In this study, we describe synthesis, characterization, and zipper assembly of yellow p-oligophenyl naphthalenediimide (POP-NDI) donor−acceptor hybrids. Moreover, we disclose, for the first time, results from the functional comparison of zipper and layer-by-layer (LBL) assembly as well as quartz crystal microbalance (QCM), atomic force microscopy (AFM), and molecular modeling data on zipper assembly. Compared to the previously reported blue and red NDIs, yellow NDIs are more π-acidic, easier to reduce, and harder to oxidize. The optoelectronic matching achieved in yellow POP-NDIs is reflected in quantitative and long-lived photoinduced charge separation, comparable to their red and much better than their blue counterparts. The direct comparison of zipper and LBL assemblies reveals that yellow zippers generate more photocurrent than blue zippers as well as LBL photosystems. Continuing linear growth found in QCM measurements demonstrates that photocurrent saturation at the critical assembly thickness occurs because more charges start to recombine before reaching the electrodes and not because of discontinued assembly. The found characteristics, such as significant critical thickness, strong photocurrents, large fill factors, and, according to AFM images, smooth surfaces, are important for optoelectronic performance and support the existence of highly ordered architectures.

The excited-state dynamics of biotin–spacer–Lucifer-Yellow (LY)constructs bound to avidin (Avi) and streptavidin (Sav) was investigatedusing femtosecond spectroscopy. Two different locations in the proteins,identified by molecular dynamics simulations of Sav, namely the entrance of the binding pocket andthe protein surface, were probed by varying the length of thespacer. A reduction of the excited-state lifetime, stronger inSav than in Avi, was observed with the long spacer construct.Transient absorption measurements show that this effect originatesfrom an electron transfer quenching of LY, most probablyby a nearby tryptophan residue. The local environment of theLY chromophore could be probed by measuring the time-dependent polarisation anisotropy and Stokes shift of the fluorescence. Substantial differences in both dynamics were observed.The fluorescence anisotropy decays analysed by using thewobbling-in-a-cone model reveal a much more constrained environment of the chromophore with the short spacer. Moreover, the dynamic Stokes shift is multiphasic in all cases, with a~ 1 ps component that can be ascribed to diffusive motion ofbulk-like water molecules, and with slower components withtime constants varying not only with the spacer, but with theprotein as well. These slow components, which depend strongly on the local environment of the probe, are ascribed to themotion of the hydration layer coupled to the conformationaldynamics of the protein.

The objective with synthetic multifunctional nanoarchitecture is to create large suprastructures with interesting functions. For this purpose, lipid bilayer membranes or conducting surfaces have been used as platforms and rigid-rod molecules as shape-persistent scaffolds. Examples for functions obtained by this approach include pores that can act as multicomponent sensors in complex matrices or rigid-rod π-stack architecture for artificial photosynthesis and photovoltaics.

Rigid p-octiphenyl rods were used to create helical tetrameric π-stacks of blue, red-fluorescent naphthalene diimides that can span lipid bilayer membranes. In lipid vesicles containing quinone as electron acceptors and surrounded by ethylenediaminetetraacetic acid as hole acceptors, transmembrane proton gradients arose through quinone reduction upon excitation with visible light. Quantitative ultrafast and relatively long-lived charge separation was confirmed as the origin of photosynthetic activity by femtosecond fluorescence and transient absorption spectroscopy. Supramolecular self-organization was essential in that photoactivity was lost upon rod shortening (from p-octiphenyl to biphenyl) and chromophore expansion (from naphthalene diimide to perylene diimide). Ligand intercalation transformed the photoactive scaffolds into ion channels.

The lessons learned from p-octiphenyl β-barrel pores are applied to the rational design of synthetic multifunctional pore 1 that is unstable but inert, two characteristics proposed to be ideal for practical applications. Nonlinear dependence on monomer concentration provided direct evidence that pore 1 is tetrameric (n = 4.0), unstable, and “invisible,â€� i.e., incompatible with structural studies by conventional methods. The long lifetime of high-conductance single pores in planar bilayers demonstrated that rigid-rod β-barrel 1 is inert and large (d ≈ 12 Ã…). Multifunctionality of rigid-rod β-barrel 1 was confirmed by adaptable blockage of pore host 1 with representative guests in planar (8-hydroxy-1,3,6-pyrenetrisulfonate, K_D = 190 μM, n = 4.9) and spherical bilayers (poly-l-glutamate, K_D ≤ 105 nM, n = 1.0; adenosine triphosphate, K_D = 240 μM, n = 2.0) and saturation kinetics for the esterolysis of a representative substrate (8-acetoxy-1,3,6-pyrenetrisulfonate, K_M = 0.6 μM). The thermodynamic instability of rigid-rod β-barrel 1 provided unprecedented access to experimental evidence for supramolecular catalysis (n = 3.7). Comparison of the obtained k_cat = 0.03 min^-1 with the k_cat ≈ 0.18 min^-1 for stable analogues gave a global K_D ≈ 39 μM³ for supramolecular catalyst 1 with a monomer/barrel ratio ≈ 20 under experimental conditions. The demonstrated “invisibilityâ€� of supramolecular multifunctionality identified molecular modeling as an attractive method to secure otherwise elusive insights into structure. The first molecular mechanics modeling (MacroModel, MMFF94) of multifunctional rigid-rod β-barrel pore hosts 1 with internal 1,3,6-pyrenetrisulfonate guests is reported.