Biomedical subjects

Kimihiko Hirao

Publications and source records attributed to Kimihiko Hirao.

At least 19 recordsLinked to original sources

PubMed2007

Polarizability and second hyperpolarizability evaluation of long molecules by the density functional theory with long-range correction.

Polarizabilities and second hyperpolarizabilities of polyacetylene and a hydrogen chain are evaluated by density functional theory (DFT) using a hybrid generalized gradient approximation functional with correct long-range electron-electron interactions. The well known catastrophic overestimate of the hyperpolarizabilities for molecular systems of enhanced length is corrected by the two-electron repulsion operator decomposition technique, integrating the distance-dependent nonlocal exchange effects for long-range interaction, while neither the asymptotically corrected exchange functional for long-range interaction nor ordinary hybrid methods seem to be capable of overcoming the serious drawback of the DFT in polarizability/hyperpolarizability evaluation.

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PubMed2006

Quantal cumulant dynamics: general theory.

The authors have derived coupled equations of motion of cumulants that consist of a symmetric-ordered product of the position and momentum fluctuation operators in one dimension. The key point is the utilization of a position shift operator acting on a potential operator, where the expectation value of the shift operator is evaluated using the cumulant expansion technique. In particular, the equations of motion of the second-order cumulant and the expectation values of the position and momentum operators are given. The resultant equations are expressed by those variables and a quantal potential that consists of an exponential function of the differential operators and the original potential. This procedure enables us to perform quantal (semiclassical) dynamics in one dimension. In contrast to a second-order quantized Hamilton dynamics by Prezhdo and Pereverzev which conserves the total energy only with an odd-order Taylor expansion of the potential [J. Chem. Phys. 116, 4450 (2002); 117, 2995 (2002)], the present quantal cumulant dynamics method exactly conserves the energy, even if a second-order approximation of the cumulants is adopted, because the present scheme does not truncate the given potential. The authors propose three schemes, (i) a truncation, (ii) a summation of derivatives, and (iii) a convolution method, for evaluating the quantal potentials for several types of potentials. The numerical results show that although the truncation method preserves the energy to some degree, the trajectory obtained gradually deviates from that of the summation scheme after 2000 steps. The phase space structure obtained by the truncation scheme is also different from that of the summation scheme in a strongly anharmonic region.

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PubMed2006

The relativistic complete active-space second-order perturbation theory with the four-component Dirac Hamiltonian.

The relativistic complete active-space second-order perturbation theory (CASPT2) is developed for the four-component relativistic Hamiltonian. The present method can describe the near-degenerated and dissociated electronic states of molecules involving atoms of heavy elements. The present approach is less expensive than the relativistic multireference configuration interaction method. The ground and low-lying excited states of TlH, Tl(2), and PtH molecules are calculated with the Dirac-Coulomb (DC) CASPT2 method and their spectroscopic constants are obtained. These spectroscopic constants are compared with experimental findings and previous theoretical work. For all the molecules, the spectroscopic constants of DC-CASPT2 show good agreement with the experimental or previous theoretical spectroscopic constants. The present theory provides accurate descriptions of bonding or dissociation states and of ground and excited states in a well-balanced way.

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PubMed2006

Franck-Condon factors based on anharmonic vibrational wave functions of polyatomic molecules.

Franck-Condon (FC) integrals of polyatomic molecules are computed on the basis of vibrational self-consistent-field (VSCF) or configuration-interaction (VCI) calculations capable of including vibrational anharmonicity to any desired extent (within certain molecular size limits). The anharmonic vibrational wave functions of the initial and final states are expanded unambiguously by harmonic oscillator basis functions of normal coordinates of the respective electronic states. The anharmonic FC integrals are then obtained as linear combinations of harmonic counterparts, which can, in turn, be evaluated by established techniques taking account of the Duschinsky rotations, geometry displacements, and frequency changes. Alternatively, anharmonic wave functions of both states are expanded by basis functions of just one electronic state, permitting the FC integral to be evaluated directly by the Gauss-Hermite quadrature used in the VSCF and VCI steps [Bowman et al., Mol. Phys. 104, 33 (2006)]. These methods in conjunction with the VCI and coupled-cluster with singles, doubles, and perturbative triples [CCSD(T)] method have predicted the peak positions and intensities of the vibrational manifold in the X 2B1 photoelectron band of H2O with quantitative accuracy. It has revealed that two weakly visible peaks are the result of intensity borrowing from nearby states through anharmonic couplings, an effect explained qualitatively by VSCF and quantitatively by VCI, but not by the harmonic approximation. The X 2B2 photoelectron band of H2CO is less accurately reproduced by this method, likely because of the inability of CCSD(T)/cc-pVTZ to describe the potential energy surface of open-shell H2CO+ with the same high accuracy as in H2O+.

