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Development of a Polarizable Intermolecular Potential Function (PIPF) for Liquid Amides and Alkanes
Version 2 2019-03-07, 12:33
Version 1 2016-02-28, 13:35
journal contribution
posted on 2007-11-13, 00:00 authored by Wangshen Xie, Jingzhi Pu, Alexander D. MacKerell, Jiali GaoA polarizable intermolecular potential function (PIPF) employing the Thole interacting dipole (TID) polarization model has been developed for liquid alkanes and amides. In
connection with the internal bonding terms of the CHARMM22 force field, the present PIPF-CHARMM potential provides an adequate description of structural and thermodynamic properties for liquid alkanes and for liquid amides through molecular dynamics simulations. The
computed heats of vaporization and liquid density are within 1.4% of experimental values.
Polarization effects play a major role in liquid amides, which are reflected by an increase of
1.5−1.8 D in molecular dipole moment for primary and secondary amides. Furthermore, the
computed polarization energies contribute to the total intermolecular interaction energy by
6−24%. The ability of the PIPF-CHARMM force field to treat protein backbone structures is
tested by examining the potential energy surface of the amide bond rotation in N-methylacetamide
and the Ramachandran surface for alanine dipeptide. The agreement with ab initio MP2
results and with the original CHARMM22 force field is encouraging, suggesting that the PIPF-CHARMM potential can be used as a starting point to construct a complete polarizable force
field for proteins.
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Polarizable Intermolecularpolarization energiesCHARMM 22 force fieldLiquid AmidesTIDab initio MP 2 resultspolarization modelalkanedynamics simulationsPolarization effectsinteraction energyprotein backbone structuresPIPF-CHARMM force fieldalanine dipeptideenergy surfaceamide bond rotationRamachandran surfacepolarizable force field
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