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Abstract: The manganese clusters have attracted much attention in relation with the oxygen evolving center (OEC) in photosystem II (PS II) system, which catalyzes the water oxidation reaction. Previously, we examined various spin-structures of Mn(II)4O4 model clusters, of which all of magnetic interactions are antiferromagnetic. In this study, we investigated electronic and magnetic structures of simple model clusters, Mn4O4(OAc)6 and Mn3CaO4(OAc)6 using spin unrestricted B3LYP (UB3LYP) method. The UB3LYP method is a standard tool for this study and has been in fact employed by many researchers. However, several peculiar features are observed for these model clusters: for instance the most stable spin state becomes the highest spin state for Mn(IV)4O4(OAc)6 although this model cluster consists of superexchange type of units, Mn(IV)2O2 that usually favors antiferromagnetic spin alignments. Implications of the comparative results are discussed in relation to the electrophilic (or radical) mechanism for the O–O bond formation in the OEC. [Copyright &y& Elsevier]

Abstract: UB3LYP calculations were first performed to elucidate electronic and spin structures of the CaMn4O5 cluster in the oxygen-evolving-complex of the PSII system refined to the 1.9Å X-ray resolution by Kamiya, Shen, and their collaborators. Eight different UB3LYP solutions with axial spin structures were constructed to obtain the energy levels of the cluster on the basis of their X-ray structure. The energy diagrams were analyzed in terms of the Heisenberg model that involves six effective-exchange integrals between manganese ions. Several characteristic features of the electronic states of the cluster are revealed from these theoretical investigations based on the UB3LYP calculations. [Copyright &y& Elsevier]

Abstract: Spin-frustrated systems has been attracted much attention from the viewpoint of their anomalous behaviors on magnetism and the relation with superconductivity. Recently, the superconductivity in Na0.35Co2O4(H2O)1.3 was observed. In this study, ab initio calculations of the electronic and magnetic structures of the fundamental triangular and hexagonal parts, Co n O x (n =3.7) of this compound have been performed using the general spin orbital density functional theory. The J value of fundamental triangular unit is computed by employing the new estimation scheme, which is applicable for all of triangular and hexagonal systems. The results are discussed in relation to T c from the viewpoint of J model. [Copyright &y& Elsevier]

We have applied the ab initio density functional theory (DFT) based on generalized spin orbital (GSO) for tetrahedral manganese clusters with a noncollinear spin structure. It was found that three-dimensional (3D) spin states become clearly ground-states by all of GSO-localized spin density approximation, GSO-generalized gradient approximation, and GSO-hybrid methods for tetrahedral Mn(II)4O4. These results are consistent with the experimental results. [Copyright &y& Elsevier]

Several key concepts and geometrical rules for the Mn–Mn and Mn–O distances of the CaMn 4 O 5 cluster in the oxygen evolving complex (OEC) of photosystem II (PSII) by previous and present theoretical calculations were examined for a clear understanding of the damage-free S 1 structure revealed by X-ray free electron laser (XFEL). A simple equation to estimate the Mn a –Mn b distance in relation to the Mn a –O (5) distance was derived taking into consideration the Jahn–Teller (JT) effects for Mn centers, indicating that the XFEL structure is regarded as a slightly right-elongated quasi-central structure in contradiction to a right-opened structure proposed by the EXAFS measurements. [ABSTRACT FROM AUTHOR]

The structure of the oxygen evolving complex (OEC) of photosystem II (PSII) was recently analyzed by crystallography at 1.95 Å resolution using X-ray free electron laser (XFEL), but the positions of hydrogen atoms were not determined. We have examined the XFEL structure theoretically under the assumption of four protonation cases. The spin densities obtained by the high-spin UB3LYP revealed that a partial internal reduction of the high-valent Mn ions in the CaMn 4 O 4 X(H 2 O) 3 Y cluster occurs for the O (5) (=X) = O 2− case, entailing its protonation (X = OH − ) in the XFEL structure. [ABSTRACT FROM AUTHOR]

Abstract: A master equation approach involving the effect of the interaction between spins and phonons is formulated in the Markov approximation in order to perform a dynamics for a spin aggregate which have the novel fractal architectures. Such a dynamics is important for elucidating the relation between the dynamical features and the architectures of spin aggregates. [Copyright &y& Elsevier]

