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Hydrogen‐bond (H‐bond) interaction energies in α‐helices of short alanine peptides were systematically examined by precise density functional theory calculations, followed by a molecular tailoring approach. The contribution of each H‐bond interaction in α‐helices was estimated in detail from the entire conformation energies, and the results were compared with those in the minimal H‐bond models, in which only H‐bond donors and acceptors exist with the capping methyl groups. The former interaction energies were always significantly weaker than the latter energies, when the same geometries of the H‐bond donors and acceptors were applied. The chemical origin of this phenomenon was investigated by analyzing the differences among the electronic structures of the local peptide backbones of the α‐helices and those of the minimal H‐bond models. Consequently, we found that the reduced H‐bond energy originated from the depolarizations of both the H‐bond donor and acceptor groups, due to the repulsive interactions with the neighboring polar peptide groups in the α‐helix backbone. The classical force fields provide similar H‐bond energies to those in the minimal H‐bond models, which ignore the current depolarization effect, and thus they overestimate the actual H‐bond energies in α‐helices. © 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Au nanoclusters (Au NCs) stabilized by poly(N‐vinyl‐2‐pyrrolidone) and poly(allylamine), abbreviated to Au:PVP and Au:PAA, catalyze the aerobic oxidation of p‐hydroxybenzyl alcohols, but the catalytic activity of Au:PVP is much higher than that of Au:PAA. To elucidate the correlations between the catalytic activities and coordination structures of the stabilizing polymer, the substrate accessibility on Au NCs was estimated by density functional theory (DFT) and molecular dynamics (MD) calculations. For MD simulations, we applied a systematic method to optimize the temperature parameters in temperature replica exchange molecular dynamics (T‐REMD), and the coordination structures were comprehensively classified by multivariate analysis. The results show that the number of open active sites on the Au NCs is a good index for predicting the catalytic activities. © 2018 Wiley Periodicals, Inc. The authors investigated the coordinate structures of polymer‐stabilized Au nanocluster (Au NC) in association with catalytic activity by using the Au NC surface coverage ratio by the polymers. The results indicate that the relative catalytic activities of polymer‐stabilized Au NCs can be largely predicted by estimating the number ratio of the adsorbed monomer molecules on Au NC by DFT calculation, when the lengths of the polymer chains are almost the same. [ABSTRACT FROM AUTHOR]

Lately, it was found that the Au nanoclusters stabilised by poly(N-vinyl-2-pyrrolidone) [PVP; (C6H9ON)n], abbreviated to Au:PVP, can oxidisep-hydroxybenzyl alcohol selectively into the corresponding aldehyde in water without degradation. This observation indicates that Au cluster can exhibit high catalytic activity without any metal oxide supports. From previous works, it was found that the anionic Au clusters played an important role for the activation of oxygen molecule on the Au clusters. However, the catalytic activity of neutral Au clusters for the aerobic oxidation reaction of alcohol is not still investigated in detail. In order to examine the catalytic activity of neutral Au clusters, the aerobic oxidation ofp-hydroxybenzyl alcohol to the corresponding aldehyde catalysed by Au6has been investigated quantum chemically using density functional theory with the PBE0 functional. Possible reaction pathways are investigated taking account of full structure relaxation of the model systems. From the calculation results, it was found that the formations of both a hydroperoxyl anion and a hydride were the important steps for the aerobic oxidation ofp-hydroxybenzyl alcohol over Au6cluster. [ABSTRACT FROM PUBLISHER]

We investigate for the first time the electronic structure of the biomimetic diiron complex 1 [Fe(IV)2(μ-O)2(5-Me3-TPA)2]4+ (5-Me3-TPA = tris(5-methyl-2-pyridylmethyl)amine) using broken-symmetry hybrid density functional theory method. According to previous studies, the Fe(IV)2(μ-O)2 core of intermediate Q of soluble methane monooxygenase shows antiferromagnetic coupling between local S = 2 states at each iron site. In contrast to Q, each local Fe(IV) ion of the synthetic complex does not have an S = 2 but has an S = 1 state based on the calculated geometric parameters and energetic stability. Our calculation supports the experimental result. [ABSTRACT FROM AUTHOR]

The chemical species of solvent molecule (WB) between two manganese ions in the active site of arginase is investigated based on the structural and magnetic property. The calculated magnetic coupling constant (Jab) values at UBH&HLYP level of theory are - 1.9 cm- 1 for WB = H2O and - 5.7 cm- 1 for WB = OH- , respectively. In comparison with the experimental value (Jab = ∼ - 2.0 cm- 1), H2O is the most likely candidate to WB in the initial structure. Natural orbital analyses reveal that WB plays an important role for keeping the geometry of the Mn-O(WB)-Mn core rigid rather than mediating superexchange interaction. The result indicates that WB does not have to shift to one Mn ion as an initiation of the hydrolysis reaction. [ABSTRACT FROM AUTHOR]

Inter-dimer magnetic interactions (J ab(D) ) between (BEDT-TTF) 2 + • dimers in the κ-(BEDT-TTF) 2 Cu 2 (CN) 3 crystal has been studied theoretically. In these crystals, triangular lattice structure with spin frustration has been discovered and experimental studies have been performed by several research groups. We have calculated the inter-dimer J ab(D) values by using several methods. In addition, we have analyzed the spin lattice with optimization of θ angle in classical Heisenberg spin model and with numerical diagonalization in quantum Heisenberg spin model. [ABSTRACT FROM AUTHOR]

Abstract: A new scheme for calculations of effective exchange integral (J) values at the complete basis set (CBS) limit is proposed based on an extrapolation method of the total energy and an approximate spin projection (AP) method. By using the scheme, the J values between oxo-vanadium units in a (VO)7 ring complex at the CBS limit are calculated with several hybrid density functional theory (DFT) functional sets that are BHandHLYP, B3LYP and CAM-B3LYP. The calculated results indicate that the J values at the CBS limit with BHandHLYP reproduces the experimental result well. In addition, some basis sets such as Dunning’s correlation-consistent polarized valence, Pople series and def2 series are also examined to elucidate which basis function reproduces the J values at the CBS limit. The results indicate that the basis sets that are larger than 6-31+G∗ level are at least required to reproduce the J values of the (VO)7 complex at the CBS limit. [Copyright &y& Elsevier]

Abstract: A theoretical method for ab initio calculations of the zero-field splitting parameters from electron spin–spin interaction contributions is described. This methodology is applied to typical organic biradicals within the density-functional theory. It is shown that this approach can provide results in good agreement with experimental values for typical organic biradicals at moderate computational cost. Magnetic properties are discussed in detail for typical organic biradicals, such as carbene, vinylmethylene, phenylcarbene, and diphenylcarbene. Their spin orbitals, magnetic axes, and effects of conformational changes are investigated. Moreover, the relationship between those three factors and the zero-filed splitting parameters (D- and E) including their signs is revealed. This method has been proved to be quite valid in studying organic ferromagnets. [Copyright &y& Elsevier]