Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    Evidence for an unidentified non-photochemical ground-level source of formaldehyde in the Po Valley with potential implications for ozone production
    Kaiser, J. ; Wolfe, G.M. ; Bohn, B. ; Ganzeveld, L.N. - \ 2015
    Atmospheric Chemistry and Physics 15 (2015). - ISSN 1680-7316 - p. 1289 - 1298.
    volatile organic-compounds - exchange cafe model - total oh reactivity - tropospheric degradation - chemical mechanism - gas-phase - part - atmosphere - forest - hydrocarbons
    Ozone concentrations in the Po Valley of northern Italy often exceed international regulations. As both a source of radicals and an intermediate in the oxidation of most volatile organic compounds (VOCs), formaldehyde (HCHO) is a useful tracer for the oxidative processing of hydrocarbons that leads to ozone production. We investigate the sources of HCHO in the Po Valley using vertical profile measurements acquired from the airship Zeppelin NT over an agricultural region during the PEGASOS 2012 campaign. Using a 1-D model, the total VOC oxidation rate is examined and discussed in the context of formaldehyde and ozone production in the early morning. While model and measurement discrepancies in OH reactivity are small (on average 3.4 ± 13%), HCHO concentrations are underestimated by as much as 1.5 ppb (45%) in the convective mixed layer. A similar underestimate in HCHO was seen in the 2002–2003 FORMAT Po Valley measurements, though the additional source of HCHO was not identified. Oxidation of unmeasured VOC precursors cannot explain the missing HCHO source, as measured OH reactivity is explained by measured VOCs and their calculated oxidation products. We conclude that local direct emissions from agricultural land are the most likely source of missing HCHO. Model calculations demonstrate that radicals from degradation of this non-photochemical HCHO source increase model ozone production rates by as much as 0.6 ppb h-1 (12%) before noon.
    A possible simplification of the Goss-modified Abraham solvation equation
    Noort, P.C.M. van - \ 2013
    Chemosphere 93 (2013)9. - ISSN 0045-6535 - p. 1742 - 1746.
    partition-coefficients - organic-compounds - gas-phase - water - thermodynamics - temperature - equilibrium - descriptors - solutes - model
    Abraham solvation equations find widespread use in environmental chemistry and pharmaco-chemistry. Recently Goss proposed a modified Abraham solvation equation. For various partitioning processes, the present study investigates the consequences for the fit when the Abraham solvation parameter V is left out of this modified solvation equation. For air-organic solvent partition, the Abraham solvation parameter V can be omitted from the Goss-modified Abraham solvation equation without any loss of statistical quality. For air–water partitioning, organic biphasic system partitioning, as well as water-organic solvent partitioning, omitting the V parameter from the Goss-modified Abraham solvation equation leads to only a small deterioration of statistic quality.
    Native tandem and ion mobility mass spectrometry highlight structural and modular similarities in CRISPR-associated protein complexes from Escherichia coli and Pseudomonas aeruginosa
    Duijn, E. van; Barbu, I.M. ; Barendregt, A. ; Jore, M.M. ; Wiedenheft, B. ; Lundgren, M. ; Westra, E.R. ; Brouns, S.J.J. ; Doudna, J.A. ; Oost, J. van der; Heck, A.J.R. - \ 2012
    Molecular and Cellular Proteomics 11 (2012). - ISSN 1535-9476 - p. 1430 - 1441.
