Quantum effects and dynamics in hydrogen-bonded systems: a first-principles approach to spectroscopic experiments

Computer simulations have become an important tool in physics. Especially systems in the solid state have been investigated extensively with the help of modern computational methods. This thesis focuses on the simulation of hydrogen-bonded systems, using quantum chemical methods combined with molecular dynamics (MD) simulations. MD simulations are carried out for investigating the energetics and structure of a system under conditions that include physical parameters such as temperature and pressure. Ab initio quantum chemical methods have proven to be capable of predicting spectroscopic quantities. The combination of these two features still represents a methodological challenge. Furthermore, conventional MD simulations consider the nuclei as classical particles. Not only motional effects, but also the quantum nature of the nuclei are expected to influence the properties of a molecular system. This work aims at a more realistic description of properties that are accessible via NMR experiments. With the help of the path integral formalism the quantum nature of the nuclei has been incorporated and its influence on the NMR parameters explored. The effect on both the NMR chemical shift and the Nuclear Quadrupole Coupling Constants (NQCC) is presented for intra- and intermolecular hydrogen bonds. The second part of this thesis presents the computation of electric field gradients within the Gaussian and Augmented Plane Waves (GAPW) framework, that allows for all-electron calculations in periodic systems. This recent development improves the accuracy of many calculations compared to the pseudopotential approximation, which treats the core electrons as part of an effective potential. In combination with MD simulations of water, the NMR longitudinal relaxation times for 17O and 2H have been obtained. The results show a considerable agreement with the experiment. Finally, an implementation of the calculation of the stress tensor into the quantum chemical program suite CP2K is presented. This enables MD simulations under constant pressure conditions, which is demonstrated with a series of liquid water simulations, that sheds light on the influence of the exchange-correlation functional used on the density of the simulated liquid.

Preparation of new crystal forms via photochemical, mechanochemical and sol-gel methods

This work of thesis involves various aspects of crystal engineering. Chapter 1 focuses on crystals containing crown ether complexes. Aspects such as the possibility of preparing these materials by non-solution methods, i.e. by direct reaction of the solid components, thermal behavior and also isomorphism and interconversion between hydrates are taken into account. In chapter 2 a study is presented aimed to understanding the relationship between hydrogen bonding capability and shape of the building blocks chosen to construct crystals. The focus is on the control exerted by shape on the organization of sandwich cations such as cobalticinium, decamethylcobalticinium and bisbenzenchromium(I) and on the aggregation of monoanions all containing carboxylic and carboxylate groups, into 0-D, 1-D, 2-D and 3-D networks. Reactions conducted in multi-component molecular assemblies or co-crystals have been recognized as a way to control reactivity in the solid state. The [2+2] photodimerization of olefins is a successful demonstration of how templated solid state synthesis can efficiently synthesize unique materials with remarkable stereoselectivity and under environment-friendly conditions. A demonstration of this synthetic strategy is given in chapter 3. The combination of various types of intermolecular linkages, leading to formation of high order aggregation and crystalline materials or to a random aggregation resulting in an amorphous precipitate, may not go to completeness. In such rare cases an aggregation process intermediate between crystalline and amorphous materials is observed, resulting in the formation of a gel, i.e. a viscoelastic solid-like or liquid-like material. In chapter 4 design of new Low Molecular Weight Gelators is presented. Aspects such as the relationships between molecular structure, crystal packing and gelation properties and the application of this kind of gels as a medium for crystal growth of organic molecules, such as APIs, are also discussed.

