Weight Averaged Anharmonic Vibrational Calculations: Applications to Polypeptide, Lipid Bilayers, and Polymer Materials

Yagi, Kiyoshi; Otaki, Hiroki; Li, Pai‐Chi; Thomsen, Bo; Sugita, Yuji

doi:10.1002/9783527814596.ch5

Cited by 3 publications

(4 citation statements)

References 85 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Recently, a number of theoretical reconstructions of NIR spectra by means of efficient vibrational second-order perturbation (VPT2) method have been reported [18]; e.g., carboxylic acids [19], fatty acids [20,21,22], aminoacids [23], nucleobases [24], nitriles [25], azines [26], phenols [27,28], and alcohols [29,30]. Considerable efforts have been undertaken in order to develop anharmonic approaches applicable to even larger molecular systems [31,32,33,34]. On the other hand, meticulous probing of vibrational potential capable of yielding nearly-exact results is also available [35,36,37,38].…”

Section: Introductionmentioning

confidence: 99%

Spectra–Structure Correlations in Isotopomers of Ethanol (CX3CX2OX; X = H, D): Combined Near-Infrared and Anharmonic Computational Study

et al. 2019

View full text Add to dashboard Cite

The effect of isotopic substitution on near-infrared (NIR) spectra has not been studied in detail. With an exception of few major bands, it is difficult to follow the spectral changes due to complexity of NIR spectra. Recent progress in anharmonic quantum mechanical calculations allows for accurate reconstruction of NIR spectra. Taking this opportunity, we carried out a systematic study of NIR spectra of six isotopomers of ethanol (CX3CX2OX; X = H, D). Besides, we calculated the theoretical spectra of two other isotopomers (CH3CD2OD and CD3CH2OD) for which the experimental spectra are not available. The anharmonic calculations were based on generalized vibrational second-order perturbation theory (GVPT2) at DFT and MP2 levels with several basis sets. We compared the accuracy and efficiency of various computational methods. It appears that the best results were obtained with B2PLYP-GD3BJ/def2-TZVP//CPCM approach. Our simulations included the first and second overtones, as well as binary and ternary combinations bands. This way, we reliably reproduced even minor bands in the spectra of diluted samples (0.1 M in CCl4). On this basis, the effect of isotopic substitution on NIR spectra of ethanol was accurately reproduced and comprehensively explained.

show abstract

Section: Introductionmentioning

confidence: 99%

Spectra–Structure Correlations in Isotopomers of Ethanol (CX3CX2OX; X = H, D): Combined Near-Infrared and Anharmonic Computational Study

et al. 2019

View full text Add to dashboard Cite

show abstract

“…This procedure, albeit at the MM level, yields essential HB structures between H 2 PO 4 – and water molecules that contributes to the spectrum, and leads to a smooth convergence of the spectrum with respect to the number of snapshot as small as 8 (one for each N wat = 9–16). The result suggests that the weight-average approach 50 combining a structural sampling using MD and vibrational calculations of IR spectra using VQDPT2 and QM/MM is a promising approach to simulate the IR spectrum of solvated molecules.…”

Section: Resultsmentioning

confidence: 99%

“…Vibrational calculations for complex systems remain a challenge, because (1) the system visits many minima with different frequencies in finite temperature, and (2) the solvent/protein environment needs to be considered. We have recently developed a weight-averaged method, − which incorporates the former effect using classical molecular dynamics (MD) simulations and vibrational calculations based on the ab initio PES. In this method, MD simulations are first carried out to sample a large number of structures in the target system.…”

Section: Introductionmentioning

confidence: 99%

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

Yagi

Yamada

Kobayashi

et al. 2019

J. Chem. Theory Comput.

Self Cite

View full text Add to dashboard Cite

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 (Fe III ) 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 III (NO) is likely a closed-shell singlet state based on a ratio of N–O and Fe–NO stretching frequencies (ν N–O and ν Fe–NO ) calculated for closed- and open-shell singlet states. The calculated ν N–O and ν Fe–NO overestimate the experimental ones by 120 and 75 cm –1 , respectively. The electronic structure and solvation of Fe III (NO) affect the structure around the heme of P450nor leading to an increase in ν N–O and ν Fe–NO .

show abstract

“…The final result is then obtained via weight averaging of these vibrational spectra. [1,45,47,48] This approach has, for instance, been applied in vibrational structure calculations on polyamides examples [1,48] in reduced vibrational space. These figure).…”

Section: The Potential Energy Surfacementioning

confidence: 99%

Tailored multilevel approaches in vibrational structure theory: A route to quantum mechanical vibrational spectra for complex systems

König

2020

Int J of Quantum Chemistry

View full text Add to dashboard Cite

Vibrational spectroscopies have emerged as important tools to elucidate structures and processes in life sciences. The interpretation of vibrational spectra requires, in most cases, computational assistance and account for anharmonic effects. Pushing the size limitations of anharmonic vibrational structure calculations is therefore of great interest. Fortunately, interpretation of the experimental results often requires only a limited part of the vibrational spectrum. Hence, it can be expected that multilevel approaches, focusing computational effort on the relevant parts, are highly beneficial. Still, such approaches are rather sparse in the field of vibrational structure theory. In this perspective, we outline the present status on multilevel static vibrational wave functions and rectilinear vibrational coordinates. We further foresee how those ingredients can be combined to formulate a comprehensive multilevel vibrational structure framework.

show abstract

Weight Averaged Anharmonic Vibrational Calculations: Applications to Polypeptide, Lipid Bilayers, and Polymer Materials

Cited by 3 publications

References 85 publications

Spectra–Structure Correlations in Isotopomers of Ethanol (CX3CX2OX; X = H, D): Combined Near-Infrared and Anharmonic Computational Study

Spectra–Structure Correlations in Isotopomers of Ethanol (CX3CX2OX; X = H, D): Combined Near-Infrared and Anharmonic Computational Study

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

Tailored multilevel approaches in vibrational structure theory: A route to quantum mechanical vibrational spectra for complex systems

Contact Info

Product

Resources

About