掲載種別：研究論文（学術雑誌）   出版者・発行元：Elsevier BV  

DOI： 10.1016/j.chemphys.2024.112478

researchmap

掲載種別：研究論文（学術雑誌）  

DOI： 10.1039/D4CY01537A

researchmap

掲載種別：研究論文（学術雑誌）   出版者・発行元：Royal Society of Chemistry (RSC)  

Tiara-like metal nanoclusters (TNCs) composed of group 10 transition metals and thiolates can easily change their number of polymerization and include various molecules and metal ions as guests within their...

DOI： 10.1039/d4nr04579c

researchmap

掲載種別：研究論文（学術雑誌）  

DOI： 10.1039/D4CP04656K

researchmap

掲載種別：研究論文（学術雑誌）  

DOI： 10.1063/5.0234050

researchmap

掲載種別：研究論文（学術雑誌）  

DOI： 10.1063/5.0225208

researchmap

掲載種別：研究論文（学術雑誌）   出版者・発行元：Elsevier BV  

DOI： 10.1016/j.carbon.2024.119838

researchmap

掲載種別：研究論文（学術雑誌）  

DOI： 10.1021/acs.jpclett.4c02306

researchmap

掲載種別：研究論文（学術雑誌）   出版者・発行元：American Physical Society (APS)  

DOI： 10.1103/physrevb.110.104104

researchmap

その他リンク： http://harvest.aps.org/v2/journals/articles/10.1103/PhysRevB.110.104104/fulltext

掲載種別：研究論文（学術雑誌）  

DOI： 10.1039/D4CP02047B

researchmap

掲載種別：研究論文（学術雑誌）   出版者・発行元：Springer Science and Business Media LLC  

DOI： 10.1140/epjd/s10053-024-00871-1

researchmap

その他リンク： https://link.springer.com/article/10.1140/epjd/s10053-024-00871-1/fulltext.html

掲載種別：研究論文（学術雑誌）   出版者・発行元：American Chemical Society (ACS)  

DOI： 10.1021/jacs.4c07091

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）  

Aromaticity is an important concept in organic chemistry, and thus, many theoretical and experimental studies have been conducted so far. However, the majority of theoretical studies have concentrated on the aromaticity of the stationary point structures. Herein, the influence of nuclear quantum fluctuation (nuclear quantum effects: NQEs) and thermal fluctuation on the aromaticity of benzene have been analyzed by path integral molecular dynamics (PIMD) simulation. The PIMD simulations revealed that the NQEs affected not only the C-H bonds but also the C-C bonds. The HOMA and NICS calculations demonstrated that the aromaticity decreased due to the NQEs of carbon atoms, attributed to an increase in the contribution from specific vibrational modes strongly correlated with benzene's aromaticity.

DOI： 10.1039/d4cp01331j

PubMed

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）  

This study explores various models of semiconductor dielectric functions, with a specific emphasis on the large wavenumber spectrum and the derivation of the screened exchange interaction. Particularly, we discuss the short-range effect of the screened exchange potential. Our investigation reveals that the short-range effect originating from the high wavenumber spectrum is contingent upon the dielectric constant of the targeted system. To incorporate dielectric-dependent behaviors concerning the short-range aspect into the dielectric density functional theory (DFT) framework, we utilize the local Slater term and the Yukawa-type term, adjusting the ratio between these terms based on the dielectric constant. Additionally, we demonstrate the efficacy of the time-dependent dielectric DFT method in accurately characterizing the electronic structure of excited states in dyes and functional molecules. Several theoretical approaches have incorporated parameters dependent on the system to elucidate short-range exchange interactions. Our theoretical analysis and discussions will be useful for those studies.

DOI： 10.1063/5.0207751

PubMed

researchmap

掲載種別：研究論文（学術雑誌）   出版者・発行元：American Chemical Society (ACS)  

DOI： 10.1021/acs.jpcc.4c01525

researchmap

掲載種別：研究論文（学術雑誌）   出版者・発行元：AIP Publishing  

The theoretical modeling of high-pressure ice remains challenging owing to the complexity in accurately reflecting its properties attributable to nuclear quantum effects. To explore the nuclear quantum effects of the phase transition between Ice VII and Ice X, we introduce an approach based on ab initio path-integral molecular dynamics. The results indicate that quantum effects facilitate the phase transition, with the observed isotope effects consistent with the experimental outcomes. We demonstrate that quantum effects manifest differently across ice phases: In Ice VII, quantum effects reduce the pressure through the centralization of protons. In contrast, in Ice X, quantum effects increase the pressure owing to the increased kinetic energy of zero-point vibration.

DOI： 10.1063/5.0205529

researchmap

掲載種別：研究論文（学術雑誌）   出版者・発行元：Elsevier BV  

DOI： 10.1016/j.chemphys.2024.112258

researchmap

掲載種別：研究論文（学術雑誌）   出版者・発行元：American Chemical Society (ACS)  

DOI： 10.1021/acs.jpca.4c00239

researchmap

掲載種別：研究論文（学術雑誌）   出版者・発行元：Oxford University Press (OUP)  

Abstract

We analyzed the difference in the structural H/D isotope effect between an excess proton in light water (H-body) and an excess deuteron in heavy water (D-body), including the nuclear quantum effect, using path integral molecular dynamics simulations. We found that the second peak of the H-body is shorter than that of the D-body in the radial distribution function of O*–O, where O* is the oxygen atom of the H3O+/D3O+ fragment. The main reason for this would be the difference in the ratio of the Zundel structure with the sp3-like configuration, where the Zundel structure in the H-body (14.0%) is greater than that in the D-body (12.0%). We also found rare occurrences of double H3O+/D3O+ configurations, mainly including Zundel–Zundel-like structures such as H7O3+/D7O3+ and H9O4+/D9O4+. The ratios of such configurations appearing in our simulations are 0.89% and 0.20% for the H-body and the D-body, respectively.

DOI： 10.1093/bulcsj/uoad009

researchmap

その他リンク： https://academic.oup.com/bcsj/article-pdf/97/1/uoad009/56616043/uoad009.pdf

掲載種別：研究論文（学術雑誌）   出版者・発行元：Society of Computer Chemistry Japan  

DOI： 10.2477/jccjie.2023-0045

researchmap

掲載種別：研究論文（学術雑誌）   出版者・発行元：American Chemical Society (ACS)  

DOI： 10.1021/acs.jpcc.3c04610

researchmap

掲載種別：研究論文（学術雑誌）   出版者・発行元：Elsevier BV  

DOI： 10.1016/j.cplett.2023.140744

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）  

A positive Mu is a useful tool for investigating the spin density of radical species. The theoretical estimation of its behavior in a molecule requires the inclusion of a quantum effect due to the small mass of muonium. Herein, we performed ab initio a path integral molecular dynamics (PIMD) simulation, which accurately included a multi-dimensional quantum effect, for muoniated 9H-xanthene-9-thione (μXT). Our results showed that the quantum effect significantly increased the hyperfine coupling constant (HFCC) value of μXT, which qualitatively improved the calculated HFCC value, compared to the experimental one. In the PIMD simulation, the bond length between muonium and sulfur in μXT is longer than that between hydrogen and sulfur in a hydrogenated 9H-xanthene-9-thione (HXT), leading to a spin density transfer from XT (9H-xanthene-9-thione) to muonium due to neutral dissociations. Additionally, we found that the S-Mu bond in μXT prefers a structure perpendicular to the molecular plane, where the interaction between Mu and the singly occupied molecular orbital of μXT is the strongest. These structural changes resulted in a larger HFCC value in the PIMD simulation of μXT.

DOI： 10.1063/5.0159207

PubMed

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：American Chemical Society (ACS)  

Extensive research has been recently conducted to improve the power conversion efficiency (PCE) of perovskite solar cells. However, the charge carriers are easily trapped by the defect sites located at the interface between the perovskite layer and the electrode, which decreases the PCE. To reduce such defect sites, the passivation technique is frequently employed to coat small molecules on the perovskite surface during the manufacturing process. To clarify the passivation mechanism from a molecular viewpoint, we performed density functional theory calculations to target Pb-free Sn perovskites (CH3NH3SnI3). We investigated the passivation effect of Lewis base/acid molecules, such as ethylene diamine (EDA) and iodopentafluorobenzene (IPFB), and discussed behaviors of the defect levels within the bandgap as they have strong negative impacts on the PCE. The adsorption of EDA/IPFB on the Sn perovskite surface can remove the defect levels from the bandgap. Furthermore, we discuss the importance of interactions with molecular orbitals.

DOI： 10.1021/acs.jpclett.3c01450

PubMed

researchmap

掲載種別：研究論文（学術雑誌）   出版者・発行元：The Chemical Society of Japan  

DOI： 10.1246/bcsj.20230085

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）  

Curcumin and its derivatives possess intramolecular low-barrier hydrogen bonds for intramolecular proton transfer. The π-delocalization in the OCCCO framework of the hydrogen bond in these compounds is reorganized concomitantly with the proton transfer. To characterize the hydrogen bond and π-delocalization, we performed path integral molecular dynamics simulations, revealing that although the proton migration and reorganization of the π-delocalized structure showed a positive correlation, the correlation was weak.

DOI： 10.1039/d3cp01821k

PubMed

researchmap

掲載種別：研究論文（学術雑誌）   出版者・発行元：AIP Publishing  

To understand the mechanism of the H–D exchange reaction for synthesizing various deuterium-labeled molecules on heterogeneous metal catalysts as a first step, we analyzed the effects of H/D isotopes on the adsorption of H2O/D2O and their dissociated OH/OD and H/D species on the Pt(111) surface. We applied the combined plane-wave and localized basis set method developed by us to directly treat the electronic structures of the surface and the localized adsorbed region and the nuclear quantum effect of H and D. The results showed that the adsorption energies for the D-compounds on the Pt surface were larger than those for the H-compounds. This is in keeping with the experimental observations. The difference in the distance between the adsorbates and the Pt surface induced by the H/D isotope effect depends on the bonding characteristics. While the distance between D2O and the Pt surface was longer than that in the H2O case, the distance between the D atom and the Pt surface was shorter than that for the H atom. This is the first report on the geometrical differences between H and D based on a systematic analysis of water and its dissociated species.

DOI： 10.1063/5.0151660

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）  

We studied the stability of a system consisting of a positron (e+) and two lithium anions, [Li-; e+; Li-], using first-principles quantum Monte Carlo calculations combined with the multi-component molecular orbital method. While diatomic lithium molecular dianions Li22- are unstable, we found that its positronic complex can form a bound state with respect to the lowest energy decay into the dissociation channel Li2- and a positronium (Ps). The [Li-; e+; Li-] system has the minimum energy at the internuclear distance of ∼3 Å, which is close to the equilibrium internuclear distance of Li2-. At the minimum energy structure both an excess electron and a positron are delocalized as orbiting around the Li2- molecular anion core. A dominant feature of such a positron bonding structure is described as the Ps fraction bound to Li2-, unlike the covalent positron bonding scheme for the electronically isovalent [H-; e+; H-] complex.

DOI： 10.1063/5.0150246

PubMed

researchmap

掲載種別：研究論文（学術雑誌）   出版者・発行元：The Chemical Society of Japan  

DOI： 10.1246/bcsj.20230081

researchmap

掲載種別：研究論文（学術雑誌）   出版者・発行元：Wiley  

DOI： 10.1002/adfm.202303321

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）  

Path integral molecular dynamics (PIMD) simulations for C6H6, C6D6, and C6T6 have been carried out to directly estimate the distribution of projected C-H(D,T) bond lengths onto the principal axis plane. The average values of raw C-H(D,T) bond lengths obtained from PIMD simulations are in the order of ⟨RC-H⟩ > ⟨RC-D⟩ > ⟨RC-T⟩ due to the anharmonicity of the potential energy curve. However, the projected C-H(D,T) bond lengths are almost the same as those reported by Hirano et al. [J. Mol. Struct. 2021, 1243, 130537]. Our PIMD simulations directly and strongly support the explanation by Hirano et al. for the experimental observations that almost the same projected C-H(D) bond lengths are found for C6H6 and C6D6. The PIMD simulations also predicted the same projected bond lengths for C6T6 as those of C6H(D)6. In addition to the previous local mode analysis, the present PIMD simulations predicted, for benzene isotopologues, that the vibrationally averaged structure is planar but non-flat.

DOI： 10.1021/acs.jpca.2c07197

PubMed

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Royal Society of Chemistry (RSC)  

Clusters of CO₂ can have positron binding states. Besides, they have various kinds of binding origins depending on the nuclear configurations.

DOI： 10.1039/d2cp03788b

PubMed

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.1039/D2NR06952K

PubMed

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）  

Gaining insight into the encapsulation mechanism is important for controlling the encapsulation rate toward the self-assembly of gear-shaped amphiphile molecules (GSAs). To this aim, we conducted molecular dynamics (MD) simulations for three different hexameric nanocubes (1612+, 2612+, and 3612+) of GSAs (12+, 22+, and 32+, respectively) to elucidate the quantitative structure-property relationship between the stability of the nanocubes and the rate of encapsulation of a guest molecule. The 12+, 22+, and 32+ monomers differ from each other in the number of methyl groups, having three, zero, and two methyl groups, respectively. The 3612+ hexamer has methyl groups only on the equatorial region. In the cases of the simulations of 1612+ and 3612+, the cubic structures are maintained due to a tight triple-π stacking around the equator region. Meanwhile, 2612+ deforms easily due to the occurrence of a large fluctuation. These results indicate that the methyl groups on the equator are crucial to stabilize the nanocubes. The encapsulation of an iodide ion as a guest molecule is revealed to occur through the pole region via a gap that is easily formed in the nanocubes without methyl groups on the poles. Our study clearly suggests that self-assembled nanocubes can be designed to attain a specific stability and encapsulation efficiency simultaneously.

DOI： 10.1021/acs.jpcb.2c07444

PubMed

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Royal Society of Chemistry (RSC)  

Decomposition analysis shows that the solvent reorientation effect causes solvatofluorochromism of TTz dyes.

DOI： 10.1039/d2ra06454e

PubMed

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Royal Society of Chemistry (RSC)  

Small hydrogen inorganic molecules such as water have no positron binding ability. We revealed that their hydrogen bonded binary molecular clusters exhibit greater positron affinities due to the increased dipole moments and polarization effect.

DOI： 10.1039/d2cp03813g

PubMed

researchmap

掲載種別：研究論文（学術雑誌）   出版者・発行元：Elsevier BV  

DOI： 10.1016/j.cplett.2022.139740

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）  

The nuclear quantum effects (NQEs) in dihydrogen bond (DHB) complexes, i.e., NH4+⋯BeH2 and NH4+⋯MgH2, have been investigated using multicomponent quantum mechanics (MC_QM) calculations and path integral molecular dynamics (PIMD) simulation. The MC_QM method considers the NQEs, whereas PIMD considers both the NQEs and the thermal effects. The linear C3v structure is maintained in the optimized structures obtained by the static MP2 and MC_MP2 calculations, whereas the average structures obtained by the PIMD simulation are nonlinear. The strong DHB interaction in NH4+⋯MgH2 suppresses the fluctuation in the Hδ+NMg and Hδ-MgN angles, and hence, the NH4+ rotation did not occur in the simulation of NH4+⋯MgH2. The analysis of the radius of gyration revealed that the nuclear quantum fluctuation in the perpendicular direction is suppressed by the formation of the DHB complex, whereas that in the parallel direction is slightly enhanced in both the Hδ+ and Hδ- nuclei.

DOI： 10.1039/d2cp01999j

PubMed

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Royal Society of Chemistry (RSC)  

The one-dimensional porphyrin chains in the cocrystal play a very important role in the hole transport properties of C₇₀/porphyrin nanoribbons.

DOI： 10.1039/d2ra02669d

Web of Science

PubMed

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：WILEY  

The optimum exponent alpha$$ \alpha $$ (alpha opt$$ {\alpha}_{\mathrm{opt } } $$) value in 1s Gaussian type function (GTF) was analyzed to develop nuclear basis function for multicomponent quantum mechanics (MC_QM) calculations, in which nuclear quantum effects are directly included, on electronic excited state. We have demonstrated that the general values proposed for MC_QM calculations (alpha ave$$ {\alpha}_{\mathrm{ave } } $$) on electronic ground state are also useful for the MC_QM calculations on excited state. In addition, we also analyzed the alpha opt$$ {\alpha}_{\mathrm{opt } } $$ value for the MC_QM calculation of transition state (TS) structures. Although the alpha opt$$ {\alpha}_{\mathrm{opt } } $$ values for TS structures are smaller than those for energy-minimum structures, indicating that the nuclear wavefunction becomes more diffusive at TS, H/D isotope effects in TS structures can be adequately analyzed using the alpha ave$$ {\alpha}_{\mathrm{ave } } $$ values. We have demonstrated that 1s GTF with the alpha ave$$ {\alpha}_{\mathrm{ave } } $$ value is useful for the MC_QM calculation on not only electronic ground state but also excited states and calculation of TS structures.

DOI： 10.1002/qua.26962

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：AMER CHEMICAL SOC  

The compounds Fujikurin A, B, and D, recently isolated from Fusarium fujikuroi, possess intramolecular low-barrier hydrogen bonds (LBHBs), which are hydrogen bonds with a very low-energy barrier for proton transfer. The isolated compounds have a hydrogen-bonded proton that appears to rapidly switch between two equilibrium states via a transition state (TS). To understand the characteristics of these intramolecular LBHBs in detail, we performed path integral molecular dynamics (PIMD) simulations, which can consider nuclear quantum effects (NQEs) under a finite temperature. The PIMD simulations predicted that the NQE completely washed out the energy barrier for the proton transfer reaction. Consequently, a single-well shape emerged in the results, along with the effective free-energy potential surface for the hydrogen-bonded proton distribution. Thus, we conclude that the hydrogen-bonded proton in Fujikurin does not in fact transfer between two equilibrium structures but widely delocalizes around the global minimum structure involving the TS region.

DOI： 10.1021/acsomega.2c0085714244

Web of Science

PubMed

researchmap

掲載種別：研究論文（学術雑誌）   出版者・発行元：American Chemical Society (ACS)  

DOI： 10.1021/acsomega.1c06976

researchmap

掲載種別：研究論文（学術雑誌）   出版者・発行元：The Chemical Society of Japan  

DOI： 10.1246/cl.210760

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：ELSEVIER  

Ab initio path integral molecular dynamics (PIMD) simulations were performed to understand the nuclear quantum effect and thermal effect on the torsional motion of H2O2 (D2O2). A broad distribution of geometrical parameters (OH and OO bond lengths [ROH and ROO] and HOO bond angle [angle HOO]) was obtained in quantum ab initio PIMD simulations, rather than in classical MD simulations. However, a modest distribution around the trans-configuration TS (angle HOOH = 180 degrees) was found in the quantum ab initio PIMD simulations of H2O2 at low temperatures. Thus, the nuclear quantum effect slightly enhanced the HOOH torsional motion at low temperatures. A series of simulations also revealed that the thermal effect enhanced the HOOH torsional motion. However, it was restrained by the primary nuclear quantum effect on the ROH in quantum simulations at high temperatures. Therefore, an interesting competitive nuclear quantum effect on the torsional motion of H2O2 was observed.

DOI： 10.1016/j.comptc.2021.113542

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：American Physical Society (APS)  

The spontaneous radiative dissociation spectrum of the second bound state of positronium hydride (PsH) located just below the H(2p) + Ps(2p) threshold energy is investigated by the variational and complex coordinate rotation methods. Convergence of the transition rates is examined in both length and velocity gauges. The spectrum indicates that the primary channel of radiative dissociation is the transition into the continuum of H(1s) + Ps(2p), and the secondary one is that into the H(2p) + Ps(1s) continuum. Radiative transition to the resonance state located close to the second bound state is found to exist. The total rate of the radiative dissociation is found to be 9.1(2) x 108 s-1.

DOI： 10.1103/physreva.105.012814

Web of Science

researchmap

その他リンク： http://harvest.aps.org/v2/journals/articles/10.1103/PhysRevA.105.012814/fulltext

記述言語：英語   掲載種別：研究論文（学術雑誌）  

Recently, deuterium-labeled drugs, such as deutetrabenazine, have attracted considerable attention. Consequently, understanding the reaction mechanisms of deuterium-labeled drugs is crucial, both fundamentally and for real applications. To understand the mechanisms of H- and D-transfer reactions, in this study, we used deuterated anisole as a deutetrabenazine model and computationally considered the nuclear quantum effects of protons, deuterons, and electrons. We demonstrated that geometrical differences exist in the partially and fully deuterated methoxy groups and hydrogen-bonded structures of intermediates and transition states due to the H/D isotope effect. The observed geometrical features and electronic structures are ascribable to the different nuclear quantum effects of protons and deuterons. Primary and secondary kinetic isotope effects (KIEs) were calculated for H- and D-transfer reactions from deuterated and undeuterated anisole, with the calculated primary KIEs in good agreement with the corresponding experimental data. These results reveal that the nuclear quantum effects of protons and deuterons need to be considered when analyzing the reaction mechanisms of H- and D-transfer reactions and that a theoretical approach that directly includes nuclear quantum effects is a powerful tool for the analysis of H/D isotope effects in H- and D-transfer reactions.

