Conjugated macrocycles have emerged as novel structural motifs that modulate the electronic properties of organic molecules because of their strained and contorted structures. Cycloparaphenylenes, known as nanohoops, are a particularly attractive scaffold for the design of new types of carbon nanomaterials because of their size-selective synthesis, radially oriented π-systems and tunable electronic properties. The development of modular syntheses of nanohoops over the past decade should enable the preparation of substituted derivatives that can be tuned for applications in biology and materials science. Chapter I provides a brief overview of conjugated macrocycles recently reported in the literature with a discussion of the structural effects that are responsible for the remarkable properties of this class of molecules. Chapter II highlights a scalable and mild synthetic approach developed in our lab to prepare nanohoop conjugated macrocycles and expands the generality of this methodology with the formal synthesis of natural product Acerogenin E. Chapter III describes the synthesis of cycloparaphenylenes with versatile functional handles and uncovers the reactivity of the strain nanohoop backbone under reaction conditions that promote the formation of radical cations. Chapter IV takes advantage of the functional groups described in chapter III to develop the first example of nanohoops as a new class of biocompatible fluorophores. Chapter V details a novel synthetic approach that enables the incorporation of the linear acene pentacene into the nanohoop backbone and reports our findings on the impact that the macrocyclic structure has on the properties of this organic semiconductor. In summary, the findings discussed in this dissertation provide synthetic strategies for the selective functionalization of nanohoops and highlight this class of molecules as a novel scaffold for the design of new types of carbon nanomaterials. This dissertation includes previously published and unpublished co-authored material.

by Xiao-Ming Chen. / Thesis (Ph.D.)--Chinese University of Hong Kong, 1992. / Includes bibliographical references (leaves 127-135). / Acknowledgements / Abstract --- p.i / Nomenclature --- p.ii / Table of Contents --- p.iii / List of Tables --- p.iv-v / List of Figures --- p.v-vii / Chapter 1. --- Introduction --- p.1-9 / Chapter 2. --- Results and Discussion --- p.10-104 / Chapter 1. --- Betaine derivatives --- p.10-19 / Chapter 2. --- "Complexes of manganese(II), cobalt(II), and nickel(II)" --- p.20-31 / Chapter 3. --- Complexes of zinc(II) --- p.32-40 / Chapter 4. --- Complexes of cadmium(II) and mercury(II) --- p.41-56 / Chapter 5. --- Complexes of silver(I) --- p.57-76 / Chapter 6. --- Complexes of copper(II) --- p.77-97 / Chapter 7. --- Mixed-metal complexes --- p.98-104 / Chapter 3. --- Conclusions --- p.105-106 / Chapter 4. --- Experimental --- p.107-126 / Chapter 5. --- References --- p.127-135 / Chapter 6. --- Appendix A --- p.136-151 / Chapter 1. --- Atomic coordinates and equivalent isotropic thermal parameters --- p.136-144 / Chapter 2. --- Anisotropic thermal parameters --- p.145-151 / Chapter 7. --- Appendix B (in a separated volume to be kept as Supplementary Data in the Department of Chemistry) Tables of structure factors

Molecules with unusual steric crowding are always interesting in chemistry. They give the opportunity to explore the limits of stable molecular structures and the synthesis of unnatural products. They also provide points of calibration for modern computational methods. This dissertation describes the design, synthesis and characterization of two types of crowded complex aromatic compounds. The goal of the first project was to synthesize in-keto cyclophanes, that is, molecules with ketone oxygens pressed toward the centers of benzene rings. Several likely precursors were synthesized and fully characterized, but attempts to make the in-keto cyclophanes themselves were unsuccessful. The nonbonded interaction between the ketone oxygen and basal benzene ring may be so close in the target structures as to prevent the formation of an in-keto cyclophane. The second project describes the design, synthesis and characterization of several macrobicyclic, bis(triarylelement)-containing cyclophanes with various bridgehead heteroatoms. Computational studies accurately predicted that when the bridgehead substituents are small (lone pairs or protons), an in,in bridgehead stereochemistry is strongly favored, but larger bridgehead substituents favor the formation of in,out stereoisomers. The NMR spectra of several of these compounds show unusual through-space spin-spin coupling between atoms along the central axis. Most importantly, one of these compounds, an in,in-bis(hydrosilane), possesses a hydrogen-hydrogen nonbonded contact distance of approximately 1.56 Å, a new “world record” for such a contact in any crystallographically characterized compound. / 1 / Jie Zong

