Atomic Orbital-Based Reformulation of MP2 Energy Gradients and Quantum-Chemical Investigations of the gauche-Effect in Proline and Polyproline Compounds

Es wird eine auf dem Laplace-Ansatz von Almlöf und Häser basierende Neuformulierung für die Energiegradienten der Møller-Plesset-Störungstheorie zweiter Ordnung (MP2) vorgestellt. Während der Rechenaufwand der konventionellen MP2-Methode mit der fünften Potenz der Molekülgröße ansteigt und deswegen die Anwendbarkeit auf kleine Systemgrößen (etwa 100 Atome) beschränkt ist, eignet sich der vorliegende Ausdruck für eine linear skalierende Umsetzung. Die Reformulierung ist vollständig atomorbitalbasiert, wobei die Berechnung der auftretenden gestörten Einteilchen-Dichtematrix mit Hilfe der Z-Vektor-Technik von Handy und Schaefer umgangen werden kann. Im Rahmen der Arbeit wurde die Z-Vektor-Methode erstmals dichtematrixbasiert formuliert und angewendet. Die Validierung des Ansatzes anhand einer Auswahl kleiner Moleküle deutet auf ein frühes Einsetzen des linearen Skalenverhaltens signifikanter Integralprodukte hin und zeigt, dass bereits vier bis sechs Quadratur-Punkte eine Genauigkeit im µHartree/Bohr-Bereich gewährleisten. Der neue atomorbitalbasierte MP2-Gradientenausdruck liefert eine Grundlage für die Strukturberechnung großer Moleküle unter Berücksichtigung von Elektronenkorrelation, insbesondere von den in der Hartree-Fock-Näherung und in heute gängigen Dichtefunktionalen vernachlässigten dispersiven Wechselwirkungen. Neben den methodischen Entwicklungen werden Untersuchungen zur Konformation und relativen Stabilität von Prolin- und Polyprolinderivaten vorgestellt, wobei vor allem Einflüsse durch Substituenten und stereoelektronische Effekte im Vordergrund stehen. Anhand substituierter Prolinderivate wird die Bedeutung des gauche-Effekts betrachtet und untersucht, welche Faktoren für das cis/trans-Isomerenverhältnis entscheidend sind, um so ein besseres Verständnis für die Prolyl-cis/trans-Isomerisierung zu erlangen, die in zahlreichen biologisch relevanten Prozessen eine zentrale Rolle spielt. Die vorgestellten Untersuchungen zeigen, dass der gauche-Effekt strukturlenkenden Einfluss in den betrachteten Prolinderivaten besitzt und dadurch auch das cis/trans-Isomerenverhältnis indirekt beeinflusst. Darüber hinaus lässt die Analyse der quantenchemisch berechneten Strukturen erkennen, dass in bestimmten Isomeren räumliche Anordnungen gegeben sind, die stabilisierende intramolekulare Wechselwirkungen gestatten und ausschlaggebend für das cis/trans-Isomerenverhältnis sind. Aufbauend auf den Monomerstudien wird der Substituenteneinfluss auf die Konformation und Helixstabilität von Oligoprolinverbindungen diskutiert. Es wird gezeigt, dass der durch entsprechende Substituenten hervorgerufene gauche-Effekt, der als vergleichsweise schwacher stereoelektronischer Effekt angesehen wird, in der Lage ist, die Struktur und somit die Stabilität oligomerer Verbindungen zu beeinflussen. Neben Untersuchungen zum Substituenteneffekt werden Studien vorgestellt, die sich mit dem Einfluss geladener Endgruppen auf die Helixstabilität von Oligoprolinen befassen. Die dabei in Einklang mit experimentellen Befunden ermittelte Stabilisierung der PPI-helikalen Struktur wird anhand systematischer Fragmentuntersuchungen und Dipolmomentberechnungen erklärt. Auf diese Weise liefern die quantenchemischen Studien einen Beitrag zum Verständnis struktur- und stabilitätsbestimmender Einflüsse in Prolin- und Oligoprolinverbindungen.A reformulation of second-order Møller-Plesset perturbation theory (MP2) energy gradients based on the Laplace ansatz of Häser and Almlöf is introduced. While the computational effort at the MP2 level conventionally increases with the fifth power of the molecular size and thus restricts the applicability onto small sized systems (about 100 atoms) the present reformulation is suitable for a linear-scaling implementation. A fully atomic orbital-based gradient expression is provided, in which the explicit computation of the emerging perturbed density matrix can be circumvented by applying the Z-vector technique of Handy and Schaefer. In the present thesis, the Z-vector method was also for the first time formulated within a density matrix-based scheme. The implementation was checked for a set of small molecules. The numerically significant integral products indicate an early onset of the linear-scaling behavior. Typically four to six Laplace points are sufficient to assure µHartree/Bohr accuracy. The new atomic orbital-based MP2 energy gradient expression provides a basis for computing the structure of large molecules while accounting for electron-correlation effects. This is particularly important, since dispersive interactions are not or not sufficiently accounted for in the Hartree-Fock approximation or currently popular density functionals. The thesis focuses in the second part on quantum chemical studies of the conformational and relative stabilities of proline and polyproline derivatives. Special emphasis is put on the influence of substituents and stereoelectronic effects. On the basis of substituted proline derivatives, the relevance of the gauche-effect and the cis/trans ratio are studied to gain a better understanding of the prolyl-cis/trans-isomerization, that plays an important role in many biological processes. The results demonstrate that within the considered proline derivatives the gauche-effect possesses structure directing influence and thus affects the cis/trans-ratio. The structural analysis reveals in certain isomers spatial arrangements which allow for stabilizing intramolecular interactions and, therefore, influence the cis/trans ratio. Based on the monomer studies, the influence of substituents on the conformation and the helix stability of oligoprolines is discussed. It is shown, that the gauche-effect, which is evoked by specific substituents and regarded as a comparatively weak stereoelectronic effect, is also able to affect the structure and thus the stability of oligomeric compounds. Moreover, studies concerning the impact of charged terminal groups on the helix stability are presented. In accordance with experimental results, a stabilization of the PPI helical structure is found and influences are studied by systematic fragment studies and dipole moment calculations. In this way, the quantum chemical studies provide insights into the structure and stability determining effects in proline and oligoproline compounds

