List of works - Yasuteru Shigeta

A Density Functional Theory Based Protocol to Compute the Redox Potential of Transition Metal Complex with the Correction of Pseudo-Counterion: General Theory and Applications.

scientific article published on 5 June 2013

A computational scheme of pKa values based on the three-dimensional reference interaction site model self-consistent field theory coupled with the linear fitting correction scheme

scientific article published on 01 November 2018

Accessing the Accuracy of Density Functional Theory through Structure and Dynamics of the Water-Air Interface

scientific article published on 13 August 2019

Accurate standard hydrogen electrode potential and applications to the redox potentials of vitamin C and NAD/NADH.

scientific article

Agonist and Antagonist-Diverted Twisting Motions of a Single TRPV1 Channel

scientific article published on 09 December 2020

An accurate density functional theory based estimation of pKa values of polar residues combined with experimental data: from amino acids to minimal proteins ⬇️

scientific article published on February 15, 2012

Atom-Scale Reaction Pathways and Free-Energy Landscapes in Oxygen Plasma Etching of Graphene

scientific article published on 25 April 2013

Binding of a positron to nucleic base molecules and their pairs

scientific article published on 12 September 2013

Catalytic Mechanism of Nitrile Hydratase Subsequent to Cyclic Intermediate Formation: A QM/MM Study

scientific article published on 23 March 2016

Common folding processes of mini-proteins: Partial formations of secondary structures initiate the immediate protein folding.

scientific article published on 13 February 2017

Conformation-Changeable π-Electronic Systems with Metastable Bent-Core Conformations and Liquid-Crystalline-State Electric-Field-Responsive Properties

scientific article published on 11 December 2020

Consistent scheme for computing standard hydrogen electrode and redox potentials

scientific article published on 24 August 2012

Cooperatively Interlocked [2+1]-Type π-System-Anion Complexes

scientific article published on 24 February 2017

Correlation functions in quantized Hamilton dynamics and quantal cumulant dynamics

scientific article published on 01 October 2008

Development of an Analysis Toolkit, AnalysisFMO, to Visualize Interaction Energies Generated by Fragment Molecular Orbital Calculations

scientific article published on 20 December 2018

Development of calculation and analysis methods for the dynamic first hyperpolarizability based on the ab initio molecular orbital-quantum master equation method.

scientific article published on 23 April 2012

Distribution function in quantal cumulant dynamics

scientific article published on 01 April 2008

Doubly N-Methylated Porphyrinoids

scientific article published on 6 June 2016

Dynamic charge fluctuation of endohedral fullerene with coencapsulated Be atom and H2

scientific article published on 01 October 2005

Effects of mercury(II) on structural properties, electronic structure and UV absorption spectra of a duplex containing thymine-mercury(II)-thymine nucleobase pairs.

scientific article published on 7 December 2009

Efficient Conformational Sampling of Collective Motions of Proteins with Principal Component Analysis-Based Parallel Cascade Selection Molecular Dynamics

scientific article published on 13 August 2020

Efficient Conformational Search Based on Structural Dissimilarity Sampling: Applications for Reproducing Structural Transitions of Proteins.

scientific article published on 7 February 2017

Enhanced conformational sampling method for proteins based on the TaBoo SeArch algorithm: application to the folding of a mini-protein, chignolin.

scientific article published on 18 February 2015

Enhancement of Second Hyperpolarizabilities in Open-Shell Singlet Slipped-Stack Dimers Composed of Square Planar Nickel Complexes Involvingo-Semiquinonato Type Ligands

scientific article published on 19 January 2011

Enhancement of the third-order nonlinear optical properties in open-shell singlet transition-metal dinuclear systems: effects of the group, of the period, and of the charge of the metal atom

scientific article published on 25 May 2012

Excitonic Coupling on a Heliobacterial Symmetrical Type-I Reaction Center: Comparison with Photosystem I

scientific article published on 07 January 2020

Finite-field method with unbiased polarizable continuum model for evaluation of the second hyperpolarizability of an open-shell singlet molecule in solvents.

