Source: http://truhlar.chem.umn.edu/journal-articles/2000-2009
Timestamp: 2019-04-20 02:42:28+00:00

Document:
570. "A Universal Solvation Model Based on Class IV Charges and the Intermediate Neglect of Differential Overlap for Spectroscopy Molecular Orbital Method," J. Li, T. Zhu, C. J. Cramer, and D. G. Truhlar, Journal of Physical Chemistry A 104, 2178-2182 (2000). (W. A. Goddard III Birthday Issue).
571. "A Two-Response-Time Model Based on CM2/INDO/S2 Electrostatic Potentials for the Dielectric Polarization Component of Solvatochromic Shifts on Vertical Excitation Energies," J. Li, C. J. Cramer, and D. G. Truhlar, International Journal of Quantum Chemistry 77, 264-280 (2000). (Festschrift in Honor of Michael C. Zerner's 60th Birthday).
572. "A Universal Solvation Model Based on the Conductor-like Screening Model," D. M. Dolney, G. D. Hawkins, P. Winget, D. A. Liotard, C. J. Cramer, and D. G. Truhlar, Journal of Computational Chemistry 21, 340-366 (2000).
573. "Prediction of Vapor Pressures from Self-Solvation Free Energies Calculated by the SM5 Series of Universal Solvation Models," P. Winget, G. D. Hawkins, C. J. Cramer, and D. G. Truhlar, Journal of Physical Chemistry B 104, 4726-4734 (2000).
576. "Statistical Thermodynamics of Bond Torsion Modes," Y.-Y. Chuang and D. G. Truhlar, Journal of Chemical Physics 112, 1221-1228 (2000); erratum: 121, 7036 (2004), 124, 179903/1-2 (2006).
577. "Multidimensional Transition State Theory and the Validity of Grote-Hynes Theory the Validity of Grote-Hynes Theory," D. G. Truhlar and B. C. Garrett, Journal of Physical Chemistry B 104, 1069-1072 (2000).
578. "Computational Electrochemistry: Aqueous One-Electron Oxidation Potentials for Substituted Anilines," P. Winget, E. J. Weber, C. J Cramer, and D. G. Truhlar, Physical Chemistry Chemical Physics 2, 1231-1239 (2000), 2, 1871(E) (2000).
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579. "Do Semiclassical Trajectory Theories Provide an Accurate Picture of Radiationless Decay for Systems with Accessible Surface Crossings?" M. D. Hack, A. Jasper, Y. L. Volobuev, D. W. Schwenke, and D. G. Truhlar, Journal of Physical Chemistry A 104, 217-232 (2000).
580. "Multilevel Geometry Optimization," J. M. Rodgers, P. L. Fast, and D. G. Truhlar, Journal of Chemical Physics 112, 3141-3147 (2000).
581. "Comment on Rate Constants for Reactions of Tritium Atoms with H2, D2, and HD," J. Srinivasan and D. G. Truhlar, Journal of Physical Chemistry A 104, 1965-1967 (2000).
582. "How Should We Calculate Transition State Geometries for Radical Reactions? The Effect of Spin Contamination on the Prediction of Geometries for Open-Shell Saddle Points," Y.-Y. Chuang, E. L. CoitiÒo, and D. G. Truhlar, Journal of Physical Chemistry A 104, 446-450 (2000).
587. "Potential Energy Surface, Thermal and State-Selected Rate Constants, and Kinetic Isotope Effects for Cl + CH4 -> HCl + CH3" J. C. Corchado, D. G. Truhlar, and J. Espinosa-Garcia, Journal of Chemical Physics 112, 9375-9389 (2000).
588. "Multi-configuration Molecular Mechanics Algorithm for Potential Energy Surfaces of Chemical Reactions" Y. Kim, J. C. Corchado, J. Villa, J. Xing, and D. G. Truhlar, Journal of Chemical Physics 112, 2718-2735 (2000).
589. "Dynamics of the Cl + H2/D2 Reaction: A Comparison of Crossed Molecular Beam Experiments with Quasiclassical Trajectory and Quantum Mechanical Calculations," M. Alagia, N. Balucani, L. Cartechini, P. Casavecchia, G. G. Volpi, F. J. Aoiz, L. Banares, T. C. Allison, S. L. Mielke, and D. G. Truhlar, Physical Chemistry Chemical Physics 2, 599-612 (2000).
590. "Quantized Dynamical Bottlenecks and Transition State Control of the Reaction of D with H2. Effect of Varying the Total Angular Momentum," D. C. Chatfield, S. L. Mielke, T. C. Allison, and D. G. Truhlar, Journal of Chemical Physics 112, 8387-8408 (2000).
591. "Continuous Surface Switching: An Improved Time-Dependent Self-Consistent-Field Method for Nonadiabatic Dynamics," Y. L. Volobuev, M. D. Hack, M. S. Topaler, and D. G. Truhlar, Journal of Chemical Physics 112, 9716-9726 (2000).
592. "Extrapolation and Perturbation Schemes for Accelerating the Convergence of Quantum Mechanical Free Energy Calculations via the Fourier Path-Integral Monte Carlo Method," S. L. Mielke, J. Srinivasan, and D. G. Truhlar, Journal of Chemical Physics 112, 8758-8764 (2000).
593. "Prediction of Soil Sorption Coefficients Using a Universal Solvation Model," P. Winget, C. J. Cramer, and D. G. Truhlar, Environmental Science and Technology 34, 4733-4740 (2000).
594. "Thermochemical Analysis of Core Correlation and Scalar Relativistic Effects on Molecular Atomization Energies," J. M. L. Martin, A. Sundermann, P. L. Fast, and D. G. Truhlar, Journal of Chemical Physics 113, 1348-1358 (2000).
595. "MC-QCISD: Multi-Coefficient Correlation Method Based on Quadratic Configuration Interaction with Single and Double Excitations," P. L. Fast and D. G. Truhlar, Journal of Physical Chemistry A 104, 6111-6116 (2000).
596. "Adiabatic Connection for Kinetics," B. J. Lynch, P. L. Fast, M. Harris, and D. G. Truhlar, Journal of Physical Chemistry A 104, 4811-4815 (2000).
597. "Quantum Dynamics of Hydride Transfer in Enzyme Catalysis," C. Alhambra, J. C. Corchado, M. L. Sanchez, J. Gao, and D. G. Truhlar, Journal of the American Chemical Society 122, 8197-8203 (2000).
599. "Analysis of the Resonance in H + D2 -> HD(v' =3) + D," T. C. Allison, R. S. Friedman, D. J. Kaufman, and D. G. Truhlar, Chemical Physics Letters 327, 439-445 (2000).
600. "Convergence of Variational Calculations of the Ground State Energy of HF Dimer," Y. Volobuev, W. C. Necoechea, and D. G. Truhlar, Chemical Physics Letters 330, 471-474 (2000).
601. "On the Nonexistence of Strictly Diabatic Molecular Electronic Bases," B. K. Kendrick, C. A. Mead, and D. G. Truhlar, Chemical Physics Letters 330, 629-632 (2000).
602. "A New Fourier Path Integral Method, A More General Scheme for Extrapolation, and Comparison of Eight Path Integral Methods for the Quantum Mechanical Calculation of Free Energies," S. L. Mielke and D. G. Truhlar, Journal of Chemical Physics 114, 621-630 (2001).
603. "Improved Algorithm for Corner Cutting Calculations," A. Fernandez-Ramos and D. G. Truhlar, Journal of Chemical Physics 114, 1491-1496 (2001).
604. "Quantum Mechanical Dynamics of Hydride Transfer in Polycyclic Hydoxy Ketones in the Condensed Phase," R. M. Nicoll, I. H. Hillier, and D. G. Truhlar, Journal of the American Chemical Society 123, 1459-1463 (2001).
605. "Electronically Nonadiabatic Trajectories: Continuous Surface Switching II," M. D. Hack and D. G. Truhlar, Journal of Chemical Physics 114, 2894-2902 (2001).
606. "Convex Arrhenius Plots and their Interpretation," D. G. Truhlar and A. Kohen, Proceedings of the National Academy of Sciences, U.S.A. 98, 848-851 (2001).
607. "Reductive Dechlorination of Hexachloroethane in the Environment. Mechanistic Studies via Computational Electrochemistry," E. V. Patterson, C. J. Cramer, and D. G. Truhlar, Journal of the American Chemical Society 123, 2025-2031 (2001).
609. "How Well Can Hybrid Density Functional Methods Predict Transition State Geometries and Barrier Heights?" B. J. Lynch and D. G. Truhlar, Journal of Physical Chemistry A 105, 2936-2941 (2001).
610. "Multi-Coefficient Correlation Method: Comparison of Specific-Range Reaction Parameters to General Reaction Parameters for CnHxOy Compounds," P. L. Fast, N. Schultz, and D. G. Truhlar, Journal of Physical Chemistry A 105, 4143-4149 (2001).
