List of works - Yihan Shao

A Quantum Chemical Study of the Ground and Excited State Electronic Structures of Carbazole Oligomers with and without Triarylborane Substitutes

scientific article published on 21 May 2012

A combined density functional theory and molecular mechanics (QM/MM) study of FeCO vibrations in carbonmonoxy myoglobin

scientific article published in February 2006

A parallel implementation of the analytic nuclear gradient for time-dependent density functional theory within the Tamm–Dancoff approximation

scholarly article by Fenglai Liu published in October 2010

Accelerated Computation of Free Energy Profile at <i>Ab Initio</i> Quantum Mechanical/Molecular Mechanics Accuracy via a Semiempirical Reference Potential. 4. Adaptive QM/MM

scientific article published on 18 February 2021

Accelerated Computation of Free Energy Profile at ab Initio Quantum Mechanical/Molecular Mechanics Accuracy via a Semi-Empirical Reference Potential. I. Weighted Thermodynamics Perturbation

scientific article published on 18 October 2018

Accelerated computation of free energy profile at ab initio quantum mechanical/molecular mechanical accuracy via a semi-empirical reference potential. II. Recalibrating semi-empirical parameters with force matching

scientific article published on 11 September 2019

Accelerating <i>Ab Initio</i> Quantum Mechanical and Molecular Mechanical (QM/MM) Molecular Dynamics Simulations with Multiple Time Step Integration and a Recalibrated Semiempirical QM/MM Hamiltonian

scientific article published in 2022

Accelerating Correlated Quantum Chemistry Calculations Using Graphical Processing Units and a Mixed Precision Matrix Multiplication Library

scientific article published in January 2010

Accelerating MP2C dispersion corrections for dimers and molecular crystals.

scientific article published in June 2013

Accelerating resolution-of-the-identity second-order Møller-Plesset quantum chemistry calculations with graphical processing units

scientific article published on 30 January 2008

Accurate local approximations to the triples correlation energy: formulation, implementation and tests of 5th-order scaling models

scientific article published on 20 January 2005

Advanced Potential Energy Surfaces for Molecular Simulation

scientific article published on 11 August 2016

Advances in methods and algorithms in a modern quantum chemistry program package.

scientific article

Advances in molecular quantum chemistry contained in the Q-Chem 4 program package

article

An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches.

scientific article published on 12 January 2017

An efficient method for calculating maxima of homogeneous functions of orthogonal matrices: applications to localized occupied orbitals

scientific article published in November 2004

An efficient protocol for obtaining accurate hydration free energies using quantum chemistry and reweighting from molecular dynamics simulations

scientific article published on 22 August 2016

An improved J matrix engine for density functional theory calculations

scientific article published in June 2000

An improved algorithm for analytical gradient evaluation in resolution-of-the-identity second-order Møller-Plesset perturbation theory: Application to alanine tetrapeptide conformational analysis

scientific article (publication date: 15 April 2007)

Analysis and visualization of energy densities. I. Insights from real-time time-dependent density functional theory simulations

scientific article published on 10 November 2020

Analysis and visualization of energy densities. II. Insights from linear-response time-dependent density functional theory calculations

scientific article published on 20 November 2020

Analysis of Localized Diabatic States beyond the Condon Approximation for Excitation Energy Transfer Processes

scientific article published on 21 January 2014

Analytic Derivatives of Quartic-Scaling Doubly Hybrid XYGJ-OS Functional: Theory, Implementation, and Benchmark Comparison with M06-2X and MP2 Geometries for Nonbonded Compelexes

scientific article published on April 2013

Analytic derivative couplings between configuration-interaction-singles states with built-in electron-translation factors for translational invariance

scientific article published in December 2011

Are Explicit Solvent Models More Accurate than Implicit Solvent Models? A Case Study on the Menschutkin Reaction

scientific article published on 25 June 2019

Are both symmetric and buckled dimers on Si(100) minima? Density functional and multireference perturbation theory calculations