DOI： 10.1021/acs.jpca.1c08514

PubMed

researchmap

掲載種別：研究論文（学術雑誌）   出版者・発行元：Elsevier BV  

DOI： 10.1016/j.chemphys.2021.111381

researchmap

掲載種別：研究論文（学術雑誌）   出版者・発行元：Elsevier BV  

DOI： 10.1016/j.cplett.2021.139263

researchmap

掲載種別：研究論文（学術雑誌）   出版者・発行元：Royal Society of Chemistry (RSC)  

The ambipolar triclinic C₆₀/Fc nanosheet FETs were converted to n-type face-centered cubic C₆₀ nanosheet FETs due to the loss of ferrocene with void formation upon heating at 150 °C.

DOI： 10.1039/d1tc05545c

researchmap

掲載種別：研究論文（学術雑誌）   出版者・発行元：American Physical Society (APS)  

DOI： 10.1103/physreva.104.062807

researchmap

その他リンク： http://harvest.aps.org/v2/journals/articles/10.1103/PhysRevA.104.062807/fulltext

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：SPRINGER WIEN  

Among the hydrogen bonds, which are critical to sustaining life, the interaction between ammonium ions (NH4+) and water is considered a model interaction in biological systems. Although this interaction has been examined in earlier studies on molecular dynamics, the nuclear quantum effect was not considered in those studies. In this study, we investigate the nuclear quantum effect of a singly-hydrated ammonium ion cluster, NH4+ (H2O), using an ab initio on-the-fly path integral molecular dynamics (PIMD) simulation with a BHandHLYP/6-31++G(d,p) level of calculations. We find that the nuclear quantum effect shortens the N-O bond and increases the angle of the O-N-H-b bond. The results indicate that the nuclear quantum effect has two competing contributions. The first contribution involves strengthening the intermolecular interaction, which reduces the intermolecular distance, and the other contribution involves weakening the interaction, and it facilitates the rotation of NH4+.

DOI： 10.1007/s00601-021-01689-y

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）  

Despite the fact that the positron annihilation has been used in biomedical applications, the detailed mechanism of the positron annihilation on biological molecules remains poorly understood so far. In this work, we investigated the positron binding and positron annihilation properties for both global minimum and hydrogen-bonded structures of 20 amino acid molecules using the multicomponent molecular orbital method. By regression analysis, we confirmed that positron affinity can increase with an increase of the permanent dipole moment of the parent amino acids as reported in previous studies, while the annihilation rate linearly increases with respect to the square root of positron affinity. By the one-particle property analyses for probabilities of electron-positron contacts, we found that delocalization characteristics of both electrons and positrons play key roles to enhance the positron annihilation rate arising from both the valence electrons in σ- and π-type molecular orbitals from 2p atomic orbitals but not from the highest occupied molecular orbital electrons, particularly for comparatively weakly bound positronic amino acid systems.

DOI： 10.1021/acsomega.1c03409

PubMed

researchmap

掲載種別：研究論文（学術雑誌）  

To understand detailed geometrical changes and electronic structures of the adsorbed water molecules (H2O, D2O, and HDO) and H2O- and D2O-ice Ih(0 0 0 1) basal surfaces induced by the H/D isotope effect, nuclear quantum effects of the proton and deuteron in the first-principles calculations should be considered. We applied our developed combined plane wave and localized basis set (CPLB) method, which can directly treat the electronic structures of the surface and the localized adsorbed region with the nuclear quantum effect, to analyze the H/D isotope effect of adsorbed water molecules on ice. We demonstrated the geometrical change in the adsorbed water and H2O-ice surface due to the H/D isotope effect because the hydrogen bonds involving D (D2O and HDO) were longer than those involving H. Hence, the adsorption energies of D2O and HDO molecules were smaller than those of H2O because of the geometrical changes induced by the H/D isotope effect. The H/D isotope effect led to weaker adsorption energy and longer hydrogen bonds on the D2O-ice surface than those on the H2O-ice surface. We successfully described the H/D isotope effect of water adsorption on the ice Ih(0 0 0 1) surface by directly considering the quantum effect of the proton and deuteron.

DOI： 10.1016/j.apsusc.2021.150100

Scopus

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）  

In this work, the excitation energies of asymmetric thiazolothizaole (TTz) dye molecules have been theoretically studied using dielectric-dependent density functional theory (DFT). In the dielectric-dependent DFT approach, the ratio (fraction) of the nonlocal Hartree exchange term incorporated into the DFT exchange-correlation functional is a system-dependent parameter, which is inversely proportional to the dielectric constant of the target material. The dielectric-dependent DFT method is closely related to the Coulomb hole and screened exchange (COHSEX) approximation in the GW method and therefore has been applied to crystalline systems with periodic boundary conditions, such as semiconductors and inorganic materials. By focusing on the solvatofluorochromic phenomena of asymmetric TTz dyes, we show that excitation energy calculations obtained from the dielectric-dependent DFT method can reproduce the corresponding experimental UV-vis absorption and emission spectra of dyes in solvents.

DOI： 10.1039/d1cp02047a

PubMed

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）  

The positronic bound state for the non-polar carbon disulfide (CS2) has been experimentally identified, although previous theoretical investigations, which were dedicated to studying the positronic CS2 monomer, could not reasonably reproduce the experimentally measured positron affinity. In the present study, we performed analysis of the vibrational averaged positron affinity for the positronic CS2 dimer, [C2S4; e+], using the Hartree-Fock and configuration interaction levels of the multi-component molecular orbital method combined with the self-consistent field level of the vibrational variational Monte Carlo method. We demonstrated that the equilibrium structure of the non-polar C2S4 can have the positronic bound state with a positron affinity of about 46.18 meV in the configuration interaction level, while this is 0 meV in the Hartree-Fock level. Furthermore, by taking into account the vibrational effect, we succeeded in reproducing the resonant positron kinetic energies lying close to the experimental value, where the vibrational averaged positron affinity becomes greater with an increased dipole moment and dipole polarizability. We also showed possible mechanisms to effectively enhance the resonant positron capture for [C2S4; e+], associated with both the infrared active and infrared inactive vibrational modes.

DOI： 10.1039/d1cp02808a

PubMed

researchmap

掲載種別：研究論文（学術雑誌）   出版者・発行元：Springer Science and Business Media {LLC}  

DOI： 10.1007/s00601-021-01636-x

researchmap

掲載種別：研究論文（学術雑誌）  

Deuterium isotope effects in the keto-enol tautomerism of β-dicarbonyl compounds (malonaldehyde, acetylacetone, dibenzoylmethane, and avobenzone) have been studied using a B3LYP+D functional level of multi-component density functional theory (MC_DFT), which can directly take nuclear quantum effects (NQEs) of the hydrogen nuclei into account. We clearly show that the keto-enol energy difference becomes smaller by deuterium substitution, which is in reasonable agreement with the corresponding experimental evidence. Our MC_DFT study also reveals the hydrogen/deuterium (H/D) isotope effect in geometries and shows that the deuterium substitution weakens the intramolecular hydrogen-bonded interaction in the enol form. Direct treatment of NQEs of hydrogen nuclei via the MC_DFT method is essential for analyzing the H/D isotope effect in keto-enol tautomerism of β-dicarbonyl compounds. Such isotope effects cannot be reproduced in the conventional DFT scheme with harmonic zero-point vibrational corrections.

DOI： 10.1246/bcsj.20210083

Scopus

researchmap

掲載種別：研究論文（学術雑誌）  

We analysed the H/D isotope effect of CH4/CD4adsorption on a Rh(111) surface using our combined plane wave and localized basis sets method, that we proposed for the consideration of delocalized electrons on a surface and the quantum effect of protons (deuterons) in metal-molecule interactions. We observed that the adsorption distance and energy of CD4were larger and lower than those of CH4, respectively. This is in reasonable agreement with the corresponding experimental results of cyclohexane adsorption. We clearly found that the trend of the H/D isotope effect in the geometrical and energetic difference was similar to that of the hydrogen-bonded systems.

DOI： 10.1039/d0ra10796d

Scopus

researchmap

掲載種別：研究論文（学術雑誌）  

We investigated H-spillover mechanisms on Pt atoms decorating defective carbon nanocones (Pt/dCNC) using the multicomponent B3LYP (MC_B3LYP) method, which can take account of the nuclear quantum effect (NQE) of light nuclei. MC_B3LYP shows reduced relative energies for all stationary-point structures and lower energy barriers to H-spillover reactions. Interestingly, MC_B3LYP calculations reveal that the activation energy for H2 dissociation completely vanishes indicating that H2 molecules dissociate readily on Pt/dCNC. Our crucial finding is that the different metal (Pt and Pd) on dCNC surface has affected the thermodynamic favorability of the hydrogen dissociation process, on Pt/dCNC is facile and highly exothermic, while on Pd/dCNC is dramatically endothermic. Furthermore, comparison of combined dissociation-spillover mechanism on Pt decorated on carbon nanocone (Pt/dCNC) and Pt decorated on graphene (Pt/dG) catalysts have been focused to explain the curvature effect which can facilitate the hydrogen spillover process and provide a highly exothermic reaction, which is more thermodynamically favorable than that of a metal-graphene surface. Our new understanding of this reaction mechanism and the influence of NQEs on electronic properties will be useful for the future development of the spillover mechanism as well as the synthesis of high-performance Pt/dCNC for H2 energy applications.

DOI： 10.1016/j.mcat.2021.111486

Scopus

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：American Chemical Society (ACS)  

The H/D isotope effect in the CH···O interactions of several systems is systematically analyzed to determine whether it exerts control over reaction selectivity. Our theoretical study demonstrates that deuterium substitution has a negligible effect on CH···O interactions; thus, reaction selectivity likely cannot be controlled by the H/D isotope effect in these CH···O interactions.

DOI： 10.1021/acs.orglett.0c03351

PubMed

researchmap

担当区分：最終著者,　責任著者   記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：The Chemical Society of Japan  

The nuclear quantum effect of a singly hydrated ammonium ion cluster, NH4+(H2O), is investigated using an ab initio on-the-fly path integral molecular dynamics (PIMD) simulation with a BHandHLYP/6-31++G(d,p) level of calculations. Owing to the nuclear quantum effect with a PIMD simulation, the bond length of N-O (R-NO) is shortened and the distribution of the angle of O-N-H-b (theta(ONHb)) is greater. These results indicate that the nuclear quantum effect has two apparent contradictory contributions. One is the strengthening of the hydrogen bond arising from the zero-point energy (ZPE), whereas the other is facilitating the rotation of NH4+ in water owing to a quantum fluctuation.

DOI： 10.1246/bcsj.20200120

Web of Science

researchmap

担当区分：最終著者,　責任著者   記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：AIP Publishing  

We studied the positron (e+) interaction with the hydrogen molecular dianion H2 2- to form the positronic bound state of [H-; e+; H-] using the first-principles quantum Monte Carlo method combined with the multi-component molecular orbital one. H2 2- itself is unstable, but it was shown that such an unbound H2 2- may become stable by intermediating a positron and forming the positronic covalent bond of the [H-; e+; H-] system [J. Charry et al., Angew. Chem., Int. Ed. 57, 8859-8864 (2018)]. We newly found that [H-; e+; H-] has double minima containing another positronic bound state of [H2; Ps-]-like configuration with the positronium negative ion Ps- at the bond distance approximately equal to the equilibrium H2 molecule. Our multi-component variational Monte Carlo calculation and the multi-component configuration interaction one resulted in the positronic covalent bonded structure being the global minimum, whereas a more sophisticated multi-component diffusion Monte Carlo calculation clearly showed that the [H2; Ps-]-like structure at the short bond distance is energetically more stable than the positronic covalent bonded one. The relaxation due to interparticle correlation effects pertinent to Ps- (or Ps) formation is crucial for the formation of the Ps-A2-like structure for binding a positron to the non-polar negatively charged dihydrogen.

DOI： 10.1063/5.0022673

PubMed

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：American Physical Society (APS)  

Positron binding energies and annihilation spectra are calculated using the positron-electron correlation-polarization potential model for a series of six chloroethene molecules. From detailed analysis of the positron densities and positron-molecule interactions, it was found that the positron is attracted by both the potential well around the negative end of the dipole moment and the π electrons of the C=C double bond. The positron annihilation spectra were simulated using the Feshbach resonance widths, which can be calculated from the couplings between the positron motion and vibrational motion. The importance of π electrons in positron binding is discussed in terms of the calculated resonance widths.

DOI： 10.1103/physreva.102.052830

Scopus

researchmap

その他リンク： http://harvest.aps.org/v2/journals/articles/10.1103/PhysRevA.102.052830/fulltext

掲載種別：研究論文（学術雑誌）  

The positron-electron correlation-polarization potential model is used to calculate annihilation spectra of carbon disulfide and benzene. We assume that the positron is captured in the vibrationally excited states of the target molecule through vibrational Feshbach resonances. Using the standard normal mode representation, we calculated the resonance energies and widths for each vibrational mode. The resonance widths were calculated with Fermi's Golden Rule approximation, where the time-dependent wave packet approach has been applied. We found that vibrational resonances of infrared-active modes play a dominant role in resonant annihilation; however, infrared-inactive modes also contribute to the annihilation spectrum through polarizability changes along normal mode coordinates.

DOI： 10.1002/qua.26376

Scopus

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Wiley  

Detailed information on the H/D isotope effects for adsorption on the surface and absorption in the bulk is important for understanding the nuclear quantum effect. To achieve this, we developed a new theoretical approach, namely, the combined plane wave and localized basis set (CPLB) method. By using the multicomponent quantum chemical method, which takes into account the quantum effect of a proton or deuteron, with the localized part of the CPLB method, direct analysis of the H/D isotope effect about adsorption and absorption is carried out. In this study, we performed a theoretical investigation of the H/D isotope effects for adsorption on a Pd(111) surface and absorption in bulk Pd. We clearly showed an H/D isotope effect on geometry during adsorption and absorption. Our developed CPLB approach is a powerful tool for analyzing the quantum nature of H/D in surface, bulk, and inhomogeneous systems.

DOI： 10.1002/qua.26275

Scopus

researchmap

その他リンク： https://onlinelibrary.wiley.com/doi/full-xml/10.1002/qua.26275

担当区分：最終著者,　責任著者   記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：American Chemical Society (ACS)  

Polysilanes are important materials for photoresist masks used in semiconductor chipmaking processes. As the oxidation of a polyalkylsilane can lead to the failure of the chipmaking process, it is important that the oxidation reaction mechanism is understood to suppress undesired reactions. In this paper, the oxidation mechanism of polysilanes is elucidated both experimentally and computationally. X-ray photoelectron spectroscopy was used to show that polysilanes with phenyl groups tend to become more oxidized than those with methyl groups. Furthermore, thermal desorption spectroscopy also revealed that the phenyl groups are lost from the polysilanes. Our computational study revealed that the oxidation mechanism proceeds by dearylation initiated by the addition of 3O2 to the phenyl or methyl group and the oxidation of the polysilane backbone by phenylperoxyl radicals that depart from the backbone, which was found to involve a two-step reaction involving the cleavage of the O-O bond of the phenylperoxyl radical followed by the formation of the Si-O-Si structure. Therefore, the mechanism for the oxidation of the polysilane involves the phenyl group.

DOI： 10.1021/acs.jpcc.0c02416

Scopus

researchmap

担当区分：最終著者   記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Wiley  

Positron binding energies (PBEs) of 41 polyatomic molecules were calculated using the positron-electron correlation-polarization potential (CPP) approach and compared with experimentally measured values. In this approach, the short-range positron-electron potential is modeled using the density-functional expression, whereas the long-range potential is approximated by the attractive polarization potential. The positron-electron CPP model based on local-density approximation yields larger PBEs than experimental values; however, the calculated values can be substantially improved by introducing generalized gradient approximation. We also investigated the conformational dependence of PBEs for representative molecules.

DOI： 10.1002/jcc.26200

PubMed

researchmap

その他リンク： https://onlinelibrary.wiley.com/doi/full-xml/10.1002/jcc.26200

掲載種別：研究論文（国際会議プロシーディングス）  

Synopsis Theoretical understanding of hyperfine coupling constant (HFCC) is important to analyze muon spin rotation/relaxation/resonance (μSR) spectrum. We performed ab initio path integral molecular dynamics simulations to predict and analyze the reduced HFCCs of muoniated thioacetone radical (Mu-TACE) and hydrogenated thioacetone radical (H-TACE). Our predicted HFCC value of Mu in Mu-TACE was larger than that of H in HTACE, because of the larger nuclear quantum effect of positive muon.

DOI： 10.1088/1742-6596/1412/22/222011

Scopus

researchmap

掲載種別：研究論文（国際会議プロシーディングス）  

Synopsis We theoretically analyzed the positron affinity (PA) of acetaldehyde molecule at several vibrational excited states toward the elucidation of physical and chemical origin of H/D isotope shift in the molecular PA value. We found that (i) the acetaldehyde molecule has different PA values and its H/D isotope shift for each vibrational state, and (ii) H/D isotope shift in the PA values at vibrational excited states are mainly due to the change in the dipole moment by the vibrational excitations.

DOI： 10.1088/1742-6596/1412/22/222012

Scopus

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：The Chemical Society of Japan  

We have theoretically analyzed the geometrical H/D isotope effect of HNO£XH2NH2 (X = B or Al) and HNO£BH3NH3 systems with the aid of multicomponent quantum mechanics (MC_QM) method, which can directly include the nuclear quantum effect of hydrogen nuclei. We demonstrate that deuterium substitution of positively charged hydrogen in blue-shifting dihydrogen-bonded clusters leads to elongation of the dihydrogen-bonded distance, whereas the substitution of negatively charged hydrogen leads to contraction, as is the case in red-shifting dihydrogen-bonded clusters.

DOI： 10.1246/cl.200198

Scopus

researchmap

担当区分：最終著者,　責任著者   記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Wiley  

Nuclear quantum and H/D isotope effects of bridging and terminal hydrogen atoms of diborane (B2H6) molecules were systematically studied by classical ab initio molecular dynamics (CLMD) and ab initio path integral molecular dynamics (PIMD) simulations with BHandHLYP/6-31++G** level of theory at room temperature (298.15 K). Calculated results clearly show that H/D isotope effect appears in the distribution of hydrogen (deuterium) of B2H6 (B2D6). Geometry of B2H6 also plays a significant role in the nuclear quantum effect proved by PIMD simulations, but slightly deviated from its equilibrium structure when simulated via CLMD simulation. The bond lengths between boron atoms R (B1 … B2) and the bridging hydrogen atoms RHH (HB1 … HB2) of the B2H6 molecule obtained from PIMD simulations are slightly longer than those of the deuterated form of the diborane (B2D6) molecule. The principal component analysis (PCA) was also employed to distinguish the important modes of bridging hydrogen as related to the nuclear quantum and H/D isotope effects. The highest level of contribution obtained from PCA of PIMD simulations is bending, while various mixed vibrations with less contribution were also found. Therefore, the nuclear quantum and H/D isotope effects need to be taken into account for a better understanding of diborane geometry.

DOI： 10.1002/qua.26179

Scopus

researchmap

その他リンク： https://onlinelibrary.wiley.com/doi/full-xml/10.1002/qua.26179

担当区分：最終著者,　責任著者   記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Springer Science and Business Media LLC  

DOI： 10.1140/epjd/e2020-100538-3

researchmap

その他リンク： http://link.springer.com/article/10.1140/epjd/e2020-100538-3/fulltext.html

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Elsevier BV  

In order to investigate the possibility of the electric field control of proton transfer in the interface hydrogen-bond on self-assembled monolayer, we computationally evaluated the dependence of the potential energy curve along the proton transfer coordinate on the external electric field. It was demonstrated that the stable position of the proton can be switched from the hydrogen-bonding donor to acceptor according to the electric field, via the formation of the low-barrier hydrogen bond. By comparing with several hydrogen-bonding moieties from biomolecules, we confirmed that the switching threshold field is correlated with the pKa difference of the donor and acceptor.

