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FMO-MO (Molecular orbitals (MOs) of the fragment MO (FMO) method) for (-)-epicatechin gallate were calculated to examine the dependency of the accuracy on the fragmentation patterns and on the basis set, and the results were compared to those obtained using conventional MO calculations. Results also show that the FMO-MO can be used as the initial guess in self-consistent field calculations.

DOI： 10.1246/bcsj.81.254

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We performed ab initio MO-MD simulation based on the fragment MO (FMO) method using the (-)-epicatechin Gallate in order to examine the efficiency of fragmentation pattern in comparison with conventional MO-MD. We clearly demonstrated that the FMO-MD simulation gave sufficient results concerning the trajectory of the total energy and the geometry difference.

DOI： 10.1246/bcsj.81.110

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：CHEMICAL SOC JAPAN  

Difference in the potential energy surfaces (Delta E) obtained from the fragment MO (FMO) method and conventional ab initio Hartree-Fock SCF-MO (HFMO) method was investigated using the best fragmentation pattern of (-)epicatechin gallate. In the lower energy region (< 23.06 kcal mol(-1) from the minimum), the average Delta E at each grid point was 1.1 kcal mol(-1). The FMO method is applicable to quantum MD calculation of large molecular system at around the standard temperature.

DOI： 10.1246/bcsj.80.1939

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Language：Japanese   Publisher：Society of Computer Chemistry, Japan  

We have been developing a computational tool to obtain the molecular orbitals for large molecules such as proteins and molecular clusters without excessive calculation costs. In our method, the entire Fock matrix is generated using density matrix obtained from the fragment molecular orbital method, which is applicable to large systems and suitable for parallel processing. To solve the large scale generalized eigenproblem, we use the Sakurai-Sugiura method. This method solves several liner equations which have large granularity and is well suited to master-worker type execution. It is suffic...

DOI： 10.2477/jccj.6.217

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Molecular orbital calculations of the complex between DNA-ERE (estrogen response element) and ER (estrogen receptor)-DBD (DNA-binding domain) were performed using the fragment molecular orbital (FMO) method, which enables large-scale MO (molecular orbital) calculations by reducing the computational cost and by significantly increasing efficiency for parallel computation. Such a large system, which contains 3354 atoms, is impractical via conventional MO methods due to the immense computational cost. Details of the interaction between DNA-ERE and ER-DBD were revealed in this study as follows by using the FMO calculations to analyze the interfragment interaction energies (IFIEs) and the electrostatic potentials (ESPs). An area with a high positive ESP is identified on the DNA-binding side of ER-DBD and is the main driving force behind access to the DNA. The position of the ER-DBD monomer can be fixed on a phosphate group of DNA-ERE by the strong electrostatic interactions, whereas the rotation cannot be fixed. In contrast, both the position and rotation of the ER-DBD dimer can be fixed and can therefore form the stable (ER-DBD)(2)center dot center dot center dot DNA-ERE complex. Dimerization of the ER-DBD monomers, each of which have a charge of +5 , is mainly due to large attractive interaction energies of the second Zn fragments. The base pairs in the consensus sequence of DNA-ERE interact only with the recognition helix located in the major groove due to the large shielding effect of the phosphate groups of DNA. The recognition helix has weaker interactions with the base pairs than the electrostatic interactions with the phosphate groups. Thus, the DNA-binding machinery of the ER-DBD dimer, which can secure the recognition helix in the major groove of DNA, is crucial for interactions between the recognition helix and base pairs.

