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Sacramento MMA, Oliveira MB, Gomes JRB, Borges J, Freedman BR, Mooney DJ, Rodrigues JMM, Mano JF. Natural Polymer-Polyphenol Bioadhesive Coacervate with Stable Wet Adhesion, Antibacterial Activity, and On-Demand Detachment. Adv Healthc Mater 2024:e2304587. [PMID: 38334308 DOI: 10.1002/adhm.202304587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/02/2024] [Indexed: 02/10/2024]
Abstract
Medical adhesives are emerging as an important clinical tool as adjuvants for sutures and staples in wound closure and healing and in the achievement of hemostasis. However, clinical adhesives combining cytocompatibility, as well as strong and stable adhesion in physiological conditions, are still in demand. Herein, a mussel-inspired strategy is explored to produce adhesive coacervates using tannic acid (TA) and methacrylate pullulan (PUL-MA). TA|PUL-MA coacervates mainly comprise van der Waals forces and hydrophobic interactions. The methacrylic groups in the PUL backbone increase the number of interactions in the adhesives matrix, resulting in enhanced cohesion and adhesion strength (72.7 Jm-2 ), compared to the non-methacrylated coacervate. The adhesive properties are kept in physiologic-mimetic solutions (72.8 Jm-2 ) for 72 h. The photopolymerization of TA|PUL-MA enables the on-demand detachment of the adhesive. The poor cytocompatibility associated with the use of phenolic groups is here circumvented by mixing reactive oxygen species-degrading enzyme in the adhesive coacervate. This addition does not hamper the adhesive character of the materials, nor their anti-microbial or hemostatic properties. This affordable and straightforward methodology, together with the tailorable adhesivity even in wet environments, high cytocompatibility, and anti-bacterial activity, enables foresee TA|PUL-MA as a promising ready-to-use bioadhesive for biomedical applications.
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Affiliation(s)
- Margarida M A Sacramento
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, Aveiro, 3810-193, Portugal
| | - Mariana B Oliveira
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, Aveiro, 3810-193, Portugal
| | - José R B Gomes
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, Aveiro, 3810-193, Portugal
| | - João Borges
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, Aveiro, 3810-193, Portugal
| | - Benjamin R Freedman
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, 02138, USA
- Department of Orthopaedic Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - David J Mooney
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, 02138, USA
| | - João M M Rodrigues
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, Aveiro, 3810-193, Portugal
| | - João F Mano
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, Aveiro, 3810-193, Portugal
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2
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Zêzere B, Fonseca TVB, Portugal I, Simões MMQ, Silva CM, Gomes JRB. Influence of Ethanol Parametrization on Diffusion Coefficients Using OPLS-AA Force Field. Int J Mol Sci 2023; 24:ijms24087316. [PMID: 37108479 PMCID: PMC10138630 DOI: 10.3390/ijms24087316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 04/03/2023] [Accepted: 04/08/2023] [Indexed: 04/29/2023] Open
Abstract
Molecular dynamics simulations employing the all-atom optimized potential for liquid simulations (OPLS-AA) force field were performed for determining self-diffusion coefficients (D11) of ethanol and tracer diffusion coefficients (D12) of solutes in ethanol at several temperature and pressure conditions. For simulations employing the original OPLS-AA diameter of ethanol's oxygen atom (σOH), calculated and experimental diffusivities of protic solutes differed by more than 25%. To correct this behavior, the σOH was reoptimized using the experimental D12 of quercetin and of gallic acid in liquid ethanol as benchmarks. A substantial improvement of the calculated diffusivities was found by changing σOH from its original value (0.312 nm) to 0.306 nm, with average absolute relative deviations (AARD) of 3.71% and 4.59% for quercetin and gallic acid, respectively. The new σOH value was further tested by computing D12 of ibuprofen and butan-1-ol in liquid ethanol with AARDs of 1.55% and 4.81%, respectively. A significant improvement was also obtained for the D11 of ethanol with AARD = 3.51%. It was also demonstrated that in the case of diffusion coefficients of non-polar solutes in ethanol, the original σOH=0.312 nm should be used for better agreement with experiment. If equilibrium properties such as enthalpy of vaporization and density are estimated, the original diameter should be once again adopted.
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Affiliation(s)
- Bruno Zêzere
- CICECO-Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Tiago V B Fonseca
- CICECO-Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Inês Portugal
- CICECO-Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Mário M Q Simões
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Carlos M Silva
- CICECO-Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - José R B Gomes
- CICECO-Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
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3
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Bordonhos M, Galvão TLP, Gomes JRB, Gouveia JD, Jorge M, Lourenço MAO, Pereira JM, Pérez‐Sánchez G, Pinto ML, Silva CM, Tedim J, Zêzere B. Multiscale Computational Approaches toward the Understanding of Materials. Advcd Theory and Sims 2022. [DOI: 10.1002/adts.202200628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marta Bordonhos
- CICECO ‐ Aveiro Institute of Materials Department of Chemistry University of Aveiro Campus Universitário de Santiago Aveiro 3810‐193 Portugal
- CERENA, Department of Chemical Engineering Instituto Superior Técnico University of Lisbon Avenida Rovisco Pais, No. 1 Lisbon 1049‐001 Portugal
| | - Tiago L. P. Galvão
- CICECO ‐ Aveiro Institute of Materials Department of Materials and Ceramic Engineering University of Aveiro Campus Universitário de Santiago Aveiro 3810‐193 Portugal
| | - José R. B. Gomes
- CICECO ‐ Aveiro Institute of Materials Department of Chemistry University of Aveiro Campus Universitário de Santiago Aveiro 3810‐193 Portugal
| | - José D. Gouveia
- CICECO ‐ Aveiro Institute of Materials Department of Chemistry University of Aveiro Campus Universitário de Santiago Aveiro 3810‐193 Portugal
| | - Miguel Jorge
- Department of Chemical and Process Engineering University of Strathclyde 75 Montrose Street Glasgow G1 1XJ UK
| | - Mirtha A. O. Lourenço
- CICECO ‐ Aveiro Institute of Materials Department of Chemistry University of Aveiro Campus Universitário de Santiago Aveiro 3810‐193 Portugal
| | - José M. Pereira
- CICECO ‐ Aveiro Institute of Materials Department of Chemistry University of Aveiro Campus Universitário de Santiago Aveiro 3810‐193 Portugal
| | - Germán Pérez‐Sánchez
- CICECO ‐ Aveiro Institute of Materials Department of Chemistry University of Aveiro Campus Universitário de Santiago Aveiro 3810‐193 Portugal
| | - Moisés L. Pinto
- CERENA, Department of Chemical Engineering Instituto Superior Técnico University of Lisbon Avenida Rovisco Pais, No. 1 Lisbon 1049‐001 Portugal
| | - Carlos M. Silva
- CICECO ‐ Aveiro Institute of Materials Department of Chemistry University of Aveiro Campus Universitário de Santiago Aveiro 3810‐193 Portugal
| | - João Tedim
- CICECO ‐ Aveiro Institute of Materials Department of Materials and Ceramic Engineering University of Aveiro Campus Universitário de Santiago Aveiro 3810‐193 Portugal
| | - Bruno Zêzere
- CICECO ‐ Aveiro Institute of Materials Department of Chemistry University of Aveiro Campus Universitário de Santiago Aveiro 3810‐193 Portugal
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Tedim J, Galvão TLP, Yasakau KA, Bastos A, Gomes JRB, Ferreira MGS. Layered double hydroxides for corrosion-related applications—Main developments from 20 years of research at CICECO. Front Chem 2022; 10:1048313. [DOI: 10.3389/fchem.2022.1048313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 10/25/2022] [Indexed: 11/19/2022] Open
Abstract
This work describes the main advances carried out in the field of corrosion protection using layered double hydroxides (LDH), both as additive/pigment-based systems in organic coatings and as conversion films/pre-treatments. In the context of the research topic “Celebrating 20 years of CICECO”, the main works reported herein are based on SECOP’s group (CICECO) main advances over the years. More specifically, this review describes structure and properties of LDH, delving into the corrosion field with description of pioneering works, use of LDH as additives to organic coatings, conversion layers, application in reinforced concrete and corrosion detection, and environmental impact of these materials. Moreover, the use of computational tools for the design of LDH materials and understanding of ion-exchange reactions is also presented. The review ends with a critical analysis of the field and future perspectives on the use of LDH for corrosion protection. From the work carried out LDH seem very tenable, versatile, and advantageous for corrosion protection applications, although several obstacles will have to be overcome before their use become commonplace.
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Novell Leruth G, Kuznetsova A, Tedim J, Gomes JRB, Galvão TLP. Molecular Dynamics Model to Explore the Initial Stages of Anion Exchange involving Layered Double Hydroxide Particles. Nanomaterials (Basel) 2022; 12:4039. [PMID: 36432324 PMCID: PMC9695576 DOI: 10.3390/nano12224039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/10/2022] [Accepted: 11/14/2022] [Indexed: 06/16/2023]
Abstract
A classical molecular dynamics (MD) model of fully unconstrained layered double hydroxide (LDH) particles in aqueous NaCl solution was developed to explore the initial stages of the anion exchange process, a key feature of LDHs for their application in different fields. In particular, this study focuses on the active corrosion protection mechanism, where LDHs are able to entrap aggressive species from the solution while releasing fewer corrosive species or even corrosion inhibitors. With this purpose in mind, it was explored the release kinetics of the delivery of nitrate and 2-mercaptobenzothiazole (MBT, a typical corrosion inhibitor) from layered double hydroxide particles triggered by the presence of aggressive chloride anions in solution. It was shown that the delamination of the cationic layers occurs during the anion exchange process, which is especially evident in the case of MBT-.
