José R. B. Gomes

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.

Aim: Using advanced computational techniques to drive innovation in chemistry and materials science, with a focus on multiscale approaches that bridge different length and time scales.

Keywords: Molecular Structure, Gas-Phase Thermochemistry, Reaction Pathways, Adsorption (Chemisorption and Physisorption), Catalysis

Multiscale Computational Approaches

Our collaborative research efforts focus on developing and deploying computational methods that operate across various length and time scales. We utilize techniques ranging from quantum mechanical approaches, such as density functional theory (DFT), to classical atomistic and coarse-grained force field methods. These approaches allow us to study molecular systems ranging from a few atoms to several million, at different levels of detail. Our goal is to provide the computational materials science community with robust tools and molecular models that enable more realistic simulations of material properties and reveal how subtle structural changes influence these properties.

Reactions at Interfaces

We employ a range of computational methods—such as quantum mechanics (QM), molecular mechanics (MM), hybrid QM/MM approaches, molecular dynamics (MD), coarse-grained (CG) simulations, docking, and microkinetic modeling—to explore the intricate interactions and reactions of adsorbates (both in gas and solution phases) with various substrates, including inorganic and hybrid materials as well as enzymes. Our goal is to predict the potential of different substrates for applications in e.g. sensing and catalysis.

Gas Adsorption in Porous Materials

We predict equilibrium adsorption for pure and mixed gases on porous materials—including those synthesized at CICECO—using grand canonical Monte Carlo (GCMC) simulations. Our goal is to identify and optimize materials for critical gas separations, such as ethane/ethylene and CO₂/CH₄. Density functional theory (DFT) also plays a key role in analyzing the specific interactions between gases and their substrates.

Interactions of Ionic Liquids with (Bio)organics

Our research delves into the liquid-liquid equilibrium and solubility characteristics of ionic liquid mixtures with (bio)organic molecules. We utilize DFT and MD simulations to understand these complex systems. Our goal is to analyze the preferred interactions between the components of these intricate systems and to obtain data (e.g diffusivities) that are key in the design and optimization of e.g. supercritical fluid extraction processes.

Bridging Theory and Experiment

Our efforts culminate in a series of studies that shed light on the synthesis of materials, interpretation of unexpected experimental results, prediction of material properties, and selection of materials for targeted applications, including gas adsorption/separation, corrosion protection, and catalysis. By integrating these advanced computational models into practical research scenarios, we have been enabling a deeper understanding of material behavior, guiding the design and optimization of next-generation materials for diverse technological applications.

For a comprehensive account of our recent successful case studies, please refer to the review article: "Multiscale Computational Approaches Towards the Understanding of Materials" by M. Bordonhos, T. L. P. Galvão, José R. B. Gomes, J. D. Gouveia, M. Jorge, M. Lourenço, J. M. Pereira, G. Pérez-Sánchez, M. L. Pinto, C. M. Silva, J. Tedim, and B. Zêzere, published in Advanced Theory and Simulations, 6 (2023) 2200628.

ON-GOING

Co-principal investigator of project Hydrogen production via formic acid decomposition using MXenes (Rede Nacional de Computação Avançada, Call on Advanced Computing Projects (4th edition), Fundação para a Ciência e a Tecnologia, ref. 2023.10404.CPCA.A2).

Core team member of project Machine learning from computational materials science data for modelling nanocrystal catalysts (COST Innovators Grant 18234, ref. CIG18234).

Principal Investigator of project The surface chemistry of MXenes under explicit water solvent conditions (Rede Nacional de Computação Avançada, Call on Advanced Computing Projects (4th edition), Fundação para a Ciência e a Tecnologia, ref. 2024.13633.CPCA.A3).

Team member of project Exploring layered carbide-nitride systems for ammonia synthesis combining experiment and theory (KAUST, ref. ORFS-2022-CRG11-5075.2).

CONCLUDED

Principal Investigator of project ForTheShift: MXenes catalysts for the water gas shift reaction (Fundação para a Ciência e a Tecnologia, ref. 2022.02949.PTDC).

Co-principal Investigator of project MXene-based transition metal single atom catalysts for nitrogen dissociation (Rede Nacional de Computação Avançada, Call on Advanced Computing Projects (3rd edition), Fundação para a Ciência e a Tecnologia, ref. 2022.15802.CPCA.A2).

Principal Investigator of project Structural, energetic and catalytic properties of vacancy defects in MXene surfaces (Rede Nacional de Computação Avançada, Call on Advanced Computing Projects (2nd edition), Fundação para a Ciência e a Tecnologia, ref. 2021.09799.CPCA, A2 access).

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

Principal Investigator of project Structural, energetic and catalytic properties of vacancy defects in MXene surfaces (Rede Nacional de Computação Avançada, Call FCT/CPCA/2021/01, Fundação para a Ciência e a Tecnologia, ref. 2021.09799.CPCA).

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)

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).

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

Most recent publications:

2025

2024

• National:
  • Professor Carlos Manuel Silva (Universidade de Aveiro);
  • Professor Moisés Luzia Pinto (Instituto Superior Técnico);
  • Professor João Tedim (Universidade de Aveiro).

• International:
  • Professor Francesc Illas (Universidade de Barcelona, Spain);
  • Professor Francesc Viñes (Universidade de Barcelona, Spain);
  • Professor Miguel Jorge (Universidade de Strathclyde, UK).

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.

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).