Computational study of conformational preferences of thioamide-containing azaglycine peptides

The effect of thioamide substitution on the conformational stability of an azaglycine-containing peptide, For-AzaGly-NH2 (1), was investigated for the sake of finding possible applications by using ab initio and DFT methods. As model compounds, For-[psiCSNH]-AzaGly-NH2 (2), For-AzaGly-[psiCSNH]-NH2 (3), and For-[psiCSNH]-AzaGly-[psiCSNH]-NH2 (4) were used. Two-dimensional phi-psi potential energy surfaces (PESs) for 2-4 were calculated at the B3LYP/6-31G*//HF/6-31G* level in gas (epsilon = 1.0) and in water (epsilon = 78.4) by applying the isodensity polarizable continuum model (IPCM) method. On the basis of these PESs, the minimum energy conformations for 2-4 were characterized at the B3LYP level with 6-31G*, 6-311G**, and 6-31+G** basis sets. The remarkable structural effect of thioamide substitution for 2-4 is that beta-strand structure is observed as a global or local minimum. The minima of 2-4 are also compared with those for glycine and thioamide-containing glycine peptides. Our theoretical results demonstrate that compounds 2-4 would be used to design controllable secondary structures.     

Size-based analysis of incinerator fly ash using gravitational SPLITT fractionation, sedimentation field-flow fractionation, and inductively coupled plasma-atomic emission spectroscopy

Fly ash has been regarded as hazardous because of its high adsorption of toxic organic and/or inorganic pollutants. Fly ash is also known to have broad distributions of different chemical and physical properties, such as size and density. In this study, fly ash emitted from a solid waste incinerator was pre-fractionated into six sub-populations by use of gravitational SPLITT fractionation (GSF). The GSF fractions were then analyzed by sedimentation field-flow fractionation (SdFFF) and ICP–AES. SdFFF analysis showed the fly ash has a broad size distribution ranging from a few nanometers up to about 50 µm. SdFFF results were confirmed by electron microscopy. Inductively coupled plasma–atomic emission spectroscopy (ICP–AES) analysis of the GSF fractions showed the fly-ash particles contain a variety of inorganic elements including Ca, Si, Mg, Fe, and Pb. The most abundant in fly ash was Ca, followed by Si then Mg. No correlations were found between trace element concentration and particle size.     

Rapidly converging lattice sums for nonelectrostatic interactions

The relative energies of one-, two-, and three-dimensional Bravais lattice Lennard-Jones particles can be calculated by lattice sums. The expression of lattice sums over a Lennard-Jones potential can be manipulated into a form that converges rapidly. A formalism capable of calculating the lattice potential at arbitrary points of a completely general lattice has been developed. This method provides an alternative way to calculate the relative energies from the surface and the interior bulk sites of many chemical systems. The method is illustrated with application to hcp and fcc Lennard-Jonesium, both for the relative binding energy and for calculating the potential along the geometric diffusion pathway between tetrahedral and octahedral interstitial sites. Diffusion from the tetrahedral site to the octahedral site experiences a barrier of 752.600 in units of 4 epsilon. The reverse pathway experiences a barrier of 1035.614 in units of 4 epsilon.     

Roles of TNF-alpha and IgE in the late phase of contact hypersensitivity induced by trimellitic anhydride

Trimellitic anhydride (TMA) is widely used industrially to make epoxy and alkyd resins, plasticizers and surfactants. The purpose of this study was to investigate whether contact hypersensitivity (CHS) is induced by repeated TMA challenge and the role of TNF-alpha and IgE in the TMA-induced CHS. The repetition of the challenge enlarged the extent of an early and a late phase of CHS in TNF-alpha+/+ (B6129SF2/J) and Balb/c mice. In the late phase of TMA-induced CHS, the peak of ear swelling responses by single challenge showed at 24 h after challenge, but the peak was observed at 8 h after repeated challenge. In the TNF-alpha knockout TNF-alpha-/- (B6;129S-Tnftm1Gk1) mice, the repetition of the TMA challenges enlarged the extent of the late phase of CHS, but less than those in TNF-alpha+/+ mice. Injection of anti-TNF-alpha antibody into the peritoneal cavity of Balb/c mice significantly decreased the extent of the late phase of CHS. Subcutaneous injection of anti-IgE antibody into Balb/c mice also decreased the extent of the late phase of CHS in dose-dependent manner. Histologically, infiltration of polymorphonuclear leukocytes and eosinophils was more pronounced in repeatedly TMA-challenged TNF-alpha+/+ and Balb/c mice than in the TNF-alpha-/- mice and anti-TNF-alpha or anti-IgE antibodies treated Balb/c mice. These results indicate that mice sensitized by TMA could possibly offer a useful model to study the mechanism of CHS, and TNF-alpha and IgE may act as potential modulators in the late phase of TMA-induced CHS. Neutralization of TNF-alpha and IgE by anti-TNF-alpha or anti-IgE antibodies may provide therapeutic tools for the treatment of TMA-induced CHS.     

