<p>This thesis is based on ten publications (Papers I-X). The phosphodiester backbone makes DNA or RNA to behave as polyelectrolyte, the pentose sugar gives the flexibility, and the aglycones promote the self-assembly or the ligand-binding process. The hydrogen bonding, stacking, stereoelectronics and hydration are few of the important non-covalent forces dictating the self-assembly of DNA/RNA. The pH-dependent thermodynamics clearly show (Papers I and II) that a change of the electronic character of aglycone modulates the conformation of the sugar moiety by the tunable interplay of stereoelectronic anomeric and <i>gauche</i> effects, which are further transmitted to steer the sugar-phosphate backbone conformation in a cooperative manner. 3'<i>-</i>anthraniloyl<b> </b>adenosine<b> </b>(a mimic of 3'-teminal CC<u>A</u>_OH of the aminoacyl-tRNA^Phe) binds to EF-Tu*GTP in preference over 2'<i>-</i>anthraniloyl<b> </b>adenosine<b>, </b>thereby showing (Paper III) that the 2’-<i>endo</i> sugar conformation is a more suitable mimic of the transition state geometry than the 3’<i>-endo</i> conformation in discriminating between correctly and incorrectly charged aminoacyl-tRNA^Phe by EF-Tu during protein synthesis. The presence of 2'-OH in RNA distinguishesit from DNA both functionallyas well as structurally. This work (Paper IV) provides straightforward NMR evidence to show that the 2'-OH is intramolecularly hydrogen bonded with the vicinal 3'-oxygen, and the exposure of the 3'<i>-</i>phosphate of the ribonucleotides to the bulk water determines the availability of the bound water around the vicinal 2'-OH, which then can play various functional role through inter- or intramolecular interactions. The pH-dependent ¹H NMR study with nicotinamide derivatives demonstrates (Paper V) that the cascade of intramolecular cation (pyridinium)-π(phenyl)-CH(methyl) interaction in edge-to-face geometry is responsible for perturbing the p<i>K</i>_a of the pyridine-nitrogen as well as for the modulation of the aromatic character of the neighboring phenyl moiety, which is also supported by the T₁ relaxation studies and <i>ab initio</i> calculations. It has been found (Papers VI-IX) that the variable intramolecular electrostatic interaction between electronically coupled nearest neighbor nucleobases (steered by their respective microenvironments) can modulate their respective pseudoaromatic characters. The net result of this pseudoaromatic cross-modulation is the creation of a unique set of aglycones in an oligo or polynucleotide, whose physico-chemical properties are completely dependent upon the propensity and geometry of the nearest neighbor interactions (extended genetic code). The propagation of the interplay of these electrostatic interactions across the hexameric ssDNA chain is considerably less favoured (effectively up to the fourth nucleobase) compared to that of the isosequential ssRNA (up to the sixth nucleobase). The dissection of the relative strength of basepairing and stacking in a duplex shows that stability of DNA-DNA duplex weakens over the corresponding RNA-RNA duplexes with the increasing content of A-T/U base pairs, while the strength of stacking of A-T rich DNA-DNA duplex increases in comparison with A-U rich sequence in RNA-RNA duplexes (Paper X).</p>

