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Anharmonic Vibrational Analysis of Biomolecules and Solvated Molecules Using Hybrid QM/MM Computations.

07:00 EST 7th February 2019 | BioPortfolio

Summary of "Anharmonic Vibrational Analysis of Biomolecules and Solvated Molecules Using Hybrid QM/MM Computations."

Quantum mechanics / molecular mechanics (QM/MM) calculations are applied for anharmonic vibrational analyses of biomolecules and solvated molecules. The QM/MM method is implemented into a molecular dynamics (MD) program, GENESIS, by interfacing with external electronic structure programs. Following the geometry optimization and the harmonic normal mode analysis based on a partial Hessian, the anharmonic potential energy surface (PES) is generated from QM/MM energies and gradients calculated at grid points. The PES is used for vibrational self-consistent field (VSCF) and post-VSCF calculations to compute the vibrational spectrum. The method is first applied to a phosphate ion in solution. By taking both the ion and neighboring water molecules as a QM region, IR spectra of representative hydration structures are calculated by the second-order vibrational quasi-degenerate perturbation theory (VQDPT2) at the level of B3LYP/cc-pVTZ and TIP3P force field. A weight average of IR spectra over the structures reproduces the experimental spectrum with a mean absolute deviation of 16 cm. Then, the method is applied to an enzyme, P450 nitric oxide reductase (P450nor), with the NO molecule bound to a ferric (Fe) heme. Starting from snapshot structures obtained from MD simulations of P450nor in solution, QM/MM calculations have been carried out at the level of B3LYP-D3/def2-SVP(D). The spin state of Fe(NO) is likely a closed-shell singlet state based on a ratio of N-O and Fe-NO stretching frequencies (ν and ν) calculated for closed- and open-shell singlet states. The calculated ν and ν overestimate the experimental ones by 120 and 75 cm, respectively. The electronic structure and solvation of Fe(NO) affect the structure around the heme of P450nor leading to an increase in ν and ν.

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This article was published in the following journal.

Name: Journal of chemical theory and computation
ISSN: 1549-9626
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