The self-assembly process is governed by the individual constituents of molecules through precise non-covalent interactions. Amphiphilic cyanines are intriguing in supramolecular chemistry due to the large polarizability of their delocalized π-electron systems, their tuneable optical properties and their ability to form well-defined self-assembled structures in different media. Here we present the synthesis of a novel tetrahydroxy amphiphilic carbocyanine dye with perfluoro alkylated chains -(CH2)2-(CF2)5-CF3 as hydrophobic segments and aminoproanediol as hydrophilic segment. The target molecule was synthesized in a multi-step process, which illustrates the complexity and precision required to achieve the desired structure. This study focuses on the comparison of the influence of C8H17 and C8H4F13 tails and the effects of carboxylated and non-ionic aminopropanediol head groups as substituents on self-assembly of the TBC dye. Absorption and fluorescence measurements show similar spectroscopic properties to cyanine dyes studied previously. Cryogenic transmission electron microscopy (cryo-TEM) reveals formation of multiple supramolecular aggregates. As supramolecular assembly is very sensitive to sample preparation, multilamellar or multivesicular vesicles are obtained preferentially in vigorously vortexed solutions. Moreover, time-dependent tube formation was observed in gently mixed solutions. Thereby, we could follow the growing mechanism of the unprecedented Y-junctions of supramolecular tubes.

Synthetic multichromophore systems are of great importance in artificial light harvesting devices, organic optoelectronics, tumor imaging and therapy. Here, we introduce a promising strategy for the construction of self-assembled peptide templated dye stacks based on coupling of a de novo designed pH sensitive peptide with a cyanine dye Cy5 at its N-terminus. Microscopic techniques, in particular cryogenic TEM (cryo-TEM) and cryo-electron tomography technique (cryo-ET), reveal two types of highly ordered three-dimensional assembly structures on the micrometer scale. Unbranched compact layered rods are observed at pH 7.4 and two-dimensional membrane-like assemblies at pH 3.4, both species displaying spectral features of H-aggregates. Molecular dynamics simulations reveal that the coupling of Cy5 moieties promotes the formation of both ultrastructures, whereas the protonation states of acidic and basic amino acid side chains dictates their ultimate three-dimensional organization.

The synthesis of a new amphiphilic 5,5',6,6'-tetrachlorobenzimidacarbocyanine dye derivative with -(CH2)2-(CF2)5-CF3 chains attached to the nitrogen atoms in the 1,1'-position, CF8O3, is reported. Depending on the dye concentration and the addition of MeOH, CF8O3 forms J- and H-aggregates in aqueous solutions. The aggregation behavior was investigated using steady-state absorption, linear dichroism, and fluorescence spectroscopy, as well as by cryogenic transmission electron microscopy (cryo-TEM). The J-band of the MeOH-free solution is monomer-like, rather broad, and less red-shifted with respect to the monomer absorption, indicating weak excitonic coupling and disorder effects. Cryo-TEM reveals a diversity of supramolecular structures, wherein linear and branched cylindrical micelles dominate. It is concluded that the high stiffness of fluoroalkyl chains does not allow the chains to splay and completely fill up the hydrophobic gap between opposing chromophores. This destabilizes the bilayers and favors the micellar structure motifs instead. The aggregates appearing at 30% MeOH show a split absorption spectrum consisting of a broad blue-shifted H-band and an accompanying sharp red-shifted J-band with perpendicular polarizations. These HJ-type aggregates are also composed of micellar fibers, but these bundle into rope-like strands. For 10% MeOH, a narrow bilayered tube is the dominating morphology. The observed MeOH dependence of aggregation reveals a clear cosolvent effect.

The syntheses of novel amphiphilic 5,5 ',6,6 '-tetrachlorobenzimidacarbocyanine (TBC) dye derivatives with aminopropanediol head groups, which only differ in stereochemistry (chiral enantiomers, meso form and conformer), are reported. For the achiral meso form, a new synthetic route towards asymmetric cyanine dyes was established. All compounds form J aggregates in water, the optical properties of which were characterised by means of spectroscopic methods. The supramolecular structure of the aggregates is investigated by means of cryo-transmission electron microscopy, cryo-electron tomography and AFM, revealing extended sheet-like aggregates for chiral enantiomers and nanotubes for the mesomer, respectively, whereas the conformer forms predominately needle-like crystals. The experiments demonstrate that the aggregation behaviour of compounds can be controlled solely by head group stereochemistry, which in the case of enantiomers enables the formation of extended hydrogen-bond chains by the hydroxyl functionalities. In case of the achiral meso form, however, such chains turned out to be sterically excluded.