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Affiliation(s)
- Gerard Novell Leruth
- CICECO-Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
- CICECO-Aveiro Institute of Materials, Department of Materials and Ceramic Engineering, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Alena Kuznetsova
- CICECO-Aveiro Institute of Materials, Department of Materials and Ceramic Engineering, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
- Smallmatek—Small Materials and Technologies Lda., Rua dos Canhas, 3810-075 Aveiro, Portugal
| | - João Tedim
- CICECO-Aveiro Institute of Materials, Department of Materials and Ceramic Engineering, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - José R. B. Gomes
- CICECO-Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Tiago L. P. Galvão
- CICECO-Aveiro Institute of Materials, Department of Materials and Ceramic Engineering, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
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Zêzere B, Portugal I, Gomes JRB, Silva CM. Modeling Tracer Diffusion Coefficients of Any Type of Solutes in Polar and Non-Polar Dense Solvents. Materials (Basel) 2022; 15:ma15186416. [PMID: 36143725 PMCID: PMC9502877 DOI: 10.3390/ma15186416] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 05/13/2023]
Abstract
In this work, a simple two-parameters correlation based on the Rice and Gray, Lennard-Jones, and Stockmayer theories was devised for the calculation of binary diffusion coefficients (D12) of any type of solutes at infinite dilution in polar and non-polar solvents. This equation can be relevant for systems with polar solvents, since most models in the literature fail when strong intermolecular forces predominate in solution. The new correlation embodies the Stockmayer potential without requiring the dipole moments of any component, which significantly enlarges its application. It was validated with the largest D12 database of polar and non-polar dense systems, with 8812 data points (NDP) spanning 553 systems, of which 133 have water as solvent (NDP = 1266), 89 contain polar solvents excluding water (NDP = 1405), 177 have supercritical carbon dioxide (SC-CO2) as solvent (NDP = 5028), and 154 have non-polar or weakly polar solvents excluding SC-CO2 (NDP = 1113). Overall, the model achieved an average deviation of only 3.43%, with accurate and unbiased behavior even for polar systems.
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Zêzere B, Buchgeister S, Faria S, Portugal I, R. B. Gomes J, Manuel Silva C. Diffusivities of linear unsaturated ketones and aldehydes in compressed liquid ethanol. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Aliyeva M, Brandão P, Gomes JRB, Coutinho JA, Ferreira O, Pinho SP. Solubilities of Amino Acids in Aqueous Solutions of Chloride or Nitrate Salts of Divalent (Mg 2+ or Ca 2+) Cations. J Chem Eng Data 2022; 67:1565-1572. [PMID: 36568723 PMCID: PMC9777878 DOI: 10.1021/acs.jced.2c00148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The solubilities of glycine, l-leucine, l-phenylalanine, and l-aspartic acid were measured in aqueous MgCl2, Mg(NO3)2, CaCl2,, and Ca(NO3)2 solutions with concentrations ranging from 0 to 2 mol/kg at 298.2 K. The isothermal analytical method was used combined with the refractive index measurements for composition analysis guaranteeing good accuracy. All salts induced a salting-in effect with a higher magnitude for those containing the Ca2+ cation. The nitrate anions also showed stronger binding with the amino acids, thus increasing their relative solubility more than the chloride anions. In particular, calcium nitrate induces an increase in the amino acid solubility from 2.4 (glycine) to 4.6 fold (l-aspartic acid) compared to the corresponding value in water. Amino acid solubility data in aqueous MgCl2 and CaCl2 solutions collected from the open literature were combined with that from this work, allowing us to analyze the relations between the amino acid structure and the salting-in magnitude.
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Affiliation(s)
- Mehriban Aliyeva
- Centro
de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
- CICECO
− Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Paula Brandão
- CICECO
− Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - José R. B. Gomes
- CICECO
− Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - João A.
P. Coutinho
- CICECO
− Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Olga Ferreira
- Centro
de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
| | - Simão P. Pinho
- Centro
de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
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Aliyeva M, Brandão P, Gomes JRB, Coutinho JAP, Ferreira O, Pinho SP. Electrolyte Effects on the Amino Acid Solubility in Water: Solubilities of Glycine, l-Leucine, l-Phenylalanine, and l-Aspartic Acid in Salt Solutions of (Na +, K +, NH 4+)/(Cl –, NO 3–). Ind Eng Chem Res 2022. [DOI: 10.1021/acs.iecr.1c04562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Mehriban Aliyeva
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
- CICECO − Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Paula Brandão
- CICECO − Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - José R. B. Gomes
- CICECO − Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - João A. P. Coutinho
- CICECO − Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Olga Ferreira
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
| | - Simão P. Pinho
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
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Thomas JA, Zubi A, Alnafisah HA, Turega S, Marques I, Gomes JRB, Félix V. Being positive is not everything - experimental and computational studies on the selectivity of a self-assembled, multiple redox-state, receptor that binds anions with up to picomolar affinities. Chemistry 2021; 28:e202102465. [PMID: 34755915 DOI: 10.1002/chem.202102465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Indexed: 11/06/2022]
Abstract
The interaction of the self-assembled trinuclear ruthenium bowl 1 3+ , that displays three other accessible oxidation states, with oxo-anions is investigated. Using a combination of NMR and electrochemical experimental data, estimates of the binding affinities of 1 4+ , 1 5+ , and 1 6+ for both halide and oxo-anions were derived. This analysis revealed that, across the range of oxidation states of the host, both high anion binding affinities (>10 9 M -1 for specific guests bound to 1 6+ ) and high selectivities (a range of >10 7 M -1 ) were observed. As the crystal structure of binding of the hexafluorophosphate anion revealed that the host has two potential binding sites (named the α and β pockets), the host-guest properties of both putative binding sites of the bowl, in all of its four oxidation states, were investigated through detailed quantum-based computational studies. These studies revealed that, due to the interplay of electrostatically assisted hydrogen-bonding and anion-π interactions, binding to the α pocket is generally preferred, except for the case of the relatively large and lipophilic hexafluorophosphate anionic guest and the host in the highest oxidation states, where the β pocket becomes relatively favourable. This analysis confirms that host-guest interactions involving structurally complex supramolecular architectures are driven by a combination of non-covalent interactions and, even in the case of charged binding pairs, electrostatics alone cannot accurately define these recognition processes.
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Affiliation(s)
- Jim Antony Thomas
- University of Sheffiled, Department of Chemistry, Brook Hill, S3 7HF, Sheffield, UNITED KINGDOM
| | - Ahmed Zubi
- The University of Sheffield, Chemistry, UNITED KINGDOM
| | | | - Simon Turega
- Sheffield Hallam University, Chemistry, UNITED KINGDOM
| | - Igor Marques
- University of Aveiro CICECO: Universidade de Aveiro CICECO, Chemistry, PORTUGAL
| | - José R B Gomes
- Centro de Investigação em Materiais Cerâmicos e Compósitos: Universidade de Aveiro CICECO, Chemistry, PORTUGAL
| | - Vítor Félix
- University of Aveiro CICECO: Universidade de Aveiro CICECO, Chemistry, PORTUGAL
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Affiliation(s)
- Raul Morales-Salvador
- Departament de Ciència de Materials i Química Física & Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, c/Martí i Franquès 1-11, 08028 Barcelona, Spain
| | - José D. Gouveia
- CICECO─Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Ángel Morales-García
- Departament de Ciència de Materials i Química Física & Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, c/Martí i Franquès 1-11, 08028 Barcelona, Spain
| | - Francesc Viñes
- Departament de Ciència de Materials i Química Física & Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, c/Martí i Franquès 1-11, 08028 Barcelona, Spain
| | - José R. B. Gomes
- CICECO─Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Francesc Illas
- Departament de Ciència de Materials i Química Física & Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, c/Martí i Franquès 1-11, 08028 Barcelona, Spain
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Morales‐García Á, Viñes F, Gomes JRB, Illas F. Concepts, models, and methods in computational heterogeneous catalysis illustrated through
CO
2
conversion. WIREs Comput Mol Sci 2021. [DOI: 10.1002/wcms.1530] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Ángel Morales‐García
- Departament de Ciència de Materials i Química Física & Institut de Química Teòrica i Computacional (IQTCUB) Universitat de Barcelona Barcelona Spain
| | - Francesc Viñes
- Departament de Ciència de Materials i Química Física & Institut de Química Teòrica i Computacional (IQTCUB) Universitat de Barcelona Barcelona Spain
| | - José R. B. Gomes
- CICECO—Aveiro Institute of Materials, Department of Chemistry University of Aveiro Aveiro Portugal
| | - Francesc Illas
- Departament de Ciència de Materials i Química Física & Institut de Química Teòrica i Computacional (IQTCUB) Universitat de Barcelona Barcelona Spain
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Sardo M, Afonso R, Juźków J, Pacheco M, Bordonhos M, Pinto ML, Gomes JRB, Mafra L. Unravelling moisture-induced CO 2 chemisorption mechanisms in amine-modified sorbents at the molecular scale. J Mater Chem A Mater 2021; 9:5542-5555. [PMID: 34671479 PMCID: PMC8459418 DOI: 10.1039/d0ta09808f] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 01/08/2021] [Indexed: 05/03/2023]
Abstract
This work entails a comprehensive solid-state NMR and computational study of the influence of water and CO2 partial pressures on the CO2-adducts formed in amine-grafted silica sorbents. Our approach provides atomic level insights on hypothesised mechanisms for CO2 capture under dry and wet conditions in a tightly controlled atmosphere. The method used for sample preparation avoids the use of liquid water slurries, as performed in previous studies, enabling a molecular level understanding, by NMR, of the influence of controlled amounts of water vapor (down to ca. 0.7 kPa) in CO2 chemisorption processes. Details on the formation mechanism of moisture-induced CO2 species are provided aiming to study CO2 : H2O binary mixtures in amine-grafted silica sorbents. The interconversion between distinct chemisorbed CO2 species was quantitatively monitored by NMR under wet and dry conditions in silica sorbents grafted with amines possessing distinct bulkiness (primary and tertiary). Particular attention was given to two distinct carbonyl environments resonating at δ C ∼161 and 155 ppm, as their presence and relative intensities are greatly affected by moisture depending on the experimental conditions. 1D and 2D NMR spectral assignments of both these 13C resonances were assisted by density functional theory calculations of 1H and 13C chemical shifts on model structures of alkylamines grafted onto the silica surface that validated various hydrogen-bonded CO2 species that may occur upon formation of bicarbonate, carbamic acid and alkylammonium carbamate ion pairs. Water is a key component in flue gas streams, playing a major role in CO2 speciation, and this work extends the current knowledge on chemisorbed CO2 structures and their stabilities under dry/wet conditions, on amine-modified solid surfaces.
