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Titanosilicate-supported Au-cluster catalysts can be used to selectively synthesize propylene oxide from propylene using O2 and H2. However, the details of the catalytic reaction mechanism have not yet been elucidated. Thus, the reaction mechanism was investigated using density functional theory calculations. The calculation results revealed that active Ti-OOH forms on the surface Ti site, which is active as an oxidant and acts as an anchorage site for Au nanoclusters. The rate-determining step of propylene oxide synthesis on Au/titanosilicate is O insertion into propylene, with an activation energy of 1.37 eV. The propylene involved in this reaction is activated by adsorption on Au nanoclusters. Moreover, it was also found that the formation of Ti-OOH on Au/titanosilicate requires an activation energy of 0.48 eV, while it is barrierless on Au/anatase-TiO2. However, the decomposition energy of Ti-OOH on Au/titanosilicate is −0.16 eV, which is smaller than that on Au/anatase-TiO2 (−1.12 eV). The results indicate that Ti-OOH decomposes more readily on Au/titanosilicate than on Au/anatase-TiO2 but is easily regenerated because the reaction energy is significantly smaller than that on Au/anatase-TiO2. Therefore, these calculations are qualitatively in good agreement with the experimental results for Au/titanosilicate, which exhibited high catalytic activity at high temperatures. [ABSTRACT FROM AUTHOR]

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]

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]

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 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]

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]

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]

We examined nearsightedness of electronic matter (NEM) of finite systems on the basis of linear response function (LRF). From the computational results of a square-well model system, the behavior of responses obviously depends on the number of electrons (N): as N increases, LRF, δρ(r)/δv(r′), decays rapidly for the distance, ∣r−r′∣. This exemplifies that the principle suggested by Kohn and Prodan holds even for finite systems: the cause of NEM is destructive interference among electron density amplitudes. In addition, we examined double-well model systems, which have low-lying degenerate levels. In this case, there are two types of LRF: the cases of the half-filled and of full-filled in low-lying degenerate levels. The response for the former is delocalized, while that of the later is localized. These behaviors of model systems are discussed in relation to the molecular systems’ counterparts, H2, He22+, and He2 systems. We also see that NEM holds for the dissociated limit of H2, of which the mechanism is similar to that of the insulating state of solids as suggested by Kohn. We also examined LRF of alanine tripeptide system as well as butane and butadiene molecules, showing that NEM of the polypeptide system is caused by sp3 junctions at Cα atoms that prevent propagation of amplitudes of LRF, which is critically different from that of NEM for finite and infinite homogeneous systems. [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]

Residual chlorines, which originate from HAuCl4, enhance the aggregation of gold (Au) nanoparticles and clusters, preventing the generation of highly active supported Au catalysts. However, the detailed mechanism of residual-chlorine-promoted aggregation of Au is unknown. Herein to investigate this mechanism, density functional theory (DFT) calculations of Au and Cl adsorption onto a reduced rutile TiO2(110) surface were performed using a generalised gradient approximation Perdew, Burke, and Ernzerhof formula (GGA–PBE) functional and plane-wave basis. Although both Au and Cl atoms prefer to mono-absorb onto oxygen defect sites, Cl atoms have a stronger absorption onto a reduced TiO2(110) surface, abbreviated as rTiO2(110) in the following, than Au atoms. Additionally, co-adsorption of a Cl atom and a Au atom or Au nanorod onto a rTiO2surface was investigated; Cl adsorption onto an oxygen defect site weakens the interaction between a Au atom or Au nanorod and rTiO2(110) surface. The calculation results suggest that the depletion of interaction between Au and rTiO2surface is due to strong interaction between Cl atoms at oxygen defect sites and neighbouring bridging oxygen (OB) atoms. [ABSTRACT FROM PUBLISHER]

We present a simple approach to treat the boundary problem in quantum mechanics and molecular mechanical (QM/MM) methods. The method is based on ab initio calculations of linear response functions, which indicate nonlocal polarization of densities due to the perturbations at the specific site. We describe basic ideas as well as some numerical results. The computational results will be discussed with the boundary problem in QM/MM methods. © 2012 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

