Publications

For more detail, please go Google Scholar

2019

165

The generalized Boltzmann distribution is the only distribution in which the Gibbs-Shannon entropy equals the thermodynamic entropy

Xiang Gao, Emilio Gallicchio, Adrian E. Roitberg.
The Journal of Chemical Physics, 151:034113 (2019)

164

Fast Implementation of the Nudged Elastic Band Method in AMBER

Delaram Ghoreishi, David S. Cerutti, Zachary Fallon, Carlos Simmerling, Adrian E. Roitberg.
Journal of Chemical Theory and Computation, 15:4699-4707 (2019)

163

Approaching coupled cluster accuracy with a general-purpose neural network potential through transfer learning

Justin S. Smith, Benjamin T. Nebgen, Roman Zubatyuk, Nicholas Lubbers, Christian Devereux, Kipton Barros, Sergei Tretiak, Olexandr Isayev, Adrian E. Roitberg.
Nature Communications, 10:2903 (2019)

162

pH-Dependent Conformational Changes Due to Ionizable Residues in a Hydrophobic Protein Interior: The Study of L25K and L125K Variants of SNase

Ankita Sarkar, Pancham Lal Gupta, Adrian E. Roitberg.
The Journal of Physical Chemistry B, 123:5742-5754 (2019)

161

Can the Electrostatically Embedded Many-Body Expansion be applied for fast and accurate ab initio Molecular Dynamics

Cruzeiro, Vinícius Wilian; Georg, Herbert; Cabral, Benedito; Roitberg, Adrian.
Journal of Chemical Theory and Computation, Submitted (2019)

160

Multidimensional Replica Exchange Simulations for Efficient Constant pH and Redox Potential Molecular Dynamics

Vinícius Wilian D. Cruzeiro, Adrian E. Roitberg.
Journal of Chemical Theory and Computation, 15:871-881 (2019)

2018

159

Energy transfer and spatial scrambling of an exciton in a conjugated dendrimer

D. Ondarse-Alvarez, N. Oldani, A. E. Roitberg, V. Kleiman, S. Tretiak, S. Fernandez-Alberti.
Physical Chemistry Chemical Physics, 20:29648-29660 (2018)

158

Transforming Computational Drug Discovery with Machine Learning and AI

Justin S. Smith, Adrian E. Roitberg, Olexandr Isayev.
ACS Medicinal Chemistry Letters, 9:1065-1069 (2018)

157

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

Tai-Sung Lee, David S. Cerutti, Dan Mermelstein, Charles Lin, Scott LeGrand, Timothy J. Giese, Adrian Roitberg, David A. Case, Ross C. Walker, Darrin M. York.
Journal of Chemical Information and Modeling, 58:2043-2050 (2018)

156

Investigating Saccharomyces cerevisiae alkene reductase OYE 3 by substrate profiling, X-ray crystallography and computational methods

Robert W. Powell, III, M. Pilar Buteler, Sunidhi Lenka, Michele Crotti, Sara Santangelo, Matthew J. Burg, Steven Bruner, Elisabetta Brenna, Adrian E. Roitberg, Jon D. Stewart.
Catalysis Science & Technology, 8:5003-5016 (2018)

155

Probing the Structures of Solvent-Complexed Ions Formed in Electrospray Ionization Using Cryogenic Infrared Photodissociation Spectroscopy

Matthew R. Bell, Vinícius Wilian D. Cruzeiro, Adam P. Cismesia, Larry F. Tesler, Adrian E. Roitberg, Nicolas C. Polfer.
The Journal of Physical Chemistry A, 122:7427-7436 (2018)

154

Redox potential replica exchange molecular dynamics at constant pH in AMBER: Implementation and validation

Vinícius Wilian D. Cruzeiro, Marcos S. Amaral, Adrian E. Roitberg.
The Journal of Chemical Physics, 149:072338 (2018)

153

Transferable Dynamic Molecular Charge Assignment Using Deep Neural Networks

Benjamin Nebgen, Nicholas Lubbers, Justin S. Smith, Andrew E. Sifain, Andrey Lokhov, Olexandr Isayev, Adrian E. Roitberg, Kipton Barros, Sergei Tretiak.
Journal of Chemical Theory and Computation, 14:4687-4698 (2018)

152

Discovering a Transferable Charge Assignment Model Using Machine Learning

Andrew E. Sifain, Nicholas Lubbers, Benjamin T. Nebgen, Justin S. Smith, Andrey Y. Lokhov, Olexandr Isayev, Adrian E. Roitberg, Kipton Barros, Sergei Tretiak.
The Journal of Physical Chemistry Letters, 9:4495-4501 (2018)

151

Coherent exciton-vibrational dynamics and energy transfer in conjugated organics

Tammie R. Nelson, Dianelys Ondarse-Alvarez, Nicolas Oldani, Beatriz Rodriguez-Hernandez, Laura Alfonso-Hernandez, Johan F. Galindo, Valeria D. Kleiman, Sebastian Fernandez-Alberti, Adrian E. Roitberg, Sergei Tretiak.
Nature Communications, 9: (2018)

150

Photoexcited Nonadiabatic Dynamics of Solvated Push–Pull π-Conjugated Oligomers with the NEXMD Software

Andrew E. Sifain, Josiah A. Bjorgaard, Tammie R. Nelson, Benjamin T. Nebgen, Alexander J. White, Brendan J. Gifford, David W. Gao, Oleg V. Prezhdo, Sebastian Fernandez-Alberti, Adrian E. Roitberg, Sergei Tretiak.
Journal of Chemical Theory and Computation, 14:3955-3966 (2018)

149

Less is more: Sampling chemical space with active learning

Justin S. Smith, Ben Nebgen, Nicholas Lubbers, Olexandr Isayev, Adrian E. Roitberg.
The Journal of Chemical Physics, 148:241733 (2018)

148

Cation-dependent conformations in 25-hydroxyvitamin D3-cation adducts measured by ion mobility-mass spectrometry and theoretical modeling

