This thesis explores fundamental design strategies in the field of synthetic ion channel research from two different perspectives. In the first part the synthesis of complex, shape persistent and thermodynamically stable structures based on metal-ligand self-assembly is explored. The second part examines transport systems with dynamic transport behavior in response to chemical inputs which more closely mimic the dissipative assembly of Natural ion channels. In part one, two model systems, the ethylenediamine palladium(II) - 4,4’-bipyridine squares of Fujita and the trimeric bis(terpyridine) - iron(II) hexagonal macrocycles of Newkome, were targeted for structural modification towards becoming transport competent systems via improving the membrane partitioning characteristics of the final coordination compounds by increasing their lipophilicity. Modifications of the Fujita system involved the generation of two lipophilic 4,4’-bipyridines with addition of lipophilic groups of 13 and 17 carbon long alkyl chains respectively at the 3 and 3’ positions. After pursuing multiple unsuccessful synthetic routes the successful syntheses afforded the final lipophilic 4,4’-bipyridines in overall yields of 19 to 21% over two synthetic steps. Mixtures of the newly generated lipophilic 4,4’-bipyridines with a known lipophilic ethylenediamine palladium(II) “corner” exhibited evidence of self-assembly from NMR spectroscopy experiments however attempts at further characterization by ESI-MS and X-ray crystallography were unproductive. The putative self-assembled structures were inactive in HPTS vesicle assays but showed erratic conductance activity in bilayer clamp experiments. However, the magnitude of the conductance observed was not indicative of the passage of ions through the internal pore of the square complex. Modifications to the Newkome hexagons were aimed at generating overall neutral assemblies with external lipophilic groups. These modifications involved imparting a net -2 charge to the ligand via modifications to the terminal tridentate ligands so that upon coordination to octahedral metal centers in the +2 oxidation state the overall hexagonal complex would be neutrally charged. Two bis-polydentate ligands were generated; a dissymmetric molecule comprising one terpyridine and one dipicolinate tridentate ligand (TERPY-DPA) and a symmetrical molecule comprising two 2,2’-bipyridine-6-carboxylate tridentate ligands (BIPYA-BIPYA). The successful syntheses provided the desired trimethylsilylethyl ester protected compounds in yields of 9.2 and 7.5 % over 6 and 8 total synthetic steps for TERPY-DPA and BIPYA-BIPYA respectively. A new approach to metal-ligand complex formation by concomitant fluoride deprotection and assembly was demonstrated with a monomeric complex. Polymetallic complexes formed with a variety of transition metals based on colorimetric changes but the products were very intractable and resisted full structural or transport characterization. Part two develops a system potentially capable of exhibiting dissipative assembly of active transporters. A library of six thioester containing compounds structurally related to known active oligoester compounds was synthesized. The successful syntheses provided the desired compounds in overall yields of 1.0 to 17.7% over 11 to 13 total synthetic steps. The intramolecular cyclization - truncation and thioester exchange reactions central to the dissipative assembly strategy were explored using a model compound. The full length compounds showed transport activity via the HPTS vesicle assay that was significantly below that of the lead compound. Bilayer clamp experiments however, revealed significant transport activity for both the full length as well as the truncated thiol molecules. In the case of the latter the transport events had exceedingly high conductivity for such a small molecule. This unexpected activity for both the full length and truncated compounds, although different, prevented a full implementation of dissipative assembly of transport. / Graduate / 0490 / 0485 / 0494

This Thesis presents the synthesis, characterization and mechanistic explorations into a series of diphenylacetylene-containing oligoester ion channels. Eighteen final compounds were synthesized and tested for ion transport activity utilizing both vesicle and planar bilayer assays. The oligomers varied in length, hydrophobicity and the nature of the aromatic moiety. Compounds incorporating a modified diphenylacetylene (‘Dip’), or a novel phenyl-extended fluorophore (‘Trip’) were made using a reliable, modular synthesis. The final compounds were prepared in a total of 5 to 11 steps from commercial materials in yields ranging from 10 to 40%. The compounds’ activity varied considerably; both highly active and completely inactive compounds were discovered. The differences in