An accurate prediction of hydration free energies by combination of molecular integral equations theory with structural descriptors

Journal of Physical Chemistry B

Volumn 114, Issue 37, 2010, Pages 12068-12079

  Ratkova, Ekaterina L ^a   Chuev, Gennady N ^a,b   Sergiievskyi, Volodymyr P ^a   Fedorov, Maxim V ^a  

^a MAX PLANCK INSTITUTE FOR MATHEMATICS IN THE SCIENCES   (Germany)

^b INSTITUTE OF THEORETICAL AND EXPERIMENTAL BIOPHYSICS   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

ALDEHYDES; BENZENE; CHEMICAL BONDS; ETHERS; FREE ENERGY; KETONES; MOLECULES; PHENOLS;

ACCURATE PREDICTION; BENZENE RING; CHEMICAL CLASS; CHEMICAL DESCRIPTORS; CHEMICAL STRUCTURE; DOUBLE BONDS; ENERGY EXPRESSION; ETHER GROUP; EXCLUDED VOLUME; HALOGEN ATOMS; HYDRATION FREE ENERGIES; HYDROXYL GROUPS; KETONE GROUP; MOLECULAR INTEGRALS; NEW MODEL; NOVEL METHODS; OPTIMUM MODEL; ORGANIC MOLECULES; ORGANIC SOLUTES; REFERENCE INTERACTION SITE MODELS; STANDARD DEVIATION; STRUCTURAL DESCRIPTORS; TEST SETS; TRAINING SETS;

HYDRATION;

EID: 77956715805     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp103955r     Document Type: Article

References (126)