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Affiliation(s)
- Mariana Sardo
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago 3810-193 Aveiro Portugal
| | - Rui Afonso
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago 3810-193 Aveiro Portugal
| | - Joanna Juźków
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago 3810-193 Aveiro Portugal
| | - Marlene Pacheco
- CERENA, Instituto Superior Técnico, University of Lisbon Av. Rovisco Pais 1049-001 Lisboa Portugal
| | - Marta Bordonhos
- CERENA, Instituto Superior Técnico, University of Lisbon Av. Rovisco Pais 1049-001 Lisboa Portugal
| | - Moisés L Pinto
- CERENA, Instituto Superior Técnico, University of Lisbon Av. Rovisco Pais 1049-001 Lisboa Portugal
| | - José R B Gomes
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago 3810-193 Aveiro Portugal
| | - Luís Mafra
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago 3810-193 Aveiro Portugal
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14
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Sladekova K, Campbell C, Grant C, Fletcher AJ, Gomes JRB, Jorge M. Correction to: The effect of atomic point charges on adsorption isotherms of CO2 and water in metal organic frameworks. ADSORPTION 2021. [DOI: 10.1007/s10450-021-00301-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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15
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Vilela SMF, Navarro JAR, Barbosa P, Mendes RF, Pérez-Sánchez G, Nowell H, Ananias D, Figueiredo F, Gomes JRB, Tomé JPC, Paz FAA. Multifunctionality in an Ion-Exchanged Porous Metal–Organic Framework. J Am Chem Soc 2021; 143:1365-1376. [DOI: 10.1021/jacs.0c10421] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sérgio M. F. Vilela
- Department of Chemistry, CICECO−Aveiro Institute of Materials, University of Aveiro, 3810-193 Aveiro, Portugal
- Department of Chemistry, LAQV-REQUIMTE, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Jorge A. R. Navarro
- Department of Inorganic Chemistry, University of Granada, 18071 Granada, Spain
| | - Paula Barbosa
- Department of Materials & Ceramic Engineering, CICECO−Aveiro Institute of Materials, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Ricardo F. Mendes
- Department of Chemistry, CICECO−Aveiro Institute of Materials, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Germán Pérez-Sánchez
- Department of Chemistry, CICECO−Aveiro Institute of Materials, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Harriott Nowell
- Diamond Light Source, Didcot OX11 0DE, Oxfordshire, United Kingdom
| | - Duarte Ananias
- Department of Chemistry, CICECO−Aveiro Institute of Materials, University of Aveiro, 3810-193 Aveiro, Portugal
- Department of Physics, CICECO−Aveiro Institute of Materials, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Filipe Figueiredo
- Department of Materials & Ceramic Engineering, CICECO−Aveiro Institute of Materials, University of Aveiro, 3810-193 Aveiro, Portugal
| | - José R. B. Gomes
- Department of Chemistry, CICECO−Aveiro Institute of Materials, University of Aveiro, 3810-193 Aveiro, Portugal
| | - João P. C. Tomé
- Departamento de Engenharia Química, Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal
| | - Filipe A. Almeida Paz
- Department of Chemistry, CICECO−Aveiro Institute of Materials, University of Aveiro, 3810-193 Aveiro, Portugal
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16
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Gouveia JD, Novell-Leruth G, Reis PMLS, Viñes F, Illas F, Gomes JRB. First-Principles Calculations on the Adsorption Behavior of Amino Acids on a Titanium Carbide MXene. ACS Appl Bio Mater 2020; 3:5913-5921. [DOI: 10.1021/acsabm.0c00621] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- José D. Gouveia
- Department of Chemistry, CICECO—Aveiro Institute of Materials, University of Aveiro, Campus Universitário de Santiago, Aveiro 3810-193, Portugal
| | - Gerard Novell-Leruth
- Department of Chemistry, CICECO—Aveiro Institute of Materials, University of Aveiro, Campus Universitário de Santiago, Aveiro 3810-193, Portugal
| | - Pedro M. L. S. Reis
- Department of Chemistry, CICECO—Aveiro Institute of Materials, University of Aveiro, Campus Universitário de Santiago, Aveiro 3810-193, Portugal
| | - Francesc Viñes
- Departament de Ciència de Materials i Quı́mica Fı́sica & Institut de Quı́mica Teòrica i Computacional (IQTCUB), Universitat de Barcelona, c/Martı́ i Franqués 1, 08028 Barcelona, Spain
| | - Francesc Illas
- Departament de Ciència de Materials i Quı́mica Fı́sica & Institut de Quı́mica Teòrica i Computacional (IQTCUB), Universitat de Barcelona, c/Martı́ i Franqués 1, 08028 Barcelona, Spain
| | - José R. B. Gomes
- Department of Chemistry, CICECO—Aveiro Institute of Materials, University of Aveiro, Campus Universitário de Santiago, Aveiro 3810-193, Portugal
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17
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Affiliation(s)
- José D. Gouveia
- CICECO—Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Ángel Morales-García
- Departament de Ciència de Materials i Quı́mica Fı́sica & Institut de Quı́mica Teòrica i Computacional (IQTCUB), Universitat de Barcelona, c/Martı́ i Franquès 1-11, 08028 Barcelona, Spain
| | - Francesc Viñes
- Departament de Ciència de Materials i Quı́mica Fı́sica & Institut de Quı́mica Teòrica i Computacional (IQTCUB), Universitat de Barcelona, c/Martı́ i Franquès 1-11, 08028 Barcelona, Spain
| | - José R. B. Gomes
- CICECO—Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Francesc Illas
- Departament de Ciència de Materials i Quı́mica Fı́sica & Institut de Quı́mica Teòrica i Computacional (IQTCUB), Universitat de Barcelona, c/Martı́ i Franquès 1-11, 08028 Barcelona, Spain
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18
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Teixeira C, Ventura C, Gomes JRB, Gomes P, Martins F. Cinnamic Derivatives as Antitubercular Agents: Characterization by Quantitative Structure-Activity Relationship Studies. Molecules 2020; 25:molecules25030456. [PMID: 31973244 PMCID: PMC7037561 DOI: 10.3390/molecules25030456] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 01/15/2020] [Accepted: 01/17/2020] [Indexed: 11/22/2022] Open
Abstract
Tuberculosis, caused by Mycobacterium tuberculosis (Mtb), remains one of the top ten causes of death worldwide and the main cause of mortality from a single infectious agent. The upsurge of multi- and extensively-drug resistant tuberculosis cases calls for an urgent need to develop new and more effective antitubercular drugs. As the cinnamoyl scaffold is a privileged and important pharmacophore in medicinal chemistry, some studies were conducted to find novel cinnamic acid derivatives (CAD) potentially active against tuberculosis. In this context, we have engaged in the setting up of a quantitative structure–activity relationships (QSAR) strategy to: (i) derive through multiple linear regression analysis a statistically significant model to describe the antitubercular activity of CAD towards wild-type Mtb; and (ii) identify the most relevant properties with an impact on the antitubercular behavior of those derivatives. The best-found model involved only geometrical and electronic CAD related properties and was successfully challenged through strict internal and external validation procedures. The physicochemical information encoded by the identified descriptors can be used to propose specific structural modifications to design better CAD antitubercular compounds.
