Curriculum Vitae

Education

• Ph.D in Chemistry, University of California, Irvine, 2018

  • Thesis Topics: hydration and solvation free energies of small organic molecules of pharmacological interest; prediction of solubility of molecular solids from absolute free energy calculations; reproducibility of relative hydration calculations across different software; use of infinite dilution activity coefficients as alternative parameters for force field and method development.

  • Adviser: David L. Mobley

• M.S. in Chemistry, Universidade de Brasília, 2013

  • Dissertation Topic: use of conceptual DFT and molecular fingerprints obtained from ab initio calculations to predict reaction paths to understand the reactivity of ambidented nucleofiles.

  • Advisers: Fernando C. Rangel and Kleber C. Mundim

• B.S. in Chemistry, Universidade de Brasília, 2011

Work experience

• 2021-Present: Visiting Scholar

  • Department of Applied Mathematics and Statistics, SUNY Stony Brook

  • Duties included: Development and resting of DOCK6’s descriptor-driven de novo design algorithm.

• 2022-Present: Voluntary Professor

  • Instituto de Química, Universidade de Brasília (UnB).

  • Duties included: Joined the LMSC (Laboratório de Modelagem de Sistemas Complexos) to assist the design NLO materials and to continue my personal research on 5-HT receptors. Taught IQD1010.

• 2019-2021: Postdoctoral Fellow

  • Department of Applied Mathematics and Statistics, SUNY Stony Brook.

  • Duties included: The Rizzo Lab works with protein-ligand docking and with the development of the DOCK6 software. Design of drugs targeting the 6-HB subdomain of the SARS-CoV-2 spike protein. Implementation of descriptor-driven de novo design methodology using an RDKit interface with DOCK6. Directly mentored two graduate students, Steven Pak and Christopher Corbo (2020-2021). Assisted in mentoring two senior graduate students, Lauren Prentis and John Bickel (2019-2021). Taught AMS 535 and AMS 536.
  • Supervisor: Prof. Robert C. Rizzo

• 2013-2018: Research Assistant

  • Department of Chemistry, University of California, Irvine.

  • Duties included: Worked with free energy calculations in systems of pharmacological interest – solvation free energies of small organic molecules and solubility prediction from absolute chemical potentials of molecular solids and their solution phases. Innovated by using infinite dilution activity coefficients as alternatives to hydration free energies as method validation tools. Curated and updated FreeSolv, the hydration free energy database, with the addition of hydration enthalpies and entropies. Mentored two undergraduate students, Daisy Y. Kyu (2015-2016), Nam Thi (2016). Taught CHEM H2LA, H2LB, 138, 1LC and PHARMSCI 170B.
  • Supervisor: Professor David L. Mobley

• 2013: Independent Scientific Consultant

  • Consulted for the work published by F. A. R. Silva and E. R. Maia on polymer-clay nanocomposites.

Certifications

• 2018: Improv for Teaching, U. C. Irvine (10h)
• 2018: Activate to Captivate, U. C. Irvine (16h)
• 2017: Fundamentals of Business Analysis, U. C. Irvine (25h)
• 2016: Principles of Financial Analysis, U. C. Irvine (30h)
• 2016: The Business of Science: Core Professional Skills, SciPhD Certificate Program (40h)
• 2010: Nuclear Magnetic Resonance: theory and practice, NMR Users Association (AUREMN) (72h)
• 2008: C/C++, Universidade de Brasília (21h)

Publications

Approaches for Calculating Solvation Free Energies and Enthalpies Demonstrated with an Update of the FreeSolv Database

G. Duarte Ramos Matos, et al. (2017). "Approaches for Calculating Solvation Free Energies and Enthalpies Demonstrated with an Update of the FreeSolv Database." J. Chem. Eng. Data. 62 (5) 1559-1569.

Molecular dynamics simulations of montmorillonite reinforcing amylose plasticized by Brazilian Cerrado oils: polymer-clay nanocomposite

F. A. R. Silva, M. J. A. Sales, M. Ghoul, L. Chebil, G. Duarte Ramos Matos, E. R. Maia (2018). "Molecular dynamics simulations of montmorillonite reinforcing amylose plasticized by Brazilian Cerrado oils: polymer-clay nanocomposite." MRS Communications. 8, 266-274.