This thesis is concerned with the reactions of sulfur-centred radicals and alkynes. The first objective of this work was to extend the scope of “self-terminating radical cyclisations” to sulfur-centred radicals, such as thiyl radicals. Preliminary experiments revealed that the reaction of thiyl radicals with alkynes was sensitive to residual oxygen. In the absence of oxygen, the reactions of photochemically generated phenylthiyl radicals with cyclodecyne (1) resulted in three isomeric sulfides, which were identified through a combination of techniques. (1S,6S)-2-phenylthiobicyclo[4.4.0]decane (trans-49a, unknown stereochemistry at C2) was identified by synthesis of an authentic sample, while the structure of (1S,2R,6S)-2-phenylthiobicyclo[4.4.0]decane (cis-49a1) was determined by X-ray analysis of the corresponding crystalline sulfone, cis-69. The third sulfide, (1S,2S,6S)-2-phenylthio-bicyclo[4.4.0]decane (cis-49a2), was assigned based on computational studies. / In addition, the reactions of benzylthiyl, tert-butylthiyl and allylthiyl radicals with cyclodecyne (1) were investigated. Various sources of thiyl radical generation were utilized, such as the photolysis of disulfides and thiols, hydrogen atom abstraction of thiols using radical initiators, as well as thiol autoxidation in the presence of oxygen. The radical cascade initiated by the addition of thiyl radicals to alkyne 1 was typically terminated by either reduction or disproportionation, whereas “self-termination” was only observed in one particular instance where the tert-butylthiyl radical was generated by autoxidation. However, this was only a minor pathway. / The second objective of this work was to investigate the reactions of thiyl radicals with alkynes in the presence of oxygen. For this purpose, phenylthiyl radicals were generated in the presence of diphenylacetylene (89) and molecular oxygen. Benzil (91), an α-diketone, and 1,2-diphenyl-2-(phenylthio)ethanone (93), an α-ketosulfide, were formed. The novel thiyl radical-mediated oxidation of diphenylacetylene to benzil mediated proceeds under mild and metal-free conditions, using various methods of thiyl radical generation. The product ratio of diketone to ketosulfide varied with the reaction conditions. Under photochemical conditions, benzil was formed but its photodegradation was also observed. Using autoxidation, moderate to good yields of both diketone 91 and ketosulfide 93 were obtained, although the product ratios varied with solvent and reaction conditions. Diketone 91 was the major product when the thiyl radical was generated electrochemically. Following investigation of the reaction mechanism using experimental and computational studies, the phenylthiyl peroxyl radical was identified as the key reactive intermediate. This represents the first synthetic application of thiyl peroxyl radicals. / Using autoxidation conditions, the oxidation was explored using substituted aromatic thiyl radicals, e.g. 2,6-dimethylbenzene, 2,4,6-tri-tert-butylbenzene, 4-methoxybenzene and 4-nitrobenzene thiyl radicals. Except for the case of 4-methoxybenzene thiyl radicals, where generation of the thiyl radicals was inefficient, diketone 91 was formed as the dominant product. This oxidation of alkynes to ketones, via thiyl radical-mediated activation of oxygen, was then applied to cyclodecyne (1). Bicyclic ketones 7/8 were found as the major products under photochemical conditions, while sulfides 152/trans-49a were the dominant products under autoxidation conditions. Bicyclic ketones 7/8 were formed due to the intramolecular radical processes directed by the transannular strain of the ten-membered carbon framework. Only trace amounts of the cyclic α-diketone 151 were detected under autoxidation conditions.

Thesis (Ph.D.)--University of Melbourne, School of Chemistry, 2009. / Typescript. Includes bibliographical references.

