José Richard Baptista Gomes
  Principal Researcher  
   
  phone: 234 401 423  
  extension: 24 923  
  e-mail: jrgomes@ua.pt  
  department: Chemistry  
  office: 29.3.34  
   
  group: 6 - computer simulation and multiscale modeling
 
  line: 1 - information and communication technology
 
  direct url: http://www.ciceco.ua.pt/JoseRGomes  
   
Short CV

Researcher ID
ORCID

José obtained his Ph.D. in 2000, University of Porto, in the group of Prof. JAN Ferreira Gomes. In the period 2000-2007, José was a post-doc researcher in Barcelona (Faculty of Chemistry) under supervision of Prof. F. Illas, and in the University of Porto, viz. group of Prof. MAV Ribeiro da Silva. José is a researcher at CICECO, University of Aveiro, since December 2007.

José is deeply interested in the application of computational chemistry to several different areas, such as, heterogeneous catalysis, materials science, surface science and physical organic chemistry.

José got two prizes at the Faculty of Sciences, University of Porto (Teresa da Fonseca, 1995, and Mendonça Monteiro, 1994) and has been awarded the 2010 Vicente de Seabra Medal by the Portuguese Chemical Society (SPQ).

José is the coordinator of Group 6.

Scientific Interests
Aim: To use computers and computational methods in chemistry and in materials science.
Keywords: Molecular Structure; Gas-phase thermochemistry; Reaction profiles; Adsorption (chemisorption and physisorption); Catalysis
Reactions at Interfaces: Several different computational techniques (quantum mechanical (QM), molecular mechanics (MM), QM/MM, molecular dynamics (MD) or coarse-grained (CG) simulations, docking, 3D-QSAR, microkinetic modelling, ...) are being used to analyze the interactions and reactions of adsorbates (in gaseous or in solution) with materials or enzymes. The calculations are being used to interpret experimental results obtained for heterogeneous catalysis at pure metallic, bimetallic or metal supported surfaces, to design new compounds with capability to inhibit falcipains and to understand the templated condensation of silica in the synthesis of periodic mesoporous (organo)silicas (PMO or PMS materials).



Adsorption of Gases in Porous Materials: Predictions of equilibrium adsorption and permeabilities for pure- and multi-components on porous materials (some synthesized at CICECO, e.g. PMO materials) are being obtained from grand canonical Monte Carlo (GCMC) and molecular dynamics (MD) simulations. The isotherms are compared with experimentally measured curves in order to improve the models. The idea is to find/optimize materials for gas separation (propane/propylene; CO2/CH4; ...). Density functional theory (DFT) is also being employed to analyze specific gas-substrate interactions.



Interactions of Ionic Liquids with (Bio)organics: The liquid-liquid equilibrium and solubility behaviors of mixtures of ionic liquids and (bio)organic molecules are being analyzed by density functional theory (DFT) and by molecular dynamics (MD) simulations. These studies are being conducted in collaboration with experimental work (nuclear magnetic resonance shifts, density measurements, excess volumes, etc.) performed at CICECO. The computational techniques are being employed to analyze which are the preferred interactions between the constituting species.
Scientific projects

ON-GOING

STSM Coordinator of COST Action Computational materials sciences for efficient water splitting with nanocrystals from abundant elements (CA 18234).

Co-principal Investigator of project DataCor - Smart Data to Design Corrosion Inhibitors (Compete 2020, ref. POCI-01-0145-FEDER-030256).

Team member of project Delivery vehicles of therapeutic gasotransmitters NO and H2S based on nanoporous materials (Portugal 2020, ref. PTDC/MED-QUI/28721/2017).

Principal Investigator of project SILVIA - Modeling the synthesis of silica materials via multiscale computer simulations (Programa Operacional Centro 2020, ref. CENTRO-01-0145-FEDER-31002)

 

CONCLUDED

Principal Investigator of project Modeling the synthesis of silica materials with a novel reactive coarse-grained model (RES - Red Española de Supercomputación, ref. QS-2019-2-0034).

Team member of project Dissociation mechanism of water on two-dimensional transition metal carbides (MXenes) (RES - Red Española de Supercomputación, ref. QS-2019-2-0019).

Principal Investigator of project SELMA - Unveiling the self-healing mechanisms associated with smart nanocontainers (Fundação para a Ciência e a Tecnologia, ref. PTDC/QEQ-QFI/4719/2014).

