Biomedical subjects

Shiro Koseki

Publications and source records attributed to Shiro Koseki.

7 recordsLinked to original sources

PubMed2006

Density functional theoretical study on enantiomerization of 2,2'-biphenol.

The S-R enantiomerization processes of 2,2'-biphenol (biphenol) have been investigated using density functional theory (DFT). Five isomers for biphenol were identified: I0, which is the most stable isomer; I1a and I1b, which are formed by a restricted rotation of one OH group; and I2a and I2b, which are formed by a restricted rotation of the two OH groups where a and b denote cis and trans configurations, respectively. Each isomer has R- and S-enantiomers. The energies relative to the most stable isomer I0 are 1.6, 3.3, 5.3, and 5.5 kcal mol(-1) for I1a, I1b, I2a, and I2b, respectively. The direct enantiomerization of I0, in which the phenol-ring rotation is considered to be the reaction coordinate while the OH rotations are frozen, is forbidden because of the repulsion between the two OH groups. The transition states for isomerizations of I0 to other isomers (I1a, I1b, I2a, or I2b) were calculated as well as those for the other direct enantiomerizations except for that of I0. From the viewpoint of the least number of the transition states and their low energy levels, the probable S-R enantiomerization of I0 is expressed as a sequential process of isomerization: I0,S --> I1a,S, a direct enantiomerization induced by one of the two OH rotations, I1a,S --> I1a,R, and another isomerization, I1a,R --> I0,R, that is, I0,S --> I1a,S --> I1a,R --> I0,R as the whole process. This process is effective in quantum control of the enantiomerization of biphenol and can be carried out by a sequence of a pump-dump IR laser-pulse scheme.

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PubMed2006

Dissociation potential curves of low-lying states in transition metal hydrides. 3. Hydrides of groups 6 and 7.

The dissociation curves of low-lying spin-mixed states in monohydrides of groups 6 and 7 were calculated by using an effective core potential (ECP) approach. This approach is based on the multiconfiguration self-consistent field (MCSCF) method, followed by first-order configuration interaction (FOCI) calculations, in which the method employs an ECP basis set proposed by Stevens and co-workers (SBKJC) augmented by a set of polarization functions. Spin-orbit coupling (SOC) effects are estimated within the one-electron approximation by using effective nuclear charges, since SOC splittings obtained with the full Breit-Pauli Hamitonian are underestimated when ECP basis sets are used. The ground states of group 6 hydrides have Omega = (1)/(2)(X(6)Sigma(+)(1/2)), where Omega is the z component of the total angular momentum quantum number. Although the ground states of group 7 hydrides have Omega = 0(+), their main adiabatic components are different; the ground state in MnH originates from the lowest (7)Sigma(+), while in TcH and ReH the main component of the ground state is the lowest (5)Sigma(+). The present paper reports a comprehensive set of theoretical results including the dissociation energies, equilibrium distances, electronic transition energies, harmonic frequencies, anharmonicities, and rotational constants for several low-lying spin-mixed states in these hydrides. Transition dipole moments were also computed among the spin-mixed states and large peak positions of electronic transitions are suggested theoretically for these hydrides. The periodic trends of physical properties of metal hydrides are discussed, based on the results reported in this and other recent studies.

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PubMed2004

Improvement of parallelization performance of GAMESS: global sum and (semi-)direct integral calculation in multireference perturbation calculation.

Performance benchmark tests of the multireference perturbation theory (MRPT2) calculation in the GAMESS suite of programs have been performed on a 128-node PC cluster system. The benchmark results point to two kinds of problems with GAMESS: network delay and slow access to disk files. To overcome these bottlenecks, we employ (semi-)direct atomic orbital integral calculations and a new algorithm for the "global sum" operation. These modifications produce remarkable performance improvements, especially in the 128-node PC cluster system, which was almost twice as fast in our version as in the original version. The modification of "global sum" also improved the performance of other types of molecular orbital calculations in GAMESS, such as density functional theory.

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PubMed2004

A new hierarchical parallelization scheme: generalized distributed data interface (GDDI), and an application to the fragment molecular orbital method (FMO).

A two-level hierarchical scheme, generalized distributed data interface (GDDI), implemented into GAMESS is presented. Parallelization is accomplished first at the upper level by assigning computational tasks to groups. Then each group does parallelization at the lower level, by dividing its task into smaller work loads. The types of computations that can be used with this scheme are limited to those for which nearly independent tasks and subtasks can be assigned. Typical examples implemented, tested, and analyzed in this work are numeric derivatives and the fragment molecular orbital method (FMO) that is used to compute large molecules quantum mechanically by dividing them into fragments. Numeric derivatives can be used for algorithms based on them, such as geometry optimizations, saddle-point searches, frequency analyses, etc. This new hierarchical scheme is found to be a flexible tool easily utilizing network topology and delivering excellent performance even on slow networks. In one of the typical tests, on 16 nodes the scalability of GDDI is 1.7 times better than that of the standard parallelization scheme DDI and on 128 nodes GDDI is 93 times faster than DDI (on a multihub Fast Ethernet network). FMO delivered scalability of 80-90% on 128 nodes, depending on the molecular system (water clusters and a protein). A numerical gradient calculation for a water cluster achieved a scalability of 70% on 128 nodes. It is expected that GDDI will become a preferred tool on massively parallel computers for appropriate computational tasks.

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PubMed2003

Description of molecular dynamics in intense laser fields by the time-dependent adiabatic state approach: application to simultaneous two-bond dissociation of CO2 and its control.

