Misako Aida

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Organization: Hiroshima University , Japan

Department: Center for Quantum Life Sciences and Department of Chemistry

Title: Professor(PhD)

TOPICS

Physical Chemistry

Chemicals
References

A comprehensive search of topologically distinct local minimum structures of protonated water octamer and the classification of OH topological types

Co-reporter:Dai Akase, Hiroyuki Teramae, Misako Aida

Chemical Physics Letters 2015 Volume 618() pp:51-56

Publication Date(Web):2 January 2015

DOI:10.1016/j.cplett.2014.10.071

•Rooted digraphs correspond to topological isomers of protonated water clusters.•134 topologically distinct isomers of protonated water octamer are obtained.•OH bonds are classified into 10 topological types by local HB patterns.•Topological type of OH bond can be used as a vibrational spectral signature.The rooted digraph is used to topologically distinguish the isomers of protonated water (PW) cluster. We generated many PW octamer geometries and obtained 134 topologically distinct geometries of the PW octamers at the theoretical level of MP2/aug-cc-pVDZ. The temperature-dependent population ratios of those isomers were calculated. Dominant structures of PW octamers vary according to the temperature. The OH bonds of PW cluster were classified into 10 topological types according to the local hydrogen-bonding network. The vibrational frequency of the same topological type of the OH bond, which is transferable in different isomers, can be used as a vibrational spectral signature.

A new variant of multicanonical Monte Carlo algorithm with specifying the temperature range and its application to the hydration free energy change of fluorinated methane derivatives

Co-reporter:Hideo Doi, Misako Aida

Chemical Physics Letters 2014 Volumes 595–596() pp:55-60

Publication Date(Web):18 March 2014

DOI:10.1016/j.cplett.2014.01.044

•Selected-multicanonical Monte Carlo (SMMC) method is presented.•The temperature range is specified in the weight factor determination process.•SMMC is applied to hydration free energy changes of fluorinated methane derivatives.The multicanonical Monte Carlo simulation is often carried out making use of a weight factor which is decided with specifying the energy range. Here we present a new variant of multicanonical Monte Carlo algorithm, ‘selected-multicanonical Monte Carlo’, in which the range of temperature is specified instead of the energy range and the configurations are selected which fit the desired temperature range. The new method has the advantage of adequately deciding the weight factor to create multicanonical ensemble. The new method is applied to free energy perturbation calculation to obtain the hydration free energy changes of methane derivatives.

Distribution of Topologically Distinct Isomers of Water Clusters and Dipole Moments of Constituent Water Molecules at Finite Atmospheric Temperatures

Co-reporter:Dai Akase and Misako Aida

The Journal of Physical Chemistry A 2014 Volume 118(Issue 36) pp:7911-7924

Publication Date(Web):August 11, 2014

DOI:10.1021/jp504854f

Hydrogen-bonding (HB) patterns correspond to topologically distinct isomers of a water cluster and can be expressed by digraphs. We make use of the HB pattern to divide the configuration space of a water cluster ((H2O)n, n = 3–8) at a finite temperature. Each configuration of a water cluster generated in Monte Carlo (MC) simulation is classified into an HB pattern. The number of observed HB patterns increases exponentially with the cluster size, whereas the population of the most abundant HB pattern decreases. The populations of the HB patterns are transformed into the relative Helmholtz energies. At a finite temperature, it can be observed that isomers other than local minimum structures on the potential energy surface are highly populated. The dipole moment of a constituent molecule in a water cluster is enhanced, depending on the molecular circumstance. The change is rationalized by the difference in the local HB type of the water molecule in the HB network.

Solvent distributions, solvent orientations and specific hydration regions around 1-adamantyl chloride and adamantane in aqueous solution

Co-reporter:Masayuki Ohisa, Misako Aida

Chemical Physics Letters 2011 Volume 511(1–3) pp:62-67

Publication Date(Web):26 July 2011

DOI:10.1016/j.cplett.2011.06.020

Abstract

Ab initio molecular orbital theory and Monte Carlo method with molecular mechanics are used to calculate the hydration numbers and solvent configurations around 1-adamantyl chloride in 324 water molecules. In the highest probability region for distribution of water molecules, a water molecule forms two hydrogen bonds with Cl and the adamantane skeleton; in the second highest probability region, a water molecule is located at the rear side. The CH⋯ $\dots$ O interaction in the rear side is enhanced by the Cl substitution. The water orientation in the rear side of 1-adamantyl chloride is different from that around a hydrophobic adamantane molecule.

