Relative stability of major types of beta-turns as a function of amino acid composition: a study based on Ab initio energetic and natural abundance data

Folding properties of small globular proteins are determined by their amino acid sequence (primary structure). This holds both for local (secondary structure) and for global conformational features of linear polypeptides and proteins composed from natural amino acid derivatives. It thus provides the rational basis of structure prediction algorithms. The shortest secondary structure element, the beta-turn, most typically adopts either a type I or a type II form, depending on the amino acid composition. Herein we investigate the sequence-dependent folding stability of both major types of beta-turns using simple dipeptide models (-Xxx-Yyy-). Gas-phase ab initio properties of 16 carefully selected and suitably protected dipeptide models (for example Val-Ser, Ala-Gly, Ser-Ser) were studied. For each backbone fold most probable side-chain conformers were considered. Fully optimized 321G RHF molecular structures were employed in medium level [B3LYP/6-311++G(d,p)//RHF/3-21G] energy calculations to estimate relative populations of the different backbone conformers. Our results show that the preference for beta-turn forms as calculated by quantum mechanics and observed in Xray determined proteins correlates significantly.     

A comparative study between inductively and capacitively coupled plasma deposited polystyrene films: chemical and morphological characterizations

Thin polystyrene films were deposited on stainless steel substrates by capacitively and inductively coupled radio frequency glow discharge plasma, in order to compare their chemical and morphological properties. The films were characterized by Fourier‐transform infrared spectroscopy (FTIR), X‐Ray photoelectron spectroscopy (XPS), time‐of‐flight secondary ion mass spectrometry (ToF‐SIMS), atomic force microscopy (AFM) and scanning electron microscope (SEM). Wettability properties were also determined by contact angle measurements. Ageing effect was studied by analysing films aged for 15 min and for 1 week. Results from both capacitively and inductively plasma polymerized polystyrene (pPS) films aged for 15 min showed that the chemical structure of the bulk, chemical composition of the surface (depth < 10 nm) and wettability properties were rather similar. Only their microstructures were very different: the pPS_capa film's microstructure showed homogeneous distribution of spherical particles of about 100 nm in diameter but the pPS_ind film's microstructure seemed to be mainly influenced by the surface of the metallic substrate: orientated ‘lamellae‐like layers’ of polymers were observed on each metallic grain. Ageing for 1 week in ambient air induced low oxygen uptake in the surface of both pPS films. The pPS_ind topmost surface (depth < 3 nm) was more oxidized than that of pPS_capa but no modification of the chemical structure of the bulk or of the morphology was noticed after ageing. Copyright © 2006 John Wiley & Sons, Ltd.     

A density functional study of propylene glycol conversion to propanal and propanone of various acid-catalyzed reaction models: a water-addition effect

The acid-catalyzed models on reaction mechanisms of pinacol rearrangement of propylene glycol conversion to propanal and propanone have been investigated using the density functional method at 298.15 K. Thermodynamic quantities of activation steps of four water-addition models were obtained. The number of added water interacting with the transition states of three concerted pathways has obviously affected the product ratio. The relative energetic profiles of the conversion reactions of all solvation models have been comparatively displayed. Estimation of the percent ratio of product composition computed from activation free energies of each acid-catalyzed reaction model was carried out. The percent ratios of propanal and propanone were decreased as the number of added water increased.     

Stille Cross‐Coupling of a Racemic Planar‐Chiral Ferrocene and Crystallographic Trace Analysis of Catalysis Intermediates and By‐products

A pressure‐controlled procedure for the S_N1 reaction of rac‐1‐[(dimethylamino)methyl]‐2‐(tributylstannyl)ferrocene ( 1 ) to rac‐1‐(phthalimidomethyl)‐2‐(tributylstannyl)ferrocene ( 2 ) was developed. Pd⁰‐Catalyzed Stille coupling of 2 with iodobenzene afforded rac‐1‐phenyl‐2‐(N‐phthalimidomethyl)ferrocene ( 5 ) in 74% yield; after trace enrichment by crystallization of the combined mother liquors, one single crystal of each, 5 , catalysis intermediate trans‐iodo(σ‐phenyl)bis(triphenylarsino)palladium(II) ( 7 ), trans‐diiodobis(triphenylarsino)palladium(II) ( 8 ), and rac‐2,2′‐bis(phthalimidomethyl)‐1,1′‐biferrocene ( 9 ) could be isolated by crystal sorting under a microscope and characterized by X‐ray crystal structure analysis. Furthermore, 5 was deprotected to amine ( 11 ), which does even survive the Birch reduction to rac‐1‐(aminomethyl)‐2‐(cyclohexa‐2,5‐dienyl)ferrocene ( 12 ).     

