List of works - Misako Aida

A Comment on ‘Promoting Equal Participation of Men and Women in Science and Engineering’

A Quantum Chemical Study of the Catalysis for Cytidine Deaminase: Contribution of the Extra Water Molecule

scientific article published on 01 May 2006

A Theoretical Insight into the Interaction of Fatty Acids Involved in Royal Jelly with the Human Estrogen Receptor β

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

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

A polarizable mixed Hamiltonian model of electronic structure for micro-solvated excited states. I. Energy and gradients formulation and application to formaldehyde (1A2)

Ab Initio Direct Molecular Dynamics Simulations and QM/MM Computations in Search of Organic Reaction Mechanisms

article

Ab Initio QM/MM-MC Study on Hydrogen Transfer of Glycine Tautomerization in Aqueous Solution: Helmholtz Energy Changes along Water-mediated and Direct Processes

Ab initio MO and quasi-classical direct ab initio MD studies on the nitrogen inversion of trimethylamine

Ab initio ONIOM-molecular dynamics (MD) study on the deamination reaction by cytidine deaminase

scientific article published on 28 July 2007

Ab initio force field for simulations of proteins and nucleic acids

article published in 1992

Ab initio mo study on base stacking: Adenine-adenine interaction in single-stranded polyadenylic acid (Poly A)

Ab initio molecular dynamics studies on substitution vs electron transfer reactions of substituted ketyl radical anions with chloroalkanes: how do the two products form in a borderline mechanism?

Ab initio molocular orbital study on the mechanism of the Haber-Weiss reaction

An ab initio MO study on the disulfide bond: properties concerning the characteristic S-S dihedral angle

An ab initio MO study on the hydrolysis of methyl chloride

An ab initio MO study on the thiol—disulphide exchange reaction

An ab initio molecular orbital study on the characteristics of 8-hydroxyguanine

scientific article published on 01 October 1987

An insight into the environmental effects of the pocket of the active site of the enzyme.Ab initio ONIOM-molecular dynamics (MD) study on cytosine deaminase

scientific article published on 01 February 2008

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

Association Behavior of Poly(ethylene oxide)-Poly(propylene oxide) Alternating Multiblock Copolymers in Water toward Thermally Induced Phase Separation

scientific article published on 13 December 2017

BSSE-corrected Three-body Interaction Energy in the Recognition of GC Base Pair by Asparagine

Characteristics of the Watson-Crick type hydrogen-bonded DNA base pairs: An ab initio molecular orbital study

Chemical Modification of the siRNA Seed Region Suppresses Off-Target Effects by Steric Hindrance to Base-Pairing with Targets

scientific article published on 12 May 2017

Chiral Sum Frequency Spectroscopy of Thin Films of Porphyrin J-Aggregates

scientific article published on 01 April 2009

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

scientific article published on 04 February 2009

Correction to “Chemical Modification of the siRNA Seed Region Suppresses Off-Target Effects by Steric Hindrance to Base-Pairing with Targets”.

scientific article published on 5 June 2017

Crosslinking reactions of 4-amino-6-oxo-2-vinylpyrimidine with guanine derivatives and structural analysis of the adducts.

scientific article

Dimerization and Double Proton Transfer-Induced Tautomerism of 4(3H)-Pyrimidinone in Solution Studied by IR Spectroscopy and Quantum Chemical Calculations

scientific article published on 01 December 2006

Dipole Moments of Amino Acid Residues, Gly and Ala, in α-Helix: Quantum Chemical Building Blocks for Macrodipole Moment of α-Helical Polypeptide

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

scientific article published on 21 August 2014

Electronic origin of the dependence of hydrogen bond strengths on nearest-neighbor and next-nearest-neighbor hydrogen bonds in polyhedral water clusters (H2O)n, n = 8, 20 and 24

scientific article published on 01 July 2016

Electronic states of the DNA polynucleotides poly(dG)-poly(dC) in the presence of iodine

scholarly article in Physical Review B, vol. 75 no. 4, January 2007

Enumeration of Topology-Distinct Structures and Possible Stable Structures of Protonated Water Clusters, H3O+(H2O)n−1(n≤5)

