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Surface Spectroscopic Studies of Molecular Recognition on Bare and Functionalized Silica Open Access


Other title
Functionalized Silica
Immobilized DNA
Specific Ion Effects
Bifunctional Surface
Type of item
Degree grantor
University of Alberta
Author or creator
Azam, Md Shafiul
Supervisor and department
Gibbs-Davis, Julianne (Chemistry)
Examining committee member and department
Borguet, Eric (Chemistry, Temple University)
Hanna, Gabriel (Chemistry)
Cairo, Christopher (Chemistry)
Xu, Yunjie (Chemistry)
Department of Chemistry

Date accepted
Graduation date
Doctor of Philosophy
Degree level
Understanding the molecular recognition processes at the solid/liquid interface is of central importance in numerous environmental, biological and materials applications. We studied the unorthodox behavior of molecules and ions at the silica/liquid interfaces using surface specific spectroscopic techniques. For instance, we used nonresonant second harmonic generation (SHG) spectroscopy to investigate the effect of specific cations on the acid-base equilibria of the silica/water interface. The silanol groups on planar silica are known to exhibit two acid dissociation constants with pKa values of ~4 and ~9. We observed that varying the alkali chloride significantly changed the effective pKa values for the less acidic silanols by as much as 2.5 log units. The effect of anions on the acid-base behavior of the silica/water interface was even more striking. Varying the halides in the aqueous phase led to drastically different effective pKa values for both types of silanol sites. The acid-base titration curves became increasingly sharp with increasing halide size, which was indicative of cooperative acid-base behavior. This has been the first clear observation of cooperative acid-base behavior at a mineral oxide interface. Next, to study the molecular recognition processes on a functionalized surface we selected DNA-tethered silica as our surface of interest. Utilizing the molecular specificity of resonant SHG we monitored the hybridization and thermal dissociation of DNA immobilized at the silica/water interface in real time. The timescale of hybridization for immobilized DNA was comparable to that of gold-supported DNA. However, the measured dissociation temperature of DNA immobilized at the silica/water interface was significantly lower than what is usually observed for gold tethered DNA, which we attributed to the additional charge repulsion between silica and the hybridizing complementary DNA. To increase complexity at the silica/liquid interface we introduced an orthogonally reactive azide-amine mixed monolayer, which provided a general starting point for synthesizing mixed monolayers with controlled ratios. Using X-ray photoelectron spectroscopy, we determined the azide/amine surface ratio as well as the reactivity of the functional groups in the mixed self-assembled monolayer (SAM). The subsequent functionalization of this mixed monolayer generated a bifunctional surface with a similar functional group ratio to the azide-amine precursor SAM.
Permission is hereby granted to the University of Alberta Libraries to reproduce single copies of this thesis and to lend or sell such copies for private, scholarly or scientific research purposes only. Where the thesis is converted to, or otherwise made available in digital form, the University of Alberta will advise potential users of the thesis of these terms. The author reserves all other publication and other rights in association with the copyright in the thesis and, except as herein before provided, neither the thesis nor any substantial portion thereof may be printed or otherwise reproduced in any material form whatsoever without the author's prior written permission.
Citation for previous publication
Azam, M. S.; Gibbs-Davis, J. M. “Monitoring DNA Hybridization and Thermal Dissociation at the Silica/Water Interface Using Resonantly Enhanced Second Harmonic Generation Spectroscopy,” 2013, Anal. Chem. 85, ASAP Article.Azam, M. S.; Weeraman, C. N.; Gibbs-Davis, J. M. “Halide-Induced Cooperative Acid-Base Behavior of the Silica/Water Interface,” 2013, 117, 8840-8850.Azam, M. S.; Weeraman, C. N.; Gibbs-Davis, J. M. “Specific Cation Effects on the Bimodal Acid-Base Behavior of the Silica/Water Interface,” J. Phys. Chem. Lett., 2012, 3, 1269-1274.Azam, M. S.; Fenwick, S. L.; Gibbs-Davis, J. M. “Orthogonally Reactive SAMs as a General Platform for Bifunctional Silica Surfaces,” Langmuir, 2011, 27(2), 741-750.

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