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PubMed2006

Theoretical study of valence photoelectron spectra of Re(CO)5X (X=Cl, Br, and I): a spin-orbit DK3 symmetry-adapted cluster/symmetry-adapted cluster-configuration interaction study.

The valence photoelectron spectra of Re(CO)(5)X (X=Cl, Br, and I) are studied theoretically using symmetry-adapted cluster (SAC)/SAC-configuration interaction (SAC-CI) theory. The relativistic effects are included by the third-order Douglas-Kroll (DK3) method, and the spin-orbit coupling is also considered. Both electron correlation and relativistic effects are significant in assigning the valence photoelectron spectra of Re(CO)(5)X (X=Cl, Br, and I). DK3-SAC/SAC-CI provides values for the relative peak positions in a reasonable agreement with the observed photoelectron spectra. The sequence of ionization energies for Re(CO)(5)Cl, Re(CO)(5)Br, and Re(CO)(5)I are calculated as e(')[a(1)(Cl)]>e(')[e(Re+Cl)] approximately e(")[e(Re+Cl)]>e(")[b(2)(Re)]>e(')[e(Re-Cl)]>e(")[e(Re-Cl)], e(')[a(1)(Br)]>e(')[e(Re+Br)]>e(")[e(Re+Br)+b(2)(Re)]>e(")[b(2)(Re)+e(Re+Br)]>e(')[e(Re-Br)]>e(")[e(Re-Br)], and e(')[e(Re+I)+a(1)(I)]>e(")[b(2)(Re)+e(Re+I)] approximately e(')[a(1)(I)+e(Re+I)]>e(")[e(Re+I)+b(2)(Re)]>e(')[e(Re-I)]>e(")[e(Re-I)], respectively. These assignments are quite new and different from previous assignments.

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PubMed2006

A dual-level approach to density-functional theory.

An efficient approximate scheme for density-functional theory (DFT) calculations, which eliminates the time-consuming self-consistent-field (SCF) procedure, is proposed using a dual-level DFT approach. In this approach, dual levels of basis sets and exchange-correlation functionals are adopted. The dual-level DFT approach is based on the idea that the total electron density in the ground state can be represented in terms of the density evaluated using the low-quality basis set and the low-cost exchange-correlation functional. Since the SCF procedure is avoided in the total energy evaluation, the dual-level DFT approach drastically reduces the computational cost. The applications of several dual-level DFT calculations to molecular systems show that our approach is more efficient than the self-consistent DFT approach with a moderate accuracy.

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PubMed2006

Acetalization and thioacetalization of cabonyl compounds: a case study based on global and local electrophilicity descriptors.

Acetalization of benzaldehyde and substituted benzaldehydes (containing both electron-donating and electron-withdrawing groups) is explained qualitatively on the basis of global electrophilicity descriptor, w, as proposed by Parr and coworkers. The generated values of w can explain qualitatively the preferential electrophilic addition, and hence, the yield of acetalization obtained in an earlier experimental study carried by Patel and coworkers. The present study also reveals that although both steric and electronic factors affect the yield, only later can be taken care of by w. In the case of a competitive formation of cyclic acetals and cyclic thioacetals from a reaction mixture containing p-hydroxybenzaldehyde, p-nitrobenzaldehyde, 1,2-ethanediol (i.e., glycol), and 1,2-ethanedithiol, the relative experimental yields could be explained from the difference of the global electrophilicity values between aldehydes and acetalizing agents in the same line of arguments of Maynard et al.

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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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PubMed2006

Highly accurate potential-energy and dipole moment surfaces for vibrational state calculations of methane.

