Molecular recognition and host-guest interactions in complexes of O-bistren,C-bistren,and bisdien

The host-guest relationships of the complexes of the cryptand ligands O-BISTREN and C-BISTREN, and of the analogous macrocyclic ligand BISDIEN are compared. The affinities of their binuclear copper(II) complexes for the bridging ligands (OH^–, F^–) as cascade type guests (i.e., guests of guests) are reported. The ability of the dicobalt(II)-BISDIEN complex to coordinate dioxygen and an additional bifunctional guest simultaneously, leads to the possibility of a new type of catalysis occurring within the cavity of a macrocyclic complex.     

Thermodynamic stability of polyacrylamide and poly(N,N‐dimethyl acrylamide)

Based on theoretical thermodynamic principles, the possibility of environmental degradation of polyacrylamide to its starting monomer was investigated. Theoretical electronic structure studies on the geometry and fragmentation energy of acrylamide and N,N‐dimethyl acrylamide tetramer models were carried out using a first principles gradient corrected density functional approach. Thermal degradation to form a radical would require the cleavage of carbon–carbon bonds in the polymer chain; the energy needed for this cleavage was found to depend on the structure of the repeat unit which ranged from low of 72.5 kcal for a rare head‐to‐head construct to 86.2 kcal for a normal head‐to‐tail polymer construct (therefore, for the cleavage of a normal head‐to‐tail repeat unit, temperatures of approximately 450°C would be required). The thermodynamics of the unzipping, disproportionation, and back‐biting reactions in the resulting radical fragments were also investigated; the back‐biting process was found to require the least energy and provided the most stable radical fragment with a low probability for disproportionation or releasing of monomer to occur. The effect of solvation on the hydrogen‐bonding network in the acrylamide tetramer was studied by adding explicit molecules of water to the tetramer models. The addition of water had a significant effect on the stability of the model polymer slightly stabilizing the head‐to‐head polymer, and slightly destabilizing the head to tail polymer. Copyright © 2007 John Wiley & Sons, Ltd.     

Quantum mechanical description of electrode reactions: Part II. Treatment of compact layer structure at platinum electrodes by means of the extended Hückel molecular orbital method. Pt(111) surfaces

The Iteraltive Extended Hückel Molecular Orbital method has been adapted to calculation of the properties of an electrode and compact layer. Predictions of the stablest orientations, on the Pt(111) surface of species such as H₂O, Pt, OH^?, H, and the halides, F^?, Cl^?, Br^? and I^?, based upon calculation of the total energy corresponding to various internuclear distances, are reported. The calculations correctly predict self-adsorption of Pt on the Pt(111) surface at the face-centered cubic closest-packing position. The H₂O molecule is predicted to locate itself above three adjoining Pt atoms, with the O atom closest to the surface and the H atoms opposite the O. Similar results were obtained for OH^? and the halides. Atomic H, however, is predicted to drop into the plane of centers of the Pt surface atoms, where it would lie between, three adjacent Pt atoms. Application of the method to electrode studies requires only modest amounts of computer time but produces surprisingly reliable qualitative predictions. Compulation of electrochemical quantities such as charge, differential capacitance, surface tension and potential energy as a function of electrode potential will be described in future work.     

Evaluation of docking/scoring approaches: A comparative study based on MMP3 inhibitors

An increasing number of docking/scoring programs are available that use different sampling and scoring algorithms. A reliable scoring function is the crucial element of such approaches. Comparative studies are needed to evaluate their current capabilities. DOCK4 with force field and PMF scoring as well as FlexX were used to evaluate the predictive power of these docking/scoring approaches to identify the correct binding mode of 61 MMP-3 inhibitors in a crystal structure of stromelysin and also to rank them according to their different binding affinities. It was found that DOCK4/PMF scoring performs significantly better than FlexX and DOCK4/FF in both ranking ligands and predicting their binding modes. Most notably, DOCK4/PMF was the only scoring/docking approach that found a significant correlation between binding affinity and predicted score of the docked inhibitors. However, comparing only those cases where the correct binding mode was identified (scoring highest among sampled poses), FlexX showed the best `fine tuning' (lowest rmsd) in predicted binding modes. The results suggest that not so much the sampling procedure but rather the scoring function is the crucial element of a docking program.     