Benchmarking the Performance of Time-Dependent Density Functional Theory Methods on Biochromophores

scientific article published on 26 December 2019

Blind prediction of distribution in the SAMPL5 challenge with QM based protomer and pK a corrections

scientific article published on 19 September 2016

Bonding Patterns in Benzene Triradicals from Structural, Spectroscopic, and Thermochemical Perspectives

scientific article published in August 2004

Boramino acid as a marker for amino acid transporters

scientific article published on 11 September 2015

Calculating distribution coefficients based on multi-scale free energy simulations: an evaluation of MM and QM/MM explicit solvent simulations of water-cyclohexane transfer in the SAMPL5 challenge

scientific article published on 30 August 2016

Calculating electron transfer couplings by the Spin-Flip approach: energy splitting and dynamical correlation effects

scientific article published in May 2004

Calculations of Solvation Free Energy through Energy Reweighting from Molecular Mechanics to Quantum Mechanics

scientific article published on 5 January 2016

Combined QM/MM calculations of active-site vibrations in binding process of P450cam to putidaredoxin

scientific article published on 28 November 2007

Communication: Adjusting charge transfer state energies for configuration interaction singles: without any parameterization and with minimal cost

scientific article published in April 2012

Comparison of Three Chain-of-States Methods: Nudged Elastic Band and Replica Path with Restraints or Constraints

scientific article published on 27 September 2012

Complex absorbing potentials within EOM-CC family of methods: theory, implementation, and benchmarks.

scientific article published in July 2014

Computation of Hydration Free Energies Using the Multiple Environment Single System Quantum Mechanical/Molecular Mechanical Method

scientific article published on 23 November 2015

Computational Insights into Endo/Exo Selectivity of the Diels-Alder Reaction in Explicit Solvent at Ab Initio Quantum Mechanical/Molecular Mechanical Level

scientific article published on 11 June 2019

Computing the Free Energy along a Reaction Coordinate Using Rigid Body Dynamics

scientific article published on 15 August 2014

Controlling the Cleavage of Carbon-Carbon Bonds To Generate α,α-Difluorobenzyl Carbanions for the Construction of Difluoromethylbenzenes

scientific article published on 06 September 2019

Curvy steps for density matrix based energy minimization: tensor formulation and toy applications

scientific article published on 10 January 2003

Curvy steps for density matrix-based energy minimization: Application to large-scale self-consistent-field calculations

scientific article published on 8 April 2003

Derivative couplings between TDDFT excited states obtained by direct differentiation in the Tamm-Dancoff approximation

scientific article published in July 2014

Design, Synthesis, and Evaluation of 18F-Labeled Monoacylglycerol Lipase Inhibitors as Novel Positron Emission Tomography Probes

scientific article published on 26 September 2019

Design, Synthesis, and Evaluation of Reversible and Irreversible Monoacylglycerol Lipase Positron Emission Tomography (PET) Tracers Using a "Tail Switching" Strategy on a Piperazinyl Azetidine Skeleton

scientific article published on 21 March 2019

Do Better Quality Embedding Potentials Accelerate the Convergence of QM/MM Models? The Case of Solvated Acid Clusters

scientific article published on 26 September 2018

Doubly Polarized QM/MM with Machine Learning Chaperone Polarizability

scientific article published on 01 November 2021

Dual-basis analytic gradients. 1. Self-consistent field theory

scientific article published in December 2006

Dual-basis second-order Moller-Plesset perturbation theory: A reduced-cost reference for correlation calculations

scientific article published in August 2006

Effective fragment potential method in Q-CHEM: a guide for users and developers.

scientific article

Efficient Calculation of QM/MM Frequencies with the Mobile Block Hessian

scientific article published on 6 January 2011

Efficient Computation of Free Energy Surfaces of Diels⁻Alder Reactions in Explicit Solvent at Ab Initio QM/MM Level

scientific article published on 28 September 2018

Efficient Strategy for the Calculation of Solvation Free Energies in Water and Chloroform at the Quantum Mechanical/Molecular Mechanical Level

scientific article published on 21 September 2017

Efficient evaluation of the Coulomb force in density-functional theory calculations

scientific article published on 15 April 2001

Efficient self-consistent DFT calculation of nondynamic correlation based on the B05 method

scientific article published in June 2010

Efficient treatment of induced dipoles

scientific article published in August 2015

Enumeration and Symmetry of Substitution Isomers

scientific article published in January 1996

Enumeration of B24-mNmCages

scientific article published in January 1996

Erratum: "Complex absorbing potentials within EOM-CC family of methods: Theory, implementation, and benchmarks" [J. Chem. Phys. 141, 024102 (2014)].

scientific article published in October 2015

Ewald mesh method for quantum mechanical calculations

scientific article published in March 2012

Extension of the Effective Fragment Potential Method to Macromolecules

scientific article published on 17 June 2016

Fast evaluation of a linear number of local exchange matrices

Fast evaluation of scaled opposite spin second-order Møller-Plesset correlation energies using auxiliary basis expansions and exploiting sparsity

scientific article published in September 2007

Fast methods for resumming matrix polynomials and Chebyshev matrix polynomials

General formulation of spin-flip time-dependent density functional theory using non-collinear kernels: theory, implementation, and benchmarks

scientific article

General implementation of the resolution-of-the-identity and Cholesky representations of electron repulsion integrals within coupled-cluster and equation-of-motion methods: theory and benchmarks

scientific article published in October 2013

How accurate are approximate quantum chemical methods at modelling solute-solvent interactions in solvated clusters?

