Intramolecular singlet-singlet (SSET) and triplet-triplet (TTET) energy transfer have been studied in two cyclic octapeptides, 1A and 2A, and their open chain analogs, 1B and 2B. The peptides are constructed by a solid phase synthetic technique from enantiomerically pure amino acids with alternating chirality. Cyclic peptides with this arrangement of amino acids preferentially adopt flat, disk-like conformations where the peptide side chains lie on the outside of the ensemble. In 1A, benzophenone and naphthalene chromophores are incorporated as 4-benzoyl-L-phenylalanine and 2-naphtyl-L-alanine at positions 1 and 5 in the peptide sequence while in 2A, these chromophores occupy positions 1 and 3. Molecular modeling studies indicate that the interchromophore separation is larger in 1A than in 2A. This difference in separation is apparent from the observation of TTET energy transfer in 2A, which is consistent with the short range nature of TTET. Low temperature phosphorescence results indicate that intramolecular TTET is efficient in 2A and 2B and occurs with a rate of kTTET > 9.4x103 s-1. Intramolecular SSET occurs efficiently within these cyclic and open chain peptides. 1A undergoes intramolecular SSET from the naphthalene chromophore to the benzophenone chromophore with kSSET > 3.7x107 s-1, while in 2A with kSSET >3.0x107 s-1. Results obtained by modeling, UV-Visible spectroscopy, fluorescence and phosphorescence spectroscopies and transient absorption experiments are described.

This thesis aims to provide insights into two challenging problems in the field of molecular electronics: Understanding the role of the electronic and the mechanical properties of electrodes in determining the charge transport dynamics of molecular devices and achieving the optical control of charge transport through single-molecule junctions by exploiting the optical properties of electrodes. We start by investigating the impact of electrode band structure on the charge transport characteristics of molecular devices. To this end, we conduct two independent, yet highly related studies. In the first study, we demonstrate how the metallic band structure dictates the molecular orbital coupling at metal-molecule interfaces by studying charge transport through pyridine-based single-molecule junctions with Au and Ag electrodes using a newly developed scanning tunneling microscope-based spectroscopy technique and performing density functional theory calculations. We find that pyridine derivatives couple well to Au electrodes compared with Ag electrodes. The density functional theory calculations show that the increase in the molecular orbital coupling to Au compared with Ag is due to an enhanced density of d-states near the Fermi level resulting from relativistic effects. Second, we study the interfacial charge transport properties of molecular devices with metal, semimetal and semiconductor electrodes using X-ray photoemission based spectroscopy techniques. In particular, we probe the hot electron dynamics of 4,4'-bipyrdine on Au (metal), epitaxial graphene (semimetal) and graphene nanoribbon (semiconductor) surfaces. We find that charge transfer from the molecule to the substrate is fastest on the metal surface and slowest on the semiconductor surface. We attribute this trend to a reduced electronic interaction between the molecule and the surface as a results of a decrease in the density of electronic states near the Fermi level as the metallic character of the substrate is reduced. Furthermore, we provide evidence for fast phase decoherence of hot electrons via an interaction with the substrate in these systems. Third, we shed light onto the origin of flicker noise in single-molecule junctions, tunnel junctions and gold point-contacts at room temperature. We find that the switching of gold atoms between metastable sites in the electrodes due to the thermal energy leads to conductance fluctuations in these systems. We further demonstrate how the flicker noise characteristics of single-molecule junctions can be used to infer the nature of the electronic interaction at metal-molecule interfaces. Specifically, we find that flicker noise exhibits a power dependence on junction conductance that can distinguish between through-space and through-bond charge transport. This work demonstrates how the mechanical properties of electrodes affect charge transport through single-molecule junctions and how noise can be used to understand the electronic properties of metal-molecule interfaces. Lastly, we explore the possibility of driving currents through single-molecule junctions using electromagnetic radiation. To this end, we perform photocurrent measurements on single-molecule junctions, tunnel junctions and gold point-contacts obtained using the scanning tunneling microscope-based break-junction technique. We find that the primary source of photocurrents in these systems is the laser induced local heating and the subsequent thermal expansion when probed using a lock-in type technique in which the light intensity is being modulated. We further develop an experimental method that differentiates between the photocurrents due to thermal expansion and the optical currents in single-molecule junctions, and provide evidence for optical currents due to electron-photon interaction during charge transport through single-molecule junctions. By using this method we estimate the plasmonic electric field enhancement factor in single-molecule junctions formed by 4,4'-bipyridine. Our estimate is in very good agreement with values inferred from tip enhanced Raman spectroscopy measurements and field emission measurements. We believe that the results presented in this thesis provide original insights into the fundamentals of the physics that govern charge transport across metal-molecule interfaces. Furthermore, the new experimental techniques introduced in this thesis offer new ways for investigating the rich physics present in nanoscale systems.

