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.     

Organocatalyzed Domino [3+2] Cycloaddition/Payne‐Type Rearrangement using Carbon Dioxide and Epoxy Alcohols

An unprecedented organocatalytic approach towards highly substituted cyclic carbonates from tri‐ and tetrasubstituted oxiranes and carbon dioxide has been developed. The protocol involves the use of a simple and cheap superbase under mild, additive‐ and metal‐free conditions towards the initial formation of a less substituted carbonate product that equilibrates to a tri‐ or even tetrasubstituted cyclic carbonate under thermodynamic control. The latter are conveniently trapped in situ, providing overall a new domino process for synthetically elusive heterocyclic scaffolds. Control experiments provide a rationale for the observed cascade reactions, which demonstrate similarity to the well‐known Payne rearrangement of epoxy alcohols.     

A study on the essential oil of Ferulago campestris: How much does extraction method influence the oil composition?

The essential oil of different parts of Ferulago campestris (Bess.) collected in Sicily has been extracted by microwave-assisted hydrodistillation (MAHD) and by classic hydrodistillation (HD). A comparative qualitative-quantitative study on the composition of the oils was carried out. A total of 100 compounds were identified in the oils obtained by MAHD, whereas 88 compounds characterized the HD oils. The most prominent components were, in all different parts of F. campestris and in both extraction methods, 2,4,5-trimethylbenzaldehyde and 2,4,6-trimethylbenzaldehyde isomers; the latter was not previously found. The attempt to evaluate where the oil components are located in all parts of the plant was carried out by means of a kinetic study. Then, electron microscopy observation on the different parts before and after MAHD and HD was performed.     

Trimethoxysilylpolymethacrylate as new material for stone conservation. Porosimetric and colorimetric investigations

Aimed to obtain new materials for the conservation of stone substrates, we report here on the synthesis of a polymer which has been obtained by inducing polymerization on a methacrylate monomer functionalized by alchoxysilane groups. Two lithotypes, the Comiso calcarenite and Mistretta quartzite, stones largely used in artworks of north-eastern Sicily, were treated with the above polymer and its conserving efficacy evaluated in terms of porosimetric features, hydric properties and appearance. The collected data were compared to those provided, under the same experimental conditions, by an ethylmethacrylate/methylmethacrylate copolymer and an alkylalchoxysilane, products widely employed in the protection of stones. Experiments aimed to test the durability of the above polymer against UV artificial ageing are also reported.     

Field-amplified sample stacking and nonaqueous capillary electrophoresis determination of complex mixtures of polar aromatic sulfonates

Nonaqueous CE and field-amplified sample stacking have been used in the determination of complex mixtures of polar aromatic sulfonates (AS; mainly benzene- and naphthalenesulfonates) of environmental concern. The analytical procedure consists of an on-column aqueous sample enrichment, followed by the nonaqueous electrophoretic determination of stacked aromatic sulfonates. Various organic solvents were used as separation medium, acetonitrile and N-methylformamide gave the best results. Optimum capillary electrophoresis separation is obtained with ammonium acetate (25 mM) dissolved in N-methylformamide-methanol (90:10) as background electrolyte. This combined method was applied to the analysis of surface water samples spiked with selected aromatic sulfonates derivatives.     

Transition-metal nanoparticles in imidazolium ionic liquids: recyclable catalysts for biphasic hydrogenation reactions

1-n-Butyl-3-methylimidazolium hexafluorophosphate room-temperature ionic liquid is not only suitable as a medium for the preparation and stabilization of iridium nanoparticles but also ideal for the generation of recyclable biphasic catalytic systems for hydrogenation reactions. Thus, Ir(0) nanoparticles with a mean diameter of 2 nm have been prepared by reduction of Ir(I) dissolved in the ionic liquid with H2. This catalytic solution can be reused several times for the biphasic hydrogenation of olefins under mild reaction conditions.