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(gc3565)Reliable Electronic Structure Prediction of Molecular Properties


EMSL Project ID
3565

Abstract

The area of environmental chemical science is dominated by issues of scaling in space and time. The goal of environmental science is to understand the current state of the environment based on our knowledge of the past and to use this information to be able to predict the future state. For example, given current practices for manufacturing, what will be their long-term environmental impact? Given potential environmental remediation strategies, what will these lead to? One does not want to use a remediation strategy that will have unforeseen consequences and introduce new environmental issues. No one wants to repeat the mistakes of the past, for example, the widespread release of chlorofluorocarbons (CFC?s) into the atmosphere. Although, we are interested in the results at large spatial and temporal scales, detailed insight into behavior at the molecular scale is key to understanding (1) how humans have impacted the environment, (2) how to remediate anthropogenic impacts on the environment, and (3) how to minimize future anthropogenic impacts. Of particular interest are reliable, accurate values for thermodynamic and kinetic properties of molecules that can be used in molecular design, in process design and in remediation models. Computational chemistry is a key technology for addressing the complex environmental cleanup problems facing the Department of Energy?s nuclear production sites, as well as the problems associated with other polluted sites in the United States and the prevention of further pollution. High accuracy from a simulation is important. A factor of 2 to 4 in catalyst efficiency may determine whether a chemical process is economically feasible or not and a factor of 4 in a rate constant at room temperature (25oC) corresponds to a change in the activation energy on the order of just less than 1 kcal/mol. Given a 50:50 starting mixture of two components, a change in the free energy, G, of less than 1.5 kcal/mol leads to a change in the equilibrium constant by a factor of 10, leading to a 90:10 mixture at 25oC. The requirement for such accuracy means that we must be able to predict thermodynamic quantities such as bond dissociation energies (De or D00) and heats of formation (Hf) to better than 1 kcal/mol and activation energies to within a few tenths of a kcal/mol ? a daunting computational task. Our goal is to develop and test the procedures needed to provide accurate predictions of such molecular properties. We will then apply such tools to the prediction of a variety of molecular properties and systems including: transition metal compounds, host/guest complexes for the design of separation systems, combustion related compounds including the propargyl potential energy surface, anionic states of solvated nucleic acid bases and amino acids related to low dose biochemistry, development of flexible, polarizable interaction potentials for water-water and ion-water interactions, high cccuracy thermochemistry for molecules including fluorinated compounds and biological molecules relevant to phosphorylation processes, novel gas phase anion including clusters, inorganic complexes, and the effects of solvation, and theoretical studies of the mechanisms of hydrolytic reactions.

Project Details

Project type
Capability Research
Start Date
2006-02-03
End Date
2006-10-25
Status
Closed

