Characterization of activated carbon fibers using argon adsorption

In this paper, we present results of the internal structure (pore size and pore wall thickness distributions) of a series of activated carbon fibers with different degrees of burn-off, determined from interpretation of argon adsorption data at 87 K using infinite and finite wall thickness models. The latter approach has recently been developed in our laboratory. The results show that while the low bun-off samples have nearly uniform pore size (

Accurate prediction of scorpion toxin functional properties from primary structures

Scorpion toxins are common experimental tools for studies of biochemical and pharmacological properties of ion channels. The number of functionally annotated scorpion toxins is steadily growing, but the number of identified toxin sequences is increasing at much faster pace. With an estimated 100,000 different variants, bioinformatic analysis of scorpion toxins is becoming a necessary tool for their systematic functional analysis. Here, we report a bioinformatics-driven system involving scorpion toxin structural classification, functional annotation, database technology, sequence comparison, nearest neighbour analysis, and decision rules which produces highly accurate predictions of scorpion toxin functional properties. (c) 2005 Elsevier Inc. All rights reserved.

Structural and stereochemical revision of isocyanide and isothiocyanate amphilectenes from the Caribbean marine sponge Cribochalina sp.

The absolute stereochemistry of amphilectene metabolites from Cribochalina sp. has been revised by a detailed NMR spectroscopic study of the Mosher ester derivatives of a related alcohol. The relative stereochemistry of the previously described amphilectenes has been reinvestigated and reassigned on the basis of the X-ray structural analysis carried out on one of them. The structure of a new amphilectene metabolite, which is an isothiocyanato analogue is also presented. (c) 2005 Elsevier Ltd. All rights reserved.

Highly-ordered hybrid organic-inorganic isoporous membranes from polymer modified nanoparticles

atomic force microscopy (AFM); atom transfer radical polymerization (ATRP); block copolymers; self-assembly; silica nanoparticles.

Why H Atom Prefers the On-Top Site and Alkali Metals Favor the Middle Hollow Site on the Basal Plane of Graphite

In this work, the different adsorption properties of H and alkali metal atoms on the basal plane of graphite are studied and compared using a density functional method on the same model chemistry level. The results show that H prefers the on-top site while alkali metals favor the middle hollow site of graphite basal plane due to the unique electronic structures of H, alkali metals, and graphite. H has a higher electronegativity than carbon, preferring to form a covalent bond with C atoms, whereas alkaline metals have lower electronegativity, tending to adsorb on the highest electrostatic potential sites. During adsorption, there are more charges transferred from alkali metal to graphite than from H to graphite.

Facile synthesis of rhodamine esters using acetyl chloride in alcohol solution

The rhodamines are a highly fluorescent class of compound used in many different fields of research, from the lasing medium in dye lasers to biological stains and markers for cellular drug resistance. In this study, esters (2-7) of rhodamine 110 (1) were conveniently prepared via the addition of acetyl chloride to a solution of the free acid (1) in the appropriate alcohol. This method conferred several advantages over previous preparations, namely that for low boiling alcohols, simple evaporation of the solution afforded the ester in quantitative yield with no need for purification. For higher boiling point alcohols, a method has been developed which allows the separation of longer chain esters from the alcohol solvent.

A gradient descent algorithm for minimizing amino acid coupling reactions when synthesizing cyclic-peptide libraries

Combinatorial chemistry has become an invaluable tool in medicinal chemistry for the identification of new drug leads. For example, libraries of predetermined sequences and head-to-tail cyclized peptides are routinely synthesized in our laboratory using the IRORI approach. Such libraries are used as molecular toolkits that enable the development of pharmacophores that define activity and specificity at receptor targets. These libraries can be quite large and difficult to handle, due to physical and chemical constraints imposed by their size. Therefore, smaller sub-libraries are often targeted for synthesis. The number of coupling reactions required can be greatly reduced if the peptides having common amino acids are grouped into the same sub-library (batching). This paper describes a schedule optimizer to minimize the number of coupling reactions by rotating and aligning sequences while simultaneously batching. The gradient descent method thereby reduces the number of coupling reactions required for synthesizing cyclic peptide libraries. We show that the algorithm results in a 75% reduction in the number of coupling reactions for a typical cyclic peptide library.

Antimicrobial peptides in action

Molecular dynamics simulations of the magainin MG-H2 peptide interacting with a model phospholipid membrane have been used to investigate the mechanism by which antimicrobial peptides act. Multiple copies of the peptide were randomly placed in solution close to the membrane. The peptide readily bound to the membrane, and above a certain concentration, the peptide was observed to cooperatively induce the formation of a nanometer- sized, toroidally shaped pore in the bilayer. In sharp contrast with the commonly accepted model of a toroidal pore, only one peptide was typically found near the center of the pore. The remaining peptides lay close to the edge of the pore, maintaining a predominantly parallel orientation with respect to the membrane.

Characterization of heat-treated porous carbons using argon adsorption

The microstructural variation of Norit RI Extra activated carbon, progressively heated at 1373 K, was explored in terms of pore size and pore wall thickness distributions, for various periods of heating time, determined by argon adsorption at 87 K, both using an infinite as well as and finite wall thickness model. The latter approach has recently been developed in our laboratory and has been applied to several virgin carbons. The current results show significant variations in small pore size regions (< 7 angstrom) in association with strong growth of thick walls having at least three carbon sheets, as a result of heat treatment. In particular, shrinkage of the smallest pores due to strong interaction between their opposite walls as well as smoothening of carbon wall surfaces due to an increase in graphitization degree under thermal treatment have been found. Further, the results of pore wall thickness distribution are well corroborated by X-ray diffraction. The results of pore size and pore wall thickness distributions are also shown to be consistent with transmission electron microscopy analyses. (c) 2005 Elsevier Ltd. All rights reserved.

