New Publications

Using AMBER18 for Relative Free Energy Calculations

J. Chem. Inf. Model., (Accepted) ,
DOI: 10.1021/acs.jcim.9b00105

Quantum Suppression of Intramolecular Deuterium Kinetic Isotope Effects in a Pericyclic Hydrogen Transfer Reaction

J. Phys. Chem. A, (2019) 123, 3647-3654
DOI: 10.1021/acs.jpca.9b00172

Predicting site-binding modes of ions and water to nucleic acids using molecular solvation theory

J. Am. Chem. Soc., (2019) 141, 2435
DOI: 10.1021/jacs.8b11474

A Comparison of QM/MM Simulations with and without the Drude Oscillator Model Based on Hydration Free Energies of Simple Solutes

Molecules, (2018) 23, 2695-2719
DOI: 10.3390/molecules23102695

GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features

J. Chem. Inf. Model., (2018) 58, 2043-2050
DOI: 10.1021/acs.jcim.8b00462

On the convergence of multi-scale free energy simulations

Mol Simul, (2018) 44, 1062-1081
DOI: 10.1080/08927022.2018.1475741

A Multidimensional B-Spline Correction for Accurate Modeling Sugar Puckering in QM/MM Simulations

J. Chem. Theory Comput., (2017) 13, 3975-3984
DOI: 10.1021/acs.jctc.7b00161 Download PDF

Quantum mechanical force fields for condensed phase molecular simulations

J. Phys.: Condens. Matter, (2017) 29, 383002-383016
DOI: 10.1088/1361-648X/aa7c5c Download PDF

Toward Fast and Accurate Binding Affinity Prediction with pmemdGTI: An Efficient Implementation of GPU-Accelerated Thermodynamic Integration

J. Chem. Theory Comput. , (2017) 13, 3077-3084
DOI: 10.1021/acs.jctc.7b00102 Download PDF

Improved ligand geometries in crystallographic refinement using AFITT in PHENIX

Acta Crystallogr. D Struct Biol., (2016) 72, 1062-1072
DOI: 10.1107/S2059798316012225 Download PDF

The importance of protonation and tautomerization in relative binding affinity prediction: a comparison of AMBER TI and Schrödinger FEP

J. Comput. Aided Mol. Des., (2016) 30, 533-539
DOI: 10.1007/s10822-016-9920-5 Download PDF

Ambient-Potential Composite Ewald Method for ab Initio Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulation

J. Chem. Theory Comput., (2016) 12, 2611-2632
DOI: 10.1021/acs.jctc.6b00198 Download PDF

VR-SCOSMO: A smooth conductor-like screening model with charge-dependent radii for modeling chemical reactions

J. Chem. Phys., (2016) 144, 164115
DOI: 10.1063/1.4946779 Download PDF

A Modified Divide-and-Conquer Linear-Scaling Quantum Force Field with Multipolar Charge Densities

DOI: 10.4032/9789814613934 Download PDF

Charge-dependent many-body exchange and dispersion interactions in combined QM/MM simulations

J. Chem. Phys, (2015) 143, 234111
DOI: 10.1063/1.4937166 Download PDF

Enzyme transition states from theory and experiment

Biochim. Biophys. Acta, (2015) 1854, 1727–1728
DOI: 10.1016/j.bbapap.2015.08.006 Download PDF

Effect of Zn2+ binding and enzyme active site on the transition state for RNA 2'-O-transphosphorylation interpreted through kinetic isotope effects

Biochim. Biophys. Acta, (2015) 1854, 1795-1800
DOI: 10.1016/j.bbapap.2015.02.022. Download PDF

Heavy Atom Labeled Nucleotides for Measurement of Kinetic Isotope Effects

Biochim. Biophys. Acta, (2015) 1854, 1737-1745
DOI: 10.1016/j.bbapap.2015.03.007 Download PDF

Nucleic acid reactivity: challenges for next-generation semiempirical quantum models

J. Comput. Chem., (2015) 36, 1370-1389
DOI: 10.1002/jcc.23933 Download PDF

Multipolar Ewald Methods. II. Applications Using a Quantum Mechanical Force Field