This thesis comprises eight chapters in two parts: the first part, chapters 1 to 6, details the design, synthesis, self-assembly and electrical properties of a new class of contorted polyheteroaromatic molecules, and the chapters 7 and 8 in the second part describes the design and fabrication of the first nanoscale field-effect transistor for single-molecule kinetics study. Chapter 1 is an introductory chapter. It first introduces the concept of organic photovoltaics (OPV), including the operation principles, important parameters, device structures, and relevant studied small molecules for the active layer in OPV devices. The second part of the chapter will be an overview of single-molecule biosensors involving various techniques and some important aspects on the design and fabrication. Chapter 2 details the development of a new synthetic methodology for polyheteroaromatic compounds. As one example, contorted dibenzotetrathienocoronenes (c-DBTTC) have been efficiently synthesized in three steps with high yields (>80%). Importantly this class of molecules displays an unusual intermolecular stacking in solid state and intimate interaction with n-type materials (TCNQ and C60) due to their shape-shifting ability. Chapter 3 will describe an unusual molecular conformation in highly fluorinated contorted hexa-cata-hexabenzocoronenes (c-HBC) via the fluorine-fluorine repulsive interaction. Chapter 4 describes the self-assembly properties of a new class of materials, chalcogenide-fused c-DBTTC, investigated by grazing incidence X-ray diffraction (GIXD), fluorescence microscopy and scanning electron microscopy (SEM). In chapter 5 a reticulated heterojunction OPV device applying c-DBTTC as the p-type active layer will be detailed. Combining the excellent self-assembly of c-DBTTC with the patterned graphene electrodes gives improved field-effect mobility in devices and will be described in chapter 6. In chapter 7, a field-effect transistor using a carbon nanotube (CNTFET) will be introduced. DNA hybridization kinetics will be detected using this "label-free" nanoscale device that represents a breakthrough in the field of single-molecule techniques by delivering high sensitivity and bandwidth. In chapter 8, a basic scientific research concerning Debye screening in buffer solution will be demonstrated utilizing above-mentioned DNA devices. Again, this nanoscale device uses its ability of single-molecule detection to correlate Debye length with buffer concentrations and charge distances, respectively; the correlations will serve as important references for the design of nanoscale biosensors using carbon nanotubes.

