Computational Chemical Dynamics of Complex Systems


Funding and resources:

     "Computational Chemical Dynamics of Complex Systems" is a Computational Grand Challenge project of The William R. Wiley Environmental Molecular Sciences Laboratory (EMSL), a U.S. Department of Energy national scientific user facility located at Pacific Northwest National Laboratory (PNNL) in Richland, Washington. Resources are provided by EMSL's Molecular Science Computing Facility (MSCF). The MSCF houses an 11.8 Teraflop Hewlett Packard Linux Itanium2 Cluster with 980 nodes and 1960 processors along with a suite of compatible and innovative computational chemistry software.

http://mscf.emsl.pnl.gov/research/intro_cgca.shtml

     The project is a collaborative effort involving scientists in the Department of Chemistry at the University of Minnesota and scientists at PNNL.

Participants:

Group Name
Truhlar Donald G. Truhlar, 41608, Primary Investigator
Yan Zhao, 41620, Project Manager for University of Minnesota
Elizabeth Amin
Erin E. Dahlke, 41612
Andreas Heyden, 41613
Mark A. Iron, 41614
Pablo Jaque, 41615
Zhen Hua Li, 41616
Benjamin Lynch
Anastassia Sorkin, 41618
Oksana Tishchenko, 41619
Rosendo Valero, 41617
Cramer Christopher J. Cramer, 41609
Ashley Jay
Joseph D. Scanlon, 41621
Gao Jiali Gao, 41610
Alessandro Cembran, 41625
Shuhua Ma, 41626
Kiniu Wong, 41622
Wangshen Xie, 41623
Yan Zhou, 41624
Siepmann J. Ilja Siepmann, 19941
Kelly Anderson
Jake L. Rafferty, 41627
York Darrin M. York, 41611
PNNL Marat Valiev, 9780, Site Manager for PNNL
Bruce C. Garrett, Chemical Sciences Division Director, PNNL
Michel Dupuis, 19960
Bojana Ginovska
Vassiliki-Alexandra Glezakou
Shawn M. Kathmann, 19120
Karol Kowalski
Chris Mundy
Gregory K. Schenter, 19180
Ming Tsai

Project Summary:

     New research capabilities in computational chemical dynamics are expected to play a significant role in enabling environmental scientists worldwide to address environmental challenges facing DOE and the nation. The goal of this project is to apply powerful new simulation techniques to tackle computationally challenging problems in chemical dynamics, with special emphasis on electrochemistry, heterogeneous catalysis, nanoparticles, solid-state dynamics, and photochemistry. These calculations are being carried out with new high-throughput integrated software that we are developing.

     Recent advances in computer power and algorithms have made possible accurate calculations of many chemical properties for both equilibria and kinetics. Nonetheless, applications to complex chemical systems, such as reactive processes in the condensed phase, remain problematic due to the lack of a seamless integration of computational methods that allow modern quantum electronic structure calculations to be combined with state-of-the-art methods for chemical thermodynamics and reactive dynamics. These problems are often exacerbated by unvalidated methods and limited software reliability. Our consortium is developing an integrated software suite that combines electronic structure packages with dynamics codes and efficient sampling algorithms for a variety of condensed-phase modeling problems including thermochemical kinetics and rate constants, photochemistry and spectroscopy, chemical and phase equilibria, electrochemistry, and heterogeneous catalysis. These fundamental areas of research are important for solar energy, fuel- cell technology, environmental remediation, weather modeling, pollution modeling, and atmospheric chemistry.

     Photochemical creation of excited states offers a means to control chemical transformations because different wavelengths of light can be used to create different vibronic states, thereby directing chemical reactions along different pathways. It is crucial to understand how energy deposited into the system is used; this is particularly complicated in condensed phase systems where there are many ways to dissipate excess energy. Similar opportunities and challenges present themselves in the areas of electrochemistry and catalysis. We are therefore carrying out prototype large-scale applications on environmental problems as well as other applications to complex chemical dynamics processes, focusing on three high-impact areas. In the computational electrochemistry area, are especially concerned with processes that enhance the design of fuel cell technology and with the calculation of in situ reduction potentials. For heterogeneous, nanoparticle, and solid-state dynamics, we are developing an array of methods for multi-time-scale simulation of nucleation of crystals in solution, reactions of radicals at solution-phase interfaces and in ice, zeolite catalysis, structure and dynamics of gallazane precursors to gallium nitride nanocrystals, the regulatory role of metal ions in the reactivity of inorganic phosphates, nanoparticles structure and dynamics, and ice dynamics. In the computational photochemistry area, we are constructing potential energy surfaces for a number of photochemical reactions and employing them for dynamics calculations based on the new decay of mixing with coherent switches algorithm. We are also considering solvatochromic shifts on conical intersections that govern selected photochemical processes.