Christopher D. Chouinard, Vinícius Wilian D. Cruzeiro, Robin H.J. Kemperman, Nicholas R. Oranzi, Adrian E. Roitberg, Richard A. Yost.
International Journal of Mass Spectrometry, 432:1-8 (2018)

147

Bounds on the Jensen Gap, and Implications for Mean-Concentrated Distributions

Xiang Gao, Meera Sitharam, Adrian E. Roitberg.
The Australian Journal of Mathematical Analysis and Applications, Submitted (2018)

146

A Coupled Ionization-Conformational Equilibrium Is Required To Understand the Properties of Ionizable Residues in the Hydrophobic Interior of Staphylococcal Nuclease

Jinfeng Liu, Jason Swails, John Z. H. Zhang, Xiao He, Adrian E. Roitberg.
Journal of the American Chemical Society, 140:1639-1648 (2018)

2017

145

ANI-1, A data set of 20 million calculated off-equilibrium conformations for organic molecules

Justin S. Smith, Olexandr Isayev, Adrian E. Roitberg.
Scientific Data, 4:170193 (2017)

144

Experimental and Theoretical Investigation of Sodiated Multimers of Steroid Epimers with Ion Mobility-Mass Spectrometry

Christopher D. Chouinard, Vinícius Wilian D. Cruzeiro, Adrian E. Roitberg, Richard A. Yost.
Journal of The American Society for Mass Spectrometry, 28:323-331 (2017)

143

Electronic Delocalization, Vibrational Dynamics, and Energy Transfer in Organic Chromophores

Tammie Nelson, Sebastian Fernandez-Alberti, Adrian E. Roitberg, Sergei Tretiak.
The Journal of Physical Chemistry Letters, 8:3020-3031 (2017)

142

Investigating Differences in Gas-Phase Conformations of 25-Hydroxyvitamin D3 Sodiated Epimers using Ion Mobility-Mass Spectrometry and Theoretical Modeling

Christopher D. Chouinard, Vinícius Wilian D. Cruzeiro, Christopher R. Beekman, Adrian E. Roitberg, Richard A. Yost.
Journal of The American Society for Mass Spectrometry, 28:1497-1505 (2017)

141

ANI-1: an extensible neural network potential with DFT accuracy at force field computational cost

J. S. Smith, O. Isayev, A. E. Roitberg.
Chemical Science, 8:3192-3203 (2017)

2016

140

Theoretical Insights into the Reaction and Inhibition Mechanism of Metal-Independent Retaining Glycosyltransferase Responsible for Mycothiol Biosynthesis

Juan I. Blanco Capurro, Chad W. Hopkins, Gustavo Pierdominici Sottile, Mariano C. González Lebrero, Adrian E. Roitberg, Marcelo A. Marti.
The Journal of Physical Chemistry B, 121:471-478 (2016)

139

Structure-Activity Relationships of Benzenesulfonamide-Based Inhibitors towards Carbonic Anhydrase Isoform Specificity

Avni Bhatt, Brian P. Mahon, Vinicius Wilian D. Cruzeiro, Benedetta Cornelio, Marie Laronze-Cochard, Mariangela Ceruso, Janos Sapi, Graham A. Rance, Andrei N. Khlobystov, Antonella Fontana, Adrian Roitberg, Claudiu T. Supuran, Robert McKenna.
ChemBioChem, 18:213-222 (2016)

138

Interactively Applying the Variational Method to the Dihydrogen Molecule: Exploring Bonding and Antibonding

Vinícius Wilian D. Cruzeiro, Adrian Roitberg, Nicolas C. Polfer.
Journal of Chemical Education, 93:1578-1585 (2016)

137

Ultrafast electronic energy relaxation in a conjugated dendrimer leading to inter-branch energy redistribution

D. Ondarse-Alvarez, S. Kömürlü, A. E. Roitberg, G. Pierdominici-Sottile, S. Tretiak, S. Fernandez-Alberti, V. D. Kleiman.
Physical Chemistry Chemical Physics, 18:25080-25089 (2016)

136

Structured and Unstructured Binding of an Intrinsically Disordered Protein as Revealed by Atomistic Simulations

Raúl Esteban Ithuralde, Adrián Enrique Roitberg, Adrián Gustavo Turjanski.
Journal of the American Chemical Society, 138:8742-8751 (2016)

135

Steered Molecular Dynamics Methods Applied to Enzyme Mechanism and Energetics

C.L. Ramírez, M.A. Martí, A.E. Roitberg.
Methods in Enzymology, 578:123-143 (2016)

134

Coarse-Grained Simulations of Heme Proteins: Validation and Study of Large Conformational Transitions

Claudia L. Ramírez, Ariel Petruk, Mauro Bringas, Dario A. Estrin, Adrian E. Roitberg, Marcelo A. Marti, Luciana Capece.
Journal of Chemical Theory and Computation, 12:3390-3397 (2016)

133

Structural Study of a Flexible Active Site Loop in Human Indoleamine 2,3-Dioxygenase and Its Functional Implications

Lucía Álvarez, Ariel Lewis-Ballester, Adrián Roitberg, Darío A. Estrin, Syun-Ru Yeh, Marcelo A. Marti, Luciana Capece.
Biochemistry, 55:2785-2793 (2016)

2015

132

Oxygen diffusion pathways in a cofactor-independent dioxygenase

Natali V. Di Russo, Heather L. Condurso, Kunhua Li, Steven D. Bruner, Adrian E. Roitberg.
Chemical Science, 6:6341-6348 (2015)

131

Enhancement in Organic Photovoltaic Efficiency through the Synergistic Interplay of Molecular Donor Hydrogen Bonding and π-Stacking

Nathan T. Shewmon, Davita L. Watkins, Johan F. Galindo, Raghida Bou Zerdan, Jihua Chen, Jong Keum, Adrian E. Roitberg, Jiangeng Xue, Ronald K. Castellano.
Advanced Functional Materials, 25:5166-5177 (2015)

130

Simulating the inhibition reaction of Mycobacterium tuberculosisl,d-transpeptidase 2 by carbapenems