Team

Principal Investigator

David Dixon
Institution
University of Alabama

Team Members

Minh Nguyen
Institution
University of Alabama

Myrna Hernandez Matus
Institution
University of Alabama

Nathan Stibrich
Institution
University of Georgia

Lucas Speakman
Institution
University of Georgia

Maria Lind
Institution
University of Georgia

Si-dian Li
Institution
Xinzhou Teachers University

Aleksandr Oliferenko
Institution
Pacific Northwest National Laboratory

Lawrence Haselmaier
Institution
University of Alabama

Nicholas Marshall
Institution
University of Georgia

Justin Ingels
Institution
University of Georgia

William Shaffer
Institution
University of Alabama

Daniel Grant
Institution
University of Alabama

Veronika Kasalova
Institution
University of Georgia

Johnathan Keenum
Institution
University of Alabama

Vyacheslav Bryantsev
Institution
California Institute of Technology

Han Lee
Institution
Washington State University Tri-Cities

Amanda Holland
Institution
University of Alabama

Ryan House
Institution
University of Alabama

Sarah Dickinson
Institution
University of Alabama

Xin Huang
Institution
Washington State University Tri-Cities

Thomas Kelly
Institution
University of Alabama

Raluca Craciun
Institution
University of Alabama

Bing Dai
Institution
Pacific Northwest National Laboratory

Shenggang Li
Institution
University of Alabama

Charnita Peoples
Institution
University of Alabama

Lesley Magee
Institution
University of Alabama

Keith Gutowski
Institution
University of Notre Dame

Justin Turney
Institution
University of Georgia

Steven Wheeler
Institution
University of Georgia

Kevin Kennedy
Institution
US Army Research Development and Engineering Command

Suyun Wang
Institution
University of Georgia

Se Li
Institution
University of Georgia

Ge Yan
Institution
University of Georgia

Lisa Pollack
Institution
Environmental Molecular Sciences Laboratory

Jason Spruell
Institution
University of Alabama

Claire Chisolm
Institution
University of Alabama

Georgios Fanourgakis
Institution
Pacific Northwest National Laboratory

Rafal Bachorz
Institution
Universitaet Karlsruhe

Maciej Haranczyk
Institution
Lawrence Berkeley National Laboratory

Alexander Boldyrev
Institution
Utah State University

Theresa Windus
Institution
Iowa State University

Yuri Alexeev
Institution
Universite Louis Pasteur Strasbourg

Anthony Arduengo
Institution
University of Alabama

Kai-Chung Lau
Institution
City University of Hong Kong

Cheuk-Yiu Ng
Institution
University of California, Davis

Reijo Suontamo
Institution
University of Jyvaskyla

Maciej Gutowski
Institution
Heriot-Watt University

Michael Schuurman
Institution
University of Georgia

Nathan DeYonker
Institution
University of North Texas

Chang-guo Zhan
Institution
University of Kentucky

Benjamin Hay
Institution
Oak Ridge National Laboratory

Kiran Boggavarapu
Institution
Virginia Commonwealth University

David Feller
Institution
Pacific Northwest National Laboratory

Sotiris Xantheas
Institution
Pacific Northwest National Laboratory

Kirk Peterson
Institution
Washington State University

Wibe De Jong
Institution
Lawrence Berkeley National Laboratory

Tom Waters
Institution
Washington State University Tri-Cities

Henry Schaefer
Institution
University of Georgia

Shuqiang Niu
Institution
Texas A&M University

Lai-Sheng Wang
Institution
Brown University

Jun Li
Institution
Tsinghua University

Gary Schrobilgen
Institution
McMaster University

Peter Armentrout
Institution
University of Utah

Janusz Rak
Institution
University of Gdansk

Toshiko Ichiye
Institution
Georgetown University

Related Publications

Bachorz RA, J Rak, and MS Gutowski. 2005. "Stabilization of very rare tautomers of uracil by an excess electron." Physical Chemistry Chemical Physics. PCCP 7(10):2116-2125.
Bachorz RA, WM Klopper, and MS Gutowski. 2007. "Coupled-Cluster and Explicitly Correlated Perturbation-Theory Calculations of the Uracil Anion ." Chinese Journal of Chemical Physics 126(8):Art No. 085101.
Berryman OB, V Bryantsev, DP Stay, DW Johnson, and BP Hay. 2007. "Structural Criteria for the Design of Anion Receptors: The Interaction of Halides with Electron-Deficient Arenes." Journal of the American Chemical Society 129(1):48-58.
Bryantsev V, and BP Hay. 2005. "Influence of substituents on the strength of aryl C-H anion hydrogen bonds ." Organic Letters 7(22):5031-5034.
