Rui Sun
The University of Chicago
Chicago, Illinois 60637
H (806) 786 7627
B ruisun@uchicago.edu
Experience
2015–present Postdoctoral Scholar, The University of Chicago,
Advisor: Dr. Gregory Voth
2009–2014 Ph.D. of Chemistry, Texas Tech University,
Advisor: Dr. William Hase
2013 Summer Student, Virginia Tech University, Sustainable Software Innovation
Institute for Computational Chemistry
Supervisor: Dr. Daniel Crawford
2012 Exchange Scholar, University of Pisa, Partnerships for International Research
and Education
Supervisor: Dr. Maurizio Persico and Dr. Giovanni Granucci
2008 Exchange Student, University of California, Los Angeles,
Supervisor: Dr. Daniel Neuhauser
2005–2009 Bachelor of Chemistry, Shandong University,
Disciplines of Research Experiences
Classical Direct Dynamics Simulations
Trajectories are propagated using the energy gradient calculated with quantum
mechanical methods, through which atomic level chemical dynamics are used to
investigate the properties of unimolecular and bimolecular reactions. I develop
algorithms for obtaining product properties in direct dynamics simulations and
compare them to molecular beam experiments.
Scientific Software Development and Parallel Computing
Improved the interface between the classical trajectory simulation program
(VENUS) and quantum chemical programs (NWChem and GAMESS) by adding
a trajectory restart capability and alternate initial SCF guesses. I have acquired
knowledge of parallel compilation, optimization and execution by developing a
parallel version of VENUS/NWChem and VENUS/GAMESS for simulations.
Quantum Chemistry Calculation
Different levels of theories, e.g. CCSD(T), CASSCF, DFT and MP2, have been
used extensively in my research. I have experiences of comparing multiple levels
of theories and selecting the best fit for the simulation purpose.
QM/MM Direct Dynamics in the Liquid Phase
Developed and applied software to study: (1) energy transfer from a highly
vibrationally excited solute molecule to the solvent; and (2) the effect of solvation
on post transition state reaction dynamics.
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Kinetics and Rate Constant Theory
Learned and applied various rate constant theories on different chemical reaction
systems. Variational Transition State Theory (VTST) was used to calculate
bimolecular rate constants for association reactions without potential energy
barriers and Rice-Ramsperger-Kassel-Marcus (RRKM) theory was used to interpret
lifetimes of intermediates with well-defined transition states.
QM/MM Direct Dynamics Simulations for Different Spin-Orbit States
The potential energy surface is represented as a summation of the QM spin-orbit
free potential energy and the spin-orbit coupling energy, represented by a MM-like
analytic function. The latter is calculated using CASSCF method.
Current Research Projects and Interest
1 Metadynamics Simulations of Drug Molecules Passing through Membrane, Rui
Sun, James Dama, Anand Srivastava and Gregory Voth
2 Direct Dynamics Simulation of CH3 CCl3 → CH2 CCl2 + HCl Product Energy
Partitioning. Comparison with Experiment, Rui Sun, Kyoyeon Park and William
Hase
3 Inefficient Post-Transition State Intermolecular Energy Transfer and NonEquilibrium Kinetics for a Hydroboration Reaction in Solution, Swapnil Kohale,
Rui Sun, Daniel Denslow, Maurizio Persico, Daniel Singleton and William Hase
Numerical Calculation Skills
Classical Chemical Dynamics: VENUS, GROMACS
Ab Initio Calculations: NWChem, GAMESS, Gaussion, MolPro
Programming/Scripting: FORTRAN, C/C++, Bash, Parallel Computing
