The SAMP1 Solvation Challenge: Further Lessons Regarding the Pitfalls of Parametrization

被引：33

作者：

Nicholls, Anthony ^{[1
]}

Wlodek, Stanislaw ^{[1
]}

Grant, J. Andrew ^{[2
]}

机构：

[1] OpenEye Sci Software Inc, Santa Fe, NM 87508 USA

[2] AstraZeneca, Macclesfield SK10 4TF, Cheshire, England

来源：

JOURNAL OF PHYSICAL CHEMISTRY B | 2009年 / 113卷 / 14期

关键词：

CRYSTAL-STRUCTURE PREDICTION; SMALL ORGANIC-MOLECULES; BLIND TEST; EFFICIENT GENERATION; AM1-BCC MODEL; SIMULATIONS; CHEMISTRY; ENERGIES; ENTROPY;

D O I：

10.1021/jp806855q

中图分类号：

O64 [物理化学（理论化学）、化学物理学];

学科分类号：

070304 ; 081704 ;

摘要：

This paper describes an investigation into the performance of different charges and radii with the Poisson-Boltzmann method for the calculation of vacuum-water transfer energies. The test set consisted of 63 drug-like molecules used in a blind-test challenge. The results are consistent with earlier reports, namely, that more physical charges perform better and that radii parametrization can both improve and also dramatically worsen results. with the latter suggesting a failure to capture all of the basic physics of solvation.

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页码：4521 / 4532

页数：12

相关论文

共 30 条

[1] The accuracy of molecular dipole moments in standard electronic structure calculations [J].

Bak, KL ;

Gauss, J ;

Helgaker, T ;

Jorgensen, P ;

Olsen, J .

CHEMICAL PHYSICS LETTERS, 2000, 319 (5-6) :563-568

[2] DENSITY-FUNCTIONAL THERMOCHEMISTRY .3. THE ROLE OF EXACT EXCHANGE [J].

BECKE, AD .

JOURNAL OF CHEMICAL PHYSICS, 1993, 98 (07) :5648-5652

[3] VAN DER WAALS VOLUMES + RADII [J].

BONDI, A .

JOURNAL OF PHYSICAL CHEMISTRY, 1964, 68 (03) :441-+

[4] ELECTROSTATICS AND DIFFUSION OF MOLECULES IN SOLUTION - SIMULATIONS WITH THE UNIVERSITY-OF-HOUSTON-BROWNIAN DYNAMICS PROGRAM [J].

DAVIS, ME ;

MADURA, JD ;

LUTY, BA ;

MCCAMMON, JA .

COMPUTER PHYSICS COMMUNICATIONS, 1991, 62 (2-3) :187-197

[5] A third blind test of crystal structure prediction [J].

Day, GM ;

Motherwell, WDS ;

Ammon, HL ;

Boerrigter, SXM ;

Della Valle, RG ;

Venuti, E ;

Dzyabchenko, A ;

Dunitz, JD ;

Schweizer, B ;

van Eijck, BP ;

Erk, P ;

Facelli, JC ;

Bazterra, VE ;

Ferraro, MB ;

Hofmann, DWM ;

Leusen, FJJ ;

Liang, C ;

Pantelides, CC ;

Karamertzanis, PG ;

Price, SL ;

Lewis, TC ;

Nowell, H ;

Torrisi, A ;

Scheraga, HA ;

Arnautova, YA ;

Schmidt, MU ;

Verwer, P .

ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE CRYSTAL ENGINEERING AND MATERIALS, 2005, 61 :511-527

[6] The role of occam's razor in knowledge discovery [J].

Domingos, P .

DATA MINING AND KNOWLEDGE DISCOVERY, 1999, 3 (04) :409-425

[7]

Frisch M. J., 2004, GAUSSIAN 03

[8] The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators [J].

Gallicchio, E ;

Zhang, LY ;

Levy, RM .

JOURNAL OF COMPUTATIONAL CHEMISTRY, 2002, 23 (05) :517-529

[9] ON THE CALCULATION OF ELECTROSTATIC INTERACTIONS IN PROTEINS [J].

GILSON, MK ;

RASHIN, A ;

FINE, R ;

HONIG, B .

JOURNAL OF MOLECULAR BIOLOGY, 1985, 184 (03) :503-516

[10] A simple formula for dielectric polarisation energies: The Sheffield Solvation Model [J].

Grant, J. A. ;

Pickup, B. T. ;

Sykes, M. J. ;

Kitchen, C. A. ;

Nicholls, A. .

CHEMICAL PHYSICS LETTERS, 2007, 441 (1-3) :163-166