Dr. Hai Lin
Assistant Professor, Chemistry Department,
University of Colorado Denver,
NC 3103C, Campus Mail 194, PO Box 173364

Denver, CO 80217
 
Tel: +1-303-556-4885 
Fax: +1-303-556-4776 
E-mail: hai.lin@cudenver.edu

 

(Updated 5/24/2009) (Publication Updated 5/24/2009)

 

Group website Computational Chemistry at CU-Denver

 

Education

 

1993

BSc. Eng.

Computer Science

University of Science and Technology of China

1995

M. S.

Physics

University of Science and Technology of China

1998

Ph. D.

Chemistry

University of Science and Technology of China

Positions and Appointments

 

2005-now

Assistant Professor

Chemistry Department, University of Colorado Denver

2003-2005

Minnesota Supercomputing Institute Research Scholar

Chemistry Department, University of Minnesota

2005

Project Manager for Integrated Tools for Computational Chemical Dynamics

Chemistry Department, University of Minnesota

2001-2003

Max-Planck Postdoctoral Fellow

Max-Planck Institut für Kohlenforschung, Mülheim an der Ruhr, Germany

2000-2001

Alexander von Humboldt Fellow

Department of Chemistry, Universität-Wuppertal, Germany

1998-2000

Assistant Professor

Department of Chemical Physics, University of Science and Technology of China

Research Interests

We develop computational methods for modeling and simulation of complex systems, and we apply those methods to address a broad range of problems in chemistry, biochemistry, and biophysics, such as enzymatic reactions and ion transports. Our research plan features:

 

(1) Combination of quantum mechanics and classical mechanics

(2) Combination of accurate potential with reliable dynamical algorithms.

Method Development

  • Combined quantum-mechanical / molecular-mechanical (QM/MM) methods
  • Multi-configuration molecular mechanics (MCMM)
  • Reaction dynamics with multi-dimensional tunneling
  • Many-body expansion for condensed-phase simulation

Applications

  • Properties and functionalities of enzymes, ion channels, and protein/DNA/RNA complex
  • Highly accurate potential energy, dipole moment, spectroscopy, and dynamics for polyatomic molecules and clusters

 

More about Research  

 

Interested students are very welcomed to contact me via email (hai.lin@ucdenver.edu) for research projects as well as research positions.

 

Publications

Selected Peer-reviewed Articles

·     Zhang, Y.; Lin, H. “Quantum tunneling in testosterone 6β-hydroxylation by cytochrome P450: Reaction dynamics calculations employing multiconfiguration molecular-mechanical potential energy surfaces.” J. Phys. Chem. A. in press.

·         Zhang, Y.; Lin, H. “Flexible-boundary quantum-mechanical/molecular-mechanical calculations: Partial charge transfer between the quantum-mechanical and molecular-mechanical subsystems.” J. Chem. Theory Comput. 2008, 4, 414-425.

  • Zhang, Y.; Morisetti, P.; Kim, J.; Smith, L., Lin, H. “Regioselectivity preference of testosterone hydroxylation by cytochrome P450 3A4.” Theor. Chem. Acc. 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.” J. Chem. Theory Comput. 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?” Theor. Chem. Acc. 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.” J. Phys. Chem. 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.” J. Chem. Theory Comput. 2006, 2, 1237-1254.

·     Lin, H.; Truhlar, D. G. “Redistributed charge and dipole schemes for combined quantum-mechanical and molecule mechanical calculations.” J. Phys. Chem. A 2005, 109, 3991-4004.

·     Lin, H.; Schöneboom, J. C.; Cohen, S.; Shaik, S.; Thiel, W. “QM/MM study of the product-enzyme complex in P450cam catalysis.” J. Phys. Chem. B 2004, 108, 10083-10088.

·         Lin, H.; Pu, J.; Albu, T. V.; Truhlar, D. G. “Efficient molecular mechanics for chemical reactions:  multi-configuration molecular mechanics using partial electronic structure Hessians.” J. Phys. Chem. A 2004, 108, 4112-4124.

