Atmospheric hydrocarbon activation by the hydroxyl radical: a simple yet accurate computational protocol for calculating rate coefficients

The overall rate coefficient at standard temperature and pressure for the hydrogen abstraction reaction by the hydroxyl radical (HO˙) from common saturated volatile organic compounds (VOCs) is derived theoretically using electronic structure calculations and transition state theory (TST). The computational approach used is based on relatively efficient methods, and hence is applicable to a large number of compounds with only a modest use of computer resources. The key methods used are density functional theory (for the calculation of barrier heights) and simple transition state theory (TST), including a simple correction for tunnelling. All thermally relevant conformers of the reactant and the abstraction TS are included in the study. For all compounds in a test set of thirty-four, the calculated rate coefficient agrees with the experimental value to within better than an order of magnitude, and to within better than a factor of three for all but six cases, so that the accuracy is of predictive utility.     

Biosynthetically intriguing chlorinated lipophilic metabolites from geographically distant tropical marine cyanobacteria

Five new vinylchlorine-containing metabolites, the lipoamides janthielamide A and kimbeamides A-C and the ketide-extended pyranone kimbelactone A, have been isolated from collections of marine cyanobacteria made in Cura?ao and Papua New Guinea. Both janthielamide A and kimbeamide A exhibited moderate sodium channel blocking activity in murine Neuro-2a cells. Consistent with this activity, janthielamide A was also found to antagonize veratridine-induced sodium influx in murine cerebrocortical neurons. These lipoamides represent the newest additions to a relatively rare family of marine cyanobacterial-derived lipoamides and a new structural class of compounds exhibiting neuromodulatory activities from marine cyanobacteria.     

Managing, profiling and analyzing a library of 2.6 million compounds gathered from 32 chemical providers

Summary The data for 3.8 million compounds from structural databases of 32 providers were gathered and stored in a single chemical database. Duplicates are removed using the IUPAC International Chemical Identifier. After this, 2.6 million compounds remain. Each database and the final one were studied in term of uniqueness, diversity, frameworks, ‘drug-like’ and ‘lead–like’ properties. This study also shows that there are more than 87 000 frameworks in the database. It contains 2.1 million ‘drug-like’ molecules among which, more than one million are ‘lead-like’. This study has been carried out using ‘ScreeningAssistant’, a software dedicated to chemical databases management and screening sets generation. Compounds are stored in a MySQL database and all the operations on this database are carried out by Java code. The druglikeness and leadlikeness are estimated with ‘in–house’ scores using functions to estimate convenience to properties; unicity using the InChI code and diversity using molecular frameworks and fingerprints. The software has been conceived in order to facilitate the update of the database. ‘ScreeningAssistant’ is freely available under the GPL license.     

Efficient DNA Extraction and Amplification of Samples from the Archeological Site of Pompei (Italy)

Due to their growth and metabolism, microorganisms can cause severe damage to Cultural Heritage, through mechanical and chemical processes. In this paper we used molecular approaches to study bacterial communities on samples from the archeological site of Pompei (Italy). In particular four DNA extraction methods without prior cultivation of the microflora were compared. In terms of efficiency, the DNA extraction method based on the Tri-Reagent™ kit gave the best results. All extraction protocols coupled with 16S rDNA fragments PCR amplification were satisfactory; but the best results were obtained by Klentaq DNA LA Polymerase™; this enzyme can be considered an effective tool for amplification of DNA from Cultural Heritage and possibly other environmental samples.     

Polymeric nanoparticles based on polylactide and related copolymers

The preparation of nanoparticle suspensions was carried out by using commercial biodegradable polymers as poly(d,l-lactide), poly(d,l-lactide-co-glycolide) and poly(d,l-lactide-co-ϵ-caprolactone). The method of preparation was based on the controlled addition of polymer organic solution to an aqueous phase containing dispersing agents. Poly(ethylene glycol) (10, 20, and 35 kDa grade), Tween 20, and Pluronic F-127 were used as dispersing agents in the aqueous phase. Content and type of both polymeric matrix and dispersing agent resulted of paramount relevance for the attainment of monodispersed nanoparticles with average diameter of about 130 nm. The addition of a steric stabilizer allowed for nanoparticle purification and isolation while preventing their agglomeration. The best results were obtained by using 35 kDa grade poly(ethylene glycol) as dispersing agent and either mannitol or glycidylisopropylidenglyceryl-β-cyclo-dextrin as steric stabilizer. The adopted procedure afforded biodegradable nanoparticle suspensions that could be used for the incapsulation and intravenous administration of biologically active proteins and oligopeptides.