Bryantsev V, and BP Hay. 2006. "Conformational Preferences and Internal Rotation in Alkyl- and Phenyl-Substituted Thiourea Derivatives." Journal of Physical Chemistry A 110(14):4678-4688.
Bulusu S, S Yoo, E Apra, SS Xantheas, and X Zeng. 2006. "Lowest-energy structures of water clusters (H2O)(11) and (H2O)(13)." Journal of Physical Chemistry A 110(42):11781-11784.
Cui L, X Huang, L Wang, DY Zubarev, AI Boldyrev, J Li, and LS Wang. 2006. "Sn₁₂²⁻: Stannaspherene." Journal of the American Chemical Society 128(26):8390-8391. doi:10.1021/ja062052f
Custelcean R, BA Moyer, V Bryantsev, and BP Hay. 2005. "Anion Coordination in Metal-Organic Frameworks Functionalized with Urea Hydrogen-Bonding Groups." Crystal Growth & Design 6(2):555-563.
DeYonker NJ, Li S, Yamaguchi Y, Schaefer HF, Crawford TD, King RA, and Peterson KA,"Application of equation-of-motion coupled-cluster methods to low-lying singlet and triplet electronic states of HBO and BOH" JOURNAL OF CHEMICAL PHYSICS 122 (23): Art. No. 234316 JUN 15 2005
DeYonker NJ, Yamaguchi Y, Allen WD, Pak C, Schaefer HF and Peterson KA. "Low-lying electronic states of FeNC and FeCN: A theoretical journey into isomerization and quartet/sextet competition" JOURNAL OF CHEMICAL PHYSICS 120 (10): 4726-4741 MAR 8 2004
Dixon DA, JS Francisco, and Y Alexeev. 2006. "Thermochemical Properties of HxNO Molecules and Ions from ab Initio Electronic Structure Theory." Journal of Physical Chemistry A 110(1):185-191. doi:10.1021/jp054642q
Fanourgakis GS, and SS Xantheas. 2006. "The bend angle of water in ice Ih and liquid water: The significance of implementing the nonlinear monomer Dipole Moment Surface in classical interaction potentials." Journal of Chemical Physics 124(17):Art. no. 174504.
Fanourgakis GS, and SS Xantheas. 2006. "The flexible, polarizable, thole-type interaction potential for water (TTM2-F) Revisited." Journal of Physical Chemistry A 110(11):4100-4106. doi:10.1021/jp056477k
Fanourgakis GS, GK Schenter, and SS Xantheas. 2006. "A quantitative account of quantum effects in liquid water." Journal of Chemical Physics 125(14 ):Art. No. 141102.
Fanourgakis GS, V Tipparaju, J Nieplocha, and SS Xantheas. 2006. "An efficient parallelization scheme for molecular dynamics simulations with many-body, flexible, polarizable empirical potentials: Application to water." Theoretical Chemistry Accounts 117(1):73-84.
Gutowski KE, RD Rogers, and DA Dixon. 2006. "Accurate Thermochemical Properties for Energetic Materials Applications. I. Heats of Formation of Nitrogen-Containing Heterocycles and Energetic Precursor Molecules from Electronic Structure Theory." Journal of Physical Chemistry A 110(42):11890-11897. doi:10.1021/jp0643698
Gutowski KE, VA Cocalia, ST Griffin, NJ Bridges, DA Dixon, and RD Rogers. 2007. "Interactions of 1-Methylimidazole with UO₂(CH₃CO₂)₂ and UO₂(NO₃)₂: Structural, Spectroscopic, and Theoretical Evidence for Imidazole Binding to the Uranyl Ion." Journal of the American Chemical Society 129(3):526-536. doi:10.1021/ja064592i
Haranczyk M, and MS Gutowski. 2005. "Finding Adiabatically Bound Anions of Guanine through a Combinatorial Computational Approach." Angewandte Chemie International Edition 44(40):6585-6588.
Haranczyk M, and MS Gutowski. 2007. "Quantum Mechanical Energy-based Screening of Combinatorially Generated Library of Tautomers. TauTGen: A Tautomer Generator Program." Journal of Chemical Information and Modeling 47(2):686-694.
Haranczyk M, MS Gutowski, X Li, and KH Bowen. 2007. "Bound anionic states of adenine." Proceedings of the National Academy of Sciences of the United States of America 104(12):4804-4807. doi:10.1073/pnas.0609982104
Hay BP, AA Oliferenko, J Uddin, C Zhang, and TK Firman. 2005. "Search for Improved Host Architectures: Application of de Novo Structure-Based Design and High-Throughput Screening Methods to Identify Optimal Building Blocks for Multidentate Ethers.." Journal of the American Chemical Society 127(48):17043-17053.
Kasalova V, Allen WD, Schaefer HF, Czinki E, and Csaszar AG, "Molecular structures of the two most stable conformers of free glycine" JOURNAL OF COMPUTATIONAL CHEMISTRY 28 (8): 1373-1383 JUN 2007
Kim S, Wheeler SE, DeYonker NJ and Henry F. Schaefer III "The extremely flat torsional potential energy surface of oxalyl chloride" JOURNAL OF CHEMICAL PHYSICS 122 (23): Art. No. 234313 JUN 15 2005