611. "A Natural Decay of Mixing Algorithm for Non-Born Oppenheimer Trajectories," M. D. Hack and D. G. Truhlar, Journal of Chemical Physics 114, 9305-9314 (2001).
612. "Inclusion of Quantum Mechanical Vibrational Energy in Reactive Potentials of Mean Force," M. Garcia-Viloca, C. Alhambra, D. G. Truhlar, and J. Gao, Journal of Chemical Physics 114,9953-9958 (2001).
613. "Displaced-Points Path Integral Methods for Including Quantum Effects in the Monte Carlo Evaluation of Free Energies," S. L. Mielke and D. G. Truhlar, Journal of Chemical Physics 115, 652-682 (2001).
614. "Comparison of Full Multiple Spawning, Trajectory Surface Hopping, and Converged Quantum Mechanics for Electronically Nonadiabatic Dynamics," M. D. Hack, A. M. Wensmann, D. G. Truhlar, M. Ben-Nun, and T. J. Martínez, Journal of Chemical Physics 115, 1172-1186 (2001).
615. "The Treatment of Classically Forbidden Electronic Transitions in Semiclassical Trajectory Surface Hopping Calculations," A W. Jasper, M. D. Hack, and D. G. Truhlar, Journal of Chemical Physics 115, 1804-1816 (2001).
616. "Solvent-Dependent Transition States for Decarboxylations," D. Sicinska, D. G. Truhlar, and P. Paneth, Journal of the American Chemical Society 123, 7683-7686 (2001).
617. "The Direct Calculation of Diabatic States Based on Configurational Uniformity," H. Nakamura and D. G. Truhlar, Journal of Chemical Physics 115, 10353-10372 (2001).
618. "Variational Transition State Theory Evaluation of the Rate Constant for Proton Transfer in a Polar Solvent," R. P. McRae, G. K. Schenter, B. C. Garrett, Z. Svetlicic, and D. G. Truhlar, Journal of Chemical Physics 115, 8460-8480 (2001).
620. "POTLIB 2001: A Potential Energy Surface Library for Chemical Systems," R. J. Duchovic, Y. L. Volobuev, G. C. Lynch, T. C. Allison, J. C. Corchado, D. G. Truhlar, A. F. Wagner, and B. C. Garrett, Computer Physics Communications 144, 169-187 (2002). Erratum: 156, 319-322 (2004).
621. "Molecular Mechanics for Chemical Reactions. A Standard Strategy for Using Multi-Configuration Molecular Mechanics for Variational Transition State Theory with Optimized Multidimensional Tunneling," T. Albu, J. C. Corchado, and D. G. Truhlar, Journal of Physical Chemistry A 105, 8465-8487 (2001).
622. "Test of Variational Transition State Theory with Multidimensional Tunneling Contributions Against an Accurate Full-dimensional Rate Constant Calculation for a Six-Atom System," J. Pu, J. C. Corchado, and D. G. Truhlar, Journal of Chemical Physics 115, 6266-6267 (2001).
623. "Canonical Variational Theory for Enzyme Kinetics with the Protein Mean Force and Multidimensional Quantum Mechanical Tunneling Dynamics. Theory and Application to Liver Alcohol Dehydrogenase," C. Alhambra, J. Corchado, M. L. Sánchez, M. Garcia-Viloca, J. Gao, and D. G. Truhlar, Journal of Physical Chemistry B 105, 11326-11340 (2001).
624. "Quantum Mechanical Tunneling in Methylamine Dehydrogenase," C. Alhambra, M. L. Sánchez, J. C. Corchado, J. Gao, and D. G. Truhlar, Chemical Physics Letters 347, 512-518 (2001); reprinted correctly: 355, 388-394 (2002).
625. "MIDIX Basis Set for Lithium Atom: Accurate Geometries and Atomic Partial Charges for Lithium Compounds with Minimal Computational Cost," J. D. Thompson, P. Winget, and D. G. Truhlar, PhysChemComm, 4 (16), 72-77 http://dx.doi.org/10.1039/b105076c . Supplementary information: http://www.rsc.org/suppdata/qu/b1/b105076c (2001).
626. "Properties of Nonadiabatic Couplings and the Generalized Born-Oppenheimer Approximation," B. K. Kendrick, C. A. Mead, and D. G. Truhlar, Chemical Physics 277, 31-41 (2002).
627. "Photodissociation of LiFH and NaFH van der Waals Complexes: A Semiclassical Trajectory Study," A W. Jasper, M. D. Hack, A. Chakraborty, D. G. Truhlar, and P. Piecuch, Journal of Chemical Physics 115, 7945-7952 (2001); erratum: 119, 9321 (2003).
629. "Parameterization of a Universal Solvation Model for Molecules Containing Silicon," P. Winget, J. D. Thompson, C. J. Cramer, and D. G. Truhlar, Journal of Physical Chemistry B 106, 5160-5168 (2002).
630. "Parameterized Direct Dynamics Study of Rate Constants of H with CH4 from 250 to 2400 K," J. Pu and D. G. Truhlar, Journal of Chemical Physics 116, 1468-1478 (2002).
631. "Charge Model 3: A Class IV Charge Model Based on Hybrid Density Functional Theory with Variable Exchange," P. Winget, J. D. Thompson, J. D. Xidos, C. J. Cramer, and D. G. Truhlar, Journal of Physical Chemistry A 106, 10707-10717 (2002).
632. "What are the Best Affordable Multi-Coefficient Strategies for Calculating Transition State Geometries and Barrier Heights?" B. J. Lynch and D. G. Truhlar, Journal of Physical Chemistry A 106, 842-846 (2002).
633. "How Well Does Microsolvation Represent Macrosolvation? A Test Case: Dynamics of Decarboxylation of 4-Pyridylacetic Acid Zwitterion" D. Sicinska, P. Paneth, and D. G. Truhlar, Journal of Physical Chemistry B 106, 2708-2713 (2002).
634. "Interpolated Algorithms for Large-Curvature Tunneling Calculations," A. Fernandez-Ramos, D. G. Truhlar, J. C. Corchado, and J. Espinosa-Garcia, Journal of Physical Chemistry A 106, 4957-4960 (2002).
635. "Coupled Quasidiabatic Potential Energy Surfaces for LiFH," A. W. Jasper, M. D. Hack, D. G. Truhlar, and P. Piecuch, Journal of Chemical Physics 116, 8353-8366 (2002).
636. "Fewest Switches with Time Uncertainty: A Modified Trajectory Surface Hopping Algorithm with Better Accuracy for Classically Forbidden Electronic Transitions," A. W. Jasper, S. N. Stechmann, and D. G. Truhlar, Journal of Chemical Physics 116, 5424-5431 (2002); erratum: 117, 10427 (2002).
637. "Tests of Potential Energy Surfaces for H + CH4 <-> CH3 + H2: Deuterium and Muonium Kinetic Isotope Effects for the Forward and Reverse Reaction," J. Pu and D. G. Truhlar, Journal of Chemical Physics 117, 10675-10687 (2002).
638. "Obtaining the Right Orbitals is the Key to Calculating Accurate Binding Energies for Cu+ Ion," B. J. Lynch and D. G. Truhlar, Chemical Physics Letters 361, 251-258 (2002).
639. "Dynamics of 1,2-Hydrogen Migration in Carbenes and Ring Expansion in Cyclopropylcarbenes," T. V. Albu, B. J. Lynch, D. G. Truhlar, A. C. Goren, D. A. Hrovat, W. T. Borden, and R. A. Moss, Journal of Physical Chemistry A 106, 5323-5338 (2002).
640. "Validation of Variational Transition State Theory with Multidimensional Tunneling Contributions Against Accurate Quantum Mechanical Dynamics for H + CH4 -> H2+ CH3 in an Extended Temperature Interval," J. Pu and D. G. Truhlar, Journal of Chemical Physics 117, 1479-1481 (2002).
641. "Reply to Comment on Molecular Mechanics for Chemical Reactions," D. G. Truhlar, Journal of Physical Chemistry A 106, 5048-5051 (2002).
644. "Direct Diabatization of Electronic States by the Fourfold Way. II. Dynamical Correlation and Rearrangement Processes," H. Nakamura and D. G. Truhlar, Journal of Chemical Physics 117, 5576-5593 (2002).
645. "Electrostatic Component of Solvation: Comparison of SCRF Models," C. Curutchet, C. J. Cramer, D. G. Truhlar, M. F. Ruiz-Lopez, M. Orozco, and F. J. Luque, Journal of Computational Chemistry 24, 284-297 (2003).
646. "Reduced Mass in the One-Dimensional Treatment of Tunneling," D. G. Truhlar and B. C. Garrett, Journal of Physical Chemistry A, 107, 4006-4007 (2003).
