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Darrin M. York

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Position: Principal Investigator
Education:

UNC Chapel Hill (B.S.) 1989, UNC Chapel Hill (Ph.D.) 1993

Email: Darrin.York[at]rutgers.edu
Office: CIPR-308G


About Me:

I have deep interests in the development of new theoretical methods to gain a molecular level understanding of complex biomolecular processes and guide design of new technology. My graduate work at the University of North Carolina at Chapel Hill involved the development of molecular simulation methods, including new methods for calculating electrostatic interactions of large systems such as the widely used particle-mesh Ewald method.  After graduating, I was an NSF postdoctoral fellow with Prof. Weitao Yang at Duke University, here I worked on linear-scaling electronic structure methods. Next, I took an NIH postdoctoral fellowship to work with Prof. Martin Karplus at Harvard to begin work on multiscale models to study complex biological problems (Prof. Karplus was a recipient of the 2013 Nobel Prize in Chemistry for his far-reaching work on multi-scale modeling). My work with Prof. Karplus continued with an EMBO fellowship at the Universite Louis Pasteur in Strasbourg, France, until I moved to my first faculty position at the University of Minnesota Twin Cities in 2000. In 2010, I was recruited to Rutgers along with with my research group, where we embarked on some extremely exciting new research directions in the development and application of multi-scale models. I am now Henry Rutgers University Professor, and Director of the laboratory for Biomolecular Simulation Research.  My research lab has several exciting active projects ranging from the development of novel multi-scale models, quantum mechanical and machine learning force fields and free energy methods, to cutting edge biological and biomedical applications ranging from biocatalysis mechanisms and enzyme design to drug discovery.  See our Research page for further details.





Publications:

Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery

(2020)
DOI: 10.1021/acs.jcim.0c00613
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Through the Looking CLASS: When Peer Leader Learning Attitudes Are Not What They Seem

(2020) 97, 2078-2090
DOI: 10.1021/acs.jchemed.0c00129
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Improved Alchemical Free Energy Calculations with Optimized Smoothstep Softcore Potentials

(2020) 16, 5512-5525
DOI: 10.1021/acs.jctc.0c00237
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Validation of Free Energy Methods in AMBER

(2020)
DOI: 10.1021/acs.jcim.0c00285
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Fast, Accurate, and Reliable Protocols for Routine Calculations of Protein−Ligand Binding Affinities in Drug Design Projects Using AMBER GPU-TI with ff14SB/GAFF

(2020) 5, 4611-4619
DOI: 10.1021/acsomega.9b04233
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Confluence of theory and experiment reveals the catalytic mechanism of the Varkud satellite ribozyme

(2020) 12, 193-201
DOI: 10.1038/s41557-019-0391-x
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The L-platform/L-scaffold framework: a blueprint for RNA-cleaving nucleic acid enzyme design

(2020) 26, 111-126
DOI: 10.1261/rna.071894.119
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Evidence for a Catalytic Strategy to Promote Nucleophile Activation in Metal-Dependent RNA-Cleaving Ribozymes and 8-17 DNAzyme

(2019) 9, 10612-10617
DOI: 10.1021/acscatal.9b02035
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Development of a Robust Indirect Approach for MM → QM Free Energy Calculations That Combines Force-Matched Reference Potential and Bennett’s Acceptance Ratio Methods

(2019) 15, 5543-5562
DOI: 10.1021/acs.jctc.9b00401
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Dynamical ensemble of the active state and transition state mimic for the RNA-cleaving 8–17 DNAzyme in solution

(2019) 47, 10282-10295
DOI: 10.1093/nar/gkz773
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Molecular simulations of the pistol ribozyme: unifying the interpretation of experimental data and establishing functional links with the hammerhead ribozyme

(2019) 25, 1439-1456
DOI: 10.1261/rna.071944.119
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Using AMBER18 for Relative Free Energy Calculations

(2019) 59, 3128-3135
DOI: 10.1021/acs.jcim.9b00105
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An Ontology for Facilitating Discussion of Catalytic Strategies of RNA-Cleaving Enzymes