Enumeration of topology-distinct structures of hydrogen bonded water clusters

Fundamental absorption frequencies and mean structures at vibrational ground state from quasi-classical direct ab initio MD: Triatomic molecule

article

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

article

Fundamental frequency from classical molecular dynamics

article

H-bond patterns and structure distributions of water octamer (H2O)8 at finite temperatures

Helmholtz Energy Change between Neutral and Zwitterionic Forms of Glycine in Aqueous Solution Using Ab Initio Expanded QM/MM-MC with QM Solvent

Hydration of Adamantane Skeleton: Water Assembling around Amantadine and Halo-substituted Adamantanes

Hydration structure of trimethylamine N-oxide in aqueous solutions revealed by soft X-ray emission spectroscopy and chemometric analysis.

scientific article

IR and Raman intensities in vibrational spectra from direct ab initio molecular dynamics: D2O as an illustration

article

Identification of chemical species of fluorescein isothiocyanate isomer-I (FITC) monolayers on platinum by doubly resonant sum-frequency generation spectroscopy

Influence of Trimethylamine N-Oxide (TMAO) on the Three-dimensional Distribution and Alignment of Solvent Molecules in Aqueous Solution

Kinetic investigations of the process of encapsulation of small hydrocarbons into a cavitand-porphyrin

scientific article published on 3 November 2007

Macrodipole Moment of Polypeptides in β-Sheet and Its Prediction from Dipole Moments of Amino Acid Residues as Building Blocks: Alanine and Glycine in β-Strand

Molecular dynamics simulation in vacuo and in solution of cyclolinopeptide A: A conformational study

article

ONIOM Study of the Mechanism of the Enzymatic Hydrolysis of Biodegradable Plastics

scholarly article by Yoshitake Sakae et al published 15 March 2009 in Bulletin of the Chemical Society of Japan

Photo-Induced Ring-Opening Reaction of Flav-3-en-2-ol Monitored by Time-Resolved Infrared Spectroscopy

scientific article published on 27 September 2019

Photochemistry of 2-(methylamino)pyridine in a low-temperature argon matrix: Amino–imino tautomerism and rotational isomerism

Photochemistry of p-toluidine in a low-temperature argon matrix. Infrared spectrum and geometrical structure of 4-methylanilino radical

Photoinduced Amino−Imino Tautomerism: An Infrared Study of 2-Amino-5-methylpyridine in a Low-Temperature Argon Matrix

scientific article published on 01 May 2006

Photoinduced amino–imino tautomerism of 2-aminopyridine in a low-temperature argon matrix

Population of 6-Enol Form is Higher in 8-Oxoguanine than in Guanine

Quantum chemical study of the interaction of the short-chain poly(oxyethylene)s CH3(OCH2CH2)mOCH3 (C1EmC1; m = 1 and 2) with a water molecule in the gas phase and in solutions

scientific article published in January 2006

Reconsidering the activation entropy for anomerization of glucose and mannose in water studied by NMR spectroscopy

article published in 2015

Self-assembled monolayers of cyanoterphenyl terminated alkyl disulfides studied by vibrationally and electronically doubly-resonant sum-frequency generation spectroscopy

article

Self-assembled monolayers of double-chain disulfides of adenine on Au: an IR-UV sum-frequency generation spectroscopic study

scientific article published in January 2010

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

Structure and hypochromism of (6,9) (9′,6′) purinophanes

Structures of molecules in ground and excited vibrational states from quasiclassical direct ab initio molecular dynamics

scientific article published in June 2010

Synthesis and biological activities of the amide derivative of aplog-1, a simplified analog of aplysiatoxin with anti-proliferative and cytotoxic activities

scientific article

The ONIOM molecular dynamics method for biochemical applications: Cytidine deaminase