scientific article published in August 2013

First-Principles Study of the Reaction Mechanism of CHO + H on Graphene Surface

scientific article published on 19 June 2019

First-principles molecular dynamics study on the atomistic behavior of His503 in bovine cytochrome c oxidase

scientific article published on 01 May 2011

Fluctuation Flooding Method (FFM) for accelerating conformational transitions of proteins

scientific article published on March 2014

Full configuration interaction calculations of the second hyperpolarizabilities of the H4 model compound: summation-over-states analysis and interplay with diradical characters

scientific article published on 01 January 2012

Halide ion complexes of decaborane (B10H14) and their derivatives: noncovalent charge transfer effect on second-order nonlinear optical properties

scientific article published on 25 January 2012

How low-resolution structural data predict the conformational changes of a protein: a study on data-driven molecular dynamics simulations

scientific article published on 01 July 2018

Hybrid Cascade-Type Molecular Dynamics with a Markov State Model for Efficient Free Energy Calculations

scientific article published on 07 December 2018

Identification of the key interactions in structural transition pathway of FtsZ from Staphylococcus aureus.

scientific article published on 26 April 2017

In Silico Structural Modeling and Analysis of Elongation Factor-1 Alpha and Elongation Factor-like Protein

scientific article published on 23 April 2019

Independent Nontargeted Parallel Cascade Selection Molecular Dynamics (Ino-PaCS-MD) to Enhance the Conformational Sampling of Proteins

scientific article published on 19 August 2021

Interplay between the diradical character and third-order nonlinear optical properties in fullerene systems

scientific article published on 18 December 2012

Ion-Pairing Crystal Polymorphs of Interlocked [2 + 1]-Type Receptor-Anion Complexes

scientific article published on 15 August 2016

Molecular Mechanism of the Reaction Specificity in Threonine Synthase: Importance of the Substrate Conformations

scientific article published on 10 May 2017

Molecular dynamics studies on the mutational structures of a nylon-6 byproduct-degrading enzyme

Multiple proton-transfer reactions in DNA base pairs by coordination of pt complex

scientific article published in February 2007

Mutations affecting the internal equilibrium of the reaction catalyzed by 6-aminohexanoate-dimer hydrolase.

scientific article published on 16 August 2016

Nontargeted Parallel Cascade Selection Molecular Dynamics Based on a Nonredundant Selection Rule for Initial Structures Enhances Conformational Sampling of Proteins

scientific article published on 21 November 2019

Nontargeted Parallel Cascade Selection Molecular Dynamics Using Time-Localized Prediction of Conformational Transitions in Protein Dynamics

scientific article published on 27 August 2019

Nylon-Oligomer Hydrolase Promoting Cleavage Reactions in Unnatural Amide Compounds

scientific article published on 21 March 2014

On the induced-fit mechanism of substrate-enzyme binding structures of nylon-oligomer hydrolase

scientific article published on 21 April 2014

Open-Shell Characters and Second Hyperpolarizabilities of One-Dimensional Graphene Nanoflakes Composed of Trigonal Graphene Units

scientific article published on 17 May 2011

Open-shell character and second hyperpolarizabilities of one-dimensional chromium(II) chains: size dependence and bond-length alternation effect

scientific article

Photosubstitution Reaction of cis-[Ru(bpy)2(CH3CN)2]2+ and cis-[Ru(bpy)2(NH3)2]2+ in Aqueous Solution via Monoaqua Intermediate

scientific article published on 13 March 2019

Phototransformative Supramolecular Assembly of Amphiphilic Diarylethenes Realized by a Combination of Photochromism and Lower Critical Solution Temperature Behavior

scientific article published on 11 July 2017

Protein Dynamics and the Folding Degree

scientific article published on 24 February 2020

Protein Residue Networks from Energetic and Geometric Data: Are They Identical?

