Masanori Tachikawa

Yokohama City University, Yokohama, Kanagawa, Japan

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Publications (147)304.91 Total impact

  • Chinese Journal of Physics- Taipei- 12/2013; 51(6):1336. DOI:10.6122/CJP.51.1336 · 0.43 Impact Factor
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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.
    Chemical Physics 11/2013; 426:38–47. DOI:10.1016/j.chemphys.2013.10.003 · 2.03 Impact Factor
  • 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.
    Journal of Computational Chemistry 10/2013; 34(28). DOI:10.1002/jcc.23399 · 3.60 Impact Factor
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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.
    ChemPhysChem 10/2013; 14(15). DOI:10.1002/cphc.201300549 · 3.36 Impact Factor
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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.
    Physical Chemistry Chemical Physics 09/2013; 15(38). DOI:10.1039/c3cp52572d · 4.20 Impact Factor
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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.
    Chemical Physics 06/2013; 419:229–236. DOI:10.1016/j.chemphys.2013.02.025 · 2.03 Impact Factor
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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.
    Chemical Physics 06/2013; 419:50–53. DOI:10.1016/j.chemphys.2012.11.022 · 2.03 Impact Factor
  • Akihito Koizumi, Masanori Tachikawa, Motoyuki Shiga
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    ABSTRACT: 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.
    Chemical Physics 06/2013; 419:44–49. DOI:10.1016/j.chemphys.2013.03.005 · 2.03 Impact Factor
  • Yukio Kawashima, Kimichi Suzuki, Masanori Tachikawa
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    ABSTRACT: Small hydrated fluoride ion complexes, F-(H2O)n (n=1-3), have been studied by ab initio hybrid Monte Carlo (HMC) and ab initio path integral hybrid Monte Carlo (PIHMC) simulations. Due to the quantum effect, our simulation shows that the average hydrogen-bonded F-…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 kind of hydrogen bonds, F--water and water-water hydrogen bonds, competes against each other. In F-(H2O)3, thus, the nuclear quantum effect on water-water hydrogen bond leads to the elongation of hydrogen-bonded F-…HO distance, which we suggest as the possible origin of the structural inversion from F-(H2O) to F-(H2O)3.
    The Journal of Physical Chemistry A 05/2013; 117(24). DOI:10.1021/jp403295h · 2.77 Impact Factor
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    Kimichi Suzuki, Masanori Tachikawa, Motoyuki Shiga
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    ABSTRACT: 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.
    The Journal of Chemical Physics 05/2013; 138(18):184307. DOI:10.1063/1.4803655 · 3.12 Impact Factor
  • Yukio Kawashima, Masanori Tachikawa
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    ABSTRACT: 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.
    Chemical Physics Letters 05/2013; 571:23–27. DOI:10.1016/j.cplett.2013.03.080 · 1.99 Impact Factor
  • Taro Udagawa, Takayoshi Ishimoto, Masanori Tachikawa
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    ABSTRACT: We have theoretically analyzed the nuclear quantum effect on the nuclear magnetic shieldings for the intramolecular hydrogen-bonded systems of σ-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 13C chemical shift.
    Molecules 05/2013; 18(5):5209-20. DOI:10.3390/molecules18055209 · 2.10 Impact Factor
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    ABSTRACT: 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.
    International Journal of Quantum Chemistry 01/2013; 113(2). DOI:10.1002/qua.24296 · 1.17 Impact Factor
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    ABSTRACT: 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.
    Chemical Physics Letters 01/2013; 555:84 - 86. DOI:10.1016/j.cplett.2012.11.017 · 1.99 Impact Factor
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    ABSTRACT: Several semiempirical methods were utilized to analyze the structures and stabilities of X −(H2O)n (X = F, Cl; n = 1–4) clusters with respect to the number of water molecules through their comparison with ab initio molecular orbital calculations. Our results show that the recently developed PM6-DH+ semiempirical method can provide reasonable binding energies of hydrated fluoride and chloride ion clusters, which are consistent with the corresponding experimental results. For the optimized geometries of X = F, however, the semiempirical methods show that the global minima are close to HF(OH)−(H2O)n−1 structures, which are different from the ab initio calculations. Meanwhile, the topological characteristics for the global minima of X = Cl obtained by semiempirical methods have the same symmetries with ab initio calculations. All calculation levels agree on the trend of decreasing ion-water interaction with the increasing number of water molecules. We also found a new structure of Cl−(H2O)4 with a second hydration shell as a complement of previous studies. Those are very important data for our near-future study of on-the-fly semiempirical molecular dynamics (MD) or path integral MD simulation. PACS 36.40.Mr, 31.15.bu, 31.15.A-
    01/2013; 7(1). DOI:10.1186/2251-7235-7-7
  • Takayoshi Ishimoto, Masanori Tachikawa
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    ABSTRACT: 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.
    Solid State Phenomena 06/2012; 189:169-177. DOI:10.4028/www.scientific.net/SSP.189.169
  • K. Koyanagi, Y. Kita, M. Tachikawa
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    ABSTRACT: 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 multi-component 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.
    The European Physical Journal D 05/2012; 66(5). DOI:10.1140/epjd/e2012-20638-y · 1.40 Impact Factor
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    Masanori Tachikawa, Yukiumi Kita, Robert J Buenker
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    ABSTRACT: 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 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.
    New Journal of Physics 03/2012; 14(3). DOI:10.1088/1367-2630/14/3/035004 · 3.67 Impact Factor
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    ABSTRACT: a b s t r a c t Path-integral molecular dynamics simulations have been performed for porphycene and its isotopic vari-ants in order to understand the effect of isotopic substitution of inner protons on the double proton trans-fer 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 tem-perature 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 sim-ulations 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.
    Chemical Physics 02/2012; 394(1). DOI:10.1016/j.chemphys.2011.12.007 · 2.03 Impact Factor
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    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 1 6 consisting of methylated gear-shaped molecules (1) is a nearly cubic structure, whereas the distorted structure is found for the capsule 2 6 consisting of ones lacking three methyl groups, (2) so as to maximize the contact surface. Disassembly temperature for the demethylated capsule 2 6 , $210 K, is much lower than that for the methylated one 1 6 , $340 K, which is consistent with the corresponding experimental result that 1 6 is stable, whereas 2 exists as a monomer in aqueous methanol. V C 2012 Wiley Periodicals, Inc.
    International Journal of Quantum Chemistry 01/2012; 113(4). DOI:10.1002/qua.24108 · 1.17 Impact Factor

Publication Stats

1k Citations
304.91 Total Impact Points

Institutions

  • 2003–2015
    • Yokohama City University
      • Graduate School of Nanobioscience
      Yokohama, Kanagawa, Japan
  • 2007
    • Ibaraki University
      Mito-shi, Ibaraki, Japan
  • 1999–2006
    • Rikkyo University
      • Department of Chemistry
      Edo, Tōkyō, Japan
  • 2004
    • The University of Aizu
      • School of Computer Science and Engineering
      Hukusima, Fukushima, Japan
  • 2000–2002
    • RIKEN
      Вако, Saitama, Japan
  • 1994–1998
    • Waseda University
      • Department of Chemistry and Biochemistry
      Edo, Tōkyō, Japan