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

• Published in: Journal of chemical theory and computation 2019-03, Vol.15 (3), p.1924-1938
• Main Authors: Yagi, Kiyoshi, Yamada, Kenta, Kobayashi, Chigusa, Sugita, Yuji
• Format: Article
• Language: English
• Subjects: Anharmonicity; Biomolecules; Computer simulation; Cytochrome P-450 Enzyme System - chemistry; Electronic structure; Fusarium - chemistry; Fusarium - enzymology; Infrared spectroscopy; Mathematical analysis; Molecular dynamics; Molecular Dynamics Simulation; Nitric oxide; Optimization; Perturbation theory; Phosphates - chemistry; Potential energy; Protein Conformation; Quantum mechanics; Quantum Theory; Self consistent fields; Solutions; Solvation; Spectrophotometry, Infrared - methods; Thermodynamics; Water - chemistry; Weight
• ISSN: 1549-9618; 1549-9626
• DOI: 10.1021/acs.jctc.8b01193

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. With both the ion and neighboring water molecules taken 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–1. Then, the method is applied to an enzyme, P450 nitric oxide reductase (P450nor), with the NO molecule bound to a ferric (FeIII) 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 FeIII(NO) is likely a closed-shell singlet state based on a ratio of N–O and Fe–NO stretching frequencies (νN–O and νFe–NO) calculated for closed- and open-shell singlet states. The calculated νN–O and νFe–NO overestimate the experimental ones by 120 and 75 cm–1, respectively. The electronic structure and solvation of FeIII(NO) affect the structure around the heme of P450nor leading to an increase in νN–O and νFe–NO.