(2019) 14, 1068-1076
DOI: 10.1021/acschembio.9b00202
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Cleaning Up Mechanistic Debris Generated by Twister Ribozymes Using Computational RNA Enzymology

(2019) 9, 5803-5815
DOI: 10.1021/acscatal.9b01155
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Framework for Conducting and Analyzing Crystal Simulations of Nucleic Acids to Aid in Modern Force Field Evaluation

(2019) 123, 4611-4624
DOI: 10.1021/acs.jpcb.8b11923
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Quantum Suppression of Intramolecular Deuterium Kinetic Isotope Effects in a Pericyclic Hydrogen Transfer Reaction

(2019) 123, 3647-3654
DOI: 10.1021/acs.jpca.9b00172
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Predicting site-binding modes of ions and water to nucleic acids using molecular solvation theory

(2019) 141, 2435
DOI: 10.1021/jacs.8b11474
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A Comparison of QM/MM Simulations with and without the Drude Oscillator Model Based on Hydration Free Energies of Simple Solutes

(2018) 23, 2695-2719
DOI: 10.3390/molecules23102695
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GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features

(2018) 58, 2043-2050
DOI: 10.1021/acs.jcim.8b00462
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On the convergence of multi-scale free energy simulations

(2018) 44, 1062-1081
DOI: 10.1080/08927022.2018.1475741
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Catalytic Strategies of Nucleolytic Ribozymes

(2018) Session 6, 341-344
ISBN: 12345
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A GPU-Accelerated Parameter Interpolation Thermodynamic Integration Free Energy Method

(2018) 14, 1564–1582
DOI: 10.1021/acs.jctc.7b01175
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Model for the Functional Active State of the TS Ribozyme from Molecular Simulation

(2017) 56, 13392-13395
DOI: 10.1002/anie.201705608
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A Multidimensional B-Spline Correction for Accurate Modeling Sugar Puckering in QM/MM Simulations

(2017) 13, 3975-3984
DOI: 10.1021/acs.jctc.7b00161
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Quantum mechanical force fields for condensed phase molecular simulations

(2017) 29, 383002-383016
DOI: 10.1088/1361-648X/aa7c5c
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Toward Fast and Accurate Binding Affinity Prediction with pmemdGTI: An Efficient Implementation of GPU-Accelerated Thermodynamic Integration

(2017) 13, 3077-3084
DOI: 10.1021/acs.jctc.7b00102
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Divalent Metal Ion Activation of a Guanine General Base in the Hammerhead Ribozyme: Insights from Molecular Simulations

(2017) 56, 2985-2994
DOI: 10.1021/acs.biochem.6b01192
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Improved ligand geometries in crystallographic refinement using AFITT in PHENIX

(2016) 72, 1062-1072
DOI: 10.1107/S2059798316012225
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A Two-Metal-Ion-Mediated Conformational Switching Pathway for HDV Ribozyme Activation

(2016) 6, 1853-1869
DOI: 10.1021/acscatal.5b02158
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Creation of Academic Social Networks (ASNs) for Effective Online eLearning Communities

(2016) Chapter 9, 109-126
ISBN: 12345
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The importance of protonation and tautomerization in relative binding affinity prediction: a comparison of AMBER TI and Schrödinger FEP

(2016) 30, 533-539
DOI: 10.1007/s10822-016-9920-5
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Ambient-Potential Composite Ewald Method for ab Initio Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulation

(2016) 12, 2611-2632
DOI: 10.1021/acs.jctc.6b00198
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VR-SCOSMO: A smooth conductor-like screening model with charge-dependent radii for modeling chemical reactions

(2016) 144, 164115
DOI: 10.1063/1.4946779
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A Modified Divide-and-Conquer Linear-Scaling Quantum Force Field with Multipolar Charge Densities

(2016) Chapter 2, 1-32
ISBN: 12345
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Ribozyme catalysis with a twist: the active state of the twister ribozyme in solution predicted from molecular simulation

(2016) 138, 3058-3065
DOI: 10.1021/jacs.5b12061
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Isotope effect analyses provide evidence for an altered transition state for RNA 2'-O-transphosphorylation catalyzed by Zn2+

(2016) 52, 4462-4465
DOI: 10.1039/C5CC10212J
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An active site rearrangement within the Tetrahymena group I ribozyme releases nonproductive interactions and allows formation of catalytic interactions.

