HTMoL: full-stack solution for remote access,visualization, and analysis of molecular dynamics trajectory data

Research on biology has seen significant advances with the use of molecular dynamics (MD) simulations. The MD methodology enables explanation and discovery of molecular mechanisms in a wide range of natural processes and biological systems. The need to readily share the ever-increasing amount of MD data has been hindered by the lack of specialized bioinformatic tools. The difficulty lies in the efficient management of the data, i.e., in sending and processing 3D information for its visualization. In this work, we present HTMoL, a plug-in-free, secure GPU-accelerated web application specifically designed to stream and visualize MD trajectory data on a web browser. Now, individual research labs can publish MD data on the Internet, or use HTMoL to profoundly improve scientific reports by including supplemental MD data in a journal publication. HTMoL can also be used as a visualization interface to access MD trajectories generated on a high-performance computer center directly. Furthermore, the HTMoL architecture can be leveraged with educational efforts to improve learning in the fields of biology, chemistry, and physics.     

Electrochemical C−H/N−H Activation by Water‐Tolerant Cobalt Catalysis at Room Temperature

Electrochemistry enabled C?H/N?H functionalizations at room temperature by external oxidant‐free cobalt catalysis. Thus, the sustainable cobalt electrocatalysis manifold proceeds with excellent levels of chemoselectivity and positional selectivity, and with ample scope, thus allowing electrochemical C?H activation under exceedingly mild reaction conditions at room temperature in water.     

On the influence of fatty acid chain unsaturation on supramolecular gelation of aminocarbohydrate-based supra-amphiphiles

Supramolecular gels are soft materials formed mainly by low molecular weight units held together by intermolecular interactions. Stabilizing these kinds of materials is quite a challenge due to the influence of multiple factors interfering with the integrity of the supramolecular structure. In our previous studies, we have shown that the aminocarbohydrate meglumine (MEG) interacts with organic acids by ion-pairing leading to the formation of MEG–carboxylate adducts. These adducts undergo supramolecular polymerization by heat treatment, but the macromolecular assembly was stable for a short period due to hydrogen bond (H-bond) breakup. Herein, we attempt to study the influence of hydrophobic building blocks on the formation of these compounds aiming to stabilize H-bonds to produce polymerizable supra-amphiphiles in water. Oleic acid and stearic acid are two analogous fatty acids differing only in the presence of unsaturation that were used in our studies. Results demonstrated that the presence of unsaturation hinders gelation in water by interfering with the self-assembly behavior of supra-amphiphiles. Thus, unsaturated supra-amphiphiles behave like traditional surfactants and gelify water at high concentrations (above 30% w/w). On the other hand, supramolecular gels with a polymer-like behavior could be produced with a saturated supra-amphiphile in water (above 4% w/w). The material was characterized by a lamellar arrangement that facilitates the alignment of H-bonds necessary to stabilize the self-assembled structure. These results have pivotal importance on the design of polymerizable supra-amphiphiles and demonstrate that the double bond of hydrophobic building blocks is an important design factor to be considered by scientists studying similar materials.     

Transport coefficients, Raman spectroscopy, and computer simulation of lithium salt solutions in an ionic liquid

Lithium salt solutions of Li(CF3SO2)2N, LiTFSI, in a room-temperature ionic liquid (RTIL), 1-butyl-2,3-dimethyl-imidazolium cation, BMMI, and the (CF3SO2)2N(-), bis(trifluoromethanesulfonyl)imide anion, [BMMI][TFSI], were prepared in different concentrations. Thermal properties, density, viscosity, ionic conductivity, and self-diffusion coefficients were determined at different temperatures for pure [BMMI][TFSI] and the lithium solutions. Raman spectroscopy measurements and computer simulations were also carried out in order to understand the microscopic origin of the observed changes in transport coefficients. Slopes of Walden plots for conductivity and fluidity, and the ratio between the actual conductivity and the Nernst-Einstein estimate for conductivity, decrease with increasing LiTFSI content. All of these studies indicated the formation of aggregates of different chemical nature, as it is corroborated by the Raman spectra. In addition, molecular dynamics (MD) simulations showed that the coordination of Li+ by oxygen atoms of TFSI anions changes with Li+ concentration producing a remarkable change of the RTIL structure with a concomitant reduction of diffusion coefficients of all species in the solutions.     