DOI： 10.1016/j.cplett.2020.137091

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：American Chemical Society (ACS)  

Recently, organic donor-acceptor (D-A) cocrystals have attracted special interest as functional materials because of their unique chemical and physical properties that are not exhibited by simple mixtures of their components. Herein, we report the preparation of one-dimensional novel D-A cocrystals from C60 and 5,10,15,20-tetrakis(3,5-dimethoxyphenyl)porphyrin (3,5-TPP); these cocrystals have near-infrared (NIR) light-sensing abilities, despite each of their component molecule individually having no NIR light-sensing properties. Micrometer-sized rectangular columnar C60-3,5-TPP cocrystals were produced by a simple liquid-liquid interfacial precipitation method. The cocrystals exhibit a new strong transition in the NIR region indicative of the existence of charge-transfer interactions between C60 and 3,5-TPP in the cocrystals. The C60-3,5-TPP cocrystals showed n-type transport characteristics with NIR light-sensing properties when the cocrystals were incorporated in bottom-gate/bottom-contact organic phototransistors, revealing that organic cocrystals with suitable charge-transfer interaction are useful as functional materials for the creation of novel NIR-light-sensing devices.

DOI： 10.1021/acsami.9b18784

PubMed

researchmap

担当区分：最終著者,　責任著者   記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Royal Society of Chemistry (RSC)  

<p>Dipyrrolyldiketone BF₂ complexes have a characteristic association mechanism with anions; an anion is tightly captured by the NH bonding of the two rotated pyrrole rings and the CH bonding of the backbone.</p>

DOI： 10.1039/c9ra09285d

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Springer Science and Business Media LLC  

<title>Abstract</title>True understanding of dispersion interaction in solution remains elusive because of difficulty in the precise evaluation of its interaction energy. Here, the effect of substituents with different polarizability on dispersion interactions in water is discussed based on the thermodynamic parameters determined by isothermal titration calorimetry for the formation of discrete aggregates from gear-shaped amphiphiles (GSAs). The substituents with higher polarizability enthalpically more stabilize the nanocube, which is due to stronger dispersion interactions and to the hydrophobic effect. The differences in the thermodynamic parameters for the nanocubes from the GSAs with CH₃ and CD₃ groups are also discussed to lead to the conclusion that the H/D isotope effect on dispersion interactions is negligibly small, which is due to almost perfect entropy-enthalpy compensation between the two isotopomers.

DOI： 10.1038/s42004-019-0242-0

Web of Science

researchmap

その他リンク： http://www.nature.com/articles/s42004-019-0242-0

担当区分：最終著者,　責任著者   記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：American Chemical Society (ACS)  

DOI： 10.1021/acs.jpca.9b04407

researchmap

担当区分：最終著者   記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Springer Science and Business Media LLC  

DOI： 10.1140/epjd/e2019-100147-y

researchmap

その他リンク： http://link.springer.com/article/10.1140/epjd/e2019-100147-y/fulltext.html

担当区分：最終著者,　責任著者   記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：American Chemical Society (ACS)  

DOI： 10.1021/acs.jpcb.9b02156

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：The Chemical Society of Japan  

DOI： 10.1246/bcsj.20180308

researchmap

担当区分：最終著者   記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：American Chemical Society (ACS)  

DOI： 10.1021/acs.jpca.8b11653

researchmap

掲載種別：研究論文（学術雑誌）   出版者・発行元：Wiley  

DOI： 10.1002/jcc.25562

researchmap

掲載種別：研究論文（学術雑誌）   出版者・発行元：Elsevier BV  

DOI： 10.1016/j.comptc.2018.11.013

researchmap

記述言語：日本語   掲載種別：研究論文（学術雑誌）   出版者・発行元：SOC COMPUTER CHEMISTRY, JAPAN  

Plants can produce various types of compounds classified as primary and secondary metabolites to survive and adapt against their given environments. These plant secondary metabolites have large chemical diversities in terms of their physicochemical properties. However, in most of the cases, information on the physicochemical properties of these compounds can be obtained by referring to articles. As it takes a tremendous amount of time due to curating published papers manually, the development of novel computational methods for prediction of these properties to shorten time with high accuracy, is needed. One of the key scientific fields, quantum chemical calculation has a potential ability because compound structures can be directly used as parameters to represent compounds' physicochemical characteristics. Thus, we aimed to develop a novel method for improving the accuracy of spectroscopic data of secondary metabolites predicted by quantum chemical calculation when comparing publicly-available data. We chose the six representative metabolites that are accumulated by UV-B irradiation for this study. The UV-vis absorption spectrum of each compound was obtained by CNDO/S semi-empirical molecular orbital calculation at the optimized structure by PM3 one. Subsequently, obtained data for several excited states were corrected by Gaussian fitting and the regression analysis was employed for these data. The absorption maximum of the corrected UV-vis spectrum was corresponded reasonably well with the reported experimental data. Our method enables us not only to shorten the data acquisition time, but also to predict spectroscopic data of every compound from the corresponding chemical structures.

DOI： 10.2477/jccj.2019-0002

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.1002/qua.25895

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.1002/jcc.25387

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.1002/chem.201801376

Scopus

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：American Chemical Society  

The effect of the methyl groups in neutral gear-shaped amphiphiles (GSAs) on the stability of nanocubes was investigated using a novel C2v-symmetric GSA, which was synthesized using selective alternate trilithiation of a pentabrominated hexaphenylbenzene derivative. The lack of only one methyl group in the GSA decreased the association constant for the assembly of the nanocube by 3 orders of magnitude. A surface analysis recently developed by the authors (SAVPR: surface analysis with varying probe radii) was carried out for characteristic isomers of the nanocube consisting of C2v-symmetric GSAs. It was found that the methyl groups near the equator of the nanocube play a significant role in the stabilization of the nanocubes.

DOI： 10.1021/acs.joc.8b00495

Scopus

researchmap

記述言語：英語   掲載種別：研究論文（国際会議プロシーディングス）  

DOI： 10.1007/978-3-319-74582-4_10

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.1039/c8ra02679c

Scopus

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.1038/s42004-018-0014-2

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Royal Society of Chemistry  

Self-organization processes of a gear-shaped amphiphile molecule (1) to form a hexameric structure (nanocube, 16) were inferred from sequential dissociation processes by using molecular dynamics (MD) simulations. Our MD study unveiled that programed dynamic ordering exists in the dissociation processes of 16. According to the dissociation processes, it is proposed that triple π-stacking among three 3-pyridyl groups and other weak molecular interactions such as CH-π and van der Waals interactions, some of which arise from the solvophobic effect, were sequentially formed in stable and transient oligomeric states in the self-organization processes, i.e.12, 13, 14, and 15. By subsequent analyses on structural stabilities, it was found that 13 and 14 are stable intermediate oligomers, whereas 12 and 15 are transient ones. Thus, the formation of 13 from three monomers and of 16 from 14 and two monomers via corresponding transients is time consuming in the self-assembly process.

DOI： 10.1039/c8cp00284c

Scopus

PubMed

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：American Chemical Society  

Hydrogen-bonding heterogeneous bilayers on substrates have been studied as a base for new functions of molecular adlayers by means of atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), infrared reflection absorption spectroscopy (IRAS), and density functional theory (DFT) calculations. Here, we report the formation of the catechol-fused bis(methylthio)tetrathiafulvalene (H2Cat-BMT-TTF) adlayer hydrogen bonding with an imidazole-terminated alkanethiolate self-assembled monolayer (Im-SAM) on Au(111). The heterogeneous bilayer is realized by sequential two-step immersions in solutions for the individual Im-SAM and H2Cat-BMT-TTF adlayer formations. In the measurements by AFM, a grained H2Cat-BMT-TTF adlayer on Im-SAM is revealed. The coverage and the chemical states of H2Cat-BMT-TTF on Im-SAM are specified by XPS. On the vibrational spectrum measured by IRAS, the strong hydrogen bonds between H2Cat-BMT-TTF and Im-SAM are characterized by the remarkably red-shifted OH stretching mode at 3140 cm-1, which is much lower than that for hydrogen-bonding water (typically ∼3300 cm-1). The OH stretching mode frequency and the adsorption strength for the H2Cat-BMT-TTF molecule hydrogen bonding with imidazole groups are quantitatively examined on the basis of DFT calculations.

DOI： 10.1021/acs.langmuir.7b03451

Scopus

PubMed

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Royal Society of Chemistry  

A novel method for the semi-quantitative evaluation of molecular meshing in molecular complexes and assemblies (SAVPR: surface analysis with varying probe radii) is proposed. SAVPR revealed that the extremely high stability of hexameric assemblies (nanocubes) is due to tight molecular meshing between the components in the assemblies, indicating the importance of van der Waals interactions in hydrophobic molecular assemblies.

DOI： 10.1039/c8cc00695d

Scopus

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Wiley-VCH Verlag  

The self-assembly process of a Pd2L4 cage complex consisting of rigid ditopic ligands, in which two 3-pyridyl groups are connected to a benzene ring through acetylene bonds and PdII ions was revealed by a recently developed quantitative analysis of self-assembly process (QASAP), with which the self-assembly process of coordination assemblies can be investigated by monitoring the evolution with time of the average composition of all the intermediates. QASAP revealed that the rate-determining steps of the cage formation are the intramolecular ligand exchanges in the final stage of the self-assembly: [Pd2L4Py*2]4+→[Pd2L4Py*1]4++Py* and [Pd2L4Py*1]4+→[Pd2L4]4++Py* (Py*: 3-chloropyridine, which was used as a leaving ligand on the metal source). The energy barriers for the two reactions were determined to be 22.3 and 21.9 kcal mol−1, respectively. DFT calculations of the transition-state (TS) structures for the two steps indicated that the distortion of the trigonal-bipyramidal PdII center at the TS geometries increases the activation free energy of the two steps.

DOI： 10.1002/chem.201704285

Scopus

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Elsevier B.V.  

We theoretically discuss the dynamics of the chemical reaction process induced by positron attachment, e+ + LiH → Li+ + [H−
e+]. Simple model pseudopotentials were developed on the basis of the electrostatic interaction between e+ and LiH with a large dipole moment, where some numerical parameters were chosen to qualitatively reproduce the previous-reported ab initio positron-bound adiabatic potential energy curve of [LiH
e+]. Using the developed pseudopotential models, we have performed time-independent quantum scattering calculations using the hyperspherical coordinate. Although the main scattering processes of the e+ + LiH collision are rotational and vibrational excitation processes, it is found that the calculated probabilities for the dissociative positron attachment (DPA) process are not very small within the present pseudopotential framework. This suggest that the DPA process to LiH can be observed in the future experiments.

DOI： 10.1016/j.comptc.2017.11.023

Scopus

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Royal Society of Chemistry  

To investigate the effect of quantum fluctuations on the magnetic environment inside a C60 fullerene cage, we have calculated the nuclear magnetic shielding constant of protons in H2@C60 and HD@C60 systems by on-the-fly ab initio path integral simulation, including both thermal and nuclear quantum effects. The most dominant upfield from an isolated hydrogen molecule occurs due to the diamagnetic current of the C60 cage, which is partly cancelled by the paramagnetic current, where the paramagnetic contribution is enlarged by the zero-point vibrational fluctuation of the C60 carbon backbone structure via a widely distributed HOMO-LUMO gap. This quantum modulation mechanism of the nuclear magnetic shielding constant is newly proposed. Because this quantum effect is independent of the difference between H2 and HD, the H2/HD isotope shift occurs in spite of the C60 cage. The nuclear magnetic constants computed for H2@C60 and HD@C60 are 32.047 and 32.081 ppm, respectively, which are in reasonable agreement with the corresponding values of 32.19 and 32.23 ppm estimated from the experimental values of the chemical shifts.

DOI： 10.1039/c7cp06401b

Scopus

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Royal Society of Chemistry  

The mechanism of hydrogen-tritium (H-T) exchange reactions between several small organic and HTO molecules have been investigated using M06-2X/6-311++G(d,p) method. The second HTO molecule is taken into account for both direct and addition-elimination H-T exchange reactions. The reactivity of small organic molecules for H-T exchange reactions is in the order of CH3COOH &gt
CH3CH2OH &gt
CH3CHO ≈ CH3COCH3 ≈ C2H4 and C3H6 &gt
CH4, C2H6, and C3H8. In particular, the energies of activation in addition-elimination H-T exchange reactions of alkene with two HTO molecules become lower than those of direct H-T exchange ones. Our study reveals that (i) the reactivity of alkene with HTO molecules is comparable to that of aldehyde and ketone when the effect of the second HTO molecule is taken into account and (ii) the H-T exchange reactions between alkene and HTO molecules prefer addition-elimination H-T exchange mechanism, whereas other organic molecules favor a direct one.

DOI： 10.1039/c7ra13110k

Scopus

researchmap

出版者・発行元：Springer Singapore  

DOI： 10.1007/978-981-10-5651-2_16

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：AMER CHEMICAL SOC  

The effect of reaction environment on the self assembly process of an octahedron-shaped Pd6L8 capsule was investigated. Quantitative analysis of self-assembly process with H-1 NMR spectroscopy revealed that the self-assembly , pathway of the capsule was altered by solvent and a leaving ligand coordinating to the metal source, which are not the components of the final self-assembly. Solvents definitively determine the pathway of the self-assembly at a very early stage intermediates of the self-assembly. Contrary to the expectation that the weaker the coordination ability of the leaving ligand is, the faster the formation of the final assembly becomes, a leaving ligand with weak coordination ability tends to generate a kinetically trapped species to prevent the capsule formation under mild conditions.

DOI： 10.1021/acs.inorgchem.7b02152

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：AMER CHEMICAL SOC  

Solvent dependence of double proton transfer in the formic acid-formamidine (FA-FN) complex at room temperature was investigated by means of ab initio path integral molecular dynamics (AIPIMD) simulation with taking nuclear quantum and thermal effects into account. The conductor-like screening model (COSMO) was applied for solvent effect. In comparison with gas phase, double proton delocalization between two heavy atoms (O and N) in FA-FN were observed with reduced proton transfer barrier height in low dielectric constant medium (&lt;4.8). For dielectric constant medium at 4.8, the chance of finding these two protons are more pronounced due to the solvent effect which completely washes out the proton transfer barrier. In the case of higher dielectric constant medium (&gt;4.8), the ionic species becomes more stable than the neutral ones and the formate anion and formamidium cation are thermodynamically stable. For ab initio molecular dynamics simulation, in low dielectric constant medium (&lt;4.8) a reduction of proton transfer barrier with solvent effect is found to be less pronounced than the AIPIMD due to the absence of nuclear quantum effect. Moreover, the motions of FA-FN complex are significantly different with increasing dielectric constant medium. Such a difference is revealed in detail by the principal component analysis.

DOI： 10.1021/acs.jpca.7b07010

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：ELSEVIER SCIENCE BV  

We present computational results of vibrationally enhanced positron annihilation in the e(+) + HCN/DCN collisions within a local complex potential model. Vibrationally elastic and inelastic cross sections and effective annihilation rates were calculated by solving a time-dependent complex-potential Schrodinger equation under the ab initio potential energy surface for the positron attached HCN molecule, [HCN; e(+)], with multi-component configuration interaction level (Kita and Tachikawa, 2014). We discuss the effect of vibrational excitation on the positron affinities from the obtained vibrational resonance features. (c) 2017 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2017.03.025

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.1016/j.cplett.2017.02.073

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：SPRINGER  

Heterodimer of formic acid and nitric acid, of which the monomer acidity has large difference, was studied by on-the-fly ab initio molecular dynamics (AIMD) and path integral molecular dynamics (PIMD) simulations with RI-BVWN/SVP level of density functional theory, to elucidate the nuclear quantum effect and isotopic effect on the structural dynamics of the heterodimer. At 300 K, the two hydrogen bonds were maintained in both AIMD and PIMD regimes. Analyses in structural parameters suggested that this heterodimer should exist in the asymmetric binding mode, where hydrogen bonding is stronger on the C=O center dot center dot center dot H-O-N side. The asymmetry in the binding can be observed even more when the nuclear quantum effect was introduced. Although the complex has an equal conformation connected by a double hydrogen bonding, analyses in the principal component modes revealed the dominance of the dimer opening and twisting motions, which were suggested to obstruct double-proton transfer.

DOI： 10.1007/s00214-017-2057-3

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：ROYAL SOC CHEMISTRY  

Isomerization and keto-enol tautomerism reactions of the pyruvic acid molecule have been investigated using the multicomponent B3LYP (MC_B3LYP) methods, which can take account of the nuclear quantum effect (NQE) of a light nucleus, such as a proton and a deuteron. While the conventional harmonic zero point vibrational energy (ZPVE) correction makes the activation energies of all the reactions in this system lower, a contrasting behavior is found in our MC_B3LYP results for several rotational reactions. In such cases, the H/D isotope effect on the activation energy is also completely opposite between harmonic ZPVE-corrected B3LYP and MC_B3LYP calculations. In our MC_B3LYP calculation, the activation energies of several C-C or O-H rotational reactions of H species are slightly higher than those of D species, since the NQE of a hydrogen-bonded proton strengthens the hydrogen-bonded interaction more than that of a deuteron, and, thus, the rotational motion of H species is restricted. Such an "unusual" H/D isotope effect on the activation energies can be observed only in the MC_B3LYP results. Our MC_B3LYP calculations clearly demonstrate that direct inclusion of NQE is indispensable to analyze H/D isotope effects on activation energies of not only hydrogen transfer reactions but also C-C and O-H rotational reactions in the isomerization and keto-enol tautomerism of pyruvic acid molecule.

DOI： 10.1039/c6ra28271g

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：ROYAL SOC CHEMISTRY  

Gear-shaped amphiphile molecules (1) recently synthesized by Hiraoka et al. self-assemble into a hexameric structure, nanocubes (16), in 25% aqueous methanol due to a solvophobic effect. Here we have carried out molecular dynamic simulations to elucidate the stability of these hexameric capsules (16 and 26) in water, 25% aqueous methanol, and methanol. In all solvents, the 16 nanocubes are maintained for all trajectories. On the other hand, 26 was found to collapse for one trajectory in water and seven trajectories in 25% aqueous methanol. In a pure methanol solvent, 26 was found to collapse for all trajectories. The number of collapsed trajectories of 26 increased with the amount of methanol in the solvent. We therefore focused on the structure of the p-p stacking between pyridyl groups and the CH-p interactions between the methyl and pyridyl groups within the nanocube. Our study clearly shows the role played by the methanol solvent molecules in the assembly of the nanocube in terms of the substituent and solvent effects at the molecular level, and that these substituent and solvent effects are important for the self-assembly of the nanocubes.

DOI： 10.1039/c6cp07754d

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（国際会議プロシーディングス）   出版者・発行元：IOP PUBLISHING LTD  

We theoretically analyzed the effect of the anharmonicity and the inter-mode couplings of molecular vibrations on a positron affinity (PA), which is the binding energy of a positron, of HCN and CH2O molecules. Based on the different theoretical approaches for describing vibrational wave functions, we confirmed that (i) not only the anharmonicity but also the inter-mode couplings on potential energy surface are indispensable for the accurate calculation of PA values, and (ii) the effect of inter-mode couplings on a positron affinity surface is sufficiently weaker than that on potential energy surface.

DOI： 10.1088/1742-6596/791/1/012015

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（国際会議プロシーディングス）   出版者・発行元：ELSEVIER SCIENCE BV  

H-2 dissociation on small aluminum cluster, Al-2, is studied using our multicomponent quantum-mechanical (MC_QM) method, which can take account of the nuclear quantum effect (NQE) of light nucleus, such as proton and deuteron. We demonstrate that no standard density functionals can reproduce CCSD(T) geometry of van der Waals Al-2. H-2 complex well, even though the empirical dispersion correction is included. Our MC_QM calculations reveal that NQE stabilizes structures at each stationary point, and H-2 dissociation reaction is the barrierless reaction on the MC_QM effective potential energy hypersurface. The H/D isotope effect on the dissociation reaction are also analyzed. (C) 2017 The Authors. Published by Elsevier B.V.

DOI： 10.1016/j.procs.2017.05.180

Web of Science

Scopus

researchmap

その他リンク： http://orcid.org/0000-0002-4080-5036

記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.1039/c6cp05414e

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.1063/1.4966162

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：AMER CHEMICAL SOC  

The sialyltransferase is an enzyme that transfers the sialic acid moiety from cytidine 5'-monophospho-N-acetyl-neuraminic acid (CMP-NeuAc) to the terminal position of glycans. To elucidate the catalytic mechanism of sialyltransferase, we explored the potential energy surface along the sialic acid transfer reaction coordinates by the hybrid quantum mechanics/molecular mechanics method on the basis of the crystal structure of sialyltransferase CstII. Our calculation demonstrated that CstII employed an S(N)1-like reaction mechanism via the formation of a short-lived oxocarbenium ion intermediate. The computational barrier height was 19.5 kcal/mol, which reasonably corresponded with the experimental reaction rate. We also found that two tyrosine residues (T-yr156 and Tyr162) played a vital role in stabilizing the intermediate and the transition states by quantum mechanical interaction with CMP.

