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
[11]   PARTICLE MESH EWALD - AN N.LOG(N) METHOD FOR EWALD SUMS IN LARGE SYSTEMS [J].
DARDEN, T ;
YORK, D ;
PEDERSEN, L .
JOURNAL OF CHEMICAL PHYSICS, 1993, 98 (12) :10089-10092
[12]   DIFFUSION IN PARAFFIN HYDROCARBONS [J].
DOUGLASS, DC ;
MCCALL, DW .
JOURNAL OF PHYSICAL CHEMISTRY, 1958, 62 (09) :1102-1107
[13]   Approximating the basis set dependence of coupled cluster calculations: Evaluation of perturbation theory approximations for stable molecules [J].
Dunning, TH ;
Peterson, KA .
JOURNAL OF CHEMICAL PHYSICS, 2000, 113 (18) :7799-7808
[14]   SOLVENT-INDUCED FORCES BETWEEN 2 HYDROPHILIC GROUPS [J].
DURELL, SR ;
BROOKS, BR ;
BENNAIM, A .
JOURNAL OF PHYSICAL CHEMISTRY, 1994, 98 (08) :2198-2202
[15]   An improved empirical potential energy function for molecular simulations of phospholipids [J].
Feller, SE ;
MacKerell, AD .
JOURNAL OF PHYSICAL CHEMISTRY B, 2000, 104 (31) :7510-7515
[16]   Computer simulation of a DPPC phospholipid bilayer: Structural changes as a function of molecular surface area [J].
Feller, SE ;
Venable, RM ;
Pastor, RW .
LANGMUIR, 1997, 13 (24) :6555-6561
[17]  
Flory P. J., 1969, STAT MECH CHAIN MOL
[18]  
Frisch M. J., 2016, J AM CHEM SOC, DOI DOI 10.1021/JA205566W
[19]   On the use of ab initio interaction energies for the accurate calculation of thermodynamic properties [J].
Garrison, SL ;
Sandler, SI .
JOURNAL OF CHEMICAL PHYSICS, 2002, 117 (23) :10571-10580
[20]   CONFORMATION OF THE HYDROCARBON CHAINS OF SODIUM DODECYL-SULFATE MOLECULES IN MICELLES - AN FTIR STUDY [J].
HOLLER, F ;
CALLIS, JB .
JOURNAL OF PHYSICAL CHEMISTRY, 1989, 93 (05) :2053-2058