Masanori Tachikawa

Yokohama City University, Yokohama, Kanagawa, Japan

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Publications (168)338.83 Total impact

  • Yukiumi Kita · Masanori Tachikawa
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    ABSTRACT: 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.
    No preview · Article · May 2014 · The European Physical Journal D
  • Taro Udagawa · Takao Tsuneda · Masanori Tachikawa
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    ABSTRACT: 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 hydrogen-containing 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.
    No preview · Article · May 2014 · Physical Review A
  • Yusuke Kanematsu · Masanori Tachikawa
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    ABSTRACT: 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.
    No preview · Article · Apr 2014 · The Journal of Chemical Physics
  • Masanori Tachikawa
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    ABSTRACT: 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.
    No preview · Article · Apr 2014 · Journal of Physics Conference Series
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    ABSTRACT: Molecular dynamics (MD) simulations in aqueous solution were performed for hexameric nanocubes of methylated (1(6)) and demethylated (2(6)) gear-shaped amphiphiles. To elucidate the difference between these nanocubes, the principal component analysis for the MD simulation results in aqueous solution and the normal mode analysis in the gas phase were also applied to the nanocube, 1(6) and 2(6). The structural fluctuation of the lowest-frequency motion on 2(6) is larger than that on 1(6) around the triple it stacking of 3-pyridyl groups. For the structural stability and fluctuation of the nanocube, interactions among the constituent gear-shaped molecules play more important roles than the solvophobic effect due to solvent molecules.
    No preview · Article · Mar 2014 · Chemistry Letters
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    ABSTRACT: 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.
    No preview · Article · Feb 2014 · The European Physical Journal D
  • Source
    Katsuhiko Koyanagi · Yukiumi Kita · Masanori Tachikawa
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    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.
    Preview · Article · Feb 2014 · International Journal of Quantum Chemistry
  • Taro Udagawa · Masanori Tachikawa
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    ABSTRACT: The partial isotope substitution for the change of geometrical parameters, interaction energies, and nuclear magnetic shielding tensors (σ) of dihydrogen-bonded NH3 X(+) ···YBeH (X, Y = H, D, and T) systems is analyzed. Based on the theoretical calculation, the distance between heavy atoms RN···Be of NH3 H(+) ···DBeH is clearly found to be shorter than that in NH3 D(+) ···HBeH. Such apparently paradoxical geometrical isotope effect (GIE) on RN···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 RX···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 NH3 H(+) ···DBeH is stronger than that of NH3 D(+) ···HBeH and isotopic deshielding effect of magnetic shielding becomes large in lighter isotope. © 2013 Wiley Periodicals, Inc.
    No preview · Article · Feb 2014 · Journal of Computational Chemistry
  • Kenta Yamada · Yukio Kawashima · Masanori Tachikawa
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    ABSTRACT: 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.
    No preview · Article · Feb 2014 · Chinese Journal of Physics- Taipei-
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    Yukio Kawashima · Masanori Tachikawa
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    ABSTRACT: 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.
    Full-text · Article · Jan 2014 · Journal of Chemical Theory and Computation
  • Masanori Tachikawa · Yukiumi Kita

