Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/acs.jpcb.3c05564

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Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1039/D4CC01030B

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Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：Wiley  

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Authorship：Last author,　Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：IOP Publishing  

Abstract

We have developed a reverse mapping system to convert mesoscale structures generated by dissipative particle dynamics (DPD) simulations into nanoscale structures. This system is called DSRMS (DPD-based Structure Reverse Mapping System) and is controlled by Python3 scripts using OCTA's COGNAC program for DPD and molecular dynamics (MD). The restored structures can be subjected to fragment molecular orbital (FMO) calculations using the ABINIT-MP program for detailed nanoscale interaction analysis. Polyelectrolyte and lipid membranes have been used as illustrative example.

DOI： 10.35848/1347-4065/ad0601

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Other Link： https://iopscience.iop.org/article/10.35848/1347-4065/ad0601/pdf

Language：English   Publishing type：Research paper (scientific journal)   Publisher：IOP Publishing  

Abstract

Despite rapid progress in the development of quantum algorithms in quantum computing as well as numerical simulation methods in classical computing for atomic and molecular applications, no systematic and comprehensive electronic structure study of atomic systems that covers almost all of the elements in the periodic table using a single quantum algorithm has been reported. In this work, we address this gap by implementing the recently-proposed quantum algorithm, the Bayesian Phase Difference Estimation (BPDE) approach, to determine fine structure splittings of a wide range of boron-like atomic systems. Since accurate estimate of fine structure splittings strongly depend on the relativistic as well as quantum many-body effects, our study can test the potential of the BPDE approach to produce results close to the experimental values. Our numerical simulations reveal that the BPDE algorithm, in the Dirac–Coulomb–Breit framework, can predict fine structure splittings of ground states of the considered systems quite precisely. We performed our simulations of relativistic and electron correlation effects on Graphics Processing Unit by utilizing NVIDIA’s cuQuantum, and observe a ×42.7 speedup as compared to the Central Processing Unit-only simulations in an 18-qubit active space.

DOI： 10.1088/2516-1075/acf909

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Other Link： https://iopscience.iop.org/article/10.1088/2516-1075/acf909/pdf

Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：IOP Publishing  

Abstract

Peptoids are biomimetic materials in which the substituent groups are located on the nitrogen atom of the peptide bond, facilitating the formation of nanosheet structures as reported by Mannige et al. (Nature, 526 (2015) 415). Dissipative particle dynamics (DPD) simulations were performed to investigate the aggregation stability of peptoids with different unit lengths. The crucial effective interaction parameters were determined by fragment molecular orbital (FMO) calculations, which allowed to evaluate different molecular interactions (electrostatic and dispersion) in a balanced way. The experimental observation of the unit length dependence was finally reproduced by this FMO-DPD method.

DOI： 10.35848/1347-4065/acf356

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Other Link： https://iopscience.iop.org/article/10.35848/1347-4065/acf356/pdf

Authorship：Last author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：IOP Publishing  

Abstract

We have attempted to use machine learning to streamline the calculation of non-empirical 
parameters for use in dissipative particle dynamics (DPD) simulations. We replaced the 
calculation of molecular interaction energies by the non-empirical molecular orbital method, 
which requires a lot of computational resources, with predictions by machine learning. We 
developed two methods for prediction replacement, which are a 1-step method and a 2-step 
method. The prediction accuracy of the results obtained with these methods was investigated. 
A reduction of about half of the computational cost was expected.

DOI： 10.35848/1347-4065/ace575

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Other Link： https://iopscience.iop.org/article/10.35848/1347-4065/ace575/pdf

Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/acs.cgd.3c00302

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ACS  

DOI： 10.1021/acs.jchemed.2c00837

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Authorship：Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：Society of Computer Chemistry Japan  

DOI： 10.2477/jccjie.2022-0036

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Authorship：Last author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：RSC  

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Other Link： https://chemrxiv.org/engage/chemrxiv/article-details/60d448e8926ad00c6e02e5c3

Language：English   Publishing type：Research paper (scientific journal)  

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Authorship：Last author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/acs.jpclett.1c02788

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Authorship：Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.35848/1347-4065/ac1857.

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Other Link： https://doi.org/10.26434/chemrxiv.14318459.v1

Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society ({ACS})  

DOI： 10.26434/chemrxiv-2021-w7n78

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Authorship：Last author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

By the splendid advance in computation power realized with Fugaku supercomputer, it has become
possible to perform ab initio fragment molecular orbital (FMO) calculations for thousands of
dynamical structures of a protein-ligand complex in a parallelized way. We have thus carried out the
electron-correlated FMO calculations for a complex of the 3C-like (3CL) main protease (Mpro) of the
new coronavirus (SARS-CoV-2) and its inhibitor N3 incorporating the structural fluctuations sampled
by classical molecular dynamics (MD) simulation in hydrated condition. Along with a statistical
evaluation of inter-fragment interaction energies (IFIEs) between the N3 ligand and surrounding
amino-acid residues for a thousand of dynamical structure samples, we have applied in this study a
novel approach based on the principal component analysis (PCA) and the singular value
decomposition (SVD) to the analysis of IFIE data in order to extract the dynamically cooperative
interactions between the ligand and residues. We have found that the relative importance of each
residue is modified via the structural fluctuations and that the ligand is bound in the pharmacophore
in a dynamical manner through collective interactions formed by multiple residues, thus providing a
new insight into structure-based drug discovery

DOI： 10.1021/acs.jpcb.1c03043

DOI： 10.26434/chemrxiv.13775182.v1

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Physical Society of Japan  

DOI： 10.7566/JPSJ.90.064301

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Language：Japanese   Publisher：(公社)日本薬学会  

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Authorship：Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：RSC  

At the stage of SARS-CoV-2 infection in human cells, the spike protein consisting of three chains, A, B, and C, with a total of 3300 residues plays a key role, and thus its structural properties and the binding nature of receptor proteins to host human cells or neutralizing antibodies has attracted considerable interest. Here, we report on interaction analyses of the spike protein in both closed (PDB-ID: 6VXX) and open (6VYB) structures, based on large-scale fragment molecular orbital (FMO) calculations at the level of up to the fourth-order Møller–Plesset perturbation with singles, doubles, and quadruples (MP4(SDQ)). Inter-chain interaction energies were evaluated for both structures, and a mutual comparison indicated considerable losses of stabilization energies in the open structure, especially in the receptor binding domain (RBD) of chain-B. The role of charged residues in inter-chain interactions was illuminated as well. By two separate calculations for the RBD complexes with angiotensin-converting enzyme 2 (ACE2) (6M0J) and B38 Fab antibody (7BZ5), it was found that the binding with ACE2 or antibody partially compensated for this stabilization loss of RBD.

DOI： 10.1039/D0RA09555A

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Other Link： https://chemrxiv.org/articles/preprint/Interaction_Analyses_on_SARS-CoV-2_Spike_Protein_Based_on_Large-Scale_Correlated_Fragment_Molecular_Orbital_Calculations/12941606

Authorship：Corresponding author   Language：English  

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Authorship：Last author  

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Authorship：Last author  

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Authorship：Lead author,　Corresponding author   Publishing type：Part of collection (book)   Publisher：Springer Singapore  

DOI： 10.1007/978-981-15-9235-5_4

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：The Chemical Society of Japan  

DOI： 10.1246/bcsj.20200227

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Authorship：Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

The worldwide spread of COVID-19 (new coronavirus found in 2019) is an emergent issue to be tackled. In fact, a great amount of works in various fields have been made in a rather short period. Here, we report a fragment molecular orbital (FMO) based interaction analysis on a complex between the SARS-CoV-2 main protease (Mpro) and its peptide-like inhibitor N3 (PDB ID: 6LU7). The target inhibitor molecule was segmented into five fragments in order to capture site specific interactions with amino acid residues of the protease. The interaction energies were decomposed into several contributions, and then the characteristics of hydrogen bonding and dispersion stabilization were made clear. Furthermore, the hydration effect was incorporated by the Poisson-Boltzmann (PB) scheme. From the present FMO study, His41, His163, His164, and Glu166 were found to be the most important amino acid residues of Mpro in interacting with the inhibitor, mainly due to hydrogen bonding. A guideline for optimizations of the inhibitor molecule was suggested as well based on the FMO analysis.

DOI： 10.1021/acs.jcim.0c00283

PubMed

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY-V C H VERLAG GMBH  

RNA-based therapeutics is a promising approach for curing intractable diseases by manipulating various cellular functions. For eliciting RNA (i.e., mRNA and siRNA) functions successfully, the RNA in the extracellular space must be protected and it must be delivered to the cytoplasm. In this study, the development of a self-degradable lipid-like material that functions to accelerate the collapse of lipid nanoparticles (LNPs) and the release of RNA into cytoplasm is reported. The self-degradability is based on a unique reaction "Hydrolysis accelerated by intra-Particle Enrichment of Reactant (HyPER)." In this reaction, a disulfide bond and a phenyl ester are essential structural components: concentrated hydrophobic thiols that are produced by the cleavage of the disulfide bonds in the LNPs drive an intraparticle nucleophilic attack to the phenyl ester linker, which results in further degradation. An oleic acid-scaffold lipid-like material that mounts all of these units (ssPalmO-Phe) shows superior transfection efficiency to nondegradable or conventional materials. The insertion of the aromatic ring is unexpectedly revealed to contribute to the enhancement of endosomal escape. Since the intracellular trafficking is a sequential process that includes cellular uptake, endosomal escape, the release of mRNA, and translation, the improvement in each process synergistically enhances the gene expression.

DOI： 10.1002/adfm.201910575

Scopus

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Language：Japanese   Publisher：(公社)日本薬学会  

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Authorship：Last author   Language：English   Publishing type：Research paper (scientific journal)  

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Language：English  

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Authorship：Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：Society of Computer Chemistry Japan  

DOI： 10.2477/jccj.2019-0030

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Authorship：Corresponding author   Publisher：Japan Society of Applied Physics  

DOI： 10.7567/1882-0786/ab5e0a

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Publishing type：Research paper (scientific journal)   Publisher：IOP Publishing  

DOI： 10.7567/1347-4065/ab5335

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Other Link： http://iopscience.iop.org/article/10.7567/1347-4065/ab5335/pdf

Authorship：Lead author   Language：English  

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Language：English   Publishing type：Research paper (scientific journal)  

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Language：Japanese   Publisher：日本DDS学会  

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Language：Japanese   Publisher：(公社)日本薬学会  

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Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society ({ACS})  

DOI： 10.1021/acs.jpcb.8b09326

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Publisher：Royal Society of Chemistry ({RSC})  

DOI： 10.1039/C8CC09329F

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Language：Japanese  

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Language：Japanese   Publishing type：Research paper (scientific journal)   Publisher：Division of Chemical Information and Computer Sciences  

DOI： 10.2751/jcac.20.1

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society ({ACS})  

In modern praxis, a knowledge-driven design of pharmaceutical compounds relies heavily on protein structure data. Nonetheless, quantification of the interaction between protein and ligand is of great importance in the theoretical evaluation of the ability of a pharmaceutical compound to comply with certain expectations. The FMO (fragment molecular orbital) method is handy in this regard. However, the physical complexity and the number of the interactions within a protein-ligand complex renders analysis of the results somewhat complicated. This situation prompted us to develop the 3D-visualization of interaction energies in protein (3D-VIEP) method; the toolkit AnalysisFMO, which should enable a more efficient and convenient workflow with FMO data generated by quantum-chemical packages such as GAMESS, PAICS, and ABINIT-MP. AnalysisFMO consists of two separate units, RbAnalysisFMO, and the PyMOL plugins. The former can extract interfragment interaction energies (IFIEs) or pair interaction energies (PIEs) from the FMO output files generated by the aforementioned quantum-chemical packages. The PyMOL plugins enable visualization of IFIEs or PIEs in the protein structure in PyMOL. We demonstrate the use of this tool on a lectin protein from Burkholderia cenocepacia in which FMO analysis revealed the existence of a new interaction between G1y84 and fucose. Moreover, we found that second-shell interactions are crucial in forming the sugar binding site. In the case of bilirubin oxidase from Myrothecium verrucaria (MvBO), we predict that interactions between Asp105 and three His residues (His401, His403, and His136) are essential for optimally positioning the His residues to coordinate Cu atoms to form one Type 2 and two Type 3 Cu ions.

DOI： 10.1021/acs.jcim.8b00649

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Language：Japanese  

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Publishing type：Research paper (scientific journal)   Publisher：The Chemical Society of Japan  

DOI： 10.1246/bcsj.20180150

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Authorship：Last author   Publishing type：Research paper (scientific journal)   Publisher：Chem-Bio Informatics Society  

DOI： 10.1273/cbij.18.119

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Authorship：Corresponding author   Publisher：Royal Society of Chemistry  

DOI： 10.1039/C8RA07428C

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DOI： 10.1002/jcc.25368

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Language：Japanese  

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Authorship：Corresponding author  

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Other Link： http://orcid.org/0000-0002-7310-5183

Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society ({ACS})  

DOI： 10.1021/acs.jpcb.8b01172

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society  

We developed the fragment-based method for calculating nonlocal excitations in large molecular systems. This method is based on the multilayer fragment molecular orbital method and the configuration interaction single (CIS) wave function using localized molecular orbitals. The excited-state wave function for the whole system is described as a superposition of configuration state functions (CSFs) for intrafragment excitations and for interfragment charge-transfer excitations. The formulation and calculations of singlet excited-state Hamiltonian matrix elements in the fragment CSFs are presented in detail. The efficient approximation schemes for calculating the matrix elements are also presented. The computational efficiency and the accuracy were evaluated using the molecular dimers and molecular aggregates. We confirmed that absolute errors of 50 meV (relative to the conventional calculations) are achievable for the molecular systems in their equilibrium geometries. The perturbative electron correlation correction to the CIS excitation energies is also demonstrated. The present theory can compute a large number of excited states in large molecular systems
in addition, it allows for the systematic derivation of a model exciton Hamiltonian. These features are useful for studying excited-state dynamics in condensed molecular systems based on the ab initio electronic structure theory.

DOI： 10.1021/acs.jpca.8b00446

Scopus

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Publisher：SOC COMPUTER CHEMISTRY, JAPAN 2-1-13 HIGASHIUENO, TAITO-KU, TOWA HIGH TOWN UENO 607, TOKYO, 110-0015, JAPAN  

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Publisher：SOC COMPUTER CHEMISTRY, JAPAN 2-1-13 HIGASHIUENO, TAITO-KU, TOWA HIGH TOWN UENO 607, TOKYO, 110-0015, JAPAN  

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society  

In the analyses of miscibility behaviors of macromolecules and polymers, dissipative particle dynamics (DPD) simulations are generally performed. In these simulations, the so-called χ parameters describing the effective interactions among particles are crucial. It has been known that such parameters can be obtained within the classical or empirical force field frameworks. However, there is a potential problem that charge transfer and polarization occasionally occur. Additionally, satisfactory reference parameters are not available for some cases. Therefore, we developed a new procedure to evaluate the set of parameters by using the ab initio fragment molecular orbital (FMO) method which can provide the set of interaction energies among segments as polymer units. Moreover, we evaluated the anisotropy of molecules by using the FMO-based effective interaction parameters for three standard binary mixture systems (hexane-nitrobenzene, polyisobutylene-diisobutyl ketone, and polyisoprene-polystyrene). The calculated values showed good agreement with the experimental values with about 10% errors.

DOI： 10.1021/acs.jpcb.7b08461

Scopus

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Other Link： http://orcid.org/0000-0002-7310-5183

Language：Japanese  

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Authorship：Corresponding author   Language：Japanese  

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Language：Japanese  

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Authorship：Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：Chem-Bio Informatics Society  

We have applied Google’s TensorFlow deep learning toolkit to recognize the visualized results of the fragment molecular orbital (FMO) calculations. Typical protein structures of α-helix and β-sheet provide some characteristic patterns in the two-dimensional map of inter-fragment interaction energy termed as IFIE-map (Kurisaki et al., Biophys. Chem. 130 (2007) 1). A thousand of IFIE-map images with labels depending on the existences of α-helix and β-sheet were prepared by employing 18 proteins and 3 non-protein systems and were subjected to training by TensorFlow. Finally, TensorFlow was fed with new data to test its ability to recognize the structural patterns. We found that the characteristic structures in test IFIE-map images were judged successfully. Thus the ability of pattern recognition of IFIE-map by TensorFlow was proven.

DOI： 10.1273/cbij.18.58

Scopus

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DOI： 10.2477/jccj.2018-0020

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Other Link： http://orcid.org/0000-0002-4510-5717

Language：Chinese   Publishing type：Research paper (scientific journal)   Publisher：SOC COMPUTER CHEMISTRY, JAPAN  

In order to perform efficient nanoparticle design in drug delivery systems, prediction of physical properties and elucidation of the molecular mechanism are expected by using molecular simulation. In this study, we investigated the molecular mechanism of lipid bilayer formation and mixed lipid vesicle formation using the dissipative particle dynamics (DPD) method and small angle X-ray scattering measurement. Parameters of inter-molecular interaction used for the DPD simulation were estimated in quantum mechanical level by the fragment molecular orbital method (FMO-DPD method). In lipid bilayer formation, it was found that the phospholipid having an unsaturated bond (DOPC) has higher membrane fluidity than the phospholipid (DPPC) having only saturated bonds. In the vesicle formation mixed with phospholipid and positively charged lipid, it was also found that as the proportion of positively charged lipid increases, the fluidity of the membrane increases and the shape changes from a sphere to a flat sphere.