Team member of project Variable pressure solid-state NMR methods to study gas-surface interactions in nanoporous sorbent materials for industrial post/pre-combustion CO2 capture (Fundação para a Ciência e a Tecnologia, ref. PTDC/QEQ-QAN/6373/2014).

Team member of project TUBITAK - Phase transitions and ferroelectricity in self-assembled peptides nanotubes (Fundação para a Ciência e a Tecnologia, ref. TUBITAK/0006/2014).

Team member of project UNIRCELL - Unitised regenerative fuel cell for efficient renewable energy supply: from materials to device (FCT-COMPETE / Programas de Atividades Conjuntas do Portugal 2020, ref. POCI-01-0145-FEDER-016422).

Team member of project SUSPHOTOSOLUTIONS - Soluções Fotovoltaicas Sustentáveis (Programa Operacional Centro 2020, ref. CENTRO-01-0145-FEDER-000005).

Team member of project SGH - Smart Green Homes (Sistema de Incentivos à I&D Empresarial, ref. POCI-01-0247-FEDER-007678).

Participant of project CO adsorption in MXenes (European Commission - HPC-EUROPA3, ref. INFRAIA-2016-1-730897).

Team member of project FISHING - Fishing falcipain hit inhibitors from Malaria Boxes: in silico target deconvolution model development and validation (Fundação para a Ciência e a Tecnologia, ref. EXPL/QEQ-COM/0927/2013).

Principal Investigator of project CODECAT - COmputational DEsign of new CATalysts for the water gas shift reaction (Fundação para a Ciência e a Tecnologia, ref. PTDC/QUI-QUI/117439/2010).

Principal Investigator of project SILICAT - Theoretical Study of Silicate Chemistry in the Synthesis of Nanoporous Materials (Fundação para a Ciência e a Tecnologia, ref. PTDC/QUI-QUI/109914/2009).

Team member of project Development of high-resolution 1H solid-state NMR methods and applications on materials and molecules of biological interest (Fundação para a Ciência e a Tecnologia, ref. PTDC/QUI-QUI/100998/2008).

Team member of project Synthesis and Characterization of New Microporous Niobium Silicate and Titanosilica Membranes and Their Application to the Separation of Hydrogen-containing Mixtures (Fundação para a Ciência e a Tecnologia, ref. PTDC/EQU-EQU/100476/2008).

Team member of project Intelligent Design of Mesoporous Organosilicas for Adsorptive Separation Processes (Fundação para a Ciência e a Tecnologia, ref. PTDC/EQU-EQU/099423/2008).

 

Selected Publications

Full list: http://sweet.ua.pt/jrgomes/publications.html

Most recent publications:

2020

Self-Consistent Electrostatic Embedding for Liquid Phase Polarization
M. Jorge, José R. B. Gomes, Andrew W. Milne
J. Mol. Liquids, accepted for publication. []

Revisiting Tracer Liu-Silva-Macedo model for binary diffusion coefficient using the largest database of liquid and supercritical systems
B. Zêzere, I. Portugal, José R. B. Gomes, Carlos M. Silva
J. Supercrit. Fluid. , accepted for publication. []

Unveiling the local structure of 2-mercaptobenzothiazole intercalated in (Zn2Al) layered double hydroxides
G. Novell-Leruth, G. Pérez-Sánchez, T. L. P. Galvão, D. Boiba, P. Syargei, J. Carneiro, J. Tedim, José R. B. Gomes
Appl. Clay Sci., 198 (2020) 105842. [link]

First-principles calculations of the adsorption behavior of amino acids on a titanium carbide MXene
J. D. Gouveia, G. Novell-Leruth, P. Reis, F. Viñes, F.Illas, José R. B. Gomes
ACS Appl. Bio Mater., 3 (2020) 5913. [link]

Mesoscale model of the synthesis of periodic mesoporous benzene-silica
J. D. Gouveia, G. Pérez-Sánchez, S. M. Santos, A. P. Carvalho, José R. B. Gomes, M. Jorge
J. Mol. Liquids, 316 (2020) 113861. [link]

Surface Enhanced Raman Scattering Due to a Synergistic Effect in ZnS and Graphene Oxide
J. Lopes, S. Fateixa, A. Estrada, J. D. Gouveia, José R. B. Gomes, T. Trindade
J. Phys. Chem. C, 124 (2020) 12742. [link]

MXenes atomic layer stacking phase transitions and their chemical activity consequences
J. D. Gouveia, F. Viñes, F.Illas, José R. B. Gomes
Phys. Rev. Materials, 4 (2020) 054003. [link]