José Rogério A. Silva, Thavendran Govender, Glenn E. M. Maguire, Hendrik G. Kruger, Jerônimo Lameira, Adrian E. Roitberg, Cláudio Nahum Alves.
Chemical Communications, 51:12560-12562 (2015)

129

Dynamics of Energy Transfer in a Conjugated Dendrimer Driven by Ultrafast Localization of Excitations

Johan F. Galindo, Evrim Atas, Aysun Altan, Daniel G. Kuroda, Sebastian Fernandez-Alberti, Sergei Tretiak, Adrian E. Roitberg, Valeria D. Kleiman.
Journal of the American Chemical Society, 137:11637-11644 (2015)

128

On the analysis and comparison of conformer-specific essential dynamics upon ligand binding to a protein

Marcos Grosso, Adrian Kalstein, Gustavo Parisi, Adrian E. Roitberg, Sebastian Fernandez-Alberti.
The Journal of Chemical Physics, 142:245101 (2015)

127

Insights into the mechanism of oxidation of dihydroorotate to orotate catalysed by human class 2 dihydroorotate dehydrogenase: a QM/MM free energy study

Cláudio Nahum Alves, José Rogério A. Silva, Adrian E. Roitberg.
Physical Chemistry Chemical Physics, 17:17790-17796 (2015)

126

Long-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning

Chad W. Hopkins, Scott Le Grand, Ross C. Walker, Adrian E. Roitberg.
Journal of Chemical Theory and Computation, 11:1864-1874 (2015)

125

Applicability of fluorescence-based sensors to the determination of kinetic parameters for O2 in oxygenases

Natali V. Di Russo, Steven D. Bruner, Adrian E. Roitberg.
Analytical Biochemistry, 475:53-55 (2015)

124

Hydrogen bond directed assembly of oligothiophene/fullerene superstructures on Au(111)

Xueying Zhao, Davita L. Watkins, Johan F. Galindo, Nathan T. Shewmon, Adrian E. Roitberg, Jiangeng Xue, Ronald K. Castellano, Scott S. Perry.
Organic Electronics, 19:61-69 (2015)

123

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

Thakshila Dissanayake, Jason M. Swails, Michael E. Harris, Adrian E. Roitberg, Darrin M. York.
Biochemistry, 54:1307-1313 (2015)

122

A QM/MM Free Energy Study of the Oxidation Mechanism of Dihydroorotate Dehydrogenase (Class 1A) from Lactococcus lactis

José Rogério A. Silva, Adrian E. Roitberg, Cláudio Nahum Alves.
The Journal of Physical Chemistry B, 119:1468-1473 (2015)

2014

121

Defective Hydrophobic Sliding Mechanism and Active Site Expansion in HIV-1 Protease Drug Resistant Variant Gly48Thr/Leu89Met: Mechanisms for the Loss of Saquinavir Binding Potency

Nathan E. Goldfarb, Meray Ohanessian, Shyamasri Biswas, T. Dwight McGee, Brian P. Mahon, David A. Ostrov, Jose Garcia, Yan Tang, Robert McKenna, Adrian Roitberg, Ben M. Dunn.
Biochemistry, 54:422-433 (2014)

120

Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide

Christina Bergonzo, Niel M. Henriksen, Daniel R. Roe, Jason M. Swails, Adrian E. Roitberg, Thomas E. Cheatham.
Journal of Chemical Theory and Computation, 10:492-499 (2014)

119

Underlying Thermodynamics of pH-Dependent Allostery

Natali V. Di Russo, Marcelo A. Martí, Adrian E. Roitberg.
The Journal of Physical Chemistry B, 118:12818-12826 (2014)

118

pH-REMD Simulations Indicate That the Catalytic Aspartates of HIV-1 Protease Exist Primarily in a Monoprotonated State

T. Dwight McGee, Jesse Edwards, Adrian E. Roitberg.
The Journal of Physical Chemistry B, 118:12577-12585 (2014)

117

Improving Efficiency in SMD Simulations Through a Hybrid Differential Relaxation Algorithm

Claudia L. Ramírez, Ari Zeida, Gabriel E. Jara, Adrián E. Roitberg, Marcelo A. Martí.
Journal of Chemical Theory and Computation, 10:4609-4617 (2014)

116

Catalytic Mechanism of L,D-Transpeptidase 2 from Mycobacterium tuberculosis Described by a Computational Approach: Insights for the Design of New Antibiotics Drugs

José Rogério A. Silva, Adrian E. Roitberg, Cláudio Nahum Alves.
Journal of Chemical Information and Modeling, 54:2402-2410 (2014)

115

Fitting of Dihedral Terms in Classical Force Fields as an Analytic Linear Least-Squares Problem

Chad W. Hopkins, Adrian E. Roitberg.
Journal of Chemical Information and Modeling, 54:1978-1986 (2014)

114

Signature of Nonadiabatic Coupling in Excited-State Vibrational Modes

Miguel A. Soler, Tammie Nelson, Adrian E. Roitberg, Sergei Tretiak, Sebastian Fernandez-Alberti.
The Journal of Physical Chemistry A, 118:10372-10379 (2014)

113

Unraveling the Differences of the Hydrolytic Activity of Trypanosoma cruzi trans-Sialidase and Trypanosoma rangeli Sialidase: A Quantum Mechanics–Molecular Mechanics Modeling Study

Juan A. Bueren-Calabuig, Gustavo Pierdominici-Sottile, Adrian E. Roitberg.
The Journal of Physical Chemistry B, 118:5807-5816 (2014)

112

Nonadiabatic Excited-State Molecular Dynamics: Modeling Photophysics in Organic Conjugated Materials

Tammie Nelson, Sebastian Fernandez-Alberti, Adrian E. Roitberg, Sergei Tretiak.
Accounts of Chemical Research, 47:1155-1164 (2014)

111

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

Jason M. Swails, Darrin M. York, Adrian E. Roitberg.
Journal of Chemical Theory and Computation, 10:1341-1352 (2014)

2013

110

Electronic Excited State Specific IR Spectra for Phenylene Ethynylene Dendrimer Building Blocks

