Clustering of chemical databases by means of the projection of maximum overlapping sets similarity measurements onto multidimensional spaces

In this paper, we propose a new method for clustering of chemical databases based on the representation of measurements of structural similarity onto multidimensional spaces. The proposed method permits the tuning of the clustering process through the selection of the dimension of the projection space, the normal vectors and the sensibility of the projection process. The structural similarity of each element regarding to the database elements is projected onto the defined spaces generating clusters that represent the characteristics and diversity of the database and whose size and characteristics can be easily adjusted.     

New aspects of the electroadsorption of ethyl xanthate on copper electrodes

The interaction of the ethyl xanthate (EX) anion with a copper electrode in a borate buffer solution, pH 9.2, has been investigated by cyclic voltammetry (CV), electrochemical quartz crystal microbalance (EQCM), electrochemical impedance spectroscopy (EIS), and measurements of contact angle (CA) under controlled potential. The results obtained allow establishing that, in the potential range from -0.80 and -0.60 V, two parallel reactions were characterized. These reactions were the ethyl xanthate electroadsorption and the hydrogen evolution reaction (HER). This last reaction has not been described by previous authors. Besides, the EIS measurements show that the mechanism of the HER on copper electrodes is not affected by the presence of a ethyl xanthate species. The EQCM study shows that in the electrodesorption process the departure of each ethyl xanthate species from the copper electrode is accompanied with the simultaneous entry of four to five water molecules. This fact is in accordance with the number of copper atoms involved in the adsorption of one ethyl xanthate species.     

Hexaruthenium carbonyl cluster complexes with basal edge-bridged square pyramidal metallic skeleton: efficient synthesis of 2-imidopyridine derivatives and determination of their reactive sites in carbonyl substitution reactions

The reactions of [Ru(3)(CO)(12)] with half equivalent of 2-amino-6-methylpyridine (H(2)ampy) or 2-aminopyridine (H(2)apy) in refluxing xylene give the hexanuclear products [Ru(6)(mu(3)-H)(2)(mu(5)-eta(2)-L)(mu-CO)(2)(CO)(14)] (L = ampy, 1; apy, 2). These reactions represent the first high-yield syntheses of hexanuclear complexes with a basal edge-bridged square pyramidal metallic skeleton. Five metal atoms of these complexes are bridged by the N-donor ligand in such a way that the edge-bridging metal atom is attached to the pyridine nitrogen, while the basal atoms of the square pyramid are capped by an imido fragment that arises from the activation of both N-H bonds of the NH(2) group. The reactive sites of these complexes in CO substitution reactions have been determined by studying the reactivity of 1 with triphenylphosphine. Two kinetically controlled monosubstitutions take place on the edge-bridging metal atom in positions cis to the pyridine nitrogen, leading to a mixture of two isomers of formula [Ru(6)(mu(3)-H)(2)(mu(5)-eta(2)-ampy)(mu-CO)(2)(CO)(13)(PPh(3))] (3 and 4). On heating at 80 degrees C, these monosubstituted isomers are transformed, via a dissociative pathway, into the product of thermodynamic control (5), which has the PPh(3) ligand on the apical Ru atom. The di- and trisubstituted derivatives [Ru(6)(mu(3)-H)(2)(mu(5)-eta(2)-ampy)(mu-CO)(2)(CO)(12)(PPh(3))(2)] (6) and [Ru(6)(mu(3)-H)(2)(mu(5)-eta(2)-ampy)(mu-CO)(2)(CO)(11)(PPh(3))(3)] (7) are stepwise formed from 3-5 and PPh(3). Compound 6 has the PPh(3) ligands on the edge-bridging and apical Ru atoms, and compound 7 has an additional PPh(3) ligand on an unbridged basal Ru atom. The compound [Ru(6)(mu(3)-H)(2)(mu(5)-eta(2)-ampy)(mu-CO)(2)(CO)(12)(mu-dppm)] (8), in which a basal and the apical Ru atoms are spanned by the dppm ligand, has been isolated from the reaction of 1 with bis(diphenylphosphino)methane.     

