"A polarizable QM/MM approach to the molecular dynamics of amide groups solvated in water" Magnus Schwörer, Christoph Wichmann, and Paul Tavan
J. Chem. Phys. 144, 114504 (2016).
Abstract: The infrared (IR) spectra of polypeptides are dominated by the socalled amide bands. Because they originate from the strongly polar and polarizable amide groups (AGs) making up the backbone, their spectral positions sensitively depend on the local electric fields. Aiming at accurate computations of these IR spectra by molecular dynamics (MD) simulations, which derive atomic forces from a hybrid quantum and molecular mechanics (QM/MM) Hamiltonian, here we consider the effects of solvation in bulk liquid water on the amide bands of the AG model compound Nmethylacetamide (NMA). As QM approach to NMA we choose gridbased density functional theory (DFT). For the surrounding MM water, we develop, largely based on computations, a polarizable molecular mechanics (PMM)model potential called GP6P, which features six Gaussian electrostatic sources (one induced dipole, five static partial charge distributions) and, therefore, avoids spurious distortions of the DFT electron density in hybrid DFT/PMM simulations. Bulk liquid GP6P is shown to have favorable properties at the thermodynamic conditions of the parameterization and beyond. LennardJones (LJ) parameters of the DFT fragment NMA are optimized by comparing radial distribution functions in the surrounding GP6P liquid with reference data obtained from a “firstprinciples” DFTMD simulation. Finally, IR spectra of NMA in GP6P water are calculated from extended DFT/PMMMD trajectories, in which the NMA is treated by three different DFT functionals (BP, BLYP, B3LYP). Methodspecific frequency scaling factors are derived from DFTMD simulations of isolated NMA. The DFT/PMMMD simulations with GP6P and with the optimized LJ parameters then excellently predict the effects of aqueous solvation and deuteration observed in the IR spectra of NMA. As a result, the methods required to accurately compute such spectra by DFT/PMMMD also for larger peptides in aqueous solution are now at hand.
BMO authors (in alphabetic order): Magnus Schwörer Paul Tavan Christoph Wichmann
Assoziierte Projekte: QM/MM hybrid descriptions of solutes in complex solvents Polarizable force fields for molecular mechanics from first principles
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