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ADRIAN E. ROITBERG Full Professor

Department of Chemistry, University of Florida.

Gainesville, FL. 32611-7200 Phone: (352) 392-6972

roitberg@ufl.edu

Education University of Illinois at Chicago. Chemistry. PhD. 1992

Universidad de Buenos Aires, Argentina. Chemistry. Licenciado 1987

Research Experience 1/1/2020-Present V.T. and Louise Jackson Professor in Chemistry. University of Florida 8/2011-Present Full Professor, Department of Chemistry, University of Florida. 2016-2019 University of Florida Research Foundation Professor, Department of

Chemistry, University of Florida. 8/2011-Present Affiliate Full Professor. Department of Physics, University of Florida 8/2013-8/2014 Colonel Allan R. and Margaret G. Crow Term Professor. College of

Liberal Arts and Sciences, University of Florida. 1/2004-8/2011 Associate Professor, Quantum Theory Project and Department of

Chemistry, University of Florida. 1/2005-2011 Affiliate Associate Professor. Department of Physics, University of

Florida 8/2003-1220/03 Associate Scientist, Quantum Theory Project and Department of

Chemistry, University of Florida. 1/2001-8/2003 Assistant Scientist, Quantum Theory Project and Department of

Chemistry, University of Florida. 3/1998-12/2000 Affiliate Assistant Professor. Computational Sciences Institute, George

Mason University. 1/1996-12/2000 Guest Research Scientist. Biotechnology Division, National Institute of

Standards and Technology. 10/1992-12/1995 Postdoctoral Fellow. Chemistry Department, Northwestern University.

Advisor: Prof. Mark Ratner. Honors and Awards 2020 V.T. and Louise Jackson Professor in Chemistry. University of Florida 2020 Doctoral Dissertation Advisor/Mentoring Award. University of Florida. 2016 Ulam Scholar. Center for Non-linear Sciences. Los Alamos National

Laboratory. New Mexico. 2016 University of Florida Research Foundation Professor.

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2014 Elected Fellow of the American Chemical Society. 2014 Elected Fellow of the American Physical Society. 2012 ‘Ulam Fellow’. Los Alamos National Laboratory. 2011 ‘Raices Prize’. Ministry of Science and Technology of Argentina. 2007 Howard Hughes Medical Institute Distinguished Mentor Award.

University of Florida. 2006 Fulbright Fellow (research place in Argentina). 2006 Invited Professor. University of Buenos Aires. Argentina. 2004 Invited Professor. University of Buenos Aires. Argentina Mentoring Current PhD students Chemistry: Sunidhi Lenka (UF Alumni Fellow) Maria del Pilar Buteler Christian Devereux Kavindri Ranasinghe (UF Alumni Fellow) Ignacio Pickering Yinuo Yang Jinze Xue Nicholas Terrel Farhad Ramezanghorbani Katherine Davis (UF Alumni Fellow) Physics: Dustin Tracy (UF Alumni Fellow) Graduated Ph.D. students (22 total) 2006 Alejandro Crespo. Merck Research Laboratories. New Jersey. 2007 Seonah Kim. Staff Member. National Renewable Energy Laboratory. Golden, CO 2008 Christina Crecca. Assistant Professor. Gloucester County College. Pennsylvania. 2008 Ozlem Demir. Postdoctoral Fellow at University of California San Diego. Prof.

Rommie Amaro 2008 Giorgios Leonis. Postdoctoral Fellow at Hellenic Research Institute, Greece. 2009 Elena Dolghih. Eli Lilly. Indiana. 2009 Dan Sindhikara. Schrodinger Company, New York. 2010 Maria Ana Castro. Postdoctoral Fellow. University of Buenos Aires, Argentina. Prof.

Dario Estrin. 2010 Yilin Meng. Senior Scientist. Pfizer. 2013 Jason Swails (NSF Pre-Doctoral Fellow). Lutron Electronics 2013 Danial Sabri-Dashti. Senior Scientist. Amazon Inc. 2013 Bill Miller III . Assistant Professor. Truman State University. 2013 Dwight McGee (Bridge to Doctorate Fellow). Senior Scientist at Silicon Therapeutics 2014 Johan Galindo-Cruz. Faculty in Colombia.

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2015 Natali Di Russo. Intel Corporation. (UF Alumni Fellow and HHMI award for International Graduate Student)

2016 Chad Hopkins. Senior Software Engineer, Raytheon Corporation. 2018 Justin Smith. Postdoctoral Fellow at Los Alamos National Laboratory. 2019 Vinicius Cruzeiro. Postdoctoral Fellow. U California San Diego. 2019 Xiang Gao. Engineer. NVIDIA, California 2019 Ankita Sarkar. Postdoctoral Fellow, Italian Institute of Technology 2019 Delaram Goreishi, Senior Scientist, Schrodinger Co. 2019 Pancham Lal Gupta. Postdoc at U Michigan. 2020 Farhad Ramezanghorbani Undergraduate students Dominic Rufa Doing PhD at Sloan-Kettering Cancer center, NY Abia Abia MD student Eva Rivera PhD awarded from Boston University. Prof. John Straub Robert Abel PhD awarded from Columbia University. Prof Rich Friesner Mikolai Fajer PhD awarded from UCSD. Prof. Andy Mc Cammon Mehrnoosh Arrar PhD awarded from UCSD. Prof. Andy Mc Cammon Mallory Gerace PhD student at Cornell University. Daniel Emerson PhD student at University of Pennsylvania. Professional Experience Editorial Positions 2016- Advisory Board. Chem Cell Press. 2007-2010 Senior Editor. Journal of Physical Chemistry. American Chemical Society 2012-2014 Editorial Board. Computational Chemistry Highlights 2010-active Editorial Board: Journal of Molecular Modeling. 2004-active Editorial Board: International Journal of Quantum Chemistry. 2004-active Editorial Board: Advances in Quantum Chemistry. 2004 Editor. Special Issue of “Journal of Molecular Graphics and Modeling” on Conformational Sampling Review Panels 2001- Several NIH and NSF panels, usually twice/year 2007-2009 Permanent Member NIH Study Section: Macromolecular Structure and

Function-(MSFE) 2004-2006 External Scientific Advisory Committee. MBRS-SCORE-NIH program.

University of Puerto Rico. Mayaguez, PR. 2002-20006 NSF review panel for the Supercomputing National Resources Allocation

Committee. (LRAC/MRAC). 2001-active Advisor and Reviewer for the “National Science Agency” in Argentina.

Conference Organizer 2001-2014 Co-Organizer. Sanibel Symposium in Theoretical Chemistry. Florida and

Georgia

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2007 International Organizing committee. Quitel 33. Theoretical Chemists of Latin Expression. Havana, Cuba.

2007 International Organizing Committee. Panamerican Workshop in Theoretical Chemistry. Cuernavaca, Mexico.

2002 Organizer of an ACS symposium and the National American Chemical Society meeting. “Enhanced Sampling Techniques for Monte Carlo and Molecular Dynamics”. Orlando, FL.

Service to the profession 2018- Member, Scientific Advisory Board, Schrödinger Co. 2016-2018 Member, Science Advisory Board. D3R collaborative. 2016 Chair Elect. Gordon Conference in Computational Chemistry 2020. 2016 Past Chair. American Chemical Society. Computers in Chemistry

Division. 2015 Chair. American Chemical Society. Computers in Chemistry Division. 2014 Chair-Elect. American Chemical Society. Computers in Chemistry

Division. 2006- 2012 Alternate Councilor. American Chemical Society. Computers in

Chemistry Division. 2006-2012 Member. Executive Committee. Computers in Chemistry Division.