Idealtypische subjektive Theorien - eine theoretisch fundierte Konkretisierung der Kombination von zusammenfassender qualitativer Inhaltsanalyse und empirisch begründeter Typenbildung

In diesem Beitrag stellen wir einen konzeptionellen Vorschlag für ein methodisches Verfahren zur qualitativ-theoriegenerierenden Herausarbeitung idealtypischer subjektiver Theorien vor. Vor dem Hintergrund von Annahmen zu subjektiven Theorien zeigen wir auf, dass sich die Qualität dieses Erkenntnisziels durch eine Methodenkombination von zusammenfassender qualitativer Inhaltsanalyse und empirisch begründeter Typenbildung angemessen erfassen lässt und welche Funktion den einzelnen Verfahrensschritten dabei zukommt. Mit dieser theoretisch begründeten Konkretisierung, was kategorisiert und typisiert wird, reagieren wir zum einen auf ein methodisches Desiderat und regen zum anderen an, die qualitative Inhaltsanalyse hinsichtlich des vorhandenen Potenzials - wie der abduktiven Kategorienbildung - sowie mit Blick auf eine theoretische Fundierung anhand der epistemischen Qualität des Ergebnisses weiterzuentwickeln.In this article, we present a conceptual proposal for a methodological procedure for a qualitative theory generating elaboration of ideal-typical subjective theories. Against the background of assumptions on subjective theories we show that the quality of this epistemological goal can be adequately captured by a combination of a qualitative content analysis and an empirically grounded construction of types and what function the individual procedural steps have in this respect. With this theoretically substantiated concretization of what is categorized and typified we react on the one hand to a methodological desideratum and on the other hand encourage the further development of qualitative content analysis with regard to the existing potential - such as abductive category formation - also in respect of a theoretical foundation based on the epistemic quality of the result

Post-mortem computed tomographic angiography in equine distal forelimbs: A feasibility study

