This thesis reports on unsaturated silicon compounds, as well as excursions from these into germanium chemistry, single molecule electronics, and silyl protective group chemistry. Both experimental and computational investigations were performed. Potassium germenolates were synthesized through reactions of tris(timethylsilyl) substituted acyl- and carbamylgermanes with potassium tert-butoxide. The potassium germenolates calculated by density functional theory have pyramidal structures at the Ge atoms, similar to the Si in the corresponding potassium silenolates, indicating negative charge on germanium rather than on oxygen. Germenolates also display germyl anion-like reactivity instead of germene-like reactivity as they are alkylated at Ge and initiate anionic polymerization of dienes rather than form [4+2] cycloadducts. The NMR chemical shifts reveal more negative charge at Ge in germenolates than at Si in analogous silenolates. Computations indicate that silabenzenes and silapyridines are reachable via [1,3]-silyl shifts from cyclic conjugated acylsilanes. Differently sized substituents were considered to prevent dimerizations, and 1-triisopropylsilyl-2-triisopropylsiloxy-6-tert-butylsilabenzene is a good synthetic target. Computations also show that silaphenolates are species with negative charge primarily localized at oxygen atom. Their planar structures, bond lengths, and NICS values reveal significant influence of aromaticity. Electrostatic repulsion should increase their stability, however, steric bulk is also important. Furthermore, it was found computationally that [1,3]-silyl shift from an acylsilane to a silene can function as a molecular switch reaction. Conductance calculations support this proposition.   Finally, tris(trimethylsilyl)silylmethaneamide (hypersilylamide) together with catalytic amounts of triflic acid were found to be efficient for protection of a range of alkyl and aryl alcohols and thiols in good to excellent yields. The protocol can be used to protect the less hindered OH group of a diol and has a broad functional group tolerance. A catalytic cycle is proposed. Hypersilyl protected alcohols and thiols are deprotected efficiently under photolytic conditions.

The ability to rationally or randomly modify proteins has expanded their employment in various bioanalytical applications. The bioluminescent protein, aequorin, has been employed as a reporter for decades due to its simplistic, non-hazardous nature and its high sensitivity of detection. More recently aequorin has been subject to spectral tuning. Techniques such as random and site-directed mutagenesis, the incorporation of coelenterazine analogues and the incorporation of non-natural amino acids have expanded the palette of aequorin by altering their emission wavelengths and/or half-lifes. Due to the increased diversity of aequorin, it can be used in multianalyte detection. Although aequorin has been studied extensively and has been used as a reporter in a wide array of applications, it has never been employed as a reporter in systems that involve the splitting of aequorin. Herein we describe the splitting of aequorin in such a way where it becomes the reporter protein in the development of protein-based molecular switches. We have created two distinct protein switches by genetically inserting the glucose-binding protein and the sulfate-binding protein into the aequorin sequence, splitting it in such a manner that it allows for the selective detection of glucose and sulfate, respectively. In a separate investigation, we developed a bioluminescence inhibition binding assay for the detection of hydroxylated polychlorinated biphenyls. These systems have shown that they can be employed in the detection of the respective analyte in biological as well as in environmental samples, which demonstrated a sensitive, fast alternative approach to current methods for on-site screening. Furthermore, we propose the rational design, preparation and use of truncated aequorin fragments in bioanalytical platforms such as multi-analyte detection, protein complementation assays and protein tagging assays based on our discovery that truncated aequorin retains partial bioluminescence emission. One such truncated aequorin demonstrated a large red shift in the emission maximum. It is envisioned that this new red-shifted truncated aequorin will find applications in multi-analyte detection. We anticipate that this work will lead to the discovery of additional functional truncated aequorin fragments that can be employed in novel protein-protein interactions or protein folding systems.

The research presented in this thesis introduces design criteria for development of a new type of self-contained optical biosensor. The study begins with evaluation of a dual label, fluorescence resonance energy transfer (FRET) bioassay format, and then goes on to demonstrate a signalling platform that uses an immobilized fluorescent intercalating dye so as to avoid labelling of both the target and probe strands. An extensive survey of FRET pairs that can be used to monitor hybridization events in solution and at solid interfaces was conducted in solution to provide a set of calculated Förster distances for the extrinsic labels Cyanine 3 (Cy3), Cyanine 5 (Cy5), Carboxytetramethylrhodamine (TAMRA), Iowa Black Fluorescence Quencher (IabFQ) and Iowa Black RQ (IabRQ). FRET parameters using thiazole orange (TO) intercalating dye as a FRET donor for various acceptor dye-labelled DNA conjugates in solution were determined. Limitations associated with quenching mechanisms other than those mediated by FRET motivated the development of a molecular switch that contained intercalating dye. The four binding sites associated with Neutravidin served for assembly of the switch using biotin interactions. One binding site was used to immobilize an unlabelled oligonucleotide probe. The adjacent site was used to immobilize a novel biotinylated TO derivative that could physically reach the probe. On hybridization of the probe with target, the intercalating dye was captured by the hybrid, leading to a change of fluorescence. This reversible signalling mechanism offers a method without nucleic acid labelling to detect nucleic acid association at an interface. A SNP discrimination strategy involving TO and formamide was investigated, and SNP discrimination without the requirement of thermal denaturation was achieved for multiple target lengths, including a 141-base pair PCR amplicon in solution. It was determined that formamide could also provide improvements of signal-to-noise when using thiazole orange to detect hybridization.

