Assembly Of Chromophores Research Articles

A dynamic supramolecular polymer with stimuli-responsive handedness for in situ probing of enzymatic ATP hydrolysis.

Design of artificial systems, which can respond to fluctuations in concentration of adenosine phosphates (APs), can be useful in understanding various biological processes. Helical assemblies of chromophores, which dynamically respond to such changes, can provide real-time chiroptical readout of various chemical transformations. Towards this concept, here we present a supramolecular helix of achiral chromophores, which shows chiral APs responsive tunable handedness along with dynamically switchable helicity. This system, composing of naphthalenediimides with phosphate recognition unit, shows opposite handedness on binding with ATP compared with ADP or AMP, which is comprehensively analysed with molecular dynamic simulations. Such differential signalling along with stimuli-dependent fast stereomutations have been capitalized to probe the reaction kinetics of enzymatic ATP hydrolysis. Detailed chiroptical analyses provide mechanistic insights into the enzymatic hydrolysis and various intermediate steps. Thus, a unique dynamic helical assembly to monitor the real-time reaction processes via its stimuli-responsive chiroptical signalling is conceptualized.

Organized Chromophoric Assemblies for Nonlinear Optical Materials: Towards (Sub)wavelength Scale Architectures

Photonic circuits are expected to greatly contribute to the next generation of integrated chips, as electronic integrated circuits become confronted with bottlenecks such as heat generation and bandwidth limitations. One of the main challenges for the state-of-the-art photonic circuits lies in the development of optical materials with high nonlinear optical (NLO) susceptibilities, in particular in the wavelength and subwavelength dimensions which are compatible with on-chip technologies. In this review, the varied approaches to micro-/nanosized NLO materials based on building blocks of bio- and biomimetic molecules, as well as synthetic D-π-A chromophores, have been categorized as supramolecular self-assemblies, molecular scaffolds, and external force directed assemblies. Such molecular and supramolecular NLO materials have intrinsic advantages, such as structural diversities, high NLO susceptibilities, and clear structure-property relationships. These "bottom-up" fabrication approaches are proposed to be combined with the "top-down" techniques such as lithography, etc., to generate multifunctionality by coupling light and matter on the (sub)wavelength scale.

Aqueous self-assembly of chromophore-conjugated amphiphiles.

The self-assembly of π-conjugated building blocks has been a topic of interest in last few years owing to their close relevance to optoelectronic device applications. If such building blocks are made amphiphilic by appropriate derivatization, then the self-assembly can be realized in water by the strong hydrophobic repulsive forces between the polar medium and the rigid π-surface. On the other hand, as π-π interactions are directional, such self-assembly can produce structurally precise nano-structures, compared to classical surfactants. With these objectives, the self-assembly of several amphiphilic π-systems has been studied in the recent past and is described in this article. Examples include electron-deficient, electron-rich and also mixed assemblies of donor and acceptor type chromophores which produce many elegant soft structures such as micelles, vesicle, nanotubes and fibres etc.

Self-assembling hydrogel scaffolds for photocatalytic hydrogen production.

Integration into a soft material of all the molecular components necessary to generate storable fuels is an interesting target in supramolecular chemistry. The concept is inspired by the internal structure of photosynthetic organelles, such as plant chloroplasts, which colocalize molecules involved in light absorption, charge transport and catalysis to create chemical bonds using light energy. We report here on the light-driven production of hydrogen inside a hydrogel scaffold built by the supramolecular self-assembly of a perylene monoimide amphiphile. The charged ribbons formed can electrostatically attract a nickel-based catalyst, and electrolyte screening promotes gelation. We found the emergent phenomenon that screening by the catalyst or the electrolytes led to two-dimensional crystallization of the chromophore assemblies and enhanced the electronic coupling among the molecules. Photocatalytic production of hydrogen is observed in the three-dimensional environment of the hydrogel scaffold and the material is easily placed on surfaces or in the pores of solid supports.

Enhanced light-harvesting capacity by micellar assembly of free accessory chromophores and LH1-like antennas.