American Chemical Society. 2006-2009 Assistant Program Chair. National meetings. Computers in Chemistry

Division. American Chemical Society. Memberships American Chemical Society American Physical Society Grants Active 1. "Convergence Accelerator Phase I (RAISE): MPrint-OKN," PIs: David T. McQuade, James K. Ferri, Carol A. Parish, Adrian E. Roitberg. National Science Foundation. NSF-1937017. $994,433 total. $200,000 to Roitberg. 9/1/2019-5/31/2020 2. “Neural Network Potentials”. Genentech. PI Roitberg. 7/10/2019-7/09/2021. $177,000 (total direct costs) 3. "D3SC: CDS&E: Collaborative Research: Development and application of accurate, transferable and extensible deep neural network potentials for molecules and reactions.". National Science Foundation. CHE-1802831. PI Roitberg. 7/15/2018-7/14/2021. $435,561 (Total costs)

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4. "SusChem: New Methodologies in Biocatalysis", national Science Foundation. CBET-1705918. P.I. (with Jon Stewart) NSF 7/1/17 – 6/30/20, $486,644 (total direct costs) 5. “i-REU: The US/France Exchange Program in Chemistry: Forming Global Scientists for the 21st Century”. National Science Foundation. NSF-1156907. 2017-2020. PI Valeria Kleiman, co-PI Adrian E. Roitberg. $ 613,217 total 6. “Studies on thymidylate synthase as tumor-promoting oncogene for development of new allosteric inhibitors for cancer treatment.”. National Institute of Health. National Cancer Insitute. 1R01CA188132. 2016-2020. PI: Maria Zajac-Kaye. Co-PI: Adrian E. Roitberg. Completed 1. “Infrared laser spectroscopy of mass-separated metabolites” National Institutes of Health, 1R01GM110077, 2014-2018. PI: Polfer. co-Investigator: Roitberg; Total: $1,080,000; Roitberg: $75,000 2. “PRAC - Ensembles of molecular dynamics engines for assessing force fields, conformational change, and free energies of proteins and nucleic acids.” National Science Foundation. ACI-1440031. 2014-2018. Adrian E. Roitberg. Co-PI $40,000 total. 3. “Collaborative: SI2-SSE - A Plug-and-Play Software Platform of Robotics-Inspired Algorithms for Modeling Biomolecular Structures and Motion”. National Science Foundation. ACI-1440523. 2014-2017. Adrian E. Roitberg. PI $67,235 total 4. "Research and Development work identified as quantum mechanical methods for studying excited state processes." PI. Los Alamos National Laboratory. 8/2016-8/2017. $160,447 (total costs) 5. “iREU Site: The US/France REU Site in Chemistry”. National Science Foundation. NSF-1156907. 2012-2016. Adrian E. Roitberg. PI $ 300,000 6. “Mechanism of Trypanosoma cruzi's Transsialidase in Chagas' Disease”. National Institutes of Health. R01 AI073674. Adrian E. Roitberg. PI $945,394 (2008-2014) 7. “Collaborative Research: CRIF:CRF: Extensible Cyberenvironments for Empirical and Semiempirical Hamiltonian Parameter Optimization and Dissemination.” National Science Foundation. CHE-0822935. Adrian E. Roitberg. PI share $634,486.00 (2008-2013). 8. "Collaborative Research SI2-SSE: Sustained Innovation in Acceleration of Molecular Dynamics on Future Computational Environments: Power to the People in the Cloud and on Accelerators”. National Science Foundation. (2012-2015). Adrian E. Roitberg. PI $179,102. 9. Supplemental to “Collaborative Research SI2-SSE: Sustained Innovation in Acceleration of Molecular Dynamics on Future Computational Environments: Power to the People in the Cloud and on Accelerators”. National Science Foundation. (2013-2015). Adrian E. Roitberg. PI $48,532 10. “PRAC - Hierarchical molecular dynamics sampling for assessing pathways and free energies of RNA catalysis, ligand binding, and conformational change”. National Science Foundation. ACI-1036208 (2010-2014). Adrian E. Roitberg. Co-PI $40,000 total

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11. “US–Argentina, Brazil, Chile: Planning Visit to Extend Chemistry opportunities to South America”. National Science Foundation. NSF-0725310. Adrian E. Roitberg. Co-PI $18,216, (2007). 12. “Towards an LSAMP Discovery and Innovation Center for International Undergraduate Research Experiences.” National Science Foundation. NSF-0848089. Adrian E. Roitberg. PI $ 272,000 (2008-2010). 13. “iREU Site: The US/France REU Site in Chemistry”. National Science Foundation. NSF-0755225. Adrian E. Roitberg. PI $ 280,089 (2008-2011). 14. iREU Site: The US/South America REU Site in Chemistry and Molecular Biodiversity”. National Science Foundation. NSF-0755022. Adrian E. Roitberg. Co-PI $ 535,912 (2008-2011). 15. “Molecular wires and nano-wires: properties and control”. Department of Energy. Office of Basic Energy Sciences. Nano-Scale Science, Engineering and Technology Program. DE-FG02-02ER45995. Adrian E. Roitberg. Co-PI $750,000, 2002-2005 16. “Peptide and protein folding: the view from the energy minima.” College of Liberal Arts and Sciences Research Award. $10,900. Adrian E. Roitberg. PI 2001. 17. Support for an ACS symposium titled “Enhanced sampling techniques for Monte Carlo and molecular dynamics”. Petroleum Research Fund. $2,400. Adrian E. Roitberg. PI 2001.

Publications (175 published, ~28000 citations) h-index=61 a. Submitted 1. “The Density-of-States and Equilibrium Charge Dynamics of Redox-Active Switches” Bueno, Paulo; Cruzeiro, Vinícius Wilian; Roitberg, Adrian; Feliciano, Gustavo. Journal of the American Chemical Society (January 2021) b. Accepted

c. Published 1. "pH-Dependent Conformational Changes Lead to a Highly Shifted pKa for a Buried Glutamic Acid mutant of SNase”. Ankita Sarkar and Adrian E. Roitberg. The Journal of Physical Chemistry. doi: 10.1021/acs.jpcb.0c07136 (December 2020)

2. "Steered molecular dynamic simulations reveal Marfan syndrome mutations disrupt fibrillin-1 cbEGF domain mechanosensitive calcium binding” Haller, S.J., Roitberg, A.E. & Dudley, A.T. Scientific Reports 10, 16844 (2020). https://doi.org/10.1038/s41598-020-73969-2

3. “Exploring the Concerted Mechanistic Pathway for HIV-1 PR—Substrate Revealed by Enhanced Umbrella Sampling Simulation" Authors: Sanusi, Zainab; Lawal, Monsurat;

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Gupta, Pancham Lal; Govender, Thavendran; Baijnath, Sooraj; Naicker, Tricia; Maguire, Glenn; Honarparvar, Bahareh; Roitberg, Adrian; Kruger, Hendrik. Journal of Biomolecular Structure and Dynamics (2020) doi: 10.1080/07391102.2020.1832578

4. “Unraveling Direct and Indirect Energy Transfer Pathways in a Light-harvesting Dendrimer” by Maria Camila Aguilera, Adrian E. Roitberg, Valeria D. Kleiman, Sebastian Fernandez-Alberti and Johan F. Galindo. The journal of physical chemistry C. (September 2020) doi: 10.1021/acs.jpcc.0c06539

5. “Selective ring-rearrangement or ring-closing metathesis of bicyclo[3.2.1]octenes.” Semenova, Evgeniya; Lahtigui, Ouidad; Scott, Sarah; Albritton, Matthew; Abboud, Khalil; Ghiviriga, Ion; Roitberg, Adrian; Grenning, Alexander. ChemComm. (2020) doi: 10.1039/D0CC04624H

6. “NEXMD Software Package for Non-adiabatic Excited State Molecular Dynamics Simulations” Walter Malone, Benjamin Nebgen, Alexander White, Yu Zhang, Huajing Song, Josiah Bjorgaard, Andrew Sifain, Beatriz Rodriguez-Hernandez, Victor M. Freixas, Sebastian Fernandez-Alberti, Adrian E. Roitberg, Tammie Nelson and Sergei Tretiak. Journal of Chemical Theory and Computation (2020) doi: 10.1021/acs.jctc.0c00248

7. “TorchANI: A Free and Open Source PyTorch Based Deep Learning Implementation of the ANI Neural Network Potentials” Xiang Gao, Farhad Ramezanghorbani, Olexander Isayev,Justin S. Smith, and Adrian E. Roitberg. Journal of Chemical Information and Modeling (2020) 60:3408–3415 doi: 10.1021/acs.jcim.0c00451

8. “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 and Adrian E. Roitberg. Journal of Theoretical Chemistry and Computation (2020) doi: 10.1021/acs.jctc.0c00121

9. “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 and Sergei Tretiak. Scientific Data 7: 134 (2020). doi: 10.1038/s41597-020-0473-z

10. “QSAR without Borders” Muratov, Eugene; Bajorath, J.; Sheridan, Robert; Tetko, Igor; Filimonov, Dmitry; Poroikov, Vladimir ; Oprea, Tudor; Baskin, Igor; Varnek, Alexandre; Roitberg, Adrian; Isayev, Olexandr; Curtarolo, Stefano; Fourches, Denis; Cohen, Yoram; Aspuru Guzik, Alan; Winkler, David; Agrafiotis, Dimitris; Cherkasov, Artem; Tropsha,A. Chemical Society Reviews (May 2020) doi: org/10.1039/D0CS00098A

11. “Axially-Chiral Cannabinols: A New Platform for Cannabinoid-Based Drug Discovery” Navaratne, Primali; Wilkerson, Jenny; Ranasinghe, Kavindri ; Semenova, Evgeniya; Felix, Jasmine; McMahon, Lance; Roitberg, Adrian; Ghiviriga, Ion; Grenning, Alexander. ChemMedChem doi: 10.1002/cmdc.202000025 (2020)