J. Chem. Theory Comput., (2015) 11, 451-461
DOI: 10.1021/ct500799g Download PDF

Multipolar Ewald Methods. I. Theory, Accuracy, and Performance

J. Chem. Theory Comput., (2015) 11, 436-450
DOI: 10.1021/ct5007983 Download PDF

Recent advances toward a general purpose linear-scaling quantum force field

Acc. Chem. Res., (2014) 47, 2812–2820
DOI: 10.1021/ar500103g Download PDF

Linear Free Energy Relationships in RNA Transesterification: Theoretical Models to Aid Experimental Interpretations

Phys. Chem. Chem. Phys., (2014) 16, 15846-15855
DOI: 10.1039/C4CP01050G Download PDF

Ab Initio Path-Integral Calculations of  Kinetic and Equilibrium Isotope Effects on Base-Catalyzed RNA Transphosphorylation Models 

J. Comput. Chem., (2014) 35, 1302-1316
DOI: 10.1002/jcc.23628 Download PDF

Molecular Dynamics Simulation of Nitrobenzene Dioxygenase Using AMBER Force Field

J. Chem. Theory Comput., (2014) 10, 2246-2254
DOI: 10.1021/ct500205z Download PDF

Improvement of DNA and RNA sugar pucker profiles from semiempirical quantum methods

J. Chem. Theory Comput., (2014) 10, 1538–1545
DOI: 10.1021/ct401013s Download PDF

Parametrization of an Orbital-Based Linear-Scaling Quantum Force Field for Noncovalent Interactions

J. Chem. Theory Comput., (2014) 10, 1086–1098
DOI: 10.1021/ct401035t Download PDF

Quantum mechanical study of solvent effects in prototype SN2 reactions in solution: Cl- attack on CH3Cl

J. Chem. Phys., (2014) 140, 054109
DOI: 10.1063/1.4863344 Download PDF

A Variational Linear-Scaling Framework to Build Practical, Efficient Next-Generation Orbital-Based Quantum Force Fields

J. Chem. Theory Comput., (2013) 9, 1417-1427
DOI: 10.1021/ct3010134 Download PDF

Extended Polarization in Third-Order SCC-DFTB from Chemical-Potential Equalization

J. Phys Chem. A, (2012) 116, 9131-9141
DOI: 10.1021/jp306239c Download PDF

Density-functional expansion methods: Grand challenges

Theory. Chem. Acc., (2012) 131, 1145-1161
DOI: 10.1007/s00214-012-1145-7 Download PDF

Density-functional expansion methods: Generalization of the auxiliary basis

J. Chem. Phys., (2011) 134, 194103
DOI: 10.1063/1.3587052 Download PDF

Influence of C-5 substituted cytosine and related nucleoside analogs on the formation of benzo[a]pyrene diol epoxide-dG adducts 

Nucleic Acids Res., (2011) 39, 3988-4006
DOI: 10.1093/nar/gkq1341 Download PDF

Accurate proton affinity and gas-phase basicity values of molecules important in biocatalysis

J. Phys Chem. B, (2010) 114, 13911-13921
DOI: 10.1021/jp107450n Download PDF

Exocyclic deoxyadenosine adducts of 1,2,3,4-Diepoxybutane: Synthesis, structural elucidation, and mechanistic studie

Chem. Res. Toxicol., (2010) 23, 118-133
DOI: 10.1021/tx900312e Download PDF

Density functional study of the C5 cytosine substitution influence on base paired guanine

Theory. Chem. Acc., (2009) 122, 179-188
DOI: 10.1007/s00214-008-0497-5 Download PDF

Description of phosphate hydrolysis reactions with the self-consistent-charge density-functional-tight-binding (SCC-DFTB) theory. 1. Parameterization

J. Chem. Theory Comput., (2008) 4, 2067-2084
DOI: 10.1021/ct800330d Download PDF

Extension of adaptive tree code and fast multipole methods to high angular momentum particle charge densities

J. Comput. Chem., (2008) 29, 1895-1904
DOI: 10.1002/jcc.20946 Download PDF

Spherical tensor gradient operator method for integral rotation: A simple, efficient, and extendable alternative to Slater-Koster tables

