curr. Opin Neurobiol. 2003, 13, 264-270
79. Siegel, J. B. Science 2010, 329, 309-313
80. Privett, H. K. Proc. Natl. Acad. Sci. U.S.A. 2012, 109, 3790-3795