On the mechanism and rate of spontaneous decomposition of amino acids

Journal of Physical Chemistry B

Volumn 115, Issue 46, 2011, Pages 13624-13632

  Alexandrova, Anastassia N ^a   Jorgensen, William L ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b YALE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVATION ENERGY; AMIDES; AMINES; CALCULATIONS; CARBON DIOXIDE; CARBOXYLATION; COMPUTER SIMULATION; DENSITY FUNCTIONAL THEORY; FREE ENERGY; MONTE CARLO METHODS; PERTURBATION TECHNIQUES; RATE CONSTANTS; REACTION KINETICS;

AB INITIO AND DFT CALCULATIONS; AMIDE BOND; ENERGY OF ACTIVATION; FREE ENERGY PERTURBATION; HYDRATION MODELS; KINETICS AND MECHANISM; MONTE CARLO SIMULATION; QM/MM CALCULATIONS;

AMINO ACIDS;

EID: 81555228449     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp2081808     Document Type: Article

References (85)

1. Snider, M. J.; Wolfenden, R. J. Am. Chem. Soc. 2000, 122, 11507-11508
2. Conway, D.; Libby, W. F. J. Am. Chem. Soc. 1958, 80, 1077-1080
3. Abelson, P. H. Sci. Am. 1956, 195, 83-91
4. Kahne, D.; Still, W. C. J. Am. Chem. Soc. 1988, 110, 7529-7534
5. Bryant, R. A. R.; Hansen, D. E. J. Am. Chem. Soc. 1996, 118, 5498-5499
6. Radzicka, A.; Wolfenden, R. J. Am. Chem. Soc. 1996, 118, 6105-6109
7. Bauwe, H.; Kolukisaoglu, U. J. Exp. Botany 2003, 54, 1523-1535
8. Rawsthorne, S.; Douce, R.; Oliver, D. Soc. Exp. Biol. Semin. Ser. 1995, 56, 87-109
9. Tcherkez, G. Func. Plant Biol. 2006, 33, 911-920
10. Hausler, R. E.; Lea, P. J.; Leegood, R. C. Planta 1994, 194, 418-35
11. Hausler, R. E.; Blackwell, R. D.; Lea, P. J.; Leegood, R. C. Planta 1994, 194, 406-417
12. Devi, M. T.; Raghavendra, A. S. Photosyn. Res. 1993, 38, 177-184
13. Hiraga, K.; Kikuchi, G. J. Biochem. (Tokyo, Japan) 1982, 92, 937-944
14. Klein, S. M.; Sagers, R. D. Biol. Chem. 1966, 241, 206-209
15. Higara, K.; Kikuchi, G. Biol. Chem. 1980, 255, 11671-11676
16. Kikuchi, G. Mol. Cell. Biochem. 1973, 1, 169-186
17. Sagers, R. D.; Gunsalus, J. C. J. Bacteriol. 1961, 81, 541-549
18. Cetin, I.; Fennessey, P. V.; Quick, A. N., Jr.; Marconi, A. M.; Meschia, G.; Battaglia, F. C.; Sparks, J. W. Am. J. Physiol. 1991, 260, E371-E378
19. Zieske, L. R.; Davis, L. J. Biol. Chem. 1983, 258, 10355-10359
20. Shingles, R.; Woodrow, L.; Grodzinski, B. Plant Physiol. 1984, 74, 705-710
21. Walton, N. J.; Woolhouse, H. W. Planta 1986, 167, 119-128
22. Kikuchi, G. Mol. Cell. Biochem. 1973, 1, 169-187
23. Yoshida, T.; Kikuchi, G. J. Biochem. 1972, 72, 1503-1516