Structures of Molecules in Ground and Excited Vibrational States from Quasiclassical Direct ab Initio Molecular Dynamics

Co-reporter:Tomonori Yamada and Misako Aida

The Journal of Physical Chemistry A 2010 Volume 114(Issue 21) pp:6273-6283

Publication Date(Web):May 10, 2010

DOI:10.1021/jp912269v

We demonstrate that the mean structures of molecules derived from quasiclassical direct ab initio molecular dynamics (MD) simulation, the classical simulation that takes into account quantum vibrational levels, agree well with those determined from quantum-mechanical (QM) expectation values and/or experimentally observed values. First, for a one-dimensional model potential that includes anharmonicity as the third-order potential energy term, we show that the time-averaged structure over the classical trajectory with taking account of a quantum vibrational energy level correlates with a QM structure averaged using a vibrational wave function based on the first-order perturbation theory. Next, quasiclassical direct ab initio MD and Fourier grid Hamiltonian method are applied to OH and OD radicals; the mean structures at several vibrational levels of both classical and QM methods coincide, and they are in good agreement with the structures determined experimentally. Quasiclassical direct ab initio MD is then applied to H2O, C2H2, and C6H6. For H2O and C2H2, the classical mechanically calculated mean structural parameters agree well with the experimental values and the QM values obtained from vibrational self-consistent field. For C2H2, we find that rg(C−H) is longer than re(C−H), whereas rmean(0)(C−H), which is equal to rz(C−H), is slightly shorter than re(C−H).

Classification of OH Bonds and Infrared Spectra of the Topology-Distinct Protonated Water Clusters H3O+(H2O)n−1 (n ≤ 7)

Co-reporter:Maihemutijiang Jieli and Misako Aida

The Journal of Physical Chemistry A 2009 Volume 113(Issue 8) pp:1586-1594

Publication Date(Web):February 4, 2009

DOI:10.1021/jp810735m

Rooted digraphs are used to represent the features of a protonated water (PW) cluster, and we obtain all possible topology-distinct patterns corresponding to PW clusters containing up to seven water molecules. From close investigation of the structural patterns obtained, several restrictions that should be satisfied in the stable structures of PW clusters are found. The generated hydrogen bond (HB) matrices of the restrictive rooted digraph are used as the theoretical framework to obtain all of the local minima on the potential energy surfaces of those PW clusters by the use of ab initio MO and DFT methods. For PW pentamers, hexamers, and heptamers, some new local minimum structures were found that were not previously obtained. We classify all of the O−H bonds in PW clusters up to heptamer into nine types according to the difference in the hydrogen bonding pattern; each type is accompanied by a specific range of stretching frequency. The ranges of stretching frequencies of different types of O−H in PW clusters are systematically classified.

Two-dimensional free-energy surface on the exchange reaction of alkyl chloride/chloride using the QM/MM-MC method

Co-reporter:Masayuki Ohisa, Hiroshi Yamataka, Michel Dupuis and Misako Aida

Physical Chemistry Chemical Physics 2008 vol. 10(Issue 6) pp:844-849

Publication Date(Web):05 Dec 2007

DOI:10.1039/B712565H

Two-dimensional free-energy surfaces are calculated for alkyl chloride/chloride exchange/inversion reactions: Cl− + RCl (R = Me and t-Bu) surrounded by one hundred H2O molecules as a model of solvent. The methodology of free-energy calculation by perturbation theory based on a mixed-Hamiltonian model (QM/MM) combined with Monte Carlo sampling of the solvent configurations was used to obtain the changes in solvation free energy. We devised a special procedure to analyze the two-dimensional free-energy surfaces to gain unique insight into the differences in the reaction mechanisms between the two systems. The inversion reaction path for R = t-Bu on the free-energy surface is found to proceed in an asynchronous way within a concerted framework via the ion-pair region. This is in contrast to the R = Me system that proceeds as a typical SN2 reaction.