(2016) 22, 32-48
DOI: 10.1261/rna.053710.115
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Charge-dependent many-body exchange and dispersion interactions in combined QM/MM simulations

(2015) 143, 234111
DOI: 10.1063/1.4937166
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Force Field for Mg2+, Mn2+, Zn2+, and Cd2+ Ions That Have Balanced Interactions with Nucleic Acids

(2015) 119, 15460-15460
DOI: 10.1021/acs.jpcb.5b10423
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Multiscale methods for computational RNA enzymology

(2015) 553, 335-374
ISBN: 12345
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Multipolar Ewald Methods. II. Applications Using a Quantum Mechanical Force Field

(2015) 11, 451-461
DOI: 10.1021/ct500799g
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Multipolar Ewald Methods. I. Theory, Accuracy, and Performance

(2015) 11, 436-450
DOI: 10.1021/ct5007983
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Structural fidelity and NMR relaxation analysis in a prototype RNA hairpin

(2015) 21, 963-974
DOI: 10.1261/rna.047357.114
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Integration of kinetic isotope effect analyses to elucidate ribonuclease mechanism

(2015) 1854, 1801-1808
DOI: 10.1016/j.bbapap.2015.04.022
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Enzyme transition states from theory and experiment

(2015) 1854, 1727–1728
DOI: 10.1016/j.bbapap.2015.08.006
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Heavy Atom Labeled Nucleotides for Measurement of Kinetic Isotope Effects

(2015) 1854, 1737-1745
DOI: 10.1016/j.bbapap.2015.03.007
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Effect of Zn2+ binding and enzyme active site on the transition state for RNA 2'-O-transphosphorylation interpreted through kinetic isotope effects

(2015) 1854, 1795-1800
DOI: 10.1016/j.bbapap.2015.02.022.
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Cation–Anion Interactions within the Nucleic Acid Ion Atmosphere Revealed by Ion Counting

(2015) 137, 14705-14715
DOI: 10.1021/jacs.5b08395
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Competitive interaction of monovalent cations with DNA from 3D-RISM

(2015) 43, 8405-8415
DOI: 10.1093/nar/gkv830
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Determination of hepatitis delta virus ribozyme N(–1) nucleobase and functional group specificity using internal competition kinetics

(2015) 483, 12-20
DOI: 10.1016/j.ab.2015.04.024
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Assessment of Metal-Assisted Nucleophile Activation in the Hepatitis Delta Virus Ribozyme from Molecular Simulation and 3D-RISM

(2015) 21, 1-12
DOI: 10.1261/rna.051466.115
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Nucleic acid reactivity: challenges for next-generation semiempirical quantum models

(2015) 36, 1370-1389
DOI: 10.1002/jcc.23933
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Comparison of Structural, Thermodynamic, Kinetic and Mass Transport Properties of Mg2+ Models Commonly Used in Biomolecular Simulations

(2015) 36, 970-982
DOI: 10.1002/jcc.23881
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Characterization of the three-dimensional free energy manifold for the uracil ribonucleoside from asynchronous replica exchange simulations

(2015) 11, 373-377
DOI: 10.1021/ct500776j
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Interpretation of pH–Activity Profiles for Acid–Base Catalysis from Molecular Simulations

(2015) 54, 1307-1313
DOI: 10.1021/bi5012833
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Mechanistic insights into RNA transphosphorylation from kinetic isotope effects and linear free energy relationships of model reactions

(2014) 20, 1-9
DOI: 10.1002/chem.201403862
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Recent advances toward a general purpose linear-scaling quantum force field

(2014) 47, 2812–2820
DOI: 10.1021/ar500103g
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Linear Free Energy Relationships in RNA Transesterification: Theoretical Models to Aid Experimental Interpretations

