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DommiMOE: An implementation of ligand field molecular mechanics in the molecular operating environment
Author(s) -
Deeth Robert J.,
Fey Natalie,
Williams–Hubbard Benjamin
Publication year - 2004
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.20137
Subject(s) - molecular mechanics , force field (fiction) , computer science , field (mathematics) , set (abstract data type) , interface (matter) , computational science , software , molecular dynamics , atom (system on chip) , potential energy , computational chemistry , chemistry , statistical physics , physics , programming language , mathematics , quantum mechanics , parallel computing , artificial intelligence , pure mathematics , bubble , maximum bubble pressure method
Abstract The ligand field molecular mechanics (LFMM) model, which incorporates the ligand field stabilization energy (LFSE) directly into the potential energy expression of molecular mechanics (MM), has been implemented in the “chemically aware” molecular operating environment (MOE) software package. The new program, christened DommiMOE, is derived from our original in‐house code that has been linked to MOE via its applications programming interface and a number of other routines written in MOE's native scientific vector language (SVL). DommiMOE automates the assignment of atom types and their associated parameters and popular force fields available in MOE such as MMFF94, AMBER, and CHARMM can be easily extended to provide a transition metal simulation capability. Some of the unique features of the LFMM are illustrated using MMFF94 and some simple [MCl 4 ] 2− and [Ni(NH 3 ) n ] 2+ species. These studies also demonstrate how density functional theory calculations, especially on experimentally inaccessible systems, provide important data for designing improved LFMM parameters. DommiMOE treats Jahn–Teller distortions automatically, and can compute the relative energies of different spin states for Ni(II) complexes using a single set of LFMM parameters. © 2004 Wiley Periodicals, Inc. J Comput Chem 26: 123–130, 2005