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Tannins and humic substances commonly referred to as natural organic matter (NOM), constitute an important component of natural water and soil systems. These species contain numerous phenol and carboxyl functional groups whose reactivity is strongly dependent on both the quantity and location of these moieties on the aromatic ring. In the realistic environmental conditions, both phenolic and carboxylic functional groups are adsorbed on a variety of colloidal metal oxide surfaces. Unfortunately, due to the complexity of humic-based substances, experimental data involving mineral-humate interactions are difficult to interpret. Here, we aim to develop a more detailed understanding of mineral-NOM interactions in aquatic systems, using self-assembled monolayers (SAMs) of simple organic acids having functional groups similar to those found in humic substances. SAMs of 4-(12-mercaptododecyl)benzene-1,2-diol (o-hydroxyphenol-terminated), 5-(12-mercaptododecyl)benzene-1,3-diol (m-hydroxyphenol-terminated), bis(11-thioundecyl) hydrogen phosphate (monoprotic phosphate) and 11-thioundecyl dihydrogen phosphate (diprotic phosphate) were prepared and deposited on a Au(111) surface. The composition of elements present on the surface were determined by X-ray Photoelectron Spectroscopy (XPS) and the orientation of monolayers on the Au(111) surface was explored by Attenuated Total Reflectance-Fourier Transform Infrared (ATR-FTIR) Chemical force spectrometry has been used to determine the surface pKa of the monolayers and further used to explore the role of phenolic groups in the surface complexation of NOM by monitoring adhesion forces between iron and aluminum oxide sample and hydroxyphenol-terminated Atomic Force Microscopy (AFM) modified tip. The results are discussed in the context of hydrogen bonding between corresponding species. The system in which there are multiple hydroxyl groups ortho to the carboxylic groups or adjacent to one another on the benzene ring results in significantly different force-distance profiles when interacting with the hydroxyphenol tip. / Thesis (Ph.D, Chemistry) -- Queen's University, 2013-06-18 00:22:06.646

Recently, a one-chain monoclinic unit cell for Cellulose IIII having a single glucose in the asymmetric unit was proposed based on high-resolution diffraction patterns. The new work challenged a two-chain structure published 25 years earlier, although it did not provide new three-dimensional coordinates. Our goals were to solve the structure by modeling, find whether modeling would reject the previously determined two-chain unit cell, and compare the model with the anticipated experimental structure. Combinations of the O2, O3, and O6 hydroxyls produced 54 starting structures. Clusters of 13 cellotetraose chains terminated by methyl groups for each of the 54 starting structures were optimized with MM3(96). Hydroxyl groups on 16 of these 54 structures reoriented to give very similar hydrogenbonding schemes in the interiors, along with the lowest energies. The one-chain cell models had much lower energy. The eight best “up” one-chain models agree well with the structure newly determined by experiment.

Thesis (Master of Applied Science in Chemistry)--Cape Peninsula University of Technology, 2018. / Physicochemical property enhancement of drugs is one of the focus areas of the pharmaceutical industry. This research demonstrates how crystal engineering methods offer a practical way to make systematic solid state modifications of active pharmaceutical ingredients. Nitrofurazone ((5-nitro-2-furaldehydesemicarbazone), NFZ) was selected for multicomponent crystal formation, in order to improve its aqueous solubility without modification of its molecular structure. NFZ has both hydrogen bond donor and hydrogen bond acceptor groups on its semicarbazone chain; therefore, it seemed to be a suitable target to use synthon engineering principles to form a series of multicomponent crystals. Also, the torsional flexibility of the NFZ molecule suggested great adaptability of the molecule and thus good potential for forming a variety of crystalline solids with the selected co-formers. Surprisingly, 95% of the time the co-crystallisation experiments failed and the ,  or polymorph of NFZ were obtained. The polymorph of NFZ was known since 1994. Parallel to this work, room temperature crystal structures of the and -polymorphs were reported by an independent research group. Although the crystal structures presented in this thesis were collected at 173 K, they are essentially the same as the already published ones with the obvious difference between the atomic thermal ellipsoids. Multicomponent crystals of NFZ were formed only when the API was exposed to perchloric acid (HClO4), phosphoric acid (H3PO4) and propionic acid (PA). These crystallisations resulted in the formation of 4NFZ•[H3O+][ClO4-], NFZ•H3PO4 and NFZ•PA crystals, respectively. The crystal structures were analysed with single crystal X-ray diffraction and the bulk properties of the material were analysed using powder X-ray diffraction, thermo-analytical methods and Fourier transform infrared spectroscopy. The most significant observation of the project was the extreme difficulty of the multicomponent crystal formation of NFZ, even though the API has great hydrogen bonding capabilities associated with torsional flexibility. To understand this behaviour, the solid state behaviour of the semicarbazone moiety was analysed with the aid of data retrieved from the Cambridge Structural Database. The torsional flexibility of the semicarbazone moiety was also investigated and the most common conformers were identified; and these results were supported by the findings of computational methods.