J. Chem. Phys., (2008) 129, 016102
DOI: 10.1063/1.2945897 Download PDF

Solvent structure and hammerhead ribozyme catalysis

Chem. Biol., (2008) 15, 332-342
DOI: 10.1016/j.chembiol.2008.03.010 Download PDF

Role of Mg2+ in hammerhead ribozyme catalysis from molecular simulation

J. Am. Chem. Soc., (2008) 130, 3053-3064
DOI: 10.1021/ja076529e Download PDF

Insight into the role of Mg2+in hammerhead ribozyme catalysis from x-ray crystallography and molecular dynamics simulation

J. Chem. Theory Comput., (2007) 3, 325-327
DOI: 10.1021/ct6003142 Download PDF

Specific reaction parametrization of the AM1/d Hamiltonian for phosphoryl transfer reactions: H, O, and P atoms

J. Chem. Theory Comput., (2007) 3, 486-504
DOI: 10.1021/ct6002466 Download PDF

Enzyme dynamics and tunneling enhanced by compression in the hydrogen abstraction catalyzed by soybean lipoxygenase-1

J. Phys. Chem. B., (2006) 110, 24708-24719
DOI: 10.1021/jp066263i Download PDF

Transesterification thio effects of phosphate diesters: free energy barriers and kinetic and equilibrium isotope effects from density-functional theory

Biochemistry, (2006) 45, 10043-10053
DOI: 10.1021/bi060869f Download PDF

Nucleophilic attack on phosphate diesters: a density functional study of in-line reactivity in dianionic, monoanionic, and neutral systems

J. Phys. Chem. B., (2006) 110, 11525-11539
DOI: 10.1021/jp0603942 Download PDF

Normal modes of redox-active tyrosine: conformation dependence and comparison to experiment

J. Phys. Chem. B, (2006) 110, 10970-10981
DOI: 10.1021/jp061503f Download PDF

Multi-level and density functional electronic structure calculations of proton affinities and gas-phase basicities involved in biological phosphoryl transfer

J. Phys. Chem. A, (2006) 110, 7910797
DOI: 10.1021/jp054360q Download PDF

A charge-scaling implementation of the variational electrostatic projection method

J. Comput. Chem., (2006) 27, 103-115
DOI: 10.1002/jcc.20318 Download PDF

Solvent polarization and kinetic isotope effects in nitroethane deprotonation and implications to the nitroalkane oxidase reaction

J. Am. Chem. Soc., (2005) 127, 16374-16375
DOI: 10.1021/ja055881u Download PDF

A semiempirical quantum model for hydrogen bonded nucleic acid base pairs

J. Chem. Theory Comput., (2005) 1, 1275-1285
DOI: 10.1021/ct050102l Download PDF

Improvement of semiempirical response properties with charge-dependent response density

J. Chem. Phys., (2005) 123, 164108
DOI: 10.1063/1.2080007 Download PDF

Smooth solvation method for d-orbital semiempirical calculations of biological reactions. 1. Implementation

J. Phys. Chem. B., (2005) 109, 9799-9809
DOI: 10.1021/jp044062d Download PDF

Smooth solvation method for d-orbital semiempirical calculations of biological reactions. 2. Application to transphosphorylation thio effects in solution

J. Phys. Chem. B., (2005) 109, 9810-9817
DOI: 10.1021/jp044061l Download PDF

High-order discretization schemes for biochemical applications of boundary element solvation and variational electrostatic projection methods

J. Chem. Phys., (2005) 122, 194110
DOI: 10.1063/1.1899146 Download PDF

Pseudorotation barriers of biological oxyphosphoranes: a challenge for simulations of ribozyme catalysis

Chemistry, (2005) 11, 2081-2093
DOI: 10.1002/chem.200400790 Download PDF

Ellipticity: a convenient tool to characterize electrocyclic reactions

Chemistry, (2005) 11, 1734-1738
DOI: 10.1002/chem.200401026 Download PDF

Variational Electrostatic Projection (VEP) methods for efficient modeling of the macromolecular electrostatic and solvation environment in activated dynamics simulations

J. Phys. Chem. B., (2005) 109, 536-556
DOI: 10.1021/jp0469968 Download PDF

Kinetic isotope effects on thio-substituted biological phosphoryl transfer reactions from density-functional theory

