Publications
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2024
199 The need to implement FAIR principles in biomolecular simulations
Rommie Amaro, … Adrian Roitberg, … Modesto Orozco.
Nature Methods, Submitted (2024)
198 AQuaRef: Machine learning accelerated quantum refinement of protein structures
Roman Zubatyuk, Malgorzata Biczysko, Kavindri Ranasinghe, Nigel Moriarty, Hatice Gokcan, Holger Kruse, Billy Poon, Paul Adams, Mark Waller, Adrian Roitberg, Olexandr Isayev, Pavel Afonine.
Nature Methods, Submitted (2024)
197 Guided Multi-objective Generative AI to Enhance Structure-based Drug Design
Amit Kadan, Kevin Ryczko, Adrian Roitberg and Takeshi Yamazaki.
Nature Communications, Submitted (2024)
196 Nonadiabatic Excited State Molecular Dynamics with explicit solvent: NEXMD-SANDER implementation
Dustin Tracy, Sebastian Fernandez-Alberti, Johan Fabian Galindo, Sergei Tretiak, Adrian Roitberg.
J Phys Chem B, Submitted (2024)
195 Machine Learning of Reactive Potentials
Yinuo Yang, Shuhao Zhang, Kavindri D. Ranasinghe, Olexandr Isayev, Adrian E. Roitberg.
Annual Review of Physical Chemistry, 75:371-395 (2024)
194 Assessment of Embedding Schemes in a Hybrid Machine Learning/Classical Potentials (ML/MM) Approach
Juan S. Grassano, Ignacio Pickering, Adrian E. Roitberg, Mariano C. González Lebrero, Dario A. Estrin, Jonathan A. Semelak.
Journal of Chemical Information and Modeling, 64:4047-4058 (2024)
2023
193 Accelerated Organic Crystal Structure Prediction with Genetic Algorithms and Machine Learning
Amit Kadan, Kevin Ryczko, Andrew Wildman, Rodrigo Wang, Adrian Roitberg, Takeshi Yamazaki.
Journal of Chemical Theory and Computation, 19:9388-9402 (2023)
192 AmberTools
David A. Case, … Vinícius Wilian D. Cruzeiro, … Adrian Roitberg, Carlos Simmerling, Darrin M. York, Maria C. Nagan, Kenneth M. Merz.
Journal of Chemical Information and Modeling, 63:6183-6191 (2023)
191 Axially Chiral Cannabinoids: Design, Synthesis, and Cannabinoid Receptor Affinity
Sara E. Kearney, Anghelo J. Gangano, Daniel G. Barrus, Kyle J. Rehrauer, Terry-Elinor R. Reid, Primali V. Navaratne, Emily K. Tracy, Adrian Roitberg, Ion Ghiviriga, Christopher W. Cunningham, Thomas Gamage, Alexander J. Grenning.
Journal of the American Chemical Society, 145:13581-13591 (2023)
190 First-in-class multifunctional TYMS nonclassical antifolate inhibitor with potent in vivo activity that prolongs survival
Maria V. Guijarro, Patrick C. Kellish, Peter E. Dib, Nicholas G. Paciaroni, Akbar Nawab, Jacob Andring, Lidia Kulemina, Nicholas V. Borrero, Carlos Modenutti, Michael Feely, Elham Nasri, Robert P. Seifert, Xiaoping Luo, Richard L. Bennett, Daniil Shabashvili, Jonathan D. Licht, Robert McKenna, Adrian Roitberg, Robert W. Huigens, Frederic J. Kaye, Maria Zajac-Kaye.
JCI Insight, 8: (2023)
189 Novel Lennard-Jones Parameters for Cysteine and Selenocysteine in the AMBER Force Field
Federico N. Pedron, Andresa Messias, Ari Zeida, Adrián E. Roitberg, Darío A. Estrin.
Journal of Chemical Information and Modeling, 63:595-604 (2023)
2022
188 Elucidating the Protonation State of the γ-Secretase Catalytic Dyad
Dulce C. Guzmán-Ocampo, Rodrigo Aguayo-Ortiz, José-Luis Velasco-Bolom, Pancham Lal Gupta, Adrian E. Roitberg, Laura Dominguez.
ACS Chemical Neuroscience, 14:261-269 (2022)
187 Auto3D: Automatic Generation of the Low-Energy 3D Structures with ANI Neural Network Potentials
Zhen Liu, Tetiana Zubatiuk, Adrian Roitberg, Olexandr Isayev.
