Versatile binding properties of a di-2-pyridyl ketone nicotinoylhydrazone ligand: Crystal structure of a Cu(II) complex

Six new copper complexes of di-2-pyridyl ketone nicotinoylhydrazone (HDKN) have been synthesized. The complexes have been characterized by a variety of spectroscopic techniques and the structure of [Cu(DKN)2]·H2O has been determined by single crystal X-ray diffraction. The compound [Cu(DKN)2]·H2O crystallized in the monoclinic space group P21 and has a distorted octahedral geometry. The IR spectra revealed the presence of variable modes of chelation for the investigated ligand. The EPR spectra of compounds [Cu2(DKN)2( -N3)2] and [Cu2(DKN)2( -NCS)2] in polycrystalline state suggest a dimeric structure as they exhibited a half field signal, which indicate the presence of a weak interaction between two Cu(II) ions in these complexes

Studies on Transition Metal Chelates of some Tridentate Aroylhydrazones

The ability of aroylhydrazones to bind with transition metals is a developing area of research interest and the coordinating properties of hydrazones can be tuned by the appropriate choice of parent aldehyde or ketone and the hydrazide. So in the present work we selected four different aroylhydrazones as principal ligands. Introduction of heterocyclic bases like 1,10-phenanthroline, 2,2′-bipyridine, 3-picoline and pyridine leads to the syntheses of mixed ligand metal chelates which can cause different bonding modes, spectral properties and geometries in coordination compounds. The importance of aroylhydrazones and their complexes in various fields and their interesting coordinating properties stimulate our interest in the investigation of transition metal chelates with four different aroylhydrazones. The aroylhydrazones selected are 4-benzyloxy-2-hydroxybenzaldehyde-4-nitrobenzoylhydrazone dimethylformamide monosolvate, 5-bromo-2-hydroxy-3-methoxybenzaldehyde nicotinoylhydrazone dihydrate methanol monosolvate, 4-diethylamino-2- hydroxybenzaldehyde nicotinoylhydrazone monohydrate and 2-benzoylpyridine- 4-nitrobenzoylhydrazone. The selection of 4-benzyloxy-2-hydroxybenzaldehyde- 4-nitrobenzoylhydrazone was based on the idea of developing ligands having D-π-A general structure, so that the proligand and metal complexes exhibit NLO activity. Hence it is interesting to explore the coordinating capabilities of the synthesized hydrazones and to study the NLO activity of hydrazones and some of the metal complexes.

Occurrence of filamentous algae and soil characteristics in the paddy fields of Kuttanad and Kole lands of Kerala

The present work is the study of filamentous algae in the paddy fields of Kuttanad and Kole lands of Kerala. This investigation was initiated by sampling of filamentous algae in Kuttanad during December 2010 to February 2011. A second phase of sampling was done from November 2011 to February 2012. The sampling periodicity corresponded to the crop growth starting from field preparation through sowing, and continued till the harvest. Sampling locations were selected from the active paddy cultivation regions of the six agronomic zones of Kuttanad. The numbers of sampling locations were proportional to the area of each zone. Algae of the Kole lands were collected during from October 2011 to January 2012. It was observed that blue-green algae dominated in both Kuttanad and Kole lands. Thirty two species of blue-green algae and eight species of green algae were identified from Kuttanad. The highest number of algal species was observed from Kayal lands in Kuttanad throughout the cropping season. Among the thirty two species of blue-green algae twenty five species are nonheterocystous and seven species are heterocystous. Twenty eight species of blue-green and six species of green algae were identified from Kole lands, and highest number of species was observed in Palakkal throughout the cropping season. Among the twenty eight species of blue-green algae collected from Kole lands twenty one species are non-heterocystous, and only seven species are heterocystous filamentous algae. Blooms of Spirogyra were observed during the second phase of sampling in Kuttanad and also in the Kole lands. The results of the germination study revealed that the extract of Spirogyra sp. inhibited seed germination and reduced seedling vigour. The growth of the treated seedlings was evaluated by pot experiments. The results clearly showed that Spirogyra sp. can negatively affect the seed germination, seedling vigour, and the yield of rice.