1. Perlovich, G. L.; Bauer-Brandl, A. Curr. Drug Delivery 2004, 1, 213-226
2. Perlovich, G. L.; Volkova, T. V.; Bauer-Brandl, A. J. Pharm. Sci. 2006, 95, 2158-2169
3. Reynolds, C. A.; King, P. M.; Richards, W. G. Mol. Phys. 1992, 76, 251-275
4. Kollman, P. Chem. Rev. 1993, 93, 2395-2417
5. Palmer, D. S.; Llinas, A.; Morao, I.; Day, G. M.; Goodman, J. M.; Glen, R. C.; Mitchell, J. B. O. Mol. Pharmaceutics 2008, 5, 266-279
6. Perlovich, G. L.; Hansen, L. K.; Volkova, T. V.; Mirza, S.; Manin, A. N.; Bauer-Brandl, A. Cryst. Growth Des. 2007, 7, 2643-2648
7. Kerns, E. H.; Di, L. Drug-like properties: concepts, structure design and methods: from ADME to toxicity optimization; Academic Press: San Diego, CA, 2008.
8. Hughes, L. D.; Palmer, D. S.; Nigsch, F.; Mitchell, J. B. O. J. Chem. Inf. Model. 2008, 48, 220-232
9. Cramer, C. J.; Truhlar, D. G. J. Comput.-Aided Mol. Des. 1992, 6, 629-666
10. Abraham, M. H.; Andonianhaftvan, J.; Whiting, G. S.; Leo, A.; Taft, R. S. J. Chem. Soc., Perkin Trans. 1994, 2, 1777-1791
11. Jorgensen, W. L.; Ulmschneider, J. P.; Tirado-Rives, J. J. Phys. Chem. B 2004, 108, 16264-16270
12. Perlovich, G. L.; Volkova, T. V.; Manin, A. N.; Bauer-Brandl, A. AAPS PharmSciTech 2008, 9, 205-216
13. Ionic solvation; Krestov, G. A.; Novosyolov, N. P.; Perelygin, I. S.; Kolker, A. M.; Safonova, L. P.; Ovchinnikova, V. D.; Trostin, V. N., Eds.; Ellis Horwood Series in Inorganic Chemistry; Horwood: New York, 1994.
14. Zielenkiewicz, X.; Perlovich, G. L.; Wszelaka-Rylik, M. J. Therm. Anal. Calorim. 1999, 57, 225-234
15. Mota, F. L.; Carneiro, A. R.; Queimada, A. J.; Pinho, S. P.; Macedo, E. A. Eur. J. Pharm. Sci. 2009, 37, 499-507
16. Perlovich, G. L.; Volkova, T. V.; Bauer-Brandl, A. J. Pharm. Sci. 2006, 95, 1448-1458
17. Perlovich, G. L.; Volkova, T. V.; Manin, A. N.; Bauer-Brandl, A. J. Pharm. Sci. 2008, 97, 3883-3896
18. Duffy, E. M.; Jorgensen, W. L. J. Am. Chem. Soc. 2000, 122, 2878-2888
19. Orozco, M.; Luque, F. J. Chem. Rev. 2000, 100, 4187-4225
20. Westergren, J.; Lindfors, L.; Hoglund, T.; Luder, K.; Nordholm, S.; Kjellander, R. J. Phys. Chem. B 2007, 111, 1872-1882
21. 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
22. Guthrie, J. P. J. Phys. Chem. B 2009, 113, 4501-4707
23. Klamt, A.; Eckert, F.; Diedenhofen, M. J. Phys. Chem. B 2009, 113, 4508-4510
24. Marenich, A. V.; Cramer, C. J.; Truhlar, D. G. J. Phys. Chem. B 2009, 113, 4538-4543
25. Mobley, D. L.; Bayly, C. I.; Cooper, M. D.; Dill, K. A. J. Phys. Chem. B 2009, 113, 4533-4537
26. Sulea, T.; Wanapun, D.; Dennis, S.; Purisima, E. O. J. Phys. Chem. B 2009, 113, 4511-4520
27. Encyclopedia of Computational Chemistry; Schleyer, P., Ed.; John Wiley & Sons: Chichester, U.K., 1998; Vol. 4, Chapter "Solvation: Modeling".
28. Tomasi, J.; Persico, M. Chem. Rev. 1994, 94, 2027-2094
29. Roux, B.; Simonson, T. Biophys. Chem. 1999, 78, 1-20
30. Tomasi, J.; Mennucci, B.; Cammi, R. Chem. Rev. 2005, 105, 2999-3094
31. Matubayasi, N. Front. Biosci. 2009, 14, 3536-3549
32. Jorgensen, W. L.; Duffy, E. M. Adv. Drug Delivery Rev. 2002, 54, 355-366
33. Jorgensen, W. L.; TiradoRives, J. Perspect. Drug Discovery Des. 1995, 3, 123-138
34. Matubayasi, N.; Nakahara, M. J. Chem. Phys. 2000, 113, 6070-6081
35. Matubayasi, N.; Nakahara, M. J. Mol. Liq. 2005, 119, 23-29
36. Shirts, M. R.; Pande, V. S. J. Chem. Phys. 2005, 122, 134508
37. Knight, J. L.; Brooks, C. L. J. Comput. Chem. 2009, 30, 1692-1700
38. Pisliakov, A. V.; Sharma, P. K.; Chu, Z. T.; Haranczyk, M.; Warshel, A. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 7726-7731
39. Ulmschneider, M. B.; Ulmschneider, J. P.; Sansom, M. S. P.; Di Nola, A. Biophys. J. 2007, 92, 2338-2349