DOI： 10.1021/acs.biochem.6b00267

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：WILEY-BLACKWELL  

The short hydrogen bond between tyrosine Y-z and D1-His190 of photosystem II (PSII) was investigated using multicomponent quantum mechanics, where the quantum fluctuation of a hydrogen nucleus was incorporated into electronic structure calculation. Our computation demonstrated that the deuteration for hydrogen in the short hydrogen bond of PSII led to the reduction of the O...N distance. It indicated an inverse Ubbelohde effect typically recognized in strong and symmetric hydrogen-bonding clusters such as FHF- and H3O2-. We confirmed that the relation between the geometric isotope effect and the symmetry of the potential energy profile of FHF- was reasonably agreed with that of PSII. According to this agreement, the short hydrogen bond in PSII can be regarded as a short strong hydrogen bond. (c) 2016 Wiley Periodicals, Inc.

DOI： 10.1002/jcc.24438

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：SPRINGER  

Nuclear quantum effect and thermal effect on deprotonated hydrogen sulfide dimer anion H3S2-, composed of a second row element, are widely explored by ab initio on-the-fly path integral molecular dynamics simulation. At low temperature, the hydrogen-bonded proton tends to be diffusively located at the central position between two sulfur atoms, which is the typical characteristic feature of so-called low-barrier hydrogen bond (LBHB). This is the first case of the LBHB systems composed of the second row elements, although the hydrogen-bonded distance in H3S2- (over 3.4 angstrom) is much longer than the previously reported LBHB composed of first row elements (&lt;2.5 angstrom). At high temperature, the distance between two sulfur atoms is longer than that at low temperature, and the hydrogen-bonded proton localizes to each sulfur atom. Similar tendency is obtained in the deuterated D3S2- species at all temperature. Analyzing the relationship between the position of the hydrogen-bonded proton and the quantum fluctuation effect of the proton, we elucidate that the LBHB is induced by the quantum tunneling at low temperature, while such trend becomes weak and the character of LBHB vanishes at room temperature for H3S2-.

DOI： 10.1007/s00214-016-1958-x

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：AMER INST PHYSICS  

The on-the-fly ab initio density functional path integral molecular dynamics (PIMD) simulations, which can account for both the nuclear quantum effect and thermal effect, were carried out to evaluate the structures and "reduced" isotropic hyperfine coupling constants (HFCCs) for muoniated and hydrogenated acetone radicals (2-muoxy-2-propyl and 2-hydoxy-2-propyl) in vacuo. The reduced HFCC value from a simple geometry optimization calculation without both the nuclear quantum effect and thermal effect is -8.18 MHz, and that by standard ab initio molecular dynamics simulation with only the thermal effect and without the nuclear quantum effect is 0.33 MHz at 300 K, where these two methods cannot distinguish the difference between muoniated and hydrogenated acetone radicals. In contrast, the reduced HFCC value of the muoniated acetone radical by our PIMD simulation is 32.1 MHz, which is about 8 times larger than that for the hydrogenated radical of 3.97 MHz with the same level of calculation. We have found that the HFCC values are highly correlated with the local molecular structures; especially, the Mu-O bond length in the muoniated acetone radical is elongated due to the large nuclear quantum effect of the muon, which makes the expectation value of the HFCC larger. Although our PIMD result calculated in vacuo is about 4 times larger than the measured experimental value in aqueous solvent, the ratio of these HFCC values between muoniated and hydrogenated acetone radicals in vacuo is in reasonable agreement with the ratio of the experimental values in aqueous solvent (8.56 MHz and 0.9 MHz); the explicit presence of solvent molecules has a major effect on decreasing the reduced muon HFCC of in vacuo calculations for the quantitative reproduction. Published by AIP Publishing.

DOI： 10.1063/1.4960077

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：WILEY-BLACKWELL  

We previously reported l--aminooxy-phenylpropionic acid (AOPP) to be an inhibitor of auxin biosynthesis, but its precise molecular target was not identified. In this study we found that AOPP targets TRYPTOPHAN AMINOTRANSFERASE of ARABIDOPSIS 1 (TAA1). We then synthesized 14 novel compounds derived from AOPP to study the structure-activity relationships of TAA1 inhibitors invitro. The aminooxy and carboxy groups of the compounds were essential for inhibition of TAA1 invitro. Docking simulation analysis revealed that the inhibitory activity of the compounds was correlated with their binding energy with TAA1. These active compounds reduced the endogenous indole-3-acetic acid (IAA) content upon application to Arabidopsis seedlings. Among the compounds, we selected 2-(aminooxy)-3-(naphthalen-2-yl)propanoic acid (KOK1169/AONP) and analyzed its activities invitro and invivo. Arabidopsis seedlings treated with KOK1169 showed typical auxin-deficient phenotypes, which were reversed by exogenous IAA. In vitro and invivo experiments indicated that KOK1169 is more specific for TAA1 than other enzymes, such as phenylalanine ammonia-lyase. We further tested 41 novel compounds with aminooxy and carboxy groups to which we added protection groups to increase their calculated hydrophobicity. Most of these compounds decreased the endogenous auxin level to a greater degree than the original compounds, and resulted in a maximum reduction of about 90% in the endogenous IAA level in Arabidopsis seedlings. We conclude that the newly developed compounds constitute a class of inhibitors of TAA1. We designated them pyruvamine'.
Significance Statement It is difficult to evaluate the functions of auxin and the biosynthesis pathways of indole-3-acetic acid using genetic approaches; chemical genetics is an alternative method. Here we show that L--aminooxy-phenylpropionic acid (AOPP), an inhibitor of auxin biosynthesis, targets tryptophan aminotransferase. We synthesized novel compounds derived from AOPP to study the structure-activity relationships of inhibitors of tryptophan aminotransferase invitro, and identified some that were more potent, and more specific, in inhibiting auxin levels. We designate these compounds pyruvamines'.

DOI： 10.1111/tpj.13197

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：AMER CHEMICAL SOC  

We investigate positron binding to glycine and its aqueous complexes by first-principles calculation. We show that while glycine in its ground state (Gly) does not bind positrons, several of its strongly polar conformers do, and in particular, its zwitterion form (GlyZI) binds positrons strongly. Aqueous complexes Gly center dot nH(2)O and GlyZI center dot nH(2)O also bind positrons, if their dipole moment mu &gt; mu(cr). However, mu is not a sufficient quantity to describe positron binding to thee complexes. We show that in addition to mu, positron binding strongly depends on the intramolecular bonding of glycine. In Gly center dot H2O, positrons are weakly bound to the nitrogen in Gly, whereas in GlyZI center dot nH(2)O, the ionic oxygen in GlyZI is a strong "positron attractor".

DOI： 10.1021/acs.jpca.6b01780

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：WILEY-BLACKWELL  

The optimal exponent alpha values (alpha(opt)) in s-type Gaussian-type functions (GTFs) for quantum protons and deuterons, which are used for multicomponent molecular orbital calculations including nuclear quantum nature of protons and deuterons, are analyzed for several charged or polarized systems and their deuterated species. Ishimoto and coworkers (Ishimoto, Int. J. Quantum Chem. 2006, 106, 1465) have already proposed the average exponent values for five neutral molecules (alpha(ave)), and demonstrated that their alpha(ave) enables us to evaluate the H/D isotope effect on energies and geometries of various neutral species. The differences between total energies of several charged or polarized systems with previous alpha(ave) and our alpha(opt) correspond to only less than 0.004% of the total energy (0.47 kcal.mol(-1)) except for HeH+ and HeD+ molecules, while the difference between interaction energies of H2OH+...OH2 and H2OD+...OH2 systems with previous alpha(ave) is 19% (0.22 kcal.mol(-1)) smaller than that with our alpha(opt). Meanwhile, the difference between OH bond lengths in H2OH+center dot center dot center dot OH2 system with alpha(ave) and alpha(opt) values is 0.027 angstrom. We also found that the interaction energies with alpha(opt) value at the geometry optimized with previous alpha(ave) value (alpha(sp)) well reproduce those at the geometry optimized with alpha(opt) value. We have demonstrated that the nuclear basis functions based on s-type GTFs with previous alpha(ave) values enable us to evaluate the H/D isotope effect on energies and geometries of charged or polarized systems. (C) 2016 Wiley Periodicals, Inc.

DOI： 10.1002/qua.25117

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：SPRINGER  

We theoretically analyzed a positron affinity (PA), which is the binding energy of a positron, of the non-polar carbon disulfide (CS2) molecule at vibrational excited states to elucidate the effect of molecular vibrations on the binding of positron to the molecule. Using the configuration interaction method of the multi-component molecular orbital theory and anharmonic vibrational state analysis with vibrational quantum Monte Carlo technique, the vibrational averaged PA values are calculated as 0.39, 2.03, and 5.02 meV for the ground state, fundamental tone, and overtone states of asymmetric stretching mode, respectively. The PA value of CS2 molecule is found to be enhanced by the vibrational excitation of only asymmetric stretching mode compared to the value at the vibrational ground state. With the linear regression analysis, we have confirmed that such enhancement of vibrational averaged PA values mainly arises from the increment of molecular permanent dipole moment due to the vibrational excitations of the asymmetric stretching mode.

DOI： 10.1140/epjd/e2016-70140-7

Web of Science

researchmap

記述言語：日本語   掲載種別：研究論文（学術雑誌）  

最も軽い水素の原子核の運動においては, 量子効果が顕著に現れる. 原子核運動の量子効果を直接的に取り込んだ理論として多成分分子理論を開発してきた．また近年では, 計算時間のかからない密度汎関数理論が分子理論の中心理論となりつつある．我々は, 多成分密度汎関数理論のための簡便な電子-核相関汎関数を開発した. この汎関数は, 相関波動関数から簡単かつ正当な物理条件のみにもとづいて導出した汎用性の高い汎関数であり，パラメータを1つしか含まない．にもかかわらず，水素原子を含む小分子の電子-プロトン相関エネルギーを化学的精度（1～2 kcal/mol程度の誤差）で再現する．

DOI： 10.2477/jccj.2016-0018

researchmap

記述言語：英語   掲載種別：研究論文（国際会議プロシーディングス）   出版者・発行元：SPRINGER-VERLAG BERLIN  

We analyzed the monohydration effect on the hydrogen-bonded structure between the adenine-thymine base pair using path integral molecular dynamics simulations including the nuclear quantum and thermal effects. We focused on two monohydration models for an adenine-thymine base pair with a water molecule bound to each adenine and thymine site. The adenine-thymine base pair without a water molecule was also discussed to reveal the role of a water molecule in monohydrated models. We found that the monohydration effect varies depending on the location of the water molecule. The monohydration effect on the inter-molecular motions is also investigated using the principle component analysis. The monohydration alters the inter-molecular motions of adenine-thymine base pair. We found that the nuclear quantum effect on the motion depends on the positions of the bound water molecule. The nuclear quantum effect on the hydrogen-bonded structure of adenine, thymine and water molecules is rather small, but we found significantly large nuclear quantum effect on the inter-molecular motions of the monohydrated base pair systems.

DOI： 10.1007/s00214-015-1686-7

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：ELSEVIER SCIENCE BV  

Photoactive yellow protein (PYP) has a characteristic hydrogen bond (H bond) between p-coumaric acid chromophore and Glu46, whose OH bond length has been observed to be 1.21 angstrom by the neutron diffraction technique [Proc. Natl. Acad. Sci. 106, 440-4]. Although it has been expected that such a drastic elongation of the OH bond could be caused by the quantum effect of the hydrogen nucleus, previous theoretical computations including the nuclear quantum effect have so far underestimated the bond length by more than 0.07 angstrom. To elucidate the origin of the difference, we performed a vibrational analysis of the H bond on potential energy curve with OO distance of 2.47 on the equilibrium stStructuand that with OO distance of 2.56 A on the experimental crystal structure. While the vibrationally averaged OH bond length for equilibrium structure was underestimated, the corresponding value for crystal structure was in reasonable agreement with the corresponding experimental values. The elongation of the OO distance by the quantum mechanical or thermal fluctuation would be indispensable for the formation of a low-barrier hydrogen bond in PYP. (C) 2015 The Authors. Published by Elsevier B.V. on behalf of the Research Network of Computational and Structural Biotechnology.

DOI： 10.1016/j.csbj.2015.10.003

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（国際会議プロシーディングス）   出版者・発行元：AMER INST PHYSICS  

The on-the-fly ab initio density functional path integral molecular dynamics (PIMD) simulations, which can take account of both nuclear quantum effect and thermal effect, were carried out, to analyze the thermal dependence on the structural distributions of muoniated and hydrogenated acetone radicals. We have found that the nuclear quantum effect strongly influences to the bondlength between the muonium (hydrogen) and oxygen atoms. In contrast, the rotational angle of the muonium around the oxygen-carbon axis comparably depends on both the nuclear quantum effect and thermal effect at the room temperature. Such change of the rotational angular distribution of the muonium can originate the thermal dependence on the hyperfine coupling constant value of the muoniated acetone.

DOI： 10.1063/1.4968648

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（国際会議プロシーディングス）   出版者・発行元：SPRINGER-VERLAG BERLIN  

We carried out ab initio path integral molecular dynamics simulations at room temperature for OH-(H2O)(n) (n = 1, 2) clusters to elucidate the ionic hydrogen bond structure with full thermal and nuclear quantum effects. We found that the hydrogen-bonded proton is located near the water molecule in the case of n = 2, while the proton is located at the center between hydroxide ion and the water molecule in the case of n = 1. Thus, the solvated hydroxide structure HO-H center dot center dot center dot OH is found in n = 2, while the proton sharing hydroxide structure HO center dot center dot center dot H center dot center dot center dot OH is in n = 1. We found that the nature of hydrogen bonds significantly changes with the number of water molecules around the hydroxide. We also compared these results with those of F-(H2O)(n) (n = 1, 2) clusters.

DOI： 10.1007/s00214-014-1587-1

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（国際会議プロシーディングス）   出版者・発行元：AMER CHEMICAL SOC  

Positron affinities (PAs), which is the binding energy of a positron, of hydrogen cyanide (HCN) and formaldehyde (CH2O) molecules at vibrational excited states were theoretically analyzed with both the multi-component molecular orbital and vibrational quantum Monte Carlo methods, in order to elucidate the effect of molecular vibrations on the binding of a positron to the molecules. For HCN molecule, we found that the vibrational excitations of the CN and CH stretching modes enhance PA values in comparison to the value at the ground state, whereas the excitation of bending mode deenhances it. For CH2O molecule, the vibrational excitation of C=0 stretching mode gives the largest contribution to the PA enhancement among all vibrational modes. Using the linear regression analysis, we confirmed that the PA variations at each vibrational state mainly arise from the changes in the permanent dipole moment by vibrational excitations.

Web of Science

researchmap

記述言語：日本語   出版者・発行元：一般社団法人日本物理学会  

DOI： 10.11316/jpsgaiyo.71.1.0_799

CiNii Books

researchmap

記述言語：日本語   出版者・発行元：一般社団法人日本物理学会  

DOI： 10.11316/jpsgaiyo.71.1.0_711

CiNii Books

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.1038/srep17900

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：WILEY-V C H VERLAG GMBH  

To analyze the H/D isotope effects on hydrogen transfer reactions in XHCHCHCHYXCHCHCHYH (X, Y=O, NH, or CH2) including the nuclear quantum effect of proton and deuteron, we propose a multicomponent molecular orbital-climbing image-nudged elastic band (MC_MO-CI-NEB) method. We obtain not only transition state structures but also minimum-energy paths (MEPs) on the MC_MO effective potential energy surface by using MC_MO-CI-NEB method. We find that nuclear quantum effect affects not only stationary-point geometries but also MEPs and electronic structures in the reactions. We clearly demonstrate the importance of including nuclear quantum effects for H/D isotope effect on rate constants (k(H)/k(D)).

DOI： 10.1002/cphc.201500498

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：ROYAL SOC CHEMISTRY  

We performed ab initio path integral molecular dynamics simulations for the hydroxide-water cluster, OH-(H2O)(2), at 50 K, 100 K, and 150 K to investigate its flexible structure. From our simulations, we found that nuclear quantum effects enhance hydroxide hydrogen atom inversion and the conformational change between isomers occurs by simultaneous rotation of the free hydrogen atom. We propose the importance of including the transition state conformer with C-2 symmetry, for the description of this system at temperatures realized in predissociation experiments. Temperature dependence of relative populations of each conformer along with multidimensional vibrational calculations were used to simulate the vibrational spectra and compare with the experimental spectra of Johnson and coworkers. We assign the doublet peaks seen in the experiment at 2500 to 3000 cm(-1), as the mixture of the ionic hydrogen bonded OH stretching overtone, ionic hydrogen bonded OH bending overtone, and the combination band of the ionic hydrogen bonded OH stretch and bend, which are modulated by the van der Waals OO vibrations. We concluded that for OH-(H2O)(2), the vibrational couplings between the ionic hydrogen bonded motion and floppy modes contribute to the broadening of peaks observed in the 2500 to 3000 cm(-1) region.

DOI： 10.1039/c5cp03632a

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：TAYLOR & FRANCIS LTD  

We have combined ab initio path integral molecular dynamics (PIMD) simulation and the polarizable continuum model (PCM) method to efficiently incorporate solvent effects into nuclear quantum fluctuation of molecular systems. Our combined ab initio PIMD-PCM simulation was applied to muoniated and deuterated methyl radical immersed in implicit water solvent to gain information on solvent and isotope effects from one simulation run. We found that solvent effects lead to the bond elongation and a decrease in the magnitude of isotropic hyperfine coupling constants. These are consistent with the trends in conventional static calculations and experiments. In addition, the performance of cavity models (universal force field, united atom specified for Kohn-Sham and these hybrid models) and the conservation of the PIMD-PCM Hamiltonian were accessed. We confirmed that solvent effects on nuclear quantum fluctuation are efficiently computed using our combined simulation of quantum solute in implicit solvent.

DOI： 10.1080/08927022.2014.938070

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：WILEY-BLACKWELL  

Three different H/D isotope effect in nine H3XH(D)(YH3)-Y-... (X = C, Si, or Ge, and Y = B, Al, or Ga) hydrogen-bonded (HB) systems are classified using MP2 level of multicomponent molecular orbital method, which can take account of the nuclear quantum nature of proton and deuteron. First, in the case of H3CH(D)(YH3)-Y-... (Y = B, Al, or Ge) HB systems, the deuterium (D) substitution induces the usual H/D geometrical isotope effect such as the contraction of covalent R(CH(D)) bonds and the elongation of intermolecular R(H(D)Y-...) and R((CY)-Y-...) distances. Second, in the case of H3XH(D)(YH3)-Y-... (X = Si or Ge, and Y = Al or Ge) HB systems, where H atom is negatively charged called as charge-inverted hydrogen-bonded (CIHB) systems, the D substitution leads to the contraction of intermolecular R(H(D)Y-...) and R((XY)-Y-...) distances. Finally, in the case of H3XH(D)(BH3)-B-... (X = Si or Ge) HB systems, these intermolecular R(H(D)Y-...) and R((XY)-Y-...) distances also contract with the D substitution, in which the origin of the contraction is not the same as that in CIHB systems. The H/D isotope effect on interaction energies and spatial distribution of nuclear wavefunctions are also analyzed. (c) 2015 Wiley Periodicals, Inc.

DOI： 10.1002/jcc.23978

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：TAYLOR & FRANCIS LTD  

Molecular dynamics simulations were performed for the hexameric nanocubes of methylated (1(6)) and demethylated (2(6)) gear-shaped amphiphiles in pure methanol to reveal the difference in structural fluctuation between 1(6) and 2(6). Within our simulation time of 2.0ns, the cubic structure of 1(6) in methanol is maintained, whereas that of 2(6) is collapsed. We found that the triple pi-stacking moieties consisting of the three 3-pyridyl groups in 2(6) are more fluctuated than those in 1(6). This suggests that methyl groups serve to reduce structural fluctuation for nanocubes. We also found that the existence of the solvent molecules near the nanocube is an important factor for the collapse of the 2(6) structure.

DOI： 10.1080/08927022.2014.940523

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：SPRINGER  

We analyzed the monohydration effect on the hydrogen-bonded structure between the adenine-thymine base pair using path integral molecular dynamics simulations including the nuclear quantum and thermal effects. We focused on two monohydration models for an adenine-thymine base pair with a water molecule bound to each adenine and thymine site. The adenine-thymine base pair without a water molecule was also discussed to reveal the role of a water molecule in monohydrated models. We found that the monohydration effect varies depending on the location of the water molecule. The monohydration effect on the inter-molecular motions is also investigated using the principle component analysis. The monohydration alters the inter-molecular motions of adenine-thymine base pair. We found that the nuclear quantum effect on the motion depends on the positions of the bound water molecule. The nuclear quantum effect on the hydrogen-bonded structure of adenine, thymine and water molecules is rather small, but we found significantly large nuclear quantum effect on the inter-molecular motions of the monohydrated base pair systems.