DOI： 10.2477/jccj.2018-0012

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

In dissipative particle dynamics (DPD) simulations, it is necessary to use the so-called chi parameter set that express the effective interactions between particles. Recently, we have developed a new scheme to evaluate the chi parameters in a non-empirical way through a series of fragment molecular orbital (FMO) calculations. As a challenging test, we have performed the DPD simulations using the FMO-based chi parameters for a mixture of 1-Palmitoyl-2-oleoyl phosphatidyl choline (POPC) and water. The structures of both membrane and vesicle were formed successfully. The calculated structural parameters of membrane were in good agreement with experimental results. (C) 2017 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2017.07.032

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Language：Japanese   Publisher：SOC COMPUTER CHEMISTRY, JAPAN 2-1-13 HIGASHIUENO, TAITO-KU, TOWA HIGH TOWN UENO 607, TOKYO, 110-0015, JAPAN  

<p>Peptoids are of peptide mimetics whose side chains are located not on α-carbon atoms but on nitrogen atoms. Recently, a new class macrocyclic peptoid containing phenyl rings in the main chain has been developed, and an interesting ability of cation capturing was shown. In this paper, theoretical calculations are performed on the capturing of twin cations with phenyl rings of this new peptoid moiety. The importance of π-electron donation toward cations was then revealed.</p>

DOI： 10.2477/jccj.2017-0014

CiNii Article

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Language：Japanese   Publisher：SOC COMPUTER CHEMISTRY, JAPAN 2-1-13 HIGASHIUENO, TAITO-KU, TOWA HIGH TOWN UENO 607, TOKYO, 110-0015, JAPAN  

<p>Dissipative particle dynamics (DPD) simulation is used for research in a wide range of science fields such as biological membranes. Conventionally, in such DPD simulations, both bulk water and interfacial water were treated by the same properties. However, such an approach could not well reproduce several properties of the target system, because some experimental and theoretical researches show the properties of water molecules near interfaces are considerably different from those of bulk water molecules. Therefore, in order to solve such a problem, we propose a new approach for interfacial water. We apply this approach to the DPD simulation of lipid membrane - silica - water system. As result, we could model the adsorption of lipid membrane on silica surface.</p>

DOI： 10.2477/jccj.2017-0003

CiNii Article

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Authorship：Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：Elsevier {BV}  

DOI： 10.1016/j.comptc.2016.12.008

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Authorship：Lead author,　Corresponding author   Language：Japanese   Publishing type：Research paper (scientific journal)   Publisher：Society of Computer Chemistry Japan  

DOI： 10.2477/jccj.2017-0051

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Language：Japanese   Publishing type：Research paper (scientific journal)   Publisher：Division of Chemical Information and Computer Sciences  

DOI： 10.2751/jcac.18.143

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Language：Japanese   Publisher：Society of Computer Chemistry, Japan  

<p>Peptoids are of peptide mimetics whose side chains are located not on α-carbon atoms but on nitrogen atoms. Recently, a new class macrocyclic peptoid containing phenyl rings in the main chain has been developed, and an interesting ability of cation capturing was shown. In this paper, theoretical calculations are performed on the capturing of twin cations with phenyl rings of this new peptoid moiety. The importance of π-electron donation toward cations was then revealed.</p>

DOI： 10.2477/jccj.2017-0014

CiNii Article

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Language：Japanese  

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Language：Japanese   Publisher：Society of Computer Chemistry, Japan  

<p>Dissipative particle dynamics (DPD) simulation is used for research in a wide range of science fields such as biological membranes. Conventionally, in such DPD simulations, both bulk water and interfacial water were treated by the same properties. However, such an approach could not well reproduce several properties of the target system, because some experimental and theoretical researches show the properties of water molecules near interfaces are considerably different from those of bulk water molecules. Therefore, in order to solve such a problem, we propose a new approach for interfacial water. We apply this approach to the DPD simulation of lipid membrane - silica - water system. As result, we could model the adsorption of lipid membrane on silica surface.</p>

DOI： 10.2477/jccj.2017-0003

CiNii Article

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Publishing type：Research paper (scientific journal)   Publisher：Chem-Bio Informatics Society  

DOI： 10.1273/cbij.17.72

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Publishing type：Research paper (scientific journal)   Publisher：Society of Computer Chemistry Japan  

DOI： 10.2477/jccj.2016-0047

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Language：Japanese   Publisher：Society of Computer Chemistry, Japan  

<p>The so-called oxocarbons, with cyclic polymer form of CO unit as (CO)_n, have attracted considerable interest for many years. However, pseudo-oxocarbons of chalcogen substitutions, (CCh)_n(Ch=S, Se, Te) have not yet been investigated by theoretical calculations in a systematic way. In this contribution, we report the DFT-based evaluations of molecular structures and NICS values for (CCh)₅ and (CCh)₆. It is shown that the planarity of molecules is enhanced for heavier chalcogens. Additionally, the NICS evaluation indicates that (CTe)₆ has an aromaticity comparable to that of benzene as a reference.</p>

DOI： 10.2477/jccj.2016-0042

CiNii Article

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DOI： 10.2477/jccj.2016-0034

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Language：Japanese   Publisher：Society of Computer Chemistry, Japan  

<p>Peptoids are a class of peptide mimetics whose side chains contain nitrogen atoms rather than α-carbon atoms. This structural feature restricts the intrinsic capacity to form hydrogen bond networks of α-helix, therefore peptoid oligomers are attracting attention due to the ability to design chemical properties such as self-assembling by selecting proper side chains. This paper shows some illustrative peptoid calculations, based on the fragment molecular orbital (FMO) method.</p>

DOI： 10.2477/jccj.2016-0032

CiNii Article

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Publishing type：Research paper (scientific journal)   Publisher：Elsevier {BV}  

DOI： 10.1016/j.jmgm.2016.08.004

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Language：Japanese   Publishing type：Research paper (scientific journal)   Publisher：Society of Computer Chemistry Japan  

DOI： 10.2477/jccj.2016-0047

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Language：Japanese   Publisher：Society of Computer Chemistry, Japan  

<p>The so-called oxocarbons, with cyclic polymer form of CO unit as (CO)_n, have attracted considerable interest for many years. However, pseudo-oxocarbons of chalcogen substitutions, (CCh)_n(Ch=S, Se, Te) have not yet been investigated by theoretical calculations in a systematic way. In this contribution, we report the DFT-based evaluations of molecular structures and NICS values for (CCh)₅ and (CCh)₆. It is shown that the planarity of molecules is enhanced for heavier chalcogens. Additionally, the NICS evaluation indicates that (CTe)₆ has an aromaticity comparable to that of benzene as a reference.</p>

DOI： 10.2477/jccj.2016-0042

CiNii Article

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Language：Japanese  

DOI： 10.2477/jccj.2016-0034

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Language：Japanese   Publisher：Society of Computer Chemistry, Japan  

<p>Peptoids are a class of peptide mimetics whose side chains contain nitrogen atoms rather than α-carbon atoms. This structural feature restricts the intrinsic capacity to form hydrogen bond networks of α-helix, therefore peptoid oligomers are attracting attention due to the ability to design chemical properties such as self-assembling by selecting proper side chains. This paper shows some illustrative peptoid calculations, based on the fragment molecular orbital (FMO) method.</p>

DOI： 10.2477/jccj.2016-0032

CiNii Article

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DOI： 10.2477/jccj.2015-0033

J-GLOBAL

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

Platinum complexes with 1,4,7-triazacyclononane (tacn) as facial ligands, [(PtCl3)-Cl-Iv(tacn)](ClO4), [(PtCl)-Cl-Iv(bpy)-(tacn)](ClO4)(3) ([1](ClO4), and [2](ClO4)(3), bpy: 2,2'-bipyridine) were prepared, and their hexa-coordinated octahedral structures were determined via single-crystal X-ray analysis. In aqueous solutions containing NaCl as the electrolyte, [2](3+) exhibited a quasi-reversible two-electron redox wave at +0.22 V (vs. SCE) with a large peak separation Delta E = E-pc - E-pa = 0.28 V). In addition, controlled-potential reduction of [2](3+) at -0.30 V in aqueous solutions containing NaCl afforded [Pt-II(bpy)(tacn)](2+) ([3](2+)), which was then re-oxidized to regenerate [2](3+). X-ray analysis of [3](2+) revealed a tetra-coordinated square-planar structure in which both tacn and bpy were bound to the central Pt as bidentate ligands. The redox potential of this reaction is coupled with dissociation/association of Cl- from/to Pt in the solution. MO/DFT calculations indicate that structural changes in tacn promote the reversible two-electron redox reaction between the octahedral Pt(IV) and square planar Pt(II) complexes.

DOI： 10.1246/bcsj.20150097

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

We have applied the four-body corrected fragment molecular orbital (FMO4) calculations to analyze the interaction between a designed peptide motif (Glu1-Ser2-Gln3-Glu4-Ser5) and the hydroxyapatite (HA) solid mimicked by a cluster model consisting of 1408 atoms. To incorporate statistical fluctuations, a total of 30 configurations were generated through classical molecular dynamics simulation with water molecules and were subjected to FMO4 calculations at the MP2 level. It was found that Ser5 plays a leading role in interacting with the phosphate moieties of HA via charge transfer and also that negatively charged Glu1 and Glu4 provide electrostatic stabilizations with the calcium ions. (C) 2015 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2015.03.057

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Language：Japanese  

J-GLOBAL

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Publishing type：Research paper (scientific journal)   Publisher：Elsevier {BV}  

DOI： 10.1016/j.comptc.2014.11.020

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Language：Japanese  

DOI： 10.2477/jccj.2015-0033

J-GLOBAL

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Language：Japanese   Publishing type：Research paper (scientific journal)   Publisher：Society of Computer Chemistry Japan  

DOI： 10.2477/jccj.2014-0039

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Publishing type：Research paper (scientific journal)   Publisher：Society of Computer Chemistry Japan  

DOI： 10.2477/jccj.2014-0039

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Chem-Bio Informatics Society  

We have developed a couple of optimal damping algorithms (ODAs) for unrestricted Hartree-Fock (UHF) calculations of open-shell molecular systems. A series of equations were derived for both concurrent and alternate constructions of α and β Fock matrices in the integral-direct self-consistent-field (SCF) procedure. Several test calculations were performed to check the convergence behaviors. It was shown that the concurrent algorithm provides better performance than does the alternate one.

DOI： 10.1273/cbij.14.14

Scopus

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

On the basis of available molecular structures registered in Protein Data Bank, we have theoretically carried out the interaction energy analysis for the complexes of influenza virus hemagglutinin (HA) proteins and sialosaccharide receptor analogs of host cells. Employing the fragment molecular orbital method for quantum-chemical calculations, the differences in magnitude and pattern of the interactions between the amino acid residues of avian-type (H7N3) or human-type (H7N9) HA and each saccharide part of avian or human receptor were studied in order to elucidate the molecular mechanism of avian-to-human infectious transmission of influenza virus. We have thus confirmed quantitatively that the mutations from the avian HA to the human HA significantly strengthened the binding affinity of human HA to human receptor, while retaining the affinity to avian receptor. In addition to direct effects regarding the changes of interactions between the altered residues and the receptors, we have also found the importance of indirect effects in which structural changes caused by the mutations play vital roles to modify the intermolecular interactions. (C) 2014 Elsevier Inc. All rights reserved.

DOI： 10.1016/j.jmgm.2014.07.004

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Publishing type：Research paper (scientific journal)   Publisher：Informa {UK} Limited  

DOI： 10.1080/00268976.2014.941311

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY-BLACKWELL  

The self-energy shift in the orbital relaxation (OR) term of the polarization propagator complete through the second-order is presented. In combination with the optimal damping parameter in the OR term, the modified propagator produces the excitation energy of the coupled-cluster with singles and doubles (CCSD) accuracy. The self-energy shift requires the floating-point operation of O(N4), where N refers to the magnitude of the molecular size. Because the second-order polarization propagator requires the floating-point operation of O(N5), the additional O(N4) computational effort to construct the self-energy is negligibly small. Numerical results are shown for several molecules including glycine, 2,3,5,6-tetrafluorobenzene, and naphthalene, and promising agreements with those of CCSD are confirmed within less than 0.2 eV. The basis set dependence is also tested for the water molecule using aug-cc-pV NZ (N=D-7), where this newly developed approach mimics the behavior of the CCSD values. The self-energy shifting for the second-order response matrix in combination with the use of a dumping parameter is efficiently implemented for calculations of medium-sized molecular systems, including glycine and naphthalene. The developed approach provides CCSD-like accuracy at a more affordable computational expense. (c) 2014 Wiley Periodicals, Inc.

DOI： 10.1002/qua.24625

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

The fragment molecular orbital (FMO) method can calculate the electronic structure of macromolecules such as DNA by dividing them into several fragments and introducing suitable approximations. To establish guiding principles for FMO calculation of DNA, benchmark tests were performed for several small DNA models consisting of one or two bases or two base pairs. The effects of several factors on the accuracy of FMO calculations were investigated, including the methods used to fragment the nucleotide units, approximations for the electrostatic potential, charge neutralization, and electron correlation. It was found that charge neutralization is indispensable for the reliable calculation of energies and spatial distribution of molecular orbitals, but not necessarily so for inter-fragment interaction energy analyses, such as calculation of the base-base interaction. The electrostatic approximations were shown to have only an insignificant effect on the qualitative nature of the calculations. It was also confirmed that the base-base stacking energy can be reproduced semi-quantitatively by the Moller-Plesset second-order perturbation (MP2) method though with some overestimation, and that the overestimation can be alleviated by the spin-component-scaled MP2 method. (C) 2014 Elsevier B.V. All rights

DOI： 10.1016/j.comptc.2014.02.002

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Language：Japanese  

J-GLOBAL

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Publishing type：Research paper (scientific journal)   Publisher：Royal Society of Chemistry ({RSC})  

DOI： 10.1039/c4cp00316k

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Publishing type：Research paper (scientific journal)   Publisher：Chem-Bio Informatics Society  

DOI： 10.1273/cbij.14.1

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Publishing type：Research paper (scientific journal)   Publisher：Elsevier {BV}  

DOI： 10.1016/j.cplett.2013.02.020

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Publishing type：Research paper (scientific journal)   Publisher：Elsevier {BV}  

DOI： 10.1016/j.jmgm.2013.01.006

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

Electronic excitation spectra of cis-platin (cis-[(PtCl2)-Cl-II(NH3)(2)]), which is a well-known antitumor drug, and trans-platin (trans-[(PtCl2)-Cl-II(NH3)(2)]) were experimentally observed and theoretically analyzed using ab initio spin-orbit CASPT2 (SO-CASPT2) calculations. Cis-platin showed two series of absorption bands in the wavelength regions of 250-350 nm and 350-450 nm. On the other hand, trans-platin showed three series of absorption bands in the wavelength regions of 260-280 nm, 300-340 nm and 360-400 nm. Comparing SO-CASPT2 calculations at the optimum structures in gas-phase conditions with those in DMF solvent, which were obtained by PCM implicit solvation model, it was clarified that both spin-orbit effect and solvent effect cannot be negligible even for quantitative assignments of electronic excitation spectra of cis/trans-platin. (c) 2012 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.molstruc.2012.11.027

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Publisher：Google Patents  

US Patent App. 14/442,321

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Language：Japanese  

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Language：Japanese  

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Language：Japanese  

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Publishing type：Research paper (scientific journal)   Publisher：Chem-Bio Informatics Society  

DOI： 10.1273/cbij.13.45

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

We have performed ab initio path integral Monte Carlo simulations for water trimer (H2O)(3) system. The electron correlation effects have been taken into account up to the level of third-order Moller-Plesset (MP3) perturbation theory. Through comparisons of calculated geometrical properties of water trimer such as O-O distance, O-H-O angle, and torsional angle between O-H and O-O-O plane, the interplays among the nuclear quantum, thermal and electron correlation effects are analyzed quantitatively. (c) 2012 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.comptc.2012.07.029

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Publisher：Google Patents  

US Patent App. 14/356,744

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY-V C H VERLAG GMBH  

Full-quantum mechanical fragment molecular orbital-based molecular dynamics (FMO-MD) simulations were applied to the hydration reaction of formaldehyde in water solution under neutral conditions. Two mechanisms, a concerted and a stepwise one, were considered with respect to the nucleophilic addition and the proton transfer. Preliminary molecular orbital calculations by means of polarized continuum model reaction field predicted that the hydration prefers a concerted mechanism. Because the calculated activation barriers were too high for free FMO-MD simulations to give reactive trajectories spontaneously, a More OFerrallJencks-type diagram was constructed from the statistical analysis of the FMO-MD simulations with constraint dynamics. The diagram showed that the hydration proceeds through a zwitterionic-like (ZW-like) structure. The free energy changes along the reaction coordinate calculated by means of the blue moon ensemble for the hydration and the amination of formaldehyde indicated that the hydration proceeds through a concerted process through the ZW-like structure, whereas the amination goes through a stepwise mechanism with a ZW intermediate. In inspection of the FMO-MD trajectories, water-mediated cyclic proton transfers were observed in both reactions on the way from the ZW-like structure to the product. These proton transfers also have an asynchronous character, in which deprotonation from the nucleophilic oxygen atom (or nitrogen atom for amination) precedes the protonation of the carbonyl oxygen atom. The results showed the strong advantage of the FMO-MD simulations to obtain detailed information at a molecular level for solution reactions.

