An electrodynamics-based model for ion diffusion in microbial polysaccharides

An electrodynamics-based model was formulated for simulation of ion diffusion in microbial polysaccharides. The fixed charges and electrostatic double layers that may associate with microbial polysaccharides and their effects on ion diffusion were explicitly built into the model. The model extends a common multicomponent ion diffusion formulation that is based on irreversible thermodynamics under a zero ionic charge flux condition, which is only applicable to the regions without fixed charges and electrostatic double layers. An efficient numerical procedure was presented to solve the differential equations in the model. The model well described key features of experimental observations of ion diffusion in negatively charged microbial polysaccharides including accelerated diffusive transport of cations, exclusion of anions, and increased rate of cation transport with increasing negative charge density. The simulated diffusive fluxes of cations and anions were consistent with a cation exchange diffusion concept in negatively charged polysaccharides at the interface of plant roots and soils; and the developed model allows to mathematically study such diffusion phenomena. An illustrative example was also provided to simulate dynamic behavior of ionic current during ion diffusion within a charged bacterial cell wall polysaccharide and the effects of the ionic current on the compression or expansion of the bacterial electrostatic double layer at the interface of the cell wall and bulk solution.     

Identification of 4-amino-4-deoxychorismate synthase as the molecular target for the antimicrobial action of (6s)-6-fluoroshikimate

(6S)-6-Fluoroshikimate has antimicrobial activity. The molecular basis of this effect had not been identified, but there was speculation that (6S)-6-fluoroshikimate is first converted in vivo into 2-fluorochorismate, which then could inhibit 4-amino-4-deoxychorismate synthase (ADCS). 2-Fluorochorismate was prepared from E-fluorophosphoenolpyruvate and erythose-4-phosphate by the sequential reactions of DAHP synthase, dehydroquinate synthase, dehydroquinase, shikimate dehydrogenase, EPSP synthase, and chorismate synthase. Inhibition studies on ADCS showed that it was inhibited rapidly and irreversibly by 2-fluorochorismate. Electrospray mass spectrometry of the inactivated enzyme showed an additional mass of 198 +/- 10 Da. A novel peptide of 1087.6 Da was identified in the HPLC trace for the tryptic digest of 2-fluorochorismate-inactivated ADCS. Sequencing of this peptide by MS/MS showed that the peptide corresponded to residues 272-279 with a modification of 206.1 Da on Lys-274. This observation is particularly exciting in the context of a recent proposal for the catalytic mechanism of ADCS.     

ESOL: estimating aqueous solubility directly from molecular structure

This paper describes a simple method for estimating the aqueous solubility (ESOL--Estimated SOLubility) of a compound directly from its structure. The model was derived from a set of 2874 measured solubilities using linear regression against nine molecular properties. The most significant parameter was calculated logP(octanol), followed by molecular weight, proportion of heavy atoms in aromatic systems, and number of rotatable bonds. The model performed consistently well across three validation sets, predicting solubilities within a factor of 5-8 of their measured values, and was competitive with the well-established "General Solubility Equation" for medicinal/agrochemical sized molecules.     

Selective tryptophan modification with rhodium carbenoids in aqueous solution

A new transition metal-based reaction has been developed for the selective modification of tryptophan residues on protein substrates. After activation of vinyl-substituted diazo compounds by Rh2(OAc)4, the resulting metallocarbenoid intermediates were found to modify indoles in aqueous media despite competing reactions with water. Both N- and 2-substituted indole products were observed in the reaction. Following initial small-molecule studies, the reaction was performed on two protein substrates. Both myoglobin and subtilisin Carlsberg were modified readily in aqueous solution, and the tryptophan selectivity of the reactions was confirmed through MS analyses of trypsin digest fragments. It was also demonstrated that myoblobin concentrations as low as 10 muM still led to appreciable levels of modification. Reconstitution experiments confirmed that myoglobin retained its ability to bind heme following modification.     

Total synthesis of ingenol

A total synthesis of the biologically important diterpene ingenol has been completed. Ring-closing olefin metathesis was used to construct the strained "inside-outside" tetracyclic skeleton, and a series of diastereoselective reactions were employed to complete the synthesis. Another naturally occurring ingenane, 20-deoxyingenol, has also been prepared.     

Metallaborane reaction chemistry. A facile and reversible dioxygen capture by a B-frame-supported bimetallic: structure of [(PMe2Ph)4(O2)Pt2B10H10

[(PMe2Ph)4Pt2B10H10] reversibly takes up atmospheric dioxygen to give the fluxional dioxygen-dimetallaborane complex [(PMe2Ph)4(O2)Pt2B10H10], which has Pt-Pt 2.7143(3), Pt-O 2.141(4) and 2.151(4) and O-O 1.434(6)A.     

Formation of benzynes from 2,6-dihaloaryllithiums: mechanistic basis of the regioselectivity

The key elimination step for the formation of 3-chloro- and 3-fluorobenzyne from 2-chloro-6-fluorophenyllithium displays a pronounced solvent-dependent regioselectivity. 6Li and 13C NMR spectroscopic studies on 2-chloro-6-fluorophenyllithium reveal a single monomeric aryllithium, suggested by DFT computational studies to be a trisolvate. Rate studies indicate that the elimination of LiCl and LiF proceeds via trisolvated and disolvated monomers, respectively.     

Measurement of cell migration on surface-bound fibronectin gradients

A novel technique for the quantitative observation of cell migration along linear gradient substrates functionalized with adhesive proteins is presented. Gradients of the cell adhesion molecule fibronectin are generated by the cross diffusion of functionalizable alkanethiols on gold and characterized by X-ray photoelectron spectroscopy and surface plasmon resonance. Two distinct migration assays are described that characterize the movement of either sparsely populated noncontacting cells or a confluent monolayer of cells into free space. The drift speed of bovine aortic endothelial cells is measured and shown to increase along a fibronectin gradient when compared to a uniform control substrate using both assays. The results of these experiments establish reproducible conditions for studies of cell migration on gradients of surface-bound ligands.     

The propionyl cation heat of formation revisited

The 298 K heat of formation for the propionyl cation (C₂H₅CO⁺) has been measured previously by dissociative photoionization mass spectrometry. However, recent theoretical and experimental studies involving methylketene suggest that this may be significantly underestimated, resulting in a methylketene proton affinity that is too high by ∼30 kJ mol⁻¹. In this study, the previous m/z 57 appearance energies were carefully re-evaluated, with various possible sources of error being investigated. These include factors such as sample purity, carbon-13 contamination from lower energy m/z 56 processes, kinetic and/or competitive shifts, reverse activation energies, ionizing energy calibration errors and the availability of accurate supplementary thermochemical data. In addition, high-level ab initio calculations are used to model the relevant unimolecular fragmentation processes for each of the ionized precursor molecules. As a result, it is found that only the 2-butanone appearance energy can be used to provide a reliable value for the propionyl cation heat of formation. From the 298 K m/z 57 appearance energy of 10.199 ± 0.003 eV for 2-butanone measured here, a value of 617.8 ± 0.9 kJ mol⁻¹ is derived for , which corresponds to 845.4 ± 4.8 kJ mol⁻¹ for the proton affinity of methylketene. This is in good agreement with previous theoretical calculations and thermokinetic proton affinity measurements, indicating that a significant upward revision to the propionyl cation heat of formation is warranted. Copyright © 2004 John Wiley & Sons, Ltd.