<p>This thesis is based on nine research publications (<b>I – IX</b>) on structure and reactivity of RNA vis-à-vis DNA. The DNA and RNA are made of flexible pentose sugar units, polyelectrolytic phosphodiester backbone, and heterocyclic nucleobases. DNA stores our genetic code, whereas RNA is involved both in protein biosynthesis and catalysis. Various ligand-binding and recognition properties of DNA/RNA are mediated through inter- and intra-molecular H-bonding and stacking interactions, beside hydration, van der Waal and London dispersion forces. In this work the pH dependant chemical shift, p<i>K</i>_a values of 2'-OH group as well as those the nucleobases in different sequence context, alkaline hydrolysis of the internucleotidic phosphodiester bonds and analysis of NOESY footprints along with NMR constrained molecular dynamics simulation were used as tools to explore and understand the physico-chemical behavior of various nucleic acid sequences, and the forces involved in their self-assembly process. <b>Papers I – II</b> showed that the ionization of 2'-OH group is nucleobase-dependant. <b>Paper III</b> showed that the chemical characters of internucleotidic phosphate are non-identical in RNA compared to that of DNA. <b>Papers IV – VI</b> show that variable intramolecular electrostatic interactions between electronically coupled nearest neighbor nucleobases in a ssRNA can modulate their respective pseudoaromatic character, and result in creation of a unique set of aglycons with unique properties depending on propensity and geometry of nearest neighbor interaction. <b>Paper VII</b> showed that the cross-modulation of the pseudoaromatic character of nucleobases by the nearest neighbor is sequence-dependant in nature in oligonucleotides. <b>Paper VIII</b> showed that the purine-rich hexameric ssDNA and ssRNA retain the right-handed helical structure (B-type in ssDNA and A-type in ssRNA) in the single-stranded form even in absence of intermolecular hydrogen bonding. The directionality of stacking geometry however differs in ssDNA compared to ssRNA. In ssDNA the relatively electron-rich imidazole stacks above the electron-deficient pyrimidine in the 5' to 3' direction, in contradistinction, the pyrimidine stacks above the imidazole in the 5' to 3' direction in ssRNA. <b>Paper IX</b> showed that the p<i>K</i>_a values of the nucleobases in monomeric nucleotides can be used to show that a RNA-RNA duplex is more stable than a DNA-DNA duplex. The dissection of the relative strength of base-pairing and stacking showed that the relative contribution of former compared to that of the latter in an RNA-RNA over the corresponding DNA-DNA duplexes decreases with the increasing content of A-T/U base pairs in a sequence.</p>

This thesis is based on ten publications (Papers I-X). The phosphodiester backbone makes DNA or RNA to behave as polyelectrolyte, the pentose sugar gives the flexibility, and the aglycones promote the self-assembly or the ligand-binding process. The hydrogen bonding, stacking, stereoelectronics and hydration are few of the important non-covalent forces dictating the self-assembly of DNA/RNA. The pH-dependent thermodynamics clearly show (Papers I and II) that a change of the electronic character of aglycone modulates the conformation of the sugar moiety by the tunable interplay of stereoelectronic anomeric and gauche effects, which are further transmitted to steer the sugar-phosphate backbone conformation in a cooperative manner. 3'-anthraniloyl<b> </b>adenosine<b> </b>(a mimic of 3'-teminal CC<u>A</u>OH of the aminoacyl-tRNAPhe) binds to EF-Tu*GTP in preference over 2'-anthraniloyl<b> </b>adenosine<b>, </b>thereby showing (Paper III) that the 2’-endo sugar conformation is a more suitable mimic of the transition state geometry than the 3’-endo conformation in discriminating between correctly and incorrectly charged aminoacyl-tRNAPhe by EF-Tu during protein synthesis. The presence of 2'-OH in RNA distinguishes it from DNA both functionally as well as structurally. This work (Paper IV) provides straightforward NMR evidence to show that the 2'-OH is intramolecularly hydrogen bonded with the vicinal 3'-oxygen, and the exposure of the 3'-phosphate of the ribonucleotides to the bulk water determines the availability of the bound water around the vicinal 2'-OH, which then can play various functional role through inter- or intramolecular interactions. The pH-dependent 1H NMR study with nicotinamide derivatives demonstrates (Paper V) that the cascade of intramolecular cation (pyridinium)-π(phenyl)-CH(methyl) interaction in edge-to-face geometry is responsible for perturbing the pKa of the pyridine-nitrogen as well as for the modulation of the aromatic character of the neighboring phenyl moiety, which is also supported by the T1 relaxation studies and ab initio calculations. It has been found (Papers VI-IX) that the variable intramolecular electrostatic interaction between electronically coupled nearest neighbor nucleobases (steered by their respective microenvironments) can modulate their respective pseudoaromatic characters. The net result of this pseudoaromatic cross-modulation is the creation of a unique set of aglycones in an oligo or polynucleotide, whose physico-chemical properties are completely dependent upon the propensity and geometry of the nearest neighbor interactions (extended genetic code). The propagation of the interplay of these electrostatic interactions across the hexameric ssDNA chain is considerably less favoured (effectively up to the fourth nucleobase) compared to that of the isosequential ssRNA (up to the sixth nucleobase). The dissection of the relative strength of basepairing and stacking in a duplex shows that stability of DNA-DNA duplex weakens over the corresponding RNA-RNA duplexes with the increasing content of A-T/U base pairs, while the strength of stacking of A-T rich DNA-DNA duplex increases in comparison with A-U rich sequence in RNA-RNA duplexes (Paper X).

