Date of Award


Document Type

Open Access Dissertation


Chemistry and Biochemistry


College of Arts and Sciences

First Advisor

Linda S. Shimizu


The self-assembly of macrocyclic molecules in solution and in the solid state modulates and in many cases enhances their properties for applications in sensing, catalysis and optoelectronics. The self-assembled structures are typically organized by non-covalent interactions such as hydrogen bonding, π-π stacking and dipole-dipole interactions. Our group has focused on the design and synthesis of bis-urea macrocycles that can self-assemble into solid cylinders or tubular structures affording crystalline materials. These macrocycles consist of two urea groups and two rigid C-shaped spacers. Easy functionalization of this system enables access to bis-urea macrocycle structures that could serve as molecular reactors, coordinating ligands and co-crystalizing agents.

This dissertation focuses on probing the utility of pyridyl functionalized bis-urea macrocycles as well as expanding applications of the largest self-assembled phenylethynylene bis-urea macrocycle. Chapters 1-3 examine the utilization of a smaller pyridyl bis-urea macrocycle that self-assembles into strong pillars as a co-crystal former for hydrogen/halogen bond donors. In these pillars, the individual macrocycle units are held together by two different hydrogen bonds (N-H····N and N-H····O) where the urea NHs interact with the urea carbonyl oxygen and the pyridine nitrogen. This affords pillars with basic lone pairs on carbonyl oxygen that can be used to absorb guest molecules in the solid-state. Guest binding occurs through non-covalent interactions, which are either hydrogen bonding or halogen bonding. Co-crystals and molecular salts were successfully synthesized from this macrocycle combined with diiodotetrafluorobenzenes or naphthalene-1,5-disulfonic acid respectively (chapter 2-3). These demonstrated the utility of the pyridyl bis-urea macrocycle motif to control the organization and properties of guests by co-crystallization.

To further investigate this idea, we redesigned and successfully synthesized a constitutional isomer of the pyridyl macrocycle that incorporates the pyridyl N on the exterior of the macrocycle. Chapter 5 reports the synthesis of the key protected bis-urea and tris-urea macrocyclic intermediate as well as their crystal structures. We explore the urea protected versions of these new bis-urea and tris-urea macrocycles as ligands to synthesize copper(I) and silver(I) coordination polymers. Two coordination polymers were obtained with protected pyridyl bis-urea macrocyclic ligand 4; [Cu2I2(4)2·(CH3CN)1.63(1)] and [Ag(4)(NO3)(H2O)2.5] as 2D and 3D coordination networks respectively. Initial photoluminescence studies showed that only complex [Cu2I2(4)2·(CH3CN)1.63(1)] exhibit fluorescence properties in the solid state at ambient temperature. In addition, the new pyridyl bis-urea macrocycle was successfully deprotected and crystallized by heating 6.0 mg of it in a DMSO-acetonitrile (1:1.5 v/v) mixture (5 mL) in a pressure tube to dissolve completely at 120 ˚C, then slowly cooled to room temperature at a rate of 1 °C/h. This crystal structure analysis revealed that this redesigned pyridyl bis-urea macrocycle also self-assembles into pillars (columns) using the urea···urea bifurcated hydrogen bonds as shown in Appendix D.

Also, in this dissertation (chapter 4), we investigated the loading of a small dye, 5-(dimethylamino)-5’-nitro-2,2-bithiophene into the 1D channels of our self-assembled phenylethynylene bis-urea macrocyclic host, which has no pyridyl functional groups. These 1D nanochannels have a round cross-section with a diameter of ~9 Å. Here, we were interested in understanding how the guest molecules aligned inside the host channels and the properties of the host-guest complex. The complex was prepared by soaking the crystalline host in an acetonitrile solution of the dye for 24 hours to give a purple solid. This complex was then characterized by 1H NMR, UV-visible absorption and fluorescence emission spectroscopies, and wide-angle X-ray scattering. The organization of the guest was probed using linear polarization fluorescence microscopy and time-dependent density functional theory (TDDFT) calculations at the B3LYP/TZ2P level of theory. The guest fluorescence was shown to be polarized along the fiber axis with emission polarization values up to 0.729, indicating a high degree of orientation within the 1D channels.

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