On the interaction of aliphatic amines and ammonium ions with carboxylic acids in solution and in receptor pockets

Journal of Physical Chemistry B

Volumn 116, Issue 18, 2012, Pages 5425-5436

  Nagy, Peter I ^a   Erhardt, Paul W ^a,b  

^a UNIVERSITY OF TOLEDO   (United States)

^b MEDICAL COLLEGE OF OHIO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINES; CARBOXYLATION; CHAINS; CHLORINE COMPOUNDS; COMPLEXATION; FREE ENERGY; HYDROGEN BONDS; MOLECULES; ORGANIC SOLVENTS; SOLUTIONS; STABILIZATION;

ASSOCIATION ENERGIES; BOUND WATER MOLECULES; ELECTROSTATIC INTERACTION ENERGY; FREE ENERGY PERTURBATION; INTERMOLECULAR HYDROGEN BONDS; SOLVATION FREE ENERGIES; STABILIZATION ENERGY; STABILIZATION FACTORS;

IONS;

EID: 84961977344     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp300588q     Document Type: Article

References (60)

1. Brejc, K.; Van Dijk, W. J.; Klaassen, R. V.; Schuurmans, M.; Van der Oost, J.; Smit, A. B.; Sixma, L. K. Nature (London) 2001, 411 (6835) 269-276
2. Cashin, A, L.; Petersson, E. J.; Lester, H. A.; Dougherty, D. A. J. Am. Chem. Soc. 2005, 127, 350-356
3. Goodman and Gilman's The Pharmacological Basis of Therapeutics, 9 th ed.; Hardman, J. G.; Limbird., L. E.; Molinoff, P. B.; Goodman Gilman, A., Eds.; McGraw-Hill: New York, 1996.
4. Foyes Principles of Medicinal Chemistry, 5 th ed.; Williams, D. A.; Lemke, T. L., Eds.; Lippincott, Williams & Wilkins: Baltimore, MD, 2002.
5. CRC Handbook of Chemistry and Physics, 88 th ed.; Lide, D. R., Ed.; CRC Press Taylor and Francis Group: Boca Raton, FL, 2007-2008.
6. Woods, C. J.; Manby, F. R.; Mulholland, A. J. J. Chem. Phys. 2008, 128, 014109-1-014109-8
7. Nagy, P. I.; Erhardt, W. P. J. Phys. Chem. B 2010, 114, 16436-16442
8. Náray-Szabó., G.; Nagy, P. Int. J. Quantum Chem. 1989, 35, 215-221
9. Okamoto, R.; Souma, S.; Kajihara, Y. J. Org. Chem. 2008, 73, 3460-3466
10. Nagy, P. I.; Messer, W. S., Jr. J. Phys. Chem. B 2011, 115, 4758-4767
11. Nagy, P. I. J. Phys. Chem. B 2011, 115, 9634-9645
12. Miertus, S.; Scrocco, E.; Tomasi, J. Chem. Phys. 1981, 55, 117-129
13. Tomasi, J.; Persico, M. Chem. Rev. 1994, 94, 2027-2094
14. Cancès, E.; Mennucci, B.; Tomasi, J. J. Chem. Phys. 1997, 107, 3032-3041
15. Cancès, E.; Mennucci, B. J. Chem. Phys. 1998, 109, 249-259
16. Cancès, E.; Mennucci, B. J. Chem. Phys. 1998, 109, 260-266
17. Tomasi, J.; Mennucci, B.; Cammi, R. Chem. Rev. 2005, 105, 2999-3094
18. Bondi, A. J. Phys. Chem. 1964, 68, 441-451
19. Nagy, P. I.; Alagona, G.; Ghio, C. J. Chem. Theory Comput. 2007, 3, 1249-1266
20. Hehre, W. J.; Radom, L.; Schleyer, P. v. R.; Pople, J. A. Ab Initio Molecular Orbital Theory; Wiley: New York, 1986.
21. Dunning, T. H., Jr. J. Chem. Phys. 1989, 90, 1007-1023
22. Kendall, R. A.; Dunning, T. H., Jr.; Harrison, R. J. J. Chem. Phys. 1992, 96, 6796-6806
23. Peterson, K. A. Annu. Rep. Comput. Chem. 2007, 3, 195-206
24. McQuarrie, D. A. Statistical Mechanics; University Science Books: Sausalito, CA, 2000.
