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.     

Organoruthenaborane Chemistry. X. The SM2-catalysed formation of [ l-(η6-C6Me6)-isocloso-RuB9H9], and some B-phenylamino derivatives. NMR and X-ray diffraction studies

The action of SMe₂ on the ten-vertex nido-ruthenaborane [6-(η⁶-C₆Me₆)RuB₉H_l3] ( 1 ) provides a high-yield route to the unsubstituted isocloso-ruthenaborane [1-(η⁶-C₆Me₆)RuB₉H₉] (2). The benzene analogue [1-(η⁶-C₆Me₆)RuB₉H₉] is prepared similarly. By contrast, reaction of (1) with PhNH₂ gives a variety of B-phenylamino isocloso derivatives, including orange crystals of [1-(η⁶-C₆Me₆)-2-(PhNH)-isocloso-1-RuB 9 H₈] ( 3 ), red-orange [1-(η⁶-C₆Me₆)-2,3-(PhNH)₂-isocloso-1-RuB₉H₇] ( 4 ) and dark-red [1-(η⁶-C₆Me₆)-5,6,7-(PhNH)₃-isocloso-1-RuB₉H₆] ( 5 ). Detailed ¹H and ¹¹B nmr properties of these various compounds are described. The structure of ( 3 ) has been established by a single-crystal X-ray diffraction study of the solvate [1-(η⁶-C₆Me₆)-2-(PhNH)-isocloso-1-RuB₉H₈] · 1/2 CH₂Cl₂; the crystals were monoclinic, space group C2/c, with a = 1895.1(3), b = 1556.6(3), c = 1716.4(3) pm, β = 104.37(1)° and z = 8.     

Time shift correction in second-order liquid chromatographic data with iterative target transformation factor analysis

When the generalized rank annihilation method (GRAM) is applied to liquid chromatographic data with diode-array detection, an important problem is the time shift of the peak of the analyte in the test sample. This problem leads to erroneous predictions. This time shift can be corrected if a time window is selected so that the chromatographic profile of the analyte in the test sample is trilinear with the peak of the analyte in the calibration sample. In this paper we present a new method to determine when this condition is met. This method is based on the curve resolution with iterative target transformation factor analysis (ITTFA). The calibration and test matrices are independently decomposed into profiles and spectra, and aligned before GRAM is applied. Here we study two situations: first, when the calibration matrix has one analyte and second, when it has two analytes. When the calibration matrix has two analytes, we selectively determine the time window for the analyte to be quantified. There were considerably fewer prediction errors after correction.     

Nouvelle methode de dosage du gaz carbonique dans les produits alimentaires et application au fromage

The determination of carbon dioxide in food products with particular application to cheese Samples are emulsified under reduced pressure in an alkaline citrate medium in an airtight mixer and CO₂ is quantitatively displaced into the head space by addition of an excess of sulphuric acid. A small gas pump ensures gas circulation to a specific nondispersive infrared detector mounted in a by-pass for measurement. The residual depression in the head space is suppressed shortly before measuring. The equipment is calibrated with standard gases and standard additions of sodium carbonate. The method is sufficiently simple and rapid for routine use (about 30 samples/day). The coefficient of variation is less than 1% for standard solutions and less than 2% for cheese. The matrix has practically no influence on the accuracy of the measurements.     

Synthesis and structure of Pt(II) phosphonato-phosphine complexes and of a P,O-stabilized metal-metal-bonded Pt2Ag2 complex

