Publications

Abstract While brown carbon is a strongly-light-absorbing type of organic aerosol that is capable of significant regional radiative forcing, it has been neglected from climate models, which results in differences between model predictions and measured data. This also results from uncertainty regarding the relationship between the chemical composition of brown carbon and its optical properties. Herein, here was utilized a time-dependent density functional theory (TD-DFT) approach to model the "real-world" absorption of thirty polycyclic aromatic hydrocarbons (PAHs) and twenty-five derivatives (ten nitro-PAHs and fifteen oxygenated-PAHs) present in the atmosphere over three Southern European cities (Porto, Florence and Athens). These data were corrected both for "real-world" experimental concentration of these molecules over these cities, and for their theoretical fluorescence yield. These results indicate that the absorption of the molecules more relevant for climate forcing are at similar to 330, similar to 360 and similar to 440 nm. Furthermore, the absorption is explained mainly by PAH and oxygenated-PAH molecules, while nitro-PAHs provide only negligible contributions. Porto should be the city to be most affected by radiative forcing induced by these molecules, while Florence and Athens appear to be similarly affected. Finally, these models also demonstrate that absorption at similar to 330 nm is explained by both PAH and oxygenated-PAH-molecules, while absorption at similar to 360 and similar to 440 nmis only attributed to oxygenated-PAHs. More specifically, from the fifty-five studied molecules, only coronene (a PAH), 1,8-naphthalic anhydride, 6-H-benzo[cd]pyrene-6-one and 7H-benz[de]anthracence-7-one (three oxygenated-PAHs) provide relevant contributions to radiative forcing.

Abstract Cypridina bioluminescence has been increasingly used in bioimaging, bioanalysis, and biomedicine, due to high quantum yield and high signal-to-noise ratio. However, there is still no consensus regarding different aspects of the chemiluminescent mechanism of this system, which impairs the development of new applications. Herein, we have used a theoretical DFT and TD-DFT approach to (i) determine the identity of the dioxetanone species responsible for efficient chemiexcitation and (ii) identify the bioluminescent emitter and determine if light-emission occurs from the fluorescent or chemiluminescent state. Our results demonstrate that upon oxygenation of the imidazopyrazinone scaffold, a dioxetanone with a neutral amide group and a cationic guanidinopropyl group is formed. This species is efficiently chemiexcited (with no obvious charge transfer step) to the corresponding oxyluciferin with a neutral amide and cationic guanidinopropyl groups. After the "dark" chemiluminescent state, this oxyluciferin species is converted into a bright blue-emitting fluorescent state.

Abstract <jats:p>Dissolved carbon dioxide (dCO2) evaluation is very important in many different fields. In this work, a new, integrated, colorimetric-optical fiber-based system for dCO2 monitoring in aquaculture industry was developed. The sensing chemistry is based on colorimetric changes of the used indicator—poly p-nitrophenol (pNPh)—in contact with CO2. Preliminary tests were done in a laboratory environment (calibration) and in a laboratory Recirculating Aquaculture System (RAS) with controlled CO2 injection. The results have shown the suitability of the new sensor for assessing dCO2 dynamics in RAS and its fast detection of low dCO2 concentrations in an appropriate operation range.</jats:p>

Abstract A sensing configuration for the real-time monitoring, detection, and quantification of dissolved carbon dioxide (dCO(2)) was developed for aquaculture and other applications in freshwater and saline water. A chemical sensing membrane, based on a colorimetric indicator, is combined with multimode optical fiber and a dual wavelength light-emitting diode (LED) to measure the dCO(2)-induced absorbance changes in a self-referenced ratiometric scheme. The detection and processing were achieved with an embeded solution having a mini spectrometer and microcontroller. For optrode calibration, chemical standard solutions using sodium carbonate in acid media were used. Preliminary results in a laboratory environment showed sensitivity for small added amounts of CO2 (0.25 mg.L-1). Accuracy and response time were not affected by the type of solution, while precision was affected by salinity. Calibration in freshwater showed a limit of detection (LOD) and a limit of quantification (LOQ) of 1.23 and 1.87 mg.L-1, respectively. Results in saline water (2.5%) showed a LOD and LOQ of 1.05 and 1.16 mg.L-1, respectively. Generally, performance was improved when moving from fresh to saline water. Studies on the dynamics of dissolved CO2 in a recirculating shallow raceway system (SRS+RAS) prototype showed higher precision than the tested commercial sensor. The new sensor is a compact and robust device, and unlike other sensors used in aquaculture, stirring is not required for correct and fast detection. Tests performed showed that this new sensor has a fast accurate detection as well as a strong potential for assessing dCO(2) dynamics in aquaculture applications.

Abstract The co-precipitation synthesis assisted YF3: Er3+/Yb3+ upconversion nanoparticles were examined as a function of pump power which showed a tuneable emission efficiency through 976 nm diode laser excitation. Different emission bands in the visible range corresponding to the F-4(7/2) -> I-4(15/2) (490 nm), H-2(11/2) -> I-4(15/2) (522 nm), S-4(3/ 2) -> I-4(15/2) (548 nm) and F-4(9/2) -> I-4(15/2) (659 nm) transitions were observed. The sample crystal structure, particle morphology and optical properties were characterized. The applications of the present sample in latent fingermarks detection and security ink demonstration were successfully examined through the optimized annealing temperature and pump power of excitation. This demonstration claimed the highly utilization of the YF3:Er3+/Yb3+ upconversion nanoparticles for possible crime scene and anti-counterfeiting practitioners.