25. Purvis, G. D.; Bartlett, R. J. J. Chem. Phys. 1982, 76, 1910-1918
26. Raghavachari, K.; Trucks, G. W.; Pople, J. A.; Head-Gordon, M. Chem. Phys. Lett. 1989, 157, 479-483
27. Hobza, P. Annu. Rep. Prog. Chem., Sect. C: Phys. Chem. 2004, 100, 3-27
28. Halkier, A.; Koch, H.; Jorgensen, P.; Christiansen, O.; Beck-Nielsen, I. M.; Helgaker, T. Theor. Chem. Acc. 1997, 97, 150-157
29. Wilson, A.; Dunning, T. H., Jr. J. Chem. Phys. 1997, 106, 8718-8726
30. Helgaker, T.; Klopper, W.; Koch, H.; Noga, J. J. Chem. Phys. 1997, 106, 9639-9646
31. Grimme, S. J. Comput. Chem. 2006, 27, 1787
32. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Gaussian 09, revision A.01; Gaussian, Inc.: Wallingford, CT, 2009.
33. Jorgensen, W. L.; Madura, J. D. J. Am. Chem. Soc. 1983, 105, 1407-1413
34. Jorgensen, W. L.; Swenson, C. J. J. Am. Chem. Soc. 1985, 107, 1489-1496
35. Jorgensen, W. L.; Gao, J. J. Phys. Chem. 1986, 90, 2174-2182
36. Jorgensen, W. L.; Briggs, J. M.; Contreras, M. L. J. Phys. Chem. 1990, 94, 1683-1686
37. Nagy, P. I.; V̈lgyi, G.; Takács-Novák, K. J. Phys. Chem. B 2008, 112, 2085-2094
38. Nagy, P. I.; Dhananjeyan, M. R.; Erhardt, P. W. THEOCHEM 2009, 895, 116-126
39. Zwanzig, R. W. J. Chem. Phys. 1954, 22, 1420-1426
40. Jorgensen, W. L.; Ravimohan, C. J. Chem. Phys. 1985, 83, 3050-3054
41. Jorgensen, W. L. BOSS, version 4.8; Biochemical and Organic Simulation System Users Manual; Yale University: New Haven, CT, 2007.
42. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926-935
43. Essex, J.; Jorgensen, W. J. Phys. Chem. 1995, 99, 17956-17962
44. Ewald, P. P. Ann. Phys. 1921, 369, 253-287
45. Allen, M. P.; Tildesley, D. Computer Simulations of Liquids; Oxford University Press: Oxford, U.K., 1987.
46. Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. J. Am. Chem. Soc. 1996, 118, 11225-11236
47. Rizzo, R. C.; Jorgensen, W. L. J. Am. Chem. Soc. 1999, 121, 4827-4836
48. Breneman, C. M.; Wiberg, K. B. J. Comput. Chem. 1990, 11, 361-373
49. Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. B 1988, 37, 785-789
50. Becke, A. D. J. Chem. Phys. 1993, 98, 5648-5652
51. Nagy, P. I.; Takács-Novák, K. J. Am. Chem. Soc. 2000, 122, 6583-6593
52. Nagy, P. I.; Maheshwari, A.; Kim, Y.-W.; Messer, W. S., Jr. J. Phys. Chem. B 2010, 114, 349-360
53. Ho, J.; Klamt, A.; Coote, M. L. J. Phys. Chem. A 2010, 114, 13442-13444
54. Ben-Nun, M.; Levine, R. D. Int. Rev. Phys. Chem. 1995, 14, 215-270
55. Moriyasu, M.; Kato, A.; Hashimoto, Y. J. Chem. Soc., Perkin Trans. 2 1986, 515-520
56. De Oliveira, P. R.; Viesser, R. V.; Guerrero, P. G., Jr.; Rittner, R. Spectrochim. Acta, Part A 2011, 78, 1599-1605
57. Monti, S.; Nagy, P. I. Phys. Chem. Chem. Phys. 2011, 13, 6270-6279
58. Nagy, P. I. Phys. Chem. Chem. Phys. 2012, 14, 849-857
59. Cramer, C. J. Essentials of Computational Chemistry; Wiley: New York, 2002; pp 78-80.
60. Jensen, K. P.; Jorgensen, W. L. J. Chem. Theory Comput. 2006, 2, 1499-1509