As part of our interest in the design and reactivity of P,O ligands, and because the insertion chemistry of small molecules into a metal alkyl bond is very dependent on the ancillary ligands, the behavior of Pt-methyl complexes containing the beta-phosphonato-phosphine ligand rac-Ph2PCH(Ph)P(O)(OEt)2 (abbreviated PPO in the following) toward CO insertion has been explored. New, mononuclear Pt(II) complexes containing one or two PPO ligands, [PtClMe(kappa2-PPO)] (1), [Pt{C(O)Me}Cl(kappa2-PPO)] (2), [PtMe(CO)(kappa2-PPO)]OTf (3 x OTf), [PtMe(OTf)(kappa2-PPO)] (4), trans-[PtClMe(kappa1-PPO)2] (5), [PtMe(kappa2-PPO)(kappa1-PPO)]BF4 (6 x BF4), [PtMe(kappa2-PPO)(kappa1-PPO)]OTf (6 x OTf), and [Pt{C(O)Me}(kappa2-PPO)(kappa1-PPO)]BF4 (7 x BF4) have been prepared and characterized. Hemilability of the ligands is observed in the cations 6 and 7 in which the terminally bound and chelating PPO ligands exchange their role on the NMR time-scale. The acetyl complexes 2 and 7 are stable in solution, but the former deinserts CO upon chloride abstraction. We also demonstrate the ability of PPO to behave as an assembling ligand and to stabilize a heterometallic Pt-Ag metal complex, [PtMe(kappa2-PPO){mu-(eta1-P;eta1-O)PPO)}Ag(OTf)(Pt-Ag)]OTf (8 x OTf), which was obtained by reaction of 5 with AgOTf to generate more reactive, cationic complexes. Whereas the first equivalent of AgOTf abstracted the chloride ligand, the second equivalent added to the cationic complex with formation of a Pt-Ag bond (2.819(1) A). The complexes 1, 2, 4, 5 x CH2Cl2, and (8 x OTf)2 have been structurally characterized by single-crystal X-ray diffraction. The latter has a dimeric nature in the solid state, with two silver-bound triflates acting as bridging ligands between two Pt-Ag moieties. In addition to the Ag-Pt bond, the Ag+ cation is stabilized by a dative O -->Ag interaction involving one of the PPO ligands.     

Amberlite XAD-2 functionalized with 2-aminothiophenol as a new sorbent for on-line preconcentration of cadmium and copper

A new functionalized resin has been applied in an on-line preconcentration system for copper and cadmium determination. Amberlite XAD-2 was functionalized by coupling it to 2-aminothiophenol (AT-XAD) by means of an NN spacer. This resin was packed in a minicolumn and used as sorbent in the on-line system. Metal ions were sorbed in the minicolumn, from which it could be eluted directly to the nebulizer-burner system of the flame atomic absorption spectrometer (FAAS). Elution of Cd(II) and Cu(II) from minicolumn can be made with 0.50 mol l⁻¹ HCl or HNO₃. The enrichment factors obtained were 28 (Cd) and 14 (Cu), for 60 s preconcentration time, and 74 (Cd) and 35 (Cu), if used 180 s preconcentration time. The proposed procedure allowed the determination of cadmium and copper with detection limits of 0.14 and 0.54 μg l⁻¹, respectively, when used preconcentration periods of 180 s. The effects of foreign ions on the adsorption of these metal ions are reported. The validation of the procedure was carried out by analysis of certified reference material. This procedure was applied to cadmium and copper determination in natural, drink and tap water samples.     

Density functional theory study of vibrational spectra, and assignment of fundamental vibrational modes of succinimide and N-bromosuccinimide

This work deals with the vibrational spectroscopy of succinimide and N-bromosuccinimide. The mid and far FTIR and FT-Raman spectra were measured in the condensed state. The fundamental vibrational frequencies and intensity of vibrational bands were evaluated using density functional theory (DFT) using standard B3LYP/6-31G(*) and B3LYP/6-311+G(**) methods and basis set combinations. The vibrational spectra were interpreted, with the aid of normal coordinate analysis based on a scaled quantum mechanical force field. The infrared and Raman spectra were also predicted from the calculated intensities. Comparison of simulated spectra with the experimental spectra provides important information about the ability of the computational method to describe the vibrational modes. Unambiguous vibrational assignment of all the fundamentals were made using the total energy distribution (TED).     

