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  • 1
    Electronic Resource
    Electronic Resource
    Unification of box shapes in molecular simulations (1997)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 18 (1997), S. 1930-1942 
    Details
    ISSN: 0192-8651
    Keywords: molecular simulation ; periodic boundary conditions ; box shape ; lattice ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: In molecular simulations with periodic boundary conditions the computational box may have five different shapes: triclinic; the hexagonal prism; two types of dodecahedrons; and the truncated octahedron. In this article, we show that every molecular simulation, formulated in one of these boxes, can be transformed into a simulation in one of the other ones. The transformation can be done in a preprocessing phase. The simulation in the new box is exactly identical to the simulation in the original one. This means that every molecular simulation may be done in the same type of box. Because the triclinic box is the easiest one to implement, we pay special attention to how to transform the other four box types into triclinic boxes. As a consequence, simulations in the often used truncated octahedron are superfluous; they may be done in a much simpler way in a triclinic box.   © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1930-1942, 1997
    Additional Material: 15 Ill.
    Type of Medium: Electronic Resource
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    Paper (German National Licenses)
  • 2
    Electronic Resource
    Electronic Resource
    LINCS: A linear constraint solver for molecular simulations (1997)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 18 (1997), S. 1463-1472 
    Details
    ISSN: 0192-8651
    Keywords: constraints ; molecular dynamics ; Langevin dynamics ; SHAKE ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: In this article, we present a new LINear Constraint Solver (LINCS) for molecular simulations with bond constraints. The algorithm is inherently stable, as the constraints themselves are reset instead of derivatives of the constraints, thereby eliminating drift. Although the derivation of the algorithm is presented in terms of matrices, no matrix matrix multiplications are needed and only the nonzero matrix elements have to be stored, making the method useful for very large molecules. At the same accuracy, the LINCS algorithm is three to four times faster than the SHAKE algorithm. Parallelization of the algorithm is straightforward.   © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1463-1472, 1997
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    Application of paramagnetic shift reagents to the conformational analysis of isomeric dienones (1980)
    Chichester : Wiley-Blackwell
    Organic Magnetic Resonance 14 (1980), S. 337-343 
    Details
    ISSN: 0030-4921
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Paramagnetic NMR shift reagents, Eu(fod)3 and Pr(fod)3, have been applied to study the one-ene conformations of isomeric dienones. The results obtained using various complex formation models are analysed. The preferred model suggests participation of both carbonyl oxygen Ione pairs in binding with the shift reagents. Criteria for the estimation of errors in the determination of the structure parameters of the substrate-paramagnetic reagent complexes are suggested. The data obtained using NMR shift reagents are consistent with the existence of dienone α,β-cis-isomers as s-cis-conformers only, with the carbonyl group lying out of the plane of all the other atoms of the molecule. Both s-cis and s-trans conformers occur in dienone α,β-trans-isomers.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/mrc.1270140503
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  • 4
    Electronic Resource
    Electronic Resource
    Kinetics and mechanisms of substitution reactions with sulfur-containing nucleophiles in aqueous acid solutions. I - rates of reactions of some tetrahalopalladate (II) anions with thiourea and selenourea (1975)
    New York, NY : Wiley-Blackwell
    International Journal of Chemical Kinetics 7 (1975), S. 87-98 
    Details
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The activation energy parameters for the reaction of PdX42- (X=Cl-, Br-) in aqueous halide acid solution with thiourea (tu) and selenourea (seu) have been determined. High rates of reaction parallel low enthalpies and appreciable negative entropy of activation. The rate law in each case simplifies to kobs=k[L] where L=tu or seu, and only ligand-dependent rate constants are observed at 25°C. The ligand-dependent rate constants for the first identifiable step in the PdCl42- + X system is (9.1±0.1) × 103 M-1 sec-1 and (4.5±0.1) × 104 M-1 sec-1 for X=tu and seu, respectively, while for the PdBr42- + X system it is (2.0±0.1) × 104 M-1 sec-1 and (9.0±0.1) × 104 M-1 sec-1 for X=tu and seu, respectively.
