The Density-of-States and Equilibrium Charge Dynamics of Redox-Active Switches
Paulo Bueno, Vinícius Wilian Cruzeiro, Adrian Roitberg, Gustavo Feliciano.
Journal of the AmericanChemical Society, Submitted (2021)
Publications
2021
180
The Density-of-States and Equilibrium Charge Dynamics of Redox-Active Switches
Paulo Bueno, Vinícius Wilian Cruzeiro, Adrian Roitberg, Gustavo Feliciano.
Journal of the AmericanChemical Society, Submitted (2021)
2020
179
Ankita Sarkar, Adrian E. Roitberg.
The Journal of Physical Chemistry B, 124:11072-11080 (2020)
178
Zainab K. Sanusi, Monsurat M. Lawal, Pancham Lal. Gupta, Thavendran Govender, Sooraj Baijnath, Tricia Naicker, Glenn E. M. Maguire, Bahareh Honarparvar, Adrian E. Roitberg, Hendrik G. Kruger.
Journal of Biomolecular Structure and Dynamics, :1-12 (2020)
177
Stephen J. Haller, Adrian E. Roitberg, Andrew T. Dudley.
Scientific Reports, 10:16844 (2020)
176
Unraveling Direct and Indirect Energy Transfer Pathways in a Light-Harvesting Dendrimer
Maria Camila Aguilera, Adrian E. Roitberg, Valeria D. Kleiman, Sebastian Fernandez-Alberti, Johan F. Galindo.
The Journal of Physical Chemistry C, 124:22383-22391 (2020)
175
Selective ring-rearrangement or ring-closing metathesis of bicyclo[3.2.1]octenes
Evgeniya Semenova, Ouidad Lahtigui, Sarah K. Scott, Matthew Albritton, Khalil A. Abboud, Ion Ghiviriga, Adrian E. Roitberg, Alexander J. Grenning.
Chemical Communications, 56:11779-11782 (2020)
174
NEXMD Software Package for Nonadiabatic Excited State Molecular Dynamics Simulations
Walter Malone, Benjamin Nebgen, Alexander White, Yu Zhang, Huajing Song, Josiah A. Bjorgaard, Andrew E. Sifain, Beatriz Rodriguez-Hernandez, Victor M. Freixas, Sebastian Fernandez-Alberti, Adrian E. Roitberg, Tammie R. Nelson, Sergei Tretiak.
Journal of Chemical Theory and Computation, 16:5771-5783 (2020)
173
Xiang Gao, Farhad Ramezanghorbani, Olexandr Isayev, Justin S. Smith, Adrian E. Roitberg.
Journal of Chemical Information and Modeling, 60:3408-3415 (2020)
172
Extending the Applicability of the ANI Deep Learning Molecular Potential to Sulfur and Halogens
Christian Devereux, Justin S. Smith, Kate K. Davis, Kipton Barros, Roman Zubatyuk, Olexandr Isayev, Adrian E. Roitberg.
Journal of Chemical Theory and Computation, 16:4192-4202 (2020)
171
Eugene N. Muratov, Jürgen Bajorath, Robert P. Sheridan, Igor V. Tetko, Dmitry Filimonov, Vladimir Poroikov, Tudor I. Oprea, Igor I. Baskin, Alexandre Varnek, Adrian Roitberg, Olexandr Isayev, Stefano Curtalolo, Denis Fourches, Yoram Cohen, Alan Aspuru-Guzik, David A. Winkler, Dimitris Agrafiotis, Artem Cherkasov, Alexander Tropsha.
Chemical Society Reviews, 49:3525-3564 (2020)
170
Justin S. Smith, Roman Zubatyuk, Benjamin Nebgen, Nicholas Lubbers, Kipton Barros, Adrian E. Roitberg, Olexandr Isayev, Sergei Tretiak.
Scientific Data, 7: (2020)
169
Axially Chiral Cannabinols: A New Platform for Cannabinoid‐Inspired Drug Discovery
Primali V. Navaratne, Jenny L. Wilkerson, Kavindri D. Ranasinghe, Evgeniya Semenova, Jasmine S. Felix, Ion Ghiviriga, Adrian Roitberg, Lance R. McMahon, Alexander J. Grenning.
ChemMedChem, 15:728-732 (2020)
168
Tammie R. Nelson, Alexander J. White, Josiah A. Bjorgaard, Andrew E. Sifain, Yu Zhang, Benjamin Nebgen, Sebastian Fernandez-Alberti, Dmitry Mozyrsky, Adrian E. Roitberg, Sergei Tretiak.
Chemical Reviews, : (2020)
167
Vinícius Wilian D. Cruzeiro, Gustavo Troiano Feliciano, Adrian E. Roitberg.