Thermally induced double proton transfer in GG and wobble GT base pairs: A possible origin of the mutagenic guanine

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

scientific article published on 05 December 2007

Vibrational anharmonicity of acetic acid studied by matrix-isolation near-infrared spectroscopy and DFT calculation

article

Why O6-alkylguanine is specifically promutagenic?

scientific article published on 01 August 1982

List of works by Misako Aida

A Comment on ‘Promoting Equal Participation of Men and Women in Science and Engineering’

A Quantum Chemical Study of the Catalysis for Cytidine Deaminase: Contribution of the Extra Water Molecule

A Quantum Chemical Study of the Catalysis for Cytidine Deaminase: Contribution of the Extra Water Molecule

A Theoretical Insight into the Interaction of Fatty Acids Involved in Royal Jelly with the Human Estrogen Receptor β

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

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

A polarizable mixed Hamiltonian model of electronic structure for micro-solvated excited states. I. Energy and gradients formulation and application to formaldehyde (1A2)

Ab Initio Direct Molecular Dynamics Simulations and QM/MM Computations in Search of Organic Reaction Mechanisms

Ab Initio QM/MM-MC Study on Hydrogen Transfer of Glycine Tautomerization in Aqueous Solution: Helmholtz Energy Changes along Water-mediated and Direct Processes

Ab initio MO and quasi-classical direct ab initio MD studies on the nitrogen inversion of trimethylamine

Ab initio ONIOM-molecular dynamics (MD) study on the deamination reaction by cytidine deaminase

Ab initio force field for simulations of proteins and nucleic acids

Ab initio mo study on base stacking: Adenine-adenine interaction in single-stranded polyadenylic acid (Poly A)

Ab initio molecular dynamics studies on substitution vs electron transfer reactions of substituted ketyl radical anions with chloroalkanes: how do the two products form in a borderline mechanism?

Ab initio molocular orbital study on the mechanism of the Haber-Weiss reaction

An ab initio MO study on the disulfide bond: properties concerning the characteristic S-S dihedral angle

An ab initio MO study on the hydrolysis of methyl chloride

An ab initio MO study on the thiol—disulphide exchange reaction

An ab initio molecular orbital study on the characteristics of 8-hydroxyguanine

An insight into the environmental effects of the pocket of the active site of the enzyme.Ab initio ONIOM-molecular dynamics (MD) study on cytosine deaminase

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

Association Behavior of Poly(ethylene oxide)-Poly(propylene oxide) Alternating Multiblock Copolymers in Water toward Thermally Induced Phase Separation

BSSE-corrected Three-body Interaction Energy in the Recognition of GC Base Pair by Asparagine

Characteristics of the Watson-Crick type hydrogen-bonded DNA base pairs: An ab initio molecular orbital study

Chemical Modification of the siRNA Seed Region Suppresses Off-Target Effects by Steric Hindrance to Base-Pairing with Targets

Chiral Sum Frequency Spectroscopy of Thin Films of Porphyrin J-Aggregates

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

Correction to “Chemical Modification of the siRNA Seed Region Suppresses Off-Target Effects by Steric Hindrance to Base-Pairing with Targets”.

Crosslinking reactions of 4-amino-6-oxo-2-vinylpyrimidine with guanine derivatives and structural analysis of the adducts.