Journal of Chemical Information and Modeling, 62:5373-5382 (2022)
186 Adiabatic Excited-State Molecular Dynamics with an Explicit Solvent: NEXMD-SANDER Implementation
Dustin A. Tracy, Sebastian Fernandez-Alberti, Sergei Tretiak, Adrian E. Roitberg.
Journal of Chemical Theory and Computation, 18:5213-5220 (2022)
185 Diastereoselective Indole-Dearomative Cope Rearrangements by Compounding Minor Driving Forces
Subhadip De, Breanna M. Tomiczek, Yinuo Yang, Kenneth Ko, Ion Ghiviriga, Adrian Roitberg, Alexander J. Grenning.
Organic Letters, 24:3726-3730 (2022)
184 Anticancer Agents Derived from Cyclic Thiosulfonates: Structure‐Reactivity and Structure‐Activity Relationships
Amanda F. Ghilardi, Elham Yaaghubi, Renan B. Ferreira, Mary E. Law, Yinuo Yang, Bradley J. Davis, Christopher M. Schilson, Ion Ghiviriga, Adrian E. Roitberg, Brian K. Law, Ronald K. Castellano.
ChemMedChem, 17: (2022)
183 Construction of vicinal 4°/3°-carbons via reductive Cope rearrangement
Kristin M. Sobie, Matthew Albritton, Yinuo Yang, Mariana M. Alves, Adrian Roitberg, Alexander J. Grenning.
Chemical Science, 13:1951-1956 (2022)
182 Development and Evaluation of Geometry Optimization Algorithms in Conjunction with ANI Potentials
Dongxiao Hao, Xibing He, Adrian E. Roitberg, Shengli Zhang, Junmei Wang.
Journal of Chemical Theory and Computation, 18:978-991 (2022)
2021
181 pH Effects and Cooperativity among Key Titratable Residues for Escherichia coli Glycinamide Ribonucleotide Transformylase
Pancham Lal Gupta, Justin S. Smith, Adrian E. Roitberg.
The Journal of Physical Chemistry B, 125:9168-9185 (2021)
180 The density-of-States and equilibrium charge dynamics of redox-active switches
Paulo Roberto Bueno, Vinícius Wilian D. Cruzeiro, Adrian E. Roitberg, Gustavo T. Feliciano.
Electrochimica Acta, 387:138410 (2021)
2020
179 pH-Dependent Conformational Changes Lead to a Highly Shifted pKa for a Buried Glutamic Acid Mutant of SNase
Ankita Sarkar, Adrian E. Roitberg.
The Journal of Physical Chemistry B, 124:11072-11080 (2020)
178 Exploring the concerted mechanistic pathway for HIV-1 PR—substrate revealed by umbrella sampling simulation
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 Steered molecular dynamic simulations reveal Marfan syndrome mutations disrupt fibrillin-1 cbEGF domain mechanosensitive calcium binding
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 TorchANI: A Free and Open Source PyTorch-Based Deep Learning Implementation of the ANI Neural Network Potentials
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 QSAR without borders
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 The ANI-1ccx and ANI-1x data sets, coupled-cluster and density functional theory properties for molecules
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 Non-adiabatic Excited-State Molecular Dynamics: Theory and Applications for Modeling Photophysics in Extended Molecular Materials
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 Exploring Coupled Redox and pH Processes with a Force-Field-Based Approach: Applications to Five Different Systems
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 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)
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 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)
160 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)
159 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
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 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)
155 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)
154 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)
153 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)
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 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)
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 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)
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
82 Proton Transfer Facilitated by Ligand Binding. An Energetic Analysis of the Catalytic Mechanism ofTrypanosoma cruziTrans-Sialidase
Gustavo Pierdominici-Sottile, Adrian E. Roitberg.Biochemistry, 50:836-842 (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 Apo and Nickel-Bound Forms of thePyrococcus horikoshiiSpecies of the Metalloregulatory Protein: NikR Characterized by Molecular Dynamics Simulations
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 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)
60 Modulation of Catalytic Function by Differential Plasticity of the Active Site: Case Study ofTrypanosoma cruzitrans-Sialidase andTrypanosoma rangeliSialidase†
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 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
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 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
2 Modeling side chains in peptides and proteins: Application of the locally enhanced sampling and the simulated annealing methods to find minimum energy conformations
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)