Fundamental absorption frequency from quasi-classical direct ab initio molecular dynamics: diatomic molecule

Co-reporter:Misako Aida, Michel Dupuis

Chemical Physics Letters 2005 Volume 401(1–3) pp:170-174

Publication Date(Web):1 January 2005

DOI:10.1016/j.cplett.2004.11.046

Abstract

A new approach is proposed to extract the fundamental absorption frequency from classical molecular dynamics simulation in which the oscillator amplitude is specified by setting the total energy equal to the harmonic zero-point energy. This approach is applied to D₂ molecule. The fundamental absorption frequency and the anharmonic constant of D₂, obtained from the quasi-classical direct ab initio molecular dynamics simulation method with the full Configuration Interaction level of theory with the aug-cc-pVTZ basis set, compare well with the experimentally observed values.

Analysis of borderline substitution/electron transfer pathways from direct ab initio MD simulations

Co-reporter:Hiroshi Yamataka, Misako Aida, Michel Dupuis

Chemical Physics Letters 2002 Volume 353(3–4) pp:310-316

Publication Date(Web):19 February 2002

DOI:10.1016/S0009-2614(02)00041-6

Ab initio molecular dynamics simulations were carried out for the borderline reaction pathways in the reaction of CH2O− with CH3Cl. The simulations reveal distinctive features of three types of mechanisms passing through the SN2-like transition state (TS): (i) a direct formation of SN2 products, (ii) a direct formation of ET products, and (iii) a two-step formation of ET products via the SN2 valley. The direct formation of the ET product through the SN2-like TS appears to be more favorable at higher temperatures. The two-step process depends on the amount of energy that goes into the C–C stretching mode.

Evaluation of free energy landscape for base–amino acid interactions using ab initio force field and extensive sampling

Co-reporter:T. Yoshida;T. Nishimura;M. Aida;F. Pichierri;M. M. Gromiha;A. Sarai

Biopolymers 2001 Volume 61(Issue 1) pp:

Publication Date(Web):15 FEB 2002

DOI:10.1002/1097-0282(2001)61:1<84::AID-BIP10045>3.0.CO;2-X

Structural data of protein–DNA complex show redundancy and flexibility in base–amino acid interactions. To understand the origin of the specificity in protein–DNA recognition, we calculated the interaction free energy, enthalpy, entropy, and minimum energy maps for AT-Asn, GC-Asn, AT-Ser, and GC-Ser by means of a set of ab initio force field with extensive conformational sampling. We found that the most preferable interactions in these pairs are stabilized by hydrogen bonding, and are mainly enthalpy driven. However, minima in the free energy maps are not necessarily the same as those in the minimum energy map or enthalpy maps, due to the entropic effect. The effect of entropy is particularly important in the case of GC-Asn. Experimentally observed structures of base–amino acid interactions are within preferable regions in the calculated free energy maps, where there are many different interaction configurations with similar energy. The full geometry optimization procedure using ab initio molecular orbital method was applied to get the optimal interaction geometries for AT-Asn, GC-Asn, AT-Ser, and GC-Ser. We found that there are various base–amino acid combinations with similar interaction energies. These results suggest that the redundancy and conformational flexibility in the base–amino acid interactions play an important role in the protein–DNA recognition. © 2002 Wiley Periodicals, Inc. Biopoly (Nucleic Acid Sci) 61: 84–95, 2002; DOI 10.1002/bip.10045

Two-dimensional free-energy surface on the exchange reaction of alkyl chloride/chloride using the QM/MM-MC method

Co-reporter:Masayuki Ohisa, Hiroshi Yamataka, Michel Dupuis and Misako Aida

Physical Chemistry Chemical Physics 2008 - vol. 10(Issue 6) pp:NaN849-849

Publication Date(Web):2007/12/05

DOI:10.1039/B712565H