The nature of chemical bonds of ruthenium(Ru)-quinine(Q) complexes, mononuclear [Ru(trpy)(3,5-f-Bu2Q)(OH2)](CIO4)2 (trpy = 2,2 ' : 6 ',2"-terpyridine, 3,5-di-tert-butyl-1,2-benzoquinone) (1), and binuclear [Ru2(btpyan)(3,6-di-Bu2Q)2(OH2)]2+ (btpyan = 1,8-bis( 2,2 ' : 6 ',2 "-terpyrid-4 '-yi)anthracene, 3,6-t-Bu2Q = 3,6-di-tert-butyl-1,2-benzoquinone) (2), has been investigated by broken-symmetry (BS) hybrid density functional (DFT) methods. BS DFT compu-tations for the Ru complexes have elucidated that the closed-shell structure (2b) Ru(ll)-Q complex is less stable than the open-shell structure (2bb) consisting of Ru(lll) and semiquinone (SQ) radical fragments. These computations have also elucidated eight different electronic and spin structures of tetraradical intermediates that may be generated in the course of water splitting reaction. The Heisen-berg spin Hamiltonian model for these species has been derived to elucidate six different effective exchange interactions (J) for four spin systems. Six J values have been determined using total energies of the eight (or seven) BS solutions for different spin configurations. The natural orbital analyses of these BS DFT solutions have also been performed in order to obtain natural orbitals and their occupation numbers, which are useful for the lucid understanding of the nature of chemical bonds of the Ru complexes. Implications of the compu-tational results are discussed in relation to the proposed reaction mechanisms of water splitting reaction in artificial photosynthesis systems and the similarity between artificial and native water splitting systems. [ABSTRACT FROM AUTHOR]

Symmetry breaking in cluster structures of manganese oxides by doping of Ca(II) ion is examined in relation to chameleonic mechanisms of water splitting reaction. The orbital and spin correlation diagrams have been depicted to clarify one-electron transfer and electron-pair transfer mechanisms for the reaction. The spin-polarized molecular orbital models have been applied to elucidate correspondence between magnetic-coupling mode and reaction mechanism of the oxygen-oxygen (OO) bond formation and oxygen evolution catalyzed by multicenter Ca(II) manganese oxides and related systems. The present UB3LYP calculations followed by the natural orbital analyses have been performed to elucidate electronic structures of the key intermediates and the transition state structure for the OO bond formation. The results indicate that the reaction proceeds through the continuous diradicaloid mechanism without discreet free radical fragments and/or electron-pair transfer mechanism induced by symmetry breaking with Ca(II) in the pure low-spin singlet state. The computational results are compatible with local singlet and triplet diradical-coupling mechanisms for the OO bond formation in the low- and high-spin states, respectively. Thus, magnetic (exchange) coupling modes in the oxygen evolution complex are directly related to the local singlet and triplet diradical mechanisms as in the case of soluble methane monooxygenase. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012 [ABSTRACT FROM AUTHOR]

