The influence of simulation conditions in molecular dynamics investigations of model β-sheet peptides

The influence of simulation methods, cutoff based and particle mesh Ewald (PME) on the accuracy by which experimentally derived nuclear Overhauser effect (NOE) data are reproduced, has been investigated using 500-ns-long molecular dynamics simulations on a model -sheet peptide in explicit solvent. The structural and conformational features under the different conditions were evaluated in terms of flexibility, secondary structure content, hydrogen-bonding pattern and percent of native contacts as a function of time. It was found that the different simulation methods strongly influence the dynamics of the peptide, confirming previous observations based on ideal peptide models simulated for much shorter times. Moreover, the results of our simulations prove once more that it is necessary to reach extremely long time scales to obtain enough statistics to accurately reproduce experimental NOE restraints even in the case of the PME method, despite its tendency to the stabilization of conformations which are structurally closely related to the ones derived through experiment. Possible implications regarding the stabilization and folding mechanisms, together with their relationship to the experimental study of peptide models, are discussed.     

Polymeric nanocomposites containing polyhedral oligomeric silsesquioxanes prepared via frontal polymerization

Frontal polymerization (FP) has been successfully applied, for the first time, to obtain polymeric nanocomposites containing polyhedral oligomeric silsesquioxanes (POSS) in an amine‐cured epoxy matrix. Variations of maximum temperature (T_max) and front velocity (V_f) have been studied. A comparison of these products with the corresponding materials, obtained by the classical batch polymerization technique, demonstrated that FP allows a higher degree of conversion than batch polymerization. The products have been characterized in terms of their thermal behavior with DSC analysis. SEM and X‐ray analyses revealed the morphology and the structures of the nanocomposites. The nanocomposites obtained by FP have the same characteristics of those synthesized, in much longer times, by batch polymerization. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 4514–4521, 2007     

A chemometric approach to the investigation of major and minor ion chemistry in Lake Como (Lombardia, Northern Italy

A chemometric approach based on Principal Component Analysis (PCA) has been proposed, in order to study chemical features (major and minor ions, total alkalinity, dissolved silica) of surface and deep waters of Lake Como (Northern Italy). The method allowed us to investigate the correlations between the analyzed ions in an easy-to-see way, using bi-dimensional graphs. In wintertime, the ionic composition of Lake Como waters seems to be mainly related to the geological composition of the lake basin, with a crystalline bedrock on the northern side and a sedimentary cover in the southern part. The presence of contaminants such as bromide and nitrite in water columns is also evidenced and discussed.     

Stimuli‐responsive polymer hydrogels containing partially exfoliated graphite

In this work, a new stimuli‐responsive composite polymer hydrogel containing partially exfoliated graphite was prepared by frontal polymerization. The materials obtained were characterized by differential scanning calorimetry, RAMAN, scan electron microscopy, transmission electron microscopy, atomic force microscopy, and in terms of swelling behavior. It was found that the maximum temperature reached by the polymerization front and the lower critical solution temperature are affected by the graphite content. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2010     

Influence of compatibilizer degradation on formation and properties of PA6/organoclay nanocomposites

Nanocomposites based on polyamide 6 (PA6) and commercial layered silicates have been prepared by both in situ polymerization and melt compounding. The main aim of the present work has been centred on compatibilizer degradation, caused by the preparation conditions, in terms of nanocomposite end features. Two montmorillonite (MMT)-type, organically-modified clays (OMLS), namely Cloisite 30B^® and Nanofil 784^®, and a sodium MMT (Cloisite Na^®) have been studied. Thermal properties of the layered silicates have been evaluated by TGA, IR, WAXD and pyrolysis-gas-mass. In order to better assess the influence of high temperature processes on clay modifications, a thermal treatment which mimics the conditions used during the in situ polymerization (4 h at 250 °C) has been applied on layered silicates. The above treatment, besides the elimination of absorbed water from all the clays, turned out to prove noteworthy differences in compatibilizer modification for the two organoclays. Indeed, in the case of Closite 30B^® only a removal of organic molecules outside the silicate galleries and a likely reorganization of those present inside the galleries have been detected, while a relevant chemical modification of Nanofil 784^® compatibilizer has been conversely found.As far as nanocomposite characteristics are concerned, the latter have been found to depend on both the preparation method and clay type. In the case of in situ polymerization, also thermally-treated layered silicates, coded (T), have been used, in order to put more clearly in evidence the role of compatibilizer decomposition on nanocomposite formation and properties. Indeed, nanocomposite samples containing Closite 30B^®(T) have been found to be completely exfoliated, while the same thermal treatment seems to make worse the properties of those based on Nanofil 784^®(T). Furthermore, with respect to nanocomposites based on pristine clays, samples containing thermally-treated silicates turned out to be different in terms of both molecular mass and crystal structure of the polymer matrix. Namely, PA6 γ-form seems to be promoted for all nanocomposites prepared in such a way, probably because of water removal at high temperature, which makes -OH groups of the layered silicate more free to interact with polyamide chains, thus causing a restriction of their mobility.     

Conformational studies of a bombolitin III-derived peptide mimicking the four-helix bundle structural motif of proteins

Bombolitins are five structurally related heptadecapeptides originally isolated from the venom of a bumblebee. In aqueous solution, bombolitins at sufficiently high concentration form oligomeric aggregates with consequent conformational transition from a random coil to the alpha-helical structure. Previous studies suggested that oligomeric aggregates could mimic the four-helix bundle structural motif of proteins. In the present work, we synthesized the following peptide sequence formed by two bombolitin III sequences linked head-to-tail by the tetrapeptide bridge -Gly-Pro-Val-Asp-: I(1)-K(2)-I(3)-M(4)-D(5)-I(6)-L(7)-A(8)-K(9)-L(10)-G(11)-K(12)-V(13)-L(14)-A(15)-H(16)-V(17)-G(18)-P(19)-V(20)-D(21)-I(22)-K(23)-I(24)-M(25)-D(26)-I(27)-L(28)-A(29)-K(30)-L(31)-G(32)-K(33)-V(3)(4)-L(35)-A(36)-H(37)-V(38)-NH(2). The tetrapeptide GPVD connecting the two helical peptide sequences was chosen to facilitate the formation of the helix-loop-helix structural motif. The conformational properties of the peptide were studied by CD, NMR, and molecular dynamics calculations. The results indicate the presence of a helix-loop-helix conformation at 10(-)(5) M concentration. At higher concentrations, NOESY connectivities were detected which are compatible with the presence of dimers or higher aggregates of peptide molecules in the helix-loop-helix structure packed in an antiparallel fashion. Molecular dynamics simulation were run either with NOE distance restraints or without restraints in explicit solvent for extended time. The results of these simulations support the dimerization of the molecules in the helix-loop-helix structure with formation of the four-helix bundle motif.     

On the effect of catalyst status in the quantitative determination of platinum in Pt-Sn/MgO materials

The development of an analytical method for the determination of platinum in MgO based Pt/Sn catalysts is described. Electrothermal atomic absorption spectroscopy (ETAAS) was chosen because of its high sensitivity and robustness against spectral interferences. All the sources of chemical interferences were statistically analyzed and corrections were adopted for the presence of magnesium oxide support. The effectiveness of different mineralization procedures was critically evaluated as a function of the chemical of the solid catalyst. Microwave digestion allowed recovery of metal of 100% for all the catalysts analyzed and exhibited significant better precision values than other digestion methods, which could nevertheless be utilized under proper conditions in selected cases. Received: 31 July 2000 / Revised: 17 October 2000 / Accepted: 24 October 2000