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The past 20 years have witnessed a renaissance of dye chemistry, moving from traditional colorant research toward functional materials. Different from traditional colorant research, the properties of functional materials are governed extensively by intermolecular interactions, thereby entailing significant limitations to the classical approach based on molecular structure-molecular property (color, emission, redox properties, etc.) relationships for the respective dye molecules. However, as discussed in this Perspective, such an approach can be pursued for dye aggregates, and in many cases already well-tailored dimers are sufficient to understand the influence of supramolecular organization on the functional properties of ground and photoexcited states. Illustrative examples will be given for exciton coupling and charge-transfer coupling and how these properties relate to desirable functions such as fluorescence, symmetry-breaking charge separation, and singlet fission in molecular aggregates. While the progress in this research so far mostly originated from studies on well-defined folded and self-assembled structures composed of only two dye molecules, future work will have to advance toward larger oligomers of specific size and geometry. Furthermore, future experimental studies should be guided to a larger extent by theoretical predictions that may be supported by machine learning algorithms and new concepts from artificial intelligence. Beyond already pursued calculations of potential energy landscapes, we suggest the development of theoretical approaches that identify the most desirable dye aggregate structures for a particular property on functional energy landscapes.

Summary In this study, the optical properties and excited-state dynamics of the unique self-assembled donor-acceptor (DA) merocyanine dye stacks from dimer up to octamer, prepared via dipole-dipole interactions, are reported in terms of coherent exciton dynamics and formation of an excimer-like state. Our findings are based on the steady-state absorption/emission, time-resolved fluorescence, and transient absorption (anisotropy) measurements, including wavepacket analysis and quantum mechanical calculations. Coherent exciton of torsional motions-restricted dye stacks rapidly localizes into the weakly emissive excimer-like state, by shortening the inter-moiety distance and changing the bond-length alternation pattern. The inner merocyanine moiety, having two neighboring units, has a reversed resonance character (non-polar (N) Z) in the ground state. This difference has led to two conclusions: (1) tetramers and octamers exhibit different features of excimer-like state than the dimer, and (2) octamers exhibit slower localization dynamics due to the enhanced homogeneity (six inner-moieties) compared with tetramers (two inner moieties).

A series of well-defined chromophore stacks is obtained upon self-assembly of merocyanine and bis(merocyanine) dyes in nonpolar solvents. Careful design of the spacer moieties linking the dipolar chromophores within the bis(merocyanine) dyes allows one to direct the dipole-dipole interaction driven aggregation into stacks of desired size from dimer up to octamer. The spacer-encoded self-assembly process was investigated by UV/vis absorption spectroscopy showing an increase of the hypsochromic shift with increasing stack size. The structure of the largest aggregate comprising eight chromophores was analyzed by 1D and 2D nuclear magnetic resonance spectroscopic studies revealing a perfectly interdigitated centrosymmetric organization of the dipolar dyes and concomitant annihilation of the ground state dipole moment is observed in the UV/vis absorption spectra. This unprecedented series of dye stacks from dimer to octamer enabled a systematic study of the optical absorption properties in dependence of the stack size disclosing that the absorption features can be rationalized by molecular exciton theory. Our results show that the noncovalent synthesis approach based on dipolar aggregation is suitable for the design of well-defined dye aggregates of specific size, allowing in-depth studies to manifest structure-property relationships.

Exciton coupling between different types of chromophores has been rarely investigated. Herein, a systematic study on the exciton coupling between merocyanine chromophores of different conjugation length with varying excited state energies is presented. In this work well-defined hetero-dimer stacks were obtained upon folding of bis(merocyanine) dyes in nonpolar solvents. They show distinctly different absorption properties in comparison with the spectra of the single chromophores, revealing a significant coupling between the different chromophores. The simulated absorption spectra obtained from time-dependent density functional theory (TD-DFT) calculations are in good agreement with the experimental spectra. Our theoretical analysis based on an extension of Kasha's exciton theory discloses strong coupling between the dyes' transition dipole moments despite of an excited-state energy difference of 0.60 eV between the chromophores.

A series of three bis(merocyanine) dyes comprising chromophores of different conjugation lengths has been synthesized and the intramolecular aggregation process was investigated by UV/Vis absorption spectroscopy. The spectral changes observed upon variation of the solvent polarity reveal a folding process resulting in a cofacial π-stack of two chromophores with a decrease of the aggregation tendency with increasing chromophore length and solvent polarity. Solvent-dependent UV/Vis studies of the monomeric reference dyes show a significant increase of the polyene-like character for dyes with longer polymethine chains in nonpolar solvents, which is reversed upon aggregation due to the polarizability effect of the adjacent chromophore within the dye stack. The pronounced hypsochromic shift of the absorption band observed upon aggregation indicates strong coupling of the dyes' transition dipole moments, which was confirmed by quantum-chemical analysis.

