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It is well known that unrestricted density functional theory (UDFT) calculations include spin contamination errors. While errors in UDFT/plane-wave calculations have not been clarified thus far, some effects of these errors are investigated. Recently, our group estimated spin contamination errors in UDFT/plane-wave calculation results by developing and applying the approximate spin projection (AP) scheme [Chem. Phys. Lett., 701: 103 (2018), Mol. Phys., 117: 2251 (2019), Molecules, 24: 505 (2019), Appl. Phys. Express, 12: 115506 (2019)]. In this study, a systematic theoretical investigation of the surface effects on the spin contamination error was performed. For this purpose, we selected model systems such as Au dimers, chains, and film adsorptions onto MgO and BaO (001) surfaces. The calculation results showed the dependence on the dimensions of the supported materials and lattice constants of the supports. In general, the effects of spin contamination errors are decreased by interaction with the surface. The effects of the errors increased by increasing dimension; i.e. the increasing order of spin contamination errors is film > chain > dimer. In addition, the spin-polarised states are stabilised because of the interaction with the surfaces, and spin contamination errors occur in some cases where the Au–Au distances are small. [ABSTRACT FROM AUTHOR]

Fundamental principles for theoretical understanding and elucidation of structure and reactivity of iron-sulfur (Fe-S) FenSm (n, m=2∼8) clusters are investigated and elucidated on the theoretical and experimental grounds. To this end, the nature of chemical bonds of these clusters is investigated by three methods; (1) the spin Hamiltonian model for analysis of EPR results, (2) broken-symmetry (BS) hybrid density functional theory (HDFT) methods for full geometry optimisations and elucidations of complete active spaces (CAS) for one-electron transfers reactions and (3) beyond HDFT methods such as CAS configuration interaction (CI) and MR CI for high precision energy calculations on classical and quantum computers. Theoretical concepts revealed are applied for elucidation of the mechanism of nitrogen fixation with FeMoco (Fe7MoS9C) cluster, indicating an important role of proton-coupled (PC) one electron spin transfer (OEST) processes instead of radical reaction mechanisms. [ABSTRACT FROM AUTHOR]

The density functional theory calculations are employed to present a theoretical study of the magnetic exchange interactions taking place in the [Ni.sub.9] complexes. The magnetic properties of the complexes are shown to be controlled by the [J.sub.3] magnetic interaction via the bridging ligand orbitals.

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]

We have investigated the free energy surface of alanine tripeptide in water. To elucidate the secondary structure of the amide chain, information on the free energy surface with explicit water at room temperature, and the multidimensional reaction coordinates are required. We studied the minimum free energy paths (MFEPs) connecting reactants, transition structures (TS) and products. To solve this problem, we used the free energy reaction root mapping (FERRMap) method. This is an automated search method to find MFEPs by using umbrella integration and the scaled hypersphere search method. We calculated the four-dimensional free energy surface for alanine tripeptide in water using FERRMap and found 61 equilibrium structures (EQ) connected by 133 TS points. After elucidating the MFEP network, we analysed the structures of the EQ points and the MFEPs connecting beta-sheet structures and beta-turn structures or left-handed helix structures. [ABSTRACT FROM AUTHOR]

The optimized geometries of the CaMn4OX (X = 5, 6) cluster in the oxygen evolving complex (OEC) of photosystem II (PSII) by large‐scale quantum mechanics (QM) and molecular mechanics (MM) calculations are compared with recent serial femtosecond crystallography (SFX) results for the Si (i = 0–3) states. The valence states of four Mn ions by the QM/MM calculations are also examined in relation to the experimental results by the X‐ray emission spectroscopy (XES) for the Si intermediates. Geometrical and valence structures of right‐opened Mn‐hydroxide, Mn‐oxo and Mn‐peroxide intermediates in the S3 state are investigated in detail in relation to recent SFX and XES experiments for the S3 state. Interplay between theory and experiment indicates that the Mn‐oxo intermediate is a new possible candidate for the S3 state. Implications of the computational results are discussed in relation to possible mechanisms of the oxygenoxygen bond formation for water oxidation in OEC of PSII. [ABSTRACT FROM AUTHOR]

