Cheminformatics and Materials

Research Publications

Total publications: 603

49. p A simple electrochemical detection of atorvastatin based on disposable screen-printed carbon electrodes modified by molecularly imprinted polymer: Experiment and simulation
Rebelo, P; Pacheco, JG; Voroshylova, IV; Melo, A; Cordeiro, MNDS; Delerue Matos, C
in ANALYTICA CHIMICA ACTA, 2022, ISSN: 0003-2670,  Volume: 1194, 
Article,  Indexed in: crossref, scopus, wos 
Atorvastatin (ATV) is a statin member consumed in high quantities worldwide. In response to that, the occurrence of ATV in environmental waters has become a reality, highlighting the need of rapid and sensitive analytical devices for its monitoring. In this work, the first electrochemical molecularly imprinted polymer (MIP) sensor for the detection of ATV in water samples is presented. Computational studies were conducted based on quantum mechanical (QM) calculations and molecular dynamics (MD) simulations for rational selection of a suitable functional monomer and to study in detail the templatemonomer interaction, respectively. The sensor was prepared by electropolymerisation of the selected 4aminobenzoic acid (ABA) monomer with ATV, acting as template, on screen printed carbon electrode (SPCE). Cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) techniques were applied to characterise the modified electrode surfaces. The quantitative measurements were carried out with differential pulse voltammetry (DPV) in 0.1 M phosphate buffer (pH = 7). After investigation and optimisation of important experimental parameters, a linear working range down to 0.05 mmol L-1 was determined with a correlation coefficient of 0.9996 and a limit of detection (LOD) as low as 0.049 mmol L-1 (S/N = 3). High sensitivity and selectivity of the prepared sensor were demonstrated with the ability to recognise ATV molecules over its closer structural analogues. Moreover, the sensor was quickly and successfully applied in spiked water samples, proving its potential for future on-site monitoring of ATV in environmental waters.
50. Predicting the Surface Tension of Deep Eutectic Solvents: A Step Forward in the Use of Greener Solvents
Halder, AK; Haghbakhsh, R; Voroshylova, IV; Duarte, ARC; Cordeiro, MNDS
in MOLECULES, 2022, ISSN: 1420-3049,  Volume: 27, 
Article,  Indexed in: crossref, scopus, wos 
Deep eutectic solvents (DES) are an important class of green solvents that have been developed as an alternative to toxic solvents. However, the large-scale industrial application of DESs requires fine-tuning their physicochemical properties. Among others, surface tension is one of such properties that have to be considered while designing novel DESs. In this work, we present the results of a detailed evaluation of Quantitative Structure-Property Relationships (QSPR) modeling efforts designed to predict the surface tension of DESs, following the Organization for Economic Co-operation and Development (OECD) guidelines. The data set used comprises a large number of structurally diverse binary DESs and the models were built systematically through rigorous validation methods, including 'mixtures-out'- and 'compounds-out'-based data splitting. The most predictive individual QSPR model found is shown to be statistically robust, besides providing valuable information about the structural and physicochemical features responsible for the surface tension of DESs. Furthermore, the intelligent consensus prediction strategy applied to multiple predictive models led to consensus models with similar statistical robustness to the individual QSPR model. The benefits of the present work stand out also from its reproducibility since it relies on fully specified computational procedures and on publicly available tools. Finally, our results not only guide the future design and screening of novel DESs with a desirable surface tension but also lays out strategies for efficiently setting up silico-based models for binary mixtures.