DOI： 10.1002/chem.201200874

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

The reliability of protein structure is a critical concern to grasp the insights with respect to residue-residue and residue-ligand interactions by computational methods. In such calculations, the molecular geometries are usually prepared by the optimization of experimental structure with empirical molecular mechanics (MM) parameters. As an alternative to MM methods, we have developed a partial geometry optimization with the fragment molecular orbital (FMO) scheme at the second-order Moller-Plesset perturbation (MP2) level. The TrpCage miniprotein was used as a demonstrative example. The geometries of the central region were partially optimized at the FMO-MP2 and Hartree-Fock (FMO-HF) levels, and the former with the correlation correction showed reasonable agreement with the experimental structure. (C) 2012 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2012.03.046

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

Differences in hydration between cis- and trans-platin were investigated using ab initio fragment molecular orbital-based molecular dynamics (FMO-MD) simulations. Analyzing quantum charge fluctuation in water, we found that the Pt-Cl bond fluctuation of cis/trans-platin, which is important for activating their anticancer functions, was induced by charge transfer interaction between an anti-bonding pi(Pt-Cl) orbital of platin complex and unoccupied orbital of solvent water molecules. The hydration number of Cl ligand in the first hydration shell was found to be larger for cis-platin than for trans-platin due to their difference in charge distribution. Our FMO-MD simulations showed that the amplitude of the Pt-Cl bond fluctuation is larger in hydrated cis-platin than in hydrated trans-platin. (C) 2012 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.comptc.2012.02.008

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

Free-base porphyrin and its derivatives have been attracting chemical interests with regard to their characteristic spectral behavior, showing two specific peaks called B- and Q-bands. In this Letter, a modification on the second order polarization propagator scheme is developed and the performance for porphyrin derivatives is examined. The modification is based on Dykstra and Davidson's partial renormalization technique in terms of the coupled-pair functional aspect and has significant resistance to the quasi-degeneracy. As a consequence, the improved scheme shows encouraging results compared with the other theoretical values as well as the experimental data. (C) 2011 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2011.12.063

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Language：Japanese   Publishing type：Research paper (scientific journal)   Publisher：Division of Chemical Information and Computer Sciences  

DOI： 10.2751/jcac.13.44

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Publishing type：Research paper (scientific journal)   Publisher：Elsevier {BV}  

DOI： 10.1016/j.cplett.2011.12.004

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

We have performed ab initio path integral molecular dynamics and Monte Carlo simulations for water trimer and oligopeptide. In the first part, we illustrate the path integral molecular dynamics method based on fragment molecular orbital (FMO-PIMD) method. The FMO-PIMD method is applied to water trimer and glycine pentamer to investigate nuclear quantum effects on the structure and molecular interactions. In the second part, we employ the Moller-Plesset perturbation theory and discuss interplay of nuclear quantum effects and electron correlations. (C) 2012 American Chemical Society

DOI： 10.1021/bk-2012-1094.ch015

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

Effective interactions between amino acid residues in antigen-antibody complex of influenza virus hemagglutinin (HA) protein can be evaluated in terms of the inter-fragment interaction energy (IFIE) analysis with the fragment molecular orbital (FMO) method, in which each fragment contains the side chain of corresponding amino acid residue. We have carried out the FMO-MP2 (second-order Moeller-Plesset) calculation for the complex of HA antigen and Fab antibody of influenza virus H3N2 A/Aichi/2/68 and obtained the IFIE values between each amino acid residue in HA and the whole antibody as the sums over the residues contained in the latter. Combining this IFIE data with experimental data for hemadsorption activity of HA mutants, we succeeded in theoretically explaining the mutations in HA observed after the emergence of influenza virus H3N2 A/Aichi/2/68 in an earlier study, except for those of THR83. In the present study, we employ an alternative way of fragment division in the FMO calculation at the carbonyl C site of the peptide bond instead of the C(alpha) site used in the previous work, which provides revised IFIE values consistent with all the historical mutation data in the antigenic region E of HA including the case of THR83 in the present prediction scheme for probable mutations in HA.

DOI： 10.1007/s00214-011-1048-z

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

We have developed a new module for higher-order correlated methods up to coupled-cluster singles and doubles with perturbative triples (CCSD(T)). The matrix-matrix operations through the DGEMM routine were pursued for a number of contractions. This code was then incorporated into the ABINIT-MPX program for the fragment molecular orbital (FMO) calculations. Intra-fragment processings were parallelized with OpenMP in a node-wise fashion, whereas the message passing interface (MPI) was used for the fragment-wise parallelization over nodes. Our new implementation made the FMO-based higher-order calculations applicable to realistic proteins. We have performed several benchmark tests on the Earth Simulator (ES2), a massively parallel computer. For example, the FMO-CCSD(T)/6-31G job for the HIV-1 protease (198 amino acid residues)-lopinavir complex was completed in 9.8 h with 512 processors (or 64 nodes). Another example was the influenza neuraminidase (386 residues) with oseltamivir calculated at the full fourth-order Moller-Plesset perturbation level (MP4), of which job timing was 10.3 h with 1024 processors. The applicability of the methods to commodity cluster computers was tested as well.

DOI： 10.1007/s00214-011-1036-3

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Publishing type：Research paper (scientific journal)   Publisher：Elsevier {BV}  

DOI： 10.1016/j.jmgm.2011.06.011

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

4f-in-core large-core model core potentials (LC-MCP), in which the effects of open shell 4f electrons as well as those of other electrons up to 4d were replaced with MCPs, were developed for the lanthanide trivalent ions. In order to achieve desired accuracy, the LC-MCPs were calibrated using static quantum-chemical calculations for LnF(3), and tested by ab initio molecular dynamics simulation on the hydration dynamics of La(3+). Comparing calculated results using the 4f-in-core LC-MCPs with those employing 4f-in-valence MCPs, we found that the 4f-in-core LC-MCPs require less computational costs than the 4f-in-valence MCPs with keeping enough accuracy for describing chemical properties of trivalent lanthanide systems. (C) 2011 Elsevier B. V. All rights reserved.

DOI： 10.1016/j.cplett.2011.05.028

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Publishing type：Research paper (scientific journal)   Publisher：Elsevier {BV}  

DOI： 10.1016/j.cplett.2011.04.070

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Publishing type：Research paper (scientific journal)   Publisher：Elsevier {BV}  

DOI： 10.1016/j.cplett.2011.01.039

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

The excitation energies of blue- and yellow-fluorescent proteins (BFP and YFP) were evaluated by the method of configuration interaction singles and perturbative doubles CIS(D) in conjunction with the fragment molecular orbital (FMO) scheme. Three amino acid residues were identified to be contributive to the excitation energy by the so-called pairwise procedure. Under the multilayer treatment (MFMO) with these selected residues, the best estimates for BFP and YFP were obtained as 3.36 and 2.53 eV, respectively, where the second-order self-energy shift was utilized to modify the CIS(D) expression [Mochizuki, Chem. Phys. Lett. 472 (2009) 143]. These values were comparable to the respective experimental values of 3.21/3.25 and 2.41 eV. (C) 2011 Elsevier B. V. All rights reserved.

DOI： 10.1016/j.cplett.2011.01.054

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Language：English   Publishing type：Research paper (international conference proceedings)  

This paper introduces QC2AS which is a newly designed and developed computer algebra system for symbolic quantum chemical computations. With the rapid advancement of computer, the concern with high-level model chemistry has been growing. To handle such models, it is necessary to manipulate huge algebraic formulas. QC2AS has been designed to handle algebraic formulas appeared in quantum chemistry and it provides an access to our computer algebraic techniques without knowing the background theories. In this paper, we introduce its features and the architecture with some illustrative examples. This is the first report about the development of QC2AS. © 2011 IEEE.

DOI： 10.1109/ICCSA.2011.39

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

We report the molecular mechanism of protein-RNA complex stabilization based on the electronic state calculation Fragment molecular orbital (FMO) method based quantum mechanical calculations were performed for neuro-oncological ventral antigen (NOVA)-RNA complex system The inter-molecular interactions and their effects on the electronic state of NOVA were examined in the framework of ab initio quantum calculation The strength of inter molecular interactions was evaluated using inter-fragment interaction energies (IFIEs) associated with residue-RNA base and residue-RNA backbone interactions Under the influence of Inter-molecular interactions the change of electronic state of NOVA upon the complex formation was examined based on IFIE values associated with ultra-NOVA residue-residue interactions and the change of atomic charges by each residue The results indicated that non-specifically recognized bases contributed to the stability of the complex as well as specifically recognized bases and that the secondary structure of NOVA was remarkably associated with the change of electronic state upon the complex formation (C) 2010 Elsevier B V All rights reserved

DOI： 10.1016/j.theochem.2010.09.013

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

We performed geometry optimization calculations and ab initio molecular dynamics calculations for hydration models of trivalent ions, Y(3+), La(3+), Gd(3+), and Lu(3+), by using molecular orbital calculations to examine the so-called gadolinium break. The geometry optimization calculations revealed that the M-O distances of Y(H(2)O)(8)(3+), Lu(H(2)O)(8)(3+), and La(H(2)O)(9)(3+) calculated at the MP2 level were 2.39 angstrom, 2.36 angstrom, and 2.63 angstrom, respectively, which agreed well with observed values. The calculated Gd-O distance (2.44 angstrom) of Gd(H(2)O)(8)(3+) also agrees reasonably well with the existing observed values. The differences in the M-O distances arise from the differences in the ionic radii. When the coordination number increased, the degree of decrease in the M-O binding energies per bond (B.E.) occurred in the following order: La(3+) &lt; Gd(3+) &lt; Y(3+) &lt; Lu(3+). This order is consistent with the order of the ionic radii&apos;s inverse. In ab initio molecular dynamics calculations, by using the Y(H(2)O)(24)(3+) model we could realize the hydration structure where eight water molecules are located around the Y(3+) ion. By using the bigger model of La(H(2)O)(64)(3+), the experimentally suggested structure coordinated by nine water molecules was reproduced. (C) 2010 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.theochem.2010.02.032

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Publishing type：Research paper (scientific journal)   Publisher：Elsevier {BV}  

DOI： 10.1016/j.cplett.2010.05.034

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：PERGAMON-ELSEVIER SCIENCE LTD  

The peroxisome proliferator-activated receptor-gamma (PPAR gamma) is a direct pharmacological target for drugs that enhance insulin sensitivity and are used clinically for the treatment of type II diabetes. Because the specificity of ligand recognition is lower for PPAR gamma than for other nuclear receptors, PPAR gamma can bind a larger variety of ligand types. In order to elucidate why the ligand recognition of PPAR gamma is so flexible, we performed correlated fragment molecular orbital calculations for complexes of PPAR gamma and each of two distinctive ligands, rosiglitazone and farglitazar. We found quite different patterns of ligand binding for these two ligands. The ligand-binding system of rosiglitazone, a drug in common clinical use, is based mainly on local electrostatic interactions around the thiazolidine ring, whereas both electrostatic interactions and van der Waals dispersion interactions with hydrophobic residues are required for the binding of farglitazar to PPAR gamma. We suggest that the development of novel ligands will require adequately hydrophobic pharmacophores. (C) 2010 Elsevier Ltd. All rights reserved.

DOI： 10.1016/j.bmcl.2010.04.031

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Publishing type：Research paper (scientific journal)   Publisher：Elsevier {BV}  

DOI： 10.1016/j.cplett.2010.03.020

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Publishing type：Research paper (scientific journal)   Publisher：Elsevier {BV}  

DOI： 10.1016/j.cplett.2010.03.001

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Publishing type：Research paper (scientific journal)   Publisher：Elsevier {BV}  

DOI： 10.1016/j.cplett.2010.03.020

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

The fragment molecular orbital-based molecular dynamics (FMO-MD) was improved by the introduction of the three-body extension (FMO3) and the generalized dynamic fragmentation. An analytical energy gradient was derived for FMO3 to realize FMO3-MD. An algorithm of generalized dynamic fragmentation was devised to treat each covalent-bonded and, optionally, hydrogen-bonded atom cluster as a fragment in the course of FMO-MD. The new algorithms were tested by performing conventional MO-MD, FMO2-MD, based on two-body extension, and FMO3-MD simulations of (H(2)O)(32) and H(+)(H(2)O)(32). FMO2-MD resulted in lower precision, especially in H(+)(H(2)O)(32), while FMO3-MD gave a precision comparable to that of MO-MD. (C) 2009 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2009.11.045

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Language：English   Publisher：CELL PRESS  

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY-V C H VERLAG GMBH  

DOI： 10.1002/chem.201000442

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

DOI： 10.2142/biophys.50.S65_4

CiNii Article

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

We discuss the accuracy of fragmentation in fragment molecular orbital (FMO) calculations for the hydrated sodium ion. Two-body expansion shows a considerable error in total energy even if water molecules in the second hydration shell are included in the same fragment as the sodium ion. Inclusion of the three-body term significantly improves both the total energy and the charge distributions. We also illustrate the dependence of the net charge of sodium ion on solvent size and the interfacial property of water molecules. The present study will thus provide fundamental information about hydrated ion to facilitate further theoretical and experimental studies. (C) 2009 Elsevier B. V. All rights reserved.

DOI： 10.1016/j.cplett.2009.07.060

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

We have performed a quantum-chemical MP2/6-31G* calculation for the hemagglutinin (HA) antigen-antibody system of the H3N2 influenza virus with the fragment molecular orbital method, which provides one of the world&apos;s largest ab initio electron-correlated calculations for biomolecular systems. On the basis of the calculated interfragment interaction energies (IFIEs) representing the molecular interactions between the amino acid residues in the antigen-antibody complex, we have identified those residues in the antigenic region E of HA protein that are significantly recognized by the Fab fragment of antibody with strongly attractive interactions. Combining these IFIE results with those of hemadsorption experiments by which the mutation-prohibited sites are specified has enabled us to explain most of the historical mutation data (five of six residues), which would thus provide a promising method for predicting the HA residues that have a high probability of forthcoming mutation.

DOI： 10.1021/jp810997c

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

Previously [Y. Mochizuki, Chem. Phys. Lett. 453 (2008) 109], the self-energy shift obtained from the Dyson equation was introduced to modify the energy denominator of the second-order perturbational estimate for orbital relaxations in the method of configuration interaction singles with perturbative doubles, CIS(D). This Dyson correction technique is then applied also to the differential second-order correlation energy in CIS(D) calculations, in conjunction with the partial renormalization (PR) of amplitudes by using the topological factor. The potential of Dyson/PR-corrected second-order perturbation itself is separately examined with a couple of small systems having elongated bonds at the ground state. (C) 2009 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2009.02.075

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

Bioluminescence spectra of firefly Luciola cruciata were theoretically analyzed on the basis of the fragment molecular orbital (FMO) method. The CIS(D) and PR-CIS(Ds) methods were employed for the calculations of emission energies of wild-type and mutant luciferase-oxyluciferin systems, and various multilayer FMO calculations were performed changing the sizes of the luciferase protein and of the chromophore to which the excited-state calculations were applied. We have thus reproduced the experimental emission energies of wild-type and mutant luciferase systems with good accuracy, which provides useful information concerning the roles of protein environment for the color tuning of the bioluminescence spectra of firefly. (C) 2009 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2009.02.076

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

Fragment Molecular Orbital-based Molecular Dynamics (FMO-MD) is an ab initio molecular dynamics method based on the Fragment Molecular Orbital method. FMO-MD is a general tool for quantum-mechanical MD simulations of large molecular systems that works because of the high parallel efficiency and accuracy of FMO. We review the methodology of FMO-MD and its applications to the conformation sampling of formaldehyde in a solvent, the direct simulation of hydrolysis of methyl diazonium cation, and the comparison of free energy profiles of the Menschutkin reaction in the presence and absence of the solvent. Based on these studies, we compare FMO-MD with other MD methods and discuss the future prospects of the FMO-MD method. (C) 2008 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.theochem.2008.07.001

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

We have performed a series of fragment molecular orbital (FMO) calculations for a family of red fluorescent proteins, DsRed and mFruits. The electronic transition energies were evaluated by the method of configuration interaction singles with perturbative doubles [CIS(D)] including higher-order corrections. The calculated values were in good agreement with the corresponding experimental peak values of spectra. Additionally, the chromophore environment was systematically analyzed in terms of the interaction energies between the pigment moiety and neighboring residues. It was&apos; theoretically revealed that the electrostatic interactions play a dominant role in the DsRed chromophore, whereas the color tunings in mFruits are controlled in a more delicate fashion.