Johan F. Galindo, Sebastian Fernandez-Alberti, Adrian E. Roitberg.
The Journal of Physical Chemistry C, 117:26517-26528 (2013)

109

Artifacts due to trivial unavoided crossings in the modeling of photoinduced energy transfer dynamics in extended conjugated molecules

Tammie Nelson, Sebastian Fernandez-Alberti, Adrian E. Roitberg, Sergei Tretiak.
Chemical Physics Letters, 590:208-213 (2013)

108

Trypanosoma cruzi trans-sialidase as a drug target against Chagas disease (American trypanosomiasis)

Bill R Miller III, Adrian E Roitberg.
Future Medicinal Chemistry, 5:1889-1900 (2013)

107

Optimization of Umbrella Sampling Replica Exchange Molecular Dynamics by Replica Positioning

Danial Sabri Dashti, Adrian E. Roitberg.
Journal of Chemical Theory and Computation, 9:4692-4699 (2013)

106

Photosensitization of Single-Crystal ZnO by a Conjugated Polyelectrolyte Designed to Avoid Aggregation

Xuzhi Zhu, Alexander B. Nepomnyashchii, Adrian E. Roitberg, B. A. Parkinson, Kirk S. Schanze.
The Journal of Physical Chemistry Letters, 4:3216-3220 (2013)

105

AM1 Specific Reaction Parameters for Reactions of Hydroxide Ion with Halomethanes in Complex Environments: Development and Testing

Shuai Liang, Adrian E. Roitberg.
Journal of Chemical Theory and Computation, 9:4470-4480 (2013)

104

Free-energy computations identify the mutations required to confer trans-sialidase activity intoTrypanosoma rangelisialidase

Gustavo Pierdominici-Sottile, Juliana Palma, Adrian E. Roitberg.
Proteins: Structure, Function, and Bioinformatics, 82:424-435 (2013)

103

Design of e-pharmacophore models using compound fragments for the trans-sialidase of Trypanosoma cruzi: Screening for novel inhibitor scaffolds

Bill R. Miller, Adrian E. Roitberg.
Journal of Molecular Graphics and Modelling, 45:84-97 (2013)

102

Nonadiabatic excited-state molecular dynamics: Treatment of electronic decoherence

Tammie Nelson, Sebastian Fernandez-Alberti, Adrian E. Roitberg, Sergei Tretiak.
The Journal of Chemical Physics, 138:224111 (2013)

101

Conformational disorder in energy transfer: beyond Förster theory

Tammie Nelson, Sebastian Fernandez-Alberti, Adrian E. Roitberg, Sergei Tretiak.
Physical Chemistry Chemical Physics, 15:9245 (2013)

100

Electronic Delocalization in Coordination Polymers Based on Bimetallic Carboxylates

María Ana Castro, Adrián E. Roitberg, Fabio D. Cukiernik.
Journal of Chemical Theory and Computation, 9:2609-2616 (2013)

99

Kinetics and computational studies of ligand migration in nitrophorin 7 and its Δ1–3 mutant

Ana Oliveira, Alessandro Allegri, Axel Bidon-Chanal, Markus Knipp, Adrian E. Roitberg, Stefania Abbruzzetti, Cristiano Viappiani, F. Javier Luque.
Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 1834:1711-1721 (2013)

98

Structures of Biomolecular Ions in the Gas Phase Probed by Infrared Light Sources

Corey N. Stedwell, Johan F. Galindo, Adrian E. Roitberg, Nicolas C. Polfer.
Annual Review of Analytical Chemistry, 6:267-285 (2013)

97

Simulation of mesogenic diruthenium tetracarboxylates: Development of a force field for coordination polymers of the MMX type

Maria Ana Castro, Adrian E. Roitberg, Fabio D. Cukiernik.
Journal of Computational Chemistry, 34:1283-1290 (2013)

96

Hydrophobic Effect Drives Oxygen Uptake in Myoglobin via Histidine E7

Leonardo Boechi, Mehrnoosh Arrar, Marcelo A. Martí, John S. Olson, Adrián E. Roitberg, Darío A. Estrin.
Journal of Biological Chemistry, 288:6754-6762 (2013)

2012

95

Enzyme dynamics and catalysis in the mechanism of DNA polymerase

Adrian J. Mulholland, Adrian E. Roitberg, Iñaki Tuñón.
Theoretical Chemistry Accounts, 131:1286 (2012)

94

pH-Dependent Conformational Changes in Proteins and Their Effect on Experimental pKas: The Case of Nitrophorin 4

Natali V. Di Russo, Dario A. Estrin, Marcelo A. Martí, Adrian E. Roitberg.
PLoS Computational Biology, 8:e1002761 (2012)

93

Analysis of State-Specific Vibrations Coupled to the Unidirectional Energy Transfer in Conjugated Dendrimers

Miguel A. Soler, Adrian E. Roitberg, Tammie Nelson, Sergei Tretiak, Sebastian Fernandez-Alberti.
The Journal of Physical Chemistry A, 116:9802-9810 (2012)

92

Conjugated Polyelectrolyte Dendrimers: Aggregation, Photophysics, and Amplified Quenching

Fude Feng, Seoung Ho Lee, Sung Won Cho, Sevnur Kömürlü, Tracy D. McCarley, Adrian Roitberg, Valeria D. Kleiman, Kirk S. Schanze.
Langmuir, 28:16679-16691 (2012)

91

Enhancing Conformation and Protonation State Sampling of Hen Egg White Lysozyme Using pH Replica Exchange Molecular Dynamics

Jason M. Swails, Adrian E. Roitberg.
Journal of Chemical Theory and Computation, 8:4393-4404 (2012)

90

Shishiodoshi unidirectional energy transfer mechanism in phenylene ethynylene dendrimers

S. Fernandez-Alberti, Adrian E. Roitberg, Valeria D. Kleiman, T. Nelson, S. Tretiak.
The Journal of Chemical Physics, 137:22A526 (2012)