·         Lin, H.; Thiel, W.; Yurchenko, S. N.; Carvajal, M.; Jensen, P. “Vibrational energies for NH3 based on high level ab initio potential energy surfaces.” J. Chem. Phys. 2002, 117, 11265-11276.

·         Lin, H.; Bürger, H.; Mkadmi, E. B.; He, S. G.; Yuan, L. F.; Breidung, J.; Thiel, W.; Huet, T. R.; Demaison, J. “The Si-H stretching-bending overtone polyads of SiHF3: assignments, band intensities, internal coordinate force field, and ab initio dipole moment surfaces.” J. Chem. Phys. 2001, 115, 1378-1391.

·         Hu, S. M.; Lin, H.; He, S. G.; Cheng, J. X.; Zhu, Q. S. “Fourier-transform intra-cavity absorption spectroscopy of HOD v(OD) = 5 overtone.” Phys. Chem. Chem. Phys. 1999, 1, 3727-3730.

 

 

Computational program packages (co-authored) qmmm, mbpac, mc-tinker, mc-tinkerate

 

Full List of Publications  

 

Awards/Fellowship

  • Excellence in Research & Creative Work Award (2008), College of Liberal Arts and Sciences, University of Colorado Denver
  • Research Corporation Cottrell College Science Award (2006)
  • Minnesota Supercomputing Institute Research Scholarship (2003)
  • Max-Planck Postdoctoral Research Fellowship (2001-2003, Germany)
  • Alexander von Humboldt Research Fellowship (1999, Germany)
  • Excellent Prize of President Scholarship of Chinese Academy of Sciences (1998, China)
  • Guang-Hua Scholarship (1996, China)
  • Xing-He Scholarship (1995, China)
  • Excellent Student Scholarship, University of science and Technology of China (1989, 1991-1993, China).

Research Supports

 

·         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.

 

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

 

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

 

  • National Natural Science Foundation of China (PI, 2000) “Study of the highly excited molecular overtones by Fourier Transform Intracavity Laser Absorption Spectroscopy (FT-ICLAS),” Grant No. 29903010

 

Internal Funding Supports:

  • University of Colorado Denver College of Liberal Arts and Sciences Research Innovation Seed Programs (2008) “Ion Solvation and Transport in Aqueous Solutions by Combined QM/MM Simulations” $14,996
  • University of Colorado Denver, Young Upwardly Mobile Professors Grant (2008), support Dr. Feng Shuang’s scientific visit to Denver
  • University of Colorado Denver, Young Upwardly Mobile Professors Grant (2007), support attending 234th ACS National Meeting at Boston, MA
  • University of Colorado Denver, Young Upwardly Mobile Professors Grant (2006), support attending 231st ACS National Meeting at Atlanta, GA

 

Other Experience

Invited Presentations

2008    Invited Talk, “Flexible-boundary QM/MM: Adaptive partition and partial charge transfer between QM and MM subsystems,” Host: Prof. Kenneth Merz, Jr., Quantum Theory Project, University of Florida

2007    Invited Talk, “Understand biochemical processes at the atomic level,” Host: Prof. Rui Zhao, Program in Biomolecular Structure Seminar, School of Medicine, University of Colorado Denver. 