647. "Structures and Aggregation States of Fluoromethyllithium and Chloromethyllithium Carbenoids in the Gas Phase and in Ethereal Solvent," L. M. Pratt, B. Ramachandran, J. D. Xidos, C. J. Cramer, and D. G. Truhlar, Journal of Organic Chemistry 67, 7607-7612 (2002).
648. "More Reliable Partial Atomic Charges When Using Diffuse Basis Functions," J. D. Thompson, J. D. Xidos, T. M. Sonbuchner, C. J. Cramer, and D. G. Truhlar, PhysChemComm 5 (18), 117-134 http://dx.doi.org/10.1039/b206369g (2002).
649. "Effectiveness of Diffuse Basis Functions for Calculating Relative Energies by Density Functional Theory," B. J. Lynch, Y. Zhao, and D. G. Truhlar, Journal of Physical Chemistry A 107, 1384-1388 (2003).
650. "Lateral Confinement of an Interfacial Electron Wavefunction by a Surface Dipole Lattice," G. Dutton, J. Pu, D. G. Truhlar, and X.-Y. Zhu, Journal of Chemical Physics 118, 4337-4340 (2003).
651. "Improved Treatment of Momentum at Classically Forbidden Electronic Transitions in Trajectory Surface Hopping Calculations," A. W. Jasper and D. G. Truhlar, Chemical Physics Letters 369, 60-67 (2003).
652. "Parameterization of Charge Model 3 for AM1, PM3, BLYP, and B3LYP," J. D. Thompson, C. J. Cramer, and D. G. Truhlar, Journal of Computational Chemistry, 24, 1291-1304 (2003).
653. "Robust and Affordable Multi-Coefficient Methods for Thermochemistry and Thermochemical Kinetics: The MCCM/3 Suite and SAC/3," B. J. Lynch and D. G. Truhlar, Journal of Physical Chemistry A, 107, 3898-3906 (2003).
654. "Generalized Transition State Theory in Terms of the Potential of Mean Force," G. K. Schenter, B. C. Garrett, and D. G. Truhlar, Journal of Chemical Physics, 119, 5828-5833 (2003).
655. "Force Field Variations along the Torsional Coordinates of CH3OH and CH3CHO," T. V. Albu and D. G. Truhlar, Journal of Molecular Spectroscopy, 219, 129-131 (2003).
656. "Importance of Substrate and Cofactor Polarization in the Active Site of Dihydrofolate Reductase," M. Garcia-Viloca, D. G. Truhlar, and J. Gao, Journal of Molecular Biology 327, 549-560 (2003).
657. "Carbon Tunneling from a Single Quantum State," P. S. Zuev, R. S. Sheridan, T. V. Albu, D. G. Truhlar, D. A. Hrovat, and W. T. Borden, Science 299, 867-870 (2003).
658. "Extension of the Fourfold Way For Calculation Of Global Diabatic Potential Energy Surfaces of Complex, Multi-Arrangement, Non-Born-Oppenheimer Systems: Application to HNCO (S0, S1)," H. Nakamura and D. G. Truhlar, Journal of Chemical Physics, 118, 6816-6829 (2003).
659. "Molecular Modeling of Environmentally Important Processes: Reduction Potentials" by A. Lewis, J. A. Bumpus, D. G. Truhlar, and C. J. Cramer, Journal of Chemical Education, 81, 596-604 (2004). Erratum in press.
660. "H + H2 Thermal Reaction: A Convergence of Theory and Experiment", S. L. Mielke, K. A. Peterson, D. W. Schwenke, B. C. Garrett, D. G. Truhlar, J. V. Michael, M.-C. Su, and J. W. Sutherland, Physical Review Letters 91, 063201/1-4 (2003).
661. "Free Energy Surface, Reaction Paths, and Kinetic Isotope Effect of Short-Chain Acyl-CoA Dehydrogenase, T. D. Poulsen, M. Garcia-Viloca, J. Gao, and D. G. Truhlar, Journal of Physical Chemistry B, 107, 9567-9578 (2003).
662. "Small Basis Sets for Calculations of Barrier Heights, Energies of Reaction, Electron Affinities, Geometries, and Dipole Moments," B. J. Lynch and D. G. Truhlar, Theoretical Chemistry Accounts, 111, 335-344 (2004). (Jacopo Tomasi Honorary Issue).
663. "A Class IV Charge Model for Boron Based on Hybrid Density Functional Theory," J. M. Brom, B. J. Schmitz, J. D. Thompson, C. J. Cramer, and D. G. Truhlar, Journal of Physical Chemistry A, 107, 6483-6488.
665. "Predicting Aqueous Solubilities from Aqueous Free Energies of Solvation and Experimental or Calculated Vapor Pressures of Pure Substances," J. D. Thompson, C. J. Cramer, and D. G. Truhlar, Journal of Chemical Physics 119, 1661-1670 (2003).
666. "Small Representative Benchmarks for Thermochemical Calculations," B. J. Lynch and D. G. Truhlar, J. Phys. Chem. A, 107, 8996-8999 (2003), erratum: 108, 1460 (2004).
667. "Sensitivity of Molecular Dynamics Simulations to the Choice of the X-ray Structure Used to Model an Enzymatic Reaction, "M. Garcia-Viloca, T. D. Poulsen, D. G. Truhlar, and J. Gao, Protein Science 13, 2341-2354 (2004).
668. "The Relative Likelihood of Encountering Conical Intersections and Avoided Intersections on the Potential Energy Surfaces of Polyatomic Molecules," D. G. Truhlar and C. A. Mead, Physical Review A 68, 032501/1-2 (2003).
669. "Reaction-Path Energetics and Kinetics of the Hydride Transfer Reaction Catalyzed by Dihydrofolate Reductase," M. Garcia-Viloca, D. G. Truhlar, and J. Gao, Biochemistry, 42, 13558-13575 (2003).
670. "A 'Path-by-Path' Monotone Extrapolation Sequence for Feynman Path Integral Calculations of Quantum Mechanical Free Energies'" S. L. Mielke and D. G. Truhlar, Chemical Physics Letters 378, 317-322 (2003).
671. "Generalized Hybrid Orbital (GHO) Method for Combining Ab Initio Hartree-Fock Wave Functions with Molecular Mechanics," J. Pu, J. Gao, and D. G. Truhlar, Journal of Physical Chemistry A, 108, 632-650 (2004).
672. "Benchmark Results for Hydrogen Atom Transfer Between Carbon Centers and Validation of Electronic Structure Methods for Bond Energies and Barrier Heights," A. Dybala-Defratyka, P. Paneth, J. Pu, and D. G. Truhlar, Journal of Physical Chemistry A, 108, 2475-2486 (2004).
673. "How Enzymes Work: Analysis by Modern Rate Theory and Computer Simulations," M. Garcia-Viloca, J. Gao, M. Karplus, and D. G. Truhlar, Science, 303, 186-195 (2004).
674. "Validation of Theoretical Methods for the Structure and Energy of Aluminum Nanoparticles," N. E. Schultz, G. Staszewska, P. Staszewski, and D. G. Truhlar, Journal of Physical Chemistry B, 108, 4850-4861 (2004).
675. "Army Ants Algorithm for Rare Even Sampling of Delocalized Nonadiabatic Transitions by Trajectory Surface Hopping and the Estimation of Sampling Errors by the Bootstrap Method," S. Nangia, A. W. Jasper, T. F. Miller III, and D. G. Truhlar, Journal of Chemical Physics, 120, 3586-3597 (2004).
676. "Calculation of Converged Rovibrational Energies and Partition Function for Methane using Vibrational-Rotational Configuration Interaction," A. Chakraborty, D. G. Truhlar, J. M. Bowman, and S. Carter, Journal of Chemical Physics, 121, 2071-2084 (2004).
677. "Predicting Adsorption Coefficients at Air-Water Interfaces Using Universal Solvation and Surface Area Models," C. P. Kelly, C. J. Cramer, and D. G. Truhlar, Journal of Physical Chemistry B 108, 12882-12897 (2004).
678. "Class IV Charge Model for the Self-Consistent Charge Density-Functional Tight-Binding Model," J. A. Kalinowski, B. Lesyng, J. D. Thompson, C. J. Cramer, and D. G. Truhlar, Journal of Physical Chemistry A 108, 2545-2549 (2004).
679. "Non-Born-Oppenheimer Trajectories with Self-Consistent Decay of Mixing," C. Zhu, A. W. Jasper, and D. G. Truhlar, Journal of Chemical Physics 120, 5543-5557 (2004).
680. "Tests of Second-Generation and Third-Generation Density Functionals for Thermochemical Kinetics, " Y. Zhao, J. Pu, B. J. Lynch and D. G. Truhlar, Phys. Chem. Chem. Phys. 6, 673-676 (2004).
682. "Efficient Molecular Mechanics for Chemical Reactions: Multiconfiguration Molecular Mechanics using Partial Electronic Structure Hessians," H. Lin, J. Pu, T. V. Albu, and D. G. Truhlar, Journal of Physical Chemistry A 108, 4112-4124 (2004).