Interfacial behavior of tetrapyridylporphyrin monolayer arrays

The behavior of monolayer films of free base 5,10,15,20-tetrapyridylporphinato (TPyP) and 5,10,15,20-tetrapyridylporphinato zinc(II) (ZnTPyP) on pure water, 0.1 M CdCl2, and 0.1 M CuCl2 subphases was investigated by surface pressure-area isotherms, specular X-ray reflectometry, and polarized total reflection X-ray absorption spectroscopy (PTRXAS). Surface pressure-area isotherms showed significant differences in the area per molecule on pure water compared to that on salt subphases, with a marked increase in the area observed on the salt solutions. This behavior was noted for both forms of the porphyrin and both salts investigated. Modeling of specular X-ray reflectometry data indicated that thinner and more electron dense layers on salt subphases best fit the observed profiles. These data suggest that the porphyrin macrocycle is oriented parallel to the interface on salt subphases and takes on a tilted conformation on pure water. In the case of ZnTPyP, PTRXAS was used to determine the orientation of the porphyrin moiety relative to the surface and to probe the coordination of the central Zn ion. In agreement with the pressure-area isotherms and reflectometry, the PTRXAS data indicate a change in orientation on the salt subphases.

Isokibdelones: Novel heterocyclic polyketides from a Kibdelosporangium sp.

The isokibdelones are an unprecedented family of polyketides produced by an Australian isolate of a rare actinomycete, Kibdelosporangium sp. The structures of the isokibdelones were assigned by spectroscopic analysis and chemical interconversion. A proposed biosynthesis requires a novel molecular twist that generates an unprecedented heterocyclic system and differentiates the isokibdelones from their kibdelone co-metabolites. SAR analysis on the isokibdelones further defines the anticancer pharmacophore of these novel polyketides.

Mechanisms influencing levitation and the scaling laws in nanopores: Oscillator model theory

We provide here a detailed theoretical explanation of the floating molecule or levitation effect, for molecules diffusing through nanopores, using the oscillator model theory (Phys. Rev. Lett. 2003, 91, 126102) recently developed in this laboratory. It is shown that on reduction of pore size the effect occurs due to decrease in frequency of wall collision of diffusing particles at a critical pore size. This effect is, however, absent at high temperatures where the ratio of kinetic energy to the solid-fluid interaction strength is sufficiently large. It is shown that the transport diffusivities scale with this ratio. Scaling of transport diffusivities with respect to mass is also observed, even in the presence of interactions.

Mimicking the action of GroEL in molecular dynamics simulations: Application to the refinement of protein structures

Bacterial chaperonin, GroEL, together with its co-chaperonin, GroES, facilitates the folding of a variety of polypeptides. Experiments suggest that GroEL stimulates protein folding by multiple cycles of binding and release. Misfolded proteins first bind to an exposed hydrophobic surface on GroEL. GroES then encapsulates the substrate and triggers its release into the central cavity of the GroEL/ES complex for folding. In this work, we investigate the possibility to facilitate protein folding in molecular dynamics simulations by mimicking the effects of GroEL/ES namely, repeated binding and release, together with spatial confinement. During the binding stage, the (metastable) partially folded proteins are allowed to attach spontaneously to a hydrophobic surface within the simulation box. This destabilizes the structures, which are then transferred into a spatially confined cavity for folding. The approach has been tested by attempting to refine protein structural models generated using the ROSETTA procedure for ab initio structure prediction. Dramatic improvements in regard to the deviation of protein models from the corresponding experimental structures were observed. The results suggest that the primary effects of the GroEL/ES system can be mimicked in a simple coarse-grained manner and be used to facilitate protein folding in molecular dynamics simulations. Furthermore, the results Sur port the assumption that the spatial confinement in GroEL/ES assists the folding of encapsulated proteins.

Molecular dynamics simulations of the hydrophobin SC3 at a hydrophobic/hydrophilic interface

Hydrophobins are small (similar to 100 aa) proteins that have an important role in the growth and development of mycelial fungi. They are surface active and, after secretion by the fungi, self-assemble into amphipathic membranes at hydrophobic/hydrophilic interfaces, reversing the hydrophobicity of the surface. In this study, molecular dynamics simulation techniques have been used to model the process by which a specific class I hydrophobin, SC3, binds to a range of hydrophobic/ hydrophilic interfaces. The structure of SC3 used in this investigation was modeled based on the crystal structure of the class II hydrophobin HFBII using the assumption that the disulfide pairings of the eight conserved cysteine residues are maintained. The proposed model for SC3 in aqueous solution is compact and globular containing primarily P-strand and coil structures. The behavior of this model of SC3 was investigated at an air/water, an oil/water, and a hydrophobic solid/water interface. It was found that SC3 preferentially binds to the interfaces via the loop region between the third and fourth cysteine residues and that binding is associated with an increase in a-helix formation in qualitative agreement with experiment. Based on a combination of the available experiment data and the current simulation studies, we propose a possible model for SC3 self-assembly on a hydrophobic solid/water interface.

Optical Bloch equations and enhanced decay of Rabi oscillations in strong driving fields

Optical Bloch equations are widely used for describing dynamics in a system consisting molecules, electromagnetic waves, and a thermal bath. We analyze applicability of these equations to a single molecule imbedded in a solid matrix. Classical Bloch equations and the limits of their applicability are derived from more general master equations. Simple and intuitively appealing picture based on stochastic Bloch equations shows that at low temperatures, contrary to common believes, a strong driving field can not only suppress but can also increase decay rates of Rabi oscillations. A physical system where predicted effects can be observed experimentally is suggested. (c) 2005 Elsevier B.V. All rights reserved.