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Affiliation(s)
- Cátia Teixeira
- LAQV-REQUIMTE, Departamento de Química e Bioquímica da Faculdade de Ciências da Universidade do Porto, P-4169-007 Porto, Portugal
- Correspondence: (C.T.); (F.M.)
| | - Cristina Ventura
- Instituto Superior de Educação e Ciências, P-1750-142 Lisboa, Portugal
| | - José R. B. Gomes
- CICECO, Departamento de Química, Universidade de Aveiro, P-3810-193 Aveiro, Portugal
| | - Paula Gomes
- LAQV-REQUIMTE, Departamento de Química e Bioquímica da Faculdade de Ciências da Universidade do Porto, P-4169-007 Porto, Portugal
| | - Filomena Martins
- Centro de Química e Bioquímica (CQB), Centro de Química Estrutural (CQE), Faculdade de Ciências da Universidade de Lisboa, P-1749-016 Lisboa, Portugal
- Correspondence: (C.T.); (F.M.)
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Pires J, Fernandes J, Dedecker K, Gomes JRB, Pérez-Sánchez G, Nouar F, Serre C, Pinto ML. Enhancement of Ethane Selectivity in Ethane-Ethylene Mixtures by Perfluoro Groups in Zr-Based Metal-Organic Frameworks. ACS Appl Mater Interfaces 2019; 11:27410-27421. [PMID: 31262167 DOI: 10.1021/acsami.9b07115] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A series of zirconium dicarboxylate-based metal-organic frameworks (Zr MOFs) of the UiO-66 (tetrahedral and octahedral cages) or MIL-140 (triangular channels) structure type were investigated for the separation of ethane/ethylene mixtures. The adsorption, investigated both experimentally and computationally, revealed that the size and type of pores have a more pronounced effect on the selectivity than the aromaticity of the linker. The increase in pore size when changing from benzene to naphthalene (NDC) dicarboxylate ligand makes UiO-NDC less selective (1.3-1.4) than UiO-66 (1.75-1.9) within the pressure range (100-1000 kPa), while the three-dimensional (3D) pores of the UiOs favor the adsorption of ethane due to the interactions between ethane with more spacers than in the case of the 1D channels of MIL-140s. The impact of the functionalization revealed a very interesting increase of selectivity when two perfluoro groups are present on the aromatic ring (UiO-66-2CF3) (value of 2.5 up to 1000 kPa). Indeed, UiO-66-2CF3 revealed a unique combination of selectivity and working capacity at high pressures. This is due to a complex adsorption mechanism involving a different distribution of the guest molecules in the different cages associated with changes in the ligand/perfluoro orientation when the pressure increases, favoring the ethane adsorption at high pressures.
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Affiliation(s)
- João Pires
- Centro de Química e Bioquímica and CQE , Faculdade de Ciências, Universidade de Lisboa , 1749-016 Lisboa , Portugal
| | - Joana Fernandes
- Centro de Química e Bioquímica and CQE , Faculdade de Ciências, Universidade de Lisboa , 1749-016 Lisboa , Portugal
| | - Kevin Dedecker
- Institut Lavoisier de Versailles, UMR CNRS 8180, Université de Versailles St-Quentin-en-Yvelines, Université Paris-Saclay , 78035 Versailles Cedex, France
- Centre de Recherche sur la Conservation, USR3224: CNRS-MNHN-MCC, Sorbonne Universités , 36 rue Geoffroy-Saint-Hilaire, 75005 Paris Cedex, France
| | - José R B Gomes
- Department of Chemistry , CICECO - Aveiro Institute of Materials, University of Aveiro, Campus Universitário de Santiagoí , 3810-193 Aveiro , Portugal
| | - Germán Pérez-Sánchez
- Department of Chemistry , CICECO - Aveiro Institute of Materials, University of Aveiro, Campus Universitário de Santiagoí , 3810-193 Aveiro , Portugal
| | - Farid Nouar
- Institut des Matériaux Poreux de Paris (IMAP), UMR CNRS 8004, Ecole Normale Supérieure de Paris, Ecole Supérieure de Physique et de Chimie Industrielles de Paris, PSL University , 75005 Paris , France
| | - Christian Serre
- Institut des Matériaux Poreux de Paris (IMAP), UMR CNRS 8004, Ecole Normale Supérieure de Paris, Ecole Supérieure de Physique et de Chimie Industrielles de Paris, PSL University , 75005 Paris , France
| | - Moisés L Pinto
- CERENA, Instituto Superior Técnico, Universidade de Lisboa , Av. Rovisco Pais, n° 1, 1049-001 Lisboa , Portugal
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20
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Martins ICB, Sardo M, Čendak T, Gomes JRB, Rocha J, Duarte MT, Mafra L. Hydrogen bonding networks in gabapentin protic pharmaceutical salts: NMR and in silico studies. Magn Reson Chem 2019; 57:243-255. [PMID: 30475406 DOI: 10.1002/mrc.4809] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 11/16/2018] [Accepted: 11/20/2018] [Indexed: 06/09/2023]
Abstract
Hydrogen bonds (HBs) play a key role in the supramolecular arrangement of crystalline solids and, although they have been extensively studied, the influence of their strength and geometry on crystal packing remains poorly understood. Here we describe the crystal structures of two novel protic gabapentin (GBP) pharmaceutical salts prepared with the coformers methanesulfonic acid (GBP:METHA) and ethanesulfonic acid (GBP:ETHA). This study encompasses experimental and computational electronic structure analyses of 1 H NMR chemical shifts (CSs), upon in silico HB cleavage. GBP:METHA and GBP:ETHA crystal packing comprise two main structural domains: an ionic layer (characterized by the presence of charge-assisted + NHGBP ⋯O-METHA/ETHA HB interactions) and a neutral layer generated in a different way for each salt, mainly due to the presence of bifurcated HB interactions. A comprehensive study of HB networks is presented for GBP:METHA, by isolating molecular fragments involved in distinct HB types (NH⋯O, OH⋯O, and CH⋯O) obtained from in silico disassembling of an optimized three-dimensional packing structure. Formation of HB leads to calculated 1 H NMR CS changes from 0.4 to ~5.8 ppm. This study further attempts to assess how 1 H NMR CS of protons engaged in certain HB are affected when other nearby HB, involving bifurcated or geminal/vicinal hydrogen atoms, are removed.
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Affiliation(s)
- Inês C B Martins
- CQE - Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Mariana Sardo
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Tomaž Čendak
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - José R B Gomes
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - João Rocha
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - M Teresa Duarte
- CQE - Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Luís Mafra
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Aveiro, Portugal
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21
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Afonso R, Sardo M, Mafra L, Gomes JRB. Unravelling the Structure of Chemisorbed CO 2 Species in Mesoporous Aminosilicas: A Critical Survey. Environ Sci Technol 2019; 53:2758-2767. [PMID: 30730709 DOI: 10.1021/acs.est.8b05978] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Chemisorbent materials, based on porous aminosilicas, are among the most promising adsorbents for direct air capture applications, one of the key technologies to mitigate carbon emissions. Herein, a critical survey of all reported chemisorbed CO2 species, which may form in aminosilica surfaces, is performed by revisiting and providing new experimental proofs of assignment of the distinct CO2 species reported thus far in the literature, highlighting controversial assignments regarding the existence of chemisorbed CO2 species still under debate. Models of carbamic acid, alkylammonium carbamate with different conformations and hydrogen bonding arrangements were ascertained using density functional theory (DFT) methods, mainly through the comparison of the experimental 13C and 15N NMR chemical shifts with those obtained computationally. CO2 models with variable number of amines and silanol groups were also evaluated to explain the effect of amine aggregation in CO2 speciation under confinement. In addition, other less commonly studied chemisorbed CO2 species (e.g., alkylammonium bicarbonate, ditethered carbamic acid and silylpropylcarbamate), largely due to the difficulty in obtaining spectroscopic identification for those, have also been investigated in great detail. The existence of either neutral or charged (alkylammonium siloxides) amine groups, prior to CO2 adsorption, is also addressed. This work extends the molecular-level understanding of chemisorbed CO2 species in amine-oxide hybrid surfaces showing the benefit of integrating spectroscopy and theoretical approaches.
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Affiliation(s)
- Rui Afonso
- CICECO - Aveiro Institute of Materials, Department of Chemistry , University of Aveiro, Campus Universitário de Santiago , 3810-193 Aveiro , Portugal
| | - Mariana Sardo
- CICECO - Aveiro Institute of Materials, Department of Chemistry , University of Aveiro, Campus Universitário de Santiago , 3810-193 Aveiro , Portugal
| | - Luís Mafra
- CICECO - Aveiro Institute of Materials, Department of Chemistry , University of Aveiro, Campus Universitário de Santiago , 3810-193 Aveiro , Portugal
| | - José R B Gomes
- CICECO - Aveiro Institute of Materials, Department of Chemistry , University of Aveiro, Campus Universitário de Santiago , 3810-193 Aveiro , Portugal
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22
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Schaeffer N, Pérez-Sánchez G, Passos H, Gomes JRB, Papaiconomou N, Coutinho JAP. Mechanisms of phase separation in temperature-responsive acidic aqueous biphasic systems. Phys Chem Chem Phys 2019; 21:7462-7473. [DOI: 10.1039/c8cp07750a] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The thermal and acid responsive behaviour of bulky phosphonium-based ILs is elucidated using a mixed experimental and computational approach.