683. "New Universal Solvation Model and Comparison of the Accuracy of Three Continuum Solvation Models, SM5.42R, SM5.43R, and C-PCM, in Aqueous Solution and Organic Solvents and for Vapor Pressures," J. D. Thompson, C. J. Cramer, and D. G. Truhlar, Journal of Physical Chemistry A 108, 6532-6542 (2004).
684. "Combining Self-Consistent-Charge Density-Functional Tight-binding (SCC-DFTB) with Molecular Mechanics by the Generalized Hybrid orbital (GHO) Method," J. Pu, J. Gao, and D. G. Truhlar, Journal of Physical Chemistry A 108, 5454-5463 (2004).
686. "Doubly Hybrid DFT: New Multi-Coefficient Correlation and Density Functional Methods for Thermochemistry and Thermochemical Kinetics," Y. Zhao, B. J. Lynch, and D. G. Truhlar. Journal of Physical Chemistry A 108, 4786-4791 (2004).
687. "Coherent Switching with Decay of Mixing: An Improved Treatment of Electronic Coherence for Non-Born-Oppenheimer Trajectories," C. Zhu, S. Nangia, A. W. Jasper, and D. G. Truhlar, Journal of Chemical Physics 121, 7658-7670 (2004).
688. "Analytic Potential Energy Functions for Aluminum Clusters," A. W. Jasper, P. Staszewski, G. Staszewska, N. E. Schultz, and D. G. Truhlar, J. Phys. Chem. B 108, 8996-9010 (2004).
689. "New Effective Core Method (Effective Core Potential and Valence Basis Set) for Aluminum Clusters and Nanoparticles and Al Molecules Containing C, H, and O," N. E. Schultz and D. G. Truhlar, Journal of Chemical Theory and Computation 1, 41-53 (2005).
690. "Ensemble-Averaged Variational Transition State Theory with Optimized Multidimensional Tunneling for Enzyme Kinetics and Other Condensed-Phase Reactions," D. G. Truhlar, J. Gao, M. Garcia-Viloca, C. Alhambra, J. Corchado, M. L. Sanchez, and T. D. Poulsen, International Journal of Quantum Chemistry 100, 1136-1152 (2004). (Proceedings of the 2004 Sanibel Symposium).
691. "Introductory Lecture: Nonadiabatic Effects in Chemical Dynamics," A. W. Jasper, C. Zhu, S. Nangia, and D. G. Truhlar, Faraday Discussions 127, 1-22 (2004).
692. "Hybrid Meta Density Functional Theory Methods for Thermochemistry, Thermochemical Kinetics, and Noncovalent Interactions: The MPW1B95 and MPWB1K Models and Comparative Assessments for Hydrogen Bonding and van der Waals Interactions," Y. Zhao and D. G. Truhlar, Journal of Physical Chemistry A 108, 6908-6918 (2004).
693. "Many-Body Tight-Binding Model for Aluminum Nanoparticles," G. Staszewska , P. Staszewski , N. E. Schultz, and Donald G. Truhlar, Physical Review B 71, 045423/1-14 (2005), erratum: 73, 39903/1 (2006).
694. "Accurate Vibrational-Rotational Partition Functions and Standard-State Free Energy Values for H2O2 from Monte Carlo Path-Integral Calculations," V. A. Lynch, S. L. Mielke, and D. G. Truhlar, Journal of Chemical Physics 121, 5148-5162 (2004).
695. "Use of Block Hessians for the Optimization of Molecular Geometries," J. Pu and D. G. Truhlar, Journal of Computational and Theoretical Chemistry 1, 54-60 (2005).
696. "Variational Transition State Theory," B. C. Garrett and D. G. Truhlar, see no. 75 in chapter list.
697. "Accurate Partial Atomic Charges for High-Energy Molecules Using Class IV Charge Models with the MIDI! Basis Set," C. P. Kelly, C. J. Cramer, and D. G. Truhlar, Theoretical Chemistry Accounts 113, 133-151 (2005).
698. "Density-Functional Theory and Hybrid| Density-Functional Theory Continuum Solvation Models for Aqueous and Organic Solvents: Universal SM5.43 and SM5.43R Solvation Models for any Fraction of Hartree-Fock Exchange," J. D. Thompson, C. J. Cramer, and D. G. Truhlar, Theoretical Chemistry Accounts 113,107-131 (2005).
699. "Conical Intersections and Semiclassical Trajectories: Comparison to Accurate Quantum Dynamics and Analyses of the Trajectories," A. W. Jasper and D. G. Truhlar, J. Chem. Phys. 122, 044101/1-16 (2005).
700. "The 6-31B(d) Basis Set and the BMC-QCISD and BMC-CCSD Multi-Coefficient Correlation Methods," B. J. Lynch, Y. Zhao, and D. G. Truhlar, Journal of Physical Chemistry A 109, 1643-1649 (2005).
701. "Multi-Coefficient Extrapolated Density Functional Theory for Thermochemistry and Thermochemical Kinetics, " Y. Zhao, B. J. Lynch, and D. G. Truhlar, Physical Chemistry Chemical Physics 7, 43-52 (2005).
702. "Benchmark Calculations of Reaction Energies, Barrier Heights, and Transition State Geometries for Hydrogen Abstraction from Methanol by a Hydrogen Atom," J. Pu and D. G. Truhlar, Journal of Physical Chemistry A 109, 773-778 (2005).
703. "Benchmark Database of Barrier Heights for Heavy Atom Transfer, Nucleophilic Substitution, Association, and Unimolecular Reactions and Their Use to Test Density Functional Theory," Y. Zhao, N. Gonz?lez-Garc?a, and D. G. Truhlar, Journal of Physical Chemistry A 109, 2012-2018 (2005), 110, 4942(E) (2006).
705. "Analytic Potential Energy Functions for Simulating Aluminum Nanoparticles," A. W. Jasper, N. E. Schultz, and D. G. Truhlar, Journal of Physical Chemistry B 109, 3915-3920 (2005).
706. "Temperature Dependence of Carbon-13 Kinetic Isotope Effects of Importance to Global Climate Change," H. Lin, Y. Zhao, B. A. Ellingson, J. Pu, and D. G. Truhlar, Journal of the American Chemical Society 127, 2830-2831 (2005).
707. "Redistributed Charge and Dipole Schemes for Combined Quantum Mechanical and Molecular Mechanical Calculations," H. Lin and D. G. Truhlar, Journal of Physical Chemistry A 109, 3991-4004 (2005).
709. "Benchmark Databases for Nonbonded Interactions and Their Use to Test Density Functional Theory," Y. Zhao and D. G. Truhlar, Journal of Chemical Theory and Computation 1, 415-432 (2005).
710. "Small Temperature Dependence of the Kinetic Isotope Effect for the Hydride Transfer Reaction Catalyzed by Escherichia coli,Dihydrofolate Reductase," J. Pu, S. Ma, J. Gao, and D. G. Truhlar, Journal of Physical Chemistry B 109, 8551-8556 (2005).
711. "Dependence of Transition State Structure on Substrate: The Intrinsic C-13 Kinetic Isotope Effect is Different for Physiological and Slow Substrate of the Ornithine Decarboxylase Reaction Because of Different Hydrogen Bonding Structures," D. Sicinska, D. G. Truhlar, and P. Paneth, Journal of the American Chemical Society 127, 5414-5422 (2005).
712. "Databases for Transition Element Bonding: Metal-Metal Bond Energies and Bond Lengths and Their Use To Test Hybrid, Hybrid Meta, and Meta Density Functionals and Generalized Gradient Approximations," N. E. Schultz, Y. Zhao, and D. G. Truhlar, Journal of Physical Chemistry A 109, 4388-4403 (2005).
713. "The Design of Density Functionals that are Broadly Accurate for Thermochemistry, Thermochemical Kinetics, and Nonbonded Interactions," Y. Zhao and D. G.. Truhlar, Journal of Physical Chemistry A 109, 5656-5667 (2005).
714. "Non-Born-Oppenheimer Liouville-von Neumann Dynamics. Evolution of a Subsystem Controlled by Linear and Population-Driven Decay of Mixing with Decoherent and Coherent Switching," C. Zhu, A. W. Jasper, and D. G. Truhlar, Journal of Chemical Theory and Computation 1, 527-540 (2005).
715."Multi-Coefficient Extrapolated DFT Studies of pi ... pi Interactions: The Benzene Dimer," Y. Zhao and D. G. Truhlar, Journal of Physical Chemistry A 109, 4209-4212 (2005).
717."High-Precision Quantum Thermochemistry on Nonquasiharmonic Potentials: Converged Path-Integral Free Energies and a Systematically Convergent Family of Generalized Pitzer-Gwinn Approximations," V. A. Lynch, S. L. Mielke, and D. G. Truhlar, Journal of Physical Chemistry A 109, 10092-10099 (2005), erratum: 110, 5965 (2006).
