Molecular cluster decay viewed as escape from a potential of mean force

We show that evaporation from a quasistable molecular cluster may be treated as a kinetic problem involving the stochastically driven escape of a molecule from a potential of mean force. We derive expressions for the decay rate, and a relationship between the depth of the potential and the change in system free energy upon loss of a molecule from the cluster. This establishes a connection between kinetic and thermodynamic treatments of evaporation, but also reveals differences in the prefactor in the rate expression. We perform constant energy molecular dynamics simulations of cluster dynamics to calculate potentials of mean force, friction coefficients and effective temperatures for use in the kinetic analysis, and to compare the results with the directly observed escape rates. We also use the simulations to estimate the escape rates by a probabilistic analysis. It is much more efficient to calculate the decay rate by the methods we have developed than it is to monitor escape directly, making these approaches potentially useful for the assessment of molecular cluster stability.     

Theoretical analysis of peptidyl alpha-ketoheterocyclic inhibitors of human neutrophil elastase: Insight into the mechanism of inhibition and the application of QM/MM calculations in structure-based drug design

It has been suggested from QSAR data (P. D. Edwards, D. J. Wolanin, D.A. Andisik and M. W. Davis, J. Med. Chem., 1995, 38, 76) that the inhibition of elastase by peptidyl alpha-ketoheterocyclic inhibitors can occur in two ways, the less potent inhibitors forming a non-bonded Michaelis complex and the more potent set a covalently bonded enzyme-substrate intermediate. We report QM/MM studies of both binding and reactivity that confirm these findings, showing that the activity of the least potent set of inhibitors correlates with the calculated binding energy, and that of the more potent set correlates with the stability of the intermediate. These calculations show that QM/MM methods can be successfully employed to understand complicated structure-activity relationships and might be employed in the design and assessment of new inhibitors.     

Analytical applications of infra-red spectroscopy : The behaviour of the oxinates of niobium,tantalum and associated elements

The behaviour of the oxinates of niobium, tantalum and associated metals in the infra-red region was studied and a method developed for the determination of niobium and tantalum. Vanadium caused no interference, but other heavy metals, such as molybdenum, manganese and cobalt, which interfered were removed by preliminary treatment when the method was applied to the determination of niobium and tantalum in steels.     

PCILO calculation of intermolecular energies: The water dimer

The PCILO (perturbative configuration interaction using localized orbitals) method for approximating the electronic structure of molecules has been used with some success for calculating intramolecular interactions in large molecules where intramolecular hydrogen bonding is involved. In this note we show that the PCILO method may be used to calculate the energy of interaction between two water molecules in selected configurations.     

Derivatisation for liquid chromatography/electrospray mass spectrometry: synthesis of pyridinium compounds and their amine and carboxylic acid derivatives

A simple method has been developed for the pre-column derivatisation of low molecular weight primary and secondary amines and carboxylic acids using quaternary nitrogen compounds to enhance their detection by liquid chromatography/electrospray ionisation mass spectrometry (LC/ESI-MS). The synthesis of seven novel quaternary nitrogen reagents is described. The derivatives are designed to be relatively small molecules to avoid some of the steric hindrance problems that may be associated with larger derivatisation reagents. The compounds have amine and carboxylic acid functional groups with which to derivatise carboxylic acids and amines, respectively. Two of the compounds contain a bromine atom in order to assess the advantages of a bromine isotope pattern in the mass spectra. This acts as a simple marker for derivatisation and enables data processing by cluster analysis.Activation of the carboxylic acid group was achieved by the use of either 1-chloro-4-methylpyridinium iodide (CMPI) or the more reactive 1-fluoro-4-methylpyridinium p-toluenesulphonate (FMP).1 Using both of these active reagents, the degree of nucleophilic substitution was investigated for the derivatisation of a variety of small molecules. Whilst giving some increase in the ESI-MS response for the derivatised compounds, the FMP itself acted as a derivatising reagent in a competing reaction. In the light of this finding, FMP was reacted with the test compounds separately and gave positive results as a derivatising reagent. Detection of the 'pre-charged' derivatives of amines and carboxylic acids by LC/ESI-MS was investigated with respect to their ESI response and chromatography.     

Factors controlling the efficiencies of photoinduced electron-transfer reactions

The overall efficiencies of photoinduced electron transfer reactions in polar solvents are usually determined by the efficiency with which separated radical ions are formed from the initially formed geminate radical-ion pairs. These separation efficiencies are determined by the competition between retum electron transfer and separation within the geminate pairs. A method is described for determining whether variations in the quantum yields for formation of separated radical ions are due to changes in the reorganization parameters for the return electron transfer reactions, or to other factors. The use of the method is illustrated in studies of the effects of varying steric bulk and molecular size of the donors, and also in studies of the effect of using a charged sensitizer.     

Thermal Gradients for the Control of Elution in RP-LC: Application to the Separation of Model Drugs

The use of temperature as a variable in liquid chromatography enables the facile alteration of eluotropic strength without the need to change solvent composition. The ability to change eluotropic strength via temperature alone means that thermal gradients can be used to mimic the effects of solvent gradients but without many of the unwanted effects of changes in solvent composition. Here we illustrate the use of thermal gradients as a means of controlling chromatographic separations using either constant flow or, with the flow rate increased to maintain isobaric conditions, constant pressure, performed using columns packed with 1.7 μm particles. A model is described that can be used to used to predict flow, pressure and temperature under gradient conditions. Practical experimental factors such as the need for post column cooling and the use of frit restrictors in order to obtain optimum results are described.     

Eta2-dba complexes of Pd(0): the substituent effect in Suzuki-Miyaura coupling

The influence of aryl substituents in dibenzylidene acetone (dba) ligands, for Pd(0) complexes, has been evaluated for Suzuki-Miyaura cross-coupling reactions. Electron-withdrawing substituents such as NO(2) or CF(3) deactivate the catalyst species whereas strongly donating substituents such as OMe increase catalytic activity over that of unsubstituted dba ligands. [reaction: see text]     

Total synthesis of (+)-discodermolide: an improved endgame exploiting a Still-Gennari-type olefination with a C1-C8 beta-ketophosphonate fragment

[structure: see text] An improved, third-generation, total synthesis of (+)-discodermolide, a potent microtubule-stabilizing anticancer agent of marine sponge origin, is achieved in 11.1% yield over 21 steps. Key steps include a Still-Gennari HWE olefination, performed using NaH as the base, between C1-C8 beta-ketophosphonate 7 and C9-C24 aldehyde 8, introducing the (8Z)-alkene with 10:1 selectivity, and K-Selectride reduction of the derived enone 16, installing the (7S)-configuration.