    Additional Material: 4 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/kin.550070110
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  • 5
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    Organic-walled microfossils in 3.2-billion-year-old shallow-marine siliciclastic deposits (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-02-09
    Description: Although the notion of an early origin and diversification of life on Earth during the Archaean eon has received increasing support in geochemical, sedimentological and palaeontological evidence, ambiguities and controversies persist regarding the biogenicity and syngeneity of the record older than Late Archaean. Non-biological processes are known to produce morphologies similar to some microfossils, and hydrothermal fluids have the potential to produce abiotic organic compounds with depleted carbon isotope values, making it difficult to establish unambiguous traces of life. Here we report the discovery of a population of large (up to about 300 mum in diameter) carbonaceous spheroidal microstructures in Mesoarchaean shales and siltstones of the Moodies Group, South Africa, the Earth's oldest siliciclastic alluvial to tidal-estuarine deposits. These microstructures are interpreted as organic-walled microfossils on the basis of petrographic and geochemical evidence for their endogenicity and syngeneity, their carbonaceous composition, cellular morphology and ultrastructure, occurrence in populations, taphonomic features of soft wall deformation, and the geological context plausible for life, as well as a lack of abiotic explanation falsifying a biological origin. These are the oldest and largest Archaean organic-walled spheroidal microfossils reported so far. Our observations suggest that relatively large microorganisms cohabited with earlier reported benthic microbial mats in the photic zone of marginal marine siliciclastic environments 3.2 billion years ago.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Javaux, Emmanuelle J -- Marshall, Craig P -- Bekker, Andrey -- England -- Nature. 2010 Feb 18;463(7283):934-8. doi: 10.1038/nature08793. Epub 2010 Feb 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Geology, University of Liege, 17 allee du 6 Aout B18, Liege 4000, Belgium. ej.javaux@ulg.ac.be〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20139963" target="_blank"〉PubMed〈/a〉
    Keywords: Acids ; Bacteria/chemistry/cytology/isolation & purification/metabolism ; Carbon/analysis/chemistry ; Carbon Isotopes ; *Ecosystem ; Eukaryotic Cells/chemistry/cytology ; *Fossils ; Geologic Sediments/*microbiology ; History, Ancient ; Oceans and Seas ; Organic Chemicals/*analysis/chemistry ; *Phylogeny ; Reproducibility of Results ; Seawater/*microbiology ; South Africa ; Spectrum Analysis, Raman ; Sunlight
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 6
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    Large colonial organisms with coordinated growth in oxygenated environments 2.1 Gyr ago (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-07-03
    Description: The evidence for macroscopic life during the Palaeoproterozoic era (2.5-1.6 Gyr ago) is controversial. Except for the nearly 2-Gyr-old coil-shaped fossil Grypania spiralis, which may have been eukaryotic, evidence for morphological and taxonomic biodiversification of macroorganisms only occurs towards the beginning of the Mesoproterozoic era (1.6-1.0 Gyr). Here we report the discovery of centimetre-sized structures from the 2.1-Gyr-old black shales of the Palaeoproterozoic Francevillian B Formation in Gabon, which we interpret as highly organized and spatially discrete populations of colonial organisms. The structures are up to 12 cm in size and have characteristic shapes, with a simple but distinct ground pattern of flexible sheets and, usually, a permeating radial fabric. Geochemical analyses suggest that the sediments were deposited under an oxygenated water column. Carbon and sulphur isotopic data indicate that the structures were distinct biogenic objects, fossilized by pyritization early in the formation of the rock. The growth patterns deduced from the fossil morphologies suggest that the organisms showed cell-to-cell signalling and coordinated responses, as is commonly associated with multicellular organization. The Gabon fossils, occurring after the 2.45-2.32-Gyr increase in atmospheric oxygen concentration, may be seen as ancient representatives of multicellular life, which expanded so rapidly 1.5 Gyr later, in the Cambrian explosion.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉El Albani, Abderrazak -- Bengtson, Stefan -- Canfield, Donald E -- Bekker, Andrey -- Macchiarelli, Roberto -- Mazurier, Arnaud -- Hammarlund, Emma U -- Boulvais, Philippe -- Dupuy, Jean-Jacques -- Fontaine, Claude -- Fursich, Franz T -- Gauthier-Lafaye, Francois -- Janvier, Philippe -- Javaux, Emmanuelle -- Ossa, Frantz Ossa -- Pierson-Wickmann, Anne-Catherine -- Riboulleau, Armelle -- Sardini, Paul -- Vachard, Daniel -- Whitehouse, Martin -- Meunier, Alain -- England -- Nature. 2010 Jul 1;466(7302):100-4. doi: 10.1038/nature09166.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratoire HYDRASA, UMR 6269 CNRS-INSU, Universite de Poitiers, 86022 Poitiers, France. abder.albani@univ-poitiers.fr〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20596019" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteria/cytology ; *Ecosystem ; Eukaryota/cytology ; *Fossils ; Gabon ; Geologic Sediments/microbiology ; History, Ancient ; Oxygen/*metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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