The research presented in this thesis introduces design criteria for development of a new type of self-contained optical biosensor. The study begins with evaluation of a dual label, fluorescence resonance energy transfer (FRET) bioassay format, and then goes on to demonstrate a signalling platform that uses an immobilized fluorescent intercalating dye so as to avoid labelling of both the target and probe strands. An extensive survey of FRET pairs that can be used to monitor hybridization events in solution and at solid interfaces was conducted in solution to provide a set of calculated Förster distances for the extrinsic labels Cyanine 3 (Cy3), Cyanine 5 (Cy5), Carboxytetramethylrhodamine (TAMRA), Iowa Black Fluorescence Quencher (IabFQ) and Iowa Black RQ (IabRQ). FRET parameters using thiazole orange (TO) intercalating dye as a FRET donor for various acceptor dye-labelled DNA conjugates in solution were determined. Limitations associated with quenching mechanisms other than those mediated by FRET motivated the development of a molecular switch that contained intercalating dye. The four binding sites associated with Neutravidin served for assembly of the switch using biotin interactions. One binding site was used to immobilize an unlabelled oligonucleotide probe. The adjacent site was used to immobilize a novel biotinylated TO derivative that could physically reach the probe. On hybridization of the probe with target, the intercalating dye was captured by the hybrid, leading to a change of fluorescence. This reversible signalling mechanism offers a method without nucleic acid labelling to detect nucleic acid association at an interface. A SNP discrimination strategy involving TO and formamide was investigated, and SNP discrimination without the requirement of thermal denaturation was achieved for multiple target lengths, including a 141-base pair PCR amplicon in solution. It was determined that formamide could also provide improvements of signal-to-noise when using thiazole orange to detect hybridization.

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.

Electronic devices, for logical and memory applications, are constructed based on bistable electronic units that can store binary information. Molecular electronics proposes the use of single molecules—with two distinctive states of conductance—as bistable units that can be used to create more complex electronic devices. The conductance of a molecule is strongly influenced by the contacts used to address it. The purpose of this work is to determine the electrical characteristics of several candidate molecular junctions, which are composed of a molecule and contacts. Specifically, we are interested in determining whether binary information, “0” or “1,” can be encoded in the low- and high-conductance states of the molecular junctions. First, we calculate quantum-mechanically the electronic structure of the molecular junction. Second, the continuous electronic states of the contacts, originated from their infinite nature, are obtained by solving the Schrödinger equation with periodic boundary conditions. Last, the electron transport through the molecular junctions is calculated based on a chemical interpretation of the Landauer formalism for coherent transport, which involves the information obtained from the molecule and the contacts. Metal-molecule-metal and metal-molecule-semiconductor junctions are considered. The molecule used is an olygo(phenylene ethynylene) composed of three benzene rings and a nitro group in the middle ring; this molecule is referred hereafter as the nitroOPE molecule. Gold, silicon, and metallic carbon nanotubes are used as contacts to the molecule. Results from the calculations show that the molecular junctions have distinctive states of conductance for different conformational and charge states. High conductance is found in the conformation in which all the benzene rings of the nitroOPE are coplanar. If the middle benzene ring is made perpendicular to the others, low conductance is found. Also, the negatively charged junctions (anion, dianion) show low conductance. Whenever a semiconducting contact is used, a flat region of zero current is found at low bias voltages. The results indicate that the use of Si contacts is possible; however, because of the flat region, the operating point of the devices needs to be moved to higher voltages.