A presente dissertação tem por objetivo o estudo dos rearranjos de Pummerer, ainda não descritos na literatura para α-alquiltio-sulfóxidos. É apresentado um apanhado bibliográfico que consta de duas partes: a) Um relato dos trabalhos sobre os rearranjos de Pummerer com os sulfóxidos que não possuem átomo de enxofre na cadeia carbônica. b) Um resumo dos trabalhos que estudam algumas reações de α-alquiltio-sulfóxidos. Na primeira parte desta revisão é dado destaque às possibilidades mecanísticas da reação de Pummerer, apontando-se a sua dependência dos diversos fatores, tais como as estruturas do sulfóxido, do reagente de Pummerer e das condições experimentais empregadas. Na segunda parte são destacadas a acidez aumentada do grupo metilena de α-alquiltio-sulfóxidos e a sua fácil hidrólise ácida, características estas de grande importância para o nosso estudo da reação de Pummerer com os referidos compostos. No presente trabalho são preparados quatro sulfóxidos: metil n-propilsulfóxido (I) metil metiltiometilsulfóxido (II) etil etiltiometilsulfóxido (III) e fenil feniltiometilsulfóxido (IV), todos eles já descritos na literatura. São descritas as reações do etil etiltiometilsulfóxido (III) com anidrido acético. O rearranjo de Pummerer não ocorre em condições brandas, havendo recuperação do sulfóxido de partida. Em condições mais enérgicas e isolado o ortotritioformiato de etila. É relatada a reação do mesmo sulfóxido (III) com ácido clorídrico aquoso, na qual houve recuperação de grande parte do produto de partida e formação de pequenas quantidades do dietildissulfeto. São apresentadas as reações do metil metiltiometilsulfóxido (II), etil etiltiometilsulfóxido (III) e fenil feniltiomtilsulfóxido (IV) com cloreto de tionila. Em todas elas, em vez do cloro ditioacetal esperado, produto normal do rearranjo de Pummerer ocorre formação de clorometil-sulfetos correspondentes em rendimentos de 70-90%, ao lado de dissulfetos correspondentes. Finalmente é relatada a reação do etil etiltiometilsulfóxido (III) com cloreto de benzoila. Nesta reação há também ausência do produto normal do rearranjo de Pummerer e formação de dois produtos principais: clorometilsulfeto e tioformiato de etila, ao lado de pequenas quantidades de dissulfeto e ácido benzoico. Na discussão dos resultados obtidos são destacados dois aspectos de maior-importância nas reações dos α-alquil-tio-sulfóxidos: a supressão do produto de rearranjo de Pummerer e a formação de clorometil-sulfetos nas reações com cloreto de tionila e cloreto de benzoila. São relatadas as medidas de basicidades relativas pelo emprego de dois doadores de prótons, pirrol e fenol, através do método de espectroscopia no infra-vermelho do etil etiltiometilsulfóxido (II) e metil metiltiometilsulfóxido (II) em comparação com os sulfóxidos correspondentes não substituidos. Os dados obtidos voNH e voOH indicam uma diminuição de basicidade do oxigênio sulfinílico, resultante da introdução de um átomo de enxofre na posição 2 dos sulfóxidos. É sugerida a diminuição de basicidade e em consequência da nucleofilicidade do oxigênio sulfinílico como responsável pela diminuição da reatividade com os reagentes de Pummerer. É proposto o mecanismo de três passos para a formação de clorometil-sulfetos nas reações com cloreto de tionila e cloreto de benzoila. A formação de ortotritioformiato de etila e tioformiato de etila nas reações com anidrido acético e cloreto de benzoila, respectivamente é interpretada como decorrente do rearranjo de Pummerer. / This thesis investigates the Pummerer rearrangements not described in the literature, for some α-alkylthio-sulphoxides. A literature report divided in two parts is presented: a) Pummerer rearrangements of the sulphoxides not containing sulphur atom in the carbon chain. b) Some investigations on the reactions of α-alkylthio-sulphoxides. In the first part, the mechanistic aspects of the Pummerer rearrangement are described being emphasized their dependence on several factors, such as the structure of the sulphoxide and Pummerer reagent, and experimental conditions. In the second part the increased acidity of the methylene group of the α-alkylthio-sulphoxides and its easy hydrolysis are appointed, as they are of great importance for our study of the Pummerer rearrangement. In the present work: 1. Four sulphoxides already described in the literature are prepared: methyl methylthiomethylsulphoxide (I), methyl n-propylsulphoxide (II), ethyl ethylthiomethylsulphoxide (IV), and phenyl phenylthiomethylsulphoxide (IV). 