First principle calculations of the effective exchange integrals ( J) in the Heisenberg model for diradical species are presented for both symmetry-adapted multi-reference (MR) and single-reference broken-symmetry (BS) methods. The Mukherjee-type state-specific MR coupled cluster singles and doubles (MkCCSD) method with several different reference orbitals including BS natural orbitals is used to calculate the singlet-triplet energy gaps (S-T energy gap or 2 J) and diradical characters for the antiaromatic molecules [ a cyclopropenyl anion (CPA), b cyclobutadiene (CBD), and c cyclopentadienyl cation (CPC)], the cyclobutadiene derivatives with polar substitutents [ d aminocyclobutadiene (ACBD), e formylcyclobutadiene (FCBD), and f 1-amino-2-formyl-cyclobutadiene (AFCBD)] and finally the cyclobutadine derivatives with radical substitutents [ g 1,2-bis(methylene)cyclobutadiene (1,2-BMCBD) and h 1,3-bis(methylene)cyclobutadiene (1,3-BMCBD)]. For the BS methods, the spin-unrestricted Hartree-Fock based CCSD (UHF-CCSD), the CCD with the spin-unrestricted Brueckner determinant (UBD), and BS density functional theory (UDFT) computations are performed. Comparison between MkCCSD and the UHF-CCSD results indicates that spin-contamination of UHF-CCSD solutions still remains. In comparison with UHF-CCSD, the UBD results show that spin-contamination involved in BS solutions is greatly suppressed. To eliminate the spin contamination, an approximate spin-projection (AP) scheme is applied to the BS solutions. The AP procedure with the use of the expectation value of the total-spin operator corresponding to UHF-CCSD and UBD results yields good agreement with the MkCCSD results. As for the AP correction of the UDFT methods, three different computational schemes for predicting the expectation value of the total-spin operator are examined. Systematic comparisons between these methods are presented for the S-T energy gaps (2 J). Implications of the present computational results have been discussed in relation to the design of magnetic oligomers and polymers. [ABSTRACT FROM AUTHOR]

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]

In this article, we performed spin-unrestricted Hartree Fock (UHF) based coupled-cluster (CC) and Bruckner CC double calculations of methylene, fluorine, H&bond;He&bond;H diradical, and ozone. Mukherjee-type (Mk) Multireference coupled-cluster (MRCC) calculations of these species were also conducted by the use of UHF natural orbital (UNO) and UHF localized natural orbitals (ULO) as reference orbitals to elucidate size-consistent error. Comparing calculated results of spin-unrestricted Hartree-Fock based coupled-cluster (UCC) and spin-unrestricted Bruckner-Double (UBD) with those of MkMRCC, it was found that spin-contamination errors of UCC and UBD solutions still remained, though this type of errors for these solutions was considered to be negligible in general. The comparison also revealed scope and applicability of approximate spin-projection (AP) scheme for UCC and UBD, indicating that the AP procedure corrected spin-contamination errors to yield good agreement with MRCC in energy. We also performed pure- and hybrid- density functional theory (DFT) calculations of the same systems, and those calculations provided reasonable singlet-triplet energy gaps, which were qualitatively good agreement with those of MRCC, AP-UCC, and AP-UBD calculations. Implications of the computational results are discussed in relation to applicability of hybrid DFT to large superexchange coupled systems. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [ABSTRACT FROM AUTHOR]

Reaction mechanisms of oxygen evolution in native and artificial photosynthesis II (PSII) systems have been investigated on the theoretical grounds, together with experimental results. First of all, our previous broken-symmetry (BS) molecular orbitals (MO) calculations are reviewed to elucidate the instability of the dπ-pπ bond in high-valent (HV) Mn(X)&dbond;O systems and the dπ-pπ-dπ bond in HV Mn&dbond;O&dbond;Mn systems. The triplet instability of these bonds entails strong or intermediate diradical characters: •Mn(IV)&dbond;O• and •Mn&bond;O&bond;Mn•; the BS MO resulted from strong electron correlation, leading to the concept of electron localizations and local spins. The BS computations have furthermore revealed guiding principles for derivation of selection rules for radical reactions of local spins. As a continuation of these theoretical results, the BS MO interaction diagrams for oxygen-radical coupling reactions in the oxygen evolution complex (OEC) in the PSII have been depicted to reveal scope and applicability of local singlet diradical (LSD) and local triplet diradical (LTD) mechanisms that have been successfully utilized for theoretical understanding of oxygenation reactions mechanisms by p450 and methane monooxygenase (MMO). The manganese-oxide cluster models examined are London, Berlin, and Berkeley models of CaMn4O4 and related clusters Mn4O4 and Mn3Ca. The BS MO interaction diagrams have revealed the LSD and/or LTD mechanisms for generation of molecular oxygen in the total low-, intermediate and high-spin states of these clusters. The spin alignments are found directly corresponding to the spin-coupling mechanisms of oxygen-radical sites in these clusters. The BS UB3LYP calculations of the clusters have been performed to confirm the comprehensive guiding principles for oxygen evolution; charge and spin densities by BS UB3LYP are utilized for elucidation and confirmation of the LSD and LTD mechanisms. Applicability of the proposed selection rules are examined in comparison with a lot of accumulated experimental and theoretical results for oxygen evolution reactions in native and artificial PSII systems. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [ABSTRACT FROM AUTHOR]

