Biomedical subjects

Takao Tsuneda

Publications and source records attributed to Takao Tsuneda.

7 recordsLinked to original sources

PubMed2006

Theoretical study on molecular property of protactinium(V) and uranium(VI) oxocations: why does protactinium(V) form monooxo cations in aqueous solution?

The stability of Pa(V) and U(VI) oxocations in aqueous solution were theoretically investigated by means of density functional theory calculations. As a result, the present calculations clearly supported an experimental result from an energetic point of view that monooxo protactinyl cation, PaO3+, is a preferable species for Pa(V) in aqueous solution, although dioxo protactinyl cation, PaO2+, is not a feasible form. By an analysis of molecular orbitals, we revealed that 6d orbitals of Pa(V) destabilize the pi orbitals of PaO2+, because 6d-2p antibonding orbital conflicts with another 5f-2p bonding orbital. For stable dioxo uranyl cation, UO2(2+), we found that 6d orbitals of U(VI), in contrast, form a bonding orbital with the 2p orbitals, and this bonding orbital coexists at an angle with the 5f-2p bonding orbital due to an electron correlation.

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PubMed2006

Excited state geometry optimizations by analytical energy gradient of long-range corrected time-dependent density functional theory.

An analytical excitation energy gradient of long-range corrected time-dependent density functional theory (LC-TDDFT) is presented. This is based on a previous analytical TDDFT gradient formalism, which avoids solving the coupled-perturbed Kohn-Sham equation for each nuclear degree of freedom. In LC-TDDFT, exchange interactions are evaluated by combining the short-range part of a DFT exchange functional with the long-range part of the Hartree-Fock exchange integral. This LC-TDDFT gradient was first examined by calculating the excited state geometries and adiabatic excitation energies of small typical molecules and a small protonated Schiff base. As a result, we found that long-range interactions play a significant role even in valence excited states of small systems. This analytical LC-TDDFT gradient was also applied to the investigations of small twisted intramolecular charge transfer (TICT) systems. By comparing with calculated ab initio multireference perturbation theory and experimental results, we found that LC-TDDFT gave much more accurate absorption and fluorescence energies of these systems than those of conventional TDDFTs using pure and hybrid functionals. For optimized excited state geometries, LC-TDDFT provided fairly different twisting and wagging angles of these small TICT systems in comparison with conventional TDDFT results.

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PubMed2005

Chemical exchange reaction of glycinatocopper(II) complex in water: a theoretical study.

The axial water exchange on glycinatocopper(II) complexes was theoretically investigated by using density functional theory (DFT) calculations. Glycinatocopper(II) complexes are well-known by the diffusion controlled exchange of axial ligands. Calculations using explicitly coordinating water molecules and solvent models showed that bis-glycinatocopper(II) complexes have a four-coordinate planar structure, in which waters are excluded from the axial positions of Cu(II) due to the Jahn-Teller effect. This may be because coordinating axial waters induce the discrepancy in the most stable ligand field splittings of inner 3d and outer 4d orbitals of the Cu(II) cation. To estimate the reactivity of the axial water exchange, we calculated the rate constant by calculating Gibbs free energies for the activation. As a result, we obtained the rate constant as k = 3.61 x 10(10) s(-1) in aqueous solution at T = 298.15 K. This rate constant is slightly larger than that of the diffusion controlled exchange of axial waters, which is experimentally observed in the order of 10(9) s(-1). Finally, we determined the structures of tris-glycinatocopper(II) complexes. It was consequently found that the third glycine is coordinated to Cu with the amino groups as experimentally observed.

Computer Simulation↗

PubMed2005

A density-functional study on pi-aromatic interaction: benzene dimer and naphthalene dimer.