DOI： 10.1021/jp808151c

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

Fragment Molecular Orbital based-Molecular Dynamics (FMO-MD, Komeiji et al., Chem Phys Lett 2003, 372, 342) is an ab initio MD method suitable for large molecular systems. Here, FMO-MD was implemented to conduct full quantum simulations of chemical reactions in explicit solvation. Several FMO-MD simulations were performed for a sphere of water to find a suitable simulation protocol. It was found that annealing of the initial configuration by a classical MD brought the subsequent FMO-MD trajectory to faster stabilization, and also that use of bond constraint in the FMO-MD heating stage effectively reduced the computation time. Then, the blue moon ensemble method (Sprik and Ciccotti, J Chem Phys 1998, 109, 7737) was implemented and was tested by calculating free energy profiles of the Menschutkin reaction (H(3)N + CH(3)Cl -&gt; (+)H(3)NCH(3) + Cl(-)) in the presence and absence of the solvent water via FMO-MD. The obtained free energy profiles were consistent with the Hammond postulate in that stabilization of the product by the solvent, namely hydration of Cl(-), shifted the transition state to the reactant-side. Based on these FMO-MD results, plans for further improvement of the method are discussed. (C) 2008 Wiley Periodicals, Inc. J Comput Chem 30: 40-50, 2009

DOI： 10.1002/jcc.21025

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Publishing type：Part of collection (book)   Publisher：CRC Press: Boca Raton, FL  

The application of quantum chemical methods to large molecules such as proteins and DNAs remains a great challenge in computational chemistry. The calculations of electronic structures for biomolecules are usually difficult due to their huge size, and some models are needed to realize quantum mechanical calculations on such systems.

DOI： 10.1201/9781420078497-6

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Publishing type：Research paper (scientific journal)   Publisher：Elsevier {BV}  

DOI： 10.1016/j.cplett.2008.11.044

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Publishing type：Part of collection (book)   Publisher：CRC Press  

In structural biology, molecular simulations have played an important role in elucidating functions of the biological system. The understanding of biological phenomena at the molecular level is expected to lead the modeling of disease, drug discovery, and various applications. A variety of life phenomena occur through the combination of site-specific molecular recognition of biomacromolecules. Computer simulations thus provide a promising approach to elucidate these molecular interactions in detail. However, most calculations carried out to date have employed classical mechanical methods based on empirical force fields. Such methods remain limited for performing an accurate analysis of intermolecular interactions such as charge redistribution and charge-transfer (CT) interactions. In contrast to the limitations of classical approaches to molecular simulation, quantum mechanical simulations have been used to successfully characterize weak intermolecular interactions and CT processes. Because several different types of interactions are involved in the interactions of biomolecules, quantum mechanical treatment is necessary to obtain an accurate and systematic understanding of these interactions. The fragment molecular orbital (FMO) method1-4 is one of the most reasonable tools with which to analyze the electronic structure of biomacromolecules.

DOI： 10.1201/9781420078497-10

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Publishing type：Part of collection (book)   Publisher：CRC Press  

A number of biochemical systems are photoactive in the visible region through electronic transitions. The rhodopsin protein in vertebrate eyes is a representative case of such photoabsorptions. As for emissions, the green fluorescent protein (GFP)1 and related derivatives are useful marker labels in the field of biotechnology. The central region in photoactive proteins is known as the chromophore, and it consists of the crucial pigment part and some neighboring residues that should provide the electrostatic or hydrogen-bonding interactions with the pigment. Surrounding residues also put some electrostatic potentials on the chromophore system. These environmental.

DOI： 10.1201/9781420078497-7

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Publisher：The Biophysical Society of Japan General Incorporated Association  

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Publisher：The Biophysical Society of Japan General Incorporated Association  

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

DOI： 10.2142/biophys.49.S161_5

CiNii Article

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

We have developed a method named &apos;fragment interaction analysis based on local MP2&apos; (abbreviated as FILM). This method enables us to decompose the interaction energy associated with dispersion interactions into contributions of localized occupied orbitals. In this study, the basis set dependence of the results derived from FILM was examined. The results suggested that the individual ratio of pair correlation energies of selected orbital pairs to the total dispersion interaction was almost independent of the basis set size. As an illustrative example, detailed analysis was performed on the human immunodeficiency virus type 1 protease complexed with lopinavir molecule. (c) 2008 Elsevier B. V. All rights reserved.

DOI： 10.1016/j.cplett.2008.08.022

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

The ab initio fragment molecular orbital calculations were performed for the (x-subtype of the human retinoid X receptor (hRXR alpha) complex with its natural ligand 9-cis retinoic acid (9cRA) to quantitatively specify the key residues with important roles for the ligand inducible information transmission of RXR. In the RXR-9cRA complex, the transactivation helix 12 (H12) adopts a canonical agonist conformation, which just corresponds to the transcriptional activation function 2 activating domain core (AF2C). Through the analyses of molecular interactions by the second-order Moller-Plesset perturbation (MP2) method, it was proved that Trp305 and Leu436 of the AF2C binding pocket would be important for the stabilization of the H12 canonical agonist conformation, and, at the same time, for the recognition of the 9cRA molecule. Besides, through the analyses of orbital interactions by the local MP2 (LMP2) method, it was found that Trp305 and Leu436 would recognize the 9cRA molecule especially at its C 19 methyl group, which has been most notably targeted to modify for agonist and antagonist design. Moreover, on the basis of the relationships of molecular interactions, it was suggested that the interactions of Trp305 and Leu436 with AF2C residues would be significantly influenced by the interactions of Trp305 and Leu436 with 9cRA. Taken together, our findings quantitatively demonstrated that Trp305 and Leu436 would be the possible key residues for the information transmission in liganded RXR, accounting for their importance suggested by experiments. Altogether, these results substantiated that our approach is useful for the understanding of the detailed molecular mechanism underlying the transcriptional regulation of RXR and related nuclear receptors at the quantum mechanical level.

DOI： 10.1021/jp803369x

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Language：English   Publisher：AMER CHEMICAL SOC  

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ELSEVIER SCI LTD  

The hemagglutinin (HA) protein of the influenza virus binds to the host cell receptor in the early stage of viral infection. A change in binding specificity from avian alpha 2-3 to human alpha 2-6 receptor is essential for optimal human-to-human transmission and pandemics. Therefore, it is important to reveal the key factors governing the binding affinity of HA-receptor complex at the molecular level for the understanding and prediction of influenza pandemics. In this work, on the basis of ab initio fragment molecular orbital (FMO) method, we have carried out the interaction energy analysis of HA-receptor complexes to quantitatively elucidate the binding specificity of HAs to avian and human receptors. To discuss the binding property of influenza HA comprehensively, a number of HAs from human H1, swine H1, avian H3 and avian H5 viruses were analyzed. We performed detailed investigations about the interaction patterns of complexes of various HAs and receptor analogues, and revealed that intra-molecular interactions between conserved residues in HA play an important role for HA-receptor binding. These results may provide a hint to understand the role of conserved acidic residues at the receptor binding site which are destabilized by the electrostatic repulsion with sialic acid. The calculated binding energies and interaction patterns between receptor and HAs are consistent with the binding specificities of each HA and thus explain the receptor binding mechanism. The calculated results in the present analysis have provided a number of viewpoints regarding the models for the HA-receptor binding specificity associated with mutated residues. Examples include the role of Glu190 and Gln226 for the binding specificity of H5 HA. Since H5 HA has not yet been adapted to human receptor and the mechanism of the specificity change is unknown, this result is helpful for the prediction of the change in receptor specificity associated with forthcoming possible pandemics. (C) 2008 Elsevier Ltd. All rights reserved.

DOI： 10.1016/j.compbiolchem.2008.03.006

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

The fragment molecular orbital (FMO) calculations have been successfully applied to a variety of realistic biochemical problems, by using our original ABINIT-MP program. In these applications, the inclusion of electron correlation through the second-order Moller-Plesset perturbation (MP2) was demonstrated to be essential to obtain qualitatively correct descriptions. Recently, the FMO calculations in ABINIT-MP were tuned for a massively parallel-vector processing. A series of FMO-MP2/6-31G calculations were performed on the Earth Simulator by which up to 4096 vector processors are available. The largest FMO-MP2 computation was carried out for an influenza hemagglutinin antigen-antibody system consisting of 921 residues, which was completed within one hour with 4096 processors. (c) 2008 Elsevier B. V. All rights reserved.

DOI： 10.1016/j.cplett.2008.03.090

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

The ab initio fragment molecular orbital (FMO) calculations were performed for retinoid X receptor (RXR) complexes with its ligand 9-cis retinoic acid (9cRA) and steroid receptor coactivator-1 (SRC1) to examine the influence of mutations in transcriptional activation function 2 activating domain core (AF2C) of RXR on molecular interactions between 9cRA liganded RXR and SRC1 coactivator. The RXR-SRC1 interactions in three types of RXR-9cRA-SRC1 complexes, namely, a wild type (WT), a mutant whose Glu453 of AF2C was substituted by Lys (E453K), and another mutant whose Glu456 of AF2C was substituted by Lys (E456K), were compared. Through the comparison of WT, E453K, and E456K, possible causes for a marked decrease in the transcriptional activity of RXR by the mutation of Glu453, which is known as a highly conserved charged residue of AF2C, were discussed. It was quantitatively demonstrated that the strength of the RXR-SRC1 interaction correlates with the degree of the transcriptional activation (WT &gt; E456K &gt; E453K). In E453K, the RXR-SRC1 interaction was substantially reduced by the AF2C-SRC1 repulsive interaction, and the charge transfer (CT) from RXR to SRC1 was also inhibited by the decreased electron donation from AF2C to SRC1. Our findings suggest that the inhibitions of the local RXR-SRC1 interaction via AF2C and of the local CT from RXR to SRC1 via AF2C would be the possible causes for the marked decrease in the transcriptional activity of RXR.

DOI： 10.1021/jp075430r

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

The ab initio fragment molecular orbital (FMO) calculations were performed for retinoid X receptor (RXR) complexes with its ligand 9-cis retinoic acid (9cRA) and steroid receptor coactivator-1 (SRC1) to examine the influence of mutations in transcriptional activation function 2 activating domain core (AF2C) of RXR on molecular interactions between 9cRA liganded RXR and SRC1 coactivator. The RXR-SRC1 interactions in three types of RXR-9cRA-SRC1 complexes, namely, a wild type (WT), a mutant whose Glu453 of AF2C was substituted by Lys (E453K), and another mutant whose Glu456 of AF2C was substituted by Lys (E456K), were compared. Through the comparison of WT, E453K, and E456K, possible causes for a marked decrease in the transcriptional activity of RXR by the mutation of Glu453, which is known as a highly conserved charged residue of AF2C, were discussed. It was quantitatively demonstrated that the strength of the RXR-SRC1 interaction correlates with the degree of the transcriptional activation (WT &gt; E456K &gt; E453K). In E453K, the RXR-SRC1 interaction was substantially reduced by the AF2C-SRC1 repulsive interaction, and the charge transfer (CT) from RXR to SRC1 was also inhibited by the decreased electron donation from AF2C to SRC1. Our findings suggest that the inhibitions of the local RXR-SRC1 interaction via AF2C and of the local CT from RXR to SRC1 via AF2C would be the possible causes for the marked decrease in the transcriptional activity of RXR.

DOI： 10.1021/jp075430r

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

An important goal of mechanistic studies of chemical reactions is to understand how atoms in reacting molecules behave at the molecular level. Toward this goal, full quantum mechanical molecular dynamics (MD) simulations, which employed the recently developed fragment molecular orbital (FMO)-MD method, were carded out for the hydrolysis of the methyl diazonium ion in water. The simulations illustrated for the first time how the solvent water molecules participate in the reaction and how the C-N bond cleavage and O-C bond formation take place during the reaction. It was revealed that this typical S(N)2 reaction does not always proceed through the energetically favorable synchronous pathway, but that it shows mechanistic diversity.

DOI： 10.1021/ja710038c

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

A practical use of self-energy is proposed for the description of orbital relaxation involving excited states. The proposal is first applied to modify the energy contribution from orbital relaxation in the method of configuration interaction singles with perturbative doubles, originated by Head-Gordon et al. as CIS(D). Namely, the self-energy shift is introduced for outer valence orbital energies in the denominator of contraction formula. This modification is found to be effective for Rydberg states with keeping a balance of correction for valence states. The second application of self-energy shift concerns the polarizability which is evaluated as a linear response (LR) property. The modified polarizability values become closer to those obtained by correlated calculations. (C) 2008 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2008.01.014

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Language：Japanese  

DOI： 10.2751/jcac.9.47

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

The nitric oxide dimer, (NO)2, has been known as an archetype with severe near-degeneracy because of the weak N-N bonding. We thus performed a series of multi-reference calculations of fourth-order coupled pair approximation (MRCPA4) and configuration interaction (MRCI). For the ground state, the molecular structure of cis form was optimized by these calculations. The MRCPA4 geometry was favorably compared with the recent experimental data, indicating the importance of higher excitations. Low-lying singlet excited states were also addressed. Through these calculations, the intrinsic MR character of this system was illustrated. (C) 2007 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2007.11.084

CiNii Article

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

We have developed a fragment interaction analysis based on local MP2 (FILM) in the context of the fragment molecular orbital (FMO) scheme. The primary purpose of this work is to provide a tool for analyzing inter-fragment interaction associated with dispersion interactions in a large molecule such as protein and DNA. Our implementation of local MP2 (LMP2) is based on the algorithm developed by Pulay and Werner. A potential of FILM was demonstrated using the human immunodeficiency virus type 1 protease (HIV-1 PR) complexed with lopinavir (LPV). The total energy, binding affinity, and inter-fragment interaction energy (IFIE) by the FMO method using LMP2 were compared with those obtained by canonical MP2 and the site-specific information in dispersion interaction was obtained. It turned out that the FILM is a useful tool for analyzing the dispersion interaction between an amino acid residue and a specific site of a ligand.

DOI： 10.1007/s00214-007-0374-7

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

We have developed a fragment interaction analysis based on local MP2 (FILM) in the context of the fragment molecular orbital (FMO) scheme. The primary purpose of this work is to provide a tool for analyzing inter-fragment interaction associated with dispersion interactions in a large molecule such as protein and DNA. Our implementation of local MP2 (LMP2) is based on the algorithm developed by Pulay and Werner. A potential of FILM was demonstrated using the human immunodeficiency virus type 1 protease (HIV-1 PR) complexed with lopinavir (LPV). The total energy, binding affinity, and inter-fragment interaction energy (IFIE) by the FMO method using LMP2 were compared with those obtained by canonical MP2 and the site-specific information in dispersion interaction was obtained. It turned out that the FILM is a useful tool for analyzing the dispersion interaction between an amino acid residue and a specific site of a ligand.