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12. “Nonadiabatic Excited State Molecular Dynamics: theory and applications for modeling photophysics in extended molecular materials” by T. Nelson, A. White, J. Bjorgaard, A. Sifain, Y. Zhang, B. Nebgen, S. Fernandez-Alberti, D. Mozyrsky, S. Tretiak, and A. Roitberg. Chemical Reviews doi: 10.1021/acs.chemrev.9b00447 (2020)

13. "Exploring coupled redox and pH processes with a force field-based approach: applications to five different systems”. Cruzeiro, Vinícius Wilian; Feliciano, Gustavo; Roitberg, Adrian. Journal of the American Chemical Society. doi: 10.1021/jacs.9b11433 (2020)

14. "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. 16:14:1-16 (2019)

15. “The APMO/MM approach”. José M. Rodas, Johan F. Galindo, Adrian E. Roitberg and Andrés Reyes. J Mol Model 25: 316. (2019)

16. “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, and Ernesto A. Roman. Journal of Physical Chemistry B 123:7676-7686 (2019)

17. "A Fast Implementation of the Nudged Elastic Band Method in AMBER". Ghoreishi, Delaram; Cerutti, David; Fallon, Zachary; Simmerling, Carlos; Roitberg, Adrian. Journal of Chemical Theory and Computation. 15:4699-4707 (2019)

18. “The Generalized Boltzmann Distribution is the Only Distribution in which the Gibbs-Shannon Entropy equals the Thermodynamic Entropy”. Xiang Gao, Emilio Gallicchio and Adrian E. Roitberg. Journal of Chemical Physics 151:034113, (2019)

19. “Approaching coupled cluster accuracy with a general-purpose neural network potential through transfer learning”. Justin Smith , Benjamin Nebgen , Roman Zubatyuk , Nicholas Lubbers , Christian Devereux , Kipton Barros , Sergei Tretiak , Olexandr Isayev, Adrian Roitberg. Nature Communications 10: 2903 (2019)

20. “pH-dependent Conformational Changes due to Ionizable Residues in a Hydrophobic Protein Interior: The case of L25K and L125K variants of SNase.” Ankita Sarkar, Pancham Lal Gupta, Adrian E. Roitberg. Journal of Physical Chemistry B. doi:10.1021/acs.jpcb.9b03816 (2019)

21. "Multidimensional Replica Exchange simulations for Efficient constant pH and Redox Potential Molecular Dynamics". Cruzeiro, Vinícius Wilian; Roitberg, Adrian. Journal of Chemical Theory and Computation. 15:871-881 (2019)

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22. "Energy transfer and spatial scrambling of an exciton in a conjugated dendrimer". Ondarse Alvarez, Dianelys, Oldani, A, Roitberg, Kleiman, Valeria, Tretiak, Sergei, Fernandez-Alberti, Sebastian. Physical Chemistry Chemical Physics doi: 10.1039/C8CP05852K (2018)

23. "Transforming Computational Drug Discovery with Machine Learning and AI". Smith, Justin; Roitberg, Adrian; Isayev, Olexandr. Medicinal Chemistry Letters. doi: 10.1021/acsmedchemlett.8b00437 (2018)

24. "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 E. Roitberg, David A. Case, Ross C Walker, and Darrin M. York. J. Chem. Inf. Model. doi: 10.1021/acs.jcim.8b00462 (2018)

25. "Investigating Saccharomyces cerevisiae Alkene Reductase OYE 3 by Substrate Profiling, X-Ray Crystallography and Computational Methods" Powell, Robert; Buteler, M. Pilar; Lenka, Sunidhi; Crotti, Michele; Santangelo, Sara; Burg, Matthew; Bruner, Steven; Brenna, Maria Elisabetta; Roitberg, Adrian; Stewart, Jon. Catalysis Science and Technology. doi: 10.1039/C8CY00440D (2018)

26. "Redox Potential Replica Exchange Molecular Dynamics at Constant pH in AMBER: Implementation, Validation and Application" Vinicius Cruzeiro, Marcos Amaral, and Adrian Roitberg. The Journal of Chemical Physics 149, 072338 (2018)

27. "Probing the Structures of Solvent-Complexed Ions Formed in Electrospray Ionization Using Cryogenic Infrared Photodissociation Spectroscopy". Bell, Matthew; Cruzeiro, Vinícius Wilian; Cismesia, Adam; Tesler, Larry; Roitberg, Adrian; Polfer, Nicolas. The Journal of Physical Chemistry A. doi: 10.1021/acs.jpca.8b05896 (2018)

28. "Transferable Dynamic Molecular Charge Assignment Using Deep Neural Networks". Benjamin Nebgen, Nick Lubbers, Justin Smith, Andrew E Sifain, Andrey Y Lokhov, Olexandr Isayev, Adrian E Roitberg, Kipton Barros, Sergei Tretiak. Journal of Chemical Theory and Computation. doi: 10.1021/acs.jctc.8b00524 (2018) 29. "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) 30. "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, and Sergei Tretiak. Journal of Chemical Theory and Computation. doi:10.1021/acs.jctc.8b00103 (2018)

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31. "Cation-Dependent Conformations in 25-Hydroxyvitamin D3-Cation Adducts Measured by Ion Mobility-Mass Spectrometry and Theoretical Modeling". Christopher Chouinard, Vinicius Cruzeiro, Robin Kemperman, Nicholas Oranzi, Adrian Roitberg and Richard Yost. International Journal of Mass Spectrometry doi:10.1016/j.ijms.2018.05.013 (2018) 32. "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) 33. "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 and Adrian E. Roitberg. The Journal of the American Chemical Society. doi:10.1021/jacs.7b08569 (2017). 34. "ANI-1: A data set of 20M off-equilibrium DFT calculations for organic molecules". Justin S. Smith, Olexandr Isayev, Adrian E. Roitberg. Nature Scientific Data. 4:170193 (2017) 35. "Electronic Delocalization, Vibrational Dynamics and Energy Transfer in Organic Chromophores". Nelson, Tammie; Fernandez-Alberti, Sebastian; Roitberg, Adrian; Tretiak, Sergei. The Journal of Physical Chemistry Letters. 8: 3020-3031 (2017) 36. "Investigating Differences in Gas-Phase Conformations of 25-Hydroxyvitamin D3 Sodiated Epimers using Ion Mobility-Mass Spectrometry and Theoretical Modeling". Chouinard, Christopher; Cruzeiro, Vinícius Wilian; Beekman, Christopher; Roitberg, Adrian; Yost, Richard. Journal of The American Society for Mass Spectrometry. 28: 1497-1505 (2017) 37. "An extensible neural network potential with DFT accuracy at force field computational cost". Smith, Justin; Isayev, Olexandr and Roitberg, Adrian. Chemical Science. 8:3192-3203 (2017) 38. "Experimental and Theoretical Investigation of Sodiated Multimers of Steroid Epimers with Ion Mobility-Mass Spectrometry". Christopher D. Chouinard, Vinicius W.D. Cruzeiro, Adrian E. Roitberg, Richard A. Yost. Journal of The American Society for Mass Spectrometry. 28: 323-331 (2017) 39. "Theoretical Insights Into the Reaction and Inhibition Mechanism of the Metal-Independent Retaining Glycosyltransferase Responsible for Mycothiol Biosynthesis". Blanco, Juan; Hopkins, Chad; Pierdominici Sottile, Gustavo; González Lebrero, Mariano; Roitberg, Adrian; Marti, Marcelo. The Journal of Physical Chemistry. 121:471-478 (2016). 40. "Structure activity relationships of benzenesulfonamide-based inhibitors towards carbonic anhydrase isoform specificity". Bhatt, Avni; Mahon, Brian; Cruzeiro, Vinícius Wilian; Cornelio, Benedetta; Laronze-Cochard, Marie; Ceruso, Mariangela; Sapi, Janos; Rance,