JAM-A belongs to a family of immunoglobulin-like proteins called junctional adhesion molecules (JAMs) that localize at epithelial and endothelial intercellular tight junctions. JAM-A is also expressed on dendritic cells, neutrophils, and platelets. Homophilic JAM-A interactions play an important role in regulating paracellular permeability and leukocyte transmigration across epithelial monolayers and endothelial cell junctions, respectively. In addition, JAM-A is a receptor for the reovirus attachment protein, sigma1. In this study, we used single molecular force spectroscopy to compare the kinetics of JAM-A interactions with itself and sigma1. A chimeric murine JAM-A/Fc fusion protein and the purified sigma1 head domain were used to probe murine L929 cells, which express JAM-A and are susceptible to reovirus infection. The bond half-life (t(1/2)) of homophilic JAM-A interactions was found to be shorter (k(off)(o) = 0.688 +/- 0.349 s(-1)) than that of sigma1/JAM-A interactions (k(off)(o) = 0.067 +/- 0.041 s(-1)). These results are in accordance with the physiological functions of JAM-A and sigma1. A short bond lifetime imparts a highly dynamic nature to homophilic JAM-A interactions for regulating tight junction permeability while stable interactions between sigma1 and JAM-A likely anchor the virus to the cell surface and facilitate viral entry.

Two identical or different merocyanine dyes were tethered by a rigid diphenylacetylene spacer unit that enables the folding of the two dyes into co-facially π-stacked structures in solvents of low polarity. Whilst the solvent-dependent absorption spectra of homodimers of identical dyes are easily interpreted as H-aggregates by exciton theory, the spectra of the heterodimers constitute a novel and more interesting case.

Reovirus attachment protein σ1 mediates engagement of receptors on the surface of target cells and undergoes dramatic conformational rearrangements during viral disassembly in the endocytic pathway. The σ1 protein is a filamentous, trimeric molecule with a globular β-barrel head domain. An unusual cluster of aspartic acid residues sandwiched between hydrophobic tyrosines is located at the σ1 subunit interface. A 1.75-A structure of the σ1 head domain now reveals two water molecules at the subunit interface that are held strictly in position and interact with neighboring residues. Structural and biochemical analyses of mutants affecting the aspartic acid sandwich indicate that these residues and the corresponding chelated water molecules act as a plug to block the free flow of solvent and stabilize the trimer. This arrangement of residues at the σ1 head trimer interface illustrates a new protein design motif that may confer conformational mobility during cell entry.

We have synthesized a large series of bis(merocyanine) dyes with varying spacer unit and investigated in detail their self-organization behavior by concentration- as well as solvent-dependent UV/Vis spectroscopy. Our in-depth studies have shown that the self-organization of the present bis(merocyanine) dyes is subtly influenced by the nature of the spacer unit. The utilization of rigid spacers results in the formation of self-associated bimolecular complexes with high binding strength, while flexible spacers drive the respective bichromophoric dyes to intramolecular folding. Our thorough investigations on the impact of alkyl spacer chain length on the folding tendency of the present series of bis(merocyanine) dyes revealed a biphasic behavior, that is, a steep increase of the folding tendency for the dyes containing C4 to C7 chains and then a gentle decrease for dyes with longer alkyl spacer chains as evidenced by free energy (ΔG) values for the folding of these dyes. Furthermore, analyses of aggregates' optical properties based on exciton theory as well as quantum chemical calculations suggest a bimolecular aggregate structure for the dye possessing a rigid spacer and a rotationally twisted pleated structure for the bis(merocyanine) dyes having spacer units with less than seven carbon atoms, while the application of longer alkyl chain linkers (≥C7) provides enough flexibility to orient the chromophores in electrostatically most favored antiparallel fashion.