DOI： 10.1007/s00214-007-0374-7

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

A visualization method for inter-fragment interaction energies (IFIEs) of biopolymers is presented on the basis of the fragment molecular orbital (FMO) method. The IFIEs appropriately illustrate the information about the interaction energies between the fragments consisting of amino acids, nucleotides and other molecules. The IFTEs are usually analyzed in a matrix form called an IFTE matrix. Analyzing the IFIE matrix, we detect important fragments for the function of biomolecular systems and quantify the strength of interaction energies based on quantum chemistry, including the effects of charge transfer, electronic polarization and dispersion force. In this study, by analyzing a protein-DNA complex, we report a visual representation of the IFTE matrix, a so-called IFTE map. We comprehensively examine what information the THE map contains concerning structures and stabilities of the protein-DNA complex. (c) 2007 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.bpc.2007.06.011

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

A visualization method for inter-fragment interaction energies (IFIEs) of biopolymers is presented on the basis of the fragment molecular orbital (FMO) method. The IFIEs appropriately illustrate the information about the interaction energies between the fragments consisting of amino acids, nucleotides and other molecules. The IFTEs are usually analyzed in a matrix form called an IFTE matrix. Analyzing the IFIE matrix, we detect important fragments for the function of biomolecular systems and quantify the strength of interaction energies based on quantum chemistry, including the effects of charge transfer, electronic polarization and dispersion force. In this study, by analyzing a protein-DNA complex, we report a visual representation of the IFTE matrix, a so-called IFTE map. We comprehensively examine what information the THE map contains concerning structures and stabilities of the protein-DNA complex. (c) 2007 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.bpc.2007.06.011

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Elsevier  

We propose a couple of modifications for the spin-adapted version of configuration interaction singles with perturbative doubles, originated by Head-Gordon et al. as CIS(D). A partial renormalization technique is first introduced for the T2 doubles operator of second-order Møller-Plesset perturbation (MP2) theory. Second, an extra correction from the T1 singles operator is taken into account. The combined modifications can be abbreviated as PR-CIS(Ds) (partially renormalized variant of configuration interaction singles with perturbative doubles and extra singles). A series of calculations with a benchmark set of molecules are performed for both singlet and triplet excited states. Through these tests, it is observed that favorable improvements are obtainable by the proposed modifications for low-lying valence states. © 2007 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2007.06.059

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

We propose a couple of modifications for the spin-adapted version of configuration interaction singles with perturbative doubles, originated by Head-Gordon et at. as CIS(D). A partial renormalization technique is first introduced for the T(2) doubles operator of second-order Moller-Plesset perturbation (MP2) theory. Second, an extra correction from the T, singles operator is taken into account. The combined modifications can be abbreviated as PR-CIS(Ds) (partially renormalized variant of configuration interaction singles with perturbative doubles and extra singles). A series of calculations with a benchmark set of molecules are performed for both singlet and triplet excited states. Through these tests, it is observed that favorable improvements are obtainable by the proposed modifications for low-lying valence states. (c) 2007 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2007.06.059

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

We have developed a parallelized integral-direct code of the perturbative doubles correction for configuration interaction with singles, proposed as CIS(D) by Head-Gordon et al. (Chem Phys Lett 219:21, 1994). The CIS(D) method provides the energy corrections both of the relaxation and differential correlation for the respective CIS excited states. The implementation of CIS(D) is based on our original algorithm for the second-order Moller-Plesset perturbation (MP2) calculations (Mochizuki et al. in Theor Chem Acc 112:442, 2004). There is no need to communicate bulky intermediate data among worker processes of the parallelized execution. This CIS(D) code is then incorporated into a developer version of ABINIT-MP program, in order to improve the overestimation in excitation energies calculated by the CIS method in conjunction with the multilayer fragment molecular orbital scheme (MLFMO-CIS) (Mochizuki et al. in Chem Phys Lett 406:283, 2005). The MLFMO-CIS(D) method is first used in evaluating the lowest n pi* excitation energy of the hydrated formaldehyde. The photoactive yellow protein (PYP) is the second target of MLFMO-CIS(D) calculation. Through these applications, it is shown that the CIS(D) correction improves the CIS results favorably.

DOI： 10.1007/s00214-006-0181-6

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

On the basis of the fragment molecular orbital method we addressed molecular interactions of liganded retinoid X receptor (RXR) with steroid receptor co-activating factor-1 (SRC1) coactivator to examine the contribution of helix 12 (H12), which contains the core of the transcriptional activation function 2 activating domain, to the coactivator binding of RXR. The interaction between H12 and SRC1 was proved to be the main cause for the stabilization of the coactivator binding. In particular, highly conserved charged (Glu453) and hydrophobic (Phe450) residues in H12 were found to have stronger electrostatic and dispersion interactions with SRC1 than the other charged and hydrophobic residues in H12, respectively. In addition, the charge transfer (CT) from RXR to SRC1 was found to occur mainly by the changes in charges of H12 residues. Large positive and negative charge changes were observed especially for Glu453 and for Lys631 and Ile632 in SRC1, respectively, indicating that Glu453 is an electron donor for Lys631 and Ile632 in this CT. Taken together, our findings quantitatively demonstrated that H12 and its highly conserved residues significantly contribute to the coactivator binding not only by the Coulomb and dispersion interactions but also by the CT described with the quantum-mechanical framework.

DOI： 10.1021/jp070054w

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

On the basis of the fragment molecular orbital method we addressed molecular interactions of liganded retinoid X receptor (RXR) with steroid receptor co-activating factor-1 (SRC1) coactivator to examine the contribution of helix 12 (H12), which contains the core of the transcriptional activation function 2 activating domain, to the coactivator binding of RXR. The interaction between H12 and SRC1 was proved to be the main cause for the stabilization of the coactivator binding. In particular, highly conserved charged (Glu453) and hydrophobic (Phe450) residues in H12 were found to have stronger electrostatic and dispersion interactions with SRC1 than the other charged and hydrophobic residues in H12, respectively. In addition, the charge transfer (CT) from RXR to SRC1 was found to occur mainly by the changes in charges of H12 residues. Large positive and negative charge changes were observed especially for Glu453 and for Lys631 and Ile632 in SRC1, respectively, indicating that Glu453 is an electron donor for Lys631 and Ile632 in this CT. Taken together, our findings quantitatively demonstrated that H12 and its highly conserved residues significantly contribute to the coactivator binding not only by the Coulomb and dispersion interactions but also by the CT described with the quantum-mechanical framework.

DOI： 10.1021/jp070054w

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

We have developed a parallelized integral-direct code of the perturbative doubles correction for configuration interaction with singles, proposed as CIS(D) by Head-Gordon et al. (Chem Phys Lett 219:21, 1994). The CIS(D) method provides the energy corrections both of the relaxation and differential correlation for the respective CIS excited states. The implementation of CIS(D) is based on our original algorithm for the second-order Moller-Plesset perturbation (MP2) calculations (Mochizuki et al. in Theor Chem Acc 112:442, 2004). There is no need to communicate bulky intermediate data among worker processes of the parallelized execution. This CIS(D) code is then incorporated into a developer version of ABINIT-MP program, in order to improve the overestimation in excitation energies calculated by the CIS method in conjunction with the multilayer fragment molecular orbital scheme (MLFMO-CIS) (Mochizuki et al. in Chem Phys Lett 406:283, 2005). The MLFMO-CIS(D) method is first used in evaluating the lowest n pi* excitation energy of the hydrated formaldehyde. The photoactive yellow protein (PYP) is the second target of MLFMO-CIS(D) calculation. Through these applications, it is shown that the CIS(D) correction improves the CIS results favorably.

DOI： 10.1007/s00214-006-0181-6

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Language：English   Publishing type：Research paper (scientific journal)  

We report a fully quantum mechanical simulation on the lowest n-π* excited state of the hydrated formaldehyde, by using the fragment molecular orbital (FMO) scheme. For a droplet cluster consisting of a formaldehyde molecule and 128 water molecules, the molecular dynamics (MD) simulation was directly carried out by the FMO-based Hartree-Fock/6-31G energy gradient. The FMO-MD run generated a series of configuration samples with geometrical fluctuation. These samples were then subjected to the excited state calculation of configuration interaction singles with perturbative doubles (CIS(D)) in the multilayer FMO (MLFMO) framework. The final estimation of the excitation energy was obtained to be 4.22 eV through averaging the MLFMO-CIS(D)/6-31G* energies. © 2007 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2007.02.016

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

We developed a spin adapted full configuration interaction (FCI) method which was expected to be effective for parallel processing. The graphical symmetric group approach (GSGA) was employed, where a configuration graph was partitioned into several sets of closed-shell and open-shell graphs. The configuration state functions (CSFs) bearing the same number of closed-shells and open-shells were assembled in a configuration group. The graphical approach provided a number to identify each CSF in a sequential order within the group. Combination of this partitioning and an intermediate configuration-driven algorithm in calculating the so-called sigma vectors allowed us to use symbolic coupling constants. Furthermore, this combination made it easy to implement an efficient algorithm suitable to task-distributed parallel procedure for evaluating sigma vectors. A program was written and some test calculations were carried out with high parallel efficiency. The largest size of FCI used 10 million CSFs (20 million determinants).

DOI： 10.1007/s00214-006-0171-8

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

We report a fully quantum mechanical simulation on the lowest n-Ti-excited state of the hydrated formaldehyde, by using the fragment molecular orbital (FMO) scheme. For a droplet cluster consisting of a formaldehyde molecule and 128 water molecules, the molecular dynamics (MD) simulation was directly carried out by the FMO-based Hartree-Fock/6-31G energy gradient. The FMO-MD run generated a series of configuration samples with geometrical fluctuation. These samples were then subjected to the excited state calculation of configuration interaction singles with perturbative doubles (CIS(D)) in the multilayer FMO (MLFMO) framework. The final estimation of the excitation energy was obtained to be 4.22 eV through averaging the MLFMO-ClS(D)/6-31G* energies. (c) 2007 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2007.02.016

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Language：English  

J-GLOBAL

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Publishing type：Research paper (scientific journal)   Publisher：World Scientific  

In spite of the numerous experimental and theoretical studies on green fluorescent protein and its modifications, there is still no definitive answer to the central question: why such systems exhibit enhanced fluorescence. Based upon detailed quantum-chemical estimations, we advocate the following hypothesis. In the green fluorescent protein ground electronic state, the protein surrounding strains the chromophore with respect to its native intramolecular conformational preference in vacuo or in solution. Absorbing a photon of the proper wavelength not only causes a joint proton-electron transfer in and around the chromophore, but also increases the intrinsic strain of the latter. Since conformational relaxation of such a structure will not require any additional energy input, the energy gained by the chromophore cannot be dissipated into the chromophore's internal non-radiative degrees of freedom, and thus it returns as a fluorescence emission. © 2007 World Scientific Publishing Company.

DOI： 10.1142/s1793048007000568

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

We have performed the calculations of configuration interaction singles with perturbative doubles correction (CIS(D)) in conjunction with the multilayer fragment molecular orbital (MLFMO) scheme for a red fluorescent protein isolated from Discosoma coral (known as DsRed). The pigment geometry of DsRed was first examined by employing several model molecules whose spectra in gas-phase were actually observed, and an adequacy was confirmed. The excitation energy was then calculated to be 2.28 eV at the MLFMO-CIS(D)/6-31G* level. The emission energy was also estimated to be 2.21 eV similarly. These theoretical values were in good agreement with the corresponding experimental values of 2.22 eV and 2.13 eV. (c) 2006 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2006.11.088

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Publishing type：Research paper (scientific journal)   Publisher：Elsevier {BV}  

DOI： 10.1016/j.cplett.2007.10.066

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Language：English   Publishing type：Research paper (international conference proceedings)   Publisher：AMER INST PHYSICS  

The: Fragment Molecular Orbital based Molecular Dynamics method (FMO-MD, Komeiji et al., Chem. Phys. Lett. 372, 342, 2003) was reimplemented by combining the latest versions of PEACH and ABINIT-MP programs. Several simulations were performed for a spherical cluster of 125 water molecules at HF/6-31G* level to examine methods in FMO-MD. It was found that use of a molecular configuration prepared by annealing with classical MD lead to a better stabilization of the subsequent FMO-MD simulation. It was also found that use RATTLE bond length constraint in the heating stage could save computational time. These data are expected to serve as a basis for future simulations of solvated molecules.

DOI： 10.1063/1.2835978

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

DOI： 10.2142/biophys.47.S127_3

CiNii Article

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

We have performed the calculations of configuration interaction singles with perturbative doubles correction (CIS(D)) in conjunction with the multilayer fragment molecular orbital (MLFMO) scheme for a red fluorescent protein isolated from Discosoma coral (known as DsRed). The pigment geometry of DsRed was first examined by employing several model molecules whose spectra in gas-phase were actually observed, and an adequacy was confirmed. The excitation energy was then calculated to be 2.28 eV at the MLFMO-CIS(D)/6-31G* level. The emission energy was also estimated to be 2.21 eV similarly. These theoretical values were in good agreement with the corresponding experimental values of 2.22 eV and 2.13 eV. (c) 2006 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2006.11.088

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Language：Japanese   Publishing type：Research paper (other academic)   Publisher：Society of Computer Chemistry, Japan  

Kitaura <I>et al</I>. (<I>Chem. Phys. Lett.</I> <B>312</B>, 319-324 (1999)) have proposed an ab initio fragment molecular orbital (FMO) method by which large molecules such as proteins can be easily treated with chemical accuracy. In the ab initio FMO method, a molecule or a molecular cluster is divided into fragments, and the MO calculations on the fragments (monomers) and the fragment pairs (dimers) are performed to obtain the total energy that is expressed as a summation of the fragment energies and inter-fragment interaction energies (IFIEs). In this paper, we provide a brief description of the ab initio FMO method and demonstrate recent applications in the nano-bio field.

DOI： 10.2477/jccj.6.173

CiNii Article

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Language：Japanese   Publishing type：Research paper (other academic)   Publisher：Society of Computer Chemistry, Japan  

This review introduces the application of the Fragment molecular orbital (FMO) method. The ABINIT-MP and BioStation Viewer programs have been used for such applications. The FMO method was applied for problems of transcriptional regulation, including interactions of nuclear receptor, ligand, transcription factor, and DNA. Detailed interactions between biomolecules and the roles of each amino acid residue were revealed through analyses of inter-fragment interaction energy (IFIE), charge distribution, and orbital configuration. Electrostatic and van der Waals dispersion interactions were found to be equally important in molecular recognition. It was found that the inclusion of electron correlation was essential to obtain appropriate pictures. Other applications such as the photo-excitation process are also introduced.

DOI： 10.2477/jccj.6.185

CiNii Article

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Other Link： https://jlc.jst.go.jp/DN/JALC/00301036791?from=CiNii

Language：English   Publishing type：Research paper (other academic)  

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Publishing type：Research paper (scientific journal)  

DOI： 10.1002/jcc.20803

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Language：English   Publisher：AMER CHEMICAL SOC  

DOI： 10.1021/jp065705n

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

The fragment molecular orbital (FMO) scheme has been successfully used for a variety of large-scale molecules such as proteins and nucleic acids so far. We have applied the FMO calculations to the silicon-containing systems like polysilanes. The error caused by the fragmentation was examined by the Hartree-Fock method and the second-order Moller-Plesset (MP2) perturbation method for the ground state energy. The dynamic polarizability as a linear response property was also evaluated with and without the fragmentation. A series of numerical comparisons showed that the FMO scheme is applicable to silicon-based molecules with reasonable accuracy. This implied a potential availability of FMO calculations for the issues relevant to nanoscience and nanotechnology. (c) 2006 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2006.09.015

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

The fragment molecular orbital (FMO) scheme has been successfully used for a variety of large-scale molecules such as proteins and nucleic acids so far. We have applied the FMO calculations to the silicon-containing systems like polysilanes. The error caused by the fragmentation was examined by the Hartree-Fock method and the second-order Moller-Plesset (MP2) perturbation method for the ground state energy. The dynamic polarizability as a linear response property was also evaluated with and without the fragmentation. A series of numerical comparisons showed that the FMO scheme is applicable to silicon-based molecules with reasonable accuracy. This implied a potential availability of FMO calculations for the issues relevant to nanoscience and nanotechnology. (c) 2006 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2006.09.015

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

The ab initio fragment molecular orbital calculations were performed for molecular interactions of the whole estrogen receptor (ER) ligand-binding domain with a natural ligand, 17 ss-estradiol (EST). The interaction energies of the ligand at the residue level were calculated using HF and MP2 methods with several basis sets. The charge-transfer (CT) interactions were also analyzed based on configuration analysis for fragment interaction. Strong electrostatic interactions were observed between the EST and surrounding charged/polarized residues, Glu353, Arg394, His524, and Thr347. Weak electrostatic and significant van der Waals dispersion interactions were observed between the EST and the many surrounding hydrophobic residues. Together with the experimental interpretations, both interactions equally contributed to the total binding energies, and it was found that the inclusion of electron correlation was essential to obtain an appropriate picture of the interaction. The strongest interaction energy was observed between Glu353 and the EST, and the CT interactions from the lone- pair orbital of the carbonyl oxygen of Glu353 to the alpha*(OH) orbital of the hydroxyl group of EST were found to be important. The CT interactions from the lone- pair orbital of EST to the alpha*(NH) of Arg394 and from the lone- pair orbital of EST to the alpha*(NH) of His524 were also observed. These CT interactions occurred through the hydrogen-bond networks between the ER and EST. Therefore, electron donations from the ER to the EST and electron back-donations from EST to the ER were characteristic of ER-ligand binding. Our approach provides a powerful tool to understanding detailed molecular interactions at the quantum mechanical level.

