Publications

Abstract Fatty acids and cholesterol compositions, in both fresh and mature cheeses, prepared in accordance with the Manchego-type cheese with different fat compositions, using milk enriched with avocado oil were evaluated. Fresh cheese enriched with avocado oil showed an increase of 52% in polyunsaturated acids in full-fat milk and 98% in skimmed milk. Mature manchego style cheeses enriched with avocado oil showed an increase of 32% in polyunsaturated acids in full-fat milk and 61% in skimmed milk. Multivariate analysis (non-linear mapping, hierarchical cluster analysis, and linear discriminating analysis) of the fatty acids composition in newly prepared cheeses confirmed that they were different from the traditional cheeses and that a small set of fatty acids (myristoleic, lauroleic, eicosenoic, caproleic, stearic, palmitoleic, and margaroleic) can be used to develop classification rules.

Abstract The present work reports an energetic and structural study of 2-fluoro-, 3-fluoro-, and 4-fluorobenzonitrile. The standard molar enthalpies of formation, in the condensed phase, of the three isomers were derived from the standard molar energies of combustion, in oxygen, at T = 298.15 K. The standard molar enthalpies of vaporization or sublimation (for 4-fluorobenzonitrile), at T = 298.15 K, were measured using high-temperature Calvet microcalorimetry. The combination of these two parameters yields the standard molar enthalpies of formation in the gaseous phase. The vapor-pressure study of the referred compounds was performed by a static method, and the enthalpies of phase transition derived from the application of the Clarke and Glew equation. Theoretically estimated gas-phase enthalpies of formation, basicities, proton and electron affinities, and adiabatic ionization enthalpies were calculated from the G3MP2B3 level of theory. In order to evaluate the electronic properties, the geometries were reoptimized at MP2/cc-pVTZ level, and the QTAIM and NICS were computed. On the basis of the donor-acceptor system, another approach for evaluating the electronic effect for these compounds, using the NBO is suggested. The UV-vis spectroscopy study for the three isomers was performed. The intensities and the band positions were correlated with the thermodynamic properties calculated computationally.

Abstract The Knudsen mass-loss effusion technique was used to measure the vapour pressures of the three crystalline isomers of methylbenzamide. From the temperature dependence of the vapour pressures, the standard molar enthalpies of sublimation and the enthalpies of the intermolecular hydrogen bonds N-H center dot center dot center dot O were calculated. The temperature and molar enthalpy of fusion of the studied isomers were measured using differential scanning calorimetry. The values of the standard (p degrees = 0.1 MPa) molar enthalpy of formation in the crystalline phase, at T = 298.15 K, of the compounds studied were derived from their standard massic energies of combustion measured by static-bomb combustion calorimetry. From the experimental values, the standard molar enthalpies of formation in the gaseous phase, at T = 298.15 K, were calculated and compared with the values estimated by employing computational calculations that were conducted using different quantum chemical methods: G3( MP2), G3, and CBS-QB3. Good agreement between experimental and theoretical results is verified. The aromaticity of the compounds has been evaluated through nucleus independent chemical shifts (NICS) calculations.

Abstract Several 3-alkylaryl mimics of the enol intermediate in the reaction catalyzed by type II dehydroquinase were synthesized to investigate the effect on the inhibition potency of replacing the oxygen atom in the side chain by a carbon atom. The length and the rigidity of the spacer was also studied. The inhibitory properties of the reported compounds against type II dehydroquinase from Mycobacterium tuberculosis and Helicobacter pylori are also reported. The binding modes of these analogs in the active site of both enzymes were studied by molecular docking using GOLD 5.0 and dynamic simulations studies. © 2012 The Royal Society of Chemistry.

Abstract Quantitative Structure-Activity Relationships (QSAR) modeling tools play acritical role today in both drug design and environmental sciences. QSAR modeling seeksto discover and use mathematical relationships between molecular properties of thecompounds (descriptors) and the often complex activity of interest. An extensive numberof molecular descriptors exist which can and have been used to model a wide range oftarget activities. This complicates the task of selecting those that will be more suitable,especially when one tries to define an accurate, robust, predictive and (most importantly)interpretable model. Lately, recognition of the importance of the three-dimensionally (3D)structure and stereochemistry of molecules to their biological activity, and awareness of thelimitations of classical approaches, led to many attempts to generate 3D descriptors eitheras a complement for 2D-QSAR models or for standalone 3D-QSAR models. This reviewdescribes the 3D descriptors available in the DRAGON software along with theirsuccessful applications primarily in Medicinal Chemistry, updating a previously publishedpaper in Current Topics in Medicinal Chemistry (Helguera, A.M.; Combes, R.D.;González, M.P.; Cordeiro, M.N.D.S., 2008, 8, 1628-1655).

Abstract Blood Serum Proteome-Mass Spectra (SP-MS) may allow detecting Proteome-Early Drug Induced Cardiac Toxicity Relationships (called here Pro-EDICToRs).However, due to the thousands of proteins in the SP, a more realistic alternative representsthe identification of general Pro-EDICToRs patterns instead of a single protein marker. Inthis sense, we introduced a novel Cartesian 2D spectrum graph for SP-MS. Next, wecalculated the graph node-overlapping parameters (nopk) to numerically characterize SPMSby using them as inputs for a Quantitative Proteome-Toxicity Relationship (QPTR)classifier for Pro-EDICToRs with accuracy higher than 80%. This QPTR approach is theresult of adapting the classic blood proteome Quantitative Property-Structure Relationshipmodels (QSPR) used in Chemometrics to low-mass molecules study. Principal ComponentAnalysis (PCA) on the QPTR nopk values explains with one factor (F1) the 82.7% ofvariance. These nopk values were used to construct for the first time a Pro-EDICToRsComplex Network having samples as nodes linked by similarity between two samplesedges. We compared the topology of two sub-networks for the cardiac toxicity and controlsamples and found extreme relative differences for the re-linking (P) and Zagreb (M2)indices (9.5 and 54.2 % respectively) out of 11 parameters. We also compared the subnetworkswith the well-known ideal random networks including Barabasi-Albert,Kleinberg Small World, Erdos-Renyi, and Epsstein Power Law models. Finally, weproposed Partial Order (PO) schemes of the 115 samples based on LDA-probabilities, F1-scores and/or network node degrees. PCA-CN and LDA-PCA based POs with Tanimoto's.

