Molecular modeling of oligopeptide adsorption onto functionalized quartz surfaces

The adsorption of an EAK 16-II oligopeptide sequence in aqueous medium onto functionalized quartz surfaces has been studied by using force field calculations and molecular dynamics methods. Two different surfaces have been simulated respectively involving fully methylated and fully silanolic quartz surfaces. Geometry optimization and molecular dynamics simulations showed that the adsorption process is mainly governed by the electrostatic interactions between SiO- surface groups and the charged residues of the oligopeptide sequence. In particular, it was found that strong electrostatic interactions (a) prompt the parallel orientation of the oligopeptide with respect to the hydrophilic charged surface, resulting in an effective physisorption process and (b) stabilize the beta-sheet configuration of the physisorbed molecules. In particular, the end-on oligopeptide orientations are demonstrated to progressively lie back onto the hydrophilic surface, but this does not happen onto the hydrophobic surface. In any case, no physisorption process was observed for the fully methylated surface, where the molecule is seen to move away from the surface during the simulation time.     

Identification of phosphoproteins and determination of phosphorylation sites by zirconium dioxide enrichment and SELDI-MS/MS

Reversible protein phosphorylation mediated by protein kinases and phosphatases is the most studied post-translational modification. Efficient characterization of phosphoproteomes is hampered by (1) low stoechiometry, (2) the dynamic nature of the phosphorylation process and (3) the difficulties of mass spectrometry to identify phosphoproteins from complex mixtures and to determine their sites of phosphorylation. Combination of the phosphopeptide enrichment method with MALDI-TOFMS, or alternatively, with HPLC-ESI-MS/MS and MS(3) analysis was shown to be a step forward for the successful application of MS in the study of protein phosphorylation. In our study we used phosphopeptide enrichment performed in a simple single-tube experiment using zirconium dioxide (ZrO(2)). A simple protein mixture containing precipitated bovine milk caseins was enzymatically digested and the mixture of tryptic fragments was analysed before and after enrichment using nanoflow HPLC-ESI-MS/MS and surface-enhanced laser desorption/ionization (SELDI)-MS/MS on QqTOF instruments to compare the efficiency of the two methods in the determination of phosphorylation sites. Both approaches confirm the high selectivity obtained by the use of batch-wise, ZrO(2)-based protocol using di-ammonium phosphate as the eluting buffer. More phosphorylation sites (five for beta-casein and three for alpha(S1)-casein) were characterized by SELDI-MS/MS than by nanoflow HPLC-ESI-MS/MS. Therefore, ZrO(2)-based phosphopeptide enrichment combined with SELDI-MS/MS is an attractive alternative to previously reported approaches for the study of protein phosphorylation in mixtures of low complexity with the advance of fast in situ peptide purification. The method was limited to successful analysis of high-abundance proteins. Only one phosphorylation site was determined for the minor casein component alpha(S2)-casein by ESI-MS/MS and none for kappa-casein. Therefore an improvement in enrichment efficiency, especially for successful phosphoproteomic applications, is needed.     

Homo‐ and Copolymerization of Butadiene Catalyzed by an Bis(imino)pyridyl Vanadium Complex

Summary: The bis(imino)pyridyl vanadium(III ) complex [VCl₃{2,6‐bis[(2,6‐iPr₂C₆H₃)NC(Me)]₂(C₅H₃N)}] activated with different aluminium cocatalysts (AlEt₂Cl, Al₂Et₃Cl₃, MAO) promotes chemoselective 1,4‐polymerization of butadiene with activity values higher than classical vanadium‐chloride‐based catalysts. The polymer structure depends on the nature of the cocatalyst employed. The MAO‐activated complex was also found to be active in ethylene‐butadiene copolymerization, producing copolymers with up to 45 mol‐% of trans‐1,4‐butadiene. Crystalline polyethylene and trans‐1,4‐poly(butadiene) segments were detected in these copolymers by DSC and ¹³C NMR spectroscopy.

     

Renormalization of non-semisimple gauge models with the background field method

We study the renormalization of non-semisimple gauge models quantized in the 't Hooft-background gauge to all orders. We analyze the normalization conditions for masses and couplings compatible with the Slavnov-Taylor and Ward-Takahashi Identities and with the IR constraints. We take into account both the problem of renormalization of CKM matrix elements and the problem of CP violation and we show that the Background Field Method (BFM) provides proper normalization conditions for fermion, scalar and gauge field mixings. We discuss the hard and the soft anomalies of the Slavnov-Taylor Identities and the conditions under which they are absent.     

