Development of a Polarizable Intermolecular Potential Function (PIPF) for Liquid Amides and Alkanes

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Abstract
A 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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