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(gc3566)Direct Dynamics Simulations: From Molecules to Macromolecules and Condensed Phases


EMSL Project ID
3566

Abstract

Time dependent atomic-level simulations will be used to study a series of chemical reactions to address a number of important environmental problems and research needs. The traditional approach for performing such atomic-level simulations is to represent the system's potential energy function V(q) by either an empirical analytic function, with adjustable parameters, or as an analytic function fit in total or in part to ab initio potential energy points. These approaches have limitations and often contain ambiguities.

With the increased speed of computers and more powerful computer algorithms, it has become possible to use direct dynamics simulations to avoid problems associated with analytic functions. This approach is the focus of this proposal. In its classical implementation, the equations of motion are integrated 'on the fly' with the potential energy V(q) and derivatives ∂V/∂qi obtained directly from an electronic structure calculation. The potential energy function for a many-atom system may be represented by a quantum mechanical/molecular mechanical (QM/MM) model, in which an electronic structure theory is used to represent the potential for part of the system and empirical potential energy terms are used for the remainder.

We propose to further develop and apply direct dynamics approaches. Algorithms for propagating the atomic-level dynamics (e.g., the VENUS classical dynamics computer program) will be interfaced with electronic structure codes (e.g., NWChem and GAMESS) so that efficient direct dynamics simulations may be performed in a high-performance multi-processor computing environment. QM/MM methods, which are applicable to large molecular systems, will continue to be integrated into these software packages so that they are available for the direct dynamics. NWChem and GAMESS are unique among electronic structure codes in that they have been designed to take optimal advantage of parallel computers. In addition, direct dynamics methods will be extended to the treatment of quantum dynamics (using semiclassical methods), and electronically excited states and nonadiabatic effects.

Project Details

Project type
Capability Research
Start Date
2003-10-01
End Date
2006-10-08
Status
Closed

Team

Principal Investigator

William Hase
Institution
Texas Tech University

Team Members

Christine Aikens
Institution
Northwestern University

Asif Rahaman
Institution
University of Iowa

Lourderaj Upakarasamy
Institution
Texas Tech University

Hui Li
Institution
Ames Laboratory

Mingying Xue
Institution
Texas Tech University

Takeshi Nagata
Institution
Ames Laboratory

Bojana Ginovska
Institution
Pacific Northwest National Laboratory

Edgar Arcia
Institution
Tri-City Prep

Jeffrey Paci
Institution
Northwestern University

Lasse Jensen
Institution
Pennsylvania State University

Lipeng Sun
Institution
Northwestern University

Jonathan Mullin
Institution
Ames Laboratory

Shengli Zou
Institution
Northwestern University

Kenley Barrett
Institution
Northwestern University

Daniel Kemp
Institution
Ames Laboratory

Grigoriy Vayner
Institution
Texas Tech University

Ayako Furuhama
Institution
Pacific Northwest National Laboratory

Tzvetelin Iordanov
Institution
Georgia Southwestern State University

Steven Mielke
Institution
University of Minnesota

Kihyung Song
Institution
Korea National University of Education

Daniel Danailov
Institution
Texas Tech University

Daniel Chang
Institution
Pacific Northwest National Laboratory

Theresa Windus
Institution
Iowa State University

Yuri Alexeev
Institution
Universite Louis Pasteur Strasbourg

George Schatz
Institution
Northwestern University

Sharon Hammes-Schiffer
Institution
Pennsylvania State University

Cheol Choi
Institution
Kyungpook National University

Michel Dupuis
Institution
University at Albany, State University of New York

Joern Siepmann
Institution
University of Minnesota

David Dixon
Institution
University of Alabama

Arora Pratima
Institution
Wayne State University

Heinrich Selzle
Institution
Institut fur Physikalische and Theoretische Chemie of the Technische Universitat Muechen

Mark Gordon
Institution
Iowa State University

Related Publications

Furuhama A, M Dupuis, and K Hirao. 2006. "Reactions associated with ionization in water: a direct ab initio dynamics study of ionization in (H2O)17." Journal of Chemical Physics 124:164310. doi:10.1063/1.2194904
Jensen L, and GC Schatz. 2006. "Resonance Raman Scattering of Rhodamine 6G as Calculated Using Time-Dependent Density Functional Theory." Journal of Physical Chemistry A 110:5973-5977. doi:10.1021/jp0610867
Jensen L, J Autschbach, and GC Schatz. 2005. "Finite Lifetime Effects on the Polarizability Within Time-dependent Density-functional Theory." Journal of Chemical Physics 122:224115 1-11. doi:10.1063/1.1929740
Lee H, K An, Y Kim, and CH Choi. 2005. "Surface SN2 Reaction by H?O on Chlorinated Si(100)-2 x 1 Surface." Journal of Physical Chemistry B 109:10909-10914.
Lopez JG, G Vayner, U Lourderaj, SV Addepalli, S Kato, WA De Jong, TL Windus, and WL Hase. 2007. "Direct Dynamics Trajectory Study of F− + CH3OOH Reactive Collisions Reveals a Major Non-IRC Reaction Path." Journal of the American Chemical Society 129(32):9976-9985.
Lourderaj U, K Song, TL Windus, Y Zhuang, and WL Hase. 2007. "Direct Dynamics Simulations using Hessian-based Predictor-corrector Integration Algorithms." Journal of Chemical Physics 126:044105 1-11. doi:10.1063/1.2437214
Paci JT, T Belytschko, and GC Schatz. 2006. "Mechanical Properties of Ultrananocrystalline Diamond Prepared in a Nitrogen-Rich Plasma: A Theoretical Study." Physical Review. B, Condensed Matter 74:184112/1-9.
Tasic U, Y Alexeev, G Vayner, T Crawford, TL Windus, and WL Hase. 2006. "Ab Initio and Analytic Intermolecular Potentials for Ar–CH3OH." Physical Chemistry Chemical Physics. PCCP 8(40):4678-4684. doi:10.1039/b609743j
Vayner G, SV Addepalli, K Song, and WL Hase. 2006. "Post-transition State Dynamics for Propene Ozonolysis: Intramolecular and Unimolecular Dynamics of Molozonide." Journal of Chemical Physics 125:014317 1-16. doi:10.1063/1.2206785
Vayner G, Y Alexeev, J Wang, TL Windus, and WL Hase. 2006. " Ab Initio and Analytic Intermolecular Potentials for Ar-CF₄." Journal of Physical Chemistry A 110(9):3174-3178. doi:10.1021/jp054592p
Wang J, and WL Hase. 2005. "Intermolecular Potential To Represent Collisions of Protonated Peptide Ions with Fluorinated Alkane Surfaces." Journal of Physical Chemistry B 109(17):8320-8324.