International audience; [small alpha],[small omega]-Bis(dicyanovinyl)quaterthiophene 1 with a median 4,4-diethyl-4H-cyclopenta[2,1-b:3,4-b[prime or minute]]dithiophene has been synthesized. UV-Vis absorption data show that the covalent bridging of the inner 2,2[prime or minute]-bithiophene leads to a significant reduction of the HOMO-LUMO gap essentially due to an increase of the HOMO level as confirmed by electrochemical and theoretical results. X-ray diffraction analysis of a single crystal of 1 shows that except for the out-of-plane ethyl groups, the conjugated system displays a quasi-planar geometry while the molecular packing exhibits strong [small pi]-stacking interactions and multiple short intermolecular contacts. Quaterthiophene 1 has been used as active donor material in organic solar cells of various architectures including bi-layer planar hetero-junctions and hybrid co-evaporated bulk hetero-junctions with C60 as electron acceptor material. A maximum conversion efficiency of 4.30% is obtained with a hybrid co-evaporated device. These results are discussed in terms of structure-properties relationships with reference to the open-chain parent [small alpha],[small omega]-bis(dicyanovinyl)quaterthiophene 2.

International audience

We have synthesized a series of dipolar squaraine dyes that contain dicyanovinyl groups as acceptor and benzannulated five-membered ring heterocycles with alkyl chains of varied length as donor moieties. Based on these squaraines, thin-film transistors (TFT) were fabricated by spin coating and solution shearing. Moreover, with one of these squaraine derivatives vacuum-deposited TFTs were prepared as well. Our detailed studies revealed that the transistor performance of the present series of squaraines is strongly dependent on their structural features as well as on the processing method of thin films. Thus, solution-sheared OTFTs of selenium squaraine bearing dodecyl substituents (denoted as Se-SQ-C12) performed best with a maximum hole mobility of 0.45 cm(2) V(-1) s(-1), which is by far the highest value yet reported for OTFTs based on squaraines. This value was even surpassed by vacuum-deposited thin films of n-butyl-substituted selenium squaraine Se-SQ-C4, the only sublimable compound in this series, exhibiting a record hole mobility of 1.3 cm(2) V(-1) s(-1). Furthermore, we have investigated the morphology of the thin films and the molecular packing of these squaraine dyes by optical spectroscopy, atomic force microscopy, and X-ray diffraction. These studies revealed a relationship between the molecular structure, packing motif, thin-film morphology, and transistor performance of the squaraine dyes. From the supramolecular point of view two packing features discovered in the single crystal structure of Se-SQ-C8 are of particular interest with regard to the structure-functionality relationship: The first is the slipped and antiparallel π-stacking motif which ensures cancellation of the molecules' dipole moments and J-type absorption band formation in thin films. The second is the presence of CN···Se noncovalent bonds which show similarities to the more common halogen-bonding interactions and which interconnect the individual one-dimensional slipped π-stacks, thus leading to two-dimensional percolation pathways along the source-drain direction.

International audience; A comprehensive experimental study is reported on the optical and electrical characteristics of 2-((5-(4-(diphenylamino)phenyl)thiophen-2-yl)methylene)malononitrile (DPTMM) when used as molecular donor in an organic solar cell (OSC) device structure. A major property of this new donor-type material is an unusually deep highest-occupied molecular orbital (HOMO) level that leads to a high open-circuit voltage (Voc). A reasonably high hole-mobility was also observed in a hole-injection diode configuration. These are both promising factors for high-performance OSCs. In order to fully explore the potential of DPTMM in bulk-heterojunction-based OSCs, a step-wise experimental strategy was applied to optimize film composition and cell architecture. By co-evaporating the DPTMM with C60 to promote exciton dissociation by maximizing the heterojunction area power conversion efficiency (PCE) of 3.0% was achieved. Finally, inserting a buffer layer and a spatial gradient of the donor/acceptor ratio was found to provide better conduction paths for charge carriers. The maximum obtained PCE was 4.0%, which compares favorably with the state-of-the-art of high-performance OSCs. All optimized devices show quite unusual high Voc values up to 1 V.

Transglutaminases (TGases) are ubiquitous enzymes that catalyze selective cross-linking between protein-bound glutamine and lysine residues; the resulting isopeptide bond confers high resistance to proteolysis. Phytophthora sojae, a pathogen of soybean, secretes a Ca(2+)-dependent TGase (GP42) that is activating defense responses in both host and non-host plants. A GP42 fragment of 13 amino acids, termed Pep-13, was shown to be absolutely indispensable for both TGase and elicitor activity. GP42 does not share significant primary sequence similarity with known TGases from mammals or bacteria. This suggests that GP42 has evolved novel structural and catalytic features to support enzymatic activity. We have solved the crystal structure of the catalytically inactive point mutant GP42 (C290S) at 2.95 Å resolution and identified residues involved in catalysis by mutational analysis. The protein comprises three domains that assemble into an elongated structure. Although GP42 has no structural homolog, its core region displays significant similarity to the catalytic core of the Mac-1 cysteine protease from Group A Streptococcus, a member of the papain-like superfamily of cysteine proteases. Proteins that are taxonomically related to GP42 are only present in plant pathogenic oomycetes belonging to the order of the Peronosporales (e.g. Phytophthora, Hyaloperonospora, and Pythium spp.) and in marine Vibrio bacteria. This suggests that a lateral gene transfer event may have occurred between bacteria and oomycetes. Our results offer a basis to design and use highly specific inhibitors of the GP42-like TGase family that may impair the growth of important oomycete and bacterial pathogens.