Asymptotics of number fields and the Cohen-Lenstra heuristics

We study the asymptotics conjecture of Malle for dihedral groups Dl of order 2l, where l is an odd prime. We prove the expected lower bound for those groups. For the upper bounds we show that there is a connection to class groups of quadratic number fields. The asymptotic behavior of those class groups is predicted by the Cohen-Lenstra heuristics. Under the assumption of this heuristic we are able to prove the expected upper bounds.

Exact algorithms for p-adic fields and epsilon constant conjectures

We develop several algorithms for computations in Galois extensions of p-adic fields. Our algorithms are based on existing algorithms for number fields and are exact in the sense that we do not need to consider approximations to p-adic numbers. As an application we describe an algorithmic approach to prove or disprove various conjectures for local and global epsilon constants.

Organic inputs and farmers' management strategies in millet fields of western Niger

Research on soil fertility management in sub-Saharan Africa was criticized lately for largely ignoring farmers’ management strategies and the underlying principles. To fill this gap of knowledge, detailed interviews were conducted with 108 farm households about their rationale in managing the soil fertility of 307 individual fields in the agro-pastoral village territory of Chikal in western Niger. To amplify the farmers’ information on manuring and corralling practices, repeated measurements of applied amounts of manure were carried out within six 1-km^2 monitoring areas from February to October 1998. The interviews revealed that only 2% of the fields were completely fallowed for a period of 1–15 years, but 40% of the fields were at least partially fallowed. Mulching of crop residues was mainly practiced to fight wind erosion but was restricted to 36% of the surveyed fields given the alternative use of straw as livestock feed. Manure application and livestock corralling, as most effective tools to enhance soil fertility, were targeted to less than 30% of the surveyed fields. The application of complete fallow and manuring and corralling practices were strongly related to the households’ endowment with resources, especially with land and livestock. Within particular fields, measures were mainly applied to spots of poor soil fertility, while the restoration of the productivity of hard pans was of secondary importance. Given the limited spatial coverage of indigenous soil fertility measures and their strong dependence on farmers’ wealth, supplementary strategies to restrict the decline of soil fertility in the drought prone areas of Niger with their heavily weathered soils are needed.

Non-Born-Oppenheimer Dynamics of Hydrogen Molecules in Strong Laser-Fields

Die Arbeit behandelt die numerische Untersuchung von Wasserstoff-Moleküldynamik in starken Laserfeldern. Im Speziellen wird die Struktur von Ionisationsspektren bei Einfach-Photoionisation betrachtet. Korrelationen zwischen Elektron- und Kernbewegung werden identifiziert und mit Effekten in den Energiespektren in Verbindung gebracht. Dabei wird stets auf die Integration der zeitabhängigen Schrödingergleichung zurückgegriffen.