Infections caused by Staphylococcal and Micrococcal species represent a major public health burden. Although treatments do exist, these tend to be associated with cytotoxic effects; furthermore, the emergence of antimicrobial resistance presents an immediate challenge. New classes of active compounds are required to address these threats to human health. Here we present a de novo peptidomimetic strategy that produces self-assembling cationic antimicrobials. To identify a candidate compound with bactericidal activity, a small library of 8 peptidomimetics comprising ultrashort peptide sequences attached to a 3,5-diaminobenzoic acid scaffold was generated and tested against Micrococcus luteus and Staphylococcus aureus. Self-assembly appears to be the driving force for increased potency, likely by contributing to increased local surface charge density and peptide mass and producing a multivalent effect that enhances electrostatic interactions with negatively charged bacterial membranes, causing membrane disruption. The most active library member C7 forms patched micellar nanoparticles and has an activity higher than that of known natural antimicrobial peptides against M luteus. C7 also shows activity comparable to that of gramicidin S and the standard antibiotic vancomycin used in antibacterial therapy, but with a greater selectivity index. Importantly, C7 is also nontoxic and nonhemolytic, unlike the currently administered vancomycin, which can cause acute renal failure, and gramicidin S, which is highly hemolytic in nature. The short sequence length, ease of design, convenient synthesis strategy, and presence of a substitutable hydrophobic residue that enables self-assembly into different nanostructures make this model compound highly attractive for generating cost-effective, rapid-acting peptide-based antimicrobials.

The adsorption of three different polycations at the negatively charged surface of tubular J-aggregates of the amphiphilic cyanine dye 3,3′-bis(2-sulfopropyl)-5,5′,6,6′-tetrachloro-1,1′-dioctylbenzimidacarbocyanine (C8S3) is investigated by means of cryogenic electron microscopy and optical absorption spectroscopy. All three polycations could be adsorbed at the tubular aggregates without flocculation or precipitation when added in molar amounts of monomers sufficiently smaller than that of the dye molecules. It is found that preferably, a minority of aggregates is coated by the polycations while a majority of aggregates is left uncoated. For the coated aggregates, the adsorption leads to charge reversal of the aggregate surface as supported by zeta potential measurements. The morphology of the coating differs significantly for the three polycations: The branched polycation polyethylenimine (PEI) attaches to the tubular aggregate by hit-and-stick adsorption of the coiled state in solution forming irregular clot-like coatings; the flexible and weakly cationic poly (allylamine hydrochloride) (PAH) forms a more homogeneous coating but destroys the integrity of the dye aggregate; the more hydrophobic and strong polycation poly (diallyldimethylammonium chloride) (PDADMAC) forms a thin and homogeneous layer, supposedly by wrapping around the tubular aggregate. For the latter growth of a second double layer of dyes is observed for the aggregates. The different morphologies of the coating layers are explained by the details of the chemical structure of the polycations. The possible adsorption of polyelectrolytes at these amphiphilic tubular structures, stabilized by means of hydrophobic forces, is far from obvious and demonstrates an applicable route to the build-up of more complex nanostructures in solution by means of a self-assembly process.

Exciton dynamics in a HJ-aggregate of cyanine dye TTBC are investigated by transient absorption with a time resolution of <60 fs and power-dependent emission spectroscopies. Both measurements are consistent with an exciton delocalization length of ~28 monomers. A model assuming diffusive exciton motion reveals that the exciton mobility is at least bimodal and restricted to one spatial dimension. J-band diffusion rates of 2.69 and 2.79e-3 cm2s-1 are found, leading to maximal diffusion lengths of 449 and 14.5 nm. The findings indicate that exciton-exciton annihilation is the origin of effective uphill transfer. This mechanism, if present under solar radiation, maybe useful for organic photovoltaic systems.