Feng Xue. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2000. / Includes bibliographical references (p. 142-145). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Mode of access: World Wide Web. / Abstracts in English and Chinese.

Ma Nap Tak. / Thesis submitted in: December 2004. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2005. / Includes bibliographical references (leaves 109-114). / Abstracts in English and Chinese. / ABSTRACT (ENGLISH) --- p.iii / ABSTRACT (CHINESE) --- p.iv / ACKNOWLEDGMENTS --- p.v / ABBREVIATION --- p.vi / TABLE OF CONTENTS --- p.vii / LIST OF FIGURES --- p.x / LIST OF TABLES AND GRAPHS --- p.xii / Chapter CHAPTER 1 --- Introduction and Background --- p.1 / Chapter 1.1 --- Introduction --- p.1 / Chapter 1.2 --- Hydrogen bonds (H-bonds) in DNA --- p.2 / Chapter 1.2.1 --- Experimental Evidences of Hydrogen Bonding --- p.3 / Chapter 1.3 --- Three-centered hydrogen bond (TCHB) --- p.4 / Chapter 1.3.1 --- Definition of Three-centered hydrogen bond (TCHB) --- p.5 / Chapter 1.3.2 --- Significance of Three-centered hydrogen bond (TCHB) --- p.6 / Chapter 1.3.3 --- Characterization of Three-centered hydrogen bond (TCHB) --- p.7 / Chapter 1.3.4 --- Classification of Three-centered hydrogen bond (TCHB) --- p.7 / Chapter 1.4 --- Charge transfer in DNA --- p.9 / Chapter 1.4.1 --- Theory of DNA charge transfer --- p.9 / Chapter 1.4.2 --- Short and long range hole transfer in DNA --- p.10 / Chapter 1.4.3 --- Electron transfer in DNA --- p.12 / Chapter 1.4.4 --- Summary of DNA charge transfer --- p.12 / Chapter 1.5 --- Thesis Scope --- p.13 / Chapter CHAPTER 2 --- Theory and methodology --- p.16 / Chapter 2.1 --- Introduction --- p.16 / Chapter 2.2 --- Theory --- p.17 / Chapter 2.2.1 --- Density Functional Theory (DFT) --- p.17 / Chapter 2.2.2 --- Basis set selection --- p.18 / Chapter 2.2.3 --- Natural Bond Orbital (NBO) --- p.19 / Chapter 2.2.3.1 --- Natural Population Analysis (NPA) --- p.20 / Chapter 2.2.3.2 --- E(2) --- p.20 / Chapter 2.2.3.2 --- bond index --- p.21 / Chapter 2.2.4 --- spin-spin coupling constants --- p.22 / Chapter 2.2.5 --- Molecular Orbital (MO) --- p.23 / Chapter 2.3 --- Methodology --- p.24 / Chapter 2.3.1 --- Test calculation for TCHBs by NBO --- p.24 / Chapter 2.3.2 --- Geometry Optimization --- p.24 / Chapter 2.3.3 --- NBO analysis --- p.25 / Chapter 2.3.4 --- J-coupling constants (lhJnx) and MO calculations --- p.26 / Chapter 2.4 --- Summary --- p.26 / Chapter CHAPTER 3 --- Results and Discussion --- Hydrogen bonding in DNA --- p.27 / Chapter 3.1 --- Introduction --- p.27 / Chapter 3.2 --- Method for extracting DNA dimer models --- p.27 / Chapter 3.3 --- Computed results of Inter H-bonds of the ten dimer models --- p.33 / Chapter 3.3.1 --- Geometric parameters --- p.33 / Chapter 3.3.2 --- Natural Bond Orbital (NBO) Analysis --- p.36 / Chapter 3.3.2.1 --- E(2) and Wiberg Bond index --- p.36 / Chapter 3.3.2.2 --- The relationship of E(2) and bond distance --- p.40 / Chapter 3.3.2.3 --- The relationship of E(2) and bond angle --- p.42 / Chapter 3.3.2.4 --- The relationship of E(2) and bond index --- p.44 / Chapter 3.3.3 --- Spin-Spin Coupling Constants of inter-H bonds --- p.46 / Chapter 3.3.3.1 --- The relationship of spin-spin coupling constant and distance --- p.49 / Chapter 3.3.3.2 --- The relationship of