Mathematical Programs: Matlab, Mathematica
Other Tools: Gnuplot, Xmgrace, ECCE, Origin
Professional References
Dr. Gregory Voth (Postdoctoral Advisor)
Department of Chemistry, The University of Chicago
Dr. William Hase (Ph.D Advisor)
Department of Chemistry and Biochemistry, Texas Tech University
Dr. Hans Lischka
Department of Chemistry and Biochemistry, Texas Tech University
also Institute for Theoretical Chemistry, University of Vienna
Dr. Theresa Windus
Department of Chemistry, Iowa State University
Dr. Maurizio Persico
University of Pisa, Italy
Dr. Giovanni Grannuci
University of Pisa, Italy
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Dr. Matthew Siebert
Chemistry Department, Missouri State University
Dr. Manikandan Paranjothy
Indian Institute of Technology Rajasthan, India
Dr. Jiaxu Zhang
Institute of Chemistry, Chinese Academy of Sciences China
List of Publications
1 Potential Energy Surfaces for the HBr+ + CO2 → Br + HOCO+ Reaction in the
HBr+ 2 Π3/2 and 2 Π1/2 Spin-Orbit States, Rui Sun, Giovanni Granucci, Amit Paul,
Matthew Siebert, Hongliang Liang, Grace Cheong, William Hase and Maurizio
Persico, The Journal of Chemical Physics, Submitted
2 Comparison of Direct Dynamics Simulations with Different Electronic Structure
Methods. F− + CH3 I with MP2 and DFT/B97-1, Rui Sun, Collin Davda, Jiaxu
Zhang and William Hase, Physical Chemistry Chemical Physics, 17, 2589 (2015)
3 Direct Dynamics Simulation of Dissociation of the [CH3 –I–OH]â ĹŠ Ion-Molecule
Complex, Jing Xie, Miranda McClellan, Rui Sun, Swapnil Kohale, Niranjan Govind
and William Hase, The Journal of Physical Chemistry A DOI: 10.1021/jp511898y
(2015)
4 Direct Dynamics Simulation of the Activation and Dissociation of 1,5-Dinitrobiuret
(HDNB), Rui Sun, Matthew R. Siebert, Lai Xu, Steven Chambreau, Ghanshyam
Vaghjiani, Hans Lischka, Jianbo Liu and William Hase, Journal of the Physical
Chemistry A. 118, 2228 (2014)
5 The F− + CH3 I → FCH3 + I− Entrance Channel Potential Energy Surface Comparison of Electronic Structure Methods, Rui Sun, Jing Xie and William Hase, International Journal of Mass Spectrometry, Published, doi:10.1016/j.ijms.2014.04.006
(2014)
6 The VENUS/NWChem Software Package. Tight Coupling between Chemical
Dynamics Simulations and Electronic Structure Theory, Upakarasamy Lourderaj,
Rui Sun, Swapnil Kohale, George Barnes, Wibe de Jong, Theresa Windus and
William Hase, Computer Physics Communications, 185, 1074 (2014)
7 A Unified Model for Simulating Liquid and Gas Phase Intermolecular Energy
Transfer. N2 + C6 F6 Collisions, Amit Paul, Swapnil Kohale, Subha Pratihar,
Rui Sun, Simon North and William Hase, Journal of the Chemical Physics, 140,
194103 (2014)
8 Direct Chemical Dynamics Simulations: Coupling of Classical and Quasiclassical
Trajectories with Electronic Structure Theory, Manikandan Paranjothy, Rui Sun,
Yu Zhuang and William Hase, WIREs Computational Molecular Science, 3, 296
(2013)
9 Direct Dynamics Simulations of the Product Channels and Atomistic Mechanisms
for the OH− + CH3 I Reaction. Comparison with Experiment, Jing Xie, Rui Sun,
Matthew R. Siebert, Rico Otto, Roland Wester and William Hase, Journal of the
Physical Chemistry, A, 117, 7162 (2013)
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10 Indirect Dynamics in a Highly Exoergic Substitution Reaction, Jochen Mikosch,
Jiaxu Zhang, Sebastian Trippel, Christoph Eichhorn, Rico Otto, Sun, Rui, Wibe
DeJong, Matthias Weidemuller, William Hase and Roland Wester, Journal of the
American Chemical Society, 135, 4250 (2013)
