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.     

Pyridazine based scorpionate ligand in a copper boratrane compound

Reaction of potassium tris(mercapto-tert-butylpyridazinyl)borate K[Tn(tBu)] with copper(II) chloride in dichloromethane at room temperature led to the diamagnetic copper boratrane compound [Cu{B(Pn(tBu))(3)}Cl] (Pn = pyridazine-3-thionyl) (1) under activation of the B-H bond and formation of a Cu-B dative bond. In contrast to this, stirring of the same ligand with copper(I) chloride in tetrahydrofuran (THF) gave the dimeric compound [Cu{Tn(tBu)}](2) (2) where one copper atom is coordinated by two sulfur atoms and one hydrogen atom of one ligand and one sulfur of the other ligand. Hereby, no activation of the B-H bond occurred but a 3-center-2-electron B-H···Cu bond is formed. The reaction of copper(II) chloride with K[Tn(tBu)] in water gave the same product 2, but a formal reduction of the metal center from Cu(II) to Cu(I) occurred. When adding tricyclohexyl phosphine to the reaction mixture of K[Tn(R)] (R = tBu, Me) and copper(I) chloride in MeOH, the distorted tetrahedral Cu complexes [Cu{Tn(R)}(PCy(3))] (R = tBu 3, Me 4) were formed. Compound 4 is exhibiting an "inverted" κ(3)-H,S,S, coordination mode. The copper boratrane 1 was further investigated by density functional theory (DFT) calculations for a better understanding of the M→B interaction involving the d(8) electron configuration of Cu.     

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.     

Synthesis and thermal degradation of some ferrocene-containing polyazines and poly-schiff bases

A series of ferrocene-containing polymeric azines and polymeric Schiff bases have been synthesized by means of acid-catalyzed solution polycondensations. The molecular structures of the polymers synthesized have been determined, and information concerning their thermal behavior has been obtained. Comparative thermal stabilities of the products of polymerization of aliphatic and aromatic diamines with 1,1′-diformylferrocene and 1,1′-diacetylferrocene were investigated by thermogravimetric analysis both in air and in an inert atmosphere. In the inert atmosphere, initial weight loss due to thermal stress did not occur below 300°C in all cases, and in many cases 50–70% residue of polymer sample remained at 700°C. The use of a fluorinated diamine led to the synthesis of a polymer which did not exhibit any significant enhancement of thermal properties. Investigation of the polymer products by direct inlet mass spectroscopy led to the observation that several of the systems contained significant amounts of cyclic dimers, although linear polymers were the major products in most cases. Extraction of the cyclic dimers followed by molecular weight determination by vapor phase osmometry confirmed their molecular structures.     

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.     

Iron-Iridium Mixed-Metal Carbonyl Clusters: A Mössbauer Study of the Structure and of the Adsorption of [Fe2Ir2(CO)12]2− on MgO

¹⁹³Ir and ⁵⁷Fe Mössbauer spectroscopy was used to investigate the structure of the [Fe₂Ir₂(CO)₁₂]^2- cluster compound and the adsorption of this cluster on hydrated MgO. Supported samples were prepared by impregnation of the magnesia with solutions of [Et₄N]₂[Fe₂Ir₂(CO)₁₂] in acetone. The Mössbauer and FT-IR spectra of the MgO-supported cluster confirm that the bimetallic carbonyl is molecularly physisorbed onto MgO without undergoing any transformation or decomposition. The easy solvent extraction of the intact cluster from the oxide surface excludes ion pairing between the cluster anion and the Mg²⁺ surface sites. Mössbauer spectra are in agreement with the refined structure of the molecular cluster and the temperature dependence of the ⁵⁷Fe Mössbauer spectra above 80 K is consistent with the low degree of interaction of the cluster with the support. This technique, therefore, appears to be promising in order to infer structural information when X-ray determination fails.