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Shigeki Kato

Publications and source records attributed to Shigeki Kato.

12 recordsLinked to original sources
PubMed2006

Quantum dynamics study on multichannel dissociation and isomerization reactions of formaldehyde.

We study quantum dynamics of the multichannel reactions of H(2)CO including the molecular and radical dissociation channels as well as the isomerization ones, H(2)CO-->trans-HCOH and trans-HCOH-->cis-HCOH. For this purpose, the previously developed potential energy function [T. Yonehara and S. Kato, J. Chem. Phys. 117, 11131 (2002)] is refined to give accurate transition state energies and to describe the radical dissociation channel. The cumulative reaction probabilities for the molecular dissociation and two isomerization channels are calculated by using the full Watson Hamiltonian. We also carry out wave packet dynamics calculations starting from the transition state region for the molecular dissociation. A contracted basis set for the angular coordinates is constructed to reduce the size of dynamics calculations. The intramolecular vibrational relaxation dynamics is found to be fast and almost complete within 300 fs. Using the energy filtered wave functions, the time propagation of HCOH population is obtained in the energy range from 81 to 94 kcal/mol. The branching ratio of the radical product is estimated by calculating the time dependent reactive fluxes to the molecular and radical dissociation products.

Journal Article↗
PubMed2006

Leucine-rich repeat-containing G protein-coupled receptor-4 (LGR4, Gpr48) is essential for renal development in mice.

Leucine-rich repeat-containing G protein-coupled receptor (LGR)-4 is a G protein-coupled receptor (GPCR) with a seven-transmembrane domain structure. LGRs are evolutionally and structurally phylogenetic, classified into three subgroups and are members of the so-called orphan receptors whose ligands have yet to be identified. We generated knockout mice lacking Lgr4(Gpr48) by targeted deletion of part of exon 18, which codes for the transmembrane and signal-transducing domains of the receptor. Lgr4 null mice were born at much less than the 25% expected frequency from crosses of Lgr4 heterozygous mice (Lgr4+/-). Lgr4 null mice that survived in utero died shortly after birth in almost all cases. We observed striking renal hypoplasia in the null mice, accompanied by elevated concentration of plasma creatinine. Histological analysis of the P0 null mouse kidney showed a notable decrease in the total number and density of the glomerulus. Thus, the function of Lgr4 is essential to regulate renal development in the mouse. This study suggests that the Lgr4 gene is a new and important member of LGRs involved in a group of genes responsible for hereditary disease in the kidney.

Animals↗
PubMed2005

Theoretical study on electronic and spin structures of [Fe2S2](2+,+) cluster: reference interaction site model self-consistent field (RISM-SCF) and multireference second-order Møller-Plesset perturbation theory (MRMP) approach.

Electronic structures of [Fe(2)S(2)(SCH(3))(4)](2-,3-) in DMSO solution are calculated using reference interaction site model complete active space self-consistent field (RISM-CASSCF)/multireference second-order Møller-Plesset perturbation theory (MRMP) method. For the reduced state, we obtain both the low-spin Fe(3+)Fe(2+) localized and high-spin Fe(2.5+)Fe(2.5+) delocalized forms, which are very close in energy. The spin interaction constants obtained from the energies of states with various spin multiplicities are in good agreement with the available experimental estimates both for the oxidized and for the reduced states. The dynamic electron correlation effect is found to be important in estimating the spin interaction between the Fe ions. The redox potentials are calculated to be 2.87 and 2.78 eV for the localized and delocalized reduced states, respectively, which are close to the experimental values. We devise a simple model for calculating the free energy curves of the reduction process based on the RISM-SCF theory. The activation barrier height is calculated to be 7.4 kcal/mol at the equilibrium geometry of oxidized state, indicating that the reduction reaction will occur efficiently in DMSO solvent. The effect of solvent fluctuation on the free energy profiles is discussed on the basis of the present calculations.

Iron↗
PubMed2005

Locating the lowest free-energy point on conical intersection in polar solvent: reference interaction site model self-consistent field study of ethylene and CH2NH2(+).

We present a theoretical method for locating the lowest free-energy points on conical intersections (CIs) in solution using the reference interaction site model self-consistent field (RISM-SCF) theory. Based on the linear-response theory, the nonequilibrium free energy is defined as a quadratic function of solvation coordinates, the parameters in which are directly obtained by ab initio RISM-SCF calculations. This free energy is easily incorporated into an efficient CI optimization procedure in gas phase. The present method is applied to the cis-trans photoisomerizations of ethylene and methaniminium cation (CH2NH2(+)) in polar solvents. We show that the geometries and energies of CIs are largely affected by the solute-solvent electrostatic interaction. In particular, the hydrogen migration of ethylene observed at CIs in the gas phase disappears in protic solvents due to the large stabilization of the zwitterionic state.

