Polarizable Atomic Multipole-Based Molecular Mechanics for Organic Molecules

An empirical potential based on permanent atomic multipoles and atomic induced dipoles is reported for alkanes, alcohols, amines, sulfides, aldehydes, carboxylic acids, amides, aromatics, and other small organic molecules. Permanent atomic multipole moments through quadrupole moments have been deriv...

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Bibliographic Details
Published in:Journal of chemical theory and computation 2011-10, Vol.7 (10), p.3143-3161
Main Authors: Ren, Pengyu, Wu, Chuanjie, Ponder, Jay W
Format: Article
Language:English
Subjects:
Molecular Mechanics
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Summary:An empirical potential based on permanent atomic multipoles and atomic induced dipoles is reported for alkanes, alcohols, amines, sulfides, aldehydes, carboxylic acids, amides, aromatics, and other small organic molecules. Permanent atomic multipole moments through quadrupole moments have been derived from gas phase ab initio molecular orbital calculations. The van der Waals parameters are obtained by fitting to gas phase homodimer QM energies and structures, as well as experimental densities and heats of vaporization of neat liquids. As a validation, the hydrogen bonding energies and structures of gas phase heterodimers with water are evaluated using the resulting potential. For 32 homo- and heterodimers, the association energy agrees with ab initio results to within 0.4 kcal/mol. The RMS deviation of the hydrogen bond distance from QM optimized geometry is less than 0.06 Å. In addition, liquid self-diffusion and static dielectric constants computed from a molecular dynamics simulation are consistent with experimental values. The force field is also used to compute the solvation free energy of 27 compounds not included in the parametrization process, with a RMS error of 0.69 kcal/mol. The results obtained in this study suggest that the AMOEBA force field performs well across different environments and phases. The key algorithms involved in the electrostatic model and a protocol for developing parameters are detailed to facilitate extension to additional molecular systems.
ISSN:1549-9618
1549-9626
DOI:10.1021/ct200304d