Abstract The adjustment of multiple criteria in hit-to-lead identification and lead optimization is a major advance in drug discovery. Thus, the development of approaches able to handle additional criteria for the early simultaneous treatment of the most important properties determining the pharmaceutical profile of a drug candidate is an emergent issue in this area. In this paper, we review a desirability-based multi-objective QSAR method allowing the joint handling of multiple properties of interest in drug discovery: the MOOP-DESIRE methodology. This methodology adapts desirability theory concepts allowing the holistic modeling of the many and conflicting biological properties determining the therapeutic utility of a drug candidate. Here we survey their suitability for key tasks involving the use of chemoinformatics methods in medicinal chemistry and drug discovery.

Abstract The standard (p degrees = 0.1 MPa) molar enthalpies of formation, in the condensed phase, of the three monoiodoanisoles, were derived from the respective enthalpies of combustion, measured by rotating-bomb combustion calorimetry. Their enthalpies of sublimation/vaporization, at T = 298.15 K, were obtained by Calvet microcalorimetry using the high-temperature vacuum sublimation technique. Moreover the standard molar enthalpy, entropy and Gibbs energy of sublimation, at T = 298.15 K, of 4-iodoanisole were derived from the Knudsen mass-loss effusion technique. Combining the former sets of experimental results, the standard molar enthalpies of formation in the gas-phase, at T = 298.15 K, of 2-, 3- and 4-iodoanisole were derived, respectively, as: (15.1 +/- 2.1) kJ . mol (1); (11.8 +/- 2.2) kJ . mol (1), and (12.4 +/- 1.6) kJ . mol (1). The experimental values of the gas-phase enthalpies of formation of each iodoanisole were also estimated by means of the empirical scheme developed by Cox and by density functional theory calculations employing the B3LYP/6-311++G(d, p) approach. Estimated values are in excellent agreement with the reported experimental ones derived in the present paper.

Abstract Fluorescent silicon nanoparticles (silicon dots) are low-toxicity nanomaterials of utmost interest to analytical and bioanalytical chemistry. Silicon dots have proved to be excellent fluorescent tags for sensor development applications. This review focuses on silicon dots and their fluorescent properties and applications. Silicon dots can be produced via nine basic synthetic methods and their fluorescent properties differ considerably, according to how they are produced and functionalized. The photoluminescent mechanism depends on the particle size, surface defects and functionalization molecules. This review presents a synopsis of the most important recent analytical and bioanalytical applications, along with the toxicity assays performed with silicon dots.

Abstract It has been outlined the need of science teachers to print a more modern approach to teaching, based on effective and relevant context. Thus, the European Project PROFILES - Professional Reflection-Oriented Focus on Inquiry Learning through Science and Education - embraced by twenty participating countries, including Portugal, arises from the urgent need to invest in further continuous professional development. The aim of the project is to stimulate the skills in teaching students that may increase, through more motivating methods, their scientific literacy. In this sense, the teacher is oriented in order to experience four stages of development - the teacher as i) learner ii) teacher; iii) reflective practitioner; iv) leader - and is invited to implement with their students, new approaches based on Inquiry-Based Science Education (IBSE). Inquiry-based learning is a process where students are involved in their learning, formulate questions, investigate widely and then build new understandings, meanings and knowledge. PROFILES, and its guidelines regarding teacher training, shows great complicity with the, already completed, European Project PARSEL - Popularity And Relevance of Science Education for scientific Literacy - in which modules were developed as a set of teaching strategies for a new science approach through the discussion of social and ethical problems. The objective of the PARSEL modules is to increase the relevance and popularity of science teaching in the eyes of students, but at the same time guarantee solid student learning headed for enhancing scientific literacy. PROFILES teacher training in Portugal, lasted 50 hours and included classroom work, independent study, participation in synchronous sessions, asynchronous forums via Moodle and project implementation in their respective schools. On this last component teachers began their training by selecting and adapting a PARSEL module followed by its application with the students, bearing in mind three key stages. At the first stage, the PARSEL module was introduced to the students through relevant and interesting social issue. The relevance was achieved when the students concluded that there was a link between the title and an ordinary society situation, rather than a formal presentation of a series of scientific terms. At the moment students noted that there was a lack of scientific ideas that need to be introduced in order to elaborate a solution for the presented problem, it was the fulcral moment to start the second stage of implementation. Teachers certificated that at this stage, all the students had clearly established the relevance of the problem. Then, teachers could apply the IBSE strategy in order to guide and involve the students in the process of obtaining the formal learning. Because it was at this stage that the students acquire the so called scientific ideas, teachers took the majority of the teaching time to explore this phase. Third stage closed the circle of the learning module. This last stage was a consolidation phase of the science learning. This was made by transferring the learning achieved to the initial social issue proposed. All PARSEL modules were evaluated using the "Questionnaires for the Assessment of "motivational Learning Environment" (MoLE)" and the results pointing to an increase in student motivation.