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Affiliation(s)
- Nicolas Schaeffer
- CICECO – Aveiro Institute of Materials
- Department of Chemistry
- University of Aveiro
- 3810-193 Aveiro
- Portugal
| | - German Pérez-Sánchez
- CICECO – Aveiro Institute of Materials
- Department of Chemistry
- University of Aveiro
- 3810-193 Aveiro
- Portugal
| | - Helena Passos
- CICECO – Aveiro Institute of Materials
- Department of Chemistry
- University of Aveiro
- 3810-193 Aveiro
- Portugal
| | - José R. B. Gomes
- CICECO – Aveiro Institute of Materials
- Department of Chemistry
- University of Aveiro
- 3810-193 Aveiro
- Portugal
| | | | - João A. P. Coutinho
- CICECO – Aveiro Institute of Materials
- Department of Chemistry
- University of Aveiro
- 3810-193 Aveiro
- Portugal
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23
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Gomes JRB, Viñes F, Illas F, Fajín JLC. Implicit solvent effects in the determination of Brønsted–Evans–Polanyi relationships for heterogeneously catalyzed reactions. Phys Chem Chem Phys 2019; 21:17687-17695. [DOI: 10.1039/c9cp02817j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The Brønsted–Evans–Polanyi relationship derived for the water dissociation reaction within an implicit solvent approach is similar to that without such effects.
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Affiliation(s)
- José R. B. Gomes
- CICECO – Aveiro Institute of Materials
- Departamento de Química
- Universidade de Aveiro
- Campus Universitário de Santiago
- 3810-193 Aveiro
| | - Francesc Viñes
- Departament de Química Física & Institut de Química Teòrica i Computacional (IQTCUB)
- Universitat de Barcelona
- c/Martí i Franquès 1
- 08028 Barcelona
- Spain
| | - Francesc Illas
- Departament de Química Física & Institut de Química Teòrica i Computacional (IQTCUB)
- Universitat de Barcelona
- c/Martí i Franquès 1
- 08028 Barcelona
- Spain
| | - José L. C. Fajín
- LAQV@REQUIMTE
- Faculdade de Ciências
- Universidade do Porto
- P-4169-007 Porto
- Portugal
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Campbell C, Gomes JRB, Fischer M, Jorge M. New Model for Predicting Adsorption of Polar Molecules in Metal-Organic Frameworks with Unsaturated Metal Sites. J Phys Chem Lett 2018; 9:3544-3553. [PMID: 29886744 DOI: 10.1021/acs.jpclett.8b00967] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Conventional molecular models fail to correctly describe interactions of adsorbates with coordinatively unsaturated sites (CUS) present in a large number of metal-organic frameworks (MOFs). Here, we confirm the failure of these models for a prototypical polar adsorbate, carbon monoxide, and show that simply adjusting their parameters leads to poor agreement with experimental isotherms when outside the fitting conditions. We propose a new approach that combines quantum mechanical density functional theory (DFT) with Monte Carlo simulations to rigorously account for specific interactions at the CUS. By explicitly including electrostatic interactions and employing accurate DFT functionals that describe dispersion interactions, our modeling approach becomes generally applicable to both polar and nonpolar molecules. We demonstrate that this CUS model leads to substantial improvement in carbon monoxide adsorption isotherm predictions, and correctly captures the coordination binding mechanism. This paper represents a major stepping stone in the development of a robust, transferable and generally applicable approach to describe the complex interactions between gas molecules and CUS, with great potential for use in large-scale screening studies.
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Affiliation(s)
- Christopher Campbell
- Department of Chemical and Process Engineering , University of Strathclyde , 75 Montrose Street , Glasgow G1 1XJ , Scotland , United Kingdom
| | - José R B Gomes
- CICECO- Aveiro Institute of Materials, Department of Chemistry , University of Aveiro , Campus Universitário de Santiago , 3810-193 Aveiro , Portugal
| | - Michael Fischer
- Crystallography Group, Department of Geosciences , University of Bremen , Klagenfurter Straße , 28359 Bremen , Germany
- MAPEX Center for Materials and Processes , University of Bremen , 28359 Bremen , Germany
| | - Miguel Jorge
- Department of Chemical and Process Engineering , University of Strathclyde , 75 Montrose Street , Glasgow G1 1XJ , Scotland , United Kingdom
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Abstract
Periodic mesoporous organosilicas (PMOs) were suggested as potential adsorbents for CO2/CH4 separation because of their large affinities towards CO2 and low interaction with CH4. Herewith, we present a comprehensive computational study on the binding properties of flue gas species with the pore walls of periodic mesoporous phenylene-silica (Ph-PMO) for understanding the possible impact of other gaseous species in the CO2/CH4 separation. The calculations considered three exchange-correlation functionals (PBE, PBE-D2 and M06-2X) based on the density functional theory and the walls of the periodic mesoporous phenylene-silica were modelled within the cluster model approach. The components of the flue gas considered were the diatomic CO, H2, N2, O2 and NO molecules, the triatomic CO2, H2O, H2S and SO2 species, the tetratomic SO3 and NH3 gases and the pentatomic CH4 molecule. The calculated data demonstrate that the presence of H2O, SO2, NH3, H2S and SO3 is a significant threat to CO2 capture by Ph-PMO and suggest that the Ph-PMO material would present high selectivity for CO2 over CH4, CO, H2 or N2 adsorption. The adsorption behaviour of flue gas components in Ph-PMO can be directly related to the experimental proton affinities, basicities or even the polarizabilities of the gaseous molecules.
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Affiliation(s)
- Mirtha A O Lourenço
- CICECO - Aveiro Institute of Materials, Department of Materials and Ceramic Engineering, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.
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Ofoegbu SU, Galvão TLP, Gomes JRB, Tedim J, Nogueira HIS, Ferreira MGS, Zheludkevich ML. Corrosion inhibition of copper in aqueous chloride solution by 1H-1,2,3-triazole and 1,2,4-triazole and their combinations: electrochemical, Raman and theoretical studies. Phys Chem Chem Phys 2018; 19:6113-6129. [PMID: 28191580 DOI: 10.1039/c7cp00241f] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Triazoles are well-known organic corrosion inhibitors of copper. 1H-1,2,3-Triazole and 1,2,4-triazole, two very simple molecules with the only difference being the positions of the nitrogen atoms in the triazole ring, were studied in this work as corrosion inhibitors of copper in 50 mM NaCl solution using a set of electrochemical and analytical techniques. The results of electrochemical tests indicate that 1H-1,2,3-triazole exhibited superior inhibitor properties but could not suppress anodic copper dissolution at moderate anodic potentials (>+300 mV SCE), while 1,2,4-triazole, although it exhibited higher anodic currents, suppressed anodic copper dissolution at very anodic potentials. Density functional theory calculations were also performed to interpret the measured data and trends observed in the electrochemical studies. The computational studies considered either the inhibitors isolated in the gaseous phase or adsorbed onto Cu(111) surface models. From the calculations, the mechanisms of the inhibitive effects of both triazoles were established and plausible mechanisms of formation of the protective films on the Cu surface were proposed. The results of this study hold positive implications for research in the areas of catalysis, and copper content control in water purification systems.
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Affiliation(s)
- Stanley Udochukwu Ofoegbu
- Department of Materials and Ceramic Engineering, CICECO-Aveiro Institute of Materials, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.
| | - Tiago L P Galvão
- Department of Materials and Ceramic Engineering, CICECO-Aveiro Institute of Materials, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.
| | - José R B Gomes
- Department of Chemistry, CICECO-Aveiro Institute of Materials, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - João Tedim
- Department of Materials and Ceramic Engineering, CICECO-Aveiro Institute of Materials, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.
| | - Helena I S Nogueira
- Department of Chemistry, CICECO-Aveiro Institute of Materials, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - M G S Ferreira
- Department of Materials and Ceramic Engineering, CICECO-Aveiro Institute of Materials, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.
| | - M L Zheludkevich
- Department of Materials and Ceramic Engineering, CICECO-Aveiro Institute of Materials, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal. and MagIC, Institute of Materials Research, Helmholtz-ZentrumGeesthacht, Max-Planck-Strasse1, 21502 Geesthacht, Germany
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Jorge M, Milne AW, Sobek ON, Centi A, Pérez-Sánchez G, Gomes JRB. Modelling the self-assembly of silica-based mesoporous materials. Molecular Simulation 2018. [DOI: 10.1080/08927022.2018.1427237] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Miguel Jorge
- Department of Chemical and Process Engineering, University of Strathclyde, Glasgow, UK
| | - Andrew W. Milne
- Department of Chemical and Process Engineering, University of Strathclyde, Glasgow, UK
| | - Olivia N. Sobek
- Department of Chemical and Process Engineering, University of Strathclyde, Glasgow, UK
| | - Alessia Centi
- Department of Chemical and Process Engineering, University of Strathclyde, Glasgow, UK
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - Germán Pérez-Sánchez
- CICECO – Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
| | - José R. B. Gomes
- CICECO – Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
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28
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Schaeffer N, Passos H, Gras M, Mogilireddy V, Leal JP, Pérez-Sánchez G, Gomes JRB, Billard I, Papaiconomou N, Coutinho JAP. Mechanism of ionic-liquid-based acidic aqueous biphasic system formation. Phys Chem Chem Phys 2018; 20:9838-9846. [DOI: 10.1039/c8cp00937f] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
This work represents a major contribution to the understanding of ionic liquid-based acidic aqueous biphasic system formation and application.