718."How Well Can New-Generation Density Functional Methods Describe Stacking Interactions in Biological Systems?" Y. Zhao and D. G. Truhlar, Phys. Chem. Chem. Phys. 7, 2701-2705 (2005).
719. "Infinite-Basis Calculations of Binding Energies for the Hydrogen Bonded and Stacked Tetramers of Formic Acid and Formamide and Their use for Validation of Hybrid DFT and Ab Initio Methods," Y. Zhao and D. G. Truhlar, Journal of Physical Chemistry A 109, 6624-6627 (2005).
720. "How Well Can Density Functional Methods Describe Hydrogen Bonds to pi Acceptors?" Y. Zhao, O. Tishchenko, and D. G. Truhlar, Journal of Physical Chemistry B 109, 19046-19051 (2005).
721. "Improved Density Functionals for Water," E. E. Dahlke and D. G. Truhlar, Journal of Physical Chemistry B 109, 15677-15683 (2005).
723. "A New Algorithm for Efficient Direct Dynamics Calculations of Large- Curvature Tunneling and Its Application to Radical Reactions with 9-15 Atoms," A. Fern?ndez-Ramos and D. G. Truhlar, Journal of Chemical Theory and Computation 1, 1063-1078 (2005).
724. "Electronic Decoherence Time for Non-Born-Oppenheimer Trajectories," A. W. Jasper and D. G. Truhlar, Journal of Chemical Physics, 123, 64103/1-4 (2005).
725."SM6: A Density Functional Theory Continuum Solvation Model for Calculating Aqueous Solvation Free Energies of Neutrals, Ions, and Solute-Water Clusters," C. P. Kelly, C. J. Cramer, and D. G. Truhlar, Journal of Chemical Theory and Computation 1, 1133-1152 (2005).
726. "Nonperfect Synchronization of Reaction Center Rehybridization in the Transition State of the Hydride Transfer Catalyzed by Dihydrofolate Reductase" J. Pu, S. Ma, M. Garcia-Viloca, J. Gao, D. G. Truhlar, and A. Kohen, Journal of the American Chemical Society 127, 14879-14886 (2005).
727. "Density functional for Inorganometallic and Organometallic Chemistry," N. E. Schultz, Y. Zhao, and D. G. Truhlar, Journal of Physical Chemistry A 109, 11127-11143 (2005).
728. "Potential of Mean Force Calculation for the Proton and Hydride Transfer Reactions Catalyzed by Medium Chain Acyl-Coa Dehydrogenase: The Effect of Mutations on Enzyme Catalysis," S. Bhattacharyya, S. Ma, M. T. Stankovich, D. G. Truhlar, and J. Gao, Biochemistry 44, 16549-16563 (2005).
This manuscript, in the accepted version, is now available free as manuscript NIHMS60097 at PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2527473/. In general we recommend accessing the published version if possible rather than than the accepted version, because we some times make post-acceptance corrections at the galley stage.
730. "Combined Valence Bond-Molecular Mechanics Potential Energy Surface and Direct Dynamics Study of Rate constants and Kinetic Isotope Effects for the H + C2H6 Reaction," A. Chakraborty, Y. Zhao, H. Lin, and D. G. Truhlar, Journal of Chemical Physics 124, 044315/1-044315/14 (2006).
Author complimentary copy and supporting information Copyright (2006) American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics.
732. "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, Journal of Physical Chemistry A 110, 2493-2499 (2006).
This manuscript, in the accepted version, is now available free as manuscript NIHMS60100 at PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2528253/. In general we recommend accessing the published version if possible rather than than the accepted version, because we some times make post-acceptance corrections at the galley stage.
733. "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, Journal of Chemical Theory and Computation 2, 364-382 (2006).
734. "Transferability of Orthogonal and Nonorthogonal Tight Binding Models for Aluminum Clusters and Nanoparticles," Ahren W. Jasper, Nathan E. Schultz, and Donald G. Truhlar, Journal of Chemical Theory and Computation 3, 210-218 (2007).
736. "Direct Calculation of Coupled Diabatic Potential Energy Surfaces for Ammonia and Mapping of a Four-Dimensional Conical Intersection Seam," S. Nangia and D. G. Truhlar, Journal of Chemical Physics 124, 124309/1-13 (2006).
Author complimentary copy Copyright (2006) American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics.
737. "Predicting Aqueous Free Energies of Solvation as Functions of Temperature, " A. C. Chamberlin, C. J. Cramer, and D. G. Truhlar, Journal of Physical Chemistry B 110, 5665-5675 (2006).
738. "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, Journal of Physical Chemistry A 110, 5121-5129 (2006).
739. "Converged Vibrational Energy Levels and Quantum Mechanical Vibrational Partition Function of Ethane," A. Chakraborty and D. G. Truhlar, Journal of Chemical Physics 124, 184310/1-6 (2006).
740. "Searching for Saddle Points by Using the Nudged Elastic Band Method: An Implementation for Application to Gas-Phase Systems," N. González-García, J. Pu, A. González-Lafont, J. M. Lluch, and D. G. Truhlar, Journal of Chemical Theory and Computation 2, 895-904 (2006).
741. "Modeling of Bimolecular Reactions," A. Fernández-Ramos, J. A. Miller, S. J. Klippenstein, and D. G. Truhlar, Chemical Reviews 106, 4518-4584 (2006).
742. "Assessment of Model Chemistries for Noncovalent Interactions," Y. Zhao and D. G. Truhlar, Journal of Chemical Theory and Computation, 2, 1009-1018 (2006).
743. "Comparative Assessment of DFT Methods for 3d Transition Metal Chemistry," Y. Zhao and D. G. Truhlar, Journal of Chemical Physics 124, 224105/1-6 (2006).
744. "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, Journal of Physical Chemistry B 110, 16066-16081 (2006).
745. "Assessment of the Pairwise Additive Approximation and Evaluation of Many-Body Terms for Water Clusters," E. A. Dahlke and D. G. Truhlar, Journal of Physical Chemistry B 110, 10595-10601 (2006).
746. "Statistical Thermodynamics of Bond Torsional Modes. Tests of Separable, Almost-Separable and Improved Pitzer-Gwinn Approximations", B. A. Ellingson, V. A. Lynch, S. L. Mielke, and D. G. Truhlar, Journal of Chemical Physics 125, 84305/1-17 (2006).
747. "Hydride Transfer Reaction Catalyzed by Hyperthermophilic Dihydrofolate Reductase is Dominated by Quantum Mechanical Tunneling and is Promoted by Both Inter- and IntramolecularCorrelated Motions," J. Pang, J. Pu, J. Gao, D. G. Truhlar, and R. Allemann, Journal of the American Chemical Society 128, 8015-8023 (2006).
748. "Multidimensional Tunneling, Recrossing, and the Transmission Coefficient for Enzymatic Reactions,” J. Pu, J. Gao, and D. G. Truhlar, Chemical Reviews 106, 3140-3169 (2006).
749. "Mechanisms and Free Energies of Enzymatic Reactions", J. Gao, S. Ma, D. T. Major, K. Nam, J. Pu, and D. G. Truhlar, Chemical Reviews 106, 3188-3209 (2006).
750. "Density Functionals for Noncovalent Interaction Energies of Biological Importance," Y. Zhao and D. G. Truhlar, Journal of Chemical Theory and Computation 3, 289-300 (2007).
751. "Assessment of Density Functionals for Pi 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, Journal of Physical Chemistry A 110, 10478-10486 (2006).
753. "Multi-Configuration Molecular Mechanics Based on Combined Quantum Mechanical and Molecular Mechanical Calculations," H. Lin, Y. Zhao, O. Tishchenko, and D. G. Truhlar, Journal of Chemical Theory and Computation 2, 1237-1254 (2006).
754. "Optimizing the Performance of the Multiconfiguration Molecular Mechanics Method," O. Tishchenko and D. G. Truhlar, Journal of Physical Chemistry A 110, 13530-13536 (2006).
755. "Phase Behavior of Elemental Aluminum using Monte Carlo Simulations," D. Bhatt, N. E. Schultz, A. W. Jasper, J. I. Siepmann, D. G. Truhlar, Journal of Physical Chemistry B 110, 26135-26142 (2006).
756. "PdnCO (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 , Journal of Physical Chemistry B 110, 24030-24036 (2006).
758. "Electrostatically Embedded Many-Body Expansion for Large Systems, with Applications to Water Clusters" E. E. Dahlke and D. G. Truhlar, Journal of Chemical Theory and Computation 3, 46-53 (2007) .
759. "A New Local Density Functional for Main Group Thermochemistry, Transition Metal Bonding, Thermochemical Kinetics, and Noncovalent Interactions" Y. Zhao, D. G. Truhlar, Journal of Chemical Physics 125, 194101/1-18 (2006).