scientific article published on 30 November 2018

Protein folding pathways extracted by OFLOOD: Outlier FLOODing method

scientific article published on 03 November 2014

Quantal cumulant dynamics: general theory

scientific article published in December 2006

Refractive indices of organo-metallic and -metalloid compounds: A long-range corrected DFT study

scientific article

Selection Rules for Outliers in Outlier Flooding Method Regulate Its Conformational Sampling Efficiency

scientific article published on 28 August 2019

Selection rules on initial structures in parallel cascade selection molecular dynamics affect conformational sampling efficiency

scientific article published on 05 September 2018

Simple, yet powerful methodologies for conformational sampling of proteins.

scientific article published on March 2015

Sparsity-weighted outlier FLOODing (OFLOOD) method: Efficient rare event sampling method using sparsity of distribution.

scientific article published on 27 November 2015

Structural origin of copper ion containing artificial DNA: a density functional study.

scientific article published on December 2008

Substitution effects on optical properties of iminonitroxide- substituted iminonitroxide diradical

Synergetic Effects of Triplet–Triplet Annihilation and Directional Triplet Exciton Migration in Organic Crystals for Photon Upconversion

TaBoo SeArch Algorithm with a Modified Inverse Histogram for Reproducing Biologically Relevant Rare Events of Proteins

scientific article published on 12 April 2016

Temperature-Shuffled Structural Dissimilarity Sampling Based on a Root-Mean-Square Deviation

scientific article published on 26 June 2018

Theoretical design of solvatochromism switching by photochromic reactions using donor-acceptor disubstituted diarylethene derivatives with oxidized thiophene rings.

scientific article published in March 2015

Theoretical insight into stereoselective reaction mechanisms of 2,4-pentanediol-tethered ketene-olefin [2 + 2] cycloaddition

scientific article published on 23 January 2012

Theoretical studies of electronic structures, magnetic properties and electron conductivities of one-dimensional Ni(n) (n = 3, 5, 7) complexes.

scientific article published on 3 October 2013

Theoretical study of the mechanism of hydrogenation of side-on coordinated dinitrogen activated by Zr binuclear complexes ([(eta5-C5Me4H)2Zr]2(mu2,eta2,eta2-N2)).

scientific article published in October 2005

Theoretical study on reaction mechanisms of nitrite reduction by copper nitrite complexes: toward understanding and controlling possible mechanisms of copper nitrite reductase

scientific article published on 16 April 2015

Theoretical study on reaction scheme of silver(I) containing 5-substituted uracils bridge formation

scientific article published on 08 July 2011

Third-Order Nonlinear Optical Properties of Open-Shell Supermolecular Systems Composed of Acetylene Linked Phenalenyl Radicals

scientific article published on 21 July 2011

Tunneling matrix element and tunneling pathways of protein electron transfer calculated with a fragment molecular orbital method

scientific article published on 01 September 2020

Unidirectional electronic ring current driven by a few cycle circularly polarized laser pulse: quantum model simulations for Mg-porphyrin

scientific article

Unraveling the degradation of artificial amide bonds in nylon oligomer hydrolase: from induced-fit to acylation processes

scientific article published on 01 February 2015

Why Are Lopinavir and Ritonavir Effective against the Newly Emerged Coronavirus 2019? Atomistic Insights into the Inhibitory Mechanisms

scientific article published on 15 April 2020

List of works by Yasuteru Shigeta

A Density Functional Theory Based Protocol to Compute the Redox Potential of Transition Metal Complex with the Correction of Pseudo-Counterion: General Theory and Applications.

A computational scheme of pKa values based on the three-dimensional reference interaction site model self-consistent field theory coupled with the linear fitting correction scheme

Accessing the Accuracy of Density Functional Theory through Structure and Dynamics of the Water-Air Interface

Accurate standard hydrogen electrode potential and applications to the redox potentials of vitamin C and NAD/NADH.

