Date of Award


Publication Type

Doctoral Thesis

Degree Name



Chemistry and Biochemistry

First Advisor

Loeb, Stephen

Second Advisor

Carmichael, Tricia




This dissertation presents the design, synthesis and characterization of a set of bis(pyridinium)ethane and dibenzo-24-crown-8 based systems that form self-assembled monolayers on a gold substrate. Chapter 1 introduces the concept of interpenetrated and interlocked molecules, molecular machines and self-assembled monolayers with representative examples found in the literature. Chapter 2 provides an introduction to the various surface characterization techniques that were employed. In chapter 3, an interpenetrated system capable of forming self-assembled monolayers on a gold substrate is described. The chapter begins with the design and synthesis of the linker molecule. The recognition site was then synthesized, stoppered at one end with 3,5-lutidine and terminated at the other end with a thioacetate protected mercaptoundecanoic acid. SAMs were formed and characterized through RAIRS. While confirmation of SAM formation was acquired, evidence that the macrocycle was present could not be obtained. Chapter 4 describes the synthesis and characterization of slippage [2]rotaxanes. The rotaxanes were stoppered at one end with cyclohexyl isonicotinate and the other end with a 3,5-substituted phenyl ring. The kinetic and thermodynamics showed association constants strong enough to isolate the [2]rotaxanes with substituted DB24C8 macrocycles. The synthesis was redesigned with diphenylmethyl as a protecting group since it is able to be removed without damaging the recognition site. SAMs, with and without the macrocycle, were formed and characterized using RAIRS, EIS, XPS, and contact angle measurements. The SAMs formed were seen to be loosely packed, even more so when the rotaxane was present. Attempts to remove the macrocycles after SAM formation were conducted. While this may have been successful, it was unclear due to intercalation of DMSO into the SAM. Chapter 5 describes attempts to improve the packing of the SAM by using a co-adsorbent. Mixed SAMs were formed with the slippage system, using mercaptoundecanoic acid as the co-adsorbate. The mixed SAMs were characterized at various ratios of the adsorbates. After determining the ideal ratios of each compound for the best packing of the SAM, further attempts at removal of the macrocycle were conducted using DMSO, however, intercalation of DMSO into the SAM was still an issue.