Ivan Tubert-Brohman - Résumé Contact Information: Ivan Tubert-Brohman Email: ivan@tubert.org URL: http://ivan.tubert.org Education: Ph. D. in Computational Chemistry, 2001-2006. Dissertation topic: The development of improved semiempirical methods; Research Advisor: William L. Jorgensen Yale University M. Sc. in Organic Chemistry, 2001-2002 Yale University B.Sc. in Chemistry, 1995-2001. Undergraduate thesis: Computer-Assisted Organic Synthesis: Development of an Educational Software Package; Thesis Advisor: José Manuel Méndez-Stivalet National Autonomous University of Mexico Overall GPA: 9.86/10 Exchange student, 1998. Education Abroad Program University of California at Berkeley Job history: Senior Scientist Schrodinger, LLC 2009-Present Research and development of computational chemistry software with applications to pharmaceutical research. Postdoctoral fellow University of Basel 2007-2008 Worked with Prof. Markus Meuwly on methods for the simulation of transition-metal catalyzed hydrogenation reactions and reactive molecular dynamics applied to proton transfer in ferredoxins. Postdoctoral fellow Harvard University 2006-2007 Worked with Prof. Alan Aspuru-Guzik on distributed computing applications for clean energy materials and quantum computing algorithms for protein folding. Honors, Fellowships, and Awards: * Marie Curie Incoming International Fellowship, The European Commission, 2007-2008 Fellowship for postdoctoral research at the University of Basel under Prof. Markus Meuwly * Richard Wolfgang Prize, Yale University, 2007 Best dissertation in Chemistry * CINF Scholarship for Scientific Excellence, ACS Division of Chemical Information, sponsored by IO Informatics, 2005 230th ACS National Meeting, Washington, DC * CCG Excellence Award, ACS Division of Computers in Chemistry and the Chemical Computing Group., 2004 227th ACS National Meeting, Anaheim, California * Gabino Barreda medal, National Autonomous University of Mexico, 2001 Given to the top student of each class * Telmex Fellowship, Telefonos de Mexico, 1997-1999 Given by the national phone company by national competition * Second place, 2nd Inter-university Math Contest (Mexico City), 1998 * Gold medal, Iberoamerican Chemistry Olympiad (Buenos Aires), 1995 * Silver medal, International Chemistry Olympiad (Beijing), 1995 * Bronze medal, International Chemistry Olympiad (Oslo), 1994 Past and current Research Interests: * Modeling of asymmetric hydrogenation reactions. Developed a force field for the simulation of iridium complexes used as catalysts for asymmetric hydrogenation reactions. * Electron-coupled proton transfer. Developed and applied a molecular-mechanics proton transfer algorithm to the electron-coupled proton transfer in Azotobacter Vinelandii Ferredoxin I. * Virtual screening. Used genetic algorithms to optimize a chemical similarity search protocol for the search of HIV non-nucleoside reverse transcriptase inhibitors. * QM/MM simulation of enzymatic reactions. Applied Monte Carlo quantum mechanical/molecular mechanical simulations to reactions catalyzed by chorismate mutase, halohalkane dehalogenase, fatty acid amide hydrolase, and artificially designed proteins. * Steric effects on acidity. Studied steric and solvent effects on pKa via density functional theory combined with Monte Carlo statistical mechanical simulations. * Semiempirical quantum molecular orbital methods. Developed improved semiempirical methods by using statistical bond and group equivalents, by modifying the core repulsion function, and by introducing orthogonalization corrections to the SCF calculation. * Computer-assisted organic synthesis. Designed and implemented a client-server Computer-Assisted Organic Synthesis system, which includes pattern recognition, a language interpreter, a graphical user interface, and a knowledge base. Publications: Tubert-Brohman, I.; Schmid, M.; Meuwly, M. "Molecular mechanics force field for octahedral organometallic compounds with inclusion of the trans influence ". J. Chem. Theory Comput.. 