Pentafluorophenyl phenyl interaction in biphenyl DNA

We prepared and investigated oligonucleotide duplexes of the sequence d(GATGAC(X)(n)GCTAG)d(CTAGC(Y)(n)GTCATC), in which X and Y designate biphenyl- (bph) and pentafluorobiphenyl- ((5F)bph) C-nucleotides, respectively, and n varies from 0-4. These hydrophobic base substitutes are expected to adopt a zipperlike, interstrand stacking motif, in which not only bph/bph or (5F)bph/(5F)bph homo pairs, but also (5F)bph/bph mixed pairs can be formed. By performing UV-melting curve analysis we found that incorporation of a single (5F)bph/(5F)bph pair leads to a duplex that is essentially as stable as the unmodified duplex (n=0), and 2.4 K more stable than the duplex with the nonfluorinated bph/bph pair. The T(m) of the mixed bph/(5F)bph pair was in between the T(m) values of the respective homo pairs. Additional, unnatural aromatic pairs increased the T(m) by +3.0-4.4 K/couple, irrespective of the nature of the aromatic residue. A thermodynamic analysis using isothermal titration calorimetry (ITC) of a series of duplexes with n=3 revealed lower (less negative) duplex formation enthalpies (DeltaH) in the (5F)bph/(5F)bph case than in the bph/bph case, and confirmed the higher thermodynamic stability (DeltaG) of the fluorinated duplex, suggesting it to be of entropic origin. Our data are compatible with a model in which the stacking of (5F)bph versus bph is dominated by dehydration of the aromatic units upon duplex formation. They do not support a model in which van der Waals dispersive forces (induced dipoles) or electrostatic (quadrupole) interactions play a dominant role

The role of the interplay between polymer architecture and bacterial surface properties on the microbial adhesion to polyoxazoline-based ultrathin films

Surface platforms were engineered from poly(L-lysine)-graft-poly(2-methyl-2-oxazoline) (PLL-g-PMOXA) copolymers to study the mechanisms involved in the non-specific adhesion of Escherichia coli (E. coli) bacteria. Copolymers with three different grafting densities (PMOXA chains/Lysine residue of 0.09, 0.33 and 0.56) were synthesized and assembled on niobia (Nb O ) surfaces. PLL-modified and bare niobia surfaces served as controls. To evaluate the impact of fimbriae expression on the bacterial adhesion, the surfaces were exposed to genetically engineered E. coli strains either lacking, or constitutively expressing type 1 fimbriae. The bacterial adhesion was strongly influenced by the presence of bacterial fimbriae. Non-fimbriated bacteria behaved like hard, charged particles whose adhesion was dependent on surface charge and ionic strength of the media. In contrast, bacteria expressing type 1 fimbriae adhered to the substrates independent of surface charge and ionic strength, and adhesion was mediated by non-specific van der Waals and hydrophobic interactions of the proteins at the fimbrial tip. Adsorbed polymer mass, average surface density of the PMOXA chains, and thickness of the copolymer films were quantified by optical waveguide lightmode spectroscopy (OWLS) and variable-angle spectroscopic ellipsometry (VASE), whereas the lateral homogeneity was probed by time-of-flight secondary ion mass spectrometry (ToF-SIMS). Streaming current measurements provided information on the charge formation of the polymer-coated and the bare niobia surfaces. The adhesion of both bacterial strains could be efficiently inhibited by the copolymer film only with a grafting density of 0.33 characterized by the highest PMOXA chain surface density and a surface potential close to zero.

