An effective fragment method for modeling solvent effects in quantum mechanical calculations

Abstract

An effective fragment model is developed to treat solvent effects on chemical properties andreactions. The solvent, which might consist of discrete water molecules, protein, or othermaterial, is treated explicitly using a model potential that incorporates electrostatics,polarization, and exchange repulsion effects. The solute, which one can most generally envision as including some number of solvent molecules as well, is treated in a fully ab initio manner, using an appropriate level of electronic structure theory. In addition to the fragment model itself, formulae are presented that permit the determination of analytic energy gradients and, therefore, numerically determined energy second derivatives (hessians) for the complete system. Initial tests of the model for the water dimer and water-formamide are in good agreement with fully abinitio calculations. An effective fragment model is developed to treat solvent effects on chemical properties and reactions. The solvent, which might consist of discrete water molecules, protein, or other material, is treated explicitly using a model potential that incorporates electrostatics, polarization, and exchange repulsion effects. The solute, which one can most generally envision as including some number of solvent molecules as well, is treated in a fully ab initio manner, using an appropriate level of electronic structure theory. In addition to the fragment model itself, formulae are presented that permit the determination of analytic energy gradients and, therefore, numerically determined energy second derivatives ͑hessians͒ for the complete system. Initial tests of the model for the water dimer and water-formamide are in good agreement with fully ab initio calculations.

Electrostatic properties in the catalytic site of papain: A possible regulatory mechanism for the reactivity of the ion pair

“…However, even considering a single static configuration, our results cannot be considered as quantitative ones because our methodological approach does not include inter-fragment polarization effects (only a local correction is introduced by the OME reassociation method in the important peptide junction region). A methodology that incorporates inter-fragment polarization effects 69,[81][82][83] and a correction for the charge penetration effect 84 is under development. These improvements are especially important to avoid significant errors when evaluating the internal ion pair energy and also when evaluating the ion pair interaction with the surrounding protein residues and water molecules.…”

Advances in molecular quantum chemistry contained in the Q-Chem 4 program package

“…The EFP method is a first-principles-based model that was originally designed to describe aqueous environments [306,307]. It was later extended to general solvents and biological environments [263,308,309].…”

QM/MM: what have we learned, where are we, and where do we go from here?

“…Since most popular MM force fields, like CHARMM [18] or OPLS-AA [17,19,20,22,24,25], have developed extensive sets of atomic-centered partial point charges for calculating electrostatic interactions at the MM level, it is usually convenient to represent the SS atoms by atomic-centered partial point charges in the effective QM Hamiltonian. However, more complicated representations involving distributed multipoles have also been attempted [46,89]. The bonded (stretching, bending, and torsional) interactions and non-bonded van der Waals interactions between the PS and SS are retained at the MM level.…”

“…In some cases, the boundary between PS and SS does not go through a covalent bound, e.g., a molecule being solvated in water, where the solute is the PS and the solvent (water) molecules are the SS [36,69]. The effective fragment potential method [46] can also be considered as a special case of MM in this catalog. In many cases, however, one cannot avoid passing the boundary between the PS and SS through covalent bonds (e.g., in enzymes or reactive polymers) or through ionic bonds (in solid-state catalysts).…”