Agonist and Antagonist-Diverted Twisting Motions of a Single TRPV1 Channel

An accurate density functional theory based estimation of pKa values of polar residues combined with experimental data: from amino acids to minimal proteins ⬇️

Atom-Scale Reaction Pathways and Free-Energy Landscapes in Oxygen Plasma Etching of Graphene

Binding of a positron to nucleic base molecules and their pairs

Catalytic Mechanism of Nitrile Hydratase Subsequent to Cyclic Intermediate Formation: A QM/MM Study

Common folding processes of mini-proteins: Partial formations of secondary structures initiate the immediate protein folding.

Conformation-Changeable π-Electronic Systems with Metastable Bent-Core Conformations and Liquid-Crystalline-State Electric-Field-Responsive Properties

Consistent scheme for computing standard hydrogen electrode and redox potentials

Cooperatively Interlocked [2+1]-Type π-System-Anion Complexes

Correlation functions in quantized Hamilton dynamics and quantal cumulant dynamics

Development of an Analysis Toolkit, AnalysisFMO, to Visualize Interaction Energies Generated by Fragment Molecular Orbital Calculations

Development of calculation and analysis methods for the dynamic first hyperpolarizability based on the ab initio molecular orbital-quantum master equation method.

Distribution function in quantal cumulant dynamics

Doubly N-Methylated Porphyrinoids

Dynamic charge fluctuation of endohedral fullerene with coencapsulated Be atom and H2

Effects of mercury(II) on structural properties, electronic structure and UV absorption spectra of a duplex containing thymine-mercury(II)-thymine nucleobase pairs.

Efficient Conformational Sampling of Collective Motions of Proteins with Principal Component Analysis-Based Parallel Cascade Selection Molecular Dynamics

Efficient Conformational Search Based on Structural Dissimilarity Sampling: Applications for Reproducing Structural Transitions of Proteins.

Enhanced conformational sampling method for proteins based on the TaBoo SeArch algorithm: application to the folding of a mini-protein, chignolin.

Enhancement of Second Hyperpolarizabilities in Open-Shell Singlet Slipped-Stack Dimers Composed of Square Planar Nickel Complexes Involvingo-Semiquinonato Type Ligands

Enhancement of the third-order nonlinear optical properties in open-shell singlet transition-metal dinuclear systems: effects of the group, of the period, and of the charge of the metal atom

Excitonic Coupling on a Heliobacterial Symmetrical Type-I Reaction Center: Comparison with Photosystem I

Finite-field method with unbiased polarizable continuum model for evaluation of the second hyperpolarizability of an open-shell singlet molecule in solvents.

First-Principles Study of the Reaction Mechanism of CHO + H on Graphene Surface

First-principles molecular dynamics study on the atomistic behavior of His503 in bovine cytochrome c oxidase

Fluctuation Flooding Method (FFM) for accelerating conformational transitions of proteins

Full configuration interaction calculations of the second hyperpolarizabilities of the H4 model compound: summation-over-states analysis and interplay with diradical characters

Halide ion complexes of decaborane (B10H14) and their derivatives: noncovalent charge transfer effect on second-order nonlinear optical properties

How low-resolution structural data predict the conformational changes of a protein: a study on data-driven molecular dynamics simulations

Hybrid Cascade-Type Molecular Dynamics with a Markov State Model for Efficient Free Energy Calculations

Identification of the key interactions in structural transition pathway of FtsZ from Staphylococcus aureus.

In Silico Structural Modeling and Analysis of Elongation Factor-1 Alpha and Elongation Factor-like Protein

Independent Nontargeted Parallel Cascade Selection Molecular Dynamics (Ino-PaCS-MD) to Enhance the Conformational Sampling of Proteins

Interplay between the diradical character and third-order nonlinear optical properties in fullerene systems

Ion-Pairing Crystal Polymorphs of Interlocked [2 + 1]-Type Receptor-Anion Complexes

Molecular Mechanism of the Reaction Specificity in Threonine Synthase: Importance of the Substrate Conformations

Molecular dynamics studies on the mutational structures of a nylon-6 byproduct-degrading enzyme

Multiple proton-transfer reactions in DNA base pairs by coordination of pt complex

Mutations affecting the internal equilibrium of the reaction catalyzed by 6-aminohexanoate-dimer hydrolase.

