Reliable Electronic Structure Prediction of Molecular Properties
EMSL Project ID
20901
Abstract
The field of environmental 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 make forward predictions. 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? The use of remediation strategies should be based on a solid understanding of their long-term impact on the environment in order to avoid unforeseen consequences such as the past widespread release of chlorofluorocarbons (CFCs) into the atmosphere. Although the interest is clearly in the results at large spatial and temporal scales, detailed insight into behavior at the molecular scale is key to the understanding of (i) how humans have impacted the environment, (ii) how to remediate anthropogenic impacts on the environment, and (iii) how to minimize future anthropogenic impacts. Of particular interest are reliable, accurate values for thermodynamic and kinetic properties of molecular systems that can be used in molecular design, in process design, for example, studies of combustion, and in remediation models. Computational chemistry is a key technology for addressing the complex environmental cleanup problems facing the Department of Energys nuclear production sites, as well as the problems associated with other polluted sites in the United States and the prevention of further pollution. The issue of accuracy as the result of a simulation is very important. For instance, 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, ΔG, 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 (ΔHf) of small molecules and molecular clusters 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 then apply such tools to the prediction of a variety of molecular properties and systems including: transition metal compounds, combustion related compounds including the propargyl potential energy surface and alkane and alkoxy radical bond energies, main group chemistry including highly reactive compounds with high oxidation states and mono-, di- and tri-phosphate compounds, host/guest complexes for the design of separation systems such as clathrate hydrates and metal ion receptors, and iron-sulfur proteins.
Project Details
Project type
Capability Research
Start Date
2006-10-01
End Date
2009-09-30
Status
Closed
Released Data Link
Team
Principal Investigator
Team Members
Related Publications
A Whiteside, C Sloan, SS Xantheas, M Gutowski. 2010. ?Electronegativity Calculations for ?Ionic? Elemental Boron?. Euroboron 5. August 29 - September 2 2011. Heriot-Watt University, Edinburgh, United Kingdom.
A Whiteside, M Gutowski, SS Xantheas, S Eustis, D Radisic, KH Bowen. 2009. ?Computational Group Electronegativity (and some electron-triggered proton transfer)?. ScotCHEM Computational Chemistry Symposium 2009. May 13 2009. Heriot-Watt University, Edinburgh, United Kingdom.
A Whiteside, SS Xantheas, M Gutowski. 2011. "Radical Ammonium: from Proton Transfer to Electronegativity". Internal presentation. January 19 2011. Heriot-Watt University, Edinburgh, United Kingdom.
A Whiteside, SS Xantheas, M Gutowski. 2011. "Radical Ammonium: from Proton Transfer to Electronegativity". ScotCHEM Computational Chemistry Symposium 2011. June 7 2011. The University of Edinburgh, Edinburgh, United Kingdom.
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.
Bachorz RA, WM Klopper, MS Gutowski, X Li, and KH Bowen. 2008. "Photoelectron Spectrum of Valence Anions of Uracil and First-principles Calculations of Excess Electron Binding Energies." Journal of Chemical Physics 129:054309. doi:10.1063/1.2965128
Blake TA, ED Glendening, RL Sams, SW Sharpe, and SS Xantheas. 2007. "High Resolution Infrared Spectroscopy in the 1200 to 1300 cm-1 Region and Accurate Theoretical Estimates for the Structure and Ring Puckering Barrier of Perfluorocyclobutane." Journal of Physical Chemistry A 111(44):11328-11341.
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.
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.
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, and MS Gutowski. 2008. "Visualization of Molecular Orbitals and the Related Electron Densities." Journal of Chemical Theory and Computation 4(5):689-693. doi:10.1021/ct800043a
Haranczyk M, MS Gutowski, X Li, and KH Bowen. 2007. "Adiabatically Bound Valence Anions of Guanine." Journal of Physical Chemistry B 111(51):14073-14076. doi:10.1021/jp077439z
Kathmann SM, GK Schenter, and SS Xantheas. 2008. "On the Determination of Monomer Dissociation Energies of Small Water Clusters from Photoionization Experiments." Journal of Physical Chemistry A 112(9):1851-1853. doi:10.1021/jp710624r
Kirov MV, GS Fanourgakis, and SS Xantheas. 2008. "Identifying the Most Stable Networks in Polyhedral Water Clusters." Chemical Physics Letters 461(4-6):180-188. doi:10.1016/j.cplett.2008.04.079
Laskin J, JH Futrell, and IK Chu. 2007. "Is Dissociation of Peptide Radical Cations an Ergodic Process?" Journal of the American Chemical Society 129(31):9598-9599.
Laskin J, Z Yang, and IK Chu. 2008. "Energetics and Dynamics of Electron Transfer and Proton Transfer in Dissociation of Metal III (salen)-Peptide Complexes in the Gas Phase." Journal of the American Chemical Society 130(10):3218-3230. doi:10.1021/ja077690s
Laskin J, Z. Yang, C. M. D. Ng, I. K. Chu ” Fragmentation of a-Radical Cations of Arginine-Containing Peptides”, J. Am. Soc. Mass Spectrom., 21, 511-521 (2010).
Lei-Ming Wang,Rhitankar Pal, Wei Huang, Xiao Cheng Zeng, and
Lai-Sheng Wang. 2010. "Observation of earlier two-to-three dimensional structural transition
in gold cluster anions by isoelectronic substitution: MAun ? (n=8–11; M=Ag,Cu)." THE JOURNAL OF CHEMICAL PHYSICS 132, 114306. doi:10.1063/1.3356046
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.