Photophysical characterization of a highly conjugated bipyridyl-based dye synthesized by a unique two-step approach

In this article, we present a new and simple, yet efficient, two-step approach to synthesize 4,4'-bis(dibutylaminostyrylstyryl)-2,2'-bipyridine with high yield, as well as its linear and nonlinear optical characterizations in THF and toluene solutions. We show that its one- and two-photon absorption spectra are similar in both solvents. Nevertheless, the relaxation processes of this compound exhibit dependence on the solvent polarity. The one- and two-photon induced fluorescence signal of this molecule in solution reveals that its excited state is highly stabilized in THF solution rather than in toluene. Analysis of the fluorescence quantum yield, lifetime, and radiative and nonradiative decay rates are in agreement with Lippert's model for solute-solvent interactions. The optical measurements demonstrate that this dye is a promising candidate for multiphoton fluorescence imaging, optical limiting, and dye lasers.     

Effect of temperature on the chromatographic retention of ionizable compounds. III. Modeling retention of pharmaceuticals as a function of eluent pH and column temperature in RPLC

We propose a general simple equation for accurately predicting the retention factors of ionizable compounds upon simultaneous changes in mobile phase pH and column temperature at a given hydroorganic solvent composition. Only four independent experiments provide the input data: retention factors measured in two pH buffered mobile phases at extreme acidic and basic pH values (e. g., at least +/- 2 pH units far from the analyte pK(a)) and at two column temperatures. The equations, derived from the basic thermodynamics of the acid-base equilibria, additionally require the knowledge of the solute pK(a )and enthalpies of acid-base dissociation of both the solute and the buffer components in the hydroorganic solvent mixture. The performance of the predictive model is corroborated with the comparison between theoretical and experimental retention factors of several weak acids and bases of important pharmacological activity, in mobile phases containing different buffer solutions prepared in 25% w/w ACN in water and at several temperatures.     

Tailoring orthogonal proteomic routines to understand protein separation during ion exchange chromatography

Surface charge, molecular weight, and folding state are known to influence protein chromatographic behaviour onto ion exchangers. Experimentally, information related to such factors can be gathered via 2-DE methods. The application of 2-D PAGE under denaturing/reducing conditions was already shown to reveal separation trends within a large protein population from cell extracts. However, ion-exchange chromatography normally runs under native conditions. A tailored protocol consisting in a first separation based on IEF on Immobiline strips under native conditions followed by a second dimension SDS-PAGE run was adopted. The chromatographic versus electrophoretic separation behaviours of two model proteins, thaumatin (TAU) and BSA, were compared to better understand which proteomic routine would be better suited to anticipate IEX chromatographic separations. It was observed that the information contained in the pI value obtained with the adapted 2-DE protocol showed better correlation with the IEX chromatographic behaviour. On the other hand, chromatographic separations performed in the presence of urea as a denaturant have demonstrated the potential influence of hydrodynamic radius/conformation on protein separation. Moreover, the information provided by such 2-D system correlated well with the chromatographic behaviour of an additional set of pure proteins. An initial prediction of protein ion-exchange chromatographic behaviour could be possible utilizing an experimental approach based on 2-DE running under milder chemical conditions. This technique provides information that more closely resembles the separation behaviour observed with a complex biotechnological feedstock.     

Symmetrization and norm of the Hardy-Littlewood maximal operator on Lorentz and Marcinkiewicz spaces

We prove that when a function on the real line is symmetricallyrearranged, the distribution function of its uncentered Hardy–Littlewoodmaximal function increases pointwise, while it remains unchangedonly when the function is already symmetric. Equivalently, if is the maximal operator and the symmetrization, then f(x)f(x)for every x, and equality holds for all x if and only if, upto translations, f(x) = f(x) almost everywhere. Using theseresults, we then compute the exact norms of the maximal operatoracting on Lorentz and Marcinkiewicz spaces, and we determineextremal functions that realize these norms.