DOI： 10.1021/jp060770i

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

We have realized a fully quantum mechanical treatment of large scale systems containing heavy metal atom, by introducing the model core potential (MCP) technique into the fragment molecular orbital (FMO) scheme. The scalar relativistic effects are incorporated by the use of MCP. This FMO/MCP method was applied to the divalent mercury ion hydrated, with 256 water molecules at the second-order Moller-Plesset (MP2) perturbation level. The complex between cisplatin and DNA was also calculated with MP2, where about a thousand of water molecules and dozens of sodium ions were employed for the explicit treatment of hydration. (c) 2006 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2006.06.103

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

We have realized a fully quantum mechanical treatment of large scale systems containing heavy metal atom, by introducing the model core potential (MCP) technique into the fragment molecular orbital (FMO) scheme. The scalar relativistic effects are incorporated by the use of MCP. This FMO/MCP method was applied to the divalent mercury ion hydrated, with 256 water molecules at the second-order Moller-Plesset (MP2) perturbation level. The complex between cisplatin and DNA was also calculated with MP2, where about a thousand of water molecules and dozens of sodium ions were employed for the explicit treatment of hydration. (c) 2006 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2006.06.103

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

The ab initio fragment molecular orbital calculations were performed for molecular interactions of the whole estrogen receptor (ER) ligand-binding domain with a natural ligand, 17 ss-estradiol (EST). The interaction energies of the ligand at the residue level were calculated using HF and MP2 methods with several basis sets. The charge-transfer (CT) interactions were also analyzed based on configuration analysis for fragment interaction. Strong electrostatic interactions were observed between the EST and surrounding charged/polarized residues, Glu353, Arg394, His524, and Thr347. Weak electrostatic and significant van der Waals dispersion interactions were observed between the EST and the many surrounding hydrophobic residues. Together with the experimental interpretations, both interactions equally contributed to the total binding energies, and it was found that the inclusion of electron correlation was essential to obtain an appropriate picture of the interaction. The strongest interaction energy was observed between Glu353 and the EST, and the CT interactions from the lone- pair orbital of the carbonyl oxygen of Glu353 to the alpha*(OH) orbital of the hydroxyl group of EST were found to be important. The CT interactions from the lone- pair orbital of EST to the alpha*(NH) of Arg394 and from the lone- pair orbital of EST to the alpha*(NH) of His524 were also observed. These CT interactions occurred through the hydrogen-bond networks between the ER and EST. Therefore, electron donations from the ER to the EST and electron back-donations from EST to the ER were characteristic of ER-ligand binding. Our approach provides a powerful tool to understanding detailed molecular interactions at the quantum mechanical level.

DOI： 10.1021/jp060770i

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY-BLACKWELL  

The ab initio fragment molecular orbital (FMO) calculations were performed for the cAMP receptor protein (CRP) complexed with a cAMP and DNA duplex to elucidate their sequence-specific binding and the stability of the DNA duplex, as determined by analysis of their inter- and intramolecular interactions. Calculations were performed with the AMBER94 force field and at the HF and MP2 levels with several basis sets. The interfragment interaction energies (IFIEs) were analyzed for interactions of CRP-cAMP with each base pair, DNA duplex with each amino acid residue, and each base pair with each residue. In addition, base-base interactions were analyzed including hydrogen bonding and stacking of DNA. In the interaction between DNA and CRP-cAMP, there was a significant charge transfer (CT) from the DNA to CRP. and this CT interaction played an important role as well as the electrostatic interactions. It is necessary to apply a quantum mechanical approach beyond the "classical" force-field approach to describe the sequence specificity. In the DNA intramolecular interaction, the dispersion interactions dominated the stabilization of the base-pair stacking interactions. Strong, attractive 1,2-stacking interactions and weak, repulsive 1,3-stacking interactions were observed. Comparison of the intramolecular interactions of free and complexed DNA revealed that the base-pairing interactions were stronger, and the stacking interactions were weaker, in the complexed structure. Therefore, the DNA duplex stability appears to change due to both the electrostatic and the CT interactions that take place under conditions of DNA-CRP binding. (c) 2006 Wiley Periodicals, Inc.

DOI： 10.1002/jcc.20399

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY-BLACKWELL  

The ab initio fragment molecular orbital (FMO) calculations were performed for the cAMP receptor protein (CRP) complexed with a cAMP and DNA duplex to elucidate their sequence-specific binding and the stability of the DNA duplex, as determined by analysis of their inter- and intramolecular interactions. Calculations were performed with the AMBER94 force field and at the HF and MP2 levels with several basis sets. The interfragment interaction energies (IFIEs) were analyzed for interactions of CRP-cAMP with each base pair, DNA duplex with each amino acid residue, and each base pair with each residue. In addition, base-base interactions were analyzed including hydrogen bonding and stacking of DNA. In the interaction between DNA and CRP-cAMP, there was a significant charge transfer (CT) from the DNA to CRP. and this CT interaction played an important role as well as the electrostatic interactions. It is necessary to apply a quantum mechanical approach beyond the "classical" force-field approach to describe the sequence specificity. In the DNA intramolecular interaction, the dispersion interactions dominated the stabilization of the base-pair stacking interactions. Strong, attractive 1,2-stacking interactions and weak, repulsive 1,3-stacking interactions were observed. Comparison of the intramolecular interactions of free and complexed DNA revealed that the base-pairing interactions were stronger, and the stacking interactions were weaker, in the complexed structure. Therefore, the DNA duplex stability appears to change due to both the electrostatic and the CT interactions that take place under conditions of DNA-CRP binding. (c) 2006 Wiley Periodicals, Inc.

DOI： 10.1002/jcc.20399

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

We have developed a linear response module to evaluate the dynamic polarizability, by accepting the fragment molecular orbital (FMO) scheme proposed by Kitaura. The module is parallelized in an integral-driven fashion with atomic-orbital indices in a local version Of ABINIT-MP program. The error caused by fragmentation was checked through test calculations on the water pentamer and the glycine pentamer. The error is shown to be small even under nonzero frequency, indicating the potential applicability of the FMO-based polarizability evaluation for large molecules. (c) 2005 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2005.11.014

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

We have developed a linear response module to evaluate the dynamic polarizability, by accepting the fragment molecular orbital (FMO) scheme proposed by Kitaura. The module is parallelized in an integral-driven fashion with atomic-orbital indices in a local version Of ABINIT-MP program. The error caused by fragmentation was checked through test calculations on the water pentamer and the glycine pentamer. The error is shown to be small even under nonzero frequency, indicating the potential applicability of the FMO-based polarizability evaluation for large molecules. (c) 2005 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2005.11.014

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

We have developed a visualized cluster analysis of protein-ligand interaction (VISCANA) that analyzes the pattern of the interaction of the receptor and ligand on the basis of quantum theory for virtual ligand screening. Kitaura et al. (Chem. Phys. Lett. 1999, 312, 319-324.) have proposed an ab initio fragment molecular orbital (FMO) method by which large molecules such as proteins can be easily treated with chemical accuracy. In the FMO method, a total energy of the molecule is evaluated by summation of fragment energies and interfragment interaction energies (IFIEs). In this paper, we have proposed a cluster analysis using the dissimilarity that is defined as the squared Euclidean distance between IFIEs of two ligands. Although the result of an ordered table by clustering is still a massive collection of numbers, we combine a clustering method with a graphical representation of the IFIEs by representing each data point with colors that quantitatively and qualitatively reflect the IFIEs. We applied VISCANA to a docking study of pharmacophores of the human estrogen receptor alpha ligand-binding domain (57 amino acid residues). By using VISCANA, we could classify even structurally different ligands into functionally similar clusters according to the interaction pattern of a ligand and amino acid residues of the receptor protein. In addition, VISCANA could estimate the correct docking conformation by analyzing patterns of the receptor-ligand interactions of some conformations through the docking calculation.

DOI： 10.1021/ci050262q

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Language：English   Publishing type：Part of collection (book)   Publisher：Elsevier  

The fragment molecular orbit (FMO) method relies on the division of a large molecular system into a collection of small fragments and on the molecular orbital (MO) calculations for the fragments (monomers) and their pairs (dimers) performed to obtain the total energy and other molecular properties. The ABINIT-MP software is a program code freely available on the web to perform the FMO calculations for biopolymers, such as proteins and nucleic acids. The chapter focuses on the recent developments of the ABINIT-MP software and some examples of its application to the MO calculations for proteins. The FMO calculations in the Hartree-Fock , the second-order Møller-Plesset perturbation , and the configuration interaction with singles approximations are now available in an efficiently parallelized fashion. The application examples are demonstrated for the virtual screening of ligand molecules for estrogen receptor and the evaluation of the excitation energy of photoactive yellow protein. ABINIT-MP software is developed to make ab initio calculations for biomolecules more efficient. © 2006 Elsevier B.V. All rights reserved.

DOI： 10.1016/B978-044452220-7/50066-6

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

We have developed a visualized cluster analysis of protein-ligand interaction (VISCANA) that analyzes the pattern of the interaction of the receptor and ligand on the basis of quantum theory for virtual ligand screening. Kitaura et al. (Chem. Phys. Lett. 1999, 312, 319-324.) have proposed an ab initio fragment molecular orbital (FMO) method by which large molecules such as proteins can be easily treated with chemical accuracy. In the FMO method, a total energy of the molecule is evaluated by summation of fragment energies and interfragment interaction energies (IFIEs). In this paper, we have proposed a cluster analysis using the dissimilarity that is defined as the squared Euclidean distance between IFIEs of two ligands. Although the result of an ordered table by clustering is still a massive collection of numbers, we combine a clustering method with a graphical representation of the IFIEs by representing each data point with colors that quantitatively and qualitatively reflect the IFIEs. We applied VISCANA to a docking study of pharmacophores of the human estrogen receptor alpha ligand-binding domain (57 amino acid residues). By using VISCANA, we could classify even structurally different ligands into functionally similar clusters according to the interaction pattern of a ligand and amino acid residues of the receptor protein. In addition, VISCANA could estimate the correct docking conformation by analyzing patterns of the receptor-ligand interactions of some conformations through the docking calculation.

DOI： 10.1021/ci050262q

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Elsevier  

A size-extensive modification is proposed for the configuration interaction with the Hartree-Fock (HF) reference plus single excitations (super-CI) for the orbital relaxation, where a partial renormalization is utilized. The way of renormalization owes to Ahlrichs's coupled pair functional. This proposal is named concurrent electron relaxation functional (CERF). The size-extensivity and performance of CERF are checked through test calculations. © 2005 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2005.05.066

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

We propose a modified version of configuration analysis (CA) for the fragment interaction in conjunction with Kitaura's fragment molecular orbital (FMO) scheme. The proposal is abbreviated as CAFI. The MO sets of fragments are merged and then orthonormalized by the use of a weighted Lowdin orthonormalization. The energy calculation is performed with the concurrent electron relaxation functional (CERF). The relaxation energy is obtained in an orbital-wise fashion and is distinguished as the charge-transfer and the polarization. The utility of CAM is demonstrated through test calculations on hydrogen-bonding systems. (c) 2005 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2005.05.079

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

A size-extensive modification is proposed for the configuration interaction with the Hartree-Fock (HF) reference plus single excitations (super-CI) for the orbital relaxation, where a partial renormalization is utilized. The way of renormalization owes to Ahlrichs's coupled pair functional. This proposal is named concurrent electron relaxation functional (CERF). The size-extensivity and performance of CERF are checked through test calculations. (c) 2005 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2005.05.066

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

We propose a modified version of configuration analysis (CA) for the fragment interaction in conjunction with Kitaura's fragment molecular orbital (FMO) scheme. The proposal is abbreviated as CAFI. The MO sets of fragments are merged and then orthonormalized by the use of a weighted Lowdin orthonormalization. The energy calculation is performed with the concurrent electron relaxation functional (CERF). The relaxation energy is obtained in an orbital-wise fashion and is distinguished as the charge-transfer and the polarization. The utility of CAM is demonstrated through test calculations on hydrogen-bonding systems. (c) 2005 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2005.05.079

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

We have developed a parallelized integral-direct solver for configuration interaction singles (CIS) in the ABINIT-MP program, by accepting the recently proposed multilayer fragment molecular orbital (MLFMO) method. In the MLFMO-CIS scheme, the region of interest in photoactive issues can be treated with the environmental potential at the Hartree-Fock (HF) level. The parallel efficiency is observed to be reasonable for the formaldehyde hydration system. A realistic applicability of the method is demonstrated for the photoactive yellow protein (PYP) including 125 amino acid residues. (c) 2005 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2005.03.008

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

We have developed a parallelized integral-direct solver for configuration interaction singles (CIS) in the ABINIT-MP program, by accepting the recently proposed multilayer fragment molecular orbital (MLFMO) method. In the MLFMO-CIS scheme, the region of interest in photoactive issues can be treated with the environmental potential at the Hartree-Fock (HF) level. The parallel efficiency is observed to be reasonable for the formaldehyde hydration system. A realistic applicability of the method is demonstrated for the photoactive yellow protein (PYP) including 125 amino acid residues. (c) 2005 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2005.03.008

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Publishing type：Research paper (international conference proceedings)  

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

We propose a parallelized integral-direct algorithm of the second-order Moller-Plesset perturbation theory (MP2) as a size-consistent correlated method. The algorithm is a modification of the recipe by Mochizuki et al. [(1996) Theor Chim Acta 93:211]. There is no need to communicate the bulky data of integrals across worker processes, keeping the formal fifth-power dependence on the number of basis functions. A multiple integral screening procedure is incorporated to reduce the operation costs effectively. An approximate MP2 density matrix can also be directly calculated through the integral contraction with orbital energies. We implement the MP2 code by accepting Kitaura&apos;s fragment molecular orbital (FMO) scheme as in the program ABINIT-MP developed by Nakano et al. [(2002) Chem Phys Lett 351:475]. The error in the FMO-MP2 energies is found to be within the order of the chemical accuracy. Timing and parallel acceleration results are shown for test molecules.

DOI： 10.1007/s00214-004-0602-3

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

We propose a parallelized integral-direct algorithm of the second-order Moller-Plesset perturbation theory (MP2) as a size-consistent correlated method. The algorithm is a modification of the recipe by Mochizuki et al. [(1996) Theor Chim Acta 93:211]. There is no need to communicate the bulky data of integrals across worker processes, keeping the formal fifth-power dependence on the number of basis functions. A multiple integral screening procedure is incorporated to reduce the operation costs effectively. An approximate MP2 density matrix can also be directly calculated through the integral contraction with orbital energies. We implement the MP2 code by accepting Kitaura&apos;s fragment molecular orbital (FMO) scheme as in the program ABINIT-MP developed by Nakano et al. [(2002) Chem Phys Lett 351:475]. The error in the FMO-MP2 energies is found to be within the order of the chemical accuracy. Timing and parallel acceleration results are shown for test molecules.

DOI： 10.1007/s00214-004-0602-3

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

We have recently developed a parallelized integral-direct algorithm for the second-order Moller-Plesset perturbation theory (MP2) and implemented it into the ABINIT-MP program of the fragment molecular orbital (FMO) scheme. A flexible parallelization is possible by combining the fragment indices (upper level) and the two-electron integral indices (lower level) on distributed computational resources, leading to an enhancement of in-core processings. In this Letter, we carry out a series of benchmark FMO-MP2 calculations of realistic proteins consisting of the tens of thousands of basis functions. The performance is shown to be high, indicating that the ABINIT-MP program is easily applicable to the realistic systems. (C) 2004 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2004.08.082

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

We have recently developed a parallelized integral-direct algorithm for the second-order Moller-Plesset perturbation theory (MP2) and implemented it into the ABINIT-MP program of the fragment molecular orbital (FMO) scheme. A flexible parallelization is possible by combining the fragment indices (upper level) and the two-electron integral indices (lower level) on distributed computational resources, leading to an enhancement of in-core processings. In this Letter, we carry out a series of benchmark FMO-MP2 calculations of realistic proteins consisting of the tens of thousands of basis functions. The performance is shown to be high, indicating that the ABINIT-MP program is easily applicable to the realistic systems. (C) 2004 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2004.08.082

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Language：Japanese   Publisher：Society of Computer Chemistry, Japan  

Integral transformation from basis functions to molecular orbitals is necessary in configuration-based correlation treatments of molecular orbital calculations. In particular, the processing of two-electron integrals having fourth power dependence of the number of basis functions can be costly, thus care should be taken to reduce the operation counts as far as possible. In this contribution, we report a development of integral transformation modules, based on Yamamoto-Nagashima's algorithm (<I>J. Comp. Chem.</I>, <B>9</B>, 627 (1988)) by which only non-zero integrals within threshold are efficiently processed. The BLAS routines, DAXPY and DDOT are used in the innermost part of the transformation step.

DOI： 10.2477/jccj.3.1

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Other Link： https://jlc.jst.go.jp/DN/JALC/00237366801?from=CiNii

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

The dehydrogenation of methanol on Pt(1 1 1)/water and Pt(1 1 1)/vacuum interfaces was investigated by using ab initio theoretical calculations. Possible reactive intermediate structures were optimized, and energetically favorable reaction pathways were traced at these two interfaces. When all products formed through the dehydrogenation remained on a Pt(1 1 1) surface, the reaction energy of a whole dehydrogenation was smaller at the Pt(1 1 1)/water interface than that at the Pt(1 1 1)/vacuum interface by about 0.7 eV. (C) 2003 Elsevier B.V. All rights reserved.

DOI： 10.1016/S0009-2614(03)01144-8

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

The dehydrogenation of methanol on Pt(1 1 1)/water and Pt(1 1 1)/vacuum interfaces was investigated by using ab initio theoretical calculations. Possible reactive intermediate structures were optimized, and energetically favorable reaction pathways were traced at these two interfaces. When all products formed through the dehydrogenation remained on a Pt(1 1 1) surface, the reaction energy of a whole dehydrogenation was smaller at the Pt(1 1 1)/water interface than that at the Pt(1 1 1)/vacuum interface by about 0.7 eV. (C) 2003 Elsevier B.V. All rights reserved.