Struktur-Dynamik-Beziehungen in amorphen festen Lösungen

Feste Lösungen homogen dispergierter Wirkstoffmoleküle in amorphen Polymermatrizen sind wichtige Materialien in vielen pharmazeutischen Anwendungen, bei denen eine kontrollierte Abgabe wasserunlöslicher Wirkstoffe in wässrige Systeme eine Rolle spielt. Die intermolekulare Bindungs-stärke zwischen Polymer- und Wirkstoffmolekülgruppen bestimmt die Stabilität der festen Lösung und steuert somit die biologische Aktivität der Wirkstoffmoleküle. In festen Lösungen, die aus acryl-säurehaltigen Copolymeren (Protonendonoren) und basischen Wirkstoffmolekülen (Protonenakzepto-ren) hergestellt werden, sind intermolekulare Wasserstoffbrücken zwischen den Systemkomponenten Triebkraft für die Bildung einer stabilen homogenen Dispersion und für die Entstehung struktureller Merkmale zwischen den Molekülgruppen der Systemkomponenten. Zudem ist die Bindungsstärke der Wasserstoffbrücken im Hinblick auf die kontrollierte Abgabe der Wirkstoffe von Bedeutung. Da dynamische chemische Gleichgewichte bei der Bildung der Wasserstoffbrücken eine wichtige Rolle spielen müssen neben strukturellen Parametern auch dynamische Faktoren beleuchtet werden. Ziel dieser Arbeit ist neben der Ermittlung von intermolekularen Bindungsstärken vor allem die Identifika-tion struktureller Verhältnisse zwischen den Systemkomponenten auf molekularer Ebene. Die Be-stimmung der Abhängigkeit dieser Parameter von der Struktur der verwendeten Polymere und einer Vielzahl weiterer Einflüsse wie z.B. Feuchtigkeit, Lagerdauer oder Wirkstoffkonzentration soll ein kontrolliertes Design fester Lösungen mit definierten anwendungsspezifischen Eigenschaften ermögli-chen. Temperaturabhängige 1H-Festkörper-MAS-NMR (Magic Angle Spinning Nuclear Magnetic Resonance) Experimente an festen Lösungen mit unterschiedlichen Copolymer-Zusammensetzungen weisen die Existenz dynamischer chemischer Gleichgewichte in den komplexen Wasserstoffbrücken-netzwerken nach. Veränderungen in der chemischen Verschiebung und in der Linienform der Reso-nanzlinien acider Protonen erlauben einen tiefen Einblick in die Architektur dieser Netzwerke und legen die Bindungsverhältnisse unter Berücksichtigung der Polymerchemie und der Mobilität der Systemkomponenten dar, wobei die Befunde mithilfe quantenchemischer Rechnungen untermauert werden können. Die Gegenwart acider Protonen ermöglicht einen einfachen 1H-2H-Austausch, wor-aufhin mithilfe rotorsynchronisierter temperaturabhängiger 2H-MAS-NMR Experimente die Wasser-stoffbrückenbindungsstärke bestimmt werden kann. Mit 1H-1H-Korrelationsexperimenten (Doppelquantenspektroskopie) stehen Methoden für die Bestimmung homonuklearer dipolarer 1H-1H-Kopplungen zur Verfügung, die strukturelle Aussagen aufgrund von bevorzugten räumlichen Kontak-ten bestimmter Molekülgruppen ermöglichen. Weiterhin können diese Experimente verwendet werden, um Wasserstoffbrücken zwischen Polymergruppen von Polymer-Wirkstoff-Wasserstoffbrücken zu unterscheiden, wodurch eine quantitative Beschreibung des Bindungsnetzwerks und der Konkurrenz-prozesse zwischen den einzelnen wasserstoffverbrückten Spezies ermöglicht wird. Eine Kristallisation der Wirkstoffmoleküle ist in vielen Anwendungen unerwünscht, da sie die biologische Verfügbarkeit des Wirkstoffs reduzieren. Mit 1H-Festkörper-MAS-NMR Experimenten können kristalline von amorph dispergierten Wirkstoffmolekülen unterschieden werden, wodurch eine Quantifizierung der Destabilisierungsprozesse ermöglicht wird, die durch Exposition der festen Lösungen mit Wasserdampf ausgelöst werden können. Die Zeit- und Konzentrationsabhängigkeit der Wasseraufnahme kann mit NMR-Experimenten verfolgt werden, wobei unterschiedlich mobile Was-serspezies an unterschiedlichen Bindungsorten identifiziert werden können, was zum molekularen Verständnis der Destabilisierungsprozesse beiträgt. Zusätzlich wird die Mobilität der Wirkstoffmole-küle bestimmt, die sich – wie auch die Wirkstoffkonzentration - als wichtige Größe in der Beschrei-bung der Destabilisierung erweist. Aufbauend auf den Beobachtungen wird ein Zusammenhang zwischen der Copolymerzusammensetzung und einer kritischen Wirkstoffkonzentration hergestellt, der für die Anwendungen amorpher fester Lösungen in biologischen Systemen von großer Bedeutung ist.

