Clustering files of chemical structures using the fuzzy k-means clustering method

This paper evaluates the use of the fuzzy k-means clustering method for the clustering of files of 2D chemical structures. Simulated property prediction experiments with the Starlist file of logP values demonstrate that use of the fuzzy k-means method can, in some cases, yield results that are superior to those obtained with the conventional k-means method and with Ward's clustering method. Clustering of several small sets of agrochemical compounds demonstrate the ability of the fuzzy k-means method to highlight multicluster membership and to identify outlier compounds, although the former can be difficult to interpret in some cases.     

Building addressable libraries: the use of electrochemistry for spatially isolating a heck reaction on a chip

Pd(0) was generated at preselected sites on an electrochemically addressable chip and then utilized to effect a Heck reaction. The Pd(0) was confined to the preselected electrodes with the use of allylmethyl carbonate. Unlike most mediated electrochemical reactions, the electrolysis in this case was not used to convert a stoichiometric process into a catalytic one by recycling the metal. Instead, the unique environment of the chip was used to interfere with a catalytic process to make it stoichiometric. This was done to gain spatial control over the reaction. The development of a strategy for conducting Pd(0)-catalyzed reactions on the chips should greatly expand the synthetic chemistry available for building chip-based libraries.     

Stereoselective discrimination and quantification of arginine and N-blocked arginine enantiomers by formation and dissociation of calcium-mediated diastereomeric trimer complexes with a chiral reference compound using electrospray ionization-ion trap tandem mass spectrometry

Chiral resolution of arginine (Arg) and Arg derivatives is demonstrated using electrospray ionization-tandem mass spectrometry (ESI-MS). Calcium ion (Ca(II))-mediated trimeric clusters are generated, which incorporate the analyte of interest and an enantiomerically pure reference molecule of similar metal ion affinity. Two methods, one based on the measurement of a competitive-dissociation-based branching ratio (R(chir)) by the kinetic method (KM) and one based on the measurement of a chiral recognition ratio (CR) by a similar method, are compared. Incorporating N-blocked Arg derivatives (Z-Arg and Boc-Arg) as chiral references provides chiral resolution greater than that previously reported for Arg enantiomers. In a reciprocal manner, pure Arg enantiomers can be used as references for discriminating enantiomers of these N-blocked Arg derivatives. Condensed-phase and gas-phase Ca(II) ion affinity relative to Arg is also addressed qualitatively for other acidic, basic, and neutral amino acids. In some cases, when only one offspring ion is observed (insufficient for KM analysis), the CR method can be applied as an alternative to obtain a measurable stereoselectivity value for the system. The results of these experiments demonstrate the applicability of, and the difference between, the KM and the CR method for improved quantitative analysis of enantiomeric excess for Arg.     

Influence of the electric field on a bio-mimetic film supported on a gold electrode

A model biological membrane was formed by fusion of mixed cholesterol and DMPC (dimyristoylphosphatidylcholine) phospholipid vesicles onto a gold-coated quartz support. The gold surface was charged and the influence of the charge at the solid support on the structure and integrity of the phospholipid bilayer was investigated using the specular reflection of neutrons and electrochemical measurements. When the surface charge density is close to zero, the lipid vesicles fuse directly on the surface to form a bilayer with a small number of defects and hence low water content. When the support's surface is negatively charged the film swells and incorporates water due to the field driven poration of the membrane. When the charge density is more negative then -8 microC cm(-2) the bilayer is detached from the metal surface. However, it remains in close proximity to the metal electrode, suspended on a thin cushion of water. The film thicknesses, calculated from neutron reflectivity, have allowed us to determine the tilt angle of the lipid molecules as a function of the support's charge density. The lipid molecules are tilted 55 degrees from the surface normal at zero charge density but become significantly more perpendicular (30 degrees tilt angle) at charge densities more negative than -8 microC cm(-2). The tilt angle measurements are in very good agreement with previous IR studies. This paper describes the highlights of a more in-depth study which is fully described in [1].     

Structure and biosynthetic implication of (S)-NHAB, a novel shunt product, from a disruptant of the actVI-ORFA gene for actinorhodin biosynthesis in Streptomyces coelicolor A3(2)

A novel shunt product was isolated from a disruptant of the actVI-ORFA gene involved in the biosynthesis of actinorhodin (ACT) in Streptomyces coelicolor A3(2). Its structure was elucidated as 1,4-naphthoquinone-8-hydroxy-3-[3(S)-acetoxy-butyric acid], (S)-NHAB, based on NMR, MS, and CD spectroscopic data as well as a single crystal X-ray crystallographic analysis. The formation of (S)-NHAB involves a retro-Claisen type C-C bond cleavage of an ACT biosynthetic intermediate. Feeding experiments with [1-¹³C] and [2-¹³C] acetates indicated its biosynthetic origin as a single octaketide chain. The relevant gene product, Act-ORFA, which is a functionally unknown protein, is proposed to play a regulatory role related to the multi-enzymatic steps to ACT production, based on the metabolic profile of its disruptant and the wide distribution of actVI-ORFA homologues in the gene clusters for Streptomyces aromatic polyketides.     

