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.     

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.     

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.     

Photolithographic synthesis of peptoids

We describe a novel photolithographic approach to the synthesis of peptoids (oligo-N-substituted glycines). This strategy enables the construction of a spatially addressable peptoid microarray, thus providing a potentially powerful tool for the discovery of protein ligands.     

Norms on Free Topological Groups

A norm on a group G is a function N mapping G into the set ofnon-negative real numbers such that for each x and y in G, N(xy^–1) N(x)+N(y) and N(e) = 0, where e is the identity element ofG. It is shown here that if F(X) is the free topological groupon any completely regular Hausdorff space X and H is a subgroupof F(X) generated by a finite subset of X, then any norm onH can be extended to a continuous norm on F(X).     

Vibrational exciton delocalization precludes the use of infrared intensities as proxies for surfactant accumulation on aqueous surfaces

Surface-sensitive vibrational spectroscopy is a common tool for measuring molecular organization and intermolecular interactions at interfaces. Peak intensity ratios are typically used to extract molecular information from one-dimensional spectra but vibrational coupling between surfactant molecules can manifest as signal depletion in one-dimensional spectra. Through a combination of experiment and theory, we demonstrate the emergence of vibrational exciton delocalization in infrared reflection–absorption spectra of soluble and insoluble surfactants at the air/water interface. Vibrational coupling causes a significant decrease in peak intensities corresponding to C–F vibrational modes of perfluorooctanoic acid molecules. Vibrational excitons also form between arachidic acid surfactants within a compressed monolayer, manifesting as signal reduction of C–H stretching modes. Ionic composition of the aqueous phase impacts surfactant intermolecular distance, thereby modulating vibrational coupling strength between surfactants. Our results serve as a cautionary tale against employing alkyl and fluoroalkyl vibrational peak intensities as proxies for concentration, although such analysis is ubiquitous in interface science.

Coupling between surfactant molecules at the air/water interface bleeds intensity into a diffuse background, such that single-wavelength vibrational intensity is effectively depleted at high surface coverage.     

Palladium-catalyzed amination of aryl nonaflates

The first detailed study of the palladium-catalyzed amination of aryl nonaflates is reported. Use of ligands 2-4 and 6 allows for the catalytic amination of electron-rich and -neutral aryl nonaflates with both primary and secondary amines. With use of Xantphos 5, the catalytic amination of a variety of functionalized aryl nonaflates resulted in excellent yields of anilines; even 2-carboxymethyl aryl nonaflate is effectively coupled with a primary alkylamine. Moderate yields were obtained when coupling halo-aryl nonaflates with a variety of amines, where in most cases the aryl nonaflate reacted in preference to the aryl halide. Overall, aryl nonaflates are an effective alternative to triflates in palladium-catalyzed C-N bond-forming processes due to their increased stability under the reaction conditions.