Atomic force microscopy of biomimetic systems

This thesis was driven by the ambition to create suitable model systems that mimic complex processes in nature, like intramolecular transitions, such as unfolding and refolding of proteins, or intermolecular interactions between different cell compo-nents. Novel biophysical approaches were adopted by employing atomic force mi-croscopy (AFM) as the main measurement technique due to its broad diversity. Thus, high-resolution imaging, adhesion measurements, and single-molecule force distance experiments were performed on the verge of the instrumental capabilities. As first objective, the interaction between plasma membrane and cytoskeleton, me-diated by the linker protein ezrin, was pursued. Therefore, the adsorption process and the lateral organization of ezrin on PIP2 containing solid-supported membranes were characterized and quantified as a fundament for the establishment of a biomimetic model system. As second component of the model system, actin filaments were coated on functionalized colloidal probes attached on cantilevers, serving as sensor elements. The zealous endeavor of creating this complex biomimetic system was rewarded by successful investigation of the activation process of ezrin. As a result, it can be stated that ezrin is activated by solely binding to PIP2 without any further stimulating agents. Additional cofactors may stabilize and prolong the active conformation but are not essentially required for triggering ezrin’s transformation into an active conformation. In the second project, single-molecule force distance experiments were performed on bis-loop tetra-urea calix[4]arene-catenanes with different loading rates (increase in force per second). These macromolecules were specifically designed to investigate the rupture and rejoining mechanism of hydrogen bonds under external load. The entangled loops of capsule-like molecules locked the unbound state of intramolecular hydrogen bonds mechanically, rendering a rebinding observable on the experimental time scale. In conjunction with Molecular Dynamics simulations, a three-well potential of the bond rupture process was established and all kinetically relevant parameters of the experiments were determined by means of Monte Carlo simulations and stochastic modeling. In summary, it can be stated that atomic force microscopy is an invaluable tool to scrutinize relevant processes in nature, such as investigating activation mechanisms in proteins, as shown by analysis of the interaction between F-actin and ezrin, as well as exploring fundamental properties of single hydrogen bonds that are of paramount interest for the complete understanding of complex supramolecular structures.

Spin-crossover in metallomesogens of iron(II)

Covalent grafting mesogenic groups to the coordination cores of the parent mononuclear low-spin and spin-crossover compounds afforded metallomesogenic complexes of iron(II). In comparison with the parent complexes the spin-crossover properties of the alkylated derivatives are substantially modified. The type of the modification was found to be dependent on the properties of the parent system and the nature of the used anion, however, the general tendency is the destabilization of the low-spin state at the favor of spin-crossover or high-spin behavior below 400 K. The structural insight revealed the micro-segregated layered organization. The effect of the alkylation of the parent compounds consists first of all in the change of the lattice to a two-dimensional lamellar one retaining significant intermolecular contacts only within the ionic bilayers. The comprehensive analysis of the structural and thermodynamic data in the homologous series pointed at the mechanism of the interplay between the structural modification on melting and the induced anomalous change of the magnetic properties. A family of one-dimensional spin-crossover polymers was synthesized and characterized using a series of spectroscopic methods, X-ray powder diffraction, magnetic susceptibility measurements and differential scanning calorimetry. The copper analogue of was also synthesized and its crystal structure solved. In comparison with the mononuclear systems, the polymeric mesogens of iron(II) are less sensitive to the glass transition, which was attributed to the moderate concomitant variation of the structure. Nevertheless, the observed increase of the magnetic hysteresis with lengthening of the alkyl substituents was ascribed to the interplay of the structural reorganization of the coordination core due to spin-crossover with the structural delay in the spatial reorganization of the mesogenic substituents. The classification of mononuclear and polymeric metallomesogens according to the interactions between the structural- and the spin-transition and analysis of the data on the reported spin-crossover metallomesogens led to the separation of three types, namely: Type i: systems with coupling between the electronic structure of the iron(II) ions and the mesomorphic behavior of the substance; Type ii: systems where both transitions coexist in the same temperature region but are not coupled due to competition with the dehydration or due to negligible structural transformation; Type iii: systems where both transitions occur in different temperature regions and therefore are uncoupled. Fine-tuning, in particular regarding the temperature at which the spin-transition occurs with hysteresis properties responsible for the memory effect, are still a major challenge towards practical implementation of spin-crossover materials. A possible answer to the problem could be materials in which the spin-crossover transition is coupled with another transition easily controllable by external stimuli. In the present thesis we have shown the viability of the approach realized in the mesogenic systems with coupled phase- and spin-transitions.