760. “Nonadiabatic effects in C-Br Bond Scission in the Photodissociation of Bromoacetyl Chloride”, R. Valero and D.G. Truhlar, Journal of Chemical Physics 125, 194305/1-22 (2006).
761. “Benchmarking Approximate Density Functional Theory for s/d Excitation Energies in 3d Transition Metal Cations”, N. Schultz, Y. Zhao, and D.G. Truhlar, Journal of Computational Chemistry 29, 185-189 (2008).
762. “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, Journal of Physical Chemistry B 111, 408-422 (2007).
This manuscript, in the accepted version, is now available free as manuscript NIHMS60109 at PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2528251/. In general we recommend accessing the published version if possible rather than than the accepted version, because we some times make post-acceptance corrections at the galley stage.
763. "Representative Benchmark Suites for Barrier Heights of Diverse Reaction Types and Assessment of Electronic Structure Methods for Thermochemical Kinetics," J. Zheng, Y. Zhao, and D. G. Truhlar, Journal of Chemical Theory and Computation 3, 569-582 (2007).
764. "How Well Can New-Generation Density Functional Methods Describe Protonated Epoxides Where Older Functionals Fail?" Y. Zhao and D. G. Truhlar, Journal of Organic Chemistry 72, 295-298 (2007).
765. "A Density Functional Theory that Accounts for Medium-Range Correlation Energies in Organic Chemistry," Y. Zhao and D. G. Truhlar, Organic Letters 8, 5753-5755 (2006).
766. "Computational Requirements for Simulating the Structures and Proton Activity of Silicaceous Materials," Y. Zhang, Z. H. Li, and D. G. Truhlar, Journal of Chemical Theory and Computation 3, 593-604 (2007).
767. "Improved Direct Diabatization and Fitting of Coupled Potential Energy Surfaces for the Photodissociation of Ammonia," Z. H. Li, R. Valero, and D. G. Truhlar, Theoretical Chemistry Accounts 118, 9-24 (2007). (Fernando Bernardi Memorial Issue).
768. "Global Potential Energy Surfaces with Correct Permutation Symmetry by Multi-Configuration Molecular Mechanics," O. Tishchenko and D. G. Truhlar, Journal of Chemical Theory and Computation 3, 938-948 (2007).
769. "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, Journal of Physical Chemistry B 111, 2231-2241 (2007).
770. "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, Journal of Physical Chemistry A 110, 13126-13130 (2006).
771. "Computational Electrochemistry: The Aqueous Ru3+ | Ru2+ Reduction Potential,” P. Jaque, A.V. Marenich, C. J. Cramer, and D. G. Truhlar, Journal of Physical Chemistry C 111, 5783-5799 (2007).
772. "The Concept of Resonance," D. G. Truhlar, Journal of Chemical Education 84, 781-782 (2007).
773. "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, Theoretical Chemistry Accounts 120, 215-241 (2008) (Contribution to the Mark S. Gordon 65th Birthday Festschrift Issue). Erratum: 119, 525 (2008).
774. "Aggregation of Alkyllithiums in Tetrahydrofuran," L. M. Pratt, D. G. Truhlar, C. J. Cramer, S. R. Kass, J. D. Thompson, and J. D. Xidos, Journal of Organic Chemistry 72, 2962-2966 (2007).
775. "Thermochemical Kinetics of Hydrogen-Atom Transfers Between Methyl, Methane, Ethynyl, Ethyne, and Hydrogen," J. Zheng, Y. Zhao, and D. G. Truhlar, Journal of Physical Chemistry A 111, 4632-4642 (2007).
776. "Attractive Noncovalent Interactions in Grubbs Second-Generation Ru Catalysts for Olefin Metathesis," Y. Zhao and D. G. Truhlar, Organic Letters 9, 1967-1970 (2007).
777. "Symmetry Numbers and Chemical Reaction Rates," A. Fernández-Ramos, B. A. Ellingson, R. Meana-Pañeda, J. M. C. Marques and D. G. Truhlar, Theoretical Chemistry Accounts 118, 813-826 (2007).
778. "Coupling of Hydrogenic Tunneling to Active-Site Motion in the Hydrogen Radical Transfer Catalyzed by a Coenzyme B12-Dependent Mutase ," A. Dybala-Defratyka, P. Paneth, R. Banerjeeand D. G. Truhlar, Proceedings of the National Academy of Sciences of the U.S.A. 104, 10774-10779 (2007).
779. "Electrostatically Embedded Many-Body Correlation Energy, with Applications to the Calculation of Accurate Second-Order Moller-Plesset Perturbation Theory Energies for Large Water Clusters" E. E. Dahlke and D. G. Truhlar, Journal of Chemical Theory and Computation 3, 1342-1348 (2007).
780. "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, Journal of Chemical Theory and Computation 3, 1378-1398 (2007).
781. "Combined Quantum Mechanical Molecular Mechanical Simulations of One- and Two-Electron Reduction Potentials,of Flavin Cofactor in Water, Medium-Chain Acyl-CoA Dehydrogenaseand Cholesterol Oxidase," S. Bhattacharyay, M. T. Stankovich, D. G. Truhlar, and J. Gao, Journal of Physical Chemistry A 111, 5729-5742 (2007) .
782. "Size-Selective Supramolecular Chemistry in a Hydrocarbon Nanoring," Y. Zhao and D. G. Truhlar, Journal of the American Chemical Society 129, 8440-8442 (2007).
783. “A Diabatic Representation Including Both Valence Nonadiabatic Interactions and Spin-Orbit Effects for Reaction Dynamics”, R. Valero and D.G. Truhlar, Journal of Physical Chemistry A 111, 8536-8551 (2007).
784. "Multi-Coefficient Gaussian-3 Calculation of the Rate Constant for the OH + CH4 Reaction and its 12C/13C Kinetic Isotope Effect with Emphasis on the Effects of Coordinate System and Torsional Treatment," B. A. Ellingson, J. Pu, H. Lin, Y. Zhao, and D. G. Truhlar, Journal of Physical Chemistry A 111, 11706-11717 (2007).
785. "Explanation of the Unusual Temperature Dependence of the Atmospherically Important OH + H2S -> H2O + SH Reaction and Prediction of the Rate Constant at Combustion Temperatures," B. A. Ellingson, and D. G. Truhlar, Journal of the American Chemical Society 129, 12765-12771 (2007).
786. "Structures, Rugged Energetic Landscapes, and Nanothermodynamics of Aln (2 ≤ n ≤ 65) Particles," Z. H. Li, A. W. Jasper, and D. G. Truhlar, Journal of the American Chemical Society 129, 14899-14910 (2007).
787. "Computational Chemistry of Polyatomic Reaction Kinetics and Dynamics: The Quest for an Accurate CH5 Potential Energy Surface," Titus V. Albu, J. Espinosa-García, D. G. Truhlar, Chemical Reviews 107, 5101-5132 (2007).
788. "Reactions of Hydrogen Atom with Hydrogen Peroxide," B. A. Ellingson, D. P. Theis, O. Tishchenko, J. Zheng, and D. G. Truhlar, J. Phys. Chem. A 111, 13554-13566 (2007).
791. "Free Energies of Formation of Metal Clusters and Nanoparticles from Molecular Simulations: Aln with n = 2-60," Z. H. Li, D. Bhatt, N. E. Schultz, J. I. Siepmann, and D. G. Truhlar, Journal of Physical Chemistry C 111, 16227-16242 (2007).
792. "Synthetic Efficiency in Enzyme Mechanisms Involving Carbocations: Aristolochene Synthase," R. K. Allemann, N. J. Young, S. Ma, D. G. Truhlar, J. Gao, Journal of the American Chemical Society 129, 13008-13013 (2007).
This manuscript, in the accepted version, is now available free as manuscript NIHMS60106 at PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2528250/. In general we recommend accessing the published version if possible rather than than the accepted version, because we some times make post-acceptance corrections at the galley stage.
793. "Charge Model 4 and Intramolecular Charge Polarization," R. M. Olson, A. V. Marenich, C. J. Cramer, and D. G. Truhlar, Journal of Chemical Theory and Computation 3, 2046-2054 (2007).
794. "Polarization Effects in Aqueous and Nonaqueous Solutions," A. V. Marenich, R. M. Olson, A. C. Chamberlin, C. J. Cramer, and D. G. Truhlar, Journal of Chemical Theory and Computation 3, 2055-2067 (2007).
801. "Non-Born–Oppenheimer Molecular Dynamics of Na...FH Photodissociation," A. W. Jasper and D. G. Truhlar, Journal of Chemical Physics 127, 194306/1-7 (2007).
Author complimentary copy Copyright (2007) American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics.
790. "Density Functionals with Broad Applicability in Chemistry," Y. Zhao and D. G. Truhlar, Accounts of Chemical Research 41, 157-167 (2008).