DOI： 10.1007/s00214-015-1686-7

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：AMER CHEMICAL SOC  

Multicomponent quantum mechanical (MC_QM) calculations with polarizable continuum model (PCM) have been tested against liquid H-1 NMR chemical shifts for a test set of 80 molecules. Improvement from conventional quantum mechanical calculations was achieved for MC_QM calculations. The advantage of the multicomponent scheme could be attributed to the geometrical change from the equilibrium geometry by the incorporation of the hydrogen nuclear quantum effect, while that of PCM can be attributed to the change of the electronic structure according to the polarization by solvent effects.

DOI： 10.1021/jp512877a

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：SPRINGER  

The H/D/T geometrical isotope effect (GIE) on XH center dot center dot center dot pi interaction in XH center dot center dot center dot benzene (X = CH3, OH, and NH2) complexes is analyzed by MP2 level of multicomponent molecular orbital calculations, which can take account of nuclear quantum nature. The distances between X atom and center of the benzene ring in XD center dot center dot center dot benzene and XT center dot center dot center dot benzene complexes are found to be shorter than that in XH center dot center dot center dot benzene complex, which shows a different trend in the conventional hydrogen-bonded complexes. Such reverse Ubbelohde effect in XH center dot center dot center dot benzene complexes is explained by the cooperative effect of two kinds of GIEs: (1) primary GIE on the covalent X-H bond and (2) secondary GIE on the H center dot center dot center dot pi distance. We have clearly revealed that the primary GIE is dominant in the GIE of XH center dot center dot center dot pi complexes.

DOI： 10.1007/s00214-015-1633-7

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：AMER INST PHYSICS  

The magnetic coupling of the chromium dimer cation, Cr-2(+), has been an outstanding problem for decades. An optical absorption spectrum of Cr-2(+) has been obtained by photodissociation spectroscopy in the photon-energy range from 2.0 to 5.0 eV. Besides, calculations have been performed by the equation-of-motion coupled-cluster singles and doubles method for vertical excitation of the species. Their coincidence supports our assignment that the ground electronic state exhibits a ferromagnetic spin coupling, which is contrary to those of neutral and negatively charged dimers, Cr-2 and Cr-2(-), in their lowest spin states. (C) 2015 AIP Publishing LLC.

DOI： 10.1063/1.4907197

Web of Science

researchmap

掲載種別：研究論文（学術雑誌）   出版者・発行元：Springer Science and Business Media LLC  

DOI： 10.1007/s00214-014-1587-1

Web of Science

researchmap

その他リンク： http://link.springer.com/article/10.1007/s00214-014-1587-1/fulltext.html

記述言語：英語   掲載種別：研究論文（国際会議プロシーディングス）   出版者・発行元：IOP PUBLISHING LTD  

To theoretically demonstrate the binding of a positron to small polarized molecules, we have calculated the vibrational averaged positron affinity (PA) values for small molecules with multi-component quantum Monte Carlo and molecular orbital methods. Our most accurate prediction of the vibrational averaged PA values at the fundamental and overtone states for formaldehyde molecule are 31 and 36 meV, respectively.

DOI： 10.1088/1742-6596/635/7/072085

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（国際会議プロシーディングス）   出版者・発行元：AMER INST PHYSICS  

To theoretically demonstrate the binding of a positron to small polarized molecules, we have calculated the vibrational averaged positron affinity (PA) values along the local vibrational contribution with the configuration interaction level of multi-component molecular orbital method. This method can take the electron-positron correlation contribution into account through single electronic - single positronic excitation configurations. The PA values are enhanced by including the local vibrational contribution from vertical PA values due to the anharmonicity of the potential.

DOI： 10.1063/1.4938847

Web of Science

researchmap

記述言語：英語  

researchmap

記述言語：英語   掲載種別：研究論文（国際会議プロシーディングス）   出版者・発行元：AMER INST PHYSICS  

A Colle-Salvetti type electron-nucleus correlation functional for multicomponent density-functional theory is proposed. We demonstrate that our correlation functional quantitatively reproduces the quantum nuclear effects of protons; the mean absolute deviation value is 2.8 millihartrees for the optimized structure of hydrogen-containing molecules. We also show other practical calculations with our new electron-deuteron and electron-triton correlation functionals. Since this functional is derived without any unphysical assumption, the strategy taken in this development will be a promising recipe to make new functionals for the potentials of other particles' interactions.

DOI： 10.1063/1.4938873

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：AMER INST PHYSICS  

Multicomponent quantum mechanical (MC_QM) calculation has been extended with ONIOM (our own N-layered integrated molecular orbital + molecular mechanics) scheme [ONIOM(MC_QM:MM)] to take account of both the nuclear quantum effect and the surrounding environment effect. The authors have demonstrated the first implementation and application of ONIOM(MC_QM:MM) method for the analysis of the geometry and the isotope shift in hydrogen-bonding center of photoactive yellow protein. ONIOM(MC_QM:MM) calculation for a model with deprotonated Arg52 reproduced the elongation of O-H bond of Glu46 observed by neutron diffraction crystallography. Among the unique isotope shifts in different conditions, the model with protonated Arg52 with solvent effect reasonably provided the best agreement with the corresponding experimental values from liquid NMR measurement. Our results implied the availability of ONIOM(MC_QM:MM) to distinguish the local environment around hydrogen bonds in a biomolecule. (C) 2014 AIP Publishing LLC.

DOI： 10.1063/1.4900987

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：WILEY  

The feature of positron binding to aspartame molecule was analyzed using the ab initio multicomponent molecular orbital method. All nine stable conformers for aspartame molecule have positive positron affinity (the binding energy of a positron) values, which means that a positron can be attached to parent aspartame molecule. Analyzing the positronic orbitals of positronic aspartame conformers and the electrostatic potential maps of the corresponding parent molecules, we found that long-range electrostatic interaction is the most crucial role in positron binding to aspartame molecule. We theoretically confirmed the possibility of positron binding to the conformers of aspartame molecule with strong dipole moment. (C) 2014 Wiley Periodicals, Inc.

DOI： 10.1002/qua.24641

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：ELSEVIER SCIENCE BV  

The H/D isotope effects on structures, binding energies, and basis set superposition errors (BSSEs) of hydrated fluoride anion clusters, F-(H2O)(n) (n = 1-3), are theoretically analyzed by using the MP2 level of multi-component molecular orbital (MC_MO-MP2) method, in which quantum nature of proton/deuteron and electron-electron correlation are directly taken account. Our results clearly show that the additional water molecule to F-(H2O)(n-1) cluster forms stronger water-water hydrogen bond than that in simple water cluster, whereas the additional F--water hydrogen bond formation in F-(H2O)(n) cluster weakens the original F--water hydrogen bonds in F-(H2O)(n-1) cluster. The BSSEs estimated in the MC_MO-MP2 calculations are slightly larger than those in the conventional MP2 calculations, due to the H/D geometrical isotope effect on the intermolecular distances. Consequently, the order of stability in several F-(H2O)(3) cluster isomers cannot be adequately evaluated without BSSE corrections in our MC_MO-MP2 calculations, rather than the conventional MP2 ones. (C) 2014 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.chemphys.2014.07.014

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：SPRINGER  

We have performed multi-component full-configuration interaction calculations to investigate the nature of chemical bonding of [LiH; e(+)] at the small and large internuclear distance R. We discuss the importance of geometrical changes in positronic compounds induced by a positron attachment in terms of the virial theorem, with a comparison of the adiabatic- and vertical-positron affinity (PA). The systematic improvement of the PA values achieved by optimisation of (i) the molecular geometry and (ii) the positronic basis centre is also discussed. The stable dissociation channel of [LiH; e(+)] is compared with the ionic- and neutral-dissociation channels of its parent molecule LiH through the analysis of the potential energy curve and the electronic and positronic densities. The vertical PA as a function of R is also presented, which is the difference between the potential energy curve of the parent molecule (LiH -&gt; Li+ + H-) and its positronic compound ([LiH; e(+)] -&gt; Li+ + [H-; e(+)]). Unlike the preceding study of [M. Mella et al., J. Chem. Phys. 113, 6154 (2000)], it took more than R = 50 bohr to converge the vertical PA due to the long-range ionic bonding interaction.

DOI： 10.1140/epjd/e2014-40708-4

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：SPRINGER  

The structure of 7-azaindole dimer (7AI(2)) as a model compound for DNA base pair has been studied by classical molecular dynamics (MD) and path integral molecular dynamics (PIMD) simulations on the semi-empirical PM6 potential energy surface at various temperatures, to investigate the nuclear quantum effect and temperature dependency on the hydrogen-bonded moiety of 7AI(2). At 75 K, two H-bondings are maintained throughout a given simulation time in both classical and PIMD (quantum) simulations. At 150 K, these two H-bondings are maintained in only quantum simulation, while in classical simulation, the two H-bondings (or one H-bonding) are sometimes broken and reformed. For 225 K, these two H-bondings are broken in both classical and quantum simulations. We have also applied a principal component analysis to MD and PIMD simulations to analyze the intermolecular motions. We found that the ratio of the second lowest (dimer butterfly out-of-plane) vibrational mode from normal mode analysis which is the most dominant motion decreases with increasing temperature, whereas that of first lowest (dimer torsion out-of-plane) vibrational mode which is the second most dominant motion increases with increasing temperature from temperature 75 to 150 K and then decreases at 225 K due to the nuclear quantum effect. Moreover, the motions of two hydrogen-bonded structures are significantly different with increasing temperature. This difference is revealed by the principal component analysis which shows that the ratio of opening in-plane motion decreases and the ratio of stretching in-plane motion decreases.

DOI： 10.1007/s00214-014-1553-y

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：AMER PHYSICAL SOC  

The vertical positron affinity (PA) value at the equilibrium position of a formaldehyde molecule is predicted as +25(3) meV with the highly accurate quantum Monte Carlo method. Applying anharmonic vibrational analysis, we have found that the vibrational excitation of the C = O stretching mode drastically enhances the PA value, due to the increment of the molecular dipole moment along this mode. Our predictions of the vibrational averaged PA values at the fundamental and overtone states are 31 and 36 meV, respectively, which strongly supports the conclusion that a positron can bind to formaldehyde.

DOI： 10.1103/PhysRevA.89.062711

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：AMER CHEMICAL SOC  

We performed ab initio path integral molecular dynamics (PIMD) simulations with a density functional theory (DFT) method to accurately predict hyperfine coupling constants (HFCCs) in the ethyl radical (C beta H3-C alpha H2) and its Mu-substituted (muoniated) compound (C(beta)H(2)Mu-C alpha H2). The substitution of a Mu atom, an ultralight isotope of the H atom, with larger nuclear quantum effect is expected to strongly affect the nature of the ethyl radical. The static conventional DFT calculations of C beta H3-C alpha H2 find that the elongation of one C beta-H bond causes a change in the shape of potential energy curve along the rotational angle via the imbalance of attractive and repulsive interactions between the methyl and methylene groups. Investigation of the methyl-group behavior including the nuclear quantum and thermal effects shows that an unbalanced C(beta)H(2)Mu group with the elongated C-beta-Mu bond rotates around the C-beta-C-alpha bond in a muoniated ethyl radical, quite differently from the C beta H3 group with the three equivalent C-beta-H bonds in the ethyl radical. These rotations couple with other molecular motions such as the methylene-group rocking motion (inversion), leading to difficulties in reproducing the corresponding barrier heights. Our PIMD simulations successfully predict the barrier heights to be close to the experimental values and provide a significant improvement in muon and proton HFCCs given by the static conventional DFT method. Further investigation reveals that the C-beta-Mu/H stretching motion, methyl-group rotation, methylene-group rocking motion, and HFCC values deeply intertwine with each other. Because these motions are different between the radicals, a proper description of the structural fluctuations reflecting the nuclear quantum and thermal effects is vital to evaluate HFCC values in theory to be comparable to the experimental ones. Accordingly, a fundamental difference in HFCC between the radicals arises from their intrinsic molecular motions at a finite temperature, in particular the methyl-group behavior.

DOI： 10.1021/ct500027z

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：AMER PHYSICAL SOC  

An electron-nucleus Colle-Salvetti-type correlation functional for multicomponent density-functional theory is proposed. We demonstrate that our correlation functional quantitatively reproduces the quantum mechanical effects of protons; the mean absolute deviation value is 2.8 millihartrees for the optimized structures of hydrogencontaining molecules, and the effective potential energy curve of the hydrogen molecule is well reproduced. Since this functional is derived without any unphysical assumption, the strategy taken in this development will be a promising recipe to make new functionals for the potentials of other particles' interactions, such as electron-positron and electron-muon.

DOI： 10.1103/PhysRevA.89.052519

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：SPRINGER  

We theoretically analyzed positron affinities (PA) of hydrogen cyanide (HCN) molecule at vibrational excited states to elucidate the effect of molecular vibrations on the binding of a positron to the molecule. Using the configuration interaction method in the multi-component molecular orbital theory and anharmonic vibrational state analysis with the variational Monte Carlo technique, we found that the vibrational excitations of the CN and CH stretching modes enhance the PA value compared to that of the vibrational ground state, whereas the excitation of bending mode deenhances it. The largest PA enhancement is found at the excited states of the CH stretching mode; the PA values are 43.02 (1) and 46.34 (2) meV for the fundamental tone and overtone states, respectively. With the linear regression analysis, we confirmed that the PA variation of HCN molecule at each vibrational state arises from the variation of permanent dipole moment and dipole-polarizability due to each vibrational excitation.

DOI： 10.1140/epjd/e2014-40799-9

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：AMER INST PHYSICS  

We have developed the multicomponent hybrid density functional theory [MC_(HF+DFT)] method with polarizable continuum model (PCM) for the analysis of molecular properties including both nuclear quantum effect and solvent effect. The chemical shifts and H/D isotope shifts of the picolinic acid N-oxide (PANO) molecule in chloroform and acetonitrile solvents are applied by B3LYP electron exchange-correlation functional for our MC_(HF+DFT) method with PCM (MC_B3LYP/PCM). Our MC_B3LYP/PCM results for PANO are in reasonable agreement with the corresponding experimental chemical shifts and isotope shifts. We further investigated the applicability of our method for acetylacetone in several solvents. (C) 2014 AIP Publishing LLC.

DOI： 10.1063/1.4872006

Web of Science

researchmap

掲載種別：研究論文（学術雑誌）   出版者・発行元：The Chemical Society of Japan  

DOI： 10.1246/cl.130928

Web of Science

Scopus

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：SPRINGER  

Energy thresholds for dissociation channels of positronic alkali-metal hydrides, [XH;e(+)] (X = Li, Na, and K), to XH + e(+)(positron dissociation), XH+ + Ps (positronium dissociation), and X+ + [H-;e(+)] (positronic hydride ion dissociation) have been calculated using quantum Monte Carlo and high-level ab initio molecular orbital methods, and including quantum zero-point vibrational energy of all of the particles. As the atomic number of X increases from Li to K, the dissociation energy to XH + e(+) increases because the dipole moment of XH increases with the atomic number of X, while the dissociation energy to XH+ + Ps decreases. The energy threshold for the ionic dissociation to X+ + [H-;e(+)] is also reduced, and we obtain 0.975 (3) eV, 0.573 (12) eV, and 0.472 (19) eV for [LiH;e(+)], [NaH;e(+)], and [KH;e(+)], respectively, for this channel. Our results strongly support the conclusion that, among these three channels, the lowest energy dissociation for [XH;e(+)] is the pathway to X+ + [H-;e(+)], where X = Li, Na, and K.

DOI： 10.1140/epjd/e2014-40734-2

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.1002/qua.24541

Scopus

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：PHYSICAL SOC REPUBLIC CHINA  

We have investigated, by on-the-fly path integral molecular dynamics (PIMD) simulations, which can take into account the nuclear quantum and thermal effects, the nuclear quantum effect on the muoniated ethyl radical, where one of the hydrogen atoms of the methyl group in the ethyl radical is substituted with a muonium. Muonium consists of a positive muon and an electron, which can be considered as an ultra-light isotope of a hydrogen atom, and we here focused on the muon spin resonance/rotation/relaxation (SR) and the hyperfine coupling constants (HFCC). Our PIMD simulation with the semiempirical PM6 method has succeeded in treating the nuclear quantum effect, which results mainly in the elongation of the bond length and the characteristic rotation of the CH(2)Mu group. Our PIMD simulation provides dramatic improvements in the characteristics of the HFCCs obtained from the conventional PM6 calculation, although the calculated HFCCs are not in qualitative agreement with the corresponding experimental ones because of the limitation of the semiempirical PM6 method for systems with an unpaired electron.

DOI： 10.6122/CJP.52.126

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：WILEY-BLACKWELL  

The partial isotope substitution for the change of geometrical parameters, interaction energies, and nuclear magnetic shielding tensors (sigma) of dihydrogen-bonded NH3X+center dot center dot center dot YBeH (X, Y = H, D, and T) systems is analyzed. Based on the theoretical calculation, the distance between heavy atoms R-N center dot center dot center dot Be of NH3H+center dot center dot center dot DBeH is clearly found to be shorter than that in NH3D+center dot center dot center dot HBeH. Such apparently paradoxical geometrical isotope effect (GIE) on R-N center dot center dot center dot Be is revealed by the cooperative effect of two kinds of (1) primary covalent-bonded GIE and (2) secondary dihydrogen-bonded one. We have demonstrated that (1) the covalent bond lengths become shorter by heavier isotope-substitution and (2) the dihydrogen-bonded distance R-X center dot center dot center dot Y becomes shorter by heavier Y and lighter X isotope-substitution due to the difference of electronic structure reflected by the nuclear distribution. We have also found that interaction energy of NH3H-center dot center dot center dot DBeH is stronger than that of NH3D+center dot center dot center dot HBeH and isotopic deshielding effect of magnetic shielding becomes large in lighter isotope. (C) 2013 Wiley Periodicals, Inc.

DOI： 10.1002/jcc.23505

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：AMER CHEMICAL SOC  

: Ab initio path integral molecular dynamics (PIMD) simulation was performed to understand the nuclear quantum effect on the out-of-plane ring deformation of hydrogen maleate anion and investigate the existence of a stable structure with ring deformation, which was suggested in experimental observation (Fillaux et al., Chem. Phys. 1999, 120, 387-403). The isotope effect and the temperature effect are studied as well. We first investigated the nuclear quantum effect on the proton transfer. In static calculation and classical ab initio molecular dynamics simulations, the proton in the hydrogen bond is localized to either oxygen atom. On the other hand, the proton is located at the center of two oxygen atoms in quantum ab initio PIMD simulations. The nuclear quantum effect washes out the barrier of proton transfer. We next examined the nuclear quantum effect on the motion of hydrogen maleate anion. Principal component analysis revealed that the out-of-plane ring bending modes have dominant contribution to the entire molecular motion. In quantum ab initio PIMD simulations, structures with ring deformation were the global minimum for the deuterated isotope at 300 K. We analyzed the out-of-plane ring bending mode further and found that there are three minima along a ring distortion mode. We successfully found a stable structure with ring deformation of hydrogen maleate for the first time, to our knowledge, using theoretical calculation. The structures with ring deformation found in quantum simulation of the deuterated isotope allowed the proton transfer to occur more frequently than the planar structure. Static ab initio electronic structure calculation found that the structures with ring deformation have very small proton transfer barrier compared to the planar structure. We suggest that the "proton transfer driven" mechanism is the origin of stabilization for the structure with out-of-plane ring deformation.

DOI： 10.1021/ct4007986

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（国際会議プロシーディングス）   出版者・発行元：IOP PUBLISHING LTD  

To theoretically demonstrate the binding of a positron to acetonitrile, acetaldehyde, and acetone molecules, we have calculated the vibrational averaged positron affinity (PA) values along the local CN or CO vibrational contribution with the configuration interaction level of multi-component molecular orbital method. This method can take the electron-positron correlation contribution into account through single electronic - single positronic excitation configurations. The PA values are enhanced by including the local vibrational contribution from vertical PA values due to the anharmonicity of the potential. For acetonitrile, acetaldehyde, and acetone molecules, the PA values after averaging over the 1st vibrational state are 136, 55, and 96 meV, which can be compared with the corresponding experimental vlues of 180, 90, and 173 meV, respectively.

