An ab initio study on the torsional surface of alkanes and its effect on molecular simulations of alkanes and a DPPC bilayer

被引:268
作者
Klauda, JB
Brooks, BR
MacKerell, AD
Venable, RM
Pastor, RW
机构
[1] FDA, Ctr Biol Evaluat & Res, Biophys Lab, Rockville, MD 20852 USA
[2] Univ Maryland, Sch Pharm, Dept Pharmaceut Sci, Baltimore, MD 21201 USA
[3] NIH, Biophys Chem Lab, Bethesda, MD 20892 USA
关键词
D O I
10.1021/jp0468096
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
Energies of 119 conformations of normal alkanes from butane to heptane were calculated at approximately the CCSD(T)/cc-pVQZ level. Energies of gauche (g) conformers relative to trans (t) decrease as chain length increases. In what is termed the "positive pentane effect", adjacent gauche conformers of the same sign are stabilized compared to nonadjacent conformers; e.g., for hexane the energies of tgt, tgg, and gtg are 0.600, 0.930, and 1.18 kcal/mol, respectively. Torsional terms in the CHARMM27 (C27) force field were fit to the calculated QM energies to yield a revised potential, C27r. Molecular dynamics simulations of normal alkanes (heptane, decane, tridecane, and pentadecane) with C27r yield higher populations of gauche states, increased transition rates, and improved agreement with experiment as compared to C27. In addition, C27r simulations of a hydrated DPPC lipid bilayer yield improved agreement with the experimental NMR deuterium order parameters for the aliphatic chain ends.
引用
收藏
页码:5300 / 5311
页数:12
相关论文
共 53 条
[1]  
Allen M. P., 1987, J COMPUTER SIMULATIO, DOI DOI 10.2307/2938686
[2]   MOLECULAR-DYNAMICS SIMULATIONS AT CONSTANT PRESSURE AND-OR TEMPERATURE [J].
ANDERSEN, HC .
JOURNAL OF CHEMICAL PHYSICS, 1980, 72 (04) :2384-2393
[3]   A combined method for determining reaction paths, minima, and transition state geometries [J].
Ayala, PY ;
Schlegel, HB .
JOURNAL OF CHEMICAL PHYSICS, 1997, 107 (02) :375-384
[4]   A WELL-BEHAVED ELECTROSTATIC POTENTIAL BASED METHOD USING CHARGE RESTRAINTS FOR DERIVING ATOMIC CHARGES - THE RESP MODEL [J].
BAYLY, CI ;
CIEPLAK, P ;
CORNELL, WD ;
KOLLMAN, PA .
JOURNAL OF PHYSICAL CHEMISTRY, 1993, 97 (40) :10269-10280
[5]  
Berne B. J., 2000, DYNAMIC LIGHT SCATTE
[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]   A comparison of the potential energy parameters of aliphatic alkanes: molecular dynamics simulations of triacylglycerols in the alpha phase [J].
Chandrasekhar, I ;
van Gunsteren, WF .
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 2002, 31 (02) :89-101
[8]   APPLICATION OF RESP CHARGES TO CALCULATE CONFORMATIONAL ENERGIES, HYDROGEN-BOND ENERGIES, AND FREE-ENERGIES OF SOLVATION [J].
CORNELL, WD ;
CIEPLAK, P ;
BAYLY, CI ;
KOLLMAN, PA .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1993, 115 (21) :9620-9631
[9]   Gaussian-3 (G3) theory for molecules containing first and second-row atoms [J].
Curtiss, LA ;
Raghavachari, K ;
Redfern, PC ;
Rassolov, V ;
Pople, JA .
JOURNAL OF CHEMICAL PHYSICS, 1998, 109 (18) :7764-7776
[10]   Gaussian-3 theory using reduced Moller-Plesset order [J].
Curtiss, LA ;
Redfern, PC ;
Raghavachari, K ;
Rassolov, V ;
Pople, JA .
JOURNAL OF CHEMICAL PHYSICS, 1999, 110 (10) :4703-4709