DOI： 10.1021/jp071710v

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We have been developing a computational tool to obtain the molecular orbitals for large molecules such as proteins and molecular clusters without excessive calculation costs. In our method, the entire Fock matrix is generated using density matrix obtained from the fragment molecular orbital method, which is applicable to large systems and suitable for parallel processing. To solve the large scale generalized eigenproblem, we use the Sakurai-Sugiura method. This method solves several liner equations which have large granularity and is well suited to master-worker type execution. It is sufficient for parallel processing on computers of distributed memory parallel architecture. The method is favorable for calculation of only a small number of eigenvalues and corresponding eigenvectors of a large scale matrix. Our method has high parallelization efficiency and the communication cost is negligible to the total calculation costs. Thus, this is one of the right applications for using Grid technology.<BR>Elapsed times to obtain MOs close to HOMO-LUMO of Lysozyme (129 amino-acid residues and solvent molecules, total 8258 atoms) with FMO/HF/STO-3G (20758 basis functions)) and model DNA (40 A-T base pairs, total 2636 atoms with FMO/HF/STO-3G (10108 basis functions)) are less than about 5 hours and 1 hour, respectively, on only 128 Dual Opteron cluster. The position of HOMO and LUMO in the Lysozyme and water cluster case is strongly dependent on distribution and the number of solvent water molecules. Careful treatment for solvent molecules is required to have consistent results. In the case of model DNA, HOMO and LUMO are located at the center and the terminal of the DNA chain, respectively.

DOI： 10.2477/jccj.6.217

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Language：English   Publishing type：Research paper (international conference proceedings)   Publisher：SPRINGER-VERLAG BERLIN  

We consider a parallel method for solving generalized eigenvalue problems that arise from molecular orbital computations. We use a moment-based method that finds several eigenvalues and their corresponding eigenvectors in a given domain, which is suitable for master-worker type parallel programming models. The computation of eigenvalues using explicit moments is sometimes numerically unstable. We show that a Rayleigh-Ritz procedure can be used to avoid the use of explicit moments. As a test problem, we use the matrices that arise in the calculation of molecular orbitals. We report the performance of the application of the proposed method with several PC clusters connected through a hybrid MPI and GridRPC system.

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The Drug discovery on grid project is aimed at developing a platform for drug discovery, on which various calculations and simulations are effectively executed at high speed. For storing and retrieving calculated and experimental information, the drug, markup language database is an extension of the chemical markup language database with appropriate figures as indicated. Before the docking of a drug molecule with its target receptor, an extensive conformational search of the drug molecule is carried out for defining the bioactive conformation. The conformational search is carried out for a series of molecules selected from the database, where information on the two-dimensional structure of molecules is stored. Then all the low energy conformers obtained in the previous procedure are subjected to the docking analysis. There are three methods for evaluating the docking energy; the fragment molecular orbital , the replica exchange molecular dynamics , and the empirical scoring function based on the energy obtained from the force field calculation and indexes of three-dimensional complementary structure between a drug and its target protein. The chapter studies CONFLEX that has been recognized as one of the most efficient conformational space search programs. The types of CONFLEX and its application to peptide folding are studied along with flowcharts. Hence, computational techniques, such as parallel computing and grid will enable to probe the drug-receptor mediated phenomenon directly. © 2006 Elsevier B.V. All rights reserved.

DOI： 10.1016/B978-044452220-7/50076-9

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：SPRINGER-VERLAG BERLIN  

In the present paper, we propose a hybrid parallel method for large sparse eigenvalue problems in a grid computing environment. A moment-based method that finds several eigenvalues and their corresponding eigenvectors in a given domain is used. This method is suitable for master-worker type parallel programming models. In order to improve the parallel efficiency of the method, we propose a hybrid implementation using a GridRPC system Ninf-C and MPI. We examined the performance of the proposed method in an environment where several PC clusters are used.

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DOI： 10.1016/j.theochem.2005.06.040

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Language：Japanese   Publisher：The Japan Society for Industrial and Applied Mathematics  

Characters of generalized eigenvalue problem in FMO-MO method, which is one of the fastest methods to calculate molecular orbitals of large molecules such as proteins, are described in order to solve it efficiently. Fock matrix to solve looks dense, because 7.6% of elements have significant value even for a large molecule. The frontier orbital energies can be estimated from fragment and fragment-pair orbital energy distributions in FMO method, which is performed in FMO-MO calculation, and then the frontier orbitals can be obtained efficiently by the method to solve eigenvalue problem in a s...