Abstract: Density functional theory (DFT) is applied to calculating zero-field splitting (ZFS) parameters caused by spin–orbit coupling (SOC). We examine the behavior and tendency of the method by applying it to some basic molecules such as carbene, binuclear single-molecule magnet (SMM), etc. It shows the method has good accuracy but it fails in particular cases. We suggest applicable region of the method. [Copyright &y& Elsevier]

In this study, the zero-field splitting parameters ( D , E ) and effective exchange integrals ( J ) for a Mn 12 /Mn 11 Cr mixed crystal were evaluated using ab initio molecular orbital (MO) computations based on the hybrid density functional theory (DFT) methods for Mn 11 Cr ∗ -acetate cluster (Mn 12 and Mn 11 Cr mixing). In this study, Mn 12 -acetate, Mn 11 Cr-acetate, and Mn 12− n Cr n -acetate clusters were focused on. The zero-field splitting (ZFS) parameters are obtained by UB3LYP methods, i.e. −0.339 cm −1 (Mn 12 -acetate) and −0.351 cm −1 (Mn 11 Cr-acetate). The energy barriers were estimated to be 53.7 K and 50.4 K, which showed good agreement with previously reported experimental values of 68.8 K and 56.8 K, respectively. The origin of such anisotropy is assumed to be the eight Mn III ions with d 4 -electrons in their outer ring subunits, where elongated conformation along the axial direction becomes very important and leads to negative D values. The spin networks in these clusters were discussed by using the effective exchange integral sets. The J s value, as estimated by the UB3LYP method revealed that the J 2 , J 3 , and J 3 ′ interactions played important roles in describing the parallel spin ordering in cubane and ring subunits as well as the antiferromagnetic coupling between two subunits. The other interactions, i.e. J 1 , J 1 ′, J 4 , and J 4 ′ somewhat disturbed the spin ordering in the Mn 12 -acetate cluster. The substitution of Mn IV by Cr III did not change the spin network. However, the total S value changed after the substitution. [ABSTRACT FROM AUTHOR]

We report a computational study on the dioxygenation reaction of the substrate flavonolate (fla) by a synthetic model complex [Cu 2+ (idpa)(fla − )] + (idpa = 3,3′-iminobis( N , N -dimethylpropylamine) and related species mimicking quercetin 2,4-dioxygenases. It is found that the reaction mechanism obtained for the present biomimetic complexes is substantially different from the plausible enzymatic reaction. All model complexes favor a single electron transfer from flavonolate to dioxygen over a valence tautomerism [Cu 2+ (idpa)(fla − ) ↔ Cu + (idpa)(fla )], and a subsequent intersystem crossing and a ring-closure lead to a formation of a 1,2-dioxetane intermediate instead of undergoing a direct formation of a precursor endoperoxide. The generation of the 1,2-dioxetane intermediate is shown to be the rate-determining step and inclusion of a carboxylate co-ligand can enhance the reactivity, rendering this process barrier-free. We have also proposed for the first time a pathway, which can circumvent a non-enzymatic reaction by involving conversion from the 1,2-dioxetane to the endoperoxide with lower barriers. [ABSTRACT FROM AUTHOR]

We report a thorough comparison between the spin-unrestricted semi-empirical molecular orbital (SE-UMO) and density functional theory (UDFT) calculations for a variety of π-conjugated diradical molecules which exhibit through-bond magnetic exchange interactions. The spin-unrestricted neglect of diatomic differential overlap (NDDO)-based methods (UPM6 and UrPM6) and self-consistent charge density functional tight-biding (UDFTB) are examined. The UCAM-B3LYP method is used as a representative of UDFT. We have found that NDDO-based and UDFTB methods give different performances with respect to the results of UCAM-B3LYP. The degree of diradical character in the target systems decreases in the order of UPM6 > UrPM6 ≈ UCAM-B3LYP > UDFTB. The conventional UPM6 and UDFTB calculations tend to overestimate and underestimate the diradical character, respectively, whereas UrPM6 is able to provide much the same results as UCAM-B3LYP. This is convincing evidence that UrPM6 will be useful for in silico screening of materials science at much lower computational cost. [ABSTRACT FROM AUTHOR]