(2014) 16, 15846-15855
DOI: 10.1039/c4cp01050g
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Altered (transition) states: mechanisms of solution and enzyme catalyzed RNA 2'-O-transphosphorylation

(2014) 21, 96-102
DOI: 10.1016/j.cbpa.2014.06.010.
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Ab Initio Path-Integral Calculations of Kinetic and Equilibrium Isotope Effects on Base-Catalyzed RNA Transphosphorylation Models

(2014) 35, 1302-1316
DOI: 10.1002/jcc.23628
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Molecular Dynamics Simulation of Nitrobenzene Dioxygenase Using AMBER Force Field

(2014) 10, 2246-2254
DOI: 10.1021/ct500205z
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Evidence for the role of active site residues in the hairpin ribozyme from molecular simulations along the reaction path

(2014) 136, 7789-7792
DOI: 10.1021/ja500180q
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Improvement of DNA and RNA sugar pucker profiles from semiempirical quantum methods

(2014) 10, 1538–1545
DOI: 10.1021/ct401013s
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Parametrization of an Orbital-Based Linear-Scaling Quantum Force Field for Noncovalent Interactions

(2014) 10, 1086–1098
DOI: 10.1021/ct401035t
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Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent Using Discrete Protonation States: Implementation, Testing, and Validation

(2014) 10, 1341–1352
DOI: 10.1021/ct401042b
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Ion counting from explicit solvent simulations and 3D-RISM

(2014) 106, 883-894
DOI: 10.1016/j.bpj.2014.01.021
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Quantum mechanical study of solvent effects in prototype SN2 reactions in solution: Cl- attack on CH3Cl

(2014) 140, 054109
DOI: 10.1063/1.4863344
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Roadmaps through Free Energy Landscapes Calculated Using the Multidimensional vFEP Approach

(2014) 10, 24-34
DOI: 10.1021/ct400691f
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Bridging the Gap Between Theory and Experiment to Derive a Detailed Understanding of Hammerhead Ribozyme Catalysis

(2013) 120, 25-91
ISBN: 12345
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Experimental and computational analysis of the transition state for ribonuclease A-catalyzed RNA 2'-O-transphosphorylation

(2013) 110, 13002-13007
ISBN: 12345
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A Framework for Flexible and Scalable Replica-Exchange on Production Distributed Cyberinfrastructure.

(2013)
ISBN: 12345
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A Variational Linear-Scaling Framework to Build Practical, Efficient Next-Generation Orbital-Based Quantum Force Fields

(2013) 9, 1417-1427
DOI: 10.1021/ct3010134
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Molecular Simulations of RNA 2'-O-Transesterification Reaction Models in Solution

(2013) 117, 94-103
DOI: 10.1021/jp3084277
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A New Maximum Likelihood Approach for Free Energy Profile Construction from Molecular Simulations

(2013) 9, 153-164
DOI: 10.1021/ct300703z
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Exact Relation between Potential of Mean Force and Free-Energy Profile

(2012) 8, 3998-4003
DOI: 10.1021/ct300392f
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Mapping L1 ligase ribozyme conformational switch

(2012) 423, 106-122
DOI: 10.1016/j.jmb.2012.06.035
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Extended Polarization in Third-Order SCC-DFTB from Chemical-Potential Equalization

(2012) 116, 9131-9141
DOI: 10.1021/jp306239c
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Density-functional expansion methods: Grand challenges

(2012) 131, 1145-1161
DOI: 10.1007/s00214-012-1145-7
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Characterization of the Reaction Path and Transition States for RNA Transphosphorylation Models from Theory and Experiment

(2012) 51, 647-651
DOI: 10.1002/anie.201104147
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Characterization of the structure and dynamics of the HDV ribozyme in different stages along the reaction path

(2011) 2, 2538-2543
DOI: 10.1021/jz201106y
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Density-functional expansion methods: Generalization of the auxiliary basis

(2011) 134, 194103
DOI: 10.1063/1.3587052
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Influence of C-5 substituted cytosine and related nucleoside analogs on the formation of benzo[a]pyrene diol epoxide-dG adducts