DOI： 10.11540/jsiamt.15.2_169

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We describe brief explanation of molecular orbitals based on fragment molecular orbital method (FMO-MO), and demonstrate its efficiency showing the result of the example FMO-MO calculation for a protain. Using FMO-MO method, molecular orbital calculations for molecules containing over 1,000 atoms can be achieved in a short time because large-scale iterative procedure for entire molecule is not required in FMO-MO calculation. FMO-MO calculation for Lysozyme molecule has been finished in almost 4.5 hours using large-scale PC cluster. The generalized eigenvalue problem is 34% of total wall clo...

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In this paper we present a parallel method for finding several eigenvalues and eigenvectors of large-scale eigenvalue problems. In this method, a small matrix pencil that has only the desired eigenvalues is derived by solving large sparse linear equations constructed from matrices of the eigenvalue problem. Since these equations can be solved independently, we solve them on remote hosts in parallel. This approach is suitable for master-worker programming models. We have implemented and tested the proposed method in a grid environment using OmniRPC.

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ELSEVIER SCIENCE BV  

The bond dissociation enthalpies (BDEs) of polyhalogenated benzenes were calculated by using the G2M(CC), B3LYP/6-311G(2dfp), and B3LYP/6-311G(d,p) methods. The BDEs of C-H and C-X (X = F, Cl, and Br) calculated by these three methods well reproduced the experimental BDEs, within 1.2, 2.3, and 4.5 kcal/mol, respectively. The analysis of the basis set dependence of the BDEs showed that the BDEs calculated by the B3LYP/6-311G(d,p) method are sufficient for the quantitative discussion. An accurate and systematic set of the BDEs of polyhalogenated benzenes was thus obtained by B3LY-P/6-311G(d,p) calculations. The substitution effects on the BDEs of polyhalogenated benzenes were analyzed by using a linear scheme with and without the correction terms for steric effect. The resulting regression equation for the C-F BDEs well reproduced the calculated C-F BDEs even without the correction term for steric effect, but the regression equations for the C-Cl and C-Br BDEs needs the correction term for steric effect. (C) 2004 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.theochem.2004.05.024

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The fully optimized calculation of dibenzo-p-dioxin (DD) and 75 polychlorinated dibenzo-dioxins (PCDDs) were carried out at the B3LYP/6-311G** level. The corresponding total energy, enthalpy, entropy and free energy were calculated. In addition, the dependences of the calculated parameters on the number and the position of chlorine substitute were discussed. By designing isodemic reactions, standard formation heat and free energy were obtained, from which the order of relative stability for PCDDs was determined. Based on the comparison of the stability order with the observed percentage of PCDDs from incinerator, a predominant thermodynamic control process for formation of tetrachlorinated dibenzo-dioxins (TCDDs), pentachlorinated dibenzo-dioxins (Penta-CDDs) and hexachlorinated dibenzo-dioxins (Hexa-CDDs) in incineration was suggested. (C) 2004 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.theochem.2003.11.030

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A combination of Monte Carlo (MC) simulation and ab initio spin-orbit coupling SCF (SOC-SCF) method was used to evaluate parity-violating energy, E-pv, of L-alanine zwitterion (L-ALAZ) in aqueous solution. In the MC simulation, the effective pair potential functions, which include the effect of the polarization of L-ALAZ caused by salvation were determined and employed. The 100 solution structures were picked up at every 1 M steps of the MC simulation of the L-ALAZ aqueous solution, and the Epv energy was calculated for the L-ALA-Z-(H2O), (n = 1-10) clusters in each solution structure by the SOC-SCF/6-31G method. The mean deviation of E-pv for the L-ALAZ-(H2O)(10) clusters was large, 2 x 10(-20) hartree, and this comes from the fact the coordination of H2O at the CO2 site brings about large effect on E-pv. Although, the small change in the orientation of H2O to the CO2 group may change the sign of Epv, the expectation value of E-pv of L-ALAZ is positive for thermally stable conformations in aqueous solution at 298 K. The present MC/MO calculations have shown that the E-pv value of L-ALAZ is positive when the solvent effect is introduced by explicit H2O molecules. This is same as that observed in previous calculations with the continuum model of solvation. The present calculations provide support for the destabilization of L-ALAZ compared to D-ALAZ at thermally accessible conformations in aqueous solution. (C) 2004 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.theochem.2003.10.060

