List of works - Hai Lin

Adaptive Partitioning QM/MM Dynamics Simulations for Substrate Uptake, Product Release, and Solvent Exchange.

scientific article published on 16 June 2016

Adaptive Partitioning QM/MM for Molecular Dynamics Simulations: 6. Proton Transport through a Biological Channel

scientific article published on 28 January 2019

Adaptive QM/MM for Molecular Dynamics Simulations: 5. On the Energy-Conserved Permuted Adaptive-Partitioning Schemes

scientific article published on 28 August 2018

Adaptive partitioning in combined quantum mechanical and molecular mechanical calculations of potential energy functions for multiscale simulations.

scientific article published on 9 February 2007

Adaptive-Partitioning Multilayer Dynamics Simulations: 1. On-the-Fly Switch between Two Quantum Levels of Theory

scientific article published on 27 August 2021

Adaptive-Partitioning QM/MM Dynamics Simulations: 3. Solvent Molecules Entering and Leaving Protein Binding Sites.

scientific article published in November 2014

Adaptive-Partitioning Redistributed Charge and Dipole Schemes for QM/MM Dynamics Simulations: On-the-fly Relocation of Boundaries that Pass through Covalent Bonds

scientific article published on 29 September 2011

Adaptive-partitioning QM/MM for molecular dynamics simulations: 4. Proton hopping in bulk water

scientific article published on 22 May 2015

Charge transfer and polarization for chloride ions bound in ClC transport proteins: natural bond orbital and energy decomposition analyses

scientific article published on 27 November 2013

Chloride Ion Transport by the E. coli CLC Cl-/H+ Antiporter: A Combined Quantum-Mechanical and Molecular-Mechanical Study.

scientific article

Combined valence bond-molecular mechanics potential-energy surface and direct dynamics study of rate constants and kinetic isotope effects for the H+C2H6 reaction

article

Computational Studies of Carbodiimide Rings

scientific article published on 21 April 2014

Dipole moment and rovibrational intensities in the electronic ground state of NH3: bridging the gap between ab initio theory and spectroscopic experiment

scientific article published in March 2005

Efficient Molecular Mechanics for Chemical Reactions: Multiconfiguration Molecular Mechanics Using Partial Electronic Structure Hessians

article by Hai Lin et al published May 2004 in Journal of Physical Chemistry A

Flexible-Boundary Quantum-Mechanical/Molecular-Mechanical Calculations: Partial Charge Transfer between the Quantum-Mechanical and Molecular-Mechanical Subsystems

scientific article published on 01 March 2008

Green Fluorescent Proteins: Empirical Force Field for the Neutral and Deprotonated Forms of the Chromophore. Molecular Dynamics Simulations of the Wild Type and S65T Mutant

article

Membrane Docking of the Synaptotagmin 7 C2A Domain: Computation Reveals Interplay between Electrostatic and Hydrophobic Contributions.

scientific article published on 2 September 2015

Membrane Docking of the Synaptotagmin 7 C2A Domain: Electron Paramagnetic Resonance Measurements Show Contributions from Two Membrane Binding Loops.

scientific article published on 31 August 2015

Molecular dynamics simulations of ion solvation by flexible-boundary QM/MM: On-the-fly partial charge transfer between QM and MM subsystems

scientific article published on 23 July 2014

Multicoefficient Gaussian-3 Calculation of the Rate Constant for the OH + CH4Reaction and Its12C/13C Kinetic Isotope Effect with Emphasis on the Effects of Coordinate System and Torsional Treatment

Multiconfiguration Molecular Mechanics Based on Combined Quantum Mechanical and Molecular Mechanical Calculations.

scientific article published in September 2006

Overtones of the Si−H Stretching−Bending Polyad in SiHD3: Internal Coordinate Force Field, ab initio Dipole Moment Surfaces, and Band Intensities

