Discrepancy in the Near-Solute Electric Dipole Moment Calculated from the Electric Field

被引:10
作者
Yang, Pei-Kun [1 ]
机构
[1] I SHOU Univ, Dept Biomed Engn, Kaohsiung 840, Taiwan
关键词
dielectric polarization; molecular solute; structural solvent; molecular dynamics simulation; continuum solvent model; MOLECULAR-DYNAMICS; SOLVENT; SOLVATION; DOCKING; MODELS; EQUATIONS; ENERGIES; WATER;
D O I
10.1002/jcc.21858
中图分类号
O6 [化学];
学科分类号
0703 ;
摘要
The electric dipole moment p(r) was computed as the integral of the permanent dipole moment of the solvent molecule mu(r) weighted by the orientational probability distribution Omega(r;O) over all orientations, where O is the orientation of the solvent molecule at r. The relationship between Omega(r;O) and the potential of the mean torque was derived; p(r) is proportional to the electric field E(r) under the following assumptions: (1) the van der Waals (vdW) interaction is independent of the orientation of the solvent molecule at r; (2) the solvent molecule and its electrical effect are modeled as a point dipole moment; (3) the solvent molecule at r is in a region far from the solute; and (4) mu E(r) << k(B)T, where k(B) is Boltzmann's constant and T is absolute temperature. The errors caused by calculating near-solute Omega(r) and p(r) from E(r) are unclear. The results show that Omega(r) is inconsistent with the value calculated from E(r) for water molecules in the first and second shells of solute with charge state Q = +/- 1 e, and a large variation in solvent molecular polarizability gamma(mol)(r), which appeared in the first valley of 4 pi r(2) E(r) for |Q| < 1 e. Nonetheless, p(r) is consistent with the values calculated from E(r) for |Q| < 1 e. The implication is that the assumptions for calculating p(r) can be ignored in the calculation of the solvation free energy of biomolecules, as they pertain to protein folding and protein-protein/ligand interactions. (C) 2011 Wiley Periodicals, Inc. J Comput Chem 32: 2783-2798, 2011
引用
收藏
页码:2783 / 2799
页数:17
相关论文
共 27 条
[1]  
[Anonymous], 1999, CLASSICAL ELECTRODYN
[2]   Water as an active constituent in cell biology [J].
Ball, Philip .
CHEMICAL REVIEWS, 2008, 108 (01) :74-108
[3]  
BERG J., 2012, Biochemistry
[4]  
BLOKZIJL W, 1993, ANGEW CHEM INT EDIT, V32, P1545, DOI 10.1002/anie.199315451
[5]   Volumes and hydration warmth of ions [J].
Born, M .
ZEITSCHRIFT FUR PHYSIK, 1920, 1 :45-48
[6]   CHARMM - A PROGRAM FOR MACROMOLECULAR ENERGY, MINIMIZATION, AND DYNAMICS CALCULATIONS [J].
BROOKS, BR ;
BRUCCOLERI, RE ;
OLAFSON, BD ;
STATES, DJ ;
SWAMINATHAN, S ;
KARPLUS, M .
JOURNAL OF COMPUTATIONAL CHEMISTRY, 1983, 4 (02) :187-217
[7]   Interfaces and the driving force of hydrophobic assembly [J].
Chandler, D .
NATURE, 2005, 437 (7059) :640-647
[8]  
Egelstaff P.A., 1992, INTRO LIQUID STATE
[9]   Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures [J].
Feig, M ;
Onufriev, A ;
Lee, MS ;
Im, W ;
Case, DA ;
Brooks, CL .
JOURNAL OF COMPUTATIONAL CHEMISTRY, 2004, 25 (02) :265-284
[10]  
Griffiths D. J., 1999, Introduction to Electrodynamics