The long-range correction (LC) scheme of density-functional theory (DFT) was applied to the calculation of the pi-aromatic interaction of the benzene dimer and naphthalene dimer. In previous calculations, it was confirmed that the LC scheme [Iikura et al., J. Chem. Phys. 115, 3540 (2001)] gives very accurate potential- energy surfaces (PESs) of small van der Waals (vdW) complexes by combining with the Anderson-Langreth-Lundqvist (ALL) vdW correlation functional [Andersson et al., Phys. Rev. Lett. 76, 102 (1996)] (LC-DFT + ALL). In this study, LC-DFT+ALL method was examined by calculating a wide range of PES of the benzene dimer including parallel, T-shaped, and parallel-displaced configurations. As a result, we succeeded in reproducing very accurate PES within the energy deviance of less than 1 kcalmol in comparison with the results of high-level ab initio molecular-orbital methods at all reference points on the PES. It was also found that LC-DFT + ALL gave accurate results independent of exchange-correlation functional used, in contrast with the strong functional dependencies of conventional pure functionals. This indicates that both exchange repulsion and van der Waals attractive interactions should be correctly incorporated in conventional pure functionals in order to calculate accurate pi-aromatic interactions. We also found that LC-DFT + ALL method has a low basis-set dependency in the calculations of pi-aromatic interactions. The present scheme was also successfully applied to the pi,[ellipsis (horizontal)],pi stacking interactions of naphthalene dimer. This may suggest that LC-DFT + ALL method would be a powerful tool in the calculations of large molecules such as biomolecules.

Journal Article↗

PubMed2005

Nonlinear optical property calculations by the long-range-corrected coupled-perturbed Kohn-Sham method.

The long-range correction (LC) scheme for the exchange functional of density-functional theory (DFT) was combined with the coupled-perturbed Kohn-Sham (CPKS) method to calculate nonlinear optical response properties. By using this LC-CPKS method, we calculated the hyperpolarizabilities of typical molecules and the dipole moments, polarizabilities, and hyperpolarizabilities of push-pull pi-conjugated systems: p-nitroaniline, 4-amino-4'-nitrostilbene, and alpha,omega-nitroaminopolyenes. It was found that the LC scheme clearly improved the calculation of these optical properties for all of these systems, which have been significantly overestimated by conventional DFTs. We therefore concluded that the long-range exchange interaction played an important role in calculating the optical properties using the DFT formalism.

Journal Article↗

PubMed2004

A long-range-corrected time-dependent density functional theory.

We apply the long-range correction (LC) scheme for exchange functionals of density functional theory to time-dependent density functional theory (TDDFT) and examine its efficiency in dealing with the serious problems of TDDFT, i.e., the underestimations of Rydberg excitation energies, oscillator strengths, and charge-transfer excitation energies. By calculating vertical excitation energies of typical molecules, it was found that LC-TDDFT gives accurate excitation energies, within an error of 0.5 eV, and reasonable oscillator strengths, while TDDFT employing a pure functional provides 1.5 eV lower excitation energies and two orders of magnitude lower oscillator strengths for the Rydberg excitations. It was also found that LC-TDDFT clearly reproduces the correct asymptotic behavior of the charge-transfer excitation energy of ethylene-tetrafluoroethylene dimer for the long intramolecular distance, unlike a conventional far-nucleus asymptotic correction scheme. It is, therefore, presumed that poor TDDFT results for pure functionals may be due to their lack of a long-range orbital-orbital interaction.

Journal Article↗

PubMed2003

Regional self-interaction correction of density functional theory.

We propose a new simple scheme for self-interaction correction (SIC) of exchange functionals in the density functional theory. In the new scheme, exchange energies are corrected by substituting exchange self-interactions for exchange functionals in regions of self-interaction. To classify the regions of self-interaction, we take advantage of the property of the total kinetic energy density approaching the Weizsäcker density in the case of electrons in isolated orbitals. The scheme differs from conventional SIC methods in that it produces optimized molecular structures. Applying the scheme to the calculation of reaction energy barriers showed that it provides a clear improvement in cases where the barriers are underestimated by conventional "pure" functionals. In particular, we found that this scheme even reproduces a transition state that is not given by pure functionals.

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