    bacterial immune-system - crispr-cas systems - gas-phase - subunit architecture - antiviral defense - small rna - dna - recognition - prokaryotes - sequence
    The CRISPR/Cas (clustered regularly interspaced short palindromic repeats/ CRISPR-associated genes) immune system of bacteria and archaea provides acquired resistance against viruses and plasmids, by a strategy analogous to RNA-interference. Key components of the defense system are ribonucleoprotein complexes, the composition of which appears highly variable in different CRISPR/Cas subtypes. Previous studies combined mass spectrometry, electron microscopy and small angle X-ray scattering to demonstrate that the E. coli Cascade complex (405 kDa) and the P. aeruginosa Csy-complex (350 kDa) are similar in that they share a central spiral-shaped hexameric structure, flanked by associating proteins and one CRISPR RNA (crRNA). Recently, a cryo-electron microscopy structure of Cascade revealed that the crRNA molecule resides in a groove of the hexameric backbone. For both complexes we here describe the use of native mass spectrometry in combination with ion mobility mass spectrometry (IMMS) to assign a stable core surrounded by more loosely associated modules. Via computational modeling subcomplex structures were proposed that relate to the experimental IMMS data. Despite the absence of obvious sequence homology between several subunits, detailed analysis of sub-complexes strongly suggests analogy between subunits of the two complexes. Probing the specific association of E. coli Cascade/crRNA to its complementary DNA target reveals a conformational change. All together these findings provide relevant new information about the potential assembly process of the two CRISPR-associated complexes
    Photochemical generation of highly destabilized vinyl cations: the effects of alpha- and beta-trifluoromethyl versus alpha- and beta-methyl substituents
    Alem, K. van; Belder, G. ; Lodder, G. ; Zuilhof, H. - \ 2005
    Journal of Organic Chemistry 70 (2005)1. - ISSN 0022-3263 - p. 179 - 190.
    alkenyl(aryl)iodonium triflate fragmentations - hydrogen atom transfer - transition-states - iodonium salts - gas-phase - carbocations - solvolysis - halides - ion - rearrangements
    The photochemical reactions in methanol of the vinylic halides 1-4, halostyrenes with a methyl or a trifluoromethyl substituent at the - or -position, have been investigated quantitatively. Next to E/Z isomerization, the reactions are formation of vinyl radicals, leading to reductive dehalogenation products, and formation of vinyl cations, leading to elimination, nucleophilic substitution, and rearrangement products. The vinyl cations are parts of tight ion pairs with halide as the counterion. The elimination products are the result of -proton loss from the primarily generated -CH3 and -CF3 vinyl cations, or from the -CH3 vinyl cation formed from the -CH3 vinyl cation via a 1,2-phenyl shift. The -CF3 vinyl cation reacts with methanol yielding nucleophilic substitution products, no migration of the phenyl ring producing the -CF3 vinyl cation occurs. The -CF3 vinyl cation, which is the most destabilized vinyl cation generated thus far, gives a 1,2-fluorine shift in competition with proton loss. The experimentally derived order of stabilization of the vinyl cations photogenerated in this study, -CF3 <-CF3 <-CH3 <-CH3, is corroborated by quantum chemical calculations, provided the effect of solvent is taken into account.
    Phthalocyanines with eight oligo(ethylene oxide) alkoxy units: thermotropic phase behavior, aggregate formation and ion complexation with redox-active ions
    Piet, D.P. ; Verheij, H.J. ; Zuilhof, H. - \ 2003
    Journal of Porphyrins and Phthalocyanines 7 (2003)2. - ISSN 1088-4246 - p. 73 - 82.
    bond-dissociation energies - cation-ether complexes - octasubstituted phthalocyanine - molecular semiconductors - crowned-phthalocyanines - equilibrium structures - copper phthalocyanine - electron-transfer - liquid-crystal - gas-phase
    The thermotropic phase behavior of phthalocyanines (Pc's) with eight oligo(ethylene oxide) alkoxy side chains has been investigated. An increase in the number of ethylene oxide units results in a decrease in the solid-to-mesophase and isotropization temperatures. The investigated compounds display a discotic hexagonally ordered (D-ho) mesophase. The solubilization of LiI/I-2 into the polar side chains of the Pc's has been studied both in solution and in spin-coated films, and the effect on the aggregate formation is discussed. At higher temperatures, the Pc - LiI/I-2 complex is not stable and small crystallites are formed. The dark direct current conductivity of these films is reported as a function of LiI/I-2 concentration in the polar side groups of the Pc's. The observed decrease in conductivity with increasing salt concentration is related to the morphology of the material. Copyright (C) 2003 Society of Porphyrins & Phthalocyanines.
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