published_or_final_version / Chemistry / Doctoral / Doctor of Philosophy

2-Benzyloxy-1-methylpyridinium trifluoromethanesulfonate (commonly referred to as benzyloxypyridinium triflate or Dudley’s salt) is a novel protecting reagent for the conversion of an alcohol functional group into a benzyl ether. This novel protecting reagent allows for protection of an alcohols, carboxylic acids, and other nucleophiles under mild conditions. The two traditional methods of forming this benzyl ether rely on either basic (Williamson ether synthesis) or acidic (coupling via trichloroacetimidate with a strong acid) conditions which may potentially decompose sensitive substrates. This research will investigate the mechanism by which benzyloxypyridinium triflate decomposes. Investigation of benzyloxypyridinium triflate will require two aspects, synthesis of various derivatives and a rate study. The synthesis of benzyloxypyridinium triflate derivatives (broadly named benzyloxypyridinium salts) will result in a series of new compounds, along with new synthetic routes to make them. Testing the derivatives to ensure they form the expected benzyl ether or ester then allows for investigation of the rate for each derivative as they form the benzyl ether. Among the various techniques that may be employed to study the mechanism, rate studies will be a significant portion of data used to draw a conclusion. Each derivative of the benzyloxypyridinium triflate is designed to affect the rate of decomposition thereby changing the rate of benzyl ether formation by either promoting or impeding the formation of a carbocation. Monitoring the rate of each derivative and comparing that rate to the rate of the benzyloxy- pyridinium triflate will give insight to a mechanistic pathway, indicating whether the pathway is more unimolecular or bimolecular. An immediate application of a known mechanism could lead to more desirable conditions for the benzyloxypyridinim triflate when forming the benzyl ether. In addition, having an understanding of the mechanism allows for the utility of arylmethylpyridinium salts to be expanded by allowing the pyridinium salt to deliver a variety of different electrophiles. The mechanism will also allow for different nucleophiles to trap the corresponding electrophile from the pyridinium salt. / No title page or introductory pages in thesis body PDF. / Department of Chemistry

No description available.

No description available.

<p>An efficient and versatile non-destructive method to analyze the progress of solid-phase glycoconjugate synthesis with gel-phase ¹⁹F NMR spectroscopy is described. The method relies on use of fluorinated linkers and building blocks carrying fluorinated protective groups. Commercially available fluorinated reagents have been utilized to attach the protective groups. </p><p>The influence of resin structures for seven commercial resins upon resolution of gel-phase ¹⁹F NMR spectra was investigated. Two different linkers for oligosaccharide synthesis were also developed and successfully employed in preparation of α-Gal trisaccharides and a n-pentenyl glycoside. Finally, reaction conditions for solid-phase peptide glycosylations were established.</p>

An efficient and versatile non-destructive method to analyze the progress of solid-phase glycoconjugate synthesis with gel-phase 19F NMR spectroscopy is described. The method relies on use of fluorinated linkers and building blocks carrying fluorinated protective groups. Commercially available fluorinated reagents have been utilized to attach the protective groups. The influence of resin structures for seven commercial resins upon resolution of gel-phase 19F NMR spectra was investigated. Two different linkers for oligosaccharide synthesis were also developed and successfully employed in preparation of α-Gal trisaccharides and a n-pentenyl glycoside. Finally, reaction conditions for solid-phase peptide glycosylations were established.

No description available.

This PhD thesis is focused on the synthesis of DNA modified with photocleavable 2- nitrobenzyl protecting groups in major groove and its applications in the regulation of gene expression in the level of transcription. In the first part of my thesis, the synthesis of photocaged 2'-deoxyribonucleosides triphosphates and their photolysis to unprotected 5-hydroxymethylated nucleotides is described. All prepared nucleoside triphosphates were good substrates for their enzymatic incorporation into DNA. Synthesized 5-(2-nitrobenzyloxy)methyl-2'-deoxyuridine-5'- monophosphate (dUNBMP) and DNA with one 5-(2-nitrobenzyloxy)methyl- modification in the sequence were used for the detailed kinetic studies of photocleavage reactions. In the second part of the thesis, the series of modified DNAs with specific sequences were prepared by primer extension (PEX) and/or polymerase chain reaction (PCR). A cleavage of prepared modified DNAs was studied by selected restriction endonucleases (REs). In all cases, the nitrobenzylated DNA fully resist the cleavage by REs. The deprotection/ photocleavage conditions for nitrobenzylated DNA were studied in the case of DNAs with positive restriction endonuclease digestion of hydroxymethylated DNA. The resulting photocleaved DNA was fully digested by REs, therefore 2-nitrobenzyl...