Both direct exchange and super‐exchange interactions cooperate to realize inter‐spin magnetic interaction in binuclear manganese complex Mn(IV)2O2(NHCHCO2)4 with a di‐μ‐oxo path. We revisited this spin system using DMRG CAS methods and CAS selection procedures. Our results indicate that our previous "dynamically extended spin polarization" (DE‐SP) procedure for organic polyradicals and so forth does not work well. Thus, we have examined another selection procedure, the "dynamically extended super‐exchange" (DE‐SE) procedure. DMRG CASCI [18,18] by UB3LYP(HS)‐UNO(DE‐SE) can realize antiferromagnetic J values similar to experimental ones (−87 cm−1). In addition, all J values between all spin states (HS[septet],IS[quintet],IS[triplet],LS[singlet])were also shown to be correct under sufficiently large M values. © 2018 Wiley Periodicals, Inc. Both direct exchange and super‐exchange interactions cooperate to realize inter‐spin magnetic interaction in binuclear manganese complex Mn(IV)2O2(NHCHCO2)4 with di‐μ‐oxo path. The authors revisit this spin system using DMRG CAS methods and CAS selection procedures. [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]

The free‐energy landscape is an important factor for understanding the conformational equilibria of chemical reactions, and many techniques have been developed to calculate the potential of the mean force. Unfortunately, these methods require a previous knowledge of the system for calculations because the results depend on the reaction coordinates. In this study, we combine the scaled hypersphere search method with the umbrella integration method to obtain the transition states on free‐energy landscapes and minimum‐free‐energy paths (MFEPs). With this approach, the MFEP connections between known and unknown equilibrium points are constructed without the prior knowledge of the free‐energy landscape. The problem of reaction coordinates can be solved by using a multidimensional, fully automated interrogation of MFEPs for acquiring the potential of mean force. The efficiency of the proposed method is demonstrated by applying it to alanine dipeptide and alanine tripeptide. © 2018 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Possible mechanisms for water cleavage in oxygen evolving complex (OEC) of photosystem II (PSII) have been investigated based on broken-symmetry (BS) hybrid DFT (HDFT)/def2 TZVP calculations in combination with available XRD, XFEL, EXAFS, XES and EPR results. The BS HDFT and the experimental results have provided basic concepts for understanding of chemical bonds of the CaMn4O5cluster in the catalytic site of OEC of PSII for elucidation of the mechanism of photosynthetic water cleavage. Scope and applicability of the hybrid DFT (HDFT) methods have been examined in relation to relative stabilities of possible nine intermediates such as Mn-hydroxide, Mn-oxo, Mn-peroxo, Mn-superoxo, etc., in order to understand the O–O (O–OH) bond formation in the S3and/or S4states of OEC of PSII. The relative stabilities among these intermediates are variable, depending on the weight of the Hartree–Fock exchange term of HDFT. The Mn-hydroxide, Mn-oxo and Mn-superoxo intermediates are found to be preferable in the weak, intermediate and strong electron correlation regimes, respectively. Recent different serial femtosecond X-ray (SFX) results in the S3state are investigated based on the proposed basic concepts under the assumption of different water-insertion steps for water cleavage in the Kok cycle. The observation of water insertion in the S3state is compatible with previous large-scale QM/MM results and previous theoretical proposal for the chemical equilibrium mechanism in the S3state . On the other hand, the no detection of water insertion in the S3state based on other SFX results is consistent with previous proposal of the O–OH (or O–O) bond formation in the S4state . Radical coupling and non-adiabatic one-electron transfer (NA-OET) mechanisms for the OO-bond formation are examined using the energy diagrams by QM calculations and by QM(UB3LYP)/MM calculations . Possible reaction pathways for the O–O and O–OH bond formations are also investigated based on two water-inlet pathways for oxygen evolution in OEC of PSII. Future perspectives are discussed in relation to post HDFT calculations of the energy diagrams for elucidation of the mechanism of water oxidation in OEC of PSII. [ABSTRACT FROM AUTHOR]

In this work, we show that the natural orbitals of unrestricted hybrid density functional theory (UHDFT) can be used as the active space orbitals to perform multireference (MR) calculations, for example, the density matrix renormalisation group (DMRG) and Mukherjee-type (Mk) MR coupled-cluster (CC) method. By including a sufficiently large number of these natural orbitals, full-valence (FV) active space can be identified without recourse of the expensive self-consistent procedures for DMRG-SCF. Several useful chemical indices are derived based on the occupation numbers of the natural orbitals for seamless continuation from broken-symmetry (BS) to symmetry-adapted (SA) methods. These procedures are used on 1,3-didehydrobenzene (meta-benzyne) to calculate its singlet (S)-triplet (T) gap. We compare our results to available experiments and computational results obtained by several other groups. We see our procedures as a seamless bridge between single-reference BS methods, such as UHDFT, and the SA MR methods, such as FV DMRG and MkMRCC. [ABSTRACT FROM AUTHOR]

