Evaluation of configurational entropy methods from peptide folding-unfolding simulation

A 4-micros molecular dynamics simulation of the second beta-hairpin of the B1 domain of streptococcal protein G is used to characterize the free energy surface and to evaluate different configurational entropy estimators. From the equilibrium folding-unfolding trajectory, 200 000 conformers are clustered according to their root-mean-square deviation (RMSD). The height of the free energy barrier between pairs of clusters is found to be significantly correlated with their pairwise RMSD. Relative free energies and relative configurational entropies of the clusters are determined by explicit evaluation of the partition functions of the different clusters. These entropies are used to evaluate different entropy estimators for the largest 20 clusters as well as a subensemble comprising exclusively extended conformers. It is found that the quasi-harmonic entropy estimator operating in dihedral angle space performs better than the one using Cartesian coordinates. A recent generalization of the quasi-harmonic approach that computes Shannon entropies of probability distributions obtained by projecting the conformers along the eigenvectors of the covariance matrix performs similarly well. For the best entropy estimators, a linear correlation coefficient between 0.92 and 0.97 is found. Unexpectedly, when correlations between dihedral angles are neglected, the agreement with the reference entropies improved.     

Synthesis of 4‐phenylbutyl‐branched polyethylene from an ethylene‐styrene feed by a half‐titanocene catalyst

Copolymerization of ethylene and styrene with the catalytic system Cp*TiMe₃‐B(C₆F₅)₃ under suitable conditions affords a new polymer having a polyethylenic backbone with 4‐phenyl‐1‐butyl branches as the main product. This unexpected result has been ascribed to the multi‐site nature of the catalytic system, containing a species able to co‐oligomerize ethylene and styrene to 6‐phenyl‐1‐hexene (which was actually identified in the polymerization mixture), and another species able to copolymerize the latter with ethylene.     

Study on the Interaction of the CpG Alternating DNA with CdTe Quantum Dots

A novel sensitive method for detection of DNA methylation was developed with thioglycollic acid (TGA)-capped CdTe quantum dots (QDs) as fluorescence probes. Recognition of methylated DNA sites would be useful strategy due to the important roles of methylation in disease occurrence and developmental processes. DNA methylation occurs most often at cytosine-guanine sites (CpG dinucleotides) of gene promoters. The QDs significantly interacted with hybridized unmethylated and methylated DNA. The interaction of CpG rich methylated and unmethylated DNA hybrid with quantum dots as an optical probe has been investigated by fluorescence spectroscopy and electrophoresis assay. The fluorescence intensity of QDs was highly dependent to unmethylated and methylated DNA. Specific site of CpG islands of Adenomatous polyposis coli (APC), a well-studied tumor suppressor gene, was used as the detection target. Under optimum conditions, upon the addition of unmethylated dsDNA, the fluorescence intensity increased in linear range from 1.0?×?10^??10 to 1.0?×?10^??6M with detection limit of 6.2?×?10^??11 M and on the other hand, the intensity of QDs showed no changes with addition of methylated dsDNA. We also demonstrated that the unmethylated and methylated DNA and QDs complexes showed different mobility in electrophoresis assay. This easy and reliable method could distinguish between methylated and unmethylated DNA sequences.     

Biocompatibility Study of Electrospun Nanocomposite Membranes Based on Chitosan/Polyvinyl Alcohol/Oxidized Carbon Nano-Onions

In recent decades, the number of patients requiring biocompatible and resistant implants that differ from conventional alternatives dramatically increased. Among the most promising are the nanocomposites of biopolymers and nanomaterials, which pretend to combine the biocompatibility of biopolymers with the resistance of nanomaterials. However, few studies have focused on the in vivo study of the biocompatibility of these materials. The electrospinning process is a technique that produces continuous fibers through the action of an electric field imposed on a polymer solution. However, to date, there are no reports of chitosan (CS) and polyvinyl alcohol (PVA) electrospinning with carbon nano-onions (CNO) for in vivo implantations, which could generate a resistant and biocompatible material. In this work, we describe the synthesis by the electrospinning method of four different nanofibrous membranes of chitosan (CS)/(PVA)/oxidized carbon nano-onions (ox-CNO) and the subdermal implantations after 90 days in Wistar rats. The results of the morphology studies demonstrated that the electrospun nanofibers were continuous with narrow diameters (between 102.1 nm ± 12.9 nm and 147.8 nm ± 29.4 nm). The CS amount added was critical for the diameters used and the successful electrospinning procedure, while the ox-CNO amount did not affect the process. The crystallinity index was increased with the ox-CNO introduction (from 0.85% to 12.5%), demonstrating the reinforcing effect of the nanomaterial. Thermal degradation analysis also exhibited reinforcement effects according to the DSC and TGA analysis, with the higher ox-CNO content. The biocompatibility of the nanofibers was comparable with the porcine collagen, as evidenced by the subdermal implantations in biological models. In summary, all the nanofibers were reabsorbed without a severe immune response, indicating the usefulness of the electrospun nanocomposites in biomedical applications.     

