A General Boundary Potential for Hybrid QM/MM Simulations of Solvated Biomolecular Systems

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Abstract

We present a general boundary potential for the efficient and accurate evaluation of electrostatic interactions in hybrid quantum mechanical/molecular mechanical (QM/MM) approaches called solvated macromolecule boundary potential (SMBP), which is designed for QM/MM calculations with any kind of QM method. The SMBP targets QM/MM single-point energy calculations and geometry optimizations. In the SMBP scheme, the outer solvent and macromolecule region is described by a boundary potential obtained with the use of Poisson-Boltzmann calculations (treating the bulk solvent as a dielectric continuum). In the QM calculations, the SMBP is represented by virtual point charges on a surface enclosing the explicitly treated inner region. These charges and their interactions with the QM density are determined through a self-consistent reaction field procedure. The accuracy of the SMBP is evaluated on three diverse test systems: the intramolecular proton transfer of glycine in water, the hydroxylation reaction in p-hydroxybenzoate hydroxylase, and the spin state energy splittings in the pentacoordinated ferric complex of cytochrome P450cam. In the case of solvated glycine, application of the SMBP turns out to be problematic since analogous QM/MM/SMBP and full QM/MM geometry optimizations lead to different close-lying local minima. In both enzymes, the SMBP performs very well and closely reproduces the results from full QM/MM optimizations of these more rigid test systems. Starting from optimized QM/MM/SMBP structures along a reaction path, one can apply the previously implemented generalized solvent boundary potential (GSBP) to sample over MM phase space in QM/MM free energy calculations within the framework of free energy perturbation theory. This reduces the overall computational costs of sampling by 1 order of magnitude while maintaining good accuracy. The combined use of SMBP and GSBP thus allows for efficient QM/MM free energy studies of enzymes.

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