spin-spin coupling constant and bond angle --- p.50 / Chapter 3.3.3.3 --- The relationship of spin-spin coupling constant and E(2) energy --- p.52 / Chapter 3.4 --- Experimental Characterization of Three-centered H-bonds --- p.54 / Chapter 3.5 --- Theoretical Characterization of Three-centered H-bonds --- p.55 / Chapter 3.5.1 --- Geometry properties (360°C Rule) --- p.55 / Chapter 3.5.2 --- NMR properties (Spin-Spin Coupling Constants) --- p.55 / Chapter 3.5.3 --- NBO properties (E(2) and Wiberg bond index) --- p.56 / Chapter 3.6 --- Computed results of Three-centered hydrogen bonds (TCHBs) of the ten dimer models --- p.56 / Chapter 3.6.1 --- Natural Bond Orbital (NBO) Analysis --- p.56 / Chapter 3.6.1.1 --- Determination of TCHBs in the ten dimer models --- p.56 / Chapter 3.6.1.2 --- Analysis of TCHB interactions (E(2) and bond index) --- p.62 / Chapter 3.6.1.3 --- The relationship between E(2) and bond distance of TCHBs --- p.63 / Chapter 3.6.1.4 --- The relationship between E(2) and bond angle of TCHBs --- p.65 / Chapter 3.6.2 --- Spin-Spin Coupling Constants of TCHBs --- p.66 / Chapter 3.6.2.1 --- The relationship between spin-spin coupling constant and bond distance of TCHBs --- p.68 / Chapter 3.6.2.2 --- The relationship between spin-spin coupling constant and E(2) energy of TCHBs --- p.69 / Chapter 3.6.3 --- Geometry of TCHBs --- p.71 / Chapter 3.7 --- Summary --- p.72 / Chapter CHAPTER 4 --- Results and Discussion --- Charge location and charge transfer in DNA --- p.77 / Chapter 4.1 --- Introduction --- p.77 / Chapter 4.2 --- Method --- p.78 / Chapter 4.3 --- Computed results of the charge location of the trimer models --- p.81 / Chapter 4.3.1 --- Location of excess positive charge --- p.81 / Chapter 4.3.2 --- Location of excess negative charge --- p.90 / Chapter 4.4 --- Role of TCHBs in charge transfer --- p.95 / Chapter 4.4.1 --- Introduction --- p.95 / Chapter 4.4.2 --- "Analysis of G1G2C3, C3A4A5 and A8A9C10 trimers" --- p.96 / Chapter 4.4.3 --- Analysis of A7A8A9 and A8A9C10 trimers --- p.103 / Chapter 4.5 --- Summary --- p.105 / Chapter CHAPTER 5 --- Concluding Remarks --- p.107 / REFERENCES / APPENDIX

Investigation on a series of hydrogen-bonded networks constructed with N-heteroaryl acids is described in Section 3.4. In this section, we focused on the connection modes within the heteroaryl dimer. The study of co-crystals and inclusion compounds based on 2-thiobarbituric acid (TBA) or trithiocyanuric acid (TCA) indicated that the dimer of TBA is present in all three crystals in the forms of ribbon, tetramer or separated dimer. In the case of 5-nitrobarbiturate, its dimer occurs in two ammonium salts and in three of its four thiourea complexes, but is absent in all three urea complexes. / Self-assembly of two-dimensional hydrogen-bonded honeycomb grids exhibiting the rosette motif has been conducted with the guanidinium cation and various anions as the building blocks, tetraalkylammonium ions of suitable bulk being employed as interlayer templates. It is noteworthy that the rosette layer constructed from three different trigonal-planar molecular components has been achieved. In addition, deviating from conventional topological design, the generation of new rosette layers, albeit highly distorted, has also been accomplished with 1,2-dithiosquarate and the