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Language：English   Publishing type：Research paper (international conference proceedings)   Publisher：NANO SCIENCE & TECHNOLOGY INST  

The fragment molecular orbital (FMO) method was applied to evaluate the interaction between estrogen response element (ERE) in DNA and DNA binding domain (DBD) of estrogen receptor (ER). In order to calculate the whole electronic state of DNA-ERE and ER-DBD, we developed the SCC-DIIS method and the field scaling method. The SCC-DIIS method is for acceleration of the self-consistent charge (SCC) convergence, and the field scaling method changes the field effect from other fragments for stable convergence. Hybridization of these two methods made it possible to calculate the whole electronic state of DNA-ERE and ER-DBD.

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Language：English   Publishing type：Research paper (international conference proceedings)   Publisher：NANO SCIENCE & TECHNOLOGY INST  

We have developed the two-dimensional particle mesh Ewald (2D-PME) algorithm for molecular dynamics (MD) simulation, and applied it to have knowledge of the behavior of DNA and its interaction on microarrays, which crucial in the design of DNA microarrays. The 2D-PME algorithm can rapidly calculate the Coulomb interaction for a 3D system with 2D periodicity, which is the most time-consuming process in the MD simulation.
The MD simulation of DNA microarrays that contain a single DNA molecule in a unit-cell was carried out under the two types of the boundary conditions, 3D systems with the 2D and 3D periodicities, in which the Coulomb interactions were calculated by using 2D-PME and 3D-PME methods, respectively. Effect of the infinite replicas in the vertical direction to the microarray surface in 3D periodic system was examined based on the results of the 3D system with 2D periodicity. Comparison of the computational efficiency and accuracy between the 2D-PME and 3D-PME methods revealed the availability of the 2D-PME method.

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Language：Chinese   Publishing type：Research paper (scientific journal)   Publisher：SCIENCE CHINA PRESS  

Molecular structures of 22 tetrachlorinated dibenzo-p-dioxins (TCDDs) were calculated by the B3LYP/6-311G** method. The structures, total energy, standard entropy, standard enthalpy and standard free energy were obtained, in which the calculated molecular configuration of 2,3,7,,8-TCDD is very close to the experimental analysis of X-ray diffraction. The results show that the total energy, the standard enthalpy and standard free energy are very well correlated with the numbers of chlorine atoms at the alpha positions and the parameters that represent the specific configurations of two chlorine atoms. The linear relation coefficient r is larger than 0.997. Based on the above result, a relative stability order of the total energy and standard free energy of all isomers was established. The total energy and the standard free energy of 1, 3, 6, 8-TCDD are the lowest compared to other isomers, so it is the most stable configuration with 1, 3, 7, 9-TCDD being the second and 1, 3, 7, 8-TCDD being the third in the stability of the configurations. Finally, the relative stability order was compared with the isomer pairs distribution produced in the fly ash emitted from municipal waste incinerators. Therefore, the most abundant isomer was predicted as the most stable isomer and the significance of thermodynamic control was suggested in the TCDD formation mechanism.

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The potential energy curve for the reaction of the ethaniminium ion (CH3CH=NH2+) and the cyanide anion (CN-) to give 2-amino-propanenitrile (APN) in aqueous solution which is the chirality-producing step of Strecker synthesis Of L-alanine was obtained by ab initio GB 6-31G** calculation including the solvent effect. The transition state was located at 2.13 Angstrom of the C-alpha-C(=-N) distance. The barrier height for this reaction was 16.6 kcal/mol and the reaction is expected to occur easily in aqueous solution. The parity-violating interaction energy (E-pv) was calculated by using the spin-orbit-coupling SCF wavefunction and the [5s2p1d/3s1p] basis set. The E-pv value of the association state of the two ions is zero, while the reaction product L-APN has the positive value of +0.17 X 10(-20) hartree. E-pv was positive for all reaction stages including the transition state, suggesting that the formation Of L-APN is not more favorable than D-APN in the Strecker synthesis of alanine due to the parity-violating weak neutral current interaction. (C) 2002 Elsevier Science B.V. All rights reserved.

