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Publication for the ONR grant - "Integrated Tools for Computational Chemical Dynamics"

2005 publications

 "Improved Density Functionals for Water," E. E. Dahlke and D. G. Truhlar, J. Phys. Chem. A 109, 15677-15683 (2005).

"Exchange-Correlation Functional with Broad Accuracy for Metallic and Nonmetallic Compounds, Kinetics, and Noncovalent Interactions," Y. Zhao, N. E. Schultz, and D. G. Truhlar, J. Chem. Phys. 123, 161103/1-4 (2005). (communication)

"Density Functional for Inorganometallic and Organometallic Chemistry," N. E. Schultz, Y. Zhao, and D. G. Truhlar, J. Phys. Chem. A 109, 11127-11143 (2005).

2006 publications

" Design of Density Functionals by Combining the Method of Constraint Satisfaction with Parametrization for Thermochemistry, Thermochemical Kinetics, and Noncovalent Interactions," Y. Zhao, N. E. Schultz, and D. G. Truhlar, J. Chem. Theory Comput. 2, 364-382 (2006)

"Comparative DFT Study of van der Waals Complexes: Rare-Gas Dimers, Alkaline-Earth Dimers, Zinc Dimer, and Zinc-Rare-Gas Dimers," Y. Zhao and D. G. Truhlar, J. Phys. Chem. A. 110, 5121-5129 (2006)

"Comparative Assessment of DFT Methods for 3d Transition Metal Chemistry," Y. Zhao and D. G. Truhlar, J. Chem. Phys. 124, 224105/1-6 (2006).

"Assessment of Model Chemistries for Noncovalent Interactions," Y. Zhao and D. G. Truhlar, J. Chem. Theory Comput. 2, 1009-1018 (2006).

"Predicting Aqueous Free Energies of Solvation as Functions of Temperature," A. C. Chamberlin, C. J. Cramer, and D. G. Truhlar, J. Phys. Chem. B, 110, 5665 (2006).

"Adding Explicit Solvent Molecules to Continuum Solvent Calculations for the Calculation of Aqueous Acid Dissociation Constants," C. P. Kelly, C. J. Cramer, D. G. Truhlar, J. Phys. Chem. A 110, 2493-2499 (2006).

"Aqueous Solvation Free Energies of Ions and Ion-Water Clusters Based on An Accurate Value for the Absolute Aqueous Solvation Free Energy of the Proton," C. P. Kelly, C. J. Cramer, and D. G. Truhlar, J. Phys. Chem. B 110, 16066-16081 (2006).

"Assessment of Density Functionals for π Systems: Energy Differences between Cumulenes and Poly-ynes, Proton Affinities, Bond Length Alternation, and Torsional Potentials of Conjugated Polyenes, and Proton Affinities of Conjugated Schiff Bases ," Y. Zhao and D. G. Truhlar, J. Phys. Chem. A 110, 10478-10486 (2006).

"Multi-Configuration Molecular Mechanics Based on Combined Quantum Mechanical and Molecular Mechanical Calculations," H. Lin, Y. Zhao, O. Tishchenko, and D. G. Truhlar, J. Chem. Theory Comput. 2, 1237-1254 (2006).

"Pd_nCO (n = 1,2): Accurate Ab Initio Bond Energies, Geometries, and Dipole Moments and the Applicability of Density Functional Theory for Fuel Cell Modeling," N. E. Schultz, B. F. Gherman, C. J. Cramer, and D. G. Truhlar , J. Phys. Chem. B 110, 24030-24036 (2006).

"A New Local Density Functional for Main Group Thermochemistry, Transition Metal Bonding, Thermochemical Kinetics, and Noncovalent Interactions," Y. Zhao, D. G. Truhlar, J. Chem. Phys. 125, 194101/1-18 (2006).

"A Density Functional Theory that Accounts for Medium-Range Correlation Energies in Organic Chemistry," Y. Zhao and D. G. Truhlar, Org. Lett. 8, 5753-5755 (2006).

"Density Functional for Spectroscopy: No Long-Range Self-Interaction Error, Good Performance for Rydberg and Charge-Transfer States, and Better Performance on Average than B3LYP for Ground States," Y. Zhao, and D. G. Truhlar, J. Phys. Chem. A 110, 13126-13130 (2006).