Biohybrid light-harvesting antennas are an emerging platform technology with versatile tailorability for solar-energy conversion. These systems combine the proven peptide scaffold unit utilized for light harvesting by purple photosynthetic bacteria with attached synthetic chromophores to extend solar coverage beyond that of the natural systems. Herein, synthetic unattached chromophores are employed that partition into the organized milieu (e.g. detergent micelles) that house the LH1-like biohybrid architectures. The synthetic chromophores include a hydrophobic boron-dipyrrin dye (A1) and an amphiphilic bacteriochlorin (A2), which transfer energy with reasonable efficiency to the bacteriochlorophyll acceptor array (B875) of the LH1-like cyclic oligomers. The energy-transfer efficiencies are markedly increased upon covalent attachment of a bacteriochlorin (B1 or B2) to the peptide scaffold, where the latter likely acts as an energy-transfer relay site for the (potentially diffusing) free chromophores. The efficiencies are consistent with a Förster (through-space) mechanism for energy transfer. The overall energy-transfer efficiency from the free chromophores via the relay to the target site can approach those obtained previously by relay-assisted energy transfer from chromophores attached at distant sites on the peptides. Thus, the use of free accessory chromophores affords a simple design to enhance the overall light-harvesting capacity of biohybrid LH1-like architectures.

Homo- and heterometallic luminescent 2-D stilbene metal–organic frameworks

Metal-organic frameworks (MOFs) can provide a matrix for the assembly of organic chromophores into well-defined geometries, allowing for tuning of the material properties and study of structure-property relationships. Here, we report on the effect of the coordinated metal ion on the luminescence properties of eight isostructural MOFs having the formula M(1)2M(2)L3(DMF)2 (M(1) = M(2) = Zn (1), Cd (2), Mn (3), Co (4); M(1) = Zn, M(2) = Cd (5), Mn (6), Co (7); M(1) = Co, M(2) = Mn (8); L = trans-4,4'-stilbene dicarboxylate), synthesized by reaction of the appropriate metal nitrate or mixtures of metal nitrates with LH2 in DMF. The crystal structures of 2, 3 and 5-8 were determined by X-ray diffraction to be composed of trinuclear metal clusters linked by stilbene dicarboxylate linkers in a paddlewheel geometry, extending to form a 2-D layered structure. In the mixed-metal cases, the larger metal ion was found to occupy the octahedral site in the cluster while the smaller ion occupies the tetrahedral positions, suggesting a selective, ligand-directed assembly process for the mixed-metal species. Variable temperature magnetic measurements for paramagnetic MOFs 3 and 6-8 were consistent with the site occupancies determined crystallographically, and indicated weak intra-cluster antiferromagnetic coupling for 3 and 8. Comparison between the crystal structures of 2, 3 and 5-8 and those reported for 1 and 4 in the literature reveal close resemblances between linker environments, with important intermolecular stilbene-stilbene geometries that are comparable in all cases. Interestingly, pale-colored 1-3 and 5-7 display very similar emission profiles upon excitation at λ(ex) = 350 nm, whereas dark-colored 4 and 8 do not exhibit detectable emission spectra. The bright, well-resolved luminescence of 1, 2 and 5 is ascribed to rigidification of the linker upon coordination to the d(10) metal ions, whereas the weaker emission observed for 3, 6 and 7 is presumably a result of quenching due to close proximity of the linker to one or more paramagnetic ions. Time-resolved measurements for 1, 2, 5 and 6 reveal biexponential emission decays, where the lifetime of the longer-lived state corresponds to observed variations in the nearest-neighbor cofacial stilbene-stilbene distances in their crystal structures. For 3, a monoexponential decay with shorter lifetime was determined, indicating significant paramagnetic quenching of its emissive state.

Self-organized porphyrin arrays on surfaces: the case of hydrophilic side chains and polar surfaces

Energy collection in photosynthetic microorganisms occurs through vectorial energy transfer along organized assemblies of chromophores. This process has inspired many research groups and yielded numerous examples of self-assembled photoactive structures. Dye sensitization of solar cells usually requires covalent anchoring of dyes onto the surface of metal oxides. A new porphyrin derivative that self-assembles upon non-covalent interaction with a surface has been designed and characterized by AFM. Interaction with metal oxide surfaces is further documented by the sensitization of metal oxide surfaces and the generation of photocurrent in non-optimized dye sensitized solar cells.