Detailed Structural Characterizations of SBA‐15 and MCM‐41 Mesoporous Silicas on a High‐Resolution Transmission Electron Microscope

Using high‐resolution transmission electronic micrograph (HR‐TEM) observation, one can clearly see the pore geometry of the MCM‐41 and SBA‐15 mesoporous silicas to determine that their pore shapes are hexagonal and round, respectively. With the perpendicular orientations of the nanochannels to the electron beam, parallel line images of the (100) and (110) repeating spacings were observed. In the SBA‐15 mesoporous silicas, there are byproducts of the granular silica and disordered mesostructures, attributed to the weak hydrogen interactions between Pluronic 123 blockcopolymer and the silica species. There are also many different and significant +π disclination defects in SBA‐15 and MCM‐41 surfactant‐silica composites. The SBA‐15 with a thicker silica wall is more stable under irradiation by high‐energy electron beams compared to MCM‐41, which has thinner wall thickness. Some carbon nanostructure impurities were found in some carbon films on the metal grids.     

Towards advanced circuit board materials: adhesion of copper foil to ultra‐high molecular weight polyethylene composite

Polyethylene based composites are attractive materials for advanced circuit board applications because of their unique combination of properties: low dielectric constant and loss factor, light weight, high flexural modulus and low thermal expansion coefficient controlled in all spatial directions. This investigation describes a process to consolidate chopped fibers of ultra‐high molecular weight polyethylene concurrently with its bonding to a copper foil. Bonding is affected by a thin sheet of low‐density polyethylene, incorporating a crosslinking agent with a concentration gradient across the sheets thickness. In this single step process, the composite material is formed and bonded to the metal foil, achieving good adhesion without the use of extraneous glue. Copyright © 2002 John Wiley & Sons, Ltd.     

Separation, identification, and interaction of heparin oligosaccharides with granulocyte-colony stimulating factor using capillary electrophoresis and mass spectrometry

A capillary electrophoresis (CE) method was developed for the separation of heparin oligosaccharides compatible to study the interactions between the oligosaccharides and granulocyte-colony stimulating factor (G-CSF). Unfractionated heparin was eliminitively degraded to heparin oligosaccharides by an endolytic heparinase. The degraded smaller oligosaccharides (M(r) < 1000) were baseline-separated by CE under a 50 mM phosphate buffer (pH 9.0) in 10 min. Standard heparin disaccharides and larger oligosaccharides (1000 < M(r) < 8000) were all separated under optimized separation conditions. Compared with standard heparin disaccharides, smaller oligosaccharides contained one nonsulfated, two monosulfated, and two disulfated disaccharides, but trisulfated disaccharides were not found. The smaller oligosaccharides were also identified and molecular mass was deduced by electrospray ionization-mass spectrometry (ESI-MS). Furthermore, interactions between G-CSF and the oligosaccharides were studied by using capillary zone electrophoresis (CZE) under the above separation conditions. It was found that larger oligosaccharides could interact with G-CSF while smaller oligosaccharides were not observed to bind to G-CSF under the experimental conditions. In conclusion, the purified heparinase could selectively degrade heparin into oligosaccharides and the interaction between G-CSF and heparin was correlated with the chain length of heparin.     

Statistical-overlap theory for elliptical zones of high aspect ratio in comprehensive two-dimensional separations

The low prediction by statistical-overlap theory of the numbers of singlets and peaks in two-dimensional separations containing zones represented by either circles of small number or eccentric ellipses of any number is shown to result from use of probability expressions for unbound spaces of infinite extent. An exact theory is derived for the probability of singlet formation in a reduced two-dimensional space of unit length, width, and area. The probability is a weighted sum of the probabilities of singlet formation in the interior, edge, and corner regions of the space, which depend only on saturation. The weighting factors are the fractions of area associated with each region and depend on the number of zones, the aspect ratio, the saturation, and the ellipse's spatial orientation. The average numbers of doublets, triplets, and peaks in the space are approximated by combining these results with Roach's equations describing the clustering of circles in an unbound two-dimensional space. Simulations show that theory predicts the number of singlets, doublets, triplets, and peaks, when the number of zones is 25 or more, the aspect ratio is 100 or less, and the saturation is 2 or less. The relationship is derived between the aspect ratios of ellipses in the reduced space and actual separation space. Calculations are presented for comprehensive two-dimensional gas chromatography.