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Affiliation(s)
- Nicolas Schaeffer
- CICECO
- Department of Chemistry
- University of Aveiro
- Campus Universitário de Santiago
- 3810-193 Aveiro
| | - Helena Passos
- CICECO
- Department of Chemistry
- University of Aveiro
- Campus Universitário de Santiago
- 3810-193 Aveiro
| | - Matthieu Gras
- LEPMI – Universite Grenoble-Alpes
- F-38000 Grenoble
- France
| | | | - João P. Leal
- C2TN
- DECN
- Instituto Superior Técnico
- Universidade de Lisboa
- 2695-066 Bobadela
| | - Germán Pérez-Sánchez
- CICECO
- Department of Chemistry
- University of Aveiro
- Campus Universitário de Santiago
- 3810-193 Aveiro
| | - José R. B. Gomes
- CICECO
- Department of Chemistry
- University of Aveiro
- Campus Universitário de Santiago
- 3810-193 Aveiro
| | | | | | - João A. P. Coutinho
- CICECO
- Department of Chemistry
- University of Aveiro
- Campus Universitário de Santiago
- 3810-193 Aveiro
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29
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Abstract
The reactivity of metallic nanotubes toward the catalysis of water dissociation, a key step in the water gas shift reaction (WGSR), was analyzed through density functional theory (DFT) calculations. Water dissociation was studied on surfaces of nanotubes based on copper, gold and platinum, and also on platinum doped copper and gold nanotubes. Gold and copper nanotubes present activities that are similar to those of their corresponding extended surfaces but, in the case of the Pt(5,3) nanotube, a significant improvement in the activity is found when compared with the extended surfaces. In fact, the calculations predict the water dissociation to be spontaneous on Pt(5,3) with a low activation energy barrier. The platinum doping of gold and copper nanotubes leads to contrasting effects, i.e., with a slight increase of activity found on gold and a slight decrease of activity in the case of copper. The consideration of a Brönsted-Evans-Polanyi (BEP) relationship to estimate the activation energy barriers for the O-H bond break leads to a satisfactory agreement between estimated and explicitly calculated values which suggests the validity of the BEP relationship for qualitative predictions of the activities of metal nanotubes towards the water dissociation reaction.
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Affiliation(s)
- José L C Fajín
- LAQV@REQUIMTE, Faculdade de Ciências, Universidade do Porto, P-4169-007 Porto, Portugal.
| | - M Natália D S Cordeiro
- LAQV@REQUIMTE, Faculdade de Ciências, Universidade do Porto, P-4169-007 Porto, Portugal.
| | - José R B Gomes
- CICECO - Aveiro Institute of Materials, Departamento de Química, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
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30
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Prates Ramalho JP, Illas F, Gomes JRB. Adsorption of CO on the rutile TiO2(110) surface: a dispersion-corrected density functional theory study. Phys Chem Chem Phys 2017; 19:2487-2494. [DOI: 10.1039/c6cp06971a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The geometry, energy and stretching frequency of carbon monoxide on the rutile TiO2(110) surface for coverages between 0.125 and 1.5 ML are investigated by means of density functional theory calculations.
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Affiliation(s)
- João P. Prates Ramalho
- Departamento de Química
- Centro de Química de Évora e Centro Hercules
- Universidade de Évora
- 7000 Évora
- Portugal
| | - Francesc Illas
- Departament de Ciència dels Materials i Química Física & Institut de Química Teòrica i Computacional (IQTCUB)
- Universitat de Barcelona
- 08028 Barcelona
- Spain
| | - José R. B. Gomes
- CICECO
- Departamento de Química
- Universidade de Aveiro
- Campus Universitário de Santiago
- P-3810-193 Aveiro
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31
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Mafra L, Čendak T, Schneider S, Wiper PV, Pires J, Gomes JRB, Pinto ML. Structure of Chemisorbed CO2 Species in Amine-Functionalized Mesoporous Silicas Studied by Solid-State NMR and Computer Modeling. J Am Chem Soc 2016; 139:389-408. [DOI: 10.1021/jacs.6b11081] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Luís Mafra
- CICECO
- Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Tomaž Čendak
- CICECO
- Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Sarah Schneider
- CICECO
- Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Paul V. Wiper
- CICECO
- Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - João Pires
- Centro
de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - José R. B. Gomes
- CICECO
- Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Moisés L. Pinto
- CERENA,
Departamento de Engenharia Quı́mica, Instituto Superior
Técnico, Universidade de Lisboa, Av. Rovisco Pais, no. 1, 1049-001 Lisboa, Portugal
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32
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Batista MLS, Passos H, Henriques BJM, Maginn EJ, Pinho SP, Freire MG, Gomes JRB, Coutinho JAP. Why are some cyano-based ionic liquids better glucose solvents than water? Phys Chem Chem Phys 2016; 18:18958-70. [PMID: 27353302 DOI: 10.1039/c6cp02538b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Among different classes of ionic liquids (ILs), those with cyano-based anions have been of special interest due to their low viscosity and enhanced solvation ability for a large variety of compounds. Experimental results from this work reveal that the solubility of glucose in some of these ionic liquids may be higher than in water - a well-known solvent with enhanced capacity to dissolve mono- and disaccharides. This raises questions on the ability of cyano groups to establish strong hydrogen bonds with carbohydrates and on the optimal number of cyano groups at the IL anion that maximizes the solubility of glucose. In addition to experimental solubility data, these questions are addressed in this study using a combination of density functional theory (DFT) and molecular dynamics (MD) simulations. Through the calculation of the number of hydrogen bonds, coordination numbers, energies of interaction and radial and spatial distribution functions, it was possible to explain the experimental results and to show that the ability to favorably interact with glucose is driven by the polarity of each IL anion, with the optimal anion being dicyanamide.
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Affiliation(s)
- Marta L S Batista
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.
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33
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Fajín JLC, Viñes F, D S Cordeiro MN, Illas F, Gomes JRB. Effect of the Exchange-Correlation Potential on the Transferability of Brønsted-Evans-Polanyi Relationships in Heterogeneous Catalysis. J Chem Theory Comput 2016; 12:2121-6. [PMID: 27111183 DOI: 10.1021/acs.jctc.6b00168] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
As more and more accurate density functional methods emerge, the transferability of Brønsted-Evans-Polanyi (BEP) relationships obtained with previous models is an open question. In this work, BEP relationships derived from different density functional theory based calculations are analyzed to answer this question. In particular, BEP relationships linking the activation energy of O-H bond breaking reactions taking place on metallic surfaces with the adsorption energy of the reaction products are chosen as a case study. These relationships are obtained with the widely used Perdew-Wang (PW91) generalized gradient approximation (GGA) exchange-correlation functional and with the more accurate meta-GGA Tao-Perdew-Staroverov-Scuseria (TPSS) one. We provide compelling evidence that BEP relationships derived from PW91 and TPSS functionals are essentially coincidental. This finding validates previously published BEP relationships and indicates that the reaction activation energy barrier can be obtained by the determination of the energy reaction descriptor value at the less computationally demanding GGA level; an important aspect to consider in future studies aimed at the computational design of catalysts with improved characteristics.
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Affiliation(s)
- José L C Fajín
- LAQV@REQUIMTE, Faculdade de Ciências, Universidade do Porto , P-4169-007 Porto, Portugal
| | - Francesc Viñes
- Departament de Química Física & Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona , c/Martí i Franquès 1, 08028 Barcelona, Spain
| | - M Natália D S Cordeiro
- LAQV@REQUIMTE, Faculdade de Ciências, Universidade do Porto , P-4169-007 Porto, Portugal
| | - Francesc Illas
- Departament de Química Física & Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona , c/Martí i Franquès 1, 08028 Barcelona, Spain
| | - José R B Gomes
- CICECO-Aveiro Institute of Materials, Departamento de Química, Universidade de Aveiro , 3810-193 Aveiro, Portugal
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34
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Teixeira C, Barbault F, Couesnon T, Gomes JRB, Gomes P, Maurel F. Striking HIV-1 Entry by Targeting HIV-1 gp41. But, Where Should We Target? PLoS One 2016; 11:e0146743. [PMID: 26785380 PMCID: PMC4718650 DOI: 10.1371/journal.pone.0146743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 12/20/2015] [Indexed: 11/17/2022] Open
Abstract
HIV-1 gp41 facilitates the viral fusion through a conformational switch involving the association of three C-terminal helices along the conserved hydrophobic grooves of three N-terminal helices coiled-coil. The control of these structural rearrangements is thought to be central to HIV-1 entry and, therefore, different strategies of intervention are being developed. Herewith, we describe a procedure to simulate the folding of an HIV-1 gp41 simplified model. This procedure is based on the construction of plausible conformational pathways, which describe protein transition between non-fusogenic and fusogenic conformations. The calculation of the paths started with 100 molecular dynamics simulations of the non-fusogenic conformation, which were found to converge to different intermediate states. Those presenting defined criteria were selected for separate targeted molecular dynamics simulations, subjected to a force constant imposing a movement towards the gp41 fusogenic conformation. Despite significant diversity, a preferred sequence of events emerged when the simulations were analyzed in terms of the formation, breakage and evolution of the contacts. We pointed out 29 residues as the most relevant for the movement of gp41; also, 2696 possible interactions were reduced to only 48 major interactions, which reveals the efficiency of the method. The analysis of the evolution of the main interactions lead to the detection of four main behaviors for those contacts: stable, increasing, decreasing and repulsive interactions. Altogether, these results suggest a specific small cavity of the HIV-1 gp41 hydrophobic groove as the preferred target to small molecules.