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Graham; Khlobystov, Andrei; Fontana, Antonella; Roitberg, Adrian; Supuran, Claudiu; McKenna, Robert. ChemBioChem 18:213 (2016) 41. "Applying the Variational Method to the Hydrogen atom and Dihydrogen molecule within the IPython notebook platform" Cruzeiro, Vinícius Wilian; Roitberg, Adrian; Polfer, Nicolas. The Journal of Chemical Education. 93:1578-1585 (2016) 42. "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, and V. Kleiman. Physical Chemistry Chemical Physics. 18:25080-25089 (2016) 43. "Structured and Unstructured binding of an Intrinsically Disordered Protein as revealed by atomistic simulations" Raul Esteban Ithuralde , Adrian E Roitberg and Adrian G Turjanski. Journal of the American Chemical Society. 138:8742-8751 (2016) 44. "Steered Molecular Dynamics Methods applied to Enzyme Mechanism and Energetics". Claudia Ramirez, Marcelo Marti and Adrian E. Roitberg. Methods in Enzymology. 578:123-143 (2016) 45. "Coarse grain simulations of heme proteins: validation and study of large conformational transitions" Ramirez, Claudia; Petruk, Ariel; Bringas, Mauro; Estrin, Dario; Roitberg, Adrian; Marti, Marcelo; Capece, Luciana. Journal of Chemical Theory and Computation. 12:3390-33978 (2016) 46. "Structural study of a flexible active site loop in human indoleamine 2,3-dioxygenase and its functional implications" Alvarez, Lucia; Lewis Ballester, Ariel; Roitberg, Adrian; Estrin, Dario; Yeh, Syun-Ru; Marti, Marcelo; Capece, Luciana. Biochemistry. 55:2785-2793 (2016) 47. "Enhancement in Organic Photovoltaic Efficiency through the Synergistic Interplay of Molecular Donor Hydrogen Bonding and pi-Stacking”. Nathan T. Shewmon, Davita L. Watkins, Johan F. Galindo, Raghida Bou Zerdan, Jihua Chen, Jong Keum, Adrian E. Roitberg, Jiangeng Xue and Ronald K. Castellano. Advanced Functional Materials. 25:5166-5177 (2015) 48. “Oxygen diffusion pathways in a cofactor-independent dioxygenase". Natali V Di Russo, Heather L Condurso, Kunhua Li, Steven Bruner and Adrian E. Roitberg. Chemical Science. 6:6341-6348 (2015) 49. “Simulating the Inhibition Reaction of Mycobacterium tuberculosis L,D-Transpeptidase 2 by Carbapenems”. José Rogério A. Silva, Thavendran Govender, Glenn E. M. Maguire, Hendrik G. Kruger, Jerônimo Lameira, Adrian E. Roitberg and Cláudio Nahum Alves. Chemical Communications. 51:12560-12562. (2015)

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50. “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, and Valeria Kleiman. Journal of the American Chemical Society. 137 :11637–11644 (2015). 51. “On the analysis and comparison of conformer-specific essential dynamics upon ligand binding to a protein”. Marcos Grosso, Adrian Kalstein, Gustavo Parisi, Adrian Roitberg, and Sebastian Fernandez-Alberti. J. Chem. Phys. 142:245101 (2015) 52. “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 and Adrian E. Roitberg. Physical Chemistry Chemical Physics. 17:17790-17796 (2015) 53. "Long Time Step Molecular Dynamics through Hydrogen Mass Repartitioning" Hopkins, Chad; LeGrand, Scott; Walker, Ross; Roitberg, Adrian. Journal of Chemical Theory and Computation. 11:1864-1874. March (2015) 54. “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) 55. "Hydrogen Bond Directed Assembly of Oligothiophene/Fullerene Superstructures on Au(111)". Zhao, Xueying; Watkins, Davita; Galindo, Johan; Shewmon, Nathan; Roitberg, Adrian; Xue, Jiangeng; Castellano, Ronald; Perry, Scott. Organic Electronics. 19:61 (2015) 56. “Interpretation of pH-activity Profiles for Acid-Base Catalysis from Molecular Simulations.” Dissanayake, Thakshila; Swails, Jason; Harris, Michael; Roitberg, Adrian; York, Darrin. Biochemistry. 54:1307-1313 (2015) 57. A QM/MM Free Energy Study of the Oxidation Mechanism of Dihydroorotate Dehydrogenase (Class 1A) from Lactococcus lactis. Silva, José; Roitberg, Adrian; Alves, Claudio. Journal of Physical Chemistry. 119:1468-1473 (2015) 58. “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”. Goldfarb, Nathan, Ohanessian, Meray, Biswas, Shya , McGee Jr., T. Dwight, Mahon, Brian, Ostrov, David, Garcia, Jose, Tang, Yan, McKenna, Robert, Roitberg, Adrian, Dunn, Ben. Biochemistry. 54:422-433 (2015) 59. “Underlying thermodynamics of pH allostery”. Natali Di Russo, Marcelo A. Marti and Adrian E. Roitberg. Journal of Physical Chemistry B, 118:12818-12826 (2014)

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60. "pH-REMD Simulations Indicate that the Catalytic Aspartates of HIV-1 Protease Exist Primarily in a Mono-protonated State”. T. Dwight McGee, Jesse Edwards and Adrian E. Roitberg. Journal of Physical Chemistry B, 118:12577-12585 (2014) 61. “Improving Efficiency in SMD Simulations Trough a Hybrid Differential Relaxation Algorithm”. Ramirez, Claudia; Roitberg Adrian and Marti, Marcelo. Journal of Chemical Theory and Computation, 10:4609-4617 (2014) 62. "Catalytic mechanism of L,D-Transpeptidase 2 from Mycobacterium tuberculosis described by a computational approach: Insights for the design of new antibiotics drugs" Silva, José; Roitberg, Adrian; Alves, Claudio. Journal of Chemical Information and Modeling. 54:2402-2410 (2014) 63. “Fitting of dihedral terms in classical force fields as an analytical linear least square problem" Chad Hopkins and Adrian E. Roitberg. Journal of Chemical Information and Modeling. 54:1978–1986 (2014) 64. “Signature of nonadiabatic coupling in excited-state vibrational modes”. Miguel A. Soler, Tammie Nelson, Adrian E. Roitberg Sergei Tretiak, Sebastian Fernandez-Alberti. Journal of Physical Chemistry A, 118:10372-10379 (2014) 65. "Unraveling the differences of the hydrolytic activity of Trypanosoma cruzi trans-Sialidase and Trypanosoma rangeli Sialidase: A QM/MM modeling study" Bueren-Calabuig, Juan, Pierdominici-Sottile, Gustavo and Roitberg, Adrian. The Journal of Physical Chemistry B. 118:5807-5816 (2014) 66. “Nonadiabatic Excited-State Molecular Dynamics: Modeling Photophysics in Organic Conjugated Materials” Nelson, Tammie; Fernandez-Alberti, Sebastian; Roitberg, Adrian; Tretiak, Sergei. Accounts of Chemical Research. 47:1155–1164 (2014) 67. “Multi-dimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide”. Bergonzo, Christina; Henriksen, Niel; Roe, Daniel; Swails, Jason; Roitberg, Adrian; Cheatham III, Thomas. Journal of Chemical Theory and Computation, 10:492-499 (2014) 68. "Constant pH replica exchange molecular dynamics in explicit solvent using discrete protonation states: implementation, testing, and validation" Swails, Jason, York, Darrin and Roitberg, Adrian. Journal of Theoretical Chemistry and Computation. 10:1341-1352 (2014) 69. “Artifacts Due to Trivial Unavoided Crossings in the Modeling of Photoinduced Energy Transfer Dynamics in Extended Conjugated Molecules”. Tammie Nelson, Sebastian Fernandez-Alberti, Adrian Roitberg, and Sergei Tretiak. Chem. Phys. Letters. 590:208-213 (2013)

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70. “Electronic Excited State-specific IR Spectra for Phenylene Ethynylene Dendrimer Building Blocks.” Authors: Galindo, Johan, Fernandez-Alberti, Sebastian and Roitberg, Adrian. The Journal of Physical Chemistry C. 117:26517-26528 (2013) 71. “Trypanosoma cruzi trans-sialidase as a drug target against Chagas’ disease (American trypanosomiasis).” Bill R. Miller III and Adrian E. Roitberg. Future Medicinal Chemistry, 5:1889-1900 (2013) 72. "Optimization of Umbrella Sampling Replica Exchange Molecular Dynamics by Replica Positioning" Sabri-Dashti, Danial and Roitberg, Adrian. Journal of Chemical Theory and Computation. 9:4692-4699 (2013) 73. "Photosensitization of Single Crystal ZnO by a Conjugated Polyelectrolyte Designed to Avoid Aggregation". Zhu, Xuzhi; Nepomnyashchii, Alexander; Roitberg, Adrian; Parkinson, Bruce; Schanze, Kirk. Journal of Physical Chemistry Letters. 4:3126-3220 (2013) 74. "Free energy computations identify the mutations required to confer trans-sialidase activity into Trypanosoma rangeli Sialidase" Gustavo Pierdominici-Sottile, Juliana Palma and Adrian E. Roitberg. Proteins: Structure, Function and Bioinformatics. 82:424-425 (2014) 75. “AM1 Specific Reaction Parameters for Reactions of Hydroxide Ion with Halomethanes in complex environments: Development and Testing.” Liang, Shuai; Roitberg, Adrian. Journal of Chemical Theory and Computation. 9:4470-4480 (2013) 76. “Design of e-pharmacophore models using compound fragments for the trans-sialidase of Trypanosoma cruzi: screening for novel inhibitor scaffolds” Bill Miller II, Adrian E. Roitberg. Journal of Molecular Graphics and Modelling. 45: 84-97 (2013) 77. “Nonadiabatic Excited-State Molecular Dynamics: Treatment of Electronic Decoherence” Tammie Nelson, Sebastian Fernandez-Alberti, Adrian E. Roitberg, and Sergei Tretiak. Journal of Chemical Physics. J. Chem. Phys. 138: 224111 (2013) 78. “Conformational Disorder in Energy Transfer: Beyond Forster Theory” Tammie Nelson, Sebastian Fernandez-Alberti, Adrian E. Roitberg, and Sergei Tretiak. Physical Chemistry Chemical Physics. 15:9245-9256 (2013) 79. “Electronic delocalization in coordination polymers based on bimetallic carboxylates” Maria Ana Castro, Adrian E Roitberg and Fabio Cukiernik. Journal of theoretical chemistry and computation. 9:2609-2616 (2013) 80. “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. Biochim Biophys Acta - Proteins and Proteomics. 1824:1711-1721 (2013)