Protein Folding Simulations: Confinement, External Fields and Sequence Design

The present Thesis looks at the problem of protein folding using Monte Carlo and Langevin simulations, three topics in protein folding have been studied: 1) the effect of confining potential barriers, 2) the effect of a static external field and 3) the design of amino acid sequences which fold in a short time and which have a stable native state (global minimum). Regarding the first topic, we studied the confinement of a small protein of 16 amino acids known as 1NJ0 (PDB code) which has a beta-sheet structure as a native state. The confinement of proteins occurs frequently in the cell environment. Some molecules called Chaperones, present in the cytoplasm, capture the unfolded proteins in their interior and avoid the formation of aggregates and misfolded proteins. This mechanism of confinement mediated by Chaperones is not yet well understood. In the present work we considered two kinds of potential barriers which try to mimic the confinement induced by a Chaperon molecule. The first kind of potential was a purely repulsive barrier whose only effect is to create a cavity where the protein folds up correctly. The second kind of potential was a barrier which includes both attractive and repulsive effects. We performed Wang-Landau simulations to calculate the thermodynamical properties of 1NJ0. From the free energy landscape plot we found that 1NJ0 has two intermediate states in the bulk (without confinement) which are clearly separated from the native and the unfolded states. For the case of the purely repulsive barrier we found that the intermediate states get closer to each other in the free energy landscape plot and eventually they collapse into a single intermediate state. The unfolded state is more compact, compared to that in the bulk, as the size of the barrier decreases. For an attractive barrier modifications of the states (native, unfolded and intermediates) are observed depending on the degree of attraction between the protein and the walls of the barrier. The strength of the attraction is measured by the parameter $\epsilon$. A purely repulsive barrier is obtained for $\epsilon=0$ and a purely attractive barrier for $\epsilon=1$. The states are changed slightly for magnitudes of the attraction up to $\epsilon=0.4$. The disappearance of the intermediate states of 1NJ0 is already observed for $\epsilon =0.6$. A very high attractive barrier ($\epsilon \sim 1.0$) produces a completely denatured state. In the second topic of this Thesis we dealt with the interaction of a protein with an external electric field. We demonstrated by means of computer simulations, specifically by using the Wang-Landau algorithm, that the folded, unfolded, and intermediate states can be modified by means of a field. We have found that an external field can induce several modifications in the thermodynamics of these states: for relatively low magnitudes of the field ($<2.06 \times 10^8$ V/m) no major changes in the states are observed. However, for higher magnitudes than ($6.19 \times 10^8$ V/m) one observes the appearance of a new native state which exhibits a helix-like structure. In contrast, the original native state is a $\beta$-sheet structure. In the new native state all the dipoles in the backbone structure are aligned parallel to the field. The design of amino acid sequences constitutes the third topic of the present work. We have tested the Rate of Convergence criterion proposed by D. Gridnev and M. Garcia ({\it work unpublished}). We applied it to the study of off-lattice models. The Rate of Convergence criterion is used to decide if a certain sequence will fold up correctly within a relatively short time. Before the present work, the common way to decide if a certain sequence was a good/bad folder was by performing the whole dynamics until the sequence got its native state (if it existed), or by studying the curvature of the potential energy surface. There are some difficulties in the last two approaches. In the first approach, performing the complete dynamics for hundreds of sequences is a rather challenging task because of the CPU time needed. In the second approach, calculating the curvature of the potential energy surface is possible only for very smooth surfaces. The Rate of Convergence criterion seems to avoid the previous difficulties. With this criterion one does not need to perform the complete dynamics to find the good and bad sequences. Also, the criterion does not depend on the kind of force field used and therefore it can be used even for very rugged energy surfaces.

Carbon and nitrogen emissions from stored manure and cropped fields in irrigated mountain oases of Oman

Little is known about gaseous carbon (C) and nitrogen (N) emissions from traditional terrace agriculture in irrigated high mountain agroecosystems of the subtropics. In an effort towards filling this knowledge gap measurements of carbon dioxide (CO_2), methane (CH_4), ammonia (NH_3) and dinitrous oxide (N_2O) were taken with a mobile photoacoustic infrared multi-gas monitor on manure-filled PE-fibre storage bags and on flood-irrigated untilled and tilled fields in three mountain oases of the northen Omani Al Jabal al Akhdar mountains. During typical 9-11 day irrigation cycles of March, August and September 2006 soil volumetric moisture contents of fields dominated by fodder wheat, barley, oats and pomegranate ranged from 46-23%. While manure incorporation after application effectively reduced gaseous N losses, prolonged storage of manure in heaps or in PE-fibre bags caused large losses of C and N. Given the large irrigation-related turnover of organic C, sustainable agricultural productivity of oasis agriculture in Oman seems to require the integration of livestock which allows for several applications of manure per year at individual rates of 20 t dry matter ha^−1.

Selbstassemblierte Monolagen und magnetisch strukturierte Submonolagen mit dia- und paramagnetischen Molekülen sowie Einzelmolekülmagneten auf Phthalocyanin- und Subphthalocyanin-Basis