scientific article published on 01 February 2020

Identification and Development of a New Positron Emission Tomography Ligand 4-(2-Fluoro-4-[11C]methoxyphenyl)-5-((1-methyl-1H-pyrazol-3-yl)methoxy)picolinamide for Imaging Metabotropic Glutamate Receptor Subtype 2 (mGlu2)

scientific article published on 22 September 2020

Improved Fermi operator expansion methods for fast electronic structure calculations

Improved self-consistent and resolution-of-identity approximated Becke'05 density functional model of nondynamic electron correlation

scientific article published on January 2012

Isomer counting and isomer permutation representation

scientific article published in January 1996

Large-Scale QM/MM Calculations of Electronic Excitations in Yellow Protein: Toward Petascale Level of Protein Calculations

scientific article published in October 2007

Lennard-Jones parameters for the combined QM/MM method using the B3LYP/6-31G*/AMBER potential

scientific article published in September 2005

Machine-Learning-Assisted Free Energy Simulation of Solution-Phase and Enzyme Reactions

scientific article published on 01 September 2021

Multiple environment single system quantum mechanical/molecular mechanical (MESS-QM/MM) calculations. 1. Estimation of polarization energies

scientific article published on 30 October 2014

Numerical study on the partitioning of the molecular polarizability into fluctuating charge and induced atomic dipole contributions

scientific article published on 18 May 2015

On the structure of Si(100) surface: importance of higher order correlations for buckled dimer

scientific article published on May 2013

Oxalate-curcumin-based probe for micro- and macroimaging of reactive oxygen species in Alzheimer's disease

scientific article published on 6 November 2017

Performance of the AMOEBA Water Model in the Vicinity of QM Solutes: A Diagnosis Using Energy Decomposition Analysis

scientific article published on 21 April 2017

Publisher's Note: “Derivative couplings between TDDFT excited states obtained by direct differentiation in the Tamm-Dancoff approximation” [J. Chem. Phys. 141, 024114 (2014)]

scientific article published on 14 August 2014

Quartic-Scaling Analytical Energy Gradient of Scaled Opposite-Spin Second-Order Møller-Plesset Perturbation Theory

scientific article published in May 2007

Reaction Path-Force Matching in Collective Variables: Determining Ab Initio QM/MM Free Energy Profiles by Fitting Mean Force

scientific article published on 20 July 2021

Representation of the QM Subsystem for Long-Range Electrostatic Interaction in Non-Periodic Ab Initio QM/MM Calculations

scientific article published on 29 September 2018

Shared memory multiprocessing implementation of resolution-of-the-identity second-order Møller–Plesset perturbation theory with attenuated and unattenuated results for intermolecular interactions between large molecules

scientific article published on 6 January 2014

Sparse matrix multiplications for linear scaling electronic structure calculations in an atom-centered basis set using multiatom blocks

scientific article published in April 2003

Superposition of Fragment Excitations for Excited States of Large Clusters with Application to Helium Clusters

scientific article published on 20 November 2015

Symmetry of hydrogenated C60

scientific article published in August 1995

Synthesis and Preliminary Evaluations of a Triazole-Cored Antagonist as a PET Imaging Probe ([18F]N2B-0518) for GluN2B Subunit in the Brain

scientific article published on 27 February 2019

Synthesis, pharmacology and preclinical evaluation of C-labeled 1,3-dihydro-2H-benzo[d]imidazole-2-ones for imaging γ8-dependent transmembrane AMPA receptor regulatory protein

scientific article published on 5 September 2018

TD-DFT spin-adiabats with analytic nonadiabatic derivative couplings

scientific article published on 01 January 2020

TINKTEP: A fully self-consistent, mutually polarizable QM/MM approach based on the AMOEBA force field

scientific article published in September 2016

The evaluation of moments for benzenoid hydrocarbons

scientific article published in January 1995

The evaluation of moments for benzenoid hydrocarbons

scientific article published in 1995

The spin–flip approach within time-dependent density functional theory: Theory and applications to diradicals

scientific article published on 15 March 2003

Topology and Stability of Trivalent Polyhedral Clusters

scientific article published in November 1994

Towards enhanced metabolomic data analysis of mass spectrometry image: Multivariate Curve Resolution and Machine Learning

scholarly article by Xiang Tian et al published 11 December 2018 in Analytica Chimica Acta