Microscopic, chemical and spectroscopic investigations on emeralds of various origins

In dieser Arbeit werden die mikroskopischen, chemischen und spektroskopischen Charakteristika von 260 natürlichen Smaragden und 66 synthetischen „Smaragden“ untersucht. Die Konzentrationen der chemischen Elemente von Smaragden wurden mit Hilfe der LA-ICP-MS und EMS bestimmt. Ergänzende Raman- und IR spektroskopische Methoden ermöglichen es, die Herkunft der verschiedenen Smaragde und ihrer synthetischen Analoga zu bestimmen. Auf Grund der verschiedenen Gehalte von Si, Al und Be können synthetische „Smaragde“ von natürlichen getrennt werden. Die Smaragde von Malipo, Chivor und auch synthetische „Smaragde“ können von allen anderen natürlichen Smaragden wegen der unterschiedlichen Cr-, V-, und Fe-Gehalte von einander getrennt werden. Wegen der unterschiedlichen Mg-, Na-, K-Gehalte lassen sich eher „schiefer-gebundene“ Smaragde identifizieren. Dabei wird festgestellt, dass die Unterscheidung in „schiefer-„ und „nichtschiefer-gebundene“ Smaragd-Vorkommen im Wesentlichen nur die Endglieder einer offensichtlich kristallchemisch sehr variablen Mineralchemie der Berylle, bzw. Smaragde beschreibt, dass damit aber keinesfalls eine petrologisch vertretbare Trennung belegbar ist, sondern dass Smaragde nur das jeweils regierende chemische Regime unter geeigneten Druck-Temperatur-Bedingungen widerspiegeln. Einschlussmerkmale spielen eine große Rolle bei der Unterscheidung verschiedener Lagerstätten und Herstellungsmethoden. Zum Beispiel können die Smaragde der drei Lagerstätten Santa Terezinha, Chivor, und Kafubu mit Hilfe ihrer charakteristischen Pyriteinschlüsse identifiziert werden. Die Band-Positionen und FWHM -Werte der Raman-Bande bei 1068 cm-1 und der IR-Bande bei 1200 cm-1 ermöglichen eine Differenzierung zwischen synthetischen und natürlichen Smaragden, und können darüber hinaus auch Auskunft geben über die Lagerstätte. Zusammen mit chemischen Messwerten kann bewiesen werden, dass diese Banden von Si-O Schwingungen verursacht werden. Die Raman- und IR-Banden im Bereich der Wasserschwingungen und insbesondere das IR-Band um 1140 cm-1 führen zur Trennung von Flux-Synthesen, Hydrothermal-Synthesen und natürlichen Smaragden.

Synthesis of hexa-peri-hexabenzocoronenes - from building blocks to functional materials

Discotic hexa-peri-hexabenzocoronene (HBC) derivatives have attracted intensive scientific interest due to their unique optoelectronic properties, which depends, to a large extend, upon the attached functional groups. The presented work covers the synthesis of novel HBC building blocks and new HBC derivatives as functional materials. The traditional preparation of HBC derivatives requires elaborate synthetic techniques and tremendous effort. Especially, more than 10 synthetic steps are usually necessary to approach HBCs with lower symmetries. In order to simplify the synthetic work and reduce the high costs, a novel synthetic strategy involving only four steps was developed based on 2,3,5,6-tetraphenyl-1,4-diiodobenzene intermediates and palladium catalyzed Suzuki cross coupling reactions. In order to introduce various functionalities and expand the diversity of multi-functionalizations, a novel C2v-symmetric dihalo HBC building block 2-47, which contains one iodine and one bromine in para positions, was prepared following the traditional intermolecular [4+2] Diels-Alder reaction route. The outstanding chemical selectivity between iodo and bromo groups in this compound consequently leads to lots of HBC derivatives bearing different functionalities. Directly attached heteroatoms will improve the material properties. According to the application of intramolecular Scholl reaction to a para-dimethoxy HPB, which leads to a meta-dimethoxy HBC, a phenomenon of phenyl group migration was discovered. Thereby, several interesting mechanistic details involving arenium cation intermediates were discussed. With a series of dipole functionalized HBCs, the molecular dynamics of this kind of materials was studied in different phases by DSC, 2D WAXD, solid state NMR and dielectric spectroscopies. High charge carrier mobility is an important parameter for a semiconductive material and depends on the degree of intramolecular order of the discotic molecules in thin films for HBC derivatives. Dipole – dipole interaction and hydrogen bonds were respectively introduced in order to achieve highly ordered supramolecular structure. The self-assembly behavior of these materials were investigated both in solution and solid state. Depending upon the different functionalities, these novel materials show either gelating or non-linear optical properties, which consequently broaden their applications as functional materials. In the field of conceivable electronic devices at a molecular level, HBCs hold high promise. Differently functionalized HBCs have been used as active component in the studies of single-molecular CFET and metal-SAMs-metal junctions. The outstanding properties shown in these materials promise their exciting potential applications in molecular devices.