Our target is the engineering of a light-gate molecular switch for the artificial ion channel, which will enable artificial ion channels to operate successfully in microfluidic systems, biomimetic sensors and various technical devices. A stable but reversible switch mechanism design is crucial, because the artificial ion channels known to date are lacking any control mechanism. Our artificial molecular switch is divided in two parts: the body part (calixarene) and a gate part based on light-responsive azo groups. The key to the controlling mechanism is the conformational change between cis and trans isomers, which is translated into movement of the gate. The gate is very robust and can either block or let the ions pass the molecular switch. Patch clamp investigations indicate successful integrations of gated artificial ion channels into lipid membranes. / Unser Ziel ist die Entwicklung eines lichtinduzierten Molekularschalters für künstliche Ionenkanäle, der als Nanobauteil für die Entwicklung von Sensoren in mikrofluiden Systemen, in biomimetischen Sensoren und in verschiedenen technischen Baugruppen eingesetzt werden soll. Für ein stabiles und zugleich reversibles System ist der Schaltmechanismus entscheidend, da die künstlichen Ionenkanäle bisher – soweit bekannt – keinen Regelmechanismus besitzen. Unser künstlicher molekularer Schalter setzt sich aus einem Rumpfteil (Calix[4]resorcinaren) und einer Schalteinheit, basierend auf lichtempfindlichen Azogruppen, zusammen. Die Schalteinheit ist sehr widerstandsfähig, kann den Ionenfluss blockieren oder die Ionen durch den Ionenkanal passieren lassen. Durch Bestrahlung wird die Kanalaktivität unterdrückt und reversibel wiederbelebt. Mittels Patch-Clamp-Untersuchungen wird das Schalten der synthetischen Ionenkanäle überprüft.

Herein we describe the regulatory significance and molecular targeting of novel non-B-DNA secondary structures formed from the PDGFR-Beta core promoter nuclease hypersensitivity element.

Although the regulation of proteins functions by allosteric interactions has been identified in many subcellular processes, long-range conformational changes in proteins are also known to be induced by molecular switches. A molecular switch based on the cis-trans isomerization of a peptidyl-prolyl bond is capable of inducing a conformational change directly to the protein backbone, which is then propagated throughout the system. However, these switches are elusive and difficult to identify due to their intrinsic dynamics in the biomolecules where they are found. Herein, we explore the conformational dynamics and free energy landscape of the SH2 domain of Interleukin-2-inducible T-Cell Kinase (ITK) to fully understand the conformational coupling between the distal cis-trans molecular switch, and its phosphotyrosine binding pocket. Using multiple microsecond-long all-atom molecular dynamics simulations in explicit water for over a total of 60 μs, we show that the cis-trans isomerization of the Asn286-Pro287 peptidyl-prolyl bond is directly correlated to the dynamics of the phosphotyrosine binding pocket, in agreement with previous NMR studies. While the cis state is localized to a single free energy basin and less dynamic, the trans state samples two distinct conformations of its binding pocket – one that recognizes the phosphotyrosine motif, and another that is similar the cis state. These results provide an atomic-level description of a less-well understood allosteric regulation by a peptidyl-prolyl cis-trans molecular switch that could aid in the understanding of normal and aberrant sub-cellular process and the identification of these elusive molecular switches in other proteins.

This communication will demonstrate the existence of a thermodynamic molecular switch in the pairwise, sequence-specific hydrophobic interaction of Ile-Ile, Leu-Ile, Val-Leu, or Ala-Leu over the temperature range of 273-333 K reported by Nemethy and Scheraga in 1962. Based on Chun's development of the Planck-Benzinger methodology, the change in inherent chemical bond energy at 0 K, ΔH°(T0), is 3.0 kcal mol-1 for Ile-Ile, 2.4 for Leu-Ile, 1.8 for Val-Leu, and 1.2 kcal mol-1 for Ala-Leu. The value of ΔH°(T0) decreases as the length of the hydrophobics side chain decreases. It is clear that the strength and stability of the hydrophobic interaction is determined by the packing density of the side chains, with Ala-Leu being the most stable. At , the thermal agitation energy, ∫0T ΔCp°(T)dT, is about five times greater than ΔH°(T0) in each case. Additionally, the thermal agitation energy for the same series, evaluated at , decreases in the same order, that is, as the length of the side chain decreases. This pairwise, sequence-specific hydrophobic interaction is highly similar in its thermodynamic behavior to that of other biological systems, except that the negative Gibbs free energy change minimum at occurs at a considerably higher temperature, 355 K compared to about 300 K. The melting temperature, , is also high, 470K compared to 343 K in a biological system. The implication is that the negative Gibbs free energy minimum at a well-defined >Ts> has it origin in the hydrophobic interactions, which are highly dependent on details of molecular structure. In addition to the four specific dipeptide interactions described, we have shown in our unpublished work the existence of a thermodynamic molecular switch in the interactions of 32 dipeptides wherein a change of sign in ΔCp°(T)reaction leads to a true negative minimum in the Gibbs free energy of reaction, and hence, a maximum in the related Keq. Indeed, all interacting biological systems that we have thus far examined using the Planck-Benzinger approach point to the universality of thermodynamic molecular switches.