Field and flow programming in frit-inlet asymmetrical flow field-flow fractionation

The separation of wide molecular mass (Mr) ranges of macromolecules using frit inlet asymmetrical flow field-flow fractionation (FI-AFlFFF) has been improved by implementing a combination of field and flow programming. In this first implementation, field strength (governed by the cross flow-rate through the membrane-covered accumulation wall) is decreased with time to obtain faster elution and improved detection of the more strongly retained (high Mr) materials. The channel outlet flow-rate is optionally held constant, increased, or decreased with time. With circulation of the flow exiting the accumulation wall to the inlet frit, the dual programming of cross flow and channel outlet flow could be implemented using just two pumps. With this flow configuration, the channel outlet flow-rate is always equal to the channel inlet flow-rate, and these may be programmed independently of the cross flow-rate through the membrane. FI-AFlFFF retains its operational advantage over conventional asymmetrical flow FFF (AFlFFF). Unlike conventional AFlFFF, FI-AFlFFF does not require time consuming, and experimentally inconvenient, sample focusing and relaxation steps involving valve switching and interruption of sample migration. The advantages of employing dual programming with FI-AFlFFF are demonstrated for sets of polystyrene sulfonate standards in the molecular mass range of 4 to 1000 kDa. It is shown that programmed FI-AFlFFF successfully expands the dynamic separation range of molecular mass.     

Cell lysis on a microfluidic CD (compact disc)

Cell lysis was demonstrated on a microfluidic CD (Compact Disc) platform. In this purely mechanical lysis method, spherical particles (beads) in a lysis chamber microfabricated in a CD, cause disruption of mammalian (CHO-K1), bacterial (Escherichia coli), and yeast (Saccharomyces cerevisiae) cells. Interactions between beads and cells are generated in the rimming flow established inside a partially filled annular chamber in the CD rotating around a horizontal axis. To maximize bead-cell interactions in the lysis chamber, the CD was spun forward and backwards around this axis, using high acceleration for 5 to 7 min. Investigation on inter-particle forces (friction and collision) identified the following parameters; bead density, angular velocity, acceleration rate, and solid volume fraction as having the most significant contribution to cell lysis. Cell disruption efficiency was verified either through direct microscopic viewing or measurement of the DNA concentration after cell lysing. Lysis efficiency relative to a conventional lysis protocol was approximately 65%. In the long term, this work is geared towards CD based sample-to-answer nucleic acid analysis which will include cell lysis, DNA purification, DNA amplification, and DNA hybridization detection.     

Biomedical significance of endothelial cell specific growth factor, angiopoietin

Until recently, vascular endothelial growth factor (VEGF) was the only growth factor proven to be specific and critical for blood vessel formation. Other long-known factors, such as the fibroblast growth factors (FGFs), platelet-derived growth factor, or transforming growth factor-beta, had profound effects in endothelial cells. But such factors were nonspecific, in that they could act on many other cells, and it seemed unlikely that these growth factors would be effective targets for treatment of endothelial cell diseases. A recently discovered endothelial cell specific growth factor, angiopoietin, has greatly contributed to our understanding of the development, physiology, and pathology of endothelial cells (Davis et al., 1996; Yancopoulos et al., 2000). The recent studies that identified and characterized the physiological and pathological roles of angiopoietin have allowed us to widen and deepen our knowledge about blood vessel formation and vascular endothelial function. Therefore, in this review, we describe the biomedical significance of these endothelial cell growth factors, the angiopoietins, in the vascular system under normal and pathological states.     

Syntheses of 1beta-methylcarbapenems bearing 5-methyl-4-hydroxypyrrolidinone

A new series of 1beta-methylcarbapenems 1a-d bearing 5-methyl-4-mercaptopyrrolidinone rings has been prepared and evaluated for in vitro antibacterial activity and pharmacokinetic parameters. Most compounds showed excellent antibacterial activity and high stability to dehydropeptidase-1. We have synthesized optically active 5-methyl-4-hydroxypyrrolidinones from enantiomerically pure aziridine esters.     

Controlled polymerization in mesoporous silica toward the design of organic-inorganic composite nanoporous materials

Free-radical polymerization inside mesoporous silica has been investigated in order to open a route to functional polymer-silica composite materials with well-defined mesoporosity. Various vinyl monomers, such as styrene, chloromethyl styrene, 2-hydroxyethyl methacrylate, and methacrylic acid, were polymerized after impregnation into mesoporous silicas with various structures, which were synthesized using polyalkylene oxide-type block copolymers. The location of the polymers was systematically controlled with detailed structures of the silica framework and the polymerization conditions. Particularly noteworthy is the polymer-silica composite structure obtained by in situ polymerization after the selective adsorption of monomers as a uniform film on silica walls. The analysis of XRD data and the N(2) adsorption isotherms indicates the formation of uniform polymer nanocoating. The resultant polymer-silica composite materials can easily be post-functionalized to incorporate diverse functional groups in high density, due to the open porous structure allowing facile access for the chemical reagent. The fundamental characteristics of the composite materials are substantiated by testing the biomolecule's adsorption capacity and catalytic reactivity. Depending on the structure and composition of polymers, the resultant polymer-silica composite materials exhibit notably distinct adsorption properties toward biomolecules, such as proteins. Furthermore, it is demonstrated that the nanocoatings of polymers deposited on the mesopore walls have remarkably enhanced catalytic activity and selectivity, as compared to that of bulk polymer resins. We believe that, due to facile functionalization and attractive textural properties, the mesoporous polymer-silica composite materials are very useful for applications, such as adsorption, separation, host-guest complexes, and catalysis.     

Recyclable self-assembly-supported catalytic system for orthoalkylation

[reaction: see text] A new recyclable supported catalyst system for orthoalkylation was devised using a self-assembly consisting of the barbiturate and 2,4,6-triaminopyrimidine H-bonding motifs. At high temperature, the system is completely homogeneous so as to give an efficient catalytic activity, while it is heterogenized at room temperature to form an insoluble solid phase for the easy recovery of the catalyst after the reaction.