(2011) 39, 3988-4006
DOI: 10.1093/nar/gkq1341
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Active participation of Mg2+ ion in the reaction coordinate of RNA self-cleavage catalyzed by the hammerhead ribozymes

(2011) 7, 1-3
DOI: 10.1021/ct100467t
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Accurate proton affinity and gas-phase basicity values of molecules important in biocatalysis

(2010) 114, 13911-13921
DOI: 10.1021/jp107450n
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Computational mutagenesis studies of hammerhead ribozyme catalysis

(2010) 132, 13505-13518
DOI: 10.1021/ja105956u
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Insights into the Role of Conformational Transitions and Metal Ion Binding in RNA Catalysis from Molecular Simulations

(2010) 6, 168-200
ISBN: 12345
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Molecular dynamics simulation of bovine pancreatic ribonuclease A - CpA and transition state-like complexes

(2010) 114, 7371-7382
DOI: 10.1021/jp909004y
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Identification of dynamical hinge points of the L1 ligase molecular switch

(2010) 16, 769-780
DOI: 10.1261/rna.1897810
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Exocyclic deoxyadenosine adducts of 1,2,3,4-Diepoxybutane: Synthesis, structural elucidation, and mechanistic studie

(2010) 23, 118-133
DOI: 10.1021/tx900312e
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CHARMM: The biomolecular simulation program

(2009) 30, 1545-1614
DOI: 10.1002/jcc.21287
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Unraveling the mechanisms of ribozyme catalysis with multi-scale simulations

(2009) 7, 377-408
ISBN: 12345
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Threshold occupancy and specific cation binding modes in the hammerhead ribozyme active site are required for active conformation

(2009) 388, 195-206
DOI: 10.1016/j.jmb.2009.02.054
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Density functional study of the influence of C5 cytosine substitution in base pairs with guanine

(2009) 122, 179-188
DOI: 10.1007/s00214-008-0497-5
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Description of phosphate hydrolysis reactions with the self-consistent-charge density-functional-tight-binding (SCC-DFTB) theory. 1. Parameterization

(2008) 4, 2067-2084
DOI: 10.1021/ct800330d
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Extension of adaptive tree code and fast multipole methods to high angular momentum particle charge densities

(2008) 29, 1895-1904
DOI: 10.1002/jcc.20946
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Electrostatic interactions in the hairpin ribozyme account for the majority of the rate acceleration without chemical participation by nucleobases

(2008) 14, 1501-1507
DOI: 10.1261/rna.863108
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Spherical tensor gradient operator method for integral rotation: A simple, efficient, and extendable alternative to Slater-Koster tables

(2008) 129, 016102
DOI: 10.1063/1.2945897
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Origin of Mutational Effects at the C3 and G8 Positions on Hammerhead Ribozyme Catalysis from Molecular Dynamics Simulations

(2008) 130, 7168-7169
DOI: 10.1021/ja711242b
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Contracted auxiliary Gaussian basis integral and derivative evaluation

(2008) 128, 064104
DOI: 10.1063/1.2821745
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Quantum mechanical/molecular mechanical simulation study of the mechanism of Hairpin ribozyme catalysis

(2008) 130, 4680-4691
DOI: 10.1021/ja0759141
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Solvent structure and hammerhead ribozyme catalysis

(2008) 15, 332-342
DOI: 10.1016/j.chembiol.2008.03.010
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Role of Mg2+ in hammerhead ribozyme catalysis from molecular simulation

(2008) 130, 3053-3064
DOI: 10.1021/ja076529e
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New QM/MM Models for Multi-scale Simulation of Phosphoryl Transfer Reactions in Solution

(2007) 201-218
ISBN: 12345
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Charge-dependent model for many-body polarization, exchange and dispersion interactions in hybrid QM/MM calculations

(2007) 127, 194101
DOI: 10.1063/1.2778428
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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

(2007) 111, 10861-10873
DOI: 10.1021/jp074167r
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Insight into the role of Mg2+in hammerhead ribozyme catalysis from x-ray crystallography and molecular dynamics simulation