Evaluation of intrinsic spectroscopic properties of chromophore assemblies by shielding with cyclohexyl base pairs within a DNA duplex

Here, we investigated spectroscopic behaviors of tetramethylrhodamine (TMR) homo- and hetero-dimers within DNA duplex. In order to shield the chromophores from natural base pairs, we used cyclohexyl base pairs as ‘insulators’; these pairs were inserted between the chromophores and nucleobases. When a single TMR moiety was sandwiched between cyclohexyl base pairs, the emission intensity increased by fivefold relative to a TMR between natural base pairs, because electron transfer from nucleobases was suppressed. Next, we inserted two TMRs between the cyclohexyl base pairs and found that they facilitated H-dimer formation of TMR; a distinct hypsochromic shift was induced only when cyclohexyl base pairs were inserted. We further examined quenching behavior of a TMR paired with a quencher dye between cyclohexyl base pairs. Interestingly, fluorescence from TMR was quenched by nitro methyl red more efficiently in the presence of cyclohexyl base pairs than in their absence. This suggests that neighboring natural base pairs disturbed electron or hole transfer between the fluorophore and the quencher. The cyclohexyl base pairs shielded the chromophore pair from the natural base pairs and allowed intrinsic electron transfer.

Mechanochemical synthesis of a fluorenone-based metal organic framework with polarized fluorescence: an experimental and computational study

The regular assembly of organic chromophores into ordered supramolecular solids has received much attention for developing high-performance luminescent materials. Herein, a fluorenone-containing dicarboxylate (FDC) has been organized into a metal organic framework (MOF) with zinc as the metal cation by a facile mechanochemical synthesis method. The obtained Zn–FDC MOF features a pillared structure, in which the fluorenone chromophore units exhibit a highly ordered arrangement. Compared with the pristine FDC sample, the Zn–FDC MOF presents blue-shifted emission, as well as enhanced photoluminescence quantum yield and fluorescence lifetime, demonstrating the ordered arrangement of the FDC within the MOF is beneficial for the improvement of the photo-related properties of the organic chromophore. Moreover, the Zn–FDC MOF film exhibits well-defined polarized photoemission with a polarized anisotropy of 0.10–0.15. Periodic density functional theoretical (DFT) calculations illustrate that no energy/electronic transfer occurs between the chromophore and the metal cation, and the valence electrons localized in the FDC are confined effectively due to the energy blocking action of the metal cations. Combining experimental and theoretical studies on the luminescent MOF system, this work not only gives a rapid and environmentally friendly way to prepare a highly ordered inorganic–organic hybrid system with improved fluorescence properties, but also provides a deep understanding of the electronic structure of the 2D pillared MOF. It is expected that the Zn–FDC MOF can be potentially applied as a polarized fluorescence material.

Design principles and fundamental trade-offs in biomimetic light harvesting

Recent developments in synthetic and supramolecular chemistry have created opportunities to design organic systems with tailored nanoscale structure for various technological applications. A key application area is the capture of light energy and its conversion into electrochemical or chemical forms for photovoltaic or sensing applications. In this work we consider cylindrical assemblies of chromophores that model structures produced by several supramolecular techniques. Our study is especially guided by the versatile structures produced by virus-templated assembly. We use a multi-objective optimization framework to determine design principles and limitations in light harvesting performance for such assemblies, both in the presence and absence of disorder. We identify a fundamental trade-off in cylindrical assemblies that is encountered when attempting to maximize both efficiency of energy transfer and absorption bandwidth. We also rationalize the optimal design strategies and provide explanations for why various structures provide optimal performance. Most importantly, we find that the optimal design strategies depend on the amount of energetic and structural disorder in the system. The aim of these studies is to develop a program of quantum-informed rational design for construction of organic assemblies that have the same degree of tailored nanoscale structure as biological photosynthetic light harvesting complexes, and consequently have the potential to reproduce their remarkable light harvesting performance.