The first part of this work reports a comparative study on electrochromic properties of two Donor-Acceptor-Donor (DAD) type polymers, namely poly(2-heptyl-4,7-di(thiophen-2-yl)-1H-benzo[d]imidazole) (BImTh) and poly(4,7-bis(2,3-dihydrothieno[3,4-b][1,4]dioxin-5-yl)-2-heptyl-1H-benzo[d]imidazole) (BImEd). DAD type polymers are designed to bear the same acceptor unit, benzimidazole and two different donor units, thiophene and 3,4-ethylenedioxy thiophene (EDOT) to make a comparison based on the donor unit effect. The resulting polymers are both multichromic and have low band gap values (1.93 eV for PBImTh and 1.74 eV for PBImEd). In the second part, 4,7-bis(2,3-dihydrothieno[3,4-b][1,4]dioxin-5-yl)-2-phenyl-1H-benzo[d]imidazole (BImBEd) is synthesized. In order to figure out the presence of an intramolecular hydrogen bonding between the amine bond of the imidazole ring and the oxygen of the EDOT molecule, different amounts of trifluoroacetic acid (TFA) and concentrated sodium hydroxide (NaOH) solutions were added during electrochemical polymerization. These treatments caused protonation of the imine and deprotonation of the amine bonds respectively. In order to prove the changes in the optical properties of the polymers due to different number of protonated and deprotonated imine and amine bonds, 1,4-bis(2,3-dihydrothieno[3,4-b][1,4]dioxin-5-yl)benzene (BEDOT-B) was also synthesized and treated with the same procedures. Results showed that it is possible to control the main chain conformation of even an insoluble polymer via acid and base treatments during in situ polymerization.

Insight into the effect of secondary interactions, fluorination, as well as substituent effects on strong ionic hydrogen bonds has been acquired through studies of FHF-, NFnH3-n•••F- (n = 0..2) and [M-H]- (M = Glycine, Alanine, Valine, Serine) clustered with ROH (R = H, CH3, C2H5). Excellent agreement was observed between thermochemical values obtained from high pressure mass spectrometry measurements and those predicted from MP2(full)/6-311++G(d,p)//B3LYP/6-311++G(d,p) calculations. In the examination of the clustering of FHF-, a strong correlation between the hydrogen bond strength and the gas phase acidity of the solvent was observed. In addition, several interesting observations on various structural and thermochemical properties were made for each of the three solvents. Upon formation of clusters with water, it was found that the large entropic advantage of one particular structure, which was not the most enthalpically favored, was significant enough to make it the predominant species within the ion source. In the case of methanol solvation, no evidence of secondary interaction of the methyl group and any other moiety could be found. The structural details revealed from calculations of the ethanol-solvated clusters indicate that secondary interactions between the terminal methyl group and FHF- had an impact on the length of both the FHF and OHF bonds present. In an attempt to gain insight into the effects of fluorination on hydrogen bonding, clusters of NFnH3-n (n = 0..2) and F- have been computationally investigated. The hydrogen bond energy in NH3∙∙∙F-, NFH2∙∙∙F- and NF2H∙∙∙F- were calculated to be -67.9 kJ∙mol-1, -120.2 kJ∙mol-1 and -181.2 kJ∙mol-1, respectively, and clearly show the effect of fluorination on hydrogen bond strength in amine-fluoride systems. The change in enthalpy and entropy for the clustering of methanol to NF2H∙∙∙F- to form the fluoride bound dimer of methanol and difluoramine has been measured via high pressure mass spectrometry to be -68.3 kJ∙mol-1 and -90.5 J∙K-1∙mol-1. These values are in excellent agreement with the calculated analogues, -70.9 kJ∙mol-1 and -88.5 J∙K-1∙mol-1. Finally, an examination of the thermochemical properties associated with the formation of a hydrogen bond linkage between protic solvents and deprotonated amino acids has been performed. In addition to observations of the effect of side chain substitution, a comparison between measured and calculated properties has provided insight into the thermochemical effects arising from the isomeric nature of this clustering system. A new theoretical model describing the impact of a distribution of isomers on thermochemical measurements made via high pressure mass spectrometry is given. When this new model was applied, and the distribution of isomers correctly accounted for, the measured values of 〖∆H〗^°, 〖∆S〗^° and 〖∆G〗_298^° consistently agreed, to a very high degree of accuracy, with those predicted by MP2(full)/6-311++G(d,p)//B3LYP/6-311++G(d,p) calculations. As well, IR spectra for the clustering of deprotonated glycine with ROH have been calculated and analyzed to demonstrate the ability of techniques such as IRMPD to identify the presence of a distribution of isomers.