Abstract Despite decades of research, it is still not clear what is the mechanism behind the efficient chemiexcitation of dioxetanones in chemiluminescent and bioluminescent reactions. In fact, long-standing theories (charge transfer-initiated luminescence and chemically induced electron-exchange luminescence) have been demonstrated to not be able to explain this phenomenon. Herein, a theoretical approach using reliable and up-to-date methodology was used to address this problem, by focusing on model dioxetanones. Time-dependent (TD)-Density functional theory (DFT) and multireference complete-active-space second-order perturbation theory (CASPT2) calculations provided evidence that points to efficient intramolecular chemiexcitation being the result of the reacting molecules having access to a long zone of the Potential energy surface (PES), within the biradicalar region, where S-0 and S-1 are degenerate. Molecules with inefficient chemiexcitation are unable to reach this zone of degeneracy. Our main finding is that access to the region of degeneracy appears to be given due to increased interaction between the keto and CO2 moieties, as supported by the use of the activation strain model and Born-Oppenheimer molecular dynamics, which extends the biradical region by delaying the rupture of the peroxide ring. Increased interaction derives from attractive electrostatic interactions between the moieties of dioxetanone. Thus, we hypothesize that efficient chemiexcitation results not only from electron/charge transfer and subsequent charge annihilation but is instead based on the degree of interaction between the keto and CO2 moieties, which controls the access to a region of degeneracy between the ground and excited states.

Abstract Herein we present a new synthesis methodology for the transprotection of the 1-phenylethyl protected tertiary amines to tert-butyloxycarbonyl (Boc) derivatives under exocyclic N-C hydrogenolysis catalyzed by Pd/C. We provide mechanistic insights into the N-dealkylation of hindered tertiary amines under the unrecognized role of tert-butyloxycarbonyl anhydride (Boc(2)O) as an additive to effectively promote the exocyclic N-C hydrogenolysis of tertiary amines by disclosing the role of Boc(2)O, which was not fully understood and studied until now. NMR and in silico experiments suggest the formation of a transient charged carbamate as the plausible intermediate. This selective transprotection enabled the development of a robust stereoselective methodology for the preparation of both enantiomers of 2-azanorbornane-3-exo-carboxylates by highly asymmetric aza-Diels-Alder reactions using (-)-8-phenylmenthol (8PM) and (+)-8-phenylneomenthol (8PnM) as chiral auxiliaries.

Abstract Novel C-60 and C70N-methyl-fulleropyrrolidine derivatives, containing both electron withdrawing and electron donating substituent groups, were synthesized by the well-known Prato reaction. The corresponding highest occupied molecular orbital (HOMO)/lowest unoccupied molecular orbital (LUMO) energy levels were determined by cyclic voltammetry, from the onset oxidation and reduction potentials, respectively. Some of the novel fullerenes have higher LUMO levels than the standards PC61BM and PC71BM. When tested in PffBT4T-2OD based polymer solar cells, with the standard architecture ITO/PEDOT:PSS/Active-Layer/Ca/Al, these fullerenes do not bring about any efficiency improvements compared to the standard PC71BM system, however they show how the electronic nature of the different substituents strongly affects the efficiency of the corresponding organic photovoltaic (OPV) devices. The functionalization of C-70 yields a mixture of regioisomers and density functional theory (DFT) calculations show that these have systematically different electronic properties. This electronic inhomogeneity is likely responsible for the lower performance observed in devices containing C-70 derivatives. These results help to understand how new fullerene acceptors can affect the performance of OPV devices.

Abstract This paper is concerned with experimental and computational thermochemical studies of epsilon-caprolactam and epsilon-caprothiolactam, molecules whose flexible ring structure provides several conformational forms. The gas-phase standard enthalpy of formation at the reference temperature of 298.15 K of the two title compounds have been determined from the enthalpy of formation in the crystalline phase, derived from bomb combustion calorimetry, and from the enthalpy of sublimation, derived from Calvet microcalorimetry and Knudsen effusion techniques. The equilibrium geometries and the thermodynamic properties of three minimum energy conformers obtained with the composite G3(MP2)//B3LYP approach were used to determine the conformational composition of the two lactam derivatives, by means of Boltzmann's distribution. The computed gas-phase standard molar enthalpies of formation of epsilon-caprolactam and epsilon-caprothiolactam have been determined using hypothetical gas-phase reactions, taking into account the conformational compositions of each one of the species. This parameter together with the corresponding experimental one are compared. (C) 2019 Elsevier Ltd.

Abstract <jats:title>Abstract</jats:title><jats:p>Consensus scoring has become a commonly used strategy within structure-based virtual screening (VS) workflows with improved performance compared to those based in a single scoring function. However, no research has been devoted to analyze the worth of docking scoring functions components in consensus scoring. We implemented and tested a method that incorporates docking scoring functions components into the setting of high performance VS workflows. This method uses genetic algorithms for finding the combination of scoring components that maximizes the VS enrichment for any target. Our methodology was validated using a dataset that contains ligands and decoys for 102 targets that has been widely used in VS validation studies. Results show that our approach outperforms other methods for all targets. It also boosts the initial enrichment performance of the traditional use of whole scoring functions in consensus scoring by an average of 45%. CompScore is freely available at: <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://bioquimio.udla.edu.ec/compscore/">http://bioquimio.udla.edu.ec/compscore/</jats:ext-link></jats:p>