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.     

Bifurcated, modular syntheses of chiral annulet triazacyclononanes

Three chiral 2,6-disubstituted tri-N-methyl azamacrocycles have been prepared by modular methods. These macrocycles were accessed from three chiral 1,4,7-triazaheptanes intermediates that were prepared by two independent routes. The first of these routes involved the benzylamine opening of chiral tosyl aziridines followed by debenzylation but was problematic on solubility grounds. A second, more effective, route was developed which avoided debenzylation by using ammonia in the nucleophilic opening of chiral tosyl aziridines.     

Organometallic compounds having metal-metal bonds : XXIII. Hydrido(triphenylgermanium)tetracarbonyliron and its conjugate base

Reaction of Ph₃GeLi with [Et₄N][HFe₃(CO)₁₁] affords the new carbonylferrate salt [Et₄N][Ph₃GeFe(CO)₄] and the same reaction provides an alternative route to the known silicon and tin analogs. Protonation of [Et₄N][Ph₃GeFe(CO)₄] with HCl in ether-THF forms the air-sensitive, thermally rather unstable cis-Ph₃GeFeH(CO)₄. The latter protonates chloride ions in dichloromethane.     

Information and organic molecules: structure considerations via integer statistics

Information in relation to organic molecules was investigated in a previous work (Graham and Schacht, J. Chem. Inf. Comput. Sci. 2000, 40, 187). The topic is given further consideration here with the help of integer statistics. Discussed are the ramifications of an integer variable Omega(t) which quantifies the total number of binding complexions for an organic molecule. Offered is a statistical view of the maximum allowed number of independent regions D expressed by the molecule, dependent on Omega(t). We illustrate the distribution properties of D along with upper limit estimates of the regioinformation mu, also dependent on Omega(t). Integer statistics based on elementary number theory establish the key distribution properties of D and mu. In so doing, the traits distinguishing high regioinformation molecules are enumerated. The statistical approach encompasses all possible molecules and conditions, not just those reported to date in chemical databases. The aim is to view the regioinformation expressed by molecules in an alternative and general way.     

Boron-containing nucleosides. 1. Synthesis of the novel heterocycle 2-benzyl-1,4-dihydro-1-hydroxythieno[3,2-c][1,5,2]diazaborin-3(2H)-one: A thieno-fused 4-borauracil

The synthesis of the novel boron-containing nucleobase 2-benzyl-1,4-dihydro-1-hydroxythieno[3,2-c]-[1,5,2]diazaborin-3(2H)-one ( 8 ), a thieno-fused 4-borauracil, is described. Compound 8 was prepared in three steps starting from 2-thiophenecarbonyl chloride ( 4 ). A multinuclear and multisolvent nmr study of 8 indicates that the boron atom maintains a trigonal geometry in the solvents used.     

The use of high-speed differential scanning calorimetry (Hyper-DSC™) to study the thermal properties of carbamazepine polymorphs

The thermal properties of two polymorphs of the drug carbamazepine, Forms I and III, were studied using high-speed differential scanning calorimetry (DSC). Previously, accurate determination of the heat enthalpy of fusion of Form III has not been possible using DSC at typical heating rates, due to concurrent exothermic recrystallisation to the higher-melting Form I. Here, it is demonstrated that heating rates of 250° C/min altered the kinetics of the melting transition of Form III such that this concurrent exothermic recrystallisation was inhibited. This allowed direct measurement of the enthalpy of the melting endotherm for Form III from a single transition. The enthalpy of this transition was found to be 109.5 J/g. Further investigations were then performed to test the utility of this technique in quantifying relative amounts of Forms I and III in mixtures of the two polymorphs. It was demonstrated that a limit of detection of 1% (w/w) was possible in this system. However, accurate quantification was not possible due to seeding effects initiating recrystallisation to Form I in these mixtures, even at these elevated heating rates. The utility of this novel technique as a fast analytical tool for studying the polymorphic behaviour of metastable polymorphs has been successfully demonstrated.     

Differentiation and quantitation of isomeric dipeptides by low-energy dissociation of copper(II)-bound complexes

Application of the kinetic method based on the dissociation of transition metal centered cluster ions is extended from chiral analysis (Tao, W. A.; Zhang, D.; Nikolaev, E. N.; Cooks, R. G. J. Am. Chem. Soc. 2000, 122, 10598) to quantitative analysis of isomeric mixtures, including those with Leu/Ile substitutions. Copper(II)-bound complexes of pairs of peptide isomers are generated by electrospray ionization mass spectrometry and the trimeric complex [CuII(ref)2(A) - H]+ (analyte A, a mixture of isomeric peptides; reference compound ref, usually a peptide) is caused to undergo collisional dissociation. Competitive loss of the neutral reference compound or the neutral analyte yields two ionic products and the ratio of rates of the two competitive dissociations, viz. the product ion branching ratio R is shown to depend strongly on the regiochemistry of the analyte in the precursor [CuII(A)(ref)2 - H]+ complex ion. Calibration curves are constructed by relating the branching ratio measured by the kinetic method, to the isomeric composition of the mixture to allow rapid quantitative isomer analysis.     

Total synthesis of (-)-callystatin A

A total synthesis of the cytotoxic polyketide marine natural product callystatin A is described. The route features chiral allenylmetal additions to construct the polypropionate C15-22 segment and an sp(2)-sp(3) Suzuki coupling to join the C1-C11 and C12-C22 subunits.     

9-BBN: An amino acid protecting group for functionalization of amino acid side chains in organic solvents

9-Borabicyclononane (9-BBN) has been utilized to protect functionalized amino acids for potential chemoselective side chain manipulation. The 9-BBN group imparts organic solubility to otherwise hydrophilic molecules and is tolerant of a wide range of reaction conditions. The high degree of solubility of these molecules in THF is particularly noteworthy. It is cleaved with either aqueous HCl or by exchange with ethylenediamine in methanol. [reaction: see text]     

The determination of free ammonia in ambient air with diffusion/denuder tubes

Ammonia is important in atmospheric chemistry because it neutralises acidic species and increases the pH of cloud droplets. Data on the concentration of free ammonia in the atmosphere are sparse because it is difficult to separate free ammonia from particulate ammonium salt aerosol. A manual method for the determination of free ammonia in air is described based on diffusion/denuder tube separation of ammonia from ammonium salt aerosol. When air is drawn through a tube coated with a selective absorbent (here oxalic acid) separation is achieved because the gaseous species diffuses much more rapidly to the tube wall than the particles. After the sampling period (usually 1–4 h, depending on the free ammonia concentration expected), the sorbed ammonia is washed from the tube and measured potentiometrically with an ammonia probe. The method is tested theoretically and experimentally. The absorption efficiency of the coated tubes is ca. 90%. In samples of room air containing 12–28 μg m^?3, the standard deviation is estimated as 1.0 μg m^?3. In field use, ammonia contents were in the range 0.53–5.0 μg m^?3.