This thesis consists of seven research publications concerning (i) pKa studies of nucleobases in model nucleotides to understand why RNA duplexes are more stable than DNA duplexes (Paper I), (ii) the role of Me(T)-π interactions in the relative stability of DNA-RNA heteroduplexes (Paper II), (iii) pKa measurements in nucleotides with different 2′-substituents (paper III), (iv) a conformation study of constrained sugars and a pKa study of 1-thyminyl to reveal effect of sugar constraints on the pKa of the nucleobase (paper IV), (v) NMR and MD studies of 1′, 2′-oxetane constrained thymidine incorporated Dickerson Drew dodecamer (paper V), (vi) the sequence dependent pKa perturbation of 9-guaninyl moeity in single stranded (ss) DNA and RNA (paper VI), (vii) the non identical chemical nature of internucleotidic phosphates in (ss) RNA using 31P NMR (paper VI), and an alkaline hydrolysis study of phosphodiesters in ssRNAs (paper VII). The architecture of DNA and RNA molecules is determined by (a) hydrogen bonding (b) base stacking (c) a variety of additional non-covalent interactions. In paper (I) we showed that A-U and G-C base pairings in RNA are more stable than A-T and G-C base pairings in DNA by 4.3 and 1 kJ mol-1 respectively. Me(T)-π interaction plays a dominant role in the relative stability of DNA-RNA duplexes (paper II). In paper III and IV, we have shown that 1′ , 2′- oxetane and azetidine rings have strong inductive effect on pyrimidine bases, and that the H2′-sugar proton can be the marker to understand the pseudoaromaticity of pyrimidine bases, as well as increasing constraints in sugar reducing the basicity of nucleobases. A 1′, 2′-oxetane locked thymidine (T) moiety deforms the local structure of Dickerson-Drew dodecamer, d(CGCGAATTCGCG)2- investigated by High resolution NMR and MD study, as is discussed in the paper V. In papers VI and VII, we showed sequence context dependent pKa (N1) of 9-guaninyl perturbation in (ss) DNAs and RNAs and the non identical chemical nature of inter-nucleotidic phosphate groups in single stranded RNAs.

Insight into the effect of secondary interactions, fluorination, as well as substituent effects on strong ionic hydrogen bonds has been acquired through studies of FHF-, NFnH3-n•••F- (n = 0..2) and [M-H]- (M = Glycine, Alanine, Valine, Serine) clustered with ROH (R = H, CH3, C2H5). Excellent agreement was observed between thermochemical values obtained from high pressure mass spectrometry measurements and those predicted from MP2(full)/6-311++G(d,p)//B3LYP/6-311++G(d,p) calculations. In the examination of the clustering of FHF-, a strong correlation between the hydrogen bond strength and the gas phase acidity of the solvent was observed. In addition, several interesting observations on various structural and thermochemical properties were made for each of the three solvents. Upon formation of clusters with water, it was found that the large entropic advantage of one particular structure, which was not the most enthalpically favored, was significant enough to make it the predominant species within the ion source. In the case of methanol solvation, no evidence of secondary interaction of the methyl group and any other moiety could be found. The structural details revealed from calculations of the ethanol-solvated clusters indicate that secondary interactions between the terminal methyl group and FHF- had an impact on the length of both the FHF and OHF bonds present. In an attempt to gain insight into the effects of fluorination on hydrogen bonding, clusters of NFnH3-n (n = 0..2) and F- have been computationally investigated. The hydrogen bond energy in NH3∙∙∙F-, NFH2∙∙∙F- and NF2H∙∙∙F- were calculated to be -67.9 kJ∙mol-1, -120.2 kJ∙mol-1 and -181.2 kJ∙mol-1, respectively, and clearly show the effect of fluorination on hydrogen bond strength in amine-fluoride systems. The change in enthalpy and entropy for the clustering of methanol to NF2H∙∙∙F- to form the fluoride bound dimer of methanol and difluoramine has been measured via high pressure mass spectrometry to be -68.3 kJ∙mol-1 and -90.5 J∙K-1∙mol-1. These values are in excellent agreement with the calculated analogues, -70.9 kJ∙mol-1 and -88.5 J∙K-1∙mol-1. Finally, an examination of the thermochemical properties associated with the formation of a hydrogen bond linkage between protic solvents and deprotonated amino acids has been performed. In addition to observations of the effect of side chain substitution, a comparison between measured and calculated properties has provided insight into the thermochemical effects arising from the isomeric nature of this clustering system. A new theoretical model describing the impact of a distribution of isomers on thermochemical measurements made via high pressure mass spectrometry is given. When this new model was applied, and the distribution of isomers correctly accounted for, the measured values of 〖∆H〗^°, 〖∆S〗^° and 〖∆G〗_298^° consistently agreed, to a very high degree of accuracy, with those predicted by MP2(full)/6-311++G(d,p)//B3LYP/6-311++G(d,p) calculations. As well, IR spectra for the clustering of deprotonated glycine with ROH have been calculated and analyzed to demonstrate the ability of techniques such as IRMPD to identify the presence of a distribution of isomers.

