A dual-mode aggregative host:guest indicator displacement sensing system has been created for the detection of trimethylated peptides and determination of histone demethylase activity. The combination of selective recognition of suitably sized trimethylammonium salts and reversible lipophilic aggregation of the host:guest complex provides a unique quenching mechanism that is not only dependent on affinity for sensitivity but the lipophilicity of the indicator. In addition, aggregation can be controlled by the application of chaotropic anions in the mixture, allowing a second level of discrimination between hard lysine groups and softer trimethyllysines.

Selective area atomic layer deposition (SA-ALD) offers the potential to replace a lithography step and provide a significant advantage to mitigate pattern errors and relax design rules in semiconductor fabrication. One class of materials that shows promise to enable this selective deposition process are self-assembled monolayers (SAMs). In an effort to more completely understand the ability of these materials to function as barriers for ALD processes and their failure mechanism, a series of SAM derivatives were synthesized and their structureproperty relationship explored. These materials incorporate different side group functionalities and were evaluated in the deposition of a sacrificial etch mask. Monolayers with weak supramolecular interactions between components (for example, van der Waals) were found to direct a selective deposition, though they exhibit significant defectivity at and below 100 nm feature sizes. The incorporation of stronger noncovalent supramolecular interacting groups in the monolayer design, such as hydrogen bonding units or pi–pi interactions, did not produce an added benefit over the weaker interacting components. Incorporation of reactive moieties in the monolayer component that enabled the polymerization of an SAM surface, however, provided a more effective barrier, greatly reducing the number and types of defects observed in the selectively deposited ALD film. These reactive monolayers enabled the selective deposition of a film with critical dimensions as low as 15 nm. It was also found that the selectively deposited film functioned as an effective barrier for isotropic etch chemistries, allowing the selective removal of a metal without affecting the surrounding surface. This work enables selective area ALD as a technology through (1) the development of a material that dramatically reduces defectivity and (2) the demonstrated use of the selectively deposited film as an etch mask and its subsequent removal under mild conditions.

Arrayed deep cavitands can be coupled to a fluorescence-based supramolecular tandem assay that allows site-selective in situ monitoring of post-translational modifications catalyzed by the lysine methyltransferase PRDM9 or the lysine demethylase JMJD2E. An arrayed sensor system containing only three cavitand components can detect the specific substrates of enzyme modification, in the presence of other histone peptides in the enzyme assay, enabling investigation of cross-reactivity over multiple methylation sites and interference from non-substrate peptides.

Arrayed, self-folding deep cavitands form a fluorescence displacement assay system for the site-selective sensing of post-translationally modified (PTM) histone peptides.

A simple three component array of host-fluorophore complexes is capable of sensitive and selective discrimination of heavy metal ions, including lanthanide and actinide salts in aqueous solution. Instead of applying optical sensors that only use "single-mode" detection, i.e., coordination of the metal to a specific ligand and monitoring the change in emission of an appended fluorophore, we exploit a series of host-fluorophore complexes that are affected by the presence of small amounts of metal ions in aqueous solution in different ways. Variable host-metal and host-guest-metal interactions lead to both turn-on and turn-off fluorescence sensing mechanisms, enhancing the discriminatory properties of the array. The limit of detection for certain metals is as low as 70 nM, and highly similar metals such as lanthanides and actinides can be easily distinguished at low micromolar concentrations in complex salt mixtures.

A reactive molecular dynamics approach is used to simulate cross-linking of acrylate polymer networks. By employing the same force field and reactive scheme and studying three representative multifunctional acrylate monomers, we isolate the importance of the nonreactive moieties within these model monomers. Analyses of reactive trajectories benchmark the estimated gel points, cyclomatic character, and spatially resolved cross-linking tendencies of the acrylates as a function of conversion. These insights into the similarities and differences of the polymerization and resulting networks suggest molecular mechanics as a useful tool in the rational design of photopolymerization resins.

Cavitands can be smoothly derivatized by CuAAC chemistry to incorporate ligand species at the upper rim. These species can coordinate metal species in a number of different conformations, leading to self-assembly. The metal-coordination confers water solubility on the cavitands, and the iron-bound species are capable of catalytic C – H oxidations of fluorene under mild conditions.

A deep cavitand is used to encapsulate the aromatic molecule pyrene in its interior while also binding Tl ions with its terminal carboxylates. Steady-state and time-resolved spectroscopic experiments, along with quantum yield measurements, quantify the enhancements of intersystem crossing and room temperature phosphorescence due to cavitand encapsulation. These results are compared to those obtained for pyrene contained in sodium dodecyl sulfate micelles, which is the usual system used to generate room temperature phosphorescence. The combination of selective binding and strong Tl recognition by the cavitand enhances the intersystem crossing and decreases the phosphorescence radiative lifetime from ∼30 to 0.23 s. The cavitand also decreases the rate of O quenching by a factor of 100. Together, these factors can boost the room temperature phosphorescence signal by several orders of magnitude, allowing it to be detected in water without O removal. Host:guest recognition provides a route to molecular-scale triplet emitters that can function under ambient conditions.