Heteroatom containing polycyclic aromatic hydrocarbons with positive charge - synthesis and characterization

The synthesis and characterization of various heteroatom containing PAHs with positive charge were investigated in this work: 1. A series of 2-phenyl-benzo[8,9]quinolizino[4,5,6,7-fed]phenanthridinylium (PQP) salts with different alkyl chains and anions were synthesized. The synthesis of the extended derivates of PQP salts with two fused benzene rings, 2-phenyl-naphthacene[1,2]quinolizino[3,4,5,6-def]benzo[i]phenanthridinium (DBPQP) tetrafluoroborate was also developed. The self-assembly behavior of these amphiphilic PAHs was investigated in methanolic solution as well as in the bulk. Various aggregates with different morphologies such as fibers, tubes and vesicals were obtained from their solution. All of these morphology changes could be ascribed to the changes in intermolecular interactions which resulting from the difference in the molecular structures such as aromatic cores, alkyl chains and counterions. 2. The synthetic strategy of oxygen containing positively charged PAHs, benzo[5,6]naphthaceno[1,12,11,10-jklmna]xanthylium (BNAX) salts and its dibenzo derivates, DBNAX salts were developed. With a similar method, sulfur containing benzo[5,6]naphthaceno[1,12,11,10-jklmna]thioxanthylium (BNATX) salts were also synthesized. Various BNAX salts with different alkyl chains could be obtained and their supramolecular behavior were investigated. A discotic liquid crystalline behavior was observed for di- (3-25) and tridodecyl (3-27) substituted BNAX salts and both compounds exhibited large unit cell in their 2D-WAXS patterns which could be attributed to the formation of dimer structures. By drop casting their methanolic solution on silicon wafers, similar nanoscaled fibers from monododecyl substituted BNAX bromide 3-24 and DBNAX bromide 3-35 could be observed. 3. A novel synthetic method toward nitrogen containing 14-phenyl-dibenzo[jk,mn]naphtho[2,1,8-fgh]thebenidinium (DBNT) salts was also developed. In this method, the undehydrogenated precursor of DBNT, dibenzoacridinium salt could be produced directly from the reaction between dibenzoxanthenylium derivates and amine/aniline in reasonable yields. Various DBNT salts with different alkyl and alkylphenyl chains on their nitrogen atom were synthesized in this two-step method. The self-assembly behavior of two alkylated DBNT salts, 4-15a and 4-18b was also studied in this work. Compound 4-15a formed nanoscaled fibers and helical aggregates were obtained from 4-18b in their methanolic solutions. 4. Various ionic complexes were derived by complexing PQP and DBPQP cations with different sulfate/sulfonate group containing anionic surfactants. The ionic complexes resulting from the ionic self-assembly (ISA) method exhibited self-assembly behavior which was controllable by the species and shape of cations and anions. Various aggregates such as nanofibers and spherical aggregates could be produced from their methanolic solution in a defined manner conveniently.

Methods for Clearance Influence Analysis in Planar and Spatial Mechanisms

This doctoral dissertation presents a new method to asses the influence of clearancein the kinematic pairs on the configuration of planar and spatial mechanisms. The subject has been widely investigated in both past and present scientific literature, and is approached in different ways: a static/kinetostatic way, which looks for the clearance take-up due to the external loads on the mechanism; a probabilistic way, which expresses clearance-due displacements using probability density functions; a dynamic way, which evaluates dynamic effects like the actual forces in the pairs caused by impacts, or the consequent vibrations. This dissertation presents a new method to approach the problem of clearance. The problem is studied from a purely kinematic perspective. With reference to a given mechanism configuration, the pose (position and orientation) error of the mechanism link of interest is expressed as a vector function of the degrees of freedom introduced in each pair by clearance: the presence of clearance in a kinematic pair, in facts, causes the actual pair to have more degrees of freedom than the theoretical clearance-free one. The clearance-due degrees of freedom are bounded by the pair geometry. A proper modelling of clearance-affected pairs allows expressing such bounding through analytical functions. It is then possible to study the problem as a maximization problem, where a continuous function (the pose error of the link of interest) subject to some constraints (the analytical functions bounding clearance- due degrees of freedom) has to be maximize. Revolute, prismatic, cylindrical, and spherical clearance-affected pairs have been analytically modelled; with reference to mechanisms involving such pairs, the solution to the maximization problem has been obtained in a closed form.

The collapse of linear polyelectrolyte chains in a poor solvent: When does a collapsing polyelectrolyte collect its counter ions?

