Kichisuke Nishimoto

The solitonic mechanism for proton transport in a hydrogen bonded chain

We find that the proton transfer in a hydrogen bonded chain subjected to the appropriate electrostatic field behaves as a soliton. The energy of soliton and the rate constant for this proton transfer process are calculated by transition state theory. We obtain the results that the energy of soliton is considerably small compared with the band gap of the polypeptide chain and the rate constant is quite large which is enough to reveal the biological function. With these results, a few biological significances are discussed.

An ab initio calculation on proton transfer in the benzoic acid dimer

Abstract We have made an ab initio calculation of the barriers for proton transfer in the hydrogen-bonded dimers of benzoic acid and acetic acid. Geometrical optimization values which are closer to the experiment one.

Hydrogen bonding of flavoprotein. I. Effect of hydrogen bonding on electronic spectra of flavoprotein

The effect of hydrogen bonding on the transition energy and the oscillator strength of the isoalloxazine nucleus of flavins was studied by the molecular orbital method. Among the possible hydrogen bondings examined, characteristic spectral shifts were found for the hydrogen bondings at N(1) and N(5) of the nucleus. The hydrogen bonding at N(1) resulted in the shift of the first absorption band towards blue and that of the second one towards red. On the other hand, the hydrogen bonding at N(5) resulted in the shifts of both the first and the second band towards red. The spectral characteristics reported on Clostridium MP and Desulfovibrio vulgaris flavodoxin coincided with the calculated results. The application of the calculated results to D-amino acid oxidase (D-amino acid: oxygen oxidoreductase (deaminating), EC 1.4.3.3) led to the conclusion that hydrogen bonding occurs at O(12), N(3)H, O(14) and N(5) of the isoalloxazine nucleus. The occurrence of hydrogen bondings at O(12), N(3)H, and O(14) is favorable for N(5) of the isoalloxazine nucleus to accept electron from an electron donor.

Monte Carlo simulations of M+Cl− (H2O)n (M = Li, Na) clusters and the dissolving mechanism of ion pairs in water

Abstract The dissolving mechanism of ion pairs in water was analyzed by means of radial distribution functions and the pair energies obtained from Monte Carlo simulations for M + Cl − (H 2 O) n (M = Li, Na) ( n = 1–8) at room temperature. The minimum-energy geometries of these clusters for n ⩾ 3 are water-shared ion pairs. Although the interionic distances for Na + Cl − (H 2 O) n clusters are about 0.2 A longer than those for Li + Cl − (H 2 O) n for n = 1–2, this reversed at n = 4. This trend originates because the water-shared structure for the Li + Cl − (H 2 O) n clusters suddenly becomes dominant at n = 4, whereas for the Na + Cl − (H 2 O) n clusters, the change is more gradual.

Ab initio MO study of benzylic cations?1. Some theoretical parameters related to the resonance demand in the Yukawa-Tsuno equation

Structures of 14 kinds of benzylic cations into which are introduced various substituents at benzylic position were optimized by means of the ab initio molecular orbital method at the RHF/6-31G* level. The theoretical indices obtained associated with the resonance interaction, such as population, bond order and bond length, were compared with the resonance demand parameter (r value) of corresponding solvolysis systems that were given by the Yukawa-Tsuno substituent effect analysis. The r value was linearly correlated with the theoretical resonance indices.

A MO-theoretical study of the hydrogen bond in (HCOOH)2, (HCONH2)2 and (B(OH)3)2

The energy decomposition scheme is used with the ab initio MO of the STO-3G minimal basis to elucidate the nature of hydrogen-bondings in (HCOOH)2, (HCONH2)2 and (B(OH)3)2. The comparison of the interaction energy and its five components, together with that of the difference density map, reveals the similarity or the difference of these three systems. Each component of the global difference density represents the characteristic role of the corresponding interaction. While the effect of the exchange and charge-transfer interaction is limited to the hydrogen-bonded region, that of the polarization and the coupling terms is spread over the intramolecular bonds of each monomer. The analysis of some orbital interactions is made with respect to (HCOOH)2 and the importance of the particular charge-transfer interaction is demonstrated.

Theoretical study of soliton dynamics of a finite one-dimensional hydrogen-bonded system

Abstract The dynamical behavior of a model for a finite one-dimensional hydrogen-bonded system has been studied by numerical calculation (RKG method). The present study shows that there exists a threshold level of the proton-proton interaction, below which the soliton will not form in the finite system. When we use the previous model, the threshold values become too large. However, when we take into consideration higher-order interaction between the nearest-neighbor protons, the width and the energy of the soliton become quite reasonable. Thus, when such a condition is fulfilled, a soliton might appear under normal physiological conditions.

Theoretical study of electron impact mass spectrometry. II. ab initio MO study of the fragmentation of ionized 1-propanol

Abstract In order to elucidate qualitatively the fragmentation mechanism of 1-propanol following low energy electron bombardment, the potential energy curves have been calculated using ab initio MO methods (4-31G//ST0-3G), The present study indicates that H 2 O elimination proceeds via the formation of a five-membered ring intermediate/transition state. A hydrogen atom of the methyl group isshifted to form H 2 O, which is in line with the deuterium labelling experiment. In the simple bond cleavage process, it is mainly the C α C β bond which is expected to be broken.

Molecular Dynamics Simulation Study on Stabilities and Reactivities of NADH Cytochrome B5 Reductase

Binding free energies between coenzyme (FAD and NADH) and the apoenzyme of NADH-cytochrome b5 reductase (b5R) were estimated by applying the continuum Poisson-Boltzmann (PB) model to structures sampled from molecular dynamics simulations in explicit water molecules. Important residues for the enzymatic catalysis were clarified using a computational alanine scanning method. The binding free energies calculated by applying an alanine scanning method can successfully reproduce the trends of the measured steady-state enzymatic activities kcatNADH/KmNADH. Significant decreases in the binding free energy are expected when one of the four residues Arg91, Lys110, Ser127, and Thr181 is mutated into Ala. According to the results of the molecular dynamics simulation, Thr181 is considered to be one of the key residues that helps NADH to approach the isoalloxazine in FAD. Finally, we have constructed very simplified model systems and carried out density functional theory calculations using B3LYP/LANL2DZ//ROHF(or RHF)/LANL2DZ level of theory in order to elucidate a realistic and feasible mechanism of the hydride-ion transfer from NADH to FAD affected by HEME(Fe3+) as an electron acceptor. Our calculated results suggest that the electron and/or hydride-ion transfer reaction from NADH to FAD can be accelerated in the presence of HEME(Fe3+).

Precise PPP molecular orbital calculations of the excitation energies of polycyclic aromatic hydrocarbons. Part 2: Evaluation of the spectrochemical softness parameter based on the spectroactive partial structure of a molecule

For precise Pariser-Parr-Pople molecular orbital (PPP MO) calculations, the values of the spectrochemical softness parameter (k) of a new two centre electron repulsion integral (new-γ) were evaluated based on an appropriate partial structure of cata-condensed polycyclic aromatic hydrocarbons (PAHs). The spectroactive aromatic sextet resonance system [ASRS] was defined as a spectroactive partial structure of a molecule. The calculated excitation energies of the p-band of the cata-condensed PAHs accurately reproduced the observed values. In particular, the calculated energies of branched PAHs were improved compared with those obtained using our previous method.