Publication Date

8-1-2025

Date of Final Oral Examination (Defense)

6-23-2025

Type of Culminating Activity

Dissertation

Degree Title

Doctor of Philosophy in Materials Science and Engineering

Department

Materials Science and Engineering

Supervisory Committee Chair

William B. Knowlton, Ph.D.

Supervisory Committee Co-Chair

Bernard Yurke, Ph.D.

Supervisory Committee Member

John A. Hall, Ph.D.

Supervisory Committee Member

Jeunghoon Lee, Ph.D.

Supervisory Committee Member

Hieu Bui, Ph.D.

Abstract

Molecular excitons have been the subject of significant research interest for nearly 100 years. Molecular excitons arise when conjugated organic molecules (dyes) are excited such that the resulting excitation is delocalized over multiple dyes in a wavelike manner. The shared excited states that allow the excitation energy to hop between molecules is of particular interest for applications that can make use of the wavelike properties of excitons, including applications in quantum information science. A key challenge for developing materials for these advanced applications is to overcome the knowledge gaps associated with precisely templating dyes with spatial control of their aggregation, separation, and orientation, which are critical factors that determine the optical response of a dye network. Deoxyribonucleic acid (DNA) has emerged as a powerful tool to self-assemble nanostructures that enables the incorporation of multitudes of substituents—including dye molecules—that affords fine control of attachments at atomic scales. Although DNA has been used to successfully induce aggregation of dyes—resulting in excitonic coupling and delocalized excitons in groups of dyes (aggregates)—much remains to be learned to gain full control of dye placement and relative orientation. Progress toward advance excitonic materials requires that we explore and understand the behavior and interactions of the dyes, the DNA template, and the interplay between the components of the system (e.g., dye-dye and DNA-dye interactions) that determine the final state of the system and resulting properties. A deep understanding of the system will lead to design rules and considerations that will allow further advances. In this work, two distinct paths are explored that each contribute to the foundational knowledge necessary to advance our understanding of assembling exciton-based materials.

In Chapter 2, the materials system was designed to directly control dye placement and orientation by linking dyes to DNA duplexes with two short linkers to restrict their movement. The dyes were templated in this way—between consecutive nucleosides—along a linear duplex to create aggregates with up to four dyes. Further, the DNA was fortified with synthetic “bridged” nucleic acids that include an additional covalent bridge across the ribose sugar in the DNA backbone that should increase hybridization affinity (and thermal stability) and suppress a degree of freedom of the DNA backbone. This work concluded that the insertion of dyes by two-linker insertion disrupted the stability of the duplex; however, the fortification imparted by the bridged nucleic acids mitigated the instability to some degree.

Chapter 3 explores a different approach to system design. In contrast to restricting dyes via multiple short linkers and fortifying the DNA to be more rigid, in this work the dyes were allowed to explore a much larger volume of space around their attachments enabled by a single—relatively long—flexible linker that enables the dyes to find their most favorable interaction with the DNA template. In this system, the disruption to the DNA caused by including dyes is minimized—relative to the two-linker approach of Chapter 2—by the expansion of the DNA template to include two DNA double helices coupled by two crossover junctions in a double-crossover (DX) tile motif. Beyond the additional stability imparted by the design, the DX tile motif has the added benefit of being well-studied as a modular building block to build up arbitrary structures via “sticky-end” assembly. The modular nature of the tile makes it an ideal platform to design modular components for future excitonic devices.

To this end, a comprehensive system-level approach is presented for templating di-chloro-squaraine (SQ-Cl_2) dyes using the DX tile motif. The analysis included a broad survey of monomer and aggregate designs and proceeded with a deeper look at several constructs of interest. Of particular note was the characterization of novel, double-tile constructs housing strongly coupled dye aggregates and elucidation of the assembly details leading to their formation. Importantly, we observed that dye-dye interactions directly participated in the self-assembly process. In addition to these insights, this work also demonstrated that exciton delocalization—an important behavior for applications of molecular excitons—can be preserved after transfer from liquid to solid phase. This holistic system-level analysis led to a collection of observations, insights, and design rules that will be broadly applicable to develop future DNA-dye systems.

Comments

Simon Roy, ORCID: 0000-0001-8652-1277

DOI

https://doi.org/10.18122/td.2429.boisestate

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