An SFG/DFG investigation of CN− adsorption at an Au electrode in 1-butyl-1-methyl-pyrrolidinium bis(trifluoromethylsulfonyl) amide ionic liquid

In this paper we report an SFG/DFG investigation of the adsorption of CN^? – used as a probe molecule to study the electrochemical double-layer structure – at a polycrystalline Au electrode in 1-butyl-1-methyl-pyrrolidinium bis(trifluoromethylsulfonyl) amide ([BMP][TFSA]) room-temperature ionic liquid (RTIL). The adsorption of CN^? yielded single SFG and DFG bands in the range from ca. 2125 to 2135 cm^?1, exhibiting a Stark tuning of ca. 3 cm^?1 V^?1. Vibrational resonances – corresponding to modes of the RTIL coadsorbed with CN^?, were found in the range from ca. 1200 to 1500 cm^?1. The study of the double-layer structure was complemented by cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) measurements, from which the differential double-layer capacity (C_DL) was estimated.     

A catalytic asymmetric reaction involving enolizable anhydrides

In the presence of a highly efficient novel bifunctional organocatalyst at low loadings under mild conditions, enolizable homophthalic anhydrides can be added to a range of aromatic and aliphatic aldehydes to give dihydroisocoumarins, with excellent yields and diastereo- and enantiocontrol (up to 99% ee).     

Understanding the role of base stacking in nucleic acids. MD and QM analysis of tandem GA base pairs in RNA duplexes

Preceding NMR experiments show that the conformation of tandem GA base pairs, an important recurrent non-canonical building block in RNA duplexes, is context dependent. The GA base pairs adopt "sheared" N3(G)-N6(A), N2(G)-N7(A) geometry in the r(CGAG)(2) and r(iGGAiC)(2) contexts while switching to "imino" N1(G)-N1(A), O6(G)-N6(A) geometry in the r(GGAC)(2) and r(iCGAiG)(2) contexts (iC and iG stand for isocytosine and isoguanine, respectively). As base stacking is likely to be one of the key sources of the context dependence of the conformation of GA base pairs, we calculated base stacking energies in duplexes containing such base pairs, to see if this dependence can be predicted by stacking energy calculations. When investigating the context dependence of the GA geometry two different conformations of the same duplex were compared (imino vs. sheared). The geometries were generated via explicit solvent MD simulations of the respective RNA duplexes, while the subsequent QM energy calculations focused on base stacking interactions of the four internal base pairs. Geometrical relaxation of nucleobase atoms prior to the stacking energy computations has a non-negligible effect on the results. The stacking energies were derived at the DFT-D/6-311++G(3df,3pd) level. We show a rather good correspondence between the intrinsic gas-phase stacking energies and the NMR-determined GA geometries. The conformation with more favorable gas-phase stacking is in most cases the one observed in experiments. This correlation is not improved when including solvent effects via the COSMO method. On the other side, the stacking calculations do not predict the relative thermodynamic stability of duplex formation for different sequences.     

Synthesis, 5-hydroxytryptamine1A receptor affinity and docking studies of 3-[3-(4-aryl-1-piperazinyl)-propyl]-1H-indole derivatives

A series of 3-[3-(4-aryl-1-piperazinyl)-propyl]-1H-indole derivatives (12a-h) was synthesized and evaluated for binding affinity at the human 5-hydroxytryptamine(1A) receptor (5-HT(1A)R) compounds (12b) and (12h) showed the highest 5-HT(1A) receptor affinity (IC(50)=15 nM). Molecular docking studies with all the compounds in a homology model of 5-HT(1A) showed that the main interaction anchoring the ligand in the receptor was a charge-reinforced bond between the protonated nitrogen atom (N-4) of the piperazine ring and Aspartate(3.32).     

Novel peptide foldameric motifs: a step forward in our understanding of the fully-extended conformation/3(10)-helix coexistence

The fully-extended, multiple C(5), conformation or 2.0(5) helix is a very appealing peptide secondary structure, in particular for its potential use as a molecular spacer, as it is characterized by the longest elevation (as high as 3.62 ?) between the α-carbon atoms of two consecutive α-amino acids. Despite this intriguing property, however, it is only poorly investigated and understood. Here, using a complete series of C(α,α)-diethylglycine (Deg) homo-oligopeptide esters to the pentamer level, we exploited the properties of a fluorophore and a quencher, synthetically positioned at the N- and C-termini of the main chain, respectively, to check the applicability of the fully-extended conformation as a rigid molecular spacer. The fluorescence study was complemented by FT-IR absorption and NMR conformational investigations. The X-ray diffraction structures of selected compounds are also reported. Unfortunately, we find that, even in a solvent of low polarity, such as chloroform, in this peptide series an equilibrium does take place between the fragile fully-extended conformation and the 3(10)-helical structure, the latter becoming more and more stable as the main chain is elongated. Since the Deg homo-peptide esters lacking any terminal aromatic group, previously investigated, are known to adopt a stable fully-extended conformation in chloroform solution, we tend to attribute the 3D-structure instability observed in this work to the presence of multiple aromatic rings in their blocking groups.     

