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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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  • 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.
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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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    The evolution of the marine phosphate reservoir (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-10-29
    Description: Phosphorus is a biolimiting nutrient that has an important role in regulating the burial of organic matter and the redox state of the ocean-atmosphere system. The ratio of phosphorus to iron in iron-oxide-rich sedimentary rocks can be used to track dissolved phosphate concentrations if the dissolved silica concentration of sea water is estimated. Here we present iron and phosphorus concentration ratios from distal hydrothermal sediments and iron formations through time to study the evolution of the marine phosphate reservoir. The data suggest that phosphate concentrations have been relatively constant over the Phanerozoic eon, the past 542 million years (Myr) of Earth's history. In contrast, phosphate concentrations seem to have been elevated in Precambrian oceans. Specifically, there is a peak in phosphorus-to-iron ratios in Neoproterozoic iron formations dating from approximately 750 to approximately 635 Myr ago, indicating unusually high dissolved phosphate concentrations in the aftermath of widespread, low-latitude 'snowball Earth' glaciations. An enhanced postglacial phosphate flux would have caused high rates of primary productivity and organic carbon burial and a transition to more oxidizing conditions in the ocean and atmosphere. The snowball Earth glaciations and Neoproterozoic oxidation are both suggested as triggers for the evolution and radiation of metazoans. We propose that these two factors are intimately linked; a glacially induced nutrient surplus could have led to an increase in atmospheric oxygen, paving the way for the rise of metazoan life.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Planavsky, Noah J -- Rouxel, Olivier J -- Bekker, Andrey -- Lalonde, Stefan V -- Konhauser, Kurt O -- Reinhard, Christopher T -- Lyons, Timothy W -- England -- Nature. 2010 Oct 28;467(7319):1088-90. doi: 10.1038/nature09485.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Earth Sciences, University of California, Riverside, California 92521, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20981096" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Aquatic Organisms/*metabolism ; Atmosphere/chemistry ; *Biological Evolution ; Ferric Compounds/analysis/metabolism ; Geologic Sediments/chemistry ; History, Ancient ; Ice Cover ; Iron/analysis/metabolism ; Marine Biology ; Oceans and Seas ; Oxidation-Reduction ; Oxygen/analysis/metabolism ; Phosphates/analysis/*metabolism ; Phosphorus/analysis/metabolism ; Seawater/chemistry ; Silicon Dioxide/analysis/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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  • 7
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    Tracing the stepwise oxygenation of the Proterozoic ocean (2008)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2008-03-28
    Description: Biogeochemical signatures preserved in ancient sedimentary rocks provide clues to the nature and timing of the oxygenation of the Earth's atmosphere. Geochemical data suggest that oxygenation proceeded in two broad steps near the beginning and end of the Proterozoic eon (2,500 to 542 million years ago). The oxidation state of the Proterozoic ocean between these two steps and the timing of deep-ocean oxygenation have important implications for the evolutionary course of life on Earth but remain poorly known. Here we present a new perspective on ocean oxygenation based on the authigenic accumulation of the redox-sensitive transition element molybdenum in sulphidic black shales. Accumulation of authigenic molybdenum from sea water is already seen in shales by 2,650 Myr ago; however, the small magnitudes of these enrichments reflect weak or transient sources of dissolved molybdenum before about 2,200 Myr ago, consistent with minimal oxidative weathering of the continents. Enrichments indicative of persistent and vigorous oxidative weathering appear in shales deposited at roughly 2,150 Myr ago, more than 200 million years after the initial rise in atmospheric oxygen. Subsequent expansion of sulphidic conditions after about 1,800 Myr ago (refs 8, 9) maintained a mid-Proterozoic molybdenum reservoir below 20 per cent of the modern inventory, which in turn may have acted as a nutrient feedback limiting the spatiotemporal distribution of euxinic (sulphidic) bottom waters and perhaps the evolutionary and ecological expansion of eukaryotic organisms. By 551 Myr ago, molybdenum contents reflect a greatly expanded oceanic reservoir due to oxygenation of the deep ocean and corresponding decrease in sulphidic conditions in the sediments and water column.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Scott, C -- Lyons, T W -- Bekker, A -- Shen, Y -- Poulton, S W -- Chu, X -- Anbar, A D -- England -- Nature. 2008 Mar 27;452(7186):456-9. doi: 10.1038/nature06811.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Earth Sciences, University of California, Riverside, California 92521, USA. cscot002@ucr.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18368114" target="_blank"〉PubMed〈/a〉
