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New Publications

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

A Two-Metal-Ion-Mediated Conformational Switching Pathway for HDV Ribozyme Activation

ACS Catal., (2016) 6, 1853-1869
DOI: 10.1021/acscatal.5b02158 Download PDF

Creation of Academic Social Networks (ASNs) for Effective Online eLearning Communities

DOI: 10.1021/bk-2016-1217.ch009

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

Ribozyme catalysis with a twist: the active state of the twister ribozyme in solution predicted from molecular simulation

J. Am. Chem. Soc., (2016) 138, 3058-3065
DOI: 10.1021/jacs.5b12061 Download PDF

Isotope effect analyses provide evidence for an altered transition state for RNA 2'-O-transphosphorylation catalyzed by Zn2+

Chem Commun (Camb)., (2016) 52, 4462-4465
DOI: 10.1039/C5CC10212J Download PDF

An active site rearrangement within the Tetrahymena group I ribozyme releases nonproductive interactions and allows formation of catalytic interactions.

RNA, (2016) 22, 32-48
DOI: 10.1261/rna.053710.115 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

Force Field for Mg2+, Mn2+, Zn2+, and Cd2+ Ions That Have Balanced Interactions with Nucleic Acids

J. Phys. Chem. B., (2015) 119, 15460-15460
DOI: 10.1021/acs.jpcb.5b10423 Download PDF

Integration of kinetic isotope effect analyses to elucidate ribonuclease mechanism

Biochim Biophys Acta, (2015) 1854, 1801-1808
DOI: 10.1016/j.bbapap.2015.04.022 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

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

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

Cation–Anion Interactions within the Nucleic Acid Ion Atmosphere Revealed by Ion Counting

J. Am. Chem. Soc., (2015) 137, 14705-14715
DOI: 10.1021/jacs.5b08395 Download PDF

Competitive interaction of monovalent cations with DNA from 3D-RISM

Nucleic Acids Res., (2015) 43, 8405-8415
DOI: 10.1093/nar/gkv830 Download PDF

Determination of hepatitis delta virus ribozyme N(–1) nucleobase and functional group specificity using internal competition kinetics

Anal. Biochem., (2015) 483, 12-20
DOI: 10.1016/j.ab.2015.04.024 Download PDF

Assessment of Metal-Assisted Nucleophile Activation in the Hepatitis Delta Virus Ribozyme from Molecular Simulation and 3D-RISM

RNA, (2015) 21, 1-12
DOI: 10.1261/rna.051466.115 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

Comparison of Structural, Thermodynamic, Kinetic and Mass Transport Properties of Mg2+ Models Commonly Used in Biomolecular Simulations

J. Comput. Chem., (2015) 36, 970-982
DOI: 10.1002/jcc.23881 Download PDF

Characterization of the three-dimensional free energy manifold for the uracil ribonucleoside from asynchronous replica exchange simulations

J. Chem. Theory Comput., (2015) 11, 373-377
DOI: 10.1021/ct500776j Download PDF

Interpretation of pH–Activity Profiles for Acid–Base Catalysis from Molecular Simulations

Biochemistry, (2015) 54, 1307-1313
DOI: 10.1021/bi5012833 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

Structural fidelity and NMR relaxation analysis in a prototype RNA hairpin

RNA, (2015) 21, 963-974
DOI: 10.1261/rna.047357.114 Download PDF

Mechanistic insights into RNA transphosphorylation from kinetic isotope effects and linear free energy relationships of model reactions

Chem. Eur. J., (2014) 20, 14336-14343
DOI: 10.1002/chem.201403862 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

Altered (transition) states: mechanisms of solution and enzyme catalyzed RNA 2'-O-transphosphorylation

Curr. Opin. Chem. Biol., (2014) 21C, 96-102
DOI: 10.1016/j.cbpa.2014.06.010. 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

Evidence for the role of active site residues in the hairpin ribozyme from molecular simulations along the reaction path

J. Am. Chem. Soc., (2014) 136, 7789-7792
DOI: 10.1021/ja500180q 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

Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent Using Discrete Protonation States: Implementation, Testing, and Validation

J. Chem. Theory Comput., (2014) 10, 1341–1352
DOI: 10.1021/ct401042b Download PDF

Ion counting from explicit solvent simulations and 3D-RISM

Biophys. J., (2014) 106, 883-894
DOI: 10.1016/j.bpj.2014.01.021 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

Roadmaps through Free Energy Landscapes Calculated Using the Multidimensional vFEP Approach

J. Chem. Theory Comput., (2014) 10, 24-34
DOI: 10.1021/ct400691f Download PDF

Bridging the Gap Between Theory and Experiment to Derive a Detailed Understanding of Hammerhead Ribozyme Catalysis

DOI: 10.1016/B978-0-12-381286-5.00002-0 Download PDF

Experimental and computational analysis of the transition state for ribonuclease A-catalyzed RNA 2'-O-transphosphorylation

Proc. Natl. Acad. Sci. USA, (2013) 110, 13002-13007
DOI: 10.1073/pnas.1215086110 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

Molecular Simulations of RNA 2′-O-Transesterification Reaction Models in Solution

J. Phys Chem. B, (2013) 117, 94-103
DOI: 10.1021/jp3084277 Download PDF

A New Maximum Likelihood Approach for Free Energy Profile Construction from Molecular Simulations

J. Chem. Theory Comput., (2013) 9, 153-164
DOI: 10.1021/ct300703z Download PDF

Exact Relation between Potential of Mean Force and Free-Energy Profile

J. Chem. Theory Comput., (2012) 8, 3998-4003
DOI: 10.1021/ct300392f Download PDF

Mapping l1 ligase ribozyme conformational switch

J. Mol. Biol., (2012) 423, 106-122
DOI: 10.1016/j.jmb.2012.06.035 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

Characterization of the Reaction Path and Transition States for RNA Transphosphorylation Models from Theory and Experiment