2. The reactions of ethyl ethylthiomethylsulphoxide (III) with acetic anhydride are described. The Pummerer rearrangement does not occur in mild conditions being recovered the starting material. In more drastic condition the ethyl trithioformate is isolated. 3. The reaction of the same sulphoxide (III) with hydrochloric diluted acid is reported to give mostly starting material and small amount of diethyldisulphide. 4. The reactions of methyl methylthiomethylsulphoxide (I), ethyl ethylthiomethylsulphoxide (III) and phenyl phenylthiomethylsulphoxide (IV) with thionyl chloride are presented. In all cases instead of the expected chloro dithioacetal, the normal Pummerer rearrangement product, chloromethylsulphides were identified in the 70-90% yield in mixture with small amounts of the corresponding disulphides. 5. The reaction of ethyl ethylthiomethylsulphoxide (III) with benzoyl chloride is reported. Again the absence of the normalPummerer rearrangement product with formation of chloromethyl sulphoxide and small amount of disulphide are observed. However, an addicional product, ethylthioformate, was also produced. 6. The suppression of the normal Pummerer rearrangement product and formation of chloromethyl-sulphides in the reaction with thionyl chloride and benzoyl chloride are discussed. The relative basicity measurements using pirrol and phenol as proton donors by IR spectroscopy are reported for ethyl ethylthiomethylsulphoxide (III) and methyl methylthiomethylsulphoxide (I) and compared to the corresponding unsubstituted sulphoxides. The obtained data (voNH and voOH) indicate a decrease of basicity of sulphinyl group by replacement of β-methylene group by sulphur atom in the sulphoxides studied. Is suggested that decrease in basicity and consequently of nucleophilicity of the oxygen atom is responsible for the decrease of reactivity toward Pummerer reagents. A three step mechanism is proposed for the formation of chloromethyl-sulphides in the reactions with thionyl chloride and benzoyl chloride. The formation of ethyl orthotriethyl thioformate and ethyl thioformate as secondary products in the reactions with acetic anhydride and benzoyl chloride respectively is interpreted as resulting from the Pummerer rearrangement.

This study focused on the preparation and characterization of new indigo diimine (Nindigo) derivatives as a new atropisomeric scaffold. Trans- and cis- indigo diimines were studied and structure-property relationships were investigated regarding N-C atropisomerism using variable temperature 1H NMR studies and density functional theory calculations. Neutral trans- and protonated cis-Nindigos were prepared featuring a variety of mono ortho-substituted aryl imine groups with varying levels of steric bulk. The neutral trans-Nindigo derivatives generally have smaller N-C rotational energy barriers than their protonated cis-congeners. This finding is consistent with the latter having closer proximity of the N-aryl groups to each other, leading to steric repulsions between the two groups. The N-C rotational energy barriers are substituent dependent; the N-C rotational energy barriers of mono ortho substituted trans-Nindigos were in the range of 6.0 – 16.4 kcal/mol and can be classified as predominantly “Class 1’ atropisomers as defined by LaPlante, while the mono ortho substituted protonated cis-Nindigo analogs have N-C rotational barriers between 12.3 – 25.5 kcal/mol and are classified as “Class 1” and “Class 2” atropisomers. The introduction of additional substituents onto the other ortho position of the aryl imine subunit has significant consequences for the N-C rotational energy barriers of both the neutral trans- and protonated cis-Nindigos making them stable, or close to being, ‘Class 3’ atropisomers, having N-C rotational energy barriers between 31.5 – 276.9 kcal/mol and 29.3 – 32.6 kcal/mol respectively. Recognizing that the protonation state induced trans- to cis-isomerization process could have significant consequences regarding the potential applicability