title: Application of a BOSS-Gaussian interface for QM/MM simulations of Henry and methyl transfer reactions.
abstract: Hybrid quantum mechanics and molecular mechanics (QM/MM) computer simulations have become an indispensable tool for studying chemical and biological phenomena for systems too large to treat with QM alone. For several decades, semiempirical QM methods have been used in QM/MM simulations. However, with increased computational resources, the introduction of ab initio and density function methods into on-the-fly QM/MM simulations is being increasingly preferred. This adaptation can be accomplished with a program interface that tethers independent QM and MM software packages. This report introduces such an interface for the BOSS and Gaussian programs, featuring modification of BOSS to request QM energies and partial atomic charges from Gaussian. A customizable C-shell linker script facilitates the interprogram communication. The BOSS-Gaussian interface also provides convenient access to Charge Model 5 (CM5) partial atomic charges for multiple purposes including QM/MM studies of reactions. In this report, the BOSS-Gaussian interface is applied to a nitroaldol (Henry) reaction and two methyl transfer reactions in aqueous solution. Improved agreement with experiment is found by determining free-energy surfaces with MP2/CM5 QM/MM simulations than previously reported investigations using semiempirical methods.
authors: Department of Chemistry, Yale University, New Haven, Connecticut, 06520-8107.
authors: Jonah Z
authors: JZ
authors: Vilseck
authors: Department of Chemistry, Yale University, New Haven, Connecticut, 06520-8107.
authors: Jakub
authors: J
authors: Kostal
authors: Department of Chemistry, Yale University, New Haven, Connecticut, 06520-8107.
authors: Julian
authors: J
authors: Tirado-Rives
authors: Department of Chemistry, Yale University, New Haven, Connecticut, 06520-8107.
authors: William L
authors: WL
authors: Jorgensen
mesh_terms: D006575:Heterocyclic Compounds, 3-Ring / Q000737:chemistry*; D008745:Methylation; D056004:Molecular Dynamics Simulation; D009010:Monte Carlo Method; D009574:Nitro Compounds / Q000737:chemistry*; D016011:Normal Distribution; D011789:Quantum Theory; D055672:Static Electricity; D013816:Thermodynamics
chemical_list: D006575:Heterocyclic Compounds, 3-Ring; D009574:Nitro Compounds; C560828:nitroaldol
keywords: BOSS; Gaussian 09; Henry reaction; charge model 5; methyl transfer reaction; quantum mechanics and molecular mechanics; reaction path