89

Crown Complexation of Protonated Amino Acids: Influence on IRMPD Spectra

Corey N. Stedwell, Johan F. Galindo, Kerim Gulyuz, Adrian E. Roitberg, Nicolas C. Polfer.
The Journal of Physical Chemistry A, 117:1181-1188 (2012)

88

MMPBSA.py: An Efficient Program for End-State Free Energy Calculations

Bill R. Miller, T. Dwight McGee, Jason M. Swails, Nadine Homeyer, Holger Gohlke, Adrian E. Roitberg.
Journal of Chemical Theory and Computation, 8:3314-3321 (2012)

87

Identification of unavoided crossings in nonadiabatic photoexcited dynamics involving multiple electronic states in polyatomic conjugated molecules

Sebastian Fernandez-Alberti, Adrian E. Roitberg, Tammie Nelson, Sergei Tretiak.
The Journal of Chemical Physics, 137:014512 (2012)

86

pH-Replica Exchange Molecular Dynamics in Proteins Using a Discrete Protonation Method

Danial Sabri Dashti, Yilin Meng, Adrian E. Roitberg.
The Journal of Physical Chemistry B, 116:8805-8811 (2012)

85

Wide-Open Flaps Are Key to Urease Activity

Benjamin P. Roberts, Bill R. Miller, Adrian E. Roitberg, Kenneth M. Merz.
Journal of the American Chemical Society, 134:9934-9937 (2012)

84

Comment on “a minimal implementation of the AMBER-GAUSSIAN interface for Ab Initio QM/MM-MD simulation”

Benjamin P. Roberts, Gustavo M. Seabra, Adrian E. Roitberg, Kenneth M. Merz, Erik Deumens, Juan Torras, Samuel B. Trickey.
Journal of Computational Chemistry, 33:1643-1644 (2012)

83

Nonadiabatic excited-state molecular dynamics: Numerical tests of convergence and parameters

Tammie Nelson, Sebastian Fernandez-Alberti, Vladimir Chernyak, Adrian E. Roitberg, Sergei Tretiak.
The Journal of Chemical Physics, 136:054108 (2012)

2011

81

Free Energy Study of the Catalytic Mechanism ofTrypanosoma cruzitrans-Sialidase. From the Michaelis Complex to the Covalent Intermediate

Gustavo Pierdominici-Sottile, Nicole A. Horenstein, Adrian E. Roitberg.
Biochemistry, 50:10150-10158 (2011)

80

Computing Alchemical Free Energy Differences with Hamiltonian Replica Exchange Molecular Dynamics (H-REMD) Simulations

Yilin Meng, Danial Sabri Dashti, Adrian E. Roitberg.
Journal of Chemical Theory and Computation, 7:2721-2727 (2011)

79

p38γ Activation Triggers Dynamical Changes in Allosteric Docking Sites

Ramiro G. Rodriguez Limardo, Dardo N. Ferreiro, Adrián E. Roitberg, Marcelo A. Marti, Adrian G. Turjanski.
Biochemistry, 50:1384-1395 (2011)

78

Nonadiabatic Excited-State Molecular Dynamics Modeling of Photoinduced Dynamics in Conjugated Molecules

Tammie Nelson, Sebastian Fernandez-Alberti, Vladimir Chernyak, Adrian E. Roitberg, Sergei Tretiak.
The Journal of Physical Chemistry B, 115:5402-5414 (2011)

77

Juvenile hormone synthesis: “esterify then epoxidize” or “epoxidize then esterify”? Insights from the structural characterization of juvenile hormone acid methyltransferase

L.A. Defelipe, E. Dolghih, A.E. Roitberg, M. Nouzova, J.G. Mayoral, F.G. Noriega, A.G. Turjanski.
Insect Biochemistry and Molecular Biology, 41:228-235 (2011)

2010

76

Electronic Spectra of the Nanostar Dendrimer: Theory and Experiment

Julio L. Palma, Evrim Atas, Lindsay Hardison, Todd B. Marder, Jonathan C. Collings, Andrew Beeby, Joseph S. Melinger, Jeffrey L. Krause, Valeria D. Kleiman, Adrian E. Roitberg.
The Journal of Physical Chemistry C, 114:20702-20712 (2010)

75

Unidirectional Energy Transfer in Conjugated Molecules: The Crucial Role of High-Frequency C≡C Bonds

S. Fernandez-Alberti, Valeria D. Kleiman, S. Tretiak, Adrian E. Roitberg.
The Journal of Physical Chemistry Letters, 1:2699-2704 (2010)

74

Exchange Often and Properly in Replica Exchange Molecular Dynamics

Daniel J. Sindhikara, Daniel J. Emerson, Adrian E. Roitberg.
Journal of Chemical Theory and Computation, 6:2804-2808 (2010)

73

Substrate stereo-specificity in tryptophan dioxygenase and indoleamine 2,3-dioxygenase

Luciana Capece, Mehrnoosh Arrar, Adrian E. Roitberg, Syun-Ru Yeh, Marcelo A. Marti, Dario A. Estrin.
Proteins: Structure, Function, and Bioinformatics, 78:2961-2972 (2010)

72

Impact of calcium on N1 influenza neuraminidase dynamics and binding free energy

Morgan Lawrenz, Jeff Wereszczynski, Rommie Amaro, Ross Walker, Adrian Roitberg, J. Andrew McCammon.
Proteins: Structure, Function, and Bioinformatics, 78:n/a-n/a (2010)

71

Constant pH Replica Exchange Molecular Dynamics in Biomolecules Using a Discrete Protonation Model

Yilin Meng, Adrian E. Roitberg.
Journal of Chemical Theory and Computation, 6:1401-1412 (2010)

2009

70

A Multiscale Treatment of Angeli’s Salt Decomposition

Juan Torras, Gustavo de M. Seabra, Adrian E. Roitberg.
Journal of Chemical Theory and Computation, 5:37-46 (2009)

69

Computational Studies of Ammonia Channel Function in Glutamine 5′-Phosphoribosylpyrophosphate Amidotransferase

Xiang S. Wang, Adrian E. Roitberg, Nigel G. J. Richards.
Biochemistry, 48:12272-12282 (2009)