X iv :1 50 2. 01 71 7v 2 [p hy si cs .c he m -p h] 1 2 Ju l 2 01 5 Vibronic origin of long-lived coherence in an artificial mol ecular light harvester James Lim1,∗, David Paleček2,3,∗, Felipe Caycedo-Soler1, Craig N. Lincoln4, Javier Prior5, Hans von Berlepsch6, Susana F. Huelga1, Martin B. Plenio1, Donatas Zigmantas2, and Jürgen Hauer4 1 Institut für Theoretische Physik, Albert-Einstein Allee 11, Universität Ulm, 89069 Ulm, Germany 2 Department of Chemical Physics, Lund University, P.O. Box 1 24, SE-22100 Lund, Sweden 3 Department of Chemical Physics, Charles University in Prag ue, Ke Karlovu 3, 121 16 Praha 2, Czech Republic 4 Photonics Institute, Vienna University of Technology, Gus shausstrasse 27, 1040 Vienna, Austria 5 Departamento de Fı́sica Aplicada, Universidad Politécni ca de Cartagena, Cartagena 30202, Spain 6 Forschungszentrum für Elektronenmikroskopie, Institut für Chemie und Biochemie, Freie Universität Berlin, Fabeckstra βe 36a, D-14195 Berlin, Germany ∗ These authors contributed equally to this work.

Amyloid fibrils are polymers formed by proteins under specific conditions and in many cases they are related to pathogenesis, such as Parkinson’s and Alzheimer’s diseases. Their hallmark is the presence of a β-sheet structure. High resolution structural data on these systems as well as information gathered from multiple complementary analytical techniques is needed, from both a fundamental and a pharmaceutical perspective. Here, a previously reported de novo designed, pH-switchable coiled coil-based peptide that undergoes structural transitions resulting in fibril formation under physiological conditions has been exhaustively characterized by transmission electron microscopy (TEM), cryo-TEM, atomic force microscopy (AFM), wide-angle X-ray scattering (WAXS) and solid-state NMR (ssNMR). Overall, a unique 2-dimensional carpet-like assembly composed of large coexisiting ribbon-like, tubular and funnel-like structures with a clearly resolved protofilament substructure is observed. Whereas electron microscopy and scattering data point somewhat more to a hairpin model of β-fibrils, ssNMR data obtained from samples with selectively labelled peptides are in agreement with both, hairpin structures and linear arrangements.

The aggregation behavior of a phenol-substituted thiacarbocyanine Cy5 dye (5-chloro-2-[5-[5-chloro-3-(4-sulfobutyl)-3H-benzothiazol-2-ylidene]-3-phenyl-penta-1,3-dienyl]-3-(4-sulfobutyl)-benzothiazol-3-ium hydroxide, inner salt, triethylammonium salt) in aqueous solution is investigated using steady-state absorption, linear dichroism, and fluorescence spectroscopies, as well as cryogenic transmission electron microscopy (cryo-TEM). By increasing the concentration, the dye self-assembles in pure water into dimers and H-aggregates, the latter being uniform particles of ∼2.6 nm size. In the presence of NaCl, two different types of J-aggregates are observed depending on salt concentration (varied from 10 to 100 mM). At low salt concentration (10 mM) a J-aggregate of extended mono-layered sheets prevails, which disappears after a few days, whereas a second type of J-aggregate emerges. Generally, the latter dominates in matured solutions in particular at high salt concentration and seems to be the thermodynamically stable species. This J-aggregate shows three perpendicularly polarized absorption bands and fluoresces in the far-red at around 800 nm. The most intensive and very narrow (fwhm of 238 cm-1) absorption band is centered at 796 nm. Cryo-TEM reveals uniform nanotubes of ∼7 nm diameter and micrometer length. They represent the first tubular cyanine dye J-aggregates that are active in the far-red. Moreover, the studied dye is a prime example of cyanine dyes showing two self-assembly pathways that lead to different species of J-aggregates with distinct optical and morphological properties.

Chiral head groups have been introduced into water-soluble hydroxyl-terminated nonionic amphiphiles and the impact of the head group stereochemistry on the supramolecular ultrastructures has been studied. Enantiomeric isomers were compared with the achiral meso form and the racemic mixture by means of cryogenic transmission electron microscopy and circular dichroism spectroscopy. Structurally, all amphiphiles are composed of the first-generation hydrophilic polyglycerol head group coupled to a single hydrophobic hexadecyl chain through an amide linkage and diaromatic spacer. The enantiomers aggregate to form twisted ribbons with uniform handedness, whereas the meso stereoisomer and racemic mixture produce elongated assemblies, namely, tubules and platelets, but without a chiral ultrastructure. Simulations on the molecular packing geometries of the stereoisomers indicate different preferential assembly routes that explain the individual supramolecular aggregation behavior.

