Performance of SM6, SM8, and SMD on the SAMPL1 test set for the prediction of small-molecule solvation free energies

Journal of Physical Chemistry B

Volumn 113, Issue 14, 2009, Pages 4538-4543

  Marenich, Aleksandr V ^a   Cramer, Christopher J ^a   Truhlar, Donald G ^a  

^a University of Minnesota   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FREE ENERGY; MOLECULES;

AQUEOUS SOLVATIONS; ATOMIC CHARGES; BASIS SETS; CHARGE MODELS; CONTINUUM SOLVATION MODELS; DENSITY FUNCTIONAL; ELECTRON DENSITIES; ELECTROSTATIC COMPONENTS; GENERALIZED BORN MODELS; QUANTUM MECHANICALS; ROOT-MEAN SQUARE DEVIATIONS; SMALL MOLECULES; SOLVATION FREE ENERGIES; SULFONYLUREAS; TEST SETS;

SOLVATION;

EID: 65249135879     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp809094y     Document Type: Article

References (71)

1. Beveridge, D. L.; DiCapua, F. M. Annu. Rev. Biophys. Biophys. Chem. 1989, 18, 431-492.
2. Kollman, P. Chem. Rev. 1993, 93, 2395-2417.
3. Orozco, M.; Luque, F. J. Chem. Rev. 2000, 100, 4187-4225.
4. Cramer, C. J.; Truhlar, D. G. Chem. Rev. 1999, 99, 2161-2200.
5. Tomasi, J.; Mennucci, B.; Cammi, R. Chem. Rev. 2005, 105, 2999- 3093.
6. Cramer, C. J. Essentials of Computational Chemistry: Theories and Models, 2nd ed.; John Wiley & Sons: Chichester, 2004.
7. Cramer, C. J.; Truhlar, D. G. In Reviews in Computational Chemistry; Lipkowitz, K. B., Boyd, D. B., Eds.; VCH: New York, 1995; Vol. 6, p 1-72.
8. Ziegler, T.; Autschbach, J. Chem. Rev. 2005, 105, 2695-2722.
9. Dill, K. A.; Truskett, T. M.; Vlachy, V.; Hribar-Lee, B. Annu. Rev. Biophys. Biomol. Struct. 2005, 34, 173-199.
10. Vitha, M.; Carr, P. W. J. Chromatogr. A 2006, 1126, 143-194.
11. Chang, T. M.; Dang, L. X. Chem. Rev. 2006, 106, 1305-1322.
12. Benjamin, I. Chem. Rev. 2006, 106, 1212-1233.
13. Cruz, L.; Urbanc, B.; M, B. J.; Lazo, N. D.; Teplow, D. B.; Stanley, H. E. Proc. Natl. Acad. Sci., USA 2005, 102, 18258-18263.
14. Gilson, M. K.; Zhou, H. X. Annu. Rev. Biophys. Biomol. Struct. 2007, 36, 21-42.
15. Jorgensen, W. L.; Duffy, E. M. Adv. Drug Deliv. Rev. 2002, 54, 355-366.
16. Raevsky, O. A. Mini-Rev. Med. Chem. 2004, 4, 1041-1052.
17. Hellou, J.; Steller, S.; Leonard, J.; Langille, M. A.; Tremblay, D. Marine Environ. Res. 2005, 59, 101-117.
18. Balakin, K. V.; Savchuk, N. P.; Tetko, I. V. Curr. Med. Chem. 2006, 13, 223-241.
19. Johnson, S. R.; Zheng, W. F. AAPS J. 2006, 8, E27-E40.
20. Nicholls, A.; Mobley, D. L.; Guthrie, J. P.; Chodera, J. D.; Bayly, C. I.; Cooper, M. D.; Pande, V. S. J. Med. Chem. 2008, 51, 769-779.
21. Marenich, A. V.; Olson, R. M.; Kelly, C. P.; Cramer, C. J.; Truhlar, D. G. J. Chem. Theory Comput. 2007, 3, 2011-2033.
22. Zhao, Y.; Truhlar, D. G. Theor. Chem. Acc. 2008, 120, 215-241.
23. Hehre, W. J.; Radom, L.; Schleyer, P. v. R.; Pople, J. A. Ab Initio Molecular Orbital Theory; Wiley: New York, 1986.
24. Olson, R. M.; Marenich, A. V.; Cramer, C. J.; Truhlar, D. G. J. Chem. Theory Comput. 2007, 3, 2046-2054.
25. Chamberlin, A. C.; Cramer, C. J.; Truhlar, D. G. J. Phys. Chem. B 2008, 112, 8651-8655.
