Flexible matching of test ligands to a 3D pharmacophore using a molecular superposition force field: Comparison of predicted and experimental conformations of inhibitors of three enzymes

Summary A computer procedure TFIT, which uses a molecular superposition force field to flexibly match test compounds to a 3D pharmacophore, was evaluated to find out whether it could reliably predict the bioactive conformations of flexible ligands. The program superposition force field optimizes the overlap of those atoms of the test ligand and template that are of similar chemical type, by applying an attractive force between atoms of the test ligand and template which are close together and of similar type (hydrogen bonding, charge, hydrophobicity). A procedure involving Monte Carlo torsion perturbations, followed by torsional energy minimization, is used to find conformations of the test ligand which cominimize the internal energy of the ligand and the superposition energy of ligand and template. The procedure was tested by applying it to a series of flexible ligands for which the bioactive conformation was known experimentally. The 15 molecules tested were inhibitors of thermolysin, HIV-1 protease or endothiapepsin for which X-ray structures of the bioactive conformation were available. For each enzyme, one of the molecules served as a template and the others, after being conformationally randomized, were fitted. The fitted conformation was then compared to the known binding geometry. The matching procedure was successful in predicting the bioactive conformations of many of the structures tested. Significant deviation from experimental results was found only for parts of molecules where it was readily apparent that the template did not contain sufficient information to accurately determine the bioactive conformation.     

Bronsted acid-promoted olefin aziridination and formal anti-aminohydroxylation

A straightforward synthesis of aziridines is reported from an electron-rich azide (alkyl or aryl azide), electron-deficient olefin, and triflic acid in cold acetonitrile. The only coproduct of the reaction is dinitrogen (N2). Active ester substrates bearing a nucleophilic carbonyl engage the putative protonated aziridine intermediate to produce the product of olefin aminohydroxylation in which the nitrogen is benzyl protected and the oxygen is acylated. The possibility that a triazoline need not be an intermediate in aziridine production is advanced.     

Reaction of tris(trimethylsilyl)methylsilicon halides with methanolic sodium methoxide. Probability of sila-olefin intermediates

The compounds TsiSiR₂X [Tsi = Me₃Si)₃C; R = Me, X = Cl, Br, I, or R = Ph, X = F, Cl, Br, I)] react with boiling 2 M MeONa-MeOH to give products of the type (Me₃Si)₂CHSiR₂OMe. It is suggested that the reaction proceeds through an elimination, analogous to E2 eliminations of alkyl halides, involving synchronous attack of MeO^? at an Me₃Si group, liberation of X^?, and formation of (Me₃Si)₂CSiR₂. The compounds TsiSiPhMeF TsiSiPhCl₂ react analogously to give (Me₃Si)₂CHSiPhMe(OMe) and (Me₃Si)₂CHSiPh(OMe)₂ [tha latter presumably by solvolysis of the initially-formed (Me₃Si)₂CHSiPhCl(OMe)]. The compounds TsiSiMe₂OMe and TsiSiMe₃ do not react, while TsiSiMe₂H gives TsiH. The compound TsiSiCl₃ reacts with 0.1 M MeONa-MeOH to give the substitution and elmination products TsiSiCl₂(OMe) and (Me₃Si)₂CHSi(OMe)₃ in ca. $\text{1}\text{2}$ ratio.     

Structural changes in the monomeric despentapeptide (B30-B26) insulin crystal

Insulin modified by the removal of its 5 B chain C terminal residues is monomeric but remains substantially potent. The crystal structures of the beef and insulin (dpi) with two molecules in the asymmetric unit has been determined by x-ray analysis. The 3-dimensional structure ofdpi proves to be generally similar to that of native molecule in 2Zn insulin. More detailed comparison reveals that the slight differences in the two independent molecules of beefdpi are distributed uniformly throughout the structure in contrast to insulin in 2Zn insulin, where the structural changes are concentrated in specific regions. The loss of symmetry in thedpi crystal appears to be the inability of the A9 serine to pack effectively in the C2 cell. The efficient packing of the sheepdpi molecule whose crystal structure has also been determined and where A9 is glycine supports this conclusion.     

A review of proton transfer reactions between various carbon-acids and amine bases in aprotic solvents

The subject of proton transfer between carbon acids and nitrogen bases in aprotic solvents is reviewed. Equilibrium and rate constants that characterize such reactions are most often determined utilizing UV-visible spectrophotometry. At ambient temperature reaction rates are sufficiently rapid that fast reaction methods, for example, the stopped-flow and temperature-jump techniques are required in many cases. Variation of the properties of the donor and acceptor reaction pairs enables electronic and steric effects upon thermodynamic and kinetic parameters of proton transfer to be assessed. Determination of the kinetic isotope effect (KIE), i.e. k(protium)/k(deuterium) led to the conclusion that, under certain circumstances and when the KIE is greater than seven, the proton undergoes reaction with a significant degree of quantum mechanical tunneling, consistent with a theoretical prediction advanced several decades earlier. In fact this aspect may be one of the most significant outgrowths of these studies. Many reactions have been characterized (by tunneling) but rarely are the reacting systems experimentally amenable to obtaining all the experimental criteria that support tunneling. Controversy that has arisen regarding treatment of experimental data and resulting conclusions from them is visited in this review. The structural nature of the product state of reaction is formulated based on spectroscopic evidence, in favorable cases, and probable structures of the transition state can be inferred.     