The binding mode of side chain- and C3-modified epothilones to tubulin

The tubulin-binding mode of C3- and C15-modified analogues of epothilone A (Epo A) was determined by NMR spectroscopy and computational methods and compared with the existing structural models of tubulin-bound natural Epo A. Only minor differences were observed in the conformation of the macrocycle between Epo A and the C3-modified analogues investigated. In particular, 3-deoxy- (compound 2) and 3-deoxy-2,3-didehydro-Epo A (3) were found to adopt similar conformations in the tubulin-binding cleft as Epo A, thus indicating that the 3-OH group is not essential for epothilones to assume their bioactive conformation. None of the available models of the tubulin-epothilone complex is able to fully recapitulate the differences in tubulin-polymerizing activity and microtubule-binding affinity between C20-modified epothilones 6 (C20-propyl), 7 (C20-butyl), and 8 (C20-hydroxypropyl). Based on the results of transferred NOE experiments in the presence of tubulin, the isomeric C15 quinoline-based Epo B analogues 4 and 5 show very similar orientations of the side chain, irrespective of the position of the nitrogen atom in the quinoline ring. The quinoline side chain stacks on the imidazole moiety of beta-His227 with equal efficiency in both cases, thus suggesting that the aromatic side chain moiety in epothilones contributes to tubulin binding through strong van der Waals interactions with the protein rather than hydrogen bonding involving the heteroaromatic nitrogen atom. These conclusions are in line with existing tubulin polymerization and microtubule-binding data for 4, 5, and Epo B.

Calculation of crystal optical properties from molecular electron density

We have recently developed a method to obtain distributed atomic polarizabilities adopting a partitioning of the molecular electron density (for example, the Quantum Theory of Atoms in Molecules, [1]), calculated with or without an applied electric field. The procedure [2] allows to obtained atomic polarizability tensors, which are perfectly exportable, because quite representative of an atom in a given functional group. Among the many applications of this idea, the calculation of crystal susceptibility is easily available, either from a rough estimation (the polarizability of the isolated molecule is used) or from a more precise estimation (the polarizability of a molecule embedded in a cluster representing the first coordination sphere is used). Lorentz factor is applied to include the long range effect of packing, which is enhancing the molecular polarizability. Simple properties like linear refractive index or the gyration tensor can be calculated at relatively low costs and with good precision. This approach is particularly useful within the field of crystal engineering of organic/organometallic materials, because it would allow a relatively easy prediction of a property as a function of the packing, thus allowing "reverse crystal engineering". Examples of some amino acid crystals and salts of amino acids [3] will be illustrated, together with other crystallographic or non-crystallographic applications. For example, the induction and dispersion energies of intermolecular interactions could be calculated with superior precision (allowing anisotropic van der Waals interactions). This could allow revision of some commonly misunderstood intermolecular interactions, like the halogen bonding (see for example the recent remarks by Stone or Gilli [4]). Moreover, the chemical reactivity of coordination complexes could be reinvestigated, by coupling the conventional analysis of the electrostatic potential (useful only in the circumstances of hard nucleophilic/electrophilic interaction) with the distributed atomic polarizability. The enhanced reactivity of coordinated organic ligands would be better appreciated. [1] R. F. W. Bader, Atoms in Molecules: A Quantum Theory. Oxford Univ. Press, 1990. [2] A. Krawczuk-Pantula, D. Pérez, K. Stadnicka, P. Macchi, Trans. Amer. Cryst. Ass. 2011, 1-25 [3] A. S. Chimpri1, M. Gryl, L. H.R. Dos Santos1, A. Krawczuk, P. Macchi Crystal Growth & Design, in the press. [4] a) A. J. Stone, J. Am. Chem. Soc. 2013, 135, 7005−7009; b) V. Bertolasi, P. Gilli, G. Gilli Crystal Growth & Design, 2013, 12, 4758-4770.

Crystal structures of isotypic poly[bis(benzimidazolium) [tetra-μ-iodido-stannate(II)]] and poly[bis(5,6-difluorobenzimidazolium) [tetra-μ-iodido-stannate(II)]]

The isostructural title compounds, {(C7H7N2)2[SnI4]}n, (1), and {(C7H5F2N2)2[SnI4]}n, (2), show a layered perovskite-type structure composed of anionic {[SnI4]2-}n sheets parallel to (100), which are decorated on both sides with templating benzimidazolium or 5,6-di­fluoro­benzimidazolium cations, respectively. These planar organic heterocycles mainly form N-H...I hydrogen bonds to the terminal I atoms of the corner-sharing [SnI6] octa­hedra (point group symmetry 2) from the inorganic layer, but not to the bridging ones. This is in contrast to most of the reported structures of related compounds where ammonium cations are involved. Here hydrogen bonding to both types of iodine atoms and thereby a distortion of the inorganic layers to various extents is observed. For (1) and (2), all Sn-I-Sn angles are linear and no out-of-plane distortions of the inorganic layers occur, a fact of relevance in view of the material properties. The arrangement of the aromatic cations is mainly determined through the direction of the N-H...I hydrogen bonds. The coherence between organic bilayers along [100] is mainly achieved through van der Waals inter­actions.