"SMx Continuum Models for Condensed Phases," C. J. Cramer and D. G. Truhlar, in Trends and Perspectives in Modern Computational Science, Lecture Series on Computer and Computational Sciences, Vol. 6, edited by G. Maroulis and T.E. Simos (Brill Academic, Amsterdam, 2006), pp. 112-140.

2007 publications

"Transition State Theory and Chemical Reaction Dynamics in Solution," D. G. Truhlar and J. R. Pliego Jr., in Continuum Solvation Models in Chemical Physics: Theory and Application, edited by B. Mennucci and R. Cammi (Wiley, Chichester, 2007), pp. 339-366.

"Density Functionals for Noncovalent Interaction Energies of Biological Importance," Y. Zhao and D. G. Truhlar, J. Chem. Theory Comp. 3, 289-300 (2007).

"Single-Ion Solvation Free Energies and the Normal Hydrogen Electrode Potential in Methanol, Acetonitrile, and Dimethyl Sulfoxide", C.P. Kelly, C.J. Cramer, and D.G. Truhlar, J. Phys. Chem. B 111, 408-422 (2007).

"How Well Can New-Generation Density Functional Methods Describe Protonated Epoxides Where Older Functionals Fail?" Y. Zhao and D. G. Truhlar, J. Org. Chem. 72, 295-298 (2007).

"Adaptive Partitioning in Combined Quantum Mechanical and Molecular Mechanical Calculations of Potential Energy Functions for Multiscale Simulations," A. Heyden, H. Lin, and D. G. Truhlar, J. Phys. Chem. B 111, 2231-2241 (2007).

"Computational Electrochemistry: The Aqueous Ru³⁺ | Ru²⁺ Reduction Potential," P. Jaque, A.V. Marenich, C. J. Cramer, and D. G. Truhlar,  J. Phys. Chem. C 111, 5783-5799 (2007).

"Specific Reaction Parametrization of the AM1/d Hamiltonian for Phosphoryl Transfer Reactions: H, O, and P Atoms," K. Nam, Q. Cui, J. Gao and D. M. York, J. Chem. Theory Comput. 3, 486-504, (2007).

"Attractive Noncovalent Interactions in Grubbs Second-Generation Ru Catalysts for Olefin Metathesis," Y. Zhao and D. G. Truhlar, Org. Lett. 9, 1967-1970 (2007).

"QM/MM: What Have We Learned, Where are We, and Where Do We Go from Here?" H. Lin and D. G. Truhlar, Theor. Chem. Acc. 117, 185-199 (2007).

"Size-Selective Supramolecular Chemistry in a Hydrocarbon Nanoring," Y. Zhao and D. G. Truhlar, J. Am. Chem. Soc. 129, 8440-8442 (2007).

"Self-Consistent Polarization of the Boundary in the Redistributed Charge and Dipole Scheme for Combined Quantum Mechanical and Molecular Mechanical Calculations," Y. Zhang, H. Lin, D. G. Truhlar, J. Chem. Theory Comput. 3, 1378-1398 (2007).

"Design of a Next Generation Force Field: The X-POL Potential," W. Xie and J. Gao, J. Chem. Theory Comput. 3, 1890-1900 (2007).

"Self-consistent Reaction Field Model for Aqueous and Nonaqueous Solutions Based on Accurate Polarized Partial Charges," A. V. Marenich, R. M. Olson, C. P. Kelly, C. J. Cramer, and D. G. Truhlar, J. Chem. Theory Comput. 3, 2011-2033 (2007).

"Charge Model 4 and Intramolecular Charge Polarization," R. M. Olson, A. V. Marenich, C. J. Cramer, and D. G. Truhlar, J. Chem. Theory Comput. 3, 2046-2054 (2007).

"Polarization Effects in Aqueous and Nonaqueous Solutions," A. V. Marenich, R. M. Olson, A. C. Chamberlin, C. J. Cramer, and D. G. Truhlar, J. Chem. Theory Comput. 3, 2055-2067 (2007).

