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Computational methodologies in the exploration of marine natural product leads
Publication . Pereira, Florbela; Aires-de-Sousa, João; LAQV@REQUIMTE; DQ - Departamento de Química; MDPI - Multidisciplinary Digital Publishing Institute
Computational methodologies are assisting the exploration of marine natural products (MNPs) to make the discovery of new leads more efficient, to repurpose known MNPs, to target new metabolites on the basis of genome analysis, to reveal mechanisms of action, and to optimize leads. In silico efforts in drug discovery of NPs have mainly focused on two tasks: dereplication and prediction of bioactivities. The exploration of new chemical spaces and the application of predicted spectral data must be included in new approaches to select species, extracts, and growth conditions with maximum probabilities of medicinal chemistry novelty. In this review, the most relevant current computational dereplication methodologies are highlighted. Structure-based (SB) and ligand-based (LB) chemoinformatics approaches have become essential tools for the virtual screening of NPs either in small datasets of isolated compounds or in large-scale databases. The most common LB techniques include Quantitative Structure–Activity Relationships (QSAR), estimation of drug likeness, prediction of adsorption, distribution, metabolism, excretion, and toxicity (ADMET) properties, similarity searching, and pharmacophore identification. Analogously, molecular dynamics, docking and binding cavity analysis have been used in SB approaches. Their significance and achievements are the main focus of this review.
Historically accurate reconstructions of Amadeo’s chrome yellows: an integrated study of their manufacture and stability
Publication . Matias, Vanessa Otero; Melo, Maria João; Vilarigues, Márcia
The subject of this PhD is the study of 19th century yellow chromate pigments, in particular chrome yellow (lead chromate), which has been frequently found in the paintings by the Portuguese Modern painter Amadeo de Souza-Cardoso (1887-1918) and by Vincent Van Gogh (1853-1890). Detailed knowledge of the materials used by artists is fundamental for the understanding of their technique and to place their works in context as well as to determine the state of preservation and authenticity of their work. For this thesis new knowledge was gained through a multidisciplinary approach which combines art technological and conservation science research. This is the first doctoral work that fully explores the Winsor & Newton (W&N) 19th Century Archive Database and provides a unique insight into the company’s choices and workshop practices. W&N had a special concern for the quality and durability of their yellow chromate pigments. A complete evaluation of their 286 production records for yellow chromate pigments was undertaken. The majority of the production records (64%) pertain to different hues of lead chromate. W&N produced essentially three lead chromate pigment types: Lemon/Pale based on mixed crystals of lead chromate and lead sulfate [PbCr1-xSxO4] where x ≤ 0.4; Middle based on pure monoclinic lead chromate [PbCrO4]; and Deep that contains the latter admixed with basic lead chromate [Pb2CrO5]. Production records for the manufacture of barium chromate, BaCrO4 (25%), zinc potassium chromate, 4ZnCrO4·K2O·3H2O (9%), and strontium chromate, SrCrO4 (2%) were also found. Despite the high number of production records, each chromate pigment type is characterised by only one or two main synthetic pathways. W&N’s addition of extenders in their lead chromate pigment formulations, indicates that they were mainly used to adjust pigment properties and not as a means to decrease costs. The reduced number of records found for the production of the light-sensitive Primrose type of lead chromate (a formulation composed of sulfur-rich PbCr1-xSxO4), and strontium chromate, suggests W&N was not manufacturing or selling these pigment formulations on a large scale; more evidence that during the 19th century W&N was committed to primarily selling high quality durable chromate pigments.
Pigment reconstructions following the main methods of synthesis were produced for this research and characterised by complementary analytical techniques: Colourimetry, Fibre Optic Reflectance Spectroscopy (FORS), micro-Energy Dispersive X-Ray Fluorescence Spectrometry (μ-EDXRF), X-Ray Diffraction (XRD), Scanning Electron Microscopy with X-ray microanalysis (SEM-EDS), micro-Raman (μ-Raman) and micro-Fourier Transform Infrared (μ-FTIR) spectroscopies. A very good correlation was found between the chemical composition of the pigment reconstructions and historic paint samples from 19th century oil paint tubes and Amadeo’s paintings. This validates their high degree of historical accuracy and attests their use as reference materials for further chemical studies.