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81. “Structures of Biomolecular Ions in the Gas Phase Probed by Infrared Light Sources” Corey N. Stedwell, Johan F. Galindo,Adrian E. Roitberg, and Nicolas C. Polfer. Annual Reviews of Analytical Chemistry. 6:267-285 (2013) 82. “Simulation of Mesogenic Diruthenium Tetracarboxylates. Development of a Force Field for Coordination Polymers of the MMX type”. Maria Ana Castro, Adrian E. Roitberg, Fabio Cukiernik. Journal of Computational Chemistry. 34:1283-1290 (2013). Journal Cover. 83. “Hydrophobic effect drives oxygen uptake in myoglobin via histidine E7”. Leonardo Boechi, Mehrnoosh Arrar, Marcelo A. Martí, John S. Olson, Adrian E. Roitberg, Darío A. Estrin. Journal of Biological Chemistry. 288:6754-6762 (2013) 84. “Conjugated Polyelectrolyte Dendrimers: Aggregation, Photophysics, and Amplified Quenching”. Feng, F.; Lee, S. H.; Cho, S. W.; Komurlu, S.; McCarley, T. D.; Roitberg, A. E.; Kleiman, V. D.; Schanze, K. S. Langmuir. 28:16679. (2012). 85. “Analysis of State-Specific Vibrations Coupled to the Unidirectional Energy Transfer in Conjugated Dendimers.” Soler, M.A.; Roitberg, A.E.; Nelson, T.; Tretiak, S.; Fernandez-Alberti, S. Journal of Physical Chemistry A. 116: 9802-9810. (2012). 86. “Enzyme dynamics and catalysis in the mechanism of DNA polymerase.” Mulholland, A.J.; Roitberg, A.E.; Tuñon, I. Theoretical Chemistry Accounts. 131:1286. (2012). 87. “pH-dependent Conformational Changes in Proteins and Their Effect on Experimental pKas: The Case of Nitrophorin 4.” Di Russo, N.V.; Estrin, D.A.; Marti, M.A.; Roitberg, A.E. PLoS Computational Biology. 8:e1002761 (2012). 88. “Enhancing Conformation and Protonation State Sampling of Hen Egg White Lysozyme Using pH Replica Exchange Molecular Dynamics.” Swails, J. M.; Roitberg, A. E. Journal of Chemical Theory and Computation. 8:4393-4404 (2012). 89. “Crown-complexation of protonated amino acids: influence on IRMPD spectra.” Stedwell, C. N.; Galindo, J. F.; Gulyuz, K.; Roitberg, A. E.; Polfer, N. C. Journal of Physical Chemistry A. 117:1181-1188 (2012). 90. “MMPBSA.py: an efficient program for end-state free energy calculations.” Miller, III, B. R.; McGee, T. D.; Swails, J. M.; Homeyer, S.; Gohlke, H.; Roitberg, A. E. Journal of Chemical Theory and Computation. 8:3314-3321 (2012). 91. “pH-replica exchange Molecular Dynamics in proteins using a discrete protonation method.” Sabri Dashti, D.; Meng, Y.; Roitberg, A. E. Journal of Physical Chemistry B. 116: 8805-8811. (2012).

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92. “Wide-Open Flaps Are Key to Urease Activity.” Roberts, B. P.; Miller, III, B. R.; Roitberg, A. E.; Merz, K. M. Journal of the American Chemistry Society. 134:9934-9937 (2012). 93. “Shishiodoshi unidirectional energy transfer mechanism in phenylene ethynylene dendrimers.” Fernandez Alberti, S.; Roitberg, A. E.; Kleiman, V. D.; Nelson. T.; Tretiak, S. Journal of Chemical Physics. 137: 22A526 (2012). 94. “Comment on “a minimal implementation of the AMBER–GAUSSIAN interface for Ab Initio QM/MM-MD simulation”.” Roberts, B. P., Seabra, G. M., Roitberg, A. E., Merz, K. M., Deumens, E., Torras, J. and Trickey, S. B., J. Comput. Chem. 33:1643-1644 (2012) 95. “Identification of unavoided crossings in nonadiabatic photoexcited dynamics involving multiple electronic states in polyatomic conjugated molecules.” Sebastian Fernandez-Alberti, Adrian Roitberg, Tammie Nelson, and Sergei Tretiak. J. Chem. Phys. 137:14512 96. “Nonadiabatic Excited-State Molecular Dynamics (NA-ESMD). Numerical tests of convergence and parameters”. Nelson T, Fernandez-Alberti S, Chernyak V, Roitberg AE and Tretiak S. J. Chem. Phys. 136:054108 (2012) 97. “Free Energy Study of the Catalytic Mechanism of Trypanosoma cruzi trans-Sialidase. From the Michaelis Complex to the Covalent Intermediate”. Pierdominici-Sottile G and Roitberg AE. Biochemistry. 50:10150-10158 (2011) 98. “p38γ Activation Triggers Dynamical Changes in Allosteric Docking Sites”. Rodriguez Limardo RG, Ferreiro DR, Roitberg AE, Marti MA, and Turjanski AG. Biochemistry. 50:1384-95 (2011) 99. “Computing Alchemical Free Energy Differences with Hamiltonian Replica Exchange Molecular Dynamics (H-REMD) Simulations”. Meng Y, Sabri-Dashti D and Roitberg AE. Journal of Chemical Theory and Computation. 7:2721-2727 (2011) 100. “Non-adiabatic excited-state molecular dynamics modeling of photoinduced dynamics in conjugated molecules”. Nelson T, Fernandez-Alberti S, Chernyak V, Roitberg AE and Tretiak S. Journal of Physical Chemistry B. 115:5402-5414 (2011) 101. “Proton transfer facilitated by ligand binding. An energetic analysis of the Catalytic Mechanism of Trypanosoma cruzi trans-Sialidase" Pierdominici-Sottile G and Roitberg AE. Biochemistry. 50:836–842 (2011) 102. “Juvenile hormone synthesis: “esterify then epoxidize” or “epoxidize then esterify”? Insights from the structural characterization of juvenile hormone acid methyltransferase”. L.A. Defelipe LA, Dolghih E, Roitberg AE, Nouzova M, Mayoral JG, Noriega FG and Turjanski AG. Insect Biochemistry and Molecular Biology, 41:228-235 (2011)