Journal of the American Chemical Society, : (2020)
2019
166
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, 16:2-14 (2019)
165
The any particle molecular orbital/molecular mechanics approach
José M. Rodas, Johan F. Galindo, Adrian E. Roitberg, Andrés Reyes.
Journal of Molecular Modeling, 25:316 (2019)
164
Folding and Dynamics Are Strongly pH-Dependent in a Psychrophile Frataxin
Rodolfo M. González-Lebrero, Lucas Defelipe, Carlos Modenutti, Adrian E. Roitberg, Nicolas A. Batastini, Martín E. Noguera, Javier Santos, Ernesto A. Roman.
The Journal of Physical Chemistry B, 123:7676-7686 (2019)
163
Xiang Gao, Emilio Gallicchio, Adrian E. Roitberg.
The Journal of Chemical Physics, 151:034113 (2019)
162
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)
161
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)
160
Ankita Sarkar, Pancham Lal Gupta, Adrian E. Roitberg.
The Journal of Physical Chemistry B, 123:5742-5754 (2019)
159
Vinícius Wilian D. Cruzeiro, Adrian E. Roitberg.
Journal of Chemical Theory and Computation, 15:871-881 (2019)
2018
158
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)
157
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)
156
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)
155
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)
154
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)
153
Vinícius Wilian D. Cruzeiro, Marcos S. Amaral, Adrian E. Roitberg.
The Journal of Chemical Physics, 149:072338 (2018)
152
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)
151
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)
150
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: 2316 (2018)
149
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)
148
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)
147
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)
146
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
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
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
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
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
Vinícius Wilian D. Cruzeiro, Adrian Roitberg, Nicolas C. Polfer.
Journal of Chemical Education, 93:1578-1585 (2016)
137
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
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
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
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
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
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
Marcos Grosso, Adrian Kalstein, Gustavo Parisi, Adrian E. Roitberg, Sebastian Fernandez-Alberti.
The Journal of Chemical Physics, 142:245101 (2015)
127
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
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
José Rogério A. Silva, Adrian E. Roitberg, Cláudio Nahum Alves.
The Journal of Physical Chemistry B, 119:1468-1473 (2015)
2014
121
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
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
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
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
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
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
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
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
Shuai Liang, Adrian E. Roitberg.
Journal of Chemical Theory and Computation, 9:4470-4480 (2013)
104
Gustavo Pierdominici-Sottile, Juliana Palma, Adrian E. Roitberg.
Proteins: Structure, Function, and Bioinformatics, 82:424-435 (2013)
103
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
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
Natali V. Di Russo, Dario A. Estrin, Marcelo A. Martí, Adrian E. Roitberg.
PLoS Computational Biology, 8:e1002761 (2012)
93
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
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
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
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
82
Gustavo Pierdominici-Sottile, Adrian E. Roitberg.
Biochemistry, 50:836-842 (2011)
81
Gustavo Pierdominici-Sottile, Nicole A. Horenstein, Adrian E. Roitberg.
Biochemistry, 50:10150-10158 (2011)
80
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
Tammie Nelson, Sebastian Fernandez-Alberti, Vladimir Chernyak, Adrian E. Roitberg, Sergei Tretiak.
The Journal of Physical Chemistry B, 115:5402-5414 (2011)
77
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
Xiang S. Wang, Adrian E. Roitberg, Nigel G. J. Richards.
Biochemistry, 48:12272-12282 (2009)
68
Daniel J. Sindhikara, Adrian E. Roitberg, Kenneth M. Merz.
Biochemistry, 48:12024-12033 (2009)
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
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
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
Daniel J. Sindhikara, Seonah Kim, Arthur F. Voter, Adrian E. Roitberg.
Journal of Chemical Theory and Computation, 5:1624-1631 (2009)
62
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)
60
Özlem Demir, Adrian E. Roitberg.
Biochemistry, 48:3398-3406 (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
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
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
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
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
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
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
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
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
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
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
S. N. Yaliraki, A. E. Roitberg, C. Gonzalez, V. Mujica, Mark A. Ratner.
The Journal of Chemical Physics, 111:6997-7002 (1999)
18
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
15
A molecular dynamics study of Fe2S2 putidaredoxin: multiple conformations of the C-terminal region
A.E. Roitberg.
Biophysical Journal, 73:2138-2148 (1997)
14
Marcia Holden, Martin Mayhew, David Bunk, Adrian Roitberg, Vincent Vilker.
Journal of Biological Chemistry, 272:21720-21725 (1997)
13
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
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
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
Ron Elber, Adrian Roitberg, Carlos Simmerling, Robert Goldstein, Gennady Verkhivker, Haiying Li, Alex Ulitsky.
NATO ASI Series, 325:165-191 (1994)
1991
2
Adrian Roitberg, Ron Elber.
The Journal of Chemical Physics, 95:9277-9287 (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)