Biomedical subjects

Shigeyoshi Yamamoto

Publications and source records attributed to Shigeyoshi Yamamoto.

6 recordsLinked to original sources

PubMed2006

Gaussian-type function set without prolapse for the Dirac-Fock-Roothaan equation (II): 80Hg through 103Lr.

We present prolapse-free universal Gaussian-type basis sets for 80Hg through 103Lr. The basis set is determined so that the Dirac-Fock-Roothaan total energy should decrease monotonically toward the numerical Dirac-Fock total energy. The difference between the Dirac-Fock-Roothaan total energy and the numerical Dirac-Fock total energy is less than 3 x 10(-6) hartree for 1H through 102No, and less than 5 x 10(-6) hartree for 103Lr. The exponents of the present sets are determined in an even-tempered manner, aiming to give total energy closer to the numerical Dirac-Fock value as the expansion term increases. The recommended set is expanded by (64, 64, 64, 46, 46, 46, 46) terms for (s+, p-, p+, d-, d+, f-, f+) symmetries, respectively. A practical set with (56, 48, 48, 36, 36, 36, 36) terms is also presented.

Journal Article↗

PubMed2006

Electronic structure of the GdF molecule by frozen-core four-component relativistic configuration interaction calculations.

The electronic structure of GdF is calculated based on frozen-core four-component relativistic configuration interactions. The resulting excitation energies are fairly close to experiment and correctly designate the excited states. For instance, the existence of the experimentally inferred state at 0.55 eV above the ground state is confirmed, having Omega=132 with (4f(7)5d(+) (1)6s(+) (1)); it is 0.58 eV above the ground state according to the present calculation.

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PubMed2006

A study of the ground state of manganese dimer using quasidegenerate perturbation theory.

We study the electronic structure of the ground state of the manganese dimer using the state-averaged complete active space self-consistent field method, followed by second-order quasidegenerate perturbation theory. Overall potential energy curves are calculated for the 1Sigmag+, 11Sigmau+, and 11Piu states, which are candidates for the ground state. Of these states, the 1Sigmag+ state has the lowest energy and we therefore identify it as the ground state. We find values of 3.29 A, 0.14 eV, and 53.46 cm(-1) for the bond length, dissociation energy, and vibrational frequency, in good agreement with the observed values of 3.4 A, 0.1 eV, and 68.1 cm(-1) in rare-gas matrices. These values show that the manganese dimer is a van der Waals molecule with antiferromagnetic coupling.

Journal Article↗

PubMed2005

Characterization of molecular orbitals by counting nodal regions.

The number of nodal regions can be used as an index for characterizing molecular orbitals. A computer program has been developed to count the number of nodal regions, based on the labeling and contraction algorithms. This program is applied to the water molecule, the hydrogen sulfide molecule, the hydrogen atomic orbitals, the Rydberg excited states of ethylene, dissociation of carbon monoxide, and CASSCF calculations of formaldehyde. Because the number of nodal regions is independent of the coordinate system, the method is applicable even when the molecular structure changes drastically as in bond rotation or bond elongation. Changes of nodal regions with bond elongation are investigated for carbon monoxide. A prescription for problems arising with basis set expansion techniques is also given.

Journal Article↗

PubMed2004

Quality of contracted Gaussian-type function basis sets.

The valence quality of contracted (C) Gaussian-type function (GTF) basis sets in molecular calculations is discussed for the first- through fourth-row atoms. The split-valence basis sets derived from minimal-type CGTF sets are compared with those derived from primitive (P) GTF sets. Using F, Cl, Br, and I atoms and their homonuclear diatomics as test species, we find that the split-valence CGTF sets have almost the same quality as PGTF sets with larger s and p expansion terms: for example, the (53/5), (533/53), (5333/533/5), and (53 333/5333/53) CGTF sets correspond approximately to the [9/5], [15/9], [19/15/5], and [22/18/7] PGTF sets for the first- to fourth-row atoms, respectively, where the slash separates the s, p, and d symmetries. For the main group atoms of the four rows, we recommend using the above-mentioned CGTFs or larger.

Journal Article↗

PubMed2004

Torsion potential works in rhodopsin.

We investigate the role of protein environment of rhodopsin and the intramolecular interaction of the chromophore in the cis-trans photoisomerization of rhodopsin by means of a newly developed theoretical method. We theoretically produce modified rhodopsins in which a force field of arbitrarily chosen part of the chromophore or the binding pocket of rhodopsin is altered. We compare the equilibrium conformation of the chromophore and the energy stored in the chromophore of modified rhodopsins with those of native rhodopsins. This method is called site-specific force field switch (SFS). We show that this method is most successfully applied to the torsion potential of rhodopsin. Namely, by reducing the twisting force constant of the C11=C12 of 11-cis retinal chromophore of rhodopsin to zero, we found that the equilibrium value of the twisting angle of the C11=C12 bond is twisted in the negative direction down to about -80 degrees. The relaxation energy obtained by this change amounts to an order of 10 kcal/mol. In the case that the twisting force constant of the other double bond is reduced to zero, no such large twisting of the bond happens. From these results we conclude that a certain torsion potential is applied specifically to the C11=C12 bond of the chromophore in the ground state of rhodopsin. This torsion potential facilitates the bond-specific cis-trans photoisomerization of rhodopsin. This kind of the mechanism is consistent with our torsion model proposed by us more than a quarter of century ago. The origin of the torsion potential is analyzed in detail on the basis of the chromophore structure and protein conformation, by applying the SFS method extensively.

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