Biomedical subjects

Kiyoshi Yagi

Publications and source records attributed to Kiyoshi Yagi.

7 recordsLinked to original sources

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

Unidirectional electronic ring current driven by a few cycle circularly polarized laser pulse: quantum model simulations for Mg-porphyrin.

A circularly polarized ultraviolet (UV) laser pulse may excite a unidirectional valence-type electronic ring current in an oriented molecule, within the pulse duration of a few femtoseconds (e.g., tau = 3.5 fs). The mechanism is demonstrated by quantum model simulation for |X = |1(1)A(1g) --> |E(+) = |4 (1)E(u+) population transfer in the model system, Mg-porphyrin. The net ring current generated by the laser pulse (I = 84.5 microA) is at least 100 times stronger than any ring current, which could be induced by means of permanent magnetic fields, with present technology.

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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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PubMed2005

Nonadiabatic chemical dynamics in an intense laser field: electronic wave packet coupled with classical nuclear motions.

Dynamics of molecules in an intense laser field is studied in terms of the quantum electronic wave packet coupled with classical nuclear motions. The equations of motion are derived taking a proper account of molecular interactions with the vector potential of a classical electromagnetic field, along with the nonadiabatic interaction due to the breakdown of the Born-Oppenheimer approximation. With the aid of electronic structure calculations, the present method enables us to track, in an ab initio manner, the dynamics of polyatomic molecules in an intense field. Preliminary calculations are carried out for the vibrational state of LiF and a collision of Li+F under an intense laser pulse, which are limited to the domain of no ionization.

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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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PubMed2004

Simple and accurate method to evaluate tunneling splitting in polyatomic molecules.

A practical and accurate semiclassical method for calculating the tunneling splitting of the ground state in polyatomic molecules is presented based on a recent version of the instanton theory [J. Chem. Phys. 115, 6881 (2001)]. The method uses ab initio quantum chemical data for the potential energy surface without any concomitant extrapolation and requires only a small number of ab initio data points to get convergence even for large molecules. This enables one to use an advanced level of electronic structure theory and achieve a high accuracy of the result. The method is applied to the 9-atomic malonaldehyde molecule by making use of the potential energy surface at the level of CCSD(T) with the hybrid basis set of aug-cc-pVTZ (for oxygen atoms and the transferred hydrogen atom) and cc-pVTZ (for other atoms).

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