of these atropisomeric Nindigo derivatives, cis-Nindigo derivatives were synthesized that contained a tether (oxalyl or palladium (II) acetylacetonate) between the two indole type nitrogens of the Nindigo, which prevent the central -C=C- from isomerizing. The N-C rotational barriers of the tethered cis-Nindigos also displayed substituent dependent N-C rotational energy barriers. The protonation state of the N, N’-oxalyl bridged cis-Nindigos has a significant impact (higher in energy by a minimum of 5.1 kcal/mol) on the N-C rotational barriers; the neutral N, N’-oxalyl bridged cis-Nindigos have N-C rotational energy barriers ranging between 11.8 – 14.9 kcal/mol, classifying them as “Class 1” atropisomers, while their protonated congeners have N-C rotational energy barriers between 16.9 – 19.8 kcal/mol, which classifies them as “Class 1” atropisomers but are on the cusp of being “Class 2” atropisomers. The size of the tether influences the N-C rotational energy barriers of cis-Nindigos; the one-atom bridged palladium (II) acetylacetonate complexes have generally lower N-C rotational energy barriers than their protonated N, N’-oxalyl bridged cis-Nindigo congeners. The palladium acetylacetonate tethered cis-Nindigo complexes displayed substituent N-C rotational energy barrier dependence and the mono ortho substituted analogs have N-C rotational energy barriers between 12.4 – 20.2 kcal/mol and are predominantly “Class 1” atropisomers, while the bulkier analogs are “Class 2” atropisomers. The palladium (II) acetylacetonate cis-Nindigo complexes that have aryl imine groups with a 2,6-disubstitution pattern have N-C rotational energy barriers greater than 19.7 and 20.2 kcal/mol and are presumed to be stable “Class 3” atropisomers like their unbridged neutral trans- and protonated cis-Nindigo counterparts. / Graduate / 2023-09-12

We report here the development of a Lewis acid catalyzed method for the dehydrative coupling of cyclic alcohols and nitriles to form amides with retention of configuration. By contrast, the formation of amides by nitrile trapping of carbocations (Ritter reaction) usually affords racemic product. The present reaction was accomplished by first converting alcohol starting materials to their corresponding chlorosulfites in situ. Even after an extensive search, only copper (II) salts were able to produce the desired conversion of these chlorosulfites to amides though with low catalytic turnover. Improving the turnover without deteriorating the stereochemical outcome was eventually accomplished by a careful selection of the reagent addition sequence and through the removal of gaseous byproducts. This Ritter-like coupling reaction proceeds in good yields with secondary cyclic alcohols under mild conditions. The stereochemical outcome likely due to fast nucleophilic capture of a non-planar carbocations (hyperconjomers) stabilized by ring hyperconjugation. / Includes bibliography. / Dissertation (Ph.D.)--Florida Atlantic University, 2014. / FAU Electronic Theses and Dissertations Collection

利用超瑞利散射，我們能夠得知有機分子的超極化率，從而幫助我們對其在液態時的結構及相互作用加深認識和了解。在此研究項目，我們將通過測量對-硝基苯胺溶劑或硝基苯之稀釋混合物的超瑞利散射退極化比，分別提取當中的相干以及非相干散射訊號，並對分子間互相的位置以及方向相關性進行研究。同時，我們將針對分子間的短程和長程相互作用，利用其分別衍生的局域相干散射與離域相干散射進行深入探討。研究顯示，退極化比會受分子間的平均距離所影響，而實驗中將利用對-硝基苯胺在溶液中的濃度或硝基苯的稀釋率對平均距離進行調整。粗略估算當分子間的相互作用能與熱能的強度可比時，退極化比將會有明顯的變化。研究中我們運用簡單的偶極硬球模型，假設分子間為經典的電偶極子相互勢能，同時只考慮一對分子之間的直接相互作用，並以球直徑作為唯一參數擬合實驗結果。另一方面，通過觀察實驗中違反局域散射的對稱性，我們證實硝基苯分子間存在著長程相關性。而以不同溶劑進行稀釋，例如甲醇和丙酮時，會破壞其長程相關性，但當其與苯類溶劑，如對-二甲苯混合時，則會保持其長程相關性。因此，分子之間的長程相關性曾被認為是來自苯環之間的π-π相互作用。過往曾經有研究提出一項將液體中的集體震動模式以震動子(libron)表示的模型，能夠解釋觀察到的不對稱性，但此模型的擬合結果與此實驗中硝基苯以甲醇稀釋，並將其相關性破壞的結果並不相符。另外，以苯甲醇稀釋的結果與純硝基苯之間的不對稱現象相反，令π-π相互作用的假設受到質疑。直至現在，仍未有一項合理的模型能解釋得到實驗中所觀察到分子間的長程相關性。 / Hyper-Rayleigh Scattering (HRS) can be used to determine the first hy-perpolarizability β and examine the structure of organic compounds in liquid states. In this research project, by studying the HRS depolarization ratios of solutions of para-nitroaniline (PNA) or diluted mixtures of nitrobenzene, coherent and incoherent scattering signals were extracted for investigation of the spatial and angular correlations between molecules in a liquid state. Both the localized coherent light scattering, which is controlled by the strength of short-range intermolecular interaction, and the delocalized coherent scattering, which is related to the long range correlation between molecules, were revealed. The depolarization ratios were found to depend on the intermolecular distance, which varied with the concentration of the PNA in the solution or the dilution ratio of pure nitrobenzene in various solvents. A rough estimation shows that significant depolarization ratio variation should occur when the interactionenergy becomes comparable to the thermal energy. With the pair correlations calculated by a dipolar hard sphere model that assumed a classical dipolar interaction potential, the experimental results can be accounted by the theory using the hard sphere diameter as the only fitting parameter. The long range correlation between molecules was confirmed to exist even in the liquid state of pure nitrobenzene by observing a deviation from the local scattering symmetries. The long range correlation between nitrobenzene molecules was found to be easily destroyed by mixing with various solvents such as methanol and acetone, but was maintained by mixing with p-xylene, which is a solvent with benzene-like molecules. The π-π inter-action between the molecules was proposed to be the origin of the long range correlations. A model of delocalized collective mode (libron) that coexists with localized orientational diffusion mode in the solution was previously introduced to explain the observed phenomena. However, break downof the long range correlation by dilution using methanol showed a disagreement with the fitting of the libron model. Furthermore, use of benzol alcohol as a dilutant gives an opposite effect on the long range correlations of the nitrobenzene molecules, which makes the π-π interaction model for long range correlation between nitrobenzene molecules questionable. Presently, there is no satisfactory model on the long range correlation between molecules that can explain all our experimental results. / Detailed summary in vernacular field only. / Chan, Yan Chun = 有機溶液之相干超瑞利散射研究 / 陳恩進. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2012. / Includes bibliographical references (leaves 129-132). / Abstracts also in Chinese. / Chan, Yan Chun = You ji rong ye zhi xiang gan chao rui li san she yan jiu / Chen Enjin. / Abstract --- p.i / 摘要 --- p.iii / Acknowledgement --- p.v / Chapter 1 --- Introduction --- p.1 / Chapter 2 --- Basic Theory --- p.7 / Chapter 2.1 --- Introduction to nonlinear optics --- p.7 / Chapter 2.2 --- Harmonic generation --- p.10 / Chapter 2.3 --- Nonlinear optical phenomena --- p.12 / Chapter 2.4 --- Frequency dependent susceptibility --- p.13 / Chapter 2.5 --- Classical model to susceptibility --- p.14 / Chapter 2.6 --- Calculation of the Nonlinear Processes using Schrödinger Equation --- p.18 / Chapter 2.7 --- Densitymatrix formulation. --- p.20 / Chapter 2.8 --- Hyper-Rayleigh Scattering (HRS) --- p.23 / Chapter 3 --- Experimental Setup and Procedures --- p.30 / Chapter 3.1 --- Experimental Setup --- p.30 / Chapter 3.2 --- Instruments --- p.32 / Chapter 3.2.1 --- Laser System --- p.32 / Chapter 3.2.2 --- Sample cells --- p.33 / Chapter 3.2.3 --- Camera Lens --- p.34 / Chapter 3.2.4 --- Numerical Aperture --- p.35 / Chapter 3.2.5 --- Monochromator --- p.35 / Chapter 3.2.6 --- Photomultiplier --- p.35 / Chapter 3.2.7 --- Photon counter --- p.36 / Chapter 3.3 --- Experimental procedures --- p.37 / Chapter 3.3.1 --- Sample preparation --- p.37 / Chapter 3.3.2 --- Focus point calibration --- p.37 / Chapter 3.3.3 --- Measurement of depolarized intensities and ratios --- p.41 / Chapter 4 --- Instrumental calibration and error analysis --- p.43 / Chapter 4.1 --- PMT applied voltage and photon counter discrimination level --- p.43 / Chapter 4.2 --- HRS wavelength and spectral width --- p.46 / Chapter 4.3 --- Polarizations --- p.50 / Chapter 4.4 --- Slit width --- p.52 / Chapter 4.5 --- Pulsed laser repetition rate --- p.53 / Chapter 4.6 --- Gate width and gate delay --- p.55 / Chapter 4.7 --- Statistical error --- p.57 / Chapter 4.8 --- Photon counting error --- p.61 / Chapter 4.9 --- Numerical aperture collimation --- p.63 / Chapter 4.10 --- Depolarization ratio bias --- p.65 / Chapter 4.11 --- Laser focusing point deviation --- p.69 / Chapter 5 --- Measurement and results of