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103. “Unidirectional Energy Transfer in Conjugated Molecules: the Crucial Role of High Frequency C=C bonds.” Fernandez-Alberti S, Kleiman VD, Tretiak S, and Roitberg AE. Journal of Physical Chemistry Letters. 1:2699-2704 (2010) 104. “Electronic Spectra of the Nanostar Dendrimer: Theory and Experiment.” Palma JL, Atas E, Hardison L, Marder TB, Collings JC, Beeby A, Melinger JS, Krause JL, Kleiman VD, and Roitberg AE. Journal of Physical Chemistry C. 114:20702-20712 (2010) 105. “Exchange Often and Properly in Replica Exchange Molecular Dynamics.” Sindhikara DJ, Emerson DJ, Roitberg AE. Journal of Chemical Theory and Computation. 6:2804-2808 (2010) 106. “Substrate Stereo-specificity in tryptophan dioxygenase and indoleamine 2,3- dioxygenase” Capece L, Arrar M, Roitberg AE, Yeh SR, Marti MA, Estrin DA. Proteins: Structure, Function, and Bioinformatics. 78:2961-2972 (2010) 107. “Impact of calcium on N1 influenza neuraminidase dynamics and binding free energy.” Lawrenz M, Wereszczynski J, Amaro R, Walker R, Roitberg AE, McCammon JA. Proteins: Structure, Function, and Bioinformatics 78:2523–2532 (2010) 108. "Constant pH Replica Exchange Molecular Dynamics in Biomolecules Using a Discrete Protonation Model". Meng Y, Roitberg AE, Journal of Chemical Theory and Computation, 6:1401–1412 (2010). 109. “Computational Studies of Ammonia Channel Function in Glutamine 5'-Phosphoribosylpyrophosphate Amidotransferase”, Wang, XS, Roitberg, AE, Richards, NG, Biochemistry, 48:12272-12282 (2009). 110. “Apo and Nickel-Bound Forms of the Pyrococcus horikoshii Species of the Metalloregulatory Protein: NikR Characterized by Molecular Dynamics Simulations”, Sindhikara DJ, Roitberg AE, Merz KM, Biochemistry, 48:12024-12033 (2009). 111. “AM1 Parameters for the Prediction of H-1 and C-13 NMR Chemical Shifts in Proteins”, Williams DE, Peters MB, Wang B, Roitberg AE, Merz KM, Journal of Physical Chemistry A, 113:11550-11559 (2009). 112. “Modulation of Catalytic Function by Differential Plasticity of the Active Site: Case Study of Trypanosoma cruzi trans-Sialidase and Trypanosoma rangeli Sialidase”. Demir O and Roitberg AE. Biochemistry. 48:3398-3406 (2009) 113. “Are Current Semiempirical Methods Better Than Force Fields? A Study from the Thermodynamics Perspective”, Seabra GD, Walker RC, Roitberg AE, Journal of Physical Chemistry A, 113:11938-11948 (2009).

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114. “Nonadiabatic Molecular Dynamics Simulations of the Energy Transfer between Building Blocks in a Phenylene Ethynylene Dendrimer”, Fernandez-Alberti S, Kleiman VD, Tretiak S, Roitberg AE, Journal of Physical Chemistry A, 113:7535-7542 (2009). 115. “Bad Seeds Sprout Perilous Dynamics: Stochastic Thermostat Induced Trajectory Synchronization in Biomolecules”, Sindhikara DJ, Kim S, Voter AF, Roitberg AE, Journal of Chemical Theory and Computation, 5:1624-1631 (2009).

116. “Theoretical Studies of Short Polyproline Systems: Recalibration of a Molecular Ruler.” Dolghih E, Ortiz W, Kim S, Krueger BP, Krause JL, Roitberg AE, Journal of Physical Chemistry A, 113: 4639-4646 (2009). 117. “Molecular Basis for the pH Dependent Structural Transition of Nitrophorin 4.” Martí MA, Estrin DA, Roitberg AE, Journal of Physical Chemistry B, 113: 2135-2142 (2009). 118. “pH-dependent mechanism of nitric oxide release in nitrophorins 2 and 4.” Swails JM, Meng Y, Walker FA, Marti MA, Estrin DA, Roitberg AE, Journal of Physical Chemistry B, 113:1192-201(2009).

119. “A Multiscale Treatment of Angeli's Salt Decomposition”. Torras J, Seabra GD, Roitberg, AE. Journal of Chemical Theory and Computation, 5: 37-46 (2009).

120. “Molecular and Functional Characterization of a Juvenile Acid Methyltransferase Expressed in the Corpora Allata of Mosquitoes.” Mayoral JG, Nouzova M, Yoshiyama M, Shinoda T, Hernandez-Martinez S, Dolghih E, Turjanski AG, Roitberg AE, Priestap H, Perez M, Impoinvil L, Li Y, Noriega FG, Journal of Insect Biochemistry and Molecular Biology. 39:31-37. (2009).

121. “Preliminary Molecular Dynamic Simulations of the Estrogen Receptor from Antagonist to Apo”. McGee TD, Edwards J, Roitberg AE. Int. J. Environ. Res. Public Health, 5: 111-114. (2008).

122. “Using the Rosetta Algorithm and selected inter-residue distances to Predict Protein Structure”. Crecca CR and Roitberg AE, International Journal of Quantum Chemistry, 108: 2793 - 2802 (2008).

123. “Using Distances between α-Carbons to Predict Protein Structure”. Crecca CR, Roitberg AE, International Journal of Quantum Chemistry. 108:2782-2792 (2008).

124. “Theoretical and experimental studies of diruthenium tetracarboxylates structure, spectroscopy and electrochemistry”. Castro MA, Roitberg AE, Cukiernik FD, Inorganic Chemistry. 47:4682–4690 (2008).

125. “A versatile AMBER-Gaussian QM/MM interface through PUPIL.” Torras J, Seabra GM, Deumens E, Trickey SB and Roitberg AE. Journal of Computational Chemistry. 29: 1564-1573 (2008).

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126. “Bond or Cage Effect: How Nitrophorins Transport and Release Nitric Oxide”. Marti MA, González Lebrero MC, Roitberg AE, Estrin DA. Journal of the American Chemical Society. 130: 1611-1618 (2008).

127. “Simulating Temperature Jumps for Protein Folding”. Kim S and Roitberg AE. Journal of Physical Chemistry B. 112: 1525-1532 (2008).

128. “Exchange frequency in replica exchange molecular dynamics”. Sindhikara D, Meng Y, Roitberg AE. Journal of Chemical Physics. 128: 024103 (2008).

129. “Coupling of Replica Exchange Simulations to a non-Boltzmann structure reservoir” Roitberg AE, Okur A, Simmerling CL. Journal of Physical Chemistry B., 111: 2415-2418(2007).

130. “Implementation of the SCC-DFTB method for hybrid QM/MM simulations within the AMBER Molecular Dynamics Package”. Seabra GM, Walker RC, Elstner M, Case DA, Roitberg AE, Journal of Physical Chemistry A. 111: 5655-5664 (2007).

131. “Molecular dynamics simulations of alkanethiol monolayers with azobenzene molecules on the Au (111).". Alkis S, Jiang P, Wang L, Roitberg AE, Krause JL, Cheng H, Journal of Physical Chemistry C, 111: 14743 - 14752 (2007).

132. “Fluorescence Resonance Energy Transfer in Dye-Labeled DNA”. Dolghih E, Roitberg AE and and Krause JL. Journal of Photochemistry and Photobiology A: Chemistry. 190: 321-327 (2007).

133. “Kinetics of internal-loop formation in polypeptide chains: a simulation study”. Doucet D, Roitberg AE and Hagen SJ. Biophys J., 92: 2281–2289 (2007).

134. “The Catalytic Mechanism of Peptidylglycine a-Hydroxylating Monooxygenase Investigated by Computer Simulation.” Crespo A, Martí MA, Roitberg AE, L. Amzel M, Estrin DA. Journal of the American Chemical Society, 128:12817-12828 (2006).

135. “Comparison of multiple Amber force fields and development of improved protein backbone parameters” Hornak V, Abel R, Okur A, Strockbine B , Roitberg AE and Simmerling CL. Proteins: Structure, Function, and Bioinformatics, 65:712-725 (2006).

136. “Structural analysis of ligand binding and catalysis in chorismate lyase”. Smith N, Roitberg AE, Rivera E, Howard A, Holden MJ, Mayhew M, Kaistha S, Gallagher DT. Archives of Biochemistry and Biophysics, 445:72-80 (2006).

137. “Theoretical Study of the Isomerization Mechanism of Azobenzene and Disubstituted Azobenzene Derivatives”. Crecca CR and Roitberg AE. Journal of Physical Chemistry A, 110:8188-8203 (2006).

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138. “Free Energy calculations with non-equilibrium methods. Applications of the Jarzynski Relationship”. Xiong H, Crespo A, Marti MA, Estrin DA, Roitberg AE. Theoretical Chemistry Accounts. 106: 338-346 (2006).

139. “Energy Transfer in the Nanostar: The Role of Coulombic Coupling and Dynamics”. Ortiz W, Krueger BP, Kleiman VD, Krause JL, Roitberg AE. Journal of Physical Chemistry B, 109:11512 -11519 (2005).

140. “Non-Equilibrium Approaches to Free Energy Calculations”. Roitberg AE. Annual Reports in Computational Chemistry, Chapter 8, page 103. Elsevier (2005).

141. “Multiple-Steering Molecular Dynamics QM-MM Free Energy Profiles in Enzymatic Reactions. Crespo A, Marti MA, Estrin DA, and Roitberg AE. Journal of the American Chemical Society, 127:6940 -6941, (2005).

142. “Special issue: Conformational sampling”. Roitberg AE and Simmerling CL. Journal of Molecular Graphics and Modelling. 22:317 (2004).

143. “Molecular Dynamics of Poly(benzylphenyl ether). Dendrimers: Efects of Backfolding on Förster Energy Transfer Rates”. Ortiz W, Jeffry Krause JL and Roitberg AE. Journal of Physical Chemistry B, 108:8218-8225 (2004).