68

67

AM1 Parameters for the Prediction of1H and13C NMR Chemical Shifts in Proteins†

Duane E. Williams, Martin B. Peters, Bing Wang, Adrian E. Roitberg, Kenneth M. Merz.
The Journal of Physical Chemistry A, 113:11550-11559 (2009)

66

Molecular and functional characterization of a juvenile hormone acid methyltransferase expressed in the corpora allata of mosquitoes

Jaime G. Mayoral, Marcela Nouzova, Michiyo Yoshiyama, Tetsuro Shinoda, Salvador Hernandez-Martinez, Elena Dolghih, Adrian G. Turjanski, Adrian E. Roitberg, Horacio Priestap, Mario Perez, Lucy Mackenzie, Yiping Li, Fernando G. Noriega.
Insect Biochemistry and Molecular Biology, 39:31-37 (2009)

65

Are Current Semiempirical Methods Better Than Force Fields? A Study from the Thermodynamics Perspective†

Gustavo de M. Seabra, Ross C. Walker, Adrian E. Roitberg.
The Journal of Physical Chemistry A, 113:11938-11948 (2009)

64

Mixed Quantum-Classical Calculations in Biological Systems

Gustavo M. Seabra, Jason Swails, Adrian E. Roitberg.
Multi-scale Quantum Models for Biocatalysis, 7:3-20 (2009)

63

Bad Seeds Sprout Perilous Dynamics: Stochastic Thermostat Induced Trajectory Synchronization in Biomolecules

Daniel J. Sindhikara, Seonah Kim, Arthur F. Voter, Adrian E. Roitberg.
Journal of Chemical Theory and Computation, 5:1624-1631 (2009)

62

Nonadiabatic Molecular Dynamics Simulations of the Energy Transfer between Building Blocks in a Phenylene Ethynylene Dendrimer†

Sebastian Fernandez-Alberti, Valeria D. Kleiman, Sergei Tretiak, Adrian E. Roitberg.
The Journal of Physical Chemistry A, 113:7535-7542 (2009)

61

Theoretical Studies of Short Polyproline Systems: Recalibration of a Molecular Ruler†

Elena Dolghih, Wilfredo Ortiz, Seonah Kim, Brent P. Krueger, Jeffrey L. Krause, Adrian E. Roitberg.
The Journal of Physical Chemistry A, 113:4639-4646 (2009)

59

Molecular Basis for the pH Dependent Structural Transition of Nitrophorin 4

Marcelo A. Martí, Dario A. Estrin, Adrián E. Roitberg.
The Journal of Physical Chemistry B, 113:2135-2142 (2009)

58

pH-Dependent Mechanism of Nitric Oxide Release in Nitrophorins 2 and 4

Jason M. Swails, Yilin Meng, F. Ann Walker, Marcelo A. Marti, Dario A. Estrin, Adrian E. Roitberg.
The Journal of Physical Chemistry B, 113:1192-1201 (2009)

2008

57

Preliminary Molecular Dynamic Simulations of the Estrogen Receptor Alpha Ligand Binding Domain from Antagonist to Apo

T. McGee, Jesse Edwards, Adrian Roitberg.
International Journal of Environmental Research and Public Health, 5:111-114 (2008)

56

Quantifying Solvation Effects on Peptide Conformations: A QM/MM Replica Exchange Study

GUSTAVO M. SEABRA, ROSS C. WALKER, ADRIAN E. ROITBERG.
Solvation Effects on Molecules and Biomolecules, 6:507-518 (2008)

55

Using the Rosetta algorithm and selected inter-residue distances to predict protein structure

Christina Crecca, Adrian E. Roitberg.
International Journal of Quantum Chemistry, 108:2793-2802 (2008)

54

Using distances between α-carbons to predict protein structure

Christina R. Crecca, Adrian E. Roitberg.
International Journal of Quantum Chemistry, 108:2782-2792 (2008)

53

Theoretical and Experimental Studies of Diruthenium Tetracarboxylates Structure, Spectroscopy, and Electrochemistry

Maria Ana Castro, Adrian E. Roitberg, Fabio D. Cukiernik.
Inorganic Chemistry, 47:4682-4690 (2008)

52

A versatile AMBER-Gaussian QM/MM interface through PUPIL

Juan Torras, Gustavo de M. Seabra, Erik Deumens, S. B. Trickey, Adrian E. Roitberg.
Journal of Computational Chemistry, 29:1564-1573 (2008)

51

Simulating Temperature Jumps for Protein Folding

Seonah Kim, Adrian E. Roitberg.
The Journal of Physical Chemistry B, 112:1525-1532 (2008)

50

Bond or Cage Effect: How Nitrophorins Transport and Release Nitric Oxide

Marcelo A. Martí, Mariano C. González Lebrero, Adrián E. Roitberg, Dario A. Estrin.
Journal of the American Chemical Society, 130:1611-1618 (2008)

49

Exchange frequency in replica exchange molecular dynamics

Daniel Sindhikara, Yilin Meng, Adrian E. Roitberg.
The Journal of Chemical Physics, 128:024103 (2008)

2007

48

Fluorescence resonance energy transfer in dye-labeled DNA

Elena Dolghih, Adrian E. Roitberg, Jeffrey L. Krause.
Journal of Photochemistry and Photobiology A: Chemistry, 190:321-327 (2007)

47

Molecular Dynamics Simulations of Alkanethiol Monolayers with Azobenzene Molecules on the Au(111) Surface

Sabri Alkis, Ping Jiang, Lin-Lin Wang, Adrian E. Roitberg, Hai-Ping Cheng, Jeffrey L. Krause.
The Journal of Physical Chemistry C, 111:14743-14752 (2007)

46

Implementation of the SCC-DFTB Method for Hybrid QM/MM Simulations within the Amber Molecular Dynamics Package†

Gustavo de M. Seabra, Ross C. Walker, Marcus Elstner, David A. Case, Adrian E. Roitberg.
The Journal of Physical Chemistry A, 111:5655-5664 (2007)