Potential-energy surface for the electronic ground state of NH3 up to 20000cm−1 above equilibrium

article by Sergei N Yurchenko et al published October 2005 in Journal of Chemical Physics

QM/MM Study of the Product−Enzyme Complex in P450camCatalysis

QM/MM: what have we learned, where are we, and where do we go from here?

article by Hai Lin & Donald Truhlar published 8 July 2006 in Theoretical Chemistry Accounts

Quantum mechanical/molecular mechanical investigation of the mechanism of C-H hydroxylation of camphor by cytochrome P450cam: theory supports a two-state rebound mechanism

scientific article published in March 2004

Quantum tunneling in testosterone 6beta-hydroxylation by cytochrome P450: reaction dynamics calculations employing multiconfiguration molecular-mechanical potential energy surfaces.

scientific article published in October 2009

Recent Progress in Adaptive-Partitioning QM/MM Methods for Born-Oppenheimer Molecular Dynamics

article

Recent developments in QM/MM methods towards open-boundary multi-scale simulations

Redistributed charge and dipole schemes for combined quantum mechanical and molecular mechanical calculations.

scientific article published in May 2005

Restrained Proton Indicator in Combined Quantum-Mechanics/Molecular-Mechanics Dynamics Simulations of Proton Transfer through a Carbon Nanotube

scientific article published on 18 August 2017

Riding elevators into and out of cells

scientific article published on 13 October 2020

Rotation–Vibration Motion of Pyramidal XY3 Molecules Described in the Eckart Frame: The Calculation of Intensities with Application to NH3

article

Rotation–vibration motion of pyramidal XY3molecules described in the Eckart frame: Theory and application to NH3

article

Self-Consistent Polarization of the Boundary in the Redistributed Charge and Dipole Scheme for Combined Quantum-Mechanical and Molecular-Mechanical Calculations

Specific Reaction Path Hamiltonian for Proton Transfer in Water: Reparameterized Semiempirical Models

scientific article published on 16 May 2013

Study of the stretching vibrational band intensities of XH4 molecules employing four-dimensionalab initio(X=C and Sn) andeffective(X=C and Si) dipole moment surfaces

Temperature dependence of carbon-13 kinetic isotope effects of importance to global climate change

scientific article

The synaptotagmin C2B domain calcium-binding loops modulate the rate of fusion pore expansion.

scientific article published on 14 February 2018

Tracking Proton Transfer through Titratable Amino Acid Side Chains in Adaptive QM/MM Simulations

scientific article published on 07 October 2019

Vibrational energies for NH3 based on high level ab initio potential energy surfaces

article

List of works by Hai Lin

Adaptive Partitioning QM/MM Dynamics Simulations for Substrate Uptake, Product Release, and Solvent Exchange.

Adaptive Partitioning QM/MM for Molecular Dynamics Simulations: 6. Proton Transport through a Biological Channel

Adaptive QM/MM for Molecular Dynamics Simulations: 5. On the Energy-Conserved Permuted Adaptive-Partitioning Schemes

Adaptive partitioning in combined quantum mechanical and molecular mechanical calculations of potential energy functions for multiscale simulations.

Adaptive-Partitioning Multilayer Dynamics Simulations: 1. On-the-Fly Switch between Two Quantum Levels of Theory

Adaptive-Partitioning QM/MM Dynamics Simulations: 3. Solvent Molecules Entering and Leaving Protein Binding Sites.

Adaptive-Partitioning Redistributed Charge and Dipole Schemes for QM/MM Dynamics Simulations: On-the-fly Relocation of Boundaries that Pass through Covalent Bonds

Adaptive-partitioning QM/MM for molecular dynamics simulations: 4. Proton hopping in bulk water

Charge transfer and polarization for chloride ions bound in ClC transport proteins: natural bond orbital and energy decomposition analyses

Chloride Ion Transport by the E. coli CLC Cl-/H+ Antiporter: A Combined Quantum-Mechanical and Molecular-Mechanical Study.