Li J, SM Kathmann, GK Schenter, and MS Gutowski. 2007. "Isomers and Conformers of H(NH?BH?)(n)H Oligomers: Understanding the Geometries and Electronic Structure of Boron-Nitrogen-Hydrogen Compounds as Potential Hydrogen Storage Materials." Journal of Physical Chemistry C 111(8):3294-3299.
Ling S, W Yu, Z Huang, Z Lin, M Haranczyk, and MS Gutowski. 2006. "Gaseous Arginine Conformers and Their Unique Intramolecular Interactions." Journal of Physical Chemistry A 110(44):12282-12291.
Li Z, MH Matus, HA Velazquez, DA Dixon, and CJ Cassady. 2007. "Gas-phase Acidities of Aspartic Acid, Glutamic Acid, and their Amino Acid Amides." International Journal of Mass Spectrometry 265(2-3):213-223. doi:10.1016/j.ijms.2007.02.009
Matus MH, AJ Arduengo, III, and DA Dixon. 2006. "The Heats of Formation of Diazene, Hydrazine, N₂H₃ ⁺, N₂H₅ +, N₂H, and N₂H₃ and the Methyl Derivatives CH₃NNH, CH₃NNCH₃, and CH₃HNNHCH₃." Journal of Physical Chemistry A 110(33):10116-10121. doi:10.1021/jp061854u
Matus MH, MT Nguyen, and DA Dixon. 2007. "Theoretical Prediction of the Heats of Formation of C₂H₅O● Radicals Derived from Ethanol and of the Kinetics of β-C-C Scission in the Ethoxy Radical." Journal of Physical Chemistry A 111(1):113-126. doi:10.1021/jp064086f
Mazurkiewicz K, M Haranczyk, MS Gutowski, and J Rak. 2007. "Can an Excess Electron Localise on a Purine Moiety in the Adenine-thymine Watson-Crick Base Pair? A Computational Study." International Journal of Quantum Chemistry 107(12):2224-2232.
Mazurkiewicz K, M Haranczyk, MS Gutowski, J Rak, D Radisic, S Eustis, D Wang, and KH Bowen. 2007. "Valence anions in complexes of adenine and 9-methyladenine with formic acid - stabilization by intermolecular proton transfer." Journal of the American Chemical Society 129(5):1216-1224.
Mazurkiewicz K, R Bachorz, MS Gutowski, and J Rak. 2006. "On the unusual stability of valence anions of thymine based on very rare tautomers. A computational study." Journal of Physical Chemistry B 110(48):24696-24707.
M. Harańczyk, J. Holliday, P. Willett, M. Gutowski. 2008. Structure and Singly Occupied Molecular Orbital Analysis of Anionic Tautomers of Guanine, J. Comput. Chem., 29(8): 1277- 1291.
M. Haranczyk, M. Gutowski. 2008. Visualization of molecular orbitals and the related electron densities, J. Chem. Theory Comput., 4(5): 689-693.
M. Haranczyk, M. Gutowski, Effect of Excess Electron and One Water Molecule on Relative Stability of the Canonical and Zwitterionic Tautomers of Glycine, J. Chem. Phys. 128, 125101 (2008);
Niu S, and T Ichiye. 2007. "Probing the Structural Effects on the Intrinsic Electronic and Redox Poperties of [2Fe-2S](+) Custers, a Broken-Symmetry Density Functional Theory Study ." Theoretical Chemistry Accounts 117(2):275-281.
Niu S, and T Ichiye.  2009.  "Insight into Environmental Effects on Bonding and Redox Properties of [4Fe-4S] Clusters in Proteins."  Journal of the American Chemical Society 131(16):5724-5725.  doi:10.1021/ja900406j
Niu S, and T Ichiye. 2009. "Probing Ligand Effects on the Redox Energies of [4Fe-4S] Clusters Using Broken-Symmetry Density Functional Theory." Journal of Physical Chemistry A 113(19):5671–5676. doi:10.1021/jp809446q
Niu S, and T Ichiye. 2011. "Density Functional Theory Calculations of Redox Properties of Iron–Sulphur Protein Analogues." Molecular Simulation 37(7):572-590. doi:10.1080/08927022.2011.582111
Shuqiang Niu and Toshiko, IchiyeCleavage of [4Fe4S]-Type Clusters: Breaking the Symmetry, J. Phys. Chem. A, 2009, 113 (19), pp 5710-5717
Shuqiang Niu, Jeffrey A. Nichols and Toshiko Ichiye, Optimization of Spin-Unrestricted Density Functional Theory for Redox Properties of Rubredoxin Redox Site Analogues, J. Chem. Theory Comput., 2009, 5 (5), pp 1361-1368
Turney JM, Sari L, Yamaguchi Y, and Schaefer HF., "The singlet electronic ground state isomers of dialuminum monoxide: AlOAl, AlAlO, and the transition state connecting them" JOURNAL OF CHEMICAL PHYSICS 122 (9): Art. No. 094304 MAR 1 2005
Wang SY, Paul A, DeYonker NJ, Yamaguchi Y, and Schaefer HF. "The ground and two lowest-lying singlet excited electronic states of copper hydroxide (CuOH)" JOURNAL OF CHEMICAL PHYSICS 123 (1): Art. No. 014313 JUL 1 2005
Zhai HJ, LS Wang, DY Zubarev, and AI Boldyrev. 2006. "Gold Apes Hydrogen. The Structure and Bonding in the Planar B7Au2- and B7Au2 Clusters." Journal of Physical Chemistry A 110(5):1689-1693.