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New Publications

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

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

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

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

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

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

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

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

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

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

DOI: 10.1021/ct100467t 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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