Modern computing and mobile device technologies are now based on semiconductor technology with nanoscale components, i.e., nanoelectronics, and are used in an increasing variety of consumer, scientific, and space-based applications. This rise to global prevalence has been accompanied by a similarly precipitous rise in fabrication cost, toxicity, and technicality; and the vast majority of modern nanotechnology cannot be repaired in whole or in part. In combination with looming scaling limits, it is clear that there is a critical need for fabrication technologies that rely upon clean, inexpensive, and portable means; and the ideal nanoelectronics manufacturing facility would harness micro- and nanoscale fabrication and self-assembly techniques. The field of molecular electronics has promised for the past two decades to fill fundamental gaps in modern, silicon-based, micro- and nanoelectronics; yet molecular electronic devices, in turn, have suffered from problems of size, dispersion and reproducibility. In parallel, advances in DNA nanotechnology over the past several decades have allowed for the design and assembly of nanoscale architectures with single-molecule precision, and indeed have been used as a basis for heteromaterial scaffolds, mechanically-active delivery mechanisms, and network assembly. The field has, however, suffered for lack of meaningful modularity in function: few designs to date interact with their surroundings in more than a mechanical manner. As a material, DNA offers the promise of nanometer resolution, self-assembly, linear shape, and connectivity into branched architectures; while its biological origin offers information storage, enzyme-compatibility and the promise of biologically-inspired fabrication through synthetic biological means. Recent advances in DNA chemistry have isolated and characterized an orthogonal DNA base pair using standard nucleobases: by bridging the gap between mismatched cytosine nucleotides, silver(I) ions can be selectively incorporated into the DNA helix with atomic resolution. The goal of this thesis is to explore how this approach to “metallize” DNA can be combined with structural DNA nanotechnology as a step toward creating electronically-functional DNA networks. This work begins with a survey of applications for such a transformative technology, including nanoelectronic component fabrication for low-resource and space-based applications. We then investigate the assembly of linear Ag+-functionalized DNA species using biochemical and structural analyses to gain an understanding of the kinetics, yield, morphology, and behavior of this orthogonal DNA base pair. After establishing a protocol for high yield assembly in the presence of varying Ag+ functionalization, we investigate these linear DNA species using electrical means. First a method of coupling orthogonal DNA to single-walled carbon nanotubes (SWCNTs) is explored for self-assembly into nanopatterned transistor devices. Then we carry out scanning tunneling microscope (STM) break junction experiments on short polycytosine, polycationic DNA duplexes and find increased molecular conductance of at least an order of magnitude relative to the most conductive DNA analog. With an understanding of linear species from both a biochemical and nanoelectronic perspective, we investigate the assembly of nonlinear Ag+-functionalized DNA species. Using rational design principles gathered from the analysis of linear species, a de novo mathematical framework for understanding generalized DNA networks is developed. This provides the basis for a computational model built in Matlab that is able to design DNA networks and nanostructures using arbitrary base parity. In this way, DNA nanostructures are able to be designed using the dC:Ag+:dC base pair, as well as any similar nucleobase or DNA-inspired system (dT:Hg2+:dT, rA:rU, G4, XNA, LNA, PNA, etc.). With this foundation, three general classes of DNA tiles are designed with embedded nanowire elements: single crossover Holliday junction (HJ) tiles, T-junction (TJ) units, and double crossover (DX) tile pairs and structures. A library of orthogonal chemistry DNA nanotechnology is described, and future applications to nanomaterials and circuit architectures are discussed.

<p>Electric current is known to flow through the π-bonds in oligothiophenes. In order to use them as molecular wires it is important to use a technique where the potential gradients can be generated and maintained in supramolecular networks. A solution to this problem can be the use of metal complexes as junction points within such a network.</p><p> In this project pathways to synthesize 2-thia-7,8-diaza-cyclopenta[<em>l</em>]phenanthrene <strong>(1)</strong> and 1-thia-7,8-diaza-cyclopenta[<em>l</em>]phenanthrene <strong>(2)</strong> for use in molecular electronic devices have been investigated. 4-(5-Bromo-thiophen-2-yl)2,2’-bipyridine <strong>(3)</strong> was prepared via Kröhnke reaction from 3-(5-bromothiophene-2-yl)acrolein and 1-(2-Oxo-2-pyridine-2-yl-ethyl)-pyridinium iodide in an overall yield of 14 %.  </p><p> Several routes towards 2-thia-7,8-diaza-cyclopenta[<em>l</em>]phenanthrene (<strong>1)</strong> and 1-thia-7,8-diaza-cyclopenta[<em>l</em>]phenanthrene <strong>(2) </strong>were tested. Since the original planned pathway did not work, lack of time made it impossible to complete the series of experiments that were needed. The synthesis of 2-thia-7,8-diaza-cyclopenta[<em>l</em>]phenanthrene (<strong>1) </strong>is almost finished. Due to the solvation problems, after the decarboxylation step, the product could not be analyzed by ¹H-NMR in a satisfactory manner. The product was sent for analysis.</p><p> A number of experiments towards 1-thia-7,8-diaza-cyclopenta[<em>l</em>]phenanthrene <strong>(2) </strong>were tested but few of them worked as planned. There is a lot of work left to be done in the synthesis of this compound but the lack of time made it impossible.</p><p> The chemistry that has been achieved is the synthesis of 1,10-phenanthroline-5,6-dione in the synthesis of 2-thia-7,8-diaza-cyclopenta[<em>l</em>]phenanthrene (<strong>1)</strong>. The following Hinsberg thiophene synthesis probably worked but due to solvation problems the product could not be isolated. The final product after hydrolysis and decarboxylation of the remaining ester groups after the Hinsberg thiophene synthesis was tested but the results were difficult to confirm.</p><p> In the synthesis of 1-thia-7,8-diaza-cyclopenta[<em>l</em>]phenanthrene <strong>(2)</strong> several attempts to make 3,4-diamino-<em>N,N</em>-diethyl-benzamide were made. The attack from the primary amines on the carbonyl carbon made it necessary to protect them. The attempt to synthesize 3,4-bis-acetylamino-<em>N,N</em>-diethyl-benzamide also failed, both the attempt directly from the carboxylic acid and through the acylchloride, even though the amines were protected.  </p>