dianionic form of 1,1'-biphenyl-2,2',6,6'-tetracarboxylate that do not conform to C3-symmetry. Although threefold molecular symmetry is regarded as a sacrosanct requirement for molecular building blocks in the construction of hydrogen-bonded rosette motif, this study shows that rosette motifs can be generated even if one of the building blocks does not have inherent threefold symmetry. / Study of compounds containing the deprotonated forms of Kemp's triacid (H3KTA) has revealed the chair or twist-boat conformation in six crystal structures. X-ray structural analysis showed that [C(NH2) 3+] · [C6H6(CH3) 3(COOH)2(COO-)] (2.2.2) exhibits a corrugated layer structure which mimics the rosette motif constructed from the guanidinium ion and the hydrogen carbonate dimer. The tricarboxylate form of Kemp's triacid KTA3- in 3[C(NH2) 3+] · [C6H6(CH3) 3(COO-)3] (2.2.4) registers a record number of eighteen acceptor hydrogen bonds involving the convergent N--H donor sites from nine guanidinium ions. The crystal structure of 3[(C2H5)4N+] · 20[C(NH 2)3+] · 11[C6H6(CH 3)3(COOH) (COO-)2] · [C6H6(CH3)3(COOH)2(COO -)]·17H2O (2.2.3) features a hydrogen-bonded aggregate with a centrosymmetric pseudo-octahedral arrangement of H2KTA- anions surrounding an inner core composed of eight guanidinium ions. The unusual twist-boat conformation of KTA3- is found in [(CH3)4N +] · 2[C(NH2)3+] · [C6H6(CH3)3(COO- )3] · 2H2O (2.2.6), which is stabilized by the co-existence of guanidinium and tetramethylammonium cations. / Systematic investigation on hydrogen-bonded supramolecular assembly using aromatic carboxylic acids bearing linear or bent skeletons with urea/guanidinium resulted in the formation of mainly R228 and R126 synthon motifs. In addition, isostructures were also constructed by varying the length of the linker between two carboxylate groups, as in naphthalene-2,6-dicarboxylate (2.3.2) and biphenyl dicarboxylate (2.3.3). / This thesis reports a systematic investigation on the generation of new inclusion compounds by the combined use of urea/thiourea, guanidinium ion and various organic anions as building blocks of hydrogen-bonded host lattices and selected quaternary ammonium ion as the enclosed guests. / Various acids bearing specific functional groups have been explored as structure building components, including boric acid, Kemp's triacid, heterocyclic (thio)urea derivatives, aryl and N-heteroaryl carboxylic acids and (dithio)squaric acid. All the co-crystals and inclusion compounds built of molecular components in the afore-mentioned categories have been characterized by single-crystal X-ray analysis. As a result, the complexes exhibit a rich variety of inclusion topologies, such as networks containing isolated cages, open channels, intersecting tunnels, double-layer systems, and sandwich-like as well as wave-like layer structures. / Han, Jie. / Adviser: Thomas C. W. Mak. / Source: Dissertation Abstracts International, Volume: 71-01, Section: B, page: 0337. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2009. / Includes bibliographical references (leaves 204-218). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Electronic reproduction. Ann Arbor, MI : ProQuest Information and Learning Company, [200-] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstracts in English and Chinese.