Highly Selective Dispersion of Carbon Nanotubes by Using Poly(phenyleneethynylene)‐Guided Supermolecular Assembly

Isolation of single-walled carbon nanotubes (SWNTs) with specific chirality and diameters is critical for achieving optimum performance of SWNTs in various applications. A water-soluble π-conjugated polymer, poly[(m-phenyleneethynylene)-alt-(p-phenyleneethynylene)], 3, is found to exhibit high selectivity in dispersing SWNT (6,5). The polymer's ability to sort out SWNT (6,5) appears to be related to the carbon-carbon triple bond, whose free rotation allows a unique assembly of chromophores in a helical conformation. The observation is consistently supported by fluorescence, Raman, and UV-vis-NIR absorption spectra. The intriguing selectivity of 3 to SWNT (6,5), however, is not observed for the vinylene analogue polymer 1, showing that the carbon-carbon triple bond could play a unique role in sorting out a specific SWNT. The observed selectivity from 3 could be attributed to a combination of the helical cavity size restrain and electronic interaction associated with the local chromophore arrangement. This strategy could be expanded for efficient SWNT sorting when the helical conformation is further finely tuned.

DNA Triplex‐Mediated Assembly of Polyaromatic Chromophores

The synthesis and characterization of intramolecular triple-helical DNA structures containing polyaromatic pyrene and perylene (perylenetetracarboxylic acid diimide, PDI) building blocks are presented. Two 1,8-dialkynylpyrene units are located in the Watson-Crick stem of the construct, while a PDI or a natural thymidine is present in the Hoogsteen strand. The triple helical structures were investigated by UV/VIS absorbance, fluorescence spectroscopy, and circular dichroism (CD) measurements. The folding of the intramolecular triple helix can be monitored by changes in the vibronic transition ratios, as well as by a change in the alkynylpyrene fluorescence (monomer vs. excimer). It is shown that thymine in the third strand has a pronounced influence on the interaction and, thus, on the fluorescence properties of two pyrene building blocks.

Influence of a GC Base Pair on Excitation Energy Transfer in DNA-Assembled Phenanthrene π-Stacks

The effect of a GC base pair on the excitation energy transfer in a DNA-based, light harvesting assembly of phenanthrene and pyrene chromophores is described. After absorption of light at 320 nm by the stacked phenanthrene building blocks, the excitation energy is transferred to the pyrene and leads to the formation of a phenanthrene-pyrene exciplex. The fluorescence intensity depends on the number of light absorbing phenanthrenes, as well as on the type of DNA base pair flanking the phenanthrene stack. In comparison to an AT base pair, a GC base pair located next to the stacked aromatic residues results in a reduction of fluorescence. The degree of quenching is dependent on the length of the phenanthrene stack that separates the GC base pair from the exciplex. Overall, a large number of stacked phenanthrenes positively affects exciplex fluorescence by increasing the quantity of absorbed light and, at the same time, reducing the effect of quenching by GC base pairs.

Preparation of supramolecular chromophoric assemblies using a DNA duplex

Organization of supramolecular assemblies of chromophores with precisely-controlled orientation and sequence remains challenging. Nucleic acids with complementary base sequences spontaneously form double-helical structures. Therefore, covalent attachment of chromophores to DNA or RNA can be used to control assembly and orientation of chromophores. In this perspective, we first review our recent work on the assemblies of fluorophores (pyrene and perylene) by using natural base pairs. The interaction between dyes can be strictly controlled by means of cluster and interstrand wedge motifs. We then discuss novel artificial base pairs that can suppress the interaction between fluorophores and nucleobases. We incorporated a cyclohexane moiety into DNA, and showed that these artificial base pairs suppressed the electron-hole transfer between fluorophores and nucleobases and enhanced the quantum yields of fluorophores. These base pairs can potentially be used to accumulate fluorophores inside DNA duplexes without decreasing quantum yields.

The DNA three-way junction as a mould for tripartite chromophore assembly

The DNA three-way junction serves as a scaffold for the molecular organization of non-nucleosidic alkynylpyrene and perylenediimide chromophores located at the branch point of the structure. Depending on the composition of the tripartite assembly, the constructs possess distinct spectroscopic properties, ranging from monomer or excimer fluorescence to completely quenched tripartite aggregates.

Two-photon absorption enhancement of polymer-templated porphyrin-based J-aggregates.