Combined valence bond-molecular mechanics potential-energy surface and direct dynamics study of rate constants and kinetic isotope effects for the H+C2H6 reaction

Computational Studies of Carbodiimide Rings

Dipole moment and rovibrational intensities in the electronic ground state of NH3: bridging the gap between ab initio theory and spectroscopic experiment

Efficient Molecular Mechanics for Chemical Reactions: Multiconfiguration Molecular Mechanics Using Partial Electronic Structure Hessians

Flexible-Boundary Quantum-Mechanical/Molecular-Mechanical Calculations: Partial Charge Transfer between the Quantum-Mechanical and Molecular-Mechanical Subsystems

Green Fluorescent Proteins: Empirical Force Field for the Neutral and Deprotonated Forms of the Chromophore. Molecular Dynamics Simulations of the Wild Type and S65T Mutant

Membrane Docking of the Synaptotagmin 7 C2A Domain: Computation Reveals Interplay between Electrostatic and Hydrophobic Contributions.

Membrane Docking of the Synaptotagmin 7 C2A Domain: Electron Paramagnetic Resonance Measurements Show Contributions from Two Membrane Binding Loops.

Molecular dynamics simulations of ion solvation by flexible-boundary QM/MM: On-the-fly partial charge transfer between QM and MM subsystems

Multicoefficient Gaussian-3 Calculation of the Rate Constant for the OH + CH4Reaction and Its12C/13C Kinetic Isotope Effect with Emphasis on the Effects of Coordinate System and Torsional Treatment

Multiconfiguration Molecular Mechanics Based on Combined Quantum Mechanical and Molecular Mechanical Calculations.

Overtones of the Si−H Stretching−Bending Polyad in SiHD3: Internal Coordinate Force Field, ab initio Dipole Moment Surfaces, and Band Intensities

Potential-energy surface for the electronic ground state of NH3 up to 20000cm−1 above equilibrium

QM/MM Study of the Product−Enzyme Complex in P450camCatalysis

QM/MM: what have we learned, where are we, and where do we go from here?

Quantum mechanical/molecular mechanical investigation of the mechanism of C-H hydroxylation of camphor by cytochrome P450cam: theory supports a two-state rebound mechanism

Quantum tunneling in testosterone 6beta-hydroxylation by cytochrome P450: reaction dynamics calculations employing multiconfiguration molecular-mechanical potential energy surfaces.

Recent Progress in Adaptive-Partitioning QM/MM Methods for Born-Oppenheimer Molecular Dynamics

Recent developments in QM/MM methods towards open-boundary multi-scale simulations

Redistributed charge and dipole schemes for combined quantum mechanical and molecular mechanical calculations.

Restrained Proton Indicator in Combined Quantum-Mechanics/Molecular-Mechanics Dynamics Simulations of Proton Transfer through a Carbon Nanotube

Riding elevators into and out of cells

Rotation–Vibration Motion of Pyramidal XY3 Molecules Described in the Eckart Frame: The Calculation of Intensities with Application to NH3

Rotation–vibration motion of pyramidal XY3molecules described in the Eckart frame: Theory and application to NH3

Self-Consistent Polarization of the Boundary in the Redistributed Charge and Dipole Scheme for Combined Quantum-Mechanical and Molecular-Mechanical Calculations

Specific Reaction Path Hamiltonian for Proton Transfer in Water: Reparameterized Semiempirical Models

Study of the stretching vibrational band intensities of XH4 molecules employing four-dimensionalab initio(X=C and Sn) andeffective(X=C and Si) dipole moment surfaces

Temperature dependence of carbon-13 kinetic isotope effects of importance to global climate change

The synaptotagmin C2B domain calcium-binding loops modulate the rate of fusion pore expansion.

Tracking Proton Transfer through Titratable Amino Acid Side Chains in Adaptive QM/MM Simulations

Vibrational energies for NH3 based on high level ab initio potential energy surfaces