Mit dieser Arbeit wurde die Selbstassemblierung von dia- und paramagnetischen Molekülen sowie Einzelmolekülmagneten auf Goldsubstraten und magnetisch strukturierten Substraten untersucht. Dazu wurden drei verschiedene Klassen an Phthalocyaninderivaten verwendet: Diamagnetische Subphthalocyanine, paramagnetische Phthalocyaninatometalle und Diphthalocyaninatolanthanidkomplexe. Alle synthetisierten Verbindungen sind peripher thioethersubstituiert. Die Alkylketten (a: n-C8H17, b: n-C12H25) vermitteln die Löslichkeit in vielen organischen Solventien und sorgen für eine geordnete Assemblierung auf einer Oberfläche, wobei die Bindung auf Gold hauptsächlich über die Schwefelatome stattfindet. Die aus Lösung abgeschiedenen selbstassemblierten Monolagen wurden mit XPS, NEXAFS-Spektroskopie und ToF-SIMS untersucht. Bei der Selbstassemblierung auf magnetisch strukturierten Substraten stehen die Moleküle unter dem Einfluss magnetischer Streufelder und binden bevorzugt nur in bestimmten Bereichen. Die gebildeten Submonolagen wurden zusätzlich mit X-PEEM untersucht. Die erstmals dargestellten Manganphthalocyanine [MnClPc(SR)8] 1 wurden ausgehend von MnCl2 erhalten. Hier fand bei der Aufarbeitung an Luft eine Oxidation zu Mangan(III) statt; +III ist die stabilste Oxidationsstufe von Mangan in Phthalocyaninen. Der Nachweis des axialen Chloridoliganden erfolgte mit Massenspektrometrie und FIR- sowie Raman-Spektroskopie. SQUID-Messungen haben gezeigt, dass die Komplexe 1 vier ungepaarte Elektronen haben. Bei den Subphthalocyaninen [BClSubpc(SR)6] 2 wurde der axiale Chloridoligand mit dem stäbchenförmigen Phenolderivat 29-H substituiert und die erfolgreiche Ligandensubstitution durch NMR- und IR-Spektroskopie sowie Massenspektrometrie an den Produkten [BSubpc(SR)6(29)] 30 belegt. Der Radikalcharakter der synthetisierten Terbiumkomplexe [Tb{Pc(SR)8}2] 3 wurde spektroskopisch nachgewiesen; SQUID-Messungen ergaben, dass es sich um Einzelmolekülmagnete mit einer Energiebarriere U des Doppelpotentialtopfs von 880 K oder 610 cm-1 bei 3a handelt. Zunächst wurden die SAMs der Komplexverbindungen 1, 2, 30 und 3 auf nicht magnetisch strukturierten Goldsubstraten untersucht. Die Manganphthalocyanine 1 bilden geordnete SAMs mit größtenteils flach liegenden Molekülen, wie die XPS-, NEXAFS- und ToF-SIMS-Analyse zeigte. Die Mehrzahl der Thioether-Einheiten ist auf Gold koordiniert und die Alkylketten zeigen ungeordnet von der Oberfläche weg. Bei der Adsorption findet eine Reduktion zu Mangan(II) statt und der axiale Chloridoligand wird abgespalten. Das beruht auf dem sog. Oberflächen-trans-Effekt. Im vorliegenden Fall übt die Metalloberfläche einen stärkeren trans-Effekt als der axiale Ligand aus, was bisher experimentell noch nicht beobachtet wurde. Die thioethersubstituierten Subphthalocyanine 2 und 30 sowie die Diphthalocyaninatoterbium-Komplexe 3 sind ebenfalls für SAMs geeignet. Ihre Monolagen wurden mit XPS und NEXAFS-Spektroskopie untersucht, und trotz einer gewissen Unordnung in den Filmen liegen die Moleküle jeweils im Wesentlichen flach auf der Goldoberfläche. Vermutlich sind bei diesen Systemen auch die Alkylketten größtenteils parallel zur Oberfläche orientiert. Im Gegensatz zu den Manganphthalocyaninen 1 tritt bei 2b, 30a, 30b und 3b neben der koordinativen Bindung der Schwefelatome auf Gold auch eine für Thioether nicht erwartete kovalente Au–S-Bindung auf, die durch C–S-Bindungsbruch unter Abspaltung der Alkylketten ermöglicht wird. Der Anteil, zu dem dieser Prozess stattfindet, scheint nicht mit der Molekülstruktur zu korrelieren. Selbstassemblierte Submonolagen auf magnetisch strukturierten Substraten wurden mit dem diamagnetischen Subphthalocyanin 2b hergestellt. Der Nachweis der Submonolagen war schwierig und gelang schließlich durch eine Kombination von ToF-SIMS, NEXAFS Imaging und X-PEEM. Die Analyse der ToF-SIMS-Daten zeigte, dass tatsächlich eine Modulation der Verteilung der Moleküle auf einem unterwärts magnetisch strukturierten Substrat eintritt. Mit X-PEEM konnte die magnetische Struktur der ferromagnetischen Schicht des Substrats direkt der Verteilung der adsorbierten Moleküle zugeordnet werden. Die Subphthalocyanine 2b adsorbieren nicht an den Domänengrenzen, sondern vermehrt dazwischen. Auf Substraten mit abwechselnd 6.5 und 3.5 µm breiten magnetischen Domänen binden die Moleküle bevorzugt in den Bereichen geringster magnetischer Streufeldgradienten, also den größeren Domänen. Solche Substrate wurden für die ToF-SIMS- und X-PEEM-Messungen verwendet. Bei größeren magnetischen Strukturen mit ca. 400 µm breiten Domänen, wie sie aufgrund der geringeren Ortsauflösung dieser Methode für NEXAFS Imaging eingesetzt wurden, binden die Moleküle dann in allen Domänen. Die diamagnetischen Moleküle werden nach dieser Interpretation aus dem inhomogenen Magnetfeld über der Probenoberfläche heraus gedrängt und verhalten sich analog makroskopischer Diamagnete. Die eindeutige Detektion der Moleküle auf den magnetisch strukturierten Substraten konnte bisher nur für die diamagnetischen Subphthalocyanine 2b erfolgen. Um die Interpretation ihres Verhaltens bei der Selbstassemblierung in einem inhomogenen Magnetfeld weiter voranzutreiben, wurde das Subphthalocyanin 37b dargestellt, welches ein stabiles organisches TEMPO-Radikal in seinem axialen Liganden enthält. Das paramagnetische Subphthalocyanin 37b sollte auf den magnetisch strukturierten Substraten in Regionen starker magnetischer Streufelder binden und damit das entgegengesetzte Verhalten zu den diamagnetischen Subphthalocyaninen 2b zeigen. Aus Zeitgründen konnte dieser Nachweis im Rahmen dieser Arbeit noch nicht erbracht werden.