Journal Article↗
PubMed2005

Electronic relaxation dynamics of Ni2+-ion aqueous solution: molecular-dynamics simulation.

Electronic relaxation dynamics of Ni2+-ion aqueous solution is investigated using molecular-dynamics (MD) simulations with the model-effective Hamiltonian developed previously. The nonadiabatic transition rates from the first three excited states to the ground state are evaluated by the golden rule formula with the adiabatic MD simulations. The MD simulations with the fewest-switch surface-hopping method are also carried out to obtain a more detailed description of the electronic relaxation dynamics among the excited states. We found out that the transitions among the three excited states are very fast, in the order of 10 fs, while the transition between the excited and ground states is slow, about 800 ps. These findings are consistent with the time scales of energy dissipation detected by the transient lens experiment. In both simulations, we explore the effects of the quantum decoherence, where the decoherence functions are derived by the energy-gap dynamics with the displaced harmonic-oscillator model.

Journal Article↗
PubMed2005

Intramolecular charge-transfer state formation of 4-(N,N-dimethylamino)benzonitrile in acetonitrile solution: RISM-SCF study.

Intramolecular charge-transfer (ICT) state formation of 4-(N,N-dimethylamino)benzonitrile in acetonitrile solution is studied by the reference interaction site model self-consistent field (RISM-SCF) method. Geometry optimizations are performed for each electronic state in solution with the complete-active-space SCF wave functions. Dynamic electron correlation effects are taken into account by using the multiconfigurational quasidegenerate perturbation theory. Two-dimensional free energy surfaces are constructed as the function of the twisting and wagging angles of the dimethylamino group for the ground and locally excited (LE) states. The calculated absorption and fluorescence energies are in good agreement with experiments. The validity of the twisted ICT (TICT) model is confirmed in explaining the dual fluorescence, and the possibility of the planar ICT model is ruled out. To examine the mechanism of the TICT state formation, a "crossing" seam between the LE and charge-transfer (CT) state surfaces is determined. The inversion of two electronic states occurs at a relatively small twisting angle. The effect of solvent reorganization is also examined. It is concluded that the intramolecular twisting coordinate is more important than the solvent fluctuation for the TICT state formation, because the energy difference between the two states is minimally dependent on the solvent configuration.

Journal Article↗
PubMed2004

Potential energy surfaces and dynamics of Ni2+ ion aqueous solution: molecular dynamics simulation of the electronic absorption spectrum.

We develop a model effective Hamiltonian for describing the electronic structures of first-row transition metals in aqueous solutions using a quasidegenerate perturbation theory. All the states consisting of 3d(n) electronic configurations are determined by diagonalizing a small effective Hamiltonian matrix, where various intermolecular interaction terms such as the electrostatic, polarization, exchange, charge transfer, and three-body interactions are effectively incorporated. This model Hamiltonian is applied to constructing the ground and triplet excited states potential energy functions of Ni(2+) in aqueous solution, based on the ab initio multiconfiguration quasidegenerate perturbation theory calculations. We perform molecular dynamics simulation calculations for the ground state of Ni(2+) aqueous solution to calculate the electronic absorption spectral shape as well as the ground state properties. Agreement between the simulation and experimental spectra is satisfactory, indicating that the present model can well describe the Ni(2+) excited state potential surfaces in aqueous solution.

Journal Article↗
PubMed2004

Excited state electronic structures and dynamics of NOCl: a new potential function set, absorption spectrum, and photodissociation mechanism.

A set of analytical potential energy surfaces (PESs) for six singlet excited states of NOCl are constructed based on multireference configuration interaction calculations. The total absorption cross section at the energy range of 2-7 eV is calculated by quantum dynamics calculations with the present PESs and transition dipole moments. The calculated absorption spectrum agrees well with the experiment. It is also found that the A band with the absorption maximum at 6.3 eV is attributed to the transition to the 4 1A' state, though the excitations to the 3 1A' and 3 1A" states contribute to the spectrum at the energy range between 4 and 5 eV. The spin-forbidden transitions are concluded to be negligibly weak. The mechanism of photodissociation reaction at the energy region corresponding to the A band is examined. The nonadiabatic transition rates from the 4 1A' state to lower singlet and triplet states are estimated by Fermi's golden rule, and the transitions to the 1 1A' and 3 1A' states induced by vibronic coupling are found to be the predominant dissociation pathways. The experimentally observed energy dependence of the recoil anisotropy of the fragments is discussed based on the calculated nonadiabatic transition rates.

Journal Article↗
PubMed2004

Role of Asp102 in the catalytic relay system of serine proteases: a theoretical study.