51. Relating the Ambient Temperature and Ionic Liquid Structure to the Changes of Capacitance Using Molecular Dynamics
Ers, H; Voroshylova, I; Pikma, P; Ivanistsev, V
in ECS Meeting Abstracts, 2022, Volume: MA2022-01, 
Article,  Indexed in: crossref 
<jats:p> Ionic liquids (ILs) are a unique class of electrolytes, which characteristics make them suitable for use in solar cells, supercapacitors, and fuel cells<jats:sup>1</jats:sup>. Due to the appealing properties such as good electrochemical stability, low vapour pressure, high concentration of ions and the lack of solvent, they have been under intense study since the early 2000s. Although numerous theoretical<jats:sup>2,3</jats:sup>, computational<jats:sup>4,5</jats:sup>, and experimental studies<jats:sup>6,7</jats:sup> have shed light on the interfacial properties of ILs, which differ noticeably from the aqueous electrolytes, multiple open questions remain. One such problem is how the interfacial capacitance is affected by the ambient temperature, as studies have shown both positive and negative temperature dependences<jats:sup>8,9</jats:sup>. Understanding the temperature dependence of interfacial capacitance is crucial as it is relevant for the description of energy storage and is one of the few quantities, which can be estimated both experimentally and computationally.</jats:p> <jats:p>In this study, we combine the density functional theory (DFT) calculations with molecular dynamics (MD) simulations of graphene (Gr) | EMImBF<jats:sub>4</jats:sub> IL interface to explain the effect of temperature on capacitance. MD simulations allow us to investigate the probable distribution of ions near the electrode’s surface and relate the changes of ILs structure to the capacitance using the interfacial bilayer model (IBL). We show that the increase of temperature affects the capacitance near the potential of zero charge by attenuating the overscreening without a notable change in the IL interfacial structure. The characteristic peaks and plateaus in the capacitance potential dependence are explained through the concepts of IL layering and saturation of the second IL layer described in the IBL. Using the DFT calculations, we estimate the impact of the quantum capacitance of Gr on the total interfacial capacitance and its temperature dependence. By accounting for the limiting quantum capacitance, the total interfacial capacitance was significantly altered in the case of the Gr electrode, as the effect of the temperature was dampened, and a V-shaped capacitance curve was obtained.</jats:p> <jats:p>Acknowledgements:</jats:p> <jats:p>This work was supported by the Estonian Research Council grant PSG249 and by the EU through the European Regional Development Fund under project TK141 (2014-2020.4.01.15-0011). The financial support from FCT/MCTES through the Portuguese national funds, project No. UID/QUI/50006/2021 (LAQV@REQUIMTE) is also acknowledged.</jats:p> <jats:p>References:</jats:p> <jats:p>1 D. R. MacFarlane, N. Tachikawa, M. Forsyth, J. M. Pringle, P. C. Howlett, G. D. Elliott, J. H. Davis, M. Watanabe, P. Simon and C. A. Angell, <jats:italic>Energy Environ. Sci.</jats:italic>, 2014, <jats:bold>7</jats:bold>, 232–250.</jats:p> <jats:p>2 A. A. Kornyshev, <jats:italic>J. Phys. Chem. B</jats:italic>, 2007, <jats:bold>111</jats:bold>, 5545–5557.</jats:p> <jats:p>3 Z. A. H. Goodwin and A. A. Kornyshev, <jats:italic>Electrochem. Commun.</jats:italic>, 2017, <jats:bold>82</jats:bold>, 129–133.</jats:p> <jats:p>4 M. Salanne, <jats:italic>Phys. Chem. Chem. Phys.</jats:italic>, 2015, <jats:bold>17</jats:bold>, 14270–14279.</jats:p> <jats:p>5 I. V. Voroshylova, H. Ers, V. Koverga, B. Docampo-Álvarez, P. Pikma, V. B. Ivaništšev and M. N. D. S. Cordeiro, <jats:italic>Electrochim. Acta</jats:italic>, 2021, <jats:bold>379</jats:bold>, 138148.</jats:p> <jats:p>6 L. Siinor, K. Lust and E. Lust, <jats:italic>J. Electrochem. Soc.</jats:italic>, 2010, <jats:bold>157</jats:bold>, F83.</jats:p> <jats:p>7 V. Lockett, M. Horne, R. Sedev, T. Rodopoulos and J. Ralston, <jats:italic>Phys. Chem. Chem. Phys.</jats:italic>, 2010, <jats:bold>12</jats:bold>, 12499–12512.</jats:p> <jats:p>8 F. Silva, C. Gomes, M. Figueiredo, R. Costa, A. Martins and C. M. Pereira, <jats:italic>J. Electroanal. Chem.</jats:italic>, 2008, <jats:bold>622</jats:bold>, 153–160.</jats:p> <jats:p>9 M. Drüschler, N. Borisenko, J. Wallauer, C. Winter, B. Huber, F. Endres and B. Roling, <jats:italic>Phys. Chem. Chem. Phys.</jats:italic>, 2012, <jats:bold>14</jats:bold>, 5090–5099. </jats:p>