DOI： 10.1016/S0166-1280(02)00023-4

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Parity-violating interaction energy (E-pv) of D-glyceraldehyde was calculated by using the spin-orbit coupling SCF wave-function and the 5s2p basis set. The E-pv value was negative for most of the low-energy conformations of D-glyceraldehyde, suggesting that D-glyceraldehyde is more stable than L-glyceraldehyde due to the parity-violating weak neutral current interaction. (C) 2002 Elsevier Science B.V. All rights reserved.

DOI： 10.1016/S0166-1280(01)00725-4

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

The reaction space map (RESMAP) representation is proposed for the comprehensive description of the chlorination and dechlorination reactions of polychlorobenzenes. By using the B3LYP/6-311G** energies and by assuming the chemical reactions which govern the chlorination and dechlorination processes of polychlorobenzenes, the relative energies of polychlorobenzenes and polychlorophenyl radicals were defined artificially. They were collected as the RESMAP which has the relative energies of polychlorobenzenes at the diagonal parts and the polychlorophenyl radicals connecting two polychlorobenzenes at the off-diagonal parts. The RESMAPs created for three models for the chlorination/dechlorination processes provided a general view of the thermodynamically controlled isomer distributions and chlorination/dechlorination reaction patterns for benzene and (poly)chlorinated benzenes.

DOI： 10.1021/ci0103119

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ELSEVIER SCIENCE BV  

Ab initio GB calculation that includes solvent effects by the generalized Born formula (GB) was applied to methyl yellow (4-dimethylaminophenylazobenzene, MY) and methyl orange (4-[4'-dimethylaminophenylazo]-benzenesulfonate, MO) and their protonated species, and the acid-catalyzed cis-trans isomerization of MY and MO was analyzed. The HF/3-21G((*))/GB calculations determined the structures and relative energies of MY and MO, their ammonium and azonium ions, and the transitions state for the cis-trans isomerization of the azonium ions in aqueous solution. The calculations indicated that (i) the energy difference between the cis and trans forms of the azonium ion is much smaller than those of the ammonium ion and the unprotonated species, (ii) the cis-azonium ion is much more stable than the cis-ammonium ion, and (iii) the cis-trans isomerization occurs easily in the azonium ion which is produced by the protonation of the azo compound or by the acid-catalyzed proton transfer from the cis-ammonium ion. (C) 2001 Elsevier Science B.V. All rights reserved.

DOI： 10.1016/S0166-1280(00)00855-1

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

A new nonempirical method of determining the effective pair potential functions which are suitable for the molecular simulation of heterolysis reactions has been proposed. The self-energy correction due to the polarization in solution was estimated by the ab initio GB calculation which includes the solvent effect by the continuum model using the generalized Born formula, and the polarization caused by solvation was incorporated in the effective pair potential functions. The method was applied to the ionic Fragmentation reaction of t-BuCl in aqueous solution. The effective pair potential functions between t-BuCl and water were determined at 12 different C-Cl distances, and expressed by analytical functions which cover the whole reaction stage, from the covalent bonding region to the dissociated free ions. The Monte Carlo simulation and statistical perturbation theory using the effective pair potential functions determined the free energy profile of the reaction with a reasonable dissociation energy.

DOI： 10.1021/jp9935790

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ELSEVIER SCIENCE BV  

Ab initio MO GB theory which includes the continuum model of solvent effect using generalized Born formula has been applied to the dimerization reaction of HCN in aqueous solution which is the starting step in prebiotic synthesis of purine precursors from aqueous hydrogen cyanide. Three steps considered were: (i) the reaction of HCN and H2O to produce the CN- anion, (ii) the reaction of CN- with HCN to give the NC-CH=N- anion, and (iii) the addition of a proton to the anion to give iminoacetonitrile. The formation of CN- ion from HCN in aqueous solution requires 15.1 kcal/mol (the experimental value estimated from the dissociation constant of HCN in water is 14.8 kcal/mol). The reaction of CN- with HCN requires the activation energy of 32.2 kcal/mol (MP2/6-31 ++ G**//HF/6-31 ++ G**) to give the dimer. This barrier height is reduced to 26.1 kcal/mol when HCN is associated with H3O+. In the presence of NH3 in aqueous solution, CN- is produced easily by the reaction of HCN and NH3 with a low activation energy of 4.3 kcal/mol. It was shown that the formation of CN- becomes easier in ammoniacal solution, and the dimerization occurs efficiently in aqueous solutions which contain NH3. (C) 2000 Elsevier Science B.V. All rights reserved.