40. Bashford, D.; Case, D. A. Annu. Rev. Phys. Chem. 2000, 51, 129-152
41. Cherstvy, A. G. J. Phys. Chem. B 2006, 110, 14503-14506
42. Cherstvy, A. G. J. Phys. Chem. B 2007, 111, 7914-7927
43. Kinoshita, M. Chem. Eng. Sci. 2006, 61, 2150-2160
44. Monson, P. A.; Morriss, G. P. Adv. Chem. Phys. 1990, 77, 451-550
45. Molecular theory of solvation; Hirata, F., Ed.; Kluwer Academic Publishers: Dordrecht, Netherlands, 2003.
46. Sumi, T.; Imai, T.; Hirata, F. J. Chem. Phys. 2001, 115, 6653-6662
47. Yokogawa, D.; Sato, H.; Imai, T.; Sakaki, S. J. Chem. Phys. 2009, 130 064111
48. Kinoshita, M. Condens. Matter Phys. 2007, 10, 387-396
49. Kinoshita, M. J. Chem. Phys. 2008, 128 024507
50. Kinoshita, M.; Suzuki, M. J. Chem. Phys. 2009, 130 014707
51. Chandler, D.; Andersen, H. C. J. Chem. Phys. 1972, 57, 1930-1937
52. Hirata, F.; Rossky, P. J. Chem. Phys. Lett. 1981, 83, 329-334
53. Hirata, F. Bull. Chem. Soc. Jpn. 1998, 71, 1483-1499
54. Chuev, G. N.; Chiodo, S.; Erofeeva, S. E.; Fedorov, M. V.; Russo, N.; Sicilia, E. Chem. Phys. Lett. 2006, 418, 485-489
55. Chiodo, S.; Chuev, G. N.; Erofeeva, S. E.; Fedorov, M. V.; Russo, N.; Sicilia, E. Int. J. Quantum Chem. 2006, 107, 265-274
56. Fedorov, M. V.; Kornyshev, A. A. Mol. Phys. 2007, 105, 1-16
57. Singer, S. J.; Chandler, D. Mol. Phys. 1985, 55, 621-625
58. Kovalenko, A.; Hirata, F. J. Phys. Chem. B 1999, 103, 7942-7957
59. Kovalenko, A.; Hirata, F. J. Chem. Phys. 1999, 110, 10095-10112
60. Lee, P. H.; Maggiora, G. M. J. Phys. Chem. 1993, 97, 10175-10185
61. Ten-no, S. J. Chem. Phys. 2001, 115, 3724-3731
62. Sato, K.; Chuman, H.; Ten-no, S. J. Phys. Chem. B 2005, 109, 17290-17295
63. Chuev, G. N.; Fedorov, M. V.; Crain, J. Chem. Phys. Lett. 2007, 448, 198-202
64. Chuev, G. N.; Fedorov, M. V.; Chiodo, S.; Russo, N.; Sicilia, E. J. Comput. Chem. 2008, 29, 2406-2415
65. Ichiye, T.; Chandler, D. J. Phys. Chem. 1988, 92, 5257-5261
66. Beglov, D.; Roux, B. J. Phys. Chem. 1997, 101, 7821-7826
67. Du, Q. H.; Beglov, D.; Roux, B. J. Phys. Chem. B 2000, 104, 796-805
68. Imai, T.; Oda, K.; Kovalenko, A.; Hirata, F.; Kidera, A. J. Am. Chem. Soc. 2009, 131, 12430-12440
69. Kovalenko, A.; Hirata, F. J. Chem. Phys. 2000, 113, 2793-2805
70. Kovalenko, A.; Hirata, F.; Kinoshita, M. J. Chem. Phys. 2000, 113, 9830-9836
71. Marucho, M.; Kelley, C. T.; Pettitt, B. M. J. Chem. Theory Comput. 2008, 4, 385-396
72. Chandler, D.; Singh, Y.; Richardson, D. M. J. Chem. Phys. 1984, 81, 1975-1982
73. Ten-no, S.; Iwata, S. J. Chem. Phys. 1999, 111, 4865-4868
74. Chuev, G. N.; Fedorov, M. V. J. Chem. Phys. 2009, 131, 1323-1329
75. McClure, K. F. J. Med. Chem. 2005, 48, 5728-5737
76. McClure, K. F. Bioorg. Med. Chem. Lett. 2006, 16, 4339-4344
77. Reiter, L. A.; Jones, C. S.; Brissette, W. H.; McCurdy, S. P.; Abramov, Y. A.; Bordner, J.; DiCapua, F. M.; Munchhof, M. J.; Rescek, D. M.; Samardjiev, I. J.; Withka, J. M. Bioorg. Med. Chem. Lett. 2008, 18, 3000-3006
78. Jain, N.; Yalkowsky, S. H. J. Pharm. Sci. 2001, 90, 234-252
79. Handbook of Chemoinformatics. 4 Bde. From Data to Knowledge, 1 st ed.; Gasteiger, J., Ed.; Wiley-VCH: Weinheim, 2003.
80. Chemoinformatics: Approaches to Virtual Screening, 1 st ed.; Varnek, A.; Tropsha, A., Eds.; RSC Publishing: Cambridge, England, 2008.
81. No, K. T.; Kim, S. G.; Cho, K. H.; Scheraga, H. A. Biophys. Chem. 1999, 78, 127-145
82. In, Y. Y.; Chai, H. H.; No, K. T. J. Chem. Inf. Model. 2005, 45, 254-263
83. Cramer, C. J.; Truhlar, D. G. J. Am. Chem. Soc. 1991, 113, 8305-8311
84. Barlow, R. J. Statistics: A Guide to the Use of Statistical Methods in the Physical Sciences, Reprint ed.; Wiley: Chichester, U.K., 1989.
85. Aqvist, J.; Medina, C.; Samuelsson, J. E. Protein Eng. 1994, 7, 385-391