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Affiliation(s)
- Cátia Teixeira
- Laboratoire Interfaces, Traitements, Organisation et Dynamique des Systèmes-ITODYS-Université Paris Diderot, Paris 7 -CNRS UMR 7086; 15 rue Jean Antoine de Baïf, 75205 Paris Cedex13, France.,CICECO-Instituto de Materiais de Aveiro, Departamento de Química, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.,UCIBIO-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre 687, 4169-007 Porto, Portugal
| | - Florent Barbault
- Laboratoire Interfaces, Traitements, Organisation et Dynamique des Systèmes-ITODYS-Université Paris Diderot, Paris 7 -CNRS UMR 7086; 15 rue Jean Antoine de Baïf, 75205 Paris Cedex13, France
| | - Thierry Couesnon
- Laboratoire Interfaces, Traitements, Organisation et Dynamique des Systèmes-ITODYS-Université Paris Diderot, Paris 7 -CNRS UMR 7086; 15 rue Jean Antoine de Baïf, 75205 Paris Cedex13, France
| | - José R B Gomes
- CICECO-Instituto de Materiais de Aveiro, Departamento de Química, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Paula Gomes
- UCIBIO-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre 687, 4169-007 Porto, Portugal
| | - François Maurel
- Laboratoire Interfaces, Traitements, Organisation et Dynamique des Systèmes-ITODYS-Université Paris Diderot, Paris 7 -CNRS UMR 7086; 15 rue Jean Antoine de Baïf, 75205 Paris Cedex13, France
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35
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Fajín JLC, Cordeiro MNDS, Gomes JRB. Methanol dissociation on bimetallic surfaces: validity of the general Brønsted–Evans–Polanyi relationship for O–H bond cleavage. RSC Adv 2016. [DOI: 10.1039/c6ra01118g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Density functional theory calculations were used to study the dissociation of the O–H bond in methanol on several bimetallic transition metal surfaces, composed of elements showing high or moderate activity towards this reaction, namely, Ni, Rh, Ru, Ir, Pd, Au, Zn and Cu.
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Affiliation(s)
- José L. C. Fajín
- LAQV@REQUIMTE
- Faculdade de Ciências
- Universidade do Porto
- P-4169-007 Porto
- Portugal
| | | | - José R. B. Gomes
- CICECO–Aveiro Institute of Materials
- Departamento de Química
- Universidade de Aveiro
- 3810-193 Aveiro
- Portugal
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36
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Batista MLS, Pérez-Sánchez G, Gomes JRB, Coutinho JAP, Maginn EJ. Evaluation of the GROMOS 56ACARBO Force Field for the Calculation of Structural, Volumetric, and Dynamic Properties of Aqueous Glucose Systems. J Phys Chem B 2015; 119:15310-9. [DOI: 10.1021/acs.jpcb.5b08155] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Marta L. S. Batista
- Departamento
de Química, CICECO, Universidade de Aveiro, Campus Universitário
de Santiago, 3810-193 Aveiro, Portugal
- Department
of Chemical and Biomolecular Engineering, 182 Fitzpatrick Hall, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Germán Pérez-Sánchez
- Departamento
de Química, CICECO, Universidade de Aveiro, Campus Universitário
de Santiago, 3810-193 Aveiro, Portugal
| | - José R. B. Gomes
- Departamento
de Química, CICECO, Universidade de Aveiro, Campus Universitário
de Santiago, 3810-193 Aveiro, Portugal
| | - João A. P. Coutinho
- Departamento
de Química, CICECO, Universidade de Aveiro, Campus Universitário
de Santiago, 3810-193 Aveiro, Portugal
| | - Edward J. Maginn
- Department
of Chemical and Biomolecular Engineering, 182 Fitzpatrick Hall, University of Notre Dame, Notre Dame, Indiana 46556, United States
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37
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Khan I, Batista MLS, Carvalho PJ, Santos LMNBF, Gomes JRB, Coutinho JAP. Vapor–Liquid Equilibria of Imidazolium Ionic Liquids with Cyano Containing Anions with Water and Ethanol. J Phys Chem B 2015; 119:10287-303. [DOI: 10.1021/acs.jpcb.5b03324] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Imran Khan
- CICECO, Aveiro Institute of Materials, Chemistry Department, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Marta L. S. Batista
- CICECO, Aveiro Institute of Materials, Chemistry Department, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Pedro J. Carvalho
- CICECO, Aveiro Institute of Materials, Chemistry Department, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Luís M. N. B. F. Santos
- Centro de Investigacão em Química, Departamento de
Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, 687, P-4169-007 Porto, Portugal
| | - José R. B. Gomes
- CICECO, Aveiro Institute of Materials, Chemistry Department, University of Aveiro, 3810-193 Aveiro, Portugal
| | - João A. P. Coutinho
- CICECO, Aveiro Institute of Materials, Chemistry Department, University of Aveiro, 3810-193 Aveiro, Portugal
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38
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Fajín JLC, Teixeira F, Gomes JRB, Cordeiro MNDS. Effect of van der Waals interactions in the DFT description of self-assembled monolayers of thiols on gold. Theor Chem Acc 2015. [DOI: 10.1007/s00214-015-1666-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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39
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Pillai RS, Pinto ML, Pires J, Jorge M, Gomes JRB. Understanding Gas adsorption selectivity in IRMOF-8 using molecular simulation. ACS Appl Mater Interfaces 2015; 7:624-637. [PMID: 25519048 DOI: 10.1021/am506793b] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Grand canonical Monte Carlo simulations were used to explore the adsorption behavior of methane, ethane, ethylene, and carbon dioxide in isoreticular metal-organic frameworks, IRMOF-1, noninterpenetrated IRMOF-8, and interpenetrated IRMOF-8. The simulated isotherms are compared with experimentally measured isotherms, when available, and a good agreement is observed. In the case of IRMOF-8, the agreement is much better for the interpenetrated model than for the noninterpenetrated model, suggesting that the experimental data was obtained on an essentially interpenetrated structure. Simulations show that carbon dioxide is preferentially adsorbed over methane, and a selective adsorption at low pressures of ethane over ethylene, especially in the case of IRMOF-8, confirm recent experimental results. Analysis of simulation results on both the interpenetrated and the noninterpenetrated structures shows that interpenetration is responsible for the higher adsorbed amounts of ethane at low pressures (<100 kPa) and for the interesting selectivity for ethane in ethane/ethylene binary mixtures. Van der Waals interactions seem to be enhanced in the interpenetrated structure, favoring ethane adsorption. This indicates that interpenetrated MOF structures may be of interest for the separation of small gas molecules.
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Affiliation(s)
- Renjith S Pillai
- Department of Chemistry, CICECO, University of Aveiro , 3810-193 Aveiro, Portugal
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40
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Batista MLS, Kurnia KA, Pinho SP, Gomes JRB, Coutinho JAP. Computational and Experimental Study of the Behavior of Cyano-Based Ionic Liquids in Aqueous Solution. J Phys Chem B 2015; 119:1567-78. [DOI: 10.1021/jp510125x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Marta L. S. Batista
- Departamento
de Química, CICECO, Universidade de Aveiro, 3810-193 Aveiro, Portugal
| | - Kiki A. Kurnia
- Departamento
de Química, CICECO, Universidade de Aveiro, 3810-193 Aveiro, Portugal
| | - Simão P. Pinho
- Associate
Laboratory LSRE/LCM, Instituto Politécnico de Bragança, 5301-857 Bragança, Portugal
| | - José R. B. Gomes
- Departamento
de Química, CICECO, Universidade de Aveiro, 3810-193 Aveiro, Portugal
| | - João A. P. Coutinho
- Departamento
de Química, CICECO, Universidade de Aveiro, 3810-193 Aveiro, Portugal
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41
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Abstract
Microwave-assisted synthesis allows preparation of nitro- and amino-functionalized phenylene–PMO in just 15 and 30 minutes, respectively, with tunable content and homogeneous distribution of functional groups.