26. Guthrie, J. P. J. Phys. Chem. B 2009, 113, 4501-4507.
27. Cramer, C. J.; Truhlar, D. G. J. Am. Chem. Soc. 1991, 113, 8305- 8311.
28. Cramer, C. J.; Truhlar, D. G. In Trends and Perspectives in Modern Computational Science; Maroulis, G., Simos, T. E., Eds.; Brill Academic: Amsterdam, 2006; Vol. 6, p 112-140.
29. Cramer, C. J.; Truhlar, D. G. Acc. Chem. Res. 2008, 41, 760-768.
30. Marenich, A. V.; Cramer, C. J.; Truhlar, D. G. J. Phys. Chem ., in press (DOI: 10.1021/jp810292n).
31. Kelly, C. P.; Cramer, C. J.; Truhlar, D. G. J. Chem. Theory Comput. 2005, 1, 1133-1152.
32. Hoijtink, G. J.; de Boer, E.; Van der Meij, P. H.; Weijland, W. P. Recl. Trav. Chim. Pays-Bas 1956, 75, 487-503.
33. Jano, I. CR. Acad. Sci. Paris 1965, 261, 103-105.
34. Tapia, O. In Quantum Theory of Chemical Reactions; Daudel, R., Pullman, A., Salem, L., Viellard, A., Eds.; Reidel: Dordrecht, 1980; Vol. 2, p 25-72.
35. Tucker, S. C.; Truhlar, D. G. Chem. Phys. Lett. 1989, 157, 164- 170.
36. Still, W. C.; Tempczyk, A.; Hawley, R. C.; Hendrickson, T. J. Am. Chem. Soc. 1990, 112, 6127-6129.
37. Chambers, C. C.; Giesen, D. J.; Hawkins, G. D.; Vaes, W. H. J.; Cramer, C. J.; Truhlar, D. G. In Rational Drug Design; Truhlar, D. G., Howe, W. J., Hopfinger, A. J., Blaney, J. M., Dammkoehler, R. A., Eds.; Springer: New York, 1999, p 51-72.
38. Liotard, D. A.; Hawkins, G. D.; Lynch, G. C.; Cramer, C. J.; Truhlar, D. G. J. Comput. Chem. 1995, 16, 422-440.
39. Giesen, D. J.; Storer, J. W.; Cramer, C. J.; Truhlar, D. G. J. Am. Chem. Soc. 1995, 117, 1057-1068.
40. Zhu, T.; Li, J.; Hawkins, G. D.; Cramer, C. J.; Truhlar, D. G. J. Chem. Phys. 1998, 109, 9117-9133.
41. Cancès, E.; Mennucci, B.; Tomasi, J. J. Chem. Phys. 1997, 107, 3032-3041.
42. Kelly, C. P.; Cramer, C. J.; Truhlar, D. G. J. Phys. Chem. B 2006, 110, 16066-16081.
43. Kelly, C. P.; Cramer, C. J.; Truhlar, D. G. J. Phys. Chem. B 2007, 111, 408-422.
44. Marenich, A. V.; Cramer, C. J.; Truhlar, D. G. J. Chem. Theor. Comput. 2008, 4, 877-887.
45. Soteras, I.; Curutchet, C.; Bidon-Chanal, A.; Orozco, M.; Luque, F. J. J. Mol. Struct. (THEOCHEM) 2005, 727, 29-40.
46. Pierotti, R. A. J. Phys. Chem. 1963, 67, 1840-1845.
47. Pierotti, R. A. Chem. Rev. 1976, 76, 717-726.
48. Claverie, P. In Intermolecular Interactions: From Diatomics to Biomolecules; Pullman, B., Eds.; Wiley: Chichester, 1978, p 69-305.
49. Bachs, M.; Luque, F. J.; Orozco, M. J. Comput. Chem. 1994, 15, 446-454.
50. Luque, F. J.; Bachs, M.; Orozco, M. J. Comput. Chem. 1994, 15, 847-857.
51. Orozco, M.; Bachs, M.; Luque, F. J. J. Comput. Chem. 1995, 16, 563-575.
52. Curutchet, C.; Cramer, C. J.; Truhlar, D. G.; Ruiz-López, M. F.; Rinaldi, D.; Orozco, M.; Luque, F. J. J. Comput. Chem. 2003, 24, 284- 297.
53. Shimizu, K.; Freitas, A. A.; Farah, J. P. S.; Dias, L. G. J. Phys. Chem. A 2005, 109, 11322-11327.
54. Basilevsky, M. V.; Leontyev, I. V.; Luschekina, S. V.; Kondakova, O. A.; Sulimov, V. B. J. Comput. Chem. 2006, 27, 552-570.