795. "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, D. G. Truhlar, Journal of Physical Chemistry A 112, 2372-2381 (2008).
796. "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, Journal of Chemical Theory and Computation 4, 33-41 (2008).
797. "A Conservative Algorithm for an Adaptive Change of Resolution in Mixed Atomistic/Coarse-Grained Multiscale Simulations," A. Heyden and D. G. Truhlar, Journal of Chemical Theory and Computation 4, 217-221 (2008).
798. "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, Journal of Physical Chemistry A 112, 3976-3984 (2008).
799. "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, Journal of Chemical Theory and Computation 4, 75-85 (2008).
800. "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, Journal of Physical Chemistry B 112, 3024-3039 (2008).
802. "Electrostatically Embedded Many-Body Expansion for Simulations," E. E. Dahlke and D. G. Truhlar, Journal of Chemical Theory and Computation 4, 1-6 (2008).
803. "Density Functional Theory in Transition-Metal Chemistry: Relative Energies of Low-Lying States of Iron Compounds and the Effect of Spatial Symmetry Breaking," A. Sorkin, M. A. Iron, and D. G. Truhlar, Journal of Chemical Theory and Computation 4, 307-315 (2008).
804. "A Comparative Assessment of the Perturbative and Renormalized Coupled Cluster Theories with a Non-Iterative Treatment of Triple Excitations for Thermochemical Kinetics, Including a Study of Basis Set and Core Correlation Effects," J. Zheng, J. R. Gour, J. J. Lutz, M. Włoch, P. Piecuch, and D. G. Truhlar, Journal of Chemical Physics 128, 044108/1-7 (2008).
Author complimentary copy Copyright (2008) American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics.
805. "A Unified Perspective of the Hydrogen Atom Transfer and Proton-Coupled Electron Transfer Mechanisms in Terms of Topographic Features of the Ground and Excited Potential Energy Surfaces As Exemplified by the Reaction Between Phenol and Radicals," O. Tishchenko, D. G. Truhlar, A. Ceulemans, and M. T. Nguyen, Journal of the American Chemical Society, 130, 7000-7010 (2008).
806. "A Prototype for Graphene Material Simulation: Structures and Interaction Potentials of Coronene Dimers," Y. Zhao and D. G. Truhlar, Journal of Physical Chemistry C, 112, 4061-4067 (2008).
807. "How Well Can New-Generation Density Functionals Describe the Energetics of Bond Dissociation Reactions Producing Radicals?" Y. Zhao and D. G. Truhlar, Journal of Physical Chemistry A 112, 1095-1099 (2008).
808. "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, Journal of Physical Chemistry C 112, 6860-6868 (2008).
810." Cluster and Nanoparticle Condensation and Evaporation Reactions. Thermal Rate Constants and Equilibrium Constants of Alm + Aln-m « Aln with n = 2 - 60 and m = 1 - 8," Z. H. Li and D. G. Truhlar, Journal of Physical Chemistry C 112, 11109-11121 (2008).
812. "Application of the Electrostatically Embedded Many-Body Expansion to Microsolvation of Ammonia in Water Clusters," A. Sorkin, E. E. Dahlke, and D. G. Truhlar, Journal of Chemical Theory and Computation 4, 683-688 (2008).
813. "Performance of the M06 Family of Exchange-Correlation Functionals for Predicting Magnetic Coupling in Organic and Inorganic Molecules," R. Valero, R. Costa, I. de P.R. Moreira, D. G. Truhlar, and Francesc Illas, Journal of Chemical Physics 128, 114103/1-8 (2008).
814. "Tight Binding Configuration Interaction (TBCI): A Non-Iterative Approach to Incorporating Electrostatics into Tight Binding," M. A. Iron, A. Heyden, G. Staszewska, and D. G. Truhlar, Journal of Chemical Theory and Computation 4, 804-818 (2008).
815. "Electrostatically Embedded Multiconfiguration Molecular Mechanics Based on the Combined Density Functional and Molecular Mechanical Method," M. Higashi and D. G. Truhlar, Journal of Chemical Theory and Computation 4, 790-803 (2008).
816. "The SM8 Solvation Model," C. J. Cramer and D. G. Truhlar, Accounts of Chemical Research, 41, 760-768 (2008).
817. "Stereochemistry of Eudesmane Cation Formation during Catalysis by Aristolochene Synthase from Penicillium roqueforti," D. J. Miller, J. Gao, D. G. Truhlar, N. J. Young, V. Gonzalez, R. K. Allemann, Organic & Biomolecular Chemistry 6, 2346-2354 (2008).
818. "Adiabatic States Derived from a Spin-Coupled Diabatic Transformation: Semiclassical Trajectory Study of Photodissociation of HBr and the Construction of Potential Curves for LiBr+," R. Valero, D. G. Truhlar, and A. W. Jasper, Journal of Physical Chemistry A 112, 5756-5769 (2008).
820. "Comment on ‘More Accurate Generalized Gradient Approximation for Solids'," Y. Zhao and D. G. Truhlar, Physical Review B 78, 197101/1-2 (2008).
821. "Construction of a Generalized Gradient Approximation by Restoring the Density-Gradient Expansion and Enforcing a Tight Lieb-Oxford Bound," Y. Zhao and D. G. Truhlar, Journal of Chemical Physics 128, 184109/1-8 (2008).
822. "Assessment of New Meta and Hybrid Meta Density Functionals for Predicting the Geometry and Binding Energy of a Challenging System: The Dimer of H2S and Benzene," H. Leverentz and D. G. Truhlar, Journal of Physical Chemistry A 112, 6009-6016 (2008).
824. "Multireference Model Chemistries for Thermochemical Kinetics," O. Tishchenko, J. Zheng, and D. G. Truhlar, Journal of Chemical Theory and Computation 4, 1208-1219 (2008).
826. "Performance of SM8 on a Test to Predict Small-Molecule Solvation Free Energies," C. J. Cramer, A. Chamberlin, and D. G. Truhlar, Journal of Physical Chemistry B 112, 8651-8655 (2008).
827. "Mixed Quantum/Classical Investigation of the Photodissociation of NH3(Ã) and a Practical Method for Maintaining Zero-Point Energy in Classical Trajectories," D. Bonhommeau and D. G. Truhlar, Journal of Chemical Physics 129, 014302/1-15 (2008).
828. "Nanosolids, Slushes, and Nanoliquids. Characterization of Nanophases in Metal Clusters and Nanoparticles," Z. H. Li and D. G. Truhlar, Journal of the American Chemical Society 130, 12698-12711 (2008).
829. "Algorithmic Decoherence Time for Decay of Mixing Non-Born-Oppenheimer Dynamics," S. C. Cheng, C. Zhu, K. K. Liang, S. H. Lin, and D. G. Truhlar, Journal of Chemical Physics 129, 24112/1-12 (2008).
This manuscript, in the accepted version, is now available free as manuscript NIHMS91029 at PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3658833/. In general we recommend accessing the published version if possible rather than than the accepted version, because we sometimes make post-acceptance corrections at the galley stage.
831. "Incorporation of a QM/MM Buffer Zone in the Variational Double Self-Consistent Field Method," W. Xie, D. G. Truhlar, and J Gao, Journal of Physical Chemistry B 112 14124-14131 (2008).
832. "Improved description of nuclear magnetic resonance shielding constants using the M06-L meta-generalized-gradient-approximation density functional," Y. Zhao and D. G. Truhlar, Journal of Physical Chemistry A 112, 6794-6799 (2008).
833. "Modeling Free Energies of Solvation in Olive Oil," A. Chamberlin, D. Levitt, C. J. Cramer, and D. G. Truhlar, Molecular Pharmceutics 5, 1064-1079 (2008).
834. "Effects of 18O Isotopic Substitution on the Rotational Spectra and Potential Splitting in the OH-H2O Complex: Improved Measurements for 16OH-16OH2 and 18OH-18OH2, New Measurements for the Mixed Isotopic Forms, and Ab Initio Calculations of the 2A' - 2A" Energy Separation," C. S. Brauer, G. Sedo, E. Dahlke, S. Wu, E. Grumstrup, K. R. Leopold, M. D. Marshall, H. O. Leung, and D. G. Truhlar, Journal of Chemical Physics 129, 104304/1-11 (2008).
Author complimentary copy Copyright (2009) American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics.
835. "Molecular Dynamics Simulation of a Solvated Protein in Water Using an Electronic Structure-based Explicit Polarization (X-POL) Potential: Polarization and Charge Redistribution in Bovine Pancreatic Trypsin Inhibitor in Water," Wangshen Xie, Modesto Orozco, Donald G. Truhlar, and Jiali Gao, Journal of Chemical Theory and Computation 5, 459-467 (2009).
836. "Exploring the Limit of Accuracy of the Global Hybrid Density Functional for Main-Group Thermochemistry, Kinetics, and Noncovalent Interactions," Y. Zhao and D. G. Truhlar, Journal of Chemical Theory and Computation 4, 1849-1868 (2008).