Unraveling substituent effects on frontier orbitals of conjugated molecules using an absolutely localized molecular orbital based analysis

scientific article published on 7 December 2018

Vibrational subsystem analysis: A method for probing free energies and correlations in the harmonic limit

scientific article published on December 2008

YinYang atom: a simple combined ab initio quantum mechanical molecular mechanical model

scientific article published on 13 April 2007

List of works by Yihan Shao

A Quantum Chemical Study of the Ground and Excited State Electronic Structures of Carbazole Oligomers with and without Triarylborane Substitutes

A combined density functional theory and molecular mechanics (QM/MM) study of FeCO vibrations in carbonmonoxy myoglobin

A parallel implementation of the analytic nuclear gradient for time-dependent density functional theory within the Tamm–Dancoff approximation

Accelerated Computation of Free Energy Profile at <i>Ab Initio</i> Quantum Mechanical/Molecular Mechanics Accuracy via a Semiempirical Reference Potential. 4. Adaptive QM/MM

Accelerated Computation of Free Energy Profile at ab Initio Quantum Mechanical/Molecular Mechanics Accuracy via a Semi-Empirical Reference Potential. I. Weighted Thermodynamics Perturbation

Accelerated computation of free energy profile at ab initio quantum mechanical/molecular mechanical accuracy via a semi-empirical reference potential. II. Recalibrating semi-empirical parameters with force matching

Accelerating <i>Ab Initio</i> Quantum Mechanical and Molecular Mechanical (QM/MM) Molecular Dynamics Simulations with Multiple Time Step Integration and a Recalibrated Semiempirical QM/MM Hamiltonian

Accelerating Correlated Quantum Chemistry Calculations Using Graphical Processing Units and a Mixed Precision Matrix Multiplication Library

Accelerating MP2C dispersion corrections for dimers and molecular crystals.

Accelerating resolution-of-the-identity second-order Møller-Plesset quantum chemistry calculations with graphical processing units

Accurate local approximations to the triples correlation energy: formulation, implementation and tests of 5th-order scaling models

Advanced Potential Energy Surfaces for Molecular Simulation

Advances in methods and algorithms in a modern quantum chemistry program package.

Advances in molecular quantum chemistry contained in the Q-Chem 4 program package

An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches.

An efficient method for calculating maxima of homogeneous functions of orthogonal matrices: applications to localized occupied orbitals

An efficient protocol for obtaining accurate hydration free energies using quantum chemistry and reweighting from molecular dynamics simulations

An improved J matrix engine for density functional theory calculations

An improved algorithm for analytical gradient evaluation in resolution-of-the-identity second-order Møller-Plesset perturbation theory: Application to alanine tetrapeptide conformational analysis

Analysis and visualization of energy densities. I. Insights from real-time time-dependent density functional theory simulations

Analysis and visualization of energy densities. II. Insights from linear-response time-dependent density functional theory calculations

Analysis of Localized Diabatic States beyond the Condon Approximation for Excitation Energy Transfer Processes

Analytic Derivatives of Quartic-Scaling Doubly Hybrid XYGJ-OS Functional: Theory, Implementation, and Benchmark Comparison with M06-2X and MP2 Geometries for Nonbonded Compelexes

Analytic derivative couplings between configuration-interaction-singles states with built-in electron-translation factors for translational invariance

Are Explicit Solvent Models More Accurate than Implicit Solvent Models? A Case Study on the Menschutkin Reaction

Are both symmetric and buckled dimers on Si(100) minima? Density functional and multireference perturbation theory calculations

Benchmarking the Performance of Time-Dependent Density Functional Theory Methods on Biochromophores

Blind prediction of distribution in the SAMPL5 challenge with QM based protomer and pK a corrections

Bonding Patterns in Benzene Triradicals from Structural, Spectroscopic, and Thermochemical Perspectives

Boramino acid as a marker for amino acid transporters

Calculating distribution coefficients based on multi-scale free energy simulations: an evaluation of MM and QM/MM explicit solvent simulations of water-cyclohexane transfer in the SAMPL5 challenge

Calculating electron transfer couplings by the Spin-Flip approach: energy splitting and dynamical correlation effects

Calculations of Solvation Free Energy through Energy Reweighting from Molecular Mechanics to Quantum Mechanics

Combined QM/MM calculations of active-site vibrations in binding process of P450cam to putidaredoxin

Communication: Adjusting charge transfer state energies for configuration interaction singles: without any parameterization and with minimal cost

Comparison of Three Chain-of-States Methods: Nudged Elastic Band and Replica Path with Restraints or Constraints

Complex absorbing potentials within EOM-CC family of methods: theory, implementation, and benchmarks.