Theoretical examinations of the ferromagnetic coupling in them-phenylene-bis-methylene molecule and its oligomer were carried out. These systems are good candidates for exchange-coupled systems to investigate strong electronic correlations. We studied effective exchange integrals (J), which indicated magnetic coupling between interacting spins in these species. First, theoretical calculations based on a broken-symmetry single-reference procedure, i.e. the UHF, UMP2, UMP4, UCCSD(T) and UB3LYP methods, were carried out with a GAUSSIAN program code under an SR wave function. From these results, theJvalue by the UHF method was largely positive because of the strong ferromagnetic spin polarisation effect. TheJvalue by the UCCSD(T) and UB3LYP methods improved an overestimation problem by correcting the dynamical electronic correlation. Next, magnetic coupling among these spins was studied using the CAS-based method of the symmetry-adapted multireference methods procedure. Thus, the UNO DMRG CASCI (UNO, unrestricted natural orbital; DMRG, density matrix renormalised group; CASCI, complete active space configuration interaction) method was mainly employed with a combination of ORCA and BLOCK program codes. DMRG CASCI calculations in valence electron counting, which included all orbitals to full valence CI, provided the most reliable result, and support the UB3LYP method for extended systems. [ABSTRACT FROM AUTHOR]

We have investigated nearsightedness of electronic matter (NEM) of finite systems on the basis of linear response function to examine theoretical foundation of contemporary computational chemistry such as quantum mechanics/molecular mechanics methods. In this study, we introduce several nearsightedness-related indices to assess the magnitude of localisability of responses for one-dimensional finite model systems. We started from two electrons' systems, which are beyond the scope of the original concept of NEM, and increased the number of electrons (N) to a hundred electrons to analyse dependency of such indices onN. In the process of construction of the indices, we analysed the factors, because of which the magnitude of nonlocal parts of linear response functions becomes small, into several ones, and extracted purely the magnitude of propagation of responses. [ABSTRACT FROM AUTHOR]

In this paper, we have investigated the catalytic mechanism of rat liver arginase using a quantum mechanics/molecular mechanics (QM/MM) approach. The enzyme catalyses the hydrolysis of L-arginine (L-Arg) to generate L-ornithine and urea. The reaction mechanism proposed by the previous experimental studies is well reproduced by the QM/MM computations. The explicit treatment of the protein environment suggests that Glu277 fulfil its role in stabilising and orienting L-Arg before nucleophilic attack by the bridging hydroxide in the first step. We have also found that the proton transfer step involving a hydrogen bond switch is the rate-limiting step. The activation energy is computed to be 9.0 and 5.9 kcal/mol at the UB3LYP-D3/CHARMM22 and UBHandHLYP-D3/CHARMM22 levels, which are comparable to the observed activation barrier of 7.2 kcal/mol. [ABSTRACT FROM AUTHOR]

We here formulate and implement linear response function (LRF) of the Mayer bond order (MBO), which is expected to be a new indicator to describe intrinsic chemical reactivity of molecules. We calculate LRFs of the MBOs of para-substituted benzoic acids, and compare the results with the Hammett substituent constants and computational results of acid dissociation constants that were previously reported. The results are discussed from the viewpoint of the applicability of LRF of the MBO to estimate the relative reactivity of the substituted benzoic acids. [ABSTRACT FROM AUTHOR]

Quantum mechanical (QM)/molecular mechanics (MM) calculations by the use of a large-scale QM model (QM Model V) have been performed to elucidate hydrogen-bonding networks and proton wires for proton release pathways (PRP) of water oxidation reaction in the oxygen evolving complex (OEC) of photosystem II (PSII). Full geometry optimisations of PRP by the QM/MM model have been carried out starting from the geometry of heavy atoms determined by the recent high-resolution X-ray diffraction (XRD) experiment of PSII refined to 1.9 Å resolution. Computational results by the QM/MM calculations have elucidated the hydrogen-bonding O···O(N) and O···H distances and O(N)–H···O angles in PRP, together with the Cl–O(N) and Cl···H distances and O(N)–H···Cl angles for chloride anions. The optimised hydrogen-bonding networks are well consistent with the XRD results and available experiments such as extended X-ray absorption fine structure, showing the reliability of channel structures of OEC of PSII revealed by the XRD experiment. The QM/MM computations have elucidated possible roles of chloride anions in the OEC of PSII. The QM/MM computational results have provided useful information for understanding and explanation of accumulated mutation experiments of key amino acid residues in the OEC of PSII. Implications of the present results are discussed in relation to three steps for theoretical modelling of water oxidation in the OEC of PSII and bio-inspired working hypotheses for developments of artificial water oxidation systems by use of 3d transition-metal complexes. [ABSTRACT FROM AUTHOR]