    Keywords: Atmosphere/chemistry ; Geologic Sediments/chemistry ; History, Ancient ; Molybdenum/analysis ; Oceans and Seas ; Oxygen/*analysis/chemistry ; Seawater/*chemistry ; Sulfides/chemistry ; Time Factors
    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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  • 8
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    Iron isotope constraints on the Archean and Paleoproterozoic ocean redox state (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-02-19
    Description: The response of the ocean redox state to the rise of atmospheric oxygen about 2.3 billion years ago (Ga) is a matter of controversy. Here we provide iron isotope evidence that the change in the ocean iron cycle occurred at the same time as the change in the atmospheric redox state. Variable and negative iron isotope values in pyrites older than about 2.3 Ga suggest that an iron-rich global ocean was strongly affected by the deposition of iron oxides. Between 2.3 and 1.8 Ga, positive iron isotope values of pyrite likely reflect an increase in the precipitation of iron sulfides relative to iron oxides in a redox stratified ocean.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rouxel, Olivier J -- Bekker, Andrey -- Edwards, Katrina J -- New York, N.Y. -- Science. 2005 Feb 18;307(5712):1088-91.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Marine Chemistry and Geochemistry Department, Geomicrobiology Group, Woods Hole Oceanographic Institution, Mail Stop 8, Woods Hole, MA 02543, USA. orouxel@whoi.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15718467" target="_blank"〉PubMed〈/a〉
    Keywords: *Atmosphere ; Chemical Precipitation ; Ferric Compounds/analysis ; Geologic Sediments/*chemistry ; Iron/*analysis ; Iron Isotopes/*analysis ; Oceans and Seas ; Oxidation-Reduction ; Oxygen ; *Seawater ; Sulfides/*analysis ; Time
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 9
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    Widespread iron-rich conditions in the mid-Proterozoic ocean (2011)
    Nature Publishing Group (NPG)
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    Publication Date: 2011-09-09
    Description: The chemical composition of the ocean changed markedly with the oxidation of the Earth's surface, and this process has profoundly influenced the evolutionary and ecological history of life. The early Earth was characterized by a reducing ocean-atmosphere system, whereas the Phanerozoic eon (less than 542 million years ago) is known for a stable and oxygenated biosphere conducive to the radiation of animals. The redox characteristics of surface environments during Earth's middle age (1.8-1 billion years ago) are less well known, but it is generally assumed that the mid-Proterozoic was home to a globally sulphidic (euxinic) deep ocean. Here we present iron data from a suite of mid-Proterozoic marine mudstones. Contrary to the popular model, our results indicate that ferruginous (anoxic and Fe(2+)-rich) conditions were both spatially and temporally extensive across diverse palaeogeographic settings in the mid-Proterozoic ocean, inviting new models for the temporal distribution of iron formations and the availability of bioessential trace elements during a critical window for eukaryotic evolution.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Planavsky, Noah J -- McGoldrick, Peter -- Scott, Clinton T -- Li, Chao -- Reinhard, Christopher T -- Kelly, Amy E -- Chu, Xuelei -- Bekker, Andrey -- Love, Gordon D -- Lyons, Timothy W -- England -- Nature. 2011 Sep 7;477(7365):448-51. doi: 10.1038/nature10327.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Earth Sciences, University of California, Riverside, California 92521, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21900895" target="_blank"〉PubMed〈/a〉
    Keywords: Biological Evolution ; Geologic Sediments/chemistry ; History, Ancient ; Iron/*analysis/chemistry ; Oceans and Seas ; Seawater/*chemistry ; Sulfur/analysis/chemistry ; Sulfur Isotopes ; Time Factors
    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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