The lead chromate pigment formulations were made into oil and poly(vinyl acetate) (PVAc) paints and irradiated with a Xenon lamp (λirr > 300 nm) to assess their photostability. The degradation process was followed by the above mentioned techniques and was further studied by Synchrotron Radiation based techniques (μ-XRF, μ-FTIR and μ-XRD). By means of micro X-ray Absorption Near-Edge Structure (μ-XANES), an innovative Light Susceptibility Index (LSI) was developed based on the ratio of the Cr K pre-edge intensity after/before irradiation with a Xenon lamp, which decreases as the quantity of Cr3+ degradation species increases. This index will enable the prediction of the stability of lead chromate pigments in works of art. Three degrees of lightfastness were identified: 1) PbCr1-xSxO4 with 0 ≤ x ≤ 0.4/0.5, 2) PbCr1-xSxO4 with x ≥ 0.4/0.5 and 3) PbCrO4 admixed with a high quantity of the extenders chalk (CaCO3) and gypsum (CaSO4.2H2O). This work demonstrates that the manufacturing conditions, in particular the pH of the production of PbCr1-xSxO4 with 0.4 ≤ x ≤ 0.5, influences their photostability.
Most importantly, this is the first work to formulate integrated mechanisms that account for the main causes of colour alteration, and which identifies the crucial role played by the pigment and binder formulations, including their additives. The combined use of the Synchrotron Radiation based techniques allowed access at the micro-scale, to the spatial distribution of the degradation products and intermediaries. This led to the discovery that the reduction of Cr6+ from lead chromate to Cr3+ species is driven by the presence of oxalic acid and/or oxalate compounds. It is proposed that these compounds result from the decomposition of carbonate compounds (present as additives) in acidic media or via decarboxylation of carboxylic acids. These degradation pathways are triggered by the photodegradation of the binder and the degradation rate is deeply dependent on the paint formulation. The presence of calcium oxalate as a degradation intermediary and/or protective patina from light absorption is also discussed in relation to these findings. For the first time, it was possible to identify a Cr3+ degradation compound, a chromium potassium sulfate, CrK(SO4)2·12H2O, by infrared spectroscopy.
Finally, it was also possible to determine that no degradation resulting from the reduction of Cr6+ to Cr3+ is currently occurring in Amadeo’s paintings which contrasts with literature reports on the degradation of lead chromate pigments in the work of Van Gogh.
Synthesis of Integrated Polymers for Soil Stabilization
Publication . Parada, Leandro Rafael de Almeida; Barroso, Telma; Ricardo, Ana
In this work, the synthesis of vinylpyrrolidone- (VP), vinyl acetate- (VA) and acrylamide- (AM) based polymers and copolymers was developed with a view to their application as drilling fluids. P(VP-co-VA), P(AM-co-VA) and P(AM-co-VP) were synthesized with different monomer ratio (87-13%, 75-25% and 50-50%) in water with the aim of obtaining a copolymer which is: (1) water soluble in a ratio of 1 g per liter of water (2) and able to exhibit a viscosity value ≥ 55 s/quart. The material fulfilling these requirements may be applied as (i) a main compound or as (ii) an additive for drilling fluids. All viscosity measurements were performed in a Marsh funnel as preliminary tests to select which was the best candidate polymer for the previous objectives. The chemical composition of all polymers and copolymers was investigated by FTIR-ATR or/and solid state 13C NMR to ensure the success of polymerization. Polymers and copolymers which achieved the previously mentioned requisites (1) and (2) were characterized by scanning electron microscopy (SEM), zeta potential and their molecular weight was determined in an Ubbelohde type I Capillar viscometer. Partially hydrolyzed P(AM-co-VA) with a weight monomer ratio of 75-25% of acrylamide and VP, respectively, and partially hydrolyzed P(AM-co-VP) with a weight monomer ratio of 87-13% of acrylamide and VP, respectively, showed a viscosity of 56 s/quart in water, gathering all needed conditions to be evaluated according to suspension and settling tests with soil. These suspension and settling tests were performed with clay in distilled-deionized and tap water.
