Hai Lin

Lin 2022
Departmental Chair and Professor
Department of Chemistry

Mailing Address:
Department of Chemistry
Campus Box 194, P.O. Box 173364
Denver, CO 80217-3364

Office Location:
Science Building
Room 4126B

Ph.D., Chemistry, University of Science and Technology of China, 1998
M.S., Physics, University of Science and Technology of China, 1995
BSc., Eng., University of Science and Technology of China, 1993

Professional Background:

  • Since 2017, Professor, University of Colorado Denver
  • 2011-2017, Associate Professor, University of Colorado Denver
  • 2005-2011, Assistant Professor, University of Colorado Denver
  • 2003 – 2005, Minnesota Supercomputing Institute Scholar, University of Minnesota 
  • 2001 – 2003, Max-Planck Postdoctoral Fellow, Max-Planck-Institut für Kohlenforschung, Germany
  • 2000 – 2001, Alexander von Humboldt Fellow, Universität-Wuppertal, Germany
  • 1998 – 2000, Assistant Professor, University of Science and Technology of China, China

Research Activities:

Our research focuses on the development and applications of computational methods to study chemical and biological processes in complex environments. Examples include enzymatic reactions, protein-ligand binding, and ion transport.


  • Cottrell Scholar, Research Corporation for Science Advancement (2015)
  • Henry Dreyfus Teacher-Scholar Award, Camille & Henry Dreyfus Foundation (2014)
  • Research Corporation for Science Advancement Cottrell College Science Multi-Investigator Award (2013)
  • NSF CAREER Award (2010, NSF)
  • Excellence in Research & Creative Work Award (2007, College of Liberal Arts and Sciences, University of Colorado Denver)
  • Research Corporation Cottrell College Science Award (2006, Research Corporation)

Duster, A.; Wang, C.-H.; Garza, C.; Miller, D.; Lin, H. "Adaptive QM/MM: Where are we, what have we learned, and where will we go from here?" Wiley Interdisciplinary Reviews: Computational Molecular Science2017, 7, e1310.

Pezeshki, S., Lin, H. "Recent developments in adaptive QM/MM," in Rivail, J.-L.; Ruiz-Lopez M.; Assfeld, X. eds. Quantum Modeling of Complex Molecular Systems, or the "Challenges and Advances in Computational Chemistry and Physics" series, 2015, published by Springer, pp 93-114, DOI:10.1007/978-3-319-21626-3_3

Chon, N. L.; Osterberg, J. R.; Henderson, J.; Khan, H.; Reuter, N.; Knight, J. D.; Lin, H. "Membrane docking of synaptotagmin-7 C2A domain: 2. Computations reveal interplay between electrostatic and hydrophobic contributions." Biochemistry2015, 54, 5696-5711. DOI: 10.1021/acs.biochem.5b00422 

Osterberg, J. R.; Chon, N. L.; Boo, A.; Maynard, F. A.; Lin, H.; Knight, J. D. "Membrane docking of synaptotagmin 7 C2A domain: 1. EPR measurements show contributions from two membrane binding loops." Biochemistry2015, 54, 5684-5695. DOI: 10.1021/acs.biochem.5b00421 

Pezeshki, S.; Lin, H. "Adaptive-partitioning QM/MM for molecular dynamics simulations: 4. Proton hopping in bulk water." Journal of Chemical Theory and Computation 201511, 2398-2411. 

Pezeshki, S.; *Davis, C.; Heyden, A.; Lin, H. "Adaptive-Partitioning QM/MM Dynamics Simulations: 3. Solvent Molecules Entering and Leaving Protein Binding Sites." Journal of Chemical Theory and Computation 2014, 10, 4765-4776. 

Pezeshki, S.; Lin, H. "Molecular dynamics simulations of ion solvation by flexible-boundary QM/MM: On-the-fly partial charge transfer between QM and MM subsystems." Journal of Computational Chemistry 2014, 35, 1778-1788. 

Pezeshki, S.; Lin, H. "Recent developments in QM/MM methods towards open-boundary multi-scale simulations." Molecular Simulations 2014, 41, 168-189. 

*Chon, N.; Lee, S.; Lin, H. "A theoretical study of temperature dependence of cluster formation from sulfuric acid and ammonia." Chemical Physics 2014, 433, 60-66. 

