Towards a universal method for calculating hydration free energies: A 3D reference interaction site model with partial molar volume correction

Journal of Physics Condensed Matter

Volumn 22, Issue 49, 2010, Pages

  Palmer, David S ^a   Frolov, Andrey I ^a   Ratkova, Ekaterina L ^a   Fedorov, Maxim V ^a  

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

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL CLASS; DATA SETS; HYDRATION FREE ENERGIES; INTEGRAL-EQUATION THEORY; LINEAR CORRELATION; MOLECULAR LIQUIDS; ORGANIC MOLECULES; PARTIAL MOLAR VOLUME; REFERENCE INTERACTION SITE MODELS; TEST SETS; UNIVERSAL METHOD;

FREE ENERGY; HYDRATION; INTEGRAL EQUATIONS; VOLUME MEASUREMENT;

THREE DIMENSIONAL;

EID: 78649896811     PISSN: 09538984     EISSN: 1361648X     Source Type: Journal    
DOI: 10.1088/0953-8984/22/49/492101     Document Type: Article

References (102)

1. Dogonadze R R, Kalman E, Kornyshev A A and Ulstrup J (ed) 1985 The Chemical Physics of Solvation. Part A: Theory of Solvation (Amsterdam: Elsevier)
2. Dogonadze R R, Kalman E, Kornyshev A A and Ulstrup J (ed) 1986 The Chemical Physics of Solvation. Part B: Spectroscopy of Solvation (Amsterdam: Elsevier)
3. Dogonadze R R, Kalman E, Kornyshev A A and Ulstrup J (ed) 1988 The Chemical Physics of Solvation. Part C: Solvation Phenomena in Specific Physical, Chemical and Biological Systems (Amsterdam: Elsevier)
4. Atkins P W 2002 Physical Chemistry 7th edn (Oxford: Oxford University Press)
5. Cramer C J and Truhlar D G 1992 J. Comput.-Aided Mol. Des. 6 629-66
6. JorgensenW L, Ulmschneider J P and Tirado-Rives J 2004 J. Phys. Chem. B 108 16264-70
7. Cabani S, Gianni P, Mollica V and Lepori L 1981 J. Solut. Chem. 10 563-95
8. Ben-Naim A and Marcus Y 1984 J. Chem. Phys. 81 2016-27
9. Abraham M H, Andonianhaftvan J, Whiting G S, Leo A and Taft R S 1994 J. Chem. Soc.-Perkin Trans. 2 8 1777-91
10. McDonald N A, Carlson H A and JorgensenW L 1997 J. Phys. Org. Chem. 10 563-76
11. Duffy E M and JorgensenW L 2000 J. Am. Chem. Soc. 122 2878-88
12. Ratkova E L, Chuev G N, Sergiievskyi V P and FedorovM V 2010 J. Phys. Chem. B 114 12068-79
13. Perlovich G L, Volkova T V, Manin A N and Bauer-Brandl A 2008 Aaps Pharmscitech. 9 205-16
14. Perlovich G L, Volkova T V and Bauer-Brandl A 2006 J. Pharm. Sci. 95 1448-58
15. Guthrie J P 2009 J. Phys. Chem. B 113 4501-7
16. Matubayasi N and NakaharaM 2005 J. Mol. Liq. 119 23-9
17. Matubayasi N, Shinoda W and NakaharaM 2008 J. Chem. Phys. 128 195107
18. Matubayasi N 2009 Front Biosci. 14 3536-49
19. Jensen J H, Li H, Robertson A D and Molina P A 2005 J. Phys. Chem. A 109 6634-43
20. Palmer D S, Llinas A, Morao I, Day G M, Goodman J M, Glen R C and Mitchell J B O 2008 Mol. Pharmaceut. 5 266-79
21. Thompson J D, Cramer C J and Truhlar D G 2003 J. Chem. Phys. 119 1661-70
22. Garrido N, Queimada A, JorgeM, Macedo E and Economou I 2009 J. Chem. Theory Comput. 5 2436-46
23. Hughes L D, Palmer D S, Nigsch F and Mitchell J B O 2008 J. Chem. Inf. Model. 48 220-32
24. Perlovich G and Bauer-Brandl A 2004 Curr. Drug Deliv. 1 213-26
25. Swanson J M J, Henchman R H and McCammon J A 2004 Biophys. J. 86 67-74
