Periodic density functional theory (DFT) based calculations were used to explore the relationship between the activation energy corresponding to RO-H bond cleavage of organic compounds on catalytically active transition metal surfaces and other simpler quantities which can be used as descriptors. Taking data for methanol on various surfaces, several Brensted-Evans-Polanyi (BEP)-like relationships linking the activation energy barrier to the reaction energy, the adsorption energy of the reaction products or to the adsorption energy of an oxygen atom were explored. The general validity of these relationships has been explored by considering cases not included in the database used to extract the BEP relationships. For the more promising BEP relationship, the database for methanol was combined with results corresponding to O-H bond breaking of ethanol, formic acid and water on a sufficiently broad number of transition metal surfaces. This extended database provided a more general and statistically meaningful general BEP type relationship connecting the activation energy for the O-H bond breakage of general RO-H compounds on catalytic transition metal systems to the adsorption energy of the reaction products. Finally, a protocol is presented that allows one to determine good candidates for bond breakage of general RO-H compounds on metallic and bimetallic surfaces limiting the explicit calculation of the activation energy barriers to a few, previously detected, interesting cases only.

The structures of self-assembled monolayers (SAMs) of short (methyl) and long (hexyl) chain alkyl thiols on the clean gold(111) surface were modeled using for the Au-S interactions either the reactive ReaxFF potential or the well-known nonreactive Morse potential, while for the Au-Au interactions either the ReaxFF potential or an embedded-atom method (EAM). Analysis of the molecular dynamics (MD) trajectories of possible SAM structures suggests that disordering of interfacial Au atoms is definitely driven by the gold-sulphur interactions. Our MD results reveal a novel structure where two methanethiol molecules are bound to a gold adatom that has been lifted from the surface at 300 K, and the same kind of RS-Au-SR motif was also observed for hexanethiol at 600 K but not at 300 K. What is more, the above motif is only observed for the reactive ReaxFF potential. Moreover, these results are in clear agreement with recent experiments and more costly first principles-based MD simulations. These findings strongly support the use of reactive potentials such as ReaxFF for gathering an accurate description of Au-S interactions in inexpensive classical MD simulations.

The structures of self-assembled monolayers (SAMs) of short (methyl) and long (hexyl) chain alkyl thiols on the clean gold (111) surface were modelled using for the Au-S interactions either the reactive ReaxFF potential or the well known non-reactive Morse potential, while for the Au-Au interactions either the ReaxFF potential or an embedded-atom method (EAM). Analysis of the MD trajectories of possible SAM structures suggests that disordering of interfacial Au atoms is definitely driven by the gold-sulphur interactions. Our MD results reveal a novel structure where two methanethiol molecules are bound to a gold adatom that has been lifted from the surface at 300 K, and the same kind of RS-Au-SR motif was also observed for hexanethiol at 600 K but not at 300 K. What is more, the above motif is only observed for the reactive ReaxFF potential. Moreover, these results are in clear agreement with recent experiments and more costly first principles-based MD simulations. These findings strongly support the use of reactive potentials such as ReaxFF for gathering an accurate description of Au-S interactions in inexpensive classical MD simulations.

The ischemic stroke cascade is composed of several pathophysiological events, providing multiple targets for pharmacological intervention. JM-20 (3-ethoxycarbonyl-2-methyl-4-(2-nitrophenyl)-4,11-dihydro-1H-pyrido[2,3-b][1,5] benzodiazepine) is a novel hybrid molecule, in which a benzodiazepine portion is covalently linked to a dihydropyridine ring, forming a new chemical entity with potential multisite neuroprotective activity. In the present study, JM-20 prevented PC-12 cell death induced either by glutamate, hydrogen peroxide or KCN-mediated chemical hypoxia. This molecule also protected cerebellar granule neurons from glutamate or glutamate plus pentylenetetrazole-induced damage at very low micromolar concentrations. In rat liver mitochondria, JM-20, at low micromolar concentrations, prevented the Ca2+-induced mitochondrial permeability transition, as assessed by mitochondrial swelling, membrane potential dissipation and organelle release of the pro-apoptotic protein cytochrome c. JM-20 also inhibited the mitochondrial hydrolytic activity of F1F0-ATP synthase and Ca2+ influx. Therefore, JM-20 may be a multi-target neuroprotective agent, promoting reductions in neuronal excitotoxic injury and the protection of the mitochondria from Ca 2+-induced impairment as well as the preservation of cellular energy balance. © 2014 Elsevier B.V.

