Biomedical subjects

Umpei Nagashima

Publications and source records attributed to Umpei Nagashima.

7 recordsLinked to original sources

PubMed2007

Quantum treatment of hydrogen nuclei in primary kinetic isotope effects in a thermal [1,5]-sigmatropic hydrogen (or deuterium) shift from (Z)-1,3-pentadiene.

The geometric and kinetic isotope effects (GIE and KIE) for thermal [1,5]-sigmatropic H and D shifts of (Z)-1,3-pentadiene were studied by including the direct quantum effect of the migrating H or D nucleus in the multi-component molecular orbital-Hartree-Fock (MC_MO-HF) method. Based on the results, the C(1)-D bond lengths are 0.007 Angstrom shorter than the C1-H bond lengths in both the reactant (A) and the transition states (TS), whereas other bond lengths resemble those between H and D. The ratio of the rate constant (k(H)/k(D)) of the reaction for the thermal [1,5]-H and D shifts determined using the MC_MO-HF method (8.28) is closer to the experimental value (12.2) than that determined using either the conventional restricted Hartree-Fock (4.10) or restricted Møller-Plesset second-order perturbation (3.79) methods.

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PubMed2006

Electron-electron and electron-nucleus correlation effects on exponent values of Gaussian-type functions for quantum protons and deuterons.

Electron-electron and electron-nucleus correlation effects on exponent (alpha) values of Gaussian-type functions (GTFs) for quantum protons and deuterons in BH3, CH4, NH3, H2O, and HF molecular systems and their deuterated counterparts were analyzed using the second-order Moller-Plesset (MP2) level of theory of the multicomponent molecular orbital (MCMO-MP2) method. This method can simultaneously determine both nuclear and electronic wave functions. Results showed that the average alpha value (alpha(ave)) of the optimized alpha in single s-type ([1s]) GTF for a proton and a deuteron is similar to that determined using the Hartree-Fock level of the MCMO (MCMO-HF) method. In contrast, due to the electron-nucleus correlation effect, the s- and p-type ([1s1p]) GTFs are delocalized compared with those determined using the MCMO-HF method. For the H-bonded complexes, differences in the interaction energy induced by the H/D isotope effect were clearly evident because the D...Y bond distance for D complex is longer than the H...Y for H complex. Also, the basis set superposition error for the interaction energy in every H complex was similar to that in every D complex. The results here clearly demonstrate that the protonic and deuteronic basis functions based on alpha(ave) values for correlation effects can be applied to the detailed analysis of the quantum effects of protons and the H/D isotope effect in widespread fields that involve H bonds and weak interactions, such as the function of biological molecules, chemical reaction processes, and the design of new materials.

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PubMed2006

Geometric isotope effect of various intermolecular and intramolecular C-H...O hydrogen bonds, using the multicomponent molecular orbital method.

The geometric isotope effect (GIE) of sp- (acetylene-water), sp(2)- (ethylene-water), and sp(3)- (methane-water) hybridized intermolecular C-H...O and C-D...O hydrogen bonds has been analyzed at the HF/6-31++G level by using the multicomponent molecular orbital method, which directly takes account of the quantum effect of proton/deuteron. In the acetylene-water case, the elongation of C-H length due to the formation of the hydrogen bond is found to be greater than that of C-D. In contrast to sp-type, the contraction of C-H length in methane-water is smaller than that of C-D. After the formation of hydrogen bonds, the C-H length itself in all complexes is longer than C-D and the H...O distance is shorter than D...O, similar to the GIE of conventional hydrogen bonds. Furthermore, the exponent (alpha) value is decreased with the formation of the hydrogen bond, which indicates the stabilization of intermolecular C-H...O hydrogen bonds as well as conventional hydrogen bonds. In addition, the geometric difference induced by the H/D isotope effect of the intramolecular C-H...O hydrogen bond shows the same tendency as that of intermolecular C-H...O. Our study clearly demonstrates that C-H...O hydrogen bonds can be categorized as typical hydrogen bonds from the viewpoint of GIE, irrespective of the hybridizing state of carbon and inter- or intramolecular hydrogen bond.