Dimerization and Double Proton Transfer-Induced Tautomerism of 4(3H)-Pyrimidinone in Solution Studied by IR Spectroscopy and Quantum Chemical Calculations

Dipole Moments of Amino Acid Residues, Gly and Ala, in α-Helix: Quantum Chemical Building Blocks for Macrodipole Moment of α-Helical Polypeptide

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

Electronic origin of the dependence of hydrogen bond strengths on nearest-neighbor and next-nearest-neighbor hydrogen bonds in polyhedral water clusters (H2O)n, n = 8, 20 and 24

Electronic states of the DNA polynucleotides poly(dG)-poly(dC) in the presence of iodine

Enumeration of Topology-Distinct Structures and Possible Stable Structures of Protonated Water Clusters, H3O+(H2O)n−1(n≤5)

Enumeration of topology-distinct structures of hydrogen bonded water clusters

Fundamental absorption frequencies and mean structures at vibrational ground state from quasi-classical direct ab initio MD: Triatomic molecule

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

Fundamental frequency from classical molecular dynamics

H-bond patterns and structure distributions of water octamer (H2O)8 at finite temperatures

Helmholtz Energy Change between Neutral and Zwitterionic Forms of Glycine in Aqueous Solution Using Ab Initio Expanded QM/MM-MC with QM Solvent

Hydration of Adamantane Skeleton: Water Assembling around Amantadine and Halo-substituted Adamantanes

Hydration structure of trimethylamine N-oxide in aqueous solutions revealed by soft X-ray emission spectroscopy and chemometric analysis.

IR and Raman intensities in vibrational spectra from direct ab initio molecular dynamics: D2O as an illustration

Identification of chemical species of fluorescein isothiocyanate isomer-I (FITC) monolayers on platinum by doubly resonant sum-frequency generation spectroscopy

Influence of Trimethylamine N-Oxide (TMAO) on the Three-dimensional Distribution and Alignment of Solvent Molecules in Aqueous Solution

Kinetic investigations of the process of encapsulation of small hydrocarbons into a cavitand-porphyrin

Macrodipole Moment of Polypeptides in β-Sheet and Its Prediction from Dipole Moments of Amino Acid Residues as Building Blocks: Alanine and Glycine in β-Strand

Molecular dynamics simulation in vacuo and in solution of cyclolinopeptide A: A conformational study

ONIOM Study of the Mechanism of the Enzymatic Hydrolysis of Biodegradable Plastics

Photo-Induced Ring-Opening Reaction of Flav-3-en-2-ol Monitored by Time-Resolved Infrared Spectroscopy

Photochemistry of 2-(methylamino)pyridine in a low-temperature argon matrix: Amino–imino tautomerism and rotational isomerism

Photochemistry of p-toluidine in a low-temperature argon matrix. Infrared spectrum and geometrical structure of 4-methylanilino radical

Photoinduced Amino−Imino Tautomerism: An Infrared Study of 2-Amino-5-methylpyridine in a Low-Temperature Argon Matrix

Photoinduced amino–imino tautomerism of 2-aminopyridine in a low-temperature argon matrix

Population of 6-Enol Form is Higher in 8-Oxoguanine than in Guanine

Quantum chemical study of the interaction of the short-chain poly(oxyethylene)s CH3(OCH2CH2)mOCH3 (C1EmC1; m = 1 and 2) with a water molecule in the gas phase and in solutions

Reconsidering the activation entropy for anomerization of glucose and mannose in water studied by NMR spectroscopy

Self-assembled monolayers of cyanoterphenyl terminated alkyl disulfides studied by vibrationally and electronically doubly-resonant sum-frequency generation spectroscopy

Self-assembled monolayers of double-chain disulfides of adenine on Au: an IR-UV sum-frequency generation spectroscopic study

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

Structure and hypochromism of (6,9) (9′,6′) purinophanes

Structures of molecules in ground and excited vibrational states from quasiclassical direct ab initio molecular dynamics

Synthesis and biological activities of the amide derivative of aplog-1, a simplified analog of aplysiatoxin with anti-proliferative and cytotoxic activities

The ONIOM molecular dynamics method for biochemical applications: Cytidine deaminase

Thermally induced double proton transfer in GG and wobble GT base pairs: A possible origin of the mutagenic guanine

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

Vibrational anharmonicity of acetic acid studied by matrix-isolation near-infrared spectroscopy and DFT calculation

Why O6-alkylguanine is specifically promutagenic?