Carbon/molecule/Cu/Au molecular junctions were fabricated on 4-inch silicon wafers using microfabrication techniques common in commercial semiconductor manufacturing. Electron-beam deposited carbon films are introduced as substrates, and the junctions exhibited high yield and excellent reproducibility. Current density-voltage characteristics of the devices were area scaling, weakly dependent on temperature and exponentially on molecular film thickness, and quantitatively similar to those of devices made with other techniques reported previously in our group, which contained pyrolyzed photoresist films as substrates. Furthermore, the test of cycle life and thermal stability reveals that the devices can survive at least under several millions of potential cycles at room temperature in air, and elevated temperature up to 150 C in vacuum for >40 hours. Parallel fabrication, thermal stability, and high yield are required for practical applications of molecular electronics, and the reported results provide important steps toward integration of molecular electronic devices with commercial processes and devices.

Single-molecular electronics and organic material electronics are expanding research fields that ultimately aim for a vast variety of different applications, ranging from organic light-emitting diodes, to novel ways to improve the performance and decrease the size of electronics components. To achieve these goals, research has to be focused both on the development of functional molecules, but also on device fabrication. The work of this thesis is focused on the development of synthetic routes towards novel molecules for potential organic electronics applications, together with an investigation of their optical and electronic properties. The first part of the thesis describes the synthesis of butadiyne-substituted and diacetylenic phosphaalkenes. Theoretical, spectroscopic and electrochemical techniques have been used to understand key steps during their synthesis, and to gain further information on the conjugative properties of their π-systems. A mechanism is proposed for the formation of the butadiyne-substituted and diacetylenic phosphaalkenes and it is shown that the phosphorus heteroatom is an intrinsic part of the π-conjugated system. The incorporation of the phosphorus heteroatom leads to decreased HOMO-LUMO gaps compared to all-carbon based reference compounds. In the second part of the thesis, acetylenic phosphaalkenes are utilized for the preparation of phosphaalkene-substituted phospholes. A first step towards the exploration of the difference in reactivity of the σ2, λ3 phosphaalkene-P and the σ3, λ3 phosphole-P is presented as the oxidation of the compounds by sulfur proceeds selectively at the σ3, λ3–P. Spectroscopic and electrochemical investigations show that the phosphaalkene is an integral part of the compounds’ π-systems, and induces a HOMO-LUMO gap decrease compared to reference compounds that lack the P=C substituent. The third part of this thesis presents an exploratory study concerning the suitability of metathesis reactions for the assembly of alkene-bridged phosphaalkenes.

Electric current is known to flow through the π-bonds in oligothiophenes. In order to use them as molecular wires it is important to use a technique where the potential gradients can be generated and maintained in supramolecular networks. A solution to this problem can be the use of metal complexes as junction points within such a network.  In this project pathways to synthesize 2-thia-7,8-diaza-cyclopenta[l]phenanthrene (1) and 1-thia-7,8-diaza-cyclopenta[l]phenanthrene (2) for use in molecular electronic devices have been investigated. 4-(5-Bromo-thiophen-2-yl)2,2’-bipyridine (3) was prepared via Kröhnke reaction from 3-(5-bromothiophene-2-yl)acrolein and 1-(2-Oxo-2-pyridine-2-yl-ethyl)-pyridinium iodide in an overall yield of 14 %.    Several routes towards 2-thia-7,8-diaza-cyclopenta[l]phenanthrene (1) and 1-thia-7,8-diaza-cyclopenta[l]phenanthrene (2) were tested. Since the original planned pathway did not work, lack of time made it impossible to complete the series of experiments that were needed. The synthesis of 2-thia-7,8-diaza-cyclopenta[l]phenanthrene (1) is almost finished. Due to the solvation problems, after the decarboxylation step, the product could not be analyzed by 1H-NMR in a satisfactory manner. The product was sent for analysis.  A number of experiments towards 1-thia-7,8-diaza-cyclopenta[l]phenanthrene (2) were tested but few of them worked as planned. There is a lot of work left to be done in the synthesis of this compound but the lack of time made it impossible.  The chemistry that has been achieved is the synthesis of 1,10-phenanthroline-5,6-dione in the synthesis of 2-thia-7,8-diaza-cyclopenta[l]phenanthrene (1). The following Hinsberg thiophene synthesis probably worked but due to solvation problems the product could not be isolated. The final product after hydrolysis and decarboxylation of the remaining ester groups after the Hinsberg thiophene synthesis was tested but the results were difficult to confirm.  In the synthesis of 1-thia-7,8-diaza-cyclopenta[l]phenanthrene (2) several attempts to make 3,4-diamino-N,N-diethyl-benzamide were made. The attack from the primary amines on the carbonyl carbon made it necessary to protect them. The attempt to synthesize 3,4-bis-acetylamino-N,N-diethyl-benzamide also failed, both the attempt directly from the carboxylic acid and through the acylchloride, even though the amines were protected.