24. Roswell, E. V.; Al-Naama, M. M.; Rowsell, K. V. Biochem. J. 1982, 204, 313-321
25. Frearon, W. R.; Montgomery, E. G. Biochem. J. 1924, 18, 576-582 and references therein.
26. Zeller, E. A. Helv. Chim. Acta 1938, 21, 880-890
27. Usha, V.; Jayaraman, R.; Toro, J. C.; Hoffner, S. E.; Das, K. S. Can. J. Microbiol. 2002, 48, 7-13
28. Stephenson, M.; Gale, E. F. Biochem. J. 1937, 31, 1316-1322
29. Janke, A.; Tayenthal, W. Biochem. Z. 1937, 289, 76-86
30. Metzler, D. E.; Snell, E. E. J. Biol. Chem. 1952, 198, 353-361
31. Ikawa, M.; Snell, E. E. J. Am. Chem. Soc. 1954, 76, 4900-4902
32. Hill, M.; Mann, P. J. G. Biochem. J. 1966, 99, 454-468
33. Nishiya, Y.; Imanaka, T. FEBS Lett. 1998, 438, 249-256
34. Molla, G.; Motteran, L.; Job, M.; Pilone, M. S.; Pollegioni, L. Eur. J. Biochem. 2003, 270, 1474-1482
35. Stadtman, T. S.; Elliott, P.; Tiemann, L. J. Biol. Chem. 1958, 231, 961-973
36. Stadtman, T. S.; Elliott, P. J. Am. Chem. Soc. 1956, 78, 2020-2021
37. Kohlstock, U.-M.; Rücknagel, K. P.; Reuter, M.; Schiethorn, A.; Andreesen, J. R.; Söhling, B. Eur. J. Biochem. 2001, 268, 6417-6425
38. Weizmann, Ch.; Bergmann, E.; Hirshberg, Y. J. Am. Chem. Soc. 1936, 58, 1675-1678 and references therein.
39. Venkatesh, M. S.; Arthur, E. M. J. Am. Chem. Soc. 1991, 113, 6479-6487
40. Donnasibilla, L. B.; Olivi, O. Acta Vitaminol. 1952, 6, 6-9
41. Saiprakash, P. K.; Rajanna, K. C.; Devi, Y. U. Ind. J. Chem. B 1984, 23B, 646-649
42. Jois, M.; Ewart, S. H.; Brosnan, J. T. Biochem. J. 1992, 283, 3435-439
43. Zou, J.; John, G.; Parkinson, J. A.; Chen, Yu.; Sadler, P. Chem. Commun. 1999, 1359-1360
44. Reddy, M. K.; Reddy, C. S.; Sundaram, E. V. Ind. J. Chem. A 1984, 23A, 197-199
45. Berrenscheen, H. K.; Danzer, W. Z. Physiol. Chem. 1933, 220, 57-60
46. Kisch, B.; Schuwirth, K. Biochem. Z. 1993, 257, 89-94
47. Hubard, S. S. J. Biol. Chem. 1938, 126, 489-492
48. Hubard, S. S. J. Am. Chem. Soc. 1939, 61, 752-753
49. Pugh, C. E. M.; Raper, H. S. Biochem. J. 1927, 21, 1370-1383
50. Austin, A. T. J. Chem. Soc. 1950, 149-150
51. Bonifacíć, M.; Štefanić, I.; Hug, G. L.; Armstrong, D. A.; Asmus, K.-D. J. Am. Chem. Soc. 1998, 120, 9930-9940
52. Voeikov, V. L.; Baskakov, I. V.; Kafkalias, K.; Naletov, V. I. Bioorg. Khim. 1996, 22, 39-47
53. Dale, W. M.; Davis, J. V.; Gilbert, C. W. Biochem. J. 1949, 45, 543-546
54. Wieland, T.; Vogelbach, C.; Bielig, H. J. Ann. 1948, 561, 116-123
55. Acevedo, O.; Jorgesen, W. L. J. Org. Chem. 2006, 71, 4896-4902
56. Acevedo, O.; Jorgesen, W. L. J. Am. Chem. Soc. 2005, 127, 8829-8834