Analyse von Protein-Ligand Interaktionen zur Charakterisierung zyklonukleotidbindender Proteine

Hyperpolarisations-aktivierte zyklonukleotid-gesteuerte (HCN) Kanäle übernehmen wichtige Funktionen in der Regulation der Herz- und Neuronalaktivität und können über einen dualen Mechanismus aus Membranhyperpolarisation und der Bindung von zyklischen Nukleotiden aktiviert werden. Ein großes Ziel der aktuellen Forschung ist die Entwicklung neuartiger Inhibitoren, die einer Fehlregulation der Kanäle entgegenwirken. In der vorliegenden Arbeit wurde die Regulation von HCN Kanälen durch zyklische Nukleotide im Detail analysiert, indem erstmals ein umfassender Screen mit 48 unterschiedlichen Zyklonukleotid-Analoga am C-terminalen Bereich (bestehend aus C-Linker und Zyklonukleotid-Bindedomäne) der drei Isoformen HCN1, HCN2 und HCN4 durchgeführt wurde. Mit Hilfe eines Fluoreszenzpolarisations-Assays wurde der Einfluss von Modifikationen in der Base, der Ribose und dem zyklischen Phosphat auf die Bindungsaffinitäten innerhalb der Zyklonukleotid-Bindedomäne untersucht. Zyklonukleotid-Analoga mit Modifikationen an der Position 7 und 8 der Base verschoben die apparenten Affinitäten im Vergleich zu den beiden natürlich vorkommenden Zyklonukleotiden cAMP und cGMP vom mikromolaren in den nanomolaren Bereich. Selektiv für die HCN4 Isoform erwiesen sich Zyklonukleotid-Analoga mit Modifikationen an der Position 6 der Base, während Modifikationen an der Position 8 der Base zu einer höheren Affinität für die HCN2 Isoform führten. Im Gegensatz zu HCN2 und HCN4 zeigte die HCN1 Isoform besonders hohe Affinitäten für Zyklonukleotid-Analoga mit Modifikationen an der Position 8 von cGMP. Eine Substitution der 2’-Hydroxylgruppe erlaubte keine Bindung an die HCN Kanäle. Mit 7-CH-cAMP konnte ein hochaffines Bindemolekül für HCN Kanäle identifiziert werden, denn der Austausch eines Stickstoffs gegen eine CH-Einheit an Position 7 der Base führte zu einer 100-fachen Steigerung der Affinität im Vergleich zu cAMP. In Übereinstimmung mit der hochaffinen Bindung konnte in kinetischen Analysen eine langsamere Dissoziationsrate für 7-CH-cAMP gemessen werden. Anhand thermodynamischer Messungen konnte ein entropisch favorisierter Bindungsmodus für 7-CH-cAMP im Vergleich zu cAMP identifiziert werden. Basierend auf einer Kristallstruktur des HCN4 CNBD:7-CH-cAMP Komplexes (2,5 Å) lässt sich erklären, dass 7-CH-cAMP durch seine höhere Lipohilie im Vergleich zu cAMP eine stärkere Präferenz für das hydrophobe Netzwerk zwischen Protein und Base besitzt. In detaillierten, vergleichenden Analysen mit den zyklonukleotidbindenden Proteinen PKA Typ I und II, hPKGIβ und Epac 1 und 2 konnte gezeigt werden, dass 7-CH-cAMP die höchsten Affinitäten für die drei Isoformen der HCN Kanäle aufwies. Somit könnte sich 7-CH-cAMP als vielversprechender Kandidat für die selektive Regulation von HCN Kanälen in vitro und in lebenden Zellen eignen und möglicherweise einen wichtigen Beitrag als krankheitsrelevanter Effektor leisten.