Facile Heterogeneously Catalyzed Nitrogen Fixation by MXenes
J. D. Gouveia, Á. Morales-García, F. Viñes, José R. B. Gomes, F. Illas
ACS Catal., 10 (2020) 5049. [link]

The Cation Effect on the Solubility of Glycylglycine and N-Acetylglycine in Aqueous Solution: Experimental and Molecular Dynamics Studies
G. Pérez-Sánchez, Y. S. Santos, O. Ferreira, J. A. P. Coutinho, José R. B. Gomes, S. P. Pinho
J. Mol. Liq., 310 (2020) 113044. [link]

Non-ionic hydrophobic eutectics - versatile solvents for tailored metal separation and valorisation
N. Schaeffer, J. H. F. Conceição, M. A. R. Martins, M. C. Neves, G. Pérez-Sánchez, José R. B. Gomes, N. Papaiconomou, J. A. P. Coutinho
Green Chem., 22 (2020) 2810. [link]

Novel insights on biomass delignification with acidic deep eutectic solvents: a mechanistic study of ß-O-4 ether bond cleavage and the role of the halide counterion on the catalytic performance
A. M. da Costa Lopes, José R. B. Gomes, J. A. P. Coutinho, A. Silvestre
Green Chem., 22 (2020) 2474. [link]

Elucidating Structure-Property Relationships in Aluminum Alloy Corrosion Inhibitors by Machine Learning
T. L. P. Galvão, G. Novell-Leuth, A. Kuznetsova, J. Tedim, José R. B. Gomes
J. Phys. Chem. C, 124 (2020) 5624. [link]
Virtual Special Issue: Machine Learning in Physical Chemistry

Cinnamic derivatives as antitubercular agents: characterization by quantitative structure-activity relationship studies
C. Teixeira, C. Ventura, José R. B. Gomes, P. Gomes, F. Martins
Molecules, 25 (2020) 456. [link]

A Computational Study of the Interaction of C2 Hydrocarbons with CuBTC
R. Afonso, J. Toda, José R. B. Gomes, M. Fischer, C. Campbell, M. Jorge
Comput. Mater. Sci., 173 (2020) 109438. [link]

The Effect of Atomic Point Charges on Adsorption Isotherms of CO2 and Water in Metal Organic Frameworks
K. Sladekova, C. Campbell, C. Grant, A. J. Fletcher, José R. B. Gomes, M. Jorge
Adsorption, 26 (2020) 663. [link]

MXenes as promising catalysts for water dissociation
J. D. Gouveia, Á. Morales-García, F. Viñes, F. Illas, José R. B. Gomes
Appl. Catal. B.: Environ., 260 (2020) 118191. [link]

Measurement of astaxanthin and squalene diffusivities in compressed liquid ethyl acetate by Taylor-Aris dispersion method
B. Zêzere, J. M. Silva, I. Portugal, José R. B. Gomes, C. M. Silva
Sep. Purif. Technol., 234 (2020) 116046. [link]

Main present collaborators
  • National:
    • Prof. Doutor João Paulo Prates Ramalho (Universidade de Évora);
    • Doutor Luís Mafra (Universidade de Aveiro);
    • Doutor Moisés Luzia Pinto (Instituto Superior Técnico);
    • Doutora Paula Ferreira (Universidade de Aveiro);
    • Prof. Doutor João Coutinho (Universidade de Aveiro);
    • Doutor João Tedim (Universidade de Aveiro);
    • Doutor Filipe Figueiredo (Universidade de Aveiro).

 

  • International:
    • Prof. Doutor Francesc Illas (Universidade de Barcelona, Espanha);
    • Doutor Francesc Viñes (Universidade de Barcelona, Espanha);
    • Doutor Miguel Jorge (Universidade de Strathclyde, Reino Unido);
    • Doutor Michael Fischer (Universidade de Bremen, Alemanha).

 

Present Research Group

Researchers:

  • Rui Vieira Afonso (Portugal) – DFT calculations on the interaction of small molecules with solid sorbents..
  • Tiago Luís Pereira Galvão (Portugal) – DFT analysis of the structure and stability of corrosion inhibitors in several substrates. Machine Learning techniques.
  • Gerard Novell-Leruth (Espanha) - DFT calculations and classical MD simulations of the interaction of corrosion inhibitors with different substrates.
  • José Daniel Gouveia (Portugal) – Molecular dynamics simulations of aqueous solutions of silicates. DFT studies of heterogeneous catalytic reactions.