Full-dimensional ab initio potential-energy surface (PES) and dipole moment surface are constructed for a methane molecule at the CCSD(T)/cc-pVTZ and MP2/cc-pVTZ levels of theory, respectively, by the modified Shepard interpolation method based on the fourth-order Taylor expansion [MSI(4th)]. The reference points for the interpolation have been set in the coupling region of CH symmetric and antisymmetric stretching modes so as to reproduce the vibrational energy levels related to CH stretching vibrations. The vibrational configuration-interaction calculations have been performed to obtain the energy levels and the absorption intensities up to 9000 cm(-1) with the use of MSI(4th)-PES. The calculated fundamental frequencies and low-lying vibrational energy levels show that MSI(4th) is superior to the widely employed quartic force field, giving a better agreement with the experimental values. The absorption bands of overtones as well as combination bands, which are caused by purely anharmonic effects, have been obtained up to 9000 cm(-1). Strongly coupled states with visible intensity have been found in the 6500-9000 cm(-1) region where the experimental data are still lacking.

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PubMed2006

Active species for Ce(IV)-induced hydrolysis of phosphodiester linkage in cAMP and DNA.

The hydrolysis of cyclic adenosine 3',5'-monophosphate and 2'-deoxythymidylyl(3'-5')2'-deoxythymidine by Ce(NH4)2(NO3)6 was kinetically studied. The rate of hydrolysis was fairly proportional to the concentration of [Ce2(IV) (OH)4]4+ , showing that this is the catalytically active species. According to quantum-chemical calculation, the two Ce(IV) ions in this [Ce2(IV) (OH)4]4+ cluster are bridged by two OH residues. Upon the complex formation with H2 PO4- (a model compound for the phosphodiesters), these two Ce(IV) ions bind the two oxygen atoms of the substrate and enhance the electrophilicity of the phosphorus atom. The catalytic mechanism of Ce(IV)-induced hydrolysis of phosphodiesters has been proposed on the basis these results.

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PubMed2005

Theoretical study of the mechanism of hydrogenation of side-on coordinated dinitrogen activated by Zr binuclear complexes ([(eta5-C5Me4H)2Zr]2(mu2,eta2,eta2-N2)).

The reaction mechanism of the reduction of dinitrogen coordinated side-on to a binuclear Zr complex, [(eta(5)-C(5)Me(4)H)(2)Zr](2)(mu(2),eta(2),eta(2)-N(2)) (T1), was investigated theoretically using a model complex, [(eta(5)-C(5)H(5))(2)Zr](2)(mu(2),eta(2),eta(2)-N(2)) (A1), employing density functional theory calculations. The effectiveness of A1 in describing T1 was confirmed by comparing the structures, distributions of charge, and frontier molecular orbitals. Our calculations showed that A1 has a twisted structure, resembling that of T1, which results in similar properties. The calculations for A1 and its derivatives on H(2) addition clearly explain the reaction mechanism and the reaction path that T1 follows, as well as the experimentally required reaction conditions. The immediate reaction of the first and second H(2) additions produces [(eta(5)-C(5)Me(4)H)(2)ZrH](2)(mu(2),eta(2),eta(2)-N(2)H(2)) (T2), and this is explained by the barrier heights of the reaction, which were calculated to be 20.4 and 10.9 kcal/mol, respectively. The latter barrier was below that of A1 + 2H(2). Complex T2 may be the initial complex for further H(2) addition under proper conditions, or it could lose one H(2) molecule followed by H migration from the Zr site to the N site. Both reactions are expected to occur, because of the closeness of the barrier heights (25.1 and 36.5 kcal/mol, respectively). Gentle warming is required for further H(2) additions, which can be understood from the energetics as well. The high reactivity of T1 with H(2) has been discussed by the comparison of the calculation of A1 and another complex with different ligands, presenting an interesting indication on the effects of the ligands. These theoretical results and discussion explaining the experiment should provide insight into the nature of the hydrogenation mechanism.

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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.

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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.

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PubMed2005

Are the local electrophilicity descriptors reliable indicators of global electrophilicity trends?