Nickel(II)-, cobalt(II)-, copper(II)-, and zinc(II)-phthalate and 1-methylimidazole coordination compounds: synthesis, crystal structures and magnetic properties

Three new coordination polymers [M(Pht)(1-MeIm)2]n (where M=Cu (1), Zn (2), Co (3); Pht2−=dianion of o-phthalic acid; 1-MeIm=1-methylimidazole) and two compounds [M(1-MeIm)6](HPht)2 · 2H2O (M=Co (4), Ni (5)) have been synthesized and characterized by X-ray crystallography. The structures of 1–3 (2 is isostructural to 3) consist of [M(1-MeIm)2] building units connected by 1,6-bridging phthalate ions to form infinite chains. In complex 1, each copper(II) center adopts a square coordination mode of N2O2 type by two O atoms from different phthalate ions and two N atoms of 1-MeIm, whereas in 3 two independent metal atoms are tetrahedrally (N2O2) coordinated to a pair of Pht ligands and a pair of 1-MeIm molecules. There are only van der Waals interactions between the chains in 1, while the three-dimensional network in 3 is assembled by C–H⋯O contacts. In contrast to polymers 1–3 the structures of 4 and 5 (complexes are also isostructural) are made up of the [M(1-MeIm)6]2+ cation, two hydrogen phthalate anions (HPht−) and two H2O solvate molecules. The coordination around each metal(II) atom is octahedral with six nitrogen atoms of 1-MeIm. Extended hydrogen bonding networks embracing the solvate water molecules and a phthalate residue as well as the weak C–H⋯O interactions stabilize the three-dimensional structures. Magnetic studies clearly show that the magnetic ions do not interact with each other. Furthermore, in compound 4 we have another example of a highly anisotropic Co2+ ion with a rhombic g-tensor and large zero-field-splitting. The complexes were also characterized by IR and 1H NMR spectroscopy, thermogravimetric analysis, and all data are discussed in the terms of known structures.

Deciphering the driving forces of erosion rates on millennial to million-year timescales in glacially impacted landscapes: An example from the Western Alps

In many regions, tectonic uplift is the main driver of erosion over million-year (Myr) timescales, but climate changes can markedly affect the link between tectonics and erosion, causing transient variations in erosion rates. Here we study the driving forces of millennial to Myr-scale erosion rates in the French Western Alps, as estimated from in situ produced cosmogenic 10Be and a newly developed approach integrating detrital and bedrock apatite fission-track thermochronology. Millennial erosion rates from 10Be analyses vary between ~0.27 and ~1.33 m/kyr, similar to rates measured in adjacent areas of the Alps. Significant positive correlations of millennial erosion rates with geomorphic measures, in particular with the LGM ice thickness, reveal a strong transient morphological and erosional perturbation caused by repeated Quaternary glaciations. The perturbation appears independent of Myr-scale uplift and erosion gradients, with the effect that millennial erosion rates exceed Myr-scale erosion rates only in the internal Alps where the latter are low (<0.4 km/Myr). These areas, moreover, exhibit channels that clearly plot above a general linear positive relation between Myr-scale erosion rates and normalized steepness index. Glacial erosion acts irrespective of rock uplift and thus not only leads to an overall increase in erosion rates but also regulates landscape morphology and erosion rates in regions with considerable spatial gradients in Myr-scale tectonic uplift. Our study demonstrates that climate change, e.g., through occurrence of major glaciations, can markedly perturb landscape morphology and related millennial erosion rate patterns, even in regions where Myr-scale erosion rates are dominantly controlled by tectonics.