Polymerization of α-olefins promoted by zirconium complexes bearing bis(phenoxy-imine) ligands with ortho-phenoxy halogen substituents

New fluorinated bis(phenoxy-imine)zirconium complexes bearing halogen substituents in the ortho and para positions of the phenolate rings, bis[N-(3,5-dibromosalycilidene)-2,3,4,5,6-pentafluoroaniline]-Zr(IV) dichloride (1) and bis[N-(3,5-dichlorosalycilidene)-2,3,4,5,6-pentafluoroaniline]-Zr(IV) dichloride (2) have been synthesized and used as precatalysts in the polymerization of propylene and 1-hexene. Their catalytic behaviour was compared with that of the analogous fluorinated zirconium complexes bearing alkyl groups in the same positions of the phenolate rings to investigate the effects produced by the introduction of additional electron-withdrawing halogen substituents. Complexes 1 and 2 produce stereoirregular, slightly syndiotactic enriched polypropylenes showing enhanced catalytic activities and an improved primary regioselectivity. Both catalysts promote efficiently the oligomerization of 1-hexene to atactic and regioregular oligomers. Interestingly for both the studied monomers it is possible to control the molecular weights and the structures of end groups of the produced polymeric chains by an appropriate choice of the cocatalyst. Functionalization reactions of the unsaturated polymeric chains selectively produced are also reported.     

Synthesis of collagen-like sequential polypeptides containing O-phospho-L-hydroxyproline and preparation of electrospun composite fibers for possible dental application

A synthetic route is described for collagen-like polypeptides constructed from O-phospho-L-hydroxyproline [Hyp(PO(3)H(2))] residues. Using the synthetic polypeptides and a natural protein, gelatin, fine fibers and their network structures (ESNWs) were prepared via electrospinning. The composite ESNWs can induce the mineralization of calcium phosphate. The phosphoryl groups of the Hyp(PO(3)H(2)) residues affect both the crystalline phase and amount of the calcium phosphate, depending on the chemical structure in the repeating sequence. The composite ESNWs can be developed as a biocompatible replacement of the extracellular matrix of hard tissues, and thus can be applied as dental materials for restoration of dental cavities or as a sealant for pits and fissures.     

Multiple Spectroscopic,Docking and Cytotoxic Study of a Synthesized 2,2′ Bipyridin Phenyl Isopentylglycin Pt(II) Nitrate Complex: Human Serum Albumin and Breast Cancer Cell Line of MDA-MB231 as Targets

In the present study, the biological activities of a new synthesized Pt(II)-complex, 2,2′ bipyridinphenyl isopentylglycin Pt(II) nitrate was investigated via its interaction with the most important blood carrier protein of human serum albumin (HSA), using fluorescence and Far-UV circular dichroism (CD) spectroscopic techniques and also molecular docking. Moreover, cytotoxicity activity of the complex was studied against breast cancer cell line of MDA MB231 using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. The Pt(II)-complex has a strong ability to quench the intrinsic fluorescence of HSA through a static quenching mechanism. According fluorescence quenching data, the binding parameters of the interaction were calculated and showed that hydrophobic interaction has an important role. The molecular docking results in coherent with fluorescence measurements illustrated that Pt(II) complex can bind to HSA at one position that located in the hydrophobic cavity of groove between drug site I and II. Also, experimental data on driving force in binding site was confirmed whereas theoretical results demonstrated Pt(II) complexinteract to HSA by hydrophobic interaction. Far-UV-CD results showed that Pt(II)-complex induced an increasing in the content of α-helical structure of the protein and stabilized it. Also, MTT assay represented growth inhibitory effect of the complex toward the breast cancer cell line.     

Synthesis and Cytotoxic Evaluation of Novel 1,2,3‐Triazole‐4‐Linked (2E,6E)‐2‐Benzylidene‐6‐(4‐nitrobenzylidene)cyclohexanones

This work describes the synthesis of novel 1,2,3‐triazole‐4‐linked (2E,6E)‐2‐benzylidene‐6‐(4‐nitrobenzylidene)cyclo‐hexanones starting from cyclohexanone. 1‐(Cyclohex‐1‐en‐1‐yl)piperidine, the enamine from cyclohexanone and piperidine, reacted with 4‐nitrobenzaldehyde to obtain 2‐(4‐nitrobenzylidene)cyclohexanone. Condensation of the latter compound with (prop‐2‐yn‐1‐yloxy)benzaldehyde derivatives under acidic conditions gave (4‐nitrobenzylidene)‐[(prop‐2‐yn‐1‐yloxy)‐benzylidene]cyclohexanones. Finally, ‘click reaction’ of these derivatives and various organic azides led to the title compounds. All compounds were examined by MTT assay for cytotoxic activity in one human breast cancer cell line, MDA‐MB‐231.     

Synthesis of Novel Isoindolo[2,1‐a]quinazolinedione Derivatives Containing a 1,2,3‐Triazole Ring System

A synthesis of isoindolo[2,1‐a]quinazolinedione derivatives, coupled with a 1,2,3‐triazole ring system, via the reaction of isatoic anhydride, HC?CCH₂NH₂, and 2‐formylbenzoic acid is described, which led to the formation of the isoindolo[2,1‐a]quinazoline‐5,11‐dione scaffold having a C?C bond that participated in a click reaction with various organic azides.     

A facile and efficient [bmim]N3 catalyzed direct oxidative esterification of arylaldehydes with alcohols

Task-specific ionic liquid, [bmim]N₃ was used as an effective catalyst and reaction medium for the direct oxidative esterification of arylaldehydes with alcohols. The oxidative esterification reaction of a variety of arylaldehydes took place smoothly with some primary and secondary alcohols in [bmim]N₃. Satisfactory results were obtained with arylaldehydes containing electron withdrawing groups. Tertiary alcohols did not react under these conditions.