DOI： 10.1016/S0009-2614(03)01144-8

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

The prolapse problem in the four-component relativistic Gaussian basis sets, recently developed by Koga, Tatewaki, and Matsuoka for the atoms H-1 through Lr-103, is discussed. Deficiency in the number of s(+), basis functions is pointed out for the atoms in the fourth and higher periods. A small prolapse is detected in the p(-) symmetry of the sixth and seventh period atoms. However, no problem is found for the remaining five symmetries. (C) 2003 Published by Elsevier Science B.V.

DOI： 10.1016/S0009-2614(03)00873-X

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

The prolapse problem in the four-component relativistic Gaussian basis sets, recently developed by Koga, Tatewaki, and Matsuoka for the atoms H-1 through Lr-103, is discussed. Deficiency in the number of s(+), basis functions is pointed out for the atoms in the fourth and higher periods. A small prolapse is detected in the p(-) symmetry of the sixth and seventh period atoms. However, no problem is found for the remaining five symmetries. (C) 2003 Published by Elsevier Science B.V.

DOI： 10.1016/S0009-2614(03)00873-X

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

Ab initio calculations have been performed to study the structures of thorium(IV) hydrate and its hydrolysis products in aqueous solution. The conductor-like polarizable continuum model (CPCM) has been used to perform geometry optimization calculations in aqueous solution. The calculated results demonstrate that the molecule geometries obtained in solvent are generally consistent with the experiments. The coordination number of thorium(IV) hydrolysis products has been investigated. The effect of the relativistic effective core potential (RECP) on the structures is also discussed. (C) 2003 Elsevier Science B.V. All rights reserved.

DOI： 10.1016/S0009-2614(03)00806-6

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

Ab initio calculations have been performed to study the structures of thorium(IV) hydrate and its hydrolysis products in aqueous solution. The conductor-like polarizable continuum model (CPCM) has been used to perform geometry optimization calculations in aqueous solution. The calculated results demonstrate that the molecule geometries obtained in solvent are generally consistent with the experiments. The coordination number of thorium(IV) hydrolysis products has been investigated. The effect of the relativistic effective core potential (RECP) on the structures is also discussed. (C) 2003 Elsevier Science B.V. All rights reserved.

DOI： 10.1016/S0009-2614(03)00806-6

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

The hydrolysis reaction of the tetravalent thorium (Th4+) ion was investigated by ab initio theoretical calculations on hydration complex models. The transition state structure was optimized, and the intrinsic reaction coordinate was traced. The results showed that the hydrolysis is highly exothermic and the transition state is close to the reactant. Reaction dependency upon the number of non-reactive water molecules was examined. (C) 2003 Elsevier Science B.V. All rights reserved.

DOI： 10.1016/S0009-2614(03)00592-X

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER INST PHYSICS  

All-electron Dirac-Hartree-Fock calculations were performed to investigate the electronic structure of curium fluoride molecules (CmFn, n = 1-4). The curium-fluorine distances, atomization energies, and Mulliken populations were all evaluated. The bonding was found to be of ionic type with the electron delocalization primarily from F 2p to Cm 6d, where the formal configurations of Cm were 7s(2)5f(7), 5f(7)7s(1), 5f(7), 5f(6) for n = 1, 2, 3, 4, respectively. The 2p-6d delocalization is significant in the tetrafluoride. For comparison, the isovalent gadolinium fluorides were also studied. CmF4 exists but GdF4 does not, reflecting the fact that 5f(7) in CmF3 is less stable than 4f(7) in GdF3. (C) 2003 American Institute of Physics.

DOI： 10.1063/1.1568075

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

The hydrolysis reaction of the tetravalent thorium (Th4+) ion was investigated by ab initio theoretical calculations on hydration complex models. The transition state structure was optimized, and the intrinsic reaction coordinate was traced. The results showed that the hydrolysis is highly exothermic and the transition state is close to the reactant. Reaction dependency upon the number of non-reactive water molecules was examined. (C) 2003 Elsevier Science B.V. All rights reserved.

DOI： 10.1016/S0009-2614(03)00592-X

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Elsevier  

Electronic structures of hydrate complex models of Th4+ and Ac3+ ions (Th(H2O)n 4+ and Ac(H2O)n 3+ (n=1,2,4,6)) were investigated by all-electron four-component relativistic calculations based on the Dirac-Hartree-Fock (DHF) method. Picture of the coordinate bond in the complexes was observed, and the difference between Th4+ and Ac3+ cases was shown. Relativistic effective-core potential (RECP) calculations were also performed on the higher hydrate models to assess the bulk solvation effect by using the conductive polarizable continuum model (CPCM) reaction-field scheme. © 2003 Elsevier Science B.V. All rights reserved.

DOI： 10.1016/S0009-2614(03)00373-7

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

Electronic structures of hydrate complex models of Th4+ and Ac3+ ions (Th(H2O)n(4)(+) and Ac(H-2)(n)(3+) (n = 1,2,4,6)) were investigated by all-electron four-component relativistic calculations based on the Dirac-Hartree-Fock (DHF) method. Picture of the coordinate bond in the complexes was observed, and the difference between Th4+ and Ac3+ cases was shown. Relativistic effective-core potential (RECP) calculations were also performed on the higher hydrate models to assess the bulk solvation effect by using the conductive polarizable continuum model (CPCM) reaction-field scheme. (C) 2003 Elsevier Science B.V. All rights reserved.

DOI： 10.1016/S0009-2614(03)00373-7

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

Adding the tight and diffuse Gaussian-type functions (GTFs), Faegri's variationally determined double-zeta-quality basis sets for molecular relativistic calculations are examined. An example atom is Cm. When the tight s-type GTF is added the total energy increases, whereas when diffuse GTFs are added the total energy decreases. The reasons for these findings are clarified. It is also pointed out that not only the Faegri's sets but also other variationally determined basis sets would show similar behavior so far as the expansion terms are not sufficient.

DOI： 10.1007/s00214-002-0412-4

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Language：English   Publishing type：Research paper (scientific journal)  

Adding the tight and diffuse Gaussian-type functions (GTFs), Faegri's variationally determined double-zeta-quality basis sets for molecular relativistic calculations are examined. An example atom is Cm. When the tight s-type GTF is added the total energy increases, whereas when diffuse GTFs are added the total energy decreases. The reasons for these findings are clarified. It is also pointed out that not only the Faegri's sets but also other variationally determined basis sets would show similar behavior so far as the expansion terms are not sufficient.

DOI： 10.1007/s00214-002-0412-4

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Language：English   Publishing type：Research paper (other academic)  

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Language：English   Publishing type：Research paper (scientific journal)  

Mono-ammine complexes of trivalent f0, f7, and f14 ions were investigated by using all-electron four-component relativistic calculations based on the Dirac-Hartree-Fock (DHF) method. Relativistic second-order Møller-Plesset perturbation (RMP2) calculations were also performed to incorporate electron correlation for the closed-shell systems. A comparison with the previous data of the aqua complexes showed that the ammine complex provides longer metal-ligand distance, larger stabilization energy, and larger amount of electron donation than the aqua complex does for a certain metal ion. © 2002 Elsevier Science B.V. All rights reserved.

DOI： 10.1016/S0009-2614(02)00727-3

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

Mono-ammine complexes of trivalent f(0), f(7), and f(14) ions were investigated by using all-electron four-component relativistic calculations based on the Dirac-Hartree-Fock (DHF) method. Relativistic second-order Mphiller-Plesset perturbation (RMP2) calculations were also performed to incorporate electron correlation for the closed-shell systems. A comparison with the previous data of the aqua complexes showed that the ammine complex provides longer metal-ligand distance, larger stabilization energy, and larger amount of electron donation than the aqua complex does for a certain metal ion. (C) 2002 Elsevier Science B.V. All rights reserved.

DOI： 10.1016/S0009-2614(02)00727-3

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER INST PHYSICS  

Dirac-Hartree-Fock (DHF) calculations were performed to investigate the hydration of the trivalent Cm ion with a 5f(7) configuration on the models of Cm(H2O)(n)(3+) (n=1,2,4,6). The curium-oxygen distances and stabilization energies were evaluated. The DHF wave functions were analyzed by the Mulliken populations and spinor projections. Hydration was found to be characterized by the coordinate bond. An increase in the number of water molecules caused an increase in the curium-oxygen distance and a reduction of the stabilization energy per water molecule. The fluorescence transition energy was also estimated using the complete open-shell configuration interaction (COSCI) method. Redshifts due to hydration were obtained and were in accord with observations of the nephelauxetic effect. The isovalent gadolinium ion Gd3+ was also studied for comparison. (C) 2002 American Institute of Physics.

DOI： 10.1063/1.1473803

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER INST PHYSICS  

Dirac-Hartree-Fock (DHF) calculations were performed to investigate the hydration of the trivalent Cm ion with a 5f(7) configuration on the models of Cm(H2O)(n)(3+) (n=1,2,4,6). The curium-oxygen distances and stabilization energies were evaluated. The DHF wave functions were analyzed by the Mulliken populations and spinor projections. Hydration was found to be characterized by the coordinate bond. An increase in the number of water molecules caused an increase in the curium-oxygen distance and a reduction of the stabilization energy per water molecule. The fluorescence transition energy was also estimated using the complete open-shell configuration interaction (COSCI) method. Redshifts due to hydration were obtained and were in accord with observations of the nephelauxetic effect. The isovalent gadolinium ion Gd3+ was also studied for comparison. (C) 2002 American Institute of Physics.

DOI： 10.1063/1.1473803

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

Iterations of the Fock matrix construction from two-electron integrals completely dominates the total cost of direct self-consistent-field (DSCF) calculations, especially for the four-component Dirac-Hartree-Fock (DHF) relativistic molecular-orbital method. We revive here the notion of vectorization as helpful to accelerate DSCF-DHF calculations. DIRAC is a representative state-of-the-art DHF code on which we consider the vectorized Fock matrix construction. While the integral generation is straightforwardly vectorizable, the contraction of generated integrals with associated densities into the Fock matrix elements is unable to vectorize simply due to frequent address conflicts. In this report, we present a vectorization of the direct Fock matrix construction by introducing a working-array technique. Total vectorization efficiency for DHF runs is improved from 50-60% by the original DIRAC to more than 90% by the modified version.

DOI： 10.3327/jnst.39.195

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

Response theory calculations in the random phase approximation are applied to linear polarizabilities and second hyperpolarizabilities of 1-, 2-, and 3-dimensional hydrogen-terminated silicon clusters. Successive enlargement of the clusters to embody on the order of 50 silicon atoms plus bond-saturating hydrogen atoms allows for extrapolation to bulk values of individual silicon atom contributions in the 1D and 3D cases. Modern effective core potentials are shown to provide excellent approximations to the all-electron values in all cases; errors for both polarizabilities and hyperpolarizabilities are on the order of 1%. The findings indicate considerable time savings in predictions of the electric polarizability properties of elements beyond the first row atoms.

DOI： 10.1021/jp012654f

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Taylor \& Francis  

We have performed a series of ab initio relativistic molecular-orbital calculations to model the hydration of trivalent curium ion. Up to the hexa-hydrate model, Dirac-Hartree-Fock calculations as a four-component recipe were used to investigate the interaction between the ion and water molecules. The fluorescence transition energy was estimated by complete open-shell configuration interaction calculations. Hydrates having more than six water molecules were treated using the B3LYP hybrid density-functional theory with effective-core potential. © 2002 Atomic Energy Society of Japan.

DOI： 10.1080/00223131.2002.10875496

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

Response theory calculations in the random phase approximation are applied to linear polarizabilities and second hyperpolarizabilities of 1-, 2-, and 3-dimensional hydrogen-terminated silicon clusters. Successive enlargement of the clusters to embody on the order of 50 silicon atoms plus bond-saturating hydrogen atoms allows for extrapolation to bulk values of individual silicon atom contributions in the 1D and 3D cases. Modern effective core potentials are shown to provide excellent approximations to the all-electron values in all cases; errors for both polarizabilities and hyperpolarizabilities are on the order of 1%. The findings indicate considerable time savings in predictions of the electric polarizability properties of elements beyond the first row atoms.

DOI： 10.1021/jp012654f

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Language：English   Publishing type：Research paper (scientific journal)  

Iterations of the Fock matrix construction from two-electron integrals completely dominates the total cost of direct self-consistent-field (DSCF) calculations, especially for the four-component Dirac-Hartree-Fock (DHF) relativistic molecular-orbital method. We revive here the notion of vectorization as helpful to accelerate DSCF-DHF calculations. DIRAC is a representative state-of-the-art DHF code on which we consider the vectorized Fock matrix construction. While the integral generation is straightforwardly vectorizable, the contraction of generated integrals with associated densities into the Fock matrix elements is unable to vectorize simply due to frequent address conflicts. In this report, we present a vectorization of the direct Fock matrix construction by introducing a working-array technique. Total vectorization efficiency for DHF runs is improved from 50–60% by the original DIRAC to more than 90% by the modified version. © 2002 Taylor and Francis Group, LTD.

DOI： 10.1080/18811248.2002.9715175

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Language：English   Publishing type：Research paper (scientific journal)  

We have performed a series of ab initio relativistic molecular-orbital calculations to model the hydration of trivalent curium ion. Up to the hexa-hydrate model, Dirac-Hartree-Fock calculations as a four-component recipe were used to investigate the interaction between the ion and water molecules. The fluorescence transition energy was estimated by complete open-shell configuration interaction calculations. Hydrates having more than six water molecules were treated using the B3LYP hybrid density-functional theory with effective-core potential. © 2002 Atomic Energy Society of Japan.

DOI： 10.1080/00223131.2002.10875496

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Language：English   Publishing type：Research paper (scientific journal)  

A simple set of rules were formulated that allows to easily transform nonrelativistic basis sets of GTFs into their relativistic analogs. The relativistic basis sets were obtained by augmenting the nonrelativistic ones by auxiliary GTFs determined from relativistic DFR calculations for hydrogen ions. By properly modifying the nonrelativistic KTS basis sets, the Dirac-Fock energies of lanthanide and actinide atoms were predicted with the accuracy up to 4-9 mhartree and 21-42 mhartree, respectively.

DOI： 10.1063/1.1415080

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Language：English   Publishing type：Research paper (scientific journal)  

Complexes between a water molecule and trivalent lanthanoid and actinoid ions were investigated by all-electron four-component relativistic calculations using the Dirac-Hartree -Fock (DHF) method. DHF-based relativistic second-order Møller-Plesset perturbation (RMP2) calculations were also performed to incorporate electron correlation for the closed-shell systems. Non-relativistic calculations using the HF and MP2 methods were carried out in parallel to compare with the DHF and RMP2 results. Metal-oxygen distances and stabilization energies were evaluated, and a separability between relativity and correlation was found. Mulliken population analysis and spinor projection were used to analyze the wave functions, and a nature of coordinate bond was revealed. © 2001 Elsevier Science B.V. All rights reserved.

DOI： 10.1016/S0301-0104(01)00483-9

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

Complexes between a water molecule and trivalent lanthanoid and actinoid ions were investigated by all-electron four-component relativistic calculations using the Dirac-Hartree-Fock (DHF) method. DHF-based relativistic second-order Moller-Plesset perturbation (RMP2) calculations were also performed to incorporate electron correlation for the closed-shell systems. Non-relativistic calculations using the HF and MP2 methods were carried out in parallel to compare with the DHF and RMP2 results. Metal-oxygen distances and stabilization energies were evaluated, and a separability between relativity and correlation was found. Mulliken population analysis and spinor projection were used to analyze the wave functions, and a nature of coordinate bond was revealed. (C) 2001 Elsevier Science B.V. All rights reserved.

DOI： 10.1016/S0301-0104(01)00483-9

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER INST PHYSICS  

A simple method is proposed in which basis sets of Gaussian-type functions (GTFs), suitable for relativistic Dirac-Fock-Roothaan (DFR) calculations, are derived from their nonrelativistic analogs. The relativistic basis set is obtained through augmenting the nonrelativistic one by several GTFs determined from relativistic calculations for hydrogen-like atoms. The usefulness and reliability of the method is illustrated by DFR calculations of the ground-state energies of lanthanide and actinide atoms. (C) 2001 American Institute of Physics.

DOI： 10.1063/1.1415080

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society  

Isobaric vapor-liquid equilibria were measured for the four binary systems of perfluoro-2-methylpentane (FC-5114mmyc2) + perfluorooctane (FC-7118mc6), 1,1,1,2,2,3,3,4,4-nonafluorohexane (HFC-569mccf) + octane, 2,2,2-trifluorodiethyl ether (HFE-356mf-f) + butyl ethyl ether, and methylperfluoroisopropyl ether (HFE-347 mmy) + heptane at atmospheric pressure. The HFE-356mf-f + butyl ethyl ether system formed a minimum boiling azeotrope. The experimental data except for those for the FC-5114mmyc2 + FC-7118mc6 system were correlated by the Wilson and NRTL activity coefficient models. The Wilson and NRTL equations gave similar results. The VLE for the FC-5114mmyc2 + FC-7118mc6 system was predicted to be an ideal solution.