DOI： 10.1016/S0166-1280(99)00356-5

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A Monte Carlo simulation with the statistical perturbation method has been employed to determine the relative stabilities among four representative conformations of the glycine zwitterion (GLYZ) in aqueous solution. The (phi,theta)=(0,0) and (60,0) conformations, in which the dihedral angle theta between the NCC and CCO planes is 0 degrees, were found to be more stable than the (0,90) and (60,90) conformations, in which theta=90 degrees. The relative stabilities of these four conformations are well elucidated on the basis of solvent-solute interactions using two-dimensional radial distribution functions. Ab initio MO/GB calculations including the solvent effect via the generalized Born formula gave similar results for the relative stabilities of the four conformations in solution. (C) 1997 Elsevier Science B.V.

DOI： 10.1016/S0166-1280(96)04942-1

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：JOHN WILEY & SONS LTD  

The conformation of the L-alanine zwitterion (ALAZ) in aqueous solution was examined by an ab initio MO method including the solvent effect with the generalized Born (GB) equation, The geometry optimization with the 6-31++G* bests set gave the (phi, theta)=(80, 8) conformation as the most stable conformation of ALAZ in aqueous solution, where phi is the HNC*C torsional angle and theta is the NC*CO torsional angle. Stabilization by the solvent is larger in the theta=90 degrees conformation than in the theta=0 degrees conformation However, the differential salvation is small and the conformation with a nearly planar NC*CO skeleton is the most stable conformation in aqueous solution. The barrier to rotation of the CO2 group (theta rotation) was calculated to be 6.7 (6-31++G*) and 5.9 (MP2/6-31++G*) kcal mol(-1), while that to rotation of the NH3 group (phi rotation) was very small (&lt;1 kcal mol(-1)). The relative free energy of solvation and relative stability among the representative conformations of ALAZ were calculated by Monte Carlo (MC) simulation with the statistical perturbation method. The energy variation along the theta rotation indicated that the value of theta = 5-10 degrees Is favorable far ALAZ in aqueous solution. The MC simulation supports the ab initio GB results for the conformational properties of ALAZ In aqueous solution. (C) 1997 by John Wiley & Sons, Ltd.

DOI： 10.1002/(SICI)1099-1395(199703)10:3<145::AID-POC885>3.0.CO;2-B

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Language：Japanese   Publisher：出版者：日本コンピュータ化学会,Society of Computer Chemistry, Japan  

In order to execute molecular dynamics (MD) simulation for the holding process and native structure of proteins efficiently, Hamiltonian algorithm (HA) was equipped to an MD program: PEACH. The difference between the conventional method and HA is evaluated using Leu-Enkephalin and Met-Enkephalin. HA was efficient for sampling a wide area of geometrical space because many low energy conformations were observed along trajectories of HA.

DOI： 10.2477/jccj.6.275

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Language：Japanese   Publisher：公益社団法人 日本化学会・情報化学部会  

DOI： 10.11546/cicsj.25.40

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タンパク質の折れ畳み過程や構造をシミュレーションする手法である分子動力学法をより効率よく行うために生体分子の分子動力学シミュレーションプログラム：PEACH に高次元アルゴリズム（HA:Hamiltonian Algorithm）を組み込み、従来の分子動力学法との差異を比較検討した。Leu-Enkephalin とMet-Enkephalin の二種類のタンパク質を計算対象とした。HA を用いると従来法のエネルギー分布よりも低いエネルギー値を多く取ることが観測され、探索空間が広がっている事が判った。Copyrightは日本コンピュータ化学会。出版社版は学会より入手。