Computation of Hydration Free Energies Using the Multiple Environment Single System Quantum Mechanical/Molecular Mechanical Method

Computational Insights into Endo/Exo Selectivity of the Diels-Alder Reaction in Explicit Solvent at Ab Initio Quantum Mechanical/Molecular Mechanical Level

Computing the Free Energy along a Reaction Coordinate Using Rigid Body Dynamics

Controlling the Cleavage of Carbon-Carbon Bonds To Generate α,α-Difluorobenzyl Carbanions for the Construction of Difluoromethylbenzenes

Curvy steps for density matrix based energy minimization: tensor formulation and toy applications

Curvy steps for density matrix-based energy minimization: Application to large-scale self-consistent-field calculations

Derivative couplings between TDDFT excited states obtained by direct differentiation in the Tamm-Dancoff approximation

Design, Synthesis, and Evaluation of 18F-Labeled Monoacylglycerol Lipase Inhibitors as Novel Positron Emission Tomography Probes

Design, Synthesis, and Evaluation of Reversible and Irreversible Monoacylglycerol Lipase Positron Emission Tomography (PET) Tracers Using a "Tail Switching" Strategy on a Piperazinyl Azetidine Skeleton

Do Better Quality Embedding Potentials Accelerate the Convergence of QM/MM Models? The Case of Solvated Acid Clusters

Doubly Polarized QM/MM with Machine Learning Chaperone Polarizability

Dual-basis analytic gradients. 1. Self-consistent field theory

Dual-basis second-order Moller-Plesset perturbation theory: A reduced-cost reference for correlation calculations

Effective fragment potential method in Q-CHEM: a guide for users and developers.

Efficient Calculation of QM/MM Frequencies with the Mobile Block Hessian

Efficient Computation of Free Energy Surfaces of Diels⁻Alder Reactions in Explicit Solvent at Ab Initio QM/MM Level

Efficient Strategy for the Calculation of Solvation Free Energies in Water and Chloroform at the Quantum Mechanical/Molecular Mechanical Level

Efficient evaluation of the Coulomb force in density-functional theory calculations

Efficient self-consistent DFT calculation of nondynamic correlation based on the B05 method

Efficient treatment of induced dipoles

Enumeration and Symmetry of Substitution Isomers

Enumeration of B24-mNmCages

Erratum: "Complex absorbing potentials within EOM-CC family of methods: Theory, implementation, and benchmarks" [J. Chem. Phys. 141, 024102 (2014)].

Ewald mesh method for quantum mechanical calculations

Extension of the Effective Fragment Potential Method to Macromolecules

Fast evaluation of a linear number of local exchange matrices

Fast evaluation of scaled opposite spin second-order Møller-Plesset correlation energies using auxiliary basis expansions and exploiting sparsity

Fast methods for resumming matrix polynomials and Chebyshev matrix polynomials

General formulation of spin-flip time-dependent density functional theory using non-collinear kernels: theory, implementation, and benchmarks

General implementation of the resolution-of-the-identity and Cholesky representations of electron repulsion integrals within coupled-cluster and equation-of-motion methods: theory and benchmarks

How accurate are approximate quantum chemical methods at modelling solute-solvent interactions in solvated clusters?

Identification and Development of a New Positron Emission Tomography Ligand 4-(2-Fluoro-4-[11C]methoxyphenyl)-5-((1-methyl-1H-pyrazol-3-yl)methoxy)picolinamide for Imaging Metabotropic Glutamate Receptor Subtype 2 (mGlu2)

Improved Fermi operator expansion methods for fast electronic structure calculations

Improved self-consistent and resolution-of-identity approximated Becke'05 density functional model of nondynamic electron correlation

Isomer counting and isomer permutation representation

Large-Scale QM/MM Calculations of Electronic Excitations in Yellow Protein: Toward Petascale Level of Protein Calculations

Lennard-Jones parameters for the combined QM/MM method using the B3LYP/6-31G*/AMBER potential

Machine-Learning-Assisted Free Energy Simulation of Solution-Phase and Enzyme Reactions

Multiple environment single system quantum mechanical/molecular mechanical (MESS-QM/MM) calculations. 1. Estimation of polarization energies

Numerical study on the partitioning of the molecular polarizability into fluctuating charge and induced atomic dipole contributions

On the structure of Si(100) surface: importance of higher order correlations for buckled dimer

Oxalate-curcumin-based probe for micro- and macroimaging of reactive oxygen species in Alzheimer's disease