A rigid linker-scaffold for solid-phase synthesis of dimeric pharmacophores

Bifunctional linker-scaffolds (compounds 1-3) were designed to meet several criteria for solid-phase syntheses of bivalent ligands. They have two amine-functionalized arms that can be differentially protected. Elaboration of these arms could give ligand-pharmacophore dimers wherein the two active components are held reasonably rigidly at around 10 A separation. Their bifunctional design also enables reactions of libraries with libraries to amplify diversity in a truly combinatorial fashion. Molecules 1-3 are also designed so that cleavage of the linker liberates the scaffold entity into solution under conditions that create only byproducts that should not interfere with biological assays. Thus they contain 2-nitrobenzene sulfonamide components that cleave in the presence of good nucleophiles. In the event, the linker-scaffolds 1-3 were prepared (Schemes 1 and 2). The N-benzyl system 2 was shown to have good stability to the types of conditions that might be used to functionalize the scaffold arms and to be sufficiently labile to the cleavage nucleophile (vide infra). The nucleophiles generally used to cleave nitrobenzene sulfonamides either generate undesirable byproducts (thiophenol or alkane thiols) or proved to be insufficiently reactive for the required solid-phase transformations (n-propylamine). However, sodium sulfide was investigated as a new alternative and shown to be a highly reactive cleavage agent that gives only volatile byproducts and sodium hydroxide. It is suggested that sodium sulfide is a highly desirable nucleophile for cleavage of 2-nitrobenzene sulfonamides, in general. The linker-scaffolds 1-3 were used to prepare a small library of bivalent ligands targeted to a protein receptor having charged cavities separated by approximately 10 A. These systems were made from guanidine, pyridinium, carboxylic acid, and sulfonic acid constituents (Tables 1 and 2).     

Synthesis of an isomer of the germacranolide isoaristolactone

Photocycloadditlon of (+)-isoplperltenone and cyclobutene-1-carboxylic acid gives an adduct which upon reduction with NaCNBH₃ followed by thermolysis yields an isomer of isoaristolactone in an overall yield of 26%.     

Multipolar excitation in triangular nanoprisms

Theoretical studies on the optical properties of gold triangular prisms in solution are presented to determine how structural modifications affect the extinction spectrum. Well-defined trends in the particle extinction are found to depend on the triangular edge length and the prism thickness. Calculations performed on large, thin triangular prisms indicate multipolar excitation and display numerous peaks in the extinction spectrum. The dominant peaks are assigned to different in-plane modes corresponding to the lowest three orders of a multipole expansion. Vector polarization plots are presented to support the peak assignments. Altering the prisms by snipping off the points of the triangular cross section significantly blueshifts the dipole peak, but the higher-order modes are only slightly affected. Snipping off large volumes can lead to the suppression of high-order multipoles in the extinction spectrum.     

The synthesis of diene and of vinyl copolymers containing predetermined quantities of polynuclear hydrocarbon or heterocyclic adducts—VI. Copolymers of butadiene,acenaphthylene or phenanthrene,and a linking agent

Reactions of tetrahydrofuran solutions of butadiene and acenaphthylene with alkali metal produce dianionic species which give quantitative yields of copolymers when subsequently titrated with alkyl dibromides. These polymers, however, crosslink on standing; this has been correlated with the presence of a proportion of 1,5-dihydroacenaphthylene adduct in the product.Similar reactions involving phenanthrene are not quantitative and yield materials containing only a small proportion of the phenanthrene added. The low efficiency has been attributed to the low electron affinity of phenanthrene and to the ability of its dianion to react with alkyl halides by electron transfer rather than metathetically.     

The synthesis of diene and of vinyl copolymers containing predetermined quantities of polynuclear hydrocarbon or heterocyclic adducts—II. The reaction of alkali metal salts of anthracene with alkyl halides

The reactions of alkali metal salts of anthracene with alkyl halides result in the formation of 9,10-dialkyl 9,10-dihydroanthracenes as the principal product, although appreciable quantities of other adducts, notably the 1,2- and 1,4-dialkyl compounds, are also formed.When the disodium salt is used, these adducts account for the total anthracene consumed, but with the dilithium salt appreciable quantities of 9,(4-hydroxybutyl) anthracene compounds are produced; they resulted from additive reaction of the salt with the tetrahydrofuran solvent. In the present experiments, these adducts account for about 20 per cent of the anthracene, but this proportion may be increased by prolonging the standing of the dilithium anthracene solution before reacting with alkyl halide.