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

Abstract: Intermolecular interactions in nano-porous crystals were studied theoretically as related to adsorption properties. The crystal [Rh2bza4pyz] n , which had been reported by Mori, Takamizawa and their co-workers in detailed, was employed in this study. As adsorbed magnetic radicals, a oxygen molecule (O2; S =1) was treated. Adsorption energies ΔE ads are defined for quantitative discussion for host–guest interaction. From the calculated results by our MO calculations, weak attractive interactions between adsorbed O2 and surrounding four ph-groups (delegated to benzene) existed. In addition, stable structure of O2 molecules over one benzene molecule was studied. From the results, parallel structure is more stable than perpendicular structure. Physisorption phenomena in intermediate distance region (R =3.4Å) contributes to energy stabilization. [Copyright &y& Elsevier]

Abstract: The effective exchange integrals (J(HB)) of the Heisenberg spin model have been evaluated by using the ab initio MO and based on Hartree–Fock (HF) and density functional theory (DFT) for organic magnetic metals, the (EDT-TTFVO)2FeBr4 crystal based on the X-ray crystallographic structures at 113K. In order to study the magnetic properties, we proposed some of the pairs, where the direct (d–d) and indirect (d–π–d) magnetic couplings between Fe(III) d-spins (S =5/2) without/with π-dimer spins (S =1/2) were calculated, respectively. The effective exchange integrals were evaluated by using UB3LYP method, and principal J values were 0.5, −0.1 and 0.4K. From these results, it is found that there were three dimensional spin arrangements of Fe(III) d-spins. The Quantum Monte Carlo (QMC) simulations had been carried out with our calculated J values to evaluate the magnetic susceptibility for this molecular crystal, reproducing the experimental tendency. [Copyright &y& Elsevier]

Abstract: Recently, graphene sheet is one of interesting systems to realize novel electronic properties. Especially, interaction between graphene and adsorbed oxygen molecule is very important to control electronic condition. In this paper, we employed some aromatic hydrocarbons as simple systems of graphene sheet and ab initio MO calculations were carried out to investigate inter-molecular interaction. It is found that not triplet but singlet O2 molecule have potential of chemisorption onto graphene surface. From the calculated potential energy surface (PES) for distance between benzene and O2 molecules, meta-stable structure is found at about 1.5Å with potential barrier. In the optimized structure of its meta-stable state, structural strain can be relaxed through bending of planer benzene ring. Its energy is estimated at 70.10kcal/mol for benzene. We also estimated the strain effects for naphthalene and pyrene molecules as larger case of graphene and they were 80.85 and 72.45kcal/mol, respectively. [Copyright &y& Elsevier]

Abstract: The barrier height for automerization of cyclobutadiene (CBD) is examined by broken-symmetry (BS) HF, post-HF, and density functional methods. To remove the spin contamination error, we use an approximate spin projection (AP) method. Comparison between the results of BS methods and those of the localized UHF natural orbital (ULO) based Mukherjee’s state-specific MRCC (ULO-MkCC) method shows that spin-unrestricted Brueckner doubles including perturbative triple excitations (UBD(T)) with the AP correction performs well within a framework of single reference approaches. On the other hand, UDFT methods except for UBLYP and UM06-2X give negative barrier heights, which are not consistent with the both the experimental and MRCC results. [ABSTRACT FROM AUTHOR]

Abstract: The electronic and spin structures of a [2Fe–2S] model complex: (1), were investigated by hybrid density functional theory (HDFT) calculations. Generalized spin orbital (GSO) approach has been examined to investigate the delocalization nature at the reduced form. The calculated results showed that the delocalization is largely dependent on the geometrical [2Fe–2S] core structure. At the symmetrical geometry, the GSO solution was a mixed-valence state: Fe2.5+Fe2.5+, with a noncollinear spin state. The energy difference between the GSO solution and an unrestricted state was extremely small (4cm−1). On the other hand at the asymmetrical geometry, the GSO solution converged into a trapped valence state: Fe3+Fe2+ with a collinear spin state, which was almost the same as an unrestricted result. Natural orbital analysis was performed to elucidate the magnetic orbital interactions at the GSO and unrestricted solutions. These results indicated that the delocalization of the odd electron is largely suppressed for the strong antiferromagnetic interactions between two irons. In conclusion, the GSO descriptions were not drastically improved the ground state energies of the [2Fe–2S] cluster, however, the GSO approach has opened to investigate a variety of electronic structures in the mixed valence states, which could not be investigated by a broken symmetry (BS) approach. [Copyright &y& Elsevier]

