Biomedical subjects

Masahiro Ehara

Publications and source records attributed to Masahiro Ehara.

8 recordsLinked to original sources

PubMed2006

C4Cl: bent or linear?

The ground state structure for the CCCCCl radical was computed by using symmetry-adapted cluster configuration-interaction (SAC-CI) theory along with density functional theory to overcome the differences raised in the recently published paper [Y. Sumiyoshi et al., Chem. Phys. Lett. 414, 82 (2005)] between the theory and the experiment. SAC-CI results clearly support the earlier experimental conclusion that the radical has the bent ground state structure corresponding to 2Pi symmetry. Contrarily, probably due to spin contamination, mixing of a bent doublet ground state with the quartet components of a linear structure, coupled-cluster singles and doubles (CCSD) calculations were unable to provide reliable results. Results obtained using density functional theory also show that the radical has a bent structure. Some low-lying doublet excited states were also studied using the SAC-CI theory. The energy difference between the ground Pi state and the nearby Sigma state is around 0.2 eV. The excitation energy for the transition with the largest oscillator strength agrees with the strongest absorption peak.

Journal Article↗

PubMed2006

Singly and doubly excited states of butadiene, acrolein, and glyoxal: Geometries and electronic spectra.

Excited-state geometries and electronic spectra of butadiene, acrolein, and glyoxal have been investigated by the symmetry adapted cluster configuration interaction (SAC-CI) method in their s-trans conformation. Valence and Rydberg states below the ionization threshold have been precisely calculated with sufficiently flexible basis sets. Vertical and adiabatic excitation energies were well reproduced and the detailed assignments were given taking account of the second moments. The deviations of the vertical excitation energies from the experiment were less than 0.3 eV for all cases. The SAC-CI geometry optimization has been applied to some valence and Rydberg excited states of these molecules in the planar structure. The optimized ground- and excited-state geometries agree well with the available experimental values; deviations lie within 0.03 A and 0.7 degrees for the bond lengths and angles, respectively. The force acting on the nuclei caused by the excitations has been discussed in detail by calculating the SAC-CI electron density difference between the ground and excited states; the geometry relaxation was well interpreted with the electrostatic force theory. In Rydberg excitations, geometry changes were also noticed. Doubly excited states (so-called 2 (1)A(g) states) were investigated by the SAC-CI general-R method considering up to quadruple excitations. The characteristic geometrical changes and large energetic relaxations were predicted for these states.

Journal Article↗

PubMed2006

Electronic spectra and photodissociation of vinyl chloride: a symmetry-adapted cluster configuration interaction study.

The vertical absorption spectrum and photodissociation mechanism of vinyl chloride (VC) were studied by using symmetry-adapted cluster configuration interaction theory. The important vertical pi --> pi* excitation was intensively examined with various basis sets up to aug-cc-pVTZ augmented with appropriate Rydberg functions. The excitation energy for pi --> pi* transition obtained in the present study, 6.96 eV, agrees well with the experimental value, 6.7-6.9 eV. Calculated excitation energies along with the oscillator strengths clarify that the main excitation in VC is the pi --> pi* excitation. Contrary to the earlier theoretical reports, the results obtained here support that the C-Cl bond dissociation takes place through the n(Cl-)sigma(C-Cl)* state.

Journal Article↗

PubMed2005

Theoretical fine spectroscopy with symmetry-adapted-cluster configuration-interaction method: outer- and inner-valence ionization spectra of furan, pyrrole, and thiophene.

Theoretical fine spectroscopy has been performed for the valence ionization spectra of furan, pyrrole, and thiophene with the symmetry-adapted-cluster configuration-interaction general-R method. The present method described that the pi(1) state interacts with the pi(3) (-2)pi*, pi(2) (-2)pi*, and pi(2) (-1)pi(3) (-1)pi* shake-up states providing the split peaks and the outer-valence satellites, both of which are in agreement with the experiments. The intensity distributions were analyzed in detail for the inner-valence region. In particular, for furan, theoretical intensities were successfully compared with the intensity measured by the electron momentum spectroscopy. The interactions of the 3b(2) and 5a(1) states with the shake-up states were remarkable for furan and pyrrole, while the 4b(2) state of thiophene had relatively large intensity.