52. Synthesis, anticancer activity, SAR and binding mode of interaction studies of substituted pentanoic acids: part II
Datta, S; Halder, AK; Adhikari, N; Amin, SA; Das, S; Jha, T
in FUTURE MEDICINAL CHEMISTRY, 2022, ISSN: 1756-8919,  Volume: 14, 
Article,  Indexed in: scopus, wos 
Aim: Our previous results suggest that phenyl/naphthylacetyl pentanoic acid derivatives may exhibit dual MMP-2 and HDAC8 inhibitory activities and show effective cytotoxic properties. Methodology: Here, 13 new compounds (C1-C13) were synthesized and characterized. Along with these new compounds, 16 previously reported phenyl/napthylacetyl pentanoic acid derivatives (C14-C29) were biologically evaluated. Results: Compounds C6 and C27 showed good cytotoxicity against leukemia cell line Jurkat E6.1. The mechanisms of cytotoxicity of these compounds were confirmed by DNA deformation assay and reactive oxygen species assay. MMP-2 and HDAC8 expression assays suggested the dual inhibiting property of these two compounds. These findings were supported by results of molecular docking studies. In silico pharmacokinetic properties showed compounds C6 and C27 have high gastrointestinal absorption. Conclusion: This study highlights the action of phenyl/naphthylacetyl pentanoic acid derivatives as anticancer agents.
53. Theoretical Study on the Diels–Alder Reaction of Fullerenes: Analysis of Isomerism, Aromaticity, and Solvation
Rodrigues, DJL; Santos, LMNBF; Melo, A; Lima, CFRAC
in Organics, 2022, Volume: 3, 
Article,  Indexed in: crossref 
<jats:p>Fullerenes are reactive as dienophiles in Diels–Alder reactions. Their distinctive molecular shape and properties result in interesting and sometimes elusive reaction patterns. Herein, to contribute to the understanding of fullerene reactivity, we evaluate the energies of reactions for Diels–Alder cycloadditions of C60, C70, and IC60MA with anthracene (Ant), by means of DFT computational analysis in vacuum and solution. The methods used showed little differentiation between the reactivity of the different fullerenes. The C70-Ant adducts where addition takes place near the edge of the fullerene were found to be the most stable regioisomers. For the IC60MA-Ant adducts, the calculated energies of reaction increase in the order: equatorial &gt; trans-3 &gt; trans-2 ≈ trans-4 ≈ trans-1 &gt; cis-3 &gt; cis-2. The change in the functional suggests the existence of stabilizing dispersive interactions between the surface of the fullerene and the addends. HOMA (harmonic oscillator model of aromaticity) analysis indicated an increase in aromaticity in the fullerene hexagons adjacent to the bonded addend. This increase is bigger in the rings of bisadduct isomers that are simultaneously adjacent to both addends, which helps explain the extra stability of the equatorial isomers. Solvation by m-xylene decreases the exothermicity of the reactions studied but has little distinguishing effect on the possible isomers. Thermal corrections reduce the exothermicity of the reactions by ~10 kJ∙mol−1.</jats:p>
54. Toxicity Assessment of the Binary Mixtures of Aquatic Organisms Based on Different Hypothetical Descriptors
Ji, M; Zhang, LH; Zhuang, XM; Tian, CY; Luan, F; Cordeiro, MNDS
in MOLECULES, 2022, ISSN: 1420-3049,  Volume: 27, 
Article,  Indexed in: crossref, scopus, wos 