    No preview · Article · Jan 2014 · Journal of Computer Chemistry Japan
  • Yudai Ogata · Masashi Daido · Yukio Kawashima · Masanori Tachikawa
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    ABSTRACT: The nuclear quantum effect on the short and asymmetric hydrogen bond of protonated lysine (LysH(+)) at room temperature is explored by ab initio path integral molecular dynamics (PIMD) simulation. From static electronic structure calculations, the barrier height of proton transfer in LysH(+) is 1.1 kcal mol(-1), which is much lower than that of typical hydrogen bonds. The hydrogen-bonded proton is delocalized in between two nitrogen atoms in the PIMD simulation including both thermal and nuclear quantum effects, while the proton is localized on a nitrogen atom in a conventional ab initio molecular dynamics simulation including thermal effects alone. We found that the proton transfer barrier found in the static calculation and conventional ab initio simulation is completely washed out in the PIMD simulation. Meanwhile, the proton distribution at the N-zeta atom was larger than that at the N atom, as found in the static calculation and conventional ab initio molecular dynamics simulation. We clarified that an asymmetric low barrier hydrogen bond exists in LysH(+) at room temperature from our PIMD simulation.
    No preview · Article · Dec 2013 · RSC Advances
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    ABSTRACT: In order to elucidate the element specificity of the S parameters of polymers containing C, O, or F atoms reported by Sato et al. with the Doppler broadening of positron annihilation radiation measurement [K. Sato, et al., 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.
    No preview · Article · Dec 2013 · Chinese Journal of Physics- Taipei-
  • Marina Takahashi · Jun Koseki · Yukiumi Kita · Yukio Kawashima · Masanori Tachikawa
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    ABSTRACT: 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.
    No preview · Article · Dec 2013 · Chinese Journal of Physics- Taipei-
  • Qi Wang · Kimichi Suzuki · Umpei Nagashima · Masanori Tachikawa · Shiwei Yan
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    ABSTRACT: The geometric isotope effects on the structures of hydrated chloride ionic hydrogen bonded clusters are explored by carrying out path integral molecular dynamics simulations. First, an outer shell coordinate is selected to display the rearrangement of single and multi hydration shell cluster structures. Next, to show the competition of intramolecular and intermolecular nuclear quantum effects, the intramolecular OH∗ stretching and intermolecular ion–water wagging motions are studied for single and multi shell structures, respectively. The results indicate that the intermolecular nuclear quantum effects stabilize the ionic hydrogen bonds in single shell structures, while they are destabilized through the competition with intramolecular nuclear quantum effects in multi shell structures. In addition, the correlations between ion–water stretching motion and other cluster vibrational coordinates are discussed. The results indicate that the intermolecular nuclear quantum effects on the cluster structures are strongly related to the cooperation of the water–water hydrogen bond interactions.
    No preview · Article · Nov 2013 · Chemical Physics
  • Masashi Daido · Yukio Kawashima · Masanori Tachikawa
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    ABSTRACT: 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. © 2013 Wiley Periodicals, Inc.
    No preview · Article · Oct 2013 · Journal of Computational Chemistry
  • Katsuhiko Koyanagi · Yukiumi Kita · Yasuteru Shigeta · Masanori Tachikawa
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    ABSTRACT: 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.
    No preview · Article · Oct 2013 · ChemPhysChem
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    ABSTRACT: To theoretically demonstrate the binding of a positron to a nonpolar or small dipole molecule, we have calculated the vibrational averaged positron affinity (PA) values along the harmonic asymmetric stretching vibrational coordinate with the configuration interaction level of multi-component molecular orbital method for CXY (X, Y = O, S, and Se) molecules. For CSe2 and CSSe molecules, a positron can even be attached at the equilibrium structures, due to the effect of the induced dipole moment with large polarizability values. For a CS2 molecule, the positive PA value is obtained at the lowest vibrational excited state in our scheme. Although there is no direct experimental evidence for the positron-binding to CO2, COS, and COSe molecules, we have predicted positron-binding for these molecules at higher vibrational excited states.
    No preview · Article · Sep 2013 · Physical Chemistry Chemical Physics
  • Qi Wang · Kimichi Suzuki · Umpei Nagashima · Masanori Tachikawa · Shiwei Yan
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    ABSTRACT: 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 rl(Cl⋯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 δ) and other cluster vibration coordinates are studied. We have found that δ strongly correlates with proton transfer motion while it has little correlation with ion–water stretching motion. Contrary to θ(H–O–H∗) coordinate, the correlations between δ 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.
    No preview · Article · Jun 2013 · Chemical Physics
  • Yukiumi Kita · Hironari Kamikubo · Mikio Kataoka · Masanori Tachikawa
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    ABSTRACT: 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.
    No preview · Article · Jun 2013 · Chemical Physics

Publication Stats

2k Citations
338.83 Total Impact Points

Institutions

  • 2003-2015
    • Yokohama City University
      • Graduate School of Nanobioscience
      Yokohama, Kanagawa, Japan
  • 2005
    • Tohoku University
      • Center for Interdisciplinary Research
      Sendai, Kagoshima, Japan
  • 2004-2005
    • Japan Science and Technology Agency (JST)
      Edo, Tokyo, Japan
  • 2000-2003
    • RIKEN
      Вако, Saitama, Japan
  • 1998-2000
    • Rikkyo University
      • Department of Chemistry
      Tokyo, Tokyo-to, Japan
  • 1994-1999
    • Waseda University
      • • Department of Chemistry and Biochemistry
      • • Advanced Research Center for Human Sciences
      Edo, Tōkyō, Japan