2008 publications

"New QM/MM Models for Multiscale Simulation of Phosphoryl Transfer Reactions in Solution," K. Nam, J. Gao, and D. M. York, in Miltiscale Simulation Methods for Nanomaterials, edited by R. B. Ross and S. S. Mohanty (Wiley, 2008), pp. 201-218.
 "Benchmarking Approximate Density Functional Theory for s/d Excitation Energies in 3d Transition Metal Cations," N. Schultz, Y. Zhao, and D.G. Truhlar, J. Comp. Chem. 29, 185-189 (2008).

"Evaluation of the Electrostatically Embedded Many-Body Expansion and the Electrostatically Embedded Many-Body Expansion of the Correlation Energy by Applications to Low-Lying Water Hexamers," E. E. Dahlke, H. R. Leverentz, D. G. Truhlar, J. Chem. Theory Comput. 4, 33-41 (2008).

"A Conservative Algorithm for an Adaptive Change of Resolution in Mixed Atomistic/Coarse-Grained Multiscale Simulations," A. Heyden and D. G. Truhlar, J. Chem. Theory Comput. 4, 217-221 (2008).

"Zn Coordination Chemistry: Development of Benchmark Suites for Geometries, Dipole Moments and Bond Dissociation Energies and Their Use to Test and Validate Density Functionals and Molecular Orbital Theory," E. A. Amin and D. G. Truhlar, J. Chem. Theory Comput. 4, 75-85 (2008).
 "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 112, 1095-1099 (2008).
 "Role of Mg²⁺ in Hammerhead Ribozyme Catalysis from Molecular Simulation," T.-S. Lee, C. S. Lopez, G. M. Giambasu, M. Martick, W. G. Scott, and D. M. York, J. Am. Chem. Soc. 130, 3053-3064 (2008).
 "Assessment of Multicoefficient Correlation Methods, Second Order Moller-Plesset Perturbation Theory, and Density Functional Theory for H₃O⁺(H₂O)_n (n=1 - 5) and OH^-(H₂O)_n (n = 1 - 4)," E. E. Dahlke, M. A. Orthmeyer, and D. G. Truhlar, J. Phys. Chem. B 112, 2372-2381 (2008).
"Extension of a Temperature-Dependent Aqueous Solvation Model to Compounds Containing Nitrogen, Fluorine, Chlorine, Bromine, and Sulfur," A. C. Chamberlin, C. J. Cramer, and D. G. Truhlar, J. Phys. Chem. B 112, 3024-3039.

submitted and in-press publications

"The M06 Suite of Density Functionals for Main Group Thermochemistry, Kinetics, Noncovalent Interactions, Excited States, and Transition Elements: Two New Functionals and Systematic Testing of Four M06 Functionals and Twelve Other Functionals," Y. Zhao and D. G. Truhlar, Theor. Chem. Acc., available at http://dx.doi.org/10.1007/s00214-007-0310-x

"Density Functionals with Broad Applicability in Chemistry," Y. Zhao and D. G. Truhlar, Acc. Chem. Res., available at http://dx.doi.org/10.1021/ar700111a
 "Quantum Mechanical/Molecular Mechanical Simulation Study of the Mechanism of Hairpin Ribozyme Catalysis," K. Nam, J. Gao, and D. M. York, J. Am. Chem. Soc., available at http://dx.doi.org/10.1021/ja0759141

"Assessment of the Accuracy of Density Functionals for the Prediction of the Relative Energies and Geometries of Low-Lying Isomers of Water Hexamers," E. E. Dahlke, R. M. Olson, H. R. Leverentz, and D. G. Truhlar, J. Phys. Chem. A, accepted in January 2008.
"VBSM: A Solvation Model Based on Valence Bond Theory," P. Su, W. Wu, C. J. Cramer, C. P. Kelly, and D. G. Truhlar, Journal of Physical Chemistry A, submitted in December 2007.

"Foundations of Solvation Modeling: The Electrostatic Contribution to the Free Energy of Solvation," A. V. Marenich, C. J. Cramer, and D. G. Truhlar, J. Chem. Theory Comput., submitted in January 2008.

"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., submitted in 2008.

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