45

Coupling of Replica Exchange Simulations to a Non-Boltzmann Structure Reservoir

Adrian E. Roitberg, Asim Okur, Carlos Simmerling.
The Journal of Physical Chemistry B, 111:2415-2418 (2007)

44

Kinetics of Internal-Loop Formation in Polypeptide Chains: A Simulation Study

Dana Doucet, Adrian Roitberg, Stephen J. Hagen.
Biophysical Journal, 92:2281-2289 (2007)

2006

43

Comparison of multiple Amber force fields and development of improved protein backbone parameters

Viktor Hornak, Robert Abel, Asim Okur, Bentley Strockbine, Adrian Roitberg, Carlos Simmerling.
Proteins: Structure, Function, and Bioinformatics, 65:712-725 (2006)

42

The Catalytic Mechanism of Peptidylglycine α-Hydroxylating Monooxygenase Investigated by Computer Simulation

Alejandro Crespo, Marcelo A. Martí, Adrian E. Roitberg, L. Mario Amzel, Darío A. Estrin.
Journal of the American Chemical Society, 128:12817-12828 (2006)

41

Theoretical Study of the Isomerization Mechanism of Azobenzene and Disubstituted Azobenzene Derivatives

Christina R. Crecca, Adrian E. Roitberg.
The Journal of Physical Chemistry A, 110:8188-8203 (2006)

40

Structural analysis of ligand binding and catalysis in chorismate lyase

Natasha Smith, Adrian E. Roitberg, Eva Rivera, Andrew Howard, Marcia J. Holden, Martin Mayhew, Salita Kaistha, D.T. Gallagher.
Archives of Biochemistry and Biophysics, 445:72-80 (2006)

39

Free Energy Calculations with Non-Equilibrium Methods: Applications of the Jarzynski Relationship

Hui Xiong, Alejandro Crespo, Marcelo Marti, Dario Estrin, Adrian E. Roitberg.
Theoretical Chemistry Accounts, 116:338-346 (2006)

2005

38

Chapter 8 Nonequilibrium Approaches to Free Energy Calculations

Adrian E. Roitberg.
Annual Reports in Computational Chemistry, 8:103-111 (2005)

37

Energy Transfer in the Nanostar: The Role of Coulombic Coupling and Dynamics

Wilfredo Ortiz, Brent P. Krueger, Valeria D. Kleiman, Jeffrey L. Krause, Adrian E. Roitberg.
The Journal of Physical Chemistry B, 109:11512-11519 (2005)

36

Multiple-Steering QM−MM Calculation of the Free Energy Profile in Chorismate Mutase

Alejandro Crespo, Marcelo A. Martí, Darío A. Estrin, Adrian E. Roitberg.
Journal of the American Chemical Society, 127:6940-6941 (2005)

2004

35

Molecular Dynamics of Poly(benzylphenyl ether) Dendrimers: Effects of Backfolding on Förster Energy-Transfer Rates

Wilfredo Ortiz, Adrian E. Roitberg, Jeffrey L. Krause.
The Journal of Physical Chemistry B, 108:8218-8225 (2004)

34

Coherent Electron Transport through an Azobenzene Molecule: A Light-Driven Molecular Switch

C. Zhang, M.-H. Du, H.-P. Cheng, X.-G. Zhang, A. E. Roitberg, J. L. Krause.
Physical Review Letters, 92:158301 (2004)

33

Special issue: Conformational sampling

Roitberg AE and Simmerling CL.
Journal of Molecular Graphics and Modelling, 22:317 (2004)

2003

32

A DFT-Based QM-MM Approach Designed for the Treatment of Large Molecular Systems: Application to Chorismate Mutase

Alejandro Crespo, Damián A. Scherlis, Marcelo A. Martí, Pablo Ordejón, Adrián E. Roitberg, Darío A. Estrin.
The Journal of Physical Chemistry B, 107:13728-13736 (2003)

31

Kinetic isotope effects in the active site ofB. subtilis chorismate mutase

Sharon E. Worthington, Adrian E. Roitberg, Morris Krauss.
International Journal of Quantum Chemistry, 94:287-292 (2003)

2002

30

Smaller and Faster: The 20-Residue Trp-Cage Protein Folds in 4 μs

Linlin Qiu, Suzette A. Pabit, Adrian E. Roitberg, Stephen J. Hagen.
Journal of the American Chemical Society, 124:12952-12953 (2002)

29

Solvent-induced symmetry breaking of nitrate ion in aqueous clusters: A quantum-classical simulation study

Mariano C. González Lebrero, Damián E. Bikiel, M. Dolores Elola, Darı́o A. Estrin, Adrian E. Roitberg.
The Journal of Chemical Physics, 117:2718-2725 (2002)

28

All-Atom Structure Prediction and Folding Simulations of a Stable Protein

Carlos Simmerling, Bentley Strockbine, Adrian E. Roitberg.
Journal of the American Chemical Society, 124:11258-11259 (2002)

27

Benzocycloarene hydroxylation by P450 biocatalysis

Martin P. Mayhew, Adrian E. Roitberg, Yadu Tewari, Marcia J. Holden, David J. Vanderah, Vincent L. Vilker.
New Journal of Chemistry, 26:35-42 (2002)

26

4,5-Dehydrooctafluoro[2.2]paracyclophane: facile generation and extraordinary Diels–Alder reactivity

Merle A. Battiste, Jian-Xin Duan, Yi-An Zhai, Ion Ghiviriga, Khalil A. Abboud, Adrian Roitberg, G.Robert Shelton, William R. Dolbier.
Tetrahedron Letters, 43:7047-7049 (2002)

2001

25

Strontium clusters: Many-body potential, energetics, and structural transitions

Guan Ming Wang, Estela Blaisten-Barojas, A. E. Roitberg, T. P. Martin.
The Journal of Chemical Physics, 115:3640-3646 (2001)

24

An MD/QM Study of the Chorismate Mutase-Catalyzed Claisen Rearrangement Reaction

Sharon E. Worthington, Adrian E. Roitberg, Morris Krauss.
The Journal of Physical Chemistry B, 105:7087-7095 (2001)