Koproduktion von Wissen in der Entwicklung des Biolandbaus - Einflüsse von Marginalisierung, Anerkennung und Markt

The empirical analysis of the historical development of transdisciplinary co-production of knowledge (CPK) in organic agriculture (OA) in Switzerland has revealed three distinct phases. The initial phase shows various characteristics of transdisciplinary CPK and a high importance of experiential knowledge. The 2nd and 3rd phases involve an in-creasing segregation of farmers’, extension agents’, and scientists’ knowledge, caused by internal and external impacts, i.e. foundation of independent research institutions, changes in agriculture policy, and new market strategies. These developments strikingly represent an ambiguous trend: the growing societal and political recognition of OA and the increasing market, which are positive achievements, are associated by a gradual loss of very precious forms of CPK. A successful re-establishment of CPK processes and re-integration of experiential knowledge would help to resolve this dilemma and thus improve future research in OA and sustainability research in general.

Sportmotorische Leistungsfähigkeit und schulische Leistung – Zum mediierenden Effekt der exekutiven Funktionen

Introduction: Die sportmotorische Leistungsfähigkeit (SMLF) hängt nicht nur positiv mit der körperlichen Gesundheit zusammen, sondern gilt auch als Prädiktor für die schulische Leistung (SL) (van der Niet, Hartmann, Smith, & Visscher, 2014). Um die Frage zu beantworten, wie denn zwei auf den ersten Blick so distale Merkmale zusammenhängen sollen, werden unterschiedliche erklärende Variablen diskutiert, wobei die kognitive Stimulationshypothese die exekutiven Funktionen (EF) als mediierende Variable im Zusammenhang zwischen SMLF und SL postuliert. Die Annahme hierbei ist, dass die mit komplexen motorischen Kontrollprozessen einhergehende kognitive Beanspruchung bei einem wiederholten Ausführen von nicht-automatisierten sportbezogenen Handlungen zu einer Aktivierung und somit Förderung der EF führt (Best, 2010). EF, verstanden als höhere kognitive Prozesse, die ein zielorientiertes und situationsangepasstes Handeln erlauben, sind für den schulischen Erfolg von zentraler Bedeutung und gleichzeitig wichtige Prädiktoren der SL (Diamond, 2013). Obwohl diese Mediation seit einigen Jahren in der Literatur diskutiert wird, wurde sie bis heute noch nicht mit Hilfe längsschnittlicher Daten geprüft. Daher wird im Folgenden der mediierende Effekt der EF im Zusammenhang zwischen SMLF und SL getestet. Methods: Im Rahmen der Studie Sport und Kognition 5.0 wurden insgesamt 237 Primarschulkinder (52.3% ♀; 11.31 ± 0.62 Jahre) zu drei Messzeitpunkten in ihrer SMLF (T1) und ihren EF (T2) getestet. Zusätzlich wurde die SL (T3) mittels objektiver Schulleistungstests (Mathematik und Deutsch) erhoben. Um die Hauptfragestellung zu prüfen, ob die SL vorwiegend mediiert über die EF durch die SMLF vorhergesagt werden kann, wurde eine bootstrapping-basierte Mediationsanalyse in AMOS 22 durchgeführt. Results: Das theoretisch abgeleitete Strukturgleichungsmodell (2 (22, N = 237) = 30.357, p = .110; CFI = .978) weist eine zufriedenstellende Anpassungsgüte auf. Erwartungsgemäss zerfällt der Zusammenhang innerhalb des Mediationsmodells zwischen der SMLF und der SL, alsbald die EF ins Modell aufgenommen werden (β = .16, p = .634). Sowohl der Zusammenhang zwischen der SMLF und den EF (β = .38, p = .039), als auch der Zusammenhang zwischen den EF und der SL fallen signifikant aus (β = .91, p = .001) und ergeben dabei eine volle Mediation über den indirekten (p = .021) und totalen Effekt (p = .001). Discussion/Conclusion: Die erstmals vorliegenden längsschnittlichen Daten bestätigen den Zusammenhang zwischen SMLF und SL bei einer Mediation über die EF und decken sich mit den, aus einem querschnittlichen Design stammenden, Befunden von van der Niet et al. (2014). Zur Steigerung der schulischen Leistung sollten zukünftige Schulsportinterventionen die SMLF von Kindern erhöhen und dabei die EF bei der Auswahl von sportlichen Aufgaben mitberücksichtigen. References: Best, J. R. (2010). Effects of physical activity on children’s executive function: Contributions of experimental research on aerobic exercise. Developmental Review, 30, 331-351. Diamond, A. (2013). Executive functions. Annual Review of Psychology, 64, 135-168. van der Niet, A. G., Hartmann, E., Smith, J. & Visscher, C. (2014). Modeling relationships between physical fitness, executive functioning, and academic achievement in primary school children. Psychology of Sport & Exercise, 15(4), 319-325.