144. “Coherent electron transport through an azobenzene molecule: A light driven molecular approach”. Zhang C, Du MH, Cheng HP, Zhang XG, Roitberg AE, Krause JL. Phys. Rev. Lett. 92:158301 (2004).

145. “A DFT based QM-MM Approach Designed for the Treatment of Large Molecular Systems: Application to Chorismate Mutase”. Crespo A, Damián A. Scherlis, Marti MA, Ordejón, P, Roitberg AE, and Estrin DA. Journal of Physical Chemistry B, 107:13728 -13736, 2003.

146. “Kinetic isotope effects in the active site of B.subtilis chorismate mutase” Worthington SE, Roitberg AE, Krauss M. International Journal of Quantum Chemistry, 94: 287-292 (2003).

147. “Smaller and faster: The 20-residue Trp-cage folds in 4 microseconds”. Qiu L, Pabit SA, Roitberg AE and Hagen SJ. Journal of the American Chemical Society, 124:12952-12953 (2002).

148. “4,5-Dehydrooctafluoro[2.2]paracyclophane: facile generation and extraordinary Diels¯Alder reactivity”, Battiste MA, Duan JX, Zhai YA, Ghiviriga I, Abboud KA, Roitberg AE, Shelton GR and Dolbier WR Tetrahedron Letters, 43:7047-7049 (2002).

149. “All atom structure prediction and folding simulations of a stable protein” Simmerling CL, Strockbine B and Roitberg AE. Journal of the American Chemical Society, 124:11258 –11259 (2002).

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150. “Solvent-induced symmetry breaking of nitrate ion in aqueous clusters: A QM/MM study”. González Lebrero MC, Bikiel, DE M. Elola D, Estrin DA and Roitberg AE. Journal of Chemical Physics, 117:2718-2722 (2002).

151. “Benzocycloarene hydroxylation by P450 biocatalysis”. Mayhew MP, Roitberg AE, Tewari Y, Holden MJ, Vanderah D and Vilker VL. New Journal of Chemistry, 26:35-42 (2002).

152. “Strontium clusters: many-body potential, energetics and structural transitions". Wang G, Blaisten-Barojas E, Roitberg AE, and Martin TP. Journal of Chemical Physics, 115:3640 (2001).

153. “An MD/QM study of the chorismate mutase catalyzed claisen rearrangement reaction”. Worthington SE, Roitberg AE and Krauss M. Journal of Physical Chemistry B, 105:7087-7095 (2001).

154. “Raman and FT-IR spectroscopies of fluorescein in solution”. Wang L, Roitberg AE, Meuse C and Gaigalas AK. Spectrochimica Acta A, 57:1781-91(2001).

155. “The electronic spectrum of the prephenate di-anion. An experimental and theoretical (MD/QM). comparison”. Roitberg AE, Worthington SE, Holden MJ, Mayhew MP and Krauss M. Journal of the American Chemical Society, 122:7312-7316, (2000).

156. “Molecular wire conductance: electrostatic potential spatial effects”. Mujica V, Roitberg AE and Ratner MA. Journal of Chemical Physics, 112:6834-6839 (2000).

157. “Pulsed terahertz spectroscopy of biomolecules”. Markelz AG, Roitberg AE and Heilweill. EH. Chemical Physics Letters, 320:42-48 (2000).

158. “The injecting energy at molecule/metal interfaces: implications for conductance of molecular junctions from an ab-initio molecular description”. Yaliraki SN, Roitberg AE, Gonzalez C, Mujica V and Ratner MA. Journal of Chemical Physics, 111:6997-7002 (1999).

159. “Electron transfer in molecules and molecular wires; geometry dependence, coherent transport and control”. Mujica V, Nitzan A, Mao Y, Davis W, Kemp M, Roitberg AE and Ratner MA. Advances in Chemical Physics, 107:403-429 (1999).

160. “Molecular wires: charge transport, mechanisms and control”. Ratner MA, Davis W, Kemp M, Mujica V, Roitberg AE and Yaliraki S. Annals of the New York Academy of Sciences, 852:22-36 (1998).

161. “Binding and electron transfer between putidaredoxin and cytochrome P450cam (CYP101). Theory and experiments”. Roitberg AE, Holden MJ, Mayhew M, Kurnikov I, Beratan D and Vilker V. Journal of the American Chemical Society, 120:8927-8932 (1998).

162. “A molecular dynamics study of Fe2S2 putidaredoxin. Multiple conformations of the C-terminal region”. Roitberg AE. Biophysical Journal, 73:2138-2148 (1997).

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163. “Probing the interactions of putidaredoxin with redox partners in camphor P450 5-monooxygenase by mutagenesis of surface residues”. Holden MJ, Mayhew M, Bunk D, Roitberg AE and Vilker V. Journal of Biological Chemistry. 272:21720-21725 (1997).

164. “A vibrational eigenfunction for a protein: The anharmonic Coupled-Mode Ground State of BPTI”. Roitberg AE, Gerber RB and Ratner MA. Journal of Physical Chemistry B, 101: 1700-1706 (1997).

165. “Molecular wires: resonances, staircases, rectification, bonding and speculation”. Kemp M, Mujica V, Roitberg AE, MaoY and Ratner MA. Atomic and Molecular Wires”, NATO ASI Series E. Applied Sciences, 341:203-217. C. Joachim (Ed.). Kluwer Academic Publishers (1997).

166. “Moller-Plesset perturbation theory applied to vibrational problems”. Norris L, Ratner MA, Roitberg AE and Gerber RB. Journal of Chemical Physics, 105:11261-11267 (1996).

167. “Molecular wires, extended couplings and disorder effects”. Kemp M, Roitberg AE, Wanta T, Mujica V and Ratner MA. Journal of Physical Chemistry, 100:8349-8355 (1996).

168. “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).

169. “Current-voltage characteristics of molecular wires. Eigenvalue staircase, coulomb blockade and rectification”. Mujica V, Kemp M, Roitberg AE and Ratner MA. Journal of Chemical Physics, 104:7296 (1996).

170. “Anharmonic wave functions of proteins: quantum self-consistent field calculations of BPTI”. Roitberg AE, Elber R, Gerber RB and Ratner MA. Science, 268:1319-1322 (1995).

171. “MOIL: a program for simulations of macromolecules”. Elber R, Roitberg AE, Simmerling CL, Goldstein R, Li H, Verkhiver G, Keasar C, Zhang J and Ulitsky A. Computer Physics Communications, 91:159 (1995).

172. “Resonances and interference effects on the effective electronic coupling in electron transfer”. Cheong A, Roitberg AE, Mujica V and Ratner MA. Journal of Photochemistry and Photobiology: A Chemistry, 82:81-86 (1994).

173. “A perturbed mean field approach to the decay rates of excited vibrational states in extended systems: an application to I2(Ne).n”. Roitberg AE, Gerber RB and Ratner MA. Journal of Chemical Physics, 100:4355-4366 (1994).

174. “Modeling side-chains In peptides and proteins - Application of the locally enhanced sampling and the simulated annealing methods to find minimum energy conformations.” Roitberg AE and Elber R. Journal of Chemical Physics, 95:9277-9287 (1991).

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175. “Reductive dissolution of neutron and gamma irradiated magnetite”. dos Santos Afonso M, Di Risio C, Roitberg AE, Marqués R and Blesa M. International Journal of Applied Instrumentation Part. C. Radiation in Physics and Chemistry, 36:3 (1990).

Book chapters 1. “Mixed Quantum-Classical Calculations in Biological Systems.” Seabra GM, Swails J, and Roitberg AE. Multi-scale Quantum Models for Biocatalysis: Modern Techniques and Applications. Tai-Sung Lee and Darrin M. York (editors). A volume in Challenges and Advances in Computational Chemistry and Physics, Jerzy Leszcynski (series editor). Springer Verlag. 7: 3-20 (2008)

2. “Quantifying Solvation Effects on Peptide Conformations: A QM/MM Replica Exchange Study”. Seabra GM, Walker RC and Roitberg AE. Solvation effects on molecules and biomolecules: Computational methods and applications. Sylvio Canuto (Editor). A volume in Springer Series: Challenges and Advances in Computational Chemistry and Physics, Jerzy Leszcynski (series editor). Springer Verlag. 6: 507-518 (2008)

3. “Mixed QM/MM Calculations in Biological Systems”. Seabra GM, Torras J, Walker RC, Roitberg AE. From Computational Biophysics to Systems Biology (CBSB07)., Proceedings of the NIC Workshop 2007, Ulrich H. E. Hansmann, Jan Meinke, Sandipan Mohanty, Olav Zimmermann (Editors)., John von Neumann Institute for Computing, Jülich. NIC Series, 36: 37-43 (2007).

