Cheminformatics and Materials

Research Publications

Total publications: 610

41. An integrated protocol to study hydrogen abstraction reactions by atomic hydrogen in flexible molecules: application to butanol isomers
Ferro Costas, D; Cordeiro, MNDS; Fernandez Ramos, A
in PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 2022, ISSN: 1463-9076,  Volume: 24, 
Article,  Indexed in: crossref, scopus, wos 
This work presents a protocol designed to study hydrogen abstraction reactions by atomic hydrogen in molecules with multiple conformations. The protocol starts with the search and location of the conformers of the equilibrium structures using the TorsiFlex program. By a simple modification of the starting geometry of reactants, a Python script generates the input for the hydrogen abstraction transition states. Initially, the search of the stationary points (reactants and transition states) is carried out at a low-level employing firstly a preconditioned search and secondly a random search. The low-level conformers were reoptimized using a higher level electronic structure method. This information allows the evaluation of the multistructural harmonic-oscillator partition functions, which are corrected for zero-point energy anharmonicity by the hybrid degeneracy-corrected second-order vibrational perturbation theory and for torsional anharmonicity by the multistructural torsional method, as implemented in the MsTor program. The structural information of the stationary points is used by Pilgrim to evaluate the multipath canonical variational transition state theory thermal rate constants with multidimensional small-curvature corrections for tunneling. Therefore, the thermal rate constants include variational (recrossing) and tunneling effects in addition to the effect of multiple conformations on the thermal rate constants. These features grant the applicability of the method to a wide range of temperatures. The method was applied to each of the hydrogen abstraction sites of the four isomers of butanol. The methodology employed allowed us to calculate the thermal rate constants in the temperature range of 250-2500 K and to accurately fit them to analytical expressions. The variety of abstraction sites shows that the protocol is robust and that it can be employed to study hydrogen abstraction reactions in molecules containing carbon and oxygen as heavy atoms.
42. An integrated protocol to study hydrogen abstraction reactions by atomic hydrogen in flexible molecules: application to butanol isomers (vol 24, pg 3043, 2022)
Ferro Costas, D; Cordeiro, MNDS; Fernandez Ramos, A
in PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 2022, ISSN: 1463-9076,  Volume: 24, 
Correction,  Indexed in: wos 
43. caso da “salicilagem dos vinhos do Porto”
in Revista Brasileira de História da Ciência, 2022, ISSN: 1983-4713,  Volume: 15, 
Article,  Indexed in: crossref 
<jats:p>No início do século XX, as ciências exatas ganharam notoriedade em Portugal por meio do seu papel como “ciência ao serviço da nação”. No caso da academia da cidade do Porto, a valorização das “artes químicas” cruza-se com a nova metodologia de ensino ministrada na Academia Politécnica do Porto e os trabalhos de segurança alimentar no recente Laboratório Químico Municipal do Porto. Um dos mais famosos ecos desta disposição revela-se no papel central da academia no desfecho de uma importante disputa comercial entre Portugal e o Brasil (1885-1905). A questão da salicilagem dos vinhos do Porto, que em muito prejudicou as exportações de vinho portuguesas para o território brasileiro, apenas se começa a desvanecer depois da intervenção dos trabalhos científicos de António Ferreira da Silva, académico e químico portuense. Este é um dos raros casos em que a construção do conhecimento científico sobre métodos analíticos tem influência central na resolução de uma disputa comercial na Europa do século XIX.</jats:p>
44. Computational Modelling and Sustainable Synthesis of a Highly Selective Electrochemical MIP-Based Sensor for Citalopram Detection
Rebelo, P; Pacheco, JG; Voroshylova, IV; Seguro, I; Cordeiro, MNDS; Delerue-Matos, C
in MOLECULES, 2022, Volume: 27, 
Article,  Indexed in: crossref, scopus, wos 
A novel molecularly imprinted polymer (MIP) has been developed based on a simple and sustainable strategy for the selective determination of citalopram (CTL) using screen-printed carbon electrodes (SPCEs). The MIP layer was prepared by electrochemical in situ polymerization of the 3-amino-4 hydroxybenzoic acid (AHBA) functional monomer and CTL as a template molecule. To simulate the polymerization mixture and predict the most suitable ratio between the template and functional monomer, computational studies, namely molecular dynamics (MD) simulations, were carried out. During the experimental preparation process, essential parameters controlling the performance of the MIP sensor, including CTL:AHBA concentration, number of polymerization cycles, and square wave voltammetry (SWV) frequency were investigated and optimized. The electrochemical characteristics of the prepared MIP sensor were evaluated by both cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) techniques. Based on the optimal conditions, a linear electrochemical response of the sensor was obtained by SWV measurements from 0.1 to 1.25 mu mol L-1 with a limit of detection (LOD) of 0.162 mu mol L-1 (S/N = 3). Moreover, the MIP sensor revealed excellent CTL selectivity against very close analogues, as well as high imprinting factor of 22. Its applicability in spiked river water samples demonstrated its potential for adequate monitoring of CTL. This sensor offers a facile strategy to achieve portability while expressing a willingness to care for the environment.