Publications:

"Thermochemical Kinetics of Hydrogen-Atom Transfers Between Methyl, Methane, Ethynyl, Ethyne, and Hydrogen,"J. Zheng, Y. Zhao, and D. G. Truhlar, J. Phys. Chem. A 2007, 111, 4632.

"Attractive Noncovalent Interactions in Grubbs Second-Generation Ru Catalysts for Olefin Metathesis,"Y. Zhao and D. G. Truhlar, Org. Lett. 2007,  9, 1967.

"Size-Selective Supramolecular Chemistry in a Hydrocarbon Nanoring ," Y. Zhao and D. G. Truhlar, J. Am. Chem. Soc. 2007, 129, 8440

"Hybrid approach for free energy calculations with high-level methods: Application to the SN2 reaction of CHCl3 and OH- in water," M. Valiev, B. C. Garrett, M.-K. Tsai, K. Kowalski, S. M. Kathmann, G. K. Schenter, and M. Dupuis J. Chem. Phys. 2007, 127, 51102

"Molecular Computational Investigation of Electron-Transfer Kinetics Across Cytochrome-Iron Oxide Interfaces," S. Kerisit, K. M. Rosso, M. Dupuis, and M. Valiev J. Phys. Chem. C 2007, 111, 11363

"Computational Characterization and Modeling of Buckeyball Tweezers: Density Functional Study of Concave-Convex π...π Interaction,"  Y. Zhao and D. G. Truhlar, Phys. Chem. Chem. Phys. in press.

 "Benchmark data for interactions in zeolite model complexes and their use for assessment and validation of electronic structure methods," Y. Zhao and D. G. Truhlar, J. Phys. Chem. C. in press.

"How Well Can New-Generation Density Functionals Describe the Energetics of Bond Dissociation Reactions Producing Radicals?" Y. Zhao and D. G. Truhlar, J. Phys. Chem. A. 2008,112, 1095 .

 "A Prototype for Graphene Material Simulation: Structures and Interaction Potential of Coronene Dimers," Y. Zhao and D. G. Truhlar, J. Phys. Chem. C, 2008, 112, 4061.

"Density Functionals with Broad Applicability in Chemistry," Y. Zhao and D. G. Truhlar, Acc. Chem. Res., 2008, 41, 157.

Research Highlights:

2007 Summary

2007 Report

2007 Highlights

PNNL contacts:

Dr. Erich R. Vorpagel
Technical Group Leader
Manager Computational Grand-Challenge and Pilot Projects
MSCF Visualization and User Services Group
Environmental Molecular Sciences Laboratory
Pacific Northwest National Laboratory
P. O. Box 999, MS: K8-91
3335 Q Ave. Phone: 509-376-0751
Richland, WA 99352 FAX: 509-376-0420
Email: erich.vorpagel@pnl.gov
Web: http://mscf.emsl.pnl.gov

Tina Foley
Visualization and User Services - Molecular Science Computing Facility
William R. Wiley Environmental Molecular Sciences Laboratory
Pacific Northwest National Laboratory
PO Box 999, MS K8-91
Richland, WA 99352
Phone: 509-376-2767 Email: tina.foley@pnl.gov
Fax: 509-376-0420 Web: http://mscf.emsl.pnl.gov

Dr. Jun Li
Senior Research Scientist II
3335 Q Avenue, K8-91
Richland, WA 99352
USA
E-mail: Jun.Li@pnl.gov
Phone: (509) 376-4354
Fax: (509) 376-0420
Web: http://emslbios.pnl.gov/id/li_j


Links:



Feedback:  Yan Zhao, Project Manager
This document last modifiedWednesday, 05-Mar-2008 16:38:06 CST