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

Printer-friendly versionPrinter-friendly versionPDF versionPDF version
TitleAn ab initio study on the torsional surface of alkanes and its effect on molecular simulations of alkanes and a DPPC bilayer.
Publication TypeJournal Article
Year of Publication2005
AuthorsKlauda, JB, Brooks, BR, Mackerell, AD, Venable, RM, Pastor, RW
JournalJ Phys Chem B
Volume109
Issue11
Pagination5300-11
Date Published2005 Mar 24
ISSN1520-6106
Keywords1,2-Dipalmitoylphosphatidylcholine, Alkanes, Lipid Bilayers, Models, Molecular
Abstract

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.

DOI10.1021/jp0468096
Alternate JournalJ Phys Chem B
PubMed ID16863197
Grant ListGM51501 / GM / NIGMS NIH HHS / United States