DOI： 10.1021/je000192d

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：MUNKSGAARD INT PUBL LTD  

The nitrogen K-shell X-ray absorption spectra of the purine bases present in nucleic acids, adenine and guanine, were analyzed by using ab initio Hartree-Fock static exchange and restricted-active-space self-consistent-field calculations. A variety of derivative molecules were calculated to investigate the energetic shifts due to environmental effects on the nitrogen atoms. Shake-up excitations were also addressed.

DOI： 10.1107/S0909049500017696

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

The polarizability of hydrogen-terminated silicon dusters derived from the silicon diamond-lattice structure was evaluated by linear response calculations. The dependences on cluster size and basis set were systematically investigated. A convergence in calculated polarizability per silicon atom toward the bulk value was found. Frequency-dependent polarizabilities were also addressed. (C) 2001 Elsevier Science B.V. All rights reserved.

DOI： 10.1016/S0009-2614(01)00176-2

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Language：English   Publishing type：Research paper (other academic)  

DOI： 10.1107/S0909049500017696

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Language：English   Publishing type：Research paper (other academic)  

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

The near-edge X-ray absorption fine structure (NEXAFS) spectrum at the sulphur K-edge of the cysteine amino acid is simulated by the ab initio Hartree-Fock static-exchange method. Several forms of cysteine are investigated, including neutral, zwitterionic and water-solvated forms. The simulations indicate that the presence of an environment induces a small lowering of the edge position in the spectrum of the neutral form. (C) 1999 Elsevier Science B.V. All rights reserved.

DOI： 10.1016/S0009-2614(99)00684-3

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

The electronic structure of the CuSi molecule was examined using the multireference coupled pair-approximation (MRCPA) following multireference single and double excitation configuration interaction calculations. We found the ground state to be the (2)Pi state, and we evaluated the bond length, dissociation energy, vibrational frequency, and dipole moment for the (2)Pi ground state and for low-lying (4)Sigma(-) and (2)Delta excited states. The dissociation energy of the (2)Pi. ground state by MRCPA is 2.13 eV, which agrees well with the experimental value of 2.26 eV. The inclusion of higher excitations by MRCPA significantly improves the description of the bonding and the accuracy of the spectroscopic constants.

DOI： 10.1007/s002140050449

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

Coupled pair approximation and configuration interaction calculations were carried out on the gallium fluoride molecule and its positive ion with flexible basis sets. Spectroscopic constants of these species were examined in detail through step-wise extensions of correlating space. The contribution from correlations of the semi-core 3d electrons in Ga was found to be sizable. The bonding character was revealed to be highly ionic even for the positive ion.

DOI： 10.1007/s002140050438

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

Fourth-order multi-reference coupled pair approximation (MRCPA-4) calculations were performed to predict spectroscopic constants of the gallium nitride (GaN) diatomic molecule. The calculations showed that the ground state is (3)Sigma(-) but that the (3)Pi state is low lying and separated from the former by 0.5 eV. The contribution of the correlations among the Ga 3d semi-core electrons was found to be crucial for a quantitative description of the molecule.

DOI： 10.1007/s002140050443

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Publisher：World Scientific  

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Publisher：Tokai  

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

Spectroscopic constants for the ground and low-lying excited electronic states of the Ga-2 molecule have been studied using MRSDCI and MRCPA methods with an extensive basis set of Gaussian-type functions. In this study, we are going to present spectroscopic constants and potential energy curves for the ground (3)Pi(u) and the excited (3)Sigma(g)(-), (1)Sigma(g)(+), (1)Pi(u), (1)Delta(g), (2) (1)Sigma(g)(+) and (3)Sigma(u)(-) states, in which electron correlation between semi-valence (3d) and valence (4s,(4) over bar p) and among valence electrons is taken into account. Our calculated vibrational frequency for the ground state, (3)Pi(u), is 175 cm(-1) by CISD with Davidson's correction and 170 cm(-1) by MRCPA, which are in good agreement with the experimental value of 180 cm(-1). The dissociation energy for the ground state, reported to be 1.28 eV, compares well with the experimental value of 1.4 eV. Avoided crossing between the two lowest (1)Sigma(g)(+) states was properly described by MRCPA. (C) 1998 Elsevier Science B.V. All rights reserved.

DOI： 10.1016/S0166-1280(98)00160-2

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

Doping profiles of pn-junctions for GaN-based laser diode structures were studied using SIMS and EBIC measurements. Mg impurity, a p-type dopant, was found to diffuse heavily into the n-type region of the order of 10(17) cm(-3) when a sample is grown on a sapphire substrate. This unwanted diffusion appears closely related to the presence of threading dislocations, and can be eliminated by using high-quality GaN substrates for epitaxial growth. (C) 1998 Elsevier Science B.V. All rights reserved.

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

The gallium monohydride (GaH) molecule and its positive ion were theoretically investigated by abinitio molecular orbital calculations with a flexible basis set including g-type functions on the Ga atom. Electron correlations among not only the valence electrons of Ga 4s4p and H 1s but also the semi-core electrons of Ga 3d were incorporated by a size-consistent scheme of the coupled pair approximation. The contribution of the 3d electron correlation was found to be considerable on spectroscopic constants of both GaH and GaH+, especially on the bond length.

DOI： 10.1007/s002140050308

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER INST PHYSICS  

Valence band structures and their strain effects in GaN have been investigated by optical spectroscopy for thick GaN films with high optical quality grown by hydride vapor phase epitaxy. Excitons associated with the A, B, and C valence bands an clearly observed in reflectance measurements without modulation techniques. It is found that the exciton energies shift with the film thickness because of the relaxation of the residual, strain. From the quantitative analysis of this behavior, we have precisely determined the valence band splitting parameters in GaN as Delta(1)=10 meV, Delta(2)=5.5 meV, and Delta(3)=6.0 meV. (C) 1998 American Institute of Physics.

DOI： 10.1063/1.367217

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Language：English   Publishing type：Research paper (international conference proceedings)   Publisher：MATERIALS RESEARCH SOCIETY  

Valence band modification by uniaxial stress in GaN is investigated by reflectance spectroscopy. It is observed that the energy separation between the A and B valence bands increases with the applied uniaxial stress in the c-plane. Changes of the wavefunctions by the stress are also investigated by the polarization characteristics of the reflectance spectra. The experimental results are analyzed on the basis of k.p theory, and deformation potential D-5 is experimentally determined as -3.3 eV. It is indicated that the uniaxial strain effect could be utilized for improving GaN-based laser performance.

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Publisher：Springer  

DOI： 10.1007/s002140050289

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Publisher：Google Patents  

US Patent 5,675,806

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

Spectroscopic constants of the ground state of the As, molecule have been evaluated using a series of complete active space self-consistent-field and second-order configuration interaction calculations with all-electron basis jets. Angular correlation is found to contribute significantly to the dissociation energy. The calculation with a set of [8s6p3d2flg] basis functions gives 3.58 eV for the dissociation energy. in contrast to the experimental value of 3.99 eV. (C) 1997 Elsevier Science B.V.

DOI： 10.1016/S0009-2614(97)00655-6

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER INST PHYSICS  

The uniaxial stress effects on valence band structures in GaN are investigated by reflectance spectroscopy. It is observed that the energy separation between A and B valence bands increases with the application of uniaxial stress in the c plane. The experimental results are analyzed on the basis of the k.p theory, and deformation potential D-5 is determined as -3.3 eV. It is indicated that the uniaxial strain effect could be utilized for improving GaN-based laser performance. (C) 1997 American Institute of Physics.

DOI： 10.1063/1.119541

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

Ab initio molecular orbital calculations are performed to investigate the three successive surface reactions of GaN with HCl. These reactions correspond to the simplest model which accounts for GaN chemical etching by HCl. We observed two characteristic points about these reactions. First, all of these reactions are exothermic and the reaction energies are about 20-29kcal/mol. Second, the activation energy of the reaction decreases as the number of Ga-Cl bonds increases. The calculation shows that the first reaction of the GaN surface with HCl is the rate-determining one and the calculated reaction barrier is less than 10kcal/mol.

DOI： 10.1143/jjap.35.L1641

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

A direct configuration interaction (CI) scheme using the generalized double symbolism both for the external space and for the internal space is proposed in an integral-driven context. The reason why the double symbolism is used in the present formulation is that the main target is in investigating large molecular systems. The integrals, configuration state functions, and energy expressions are systematically classified in terms of the orbital labels and their mutual relations. Various types of CI wavefunctions can be set up flexibly. The resulting structure of integral processings in the sigma vector construction is complicated. The number of unique loop types for two-electron integrals is 1325. Because the parallel architecture is gaining importance in the recent computational platforms, the parallelism is also addressed.

DOI： 10.1007/s002140050148

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Publisher：Google Patents  

US Patent 5,505,159

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Springer New York  

A direct configuration interaction (CI) scheme using the generalized double symbolism both for the external space and for the internal space is proposed in an integral-driven context. The reason why the double symbolism is used in the present formulation is that the main target is in investigating large molecular systems. The integrals, configuration state functions, and energy expressions are systematically classified in terms of the orbital labels and their mutual relations. Various types of CI wavefunctions can be set up flexibly. The resulting structure of integral processings in the sigma vector construction is complicated. The number of unique loop types for two-electron integrals is 1325. Because the parallel architecture is gaining importance in the recent computational platforms, the parallelism is also addressed.

DOI： 10.1007/bf01113418

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Publisher：Google Patents  

US Patent 5,469,806

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：JAPAN J APPLIED PHYSICS  

A schematic reaction mechanism is proposed to explain the Ti/TiN chemical vapor deposition (CVD) process using the TiCl4 molecule as the source species. The scheme can be considered as two successive steps: (I) TiCl4 molecules are adsorbed onto surface reactive sites through concerted electron delocalizations, (II) ambient reducing agents such as H-2 or NH3 reactively eliminate Cl atoms from Ti atoms in the form of HCl. Preliminary molecular orbital (MO) calculations indicate that step (I) is an energetically easy process. Conversely, step (II) is expected to be the rate-determining process with a considerable activation energy. As a whole, the characteristics of resultant CVD films (e.g., the conformality) are probably controlled not by the TiCl4-adsorption step (I) but by the Cl elimination step (II).

DOI： 10.1143/JJAP.34.L326

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

Ab initio molecular orbital calculations are performed to investigate the GaAs growth through a direct reaction between AsH3 and the adsorbed GaCl (symbolically written as GaClads). The formal reaction scheme is represented as GaClads + AsH3 --&gt; Ga(AsH2)(ads) + HCl, where the electron delocalization is the driving factor. The reason why the direct AsH3/GaClads reaction presents a very fast growth rate is attributed to the existence of a stable precursor state that occurs before the four-centered transtion state.

DOI： 10.1016/0022-0248(94)00644-X

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

Ab initio molecular orbital calculations were performed to systematically investigate the chloride atomic layer epitaxy (ALE) process of GaAs. In the Ga layer formation, the GaCl molecular as a source is first adsorbed onto the As dangling-bond (DB) site through electronic ''configuration mixing''. Consequently, the ambient H2 reactively eliminates the Cl atom as HCl, where the ''electron delocalization'' is the driving factor of reaction. As layer formation via As2 adsorption onto the Ga-DB site was also investigated. The results show that the pi orbitals of As2 are used to form the As-Ga bonds through ''configuration mixing'', as in the case of GaCl/As-DB. The calculated energetics are consistent with the experimental data.

DOI： 10.1016/0169-4332(94)90217-8

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

The cluster model As2-(GaH2)4 is used for ab initio complete active space self-consistent-field (CASSCF) molecular-orbital calculations, to investigate the electronic mechanism of As2 desorption from the fourfold-hollow Ga dangling-bond (DB) site. The electronic state of the adsorbed As2 is revealed to be the sigma(g)2pi(u)2pi(g)2 doubly excited configuration, where the free As2 Molecule is characterized by sigma(g)2pi(u)4 with the triple bond. Namely, the four pi orbitals of the As2 unit are used to form the four Ga-As covalent bonds with the Ga-DB site and a weak sigma bond remains between the two As atoms. The calculated CASSCF wave functions indicate that the desorption process could be just the chemical reaction of multiple bond conversions having strong electron correlations due to the near degeneracy. The single-configurational picture is completely invalid in understanding the As2 desorption. The transition state is found to be of the ''late-barrier'' type, and from this the ''cold'' vibrational distribution of the desorbed AS2 ig predicted.

DOI： 10.1103/PhysRevB.49.4658

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

The chloride ALE (atomic layer epitaxy) technique is now common to grow GaAs crystals, where the GaCl molecule is used to supply Ga atoms for the As dangling bond site. The present ab initio molecular orbital calculations predict that Cl atoms are desorbed as HCI by the single-site reaction which is induced by H-2. The reaction scheme is represented as &gt; GaCl + H-2 --&gt; &gt; GaH + HCI, which is driven by the concerted electron delocalizations among those four atoms. It is shown that the reaction is endothermic by the amount of 30 kcal/mol and occurs through the four-centred transition state of ''late-barrier'' type. The activation energy is estimated to be 37-44 kcal/mol, which agrees well with the experimental value of 40-50 kcal/mol.

DOI： 10.1016/0022-0248(94)90749-8

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Language：English   Publisher：東北大学  

CiNii Article

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMERICAN PHYSICAL SOC  

Ab initio molecular-orbital calculations have been carried out on the ground, excited, and ionized states of the gallium monochloride GaCl, which is used as a source molecule to generate Ga layers in GaAs epitaxial crystal growth. The calculated spectroscopic constants show good agreement with the experimental data. The calculated molecular properties of GaCl explain reasonably well the mechanism of its adsorption onto the As surface. The adsorption process is investigated by using a cluster model of GaCl-(AsH2)2. The adsorption is found to occur as the result of covalent-bond formation with the As atoms through electronic-configuration mixing.

DOI： 10.1103/PhysRevB.47.13420

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：JAPAN J APPLIED PHYSICS  

A new concerted mechaniSM is proposed to explain the Cl removal from the adsorbed GaCl on the outermost As surface, by the ab initio configuration interaction (CI) calculations on the simple model system of H2GaCl + H-2. The proposed reaction scheme is written as &gt;GaCl + H-2 --&gt; &gt;GaH + HCl which occurs through the single-site collision of H-2 with the adsorbed GaCl on the surface. Concerted electron delocalizations induced by H-2 is the driving force to proceed the reaction. The present calculation predicts that the reaction is endothermic with an energy of 29 kcal/mol and has a four-centered transition state. The estimated activation energy is 83 kcal/mol, which will be reduced by improving the present cluster model.

DOI： 10.1143/JJAP.32.L197

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：NEC CORPORATION  

The chloride ALE (Atomic Layer Epitaxy) process of GaAs crystals is theoretically studied by the ab initio Molecular Orbital (MO) calculations. The electron correlations are carefully considered to obtain correct descriptions of the GaAs electronic states. For the growth of Ga layers, Ga atoms are supplied as a form of GaCl to the As surface, and then the GaCl is adsorbed onto the As DB (Dangling Bond) site. The computational results are summarized as follows; (1) the GaCl overrides the potential barrier during the adsorption, (2) the valence excitation of Ga 4s --&gt; 4p pi in GaCl is essential to form the covalent bonds with the As DB site, and (3) the "self-dissociation' of the Cl atom is unlikely. From the present simulations, a concerted reaction mechanism is also predicted for the Cl-removal by the collision with H2. As a whole, the nature of the epitaxial Ga layer growth is found to be analogous to the Si epitaxial growth in which the SiCl2 is used as the Si carrier.

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：NATL RESEARCH COUNCIL CANADA  

The electronic structures of the ground state and the excited states due to the 3d-3d transition of copper acetate monohydrate are investigated by ab initio calculations. No direct bond is obtained between the two Cu ions, but they are bonded by bridges of the four acetates. The excited states represented by the one-electron excitation of an occupied 3d electron to an unoccupied 3d orbital in either of the two Cu's are located around 1.6-1.8 eV, which corresponds to the energy region of band I. Those of the simultaneous one-electron 3d-3d excitation in both Cu's (i.e., two-electron excitation) are located around 3.2-3.4 eV. They correspond to the energy region of band II.

DOI： 10.1139/v92-056

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

Ab initio configuration-interaction calculations were carried out on the copper hydroxide (CuOH) molecule in its ground and excited states. The characteristics of these states are discussed in terms of the excitation energies and the one-electron properties. Electron correlation is found to be an important factor in the energetics of this molecule.

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

The low-lying doublet states of the linear form of the copper dioxide molecule, OCuO, are investigated by the use of ab initio CASSCF (complete active space self-consistent field) and POLCI (polarization configuration interaction) calculations. The emission bands experimentally observed are discussed in terms of the calculated excitation energies of the dipole-allowed transitions from the 2-PI-g ground state.

DOI： 10.1016/0301-0104(91)80002-Y

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

DOI： 10.1016/0009-2614(89)85019-5

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMERICAN PHYSICAL SOC  

DOI： 10.1103/PhysRevB.39.11907

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

DOI： 10.1016/0009-2614(88)80441-X

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Publisher：Springer, Berlin, Heidelberg  

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Language：Japanese  

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