Guilherme Duarte

Guilherme Duarte

Ph.D. in Chemistry, UC Irvine (2018). Interested in receptor-ligand/host-guest binding under a physical organic chemistry perspective.

Publications

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

Published in Organic & Biomolecular Chemistry, 2024

In this study, we present our findings concerning solvent effects on Biginelli-like MCRs, the mechanistic pathways of these transformations, and associated side reactions. We also advocate for a comprehensive correction of the vast existing literature on this topic.

Recommended citation: 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. http://gduarter.github.io/files/2024-Biginelli.pdf

Descriptor-Driven de Novo Design Algorithms for DOCK6 Using RDKit

Published in Journal of Chemical Information and Modeling, 2023

The primary objective of the present study is three-fold: (1) implement and validate a robust interface enabling DOCK6 to communicate with the open-source cheminformatics package RDKit,22 (2) confirm that the use of DOCK_D3N protocols leads to ligand ensembles that conform to the desired target values for the descriptors under different conditions and environments, and (3) examine ligand growth behavior using very narrow ranges for descriptors derived from clinically relevant compounds.

Recommended citation: 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. http://gduarter.github.io/files/2023-D3N.pdf

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

Published in Molecules, 2023

we describe a fundamental model proposal for the future development of lipid–peptoid-based customized drug delivery systems. This proposal was built based on the synthesis of a wide variety of peptoids with structural diversity via the Ugi reaction, followed by nanoformulations through the emulsification–evaporation process and molecular dynamics simulations.

Recommended citation: 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. http://gduarter.github.io/files/2023-Nano.pdf

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

Published in Journal of Chemical Theory and Computation, 2019

Infinite dilution activity coefficients (IDACs) express the degree of non-ideality a solution has in infinitely dilute conditions and are important parameters for chemical plant design. This paper uses solvation free energy calculations to estimate IDACs and show that they are good alternatives to solvation free energies as validation tools in Computational Chemistry.

Recommended citation: 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. http://gduarter.github.io/files/2019-IDAC.pdf

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

Published in F1000Research, 2019

The solubility of molecular crystals is a challenging physical property to predict. In this paper we discuss the efforts of estimating the solubility of molecular crystals using free energy calculations.

Recommended citation: 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. http://gduarter.github.io/files/2019-Solubility.pdf

Reproducibility of Free Energy Calculations across Different Molecular Simulation Software Packages

Published in Journal of Chemical Theory and Computation, 2018

Description of relative alchemical free energy calculations and their reproducibility accross different software.

Recommended citation: Hannes Loeffler et al. (2018). "Reproducibility of Free Energy Calculations across Different Molecular Simulation Software Packages." J. Chem. Theory Comput.. 14(11) 5567-5582. http://gduarter.github.io/files/2018-Reproducibility.pdf

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

Published in MRS Communications, 2018

Study aimed at understanding the dynamics of fatty acids found in vegetable oils in montmorillonite as a means of understanding polymer-clay nanocomposites.

Recommended citation: 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. http://gduarter.github.io/files/2018-MD_montmorillonite.pdf

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

Published in Journal of Chemical & Engineering Data, 2017

Minireview about solvation free energy calculations and update of FreeSolv, a experimental and computational free energy of solvation database.

Recommended citation: 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. http://gduarter.github.io/files/2017-FreeSolv.pdf