P(AM-co-VA) were not able to suspend clay neither as main viscosifier nor as additive. P(AM-co-VP) did not reveal suspending clay capacity as main viscosifier, but when 1g of copolymer is added to one liter of PolyMud® solution (1 g/L) comprising distilled-deionized water, 100% of soil suspension was reached over a period of 24 hours. When tap water was used, P(AM-co-VP) exhibited the best performance by keeping in suspension 90% of the total clay present in solution over 24 hours.
In addition, PVP was successfully used as additive to a PolyMud® solution (1 g/L), comprising distilled-deionized water, exhibiting in suspension capacity of 90% of the total clay during 24 hours.
Extending the stability of red and blue colors of malvidin-3-glucoside-lipophilic derivatives in the presence of SDS micelles
Publication . Mendoza, Johan; Pina, Fernando; Basílio, Nuno; Guimarães, Marta; de Freitas, Victor; Cruz, Luís; LAQV@REQUIMTE; DQ - Departamento de Química; Elsevier
Anthocyanins lipophilization recently emerged as an efficient tool to deliver oil-soluble dyes aiming to expand their applications in lipophilic matrices such as cosmetics formulations. Sodium dodecyl sulfate (SDS) micelles were used to solubilize malvidin-3-glucoside derivatives bearing an ester chain derived from dodecanoic and hexanoic fatty acids. Detailed investigations on the kinetic and thermodynamic behavior of the pigments towards pH variations was carried out by means of UV-Vis spectroscopy. It was found that the pH domain of the red flavylium cation is extended in ca 0.3–0.4 pH units. The mole fraction of the quinoidal base at neutral conditions increased by 40% when compared with malvidin-3-glucoside in the same micellar media, which provides a great blue color stabilization. The results presented herein report for the first time the blue color stabilization of these lipophilic anthocyanin bioactives, opening new application fields as novel colorants for lipid-based foods and cosmetics.
Application of polyoxometalate-ionic liquids (POM-ILs) in dye-sensitized solar cells (DSSCs)
Publication . Cruz, Hugo; Pinto, Ana Lúcia; Lima, João Carlos; Branco, Luís C.; Gago, Sandra; LAQV@REQUIMTE; DQ - Departamento de Química; Elsevier BV
Polyoxometalates (POMs) as anionic metal oxides are promising candidates for application in dye-sensitized solar cells (DSSCs) due to their peculiar properties including a reversible and multi-electron redox behavior. In this work, four polyoxometalate as ionic liquids (POM-ILs) based on the combination between phosphomolybdate anion (PMo12O40 3−) and organic cations such as [BMIM]+, [BPy]+, [HDPy]+ and [P6,6,6,14]+ were prepared and characterized. A detailed chemical structural elucidation by elemental analysis, ATR-FTIR, 1H and 31P NMR spectroscopies have been performed. These POM-ILs were tested as photosensitizers by adsorption to the photoanode (TiO2 film) for different times (15 min to 17 h). The DSSCs performance can be highly improved comparing the commercially available compound and POM-ILs. The electrodeposition process is an excellent alternative to adsorption in order to improve the overall efficiencies. In general, [BPy]3[PMo12O40] and [P6,6,6,14]3[PMo12O40] are the most promissory compounds for DSSC approaches.
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Fundação para a Ciência e a Tecnologia
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5876
Número da atribuição
UID/QUI/50006/2013