Progress in the Development of Methods for Asymmetric Organic Synthesis

Methods for the enantioselective synthesis of chiral cyclohexane derivatives from aromatic carboxylic acids are presented. Birch reduction-alkylation of chiral benzamides of type 1 occur with high diastereose-lectivities to give 1,4-cyclohexadiene derivatives with quaternary centers located at C(6). Early applications of this chemistry provided target structures with a quaternary center derived from C(1) of the starting benzoic acid derivative. Herein are described 1) the development of a more versatile Birch reduction-alkylation, 2) a practical “asymmetric linkage” between aromatic carboxylic acids and chiral acyclic structures, and 3) asymmetric syntheses of unnatural alkaloids; applications to opiate receptor pharmacology.     

Standard pH values for potassium hydrogenphthalate reference buffer solutions in 10, 30 and 50% (w/w) 1,4-dioxane/water mixed solvents at temperatures from 288.15 to 318.15 K

Standard pH(S) values for 0.05 mol kg^?1 potassium hydrogenphthalate (KHpH) reference buffer solutions in 10, 30 and 50% (w/w) 1,4-dioxane/water solvent mixtures within the temperature range 288.15–318.15 K are determined from e.m.f. measurements of the cell without transference Pt|H₂|KHPh + KCl|AgCl|Ag|Pt. The consistency of the results is analysed by a recently described method of multilinear regression of the quantity p(a_Hγ_Cl) as a function of both solution composition and temperature. The standard pH(S) determined can be reproduced to within ±0.01 by the equation pH(S) - 4.004 + 3.309w + 0.408z + 1.037w³ - 14.95zw² + 27.1zw³, where w is the weight fraction of dioxane in the solvent mixture,z = (T –θ)/θ, and θ - 298.15 K. Values of the first ionization constant of phthalic acid (H₂Ph; benzene-1,2-dicarboxylic acid) in the above solvent mixtures are also determined from e.m.f. measurements of the cell without transference Pt|H₂|H₂Ph + KHPh + KCl|AgCl|Ag|Pt.     

A novel interface for variable flow nanoscale LC/MS/MS for improved proteome coverage

A variable flow "peak trapping" liquid chromatography (LC) interface has been developed for the coupling of nanoscale LC to electrospray ionization mass spectrometry (ESI-MS). The presented peak trapping LC interface allows for the extended analysis time of co-eluting compounds and has been employed for the identification of proteins via tandem mass spectrometry (MS/MS). The variable flow process can be controlled either manually or in a completely automated manner where the mass spectrometer status determines the status of the variable flow interface. When the mass spectrometer operates in MS survey mode, the interface is operated in a so-called "high-flow" mode. Alternatively, the interface is operated in a "low-flow" mode during MS/MS analysis. In the "high-flow" mode of the variable flow process the column flow rate is typically around 200 nL/min, whereas in the "low-flow" mode the column effluent is introduced into the source of the mass spectrometer at 25 nL/min. In addition to the flow reduction during MS/MS analysis, the gradient is paused to preserve the peptide separation on the analytical nanoscale LC column. The performance of the variable flow nanoscale LC/MS/MS interface is demonstrated by the automated analysis of standard peptide mixtures and protein digests utilizing variable flow, data-dependent scanning MS/MS techniques, and automated database searching.     

Level decay and orientational kinetics of the rhodamine B monomer and dimer

The population kinetics and the rotational diffusion of the rhodamine B monomer and dimer were measured by using picosecond pulses from a mode-locked Nd : YAG laser to induce and time resolve the concentration-dependent transient absorption saturation of various aqueous solutions of this organic dye.     

Synthesis of an Azasteroid Using an Acyl Iminium Ion-Initiated Tandem Cyclization

An acyl iminium ion-initiated tandem cyclization gave an unexpected dienone product, a seco-azasteroid (2). The factors governing the formation of 2 were investigated in an attempt to optimize its formation. The reaction was applied to a more elaborate system, resulting in the synthesis of the full steroid skeleton of 13-azaandrosta-1,4-diene-3,17-dione (3), which contains the unusual substitution of a chlorine atom for the axial 19-methyl.