DOI： 10.1088/1742-6596/488/1/012053

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：PHYSICAL SOC REPUBLIC CHINA  

We performed ab initio molecular orbital and density functional theory calculations for enhanced cyan fluorescent protein, gold fluorescent protein, and (4-Me)-tryptophan enhanced cyan fluorescent protein to elucidate the substituent effect on the electronic structure of the chromophore in the fluorescent proteins. The electron correlation effect on the electronic structures is investigated as well. Our calculated excitation and deexcitation energies reasonably reproduce the corresponding experimental values. The qualitative Stokes shifts for the three fluorescent proteins were realized taking the electronic correlation into account. We found that the amino group of the chromophore in gold fluorescent protein enhances charge transfer among the ground and excited states, while the substituent effect of the methyl group, which is a weak electron donor, in (4-Me)-tryptophan enhanced cyan fluorescent protein was small. The charge transfer is the origin of the Stokes shift found in gold fluorescent protein. Thus, we succeeded in elucidating the substituent effect on the electronic structure of the chromophore in three fluorescent proteins.

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：PHYSICAL SOC REPUBLIC CHINA  

In order to elucidate the element specificity of the S parameters of polymers containing C, O, or F atoms reported by Sato et a l. with the Doppler broadening of positron annihilation radiation measurement [K. Sato, et a l., Phys. Rev. B 71, 012201, (2005).], we theoretically analyzed the molecular orbitals of small size of the polymer molecules with an ab initio molecular orbital method. With a linear regression analysis, we found a strong correlation between the average kinetic energies of the valence electrons and the contribution of a free positron to the experimental S parameters for the C-, O-, and F-groups. As with a consideration of the kinetic energies of the valence electrons and the electronegativity of the C, O, and F atoms, we conclude that the element specificity of the experimental S parameters for each of the C-, O-, and F-groups is roughly explained by a difference in the electronegativity of the C, O, and F atoms.

Web of Science

researchmap

掲載種別：研究論文（学術雑誌）   出版者・発行元：Elsevier BV  

DOI： 10.1016/j.chemphys.2013.10.003

Scopus

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）  

Hole attack: A theoretical one-electron oxidation of nucleic base molecules and their pairs by positron is proposed, based on the calculations for positron-attached neutral forms of species, adenine (A), thymine (T), guanine (G), cytosine (C), and their Watson-Crick base pairs (A-T and G-C). The results reveal that binding of a positron to neutral isolated nucleic base molecules is base-selective. © 2013 WILEY-VCH Verlag GmbH &amp
Co. KGaA, Weinheim.

DOI： 10.1002/cphc.201300549

Scopus

PubMed

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：WILEY-BLACKWELL  

The structure of Watson-Crick-type adenine-thymine and guanine-cytosine pairs has been studied by hybrid Monte Carlo (HMC) and path integral hybrid Monte Carlo (PIHMC) simulations with the use of semiempirical PM6-DH+ method in the gas phase. We elucidated the nuclear quantum effect and temperature dependency on the hydrogen-bonded moiety of base pairs. It was shown that the contribution of nuclear quantum effect on the hydrogen-bonded structure is significant not only at low temperature 150 K but also at temperature as high as 450 K. The relative position of hydrogen-bonded proton between two heavy atoms and the nuclear quantum nature of the proton are also shown. Furthermore, we have applied principal component analysis to HMC and PIHMC simulations to analyze the nuclear quantum effect on intermolecular motions. We found that the ratio of Buckle mode (lowest vibrational mode from normal mode analysis) decreases due to the nuclear quantum effect, whereas that of Propeller mode (second lowest vibrational mode) increases. In addition, nonplanar structures of base pairs were found to become stable due to the nuclear quantum effect from two-dimensional free energy landscape along Buckle and Propeller modes. (c) 2013 Wiley Periodicals, Inc.

DOI： 10.1002/jcc.23399

Web of Science

researchmap

掲載種別：研究論文（学術雑誌）   出版者・発行元：Royal Society of Chemistry (RSC)  

DOI： 10.1039/c3ra44077j

Web of Science

researchmap

掲載種別：研究論文（学術雑誌）   出版者・発行元：Royal Society of Chemistry (RSC)  

DOI： 10.1039/c3cp52572d

Web of Science

PubMed

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：ELSEVIER SCIENCE BV  

The nuclear quantum effect, which plays important roles on ionic hydrogen bonded structures of Cl-(H2O)(n) (n = 1-4) clusters, was explored by carrying out path integral molecular dynamic simulations. An outer shell coordinate r(l)(Cl center dot center dot center dot O) is selected to display the rearrangement of single and multi hydration shell cluster structures. By incorporating the nuclear quantum effect, it is shown that the probability for single shell structures is decreased while the probability for multi shell structures is increased. On the other hand, the correlations between changing of bonded H* atom to Cl- (defined as delta) and other cluster vibration coordinates are studied. We have found that delta strongly correlates with proton transfer motion while it has little correlation with ion-water stretching motion. Contrary to theta(H-O-H*) coordinate, the correlations between delta and other coordinates are decreased by inclusion of nuclear quantum effect. The results indicate that the water-water hydrogen bond interactions are encouraged by quantum simulations. (C) 2013 Elsevier B. V. All rights reserved.

DOI： 10.1016/j.chemphys.2013.02.025

Web of Science

Scopus

researchmap

その他リンク： http://orcid.org/0000-0002-4080-5036

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：ELSEVIER SCIENCE BV  

The structures and infrared spectra of Ag+(H2O)(n) (n = 1-4) and Cu+(H2O) are studied by "on-the-fly" ab initio MD, ab initio PIMD, and ab initio RPMD simulations. It is found that the anharmonicity due to nuclear quantum and thermal effects acts differently depending on the system as well as the type of vibrational mode. In the low-frequency region, the spectra become a broad band as the cluster size increases due to the complex mode couplings, which is qualitatively different from the harmonic spectra. In contrast, the HOH bending modes are systematically red-shifted by a small amount due to the anharmonicity. The OH stretching modes are found to be also red-shifted, but the amount of shift is more dependent on the system. Consequently, these effects cannot be described by unique scaling of harmonic frequencies. (C) 2013 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.chemphys.2013.03.005

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：AMER CHEMICAL SOC  

Small hydrated fluoride ion complexes, F-(H2O) (n = 1-3), have been studied by ab initio hybrid Monte Carlo (HMC) and ab initio path integral hybrid Monte Carlo (PIHMC) simulations. Because of the quantum effect, our simulation shows that the average hydrogen-bonded F-center dot center dot center dot HO distance in the quantum F-(H2O) is shorter than that in the classical one, while the relation inverts at the three water molecular F-(H2O)(3) cluster. In the case of F-(H2O)(3), we have found that the nuclear quantum effect enhances the formation of hydrogen bonds between two water molecules. In F-(H2O)(2) and F-(H2O)(3), the nuclear quantum effect on two different kinds of hydrogen bonds, F--water and water-water hydrogen bonds, competes against each other. In F-(H2O)(3), thus, the nuclear quantum effect on the water-water hydrogen bond leads to the elongation of hydrogen-bonded F-center dot center dot center dot HO distance, which we suggest this as the possible origin of the structural inversion from F-(H2O) to F-(H2O)(3).

DOI： 10.1021/jp403295h

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：AMER INST PHYSICS  

Temperature dependence on the structural fluctuations of Zundel cation, H5O2+, and its isotopomers, D5O2+ and T5O2+, have been studied using path integral molecular dynamics simulations in which nuclear quantum effect is fully taken into account. It has been found that the fluctuations of hydrogen-oxygen and oxygen-oxygen distances, which are relevant to the hydrogen bonded structure, grow drastically as the temperature increases within the range of investigation between 100 K and 900 K. The fluctuation with respect to the position of non-bonded hydrogen also increases substantially as the temperature increases. The temperature dependence on the fluctuation is greater for D5O2+ or T5O2+ than that of H5O2+, since the zero-point effect of the former is less than the latter. (C) 2013 AIP Publishing LLC.

DOI： 10.1063/1.4803655

Web of Science

PubMed

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：MDPI  

We have theoretically analyzed the nuclear quantum effect on the nuclear magnetic shieldings for the intramolecular hydrogen-bonded systems of alpha-hydroxy acyl aromatic species using the gauge-including atomic orbital technique combined with our multi-component density functional theory. The effect of H/D quantum nature for geometry and nuclear magnetic shielding changes are analyzed. Our study clearly demonstrated that the geometrical changes of hydrogen-bonds induced by H/D isotope effect (called geometrical isotope effect: GIE) is the dominant factor of deuterium isotope effect on C-13 chemical shift.

DOI： 10.3390/molecules18055209

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：ELSEVIER SCIENCE BV  

Ab initio path integral molecular dynamics simulation was performed to understand the nuclear quantum effect on the hydrogen bond of hydrogen malonate anion. Static calculation predicted the proton transfer barrier as 0.12 kcal/mol. Conventional ab initio molecular dynamics simulation at 300 K found proton distribution with a double peak on the proton transfer coordinate. Inclusion of thermal effect alone elongates the hydrogen bond length, which increases the barrier height. Inclusion of nuclear quantum effect washes out this barrier, and distributes a single broad peak in the center. H/D isotope effect on the proton transfer is also discussed. (C) 2013 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2013.03.080

Web of Science

researchmap

掲載種別：研究論文（学術雑誌）  

To investigate the correlation between the wavelength dependence of ionization threshold fluence of target molecule in matrix-assisted laser desorption/ionization by infrared (IR) laser and the IR absorption spectrum of matrix molecule, we have analyzed the IR absorption spectra of four matrix molecules using density functional theory and correlated ab initio molecular orbital method. The calculated IR absorption spectra of the isolated molecules showed more qualitative correlation with the wavelength dependence of ionization threshold fluence than those of the solid state structures. We can consider that a portion of matrix molecules lost the ordered crystal structure and that the transition to the diluted or isolated state occurred at the early process of IR laser irradiation. © 2012 Wiley Periodicals, Inc.

DOI： 10.1002/qua.24296

Scopus

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：ELSEVIER SCIENCE BV  

We have first performed 'gold-standard' CCSD(T) calculations of the chromium dimer cation using a cc-pVQZ basis set in order to elucidate its electronic structures, especially for identification of its ground-state term. Our CCSD(T)/cc-pVQZ calculations have predicted that it is the highest-spin state, in contrast to a previous speculation of the lowest-spin state by density functional theory with semi-local functionals. The ground-state binding energy is found to be 1.49 eV, which reasonably agrees with the corresponding experimental value of 1.30 +/- 0.06 eV. We have also provided several spectroscopic constants for references in future theoretical and experimental works. (C) 2012 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2012.11.017

Web of Science

Scopus

J-GLOBAL

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Elsevier B.V.  

To theoretically analyze the nuclear quantum effects of protons on two hydrogen bonds around the chromophore (CRO) in the photoactive yellow protein (PYP), we have calculated simple cluster model consisting of CRO, Glu46, and Tyr42 residues in PYP with the multi-component molecular orbital method and multi-component density functional theory, which can take account of quantum fluctuations of light mass particles. The average OO distances between CRO and Glu46 and between CRO and Tyr42 with our methods are shorter than the corresponding equilibrium ones, while the OH distances become longer due to the anharmonicity of the potential. The H/D geometrical isotope effect is also found, that is, the distances between oxygen atoms are elongated by the deuterium substitution, known as Ubbelohde effect. © 2012 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.chemphys.2012.11.022

Web of Science

Scopus

researchmap

掲載種別：論文集(書籍)内論文   出版者・発行元：Springer International Publishing  

DOI： 10.1007/978-3-319-01529-3_17

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）  

The quantum nature of the strong hydrogen bonds for the F2H−and F2H3+ions and their deuterated isotopomers at the room temperature has been studied using ab initio path integral molecular dynamics (PIMD) simulations. It is found that, for both of these ions, the hydrogen-bonded H/D atoms largely fluctuate around the central position of two F atoms. The average FH/FF distances of F2H−and F2H3+are longer than the average FD/FF distances of F2D−and F2D3+due to the primary/secondary isotope effects, which stem from the difference of the quantum nature of H and D nuclei. These results are compared with the family of Zundel-type ions, O2H3−, N2H5−, O2H5+, and N2H7+, which have been studied previously with the same ab initio PIMD approach. A comparison is also made with the previous experimental and ab initio vibrational configuration interaction results of F2H−.

DOI： 10.1007/978-94-007-5297-9_10

Scopus

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：SPRINGER  

The feature of positron binding to twenty neutral amino acid molecules with the global minimum (GM) and intramoleculear hydrogen-bonded (HB) structures was analysed using the ab initio multicomponent molecular orbital method. All amino acid molecules in the intramoleculear HB structures have positive positron affinity (PA, the binding energy of a positron) values, which means that a positron can be attached to parent molecules, while in the GM structures only three amino acid molecules of Gln, Trp, and His have positive PA values. Analysing the positronic orbitals of each positronic amino acid molecule and the electrostatic potential maps of the corresponding parent molecules, we found that long-range electrostatic interaction is the most crucial role in positron binding to neutral amino acid molecules. The strong correlation is observed between the PA and dipole moment, that is, a polar molecule with a large dipole moment has a large PA value. The critical dipole moment of neutral amino acid molecules for binding a positron was found at about 3.46 Debye. From the systematic analysis of twenty kinds of amino acid molecule, we theoretically confirmed the possibility of positron binding to conformers of amino acid molecules with strong dipole moment.

DOI： 10.1140/epjd/e2012-20638-y

Web of Science

researchmap

掲載種別：研究論文（学術雑誌）   出版者・発行元：Wiley  

Abstract

To demonstrate the binding of a positron to nonpolar CX₂ (X = O and S) molecules, we have estimated the vibrational averaged positron affinity (PA) values for the harmonic asymmetric stretching vibrational coordinate with the multi‐component molecular orbital method. A positron can be attached at higher vibrational excitation levels, and vibrational averaged PA values become greater as the number of vibrational quantum number increases. The resultant PA values of carbon disulfide (CS₂) molecule are greater than those of CO₂, which is consistent with the corresponding property such as infrared (IR) intensity and polarizability of the parent species. © 2012 Wiley Periodicals, Inc.

DOI： 10.1002/qua.24111

Web of Science

researchmap

掲載種別：研究論文（学術雑誌）   出版者・発行元：Wiley  

Abstract

Molecular dynamics simulations of hexameric molecular capsules constructed from gear‐shaped amphiphile molecules with the aid of solvophobic effect and van der Waals force were performed with general AMBER force field to elucidate the thermodynamical properties of the capsules. The optimized structure of the capsule 1₆ consisting of methylated gear‐shaped molecules (1) is a nearly cubic structure, whereas the distorted structure is found for the capsule 2₆ consisting of ones lacking three methyl groups, (2) so as to maximize the contact surface. Disassembly temperature for the demethylated capsule 2₆, ∼210 K, is much lower than that for the methylated one 1₆, ∼340 K, which is consistent with the corresponding experimental result that 1₆ is stable, whereas 2 exists as a monomer in aqueous methanol. © 2012 Wiley Periodicals, Inc.

DOI： 10.1002/qua.24108

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：IOP PUBLISHING LTD  

Characteristic features of the positron-binding structure of some carbonyl and aldehyde species such as formaldehyde, acetaldehyde, acetone and propionaldehyde are discussed with the configuration interaction scheme of multi-component molecular orbital (MC_MO) calculations. This method can take the electron-positron correlation contribution into account through single electronic-single positronic excitation configurations. Our vertical positron affinity (PA) values of acetaldehyde and acetone with electronic 6-31++G(2df,2pd) and positronic [15s15p3d2f1g] basis sets are as 52 and 92 meV, which can be compared to the recent experimental values of 90 and 173 meV by Danielson et al (2010 Phys. Rev. Lett. 104 233201). For formaldehyde we have also found that the PA values are enhanced by including the local C=O vibrational contribution from the vertical PA value of 15 meV to 17, 21 and 25 meV after averaging over the zeroth, first and second vibrational states, respectively, due to the anharmonicity of the potential.

DOI： 10.1088/1367-2630/14/3/035004

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：ELSEVIER SCIENCE BV  

Path-integral molecular dynamics simulations have been performed for porphycene and its isotopic variants in order to understand the effect of isotopic substitution of inner protons on the double proton transfer mechanism. We have used an on-the-fly direct dynamics technique at the semiempirical PM6 level combined with specific reaction parameterization. Our quantum simulations show that double proton transfer of the unsubstituted porphycene at T = 300 K mainly occurs via a so-called concerted mechanism through the D-2h second-order saddle point. In addition, we found that both isotopic substitution and temperature significantly affect the double proton transfer mechanism. For example, the contribution of the stepwise mechanism increases with a temperature increase. We have also carried out hypothetical simulations with the porphycene configurations being completely planar. It has been found that out-of-plane vibrational motions significantly decrease the contribution of the concerted proton transfer mechanism. (C) 2011 Elsevier B. V. All rights reserved.

DOI： 10.1016/j.chemphys.2011.12.007

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：WILEY-BLACKWELL  

Ab initio path integral molecular dynamics simulation of MOH(H2O) (M = Cu, Ag, and Au) clusters has been performed to analyze how the hydrogen-bonded proton can be affected by the counter noble metal cation. The CuOH(H2O) cluster does not form hydrogen bonded structure even for the static equilibrium structures. Contrary to our previous article of hydrated alkali metal hydroxide clusters (Koizumi et al., J Chem Phys 2011, 134, 031101), proton transferred distribution was not observed because of the high potential barrier heights of MOH(H2O). (C) 2011 Wiley Periodicals, Inc. Int J Quantum Chem 112: 136-139, 2012

DOI： 10.1002/qua.23174

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（国際会議プロシーディングス）   出版者・発行元：AMER CHEMICAL SOC  

We report the theoretical investigations of the positron binding to alkali-metal hydrides (LiH, NaH, and KH) and hydrogen cyanide molecule (HCN) using quantum Monte Carlo (QMC) methods. We have obtained the lowest variational energies of positron-attached NaH, KH, and HCN systems so far, and larger positron affinities of these molecules than the theoretical predictions by previous configuration interaction calculations. Our study also confirms the strong correlation between the positron affinity and dipole moment of alkali-metal hydrides and the binding of a positron in the electrostatic field of the HCN molecule. In this report, we have described our methodology for analyzing a positron-attached molecule (positronic compound) using QMC techniques, and have reviewed our recent results of QMC calculations of the positron binding to these polar molecules.

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：TAYLOR & FRANCIS LTD  

We theoretically investigated the phase transition temperature (T-c) and geometrical changes of mixed K3H1-xDx(SO4)(2) and mixed (H1-xDx)(2)SQ crystals by using the first-principle multi-component molecular orbital method, which can take account of the quantum effect of light nucleus. The O center dot center dot center dot O distances in K3H1-xDx(SO4)(2) and (H1-xDx)(2)SQ crystals gradually elongate and the electronic charge density around the light nucleus becomes greater, as the deuterium concentration increases. We have also predicted the T-c values of TKHS and T(2)SQ, with the hydrogen substituted by the tritium, as about 190 and 680 K, respectively.

DOI： 10.1080/00150193.2012.696464

Web of Science

researchmap

記述言語：英語   掲載種別：論文集(書籍)内論文   出版者・発行元：Trans Tech Publications Ltd  

We investigated the phase transition and the isotope effect in squaric acid (H2C4O4, abbreviated H2SQ), a hydrogen-bonded dielectric material. Using first-principles calculation, we found that Jahn-Teller distortion of the unit structure (C4H4O4) was the major driving force for the phase transition in the H2SQ crystal. In order to elucidate the isotope effect on the phase transition in deuterated squaric acid (D2SQ), we employed the multi-component molecular orbital (MC_MO) method, which directly takes into account the quantum effects of protons and deuterons. Using this model, we successfully predicted the difference between the phase transition temperature of H2SQ and that of D2SQ to be 192K, which is in reasonable agreement with the experimental value of 145 K. We found that the isotope effect in the H2SQ/D2SQ system was based more on shrinking distribution of the deuteron wave rather than that of the proton wave. When the MC_MO method was coupled with adequate cluster models, first-principles calculations were effective to determining the origin of the phase transition and the H/D isotope effect in hydrogen-bonded dielectric materials.

DOI： 10.4028/www.scientific.net/SSP.189.169

Scopus

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：SPRINGER  

We have analyzed the basis function series in molecular systems by optimization of orbital exponents in Gaussian-type functions (GTFs) including the electron correlation effects with multiconfiguration self-consistent field (MCSCF) and Moller-Plesset second-order perturbation (MP2) methods. First, we have derived and implemented the gradient formulas of MCSCF and MP2 energies with respect to GTF exponent, as well as GTF center and nuclear geometry, based on the fully variational molecular orbital (FVMO) method. Second, we have applied these electron-correlated FVMO methods to H(2), LiH, and hydrocarbon (CH(4), C(2)H(6), C(2)H(4), and C(2)H(2)) molecules. We have clearly demonstrated that the optimized exponent values with electron-correlated methods are different from those with simple Hartree-Fock method, since adequate basis functions for adequate virtual orbitals are indispensable to describe the accurate wave function and geometry for electron-correlated calculations.