Abstract: By using broken-symmetry hybrid-DFT (UB3LYP and UB2LYP) calculation, the effective exchange integrals (J values) of [Cr(C5(CH3)5)2]+[TCNE]−[Cr(C5(CH3)5)2]+ and [Mn(C5(CH3)5)2]+[TCNQ]−[Mn(C5(CH3)5)2]+ were determined theoretically. Those calculated models were reduced to 3-spin-sites models from X-ray crystallographic data of charge transfer 3D crystal. The calculated results showed that effective exchange integrals were positive and the signs of spin densities on the cyclopentadienyl rings were negative. These results supported the so-called McConnell I mechanism for ferromagnetism proposed by Kollmar et al. and our previous calculations. Natural orbital analysis made it clear that the orbital overlap between SOMO on metals and SOMO on TCNE or TCNQ cations was nearly zero. These results indicated that orbital orthogonality was an important key factor for explaining the ferromagnetism of those systems. [Copyright &y& Elsevier]

Abstract: Strong influences of bridging ligands L on the magnetism of two Ni9 complexes, Ni9L2(O2CMe)8 {(2-py)2CO2}4 (L=OH− 1 and 2) are demonstrated by magnetic interactions. Effective exchange integrals J for 1 and 2 are determined non-empirically using UB3LYP and UBLYP. The calculated magnetic susceptibility for 1 is wholly consistent with the experimental values. Although the ground spin state of 2 obtained using the calculated J values agrees with the experimental S =9 state, fitting of the J values to the experimental magnetic susceptibility curve indicates weak antiferromagnetic interactions via the azido ligands. [Copyright &y& Elsevier]

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

Abstract: The active site structure of hemerythrin are μ-(hydro)oxo bridged diiron cores and are universal in many non-hem proteins. The magnitudes of antiferromagnetic interactions in the binuclear iron center are largely different in each oxidization states. To clarify the magnetic interactions and electronic structures in oxy-hemerythrin(Hr), deoxy-Hr and met-Hr, hybrid density-functional theory were performed in the broken symmetry way. Effective-exchange interactions are calculated by B2LYP method and they are in good agreement with experimental values. Natural orbital analyses are utilized to clarify their magnetic interactions between the iron spin sites. It is found that there are five magnetic interactions of σ, π1, π2, δ1, and δ2. Former three interactions are stronger interactions through μ-oxo. The latter two δ interactions are weaker interactions through carboxyl groups. Magnetic interaction of π1 type is most significantly changed by dioxygen bonding, where the magnetic interaction pathway is through p orbital parallel to hydrogen atom of μ-hydroxo. At dioxygen bonding state of oxy-Hr, orbital interactions between diiron spin sites and dioxygen are discussed. [Copyright &y& Elsevier]

Abstract: Electronic and spin structures of manganese clusters, Mn4O4 (1), CaMn3O4 (2), Mn3O4 (3), MnX (4), and CaMn4O4 (5), in the photosynthesis II system are investigated using the classical and quantum Heisenberg models. The molecular orbital calculations by the use of general spin orbitals (GSO) are performed for cubane-type calcium manganese cluster 2 with noncollinear spin alignment, which has also been concluded in our previous studies of 1 and 3. The calculated results, together with available experiments, enable us to propose possible electronic states (from S0 to S4) of tetranuclear manganese cluster 5, which is the active site of oxygen evolution center (OEC). The low-spin (LS) ground states of 2–5 are consistent with the ESR and other magnetic observations. A new reaction scheme for oxygen evolution from water is resulted from both theoretical and experimental results for manganese clusters 1–5 in OEC on the basis of the newly determined X-ray structure by Ferreira et al. [Science 303 (2004) 1831]. In this mechanism, both calcium and manganese ions play important roles for formation of peroxide anion bridge, which is the precursor of molecular oxygen. Implications of computational results are discussed in relation to a key role of the high-valent manganese oxo (Mn(V)s in OEC for oxygen evolution from water. Our previous and present computations conclude that Mn(V) crucial role in both native and artificial OEC systems. [Copyright &y& Elsevier]