Paramagnetic 19F chemical shift probes that respond selectively to calcium or citrate levels and signal ester hydrolysis

Paramagnetic magnetic resonance chemical shift probes containing a proximal CF(3) group have been characterised. Different systems have been created that report reversible changes in calcium ion concentrations in the millimolar regime, signal the presence of citrate selectively in competitive aqueous media and allow the monitoring of remote ester/amide hydrolysis in relayed, irreversible transformations. Chemical shift non-equivalence is amplified by the presence of the proximate lanthanide ion, with a mean separation between the CF(3) group and the metal ion of 6.4 ? found for a thulium complex, in an X-ray structure of the metal complex aqua adduct. The enhanced rate of longitudinal relaxation of the (19)F nucleus allows faster data acquisition.     

Monolithic columns with optimized pore structure for molecular size-based separations of synthetic polymers

Monolithic capillary columns based on divinylbenzene were synthesized using different alcanols as porogens. Prepared columns were tested in separation of polystyrene standards according to their molar mass (MM) and were characterized by corresponding calibration graphs. It was demonstrated that a decrease of alcanol chain length from dodecanol to octanol resulted in a decrease of column permeability and in an improved column ability to separate polystyrene standards. In contrast, removing a good solvent from porogen mixture results in an increase of column permeability and in a decrease of column performance toward polystyrene standards. Optimized synthetic conditions included porogen composed of nonanol and toluene or mesytilene, and the column prepared with this porogen was capable of separating a mixture of 14 polystyrene standards with MM ranged from several millions to oligomers.     

ToxAlerts: A Web Server of Structural Alerts for Toxic Chemicals and Compounds with Potential Adverse Reactions

The article presents a Web-based platform for collecting and storing toxicological structural alerts from literature and for virtual screening of chemical libraries to flag potentially toxic chemicals and compounds that can cause adverse side effects. An alert is uniquely identified by a SMARTS template, a toxicological endpoint, and a publication where the alert was described. Additionally, the system allows storing complementary information such as name, comments, and mechanism of action, as well as other data. Most importantly, the platform can be easily used for fast virtual screening of large chemical datasets, focused libraries, or newly designed compounds against the toxicological alerts, providing a detailed profile of the chemicals grouped by structural alerts and endpoints. Such a facility can be used for decision making regarding whether a compound should be tested experimentally, validated with available QSAR models, or eliminated from consideration altogether. The alert-based screening can also be helpful for an easier interpretation of more complex QSAR models. The system is publicly accessible and tightly integrated with the Online Chemical Modeling Environment (OCHEM, http://ochem.eu ). The system is open and expandable: any registered OCHEM user can introduce new alerts, browse, edit alerts introduced by other users, and virtually screen his/her data sets against all or selected alerts. The user sets being passed through the structural alerts can be used at OCHEM for other typical tasks: exporting in a wide variety of formats, development of QSAR models, additional filtering by other criteria, etc. The database already contains almost 600 structural alerts for such endpoints as mutagenicity, carcinogenicity, skin sensitization, compounds that undergo metabolic activation, and compounds that form reactive metabolites and, thus, can cause adverse reactions. The ToxAlerts platform is accessible on the Web at http://ochem.eu/alerts , and it is constantly growing.     

On the applicability of elastic network normal modes in small-molecule docking

Incorporating backbone flexibility into protein-ligand docking is still a challenging problem. In protein-protein docking, normal mode analysis (NMA) has become increasingly popular as it can be used to describe the collective motions of a biological system, but the question of whether NMA can also be useful in predicting the conformational changes observed upon small-molecule binding has only been addressed in a few case studies. Here, we describe a large-scale study on the applicability of NMA for protein-ligand docking using 433 apo/holo pairs of the Astex data sets. On the basis of sets of the first normal modes from the apo structure, we first generated for each paired holo structure a set of conformations that optimally reproduce its C(α) trace with respect to the underlying normal mode subspace. Using AutoDock, GOLD, and FlexX we then docked the original ligands into these conformations to assess how the docking performance depends on the number of modes used to reproduce the holo structure. The results of our study indicate that, even for such a best-case scenario, the use of normal mode analysis in small-molecule docking is restricted and that a general rule on how many modes to use does not seem to exist or at least is not easy to find.     

