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.     

Computer Scheduling of Vehicles from One or More Depots to a Number of Delivery Points

The problem of scheduling delivery vehicles from a number of depots to customers, subject to constraints on load and distance or time, is considered. A new algorithm is presented; this allows routes from several depots to be constructed simultaneously, subject to restrictions on numbers of vehicles at individual depots. Where too many customers require service, a flexible priority rule will select those to be served. Results for the single depot case are compared with other known algorithms; further results are given and discussed for cases of several depots.     

Multifrequency acoustical volume backscattering patterns in the Arabian Sea--265 kHz to 3 MHz

High-frequency acoustical volume backscattering was examined during three periods of the annual cycle of winds in the Arabian Sea-the Winter Northeast (NE) Monsoon, the Summer Southwest (SW) Monsoon, and the Fall Intermonsoon-using a multifrequency acoustic profiling system deployed on an undulating towed body. This system measured acoustical volume backscattering strengths at six frequencies ranging from 265 kHz to 3.0 MHz. Measurements were made from near the surface to 250 m depth along a ship track that paralleled the coast of Oman, then proceeded away from the coast towards the middle of the Arabian Sea. At all frequencies, volume backscattering strength was highest near the surface, decreasing with increasing depth. Contrary to expectation, backscattering was generally lower during the Summer SW Monsoon than during the Winter NE Monsoon. Also contrary to expectation, backscattering was not appreciably higher near the coast than it was offshore during the Summer SW Monsoon, although it was higher near the coast during the Winter NE Monsoon. Generally speaking, regional and seasonal differences were smaller than expected, and much smaller than the fine-scale spatial and temporal variability, particularly at frequencies below 1 MHz. There was a daily pattern of increased nighttime backscattering in the upper 100 m at 265 and 420 kHz. This pattern was less evident at 1.1 MHz and above.     

Polymerizable cationic iridium(III) complexes exhibiting color tunable light emission and their corresponding conducting metallopolymers

Cyclometalated iridium(III) complexes have been synthesized for use in a variety of photophysical applications, including polymer light emitting diodes (PLEDs). A series of new complexes with one electrochemically polymerizable ligand and two phenylpyridine(ppy)-based ligands have been prepared: [Ir(ppy)₂L][PF₆](1), [Ir(F-mppy)₂L][PF₆](2), and [Ir(Br-mppy)₂L][PF₆](3), where L = 3,8-bis(2,2′-bithien-5-yl)-1,10-phenanthroline. The ancillary ppy ligands can be easily varied synthetically to tune emission color of the monomer from blue–green to red. The solid state structure of complex 1 has been obtained by single crystal X-ray crystallography. Conducting polymer materials have been prepared by electropolymerization of monomers and were characterized through XPS analysis and spectroscopic studies.     

Gas sorption and luminescence properties of a terbium(III)-phosphine oxide coordination material with two-dimensional pore topology

The structure, stability, gas sorption properties and luminescence behaviour of a new lanthanide-phosphine oxide coordination material are reported. The polymer PCM-15 is based on Tb(III) and tris(p-carboxylated) triphenylphosphine oxide and has a 5,5-connected net topology. It exhibits an infinite three-dimensional structure that incorporates an open, two-dimensional pore structure. The material is thermally robust and remains crystalline under high vacuum at 150 °C. When desolvated, the solid has a CO(2) BET surface area of 1187 m(2) g(-1) and shows the highest reported uptake of both O(2) and H(2) at 77 K and 1 bar for a lanthanide-based coordination polymer. Isolated Tb(III) centres in the as-synthesized polymer exhibit moderate photoluminescence. However, upon removal of coordinated OH(2) ligands, the luminescence intensity was found to approximately double; this process was reversible. Thus, the Tb(III) centre was used as a probe to detect directly the desolvation and resolvation of the polymer.     

Field distribution in an electrospray ionization source determined by finite element method

Three‐dimensional computer models of electrospray ionization sources were constructed in COMSOL Multiphysics? to solve the static electric fields using finite element methods. The magnitude of the electric field strength for onset of electrospray and optimum signal was calculated under various conditions. The modification of the electric field distribution in the ion source by an atmospheric pressure ion lens was also investigated by plotting the equipotential surfaces, electric field lines and trajectories of charged droplets. Both the calculated and the experimental results demonstrate that the changes in the ion signal detected by the mass spectrometer are attributable to the focusing effect of the ion lens when appropriate voltages are applied on the sprayer and ion lens. The optimum signal was found by setting the sprayer voltage from 3000 to 5000 V while scanning the ion lens voltage. The calculated strengths of the electric field at the sprayer tip for optimum signals are similar although the applied voltages at the sprayer and ion lens are significantly different. Copyright © 2009 John Wiley & Sons, Ltd.     

Chemical markup, XML, and the world wide web. 6. CMLReact, an XML vocabulary for chemical reactions

A set of components (CMLReact) for managing chemical and biochemical reactions has been added to CML. These can be combined to support most of the strategies for the formal representation of reactions. The elements, attributes, and types are formally defined as XMLSchema components, and their semantics are developed. New syntax and semantics in CML are reported and illustrated with 10 examples.     

Physical characterization of uranium oxide pellets and powder applied in the Nuclear Forensics International Technical Working Group Collaborative Materials Exercise 4

Journal of Radioanalytical and Nuclear Chemistry - Physical characterization is one of the most broad and important categories of techniques to apply in a nuclear forensic examination. Physical...     

Comparing results of X-ray diffraction, µ-Raman spectroscopy and neutron diffraction when identifying chemical phases in seized nuclear material,during a comparative nuclear forensics exercise

Journal of Radioanalytical and Nuclear Chemistry - This work presents the results for identification of chemical phases obtained by several laboratories as a part of an international nuclear...     

Analysis and use of fragment-occurrence data in similarity-based virtual screening

Current systems for similarity-based virtual screening use similarity measures in which all the fragments in a fingerprint contribute equally to the calculation of structural similarity. This paper discusses the weighting of fragments on the basis of their frequencies of occurrence in molecules. Extensive experiments with sets of active molecules from the MDL Drug Data Report and the World of Molecular Bioactivity databases, using fingerprints encoding Tripos holograms, Pipeline Pilot ECFC_4 circular substructures and Sunset Molecular keys, demonstrate clearly that frequency-based screening is generally more effective than conventional, unweighted screening. The results suggest that standardising the raw occurrence frequencies by taking the square root of the frequencies will maximise the effectiveness of virtual screening. An upper-bound analysis shows the complex interactions that can take place between representations, weighting schemes and similarity coefficients when similarity measures are computed, and provides a rationalisation of the relative performance of the various weighting schemes.