Angew. Chem. Int. Ed., (2012) 51, 647-651
DOI: 10.1002/anie.201104147 Download PDF

Characterization of the structure and dynamics of the HDV ribozyme in different stages along the reaction path

J. Phys. Chem. Lett., (2011) 2, 2538-2543
DOI: 10.1021/jz201106y 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

Active participation of Mg2+ ion in the reaction coordinate of RNA self-cleavage catalyzed by the hammerhead ribozymes

DOI: 10.1021/ct100467t 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

Computational mutagenesis studies of hammerhead ribozyme catalysis

J. Am. Chem. Soc., (2010) 132, 13505-13518
DOI: 10.1021/ja105956u Download PDF

Insights into the Role of Conformational Transitions and Metal Ion Binding in RNA Catalysis from Molecular Simulations

DOI: 10.1016/S1574-1400(10)06001-9 Download PDF

Molecular dynamics simulation of bovine pancreatic ribonuclease A - CpA and transition state-like complexes

J. Phys. Chem. B, (2010) 21, 7371-7382
DOI: 10.1021/jp909004y Download PDF

Identification of dynamical hinge points of the L1 ligase molecular switch

RNA, (2010) 16, 769-780
DOI: 10.1261/rna.1897810 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

Threshold occupancy and specific cation binding modes in the hammerhead ribozyme active site are required for active conformation

J. Mol. Biol., (2009) 388, 195-206
DOI: 10.1016/j.jmb.2009.02.054 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

Electrostatic interactions in the hairpin ribozyme account for the majority of the rate acceleration without chemical participation by nucleobases

RNA, (2008) 14, 1501-1507
DOI: 10.1261/rna.863108 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

Origin of Mutational Effects at the C3 and G8 Positions on Hammerhead Ribozyme Catalysis from Molecular Dynamics Simulations

J. Am. Chem. Soc., (2008) 130, 7168-7169
DOI: 10.1021/ja711242b Download PDF

Contracted auxiliary Gaussian basis integral and derivative evaluation

J. Chem. Phys., (2008) 128, 064104
DOI: 10.1063/1.2821745 Download PDF

Quantum mechanical/molecular mechanical simulation study of the mechanism of Hairpin ribozyme catalysis

J. Am. Chem. Soc., (2008) 130, 4680-4691
DOI: 10.1021/ja0759141 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

New QM/MM Models for Multi-scale Simulation of Phosphoryl Transfer Reactions in Solution

DOI: 10.1002/9780470191675.ch12 Download PDF

Charge-dependent model for many-body polarization, exchange and dispersion interactions in hybrid QM/MM calculations

J. Chem. Phys., (2007) 127, 194101
DOI: 10.1063/1.2778428 Download PDF

Extension of the self-consistent-charge density-functional tight-binding method: third-order expansion of the density functional theory total energy and introduction of a modified effective coulomb interaction

J. Phys Chem. A, (2007) 111, 10861-10873
DOI: 10.1021/jp074167r 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

CHARMM force field parameters for simulation of reactive intermediates in native and thio-substituted ribozymes

J. Comput. Chem., (2007) 28, 495-507
DOI: 10.1002/jcc.20474 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

Density-functional study of the in-line mechanism of methanolysis of cyclic phosphate and thiophosphate esters in solution: insight into thio effects in RNA transesterification

J. Phys. Chem. B., (2005) 109, 19987-20003
DOI: 10.1021/jp053146z 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

Theoretical studies of dissociative phosphoryl transfer in interconversion of phosphoenolpyruvate to phosphonopyruvate: solvent effects, thio effects, and implications for enzymatic reactions

J. Phys. Chem. B, (2005) 109, 13827-13834
DOI: 10.1021/jp051042i 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

The contribution of phosphate-phosphate repulsions to the free energy of DNA bending

Nucleic Acids Res., (2005) 33, 1257-1268
DOI: 10.1093/nar/gki272 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

Pseudorotation of natural and chemically modified biological phosphoranes: implications for RNA catalysis

Chem. Phys. Chem., (2004) 5, 1045-1049
DOI: 10.1002/cphc.200400091 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

Insights into the regioselectivity and RNA-binding affinity of HIV-1 nucleocapsid protein from linear-scaling quantum methods

J. Mol. Biol., (2003) 330, 993-1004
DOI: 10.1016/S0022-2836(03)00658-2 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

Parameterization and efficient implementation of a solvent model for linear-scaling semiempirical quantum mechanical calculations of biological macromolecules

Chem. Phys. Lett., (1996) 263, 297-304
DOI: 10.1016/S0009-2614(96)01198-0 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

Toward the Accurate Modeling of DNA: The Importance of Long-Range Electrostatics

J. Am. Chem. Soc., (1995) 117, 5001-5002
DOI: 10.1021/ja00122a034 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

Molecular Modeling Studies Suggest that Zinc Ions Inhibit HIV-1 Protease by Binding at Catalytic Aspartates

Environ. Health Perspect., (1993) 101, 246-250
DOI: 10.1289/ehp.93101246 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

Molecular Dynamics Simulation of HIV-1 Protease in a Crystalline Environment and in Solution

Biochemistry, (1993) 32, 1443-1453
DOI: 10.1021/bi00057a007 Download PDF

The Interaction of Na(I), Ca(II), and Mg(II) Metal Ions with Duplex DNA: A Theoretical Modeling Study

Int. J. Quantum Chem., (1992) 44, 145-166
DOI: 10.1002/qua.560440715 Download PDF