Automatic classification of chemical structure databases using a highly parallel array processor

This article describes the use of the ICL Distributed Array Processor (DAP) for the automatic classification of chemical structure databases using the Jarvis-Patrick clustering method. This method is based upon the calculation of a table containing the nearest neighbors for each of the molecules in the database which is to be clustered. These nearest neighbors can be identified very efficiently using the DAP since it allows up to 4096 molecules to be compared with a specified molecule in parallel. Experiments with files of 4096 and 8192 structures from the Fine Chemicals Database show that clustering with the DAP is up to 6.7 times as fast as using a highly efficient, inverted file algorithm on an IBM 3083 mainframe.     

Similarity structure of wave-collapse

Similarity transformations of the cubic Schrödinger equation (CSE) are investigated. The transformations are used to remove the explicit time variation in the CSE and reduce it to differential equations in the spatial variables only. Two different methods for similarity reduction are employed and the significance of similarity in the evolution of a collapsing wave packet is investigated. Numerical solutions in radial symmetry demonstrate that the similarity behaviour is local in space and time, and that some similarity solutions must be classified as improper solutions. The nature of the collapsing singularity is reexamined.     

Metallation and reaction of 4,5-dicyanoimidazoles with alkyllithium reagents

The conditions required for selective lithiation at the 2-position of 4,5-dicyanoimidazoles are described in detail. The course of the reaction of alkyllithium reagents with 4,5-dicyanoimidazoles depends on the temperature, the number of equivalents of alkyllithium and whether the 1-nitrogen is protected. Under certain circumstances, the alkyllithium reagent adds to one of the cyano groups giving cyanoimidazole ketones.     

Enamine chemistry—XIX: Preparation and alkylation of cyclic and non-cyclic enamino-thiones

Enamino-thiones of the general type ArC(S)CH:CHNR₂,3(Ar=phenyl p-methoxyphenyl and p-bromophenyl NR₂= pyrrolidinyl piperidinol were prepared by reacting the corresponding enaminones 2 with 2,4-bis-(4-methoxyphenyl) 1,3,2,4-dithiadiphosphetane 2,4-disultide 1. The compounds 3 were reacted with methyl iodide and ethyl iodide to give exclusively S-alkylated iminium iodides 4 and 5, in quantitative overall yields N phenyl-2,3,5,6,7,8-hexahydro-4-qumolinethione, 8, and 2-methyl-N phenyl-2, 3,5,6,7,8-hexahydro-4-quinolmethione 9, were alkylated with methyl iodide ethyl iodide and benzyl bromide giving S-alkylated hexahvdro quinolinium halides. 10 and 11, respectively in high yields. The stereochemistry of the compounds of types 4 and 5 is discussed in detail.     

The relative orientation of the lipid and carbohydrate moieties of lipochitooligosaccharides related to nodulation factors depends on lipid chain saturation

Lipochitooligosaccharides (LCOs) signal the symbiosis of rhizobia with legumes and the formation of nitrogen-fixing root nodules. LCOs 1 and 2 share identical tetrasaccharide scaffolds but different lipid moieties (1, LCO-IV(C16:1[9Z], SNa) and , LCO-IV(C16:2[2E,9Z], SNa)). The conformational behaviors of both LCOs were studied by molecular modeling and NMR. Modeling predicts that a small lipid modification would result in a different relative orientation of the lipid and tetrasaccharide moieties. Diffusion ordered spectroscopy reports that both LCOs form small aggregates above 1 mM. Nuclear Overhauser spectroscopy (NOESY) data, collected under monomeric conditions, reveals lipid-carbohydrate contacts only for 1, in agreement with the modeling data. The distinct molecular structures of 1 and 2 have the potential to contribute to their selective binding by legume proteins.     

Principal component and decomposition analysis of multicomponent mixtures of carcinogenic fluorophores

A series of binary and tertiary mixtures of polycyclic aromatic hydrocarbons is analyzed by using principal component and decomposition analysis of molecular fluorescence spectra. The results demonstrate the ability to determine the number and identity of species that are present. Failures caused by high correlation among spectra are considered.     

Comprehensive two-dimensional gel protein databases offer a global approach to the analysis of human cells: the transformed amnion cells (AMA) master database and its link to genome DNA sequence data

A total of 3430 polypeptides (2592 cellular; 838 secreted) from transformed human amnion cells (AMA) labeled with [35S]methionine were separated and recorded using computer-aided two-dimensional (2-D) gel electrophoresis. A master 2-D gel database of cellular protein information that includes both qualitative and quantitative annotations has been established. The protein numbers in this database differ from those reported in an earlier version (Celis et al. Leukemia 1988, 2,561-602) as a result of changes in the scanning hardware. The reported information includes: percentage of total radioactivity recovered from the gels (based on quantitations of polypeptides labeled with a mixture of 16 14C-amino acids), protein name (including credit to investigators that aided identification), antibody against protein, cellular localization, (nuclear, 40S hnRNP, 20S snRNP U5, proteasomes, endoplasmic reticulum, mitochondria, Golgi, ribosomes, intermediate filaments, microfilaments and microtubules), levels in fetal human tissues, partial protein sequences (containing information on 48 human proteins microsequenced so far), cell cycle-regulated proteins, proteins sensitive to interferons alpha, beta, and gamma, heat shock proteins, annexins and phosphorylated proteins. The results presented should be considered as the initial phase of a joint effort between our laboratories to undertake a general and systematic analysis of human proteins. Using this integrated approach it will be possible to identify phenotype-specific proteins, to microsequence them and store the information in the database, to identify the corresponding genes, to search for homology with previously characterized proteins and to study the function of groups of proteins (pathways, organelles, etc.) that exhibit interesting regulatory properties. In particular, the 2-D gel protein database may become increasingly important in view of the concerted effort to map and sequence the entire human genome.