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.     

Laterally attached liquid-crystalline polymers as stationary phases in reversed-phase high-performance liquid chromatography. III. Effect of the local anisotropic order on the separation of polycyclic aromatic hydrocarbons

Specific stationary phases based upon non-liquid-crystalline polymers, liquid-crystalline molecules and side-on fixed liquid-crystalline polymers (SO-LCP) have been synthesized for use as silica modified stationary phases in high-performance liquid chromatography (HPLC). The mesogenic side group of the SO-LCP was composed of three phenyl ring benzoate type with terminal alkoxy chains and was laterally linked to a polysiloxane backbone via an alkyl ester spacer arm. This study demonstrated that the shape recognition of stationary phases based upon SO-LCP towards the length-to-breath ratio (L/B) was strongly connected to the existence of a local liquid-crystalline order into the pores of silica gel, warranting the interest of the collective organization of mesomorphic materials in liquid chromatography. Furthermore, the chromatographic performances depended on the kind of anisotropic order and it was more advantageous to use smectic side-on liquid-crystalline polymer than nematic and obviously non-liquid-crystalline ones. Finally, for a series of polymers having the same mesomorphism, the larger the temperature stability range of the mesophase, the more pronounced the local order effect and the higher the shape recognition.     

From allylic alcohols to aldols by using iron carbonyls as catalysts: computational study on a novel tandem isomerization-aldolization reaction

The tandem isomerization-aldolization reaction between allyl alcohol and formaldehyde mediated by [Fe(CO)3] was studied with the density functional B3LYP method. Starting from the key [(enol)Fe(CO)3] complex, several reaction paths for the reaction with formaldehyde were explored. The results show that the most favorable reaction path involves first an enol/allyl alcohol ligand-exchange process followed by direct condensation of formaldehyde with the free enol. During this process, formation of the new C-C bond takes place simultaneously with a proton transfer between the enol and the aldehyde. Therefore, the role of [Fe(CO)3] is to catalyze the allyl alcohol to enol isomerization affording the free enol, which adds to the aldehyde in a carbonyl-ene type reaction. Similar results were obtained for the reaction between allyl alcohol and acetaldehyde.     

Investigation of the nematic-isotropic transition of a liquid crystalline polymer and determination of molecular diffusion coefficients using gas chromatography

Inverse gas chromatography has been used to study the nematic-isotropic transition of a side chain liquid crystalline polymer (LCP). The mesogenic side groups are laterally attached to a polysiloxane backbone through a flexible spacer. The nematic-isotropic transition of this LCP coated onto a glass capillary column is detected by considering the variation with temperature of the retention volume and of the theoretical plate number for the several probes. The molecular diffusion coefficients, D, of naphthalene, fluorene, pyrene and o-terphenyl have been determined at different temperatures in the nematic phase of the LCP as well as in the isotropic melt. The values ranged between 10(-14) and 10(-12) m2 s(-1) for the polynuclear aromatic hydrocarbon probes tested.     

Total synthesis of zincophorin methyl ester

[reaction: see text]. A convergent total synthesis of the methyl ester of zincophorin, an ionophore antibiotic, has been realized relying on a diastereoselective titanium-mediated aldol coupling between the C1-C12 and C13-C25 subunits. The latter fragment was prepared by using a Carroll-Claisen rearrangement.     

Lignocellulosic biomass for bioethanol: Recent advances,technology trends,and barriers to industrial development

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Equilibrium and Kinetics of NO and CO Chemisorptions on Nonstoichiometric Nickel-Copper Manganites

The equilibrium and kinetics of adsorption of NO and CO on nonstoichiometric nickel-copper manganites have been investigated through volumetric measurements. The adsorption isotherms were satisfactorily fitted to the Freundlich equation. The equilibrium coverages at 298 K were found to depend closely on the chemical composition of the oxide; thus, a decrease in the coverage beyond a maximum copper extent was observed. The adsorption isotherms of NO at various temperatures in the range from 298 to 473 K showed that the equilibrium coverage decreases with increasing temperature. This behavior enabled us to follow the logarithmic decrease of the heat of adsorption of NO on such surfaces. The adsorptions of NO and CO on surfaces preadsorbed with CO and NO, respectively, were also studied. These experiments showed the ability of NO to displace CO preadsorbed molecules whereas the contrary did not hold, suggesting the existence of common adsorption sites as well as some specific CO adsorption sites. Finally, some kinetic data are reported showing that the experimental adsorption results fit the Elovich equation (with t(0) approximately 0), although two distinct rate processes could be identified. Copyright 2000 Academic Press.     