26. Gilson M K and Zhou H X 2007 Annu. Rev. Biophys. Biomol. Struct. 36 21-42
27. Kerns E H and Di L 2008 Drug-Like Properties: Concepts, Structure Design and Methods: From ADME to Toxicity Optimization (New York: Academic)
28. Mackay D, Shiu W Y and Ma K C 1992 Illustrated Handbook of Physical-Chemical Properties and Environmental Fate for Organic Chemicals vol 2 Polynuclear Aromatic Hydrocarbons, Polychlorinated Dioxins, and Dibenzofurans (Michigan, MI: Lewis Publishers)
29. HarrisonW 1999 J. Biomol. Screen. 4 61-5
30. Chandler D and Andersen H C 1972 J. Chem. Phys. 57 1930-7
31. Hirata F and Rossky P J 1981 Chem. Phys. Lett. 83 329-34
32. Singer S J and Chandler D 1985 Mol. Phys. 55 621-5
33. Kovalenko A and Hirata F 1999 J. Phys. Chem. B 103 7942-57
34. Kovalenko A and Hirata F 1999 J. Chem. Phys. 110 10095-112
35. Hirata F (ed) 2003 Molecular Theory of Solvation (Dordrecht: Kluwer Academic)
36. Lee P H and Maggiora G M 1993 J. Phys. Chem. 97 10175-85
37. Ichiye T and Chandler D 1988 J. Phys. Chem. 92 5257-61
38. Ten-no S 2001 J. Chem. Phys. 115 3724-31
39. Sato K, Chuman H and Ten-no S 2005 J. Phys. Chem. B 109 17290-5
40. Chuev G, Fedorov M and Crain J 2007 Chem. Phys. Lett. 448 198-202
41. Chuev G N, FedorovM V, Chiodo S, Russo N and Sicilia E 2008 J. Comput. Chem. 29 2406-15
42. Beglov D and Roux B 1997 J. Phys. Chem. 101 7821-6
43. Du Q H, Beglov D and Roux B 2000 J. Phys. Chem. B 104 796-805
44. Imai T, Oda K, Kovalenko A, Hirata F and Kidera A 2009 J. Am. Chem. Soc. 131 12430-40
45. Hansen J P and McDonald I R 2000 Theory of Simple Liquids 4th edn (New York: Academic)
46. Kinoshita M, Okamoto Y and Hirata F 1997 J. Comput.Chem. 18 1320-6
47. Kinoshita M, Okamoto Y and Hirata F 1998 J. Comput. Chem. 19 1724-35
48. Kinoshita M 2007 Condens. Matter Phys. 10 387-96
49. FedorovM V and Kornyshev A A 2007 Mol. Phys. 105 1-16
50. Akiyama R, Fujino N, Kaneda K and Kinoshita M 2007 Condens. Matter Phys. 10 587-96
51. Harano Y, Yoshidome T and Kinoshita M 2008 J. Chem. Phys. 129 145103
52. Kinoshita M 2008 J. Chem. Phys. 128 024507
53. Oshima H, Yoshidome T, Amano K and Kinoshita M 2009 J. Chem. Phys. 131 205102
54. Kinoshita M and Suzuki M 2009 J. Chem. Phys. 130 014707
55. Chuev G N and Fedorov M V 2009 J. Chem. Phys. 131 074503
56. Kinoshita M, Imai T, Kovalenko A and Hirata F 2001 Chem. Phys. Lett. 348 337-42
57. Beglov D and Roux B 1996 J. Chem. Phys. 104 8678-89
58. Luchko T, Gusarov S, Roe D R, Simmerling C, Case D A, Tuszynski J and Kovalenko A 2010 J. Chem. Theory Comput. 6 607-24
59. Genheden S, Luchko T, Gusarov S, Kovalenko A and Ryde U 2010 J. Phys. Chem. B 114 8505-16
60. Casanova D, Gusarov S, Kovalenko A and Ziegler T 2007 J. Chem. Theory Comput. 3 458-76
61. Chuev G N and Fedorov M V 2004 J. Comput. Chem. 25 1369-77
62. Monson P A and Morriss G P 1990 Adv. Chem. Phys. 77 451-550
63. Duh D M and Haymet A D J 1995 J. Chem. Phys. 103 2625-33
64. Kovalenko A and Hirata F 2000 J. Chem. Phys. 112 10391-402
65. Drabik P, Gusarov S and Kovalenko A 2007 Biophys. J. 92 394-403
66. Imai T, Harano Y, Kinoshita M, Kovalenko A and Hirata F 2007 J. Chem. Phys. 126 225102
67. Blinov N, Dorosh L, Wishart D and Kovalenko A 2010 Biophys. J. 98 282-96