Massive Open Online Courses (MOOC) are gaining prominence in transversal teaching-learning strategies. However, there are many issues still debated, namely assessment, recognized largely as a cornerstone in Education. The large number of students involved requires a redefinition of strategies that often use approaches based on tasks or challenging projects. In these conditions and due to this approach, assessment is made through peer-reviewed assignments and quizzes online. The peer-reviewed assignments are often based upon sample answers or topics, which guide the student in the task of evaluating peers. This chapter analyzes the grading and evaluation in MOOCs, especially in science and engineering courses, within the context of education and grading methodologies and discusses possible perspectives to pursue grading quality in massive e-learning courses. © 2015, IGI Global.

The study of quantitative structure-property relationships (QSPR) is important to study complex networks of chemical reactions in drug synthesis or metabolism or drug-target interaction networks. A difficult but possible goal is the prediction of drug absorption, distribution, metabolism, and excretion (ADME) process with a single QSPR model. For this QSPR modelers need to use flexible structural parameters useful for the description of many different systems at different structural scales (multi-scale parameters). Also they need to use powerful analytical methods able to link in a single multi-scale hypothesis structural parameters of different target systems (multi-target modeling) with different experimental properties of these systems (multi-output models). In this sense, the QSPR study of complex bio-molecular systems may benefit substantially from the combined application of spectral moments of graph representations of complex systems with perturbation theory methods. On one hand, spectral moments are almost universal parameters that can be calculated to many different matrices used to represent the structure of the states of different systems. On the other hand, perturbation methods can be used to add "small" variation terms to parameters of a known state of a given system in order to approach to a solution of another state of the same or similar system with unknown properties. Here we present one state-of-art review about the different applications of spectral moments to describe complex bio-molecular systems. Next, we give some general ideas and formulate plausible linear models for a general-purpose perturbation theory of QSPR problems of complex systems. Last, we develop three new QSPR-Perturbation theory models based on spectral moments for three different problems with multiple in-out boundary conditions that are relevant to biomolecular sciences. The three models developed correctly classify more than pairs 115,600; 48,000; 134,900 cases of the effects of in-out perturbations in intra-molecular carbolithiations, drug ADME process, or self-aggregation of micelle nanoparticles of drugs or surfactants. The Accuracy (Ac), Sensitivity (Sn), and Specificity (Sp) of these models were >90% in all cases. The first model predicts variations in the yield or enantiomeric excess due to structural variations or changes in the solvent, temperature, temperature of addition, or time of reaction. The second model predicts changes in >18 parameters of biological effects for >3000 assays of ADME properties and/or interactions between 31,723 drugs and 100 targets (metabolizing enzymes, drug transporters, or organisms). The third model predicts perturbations due to changes in temperature, solvent, salt concentration, and/or structure of anions or cations in the self-aggregation of micelle nanoparticles of drugs and surfactants.

The main objective of this study was to simulate for the first time a complex sol-gel system aimed at preparing the (S)-naproxen-imprinted xerogel with an explicit representation of all the ionic species at pH 9. For this purpose, a series of molecular dynamics (MD) simulations of different mixtures, including species never studied before using the OPLS-AA force field, were prepared. A new parametrization for these species was developed and found to be acceptable. Three different systems were simulated, representing two types of pregelification models: the first one represented the initial mixture after complete hydrolysis and condensation to cyclic trimers (model A); the second one corresponded to the same mixture after the evaporation process (model B); and the last one was a simpler initial mixture without an explicit representation of all of the imprinting-mixture constituents (model C). The comparison of systems A and C mainly served the purpose of evaluating whether an explicit representation of all of the components (model A) was needed or if a less computationally demanding system in which the alkaline forms of the silicate species were ignored (model C) would be sufficient. The results confirmed our hypothesis that an explicit representation of all of the imprinting-mixture constituents is essential to study the molecular imprinting process because a poor representation of the ionic species present in the mixture may lead to erroneous conclusions or lost information. In general, the radial distribution function (RDF) analysis and interaction energies demonstrated a high affinity of the template molecule, 2-(6-methoxynaphthalen-2-yl)propanoate (NAP(-), the conjugate base of (S)-naproxen), for the gel backbone, especially targeting the units containing the dihydroimidazolium moiety used as a functional group. Model B, representing a nearly gelled sol where the density of silicates and solvent polarity were much higher relative to the other models, allowed for much faster simulations. That gave us the chance to observe the templating effect through a comparative analysis and observation of the trajectories from simulations with the template- versus non-template-containing mixtures. Overall, a strong coherence between the imprinting-relevant interactions, aggregation, or the silicate network texturing effects taken out of the simulations and the experimentally high imprinting performance and porosity features of the corresponding gels was achieved.