Metabolite profiling in rat urine by liquid chromatography/electrospray ion trap mass spectrometry. Application to the study of heavy metal toxicity

This work reports the use of reverse-phase liquid chromatography coupled to electrospray ion trap (QIT) mass spectrometry for the analysis of the metabolome in rat urine. An injection of 20 microL of urine into the chromatographic system is followed by a slow gradient elution and mass spectrometric detection in the scanning mode from m/z 100-1000 in both positive and negative modes. Over a time scale of 90 min, 30 and 20 resolved peaks were observed in the positive and the negative modes, respectively, corresponding to the presence of a few hundred m/z ratios. By using a QIT analyzer, data-dependent tandem mass spectrometry of selected m/z ratios identified several compounds in rat urine and characterized various chemical families, including carboxylic acids, amines, sulfated compounds, glucuronides and glycosides, by the observation of characteristic fragment ions or neutral losses. The method has been applied to the investigation of the chronic toxicity of heavy metals in rat urine. A few tens of m/z ratios, differing in intensity more than threefold from control values, were observed in both positive and negative modes. The time variations for some selected ions suggest that LC/ESI-MS could allow selective characterization of biomarkers in response to specific toxic compounds.     

Generation and characterization of phenylsulfanylcarbene

A photosensitive precursor (1) to phenylsulfanylcarbene 2 has been synthesized. Laser flash photolysis (308 nm) of 1 and chemical trapping studies of 2 are reported. [structure: see text]     

Pressurised solvent extraction for organotin speciation in vegetable matrices

Because organotin compounds (OTC) are widely used in many fields of activity, they have become an ubiquitous environmental presence. The presence of organotins in the environment impacts upon food safety, making it important to monitor the levels of organotin pesticides in fruits and vegetables. Nevertheless, only a few studies have been published on organotin speciation in plants. The objective of the present study was to evaluate and optimise a specific procedure based on pressurised solvent extraction (PSE) that is suitable for monitoring organotin content in vegetables. In ASE, solvents are used at elevated temperatures and pressures to increase the rate and efficiency of the extraction process. The results from this procedure were compared to those from the technique usually employed, solid/liquid extraction (SLE) performed in an acidic solvent by mechanical shaking. Three extracting solutions were tested—methanol, ethyl acetate and a mixture of methanol and ethyl acetate—and the mixture was found to give the most quantitative results while preserving the speciation. French bean and lettuce leaves as well as potato tubers were used as the plant materials. These vegetables were considered because they are the vegatables consumed in the most quantities in Europe. The study focuses on trisubstituted OTCs, which are the most toxic tin species. The samples were spiked with four trisubstituted organotins: tributyltin (TBT), triphenyltin (TPhT), tricyclohexyltin (TcHexT) and trioctyltin (TOcT). The influence of the pressure and the temperature of the PSE on the quantitativity of the process and on species preservation was evaluated using the experimental design methodology. The optimised PSE allowed detection limits down to 1–2 ng (Sn) g^–1 to be reached. These are higher than those obtained by SLE (0.1–1 ng (Sn) g^–1). Although the repeatability is similar for both PSE and SLE (2–12% for triorganotin compounds), this appears to be highly time-dependent in the case of SLE. Comparison with SLE confirms that PSE is an interesting tool for vegetable analysis considering the satisfactory OTC preservation and repeatability obtained for a relatively short extraction duration (only 15 min against 2–12 h for SLE).