Chan, Wing Shong Thierry. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2009. / Includes bibliographical references (leaves 82-88). / Abstract also in Chinese. / Contents --- p.i / Acknowledgments --- p.iii / Abstract --- p.iv / Abbreviations --- p.vi / Chapter Chapter 1 - --- Dendronized Polymers and Supramolecular Polymers --- p.1 / Chapter 1.1 --- Introduction to Dendrons and Dendrimers --- p.1 / Chapter 1.2 --- Dendronized polymers --- p.4 / Chapter 1.2.1 --- Graft-from Method --- p.5 / Chapter 1.2.2 --- Graft-to Method --- p.7 / Chapter 1.2.3 --- Macromonomer Method --- p.8 / Chapter 1.2.3.1 --- Step Growth Polymerization --- p.9 / Chapter 1.2.3.2 --- Chain Growth Polymerization --- p.10 / Chapter 1.2.3.3 --- Living Chain Growth Polymerization --- p.11 / Chapter 1.3 --- Supramolecular Polymers --- p.12 / Chapter 1.4 --- Supramolecular Dendronized Polymers --- p.13 / Chapter Chapter 2 - --- Design of Supramolecular Dendronized Polymers --- p.18 / Chapter 2.1 --- Hydrogen Bonding --- p.19 / Chapter 2.1.1 --- Binary Characters of Hydrogen Bonding --- p.20 / Chapter 2.2 --- 2-Ureido-4[ 1H]-Pyrimidinone (UPy) --- p.22 / Chapter 2.3 --- Effects of Dendrons on Dimerization Constant of UPy --- p.25 / Chapter 2.4 --- Target Supramolecular Dendronized Polymers --- p.26 / Chapter Chapter 3 - --- Synthesis and Characterization of Supramolecular Dendronized Polymers --- p.28 / Chapter 3.1 --- Retro-Synthesis --- p.28 / Chapter 3.2 --- Synthesis of [G1]-[G3] Bifunctional Protected Monomers --- p.28 / Chapter 3.3 --- Characterization of Intermediates --- p.34 / Chapter 3.3.1 --- 1H NMR Spectroscopy --- p.34 / Chapter 3.3.2 --- 13C NMR Spectroscopy --- p.37 / Chapter 3.3.3 --- Mass Spectroscopy --- p.40 / Chapter 3.3.4 --- Size Exclusion Chromatography (SEC) --- p.40 / Chapter 3.4 --- Deprotection of [G1]-[G3] Biflmctional O-benzyl Protected Monomers --- p.41 / Chapter 3.5 --- Characterization of [G1]´ؤ[G3] Bifunctional Dendronized Monomers --- p.44 / Chapter 3.5.1 --- Characterization of [G1] Dendronized Di-UPy Monomer --- p.44 / Chapter 3.5.2 --- Characterization of [G2] Dendronized Di-UPy Monomer --- p.46 / Chapter 3.5.3 --- Characterization of [G3] Supramolecular Dendronized Di-Upy Polymer --- p.47 / Chapter 3.6 --- Conclusion --- p.49 / Chapter Chapter 4 - --- Properties of Supramolecular Dendronized Polymers --- p.50 / Chapter 4.1 --- Viscosity Measurement --- p.50 / Chapter 4.1.1 --- Introduction --- p.51 / Chapter 4.1.2 --- Viscosity Result At Room Temperature --- p.52 / Chapter 4.1.3 --- Viscosity Result At Different Temperatures --- p.53 / Chapter 4.1.4 --- Viscosity Result In Different Solvents --- p.55 / Chapter 4.2 --- Proton NMR --- p.56 / Chapter 4.3 --- Scanning Electron Microscopy --- p.59 / Chapter 4.4 --- Gelation Property --- p.61 / Chapter 4.5 --- Conclusion --- p.63 / Chapter Chapter 5 - --- Experimental Procedures --- p.66 / Chapter 5.1 --- General Information --- p.66 / Chapter 5.2 --- Experimental Procedures --- p.67 / References --- p.82 / NMR spectra --- p.89

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Errata pasted onto front end-paper. Includes bibliographical references (leaves 82-86). Describes the preparation and characterisation of a novel series of organoplatinum(II) complexes with hydrogen-bonding functionality.