Reproducibility of Free Energy Calculations across Different Molecular Simulation Software Packages

Hannes Loeffler et al. (2018). "Reproducibility of Free Energy Calculations across Different Molecular Simulation Software Packages." J. Chem. Theory Comput.. 14(11) 5567-5582.

Challenges in the use of atomistic simulations to predict solubilities of drug-like molecules

G. Duarte Ramos Matos, D. L. Mobley (2019). "Challenges in the use of atomistic simulations to predict solubilities of drug-like molecules." F1000Research. 7:686.

Challenges in the use of atomistic simulations to predict solubilities of drug-like molecules

G. Duarte Ramos Matos et al. (2019). "Infinite Dilution Activity Coefficients as Constraints for Force Field Parametrization and Method Development." J. Chem. Theory Comput.. 15 (5), 3066-3074.

Rational Design and Multicomponent Synthesis of Lipid–Peptoid Nanocomposites towards a Customized Drug Delivery System Assembly

T. P. F. Rosalba, G. Duarte Ramos Matos, C. E. M. Salvador, C. K. Z. Andrade (2023). "Rational Design and Multicomponent Synthesis of Lipid–Peptoid Nanocomposites towards a Customized Drug Delivery System Assembly." Molecules. 28, 5725.

Descriptor-Driven de Novo Design Algorithms for DOCK6 Using RDKit

G. Duarte Ramos Matos, S. Pak, R. C. Rizzo (2023). "Descriptor-Driven de Novo Design Algorithms for DOCK6 Using RDKit." J. Chem. Inf. Model.. 63, 5803-5822.

Revisiting Biginelli-like reactions: solvent effects, mechanisms, biological applications and correction of several literature reports

P. S. Beck, A. G. Leitão, Y. B. Santana, J. R. Correa, C. V. S. Rodrigues, D. F. S. Machado, G. Duarte Ramos Matos, L. M. Ramos, C. C. Gatto, S. C. C. Oliveira, C. K. Z. Andrade, B. A. D. Neto (2024). "Revisiting Biginelli-like reactions: solvent effects, mechanisms, biological applications and correction of several literature reports." Org. Biomol. Chem.. 22, 3630.

Teaching

Honors and Majors General Chemistry Lab A (CHEM H2LA/M2LA)

Honors and Majors General Chemistry Lab B (CHEM H2LB/M2LB)

Molecular Pharmacology II (PHARMSCI 170B)

Introduction to Computational Organic Chemistry (CHEM 138)

General Chemistry Lab C (CHEM 1LC)

Molecular Modeling of Biological Molecules (AMS 536)

Introduction to Computational Structural Biology and Drug Design (AMS 535)

Chemical Thermodynamics (IQD 0101)

Introduction to Modern Chemistry (IQD 0191)

Service and leadership

• 2010-2012: Academic Council Member of the Institute of Chemistry, Universidade de Brasília, Brasília, Brazil.
• 2008-2011: Fellow of the Programa de Educação Tutorial (PET) of the Ministry of Education of the Federal Republic of Brazil.

Honors, Awards and Fellowships

• 2019: Top Writer, Quora
• 2013-2017: Science without Borders Scholarship
• 2011-2013: CNPq M. Sc. Scholarship
• 2008-2011: Fellow of the Programa de Educação Tutorial (PET) of the Ministry of Education of the Federal Republic of Brazil.
• 2006-2007: Gold medal in the 5th and 6th Regional Chemistry Olympiad in Brasília, Brazil.

Skills

• Alchemical Free Energy Calculations
• Molecular Dynamics and Monte Carlo simulations
• Protein-Ligand Docking
• Computational Physical Organic Chemistry
• Science communication
• Programming languages:
  • C++, Python, Shell scripting, LaTeX
• Computational Chemistry software:
  • GROMACS, DOCK6, RDKit, Ambertools, OpenMM, Psi4, Spartan, Gaussian, GAMESS

Non-Academic Interests

• World History and Classical Art.
• Language learning.
• Financial Engineering.
• Cooking.