We theoretically investigated the dynamics of structural deformations of CO(2) and its cations in near-infrared intense laser fields (approximately 10(15) W cm(-2)) by using the time-dependent adiabatic state approach. To obtain "field-following" adiabatic potentials for nuclear dynamics, the electronic Hamiltonian including the interaction with the instantaneous laser electric field is diagonalized by the multiconfiguration self-consistent-field molecular orbital method. In the CO(2) and CO(2+) stages, ionization occurs before the field intensity becomes high enough to deform the molecule. In the CO(2)(2+) stage, simultaneous symmetric two-bond stretching occurs as well as one-bond stretching. Two-bond stretching is induced by an intense field in the lowest time-dependent adiabatic state |1> of CO(2)(2+), and this two-bond stretching is followed by the occurrence of a large-amplitude bending motion mainly in the second-lowest adiabatic state |2> nonadiabatically created at large internuclear distances by the field from |1>. It is concluded that the experimentally observed stretched and bent structure of CO(2)(3+) just before Coulomb explosions originates from the structural deformation of CO(2)(2+). We also show in this report that the concept of "optical-cycle-averaged potential" is useful for designing schemes to control molecular (reaction) dynamics, such as dissociation dynamics of CO(2), in intense fields. The present approach is simple but has wide applicability for analysis and prediction of electronic and nuclear dynamics of polyatomic molecules in intense laser fields.

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PubMed2002

Quantum control of molecular chirality: optical isomerization of difluorobenzo[c]phenanthrene.

The results of a theoretical study are presented on quantum control of a chiral exchange reaction of a polyatomic molecule by using infrared laser pulses. Difluorobenzo[c]phenanthrene was chosen to be the simplest model for its helical chirality exchange reaction. This molecule has two stable configurations: M and P forms. From the viewpoint of chemical reaction dynamics, isomerization is regarded as the movement of one of the two representative points that initially correspond to the two forms to the position of the other representative point, while the other representative point remains in its initial position. The ground-state potential energy surface and dipole moment functions required to control this reaction were evaluated at the MP2/6-31+G(d,p) and MP2/TZV+(d,p) levels of molecular orbital (MO) theory. An effective potential energy surface (PES) that is a function of twisting motion of the benzene rings and wagging motion of the CF(2) group was constructed on the basis of the MO results. An analytical expression for the effective PES and that for the dipole moment functions were prepared to make the isomerization control tractable. A quantum control method in a classical way was applied to the isomerization of preoriented difluorobenzo[c]phenanthrene in low temperature limits. The time evolution of the representative point of the M form and that of the P form are separately evaluated to determine the optimal laser fields. This means that the laser control produces pure helical enantiomers from a racemic mixture. Representative points are replaced by the corresponding nuclear wave packets in this treatment. The derived control laser field consists of two linearly polarized E(x)() and E(z)() components that are perpendicular to each other. These components are pi-phase-shifted when the representative point is in the transition-state regions. Under the irradiation of this laser pulse, one of the two representative points of the isomerization is transferred to the target position along the intrinsic reaction path between the enantiomers, while the other representative point remains in its initial potential well. This results in one-way isomerization control, that is, the M(P) to P(M) form. The isomerization is completed with yields of ca. 70% within a few picoseconds. Temporal behaviors of the nuclear wave packet whose center corresponds to the representative point are drawn to see how the desired chiral exchange reaction proceeds in the presence of the control field, while its reverse process is suppressed.

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PubMed1996

Proton-Induced Tuning of Electrochemical and Photophysical Properties in Mononuclear and Dinuclear Ruthenium Complexes Containing 2,2'-Bis(benzimidazol-2-yl)-4,4'-bipyridine: Synthesis, Molecular Structure, and Mixed-Valence State and Excited-State Properties.

A series of mono- and dinuclear Ru(bpy)(2) complexes (bpy = 2,2'-bipyridine) containing 2,2'-bis(benzimidazol-2-yl)-4,4'-bipyridine (bbbpyH(2)) were prepared. The mononuclear complex [Ru(bpy)(2)(bbbpyH(2))](ClO(4))(2).CH(3)OH.4H(2)O was characterized by an X-ray structure determination. Crystal data are as follows: triclinic, space group P&onemacr;, a = 14.443(4) Å, b = 15.392(4) Å, c = 11.675(2)Å, alpha = 101.44(2) degrees, beta = 107.85(2) degrees, gamma = 96.36(2) degrees, V = 2380(1) Å(3), Z = 2. The coordination geometry of the ruthenium(II) ion is approximately octahedral. The dihedral angle between the two pyridyl rings in bbbpyH(2) is 9.4(3) degrees, which is close to coplanar, in the complex. Mono- and dinuclear complexes exhibit broad charge-transfer absorption bands at 420-520 nm and emission at 660-720 nm in CH(3)CN solution with lifetimes of 200-800 ns at room temperature. Transient difference absorption spectra and resonance Raman (rR) spectra were used to assign the charge-transfer bands in the 420-520 nm region and to identify the lowest excited states. Both absorption and emission spectra are sensitive to solvent and solution pH. Deprotonation of the dinuclear complex raises the energies of the pi orbitals of the bbbpyH(2) ligand, so that they become closer in energy to the pi orbitals of bpy. The intervalence band of [(bpy)(2)Ru(bbbpyH(2))Ru(bpy)(2)](5+)()()is observed at 1200 nm ( epsilon = 170 M(-)(1) cm(-)(1)) in CH(3)CN. The value of the electronic coupling matrix element, H(AB), was determined as 120 cm(-)(1). Upon deprotonation, the IT band was not observed. It is therefore concluded that a superexchange pathway occurs predominantly via the Ru(II) dpi-bbbpyH(2) pi interaction, since deprotonation decreases the interaction. The role of the intervening fragments in the bridging ligand is discussed from the viewpoint of orbital energies and their orbital mixing with Ru dpi orbitals.

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