86. Carlson, H. A.; Jorgensen, W. L. J. Phys. Chem. 1995, 99, 10667-10673
87. Linear free energy relationships; Wells, P., Ed.; Academic Press: London, New York, 1968.
88. Chapman, N. B. Advances in linear free energy relationships; Plenum Press: London, New York, 1972.
89. Correlation Analysis in Organic Chemistry-An Introduction to Linear Free Energy Relationships; Shorter, J., Ed.; Clarendon Pres: Oxford, U.K., 1973.
90. Cabani, S.; Gianni, P.; V., M.; Lepori, L. J. Solution Chem. 1981, 10, 563-595
91. Ben-Naim, A.; Marcus, Y. J. Chem. Phys. 1984, 81, 2016-2027
92. McDonald, N. A.; Carlson, H. A.; Jorgensen, W. L. J. Phys. Org. Chem. 1997, 10, 563-576
93. Duh, D. M.; Haymet, A. D. J. J. Chem. Phys. 1995, 103, 2625-2633
94. Ashbaugh, H. S.; Kaler, E. W.; Paulaitis, M. E. Biophys. J. 1998, 75, 755-768
95. Ashbaugh, H. S.; Kaler, E. W.; Paulaitis, M. E. J. Am. Chem. Soc. 1999, 121, 9243-9244
96. Gallicchio, E.; Kubo, M. M.; Levy, R. M. J. Phys. Chem. B 2000, 104, 6271-6285
97. Chuev, G. N.; Sokolov, V. F. J. Phys. Chem. B 2006, 110, 18496-18503
98. Wu, J. Z.; Prausnitz, J. M. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 9512-9515
99. Perkyns, J.; Pettitt, B. J. Phys. Chem. 1996, 100, 1323-1329
100. Fedorov, M. V.; Flad, H. J.; Chuev, G. N.; Grasedyck, L.; Khoromskij, B. N. Computing 2007, 80, 47-73
101. Lue, L.; Blankschtein, D. J. Phys. Chem. 1992, 96, 8582-8594
102. Berendsen, H. J. C.; Grigera, J. R.; Straatsma, T. P. J. Phys. Chem. 1987, 91, 6269-6271
103. Chuev, G. N.; Fedorov, M. V. J. Comput. Chem. 2004, 25, 1369-1377
104. Chuev, G. N.; Fedorov, M. V. J. Chem. Phys. 2004, 120, 1191-1196
105. Chuev, G. N.; Fedorov, M. V. Phys. Rev. E 2003, 68 027702
106. Fedorov, M. V.; Hackbusch, W. A multigrid solver for the integral equations of the theory of liquids; Preprint 88, 2008.
107. Hackbusch, W. Multi-grid methods and Applications; Springer-Verlag: Berlin, 1985.
108. Fletcher, D. A.; McMeeking, R. F.; Parkin, D. J. Chem. Inf. Comp. Sci. 1996, 36, 746-749
109. Hope, H.; Ottersen, T. Acta Crystallogr., Sect. B 1978, 34, 3623-3626
110. Frisch, M. J.; et al. Gaussian 03; Gaussian, Inc.: Wallingford, CT, 2004.
111. Jorgensen, W. L.; Maxwell, D. S.; TiradoRives, J. J. Am. Chem. Soc. 1996, 118, 11225-11236
112. Kaminski, G. A.; Friesner, R. A.; Tirado-Rives, J.; Jorgensen, W. L. J. Phys. Chem. B 2001, 105, 6474-6487
113. Jacobson, M. P.; Kaminski, G. A.; Friesner, R. A.; Rapp, C. S. J. Phys. Chem. B 2002, 106, 11673-11680
114. Computer Simulation of Liquids; Allen, M. P.; Tildesley, D. J., Eds.; Clarendon Press: Oxford, U.K., 1987.
115. Foundations of organic chemistry; Hornby, M.; Peach, J., Eds.; Oxford University Press: Oxford, New York, 1993.
116. Duh, D. M.; Henderson, D. J. Chem. Phys. 1996, 104, 6742-6754
117. Sarkisov, G.; Lomba, E. J. Chem. Phys. 2005, 122, 214504
118. Tenno, S.; Hirata, F.; Kato, S. J. Chem. Phys. 1994, 100, 7443-7453
119. Sato, H.; Kovalenko, A.; Hirata, F. J. Chem. Phys. 2000, 112, 9463-9468
120. Sato, H.; Sakaki, S. J. Phys. Chem. A 2004, 108, 1629-1634
121. Ten-no, S.; Jung, J.; Chuman, H.; Kawashima, Y. Mol. Phys. 2010, 108, 327-332
122. Kovalenko, A.; Hirata, F. J. Chem. Phys. 2000, 112, 10403-10417
123. Feldman, H.; Dumontier, M.; Ling, S.; Haider, N.; Hogue, Ch. FEBS Lett. 2005, 579, 4685-4691
124. Luchko, T.; Gusarov, S.; Roe, D. R.; Simmerling, C.; Case, D. A.; Tuszynski, J.; Kovalenko, A. J. Chem. Theory Comput. 2010, 6, 607-624
125. Genheden, S.; Luchko, T.; Gusarov, S.; Kovalenko, A.; Ryde, U. J. Phys. Chem. B 2010, 114, 8505-8516
126. Palmer, D. S.; Sergiievskyi, V. P.; Jensen, F.; Fedorov, M. V. J. Chem. Phys. 2010, 133 044104