Amitriptyline (AMT) frequent presence in environmental waters reflects the continuous consumption growth and raises issues on the importance of its monitorization. In this work, a sensitive and selective electrochemiluminescence (ECL) sensor was constructed using molecularly imprinted polymer (MIP) recognition element for AMT detection. Molecular dynamics (MD) simulations were performed to select the best functional monomer. Precipitation polymerization was followed to prepare the MIP micro spheres using methacrylic acid (MAA) as functional monomer, ethylene glycol methacrylate (EGDMA) as crosslinker and chloroform (CHL) as solvent. The MIP sensor was then prepared on a low cost and disposable screen-printed electrodes (SPCEs), previously modified with single-walled carbon nanotubes (SWCNTs), by drop coating a solution containing the MIP microspheres synthesized. The mechanism of detection was based in the system Ru(bpy)(3)(2+)/AMT, where AMT acts as co-reactor of Ru(bpy)(3)(2+) ECL. Several parameters controlling the preparation process of the sensor and AMT detection were optimised. The MIP/SWCNTs/SPCE ECL sensor showed good analytical performance with a linear correlation between ECL signal and the AMT concentration ranging from 0.1 to 200 mu M (R-2 = 0.9991). The limits of detection (LOD) and quantification (LOQ) were found to be 0.4 mu M (S/N = 3) and 1.5 mu M (S/N = 10), respectively. The MIP ECL sensor displayed good selectivity to recognise AMT molecules when compared with analoge structures and it was successfully applied in real water samples with good recovery values (90 to 112%). The developed MIP ECL sensor is suitable for integration with portable devices for AMT detection in environmental waters.

In recent years, extensive sequencing and annotation of bacterial genomes has revealed an unexpectedly large number of secondary metabolite biosynthetic gene clusters whose products are yet to be discovered. For example, cyanobacterial genomes contain a variety of gene clusters that likely incorporate fatty acid derived moieties, but for most cases we lack the knowledge and tools to effectively predict or detect the encoded natural products. Here, we exploit the apparent absence of a functional beta-oxidation pathway in cyanobacteria to achieve efficient stable-isotope-labeling of their fatty acid derived lipidome. We show that supplementation of cyanobacterial cultures with deuterated fatty acids can be used to easily detect natural product signatures in individual strains. The utility of this strategy is demonstrated in two cultured cyanobacteria by uncovering analogues of the multidrug-resistance reverting hapalosin, and novel, cytotoxic, lactylate-nocuolin A hybrids-the nocuolactylates.

Herein, we present an integrated computational and experimental study to tackle the interactions between recognized beta-lactamantibiotics (cloxacillin and dicloxacillin) with the fibrinogen blood plasma protein. For this purpose, molecular docking simulation with elastic network based on collective low-frequency normal modes and perturbation response scanning maps were proposed to evaluate the conformational binding mechanism of fibrinogen under the unbound and bound states with the cited beta-lactam antibiotics. Aiming to theoretically explore the hidden biochemical mechanisms and structural attributes leading failures in therapy success with beta-lactamantibiotics. The computational results pointing that despite these conformational differences, both antibiotics exhibit very similar affinity-based free energies of binding as FEB (cloxacillin/E-region)=-8.7 kcal/mol and FEB (dicloxacillin/E-region) = -7.7 kcal/mol. We theoretically suggest that the semi-synthetic incorporation of an additional halogen CL-atom in the dicloxacillin, respect to cloxacillin molecule, and its relative docking-pose orientation in the fibrinogen E-region could significantly reduce the appearance of potential fibrinolytic off-target effects usually associated to parenterally administered beta-lactam antibiotics. Besides, the performed interactions diagrams revealed that the most relevant antibiotic binding interactions with the fibrinogen E-region (pocket 1) are mainly based on hydrophobic (C center dot center dot center dot C)-backbone-side-chain non-covalent interactions, acceptor/donor interactions with critical regulatory E-region residues SER50:Q > SER50:N associated to allosteric modulation based long-distance-based perturbations (dicloxacillin > > cloxacillin) in the E-region (Q-chain > N-chain) with remarkable conformational rigidification by decreasing the intrinsic collectivity, and leading different pattern of perturbations as allosteric signal propagation in the intrinsic conformational dynamics under bound state from both beta-lactam antibiotics. An experimental validation was carried out by using calorimetric (ITC and DSC) and spectroscopic (Raman and fluorescence) methods. These methods corroborated the computational results, adding quantitative information to explain the binding process. Finally, the obtained results open new perspectives for the "de novo rational drug-design" of new derivatives of beta-lactam antibiotics with high pharmacodynamic selectivity/specificity to avoid side-effects toward to achieve optimal benefit/risk rates beyond the antibiotic drug resistance phenomena, favoring the implementation of rigorous criteria for a more personalized antibiotic therapy.

At the core of the development of more efficient and reliable fuel cells (FCs), there are several essential chemical reactions, namely carbon monoxide (CO) oxidation. This reaction is a keystone in the cleaning of hydrogen fuel used in fuel cells due to strong poisoning by this species of the platinum catalyst used in these devices. The present work aims to provide insight regarding the activation of CO oxidation by gold or silver microfacets possessing low coordinated atoms. To achieve this, density functional theory (DFT) quantum calculations, which determined two competing reaction pathways for CO oxidation, i.e., by molecularly adsorbed oxygen, and by dissociated oxygen, are combined with first-principles kinetic Monte Carlo (1p-kMC) simulations, which employed the resulting DFT parameters in order to address the effect of temperature and partial pressures and the interplay of the elementary reaction events. The use of 1p-kMC is a step further from available works regarding the CO oxidation on gold- and silver-based catalysts for cleansing of hydrogen that is used as a fuel in FCs. Indeed, this research contributes to the conclusion that CO oxidation should preferentially occur on silver microfacets, while the obtained turnover frequencies (TOFs) reinforced such a conclusion.