DOI： 10.2477/jccj.6.275

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The fragment molecular orbital (FMO) method is one of the approximated molecular orbital (MO) method developed by Kitaura et al. In the FMO method, a target molecule is divided into small fragments and MO calculations are performed for each fragment and fragment pair to obtain the total energy and one-electron properties of entire molecule. Therefore the FMO method makes it possible to calculate the electronic structure for large molecules such as proteins, enzymes and DNA. In this study, we inspects applicability of FMO method to ab initio Molecular Dynamics (MD) method by verifying the accuracy of Potential Energy Surface(PES) of a catechine molecule between FMO method and conventional method. The accuracy of PES is 1.1kcal/mol within the range of 1eV from the energy minimum. Therefore we think that FMO method is applicable to ab initio MD.

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Language：English   Publishing type：Research paper, summary (international conference)   Publisher：AMER CHEMICAL SOC  

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Language：Japanese   Publisher：京都大学  

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.46.S108_1

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Language：Japanese   Publisher：The Japan Society of Mechanical Engineers  

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Language：Japanese   Publisher：一般社団法人日本機械学会  

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Language：Japanese   Publisher：Information Processing Society of Japan (IPSJ)  

In this paper we present a parallel method for finding several eigenvalues and eigenvectors of large-scale eigenvalue problems. In this method, a small matrix pencil that has only the desired eigenvalues is derived by solving large sparse linear equations constructed from matrices of the eigenvalue problem. Since these equations can be solved independently, we solve them on remote hosts in parallel. This approach is suitable for master-worker programming models. We have implemented and tested the proposed method in a grid environment using OmniRPC.

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Other Link： http://id.nii.ac.jp/1001/00018410/

Language：Japanese   Publisher：Information Processing Society of Japan (IPSJ)  

We describe brief explanation of molecular orbitals based on fragment molecular orbital method (FMO-MO), and demonstrate its efficiency showing the result of the example FMO-MO calculation for a protain. Using FMO-MO method, molecular orbital calculations for molecules containing over 1,000 atoms can be achieved in a short time because large-scale iterative procedure for entire molecule is not required in FMO-MO calculation. FMO-MO calculation for Lysozyme molecule has been finished in almost 4.5 hours using large-scale PC cluster. The generalized eigenvalue problem is 34% of total wall clock time in our calculation and needs significant computational time for large-scale molecular orbital calculation with FMO-MO.

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Other Link： http://id.nii.ac.jp/1001/00018405/

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Language：English   Publishing type：Research paper, summary (international conference)   Publisher：AMER CHEMICAL SOC  

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Language：English   Publishing type：Research paper, summary (international conference)   Publisher：AMER CHEMICAL SOC  

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Language：English   Publisher：日本生物物理学会  

DOI： 10.2142/biophys.44.S129_4

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Language：English   Publisher：NANO SCIENCE & TECHNOLOGY INST  

The fragment molecular orbital (FMO) method was applied to evaluate the interaction between estrogen response element (ERE) in DNA and DNA binding domain (DBD) of estrogen receptor (ER). In order to calculate the whole electronic state of DNA-ERE and ER-DBD, we developed the SCC-DIIS method and the field scaling method. The SCC-DIIS method is for acceleration of the self-consistent charge (SCC) convergence, and the field scaling method changes the field effect from other fragments for stable convergence. Hybridization of these two methods made it possible to calculate the whole electronic state of DNA-ERE and ER-DBD.

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Language：English   Publisher：Society of Computer Chemistry, Japan  

HF/6-311G&lt;SUP&gt;**&lt;/SUP&gt; and B3LYP/6-311G&lt;SUP&gt;**&lt;/SUP&gt; calculations of tetrachlorodibenzo-&lt;I&gt;p&lt;/I&gt;-dioxins (TCDDs) predicted that the lowest-energy isomer is not the most toxic 2, 3, 7, 8-TCDD isomer but l, 3, 6, 8-TCDD. This is contrary to the AM1 and PM3 predictions which are used for the elucidation of the isomer distribution of the TCDD homologue in combustion-derived samples.

DOI： 10.14827/jccj1999.13.251

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