Broken-symmetry (BS) and approximate spin-projected (AP) BS hybrid density functional theory (DFT) calculations were performed to elucidate possible mechanisms of hydroxylation reactions of methane and alkanes with soluble methane monooxygenase (sMMO) and related metalloenzymes. The BS HDFT (UB3LYP) method was employed to elucidate electronic and spin structures of the key intermediate 'Q' and to locate transition structures for hydroxylation reactions in the lowest-spin (LS) singlet and the highest-spin (HS) states of sMMO. The spin density populations and chemical indices obtained by the BS B3LYP calculations were found to be consistent with orbital interaction models for hydroxylation with MMO. However these indices in turn indicated significant spin contamination errors in the BS LS solution. The elimination of the errors with the AP procedure indeed reduced the barrier height for the recombination step of alkyl and hydroxyl radicals in the pure LS singlet state, leading to a rebound process. Then present computational results indicated that hydroxylation reactions proceed through the continuous diradical (diradicaloid) mechanism without discreet free radical fragments in the pure LS singlet state. The computational results are, respectively, compatible with local singlet (SD) and local triplet (TD) diradical mechanisms for hydroxylation in the LS and HS states; those were already applied to P450 successfully. Thus magnetic (exchange) coupling modes (LS and HS) in MMO, P450 and related metalloenzymes are directly related to local SD and TD mechanisms for hydroxylation, indicating the correspondence between the magnetic coupling mode and the radical reaction mechanism. These theoretical results enable us to examine recent BS hybrid DFT computational results for hydroxylation reactions with sMMO by several groups. Implications of the present theoretical and computational results are also discussed in relation to several experimental aspects of hydroxylation reactions. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [ABSTRACT FROM AUTHOR]

Mukherjee-type (Mk) state specific (SS) multi-reference (MR) coupled-cluster (CC) calculations of 1,n-didehydropolyene diradicals were carried out to elucidate singlet-triplet energy gaps via through-bond coupling between terminal radicals. Spin-unrestricted Hartree-Fock (UHF) based coupled-cluster (CC) computations of these diradicals were also performed. Comparison between symmetry-adapted MkMRCC and broken-symmetry (BS) UHF-CC computational results indicated that spin-contamination error of UHF-CC solutions was left at the SD level, although it had been thought that this error was negligible for the CC scheme in general. In order to eliminate the spin contamination error, approximate spin-projection (AP) scheme was applied for UCC, and the AP procedure indeed eliminated the error to yield good agreement with MRCC in energy. The CCD with spin-unrestricted Brueckner's orbital (UB) was also employed for these polyene diradicals, showing that large spin-contamination errors at UHF solutions are dramatically improved, and therefore AP scheme for UBD removed easily the rest of spin-contaminations. Pure- and hybrid-density functional theory (DFT) calculations of the species were also performed. Three different computational schemes for total spin angular momentums were examined for the AP correction of the hybrid DFT. The AP DFT calculations yielded the singlet-triplet energy gaps that were in good agreement with those of MRCC, AP UHF-CC and AP UB-CC. Chemical indices such as the diradical character were calculated with all these methods. Implications of the present computational results are discussed in relation to previous RMRCC calculations of diradical species and BS calculations of large exchange coupled systems. [ABSTRACT FROM AUTHOR]

