Quantitative molecular similarity analysis (QMSA) methods for property estimation: a comparison of property-based,arbitrary, and tailored similarity spaces

Three classes of arbitrary quantitative molecular similarity analysis (QMSA) methods have been computed using atom pairs, topological indices, and physicochemical properties. Tailored QMSA models have been developed using a selected number of TIs chosen by ridge regression. The methods have been applied to the K-nearest neighbor based estimation of log P of two sets of chemicals. Results show that the property-based and tailored QMSA methods are superior to the arbitrary similarity methods in estimating log P of both sets of chemicals     

A comparative study of proteomics maps using graph theoretical biodescriptors

This paper reports the development of new methods for mathematical characterization of effects of different toxic agents on the cellular proteome. We describe numerical characterization of proteomics maps based on mathematical invariants. A graph is first associated with a proteomics map by considering partial ordering of spots on 2-D gels by ordering proteins with respect to the mass and the charge, the two properties by which proteins are separated. The graph is then embedded over the map, and several graph theoretical invariants have been constructed. In particular we consider invariants that can be extracted from the Euclidean distance-adjacency matrix of the embedded graph, in which only Euclidean distances between adjacent vertices of a graph are considered. The approach is illustrated using proteomics patterns of normal liver cells of rats and those derived from liver cells of animals exposed to four peroxisome proliferators. In contrast to direct comparison of spot abundance our approach incorporates information on spots locations. The difference between the two approaches is that in the first case only changes in abundances are considered as a measure of perturbation of the proteome map, but in the second case not only the charge but also the mass of proteins are used for ordering protein spots.     

Studies on intramolecular Diels-Alder reactions of furo[3,4-c]pyridines in the synthesis of conformationally restricted analogues of nicotine and anabasine

En route to conformationally restricted analogues of nicotine and anabasine, a novel synthetic route to bridged anabasines is described that hinges on a domino intramolecular [4 + 2]-cycloaddition/ring opening-elimination sequence of 3-amino-substituted furo[3,4-c]pyridines. Extension of this route to bridged nicotines, however, proved abortive, even when the dienophile tether is activated by a p-tolylsulfonyl group or when the diene moiety is activated by an electron-releasing methoxy substituent. A detailed density functional theoretical study (B3LYP/6-31+G) was undertaken to provide insight into the factors that facilitate an intramolecular Diels-Alder reaction in the former case.     

On 3-D graphical representation of DNA primary sequences and their numerical characterization

In this article we (1) outline the construction of a 3-D "graphical" representation of DNA primary sequences, illustrated on a portion of the human beta globin gene; (2) describe a particular scheme that transforms the above 3-D spatial representation of DNA into a numerical matrix representation; (3) illustrate construction of matrix invariants for DNA sequences; and (4) suggest a data reduction based on statistical analysis of matrix invariants generated for DNA. Each of the four contributions represents a novel development that we hope will facilitate comparative studies of DNA and open new directions for representation and characterization of DNA primary sequences.     

Metal Complexes with Macrocyclic Ligands,XVIII. A study of steric effects in the Co2+-, Ni2+- and Cu2+-complexes with 1-(2-aminoethyl)- and 1-(2-dimethylaminoethyl)-4,8,11-trimethyl-1,4,8,11-tetraazacyclotetradecane

The two macrocycles 1-(2-aminoethyl)- and 1-[2-(dimethylamino)ethyl]-4, 8, 11-trimethyl-1, 4, 8, 11-tetraazacyclotetradecane, 1 and 2 , respectively, and their metal complexes with Co²⁺, Ni²⁺ and Cu²⁺ were prepared. The different spectral properties of the complexes with these two ligands can be rationalized by assuming that, in the case of 1 , the amino group of the pendant arm is axially coordinated to the metal ion giving a pentacoordinate structure, whereas the dimethylamino group of 2 cannot bind because of sterical hindrance. This is also corroborated by the observation that the complexes of 2 react with unidentate ligands such as N and SCN^? to give ternary species MLX⁺, whereas those of 1 do not. This indicates that the complexes of 1 have no free coordination site, their coordination sphere being completely saturated by the five N-atoms of the macrocycle, whereas the complexes of 2 having a vacant site still can add an unidentate ligand.     

A Garratt-Braverman route to isoindolines and phthalans

Garratt-Braverman (GB) cyclization, two CC bond forming reaction in a single step, has been utilized to construct several isoindoline and phthalan derivatives. The precursors were the bispropargyl protected amines and ethers with one of the propargyl arm substituted with an alkene moiety. The GB cyclizations were generally carried out in presence of DBU in refluxing toluene. In case of the bispropargyl amine systems with the alkene arm substituted with electron withdrawing ester group, the cyclization occurred at room temperature. The yields of cyclization ranged from 64 to 86% which are acceptable considering the formation of two CC bonds. The protected isoindolines could be successfully deprotected by treatment with thiophenol in presence of triethyl amine and the corresponding free amines were isolated as the TFA salts.     

Metal Complexes with Macrocyclic Ligands. Part XXVI. Synthesis and spectral properties of Cu2+ complexes with mono-N-functionalized 1,4,8-trimethyl-1,4,8,11-tetraazacyclotetradecanes

A series of mono-N-functionalized 1,4,8-trimethyl-1,4,8,11-tetraazacyclotetradecanes 3 – 14 were synthesized by alkylating the secondary N-atom of the macrocycle 1 . The spectral properties of the Cu²⁺ complexes, studied under different pH conditions, are discussed in relation to the possibility of coordination of the donor group of the side chain to the axial position of the metal ion and to the effect of the length of the side chain.     

Kinetics and mechanism of the copper(II) promoted hydrolysis of the methyl ester of ethylenediaminemonoacetate

Summary Base hydrolysis of methyl ethylenediaminemonoacetate has been studied at I=0.1 mol dm^–3 (NaClO₄) over the pH range 7.4–8.8 at 25 °C. The proton equilibria of the ligand can be represented by the equations, where E is the free unprotonated ester species. Values of pK₁ and pK₂ are 4.69 andca. 7.5 at 25° (I=0.1 mol dm^–3). For base hydrolysis of EH⁺, k_OH=1.1×10³ dm³ mol^–1 s^–1 at 25 °C. The species E is shown to undergo lactamisation to give 2-oxopiperazine (k_lact ca. 1×10^–3 s^–1) at 25 °C. Formation of the lactam is indicated both by u.v. measurements and by isolation and characterisation of the compound.Base hydrolysis of the ester ligand in the complex [CuE]²⁺ has been studied over a range of pH and temperature, k _OH ²⁵ =9.3×10⁴ dm³ mol^–1 s^–1 with H=107 kJ mol^–1 and S ₂₉₈ =209 JK^–1 mol^–1. Base hydrolysis of [CuE]²⁺ is estimated to be some 10⁵5 fold faster than that of the free ester ligand. The results suggest that base hydrolysis occursvia a chelate ester species in which the methoxycarbonyl group of the ligand is bonded to copper(II).