Polymerization of 1-vinylcyclohexene in the presence of group 4 metallocenes – MAO catalysts

1-Vinylcyclohexene was polymerized in the presence of several homogeneous catalytic systems consisting of methylaluminoxane and group 4 metallocenes such as CpTiCl₃, [isopropyl(cyclopentadienyl)(1-fluorenyl)]ZrCl₂,rac-[ethylenebis(1-indenyl)] ZrCl₂, (CH₃)₂Si(Cp)₂ZrCl₂, CpZrCl₃. The structure of the polymers depends on the catalyst. In fact, with CpTiCl₃, [isopropyl(cyclopentadienyl)(1-fluorenyl)]ZrCl₂ and rac-[ethylenebis-(1-indenyl)]ZrCl₂ the polymers are chemo-, regio- and stereoregular with 1,4 cis, 1,4 trans and 1,2 isotactic structure, respectively.     

Ab initio and DFT Study on 2H-Isoxazol-5-one: Consequences of Strong Intermolecular Hydrogen-Bond Formation in Supramolecular Structures

Ab initio and density-functional-theory (DFT) calculations on 2H-isoxazol-5-one (A), its linear dimer (LD), cyclic dimer (CD), and cyclic trimer (CT), have been performed with several basis sets in the gas phase, including electron correlation by second-order Møller-Plesset perturbation theory. The calculated complexation energy for the intermolecular H-bonded trimer as well as the corresponding geometric changes are in good agreement with the notion of resonance-assisted intermolecular H-bond formation. Bond distances and angles of the optimized geometry of CT are in accordance with the X-ray-diffraction data found on a trimeric supramolecular complex of parent compound 4-(2-methoxybenzyl)-3-phenyl-4H-isoxazol-5-one. Ab initio and DFT geometry optimizations are also reproducing exactly the large asymmetry in bond angles around the CO group that is systematically present in all literature available X-ray data for analogous heterocyclic penta-atomic compounds.     

Structural Studies of a N‐[(N‐Unsubstituted Pyrrole‐3‐carbonyl)oxy]benzamide and its Precursor Spiro[isoxazole‐4,3′‐pyrrole]

The structures of 6‐methyl‐4,8,9‐triphenyl‐2‐oxa‐3,7‐diazaspiro[4.4]nona‐3,6‐dien‐1‐one ( 3 ) and N‐[(2‐Methyl‐4,5‐diphenyl‐1H‐pyrrole‐3‐carbonyl)oxy]benzamide ( 4 ) were established by X‐ray crystal‐structure analysis. A significant improvement in the procedure currently available for the synthesis of these compounds is described. Ab initio and DFT calculations were carried out on the compound 4 and its precursor 3 , and compared with X‐ray results. In particular, to relate structural features to biological properties, the conformational characteristics and rotational barrier of compound 4 were studied.     

Non‐Newtonian viscosity in linear and star polymers

We theoretically investigate non‐Newtonian viscosity and coil deformation of linear and (regular) star polymers in dilute solution subject to large shear rates. A bead‐and‐spring model with preaveraged hydrodynamic interaction, accounting also approximately for good‐solvent expansion, is employed within the Rouse‐Zimm approach. We impose a constraint on the average spring lengths, so as to keep constant the average contour length of the arms under shear: this corresponds to assuming that the springs become increasingly stiffer. For any topology and a very large molecular mass, coil deformation modifies the hydrodynamic interaction, that goes to a maximum, and then decreases with a crossover from the Zimm to the Rouse regime with increasing shear rate. Correspondingly, the intrinsic viscosity decreases and then raises above its low‐shear value. This behavior is however much less pronounced under good‐solvent conditions. At very large shear rate, the constraint on the spring lengths becomes the dominant factor. This leads to a decrease of intrinsic viscosity with an asymptotic –2/3 power law for any draining condition. Simultaneously, the strongly elongated coil becomes fully aligned with flow.     

Thioetherphenolate group 4 metal complexes in the ring opening polymerization of rac‐β‐Butyrolactone

Group 4 complexes 1 – 3 [ 1 = (t‐BuOS)₂Ti(O‐i‐Pr)₂; 2 = (t‐BuOS)₂Zr(O‐t‐Bu)₂; 3 = (t‐BuOS)₂Hf(O‐t‐Bu)₂] supported by two phenolate bidentate ligands (t‐BuOS‐H = 4,6‐di‐tert‐butyl‐2‐phenylsulfanylphenol) promote the well‐controlled ring opening polymerization of rac‐β‐butyrolactone. In presence of isopropanol, low dispersities and molecular weights proportional to the equivalents of isopropanol are achieved. Moreover, the zirconium complex is effective in the copolymerization of rac‐β‐butyrolactone with rac‐lactide. The 13 C nuclear magnetic resonance analysis revealed that the obtained copolymers have a tapered diblock microstructure consisting of an initial block composed of lactide sequences and a terminal block composed of butyrolactone sequences. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016 , 54, 3132–3139