2007    Invited Lecture, “Toward more realistic simulations of large-size reactive systems by combining quantum mechanics and molecular mechanics in new ways,” Science Driven Petascale Computing and Capability Development, Pacific Northwest National Lab, Richland, WA

2006    Invited Talk, “An accurate and efficient computational tool for understanding enzymatic reactions,” Host: Prof. Jan Mandel, Center for Computational Mathematics Seminar, Department of Mathematics, University of Colorado Denver

2005    Invited Keynote Presentation, “QM/MM: What have we learned, where are we, and where do we go from here?” 10th Electronic Computational Chemistry Conference

2001    Invited Lecture, Host: Prof. Michael Dolg, Department of Chemistry, Bonn University, Germany

2000    Invited Talk, Host: Prof. Walter Thiel, Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany

2000    Invited Talk, “Overtone intensities of XH (X = C and Si) chromophores in some small molecules,” Workshop on Reductions of the Rovibrational Hamiltonian, Oberwolfach, Germany

2000    Invited Talk, Host: Prof. Bernd Abel, Department of Physical Chemistry, Göttingen University, Germany

1999    Invited Talk, Host: Prof. Li Li, Department of Chemistry, Tsinghua University, China

 

Reviewing Manuscript

Ad hoc reviewer for: Journal of the American Chemical Society, Journal of Chemical Theory and Computation, Computational Physics Communications, Journal of the Optical Society of America B, and Applied Optics

Reviewing Proposal

Ad hoc reviewer for: Research Corporation

Service

2005-now        Graduate Program Committee, Department of Chemistry, University of Colorado Denver

2006-2009       Faculty Council, College of Liberal Arts and Sciences, University of Colorado Denver

2007                Faculty Search Committee, Department of Chemistry, University of Colorado Denver

2005                Faculty Search Committee, Department of Mathematics, University of Colorado Denver

2005                Faculty Search Committee, Department of Chemistry, University of Colorado Denver

Professional Membership

  • American Chemical Society 

Teaching

 

Courses Taught/Scheduled

 

  • Physical Chemistry I (CHEM4511 section 001) Fall 2009
  • Molecular Modeling and Simulation (CHEM5600 section 001) Fall 2009
  • General Chemistry II (CHEM2061 section 001) Fall 2008
  • General Chemistry I (CHEM2031 section 002) Fall 2008
  • Physical Chemistry Lab II (CHEM4538 sections 001 & 002) Spring 2008
  • General Chemistry II (CHEM2061 section 002) Spring 2008
  • Physical Chemistry Lab I (CHEM4518 sections 001 & 002) Fall 2007
  • General Chemistry I (CHEM2031 section 002) Fall 2007
  • Physical Chemistry Lab II (CHEM4538 sections 001 & 002) Spring 2007
  • General Chemistry II (CHEM2061 section 002) Spring 2007
  • Physical Chemistry Lab I (CHEM4518 sections 001 & 002) Fall 2006
  • General Chemistry I (CHEM2031 section 002) Fall 2006
  • General Chemistry I (CHEM 2031) Summer 2006
  • Computational Chemistry (CHEM5510) Spring 2006

 

New Course Development

 

Grants for Teaching

  • University of Colorado Denver (2007) Capital Equipment Fund: Replacement of Fourier Transform Infrared Spectrometer for Physical Chemistry Laboratory, together with Larry Anderson, Mark Anderson, and Michael Travers, $33,200

 

  • University of Colorado Denver (2007) Faculty Development Fund: Development of the radical species UV-vis spectrometer system for Physical Chemistry Laboratory, together with Michael Travers, $4,000

 

  • University of Colorado Denver (2006) SITFAC Fund: Upgrade Computational Chemistry Program Spartan, $2,000

 

Teaching-Skill Enhancement

  • Participate in Prepare Future Faculty (PFF) program, University of Minnesota (2004)

 

Graduate Students Thesis/Research Supervised

  • Phani Morisetti            (2008)
  • Jeffery Kim                  (2007)
  • KunTae Pak                (2006)

Undergraduate Students Thesis/Research Supervised

  • Lauren Ader                (2009)
  • Jonathan Levy             (2008)
  • Lynelle Smith              (2008)
  • Daniel Silverstein        (2008)
  • Phani Morisetti            (2007)
  • Carrie Ryan                 (2007)

 

I am also a mentor associated with the LAB COATS program. Undergraduate students participated in this program are welcome to contact me for research projects.