The role of Asp102 in the catalytic relay system of serine proteases is studied theoretically by calculating the free energy profiles of the single proton-transfer reaction by the Asn102 mutant trypsin and the concerted double proton-transfer reaction (so-called the charge-relay mechanism) of the wild-type trypsin. For each reaction, the reaction free energy profile of the rate-determining step (the tetrahedral intermediate formation step) is calculated by using ab initio QM/MM electronic structure calculations combined with molecular dynamics-free energy perturbation method. In the mutant reaction, the free energy monotonically increases along the reaction path. The rate-determining step of the mutant reaction is the formation of tetrahedral intermediate complex, not the base (His57) abstraction of the proton from Ser195. In contrast to the single proton-transfer reaction of the wild-type, MD simulations of the enzyme-substrate complex show that the catalytically favorable alignment of the relay system (the hydrogen bonding network between the mutant triad, His57, Asn102, and Ser195) is rarely observed even in the presence of a substrate at the active site. In the double proton-transfer reaction, the energy barrier is observed at the proton abstraction step, which corresponds to the rate-determining step of the single proton-transfer reaction of the wild-type. Although both reaction profiles show an increase of the activation barrier by several kcals/mol, these increases have different energetic origins: a large energetic loss of the electrostatic stabilization between His57 and Asn102 in the mutant reaction, while the lack of stabilization by the protein environment in the double proton-transfer reaction. Comparing the present results with the single proton transfer of the wild-type, Asp102 is proven to play two important roles in the catalytic process. One is to stabilize the protonated His57, or ionic intermediate, formed during the acylation, and the other is to fix the configuration around the active site, which is favorable to promote the catalytic process. These two factors are closely related to each other and are indispensable for the efficient catalysis. Also the present calculations suggest the importance of the remote site interaction between His57 and Val213-Ser214 at the catalytic transition state.

Aspartic Acid↗
PubMed2003

Theoretical perspectives on the reaction mechanism of serine proteases: the reaction free energy profiles of the acylation process.

The reaction mechanism of serine proteases (trypsin), which catalyze peptide hydrolysis, is studied theoretically by ab initio QM/MM electronic structure calculations combined with Molecular Dynamics-Free Energy Perturbation calculations. We have calculated the entire reaction free energy profiles of the first reaction step of this enzyme (acylation process). The present calculations show that the rate-determining step of the acylation is the formation of the tetrahedral intermediate, and the breakdown of this intermediate has a small energy barrier. The calculated activation free energy for the acylation is approximately 17.8 kcal/mol at QM/MM MP2/(aug)-cc-pVDZ//HF/6-31(+)G/AMBER level, and this reaction is an exothermic process. MD simulations of the enzyme-substrate (ES) complex and the free enzyme in aqueous phase show that the substrate binding induces slight conformational changes around the active site, which favor the alignment of the reactive fragments (His57, Asp102, and Ser195) together in a reactive orientation. It is also shown that the proton transfer from Ser195 to His57 and the nucleophilic attack of Ser195 to the carbonyl carbon of the scissile bond of the substrate occur in a concerted manner. In this reaction, protein environment plays a crucial role to lowering the activation free energy by stabilizing the tetrahedral intermediate compared to the ES complex. The polarization energy calculations show that the enzyme active site is in a very polar environment because of the polar main chain contributions of protein. Also, the ground-state destabilization effect (steric strain) is not a major catalytic factor. The most important catalytic factor of stabilizing the tetrahedral intermediate is the electrostatic interaction between the active site and particular regions of protein: the main chain NH groups in Gly193 and Ser195 (so-called oxyanion hole region) stabilize negative charge generated on the carbonyl oxygen of the scissile bond, and the main chain carbonyl groups in Ile212 approximately Ser214 stabilize a positive charge generated on the imidazole ring of His57.

Binding Sites↗
PubMed2003

[A case of severe Chlamydia pneumoniae pneumonia requiring mechanical ventilation and complicated with disseminated intravascular coagulation].

A previously healthy 48-year-old man presented to his primary care physician with high fever, dry cough and dyspnea. Pneumonia was diagnosed and intravenous administration of imipenem/cilastatin was begun, but his respiratory condition worsened and he was admitted to our hospital with severe hypoxia. A chest radiograph showed reticular opacity and consolidation in both lung fields. The case was complicated with disseminated intravascular coagulation. Analysis of the bronchoalveolar lavage fluid showed increases in the total cell counts and an elevated percentage of lymphocytes. Sputum, blood and bronchoalveolar lavage examinations failed to reveal etiology to explain his severe respiratory illness. Treatment consisted of mechanical ventilation and administration of steroid pulse-therapy and gabexate mesilate. On the basis of his clinical course, we suspected possible atypical pneumonia, and began therapy with intravenous minocyclin and oral erythromycin administration. On the third hospital day, the arterial blood gas data improved and the bilateral pulmonary infiltration on the chest radiographs disappeared. Using paired sera, we detected increases of 1.35 in ID for anti-Chlamydia pneumoniae IgG antibodies by ELISA, and arrived at a diagnosis of Chlamydia pneumoniae pneumonia.

Acute Disease↗