Techn. University, Diss., 2004--Berlin.

University, Diss., 2005--Bielefeld.

In dieser Arbeit wird durch Modellrechnungen gezeigt, wie die Stickstoffinversion in Azacyclen als molekularer Schalter genutzt werden könnte. Hierzu werden ein Fluorazetidin- und ein Fluorazacyclopentanderviat quantenchemisch untersucht. Das letztere Molekül wird auch quantendynamisch untersucht. Jedes der beiden Moleküle besitzt zwei stabile Konformationen. Es wird gezeigt, dass das Azabicyclopentanderivat von der einen Konformation mittels zweier linear polarisierter IR-Laserpulse durch sogenanntes “ladder climbing” in die andere überführt werden kann. / In this work it is shown by model simulation, how the nitrogon inversion in azacycles could be used as a molecular switch. For this a azetidine derivative and a fluoroazabicyclopentane derivative have been investigated quantumchemically. Both of the molecules have two stable conformers. The latter molecule is also investigated quantumdynamically. Its is shown that the azabicyclopentanederivative can be switched from one conformer to the other by using two linear polarised IR laser pulses via ladder climbing.

The aim of this thesis is the quantum dynamical study of two examples of scanning tunneling microscope (STM)-controllable, Si(100)(2x1) surface-mounted switches of atomic and molecular scale. The first example considers the switching of single H-atoms between two dangling-bond chemisorption sites on a Si-dimer of the Si(100) surface (Grey et al., 1996). The second system examines the conformational switching of single 1,5-cyclooctadiene molecules chemisorbed on the Si(100) surface (Nacci et al., 2008). The temporal dynamics are provided by the propagation of the density matrix in time via an according set of equations of motion (EQM). The latter are based on the open-system density matrix theory in Lindblad form. First order perturbation theory is used to evaluate those transition rates between vibrational levels of the system part. In order to account for interactions with the surface phonons, two different dissipative models are used, namely the bilinear, harmonic and the Ohmic bath model. IET-induced vibrational transitions in the system are due to the dipole- and the resonance-mechanism. A single surface approach is used to study the influence of dipole scattering and resonance scattering in the below-threshold regime. Further, a second electronic surface was included to study the resonance-induced switching in the above-threshold regime. Static properties of the adsorbate, e.g., potentials and dipole function and potentials, are obtained from quantum chemistry and used within the established quantum dynamical models. / Die vorliegende Doktorarbeit befasst sich mit kleinsten schaltbaren Einheiten in Form des Moleküls Cyclooctadien (COD) und dem Wasserstoff-Atom, die chemisch fest mit einer Oberfläche aus kristallinem Silizium verbunden sind. Jeder dieser Schalter kann mittels einer winzigen Spitze, eines so genannten Rastertunnelmikroskops (RTM), von atomarem Durchmesser in zwei unterscheidbare und stabile Schaltpositionen gebracht werden. Dabei besteht das Schalten entweder in einer Änderung der Geometrie des molekularen Schalters oder im Brechen und Neu-knüpfen chemischer Bindungen. Dabei ist es entscheidend, dass durch die geringe Grösse dieser Schalter eine hohe Anzahl dieser Schalter auf einer Oberfläche deponiert werden können. Mit der in den Schaltern speicherbaren Informationen an oder aus, 0 oder 1 ließen sich sehr hohe Speicherkapazitäten erreichen. Vor einer Anwendung dieser Art ist es wichtig zunächst ein grundlegendes Verständnis der Schaltprozesse auf der Oberfläche zu gewinnen. Wenn alle wesentlichen Faktoren berücksichtigt wurden und der Mechanismus des Schaltens verstanden ist, kann das Ergebnis des Experiments mit Hilfe eines theoretischen Modells vorhergesagt werden. Für die Handhabbarkeit muss sich das theoretisches Modell auf wesentliche Einflüsse beschränken und diese so einfach wie möglich beschreiben. So wurde die simultane Bewegung der 12 Atome des COD in die Bewegung eines gemittelten Massenpunktes entlang von einer oder von zwei räumlichen Freiheitsgraden übersetzt. Dabei kann der Massenpunkt im klassischen Bild anschaulich als eine rollende Kugel beschrieben werden, die in einer Seite einer Doppelmulde gefangen ist. Die Kugel kann durch äußere Anregung zum Schwingen gebracht werden und schließlich über eine Barriere in die benachbarte Mulde schalten. Nun muss die Schwingung der Kugel gebremst werden, um ein Zurück-Schwingen der Kugel zu verhindern. Die Anregung erfolgt durch elektrische Ladungen die von der Spitze des RTM zur Oberfläche wandern oder durch eine schwingende, d.h. warme Oberfläche. Das Bremsen wird über die elastische Bindung zu einer kalten Oberfläche vermittelt. Um Quanteneffekte wie das Tunneln der Kugel durch die Barriere zu beschreiben wurde die Kugel durch ein Wellenpaket beschrieben und dessen Aufenthaltswahrscheinlichkeit in der Doppelmulde untersucht. Im Fall des Wasserstoffatoms war die experimentelle Prüfung des entworfenen Modells für ein Schalten bei starkem Strom leider nicht möglich. Für das COD Molekül konnte jedoch nicht nur die Übereinstimmung mit den experimentellen Befunden, sondern im Fall des Schaltens in Abhängigkeit der Oberflächentemperatur auch die Vorhersagefähigkeit des Modells unter Beweis gestellt werden.

