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.     

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.     

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.     

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.     

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.     

Optimization of the Conditions for the Cr (III) Adsorption on Activated Carbon

In order to understand the patterns of the adsorption equilibrium of Cr (III) on activated carbon, the adsorption process was studied by two different ways: classical batch experiments on commercial Norit and Merck activated carbons and their oxidized forms in a wide range of pHs; and extended time-based tests at the same pH values on the same adsorbents. This approach allowed us to understand the role of texture, chemical carbon surface functionality and experimental conditions (initial pH of the solution, contact time and adsorbate/adsorbent ratio) on the effectiveness of Cr (III) removal. The adsorption process of Cr (III) at (24 ± 1^∘C) on Merck and Norit activated carbons and their oxidized forms were studied at pH values between 1.5 and 5 (either adjusted or buffered). Chromium concentration was fixed at 200 ppm. The carbon loading ranged from 1.2 to 20 g/l. The carbon/Cr (III) solution contact time was varied from 0.5–1 month to 5 months, to ensure that the saturation of the carbon level was reached. According to the data obtained, the presence of carboxylic groups on carbon surface seems to enhance Cr (III) uptake at initial pH of the solution in the range between 2 and 4. Depending on the nature of the adsorbent surface chemistry, the contact time to reach equilibrium may range from 3 to 5 months. There is an optimum carbon loading which limits the Cr (III) uptake/removal at given pH value. In order to understand the adsorption process, an ion exchange, surface complex and surface precipitation were considered. This paper was presented in the 5th Brazilian Meeting on Adsorption, held at Natal, Brazil, 18-21 July, 2004.     

Invertomers at nitrogen in aziridine carboxylates by mltltinuclear (1H,13C,17O,and15N) NMR study

A confrgurational and conformational study of NH, N-acetyl- and N-sulfonylaziridine carboxylates is performed by¹H ,¹³C,¹⁷O, and¹⁵N NMR spectroscopy. The presence of acetyl and su fonyl groups on the ring nitrogen atom seems to reduce greatly the configurational stability at nitrogen.Published in Khimiya Geterotsiklicheskikh Soedinenii, No. 9, pp. 1226–1234, September, 1995.     

An artificial ionophore based on a polyhydroxylated steroid dimer

The Na+ transporting properties of the first member of a new class of artificial ionophores, based on a C2-symmetric polyhydroxylated steroid dimer, are described.     

High-density lipoproteins contribute to the alpha-1-globulin zone in capillary electrophoresis of human serum proteins

Alpha-1-antitrypsin (AAT) and alpha-1-acid glycoprotein (AAG) are reported to be the main proteins contributing to the alpha-1-globulin capillary zone electrophoresis (CZE) zone, but the sum (AAT + AAG) showed lower than the alpha-1-globulin. We investigated the role of high-density lipoprotein (HDL), an additional protein migrating in the alpha-1-globulin zone, as a possible cause for such a gap. In a set of 98 sera we measured the alpha-1-globulin with a dedicated clinical capillary electrophoresis system, and AAT, AAG and apolipoprotein A-1 (ApoA) by immunonephelometry. The alpha-1-globulin were consistently higher than the sum (AAT + AAG), by (mean value +/- standard deviation) 1.70 +/- 0.88 g/L in 49 sera with low ApoA, and by 3.59 +/- 0.75 g/L in 49 sera with high ApoA. Corresponding figures in the comparison alpha-1-globulin/(AAT + AAG + ApoA) were reduced to 1.08 +/- 0.77 g/L and 1.67 +/- 0.70 g/L. It is concluded that HDL significantly contribute to the CZE alpha-1-globulin zone, but do not completely explain the differences between the electrophoretic and the immunochemical measurements. However, CZE alpha-1-globulin measurements give information about increases of the two major acute phase proteins comparable to specific protein measurements.     

Representation of the molecular topology of cyclical structures by means of cycle graphs. 3. Hierarchical model of screening of chemical databases

The increase in the size and complexity of chemical databases necessitates the proposal and development of efficient methods of classification and recovery of information, which supposes proposal of a model of classification of database records and the use of a compatible model of screening for inspection of clusters and recovery of the molecules that satisfy the search criterion. The cycle graphs model based on consideration of all the cycles and chains (and equivalent cycles and chains) present in the molecular structure has been proven appropriate for classification of chemical databases, giving rise to a generation of different classification levels depending on the structural elements (cycles and chains) that are considered. In this paper we propose a screening model, compatible with the cycle graphs model, based on a hierarchy of levels of abstraction. The set of molecules that satisfies a screening model (or selection criterion) diminishes as we advance in the hierarchy of levels of the model, which allows filtering of records and, therefore, an increase in the efficiency of the screening process. In the following work of this series we describe and validate the screening tool developed.