2009. 5. 530-539. http://dx.doi.org/10.1021/ct800392n. Perdomo, A.; Truncik, C.; Tubert-Brohman, I.; Rose, G.; Aspuru-Guzik, A. "Construction of model Hamiltonians for adiabatic quantum computation and its application to finding low energy conformations of lattice protein models". Phys. Rev. A. 2008. 78. 012320. http://dx.doi.org/10.1103/PhysRevA.78.012320. Barreiro, G.; Guimaraes, C. R. W.; Tubert-Brohman, I.; Lyons, T. M.; Tirado-Rives, J.; Jorgensen, W. L. "Search for Non-Nucleoside Inhibitors of HIV-1 Reverse Transcriptase Using Chemical Similarity, Molecular Docking, and MM-GB/SA Scoring". J. Chem. Inf. Model. 2007. 47. 2416-2428. http://dx.doi.org/10.1021/ci700271z. Tubert-Brohman, I.; Acevedo, O.; Jorgensen, W. L. "Elucidation of Hydrolysis Mechanisms for Fatty Acid Amide Hydrolase and Its Lys142Ala Variant via QM/MM Simulations.". J. Am. Chem. Soc. 2006. 128. 16904-16913. http://dx.doi.org/10.1021/ja065863s. Sattelmeyer, K.; Tubert-Brohman, I.; Jorgensen, W. L. "NO-MNDO: Reintroduction of the Overlap Matrix into MNDO". J. Chem. Theory Comput. 2006. 2. 413-419. http://dx.doi.org/10.1021/ct050174c. Tubert-Brohman, I.; Guimaraes, C. R. W.; Jorgensen, W. L. "Extension of the PDDG/PM3 Semiempirical Molecular Orbital Method to Sulfur, Silicon, and Phosphorus". J. Chem. Theory Comput. 2005. 1. 817-823. http://dx.doi.org/10.1021/ct0500287. Guimaraes, C. R. W.; Udier-Blagovic, M.; Tubert-Brohman, I.; Jorgensen, W. L. "Effects of Arg90 Neutralization on the Enzyme-Catalyzed Rearrangement of Chorismate to Prephenate". J. Chem. Theory Comput. 2005. 1. 617-625. http://dx.doi.org/10.1021/ct0500803. Tubert-Brohman, I. "Annotating CPAN". perl.com. June 2004. http://perl.com/pub/a/2005/06/30/annocpan.html. Tubert-Brohman, I. "Perl and Chemistry". The Perl Journal. June 2004. 6. 3-5. http://www.tpj.com/documents/s=9607/tpj0406/. Tubert-Brohman, I.; Guimaraes, C. R. W.; Repasky, M. P.; Jorgensen, W. L. "Extension of the PDDG/PM3 and PDDG/MNDO Semiempirical Molecular Orbital Methods to Halogens". J. Comput. Chem. 2004. 25. 138-150. http://dx.doi.org/10.1002/jcc.10356. Tubert-Brohman, I.; Talanquer, V. "Sobre adsorción. [About Adsorption.]". Educación Química. 1997. 8. 186-190. Presentations: Tubert-Brohman, I.; Schmid, M.; Meuwly, M. "A molecular mechanics force field for octahedral organometallic compounds with inclusion of the trans influence". American Chemical Society Fall National Meeting (also presented at the International Conference on Organometallic Chemistry and the Swiss Chemical Society National Meeting). 2008. Tubert-Brohman, I.; Acevedo, O.; Jorgensen, W. L. "Elucidation of Hydrolysis Mechanisms for Fatty Acid Amide Hydrolase and Its Lys142Ala Variant via QM/MM Simulations.". Swiss Chemical Society National Meeting. 2007. Tubert-Brohman, I. "Elucidation of Hydrolysis Mechanisms for Fatty Acid Amide Hydrolase and Its Lys142Ala Variant via QM/MM Simulations.". AMGEN. 2006. Tubert-Brohman, I.; Jorgensen, W. L. "Mok - A domain-specific language for molecular information processing". American Chemical Society 230th National Meeting. Washington, DC. 2004. Tubert-Brohman, I. "PDDG/PM3: an Improved Semiempirical Molecular Orbital Method.". Club Med Seminar. Yale University. 