Complex tissue models aim to recapitulate features of native tissues to model development, disease pathogenesis, and drug treatments. While techniques have been developed to improve the complexity of engineered tissues, it remains challenging to coordinate and spatially control multicellular phenotypes during differentiation processes. The work presented in this thesis describes the coordinated development of engineered cells and materials to enable communication via synthetic notch receptor pathways to control multi-fate differentiation. First, I will highlight the need to incorporate synthetic biology techniques to improve complex tissue engineering. Next, I will demonstrate the methods of engineering cells with synthetic pathways. Following, I will describe the development of a library of synthetic ligand-presenting material substrates with capacity to spatially activate synthetic pathways in 2D and 3D microenvironments. In the next chapter, I summarize how we utilize ligand-patterned substrates to spatially control myogenic and endothelial differentiation in the same culture. Subsequently, I detail our investigations into how substrate mechanical properties influence activation of synthetic receptors. Finally, I present the fabrication of a RNAi dual-gradient hydrogel for interfacial gene silencing of encapsulated cells. This work contributes to improving the complexity of tissue models and therapeutics by enabling engineered microenvironments to directly influence gene expression and control cell phenotypes.

Chemical exchange dynamics are often studied using a Bloch equation analysis of coalescing line shapes in nuclear magnetic resonance spectroscopy (NMR). A similar treatment has been applied to systems exchanging on the infrared (IR) vibrational timescale, where line shape analysis of coalesced FTIR and Raman spectra allow the study of reactions occurring in picoseconds (ps). In practice however, there are comparatively few examples of line shape analysis by vibrational spectra as inhomogeneous broadening, solvent environment fluctuations or other dynamic processes in addition to chemical exchange can contribute to the overall vibrational line shape. This work examines two model systems displaying exchange dynamics on the vibrational timescale and the use of vibrational spectroscopy to describe their ultrafast dynamics. The first system details electron transfer dynamics in dimers of oxo-centered triruthenium clusters that are linked by non-covalent interactions, where we have shown how electron transfer across hydrogen bonds occurs on (or approaches) the vibrational time scale. While these studies have important implications in understanding long range ET in biological systems, the importance of non-covalent interactions also extends throughout the chemical sciences and as they readily affect the stability of artificial supramolecular structures, and selectivity of catalysts. In this dissertation the fundamental relationship between non-covalent molecular interactions and ET is examined to gain new understanding of ET processes occurring across hydrogen bonds. We were also able to show that electron delocalization across hydrogen bonds imparts substantial stability (~5 kcal mol–1) to the hydrogen bonding interaction.

The second system, a penta-coordinate ruthenium dithitene complex seeks to examine vibrational lineshape coalescence and the application of an optical Bloch analysis in systems exhibiting ultrafast dynamics. The ruthenium complex undergoes structural rearrangement between three distinct structural isomers that differed only in the orientation of a carbonyl ligand about the metal center. In methylene chloride, the three isomers 1) square pyramidal equatorial, 2) trigonal bipyramidal, and 3) square pyramidal axial were found to exchange through the meta-stable trigonal bipyriamidal intermediate within picoseconds. This study was a direct validation of the mechanism and timescale of Berry pseudorotation – the pairwise exchange of ligands in a pentacoordinate complex – a process that was described nearly fifty years ago, and to our knowledge, was the first observation of an ultrafast dynamic equilibrium involving two distinct structural isomers and the intermediate connecting them.