Understanding the molecular basis of protein function is a challenging task that lays the foundation for the pharmacological intervention in many diseases originating in altered structural states of the involved proteins. Dissecting a complex functional machinery into modules is a promising approach to protein function. The motivation for this work was to identify minimal requirements for “local” switching processes in the function of multidomain proteins that can adopt a variety of structural substates of different biological activity or representing intermediates of a complex reaction path. For example, modular switches are involved in signal transduction, where receptors respond to ligand-activation by specific conformational changes that are allosterically transmitted to “effector recognition sites” distant from the actual ligand-binding site. Heptahelical receptors have attracted particular attention due to their ubiquitous role in a large variety of pharmacologically relevant processes. Although constituting switches in their own right, it has become clear through mutagenesis and functional studies that receptors exhibit substates of partial active/inactive structure that can explain biological phenotypes of different levels of activity. Here, the notion that microdomains undergo individual switching processes that are integrated in the overall response of structurally regulated proteins is addressed by studies on the molecular basis of proton-dependent (chemical) and force-dependent (mechanical) conformational transitions. A combination of peptide synthesis, biochemical analysis, and secondary structure sensitive spectroscopy (Infrared, Circular dichroism, Fluorescence) was used to prove the switching capability of putative functional modules derived from three selected proteins, in which conformational transitions determine their function in transmembrane signaling (rhodopsin), transmembrane transport (bacteriorhodopsin) and chemical force generation (kinesin-1). The data are then related to the phenotypes of the corresponding full length-systems. In the first two systems the chemical potential of protons is crucial in linking proton exchange reactions to transmembrane protein conformation. This work addresses the hypothesized involvement of lipid protein interactions in this linkage (1). It is shown here that the lipidic phase is a key player in coupling proton uptake at a highly conserved carboxylic acid (DRY motif located at the C-terminus of helix 3) to conformation during activation of class-1 G protein coupled receptors (GPCRs) independently from ligand protein interactions and interhelical contacts. The data rationalize how evolutionary diversity underlying ligand-specifity can be reconciled with the conservation of a cytosolic ‘proton switch’, that is adapted to the general physical constraints of a lipidic bilayer described here for the prototypical class-1 GPCR rhodopsin (2). Whereas the exact sequence of modular switching events is of minor importance for rhodopsin as long as the final overall active conformation is reached, the related heptahelical light-transducing proton pump bacteriorhodopsin (bR), requires the precise relative timing in coupling protonation events to conformationtional switching at the cytosolic, transmembrane, and extracellular domains to guarantee vectorial proton transport. This study has focused on the cytosolic proton uptake site of this retinal protein whose proton exchange reactions at the cytosolic halfchannel resemble that of rhodopsin. It was a prime task in this work to monitor in real time the allosteric coupling between different protein regions. A novel powerful method based on the correlation of simultaneously recorded infrared absorption and fluorescence emission changes during bR function was established here (3), to study the switching kinetics in the cytosolic proton uptake domain relative to internal proton transfer reactions at the retinal and its counter ion. Using an uptake-impaired bR mutant the data proves the modular nature of domain couplings and shows that the energy barrier of the conformational transition in the cytosolic half but not its detailed structure is under the control of proton transfer reactions at the retinal Schiff base and its counter ion Asp85 (4). Despite the different functions of the two studied retinal proteins, the protonation is coupled to local switching mechanisms studied here at two levels of complexity, [a] a single carboxylic acid side chain acting as a lipid-dependent proton switch [b] a full-length system, where concerted modular regions orchestrate the functional coupling of proton translocation reactions. Switching on the level of an individual amino acid is shown to rely on localizable chemical properties (charge state, hydrophobicity, rotamer state). In contrast, switching processes involving longer stretches of amino acids are less understood, less generalizable, and can constitute switches of mechanical, rather than chemical nature. This applies particularly to molecular motors, where local structural switching processes are directly involved in force generation. A controversy exists with respect to the structural requirements for the cooperation of many molecular motors attached to a single cargo. The mechanical properties of the Hinge 1 domain of kinesin-1 linking the “neck” and motor domain to the “tail” were addressed here to complement single molecule data on torsional flexibility with secondary structure analysis and thermal stability of peptides derived from Hinge 1 (5). It is shown that the Hinge 1 exhibits an unexpected helix-forming propensity that resists thermal forces but unfolds under load. The data resolve the paradox that the hinge is required for motor cooperation, whereas it is dispensable for single motor processivity, clearly emphasizing the modular function of the holoprotein. However, the secondary-structural data reveal the functional importance of providing high compliance by force-dependent unfolding, i.e. in a fundamentally different way than disordered domains that are flexible but yet do not support cooperativity.

Univ., Diss., 2006--Frankfurt (Main) / Enth. Sonderabdr. aus versch. Zeitschr. - Zsfassung in dt. und engl. Sprache

Regensburg, Univ., Diss., 2004.

Techn. University, Diss., 2004--Darmstadt.

Techn. Universiẗat, Diss., 2005--Darmstadt.

Zugl.: München, Techn. Univ., Diss., 2008