2004. Tubert-Brohman, I.; Guimaraes, C. R. W.; Jorgensen, W. L. "Improved Semiempirical Methods: Parameterization of PDDG/PM3 for Sulfur". American Chemical Society 227th National Meeting. Annaheim, CA. 2004. Tubert-Brohman, I.; Guimaraes, C. R. W.; Repasky, M. P.; Jorgensen, W. L. "PDDG/PM3 and PDDG/MNDO: Extension to the Halogens". American Chemical Society 226th National Meeting. New York. 2003. Tubert-Brohman, I.; Repasky, M. P.; Jorgensen, W. L. "Semiempirical Heats of Formation through the use of Bond and Group Equivalents--Extension to the Halogens". Third Metropolitan Area Poster Program for Graduate Students in Chemical Sciences. American Chemical Society, New York Section. 2003. Tubert-Brohman, I.; Mendez-Stivalet, J. M. "Síntesis Orgánica Asistida por Computadora: Desarrollo de un programa educativo". Congreso Nacional de Química. San Luis Potosí, Mexico. 2001. Teaching Experience: Math and Science Tutor Yale University 2004-2006 Helped the students of Yale's Calhoun College with problems in Chemistry, Physics, and Calculus. Teaching Fellow Yale University 2001-2004 Computational Chemistry (1 semester), Organic Chemistry (2 semesters), and Organic Chemistry Lab (2 semesters). Responsibilities included leading a lab and/or discussion section and grading. Teaching Assistant National Autonomous University of Mexico 2000-2001 Physical Chemistry (1 semester) and Heterocyclic Organic Chemistry (1 semester). Responsibilities included lecturing, leading a lab and a discussion section and grading. Mentor, Mexican Chemistry Olympiad National Autonomous University of Mexico 1996-2001 Participated in the training of the teams from Mexico City and Oaxaca, as well as a mentor of the national delegation to the Iberoamerican Chemistry Olympiad in Venezuela in 2000. Worked in design and grading of exams, logistics, website design and administration. Computer Skills: Languages: Perl (expert), C (advanced), Fortran (intermediate), JavaScript (intermediate), VBA (basic), 8086 Assembler (basic), Java (basic). Web-related technologies: HTML, XML, CSS, mod_perl, Apache. Version Control: CVS, Subversion, Perforce, VSS. Operating systems: Linux, Irix, Windows. Scientific software: Gaussian, MOPAC, CHARMM, BOSS, JMP, Matlab. Open Source Software Development Experience (volunteer projects): PerlMol 2003-Present Perl Modules for Computational Chemistry and Chemoinformatics. Available in CPAN; with subscribers in over 20 pharmaceutical companies. Languages used: Perl. Lines of Code (LOC, not counting whitespace, comments, or documentation: ca. 6000). AnnoCPAN 2005-Present A web application that presents the documentation for every module on CPAN and allows users to add annotations on the margin. Sponsored by a Perl Foundation grant. Languages used: Perl, JavaScript, SQL. LOC: 2000. dmoz.org 2002-2006 Developed search engines, anti-spam filters, and other tools for internal use. Languages used: Perl, C, JavaScript, SQL. LOC: 2000. OSET 2000-2001 Organic Synthesis Exploration Tool. An educational program for retrosynthetic analysis. Languages used: C, Java, JavaScript. LOC: 10,000. Affiliations: American Chemical Society 2001-Present Swiss Chemical Society 2007-Present Yale Mexican Student Organization Vice President 2004-2006 CPAN User ID: ITUB 2003-Present Languages: English (fluent), Spanish (native), French (basic), German (basic). Last modified September 2007.