Mammalian orthoreoviruses (reoviruses) are prototype members of the Reoviridae family of nonenveloped viruses. Reoviruses contain ten double-stranded RNA gene segments enclosed in two concentric protein shells, outer capsid and core. These viruses serve as a versatile experimental system for studies of virus cell entry, innate immunity, and organ-specific disease. Reoviruses engage cells by binding to cell-surface carbohydrates and the immunoglobulin superfamily member, junctional adhesion molecule-A (JAM-A). JAM-A is a homodimer formed by extensive contacts between its N-terminal immunoglobulin-like domains. Reo-virus attachment protein σ1 disrupts the JAM-A dimer, engaging a single JAM-A molecule by virtually the same interface used for JAM-A homodimerization. Following attachment to JAM-A and carbohydrate, reovirus internalization is promoted by β1 integrins, most likely via clathrin-dependent endocytosis. In the endocytic compartment, reovirus outer-capsid protein σ3 is removed by cathepsin proteases, which exposes the viral membrane-penetration protein, μ1. Proteolytic processing and conformational rearrangements of μ1 mediate endosomal membrane rupture and delivery of transcriptionally active reovirus core particles into the host cell cytoplasm. These events also allow the ϕ cleavage fragment of μ1 to escape into the cytoplasm where it activates NF-κB and elicits apoptosis. This review will focus on mechanisms of reovirus cell entry and activation of innate immune response signaling pathways.

Junctional adhesion molecule-A (JAM-A) serves as a serotype-independent receptor for mammalian orthoreoviruses (reoviruses). The membrane-distal immunoglobulin-like D1 domain of JAM-A is required for homodimerization and binding to reovirus attachment protein sigma1. We employed a structure-guided mutational analysis of the JAM-A dimer interface to identify determinants of reovirus binding. We purified mutant JAM-A ectodomains for solution-phase and surface plasmon resonance binding studies and expressed mutant forms of full-length JAM-A in Chinese hamster ovary cells to assess reovirus binding and infectivity. Mutation of residues in the JAM-A dimer interface that participate in salt-bridge or hydrogen-bond interactions with apposing JAM-A monomers abolishes the capacity of JAM-A to form dimers. JAM-A mutants incapable of dimer formation form complexes with the sigma1 head that are indistinguishable from wild-type JAM-A-sigma1 head complexes, indicating that sigma1 binds to JAM-A monomers. Residues Glu(61) and Lys(63) of beta-strand C and Leu(72) of beta-strand C' in the dimer interface are required for efficient JAM-A engagement of strain type 3 Dearing sigma1. Mutation of neighboring residues alters the kinetics of the sigma1-JAM-A binding interaction. Prototype reovirus strains type 1 Lang and type 2 Jones share similar, although not identical, binding requirements with type 3 Dearing. These results indicate that reovirus engages JAM-A monomers via residues found mainly on beta-strands C and C' of the dimer interface and raise the possibility that the distinct disease phenotypes produced in mice following infection with different strains of reovirus are in part attributable to differences in contacts with JAM-A.

Reovirus attachment protein sigma1 mediates engagement of receptors on the surface of target cells and undergoes dramatic conformational rearrangements during viral disassembly in the endocytic pathway. The sigma1 protein is a filamentous, trimeric molecule with a globular beta-barrel head domain. An unusual cluster of aspartic acid residues sandwiched between hydrophobic tyrosines is located at the sigma1 subunit interface. A 1.75-A structure of the sigma1 head domain now reveals two water molecules at the subunit interface that are held strictly in position and interact with neighboring residues. Structural and biochemical analyses of mutants affecting the aspartic acid sandwich indicate that these residues and the corresponding chelated water molecules act as a plug to block the free flow of solvent and stabilize the trimer. This arrangement of residues at the sigma1 head trimer interface illustrates a new protein design motif that may confer conformational mobility during cell entry.