The collapse of linear polyelectrolyte chains in a poor solvent: When does a collapsing polyelectrolyte collect its counter ions? The collapse of polyions in a poor solvent is a complex system and is an active research subject in the theoretical polyelectrolyte community. The complexity is due to the subtle interplay between hydrophobic effects, electrostatic interactions, entropy elasticity, intrinsic excluded volume as well as specific counter-ion and co-ion properties. Long range Coulomb forces can obscure single molecule properties. The here presented approach is to use just a small amount of screening salt in combination with a very high sample dilution in order to screen intermolecular interaction whereas keeping intramolecular interaction as much as possible (polyelectrolyte concentration cp ≤ 12 mg/L, salt concentration; Cs = 10^-5 mol/L). This is so far not described in literature. During collapse, the polyion is subject to a drastic change in size along with strong reduction of free counterions in solution. Therefore light scattering was utilized to obtain the size of the polyion whereas a conductivity setup was developed to monitor the proceeding of counterion collection by the polyion. Partially quaternized PVP’s below and above the Manning limit were investigated and compared to the collapse of their uncharged precursor. The collapses were induced by an isorefractive solvent/non-solvent mixture consisting of 1-propanol and 2-pentanone, with nearly constant dielectric constant. The solvent quality for the uncharged polyion could be quantified which, for the first time, allowed the experimental investigation of the effect of electrostatic interaction prior and during polyion collapse. Given that the Manning parameter M for QPVP4.3 is as low as lB / c = 0.6 (lB the Bjerrum length and c the mean contour distance between two charges), no counterion binding should occur. However the Walden product reduces with first addition of non solvent and accelerates when the structural collapse sets in. Since the dielectric constant of the solvent remains virtually constant during the chain collapse, the counterion binding is entirely caused by the reduction in the polyion chain dimension. The collapse is shifted to lower wns with higher degrees of quaternization as the samples QPVP20 and QPVP35 show (M = 2.8 respectively 4.9). The combination of light scattering and conductivity measurement revealed for the first time that polyion chains already collect their counter ions well above the theta-dimension when the dimensions start to shrink. Due to only small amounts of screening salt, strong electrostatic interactions bias dynamic as well as static light scattering measurements. An extended Zimm formula was derived to account for this interaction and to obtain the real chain dimensions. The effective degree of dissociation g could be obtained semi quantitatively using this extrapolated static in combination with conductivity measurements. One can conclude the expansion factor a and the effective degree of ionization of the polyion to be mutually dependent. In the good solvent regime g of QPVP4.3, QPVP20 and QPVP35 exhibited a decreasing value in the order 1 > g4.3 > g20 > g35. The low values of g for QPVP20 and QPVP35 are assumed to be responsible for the prior collapse of the higher quaternized samples. Collapse theory predicts dipole-dipole attraction to increase accordingly and even predicts a collapse in the good solvent regime. This could be exactly observed for the QPVP35 sample. The experimental results were compared to a newly developed theory of uniform spherical collapse induced by concomitant counterion binding developed by M. Muthukumar and A. Kundagrami. The theory agrees qualitatively with the location of the phase boundary as well as the trend of an increasing expansion with an increase of the degree of quaternization. However experimental determined g for the samples QPVP4.3, QPVP20 and QPVP35 decreases linearly with the degree of quaternization whereas this theory predicts an almost constant value.

Oligomerization and protein-protein interactions of the sensory histidine kinase DcuS in Escherichia coli