Mukherjee's type of multireference coupled-cluster (MkMRCC), approximate spin-projected spin-unrestricted CC (APUCC), and AP spin-unrestricted Brueckner's (APUBD) methods were applied to didehydronated ethylene, allyl cation, cis-butadiene, and naphthalene. The focus is on descriptions of magnetic properties for these diradical species such as S-T gaps and diradical characters. Several types of orbital sets were examined as reference orbitals for MkMRCC calculations, and it was found that the change of orbital sets do not give significant impacts on computational results for these species. Comparison of MkMRCC results with APUCC and APUBD results show that these two types of methods yield similar results. These results show that the quantum spin corrected UCC and UBD methods can effectively account for both nondynamical and dynamical correlation effects that are covered by the MkMRCC methods. It was also shown that appropriately parameterized hybrid density functional theory (DFT) with AP corrections (APUDFT) calculations yielded very accurate data that qualitatively agree with those of MRCC and APUBD methods. This hierarchy of methods, MRCC, APUCC, and APUDFT, is expected to constitute a series of standard ab initio approaches towards radical systems, among which we could choose one of them, depending on the size of the systems and the required accuracy. [ABSTRACT FROM AUTHOR]

Copyright of International Journal of Quantum Chemistry is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

We have investigated the reaction pathways for the primary hydroxylation reaction of trimethylmethane by a high-valent Fe(IV)&dbond;O porphyrin π-cation radical species known as compound I at the B3LYP/CEP-31G level. The isoelectronic analogy of the Fe(IV)&dbond;O core of compound I to a molecular oxygen (O2) has been successfully used to clarify the important roles of the singlet excited state of the Fe(IV)&dbond;O core in the alkane hydroxylation, which has hitherto been neglected. The reaction is initiated by the rate-determining hydrogen-atom abstraction from the substrate to give a discrete radical intermediate complex, in accordance with the conventional radical rebound mechanism. Similar to the chemistry of O2, however, one of the singlet excited states, i.e., the diradical component of the 1Δ state of the Fe(IV)&dbond;O core intercepts the triplet ground state (the 3Σ state) in the region of the transition state for the hydrogen abstraction. Our findings strongly indicate that the exchange polarization or intersystem crossing for the nonradiative transition to the locally singlet state is highly important to enhance the reactivity of compound I. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008 [ABSTRACT FROM AUTHOR]

A first principle investigation has been carried out for intermediate states of the catalytic cycle of a cytochrome P450. To elucidate the whole catalytic cycle of P450, the electronic and geometrical structures are investigated not only at each ground state but also at low-lying energy levels. Using the natural orbital analysis, the nature of chemical bonds and magnetic interactions are investigated. The ground state of the Compound 1 (cpd1) is calculated to be a doublet state, which is generated by the antiferromagnetic coupling between a triplet Fe(IV)&dbond;O moiety and a doublet ligand radical. We found that an excited doublet state of the cpd1 is composed of a singlet Fe(IV)&dbond;O and a doublet ligand radical. This excited state lies 20.8 kcal mol-1 above the ground spin state, which is a non-negligible energy level as compared with the activation energy barrier of ΔE# = 26.6 kcal mol-1. The reaction path of the ground state of cpd1 is investigated on the basis of the model reaction: 3O(3p) + CH4. The computational results suggest that the reactions of P450 at the ground and excited states proceed through abstraction (3O-model) and insertion (1O-model) mechanisms, respectively. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008 [ABSTRACT FROM AUTHOR]

Copyright of International Journal of Quantum Chemistry is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

A new geometry optimization method based on an approximate spin projection (AP) procedure is proposed to eliminate a spin contamination effect in an optimized structure on a low spin (LS) state of a broken symmetry (BS) method. First, an energy gradient with the AP (AP gradient) is derived and it is applied to the geometry optimization of F2, CH2, and CH2OO in order to obtain their structures without the spin contamination. The optimization method corrects H&bond;C&bond;H angle of the CH2 about 10° in comparison with the BS method, and indicates that the spin contamination in optimized geometry of the BS LS states is considerably large. Next, an active site of Urease that consists of two Ni(II) ions is optimized by the AP method. The result indicates that structure of the active site is sensitive to a water molecule called W3. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007 [ABSTRACT FROM AUTHOR]

