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.     

Comparison by capillary SFC and SFC-MS of soxhlet and supercritical fluid extraction of hamster feces

Components of hamster feces ranging from low molecular weight fatty acids through the expected range of triglycerides have been eluted in a single SFC run with simultaneous pressure and temperature programming. Temperature programming from 140°C to 240°C was required to provide optimum conditions for separation of the fatty acids and to move the elution region of the sterol esters away from that of the triglycerides. Data from chemical ionization and electron impact mass spectrometry of compounds separated by SFC were used to confirm identities suggested by retention measurements and to provide tentative identities of unknown compounds. SFC with flame ionization detection was used to compare Soxhlet extraction, off-line supercritical fluid extraction (SFE), and on-line SFE of the feces. Although samples obtained by Soxhlet extraction and SFE produced very similar chromatograms, SFE required far less time and consumed much smaller quantities of organic solvent.     

Assessing the ability of chemical similarity measures to discriminate between active and inactive compounds

Summary A method for assessing the biological discriminating power of chemical similarity measures is presented. The main concern of this work was to develop an objective way of evaluating different similarity measures in terms of how well they distinguished between active and inactive compounds. In addition, we have explored the level of similarity required for optimal separation and commented on its implications for work in the field of chemical diversity studies. The results for one simple similarity measure showed that statistically significant separation could be achieved, and indicated a reasonable similarity value for future work.     

Virtual screening using binary kernel discrimination: analysis of pesticide data

This paper discusses the use of binary kernel discrimination (BKD) for identifying potential active compounds in lead-discovery programs. BKD was compared with established virtual screening methods in a series of experiments using pesticide data from the Syngenta corporate database. It was found to be superior to methods based on similarity searching and substructural analysis but inferior to a support vector machine. Similar conclusions resulted from application of the methods to a pesticide data set for which categorical activity data were available.     

Measurement of heterogeneous reaction rates: three strategies for controlling mass transport and their application to indium-mediated allylations

We describe three new strategies for determining heterogeneous reaction rates using photomicroscopy to measure the rate of retreat of metal surfaces: (i) spheres in a stirred solution, (ii) microscopic powder in an unstirred solution, and (iii) spheres on a rotating shaft. The strategies are applied to indium-mediated allylation (IMA), which is a powerful tool for synthetic chemists because of its stereoselectivity, broad applicability, and high yields. The rate-limiting step of IMA, reaction of allyl halides at indium metal surfaces, is shown to be fast, with a minimum value of the heterogeneous rate constant of 1 × 10(-2) cm/s, an order of magnitude faster than the previously determined minimum value. The strategies described here can be applied to any reaction in which the surface is retreating or advancing, thereby broadening the applicability of photomicroscopy to measuring heterogeneous reaction kinetics.     

Isolation and Characterization of Precise Dye/Dendrimer Ratios

Fluorescent dyes are commonly conjugated to nanomaterials for imaging applications using stochastic synthesis conditions that result in a Poisson distribution of dye/particle ratios and therefore a broad range of photophysical and biodistribution properties. We report the isolation and characterization of generation 5 poly(amidoamine) (G5 PAMAM) dendrimer samples containing 1, 2, 3, and 4 fluorescein (FC) or 6‐carboxytetramethylrhodamine succinimidyl ester (TAMRA) dyes per polymer particle. For the fluorescein case, this was achieved by stochastically functionalizing dendrimer with a cyclooctyne “click” ligand, separation into sample containing precisely defined “click” ligand/particle ratios using reverse‐phase high performance liquid chromatography (RP‐HPLC), followed by reaction with excess azide‐functionalized fluorescein dye. For the TAMRA samples, stochastically functionalized dendrimer was directly separated into precise dye/particle ratios using RP‐HPLC. These materials were characterized using ¹H and ¹⁹F NMR spectroscopy, RP‐HPLC, UV/Vis and fluorescence spectroscopy, lifetime measurements, and MALDI.     

Molecular Fluorescence Imaging Spectroscopy for Mapping Low Concentrations of Red Lake Pigments: Van Gogh's Painting The Olive Orchard

Vincent van Gogh used fugitive red lake pigments that have faded in some paintings. Mapping their distribution is key to understanding how his paintings have changed with time. While red lake pigments can be identified from microsamples, in situ identification and mapping remain challenging. This paper explores the ability of molecular fluorescence imaging spectroscopy to identify and, more importantly, map residual non‐degraded red lakes. The high sensitivity of this method enabled identification of the emission spectra of eosin (tetrabromine fluorescein) lake mixed with lead or zinc white at lower concentrations than elemental X‐ray fluorescence (XRF) spectroscopy used on account of bromine. The molecular fluorescence mapping of residual eosin and two carmine red lakes in van Gogh's The Olive Orchard is demonstrated and compared with XRF imaging spectroscopy. The red lakes are consistent with the composition of paint tubes known to have been used by van Gogh.