Electronic states and nature of the chemical bond in the molecule CrC by all-electron ab initio calculations

All-electron ab initio Hartree–Fock (HF ), valence configuration interaction (CI ), and multiconfiguration self-consistent-field (CASSCF ) calculations have been applied to investigate the electronic states of the CrC molecule. The molecule is predicted as having four low-lying electronic states, ³∑^?, ⁵∑^?, ⁷∑^?, and ⁹∑^?, separated by an energy gap of 0.55 eV from the next higher-lying state, ¹∑^?, which is followed by the states ⁵Π and ⁷Π. The four lowest-lying electronic states are due to the coupling of the angular momenta of the ⁶S_g Cr⁺ ion with those of the ⁴S_u C^? anion. The chemical bond in the ³∑^? ground state can be viewed as a quadruple bond composed of two σ and two π bonds. One σ bond is due to the formation of a molecular orbital that is doubly occupied. The remaining bonds, i.e., one σ and two π bonds, arise from valence-bond couplings. The π bonds originate from the valence-bond couplings of the electrons in the C 2pπ orbitals with those in the Cr 3dπ orbitals. The σ bond originates from the valence-bond coupling of the C 2pσ electron with an electron in the Cr 4s, 4p hybrid that is polarized away from the C atom.     

Über die Strukturaufklärung von (Hydroxy-oxo-cyclopentenyl)alkansäuren,den Aldolkondensationsprodukten von Dioxoencarbonsäuren aus Rinderleber

Structure Elucidation of (Hydroxy-oxo-cyclopentenyl)alkanoic Acids, the Aldol-Condensation Products of Dioxoene Acids from Cattle Liver During homogenization of cattle liver the highly instable dioxoene acids 13a , 13b , and 13c are formed. These acids cyclize in alkaline solution to yield pairs of stable (hydroxy-oxo-cyclopentenyl)alkanoic acids, which were isolated as methyl esters 4a / 5a , 4b / 5b , and 4c / 5c . The structures of these compounds were deduced from an enriched 3-mg mixture sample by microchemical reactions combined with a GC/MS analysis of the reaction products. Compound 13a was obtained as methyl ester by oxidation of the methyl ester of the corresponding F-acid with NaOCl. It was not possible to isolate 13a in pure form due to its high sensitivity. Instead of the methyl ester of 13a , 4a and 5a were isolated, of which the structures were established.     

Adhesion between graphite and modified polyester surfaces: a theoretical study

This study examines the adhesion of graphite to functionalized polyester surfaces using a range of qualitative and quantitative measures of theoretical adhesion. Modifications to the polyester surfaces include the addition of hydroxyl, carboxyl, or fluorine substituents with coverages of 0.4 and 0.9 groups per nm(2). In each case, the introduction of substituents to the surface of the polyester was calculated to lead to reduced adhesion to graphite. Effects of surface relaxation on adhesion are studied by employing different simulation protocols. The theoretical results suggest one mechanism to reduce adhesion to carbonaceous solids is to increase atomic roughness using strongly hydrophilic or alternatively strongly hydrophobic substituents.     

Linked crystallites in the conducting topmost layer of polymer bilayer films controlled by temperature: from micro- to nanocrystallites.

Temperature has great impact on the structure and size of the linked crystallites of the conducting topmost layer formed at the surface of a polycarbonate film via the reaction BEDT-TTF+IBr [BEDT-TTF=bis(ethylenedithio)tetrathiafulvalene]. We show that fine temperature control permits formation of a semiconducting topmost layer of alpha'-(BEDT-TTF)(2)(I(x)Br(1-x))(3) crystallites with either micro- or nanometre size, a result that opens a route to miniaturized conducting plastic materials.     