In-depth understanding of pathophysiological processes occurring in the vasculature of the equine distal limb is of great importance to improve both diagnostic and therapeutic approaches to diseases. To gain further insights, a model allowing high-resolution 3D-visualization of the vasculature is necessary. This pilot study evaluated the feasibility of restoring vascular perfusion in frozen-thawed distal equine cadaver limbs without prior preparation using computer tomographic imaging (CT). Five frozen-thawed, radiographically normal forelimbs were perfused with a lipophilic contrast agent through the median artery and radial vein in three phases (arterial, venous, and arterial-venous combined (AVC) dynamic). For comparison, one additional limb was perfused with a hydrosoluble contrast agent. The CT-studies (16-slice MDCT, 140 kV, 200 mA, 2 mm slice thickness, 1 mm increment, pitch 0.688) were evaluated at 11 specified regions for visualization of the vasculature and presence of artifacts or anatomic variations. The protocol used in this study proved to be feasible and provided good visualization (93.1%) of vasculature with low rates of artifacts. During the different phases, vascular visualization was similar, but while filling defects decreased in the later phases, extravasation worsened in the 2 limbs where it was observed. Subjectively, the best quality of angiographic images was achieved during the AVC dynamic phase. Perfusion with hydrosoluble contrast resulted in significantly lower vascular visualization (74.0%) and higher artifact rates. This study shows that reperfusion of frozen-thawed equine distal limbs with a lipophilic contrast agent allows for high-quality 3D-visualization of the vasculature and may serve as a model for in situ vascular evaluation in the future

Seizures, ataxia and parvalbumin-expressing interneurons respond to selenium supply in Selenop-deficient mice

Mice with constitutive disruption of the Selenop gene have been key to delineate the importance of selenoproteins in neurobiology. However, the phenotype of this mouse model is exquisitely dependent on selenium supply and timing of selenium supplementation. Combining biochemical, histological, and behavioral methods, we tested the hypothesis that parvalbumin-expressing interneurons in the primary somatosensory cortex and hippocampus depend on dietary selenium availability in Selenop−/− mice. Selenop-deficient mice kept on adequate selenium diet (0.15 mg/kg, i.e. the recommended dietary allowance, RDA) developed ataxia, tremor, and hyperexcitability between the age of 4–5 weeks. Video-electroencephalography demonstrated epileptic seizures in Selenop−/− mice fed the RDA diet, while Selenop ± heterozygous mice behaved normally. Both neurological phenotypes, hyperexcitability/seizures and ataxia/dystonia were successfully prevented by selenium supplementation from birth or transgenic expression of human SELENOP under a hepatocyte-specific promoter. Selenium supplementation with 10 μM selenite in the drinking water on top of the RDA diet increased the activity of glutathione peroxidase in the brains of Selenop−/− mice to control levels. The effects of selenium supplementation on the neurological phenotypes were dose- and time-dependent. Selenium supplementation after weaning was apparently too late to prevent ataxia/dystonia, while selenium withdrawal from rescued Selenop−/− mice eventually resulted in ataxia. We conclude that SELENOP expression is essential for preserving interneuron survival under limiting Se supply, while SELENOP appears dispensable under sufficiently high Se status

Ketoamide Resistance and Hepatitis C Virus Fitness in Val55 Variants of the NS3 Serine Protease

ABSTRACT Drug-resistant viral variants are a major issue in the use of direct-acting antiviral agents in chronic hepatitis C. Ketoamides are potent inhibitors of the NS3 protease, with V55A identified as mutation associated with resistance to boceprevir. Underlying molecular mechanisms are only partially understood. We applied a comprehensive sequence analysis to characterize the natural variability at Val55 within dominant worldwide patient strains. A residue-interaction network and molecular dynamics simulation were applied to identify mechanisms for ketoamide resistance and viral fitness in Val55 variants. An infectious H77S.3 cell culture system was used for variant phenotype characterization. We measured antiviral 50% effective concentration (EC 50 ) and fold changes, as well as RNA replication and infectious virus yields from viral RNAs containing variants. Val55 was found highly conserved throughout all hepatitis C virus (HCV) genotypes. The conservative V55A and V55I variants were identified from HCV genotype 1a strains with no variants in genotype 1b. Topology measures from a residue-interaction network of the protease structure suggest a potential Val55 key role for modulation of molecular changes in the protease ligand-binding site. Molecular dynamics showed variants with constricted binding pockets and a loss of H-bonded interactions upon boceprevir binding to the variant proteases. These effects might explain low-level boceprevir resistance in the V55A variant, as well as the Val55 variant, reduced RNA replication capacity. Higher structural flexibility was found in the wild-type protease, whereas variants showed lower flexibility. Reduced structural flexibility could impact the Val55 variant's ability to adapt for NS3 domain-domain interaction and might explain the virus yield drop observed in variant strains

