Hai Lin
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

Office Hours:
T: 02:00-03:00 PM
R: 02:00-03:00 PM

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