Sportmotorische Leistungsfähigkeit und schulische Leistung – Zum mediierenden Effekt der exekutiven Funktionen

Die sportmotorische Leistungsfähigkeit (SMLF) gilt in jüngster Zeit als ein Prädiktor für schulische Leistung (SL) (Diamond, 2013). Um die Frage zu beantworten, wie denn zwei auf den ersten Blick so distale Merkmale zusammenhängen sollen, werden unterschiedliche erklärende Variablen diskutiert, wobei die kognitive Stimulationshypothese die exekutiven Funktionen (EF) als mediierende Variable im Zusammenhang zwischen SMLF und SL postuliert. Die Annahme hierbei ist, dass die mit komplexen motorischen Kontrollprozessen einhergehende kognitive Beanspruchung bei einem wiederholten Ausführen von nicht-automatisierten sportbezogenen Handlungen zu einer Aktivierung und somit Förderung der EF führt (Best, 2010). Der mediierende Effekt der EF im Zusammenhang zwischen der SMLF und der SL wird seit einigen Jahren in der Literatur diskutiert und wird im Folgenden innerhalb einer längsschnittlichen Untersuchung getestet. Im Rahmen der Studie SpuK wurden 237 Primarschulkinder (52.3% ♀; 11.31 ± 0.62 Jahre) zu drei Messzeitpunkten in ihrer SMLF (T1) und ihren EF (T2) getestet. Zur Ermittlung der SMLF wurden drei sportmotorische Tests in den Bereichen Koordination, Ausdauer und Schnellkraft durchgeführt. Die EF Inhibition, kognitive Flexibilität und Arbeitsgedächtnis wurden computerbasiert über den N-Back- und Flanker-Test operationalisiert. Zusätzlich wurde die SL (T3) mittels objektiver Schulleistungstests erhoben. Um die Hauptfragestellung zu prüfen, wurde eine bootstrapping basierte Mediationsanalyse in AMOS durchgeführt. Das Strukturgleichungsmodell (2 (22, N=237)=30.357, p=.110; CFI=.978) weist eine zufriedenstellende Anpassungsgüte auf. Erwartungsgemäss zerfällt der Zusammenhang innerhalb des Mediationsmodells zwischen der SMLF und der SL, alsbald die EF ins Modell aufgenommen werden (β=.16, p= .634). Sowohl der Zusammenhang zwischen der SMLF und den EF (β=.38, p= .039), als auch der Zusammenhang zwischen den EF und der SL fallen signifikant aus (β=.91, p=.001) und ergeben dabei eine volle Mediation über den indirekten (p=.021) und totalen Effekt (p=.001). Die vorliegenden längs-schnittlichen Daten bestätigen den Zusammenhang zwischen SMLF und SL bei einer Mediation über die EF und bestätigen somit die aus querschnittlichem Design stammenden Resultate von van der Niet et al. (2014). Literatur Best, J. R. (2010). Effects of physical activity on children’s executive function: Contributions of ex-perimental research on aerobic exercise. Developmental Review, 30, 331-351. Diamond, A. (2013). Executive functions. Annual Review of Psychology, 64, 135-168. van der Niet, A. G., Hartmann, E., Smith, J. & Visscher, C. (2014). Modeling relationships between physical fitness, executive functioning, and academic achievement in primary school chil-dren. Psychology of Sport & Exercise, 15(4), 319-325.