As is the case in numerous natural processes, enzymatic phosphorylation can be used in the laboratory to influence the conformational populations of proteins. In nature, this information is used for signal transduction or energy transfer, but has also been shown to play an important role in many diseases like tauopathies or diabetes. With the goal of determining the effect of phosphorylation on amyloid fibril formation, we designed a model peptide which combines structural characteristics of α-helical coiled-coils and β-sheets in one sequence. This peptide undergoes a conformational transition from soluble structures into insoluble amyloid fibrils over time and under physiological conditions and contains a recognition motif for PKA (cAMP-dependent protein kinase) that enables enzymatic phosphorylation. We have analyzed the pathway of amyloid formation and the influence of enzymatic phosphorylation on the different states along the conformational transition from random-coil to β-sheet-rich oligomers to protofilaments and on to insoluble amyloid fibrils, and we found a remarkable directing effect from β-sheet-rich structures to unfolded structures in the initial growth phase, in which small oligomers and protofilaments prevail if the peptide is phosphorylated.

Cryogenic transmission electron microscopy (cryo-TEM) studies suggest that TTBC molecules self-assemble in aqueous solution to form single-walled tubes with a diameter of about 35 Å. In order to reveal the arrangement and mutual orientations of the individual molecules in the tube, we combine information from crystal structure data of this dye with a calculation of linear absorbance and linear dichroism spectra and molecular dynamics simulations. We start with wrapping crystal planes in different directions to obtain tubes of suitable diameter. This set of tube models is evaluated by comparing the resulting optical spectra with experimental data. The tubes that can explain the spectra are investigated further by molecular dynamics simulations, including explicit solvent molecules. From the trajectories of the most stable tube models, the short-range ordering of the dye molecules is extracted and the optimization of the structure is iteratively completed. The final structural model is a tube of rings with 6-fold rotational symmetry, where neighboring rings are rotated by 30° and the transition dipole moments of the chromophores form an angle of 74° with respect to the symmetry axis of the tube. This model is in agreement with cryo-TEM images and can explain the optical spectra, consisting of a sharp red-shifted J-band that is polarized parallel to to the symmetry axis of the tube and a broad blue-shifted H-band polarized perpendicular to this axis. The general structure of the homogeneous spectrum of this hybrid HJ-aggregate is described by an analytical model that explains the difference in redistribution of oscillator strength inside the vibrational manifolds of the J- and H-bands and the relative intensities and excitation energies of those bands. In addition to the particular system investigated here, the present methodology can be expected to aid the structure prediction for a wide range of self-assembled dye aggregates.

Natural and artificial light harvesting processes have recently gained new interest. Signatures of long lasting coherence in spectroscopic signals of biological systems have been repeatedly observed, albeit their origin is a matter of ongoing debate, as it is unclear how the loss of coherence due to interaction with the noisy environments in such systems is averted. Here we report experimental and theoretical verification of coherent exciton-vibrational (vibronic) coupling as the origin of long-lasting coherence in an artificial light harvester, a molecular J-aggregate. In this macroscopically aligned tubular system, polarization controlled 2D spectroscopy delivers an uncongested and specific optical response as an ideal foundation for an in-depth theoretical description. We derive analytical expressions that show under which general conditions vibronic coupling leads to prolonged excited-state coherence.

Self-assembling peptides can be used to create tunable higher-order structures for the multivalent presentation of a variety of ligands. We describe a novel, fiber-forming coiled-coil-based peptide that assembles to display, simultaneously, carbohydrate and peptide ligands recognized by biomacromolecules. Preassembly decoration of the scaffold with a diphtheria toxin peptide epitope or a mannose motif did not interfere with self-assembly of the nanostructure. The resulting multivalent display led to tighter binding by antidiphtheria toxin antibodies and mannose-specific carbohydrate binding proteins, respectively. The potential of this self-assembling peptide to display ligands in bioanalytical assays is illustrated by its decoration with a disaccharide glycotope from the Leishmania parasite. Carbohydrate-specific antibodies produced in response to a Leishmania infection are detected more sensitively in human and canine sera due to the multivalent presentation on the self-assembled scaffold. Thus, nanofibers based on coiled-coil peptides are a powerful tool for the development of bioassays and diagnostics.