(2007) 3, 325-327
DOI: 10.1021/ct6003142
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Specific reaction parametrization of the AM1/d Hamiltonian for phosphoryl transfer reactions: H, O, and P atoms

(2007) 3, 486-504
DOI: 10.1021/ct6002466
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CHARMM force field parameters for simulation of reactive intermediates in native and thio-substituted ribozymes

(2007) 28, 495-507
DOI: 10.1002/jcc.20474
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Enzyme dynamics and tunneling enhanced by compression in the hydrogen abstraction catalyzed by soybean lipoxygenase-1

(2006) 110, 24708-24719
DOI: 10.1021/jp066263i
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Simulations of phosphoryl transfer reactions using multi-scale quantum models

(2006) 181-192
ISBN: 12345
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QCRNA 1.0: A database of quantum calculations for RNA catalysis

(2006) 25, 423-433
DOI: 10.1016/j.jmgm.2006.02.011
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Transesterification thio effects of phosphate diesters: free energy barriers and kinetic and equilibrium isotope effects from density-functional theory

(2006) 45, 10043-10053
DOI: 10.1021/bi060869f
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Nucleophilic attack on phosphate diesters: a density functional study of in-line reactivity in dianionic, monoanionic, and neutral systems

(2006) 110, 11525-11539
DOI: 10.1021/jp0603942
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Normal modes of redox-active tyrosine: conformation dependence and comparison to experiment

(2006) 110, 10970-10981
DOI: 10.1021/jp061503f
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Multi-level and density functional electronic structure calculations of proton affinities and gas-phase basicities involved in biological phosphoryl transfer

(2006) 110, 791-797
DOI: 10.1021/jp054360q
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A charge-scaling implementation of the variational electrostatic projection method

(2006) 27, 103-115
DOI: 10.1002/jcc.20318
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Solvent polarization and kinetic isotope effects in nitroethane deprotonation and implications to the nitroalkane oxidase reaction

(2005) 127, 16374-16375
DOI: 10.1021/ja055881u
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A semiempirical quantum model for hydrogen bonded nucleic acid base pairs

(2005) 1, 1275-1285
DOI: 10.1021/ct050102l
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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

(2005) 109, 19987-20003
DOI: 10.1021/jp053146z
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Improvement of semiempirical response properties with charge-dependent response density

(2005) 123, 164108
DOI: 10.1063/1.2080007
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Theoretical studies of dissociative phosphoryl transfer in interconversion of phosphoenolpyruvate to phosphonopyruvate: solvent effects, thio effects, and implications for enzymatic reactions

(2005) 109, 13827-13834
DOI: 10.1021/jp051042i
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Benchmark calculations of proton affinities and gas-phase basicities of molecules important in the study of biological phosphoryl transfer

(2005) 7, 3070-3079
DOI: 10.1039/B504941E
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Smooth solvation method for d-orbital semiempirical calculations of biological reactions. 1. Implementation

(2005) 109, 9799-9809
DOI: 10.1021/jp044062d
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Smooth solvation method for d-orbital semiempirical calculations of biological reactions. 2. Application to transphosphorylation thio effects in solution

(2005) 109, 9810-9817
DOI: 10.1021/jp044061l
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High-order discretization schemes for biochemical applications of boundary element solvation and variational electrostatic projection methods

(2005) 122, 194110
DOI: 10.1063/1.1899146
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Pseudorotation barriers of biological oxyphosphoranes: a challenge for simulations of ribozyme catalysis

(2005) 11, 2081-2093
DOI: 10.1002/chem.200400790
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Ellipticity: a convenient tool to characterize electrocyclic reactions

(2005) 11, 1734-1738
DOI: 10.1002/chem.200401026
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The contribution of phosphate-phosphate repulsions to the free energy of DNA bending

(2005) 33, 1257-1268
DOI: 10.1093/nar/gki272
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Variational Electrostatic Projection (VEP) methods for efficient modeling of the macromolecular electrostatic and solvation environment in activated dynamics simulations