Further Insight into the Photostability of the Pyrene Fluorophore in Halogenated Solvents

Pyrene fluorophores of pyrene‐functionalized CdSe quantum dots (QD@Py), as well as alkylpyrene and pyrene itself (Py), undergo fast degradation in aerated chloroform under ultraviolet‐A (UV‐A, 316<λ<400 nm) illumination. Steady‐state fluorescence studies of irradiated chloroform solutions of QD@Py show formation of new bands, red‐shifted compared to that of the pyrene moiety. Similar behaviour is observed for pyrene and the alkylpyrene system. Column chromatography of the pyrene photolysate in chloroform allowed us to isolate photoproducts arising from pyrene degradation, and to obtain information on the structure of the photoproducts responsible for the emission bands. The most predominant photoproducts were those originating from the reaction of pyrene with dichloromethyl radicals. The phototransformation of QD@Py and the alkylpyrene involves mainly detachment of the alkyl chain from the aromatic ring, induced also by dichloromethyl radicals, and oxidation of the alkyl chain at the benzylic position was detected as well. By contrast, these pyrene systems show a high photostability in aerated dichloromethane. Transient absorption measurements showed formation of both pyrene triplet and pyrene radical cation for all pyrene systems in these halogenated solvents. The yield of pyrene radical cations for Py is higher than for QD@Py and the alkylpyrene. In addition, pyrene radical cations were longer‐lived in dichloromethane than in chloroform. The reason for the pyrene photostability in dichloromethane is the different reactivity of chloromethyl and dichloromethyl radicals towards pyrene and oxygen. These studies show that the use of dichloromethane can be a suitable alternative to chloroform when the good solubility properties of these halogenated solvents are needed to dissolve pyrene when this chromophore is used as a fluorescent probe.     

Voltammetric detection of metals and metal compounds on surfaces following a new sampling technique using alkali amalgam droplets

We propose a new method for the voltammetric detection of metals and metal compounds on surfaces of sold materials. The method is based on the reduction of oxidized metal compounds using an alkali amalgam droplet, the dissolution of the metals in the amalgam droplet, finally followed by recording the voltammetric anodic dissolution of the metal. The sample collection and all the following steps, including the voltammetric measurement, are performed at the same site of the sample and without any temporal interruption as one and the same electrode system is used for all steps. The proposed method is as an easy to handle, non-destructive express analysis for a wide range of samples.     

Mean-field cooperativity in chemical kinetics

We consider cooperative reactions and we study the effects of the interaction strength among the system components on the reaction rate, hence realizing a connection between microscopic and macroscopic observables. Our approach is based on statistical mechanics models and it is developed analytically via mean-field techniques. First of all, we show that, when the coupling strength is set positive, a cooperative behavior naturally emerges from the model; in particular, by means of various cooperative measures previously introduced, we highlight how the degree of cooperativity depends on the interaction strength among components. Furthermore, we introduce a criterion to discriminate between weak and strong cooperativity, based on a measure of “susceptibility.” We also properly extend the model in order to account for multiple attachments phenomena: this is realized by incorporating within the model p-body interactions, whose non-trivial cooperative capability is investigated too.     

A quantum chemical study on the free radical scavenging activity of tyrosol and hydroxytyrosol

The free radical scavenging activity of hydroxytyrosol (HTyr) and tyrosol (Tyr) has been studied in aqueous and lipid solutions, using the density functional theory. Four mechanisms of reaction have been considered: single electron transfer (SET), sequential electron proton transfer (SEPT), hydrogen transfer (HT), and radical adduct formation. It was found that while SET and SEPT do not contribute to the overall reactivity of HTyr and Tyr toward ^·OOH and ^·OCH₃ radicals, they can be important for their reactions with ^·OH, ^·OCCl₃, and ^·OOCCl₃. The ^·OOH-scavenging activity of HTyr and Tyr was found to take place exclusively by HT, and it is also predicted to be the main mechanism for their reactions with ^·OCH₃. HT is proposed as the main mechanism for the scavenging activity of HTyr and Tyr when reacting with other ^·OR and ^·OOR radicals, provided that R is an alkyl or an alkenyl group. The major products of reaction are predicted to be the phenoxyl radicals. In addition, Tyr was found to be less efficient than HTyr as free radical scavenger. Moreover, while HTyr is predicted to be a good peroxyl scavenger, Tyr is predicted to be only moderately for that purpose.