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, M Haranczyk, P Storoniak, MS Gutowski, J Rak, D Radisic, S Eustis, D Wang, and KH Bowen. 2007. "Intermolecular proton transfer induced by excess electron attachment to adenine(formic acid)n (n = 2, 3) hydrogen-bonded complexes." Chemical Physics 342(1-3):215-222. doi:10.1016/j.chemphys.2007.10.005
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.
Ng DC, T Song, SO Siu, CK Siu, J Laskin, and IK Chu. 2010. "Formation, isomerization, and dissociation of alpha-carbon-centered and pi-centered glycylglycyltryptophan radical cations." Journal of Physical Chemistry 114(6):2270-2280. doi:10.1021/jp908599a.
Niu S, A Derecskei-Kovacs, and MB Hall. 2007. "A Unique Coplanar Multi-center Bonding Network in Doubly Acetylide-bridged Binuclear Zirconocene Complexes: A Density Functional Theory Study." Journal of Organometallic Chemistry 692(21):4760-4767. doi:10.1016/j.jorganchem.2007.07.019
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. "Cleavage of [4Fes4S]-Type Clusters: Breaking the Symmetry." Journal of Physical Chemistry A 113(19):5710-5717. doi:10.1021/jp900402y
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
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
Siu CK, J Zhao, J Laskin, IK Chu, AC Hopkinson, and KWM Siu . 2009. "Kinetics for Tautomerizations and Dissociations of Triglycine Radical Cations." Journal of the American Society for Mass Spectrometry 20(6):996-1005.
Song T, C Lam, DC Ng, G Orlova, J Laskin, DC Fang, and IK Chu. 2009. "Experimental and Computational Studies of the Macrocyclic Effect of an Auxiliary Ligand on Electron and Proton Transfers Within Ternary Copper(II)–Histidine Complexes ." Journal of the American Society for Mass Spectrometry 20(6):972-984.
Tan ML, AR Bizzarri, Y Xiao, S Cannistraro, T Ichiye, C Manzoni, G Cerullo, MW Adams, FE Jenney, and SP Cramer. 2007. "Observation of Terahertz Vibrations in Pyrococcus Furiosus Rubredoxin Via Impulsive Coherent Vibrational Spectroscopy and Nuclear Resonance Vibrational Spectroscopy – Interpretation by Molecular Mechanics." Journal of Inorganic Biochemistry 101(3):375-384. doi:10.1016/j.jinorgbio.2006.09.031
Wei Huang, Rhitankar Pal, Lei-Ming Wang, Xiao Cheng Zeng, and
Lai-Sheng Wang. 2010. " Isomer identification and resolution in small gold clusters." THE JOURNAL OF CHEMICAL PHYSICS 132, 054305. doi:10.1063/1.3299292
Whiteside A. 2012. Proton Transfer, Electron Binding and Electronegativity in Ammonium-Containing Systems . Pacific Northwest National Laboratory, Richland, WA.
Whiteside, A., Xantheas, S. S. and Gutowski, M. (2011), Is Electronegativity a Useful Descriptor for the Pseudo-Alkali Metal NH4?. Chemistry - A European Journal, 17: 13197?13205. doi: 10.1002/chem.201101949
Xantheas SS. 2011. "Low-Lying Energy Isomers and Global Minima of Aqueous Nanoclusters: Structures and Spectroscopic Features of the Pentagonal Dodecahedron (H2O)20 and the (H3O)+(H2O)20." Canadian Journal of Chemical Engineering.
Xantheas SS, and TA Blake. 2006. "Structure, Vibrational Spectra and Ring Puckering Barrier of Cyclobutane." Journal of Physical Chemistry A 110:10487-10494.
Xiao Y, ML Tan, T Ichiye, H Wang, Y Guo, MC Smith, J Meyer, W Sturhahn, EE Alp, J Zhao, Y Yoda, and SP Cramer. 2008. "Dynamics of Rhodobacter Capsulatus [2FE-2S] Ferredoxin VI and Aquifex Aeolicus Ferredoxin 5 Via Nuclear Resonance Vibrational Spectroscopy (NRVS) and Resonance Raman Spectroscopy." Biochemistry 47(25):6612-6627. doi:10.1021/bi701433m
Yang Z, C Lam, IK Chu, and J Laskin. 2008. "The Effect of the Secondary Structure on Dissociation of Peptide Radical Cations: Fragmentation of Angiotensin III and Its Analogues." Journal of Physical Chemistry B 112(39):12468-12478. doi:10.1021/jp805226x
Yoo S, MV Kirov, and SS Xantheas. 2009. "Low-energy networks of the T-cage (H2O)(24) cluster and their use in constructing periodic unit cells of the structure I (sl) hydrate lattice." Journal of the American Chemical Society 131(22):7564-7566.
Yoo S, XC Zeng, and SS Xantheas. 2009. "On the phase diagram of water with density functional theory potentials: the melting temperature of Ice I-h with the Perdew-Burke-Ernzerhof and Becke-Lee-Yang-Parr functionals." Journal of Chemical Physics 130(22):Art. No. 211102.
Yu W, L Liang, Z Lin, S Ling, M Haranczyk, and MS Gutowski. 2009. "Comparison of Some Representative Density Functional Theory and Wave Function Theory Methods for the Studies of Amino Acids." Journal of Computational Chemistry 30(4):589-6006. doi:10.1002/jcc.21091
Zhai H and LS Wang. 2007. "Probing the Electronic Structure and Band Gap Evolution of Titanium Oxide Clusters (TiO2)n- (n = 1-10) using Photoelectron Spectroscopy." Journal of the American Chemical Society 129(10):3022-3026.