(2005) 109, 536-556
DOI: 10.1021/jp0469968
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An Efficient Linear-Scaling Ewald Method for Long-Range Electrostatic Interactions in Combined QM/MM Calculations

(2005) 1, 2-13
DOI: 10.1021/ct049941i
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Kinetic isotope effects on thio-substituted biological phosphoryl transfer reactions from density-functional theory

(2005) 31, 3909-3911
DOI: 10.1039/B502568K
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Theoretical methods that help understanding the structure and reactivity of gas phase ions

(2005) 240, 37-99
DOI: 10.1016/j.ijms.2004.09.018
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Structure and binding of Mg(II) ions and di-metal bridge complexes with biological phosphates and phosphoranes

(2004) 9, 807-817
DOI: 10.1007/s00775-004-0608-2
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Quantum descriptors for biological macromolecules from linear-scaling electronic structure methods

(2004) 56, 724-737
DOI: 10.1002/prot.20171
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Pseudorotation of natural and chemically modified biological phosphoranes: implications for RNA catalysis

(2004) 5, 1045-1049
DOI: 10.1002/cphc.200400091
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Hybrid QM/MM study of thio effects in transphosphorylation reactions: the role of solvation

(2004) 126, 7504–7513
DOI: 10.1021/ja031815l
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Many-body force field models based solely on pairwise Coulomb screening do not simultaneously reproduce correct gas-phase and condensed-phase polarizability limits

(2004) 120, 9903-9906
DOI: 10.1063/1.1756583
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Theoretical Study of the Vinyl Allene Oxide to Cyclopent-2-en-1-one Rearrangement:? Mechanism, Torquoselectivity and Solvent Effects

(2004) 69, 3635-3644
DOI: 10.1021/jo049620z
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Complete basis set extrapolated potential energy, dipole, and polarizability surfaces of alkali halide ion-neutral weakly avoided crossings with and without applied electric fields

(2004) 120, 7939
DOI: 10.1063/1.1690232
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The structure and stability of biological metaphosphate, phosphate, and phosphorane compounds in the gas phase and in solution

(2004) 126, 1654–1665
DOI: 10.1021/ja0356277
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Design and application of a multicoefficient correlatiomethod for dispersion interactions

(2004) 120, 590
DOI: 10.1063/1.1630955
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High-level ab initio methods for calculation of accurate potential energy surfaces of van der Waals complexes

(2004) 98, 388-408
DOI: 10.1002/qua.20074
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Examination of the correlation energy and second virial coefficients from accurate ab initio calculations of rare-gas dimers

(2003) 119, 2618-2622
DOI: 10.1063/1.1587684
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Insights into the regioselectivity and RNA-binding affinity of HIV-1 nucleocapsid protein from linear-scaling quantum methods

(2003) 330, 993-1004
DOI: 10.1016/S0022-2836(03)00658-2
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Hybrid QM/MM study of thio effects in transphosphorylation reactions

(2003) 125, 7178-7179
DOI: 10.1021/ja035167h
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Parameterization of semiempirical methods to treat nucleophilic attacks to biological phosphates: AM1/d parameters for phosphorus

(2003) 109, 149-159
DOI: 10.1007/s00214-002-0422-2
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Preface to proceedings of the symposium on methods and applications of combined quantum mechanical and molecularmechanical potentials (2001)

(2003) 109, 99
DOI: 10.1007/s00214-002-0414-2
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Fast approximate methods for calculating nucleic acid base pair interaction energies

(2003) 24, 57-67
DOI: 10.1002/jcc.10150
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Time-dependent density functional theory calculations of molecular static and dynamic polarizabilities, cauchy coefficients and their anisotropies with atomic numerical basis functions

(2002) 591, 255-266
DOI: 10.1016/S0166-1280(02)00246-4
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Quantum Mechanical Characterization of Nucleic Acids in Solution:? A Linear-Scaling Study of Charge Fluctuations in DNA and RNA

(2002) 106, 7693-7703
DOI: 10.1021/jp0146667
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Spectroscopic Properties of Tyrosyl Radicals in Dipeptides