Nontargeted Parallel Cascade Selection Molecular Dynamics Based on a Nonredundant Selection Rule for Initial Structures Enhances Conformational Sampling of Proteins

Nontargeted Parallel Cascade Selection Molecular Dynamics Using Time-Localized Prediction of Conformational Transitions in Protein Dynamics

Nylon-Oligomer Hydrolase Promoting Cleavage Reactions in Unnatural Amide Compounds

On the induced-fit mechanism of substrate-enzyme binding structures of nylon-oligomer hydrolase

Open-Shell Characters and Second Hyperpolarizabilities of One-Dimensional Graphene Nanoflakes Composed of Trigonal Graphene Units

Open-shell character and second hyperpolarizabilities of one-dimensional chromium(II) chains: size dependence and bond-length alternation effect

Photosubstitution Reaction of cis-[Ru(bpy)2(CH3CN)2]2+ and cis-[Ru(bpy)2(NH3)2]2+ in Aqueous Solution via Monoaqua Intermediate

Phototransformative Supramolecular Assembly of Amphiphilic Diarylethenes Realized by a Combination of Photochromism and Lower Critical Solution Temperature Behavior

Protein Dynamics and the Folding Degree

Protein Residue Networks from Energetic and Geometric Data: Are They Identical?

Protein folding pathways extracted by OFLOOD: Outlier FLOODing method

Quantal cumulant dynamics: general theory

Refractive indices of organo-metallic and -metalloid compounds: A long-range corrected DFT study

Selection Rules for Outliers in Outlier Flooding Method Regulate Its Conformational Sampling Efficiency

Selection rules on initial structures in parallel cascade selection molecular dynamics affect conformational sampling efficiency

Simple, yet powerful methodologies for conformational sampling of proteins.

Sparsity-weighted outlier FLOODing (OFLOOD) method: Efficient rare event sampling method using sparsity of distribution.

Structural origin of copper ion containing artificial DNA: a density functional study.

Substitution effects on optical properties of iminonitroxide- substituted iminonitroxide diradical

Synergetic Effects of Triplet–Triplet Annihilation and Directional Triplet Exciton Migration in Organic Crystals for Photon Upconversion

TaBoo SeArch Algorithm with a Modified Inverse Histogram for Reproducing Biologically Relevant Rare Events of Proteins

Temperature-Shuffled Structural Dissimilarity Sampling Based on a Root-Mean-Square Deviation

Theoretical design of solvatochromism switching by photochromic reactions using donor-acceptor disubstituted diarylethene derivatives with oxidized thiophene rings.

Theoretical insight into stereoselective reaction mechanisms of 2,4-pentanediol-tethered ketene-olefin [2 + 2] cycloaddition

Theoretical studies of electronic structures, magnetic properties and electron conductivities of one-dimensional Ni(n) (n = 3, 5, 7) complexes.

Theoretical study of the mechanism of hydrogenation of side-on coordinated dinitrogen activated by Zr binuclear complexes ([(eta5-C5Me4H)2Zr]2(mu2,eta2,eta2-N2)).

Theoretical study on reaction mechanisms of nitrite reduction by copper nitrite complexes: toward understanding and controlling possible mechanisms of copper nitrite reductase

Theoretical study on reaction scheme of silver(I) containing 5-substituted uracils bridge formation

Third-Order Nonlinear Optical Properties of Open-Shell Supermolecular Systems Composed of Acetylene Linked Phenalenyl Radicals

Tunneling matrix element and tunneling pathways of protein electron transfer calculated with a fragment molecular orbital method

Unidirectional electronic ring current driven by a few cycle circularly polarized laser pulse: quantum model simulations for Mg-porphyrin

Unraveling the degradation of artificial amide bonds in nylon oligomer hydrolase: from induced-fit to acylation processes

Why Are Lopinavir and Ritonavir Effective against the Newly Emerged Coronavirus 2019? Atomistic Insights into the Inhibitory Mechanisms