Potential energy functions for atomic-level simulations of water and organic and biomolecular systems

被引：1131

作者：

Jorgensen, WL ^{[1
]}

Tirado-Rives, J ^{[1
]}

机构：

[1] Yale Univ, Dept Chem, New Haven, CT 06520 USA

来源：

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA | 2005年 / 102卷 / 19期

关键词：

D O I：

10.1073/pnas.0408037102

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

An overview is provided on the development and status of potential energy functions that are used in atomic-level statistical mechanics and molecular dynamics simulations of water and of organic and biomolecular systems. Some topics that are considered are the form of force fields, their parameterization and performance, simulations of organic liquids, computation of free energies of hydration, universal extension for organic molecules, and choice of atomic charges. The discussion of water models covers some history, performance issues, and special topics such as nuclear quantum effects.

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页码：6665 / 6670

页数：6

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共 101 条

[11] The role and perspective of a initio molecular dynamics in the study of biological systems [J].

Carloni, P ;

Rothlisberger, U ;

Parrinello, M .

ACCOUNTS OF CHEMICAL RESEARCH, 2002, 35 (06) :455-464

[12] QM/MM simulations for Diels-Alder reactions in water: Contribution of enhanced hydrogen bonding at the transition state to the solvent effect [J].

Chandrasekhar, J ;

Shariffskul, S ;

Jorgensen, WL .

JOURNAL OF PHYSICAL CHEMISTRY B, 2002, 106 (33) :8078-8085

[13] Hydrogen bonding in water [J].

Chen, B ;

Ivanov, I ;

Klein, ML ;

Parrinello, M .

PHYSICAL REVIEW LETTERS, 2003, 91 (21)

[14] Molecular mechanical models for organic and biological systems going beyond the atom centered two body additive approximation: Aqueous solution free energies of methanol and N-methyl acetamide, nucleic acid base, and amide hydrogen bonding and chloroform/water partition coefficients of the nucleic acid bases [J].

Cieplak, P ;

Caldwell, J ;

Kollman, P .

JOURNAL OF COMPUTATIONAL CHEMISTRY, 2001, 22 (10) :1048-1057

[15] A 2ND GENERATION FORCE-FIELD FOR THE SIMULATION OF PROTEINS, NUCLEIC-ACIDS, AND ORGANIC-MOLECULES [J].

CORNELL, WD ;

CIEPLAK, P ;

BAYLY, CI ;

GOULD, IR ;

MERZ, KM ;

FERGUSON, DM ;

SPELLMEYER, DC ;

FOX, T ;

CALDWELL, JW ;

KOLLMAN, PA .

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1995, 117 (19) :5179-5197

[16] The pluses and minuses of mapping atomic charges to electrostatic potentials [J].

Francl, MM ;

Chirlian, LE .

REVIEWS IN COMPUTATIONAL CHEMISTRY, VOL 14, 2000, 14 :1-31

[17] Enthalpy-entropy and cavity decomposition of alkane hydration free energies: Numerical results and implications for theories of hydrophobic solvation [J].

Gallicchio, E ;

Kubo, MM ;

Levy, RM .

JOURNAL OF PHYSICAL CHEMISTRY B, 2000, 104 (26) :6271-6285

[18] Ion solvation thermodynamics from simulation with a polarizable force field [J].

Grossfield, A ;

Ren, PY ;

Ponder, JW .

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2003, 125 (50) :15671-15682

[19] Towards an assessment of the accuracy of density functional theory for first principles simulations of water [J].

Grossman, JC ;

Schwegler, E ;

Draeger, EW ;

Gygi, F ;

Galli, G .

JOURNAL OF CHEMICAL PHYSICS, 2004, 120 (01) :300-311

[20] A reappraisal of what we have learnt during three decades of computer simulations on water [J].

Guillot, B .

JOURNAL OF MOLECULAR LIQUIDS, 2002, 101 (1-3) :219-260

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