Description: image024.jpgDr. Hai Lin
Associate Professor, Chemistry Department,
University of Colorado Denver,
SI 4126B, Campus Mail 194,

PO Box 173364, Denver, CO 80217

Tel: +1-303-352-3889  Fax: +1-303-556-4776 


(Updated 9/3/2015) (Publication Updated 9/3/2015)


Group website at Computational Chemistry at UC-Denver


Curriculum vitae




BSc. Eng.

Computer Science

University of Science and Technology of China


M. S.


University of Science and Technology of China


Ph. D.


University of Science and Technology of China


Positions and Appointments


Associate Professor, University of Colorado Denver


Assistant Professor, University of Colorado Denver


Minnesota Supercomputing Institute Research Scholar, University of Minnesota


Project Manager for Integrated Tools for Computational Chemical Dynamics, University of Minnesota


Max-Planck Postdoctoral Fellow, Max-Planck Institute for Carbon Research, Germany


Alexander von Humboldt Fellow, University-Wuppertal, Germany


Assistant Professor, University of Science and Technology of China





Multiscale modeling and simulations of chemical reactions in complex environments

Method Development

1.       Molecular dynamics by open-boundary quantum-mechanics/molecular-mechanics (QM/MM)

2.       Electrostatically embedded many-body expansion of potentials



1.       Chloride and proton transferred by CLC chloride ion transport proteins

2.       Association of synaptotagmin C2 domains with membranes

3.       Cytochrome P450 enzymes: substrate docking and oxidizations

4.       Cluster formation and dynamics of ammonia and sulfuric acids


More about Research  

Selected Recent Peer-reviewed Articles (* indicates undergraduate or M.S. students)

1.       *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." Biochemistry, 2015, in press, DOI: 10.1021/acs.biochem.5b00422 text

2.      Pezeshki, S.; Lin, H. "Adaptive-partitioning QM/MM for molecular dynamics simulations: 4. Proton hopping in bulk water." Journal of Chemical Theory and Computation 2015, 11, 2398-2411. text

3.       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. text

4.       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. text

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

6.       *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. text

7.       *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. text

8.       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. text

9.      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. text

10.  *Smith, M.; Lin, H. "Charge delocalization upon chloride ion binding in ClC chloride ion channels/transporters." Chemical Physics Letters, 2011, 502, 112-117. text

11.  *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. text

12.  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. text

13.  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. text

14.  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. text

15.  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. text

Computational program packages (co-authored) QMMM, MBPAC, MCSI (formerly MC-TINKER), MC-TINKERATE

Full List of Publications  

Research Supports

1.       XSEDE (PI, 2015-2016) "Multiscale Simulations of Membrane Proteins," Grant No. 140070 (renewed). CPU time 1,738,235 service units.

2.       Camille & Henry Dreyfus Foundation (PI, 2014-2019) "Open-Boundary QM/MM Methods for Multiscale Modeling and Simulations of Chemical Reactions in Complex Environments," Grant No. TH-14-028, $60,000

3.       XSEDE (PI, 2014-2015) "Multiscale Simulations of Membrane Proteins," Grant No. 140070. CPU time 1,181,576 service units.

4.       Research Corporation for Science Advancement (co-PI, 2013-2015) "Hydrophobic and electrostatic driving forces for protein-membrane docking: A combined experimental and computational approach," Grant No. 22399, $100,000

5.       XSEDE (PI, 2013-2014) "Multiscale Simulations of Chloride Transport Proteins," Grant No. 130090. CPU time 150,000 service units.

6.       National Renewal Energy Laboratory (PI, Subcontract 2013) "Catalytic Conversion of Biomass," $35,065

7.       National Science Foundation (PI, 2009-2014) "CAREER: Multiscale Simulations of Chloride Transport Proteins by Combined Quantum and Classic Mechanical Approaches," Grant No. CHE-0952337, $625,000

8.       National Science Foundation (PI, 2009) "Mathematics and Chemistry" Subcontract (NSF/1717-528-6056, $17,090) of "Institute for Mathematics and its Applications," Grant No. 9810289.

9.       William R. Wiley Environmental Molecular Sciences Laboratory (co-PI, 2009) "Computational Chemical Dynamics of Complex Systems" (Grant No. GC34900) 800,000 node-hours CPU time at the Molecular Science Computing Facility, a U.S. Department of Energy national scientific user facility located at Pacific Northwest National Laboratory.

10.    National Science Foundation (Senior Personnel, 2008) "MRI-Consortium: Acquisition of a Supercomputer by the Front Range Computing Consortium," $3,995,000.

11.    Research Corporation (PI, 2006-2011) "Reaction mechanism and dynamics of cytochrome P2450 3A4 enzyme by combined quantum mechanical/molecular mechanical computation," Grant No. CC6725, $34,950

12.    National Natural Science Foundation of China (PI, 2000) "Study of the highly excited molecular overtones by Fourier Transform Intra-cavity Laser Absorption Spectroscopy (FT-ICLAS),"Grant No. 29903010


Interested students are very welcomed to contact me via email ( for research projects and research positions.


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