 

Pre-doctoral Researchers:

  • Marcos André Carvalho (Portugal) – co-supervision with Doutor Sérgio Santos, Aveiro. Development of a reactive model for classical molecular dynamcis simulations of the synthesis of porous silica materials.

 

Ph.D. Students:

  • Manon Wilhelm (France) – co-supervision with Dr. João Tedim, Aveiro. DFT studies towards the design of novel electrocatalysts for the water splitting.
  • Mehriban Aliyeva (Azerbaijan) – co-supervision with Prof. Dr. João Coutinho, Aveiro. Molecular dynamics simulations of protein fragments in aqueous solutions.
  • Bruno Zêzere (Portugal) – co-supervision with Prof. Dr. Carlos Silva, Aveiro. Molecular dynamics simulations of the diffusion coefficients of bioactive compounds in supercritical fluids and liquids.
  • Tiago Vieites Branco Fonseca (Portugal) – co-supervision with Prof. Doutor Carlos Silva, Aveiro and com Prof. Mário Quialheiro Simões, Aveiro. Molecular dynamics simulations of the diffusion coefficients of bioactive compounds in supercritical fluids and liquids.
  • Marta Gomes Figueira de Almeida Bordonhos (Portugal) - co-supervision with Prof. Doutor Moisés Luzia Pinto, Lisboa. DFT and GCMC simulations of gas adsorption in porous materials.

 

M. Sc. Students:

  • Maria Beatriz Pedro (Portugal) – co-supervision with Dr. Cátia Teixeira, Porto. Docking and MD simulation of the intercalation of acridine derivatives in DNA.

 

Teaching Activity

Universidade do Porto

1996/97
- "Introdução à Química I", Licenciaturas de Física, de Física e Tecnologia dos Materiais e de Optoelectrónica e Lasers, Faculdade de Ciências da Universidade do Porto (experimental laboratory classes, 1 semester).

1998/99
- "Tecnologias de Informação e Comunicação", Licenciatura in Chemistry, Faculdade de Ciências da Universidade do Porto (computational laboratory classes, 1 semester).
- "Energia e Organização em Sistemas Biológicos", Licenciatura in Biochemistry, Faculdade de Ciências da Universidade do Porto (computational laboratory classes, 1 semester).

2002-2007
- Seminar (4h) “Aplicação da Química Computacional em Estudos Termoquímicos”, Licenciatura in Chemistry, Faculdade de Ciências da Universidade do Porto.

Co-authored the guide "Termoquímica: Aulas práticas (disciplina de opção do 3º ano da Licenciatura em Química)" by Maria das Dores M. C. Ribeiro da Silva and Luís M. N. B. F. Santos, José R. B. Gomes, Departamento de Química, Faculdade de Ciências da Universidade do Porto, 2005.

 

Universidade de Aveiro

2015/16
- "Bioinformática e Estrutura Molecular", Licenciaturas in Biochemistry and in Biotechnology (lectures and computational laboratory classes, 1 semester).

2016/17
- "Elementos de Química Física", 1st year students of Licenciaturas and Integrated Masters at the Universidade de Aveiro (experimental laboratory classes, 1 semester).
- "Química Geral", 1st year students of Licenciaturas and Integrated Masters at the Universidade de Aveiro (experimental laboratory classes, 1 semester).

2017/18
- "Química Geral", 1st year students of Licenciaturas and Integrated Masters at the Universidade de Aveiro (experimental laboratory classes, 1 semester).

2018/19
- "Laboratórios de Química Física / Química Orgânica", 3rd year students of of Licenciaturas and Integrated Masters of the Department of Chemistry at the Universidade de Aveiro (experimental laboratory classes, 1 semester).
- "Química Geral", 1st year students of Licenciaturas and Integrated Masters at the Universidade de Aveiro (experimental laboratory classes, 1 semester).

2019/20
- "Laboratórios de Química Física / Química Orgânica", 3rd year students of of Licenciaturas and Integrated Masters of the Department of Chemistry at the Universidade de Aveiro (experimental laboratory classes, 1 semester).
- "Modelação e Computação Científica, 4th year students of the Integrated Master in Computacional Engineering at the Universidade de Aveiro (lectures and hands-on sessions, 1 semester).
- "Química Computacional", 1st year students of the Master in Chemistry at the Universidade de Aveiro (lectures and hands-on sessions, 1 semester).

2020/21
- "Modelação e Computação Científica, 4th year students of the Integrated Master in Computacional Engineering at the Universidade de Aveiro (lectures and hands-on sessions, 1 semester).

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