55. de O. Mendes, C. L.; da Silva, C. O.; da Silva, E. C. J. Phys. Chem. A 2006, 110, 4034-4041.
56. Barone, V.; Cossi, M.; Tomasi, J. J. Chem. Phys. 1997, 107, 3210- 3221.
57. Ben-Naim, A. Solvation Thermodynamics; Plenum: New York, 1987.
58. Higashi, M.; Marenich, A. V.; Olson, R. M.; Chamberlin, A. C.; Pu, J.; Kelly, C. P.; Thompson, J. D.; Xidos, J. D.; Li, J.; Zhu, T.; Hawkins, G. D.; Chuang, Y.-Y.; Fast, P. L.; Lynch, B. J.; Liotard, D. A.; Rinaldi, D.; Gao, J.; Cramer, C. J.; Truhlar, D. G. GAMESSPLUS, version 2008-2; University of Minnesota: Minneapolis, 2008.
59. Olson, R. M.; Marenich, A. V.; Chamberlin, A. C.; Kelly, C. P.; Xidos, J. D.; Li, J.; Thompson, J. D.; Hawkins, G. D.; Winget, P. D.; Zhu, T.; Rinaldi, D.; Liotard, D. A.; Cramer, C. J.; Truhlar, D. G.; Frisch, M. J. MN-GSM, version 2008; University of Minnesota: Minneapolis, 2008.
60. Kong, J.; White, C. A.; Krylov, A. I.; Sherrill, D.; Adamson, R. D.; Furlani, T. R.; Lee, M. S.; Lee, A. M.; Gwaltney, S. R.; Adams, T. R.; Ochsenfeld, C.; Gilbert, A. T. B.; Kedziora, G. S.; Rassolov, V. A.; Maurice, D. R.; Nair, N.; Shao, Y.; Besley, N. A.; Maslen, P. E.; Dombroski, J. P.; Daschel, H.; Zhang, W.; Korambath, P. P.; Baker, J.; Byrd, E. F. C.; Voorhis, T. V.; Oumi, M.; Hirata, S.; Hsu, C.-P.; Ishikawa, N.; Florian, J.; Warshel, A.; Johnson, B. G.; Gill, P. M. W.; Head-Gordon, M.; Pople, J. A. J. Comput. Chem. 2000, 21, 1532-1548.
61. Marenich, A. V.; Hawkins, G. D.; Liotard, D. A.; Cramer, C. J.; Truhlar, D. G. GESOL, version 2008; University of Minnesota: Minneapolis, 2008.
62. Nakamura, H.; Xidos, J. D.; Chamberlin, A. C.; Kelly, C. P.; Valero, R.; Thompson, J. D.; Li, J.; Hawkins, G. D.; Zhu, T.; Lynch, B. J.; Volobuev, Y.; Rinaldi, D.; Liotard, D. A.; Cramer, C. J.; Truhlar, D. G. HONDOPLUS, v.5.1; University of Minnesota: Minneapolis, MN, 2007.
63. Chamberlin, A. C.; Kelly, C. P.; Thompson, J. D.; Lynch, B. J.; Xidos, J. D.; Li, J.; Hawkins, G. D.; Zhu, T.; Volobuev, Y.; Rinaldi, D.; Liotard, D. A.; Cramer, C. J.; Truhlar, D. G. SMxGAUSS, version 3.4.2; University of Minnesota: Minneapolis, 2007.
64. Jaguar 6.5, Release 112; Schrödinger, Inc.: Portland, OR, 2005.
65. Fendinger, N. J.; Glotfelty, D. E. Environ. Sci. Technol. 1988, 22, 1289-1293.
66. Wauchope, R. D.; Buttler, T. M.; Hornsby, A. G.; Augustijn- Beckers, P. W. M.; Burt, J. P. In Reviews of Environmental Contamination and Toxicology; Ware, G. W., Ed.; Springer Verlag: New York, 1992; Vol. 123.
67. Cramer, C. J.; Truhlar, D. G. In Free Energy Calculations in Rational Drug Design; Reddy, M. R., Erion, M. D., Eds.; Kluwer Academic/ Plenum: New York, 2001, p 63-95.
68. Schmuckler, M. E.; Barefoot, A. C.; Kleier, D. A.; Cobranchi, D. P. Pest Manage. Sci. 2000, 56, 521-532.
69. Cramer, C. J.; Truhlar, D. G. J. Comput.-Aid. Mol. Des. 1992, 6, 629-666.
70. Cramer, C. J.; Truhlar, D. G. In Solvent Effects and Chemical Reactivity; Tapia, O., Bertrán, J., Eds.; Kluwer: Dordrecht, 1996, p 1-81.
71. Adamo, C.; Barone, V. J. Chem. Phys. 1998, 108, 664-675.