Algorithms↗

PubMed2005

Iterative Cl general singles and doubles (ICIGSD) method for calculating the exact wave functions of the ground and excited states of molecules.

The iterative configuration-interaction general singles and doubles (ICIGSD) method was applied to various closed- and open-shell electronic states of molecules within finite basis sets and was shown to give the exact results that are identical to the full CI ones. The structure of the ICIGSD is unique among the ICI formalisms, that is, the singularity problem intrinsic to atomic and molecular Hamiltonians can be avoided. The convergence of the ICIGSD method was fairly good regardless of the characters of the electronic states and the qualities of the basis sets; only several iterations were enough for obtaining microhartree accuracy. These favorable properties are attributed to the unique GSD structure. The present method was shown to be applicable to various spin states and to quasidegenerate states appearing in bond dissociation process. We have also applied the ICIGSD-CI method to calculate the excited states simultaneously. We have confirmed that the ICIGSD-CI method is accurate for calculating the excited states the symmetries of which are not only similar to but also different from that of the ground state.

Algorithms↗

PubMed2005

Theoretical fine spectroscopy with symmetry adapted cluster-configuration interaction general-R method: first-row K-shell ionizations and their satellites.

Molecular core ionization spectra and their satellites were studied by the symmetry adapted cluster-configuration interaction (SAC-CI) general-R method. The core-electron binding energies of C, N, O, and F atoms of 22 molecules were calculated with an average deviation of 0.11 eV from the experimental values. The energy splittings between K-shell gerade and ungerade states were calculated and discussed in relation to the bond length. The satellite spectra of the C 1s and N 1s core ionizations of methane and ammonia were investigated. The SAC-CI general-R method gave many shake-up states with moderate intensities, reproducing the general feature of the experimental spectra, and thus enabling the detailed understanding and assignments of the core-electron ionization spectra.

Computer Simulation↗

PubMed2004

Analytical energy gradient of the symmetry-adapted-cluster configuration-interaction general-R method for singlet to septet ground and excited states.

A method of calculating analytical energy gradients of the singlet and triplet excited states, ionized states, electron-attached states, and high-spin states from quartet to septet states by the symmetry-adapted-cluster configuration-interaction general-R method is developed and implemented. This method is a powerful tool in the studies of geometries, dynamics, and properties of the states of molecules in which not only one-electron processes but also two- and multielectron processes are involved. The performance of the present method was confirmed by calculating the geometries and the spectroscopic constants of the diatomic and polyatomic molecules in various electronic states involving the ground state and the one- to three-electron excited states. The accurate descriptions were obtained for the equilibrium geometries, vibrational frequencies, and adiabatic excitation energies, which show the potential usefulness of the present method. The particularly interesting applications were to the C' 1Ag state of acetylene, the A 2Deltau and B 2Sigmau+ states of CNC and the 4B1 and a 4Piu states of N3 radical.

Journal Article↗

PubMed2003

Electronic excitations of the green fluorescent protein chromophore in its protonation states: SAC/SAC-CI study.

Two ground-state protonation forms causing different absorption peaks of the green fluorescent protein chromophore were investigated by the quantum mechanical SAC/SAC-CI method with regard to the excitation energy, fluorescence energy, and ground-state stability. The environmental effect was taken into account by a continuum spherical cavity model. The first excited state, HOMO-LUMO excitation, has the largest transition moment and thus is thought to be the source of the absorption. The neutral and anionic forms were assigned to the protonation states for the experimental A- and B-forms, respectively. The present results support the previous experimental observations.

Animals↗