Substituent-controlled photoisomerization in retinal chromophore models: Fluorinated and methoxy-substituted protonated Schiff bases

The effect of substitution on the intrinsic (i.e. in vacuo) photoisomerization ability of retinal chromophore models has been explored using CASPT2//CASSCF minimum energy path computations to map the S₁ photoisomerization paths of two substituted minimal models of the retinal chromophore: the 2-cis-penta-2,4-dieniminium and the all-trans-epta-2,4,6-trieniminium cations, which have been modified using fluorine or methoxyl substituents as representative examples of electron-withdrawing and electron-releasing groups, respectively. A systematic analysis has been performed involving substitutions in all the possible positions along the chain. It is shown that the photochemical reactivity and photoisomerization efficiency of these systems may be tuned or indeed changed, although this effect strongly depends on the position of the substituent. In particular, we have shown that (i) most of the systems preserves qualitatively the reactivity of the parent (i.e. unsubstituted) compound; (ii) substitution at positions C4 or C6 leads to a different relaxed excited state structure of the chromophore and in general to a very flat photoisomerization path (or to a tiny S₁ energy barrier in some cases); (iii) the nature of the TICT state (i.e. the S₁ → S₀ decay funnel) may be turned from a conical intersection into an excited state minimum; (iv) for the C4 methoxy-substituted system the isomerization path as well as the S₁/S₀ decay funnel involve an unusual torsional angle. Thus, substitution turns out to be a good tool not only to tune the optical properties (i.e. the absorption and emission features) of the chromophore (as we have already shown in a previous work: I. Conti, F. Bernardi, G. Orlandi, M. Garavelli, Mol. Phys. 104 (2006) 915–924), but it may also play a crucial role in tuning and controlling photoisomerization selectivity and efficiency, affecting excited state lifetime and reaction rate. A rationale for these effects is presented, which provides a basis for understanding reactivity properties and the intrinsic photochemical behavior of substituted retinal chromophores.     

Raman spectroscopic and structural studies of indigo and its four 6,6'-dihalogeno analogues

The Raman and electron impact mass spectra of synthetic indigo and its four 6,6'-dihalogeno analogues are reported and discussed. The influence of varying the halogen on these Raman spectra is considered. Particular emphasis is laid on distinguishing indigo from 6,6'-dibromoindigo and differentiating between the dihalogenocompounds, so as to develop protocols for determining whether artefacts are coloured with dyes of marine or terrestrial origin and whether such artefacts are dyed with genuine "Tyrian Purple" or with dihalogenoindigo substitutes that do not contain bromine. The value of even low resolution electron impact mass spectrometry in a forensic context as a means of identifying authentic 6,6'-dibromoindigo and distinguishing it from its dihalogenoanalogues is emphasised     

High-performance liquid chromatography of amino acids, peptides and proteins CXXV. Molecular dynamics simulation of n-butyl chains chemically bonded to silica-based reversed-phase high-performance liquid chromatography sorbents

The molecular dynamics method has been applied to investigate the conformations of n-butyl ligands immobilised onto an amorphous silica surface analogous to those utilised with silica-based RP-HPLC sorbents. Three systems were constructed which corresponded to ligand densities of 1.64, 2.67 and 3.69 μmol/m². A number of parameters related to the structure of the sorbent materials were derived in order to characterise the molecular properties of each system. These parameters included the hydrocarbon layer thickness, the frequency of gauche conformations, the distance distribution for carbon atoms and the diffusion coefficients of individual atoms in the n-butyl ligands. From these properties, the positions of chains with respect to the surface as well as their mobility were estimated. It was found that at higher densities, the n-butyl chains are predominantly perpendicular to the surface while at low density they are highly tilted or lying almost parallel to the surface. The degree of ligand flexibility decreased with increasing surface density. Mobility of individual carbon atoms as well as chain disorder increased with distance from the surface for all ligand densities. The simulated properties of n-butyl chains immobilised to a silica surface correlated well with results obtained by Fourier transform IR and ¹³C-cross polarisation magic angle spinning NMR experimental methods and statistical predictions of the behaviour of immobilised chains.