4. “Modeling side-chains in peptides and proteins with the Locally Enhanced Sampling/simulated annealing method”. Roitberg AE and Elber R. "The Protein Folding Problem and Tertiary Structure Determination“. Editors: Merz K Jr. and Le Grand S. Birkhauser Pub. 1-41 (1994).

5. “MOIL: A molecular dynamics program with emphasis in conformational searches and reaction path calculations”. Elber R, Roitberg AE, Simmerling CL, Goldstein R, Verkhivker G, Li Y and Ulistky A. NATO ASI Series B. Physics. 325:165-191 (1994).

6. “Conformational transitions”. Czerminski R, Roitberg AE, Choi C, Ulistsky A and Elber R. AIP 239. Advances in Biomolecular Simulations 153-173. (1991).

Invited Talks (listed only since 2016) 2019 1. “The ANI family of deep learned potentials: development, application to general

computational chemistry problems, and future prospects”. September 23rd. Computational Advances in Drug Discovery. Sestri Levante. Italy.

2. “Exploring pH- and redox-dependent properties of biomolecules”. Supramolecular principles in Biological Systems”. Sept 12th. Essen, Germany

3. “Is Quantum Chemistry Amenable for Machine Learning? Are the Computers Coming for Our Jobs?” Sept 5th. Computational Chemistry seminar. Oxford, UK.

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4. “The ANI family of deep learned potentials: development, application to general computational chemistry problems, and future prospects”. September 2nd. 2nd RSC-BMCS / RSC-CICAG. Artificial Intelligence in Chemistry. Cambridge, UK.

5. “Exploring pH- and redox-dependent properties of biomolecules”. August 27th. 258th ACS National Meeting. San Diego. CA

6. “Is Quantum Chemistry Amenable for Machine Learning? Are the Computers Coming for Our Jobs? July 17. Mercury Conference. Furman University.

7. “Machine Learning in Chemistry: The end of Quantum and the rise of the machines? June 18. Progress and developments of Artificial Intelligence for Drug Design. CECAM meeting. Istituto Italiano di Tecnologia, Genoa, Italy.

8. “Neural networks learning quantum chemistry: The rise of the machines”. April 29. UIUC

9. “Neural networks learning quantum chemistry: The rise of the machines”. April 3. 257th ACS National Meeting. Orlando. FL.

10. “Vibrations as seen through a neural network potential”. April 4. 257th ACS National Meeting. Orlando. FL.

11. “Can the rules of quantum chemistry be learned? A perfect force field without a functional form”. April 2. 257th ACS National Meeting. Orlando. FL.

12. “ANAKIN-ME: Using deep learning to develop a fully-transferable and chemically accurate GPU-accelerated potential”. April 1. 257th ACS National Meeting. Orlando. FL.

13. “Machine Learning in Chemistry: The end of Quantum and the rise of the machines?”. March 18th. Boston University. Chemistry Department. Boston, MA.

14. “Machine Learning in Chemistry: The end of Quantum and the rise of the machines?”. March 6th. Open Eye CUP meeting. Santa Fe, NM

15. “Neural networks learning quantum chemistry: The rise of the machines”. February 21st. Sanibel Symposium. St Simons Island. GA

2018 16. “ANAKIN-ME: Using deep learning to develop a fully-transferable and chemically

accurate GPU-accelerated potential”. October 25th. Schrödinger Users Group Meeting. Boston, MA

17. “ANAKIN-ME: Using deep learning to develop a fully-transferable and chemically accurate GPU-accelerated potential”. October 20th. NESS 2018: Biomolecular Design and Structure Prediction. University of Connecticut. CT

18. “ANAKIN-ME: Using deep learning to develop a fully-transferable and chemically accurate GPU-accelerated potential”. October 11th. Italian Institute of Technology. Genoa, Italy.

19. “ANAKIN-ME: Using deep learning to develop a fully-transferable and chemically accurate GPU-accelerated potential”. October 9th. Artificial Intelligence in Chemical Research. Stein, Switzerland

20. “ANI strikes again. New results from a grown-up Machine learning method for organic systems”. September 28-29. The Future of Enzyme Modeling. Stockholm, Sweden

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21. “Molecular dynamics with machine learning potentials. From gas phase to solution chemistry, at low cost and high accuracy”. September 3-7th. 10th International meeting on Photodynamics and related aspects. Cartagena. Colombia.

22. “ANI strikes again. New results from a grown-up Machine learning method for organic systems” August 19-23. 256th ACS National Meeting in Boston, MA

23. “Machine Learning for chemical entities”. June 13th. East China Normal University, Shanghai, China

24. “Modeling biological systems at constant pH”. May 28th. Departmento de Quimica Biologica. FCEyN. Universidad de Buenos Aires. Buenos Aires. Argentina

25. “Desarrollo y uso de redes neuronales para estudiar reacciones químicas.” May 16th. Instituto de Calculo. FCEyN. Universidad de Buenos Aires. Buenos Aires. Argentina

26. "Active learning in chemical space for the automatic improvement of the ANI deep learned potential with an application to reaction profiles. March 19-22. 255th ACS National Meeting. New Orleans, LA

27. “Molecular dynamics with machine learning potentials. From gas phase to solution chemistry, at low cost and high accuracy”. March 19-22. 255th ACS National Meeting. New Orleans, LA

28. "Machine learning in quantum chemistry: the hype and the data. Is it time for the rise of the machines?". Feb 5th, Ohio State University, Columbus, OH

29. "Using advanced molecular dynamics to understand IM/MS data". January 27th. ASMS Sanibel meeting. Tampa, FL

2017 30. "Replica Exchange and other advanced sampling techniques". Protein Simulation

Symposium. UNAM. October 11th. Mexico City, Mexico 31. "Machine learning in quantum chemistry: the hype and the data. Is it time for the rise of

the machines?". Computational Advances in Drug Discovery. September 4th. Lausanne, Zwitzerland.

32. "Machine learning in quantum chemistry: the hype and the data. Is it time for the rise of the machines?". DE Shaw Research. June 14 New York, NY

33. "Machine learning in quantum chemistry: the hype and the data. Is it time for the rise of the machines?". Schrodinger CO. June 13 New York, NY.

34. "Conformations and protonations: A day in the life of a protein". Telluride Science Research Center. June 26-30. Telluride, CO.

35. "Machine learning in quantum chemistry: the hype and the data. Is it time for the rise of the machines?". JCUP. May 25-26. 2017. Tokyo. Japan.

36. "Machine learning in quantum chemistry: the hype and the data. Is it time for the rise of the machines?". IX Congreso Internacional de Formación y Modelación en Ciencias Básicas. 3-5 May. 2017. Medellin. Colombia.

37. "Machine learning in quantum chemistry: the hype and the data. Is it time for the rise of the machines?". NIH. April 26. 2017.

38. "Machine learning in quantum chemistry: the hype and the data. Is it time for the rise of the machines?". NSF workshop on Big Data. April 17-19. 2017. Arlington, VA

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39. "ANAKIN-ME: A general purpose and chemically accurate deep learned potential". 253rd ACS National Meeting in San Francisco, California, April 2-6. 2017.

40. "Computing with international students". Workshop on promoting undergraduate chemical and biological computing. March 9-11. New Orleans. Lousiana.

2016 41. "Pushing the envelope in Molecular Dynamics of Biological Systems: Speedups and

New Ensembles" Center for Non-Linear Sciences. Los Alamos National Laboratory. Los Alamos. New Mexico. November 2016.

42. "Cheap and Accurate Energies through Machine Learning". OpenEye co. Santa Fe. New Mexico. November 2016.

43. "Redes Neuronales aplicadas a la quimica teorica". XV reunion Mexicana de Fisico-Quimica Teorica. Merida, Mexico. November 2016.

44. "Excited state energy transfer in conjugated oligomers". University of New Mexico. Alburquerque. New Mexico. October 2016

45. "Things that move, from electrons, to protons to molecules, and what that motion says about function". Frontiers of Computational Chemistry. UNAM. Mexico City, Mexico. August 2016

46. "Extending the Range of Simulations with Constant pH Methods". Gordon Research Conference in Computational Chemistry. PGA Catalunya Business and Convention Centre. Girona, Spain. July 2017

47. "Things that move, from electrons, to protons to molecules, and what that motion says about function". Universite Pierre et Marie Curie. July 2017

48. "Enhanced sampling methods in drug design". 251th ACS National Meeting. San Diego. CA. March 2016.

49. "Constant pH simulations in biomolecular systems". 251th ACS National Meeting. San Diego. CA. March 2016.

50. “Accounting for pH effects in biomolecular dynamics and reaction mechanisms through computational approaches.". Merck Co. New Jersey. February 2016