NDLI: Polarizable Atomic Multipole-based Molecular Mechanics for Organic Molecules

Content Provider	PubMed Central
Author	Ren, Pengyu Wu, Chuanjie Ponder, Jay W.
Abstract	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 hydrogen bond distance from QM optimized geometry is less than 0.06 Å. In addition, liquid self-diffusion and static dielectric constants computed from 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 parameterization process, with a RMS error of 0.69 kcal/mol. The results obtained in this study suggest 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.
Related Links	http://dx.doi.org/10.1021/ct200304d
Ending Page	3161
Page Count	19
Starting Page	3143
File Format	PDF
ISSN	15499618
e-ISSN	15499626
Journal	Journal of chemical theory and computation
Issue Number	10
Volume Number	7
Language	English
Publisher Date	2011-10-11
Access Restriction	Open
Subject Keyword	Physical and Theoretical Chemistry Computer Science Applications Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Physical and Theoretical Chemistry Computer Science Applications

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