Shusuke Yamanaka

Theoretical illumination of water-inserted structures of the CaMn4O5 cluster in the S2 and S3 states of oxygen-evolving complex of photosystem II: full geometry optimizations by B3LYP hybrid density functional.

Full geometry optimizations of several inorganic model clusters, CaMn(4)O(4)XYZ(H(2)O)(2) (X, Y, Z = H(2)O, OH(-) or O(2-)), by the use of the B3LYP hybrid density functional theory (DFT) have been performed to illuminate plausible molecular structures of the catalytic site for water oxidation in the S(0), S(1), S(2) and S(3) states of the Kok cycle for the oxygen-evolving complex (OEC) of photosystem II (PSII). Optimized geometries obtained by the energy gradient method have revealed the degree of symmetry breaking of the unstable three-center Mn(a)-X-Mn(d) bond in CaMn(4)O(4)XYZ(H(2)O)(2). The right-elongated (R) Mn(a)-X···Mn(d) and left-elongated (L) Mn(a)···X-Mn(d) structures appear to occupy local minima on a double-well potential for several key intermediates in these states. The effects of insertion of one extra water molecule to the vacant coordination site, Mn(d) (Mn(a)), for R (L) structures have also been examined in detail. The greater stability of the L-type structure over the R-type has been concluded for key intermediates in the S(2) and S(3) states. Implications of the present DFT structures are discussed in relation to previous DFT and related results, together with recent X-ray diffraction results for model compounds of cubane-like OEC cluster of PSII.

Similarities of artificial photosystems by ruthenium oxo complexes and native water splitting systems

The nature of chemical bonds of ruthenium(Ru)–quinine(Q) complexes, mononuclear [Ru(trpy)(3,5-t-Bu2Q)(OH2)](ClO4)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′-yl)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 computations for the Ru complexes have elucidated that the closed-shell structure (2b) Ru(II)–Q complex is less stable than the open-shell structure (2bb) consisting of Ru(III) 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 Heisenberg 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 computational 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.

Reinvestigation of the reaction of ethylene and singlet oxygen by the approximate spin projection method. Comparison with multireference coupled-cluster calculations.

We quantify a spin contamination error caused by a broken-symmetry (BS) method on the geometry at the stationary points and barrier heights of the [2 + 2] reaction between singlet oxygen and ethylene, which goes through a diradical intermediate. Several hybrid GGA, hybrid meta-GGA, and long-range corrected hybrid functionals, O3LYP, B3LYP, PBE0, MPW1B95, BHandHLYP, and omegaB97X, are examined to elucidate their original nature without the spin contamination error. For that purpose, the geometry of each reaction step for the BS state as well as its total energy is corrected by using an approximate spin projection method. The CCSD and CCSD(T) single-point calculations are also carried out at optimized geometries at the DFT level to confirm the results of the DFT methods. The single-point calculations by means of Mukherjees multireference coupled cluster with single and double excitations at CASSCF(10e,8o)-optimized geometries are also presented to assess the DFT methods. After the energy and geometry corrections, the barrier height of each functional is consistent with conventional closed-shell-type reactions even in the reaction involving singlet diradical species. We also find that the spin contamination error on the geometric change is not negligible especially at the early stage of the reaction ( approximately 3 kcal/mol), where the triplet state is the ground state.

A CAS-DFT study of fundamental degenerate and nearly degenerate systems

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.

Theoretical modelling of biomolecular systems I. Large-scale QM/MM calculations of hydrogen-bonding networks of the oxygen evolving complex of photosystem II

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.

Multireference character of 1,3-dipolar cycloaddition of ozone with ethylene and acrylonitrile.

In the present study, the concerted and stepwise reaction mechanisms for 1,3-dipole cycloaddition of ozone with ethylene (1) and acrylonitrile (2) are investigated. The stationary points are optimized by using four hybrid R(U)DFT methods. A geometry optimization method based on an approximate spin projection (AP-opt method) is applied to eliminate a spin contamination from the broken-symmetry (BS) solution. The AP-opt method reveals that a diradical intermediate for the stepwise pathway is spurious due to the spin contamination. The revised reaction profile with no diradical intermediate supports the stereospecificity. On the basis of the experimental data, the RCCSD(T) method outperforms AP-UCCSD(T), AP-UBD(T), and MkMRCCSD(4e,4o) for the systems, indicating that the RCCSD(T) method can describe the diradical character of ozone within a framework of single reference wave function. The subsequent single point energy calculations show that the highly synchronous transition state is much more favorable than the asynchronous one for 1. In the case of 2, there is not much difference between two transition states because of its asymmetric structure and charge separations in the transition states.

MkMRCC, APUCC and APUBD approaches to 1,n-didehydropolyene diradicals: the nature of through-bond exchange interactions

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 Brueckners 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.

Theory of chemical bonds in metalloenzymes XIX: labile manganese oxygen bonds of the CaMn4O5 cluster in oxygen evolving complex of photosystem II

Spin polarisation effects of labile manganese–oxygen bonds in the X-ray diffraction structure of the oxygen-evolving complex (OEC) of photosystem II (PSII) at 1.9 Å resolution have been investigated by the UB3LYP computations on the basis of three different theoretical models with and without hydrogen bonds: quantum-mechanical (QM) Model I, QM(Model II)/MM and QM Model III. The spin densities on the manganese and oxygen atoms of the CaMn4O5 cluster revealed by these computations have elucidated internal, semi-internal and external reductions of high-valent manganese ions in the CaMn4O5 cluster in OEC of PSII. The internal reduction of Mn(IV) ions by the back charge transfer from oxygen dianions is remarkable in the small QM Model I, whereas it is significantly reduced in the case of more realistic QM Model III including hydrogen bonding stabilisations of oxygen dianions. However, semi-internal reduction of the CaMn4O5 cluster with remote amino acid residues such as Asp61 anion occurs even in QM Model III, indicating the necessity of large QM parts for redox-active systems such as OEC of PSII. The computational results have clearly demonstrated important roles of confinement effects of the CaMn4O5 cluster with labile Mn–O bonds with protein. These computational results have been applied to molecular design of artificial robust catalysts for water oxidation by use of sunlight.

DFT calculations for Au adsorption onto a reduced TiO2 (110) surface with the coexistence of Cl

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 rTiO2 surface 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 rTiO2 surface is due to strong interaction between Cl atoms at oxygen defect sites and neighbouring bridging oxygen (OB) atoms.

DFT calculations for aerobic oxidation of alcohols over neutral Au6 cluster

Lately, it was found that the Au nanoclusters stabilised by poly(N-vinyl-2-pyrrolidone) [PVP; (C6H9ON)n], abbreviated to Au:PVP, can oxidise p-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 of p-hydroxybenzyl alcohol to the corresponding aldehyde catalysed by Au6 has 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 of p-hydroxybenzyl alcohol over Au6 cluster.