23

Raman and FTIR spectroscopies of fluorescein in solutions

Lili Wang, A. Roitberg, C. Meuse, A.K. Gaigalas.
Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 57:1781-1791 (2001)

2000

22

Pulsed terahertz spectroscopy of DNA, bovine serum albumin and collagen between 0.1 and 2.0 THz

A.G Markelz, A Roitberg, E.J Heilweil.
Chemical Physics Letters, 320:42-48 (2000)

21

Molecular wire conductance: Electrostatic potential spatial profile

Vladimiro Mujica, Adrian E. Roitberg, Mark Ratner.
The Journal of Chemical Physics, 112:6834-6839 (2000)

20

The Electronic Spectrum of the Prephenate Dianion. An Experimental and Theoretical (MD/QM) Comparison

Adrian E. Roitberg, Sharon E. Worthington, Marcia J. Holden, Martin P. Mayhew, Morris Krauss.
Journal of the American Chemical Society, 122:7312-7316 (2000)

1999

19

The injecting energy at molecule/metal interfaces: Implications for conductance of molecular junctions from an ab initio molecular description

S. N. Yaliraki, A. E. Roitberg, C. Gonzalez, V. Mujica, Mark A. Ratner.
The Journal of Chemical Physics, 111:6997-7002 (1999)

18

Electron Transfer in Molecules and Molecular Wires: Geometry Dependence, Coherent Transfer, and Control

V. Mujica, A. Nitzan, Y. Mao, W. Davis, M. Kemp, A. Roitberg, M. A. Ratner.
Advances in Chemical Physics, Part 2 107:403-429 (1999)

1998

17

Molecular Wires: Charge Transport, Mechanisms, and Control

MARK A. RATNER, BILL DAVIS, MATHIEU KEMP, VLADIMIRO MUJICA, ADRIAN ROITBERG, SOPHIA YALIRAKI.
Annals of the New York Academy of Sciences, 852:22-37 (1998)

16

Binding and Electron Transfer between Putidaredoxin and Cytochrome P450cam. Theory and Experiments

Adrian E. Roitberg, Marcia J. Holden, Martin P. Mayhew, Igor V. Kurnikov, David N. Beratan, Vincent L. Vilker.
Journal of the American Chemical Society, 120:8927-8932 (1998)

1997

14

Probing the Interactions of Putidaredoxin with Redox Partners in Camphor P450 5-Monooxygenase by Mutagenesis of Surface Residues

Marcia Holden, Martin Mayhew, David Bunk, Adrian Roitberg, Vincent Vilker.
Journal of Biological Chemistry, 272:21720-21725 (1997)

13

A Vibrational Eigenfunction of a Protein: Anharmonic Coupled-Mode Ground and Fundamental Excited States of BPTI

Adrian E. Roitberg, R. Benny Gerber, Mark A. Ratner.
The Journal of Physical Chemistry B, 101:1700-1706 (1997)

12

Molecular Wires: Resonances, Staircases, Rectification, Bonding and Speculation

Mathieu Kemp, Vladimiro Mujica, Adrian Roitberg, Yi Mao, Mark A. Ratner.
NATO ASI Series E Applied Sciences-Advanced Study Institute, 341:203-217 (1997)

1996

11

Mo/ller–Plesset perturbation theory applied to vibrational problems

Lawrence S. Norris, Mark A. Ratner, Adrian E. Roitberg, R. B. Gerber.
The Journal of Chemical Physics, 105:11261-11267 (1996)

10

Molecular Wires:  Extended Coupling and Disorder Effects

Mathieu Kemp, Adrian Roitberg, Vladimiro Mujica, Todd Wanta, Mark A. Ratner.
The Journal of Physical Chemistry, 100:8349-8355 (1996)

9

Current‐voltage characteristics of molecular wires: Eigenvalue staircase, Coulomb blockade, and rectification

Vladimiro Mujica, Mathieu Kemp, Adrian Roitberg, Mark Ratner.
The Journal of Chemical Physics, 104:7296-7305 (1996)

8

A model for coulomb interaction in electron transport in one-dimensional mesoscopic devices

Mujica V, Kemp M, Roitberg AE, and Ratner MA.
Condensed Matter Theories, 11:261-272 (1996)

1995

7

MOIL: A program for simulations of macromolecules

Ron Elber, Adrian Roitberg, Carlos Simmerling, Robert Goldstein, Haiying Li, Gennady Verkhivker, Chen Keasar, Jing Zhang, Alex Ulitsky.
Computer Physics Communications, 91:159-189 (1995)

6

Anharmonic wave functions of proteins: quantum self-consistent field calculations of BPTI

A Roitberg, R. Gerber, R Elber, M. Ratner.
Science, 268:1319-1322 (1995)

1994

5

A perturbed‐mean‐field approach to the decay rates of excited vibrational states in extended systems: An application toI2(Ne)n

Adrian E. Roitberg, R. Benny Gerber, Mark A. Ratner.
The Journal of Chemical Physics, 100:4355-4366 (1994)

4

Resonances and interference effects on the effective electronic coupling in electron transfer

Amanda Cheong, Adrian E. Roitberg, Vladimiro Mujica, Mark A. Ratner.
Journal of Photochemistry and Photobiology A: Chemistry, 82:81-86 (1994)

3

Moil: A Molecular Dynamics Program with Emphasis on Conformational Searches and Reaction Path Calculations

Ron Elber, Adrian Roitberg, Carlos Simmerling, Robert Goldstein, Gennady Verkhivker, Haiying Li, Alex Ulitsky.
NATO ASI Series, 325:165-191 (1994)

1991

1990

1

Reductive dissolution of neutron- and gamma-irradiated magnetite

Maria Dos Santos Afonso, Cecilia D. Di Risio, Adrián Roitberg, Roberto O. Marqués, Miguel A. Blesa.
International Journal of Radiation Applications and Instrumentation. Part C. Radiation Physics and Chemistry, 36:457-460 (1990)