Transferability and additivity of dihedral parameters in polarizable and nonpolarizable empirical force fields

被引:13
作者
Zgarbova, Marie [1 ]
Rosnik, Andreana M. [2 ]
Javier Luque, F. [3 ,4 ]
Curutchet, Carles [2 ]
Jurecka, Petr [1 ]
机构
[1] Palacky Univ, Fac Sci, Dept Phys Chem, Reg Ctr Adv Technol & Mat, Olomouc 77146, Czech Republic
[2] Univ Barcelona, Fac Farm, Dept Fisicoquim, E-08028 Barcelona, Spain
[3] Univ Barcelona, Fac Farm, Dept Fisicoquim, Santa Coloma De Gramenet 08921, Spain
[4] Univ Barcelona, Fac Farm, Inst Biomed IBUB, Santa Coloma De Gramenet 08921, Spain
关键词
polarizable force fields; molecular mechanics; torsion parameters; FRAGMENT POTENTIAL METHOD; ACCURATE INTERMOLECULAR POTENTIALS; BIOLOGICALLY RELEVANT LIGANDS; HYDROGEN-BONDED COMPLEXES; MOLECULAR-DYNAMICS; NUCLEIC-ACIDS; PARTITION-COEFFICIENTS; QUANTUM-CHEMISTRY; CHARGE-TRANSFER; MODEL;
D O I
10.1002/jcc.24012
中图分类号
O6 [化学];
学科分类号
0703 ;
摘要
Recent advances in polarizable force fields have revealed that major reparameterization is necessary when the polarization energy is treated explicitly. This study is focused on the torsional parameters, which are crucial for the accurate description of conformational equilibria in biomolecules. In particular, attention is paid to the influence of polarization on the (i) transferability of dihedral terms between molecules, (ii) transferability between different environments, and (iii) additivity of dihedral energies. To this end, three polarizable force fields based on the induced point dipole model designed for use in AMBER are tested, including two recent ff02 reparameterizations. Attention is paid to the contributions due to short range interactions (1-2, 1-3, and 1-4) within the four atoms defining the dihedral angle. The results show that when short range 1-2 and 1-3 polarization interactions are omitted, as for instance in ff02, the 1-4 polarization contribution is rather small and unlikely to improve the description of the torsional energy. Conversely, when screened 1-2 and 1-3 interactions are included, the polarization contribution is sizeable and shows potential to improve the transferability of parameters between different molecules and environments as well as the additivity of dihedral terms. However, to reproduce intramolecular polarization effects accurately, further fine-tuning of the short range damping of polarization is necessary. (c) 2015 Wiley Periodicals, Inc.
引用
收藏
页码:1874 / 1884
页数:11
相关论文
共 98 条
[1]   Exploring Solvent Effects upon the Menshutkin Reaction Using a Polarizable Force Field [J].
Acevedo, Orlando ;
Jorgensen, William L. .
JOURNAL OF PHYSICAL CHEMISTRY B, 2010, 114 (25) :8425-8430
[2]   Density functional theory based effective fragment potential method [J].
Adamovic, I ;
Freitag, MA ;
Gordon, MS .
JOURNAL OF CHEMICAL PHYSICS, 2003, 118 (15) :6725-6732
[3]   ELECTRONIC-STRUCTURE CALCULATIONS ON WORKSTATION COMPUTERS - THE PROGRAM SYSTEM TURBOMOLE [J].
AHLRICHS, R ;
BAR, M ;
HASER, M ;
HORN, H ;
KOLMEL, C .
CHEMICAL PHYSICS LETTERS, 1989, 162 (03) :165-169
[4]   ATOM DIPOLE INTERACTION MODEL FOR MOLECULAR POLARIZABILITY - APPLICATION TO POLYATOMIC-MOLECULES AND DETERMINATION OF ATOM POLARIZABILITIES [J].
APPLEQUIST, J ;
CARL, JR ;
FUNG, KK .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1972, 94 (09) :2952-+
[5]   Polarizable Intermolecular Potentials for Water and Benzene Interacting with Halide and Metal Ions [J].
Archambault, Fabien ;
Chipot, Christophe ;
Soteras, Ignacio ;
Javier Luque, F. ;
Schulten, Klaus ;
Dehez, Francois .
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2009, 5 (11) :3022-3031
[6]   Parametrizing a polarizable force field from ab initio data.: I.: The fluctuating point charge model [J].
Banks, JL ;
Kaminski, GA ;
Zhou, RH ;
Mainz, DT ;
Berne, BJ ;
Friesner, RA .
JOURNAL OF CHEMICAL PHYSICS, 1999, 110 (02) :741-754
[7]   Optimized Molecular Dynamics Force Fields Applied to the Helix-Coil Transition of Polypeptides [J].
Best, Robert B. ;
Hummer, Gerhard .
JOURNAL OF PHYSICAL CHEMISTRY B, 2009, 113 (26) :9004-9015
[8]   The case for steric repulsion causing the staggered conformation of ethane [J].
Bickelhaupt, FM ;
Baerends, EJ .
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 2003, 42 (35) :4183-4188
[9]   QUANTUM-MECHANICAL STUDIES ON THE ORIGIN OF BARRIERS TO INTERNAL-ROTATION ABOUT SINGLE BONDS [J].
BRUNCK, TK ;
WEINHOLD, F .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1979, 101 (07) :1700-1709
[10]   IMPLEMENTATION OF NONADDITIVE INTERMOLECULAR POTENTIALS BY USE OF MOLECULAR-DYNAMICS - DEVELOPMENT OF A WATER WATER POTENTIAL AND WATER ION CLUSTER INTERACTIONS [J].
CALDWELL, J ;
DANG, LX ;
KOLLMAN, PA .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1990, 112 (25) :9144-9147