Supramolecular structures based on organized assemblies of macrocyclic chromophores, particularly porphyrin-based dyes, have attracted widespread interest as components of molecular devices with potential applications in molecular electronics, artificial light harvesting, and pharmacology. We report the formation of J-aggregates of two porphyrin-based dyes, 5,10,15,20-tetrakis(4-sulfonatophenyl)porphyrin (TSPP, 4) and an amino tris-sulfonate analogue (5) in water using a functionalized norbornene-based homopolymer, synthesized by ring-opening metathesis polymerization (ROMP). Ionic interactions of the cationic side chains (ammonium groups) of the polymer under acidic conditions with the negatively charged sulfonate groups of the porphyrins facilitated polymer template enhanced J-aggregation of the porphyrin dyes. J-Aggregation behavior was investigated photophysically by UV-vis absorption along with steady-state and time-resolved fluorescence studies. Two-photon absorption (2PA) was enhanced by about an order of magnitude for the J-aggregated TSPP relative to its free base. Significantly, the 2PA cross section of the polymer-templated TSPP J-aggregate was up to three times higher than the J-aggregated TSPP in the absence of the polymer template while the 2PA cross section for polymer-templated J-aggregates of 5 increased substantially, up to ca. 10,000 GM, suggesting a prominent role of polymer-templating to facilitate porphyrin aggregation and greatly enhance nonlinear absorption.

Comparative self-assembly studies and self-sorting of two structurally isomeric naphthalene-diimide (NDI)-gelators

We have reported here a comparative self-assembly and gelation studies of two isomeric bis-amide functionalized NDI-derivatives. In one case (NDI-1) the two amide groups were placed symmetrically on either side of the chromophore while for the other system (NDI-2) they were located on same side. In non-polar solvent both isomers formed self-assembled structures by synergistic effect of π-stacking and hydrogen-bonding. The propensity for self-assembly of NDI-1 was greater due to symmetrical placement of two amide groups on either arms of this chromophore which allowed π-stacking in tandem with hydrogen-bonding, while NDI-2 formed thermally more stable self-assembled fibres possibly due to location of two amide groups in close proximity along single arm of this chromophore. The structural difference in these two isomers lead to distinctly different morphology of their respective self-assembled structures which was further reflected on their gelation properties. Morphology of the self-assembled array of NDI-1 showed organized and regular entangled bundles of nanorods which imparted better gelation ability to this chromophore while the self-assembled fibres of NDI-2 showed less ordered and irregular fibres. We also probed self- assembly of these two chromophores in their mixture which revealed orthogonal assembly of the individual chromophores and no molecular mixing was noticed. Hydrogen bonding mediated self-assembly and gelation of two isomeric naphthalene-diimide (NDI) gelators is reported. NDI-1 showed precisely defined self-assembly resulting in stronger gelation due to symmetric placement of the two amide groups. Contrastingly, weak gelation was noticed for unsymmetrical NDI-2 due to irregular morphology even though thermal stability of self-assembled state in solution was found to be higher in this case due to close proximity of the two amide groups.

Photoinduced processes in chromophore–gold nanoparticle assemblies

Development of nanotechnology requires that the interaction between components of nanoscale devices can be studied and understood better. Photoinduced processes between small (2–5 nm in core diameter) gold nanoparticles (GNPs) and chromophores, including porphyrin, fullerene, and phthalocyanine, were studied. Two methods were selected for controlled assembly of chromophores and gold particles at close distances: thin films and covalent attachment, which yields chromophore-functionalized particles. Time-resolved spectroscopic and photoelectrical measurements carried out further confirmed the known strong effect of GNPs on photoexcited chromophores that leads to fast photoinduced processes. When GNPs are combined with suitable chromophores, the particles can act as electron donors or acceptors. GNPs are efficient energy acceptors, and some indications of their ability to act as energy donors were obtained. The participation of the GNPs in photoinduced charge transfer in addition to energy-transfer processes makes them attractive components for photoactive devices.