Chem. Commun., (2005) 31, 3909-3911
DOI: 10.1039/B502568K Download PDF

Theoretical methods that help understanding the structure and reactivity of gas phase ions

Int. J. Mass Spectrom., (2005) 240, 37-99
DOI: 10.1016/j.ijms.2004.09.018 Download PDF

An Efficient Linear-Scaling Ewald Method for Long-Range Electrostatic Interactions in Combined QM/MM Calculations

J. Chem. Theory Comput., (2005) 1, 2-13
DOI: 10.1021/ct049941i Download PDF

Structure and binding of Mg(II) ions and di-metal bridge complexes with biological phosphates and phosphoranes

J. Biol. Inorg. Chem., (2004) 9, 807-817
DOI: 10.1007/s00775-004-0608-2 Download PDF

Quantum descriptors for biological macromolecules from linear-scaling electronic structure methods

Proteins, (2004) 56, 724-737
DOI: 10.1002/prot.20171 Download PDF

Hybrid QM/MM study of thio effects in transphosphorylation reactions: the role of solvation

J. Am. Chem. Soc., (2004) 126, 7504–7513
DOI: 10.1021/ja031815l Download PDF

Many-body force field models based solely on pairwise Coulomb screening do not simultaneously reproduce correct gas-phase and condensed-phase polarizability limits

J. Chem. Phys., (2004) 120, 9903-9906
DOI: 10.1063/1.1756583 Download PDF

Theoretical Study of the Vinyl Allene Oxide to Cyclopent-2-en-1-one Rearrangement:  Mechanism, Torquoselectivity and Solvent Effects

J. Org. Chem., (2004) 69, 3635-3644
DOI: 10.1021/jo049620z Download PDF

Complete basis set extrapolated potential energy, dipole, and polarizability surfaces of alkali halide ion-neutral weakly avoided crossings with and without applied electric fields

J. Chem. Phys., (2004) 120, 7939
DOI: 10.1063/1.1690232 Download PDF

The structure and stability of biological metaphosphate, phosphate, and phosphorane compounds in the gas phase and in solution

J. Am. Chem. Soc., (2004) 126, 1654–1665
DOI: 10.1021/ja0356277 Download PDF

Design and application of a multicoefficient correlatiomethod for dispersion interactions

J. Chem. Phys., (2004) 120, 590
DOI: 10.1063/1.1630955

Benchmark calculations of proton affinities and gas-phase basicities of molecules important in the study of biological phosphoryl transfer

Phys. Chem. Chem. Phys., (2005) 7, 3070-3079
DOI: 10.1039/B504941E Download PDF

High-level ab initio methods for calculation of accurate potential energy surfaces of van der Waals complexes

Int. J. Quantum Chem., (2004) 98, 388-408
DOI: 10.1002/qua.20074 Download PDF

Examination of the correlation energy and second virial coefficients from accurate ab initio calculations of rare-gas dimers

J. Chem. Phys., (2003) 119, 2618-2622
DOI: 10.1063/1.1587684 Download PDF

Hybrid QM/MM study of thio effects in transphosphorylation reactions

J. Am. Chem. Soc., (2003) 125, 7178-7179
DOI: 10.1021/ja035167h Download PDF

Parameterization of semiempirical methods to treat nucleophilic attacks to biological phosphates: AM1/d parameters for phosphorus

Theor. Chem. Acc., (2003) 109, 149-159
DOI: 10.1007/s00214-002-0422-2 Download PDF

Preface to proceedings of the symposium on methods and applications of combined quantum mechanical and molecularmechanical potentials (2001)

Theor. Chem. Acc., (2003) 109, 99
DOI: 10.1007/s00214-002-0414-2 Download PDF

Fast approximate methods for calculating nucleic acid base pair interaction energies

J. Comput. Chem., (2003) 24, 57-67
DOI: 10.1002/jcc.10150 Download PDF

Time-dependent density functional theory calculations of molecular static and dynamic polarizabilities, cauchy coefficients and their anisotropies with atomic numerical basis functions 

J. Mol. Struct. (Theochem.), (2002) 591, 255-266
DOI: 10.1016/S0166-1280(02)00246-4 Download PDF

Quantum Mechanical Characterization of Nucleic Acids in Solution:  A Linear-Scaling Study of Charge Fluctuations in DNA and RNA