45. Correction: An integrated protocol to study hydrogen abstraction reactions by atomic hydrogen in flexible molecules: application to butanol isomers
Ferro-Costas, D; Cordeiro, MNDS; Fernández-Ramos, A
in Physical Chemistry Chemical Physics, 2022, ISSN: 1463-9076,  Volume: 24, 
Correction,  Indexed in: crossref 
<jats:p>Correction for ‘An integrated protocol to study hydrogen abstraction reactions by atomic hydrogen in flexible molecules: application to butanol isomers’ by David Ferro-Costas <jats:italic>et al.</jats:italic>, <jats:italic>Phys. Chem. Chem. Phys.</jats:italic>, 2022, DOI: 10.1039/d1cp03928h.</jats:p>
46. Current Outlooks on Machine Learning Methods for the Development of Industrial Homogeneous Catalytic Systems
in CURRENT ORGANOCATALYSIS, 2022, ISSN: 2213-3372,  Volume: 9, 
Article,  Indexed in: crossref, scopus, wos 
This brief perspective outlines the pivotal role of Machine Learning methods in the green, digital transition of industrial chemistry. The focus on homogenous catalysis highlights the recent methodologies in the development of industrial processes, including the design of new catalysts and the enhancement of sustainable reaction conditions to lower production costs. We report several examples of Machine Learning assisted methodologies through recent Data Science trends in the innovation of industrial homogeneous organocatalytic systems. We also stress the current benefits, drawbacks, and limitations of the mass implementation of these Data Science methodologies.
47. Double layer in ionic liquids: Temperature effect and bilayer model
Ers, H; Voroshylova, I; Pikma, P; Ivanistsev, VB
in JOURNAL OF MOLECULAR LIQUIDS, 2022, ISSN: 0167-7322,  Volume: 363, 
Article,  Indexed in: crossref, scopus, wos 
This work describes the effect of potential and temperature on the grapheneionic liquid (EMImBF4) interfacial structure and properties with the focus on a novel phenomenon of ionic saturation. We apply classical molecular dynamics simulations to reproduce well-known phenomena of overscreening, mono -layer formation, and temperature-induced smearing of the interfacial structure. Using quantum density functional theory calculations, we show how quantum capacitance dampens the influence of temperature and improves the agreement with the experimental data. Using a bilayer model, we study characteristic features of capacitance-potential dependence and relate them to the changes in interfacial structure. These insights are of fundamental and practical importance for the application of similar interfaces in electrochemical energy storage and transformation devices such as capacitors and actuators. (C) 2022 The Authors. Published by Elsevier B.V.
48. First multi-target QSAR model for predicting the cytotoxicity of acrylic acid-based dental monomers
Halder, AK; Delgado, AHS; Cordeiro, MNDS
in DENTAL MATERIALS, 2022, ISSN: 0109-5641,  Volume: 38, 
Article,  Indexed in: crossref, wos 
Objective: Acrylic acid derivatives are frequently used as dental monomers and their cy- totoxicity towards various cell lines is well documented. This study aims to probe the structural and physicochemical attributes responsible for higher toxicity of dental mono- mers, using quantitative structure-activity relationships (QSAR) modeling approaches. Methods: A regression-based linear single-target QSAR (st-QSAR) model was developed with a comparatively small dataset containing 39 compounds, the cytotoxicity of which has been assessed over the Hela S3 cell line. By contrast, a classification-based multi-target QSAR model was developed with 138 compounds, the cytotoxicity of which has been re- ported against 18 different cell lines. Both models were set up following rigorous validation protocols confirming their statistical significance and robustness. Results: The performance of the linear mt-QSAR model, developed with various feature selection and post-selection similarity searching-based schemes, superseded that of all non-linear models produced with six machine learning methods by hyperparameter opti- mization. The final derived st-QSAR and mt-QSAR linear models are shown to be highly predictive, as well as revealing the crucial structural and physicochemical factors re- sponsible for higher cytotoxicity of the dental monomers. Significance: This study is the first attempt on unveiling the cytotoxicity of dental mono- mers over several cell lines by means of a single multi-target QSAR model. Further, such a model is ready to get widespread applicability in the screening of new monomers, judging from its almost accurate predictions over diverse experimental assay conditions.