DcuS is a membrane-integral sensory histidine kinase involved in the DcuSR two-component regulatory system in Escherichia coli by regulating the gene expression of C4-dicarboxylate metabolism in response to external stimuli. How DcuS mediates the signal transduction across the membrane remains little understood. This study focused on the oligomerization and protein-protein interactions of DcuS by using quantitative Fluorescence Resonance Energy Transfer (FRET) spectroscopy. A quantitative FRET analysis for fluorescence spectroscopy has been developed in this study, consisting of three steps: (1) flexible background subtraction to yield background-free spectra, (2) a FRET quantification method to determine FRET efficiency (E) and donor fraction (fD = [donor] / ([donor]+[acceptor])) from the spectra, and (3) a model to determine the degree of oligomerization (interaction stoichiometry) in the protein complexes based on E vs. fD. The accuracy and applicability of this analysis was validated by theoretical simulations and experimental systems. These three steps were integrated into a computer procedure as an automatic quantitative FRET analysis which is easy, fast, and allows high-throughout to quantify FRET accurately and robustly, even in living cells. This method was subsequently applied to investigate oligomerization and protein-protein interactions, in particular in living cells. Cyan (CFP) and yellow fluorescent protein (YFP), two spectral variants of green fluorescent protein, were used as a donor-acceptor pair for in vivo measurements. Based on CFP- and YFP-fusions of non-interacting membrane proteins in the cell membrane, a minor FRET signal (E = 0.06 ± 0.01) can be regarded as an estimate of direct interaction between CFP and YFP moieties of fusion proteins co-localized in the cell membrane (false-positive). To confirm if the FRET occurrence is specific to the interaction of the investigated proteins, their FRET efficiency should be clearly above E = 0.06. The oligomeric state of DcuS was examined both in vivo (CFP/YFP) and in vitro (two different donor-acceptor pairs of organic dyes) by three independent experimental systems. The consistent occurrence of FRET in vitro and in vivo provides the evidence for the homo-dimerization of DcuS as full-length protein for the first time. Moreover, novel interactions (hetero-complexes) between DcuS and its functionally related proteins, citrate-specific sensor kinase CitA and aerobic dicarboxylate transporter DctA respectively, have been identified for the first time by intermolecular FRET in vivo. This analysis can be widely applied as a robust method to determine the interaction stoichiometry of protein complexes for other proteins of interest labeled with adequate fluorophores in vitro or in vivo.

Qualifica a Vibrazioni di Componenti Meccanici: Studio e Verifica di una Procedura di Test Tailoring.

I test di qualifica a vibrazioni vengono usati in fase di progettazione di un componente per verificarne la resistenza meccanica alle sollecitazioni dinamiche (di natura vibratoria) applicate durante la sua vita utile. La durata delle vibrazioni applicate al componente durante la sua vita utile (migliaia di ore) deve essere ridotta al fine di realizzare test fattibili in laboratorio, condotti in genere utilizzando uno shaker elettrodinamico. L’idea è quella di aumentare l’intensità delle vibrazioni riducendone la durata. Esistono diverse procedure di Test Tailoring che tramite un metodo di sintesi definiscono un profilo vibratorio da applicare in laboratorio a partire dalle reali vibrazioni applicate al componente: una delle metodologie più comuni si basa sull’equivalenza del danno a fatica prodotto dalle reali vibrazioni e dalle vibrazioni sintetizzate. Questo approccio è piuttosto diffuso tuttavia all’autore non risulta presente nessun riferimento in letteratura che ne certifichi la validità tramite evidenza sperimentalmente. L’obiettivo dell’attività di ricerca è stato di verificare la validità del metodo tramite una campagna sperimentale condotta su opportuni provini. Il metodo viene inizialmente usato per sintetizzare un profilo vibratorio (random stazionario) avente la stessa durata di un profilo vibratorio non stazionario acquisito in condizioni reali. Il danno a fatica prodotto dalla vibrazione sintetizzata è stato confrontato con quello della vibrazione reale in termini di tempo di rottura dei provini. I risultati mostrano che il danno prodotto dalla vibrazione sintetizzata è sovrastimato, quindi l’equivalenza non è rispettata. Sono stati individuati alcuni punti critici e sono state proposte alcune modifiche al metodo per rendere la teoria più robusta. Il metodo è stato verificato con altri test e i risultati confermano la validità del metodo a condizione che i punti critici individuati siano correttamente analizzati.

Analisi dell’influenza dei moti rigidi di una trattrice agricola sulle vibrazioni a corpo intero trasmesse all’operatore

L’esposizione degli operatori in campo agricolo alle vibrazioni trasmesse al corpo intero, produce effetti dannosi alla salute nel breve e nel lungo termine. Le vibrazioni che si generano sulle trattrici agricole hanno una elevata intensità e una bassa frequenza. Le componenti orizzontali, amplificate dalla posizione elevata della postazione di guida dall’asse di rollio, presentano maggiori criticità per quanto riguarda i sistemi di smorzamento rispetto alle componenti verticali. Queste caratteristiche rendono difficoltosa la progettazione dei sistemi dedicati alla riduzione del livello vibrazionale per questa categoria di macchine agricole. Nonostante l’installazione di diversi sistemi di smorzamento, il livello di vibrazioni a cui è sottoposto l’operatore può superare, in diverse condizioni di impiego, i livelli massimi imposti dalla legge per la salvaguardia della salute. L’obiettivo di questo lavoro è quello di valutare l’influenza dei moti rigidi di una trattrice (beccheggio, rollio e saltellamento) dotata di sospensione assale anteriore, sospensione cabina e sospensione sedile, sul livello vibrazionale trasmesso all’operatore.E’ stata pertanto strumenta una trattrice con accelerometri e inclinometri installati su telaio, cabina e sedile e utilizzata in diverse condizioni di lavoro in campo e di trasporto su strada. Dall’analisi delle prove effettuate emerge che durante il trasporto su strada è predominante l’accelerazione longitudinale, a causa dell’elevata influenza del beccheggio. La sospensione riduce notevolmente il moto rigido di beccheggio mentre l’effetto della sospensione della cabina è quello di incrementare, in ogni condizione di lavoro, il livello di accelerazione trasmesso dal telaio della macchina.