DOI： 10.1007/s00214-011-1052-3

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：SPRINGER  

Ab initio molecular orbital and density functional theory calculations with inclusion of dispersion interaction effect are employed to reveal the characteristic features of intermolecular interactions for the molecular capsule (1 (6)) consisting of six gear-shaped amphiphile molecules (1) discovered by Hiraoka et al. (J Am Chem Soc 130:14368-14369, 2008). The contributions of CH-pi and pi-pi type dispersion energies are found to be indispensable for the formation of hexameric capsule 1 (6) by the analysis of decomposed interaction energies between fragmented-model species in the 1 molecule. We have also calculated the hexameric capsule (2 (6)) from demethylated 1 molecule (2). Such subtle structural difference induces the different characters of intermolecular interactions, in which the stabilization energy of hexameric 2 (6) capsule is about 40 kcal/mol smaller than that of the original 1 (6) capsule, due to the lack of three methyl groups for the CH-pi interactions in 2 molecules.

DOI： 10.1007/s00214-011-1053-2

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：ELSEVIER SCIENCE BV  

We applied the multi-component density functional theory (MC_DFT) combined with the gauge - including atomic orbital (GIAO) and continuous set of gauge transformation (CSGT) techniques to some small molecules (H-2, HD, H2O, CH4, etc.) for analyzing the nuclear quantum effect on molecular magnetic properties, such as nuclear magnetic shielding constant and molecular magnetic susceptibility. Our method clearly shows that the absolute isotropic magnetic shielding constant depends on the spatial distribution of quantum nuclei, that is, the deuteron-isotopomers have the weaker deshielding effect than the proton-isotopomers. We also found the magnetic isotope effect with respect to the molecular magnetic susceptibility, that is, the magnetic susceptibility of the deuteron-isotopomers is smaller than that of the proton-isotopomers. (C) 2011 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.comptc.2011.03.009

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：ELSEVIER SCIENCE BV  

Ab initio path integral molecular dynamics based on MP2/cc-pVTZ method has been carried out for a series of small hydrogen cluster cations, H(3)(+), F(5)(+) ,H(7)(+) and H(9)(+). Our dissociation enthalpy for the reaction H(3)(+) (H(2))(n) -&gt; H(3)(+) (H(2))(n-1) + H(2) is found to be 5.4, 2.1, and 3.2 kcal/mol, respectively, which are slightly smaller than the corresponding experimental values. It is found that energies of quantum zero-point vibration and anharmonic vibration of the respective cations are important factors to estimate the value of dissociation energy. (C) 2010 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.comptc.2010.11.033

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：AMER CHEMICAL SOC  

We have carried out path-integral molecular dynamics simulations for hydrated sulfuric acid clusters to understand acid-dissociation and hydrogen-bonded structural rearrangement processes in these clusters from a quantum mechanical viewpoint. The simulations were performed using the PM6 semiempirical electronic structure level whose parameters were modified on the basis of the specific reaction parameters strategy so that relative energies of optimized structures, as well as water binding energies reproduce ab initio and density-functional theory calculations. We have found that the acid dissociation processes, first and second deprotonation, effectively occur in a hydrated cluster with a specific cluster size. The mechanisms of the proton-transfer processes were analyzed in detail and it was found that the distance between O in sulfuric acid and O in the proton-accepting water is playing an important role. We also found that the water coordination number of the poton-accepting water is important in the proton-transfer processes.

DOI： 10.1021/jp202380h

Web of Science

PubMed

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：SPRINGER  

The structure of Watson-Crick type guanine-cytosine (G-C) base pair has been studied by classical hybrid Monte Carlo (HMC) and quantum path integral hybrid Monte Carlo (PIHMC) simulations on the semiempirical PM6 potential energy surface. For the three NHa &lt;-X hydrogen-bonded moieties, the intramolecular NH bonds are found systematically longer while the Ha &lt;-X distance shorter in the PIHMC simulation than in the HMC simulation. We found that the hydrogen bonded length Na &lt;-X correlates with the Ha &lt;-X distance, but not with the NH distance. A correlation is also between the neighboring hydrogen bonds in the G-C base pair.

DOI： 10.1007/s00214-011-1004-y

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：AMER INST PHYSICS  

Quantum Monte Carlo methods are used to investigate the binding of a positron to the alkali-metal hydrides, XH (X = Na and K). We obtain positron affinities for the NaH and KH molecules of 1.422(10) eV and 2.051(39) eV, respectively. These are considerably larger than the previous results of 1.035 eV and 1.273 eV obtained from multireference single- and double-excitation configuration interaction calculations. Together with our previous results for [LiH;e(+)] [Y. Kita , J. Chem. Phys. 131, 134310 (2009)], our study confirms the strong correlation between the positron affinity and dipole moment of alkali-metal hydrides. (C) 2011 American Institute of Physics. [doi:10.1063/1.3620151]

DOI： 10.1063/1.3620151

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：CHEMICAL SOC JAPAN  

To elucidate the irreversible photoreaction of green fluorescent protein (GFP), we have theoretically analyzed hydrogen-bonding networks and distributions of water molecules around a chromophore (CRO) of GFP before and after photoactivation. Our molecular dynamics simulation clearly shows that such irreversibility arises from the migration of water molecules to the hollowed out region due to the reorientation of amino acid residues together with the disappearance of hydrogen-bonding networks around the CRO.

DOI： 10.1246/cl.2011.476

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：WILEY-BLACKWELL  

To elucidate the mechanism of the exceptional behavior of lysine for the ionization (protonation) yields in matrix-assisted laser desorption/ionization (MALDI) observed by Nishikaze and Takayama [Rapid Commun. Mass Spectrom. 2006, 20, 376], the temperature dependences of proton affinity (PA) and gas phase basicity for 20 amino acids are theoretically analyzed with correlated ab initio molecular orbital method under ideal gas condition. We have found that two different conformations, the linear structure with elongation of the side chain and the folded one having intramolecular hydrogen bonding, play important roles for the exceptional behavior of lysine. At low temperatures of around 298 K, the most stable conformation of the protonated lysine is the folded structure due to the formation of intramolecular hydrogen bonding. Meanwhile, at high temperatures, the Gibbs free energy of linear structure of protonated lysine becomes lower than that of the folded one because of the increment of vibrational entropic contribution. To explicitly take account of the contribution of the free energies, we have proposed the effective PA values thermally averaged using the ratio of Boltzmann distributions for two conformations. Since the effective PA value for lysine drastically decreases as the temperature increases above 1000 K, the linear correlation is clearly obtained between our effective PA values at high temperature and the ion yields in MALDI. Copyright (C) 2011 John Wiley & Sons, Ltd.

DOI： 10.1002/jms.1903

Web of Science

researchmap

記述言語：英語   出版者・発行元：AMER INST PHYSICS  

DOI： 10.1063/1.3584176

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：AMER INST PHYSICS  

Ab initio path integral molecular dynamics simulation of M(+)(H(3)O(2)(-)) (M=Li, Na, and K) has been carried out to analyze how the structure and dynamics of a low-barrier hydrogen-bonded Zundel anion, H(3)O(2)(-), can be affected by the counter alkali metal cation, M(+). Our simulation predicts that the quantum proton transfer in Zundel anion can be strongly coupled to the motion of counter cation located nearby. A smaller cation can induce larger structural distortion of the Zundel anion fragment making the proton transfer barrier higher, and hence, lower the vibrational excitation energy. It is also argued that a large H/D isotope effect is present. (C) 2011 American Institute of Physics. [doi:10.1063/1.3544212]

DOI： 10.1063/1.3544212

Web of Science

PubMed

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：ROYAL SOC CHEMISTRY  

Characteristic features of the positron binding structure of some nitrile (-CN functional group) species such as acetonitrile, cyanoacetylene, acrylonitrile, and propionitrile are discussed with the configuration interaction scheme of multi-component molecular orbital calculations. This method can take the electron-positron correlation contribution into account through single electronic-single positronic excitation configurations. Our PA value of acetonitrile with the electronic 6-31 + + G(2df,2pd) and positronic [15s15p3d2f1g] basis set is calculated as 4.96 mhartree, which agrees to within 25% with the recent experimental value of 6.6 mhartree by Danielson et al. [Phys. Rev. Lett., 2010, 104, 233201]. Our PA values of acrylonitrile and propionitrile (5.70 and 6.04 mhartree) are the largest among these species, which is consistent with the relatively large dipole moments of the latter two systems.

DOI： 10.1039/c0cp01650k

Web of Science

PubMed

researchmap

記述言語：英語   掲載種別：研究論文（国際会議プロシーディングス）   出版者・発行元：ELSEVIER SCIENCE BV  

We propose a new scheme of the photoactivation and the photobleaching for Dronpa with molecular dynamics method and density functional theory. These processes can be explained by considering cis-trans isomerization in neutral state of chromophore. The proton transfer from anionic to neutral chromophore makes cis-trans isomerization possible via hula-twist rotation process, since the space for cis-trans isomerization is opened at around the region near chromophore by moving out of the imidazole ring on H193 from the position below the phenol ring on chromophore. Then the cis-trans isomerization can occur through the hula-twist process. The contributions from the protein environment around CRO, especially S142 and H193, are indispensable for photoconversion of Dronpa.

DOI： 10.1016/j.procs.2011.04.027

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：ELSEVIER SCIENCE BV  

Full-dimensional path-integral molecular dynamics simulations were performed to determine whether the double proton transfer tautomerization of porphycene is a concerted or a stepwise process. We employed an on-the-fly direct dynamics technique at the semiempirical PM6 method whose parameters were determined so as that the relative energies of the stationary points approximately reproduce previously reported electronic structure calculations. It was found that double proton transfer occurs dominantly through the concerted pathway via the second-order saddle point structure and that contribution of the stepwise mechanism increases with a temperature increase. Nuclear quantum effects play essential roles in determining the proton transfer mechanism. (C) 2010 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2010.07.009

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：AMER INST PHYSICS  

We propose an efficient path integral hybrid Monte Carlo (PIHMC) method based on fourth-order Trotter expansion. Here, the second-order effective force is employed to generate short trial trajectories to avoid computationally expensive Hessian matrix, while the final acceptance is judged based on fourth-order effective potential. The computational performance of our PIHMC scheme is compared with that of conventional PIHMC and PIMD methods based on second- and fourth-order Trotter expansions. Our method is applied to on-the-fly ab initio PIHMC calculation of fluoride ion-water complexes, F(-)(H(2)O) and F(-)(D(2)O), at ambient temperature, particularly focusing on the geometrical isotope effect.

DOI： 10.1063/1.3367724

Web of Science

PubMed

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：ELSEVIER SCIENCE BV  

We have proposed the formation of Schiff-base between R96 and chromophore (CRO) to elucidate the reaction mechanism for the irreversible red shift of green fluorescent protein (GFP) spectra under the absence of oxygen. The difference between absorption energies of reactant and product for our GFP models with CIS(D)/6-31G* level is 0.21 eV, which is in reasonable agreement with the corresponding experimental value of 0.25 eV. We have suggested the irreversible photoreaction mechanism, where the CRO excited from ground (S(0)) state to first excited singlet (S(1)) state immediately turns to the first excited triplet (T(1)) state, and the nucleophilic addition reaction occurs on the T(1) state. (C) 2010 Elsevier ay. All rights reserved.

DOI： 10.1016/j.bpc.2010.01.008

Web of Science

PubMed

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：AMER INST PHYSICS  

The (1)H NMR chemical shift in deprotonated water dimer H(3)O(2)(-) has been studied by ab initio path integral simulation. The simulation predicts that the isotropic shielding of hydrogen-bonded proton increases as a function of temperature by about 0.003 ppm/K. This change is about an order of magnitude larger than that of the nonhydrogen-bonded proton. It is concluded that this is caused by the significant difference in the quantum distribution of proton at high and low temperatures in the low barrier hydrogen bond.

DOI： 10.1063/1.3354948

Web of Science

PubMed

researchmap

出版者・発行元：Society of Computer Chemistry, Japan  

DOI： 10.2477/jccj.9.A4

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Society of Computer Chemistry, Japan  

The geometric isotope effect (GIE) on low barrier hydrogen-bonded systems of acetic acid dimer, formic acid dimer, and their anion clusters is analyzed by HF and hybrid DFT levels of the multi-component molecular orbital (MC_MO) method, which directly includes nuclear quantum effect of proton/deuteron. Our optimized geometries for both neutral and anionic species with HF level of MC_MO method have reproduced the overall tendency of the GIE of the corresponding experimental ones. On the other hand, the results for anionic clusters with hybrid BHandHLYP functional of MC_MO method give poor agreement due to the underestimation of the barrier height of hydrogen-bonding. Our multi-component analysis clearly demonstrates that the hydrogen-bonding interaction energy is strongly affected by the distribution of nuclear wavefunction.

DOI： 10.2477/jccj.H2124M

CiNii Books

researchmap

その他リンク： https://jlc.jst.go.jp/DN/JALC/00342301803?from=CiNii

記述言語：英語   出版者・発行元：Society of Computer Chemistry, Japan  

To elucidate the adequate molecular exponents for sp<SUP>3</SUP>-, sp<SUP>2</SUP>-, and sp-hybrid characters, we have performed the optimization for both geometry and Gaussian-type function (GTF) exponents using various hydrocarbon molecules. We have found that the scale factor 1.2 is significant for the p-type GTFs in sp<SUP>3</SUP>-carbon, as well as hydrogen. The optimized molecular exponents give a flexible description of σ and π bonds in C-C chemical bonds induced by the difference of hybrid states. We also confirmed the efficiency of our calculation concerning the total energy and geometrical parameters in comparison with the results using the high quality basis sets.

DOI： 10.2477/jccj.H2126M

CiNii Books

researchmap

その他リンク： https://jlc.jst.go.jp/DN/JALC/00342301797?from=CiNii

記述言語：英語   出版者・発行元：日本コンピュータ化学会  

We have applied the fully variational molecular orbital (FVMO) method to systematically improve the values of energy-components, that is, the kinetic energy of electron and potential energy, as with that of total energy. The FVMO method enables us to describe accurate values of energy-components, since the quantum-mechanical Virial and Hellmann-Feynman theorems are completely satisfied due to the optimization of the exponents and centers in Gaussian-type functions (GTFs) basis sets. In the calculation of H<SUB>2</SUB> molecule, we have found that the energy components and total energy with FVMO method using only [6s] GTFs are actually improved more than those with the conventional MO using a much larger basis set including the multiple polarization functions of [6s3p2d1f]. Additionally, drastic improvement of virial ratios for several hydride molecules with the FVMO method is demonstrated in the current work. The energy-component analysis using the FVMO method would be a powerful tool to elucidate various chemical problems.

DOI： 10.2477/jccj.H2125M

CiNii Books

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：CHEMICAL SOC JAPAN  

We have theoretically analyzed the nuclear quantum effect on the nuclear magnetic shielding (sigma) and molecular magnetic susceptibility (chi) of H3O2- and N2H7+ systems with a new implementation combined with the multicomponent density functional theory and the gauge-including atomic orbital or continuous set of gauge transformation techniques. Our method easily reproduces the "deshielding" effect of sigma on hydrogen atoms and clearly indicates the existence of the H/D isotope effect on chi in H3O2- and N2H7+ systems.

DOI： 10.1246/cl.2009.1156

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：ELSEVIER SCIENCE BV  

Path-integral molecular dynamics simulations for the hydrogen-bonded glycine center dot(H2O)(n) (n = 1-7) clusters have been carried out using an on-the-fly direct dynamics technique at the semi-empirical PM6 level of theory. In the case of smaller clusters with n = 1-3, the simulations show that the cluster structure takes exclusively the hydrogen-bonded complex between a canonical neutral glycine and a water cluster moiety. In contrast, it was found that proton-exchange processes effectively occur between the COOH carboxylic group and water cluster moiety for n = 4-6 clusters although the overall structures are the complex between a neutral glycine and water clusters. In the case of the n = 7 cluster, glycine preferentially takes a zwitterionic form having NH3+ and COO functional groups. (C) 2009 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.chemphys.2009.09.026

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：WILEY-BLACKWELL  

We present the methodology and applications of multicomponent molecular orbital (MC_MO) method, which can take into account of the quantum effect of light particles, such as proton and deuteron, directly. We summarize the equations of the MC_MO method at the Hartree-Fock (HF) level and beyond the HF. The methodology of the MC_MO with fragment molecular orbital (FMO) method for large molecular systems is also described. We discuss the development of nuclear basis function based on the GTF, which is used in MC_MO and FMO-MC_MO calculations. We present the applications of MC_MO and FMO-MC_MO method for the analysis of geometrical isotope effect and kinetic isotope effect induced by H/D isotope effect. (C) 2009 Wiley Periodicals, Inc. Int J Quantum Chem 109: 2677-2694, 2009

DOI： 10.1002/qua.22069

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：AMER INST PHYSICS  

Quantum Monte Carlo methods are used to investigate the binding of a positron to the hydrogen cyanide (HCN) and lithium hydride (LiH) molecules. Our value of the adiabatic positron affinity (PA) of LiH of 1.010(3) eV is very close to the best theoretical value of 1.005 eV, obtained from variational calculations using explicitly correlated Gaussian basis sets [K. Strasburger, J. Chem. Phys. 114, 00615 (2001)]. We have obtained a reliable estimate of 0.0378(48) eV for the PA of the HCN molecule, which is almost 20 times larger than that obtained at the Hartree-Fock level, and strongly supports the binding of a positron in the electrostatic field of the HCN molecule. Our results show the importance of correlation effects for describing weakly bound positronic molecular complexes. (C) 2009 American Institute of Physics. [doi:10.1063/1.3239502]

DOI： 10.1063/1.3239502

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：ELSEVIER SCIENCE BV  

The H/D isotope effect on adenine(A)-thymine(T) DNA base pair has been analyzed at Hartree-Fock/3-21G** level of multi-component molecular orbital (MC-MO) method, which can directly take account of the quantum effect of proton/deuteron. The difference of quantum nature between proton and deuteron in A-T base pair causes the geometric isotope effect (GIE) on the backbone structure of respective monomers, as well as the hydrogen-bonded structure (primary and secondary GIEs). Our MC_MO results clearly suggest the importance of the quantum nature in hydrogen-interacting systems. (C) 2009 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.theochem.2009.02.011

Web of Science

researchmap

記述言語：英語   出版者・発行元：AMER INST PHYSICS  

DOI： 10.1063/1.3176015

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：ELSEVIER SCIENCE BV  

A recently developed semiempirical PM6 method was applied to study small hydrated sulfuric acid clusters. Various low-energy structures of the H2SO4 center dot(H2O)(n) (n = 1-9) clusters were optimized at this level and then compared to previous ab initio and density-functional theory studies in order to understand the applicability of the PM6 method in describing proton-transfer processes as well as hydrogen-bonded Structures in the clusters. Although the PM6 method seems to somewhat overemphasize bifurcated hydrogen-bonded structures, moderately good agreement was obtained. Quantum path-integral molecular dynamics simulations for the H2SO4 center dot(H2O)(n) (n = 1-6) clusters were subsequently performed directly using PM6 potential energies and their gradients. It was found that the acid dissociation probability increases with an increase in the cluster size, as expected, and that so-called contact-ion-pair structures are dominant in the proton-dissociated clusters. The importance of nuclear quantum effects in the cluster structures and proton-transfer processes is demonstrated. (C) 2009 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.theochem.2009.01.022

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：ELSEVIER SCIENCE BV  

Path-integral molecular dynamics simulations for the HCl(H2O)(4) cluster have been performed on the ground-state potential energy surface directly obtained on-the-fly from semiempirical PM3-MAIS molecular orbital calculations. It is found that the HCl(H2O)(4) cluster has structural rearrangement above the temperature of 300 K showing a liquid-like behavior. Quantum mechanical fluctuation of hydrogen nuclei plays a significant role in structural arrangement processes in this cluster. (C) 2009 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.chemphys.2009.01.014

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：ELSEVIER SCIENCE BV  

Fragment molecular orbital calculation has been performed to elucidate the structure of the polyphosphoinositide-binding peptide 1SOL: KHVVPNEVVVQRLFQVKGRR, derived from gelsolin, which controls cytoskeletal organization. This analysis found that important intramolecular interactions between the residues form a secondary structure of 1SOL. The early part of the alpha-helical region, Val-8 to Arg-12, has higher interaction energies than other regions. (C) 2008 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.theochem.2008.12.003

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：ELSEVIER SCIENCE BV  

A recently developed semiempirical PM6 method was applied to study small glycine-water clusters. Various low-energy configurations as well as proton-transfer transition-states were optimized to understand the ability of the PM6 method in describing the electronic structures of these systems by comparing to previous density-functional theory and ab initio molecular orbital studies. Moderately good agreement was obtained for structures and energetics of the glycine-(H(2)O)(n) clusters although PM6 seems to somewhat overestimate the stability of the zwitterionic form. Molecular dynamics simulations directly using the PM6 potential surface were then carried out to determine the statistical structures of the clusters. Although we did not observe the transformation between neutral &lt;-&gt; zwitterionic forms in our simulations, an interesting proton-dissociated behavior was seen as the cluster size increases. The difference in water solvation structures around the neutral or zwitterionic glycine form is also discussed. (C) 2008 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.theochem.2008.08.016

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：AMER INST PHYSICS  

Path integral molecular dynamics simulation based on the fourth order Trotter expansion has been performed to elucidate the geometrical isotope effect of water dimer anions, H(3)O(2)(-), D(3)O(2)(-), and T(3)O(2)(-), at different temperatures from 50 to 600 K. At low temperatures below 200 K the hydrogen- bonded hydrogen nucleus is near the center of two oxygen atoms with mostly O center dot center dot center dot X center dot center dot center dot O geometry (where X = H, D, or T), while at high temperatures above 400 K, hydrogen becomes more delocalized, showing the coexistence between O center dot center dot center dot X-O and O-X center dot center dot center dot O. The OO distance tends to be shorter as the isotopomer is heavier at low temperatures, while this ordering becomes opposite at high temperatures. It is concluded that the coupling between the OO stretching mode and proton transfer modes is a key to understand such a temperature dependence of a hydrogen- bonded structure. (C) 2008 American Institute of Physics.