The radical harvesting state of a ribonucleotide reductase R2 subunit (RNR-R2) is theoretically investigated at the broken-symmetry DFT level. Recently, a high-resolution X-ray crystallography revealed a precise location of the active site structure of RNR-R2 (Class 1b) from C. ammoniagenes, and found a linking water near the tyrosine (Tyr) radical site. In this study, the magnetic interaction between the Tyr radical and the diiron core JTyr&bond;Fe is investigated for the first time. Used theoretical model for the active site is composed of diiron core, the Tyr residue, and surrounding side-chain groups. After the geometrical structure optimization of the core structures, the magnetic interaction between the iron centers was calculated to be JFe&bond;Fe = -77.82 cm-1, which was comparable to the experimental result of JFe&bond;Fe = -84 cm-1. The natural orbital analysis clearly showed that the magnetic interaction between the two iron centers mainly interact through the p orbital of the bridging μ-oxo. It was also calculated that the JTyr&bond;Fe interaction is negligibly weak, and the Tyr radical is almost in an isolated or a free radical state. These results suggest that the linking water may be used for (1) a confinement of the reactive Tyr radical in the hydrogen bonds or (2) a hydrogen-transfer coupled with electron transfer at the radical formation step of the Tyr. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007 [ABSTRACT FROM AUTHOR]

Chemical bonding and magnetic interaction of manganese dimer (Mn2) are still in controversy in experimental and theoretical studies. In this work, we examined various exchange correlation functionals of Kohn–Sham density functional theory (DFT), together with hybrid-DFT, and Hartree–Fock plus DFT approaches on description of Mn2. We found that, in contrast to pure DFT functionals, the experimentally reported features of chemical bonding and antiferromagnetic interactions of Mn2 can be reproduced by employing the Hartree–Fock exchange terms. Thus, it is recommended to employ HF plus DFT, or hybrid DFT with large HF portion approach for the case that the direct interactions among manganese atoms play a major role to determine the electronic structure, such as manganese clusters. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007 [ABSTRACT FROM AUTHOR]

We present simple CAS-DFT approaches for degenerate and nearly degenerate systems. In this method, we do not employ any auxiliary variables, but employ the effective CASCI-DFT and CASSCF-DFT equations for the ground and excited states. Simple applications for fundamental systems such as atomic multiplet states (C, N+n, and O+n), the transition metal complex V(III)L6 (L = H2O and CO) and the Cu(II) acetate dimer Cu(II)2(Ac)4(H2O)2 are presented. The results are discussed from the viewpoint of the shapes of the potential curves of several nearly degenerate spin states, the theory of molecular magnetism and the reliability of the CAS space employed. The computational results are fully compatible with the experimental results available, and also with those of ligand field theory. [ABSTRACT FROM AUTHOR]

The Rieske-type [2Fe&bond;2S] cores of electron-transfer (ET) proteins in the mitochondrial respiratory chain have unusual properties, such as redox potentials and spectroscopy. In this study, part IV of a series, the inherent molecular structures and characteristic electronic structures of the Rieske-type [2Fe&bond;2S] clusters are investigated using broken-symmetry hybrid density functional theory (BS-HDFT). Geometry optimizations for the oxidized and reduced states were performed and their characteristic vibrational modes are assigned. Magnetic properties are investigated using model Hamiltonians to describe the electron delocalization and the unsymmetric property. The parameters of the model Hamiltonian, such as exchange coupling J, valence delocalization B, and potential energy difference Δ, are evaluated from the BS-HDFT calculations. The valence localization and excitation energy (ΔE) of the Rieske-type [2Fe&bond;2S] cluster are discussed. The chemical bond nature is characterized by chemical indices from natural orbital analysis. Our theoretical results are reasonably consistent with experimental results. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007 [ABSTRACT FROM AUTHOR]