837. "Density Functional Study of Methyl Radical Association Reaction Kinetics," J. Zheng, S. Zhang, and D. G. Truhlar, Journal of Physical Chemistry A 112, 11509-11513 (2008).
838. " Study of the Ground and Excited States of Al3 and Al3-: II. Computational Analysis of the 488 nm Anion Photoelectron Spectrum and a Reconsideration of the Al_3 Bond Dissociation Energy," S. R. Miller, N. E. Schultz, D. G. Truhlar, and D. G. Leopold, Journal of Chemical Physics 130, 024304/1-23 (2009).
839. "Perspective on Diabatic Models of Chemical Reactivity as Illustrated by the Gas-Phase SN2 Reaction of Actetate Ion with 1,2-Dichloroethane," R. Valero, L. Song, J. Gao, and D. G. Truhlar, Journal of Chemical Theory and Computation 5, 1-22 (2009). Erratum: 5, 2191 (2009).
840. "Good performance of the M06 family of hybrid meta GGA density functionals on a difficult case: CO adsorption on MgO(001)," R. Valero, J. R. B. Gomes, D. G. Truhlar, and F. Illas, Journal of Chemical Physics 129, 124710/1-7 (2008). Erratum 130, 059901/1-1 (2009).
Author complimentary copy and Erratum Copyright (2008) American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics.
841. "Mechanistic Analysis of the Base-Catalyzed HF Elimination from 4-Fluoro-4-(4'-nitrophenyl)butane-2-one Based on Liquid-Phase Kinetic Isotope Effects Calculated by Dynamics Modeling with Multidimensional Tunneling," Y. Kim, A. V. Marenich, J. Zheng, K. H. Kim, M. Kołodziejska-Huben, M. Rostkowski, P. Paneth, and D. G. Truhlar, Journal of Chemical Theory and Computation 5, 59-67 (2009).
842. "Benchmark Energetic Data in a Model System for Grubbs II Metathesis Catalysis and Their Use for Assessment and Validation of Electronic Structure Methods," Y. Zhao and D. G. Truhlar, Journal of Chemical Theory and Computation 5, 324-333 (2009).
843. "Bond Angle Distributions of Carbon Dioxide in the Gas, Supercritical, and Solid Phases" K. Anderson, S. L. Mielke, J. I. Siepmann, and D. G. Truhlar, Journal of Physical Chemistry 113, 2053-2059 (2009) (Max Wolfsberg issue).
844. "Efficient Global Representations of Potential Energy Functions: Trajectory Calculations of Bimolecular Gas-Phase Reactions by Multiconfiguration Molecular Mechanics," O. Tishchenko and D. G. Truhlar, Journal of Chemical Physics 130, 024105/1-15 (2009).
845. "Performance of SM6, SM8, and SMD on the SAMPL1 Test Set for the Prediction of Small-Molecule Solvation Free Energies," A. Marenich, C. J. Cramer, and D. G. Truhlar, Journal of Physical Chemistry B 113, 4538-4543 (2009).
846. "Critical Role of Substrate Conformational Change in the Proton Transfer Process Catalyzed by 4-Oxalocrotonate Tautomerase," J. Ruiz-PernÃ­a, M. Garcia-Viloca, S. Bhattacharyay, J. Gao D. G. Truhlar, and I. Tuñon, Journal of the American Chemical Society 131, 2687-2698 (2009).
847. "Molecular Modeling of Complex Chemical Systems," D. G. Truhlar, Journal of the American Chemical Society 130, 16824-16827 (2008). (Editorial introducing JACS Select issue no. 3).
848. "Valence–Bond Order (VBO): A New Approach to Modeling Reactive Potential Energy Surfaces for Complex systems, Materials and Nanoparticles," M. Zhao, M. A. Iron, P. Staszewski, N. E. Schultz, R. Valero, and D. G. Truhlar, Journal of Chemical Theory and Computation 5, 594-604 (2009).
849. "Universal Solvation Model Based on Solute Electron Density and on a Continuum Model of the Solvent Defined by the Bulk Dielectric Constant and Atomic Surface Tensions," A. V. Marenich, C. J. Cramer, and D. G. Truhlar, Journal of Physical Chemistry B 113, 6378-6396 (2009).
850. "Reply to Comment on “A Universal Approach to Solvation Modeling," C. J. Cramer and D. G. Truhlar, Accounts of Chemical Research 42, 493-497 (2009).
851. "Calculation of Semiconductor Band Gaps with the M06-L Density Functional," Y. Zhao and D. G. Truhlar, Journal of Chemical Physics 130, 074103/1-3 (2009).
853. "Efficient Diffuse Basis Sets: cc-pVxZ+ and maug-cc-pVxZ," E. Papajak, H. R. Leverentz, J. Zheng, and D. G. Truhlar, Journal of Chemical Theory and Computation 5, 1197-1202 (2009). Errata and addendum 5, 3330-3330 (2009) .
854. "Consistent van der Waals Radii for the Whole Main Group," M. Mantina, A. C. Chamberlin, R. Valero, C. J. Cramer, and D. G. Truhlar, Journal of Physical Chemistry A 113, 5806-5812 (2009).
This manuscript, in the accepted version, is now available free as manuscript NIHMS112052 at PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3658832/. In general we recommend accessing the published version if possible rather than than the accepted version, because we some times make post-acceptance corrections at the galley stage.
855. "Thermochemical Kinetics for Multireference Systems: Addition Reactions of Ozone," Y. Zhao, O. Tishchenko, J. R. Gour, W. Li, J. J. Lutz, P. Piecuch, and D. G. Truhlar, Journal of Physical Chemistry A 113, 5786-5799 (2009).
856. "Improved methods for Feynman Path Integral Calculations of Vibrational-Rotational Free Energies and Application to Isotopic Fractionation of Hydrated Chloride Ions," S. L. Mielke and D. G. Truhlar Journal of Physical Chemistry 113, 4817-4827 (2009). (George C. Schatz Festschrift).
857. "Non-Hermitian Multiconfiguration Molecular Mechanics," O. Tishchenko and D. G. Truhlar, Journal of Chemical Theory and Computation 5, 1454-1461 (2009).
858. "Energies, Geometries, and Charge Distributions of Zn Molecules, Clusters, and Biocenters from Coupled Cluster, Density Functional, and Neglect of Diatomic Differential Overlap Models," A. Sorkin, E. A. Amin, and D. G. Truhlar, Journal of Chemical Theory and Computation 5, 1254-1265 (2009).
859. "The Electrostatically-Embedded Many-Body Approximation for Systems of Water, Ammonia, and Sulfuric Acid and the Dependence of its Performance on Embedding Charges," H. R. Leverentz and D. G. Truhlar, Journal of Chemical Theory and Computation 5, 1573-1584 (2009).
860. "Coupled-Surface Investigation of the Photodissociation of NH3(Ã): Effect of Exciting the Symmetric and Antisymmetric Stretching Modes," D. Bonhommeau, R. Valero, D. G. Truhlar, and A. Jasper, Journal of Chemical Physics 130, 234303/1-17 (2009).
863. "Validation Study of the Ability of Density Functionals to Predictthe Planar-to-Three-Dimensional Structural Transitionin Anionic Gold Clusters," M. Mantina, R. Valero, and D. G. Truhlar, Journal of Chemical Physics 131, 064706/1-5 (2009).
864. "Solvent Dependence of 14N Nuclear Magnetic Resonance Chemical Shielding Constants as a Test of the Accuracy of the Computed Polarization of Solute Electron Densities by the Solvent," R. F. Ribeiro, A. V. Marenich, C. J. Cramer, and D. G. Truhlar, Journal of Chemical Theory and Computation, Journal of Chemical Theory and Computation 5, 2284-2300 (2009).
865. "Steric Effects and Solvent Effects on SN2 Reactions," Y. Kim, C. J. Cramer, and D. G. Truhlar, Journal of Physical Chemistry A 113, 9109-9114 (2009).
866. "Universal Solvation Model Based on The Generalized Born Approximation with Asymmetric Descreening," A. V. Marenich, C. J. Cramer, and D. G. Truhlar, Journal of Chemical Theory and Computation, 5 2447-2464 (2009).
868. "Homogeneous Nucleation with Magic Numbers: Aluminum," S. L. Girshick, P. Agarwal, and D. G. Truhlar, Journal of Chemical Physics 131, 134305/1-11 (2009).
869. "Density Functional Theory for Transition Metals and Transition Metal Chemistry," C. J. Cramer and D. G. Truhlar, Physical Chemistry Chemical Physics 11, 10757-10816 (2009).
870. "Phase Space Prediction of Product Branching Ratios: Canonical Competitive Nonstatistical Model," J. Zheng, E. Papajak, and D. G. Truhlar, Journal of the American Chemical Society 131, 15754-15760 (2009).

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