Fast development in all areas of life and science over the last 50 years demands versatile, energy efficient and cheap materials with specific but easily tuneable properties which can be used for example in organic light emitting diodes (OLEDs), thin-film transistors, photovoltaic cells, etc. This thesis is devoted to the development of novel synthetic approaches to molecules with potential applications in the field of molecular electronics.  The acquisition of a detailed mechanistic understanding of the newly developed reactions is central to the work presented in this thesis. The first chapter is dedicated to the development of a new procedure for the preparation of phospha-Wittig-Horner (pWH) reagents, i.e. a reagents that has been known to convert carbonyl compounds into compounds with P=C double bonds. Each step of the synthetic sequence, i.e. preparation of the starting P,P-dichlorophosphines, their phosphorylation using the Michaelis-Arbuzov protocol, coordination to the metal centre and final hydrolysis, are presented in detail. A possible route to uncoordinated pWH reagents is also discussed. The second chapter focuses on the reactivity of the pWH reagents with acetone under different reaction conditions. The results show how changes in the ratio of starting material vs. base as well as reaction time or structure of the pWH reagent can influence the reaction outcome and the stability of the obtained products. The possibility to prepare unusual phosphaalkenes with unsaturated P-substituents is presented. The third chapter of the thesis is dedicated to the reactivity of pWH reagents towards symmetric and asymmetric ketones which contain one or two acetylene units. The proposed mechanisms of the reactions are studied by means of in situ FTIR spectroscopy as well as theoretical calculations. Physical-chemical properties of oxaphospholes, cumulenes and bisphospholes are presented. The last chapter is dedicated to reactivity studies of pWH reagents towards ketenes, and the exploration of a reliable route to 1-phosphaallenes. Detailed mechanistic studies of the pWH reaction that are based on the isolation and crystallographic characterization of unique reaction intermediates are presented. The reactivity of phosphaallenes towards nucleophiles such as water and methanol are examined. In summary, this thesis presents synthetic routes to novel phosphorus-containing molecules, together with detailed studies of the reaction mechanisms of the observed transformations.

The field of molecular electronics includes the study of conjugated oligomers and polymers that have significant potential for use in devices such as light emitting diodes (LEDS), field effect transistors (FETS), and photovoltaic solar cells. These materials may replace inorganic semiconductors in these devices, Achieving better device performance through lowering the band-gap and achieving higher field effect mobilities will benefit from a greater fundamental understanding of charge transfer through the aromatic subunits. π-stacking of segments of conjugated polymers has been identified as a key feature that influences the charge transfer through semiconducting organic materials. Optimizing the molecular architecture of conjugated polymers has the potential to provide materials with better charge mobility. While devices might benefit from materials that take advantage of π-stacking, access to π-stacked structures presents a synthetic challenge. 1,8-Disubstituted naphthalenes may serve as simple covalent bridging scaffolds which might hold conjugated oligomers in a π-stacked arrangement. The research described in this thesis focuses on the synthesis of well-defined phenylene ethynylene oligomers coupled to naphthalene to serve as experimental models of closely π-stacked aromatic units in conjugated polymers. The π-stacked molecules reported in this dissertation are characterized by NMR, IR, and mass spectrometry. The effects of π- stacking on the structure and behavior of conjugated oligomers are determined by X-ray crystallography, spectroscopy, and electrochemistry.