In an approach to creating molecular-scale structures on glass surfaces via self assembly, a strongly-dimerizing ureido-[2-(4-pyrimidone)] (UPy) quadruple hydrogen-bonding array was chemically immobilized on silica surfaces by way of a triethoxysilane functionality. The unreacted surface silanols were then thoroughly passivated with a monofunctional organosilane, resulting in isolated UPy binding sites on the glass surface. These binding sites were found to selectively bind the strongly fluorescent perylenediimide (PDI) functionalized UPy molecules from solution, thus non-covalently linking the fluorophore to the surface. The association between the self-complementary molecules was exceptionally strong, both in solution and at the surface, such that effective hydrogen-bonding was retained after most solvent treatments. The binding was also reversible, however, so that washes with polar protic and dipolar aprotic solvents with high hydrogen-bonding capabilities, such as water, alcohols, and DMSO, resulted in the removal of the non-covalently bound fluorophore-tagged UPy. The UPy:UPy dimer system was also investigated in solution, using pyrene intramolecular excimer formation as a monitor of the dissociation of the pyrene heterodimers into homodimers incapable of forming excimers at micromolar concentrations. In addition, the energy transfer process in solution between pyrene and perylenediimide fluorophores linked through UPy dimerization was studied, with the intention using FRET-based measurements on the surface at single-molecule levels in order to determine the distances between UPy binding sites. Energy transfer was found to occur, but the observed photophysical behavior was complicated by possible secondary processes, which steady-state fluorescence measurements were unable to elucidate. The benefit of using this UPy system for attaching molecules to a surface lies in its reversibility of binding and versatility in manner of molecules which van be retained on the modified surface with a strong association. In this way molecular-scale features could conceivably be constructed on a surface by self-assembly, with the option of further chemical reactions to lock them in place, thus creating structures beyond the accessibility range of the conventional lithographic methods.

Title from PDF of title page. / Document formatted into pages; contains 80 pages. / Thesis (M.S.)--University of South Florida, 2003. / Includes bibliographical references. / Text (Electronic thesis) in PDF format. / ABSTRACT: The synthesis or the interaction between two or more molecules is known as supramolecular chemistry. The concept of supramolecular chemistry can be applied to the design of new pharmaceutical materials affording new compositions of matter with desirable composition, structure and properties. The design of a two-molecule, or binary, compound using complementary molecules represents an example of an application of crystal engineering. Crystal engineering is the understanding of intermolecular interactions, in the context of crystal packing, in the design of new solid materials. By identifying reliable connectors through molecular recognition or self-assembly, one can build predictable architectures. / ABSTRACT: The study of supramolecular synthesis was accomplished using known pharmaceutical molecules such as Nifedipine (calcium channel blocker used for cardiovascular diseases) and Phenytoin (used as an anticonvulsant drug) and model compounds containing synthons common in pharmaceutical drugs (Crown ethers and Trimesic acid with ether linkages and carboxylic acid dimers, respectively) with complementary molecular additives. The co-crystals formed were characterized by various techniques (IR, m.p., XPD, single X-ray diffraction) and preliminary results were found to exhibit characteristics different from the parent compounds as a direct result of hydrogen bonding and self-assembly interactions. These crystalline assemblies could afford improved solubility, dissolution rate, stability and bioavailability. / System requirements: World Wide Web browser and PDF reader. / Mode of access: World Wide Web.

Thesis (Ph. D.)--University of Missouri-Columbia, 2000. / Typescript. Vita. Includes bibliographical references (leaves 161-175). Also available on the Internet.