(2002) 124, 5496-5505
DOI: 10.1021/ja0164327
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Theoretical studies on the hydrolysis of phosphate diesters in the gas phase, solution, and RNase A

(2002) 86, 10-26
DOI: 10.1002/qua.1601
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Electronic structure properties of solvated biomolecules: a quantum approach for macromolecular characterization

(2000) 21, 1562-1571
DOI: 10.1002/1096-987X(200012)21:16<1562::AID-JCC13>3.0.CO;2-E
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A Smooth Solvation Potential Based on the Conductor-Like Screening Model

(1999) 103, 11060-11079
DOI: 10.1021/jp992097l
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Application of Linear-Scaling Electronic Structure Methods to the Study of Polarization of Proteins and DNA in Solution

(1998) 712, 275-287
ISBN: 12345
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Quantum Mechanical Treatment of Biological Macromolecules in Solution using Linear-Scaling Electronic Structure Methods

(1998) 80, 5011-5014
DOI: 10.1103/PhysRevLett.80.5011
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Parameterization and efficient implementation of a solvent model for linear-scaling semiempirical quantum mechanical calculations of biological macromolecules

(1996) 263, 297-304
DOI: 10.1016/S0009-2614(96)01198-0
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Density-Functional Study of the Geometries, Stabilities, and Bond Energies of Group III-V (13-15) Four-Membered-Ring Compounds

(1996) 118, 5732-5736
DOI: 10.1021/ja951706+
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Quantum Mechanical Study of Aqueous Polarization Effects on Biological Macromolecules

(1996) 118, 10940-10941
DOI: 10.1021/ja961937w
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Linear-scaling semiempirical quantum calculations for macromolecules

(1996) 105, 2744
DOI: 10.1063/1.472136
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A chemical potential equalization method for molecular simulations

(1996) 104, 159-172
DOI: 10.1063/1.470886
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A new definition of atomic charges based on a variational principle for the electrostatic potential energy

(1995) 102, 7549
DOI: 10.1063/1.469086
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Toward the Accurate Modeling of DNA: The Importance of Long-Range Electrostatics

(1995) 117, 5001-5002
DOI: 10.1021/ja00122a034
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The effect of hydrostatic pressure on protein crystals investigated by molecular simulation

(1995) 27, 203-215
DOI: 10.1007/978-94-011-0497-5_17
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A generalized formulation of electronegativity equalization from density-functional theory

(1995) 56, 385-394
DOI: 10.1002/qua.560560842
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The Fast Fourier Poisson Method for Calculating Ewald Sums

(1994) 101, 3298
DOI: 10.1063/1.467576
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Atomic-level Accuracy in Simulations of Large Protein Crystals

(1994) 91, 8715-8718
ISBN: 12345
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Density-functional Calculations of the Structure and Stability of C240

(1994) 49, 8526-8528
DOI: 10.1103/PhysRevB.49.8526
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Simulations of the Solution Structure of the HIV-1 Protease in the Presence and Absence of Bound Zinc

(1994) 15, 61-71
DOI: 10.1002/jcc.540150108
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The Effect of Long-range Electrostatic Interactions in Simulations of Macromolecular Crystals: A Comparison of the Ewald and Truncated List Methods

(1993) 99, 8345
DOI: 10.1063/1.465608
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Molecular Modeling Studies Suggest that Zinc Ions Inhibit HIV-1 Protease by Binding at Catalytic Aspartates

(1993) 101, 246-250
DOI: 10.1289/ehp.93101246
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Particle Mesh Ewald: An N·log(N) Method for Ewald Sums in Large Systems

(1993) 98, 10089
DOI: 10.1063/1.464397
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Molecular Dynamics Simulation of HIV-1 Protease in a Crystalline Environment and in Solution

(1993) 32, 1443-1453
DOI: 10.1021/bi00057a007
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The Interaction of Na(I), Ca(II), and Mg(II) Metal Ions with Duplex DNA: A Theoretical Modeling Study

(1992) 44, 145-166
DOI: 10.1002/qua.560440715
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