11 Simulation Studies of the Cl− + CH3 I SN 2 Nucleophilic Substitution Reaction.
Comparison with Ion Imaging Experiments, Jiaxu Zhang, Upakarasamy Lourderaj,
Rui Sun, Jochen Mikosch, Roland Wester, and William Hase, Journal of the
Chemical Physics 138, 114309 (2013)
12 Models for Intrinsic non-RRKM Dynamics. Decomposition of the SN 2 Intermediate
Cl− —CH3 Br, Manikandan Paranjothy, Rui Sun, Amit Kumar Paul and William
Hase, ZEITSCHRIFT FUR PHYSIKALISCHE CHEMIE, 227, 1361 (2013)
13 Comparison of Cluster, Slab, and Analytic Potential Models for the Dimethyl
Methylphosphonate (DMMP)/TiO2 (110) Intermolecular Interaction, Li Yang,
Daniel Tunega, Lai Xu, Niranjan Govind, Rui Sun, Ramona Taylor, Hans Lischka,
Wibe DeJong and William Hase, Journal of the Physical Chemistry, C, 117, 17613
(2013)
14 Direct Dynamics Simulation of Dioxetane Formation and Decomposition via the
Singlet O-O-CH2 -CH2 Biradical, Rui Sun, Kyoyeon Park, Hans Lischka, Wibe de
Jong, Theresa Windus and William Hase, Journal of the Chemical Physics 137,
044305 (2012)
15 Gas-Phase Chemical Dynamics Simulations on the Bifurcating Pathway of the
Pimaradienyl Cation Rearrangement: Role of Enzymatic Steering in Abietic Acid
Biosynthesis, Matthew Siebert, Paranjothy Manikandan, Rui Sun, Dean Tantillo and William Hase, Journal of Chemical Theory and Computation, Journal
Chemical Theory and Computation, 8, 1212 (2012)
16 Use of Direct Dynamics Simulations to Determine Unimolecular Reaction Paths
and Arrhenius Parameters for Large Molecules, Li Yang, Rui Sun and William
Hase, Journal of Chemical Theory and Computation, 7, 3478 (2011)
17 Direct Dynamics Determination of the Reaction Pathways for Decomposition of
the Cross-linked Epoxy Resin Constituent CH3 -NH-CH-CH-CH3 , Li Yang, Rui Sun
and William Hase, Computational and Theoretical Chemistry, 990, 62 (2011)
Conferences, Workshops and Symposia Attended
2014 Mesilla Chemistry Workshop for Sally Chapman, Studies of the Chemical
Dynamics of Energy Transfer and Chemical Reaction, Mesilla, NM,
Organized by: Dr. Bruce Garrett, Pacific Northwest National Laboratory
Dr. William Hase, Texas Tech University
Dr. John Tully, Yale University
2013 Mesilla Chemistry Workshop, Dynamics for Chemical Reaction Pathways.
Role of Non-Statistical Effects, Mesilla, NM,
Organized by: Dr. Joel Bowman, Emory University
Dr. William Hase, Texas Tech University
Dr. Arthur Suits, Wayne State University
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2013 245th American Chemical Society National Meeting, New Orleans, Louisiana,
Organized by: American Chemical Society
Contribution of the candidate: presented poster
2013 Welch Summer Scholar Program Enclosing Workshop, Lubbock, TX,
Organized by: Robert A. Welch Foundation
Contribution of the candidate: presented poster
2013 69th SW Regional Meeting of the American Chemical Society, Waco, TX,
Organized by: American Chemical Society
Contribution of the candidate: presented poster
2012 Partnerships for International Research and Education, Pisa, Italy,
Organized by: Dr. William Hase, Texas Tech University
Dr. Maurizio Persico, University of Pisa
Contribution of the candidate: presented two talks
2011 Mesilla Chemistry Workshop, Aromatic Interactions in Chemistry and Biology, Mesilla, NM,
Organized by: Dr. Marcey Waters, University of North Carolina
Dr. Ken Houk, University of California, Los Angeles
Dr. William Hase, Texas Tech University
2011 Southwest Theoretical Chemistry Conference, Lubbock, TX,
Organized by: Dr. William Hase, Texas Tech University
Contribution of the candidate: presented poster
2010 Southwest Theoretical Chemistry Conference, Denton, TX,
Organized by: Dr. Angela Wilson, University of North Texas
Contribution of the candidate: presented poster
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