Modeling Organic Surfaces with Self-Assembled Monolayers

The interfacial properties of organic materials are of critical importance in many applications, especially the control of wettability, adhesion, tribology, and corrosion. The relationships between the microscopic structure of an organic surface and its macroscopic physical properties are, however, only poorly understood. This short review presents a model system that has the ease of preparation and the structural definition required to provide a firm understanding of interfacial phenomena. Long-chain thiols, HS(CH₂)_nX, adsorb from solution onto gold and form densely packed, oriented monolayers. By varying the terminal functional group, X, of the thiol, organic surfaces can be created having a wide range of structures and properties. More complex systems can be constructed by coadsorbing two or more thiols with different terminal functional groups or with different chain lengths onto a common gold substrate. By these techniques, controlled degrees of disorder can be introduced into model surfaces. We have used these systems to explore the relationships between the microscopic structure of the monolayers on a molecular and supramolecutar scale and their macroscopic properties. Wettability is a macroscopic interfacial property that has proven of particular interest.     

Optimization of an electrolytic conductivity detector for determination of toxic nitrogen-containing food contaminants separated by open tubular column gas chromatography

The combination of open tubular column gas chromatography with electrolytic conductivity detection has been evaluated for the determination of nitrogen-containing pesticide residues in food extracts. Optimization of the column position at the column-detector interface was crucial to the successful operation of the detector. The signal-to-noise ratio and response stability of the detector are greatly influenced by the composition of the electrolyte solvent. Large volume splitless injections using retention gaps and optimized detector operating conditions enabled pesticide residues in food extracts to be determined at sub parts-per-million levels. Although the electrolytic conductivity detector is less sensitive than the thermionic ionization detector, its greater nitrogen selectivity can he crucial to the determination of nitrogen-containing contaminants in food extracts, particularly in complex mixtures where phosphorus-containing contaminants or matrix compounds are also present.     

Heterogeneous kinetics of the dissolution of an inorganic salt, potassium carbonate, in an organic solvent, dimethylformamide

Understanding the mechanisms of solid-liquid systems is fundamental to the development and operation of processes for the production of agrochemicals and pharmaceuticals. The use of a strong inorganic base in an organic solvent, typically, potassium carbonate in dimethylformamide, is often used to facilitate the formation of a required anionic organic nucleophile. In this paper, the dissolution kinetics of potassium carbonate in dimethylformamide at elevated temperatures is studied in the presence of ultrasound, as revealed via monitoring of the deprotonation of 2-cyanophenol by dissolved K2CO3. Two independent experimental methods were employed; the loss of 2-cyanophenol was detected electrochemically at a platinum microdisk working electrode, and the formation of the 2-cyanophenolate anion was monitored via UV/visible spectroscopic analysis. The results were modeled by fitting the experimental data to a theoretical model for the surface-controlled dissolution of solid particles. The dissolution rate constant, k, for the dissolution of K2CO3 in DMF was found to have a value of (1.3 +/- 0.2) x 10(-7) mol cm(-2) s(-1) at 100 degrees C, and the activation energy for the dissolution was 44.2 +/- 0.4 kJ mol(-1) over the temperature range of 70-100 degrees C studied.     

Application of a dynamic method of minimisation in the study of reaction surfaces

This paper describes the application of Snyman's dynamic minimisation method to a fitted potential surface of H₃. Comparisons are made with conventional algorithms. A method is described to extend Snyman's method so that it will find only a particular kind of stationary point. It is emphasized that this method enables saddle points to be found without having to resort to approaches based on trial and error.     

A universal temperature controlled membrane interface for the analysis of volatile and semi-volatile organic compounds

A universal temperature controlled membrane interface (TCMI) has been constructed for hollow-fibre membranes. The membrane temperature is controllable in the range -70 to 250 degrees C using an electric heater and a flow of cooled nitrogen or helium gas. Volatile and semi-volatile organic compounds may be detected either by continuous diffusion across the membrane or by in-membrane pre-concentration followed by thermal desorption into the detector. The TCMI interface is demonstrated in combination with mass spectrometry and GC-MS, for the determination of VOCs and SVOCs in aqueous and air samples and for the on-line monitoring of a bioreactor.