In recent years, fluid transport through stacked graphene membranes has gained considerable attention due to its potential applications in water purification and desalination. Here, we are resorting to molecular dynamics (MD) simulations to elucidate the metal ion separation efficiency and mechanism of ion transport in stacked graphene membranes of varying interlayer spacing (d). Our simulation results show that metal ions, including Cd2+, Cu2+, Hg2+, and Pb2+, can permeate through wide membranes (d = 1.0 nm), but metal ion rejection is close to complete for the narrower nanochannels, irrespectively of the metal ion type. The increase of the interlayer spacing positively influences the permeance of the metal ions and water. The impact of the first hydration shell of the metal ions on ion rejection from membranes is significantly high, whereas the impact of the second hydration shell is considerably low. Even if the second hydration radius of the metal ions is greater than the half-width of the channel, the ions can pass through the membranes because of the loosely bonded water molecules in that hydration shell. Moreover, free energy analysis using steered molecular dynamics (SMD) simulation techniques show that free energy profiles of a metal atom in wider channels are almost the same, and free energy for the metal atom within the membrane channels is always higher compared to that for water. The free energy of the metal atom within the narrower channel is noticeably high, and that is the reason for complete ion rejection. To sum up, our results suggest that stacked graphene membranes with an interlayer spacing of 0.8 nm are the best for complete metal ion rejection and considerable permeation of water.

Biofilms are aggregates of microorganisms anchored to a surface and embedded in a self-produced matrix of extracellular polymeric substances and have been associated with 80% of all bacterial infections in humans. Because bacteria in biofilms are less amenable to antibiotic treatment, biofilms have been associated with developing antibiotic resistance, a problem that urges developing new therapeutic options and approaches. Interfering with quorum-sensing (QS), an important process of cell-to-cell communication by bacteria in biofilms is a promising strategy to inhibit biofilm formation and development. Here we describe and apply an in silico computational protocol for identifying novel potential inhibitors of quorum-sensing, using CviR-the quorum-sensing receptor from Chromobacterium violaceum-as a model target. This in silico approach combines protein-ligand docking (with 7 different docking programs/scoring functions), receptor-based virtual screening, molecular dynamic simulations, and free energy calculations. Particular emphasis was dedicated to optimizing the discrimination ability between active/inactive molecules in virtual screening tests using a target-specific training set. Overall, the optimized protocol was used to evaluate 66,461 molecules, including those on the ZINC/FDA-Approved database and to the Mu.Ta.Lig Virtual Chemotheca. Multiple promising compounds were identified, yielding good prospects for future experimental validation and for drug repurposing towards QS inhibition.

In this study, we evaluated the performance of Al/Zn/Cu trimetallic catalysts for the water gas shift (WGS) reaction by Density Functional Theory (DFT) calculations. A previous DFT-based study comparing the activity of a large series of trimetallic surfaces towards the catalysis of water dissociation showed that the (AlZn)(s)@Cu(111) surface is likely the most active catalysts for the WGS reaction. Note that, the water dissociation is the rate-determining step of the WGS reaction on copper surfaces. Therefore, in this work we carried out a systematic study of all possible WGS reaction steps on such catalyst model surface. The most plausible WGS reaction mechanism on the trimetallic surface was inferred by comparing the activation energies, reaction energies and rate constants computed for its different reaction steps. The latter demonstrated that the WGS evolves on this trimetallic surface following an associative mechanism through the carboxyl intermediary, which is dehydrogenated on the surface, assisted by a hydroxyl, to produce CO2. The other WGS reaction product, this is H-2, is obtained by the combination of hydrogen atoms from the water dissociation. The activation energy barriers obtained for the WGS reaction steps on that trimetallic surface are always lower than the adsorption energy of the correspondent reactants, indicating that desorption cannot compete with the catalytic process and also, that the trimetallic Al/Zn/Cu surface should be very reactive for the WGS reaction catalysis. Overall the results of this study allowed us to suggest that the active phase of commonly employed commercial catalyst based on Cu/ZnO/Al2O3 might embody a trimetallic alloy of Al/Zn/Cu.

The complex nature of electrode charge screening is well-known for ionic liquids (ILs). Due to strong ionion correlations, these electrolytes form a distinctive layered structure at interfaces. Variations in electrode potential cause structural changes that are reflected in a peculiar shape of differential capacitance-potential dependence with characteristic peaks. Although the differential capacitance for various ILs in conjunction with metal electrodes accessed via molecular dynamics (MD) simulations has been reported in the literature, retrieving a capacitance-potential curve, C(U), from the MD trajectories is not a trivial task. In this work, we present the results of the MD simulations of the IL 1-butyl-3-methylimidazolium hexafluorophosphate at a single-crystalline Au (100) surface. The discussion focuses on the simulation data treatment for C(U) curve fitting. It is shown that the resulting C strongly depends on the fitting method used. Four capacitance peaks and three structural reorganization types were identified in the studied system. With the help of a semi-quantitative approach in the framework of the original bilayer model of electric double layer (EDL), it is argued that the ions' reorientation is in the origin of the capacitance peaks. Also, it is shown that under the conditions of this study, the multilayer structure, characteristic of EDL in ILs on the whole, is far from the "lattice saturation" regime. The multilayer structure possesses a steric packing effect that impedes structural changes, decreasing the capacitance.