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.     

Charge mapping in 3(10)-helical peptide chains by oxidation of the terminal ferrocenyl group

Two series of 3(10)-helical peptides of different lengths and rigidity, based on the strongly foldameric α-aminoisobutyric acid and containing a terminal ferrocenyl unit, have been synthesized. Oxidation-state sensitive spectroscopic tags of helical peptides, the N-H groups, allowed mapping of the charge delocalization triggered by oxidation of the terminal ferrocenyl moiety and were monitored by IR spectroelectrochemistry.     

Evaluation of propolis polyphenols absorption in humans by liquid chromatography/tandem mass spectrometry

Propolis has various biological activities such as antibacterial, antiviral, antioxidant, immunostimulating and antiinflammatory, which are generally ascribed to the polyphenolic fraction. The aim of this study was to evaluate the absorption of the main polyphenols [caffeic acid (CA), pinobanksin-5methyl ether (P-5ME), pinobanksin (Pb), chrysin (C), pinocembrin (P), galangin (G), pinobanksin-3-acetate, pinobanksin esters and caffeic acid phenylethyl ester (CAPE)] from a dewaxed and standardized extract of propolis (EPID). Fifteen healthy volunteers consumed 5 mL EPID in water, corresponding to 125 mg of flavonoids. Blood samples were collected before, each hour for 8 h and 24 h after EPID intake. After deconjugation by beta-glucuronidase/sulfatase the plasma samples were analyzed by a selective liquid chromatography/tandem mass spectrometry (LC/MS/MS) method using morin as internal standard (I.S.). A kinetic profile characterized by two t(max), respectively at 1 h and about 5 h post-ingestion, was observed in all the subjects. The two peaks may be due to enterohepatic cycling. Among the various polyphenols ingested, only P-5ME, Pb, C, P and G were detected in plasma and C(max)t(1h) were 65.7 +/- 13.3, 46.5 +/- 12.7, 79.5 +/- 18.6, 168.1 +/- 16.3 and 113.7 +/- 16.8 ng/mL, respectively. These levels decreased significantly after 8 h and were no longer detectable 24 h after EPID intake. The recovery of the extraction for CA, Pb, C, P, G and I.S. from spiked plasma was 95.2 +/- 3.1, 93.1 +/- 3.6, 91 +/- 2.5, 96.4 +/- 4.2, 93.4 +/- 2.4 and 85.5 +/- 2.4%, respectively. The results of this study evidence that flavonoids from EPID are absorbed, metabolized and Pb-5ME and G seem to have apparent absorption, measured as (AUC/dose), higher than C, P and Pb.     

Sensitizing effect of bio-based chemicals from urban wastes on the photodegradation of azo-dyes

To promote bio-based products for the industry, six bio-organic substances (cHALi) isolated from yard trimmings (green) and food (humid) urban residues aged under aerobic digestion for 0–60 days were investigated for their potential to perform as sensitizers for azo-dyes photodegradation. Ethylorange (EO) was used as probe molecule at 5 mg L^?1 starting concentration and irradiated in a closed Pyrex^® cell with a Xenon (1500 W) lamp and a cut-off filter for wavelengths below 340 nm or in a cylindrical photochemical reactor equipped with a 125 W medium pressure Hg lamp. The cHALi/EO ratio in the starting EO solution varied in the 0–200 (w/w) range. The % dye abatement was found a function of the irradiation time, of the type of cHALi substance and of the cHALi/EO ratio. The best results were achieved with cHALi isolated after 7 days biomass aerobic digestion. Total dye abatement was achieved within relatively short few hours. A progressive dye mineralization was observed under the same experimental conditions. On the contrary no significant degradation was evident for the cHALi substances within the same irradiation time. Several hydroxylated azo compounds were identified as likely responsible of residual color after total EO abatement. The results, coupled to the previously reported good performance of the same cHALi substances as auxiliaries for textile dyeing, augur well for the development of both efficient and environmentally friendly textile dyeing processes.     

Synthesis and inverse virtual screening of new bi-cyclic structures towards cancer-relevant cellular targets

Structural Chemistry - We report here synthetic approaches to access new classes of small molecules based on three heterocyclic scaffolds, i.e. 3,7-dihydropyrimido[4,5-d]pyridazine-4,8-dione,...