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 MexicoOverall GPA: 9.86/10
- Exchange student, 1998. Education Abroad Program
University of California at Berkeley
Job history
Associate Principal 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
- Repasky, M. P.; Murphy, R. B; Banks, J. L.; Greenwood, J. R.; Tubert-Brohman, I.; Bhat, S.; Friesner, R. A. "Docking performance of the Glide program as evaluated on the
Astex and DUD datasets: a complete set of glide SP results and selected
results for a new scoring function integrating WaterMap and Glide
". J. Comput. Aid. Mol. Des.. 2012. 26. 787-799. http://dx.doi.org/10.1007/s10822-012-9575-9.
- Lutz, S.; Tubert-Brohman, I.; Yang, Y.; Meuwly, M. "Water-assisted proton transfer in ferredoxin I". J. Biol. Chem.. 2011. 286. 23679-23687. http://dx.doi.org/10.1074/jbc.M111.230003.
- 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. "Monte Carlo statistical analysis of the uncertainty of enrichment metrics
for ensemble docking". American Chemical Society 240th National Meeting. Boston, MA.. 2010.
- 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 236th National Meeting. Philadelphia, PA. (also
presented at the International Conference on Organometallic Chemistry, in Rennes, France,
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. 2005.
- 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), Python (advanced), Fortran (advanced), JavaScript (intermediate), VBA (basic), 8086 Assembler (basic), Java (basic).
Web-related technologies: HTML, XML, CSS, mod_perl, Apache.
Version Control: Git, CVS, Subversion, Perforce, VSS.
Operating systems: Linux, Irix, Windows.
Scientific software: Glide, Maestro, Gaussian, MOPAC, CHARMM, BOSS, 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
Languages
English (fluent), Spanish (native), French (basic), German (basic).
Last modified September 2007.