Measure Fields for Function Approximation

The computation of a piecewise smooth function that approximates a finite set of data points may be decomposed into two decoupled tasks: first, the computation of the locally smooth models, and hence, the segmentation of the data into classes that consist on the sets of points best approximated by each model, and second, the computation of the normalized discriminant functions for each induced class. The approximating function may then be computed as the optimal estimator with respect to this measure field. We give an efficient procedure for effecting both computations, and for the determination of the optimal number of components.

Evaluation of sets of oriented and non-oriented receptive fields as local descriptors

Local descriptors are increasingly used for the task of object recognition because of their perceived robustness with respect to occlusions and to global geometrical deformations. We propose a performance criterion for a local descriptor based on the tradeoff between selectivity and invariance. In this paper, we evaluate several local descriptors with respect to selectivity and invariance. The descriptors that we evaluated are Gaussian derivatives up to the third order, gray image patches, and Laplacian-based descriptors with either three scales or one scale filters. We compare selectivity and invariance to several affine changes such as rotation, scale, brightness, and viewpoint. Comparisons have been made keeping the dimensionality of the descriptors roughly constant. The overall results indicate a good performance by the descriptor based on a set of oriented Gaussian filters. It is interesting that oriented receptive fields similar to the Gaussian derivatives as well as receptive fields similar to the Laplacian are found in primate visual cortex.

SCAPA (Spacially Addressable Protein Array) – a Novel Protein Array for the Differential Profiling of Ligand-receptor Induced Signalling

While protein microarray technology has been successful in demonstrating its usefulness for large scale high-throughput proteome profiling, performance of antibody/antigen microarrays has been only moderately productive. Immobilization of either the capture antibodies or the protein samples on solid supports has severe drawbacks. Denaturation of the immobilized proteins as well as inconsistent orientation of antibodies/ligands on the arrays can lead to erroneous results. This has prompted a number of studies to address these challenges by immobilizing proteins on biocompatible surfaces, which has met with limited success. Our strategy relates to a multiplexed, sensitive and high-throughput method for the screening quantification of intracellular signalling proteins from a complex mixture of proteins. Each signalling protein to be monitored has its capture moiety linked to a specific oligo ‘tag’. The array involves the oligonucleotide hybridization-directed localization and identification of different signalling proteins simultaneously, in a rapid and easy manner. Antibodies have been used as the capture moieties for specific identification of each signaling protein. The method involves covalently partnering each antibody/protein molecule with a unique DNA or DNA derivatives oligonucleotide tag that directs the antibody to a unique site on the microarray due to specific hybridization with a complementary tag-probe on the array. Particular surface modifications and optimal conditions allowed high signal to noise ratio which is essential to the success of this approach.

Vector Fields

Exercises and solutions about vector fields. Diagrams for the questions are all together in the support.zip file, as .eps files