Density functional theory based global and local electrophilicity descriptors are used to study the reliability of local electrophilicity values of the strongest electrophilic sites in generating global intermolecular electrophilicity trends. The evaluated values on 15 different organic chlorides show that, for systems having more than one comparatively strong electrophilic site, the local electrophilicity value of the strongest site does not produce a reliable global intermolecular electrophilicity trend. But for systems having one distinctly strong electrophilic site it does. The analytical explanation in favor of the above observation is also provided. Thus, what was argued in an earlier study (Roy, R. K. J. Phys. Chem. 2004, 108, 4934) is established strongly by numerical demonstrations as well as analytical reasoning in the present one.

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PubMed2005

A theoretical study of the gas-phase chemi-ionization reaction between uranium and oxygen atoms.

The U+O chemi-ionization reaction has been investigated by quantum chemical methods. Potential-energy curves have been calculated for several electronic states of UO and UO(+). Comparison with the available spectroscopic and thermodynamic values for these species is reported and a mechanism for the chemi-ionization reaction U+O-->UO(+)+e(-) is proposed. The U+O and Sm+O chemi-ionization reactions are the first two metal-plus-oxidant chemi-ionization reactions to be studied theoretically in this way.

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PubMed2004

Pseudospectral approach to relativistic molecular theory.

The efficient relativistic Dirac-Hartree-Fock (DHF) and Dirac-Kohn-Sham (DKS) methods are proposed by an application of the pseudospectral (PS) approach. The present PS-DHF/DKS method is a relativistic extension of the PS-HF/KS method of Friesner, though we aim at higher numerical accuracy by elimination of superfluous arbitrariness. The relativistic PS-DHF/DKS method is implemented into our REL4D programs. Several PS applications to molecular systems show that the relativistic PS-DHF/DKS approach is more efficient than the traditional approach without a loss of accuracy. The present PS-DKS method successfully assigns and predicts the photoelectron spectra of hexacarbonyl complexes of tungsten and seaborgium theoretically.

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PubMed2004

Ab initio vibrational state calculations with a quartic force field: applications to H2CO, C2H4, CH3OH, CH3CCH, and C6H6.

For polyatomic molecules, n-mode coupling representations of the quartic force field (nMR-QFF) are presented, which include terms up to n normal coordinate couplings in a fourth-order polynomial potential energy function. The computational scheme to evaluate third-and fourth-order derivatives by finite differentiations of the energy is fully described. The code to generate the nMR-QFF has been implemented into GAMESS program package and interfaced with the vibrational self-consistent field (VSCF) and correlation corrected VSCF (cc-VSCF) methods. As a demonstration, fundamental frequencies have been calculated by the cc-VSCF method based on 2MR-QFF for formaldehyde, ethylene, methanol, propyne, and benzene. The applications show that 2MR-QFF is a highly accurate potential energy function, with errors of 1.0-1.9% relative to the experimental value in fundamental frequencies. This approach will help quantitative evaluations of vibrational energies of a general molecule with a reasonable computational cost.

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PubMed2004

The effect of spin-orbit coupling on fast neutral chemical reaction O(3P)+CH3-->CH3O.

The effect of nonadiabatic transitions through the spin-orbit couplings has been investigated on the fast neutral reaction, O((3)P)+CH(3)-->CH(3)O. Adiabatic potential energies and the spin-orbit coupling terms have been evaluated for the four electronic states of CH(3)O ((2)E, (2)A(2), (4)E, and (4)A(2)) that correlate with the O((3)P)+CH(3) asymptote, as a function of CO distance and OCH angle under the C(3v) symmetry, by ab initio electronic structure calculations using multireference internally contracted single and double excitation configuration interaction method with the 6-311G(2df,2pd) basis sets. Multistate quantum reactive scattering calculations have been carried out with the use of thus obtained potential energies and spin-orbit coupling matrices, based on the generalized R-matrix propagation method. The calculated thermal rate constants show a slight positive dependence on temperature in a range between 50 and 2000 K, supporting the previous experimental results. It is shown that the spin-orbit coupled excited states give rise to reflections over the centrifugal barrier due to the quantum interference. Classical capture calculations yield larger rate constants due to the neglect of quantum reflections. It is concluded that the effect of nonadiabatic transitions is of minor importance on the overall reactivity in this reaction.

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