Assessment of vibratory stimulation on neuromuscular system

The thesis analyze a subject of renewed interest in bioengineering, the research and analysis of exercise parameters that maximize the neuromuscular and cardiovascular involvement in vibration treatment. The research activity was inspired by the increasing use of device able to provide localized or whole body vibration (WBV). In particular, the focus was placed on the vibrating platform and the effect that the vibrations have on the neuromuscular system and cardiovascular system. The aim of the thesis is to evaluate the effectiveness and efficiency of vibration applied to the entire body, in particular, it was investigated the effect of WBV on: 1) Oxygen consumption during static and dynamic squat; 2) Resonant frequency of the muscle groups of the lower limbs; 3) Oxygen consumption and electromyographic signals during static and dynamic squat. In the first three chapters are explained the state of the art concerning vibration treatments, the effects of vibration applied to the entire body, with the explanation of the basic mechanisms (Tonic Vibration Reflex, TVR) and the neuromuscular system, with particular attention to the skeletal muscles and the stretch reflex. In the fourth chapter is illustrated the set-up used for the experiments and the software, implemented in LabWindows in order to control the platform and acquire the electromyographic signal. In the fifth chapter were exposed experiments undertaken during the PhD years. In particular, the analysis of Whole Body Vibration effect on neurological and cardiovascular systems showed interesting results. The results indicate that the static squat with WBV produced higher neuromuscular and cardiorespiratory system activation for exercise duration <60 sec. Otherwise, if the single bout duration was higher than 60 sec, the greater cardiorespiratory system activation was achieved during the dynamic squat with WBV while higher neuromuscular activation was still obtained with the static exercise.

Selektiv deblockierbare Diamino-D-Galactose-Scaffolds für die kombinatorische Synthese potentieller RNA-Liganden

Die Aufklärung der Schlüsselrolle der RNA in zahlreichen biologischen Prozessen, die sich aus ihren selektiven Wechselwirkungen mit anderen RNA-Molekülen, Proteinen, Peptiden bzw. Antibiotika ergibt, ist für die Wirkstoffforschung von großer Bedeutung. Die Aminoglycoside und Antibiotika, die durch eine Hemmung der Proteinbiosynthese schon seit längerem bekannt sind, dienen als Leitstrukuren für die Synthese von weiteren Wirkstoffen. Die meisten Aminoglycosid-Antibiotika beinhalten Aminozucker, die mit dem rn2-Desoxystreptamin-Gerüst verbunden sind. Die stereochemische Vielfalt der Substitutionsstellen für Amino- und Hydroxylgruppen in diesem Gerüst und deren beschränkte konformative Flexibilität bieten vielseitige Möglichkeiten, um potenzielle RNA-Liganden so zu gestalten, dass es zu einer spezifischen Erkennung von RNA-Strukturen kommen kann. Ein wichtiger Vertreter dieser Antibiotika, Neomycin B, von dessen Struktur die Entwicklung des Diaminogalactose-Templates abgeleitet wurde, wurde in dieser Arbeit als Leitstruktur gewählt. Die Synthese von Diaminogalactose-Scaffolds wurde zunächst in Lösung durchgeführt. Anschließend wurden die Bausteine 2 und 4 an einen polymeren Träger gebunden.rnNach Prüfung der orthogonalen Stabilität der Schutzgruppen wurde mit den Scaffolds 2 und 4 eine Bibliothek von 65 Verbindungen hergestellt. Mit 42 dieser Verbindungen wurden anschließend Zellassays im Rahmen des Sonderforschungsbereichs 579 (RNA-Liganden-Wechselwirkungen) durchgeführt, um ihre Cytotoxizität zu prüfen. Für einzelne Verbindungen konnten die optimalen Konzentrationen bestimmt werden, bei denen zukünftige Tests für die Tat/TAR Wechselwirkung ohne störende cytotoxische Effekte durchgeführt werden können.rn