57. Jorgensen, W. L.; Tirado-Rives, J. J. Comput. Chem. 2005, 26, 1689-1700
58. Repasky, M. P.; Chandrasekhar, J.; Jorgensen, W. L. J. Comput. Chem. 2002, 23, 1601-1622
59. Tubert-Brohman, I.; Guimarães, C. R. W.; Repasky, M. P.; Jorgensen, W. L. J. Comput. Chem. 2003, 25, 138-150
60. Vayner, G.; Houk, K. N.; Jorgensen, W. L.; Brauman, J. I. J. Am. Chem. Soc. 2004, 126, 9054-9058
61. Acevedo, O.; Jorgensen, W. L. Org. Lett. 2004, 6, 2881-2884
62. Acevedo, O.; Jorgensen, W. L. J. Am. Chem. Soc. 2005, 127, 8829-8834
63. Acevedo, O.; Jorgensen, W. L. J. Am. Chem. Soc. 2006, 128, 6141-6146
64. Acevedo, O.; Jorgensen, W. L. J. Org. Chem. 2006, 71, 4896-4902
65. Alexandrova, A. N.; Jorgensen, W. L. J. Phys. Chem. B 2007, 111, 720-730
66. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926-935
67. Jorgensen, W. L.; Jenson, C. J. Comput. Chem. 1998, 19, 1179-1186
68. Udier-Blagovic, M.; Morales de Tirado, P.; Pearlman, S. A.; Jorgensen, W. L. J. Comput. Chem. 2004, 25, 1322-1332
69. Jorgensen, W. L.; Ulmschneider, J. P.; Tirado-Rives, J. J. Phys. Chem. B 2004, 108, 16264-16270
70. Tubert-Brohman, I.; Acevedo, O.; Jorgensen, W. L. J. Am. Chem. Soc. 2006, 128, 16904-16913
71. Hermans, J.; Wang, L. J. Am. Chem. Soc. 1997, 119, 2707-2714
72. Parr, R. G.; Yang, W. Density-functional theory of atoms and molecules; Oxford University Press: Oxford, U.K., 1989.
73. Becke, A. D. J. Chem. Phys. 1993, 98, 5648-5652
74. Perdew, J. P.; Chevary, J. A.; Vosko, S. H.; Jackson, K. A.; Pederson, M. R.; Singh, D. J.; Fiolhais, C. Phys. Rev. B 1992, 46, 6671-6687
75. Clark, T.; Chandrasekhar, J.; Spitznagel, G. W.; Schleyer, P. v. R. J. Comput. Chem. 1983, 4, 294-301
76. Frisch, M. J.; Pople, J. A.; Binkley, J. S. J. Chem. Phys. 1984, 80, 3265-3269
77. Head-Gordon, M.; Pople, J. A.; Frisch, M. J. Chem. Phys. Lett. 1988, 153, 503-506
78. Frisch, M. J.; Head-Gordon, M.; Pople, J. A. Chem. Phys. Lett. 1990, 166, 275-280
79. Frisch, M. J.; Head-Gordon, M.; Pople, J. A. Chem. Phys. Lett. 1990, 166, 281-289
80. Head-Gordon, M.; Head-Gordon, T. Chem. Phys. Lett. 1994, 220, 122-128
81. Pople, J. A.; Krishnan, R.; Schlegel, H. B.; Binkley, J. S. Int. J. Quantum Chem. 1979, 13, 325
82. Handy, N. C.; Schaefer, H. F., III. J. Chem. Phys. 1984, 81, 5031-5033
83. Barone, V.; Cossi, M. J. Phys. Chem. A 1998, 102, 1995-2001
84. Cossi, M.; Rega, N.; Scalmani, G.; Barone, V. J. Comput. Chem. 2003, 24, 669-681
85. Handbook of Chemistry and Physics, 83 rd ed.; Lide, D. R., Ed.; CRC Press: Boca Raton, FL, 2002 - 2003; pp 7-1, and references therein.