68. Palmer D S, Sergiievskyi V P, Jensen F and FedorovM V 2010 J. Chem. Phys. 133 044104
69. Ten-no S, Jung J, Chuman H and Kawashima Y 2010 Mol. Phys. 108 327-32
70. Dejaegere A and Karplus M 1996 J. Phys. Chem. 100 11148-64
71. Perkyns J and Pettitt B M 1996 J. Phys. Chem. 100 1323-9
72. Chandler D, Singh Y and Richardson D M 1984 J. Chem. Phys. 81 1975-82
73. Imai T, Kinoshita M and Hirata F 2000 J. Chem. Phys. 112 9469-78
74. Imai T, Harano Y, Kovalenko A and Hirata F 2001 Biopolymers 59 512-9
75. Lue L and Blankschtein D 1992 J. Phys. Chem. 96 8582-94
76. Berendsen H J C, Grigera J R and Straatsma T P 1987 J. Phys. Chem. 91 6269-71
77. Kovalenko A and Hirata F 2000 J. Chem. Phys. 113 2793-805
78. Allen M P and Tildesley D J (ed) 1987 Computer Simulation of Liquids (Oxford: Clarendon)
79. Case D A, Cheatham T E, Darden T, Gohlke H, Luo R, MerzKM, OnufrievA, Simmerling C, Wang B and Woods R J 2005 J. Comput. Chem. 26 1668-88
80. Kovalenko A, Ten-No S and Hirata F 1999 J. Comput. Chem. 20 928-36
81. Perkyns J S and Pettitt B M 1992 Chem. Phys. Lett. 190 626-30
82. Case D A, Darden T A, Cheatham T E III, Simmerling C L, Wang J, Duke R, Luo R, Walker R C, ZhangW, Merz K M, Roberts B, Wang B, Hayik S, Roitberg A, Seabra G, Kolossváry I, Wong K F, Paesani F, Vanicek J, Liu J, Wu X, Brozell S R, Steinbrecher T, Gohlke H, Cai Q, Ye X, Wang J, Hsieh M J, Cui G, Roe D R, Mathews D H, Seetin M G, Sagui C, Babin V, Luchko T, Gusarov S, Kovalenko A and Kollman P A 2010 Amber Version 11 WWW page http://ambermd.org
83. Pearlman D A, Case D A, Caldwell J W, RossW S, Cheatham T E, DeBolt S, Ferguson D, Seibel G and Kollman P 1995 Comput. Phys. Commun. 91 1-41
84. Dewar M J S, Zoebisch E G, Healy E F and Stewart J J P 1985 J. Am. Chem. Soc. 107 3902-9
85. Wang J M, Wang W, Kollman P A and Case D A 2006 J. Mol. Graph. Modell. 25 247-60
86. Jakalian A, Bush B L, Jack D B and Bayly C I 2000 J. Comput. Chem. 21 132-46
87. Jakalian A, Jack D B and Bayly C I 2002 J. Comput. Chem. 23 1623-41
88. Wang J M, Wolf R M, Caldwell J W, Kollman P A and Case D A 2004 J. Comput. Chem. 25 1157-74
89. Chandler D 2005 Nature 437 640-7
90. Harano Y and Kinoshita M 2005 Biophys. J. 89 2701-10
91. Roth R, Harano Y and Kinoshita M 2006 Phys. Rev. Lett. 97 078101
92. Yoshidome T, Harano Y and Kinoshita M 2009 Phys. Rev. E 79 011912
93. Kinoshita M 2009 Front. Biosci. 14 3419-U48
94. Amano K and Kinoshita M 2010 Chem. Phys. Lett. 488 1-6
95. Shirts M R and Pande V S 2005 J. Chem. Phys. 122 134508
96. Westergren J, Lindfors L, Hoglund T, Luder K, Nordholm S and Kjellander R 2007 J. Phys. Chem. B 111 1872-82
97. Matubayasi N and NakaharaM 2002 J. Chem. Phys. 117 3605-16
98. Matubayasi N and NakaharaM 2003 J. Chem. Phys. 119 9686-702
99. Matubayasi N and NakaharaM 2005 J. Chem. Phys. 122 074509
100. Takahashi H, Ohno H, Yamauchi T, Kishi R, Furukawa S, Nakano M and Matubayasi N 2008 J. Chem. Phys. 128 064507
101. Karino Y, Fedorov M V and Matubayasi N 2010 Chem. Phys. Lett. 496 351-5
102. Duan Y, Wu C, Chowdhury S, Lee M C, Xiong G M, ZhangW, Yang R, Cieplak P, Luo R, Lee T, Caldwell J, Wang J M and Kollman P 2003 J. Comput. Chem. 24 1999-2012