The nature of chemical bonds in a ferredoxin-type [2Fe–2S] cluster has been investigated on the basis of natural orbitals and several bond indices developed in Parts I and II of this study. The broken-symmetry hybrid density functional theory (BS-HDFT) with spin projection approach has been applied to elucidate the natural orbitals and occupation numbers for a model compound [Fe2S2(SCH3)4] (1), which is used to calculate the indices. The molecular structure, vibration frequencies, electronic structures, and magnetic properties in both oxidized and reduced forms of 1 have been calculated and compared with the experimental values. The optimized molecular structures after approximate spin projection have been in good agreement with experimental data. The structure changes upon one-electron reduction have been slight (<0.1 Å) and only limited around one side of the Fe atom. Raman and infrared (IR) spectra have been calculated, and their vibration modes have been assigned using the bridging 34S isotope substitution. Their magnetic properties have been examined in terms of spin Hamiltonians that contain exchange interactions and double exchange interactions. The BS-HDFT methods have provided the magnetic parameters; i.e., effective exchange integral (J) values and valence delocalization (B) values, which agree with the experimental results. It is found that large charge transfer (CT) from the bridging sulfur to the iron atoms has led to the strong antiferromagnetic interactions between iron atoms. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007 [ABSTRACT FROM AUTHOR]

The features of ab initio wave function-driven multireference (MR)-density functional theory (DFT) approach based on the partially interacting reference system for ground and excited states are discussed from the viewpoint of a simple classification of electron correlation effects. Our previous MR-DFT approach covers (i) structure-free, and (ii) resonating-type correlations, but does not include (iii) orbital-dependent correlation effects. Indeed, the computational results of excitation energies of atoms imply that the state-dependent correlations remain if the CASCI wave functions are used for the wave function part of MR-DFT and semilocal correlation functional is used. Thus, we present an orbital-dependent residual correlation for complete active space (CAS) DFT to describe type (iii) of correlation effects. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006 [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]

A quantum spin-correction scheme based on spin-correlation functions is proposed for multiple bond-breaking processes described by the unrestricted single determinant (USD) approaches, such as unrestricted Hartree–Fock (UHF) and unrestricted Kohn–Sham (UKS) density functional theory (DFT). It is known that natural orbitals (NOs) and occupation numbers (ONs) contain full information of USD solutions. We introduce a bond-operator representation of UHF and UKS wave functions to exploit information about those NOs, enabling us not only to facilitate the calculus, but also to understand the essential feature of the USD and those quantum spin-corrected solutions. We found that usual spin-projected solutions do not work for multiple bonds in the Heisenberg model mapping scheme. We propose quantum spin-correction schemes to obtain the spin-symmetry allowed solutions from the spin-unrestricted KS-DFT solutions. We examine these schemes for a chromium dimer, which is a typical example exhibiting multiple bonds. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005 [ABSTRACT FROM AUTHOR]

We perform spin dynamics in strongly correlated electron–spin systems to clarify the relationship between the phase relaxation and the structure of the spin systems. The interaction among spins is considered to be Heisenberg-type exchange. The quantum Liouville approach is used for the dynamics involving the relaxation processes of the systems, which is considered to originate in spin–phonon and electron spin–nuclear spin interactions. As a first step of our study, to examine the effects of the structures on the phase relaxation, we consider the phenomenological relaxation parameters for the relaxation terms of quantum Liouville equation, and perform the spin dynamics in four types of four electron–spin systems that have linear, square, star (dendritic structure), and tetrahedral structures. The results of our calculation indicated the possibility for the control of the phase relaxation by the change of the structure in spin clusters. Possible implications of our results are related to the single-molecule magnets, ESR-STM detection of spins, and related spin-transition phenomena (decoherence and population relaxation). © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005 [ABSTRACT FROM AUTHOR]