DOI： 10.1063/1.2987445

Web of Science

PubMed

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）  

We have extended the multicomponent molecular orbital (MCMO) method to the full-configuration interaction (full-CI) fully variational molecular orbital method by elimination of translational and rotational motion components from total Hamiltonian. In the MCMO scheme, the quantum effects of protons and deuterons as well as electrons can be directly taken into account. All variational parameters in the full-CI scheme, i.e., exponents and centers (alpha and R) in the Gaussian-type function (GTF) basis set as well as the CI coefficients, are simultaneously optimized by using their analytical gradients. The total energy of the H(2) molecule calculated using the electronic [6s3p2d1f] and nuclear [1s1p1d1f] GTFs is -1.161 726 hartree, which can be compared to the energy of -1.164 025 hartree reported using a 512 term-explicitly correlated GTF calculation. Although the d- and f-type nuclear GTFs contribute to the improvement of energy convergence, the convergence of electron-nucleus correlation energy is slower than that of electron-electron one. The nuclear wave functions are delocalized due to the electron-nucleus correlation effect compared to the result of Hartree-Fock level of MCMO method. In addition, the average internuclear distances of all diatomic molecules are within 0.001 A of the previously reported experimental results. The dipole moment of the HD molecule estimated by our method is 8.4 x 10(-4) D, which is in excellent agreement with the experimental result of (8-10) x 10(-4) D.

DOI： 10.1063/1.2912939

Web of Science

PubMed

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：WILEY-V C H VERLAG GMBH  

DOI： 10.1002/cphc.200700570

Web of Science

PubMed

researchmap

記述言語：英語   出版者・発行元：AMER CHEMICAL SOC  

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）  

In order to investigate the HD isotope effect on a dihydrogen bonded cation system, we have studied NH+4...BeH2 and its isotopomers by ab initio path integral molecular dynamics. It is found that the dihydrogen bond can be exchanged by NH+(4) rotation. The deuterated isotopomer (ND+(4)...BeD(2); DD) can exchange the dihydrogen bond more easily than other isotopomers such as (NH+4...BeH2; HH). This unusual isotope effect is ascribed to the "quantum localization" which occurs when the effective energy barrier for the rotational mode becomes higher by the zero point energy of other modes. We also found that the binding energy of dihydrogen bonds for DD species is the smallest among the isotopomers.

PubMed

researchmap

記述言語：英語   出版者・発行元：AMER CHEMICAL SOC  

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（国際会議プロシーディングス）   出版者・発行元：VSP BV-C/O BRILL ACAD PUBL  

In order to analyze the positron-molecular compounds with quantitative accuracy, we have developed the Multi-Component quantum Monte Carlo method, and applied the typical positronic compound of [H-; e(+)] system. Although the variational Monte Carlo calculation gives poor results in the case of [H-; e(+)] system, the diffusion Monte Carlo result is in good agreement with that by Hylleraas-type wave function [Y.K.Ho; Phys.Rev.A, 34, 609(1986)]. Our result is -0.788949 +/- 0.000082 a.u. lower than that using the full-configuration interaction method with one-centered gaussian type basis functions [M.Tachikawa; Chem. Phys. Lett. 350, 269(2001)].

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（国際会議プロシーディングス）   出版者・発行元：VSP BV-C/O BRILL ACAD PUBL  

In order to analyze the positron-molecular compounds with quantitative accuracy, we have developed the Multi-Component quantum Monte Carlo method, and applied the typical positronic compound of [H-; e(+)] system. Although the variational Monte Carlo calculation gives poor results in the case of [H-; e(+)] system, the diffusion Monte Carlo result is in good agreement with that by Hylleraas-type wave function [Y.K.Ho; Phys.Rev.A, 34, 609(1986)]. Our result is -0.788949 +/- 0.000082 a.u. lower than that using the full-configuration interaction method with one-centered gaussian type basis functions [M.Tachikawa; Chem.Phys,Lett. 350, 269(2001)].

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：PHYSICAL SOC JAPAN  

We analyzed isotope effects on the geometrical and electronic relaxations of hydrogen/deuterium-absorbing PtnH(D)(-) (n = 1-4, 6) clusters using the first principles multi-component molecular orbital (MC-MO) method, which can take into account the quantum effect of the proton/deuteron. The average of Pt-Pt bond distances of the PtnH- clusters was calculated to be no more than 0.004 A longer than the bond distances of corresponding PtnD- clusters. Calculations on PtnH(D)(2) (n = 2-4, 6) clusters clearly demonstrated that significant geometrical differences between Pt-Pt bond distances caused by the isotope effect depend on the number of hydrogen/deuterium atoms. Slight relaxation of the electronic charge densities was observed by the replacement from H to D. The exponent values indicate that the distribution of the wavefunction of proton and deuteron reflected the geometrical changes and electronic charge densities around the proton and deuteron.

DOI： 10.1143/JPSJ.74.3112

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：ELSEVIER SCIENCE BV  

To estimate the kinetic isotope effect (KIE) for hydrogen (or deuterium) abstraction from H(D)OR (R = H, CH3, and CN) by an OH radical, we have considered the geometrical isotope effect (GIE) induced by the difference of the protonic and deuteronic wave-functions using the multi-component MO method. The difference by the GIE of hydrogen bond was about 0.005 A. The ratio (k(a)(H)/k(a)(D)) of the rate constant of the reaction for R = H, HOR -&gt; HOR HOH + OR and HO + DOR HOD -&gt; OR, is estimated as 4.4 by our calculation, which is reasonable agreement with experimental result of 6.0 +/- 2.0. We have found that the difference of the nuclear wavefunction of the proton and deuteron affects the changes of geometry and electronic charge density, which plays an important role to theoretically determine the effective potential energy surfaces and the corresponding KIE between H and D compounds. (c) 2005 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.chemphys.2005.03.007

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）  

An ab initio path integral molecular dynamics simulation has been performed to study the quantum and thermal effects of a dihydrogen bonded cation, NH4+⋯BeH2. In this system, an attractive interaction exists between two neighboring hydrogen atoms as Nδ-Hδ+⋯ Hδ-Beδ+involving large-amplitude of vibration. Some properties playing a key role for this dihydrogen bonded system, such as the bond length, bond angle, and distribution of atomic charges, are investigated in detail by comparing the results of path integral and classical molecular dynamics with those of the equilibrium structure. It was found that the atomic charges of Hδ+and Hδ-are decreased and the dihydrogen Hδ+⋯Hδ-bond length is expanded as the thermal and zero-point quantum effects. © 2005 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2005.05.035

Web of Science

Scopus

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：ELSEVIER SCIENCE BV  

An ab initio path integral molecular dynamics simulation has been performed to study the O-16 and O-18 isotopomers for a water molecule and a hydronium ion at temperature 300 K. The average O-H bond length of (H2O)-O-18 molecule is slightly shorter than that of (H2O)-O-16 molecule, while that of (H3O+)-O-18 is slightly longer than that of (H3O+)-O-16. For hydronium ions, the Walden inversion of (H3O+)-O-18, as well as (D3O+)-O-16, is found to be more restrained than that of (H3O+)-O-16. The isotope effect in the electronic structure and thermochemical properties for these isotopomers are also shown. &COPY; 2005 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2005.03.051

Web of Science

Scopus

researchmap

記述言語：英語   出版者・発行元：AMER CHEMICAL SOC  

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：WORLD SCIENTIFIC PUBL CO PTE LTD  

We have applied ab initio path integral molecular dynamics simulation to study the quantum feature and proton/deuteron isotope effect of ammonia molecule. This method treats all the rotational and vibrational degrees of freedom fully quantum mechanically, while the potential energies of the respective molecular configurations axe calculated "on the fly" using ab initio quantum chemical approach. The differences on the geometry and the electronic structure between NH3 and ND3 molecules are investigated in detail.

DOI： 10.1142/S0219633605001337

Web of Science

Scopus

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：PHYSICAL SOC JAPAN  

The isotope effect in Pd nanoparticles that absorb hydrogen or deuterium (i.e., H/D isotope effect) was studied experimentally and theoretically. First, the geometries (i.e., lattice parameters) of such Pd nanoparticles exposed to hydrogen or deuterium gas were measured by using X-ray powder diffraction to determine the lattice parameters. Then, the geometrical and electronic relaxations of PdnH- and PdnD- (n = 1-6) clusters, which modeled Pd nanoparticles exposed to hydrogen or deuterium gas, were calculated by using a multi-component molecular orbital (MC-MO) method, which uses first principles of quantum mechanics to account for the quantum effect of proton/deuteron. Experimental results from the diffraction patterns show that the bond distances of Pd nanoparticles exposed to hydrogen gas (and thus had absorbed hydrogen) were about 0.005 Angstrom longer than those of exposed to deuterium gas. These results were confirmed by analytical results from the MC-MO calculation for PdnH- and PdnD- clusters. Therefore, the local geometrical changes due to the H/D isotope effect control the geometrical changes of the entire nanoparticle. Both the experimental and analytical results also show that the nanoparticle (cluster) size influences the extent of the H/D isotope effect on the geometrical changes. Based on the analytical results, the electronic charge densities are only slightly influenced by the H/D isotope effect.

DOI： 10.1143/JPSJ.73.1775

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：ELSEVIER SCIENCE BV  

The geometrical isotope effect of C-(HO)-O-... type hydrogen bonds was analyzed using the HF/6-31++G** level of multi-component molecular orbital calculations, which take into account the quantum effect of the proton/deuteron. The results of calculation show that the bond lengths of hydrogen-bonded C-H and C-D are 0.4 and 0.5 mAngstrom shorter, respectively, than those of a methane monomer, and that the difference in electronic charge between the hydrogen-bonded proton/deuteron in the C-H(D)O-... are -0.894 and -0.893, respectively. Thus, the geometrical changes and electronic relaxation of a C-(HO)-O-... type hydrogen bond induced by the isotope effect differ from those of typical O-(HO)-O-... and N-(HO)-O-... (C) 2004 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2004.03.091

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：ELSEVIER SCIENCE BV  

The differences in molecular fluctuation of protonated water composed of hydrogen isotopes are elucidated by ab initio path integral molecular dynamics simulation, in which 'on-the-fly' calculation of potential energy surface is done accurately with the MP2 electron correlation to sample quantum nuclear configurations. It turned out that, at the room temperature 298 K, H3O+ is quite flexible in which pyramidal structure is inverted frequently with multi-dimensional molecular distortion, while the flexibility of D3O+ is much more restrained. Our analysis shows that anharmonicity in full-dimensional rovibrational motion is essential in this isotope effect. (C) 2003 Elsevier Science B.V. All rights reserved.

DOI： 10.1016/S0009-2614(03)00707-3

Web of Science

Scopus

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：ELSEVIER SCIENCE BV  

The isotope effect for the geometrical and electronical relaxations of the hydrogen/deuterium-absorbing ultra-fine particles of Pd has been investigated using an X-ray powder diffraction, which shows that the bond distances of Pd,H are longer about 0.005 Angstrom than those of PdnD. Also, the first principle multi-component molecular orbital (MC_MO) calculation, which takes account of the quantum effect of proton/deuteron, has been, employed for the optimization of PdnH- and PdnD- (n = 4,6). The H/D isotope effect of MC_MO calculation is good agreement with those of the X-ray powder diffraction and shows a little relaxation of the electronic charge densities. (C) 2003 Elsevier Science B.V. All rights reserved.

DOI： 10.1016/S0009-2614(03)00414-7

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：TAYLOR & FRANCIS LTD  

We have theoretically rationalized the origin of the isotope effect on phase transition temperature in hydrogen-bonded ferroelectric materials, KH2PO4 and KD2PO4 , using the new first-principle dynamic extended molecular orbital (DEMO) method, which can determine both electronic and nuclear wave functions simultaneously. We confirm that the origin of the isotope effect is the localization of the nuclear wave function by deuterization. The DEMO method has also universally demonstrated the isotope effect in potential energies, geometrical structures, and electronic population on hydrogen nuclei.

Web of Science

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：AMER INST PHYSICS  

We present a general approach for accurate calculation of chemical substances which treats both nuclei and electrons quantum mechanically, adopting ab initio molecular orbital theory for the electronic structure and path integral molecular dynamics for the nuclei. The present approach enables the evaluation of physical quantities dependent on the nuclear configuration as well as the electronic structure, within the framework of Born-Oppenheimer adiabatic approximation. As an application, we give the path integral formulation of electric response properties-dipole moment and polarizability, which characterize the changes both in electronic structure and nuclear configuration at a given temperature when uniform electrostatic field is present. We also demonstrate the calculation of a water molecule using the present approach and the result of temperature and isotope effects is discussed. (C) 2001 American Institute of Physics.

DOI： 10.1063/1.1407289

Web of Science

Scopus

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）  

An overview is given on the systematic derivation of atomic integrals for the hybrid GTF-PW basis set by generalizing the McMurchie-Davidson method. This type of basis function is expected to have a wide range of applications in physics and chemistry.

Scopus

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）  

A convenient formalism is developed for the evaluation of atomic integrals composed of a hybrid Gaussian type function and plane-wave (GTF-PW) basis set, based upon the recursion scheme proposed by McMurchie and Davidson [L. E. McMurchie and E. R. Davidson, J. Comput. Phys. 26, 218 (1978)] which was originally for Gaussian type basis functions. We show that revisions of recursion relations in the original article are necessary in order to allow systematic production of overlap, kinetic energy, nuclear attraction, and electron repulsion integrals in compact forms. Involving easy calculation of complex incomplete gamma functions, the recursion relations enable the use of hybrid GTF-PW basis functions with arbitrarily large angular momentum. This basis function can be applied to the first-principle calculation for solids involving localized electron orbitals. © 2001 The American Physical Society.

DOI： 10.1103/PhysRevE.64.056706

Scopus

researchmap

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：ELSEVIER SCIENCE BV  

We present an accurate calculational scheme for many-body systems composed of electrons and nuclei, by path integral molecular dynamics technique combined with the ab initio molecular orbital theory. Based upon the scheme, the simulation of a water molecule at room temperature is demonstrated, applying all-electron calculation at the Hartree-Fock level of theory. (C) 2000 Elsevier Science B.V. All rights reserved.

DOI： 10.1016/S0009-2614(00)01269-0

Web of Science

Scopus

researchmap

記述言語：日本語  

J-GLOBAL

researchmap

記述言語：日本語   出版者・発行元：一般社団法人日本物理学会  

CiNii Books

researchmap

記述言語：日本語   出版者・発行元：Society of Computer Chemistry, Japan  

我々は分子軌道法および量子モンテカルロ法といった<i>ab initio</i>手法を多成分系に理論拡張・実装した．それにより，陽電子化合物における陽電子親和力や対消滅率の精密計算を実現し，最新の実験結果と良い一致を見出すことに成功した．いくつかの中性分子への陽電子束縛状態を系統的に計算したところ，陽電子軌道は電子軌道よりも空間的に非局在化し，また陽電子親和力と双極子モーメントの間に強い相関がみられた．

DOI： 10.2477/jccj.2013-0019

J-GLOBAL

researchmap

記述言語：日本語   出版者・発行元：一般社団法人日本物理学会  

CiNii Books

researchmap

記述言語：日本語  

J-GLOBAL

researchmap

記述言語：日本語  

researchmap

記述言語：日本語  

J-GLOBAL

researchmap

記述言語：日本語  

J-GLOBAL

researchmap

記述言語：日本語  

J-GLOBAL

researchmap

記述言語：日本語   出版者・発行元：横浜市立大学学術研究会  

DOI： 10.15015/00000338

CiNii Books

J-GLOBAL

researchmap

researchmap

researchmap

researchmap

記述言語：日本語  

J-GLOBAL

researchmap

記述言語：日本語   出版者・発行元：一般社団法人日本物理学会  

CiNii Books

researchmap

記述言語：日本語  

J-GLOBAL

researchmap

researchmap

researchmap

記述言語：日本語  

J-GLOBAL

researchmap

記述言語：日本語  

J-GLOBAL

researchmap

記述言語：日本語  

J-GLOBAL

researchmap

記述言語：日本語  

J-GLOBAL

researchmap

記述言語：英語   出版者・発行元：社団法人日本物理学会  

CiNii Books

researchmap

記述言語：日本語   出版者・発行元：一般社団法人日本物理学会  

CiNii Books

researchmap

researchmap

記述言語：日本語  

J-GLOBAL

researchmap

記述言語：日本語  

J-GLOBAL

researchmap

記述言語：日本語  

J-GLOBAL

researchmap

researchmap

記述言語：日本語  

J-GLOBAL

researchmap

記述言語：日本語  

CiNii Books

researchmap

記述言語：日本語  

J-GLOBAL

researchmap

記述言語：日本語  

J-GLOBAL

researchmap

記述言語：英語   出版者・発行元：JOHN WILEY & SONS INC  

To optimize the exponent values in protonic and deuteronic Gaussian-type functions (GTF) by the elimination of translational and rotational motions, we have proposed the new scheme of an analytical gradient formula with respect to the exponent values in the multi-component molecular orbital scheme, which can take into account the quantum effects of protons and deuterons, under the Hartree-Fock level of theory. Numerical assessment of H, and D, molecules confirms that there is a clear difference between distributions of protonic and deuteronic orbitals following the elimination of translational and rotational motions. In particular, the d-type GTF in the protonic orbital drastically improves the total energy. (C) 2007 Wiley Periodicals, Inc.

DOI： 10.1002/qua.21540

Web of Science

researchmap

記述言語：英語   出版者・発行元：WILEY-BLACKWELL  

Hund's spin-multiplicity rule for the ground state of the methylene molecule CH2 is interpreted by Hartree-Fock (HF) and multi-reference configuration interaction (MRCI) methods. The stabilization of the triplet ground state ((X) over tilde B-3(1)) relative to the second singlet excited state ((b) over tilde B-3(1)) is ascribed to the greater electron-nucleus attraction energy that is gained at the cost of increasing the electron-electron repulsion energy and with the aid of a reduction in the nucleus-nucleus repulsion energy. The highest spin-multiplicity in the ground state of CH2 is accompanied by a set of three characteristic features, i.e., elongation of the internuclear distances, reduction in the bond angle, and contraction of the valence electron density distribution around the nuclei involving expansion of the core electron density distribution. The present calculations fulfill the virial theorem to an accuracy of -V/T = 2.000 for both HF and MRCI Accordingly, the molecular geometries are optimized for each of the two states. The inclusion of correlation by MRCI method reduces the energy splitting between the two states by about 14%. The energy splitting is analyzed by the correlational virial theorem 2T(C) + V-C = 0 to make a clear interpretation of the correlation effect. (c) 2007 Wiley Periodicals, Inc.

DOI： 10.1002/qua.21541

Web of Science

researchmap

記述言語：日本語   出版者・発行元：社団法人日本物理学会  

CiNii Books

researchmap

researchmap

記述言語：日本語  

J-GLOBAL

researchmap

記述言語：日本語  

J-GLOBAL

researchmap

researchmap