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PubMed2006

A fragment molecular-orbital-multicomponent molecular-orbital method for analyzing HD isotope effects in large molecules.

We have developed a fragment molecular orbital (FMO)-multi-component MO (MC_MO) method to analyze isotope effect due to differences between the quantum effects of protons and deuterons for large molecules such as proteins and DNA. The FMO-MC_MO method enables the determination of both the electronic and the protonic (deuteronic) wave functions simultaneously, and can directly express isotope effects, including coupling effects between nuclei and electrons. In our calculations of two polyglycines, which serve as prototypes for biological molecules, by this method, we clearly observed the geometrical relaxation induced by the HD isotope effect in the intramolecular hydrogen bonding portions of the molecules. The HD isotope effect on the interfragment interaction energy, including that of the hydrogen bonding parts, was also demonstrated: the hydrogen bond was weakened by replacement of hydrogen with deuterium. We also developed electrostatic potential approximations for use in the FMO-MC_MO calculations, and the accuracy of the energy differences induced by the isotope effect was independent of the approximation level of the FMO-MC_MO. Our results confirmed that the FMO-MC_MO method is a powerful tool for the detailed analysis of changes in hydrogen bonding and interaction energies induced by the HD isotope effect for large biological molecules.

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PubMed2005

Theoretical study of intramolecular interaction energies during dynamics simulations of oligopeptides by the fragment molecular orbital-Hamiltonian algorithm method.

We analyzed the interaction energies between residues (fragments) in an oligopeptide occurring during dynamic simulations by using the fragment molecular orbital-Hamiltonian algorithm (FMO-HA) method, an ab initio MO-molecular dynamics technique. The FMO method enables not only calculation of large molecules based on ab initio MO but also easy evaluation of interfragment interaction energies. The glycine pentamer [(Gly)(5)] and decamer [(Gly)(10)] were divided into five and ten fragments, respectively. alpha-helix structures of (Gly)(5) and (Gly)(10) were stabilized by attractive interaction energies owing to intramolecular hydrogen bonds between fragments n and n+3 (and n+4), and beta-strand structures were characterized by repulsive interaction energies between fragments n and n+2. We analyzed interfragment interaction energies during dynamics simulations as the peptides' geometries changed from alpha helix to beta strand. Intramolecular hydrogen bonds between fragments 2-4 and 2-5 control the geometrical preference of (Gly)(5) for the beta-strand structure. The pitch of one turn of the alpha helix of (Gly)(10) elongated and thus weakened during dynamics due to a shifting of the intramolecular hydrogen bonds, and enabled the beta-strand structure to form. Changes in interaction energies due to the intramolecular hydrogen bonds controlled the tendency toward alpha-helix or beta-strand structure of (Gly)(5) and (Gly)(10). Evaluation of interfragment interaction energies during dynamics simulations thus enabled detailed analysis of the process of the geometrical changes occurring in oligopeptides.

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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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PubMed2002

A novel parallel algorithm for large-scale Fock matrix construction with small locally distributed memory architectures: RT parallel algorithm.

We developed a novel parallel algorithm for large-scale Fock matrix calculation with small locally distributed memory architectures, and named it the "RT parallel algorithm." The RT parallel algorithm actively involves the concept of integral screening, which is indispensable for reduction of computing times with large-scale biological molecules. The primary characteristic of this algorithm is parallel efficiency, which is achieved by well-balanced reduction of both communicating and computing volume. Only the density matrix data necessary for Fock matrix calculations are communicated, and the data once communicated are reutilized for calculations as many times as possible. The RT parallel algorithm is a scalable method because required memory volume does not depend on the number of basis functions. This algorithm automatically includes a partial summing technique that is indispensable for maintaining computing accuracy, and can also include some conventional methods to reduce calculation times. In our analysis, the RT parallel algorithm had better performance than other methods for massively parallel processors. The RT parallel algorithm is most suitable for massively parallel and distributed Fock matrix calculations for large-scale biological molecules with more than thousands of basis functions.

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