Additive and classical drude polarizable force fields for linear and cyclic ethers

被引:207
作者
Vorobyov, Igor
Anisimov, Victor M.
Greene, Shannon
Venable, Richard M.
Moser, Adam
Pastor, Richard W.
MacKerell, Alexander D., Jr. [1 ]
机构
[1] Univ Maryland, Dept Pharmaceut Sci, Sch Pharm, Baltimore, MD 21201 USA
[2] NHLBI, Lab Computat Biol, NIH, Bethesda, MD 20892 USA
关键词
D O I
10.1021/ct600350s
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
Empirical force field parameters consistent with the CHARMM additive and classical Drude based polarizable force fields are presented for linear and cyclic ethers. Initiation of the optimization process involved validation of the aliphatic parameters based on linear alkanes and cyclic alkanes. Results showed the transfer to cyclohexane to yield satisfactory agreement with target data; however, in the case of cyclopentane direct transfer of the Lennard-Jones parameters was not sufficient due to ring strain, requiring additional optimization of these parameters for this molecule. Parameters for the ethers were then developed starting with the available aliphatic parameters, with the nonbond parameters for the oxygens optimized to reproduce both gas-and condensed-phase properties. Nonbond parameters for the polarizable model include the use of an anisotropic electrostatic model on the oxygens. Parameter optimization emphasized the development of transferable parameters between the ethers of a given class. The ether models are shown to be in satisfactory agreement with both pure solvent and aqueous solvation properties, and the resulting parameters are transferable to test molecules. The presented force field will allow for simulation studies of ethers in condensed phase and provides a basis for ongoing developments in both additive and polarizable force fields for biological molecules.
引用
收藏
页码:1120 / 1133
页数:14
相关论文
共 98 条
[51]   An ab initio quantum mechanical study of hydrogen-bonded complexes of biological interest [J].
Huang, N ;
MacKerell, AD .
JOURNAL OF PHYSICAL CHEMISTRY A, 2002, 106 (34) :7820-7827
[52]   Conformational pathways of saturated six-membered rings.: A static and dynamical density functional study [J].
Ionescu, AR ;
Bérces, A ;
Zgierski, MZ ;
Whitfield, DM ;
Nukada, T .
JOURNAL OF PHYSICAL CHEMISTRY A, 2005, 109 (36) :8096-8105
[53]   Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids [J].
Jorgensen, WL ;
Maxwell, DS ;
TiradoRives, J .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1996, 118 (45) :11225-11236
[54]   Specific ion effects at the air/water interface [J].
Jungwirth, P ;
Tobias, DJ .
CHEMICAL REVIEWS, 2006, 106 (04) :1259-1281
[55]   SM6: A density functional theory continuum solvation model for calculating aqueous solvation free energies of neutrals, ions, and solute-water clusters [J].
Kelly, CP ;
Cramer, CJ ;
Truhlar, DG .
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2005, 1 (06) :1133-1152
[56]   An ab initio study on the torsional surface of alkanes and its effect on molecular simulations of alkanes and a DPPC bilayer [J].
Klauda, JB ;
Brooks, BR ;
MacKerell, AD ;
Venable, RM ;
Pastor, RW .
JOURNAL OF PHYSICAL CHEMISTRY B, 2005, 109 (11) :5300-5311
[57]   FREE-ENERGY CALCULATIONS - APPLICATIONS TO CHEMICAL AND BIOCHEMICAL PHENOMENA [J].
KOLLMAN, P .
CHEMICAL REVIEWS, 1993, 93 (07) :2395-2417
[58]   THE WEIGHTED HISTOGRAM ANALYSIS METHOD FOR FREE-ENERGY CALCULATIONS ON BIOMOLECULES .1. THE METHOD [J].
KUMAR, S ;
BOUZIDA, D ;
SWENDSEN, RH ;
KOLLMAN, PA ;
ROSENBERG, JM .
JOURNAL OF COMPUTATIONAL CHEMISTRY, 1992, 13 (08) :1011-1021
[59]   Pressure-based long-range correction for Lennard-Jones interactions in molecular dynamics simulations:: Application to alkanes and interfaces [J].
Lagüe, P ;
Pastor, RW ;
Brooks, BR .
JOURNAL OF PHYSICAL CHEMISTRY B, 2004, 108 (01) :363-368
[60]   A polarizable model of water for molecular dynamics simulations of biomolecules [J].
Lamoureux, G ;
Harder, E ;
Vorobyov, IV ;
Roux, B ;
MacKerell, AD .
CHEMICAL PHYSICS LETTERS, 2006, 418 (1-3) :245-249