Responses of soil organic carbon, aggregate diameters, and hydraulic properties to long-term organic and conventional farming on a Vertisol in India

Organic matter management can improve soil structural properties. This is crucial for agricultural soils in tropical regions threatened by high rainfall intensities. Compared to conventional farming, organic farming is usually deemed to increase organic carbon and improve soil structural properties such as stability and permeability. However, how much, if any, buildup of organic carbon is possible or indeed occurring also depends on soil type and environmental factors. We compared the impact of seven years of organic farming (annually 13.6 t ha−1 of composted manure) with that of conventional practices (2 t ha−1 of farmyard manure with 150–170 kg N ha−1 of mineral fertilizers) on soil structural properties. The study was conducted on a Vertisol in India with a two-year crop rotation of cotton soybean wheat. Despite large differences in organic amendment application, organic carbon was not significantly different at 9.6 mg C g−1 on average in the topsoil. However, the size distribution of water-stable aggregates shifted toward more aggregates <137 μm in the organic systems. Cumulative water intake was lower compared to the conventional systems, leading to higher runoff and erosion. These changes might be related to the lower pH and higher exchangeable sodium in the organic systems. Our results indicate that higher application of organic amendments did not lead to higher soil organic carbon and associated improvement in soil structures properties compared to integrated fertilization in this study. Chemical properties may dominate soil aggregation retarding the uptake and integration of organic amendments for sustainable agricultural intensification in tropical, semiarid climates

Symmetric dithiodigalactoside: strategic combination of binding studies and detection of selectivity between a plant toxin and human lectins

Thioglycosides offer the advantage over O-glycosides to be resistant to hydrolysis. Based on initial evidence of this recognition ability for glycosyldisulfides by screening dynamic combinatorial libraries, we have now systematically studied dithiodigalactoside on a plant toxin (Viscum album agglutinin) and five human lectins (adhesion/growth-regulatory galectins with medical relevance e.g. in tumor progression and spread). Inhibition assays with surface-presented neoglycoprotein and in solution monitored by saturation transfer difference NMR spectroscopy, flanked by epitope mapping, as well as isothermal titration calorimetry revealed binding properties to VAA (Ka: 1560 ± 20 M-1). They were reflected by the structural model and the affinity on the level of toxin-exposed cells. In comparison, galectins were considerably less reactive, with intrafamily grading down to very minor reactivity for tandem-repeat-type galectins, as quantitated by radioassays for both domains of galectin-4. Model building indicated contact formation to be restricted to only one galactose moiety, in contrast to thiodigalactoside. The tested lycosyldisulfide exhibits selectivity between the plant toxin and the tested human lectins, and also between these proteins. Therefore, glycosyldisulfides have potential as chemical platform for inhibitor design

Interaction of cylindrical polymer brushes in dilute and semi-dilute solution

We present a systematic study of flexible cylindrical brush-shaped macromolecules in a good solvent by small-angle neutron scattering (SANS), static light scattering (SLS), and by dynamic light scattering (DLS) in dilute and semi-dilute solution. The SLS and SANS data extrapolated to infinite dilution lead to the shape of the polymer that can be modeled in terms of a worm-like chain with a contour length of 380 nm and a persistence length of 17.5 nm. SANS data taken at higher polymer concentration were evaluated by using the polymer reference interaction site model (PRISM). We find that the persistence length reduce from 17.5 nm at infinite dilution to 5.3 nm at the highest concentration (volume fraction 0.038). This is comparable with the decrease of the persistence length in semi-dilute concentration predicted theoretically for polyelectrolytes. This finding reveals a softening of stiffness of the polymer brushes caused by their mutual interaction