Limit of detection estimator for second-order bilinear calibration

A new approach is developed for estimating the limit of detection in second-order bilinear calibration with the generalized rank annihilation method (GRAM). The proposed estimator is based on recently derived expressions for prediction variance and bias. It follows the latest IUPAC recommendations in the sense that it concisely accounts for the probabilities of committing both types I and II errors, i.e. false positive and false negative declarations, respectively. The estimator has been extensively validated with simulated data, yielding promising results.     

Two New Antiferromagnetic Nickel(II) Complexes Bridged by Azido Ligands in the Cis Position. Effect of the Counteranion on the Crystal Structure and Magnetic Properties

Two new nickel(II) end-to-end azido-bridged compounds, cis-catena-[NiL(2)(&mgr;-N(3))](n)()(ClO(4))(n)().nH(2)O (1) and [Ni(2)L(4)(&mgr;-N(3))(2)](PF(6))(2) (2), were synthesized and characterized; L is 2-(aminoethyl)pyridine. The crystal structures of 1 and 2 were solved. Complex 1: monoclinic system, space group P2(1)/a, a = 8.637(2) ?, b = 18.9995(7) ?, c = 12.3093(7) ?, beta = 105.92(2) degrees, Z = 4. Complex 2: triclinic system, space group P&onemacr;, a = 9.139(7) ?, b = 10.124(3) ?, c = 12.024(2) ?, alpha = 70.407(14) degrees, beta = 84.19(2) degrees, gamma = 67.67(4) degrees, Z = 1. In the two complexes the nickel atom is situated in a similarly distorted octahedral environment. The two complexes are different; 1 is a one-dimensional helicoidal complex with the two L ligands and the two end-to-end azido bridges in a cis arrangement while complex 2 is a dinuclear system with two end-to-end azido bridges, indicating the extreme importance of the counteranion present (ClO(4)(-) for 1 and PF(6)(-) for 2). The magnetic properties of the two compounds were studied by susceptibility measurements vs temperature. The chi(M) vs T plot for 1 shows the shape for a weakly antiferromagnetically coupled nickel(II) one-dimensional complex without a maximum until 4 K. In contrast, for complex 2 the shape of the chi(M) vs T curve shows a maximum near 40 K, indicating medium antiferromagnetic coupling. From the spin Hamiltonian -J(ij)()S(i)()S(j)(), J values for 1 and 2 were less than -1 and -29.1 cm(-)(1), respectively. The magnetic behavior for 1 and 2 may be explained in terms of the overlap between magnetic orbitals, taking into account the torsion of the Ni(II) atoms and azido-bridging ligands in the two structures.     

Ferrocenoyl peptides with sulfur-containing side chains: synthesis, solid state and solution structures

The synthesis and full characterization of a number of amino acid and dipeptide derivatives with sulfur-containing side chains derived from ferrocene carboxylic acid and ferrocene-1,1′-dicarboxylic acid is presented. In particular, compounds Fc-CO-(Aaa)_n-OMe (4) and Fe[C₅H₄-CO-(Aaa)_n-OMe]₂ (3) with (Aaa)_n = Cys(Bzl) (a), Cys(Bzl)-Cys(Bzl) (b), Cys(p-OMe-Bzl) (c), Cys(p-OMe-Bzl)-Cys(p-OMe-Bzl) (d), Met (e), and Met-Met (f) were prepared. Also, the free acid derivatives Fe[C₅H₄-CO-Met-OH]₂ (6e) and Fc-CO-Met-OH (7e) were prepared and characterized. The solid state structures of 3a, 4b, and 4e were determined by single crystal X-ray diffraction. Compound 3a shows a 1,3′ substitution pattern on the Cp rings in the solid state. Structures in solution were determined by NMR, IR and CD spectroscopy, with particular emphasis on the question of hydrogen bonding and helical chirality of the metallocene. As an example, the full assignment for the Cp signals in the disubstituted derivative 3a was achieved by simulation of the ¹H NMR signals from the cyclopentadienyl ring in combination with 2D-NOESY spectra. In solution, 3a has the known 1,2′ substitution pattern, which is stabilized by intramolecular hydrogen bonds.