In-vial pyrolysis (PyroVial) with pre- and post-sample treatment combined with different chromatographic techniques

A new generic pyrolysis unit (PyroVial) is presented. Pyrolysis is carried out in a 2 mL autosampler vial placed in a XYZ robot for automated pyrolysis as well as for pre- and post-pyrolysis treatment of the sample. Analysis of the volatiles is performed by headspace analysis while the semi- and non-volatiles are extracted from the pyrolysate with an organic solvent. The features of the PyroVial are such that all chromatographic techniques can be applied. The pyrolysis unit is discussed in terms of its technical features and its performance is illustrated with applications including conventional pyrolysis, in situ and post-pyrolysis derivatization, reaction pyrolysis and catalytic cracking.     

Rational design of a Tn antigen mimic

A novel Tn antigen mimic, in which the natural underlying amino acid has been replaced by the non-natural α-methylserine analogue, is reported. This derivative exhibits a similar affinity for a natural lectin as for the natural Tn and retains the bioactive conformation observed in the Tn-containing glycopeptides with anti-MUC1 antibodies.     

A simple but effective dual redox and fluorescent ion pair receptor based on a ferrocene-imidazopyrene dyad

The ferrocene-imidazopyrene dyad, bearing the imidazole ring as the only receptor site, acts as a redox and optical molecular sensor for ion pairs, exhibiting an easily detectable signal change in the redox potential of the ferrocene/ferrocinium redox couple and in the emission spectrum. Perturbation of the emission spectrum follows the order Pb(2+) > Hg(2+) > Zn(2+) for cations and H(2)PO(4)(-) > AcO(-) for anions.     

Toward the optimization of continuous-flow aldol and α-amination reactions by means of proline-functionalized silicon packed-bed microreactors

The activity and stability under flow conditions of covalently and non-covalently silica supported proline and proline-like organocatalysts is herein described. The slow aldol reaction of cyclohexanone with p-nitro benzaldehyde and the fast α-amination of isovaleraldehyde with dibenzyl azodicarboxylate have been selected as model reactions for this study. Prospects and limitations of the disclosed continuous-flow organocatalytic approach are widely discussed.     

Neural network pairwise interaction fields for protein model quality assessment and ab initio protein folding

In order to use a predicted protein structure one needs to know how good it is, as the utility of a model depends on its quality. To this aim, many Model Quality Assessment Programs (MQAP) have been developed over the last decade, with MQAP also being assessed at the CASP competition. We present a new knowledge-based MQAP which evaluates single protein structure models. We use a tree representation of the Cα trace to train a novel Neural Network Pairwise Interaction Field (NN-PIF) to predict the global quality of a model. NN-PIF allows fast evaluation of multiple structure models for a single sequence. In our tests on a large set of structures, our networks outperform most other methods based on different and more complex protein structure representations in global model quality prediction. Moreover, given NN-PIF can evaluate protein conformations very fast, we train a separate version of the model to gauge its ability to fold protein structures ab initio. We show that the resulting system, which relies only on basic information about the sequence and the Cα trace of a conformation, generally improves the quality of the structures it is presented with and may yield promising predictions in the absence of structural templates, although more research is required to harness the full potential of the model.     

Thiazole orange (TO) as a light-switch probe: a combined quantum-mechanical and spectroscopic study

A Density Functional Theory (DFT) study of the absorbance and fluorescence emission characteristics of the cyanine thiazole orange (TO) in solution and when intercalated in DNA was carried out in combination with spectrophotometric and spectrofluorometric experiments under different conditions (temperature, concentration, solvent viscosity). T-jump relaxation kinetics of the TO monomer-dimer conversion enabled the thermodynamic parameters of this process to be evaluated. The overall data collected provided information on the features of the "light-switch" by the fluorescent TO and the comparison between experimental and calculated photo-physical properties allowed us to explain and rationalize both shifts and quenching/enhancing effects on fluorescence due to solvation, dimerisation and intercalation in the DNA.     