Modern industrialization has led to the creation of a wide range of organic chemicals, especially in the form of multicomponent mixtures, thus making the evaluation of environmental pollution more difficult by normal methods. In this paper, we attempt to use forward stepwise multiple linear regression (MLR) and nonlinear radial basis function neural networks (RBFNN) to establish quantitative structure-activity relationship models (QSARs) to predict the toxicity of 79 binary mixtures of aquatic organisms using different hypothetical descriptors. To search for the proper mixture descriptors, 11 mixture rules were performed and tested based on preliminary modeling results. The statistical parameters of the best derived MLR model were N-train = 62, R-2 = 0.727, RMS = 0.494, F = 159.537, Q(LOO)(2) = 0.727, and Q(pred)(2) = 0.725 for the training set; and N-test = 17, R-2 = 0.721, RMS = 0.508, F = 38.773, and q(ext)(2) = 0.720 for the external test set. The RBFNN model gave the following statistical results: N-train = 62, R-2 = 0.956, RMS = 0.199, F = 1279.919, Q(LOO)(2) = 0.955, and Q(pred)(2) = 0.855 for the training set; and N-test = 17, R-2 = 0.880, RMS = 0.367, F = 110.980, and q(ext)(2) = 0.853 for the external test set. The quality of the models was assessed by validating the relevant parameters, and the final results showed that the developed models are predictive and can be used for the toxicity prediction of binary mixtures within their applicability domain.
55. Turning deep-eutectic solvents into value-added products for CO2 capture: A desirability-based virtual screening study
Ambure, P; Perez-Castillo, Y; Halder, AK; Cordeiro, MNDS
in JOURNAL OF CO2 UTILIZATION, 2022, ISSN: 2212-9820,  Volume: 58, 
Article,  Indexed in: crossref, scopus, wos 
Carbon dioxide capture and storage is one of the primary mitigation approaches endorsed by current global climate change policies, since it is the largest contributing gas to the greenhouse effect. Recently, deep eutectic solvents (DESs) have been found as promising green solvents for CO(2 )capture, particularly in industrial applications. Compared to conventional ionic liquids, for example, DESs display similar solvent properties but they are far cheaper, easier to prepare, and greener. Yet their major drawback is linked to their high viscosity that impedes management not fulfilling industrial demands. Further efforts are thus required to develop new DES solvents that hold together high capacity for CO2 uptake and low viscosity. In this work, we adopted a desirability-based decision approach to jointly handle these two conflicting properties. We began by setting up Quantitative Structure-Property Relationships (QSPR) models for uncovering the two properties based on a dataset of known binary DESs. Then, desirability functions derived from the individual QSPR models were found and combined into an overall desirability-based criterion that was applied to screen and rank two libraries, one comprising experimentally reported DESs and another one with newly designed DESs. The latter enabled us to propose novel efficient DESs for CO2 uptake, i.e., with the most suitable trade-offs between CO2 absorption capacity and viscosity. Finally, but most importantly, this work demonstrates the usefulness of the desirability based approach for the rational discovery of deep eutectic solvents or other materials to suit particular sustainable applications.
56. "Ethics against Chemistry": Solving a Crime Using Chemistry Concepts and Storytelling in a History of Science-Based Interactive Game for Middle School Students
Dias, D; Ferraz Caetano, J; Paiva, J
in JOURNAL OF CHEMICAL EDUCATION, 2021, ISSN: 0021-9584,  Volume: 98, 
Article,  Indexed in: crossref, scopus, unpaywall, wos 
Designing a science activity for middle school children is a challenging task, especially if it aims to be interdisciplinary. One may ask if it is possible to craft a positive learning experience from different areas such as history of science, chemistry, or ethics. In this paper, we argue it can be achieved if we use the right tools to engage a young audience. A combination of gamification, hands-on activities, and storytelling techniques was successfully used, providing a unique form to approach chemistry and ethics subjects in an "edutainment" format. The result is a game that challenges participants to solve a crime, while addressing chemistry topics to gather pieces of evidence and facing science-related ethical conundrums. In our pilot study, participants evaluated this activity positively, identifying the innovation and entertaining features as the most relevant in their gaming experience.