molecular light harvester James Lim1,∗, David Palecek2,3,∗, Felipe Caycedo-Soler1, Craig N. Lincoln4, Javier Prior5, Hans von Berlepsch6, Susana F. Huelga1, Martin B. Plenio1, Donatas Zigmantas2, and Jurgen Hauer4 1 Institut fur Theoretische Physik, Albert-Einstein Allee 11, Universitat Ulm, 89069 Ulm, Germany 2 Department of Chemical Physics, Lund University, P.O. Box 124, SE-22100 Lund, Sweden 3 Department of Chemical Physics, Charles University in Prague, Ke Karlovu 3, 121 16 Praha 2, Czech Republic 4 Photonics Institute, Vienna University of Technology, Gusshausstrasse 27, 1040 Vienna, Austria 5 Departamento de Fisica Aplicada, Universidad Politecnica de Cartagena, Cartagena 30202, Spain 6 Forschungszentrum fur Elektronenmikroskopie, Institut fur Chemie und Biochemie, Freie Universitat Berlin, Fabeckstraβe 36a, D-14195 Berlin, Germany ∗ These authors contributed equally to this work.

The aggregation behavior of an Indocyanine Cy5 dye (2-[5-[1,1-dimethyl-3-(4-sulfobutyl)-1,3-dihydro-benzo[e]indol-2-ylidene]-penta-1,3-dienyl]-1,1-dimethyl-3-(4-sulfobutyl)-1H-benzo[e]indolium hydroxide, inner salt, sodium salt) in aqueous solution is investigated using absorption and fluorescence spectroscopies, as well as cryogenic transmission electron microscopy (cryo-TEM). The dye concentration is varied within a broad range from ∼1 μM to ∼10 mM. At moderate concentrations, typical H-aggregates are formed. After longer storage time, the absorption spectra of these solutions change dramatically. The characteristic blue-shifted absorption band at around 600 nm becomes replaced by a three-banded absorption spectrum, which spreads over a wide wavelength range of ∼600 up to 800 nm. However, at the highest dye concentration and in the presence of ∼(10 to 30) mM NaCl, the three-banded spectrum is observed directly after preparation. The spectroscopic features can be ascribed to a structural transformation of strongly to weakly coupled H-type aggregates. The transformation is promoted by an increase of the ionic strength. Cryo-TEM data reveal that the weakly coupled H'-aggregates are organized in well-ordered, extended monolayer sheets, whereas the strongly coupled H-aggregates appear to consist of particles of only a few nanometers in size.

Engineering nanostructures of defined size and morphology is a great challenge in the field of self-assembly. Herein we report on the formation of supramolecular nanostructures of defined morphologies with subtle structural changes for a new series of dendritic amphiphiles. Subsequently, we studied their application as nanocarriers for guest molecules.

The aggregation behaviour of the cationic pinacyanol chloride in aqueous solution is investigated using absorption and linear dichroism spectroscopies, optical microscopy and cryogenic transmission electron microscopy (cryo-TEM). The investigations are focused on solutions in a concentration range from 50 μM up to 1 mM. At a concentration of 0.7 mM H-aggregates are detected that are characterized by a broad absorption band centred at ∼511 nm. The aggregates possess a tubular architecture with a single-layer wall thickness of ∼2.5 nm and an outer diameter of ∼6.5 nm. Linear dichroism spectroscopy indicates that the molecules are packed with their long axis parallel to the tube axis. These H-aggregates are not stable, but transform into J-aggregates on the time scale of weeks. The kinetics of J-aggregation depends on the dye concentration and the route of sample preparation, but can also be enhanced by shear stress. J-aggregates possess a split absorption spectrum composed of two longitudinally polarized J-bands and one H-band that is polarized perpendicular to the aggregate axis. The J-aggregates are ∼9 nm wide and several micrometer long fibrils consisting of stacked pairs of ribbons with a dumbbell-shaped density cross-section. Upon aging these ribbons laterally stack face-to-face to form tape-like aggregates.

The self-assembly of amphiphilic molecules into fibrous structures has been the subject of numerous studies over past decades due to various current and promising technical applications. Although very different in their head group chemistry many natural as well as synthetic amphiphilic compounds derived from carbohydrates, carbocyanine dyes, or amino acids tend to form fibrous structures by molecular self-assembly in water predominantly twisted ribbons or tubes. Often a transition between these assembly structures is observed, which is a phenomenon already theoretically approached by Wolfgang Helfrich and still focus point in current research. With the development of suitable sample preparation and electron optical imaging techniques, cryogenic transmission electron microscopy (cryo-TEM) in combination with three-dimensional (3D) reconstruction techniques has become a particular popular direct characterization technique for supramolecular assemblies in general. Here we review the recent progress in deriving precise structural information from cryo-TEM data of particularly fibrous structures preferably in three dimensions.