Temperature effect on the structure and formation kinetics of vinyltriethoxysilane-derived organic/silica hybrids

The structure and formation kinetics of organic/silica hybrid species prepared from acid hydrolysis of vinyltriethoxisilane has been studied in situ by small-angle X-ray scattering (SAXS) at 298, 318, and 333 K in a strongly basic step of the process. The evolution of the SAXS intensity is compatible with the formation of linear chains which grow, coil, and branch to form polymeric macromolecules in solution. The SAXS data were analyzed by the scattering from a persistent chain model for polymeric macromolecules in solution using a modified branching Sharp and Bloomfield global function, which incorporates a branching probability typical of randomly and nonrandomly branched polycondensates, and in a particular case, it is also valid for polydisperse coils of linear chains. Growth of linear chains and coiling dominate the process up to the formation of likely monodisperse Gaussian coils or polydisperse coils of linear chains. The link probability to form a branching point is increased with time to form nonrandomly branched polycondensates in solution. The kinetics of the process is accelerated with temperature, but all the curves formed by the time evolution of the structural parameters in all temperatures can correspondingly be matched on a unique curve by using an appropriate time scaling factor. The activation energy of the process was evaluated as ΔE = 21 ± 1 kJ/mol. The characteristics of the kinetics are in favor of a complex overall mechanism controlled by both condensation reactions and dynamical forces driven by interfacial energy up to the final structure development of the hybrids.     

Structural evidence of anomeric effects in the anesthetic isoflurane

The conformational and structural properties of the inhalational anesthetic isoflurane (1-chloro-2,2,2-trifluoroethyl difluoromethyl ether) have been probed in a supersonic jet expansion using Fourier-transform microwave (FT-MW) spectroscopy. Two conformers of the isolated molecule were identified from the rotational spectrum of the parent and several (37)Cl and (13)C isotopologues detected in natural abundance. The two most stable structures of isoflurane are characterized by an anti carbon skeleton (τ(C(1)-C(2)-O-C(3)) = 137.8(11)° or 167.4(19)°), differing in the trans (AT) or gauche (AG) orientation of the difluoromethyl group. The conformational abundances in the jet were estimated from relative intensity measurements as (AT)/(AG) ≈ 3:1. The structural preferences of the molecule have been rationalized with supporting ab initio calculations and natural-bond-orbital (NBO) analysis, which suggest that the molecule is stabilized by hyperconjugative effects. The NBO analysis of donor-acceptor (LP → σ*) interactions showed that these stereoelectronic effects decrease from the AT to AG conformations, so the conformational preferences can be accounted for in terms of the generalized anomeric effect.     

Efficient crystallization induced emissive materials based on a simple push-pull molecular structure

Solid state luminescent materials are the subject of ever growing interest both from a scientific and a technological point of view. Aggregation caused quenching (ACQ) processes however represent an obstacle to the development of most luminogens in the condensed phase. This is why particularly fascinating are those materials showing higher emission intensity in the solid state than in solution. Here we report on three 4-dialkylamino-2-benzylidene malonic acid dialkyl esters, very simple push-pull molecules, which are hardly emissive in solution and in the amorphous phase but become good emitters in the crystalline phase according to what has been indicated as crystallization induced emission (CIE). Thanks to combined emission and NMR spectroscopies at different temperatures on the prototype compound 4-dimethylamino-2-benzylidene malonic acid dimethyl ester in solution, we give full evidence that a restricted intramolecular rotation (RIR) phenomenon, in particular the hindered rotation around the aryl main axis of the compound, is at the origin of this behaviour. In addition, solid state photophysical and X-ray diffraction structural characterization allow us to identify J-dimeric interactions as responsible for the particularly intense emission of two of the three compounds. Moreover, by exploiting the compounds' acidochromic properties, applications in sensors and optoelectronics are envisaged.