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Affiliation(s)
- Mirtha A. O. Lourenço
- CICECO
- Department of Materials & Ceramics Engineering
- University of Aveiro
- Campus Universitário de Santiago
- 3810-193 Aveiro
| | - José R. B. Gomes
- CICECO
- Department of Chemistry
- University of Aveiro
- Campus Universitário de Santiago
- 3810-193 Aveiro
| | - Paula Ferreira
- CICECO
- Department of Materials & Ceramics Engineering
- University of Aveiro
- Campus Universitário de Santiago
- 3810-193 Aveiro
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42
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Affiliation(s)
- Cátia Teixeira
- Centro de Investigação em Química da Universidade do Porto, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto , P-4169-007 Porto, Portugal.,CICECO, Departamento de Química, Universidade de Aveiro , P-3810-193 Aveiro, Portugal
| | - Nuno Vale
- Centro de Investigação em Química da Universidade do Porto, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto , P-4169-007 Porto, Portugal
| | - Bianca Pérez
- Centro de Investigação em Química da Universidade do Porto, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto , P-4169-007 Porto, Portugal
| | - Ana Gomes
- Centro de Investigação em Química da Universidade do Porto, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto , P-4169-007 Porto, Portugal
| | - José R B Gomes
- CICECO, Departamento de Química, Universidade de Aveiro , P-3810-193 Aveiro, Portugal
| | - Paula Gomes
- Centro de Investigação em Química da Universidade do Porto, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto , P-4169-007 Porto, Portugal
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43
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Pillai RS, Gomes JRB, Jorge M. Molecular simulation of the adsorption of methane in Engelhard titanosilicate frameworks. Langmuir 2014; 30:7435-7446. [PMID: 24901733 DOI: 10.1021/la501554v] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Molecular simulations were carried out to elucidate the influence of structural heterogeneity and of the presence of extra-framework cations and water molecules on the adsorption of methane in Engelhard titanosilicates, ETS-10 and ETS-4. The simulations employed three different modeling approaches, (i) with fixed cations and water at their single crystal positions, (ii) with fixed cations and water at their optimized positions, and (iii) with mobile extra-framework cations and water molecules. Simulations employing the final two approaches provided a more realistic description of adsorption in these materials, and showed that at least some cations and water molecules are displaced from the crystallographic positions obtained from single crystal data. Upon methane adsorption in the case of ETS-10, the cations move to the large rings, while in the case of ETS-4, the water molecules and cations migrate to more available space in the larger 12-membered ring channels for better accommodation of the methane molecules. For ETS-4, we also considered adsorption in all possible pure polymorph structures and then combined these to provide an estimate of adsorption in a real ETS-4 sample. By comparing simulated adsorption isotherms to experimental data, we were able to show that both the mobility of extra-framework species and the structural heterogeneity should be taken into account for realistic predictions of adsorption in titanosilicate materials.
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Affiliation(s)
- Renjith S Pillai
- CICECO, Departamento de Química, Universidade de Aveiro , Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
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Tomé LIN, Pereira JFB, Rogers RD, Freire MG, Gomes JRB, Coutinho JAP. Evidence for the Interactions Occurring Between Ionic Liquids and Tetraethylene Glycol in Binary Mixtures and Aqueous Biphasic Systems. J Phys Chem B 2014; 118:4615-29. [DOI: 10.1021/jp501718w] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Luciana I. N. Tomé
- Departamento
de Química, CICECO, Universidade de Aveiro, 3810-193 Aveiro, Portugal
| | - Jorge F. B. Pereira
- Departamento
de Química, CICECO, Universidade de Aveiro, 3810-193 Aveiro, Portugal
- Center
for Green Manufacturing and Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Robin D. Rogers
- Center
for Green Manufacturing and Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Mara G. Freire
- Departamento
de Química, CICECO, Universidade de Aveiro, 3810-193 Aveiro, Portugal
| | - José R. B. Gomes
- Departamento
de Química, CICECO, Universidade de Aveiro, 3810-193 Aveiro, Portugal
| | - João A. P. Coutinho
- Departamento
de Química, CICECO, Universidade de Aveiro, 3810-193 Aveiro, Portugal
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Jorge M, Fischer M, Gomes JRB, Siquet C, Santos JC, Rodrigues AE. Accurate Model for Predicting Adsorption of Olefins and Paraffins on MOFs with Open Metal Sites. Ind Eng Chem Res 2014. [DOI: 10.1021/ie500310c] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Miguel Jorge
- Department
of Chemical and Process Engineering, University of Strathclyde, 75 Montrose
Street, Glasgow G1 1XJ, Scotland, United Kingdom
| | - Michael Fischer
- Department
of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
- Fachbereich
Geowissenschaften, University of Bremen, Klagenfurter Straße, 28359 Bremen, Germany
| | - José R. B. Gomes
- CICECO
− Centre for Research in Ceramics and Composite Materials,
Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Christophe Siquet
- LSRE
− Laboratory of Separation and Reaction Engineering −
Associate Laboratory LSRE/LCM, Faculdade de Engenharia, Universidade do Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - João C. Santos
- LSRE
− Laboratory of Separation and Reaction Engineering −
Associate Laboratory LSRE/LCM, Faculdade de Engenharia, Universidade do Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Alírio E. Rodrigues
- LSRE
− Laboratory of Separation and Reaction Engineering −
Associate Laboratory LSRE/LCM, Faculdade de Engenharia, Universidade do Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
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Fajín JLC, D. S. Cordeiro MN, Gomes JRB. Density Functional Theory Study of the Water Dissociation on Platinum Surfaces: General Trends. J Phys Chem A 2014; 118:5832-40. [DOI: 10.1021/jp411500j] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- José L. C. Fajín
- REQUIMTE, Faculdade
de Ciências, Universidade do Porto, Rua do Campo
Alegre, 687, P-4169-007 Porto, Portugal
| | - M. Natália D. S. Cordeiro
- REQUIMTE, Faculdade
de Ciências, Universidade do Porto, Rua do Campo
Alegre, 687, P-4169-007 Porto, Portugal
| | - José R. B. Gomes
- CICECO, Departamento
de Química, Universidade de Aveiro, Campus Universitário
de Santiago, 3810-193 Aveiro, Portugal
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Pérez B, Teixeira C, Gomes JRB, Gomes P. Development of Plasmodium falciparum protease inhibitors in the past decade (2002-2012). Curr Med Chem 2014; 20:3049-68. [PMID: 23514416 DOI: 10.2174/0929867311320250003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 10/14/2012] [Indexed: 11/22/2022]
Abstract
New drug targets for the development of antimalarial drugs have emerged after the unveiling of the Plasmodium falciparum genome in 2002. Potential antimalarial drug targets can be broadly classified into three categories according to their function in the parasite's life cycle: (i) biosynthesis, (ii) membrane transport and signaling, and (iii) hemoglobin catabolism. The latter plays a key role, as inhibition of hemoglobin degradation impairs maturation of bloodstage malaria parasites, ultimately leading to remission or even cure of the most severe stage of the infection. Intraerythrocytic Plasmodia parasites have limited capacity to biosynthesize amino acids which are vital for their growth. Therefore, the parasites obtain those essential amino acids via degradation of host cell hemoglobin, making this a crucial process for parasite survival. Several plasmodial proteases are involved in hemoglobin catabolism, among which plasmepsins and falcipains are well-known examples. Hence, development of P. falciparum protease inhibitors is a promising approach to antimalarial chemotherapy, as highlighted by the present review which is focused on the Medicinal Chemistry research effort recorded in the past decade in this particular field.
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Affiliation(s)
- B Pérez
- Centro de Investigação em Química da Universidade do Porto, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, R. do Campo Alegre, 687, P-4169-007 Porto, Portugal
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Viñes F, Gomes JRB, Illas F. Understanding the reactivity of metallic nanoparticles: beyond the extended surface model for catalysis. Chem Soc Rev 2014; 43:4922-39. [DOI: 10.1039/c3cs60421g] [Citation(s) in RCA: 134] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Metallic nanoparticles (NPs) constitute a new class of chemical objects which are used in different fields as diverse as plasmonics, optics, catalysis, or biochemistry.
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Affiliation(s)
- Francesc Viñes
- Departament de Química Física & Institut de Química Teòrica i Computacional (IQTCUB)
- Universitat de Barcelona
- 08028 Barcelona, Spain
| | - José R. B. Gomes
- CICECO
- Department of Chemistry
- University of Aveiro
- 3810-193 Aveiro, Portugal
| | - Francesc Illas
- Departament de Química Física & Institut de Química Teòrica i Computacional (IQTCUB)
- Universitat de Barcelona
- 08028 Barcelona, Spain
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Tomé LIN, Pereira JFB, Rogers RD, Freire MG, Gomes JRB, Coutinho JAP. “Washing-out” ionic liquids from polyethylene glycol to form aqueous biphasic systems. Phys Chem Chem Phys 2014; 16:2271-4. [DOI: 10.1039/c3cp54047b] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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50
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Pérez B, Antunes S, Gonçalves LM, Domingos A, Gomes JRB, Gomes P, Teixeira C. Toward the discovery of inhibitors of babesipain-1, a Babesia bigemina cysteine protease: in vitro evaluation, homology modeling and molecular docking studies. J Comput Aided Mol Des 2013; 27:823-35. [DOI: 10.1007/s10822-013-9682-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 10/04/2013] [Indexed: 11/28/2022]
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