Signal control by self-assembly of fluorophores in a molecular beacon—a model study

Pyrene excimer fluorescence is efficiently regulated through formation of π-stacked aggregates between dialkynylpyrene (Y) and perylenediimide (E) residues located in the stem region of a molecular beacon (MB). The building blocks form organized, multichromophoric complexes in the native form. Hybridization to the target results in a conformational reorganization of the chromophores. The nature of the aggregates was investigated by changing the number of chromophores and natural base pairs in the beacon stem. The formation of different types of complexes (EYEY→YEY→EY) is revealed by characteristic spectroscopic changes. The data show that signal control is an intrinsic property of the interacting chromophores. The directed assembly of non-nucleosidic chromophores can be used for the generation of an on/off switch of a fluorescence signal. The concept may find applications in various types of light-based input/output systems.

Strategic Synthesis of 2,6‐Pyridylene‐Bridged β‐to‐β Porphyrin Nanorings through Cross‐Coupling

Since the crystal structure of LH2 was elucidated to be circularly arranged chromophoric assemblies, [1–3] much effort has been devoted towards the synthesis of cyclic porphyrin arrays to study the excitation energy transfer (EET) and electronic coupling along the wheel. [4] These cyclic porphyrin arrays are also interesting in host–guest chemistry, [5] single-molecule photochemistry, [6] nonlinear optical (NLO) materials [7] and so on. [8–12] Cyclic porphyrin arrays are constructed by means of covalent bonds, noncovalent bonds, or metal coordination bonds. [8–12] Although the last two are beneficial to construct cyclic porphyrin arrays, those are often unstable toward solvent change or addition of other competing species. The covalently bonded arrays are structurally robust, but often difficult to synthesize. In addition, the final macrocyclization steps are the most tedious and generally need assistance from a suitable template. [5] Although there are some reports on covalently bonded cyclic porphyrin arrays, most of them were constructed through meso-to-meso bridging methods. As rare examples, we recently reported two b,b’-bridged cyclic porphyrin arrays with a 1,3-butadiyne or a 2,5-thienyl spacer. [13] Herein, we wish to report the efficient synthesis of 2,6-pyridylene-bridged b-tob porphyrin nanorings by Suzuki–Miyaura coupling, which is particularly effective for medium to large porphyrin rings. We have achieved the synthesis of 2,5-thienylene-bridged cyclic porphyrin dimers and trimers, but it was difficult to expand the size of the macrocycle beyond trimers. We then examined the Suzuki–Miyaura coupling of b,b’-diborylated Ni II porphyrin 1 with 2,6-dibromopyridine, which provided linear oligomers as the main products. However, we noticed that bromopyridyl-terminated oligomers were selectively obtained with the use of an excess amount of 2,6-dibromopyridine. For instance, b,b’-diborylporphyrin 1–Ni II[14] was crosscoupled with 2,6-dibromopyridine (5 equiv) under standard conditions to give 1–Br in 80 % yield, along with 2–Br (10 %) and 3–Br (2 %) (Scheme 1). It is worth noting that deborylated products were hardly detected in this reaction. Compound 2–Br was also obtained in 42 % yield through the three-component coupling of 1 (1 equiv), 1–Br (2.5 equiv), and 2,6-dibromopyridine (2.5 equiv). Further cross-coupling of 1 (1 equiv) with 1–Br (5 equiv) or 2–Br (5 equiv) afforded 3–Br or 5–Br in 50 or 45 % yields, respectively. Compound 7–Br was prepared in 50 % yield from 1 and 3–Br. With the linear precursors 2–Br, 3–Br, 5–Br, and 7–Br in hand, we examined the cyclization with 1 through a 1:1 Suzuki–Miyaura coupling reaction, which worked very effectively to give porphyrin rings 3–Ni, 4–Ni, 6–Ni, and 8–Ni in 60, 58, 55, and 55 % yields, respectively, even without any template. Treatment of 3–Ni, 4–Ni, 6–Ni, and 8–Ni with sulfuric acid in chloroform at room temperature induced Ni II demetalation to provide 3–H, 4–H, 6–H, and 8–H quantitatively, which were all converted into 3–Zn, 4–Zn, 6–Zn, and 8–Zn upon treatment with ZnA2 in quantitative yields. These newly synthesized porphyrin rings were fully characterized by high-resolution mass spectrometry and