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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]

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]

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]

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]

In this study we investigated the photochemical production of hydrogen from water using three heterogeneous microporous ruthenium coordination polymers [Ru2(p-BDC)2X]n (p-BDC = 1,4-benzenedicarboxylate, X = Cl, Br and BF4) in the presence of multi-component systems. The order of catalytic performances is [Ru2(p-BDC)2Br]n>[Ru2(p-BDC)2BF4]n>[Ru2(p-BDC)2Cl]n. The most active catalyst, [Ru2(p-BDC)2Br]n, caused the evolution of 46.7 μmol hydrogen molecules with a turn-over number of 18.7 based on [Ru2(p-BDC)2Br]n under visible light irradiation for 4 h. We ascertained that the differences in catalytic activities originated from (1) the efficiency of the quenching of methyl-viologen radicals by [Ru2(p-BDC)2X]n and (2) the durability of the structure in the reaction. In order to examine the catalytic reaction mechanism, we performed theoretical calculations for neutral model structures [Ru2(HCOO)4X(H2O)] (X = Cl, Br), one-electron reduction model complexes [Ru2(HCOO)4X(H2O)]- and deduced intermediate model structures [H-Ru2(HCOO)4X] using broken-symmetry hybrid density functional theory methods. [ABSTRACT FROM AUTHOR]

The electronic structures of ground and excited states of [Rh2(CH3COO)4(H2O)2] in aqueous solution are studied using a density functional theory (DFT) with a time-dependent (TD) method. Up to now, several theoretical assignments and explanations of its excitation characters have been reported based on the absorption spectra. In this study, we reinvestigate its absorption spectrum by the TD-DFT approach with the polarisable continuum model in order to clarify the excitation characters of the complex, especially in the aqueous solution well. [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]

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]

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]

The effective exchange integrals (J[sub ab(M)]) between two cation radicals of title compounds in the Heisenberg model were calculated by ab initio molecular orbital (MO) and density functional theory (DFT) methods, together with hybrid DFT methods. The J[sub ab(D)] values between two dimer mono-cation radicals were also estimated assuming J[sub ab(D)] ≈ J[sub ab(M)]/2. It is found that the spin lattice obtained by the ab initio method is square planar and linear in BEDT-TTF and BETS planes, respectively, although other previous calculations show that spin lattice in the BEDT-TTF plane is a triangular one. The J[sub ab] and overlap integrals (s[sub ab]) values by the ab initio methods were used to determine transfer integral (t[sub ab]) and Coulomb repulsion (U[sub eff]) parameters of the Hubbard model, which were compared with those of the previous results. Implications of the calculated results are discussed in relation to the spin-mediated mechanism for superconductivity. [ABSTRACT FROM AUTHOR]

Potential curves and high and low spin energy gaps for radical clusters were calculated by spin polarized molecular orbital methods. Through-space effective exchange integrals (J[sub ab]) and relative energies of spin projected low spin states by post-Hartree-Fock (HF) calculation were reproduced by the hybrid density functional theory (DFT) method. The hybrid parameters that could reproduce post-HF values such as UCCSD(T)'s for each model had close relations with the instabilities of those systems. Information entropy and related chemical indices were used to estimate the magnitude of the instabilities. A magnetic effective density functional (MEDF) scheme for spin clusters was proposed for practical computation of J[sub ab] values in molecular magnetic materials. [ABSTRACT FROM AUTHOR]

Cooperation of antiferromagnetism and superconductivity is achieved and reported by Kobayashi and his co-workers. For the BETS related crystals, κ-(BETS) 2 FeCl 4 (BETS=bis(ethylenedithio)tetraselenafulvalene), effective exchange integrals ( J ab ) between two BETS + molecules (Step I) and between BETS + and FeCl 4 - molecules (Step II) are very important to reveal superconductivity and successfully evaluated in our treatments. organic superconductor effective exchange integral BETS ab initio MO DFT [ABSTRACT FROM AUTHOR]

Magnetic interactions between divalent chromium (Cr(II)) ions in tetra Cr(II) complex were estimated by using a magnetic effective density functional (MEDF) method. Those results were discussed in comparison with a di-Cr(II) complex to elucidate the types of magnetic interactions. Charge and spin densities and natural orbitals by MEDF were also examined in terms of the ligand effects. aligned tetrametal systems magnetic interaction effective exchange integrals Magnetic Effective Density Functional MEDF [ABSTRACT FROM AUTHOR]

The spin alignment rule for the magnetic couplings of d-π-d conjugated systems via pyrimidine has been proposed on the basis of the superexchange (SE) interaction and spin polarization (SP) effects in order to predict the sign of J ab values between transition metal ions. This rule shows that the subtle balance of σ- and π- type SE interaction and SP effects determines the magnetic interaction of these systems. M(II) 2 -pyrimidine effective exchange interaction ( J ab ) superexchange (SE) interaction spin polarization (SP) effect [ABSTRACT FROM AUTHOR]

Phase diagrams of theoretical models for CuO 2 plane and CuO chains are presented by using a two-band model. Field-induced superconductivity Two-band model High-Tc superconductivity [ABSTRACT FROM AUTHOR]

Model clusters (NH 3 ) 4 +2 and (NM 3 -H 2 NO·) 4 +2 are introduced as simple models for a pure organic conductor. Then theoretical calculations of the total energies of ab initio solution, in which the spin or charge density are arranged alternately, and intermolecular magnetic interactions are carried out by ab initio MO-DFT method. The result shows that these model clusters are efficient for ab initio investigation of the electronic properties of organomagnetic conductors. ab initio MO calculation pure organomagnetic conductors effective exchange integrals cluster model [ABSTRACT FROM AUTHOR]

SDW and CDW states of [-O-M-O-M-O-M-O-M-](M=Cu, Ag)4 site periodic model were investigated. Our theoretical attempt is to elucidate the difference among group 11 metals; Cu, Ag, from the view point of stability on SDW/CDW states, and leads to prospect of their physical properties. SDW CDW charge fluctuation periodic model Cu and Ag oxides [ABSTRACT FROM AUTHOR]

The detailed theoretical studies for TCNQ/TCNQ -· salts, which possess ferromagnetic hysteresis at relative high temperature, were carried out. The calculations based on ab initio molecular orbital (MO) and density functional (DFT) theories were carried out to evaluate the intermolecular effective exchange integrals and transfer integrals. In addition, we employed the "hybrid DFT method" based on instability of chemical bonds and successfully studied their spin densities. From the results it was found the remarkable singlet dimer structure is dominant. In addition, quasi-one-dimensional structure was found because of nonzero charge transfer. [ABSTRACT FROM AUTHOR]

The effective exchange integrals for the naked Cr(II) tetramer are calculated by using post-Hartree-Fock and the improved hybrid density functional method. The calculated values are examined in comparison with naked Cr(II) dimer. The naked Cr(II) tetramer that is arranged similar to [Cr(II) 4 (DpyF) 4 Cl 2 ]Cl 2 also examined in terms of magnetic interactions. [ABSTRACT FROM AUTHOR]