activity are controlled by structure via the influence of structural variables on the aqueous phase aggregation and the ability of the compound to insert into the bilayer membrane. These structure-activity studies uncovered two highly-active ion transporters, HO2C-Hex-Dip-Hex-Hex-OH and –OPO32- (Hex = 6-hydroxyhexanoyl) which exhibited activity almost 10-fold higher than the fully-saturated oligoesters developed in previous work. In some cases, the transport activity is initially high but declines over a period of 20-30 minutes following compound addition. This suggests that the compound slowly transitions to an environment where it cannot form active channels. In the bilayer clamp, a variety of behaviours including highly-conducting openings were observed. An apparent voltage-gated response was exhibited by one of the Trip compounds (HO2C-Trip-G(E3)-OH), a property rarely seen for synthetic ion channels. The Dip and Trip molecules exhibited environment-sensitive fluorescence. The observed Dip excimer-like emission is the second reported instance of this in solution. The Trip compounds are solvatochromic; this property was used to infer their location in the membrane. Partitioning into the membrane was followed by a blue-shifting and increased intensity of the fluorescence emission for both series of compounds. For the Trip isomers, which are significantly more emissive than the Dip molecules, this enhancement in intensity could be visualized by eye. For the Dip oligomers, the excimer emission is a broad band with variable shape and intensity; it is time-dependent under some conditions. The excimer emission has a sub-nanosecond lifetime in homogenous solution that is significantly prolonged in the presence of vesicle bilayers, in which a number of lifetimes could be detected. Both monomer and excimer emissions can be quenched by aqueous copper, the excimer emission is more efficiently quenched than is the monomer. The photophysical characteristics of these molecules allowed for a variety of experiments designed to probe their membrane partitioning and localization behaviours. The results indicate the formation of a complex mixture of interconverting monomeric and aggregate species as the compounds move from water to the bilayer. The slow evolution of the mixture is consistent with the times noted for loss of membrane activity in transport assays. From these data a new model that describes the transport process is proposed. The key feature of this model is that transport must occur via a species that forms quickly upon the mixing of the components. Possible structures of the intermediates formed are discussed. / Graduate

Two classes of ion-channels comprising 22 members were prepared. Three members were linear oligo-esters with terephthalate core designed to span both leaflets of the bilayer; these were prepared in a modular synthesis in three linear steps. 19 half-channels based on cyclodextrins with functionalized primary-rims were prepared by the Huisgen Cu+-catalyzed [3+2]-cyclization; three distinct synthetic protocols were established to be applicable to these substrates. The voltage-clamp experiment was used to characterize the ion transport properties of these 22 compounds as well as 5 oligo-esters previously prepared by solid-phase synthesis. All but two were active in bilayers, with the majority of these compounds showing highly complex conductance activities. Exponentially voltage-dependent currents were observed for two compounds (both terephthalate-derived); exclusive “square-top” activities were observed for one solid-phase–derived compound and one cyclodextrin-based channels; fractal openings were observed for at least two cyclodextrin-based channels. An “activity grid” notation was proposed as an empirical, coarse, but model-free method of treating the complex data. Through an exhaustive analysis of previously published synthetic ion channels, disparate compounds were found to share modes of activity. Supporting software were developed to facilitate the preparation of activity grids from current traces acquired for the aforementioned 27 compounds. Resulting activity grids for individual experiments were collated to generate an activity profile for each compound, from which a structure–activity map was established and could be compared to the literature data. Four core findings emerged. First, the activity grid notation is sufficiently expressive to denote highly complex mixture of activities. Second, systematic application of the notation reduces selection bias in data analysis. Third, many synthetic ion channels share highly sim- ilar activities and suggests the participation of the lipids, water, and ions in pore-formation. Lastly, the cyclodextrin half-channels are generally membrane active, and their activities are clearly modulated by structural variations. / Graduate