localized coherent Hyper-Rayleigh scatterings --- p.74 / Chapter 5.1 --- Modeling of localized coherent scattering --- p.76 / Chapter 5.2 --- Localized coherent scattering of PNA --- p.84 / Chapter 5.3 --- Localized coherent scattering of Nitrobenzene --- p.91 / Chapter 5.4 --- Study with absorption spectrum --- p.96 / Chapter 5.5 --- Non-zero hyperpolarizability off-diagonal elements --- p.101 / Chapter 6 --- Study of delocalized coherent Hyper-Rayleigh scattering --- p.105 / Chapter 6.1 --- Delocalized coherent scattering of PNA --- p.106 / Chapter 6.2 --- Delocalized coherent scattering of nitrobenzene --- p.110 / Chapter 6.3 --- Libronmodel --- p.115 / Chapter 6.4 --- Long range correlations of PNAmolecules --- p.118 / Chapter 6.5 --- Ionic contaminations --- p.120 / Chapter 6.6 --- Long range correlations of other liquids --- p.123 / Chapter 7 --- Conclusions --- p.125 / Bibliography --- p.129

This thesis describes the development and implementation of single-molecule carbon nanotube-based field-effect transistors (smFETs) for studies of nucleic acid dynamics. Single-molecule techniques, most notably fluorescence resonance energy transfer (smFRET) and single-molecule force spectroscopy, have been employed to investigate biomolecular dynamics due to their ability to directly observe discrete, rare events, as well as to characterize structural motions in a diverse ensemble. However, these techniques are hampered by difficulties in measuring millisecond-scale dynamics, such as base pair rearrangements, as well as the inability to observe unperturbed individual molecules for long times. Alternatively, smFETs allow observation of the dynamics of charged biomolecules, such as charged amino acids in proteins or the phosphate groups of nucleic acid backbones, with microsecond temporal resolution. Structural rearrangements of a single charged molecule on the surface of a single-walled carbon nanotube (CNT) transistor can lead to measureable fluctuations in conductance through the CNT. Thus, this technique allows for simultaneous characterization of fast events and, due to the label-free and minimally-invasive nature of smFET technology, the quantification of how the frequency of these events change over long time-scales. A portion of this work describes smFET fabrication, focusing on improvements to the functionalization method, a critical step to reliably generate individual attachment sites on the CNT for subsequent single-molecule studies. A new synthetic chemistry approach is performed in ultraminiaturized, nanofabricated reaction chambers; using lithographically-defined nanowells, single-point attachments are achieved on hundreds of individual carbon nanotube transistors, providing robust statistics and unprecedented spatial control in adduct positioning. Each device acts as a sensor to detect, in real-time and through quantized changes in conductance, single-point functionalization of the nanotube, as well as consecutive chemical reactions and subsequent molecular interactions molecular conformational changes. In particular, this thesis is focused on studying the dynamics of nucleic acids using smFET technology. First, the smFET technique presented is verified by studying the thermodynamics and kinetics of DNA hybridization, the results of which compare favorably both with predicted values and previous smFET studies using alternative device architectures. Next, the reversible folding of a single-stranded telomeric DNA sequence known to form a G-quadruplex structure is studied, revealing the characteristic increased stability of the G-quadruplex structure in the presence of potassium ions relative to sodium ions. Finally, smFET studies of the dynamics of the adenine-sensing pbuE riboswitch aptamer found in Bacillus subtilis are discussed. These results demonstrate how long-lived, ligand-dependent intermediates form at a base-pair level and suggest that these intermediates have consequences for riboswitch-regulation by adenine binding to the aptamer. With the increased time resolution of smFET technology, this work has achieved the first observation of RNA zipping and unzipping at the single-molecule level, as well as label-free observations of the effects of a three-way junction motif on helix zipping and unzipping.