Damrauer, R.; Lin, H.; Damrauer, N. H. "Computational studies of carbodiimide rings." Journal of Organic Chemistry 2014, 79, 3781-3788.

*Church, J.; Pezeshki, S.; *Davis, C.; Lin, H. "Charge transfer and polarization for chloride ions bound in clc transport proteins: natural bond orbital and energy decomposition analyses." Journal of Physical Chemistry B 2013, 117, 16029-16043. 

Wu, X.; Thiel, W.; Pezeshki, S.; Lin, H. "Specific Reaction Path Hamiltonian for Proton Transfer in Water: Re-parameterized Semi-empirical Methods." Journal of Chemical Theory and Computation 2013, 9, 2672-2686. 

Pezeshki, S.; Lin, H. "Adaptive-Partitioning Redistributed Charge and Dipole Schemes for QM/MM Dynamics Simulations: On-the-fly Relocation of Boundaries that Pass through Covalent Bonds."  Journal of Chemical Theory and Computation 2011, 7, 3625-3634.

Smith, M.; Lin, H. "Charge delocalization upon chloride ion binding in ClC chloride ion channels/transporters." Chemical Physics Letters2011, 502, 112-117.

Ader, L.; Jones, D. N. M.; Lin, H. "Alcohol binding to the odorant binding protein LUSH: Multiple factors affecting binding affinities." Biochemistry 2010, 49, 6136-6142.

Zhang, Y.; Lin, H. "Flexible-boundary QM/MM calculations: II. Partial charge transfer across the QM/MM boundary that passes through a covalent bond." Theoretical Chemistry Accounts 2010, 216, 315-322.

Zhang, Y.; Lin, H. "Quantum tunneling in testosterone 6β-hydroxylation by cytochrome P450: Reaction dynamics calculations employing multiconfiguration molecular-mechanical potential energy surfaces." Journal of Physical Chemistry A 2009, 113, 11501-11508.

Zhang, Y.; Lin, H. "Flexible-boundary quantum-mechanical/molecular-mechanical calculations: Partial charge transfer between the quantum-mechanical and molecular-mechanical subsystems."  Journal of Chemical Theory and Computation 2008, 4, 414-425.

Zhang, Y.; Morisetti, P.; Kim, J.; Smith, L., Lin, H. "Regioselectivity preference of testosterone hydroxylation by cytochrome P450 3A4." Theoretical Chemistry Accounts 2008, 121, 313-319.

Zhang, Y.; Lin, H.; Truhlar, D. G. "Self-consistent polarization of the boundary in the redistributed charge and dipole scheme for combined quantum mechanical and molecular mechanical calculations."  Journal of Chemical Theory and Computation 2007, 3, 1378-1398.

Lin, H.; Truhlar, D. G. "QM/MM: What have we learned, where are we, and where do we go from here?" Theoretical Chemistry Accounts 2007, 117, 185-199.

Heyden, A.; Lin, H.; Truhlar, D. G. "Adaptive partitioning in combined quantum mechanical and molecular mechanical calculations of potential energy functions for multiscale simulations." Journal of Physical Chemistry B 2007, 111, 2231-2241.

Lin, H.; Zhao, Y.; Tischchenko, O.; Truhlar, D. G. "Multiconfiguration molecular mechanics based on combined quantum mechanical and molecular mechanical calculations."  Journal of Chemical Theory and Computation 2006, 2, 1237-1254.

Lin, H.; Truhlar, D. G. "Redistributed charge and dipole schemes for combined quantum-mechanical and molecule mechanical calculations." Journal of Physical Chemistry A 2005, 109, 3991-4004.

CHEM 2031: General Chemistry I
CHEM 2061: General Chemistry II
CHEM 4511: Physical Chemistry: Thermodynamics & Kinetics
CHEM 4521: Physical Chemistry: Quantum & Spectroscopy
CHEM 4518: Physical Chemistry Lab: Thermodynamics & Kinetics
CHEM 4538: Physical Chemistry Lab II: Quantum & Spectroscopy
CHEM 5510: Computational Chemistry
CHEM 5530: Advanced Physical Chemistry
CHEM 5600: Molecular Modeling and Simulations
CHEM 5600: Molecular Modeling and Drug Design