Fluorescence quantum yields of dye aggregates: a showcase example based on self-assembled perylene bisimide dimers.

Constituting an intermediate state of matter between molecules and solid state materials, dye aggregates can give important insights into functional properties. Despite the importance of fluorescence for many applications, it turns out that the conventional methods for quantum yield determination are not applicable to dye aggregates and so far no method has been introduced for the accurate determination of the fluorescence quantum yields of dye aggregates. Here we suggest two measurement routines for the quantum yield determination of strongly absorbing dye aggregates. Both methods provide the quantum yield of the aggregated species without the necessity of reaching a fully aggregated state, which is particularly important for the most common case imparted by the low association constants of π-π-stacking interactions. The routines are experimentally validated with two perylene bisimide dyes whose self-assembly is driven by the concerted interplay of hydrogen bonding and π-π-stacking interactions, leading to structurally well defined co-facially stacked dimers at intermediate concentrations and a further growth into larger H-aggregates at a higher concentration. Compared to other H-aggregates relatively high fluorescence quantum yields of up to 28% are found for both the co-facially stacked dimers and the larger H-aggregates.

Anti-cooperative supramolecular polymerization: a new K2-K model applied to the self-assembly of perylene bisimide dye proceeding via well-defined hydrogen-bonded dimers.

A perylene bisimide dye bearing amide functionalities at the imide positions derived from amino acid l-alanine and a dialkoxy-substituted benzyl amine self-assembles into tightly bound dimers by π-π-stacking and hydrogen bonding in chloroform. In less polar or unpolar solvents like toluene and methylcyclohexane, and in their mixtures, these dimers further self-assemble into extended oligomeric aggregates in an anti-cooperative process in which even numbered aggregates are highly favoured. The stepwise transition from dimers into oligomers can not be properly described by conventional K2-K model, and thus a new K2-K aggregation model has been developed, which interpretes the present anti-cooperative supramolecular polymerization more appropriately. The newly developed K2-K model will be useful to describe self-assembly processes of a plethora of other π-conjugated molecules that are characterized by a favored dimer species.

Sensing of Double-Stranded DNA/RNA Secondary Structures by Water Soluble Homochiral Perylene Bisimide Dyes.

A broad series of homochiral perylene bisimide (PBI) dyes were synthesized that are appended with amino acids and cationic side chains at the imide positions. Self-assembly behavior of these ionic PBIs has been studied in aqueous media by UV/Vis spectroscopy, revealing formation of excitonically coupled H-type aggregates. The interactions of these ionic PBIs with different ds-DNA and ds-RNA have been explored by thermal denaturation, fluorimetric titration and circular dichroism (CD) experiments. These PBIs strongly stabilized ds-DNA/RNA against thermal denaturation as revealed by high melting temperatures of the formed PBI/polynucleotide complexes. Fluorimetric titrations showed that these PBIs bind to ds-DNA/RNA with high binding constants depending on the number of the positive charges in the side chains. Thus, spermine-containing PBIs with six positive charges each showed higher binding constants (logKs =9.2-9.8) than their dioxa analogues (logKs =6.5-7.9) having two positive charges each. Induced circular dichroism (ICD) of PBI assemblies created within DNA/RNA grooves was observed. These ICD profiles are strongly dependent on the steric demand of the chiral substituents of the amino acid units and the secondary structure of the DNA or RNA. The observed ICD effects can be explained by non-covalent binding of excitonically coupled PBI dimer aggregates into the minor groove of DNA and major groove of RNA which is further supported by molecular modeling studies.

Evidence for kinetic nucleation in helical nanofiber formation directed by chiral solvent for a perylene bisimide organogelator.

The self-assembly behavior of an achiral perylene bisimide (PBI) organogelator that bears two 3,4,5-tridodecyloxybenzoylaminoethyl substituents at the imide positions has been investigated in chiral solvents (R)- and (S)-limonene in great detail by circular dichroism (CD) spectroscopy and atomic force microscopy (AFM). CD spectroscopic studies on dilute solutions revealed a preferential population of one-handed helical assemblies in chiral solvent with an enantiomeric excess close to 100 %, whereas AFM images of more than 100 nanofibers of the organogel obtained from more concentrated solutions were found to consist of both handed helices with an enantiomeric excess of only 20 %. This discrepancy is attributed to the fast gelation process at high dye concentration that evidently proceeds through non-equilibrated nuclei in a kinetic rather than thermodynamic self-assembly process. Under these conditions the chiral induction from the homochiral solvent may not be adequate in effectively populating only one-handed helices.