Design and characterization of libraries of molecular fragments for use in NMR screening against protein targets

We have designed four generations of a low molecular weight fragment library for use in NMR-based screening against protein targets. The library initially contained 723 fragments which were selected manually from the Available Chemicals Directory. A series of in silico filters and property calculations were developed to automate the selection process, allowing a larger database of 1.79 M available compounds to be searched for a further 357 compounds that were added to the library. A kinase binding pharmacophore was then derived to select 174 kinase-focused fragments. Finally, an additional 61 fragments were selected to increase the number of different pharmacophores represented within the library. All of the fragments added to the library passed quality checks to ensure they were suitable for the screening protocol, with appropriate solubility, purity, chemical stability, and unambiguous NMR spectrum. The successive generations of libraries have been characterized through analysis of structural properties (molecular weight, lipophilicity, polar surface area, number of rotatable bonds, and hydrogen-bonding potential) and by analyzing their pharmacophoric complexity. These calculations have been used to compare the fragment libraries with a drug-like reference set of compounds and a set of molecules that bind to protein active sites. In addition, an analysis of the overall results of screening the library against the ATP binding site of two protein targets (HSP90 and CDK2) reveals different patterns of fragment binding, demonstrating that the approach can find selective compounds that discriminate between related binding sites.     

Continuous sample deposition from reversed-phase liquid chromatography to tracks on a matrix-assisted laser desorption/ionization precoated target for the analysis of protein digests

Peptide mass fingerprinting by matrix-assisted laser desorption/ionization (MALDI)-mass spectrometry (MS) is one of the standard high-throughput methods for protein identification today. Traditionally this method has been based on spotting peptide mixtures onto MALDI targets. While this method works well for more abundant proteins, low-abundance proteins mixed with high-abundance proteins tend to go undetected due to ion suppression effects, instrumental dynamic range limitations and chemical noise interference. We present an alternative approach where liquid chromatography (LC) effluent is continuously collected as linear tracks on a MALDI target. In this manner the chromatographic separation is spatially preserved on the target, which enables generation of off-line LC-MS and LC-MS/MS data by MALDI. LC-MALDI sample collection provides improved sensitivity and dynamic range, spatial resolution of peptides along the sample track, and permits peptide mass mapping of low-abundance proteins in mixtures containing high-abundance proteins. In this work, standard and ribosomal protein digests are resolved and captured using LC-MALDI sample collection and analyzed by MALDI-TOF-MS.     

Thermochemistry of fluorine compounds: IV. Rubidium tetrafluoroiodate

From measurement of the heat of hydrolysis, at 25°C , the enthalpy of formation of rubidium tetrafluoroiodate is derived: ΔH°_f [RbIF₄, cryst.]₂₉₈= ?191.12±4.43 kJ mol^?1. Heat capacity measurements for RbIF₄ over the range 273–303 K are also reported.     

Mai?analytische Bestimmung von Schwefels?ure, Salpeters?ure und salpetriger S?ure in Misch- und Abfalls?uren

Ohne Zusammenfassung     

Methyl formate oxidation: Speciation data,laminar burning velocities,ignition delay times,and a validated chemical kinetic model

The oxidation of methyl formate (CH₃OCHO) has been studied in three experimental environments over a range of applied combustion relevant conditions:

• 1. A variable‐pressure flow reactor has been used to quantify reactant, major intermediate and product species as a function of residence time at 3 atm and 0.5% fuel concentration for oxygen/fuel stoichiometries of 0.5, 1.0, and 1.5 at 900 K, and for pyrolysis at 975 K.
• 2. Shock tube ignition delays have been determined for CH₃OCHO/O₂/Ar mixtures at pressures of ≈ 2.7, 5.4, and 9.2 atm and temperatures of 1275–1935 K for mixture compositions of 0.5% fuel (at equivalence ratios of 1.0, 2.0, and 0.5) and 2.5% fuel (at an equivalence ratio of 1.0).
• 3. Laminar burning velocities of outwardly propagating spherical CH₃OCHO/air flames have been determined for stoichiometries ranging from 0.8–1.6, at atmospheric pressure using a pressure‐release‐type high‐pressure chamber.

A detailed chemical kinetic model has been constructed, validated against, and used to interpret these experimental data. The kinetic model shows that methyl formate oxidation proceeds through concerted elimination reactions, principally forming methanol and carbon monoxide as well as through bimolecular hydrogen abstraction reactions. The relative importance of elimination versus abstraction was found to depend on the particular environment. In general, methyl formate is consumed exclusively through molecular decomposition in shock tube environments, while at flow reactor and freely propagating premixed flame conditions, there is significant competition between hydrogen abstraction and concerted elimination channels. It is suspected that in diffusion flame configurations the elimination channels contribute more significantly than in premixed environments. © 2010 Wiley Periodicals, Inc. Int J Chem Kinet 42: 527–549, 2010