J. Phys. Chem. B, (2002) 106, 7693-7703
DOI: 10.1021/jp0146667 Download PDF

Spectroscopic Properties of Tyrosyl Radicals in Dipeptides

J. Am. Chem. Soc., (2002) 124, 5496-5505
DOI: 10.1021/ja0164327 Download PDF

Theoretical studies on the hydrolysis of phosphate diesters in the gas phase, solution, and RNase A

Int. J. Quantum Chem., (2002) 86, 10-26
DOI: 10.1002/qua.1601 Download PDF

Electronic structure properties of solvated biomolecules: a quantum approach for macromolecular characterization

J. Comput. Chem., (2000) 21, 1562-1571
DOI: 10.1002/1096-987X(200012)21:16<1562::AID-JCC13>3.0.CO;2-E Download PDF

A Smooth Solvation Potential Based on the Conductor-Like Screening Model

J. Phys. Chem. A, (1999) 103, 11060-11079
DOI: 10.1021/jp992097l Download PDF

Application of Linear-Scaling Electronic Structure Methods to the Study of Polarization of Proteins and DNA in Solution

ACS Symposium Series, (1998) 712, 275-287
DOI: 10.1021/bk-1998-0712.ch018 Download PDF

Quantum Mechanical Treatment of Biological Macromolecules in Solution using Linear-Scaling Electronic Structure Methods

Phys. Rev. Lett., (1998) 80, 5011-5014
DOI: 10.1103/PhysRevLett.80.5011 Download PDF

Density-Functional Study of the Geometries, Stabilities, and Bond Energies of Group III−V (13−15) Four-Membered-Ring Compounds

J. Am. Chem. Soc., (1996) 118, 5732-5736
DOI: 10.1021/ja951706+ Download PDF

Quantum Mechanical Study of Aqueous Polarization Effects on Biological Macromolecules

J. Am. Chem. Soc., (1996) 118, 10940-10941
DOI: 10.1021/ja961937w Download PDF

Linear‐scaling semiempirical quantum calculations for macromolecules

J. Chem. Phys., (1996) 105, 2744
DOI: 10.1063/1.472136 Download PDF

A chemical potential equalization method for molecular simulations

J. Chem. Phys., (1996) 104, 159-172
DOI: 10.1063/1.470886 Download PDF

A new definition of atomic charges based on a variational principle for the electrostatic potential energy

J. Chem. Phys., (1995) 102, 7549
DOI: 10.1063/1.469086 Download PDF

The effect of hydrostatic pressure on protein crystals investigated by molecular simulation

Jerus. Sym. Q., (1995) 27, 203-215
DOI: 10.1007/978-94-011-0497-5_17 Download PDF

A generalized formulation of electronegativity equalization from density-functional theory

Int. J. Quantum Chem., (1995) 56, 385-394
DOI: 10.1002/qua.560560842 Download PDF

The Fast Fourier Poisson Method for Calculating Ewald Sums

J. Chem. Phys., (1994) 101, 3298
DOI: 10.1063/1.467576 Download PDF

Atomic-level Accuracy in Simulations of Large Protein Crystals

Proc. Natl. Acad. Sci. USA, (1994) 91, 8715-8718
DOI: 10.1073/pnas.91.18.8715 Download PDF

Density-functional Calculations of the Structure and Stability of C240

Phys. Rev. B: Condens. Matter, (1994) 49, 8526-8528
DOI: 10.1103/PhysRevB.49.8526 Download PDF

Simulations of the Solution Structure of the HIV-1 Protease in the Presence and Absence of Bound Zinc

J. Comput. Chem., (1994) 15, 61-71
DOI: 10.1002/jcc.540150108 Download PDF

The Effect of Long-range Electrostatic Interactions in Simulations of Macromolecular Crystals: A Comparison of the Ewald and Truncated List Methods

J. Chem. Phys., (1993) 99, 8345
DOI: 10.1063/1.465608 Download PDF

Particle Mesh Ewald: An N⋅log(N) Method for Ewald Sums in Large Systems

J. Chem. Phys., (1993) 98, 10089
DOI: 10.1063/1.464397 Download PDF
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