Tubes or sheets: divergent aggregation pathways of an amphiphilic 2,7-substituted pyrene trimer

The self-assembly of an amphiphilic 2,7-linked pyrene trimer in an aqueous environment into two morphologically related forms is described. Supramolecular polymerization leads to the simultaneous formation of nanosheets and nanotubes.

From supramolecular sheets to fibers and back: establishing the critical parameters that govern the morphology of pyrene-based self-assembled materials

The precise arraying of functional entities in morphologically well-defined shapes remains one of the key challenges in the processing of organic molecules1. Among various π-conjugated species, pyrene exhibits a set of unique properties, which make it an attractive compound for the utilization in materials science2. In this contribution we report on properties of self-assembled structures prepared from amphiphilic pyrene trimers (Py3) consisting of phosphodiester-linked pyrenes. Depending on the geometry of a pyrene core substitution (1.6-, 1.8-, or 2.7- type, see Scheme), the thermally-controlled self-assembly allows the preparation of supramolecular architectures of different morphologies in a bottom-up approach: two-dimensional (2D) nanosheets3 are formed in case of 1.6- and 2.7-substitution4 whereas one-dimensional (1D) fibers are built from 1.8- substituted isomers. The morphologies of the assemblies are established by AFM and TEM, and the results are further correlated with spectroscopic and scattering data. Two-dimensional assemblies consist of an inner layer of hydrophobic pyrenes, sandwiched between a net of phosphates. Due to the repulsion of the negative charges, the 2D assemblies exist mostly as free-standing sheets. An internal alignment of pyrenes leads to strong exciton coupling with an unprecedented observation (simultaneous development of J- and H-bands from two different electronic transitions). Despite the similarity in spectroscopic properties, the structural parameters of the 2D aggregates drastically depend on the preparation procedure. Under certain conditions extra-large sheets (thickness of 2 nm, aspect ratio area/thickness ~107) in aqueous solution are formed4B. Finally, one-dimensional assemblies are formed as micrometer-long and nanometer-thick fibers. Both, planar and linear structures are intriguing objects for the creation of conductive nanowires that may find interest for applications in supramolecular electronics.

From supramolecular sheets to fibers and back: establishing the critical parameters that govern the morphology of pyrene-based self-assembled materials

The precise arraying of functional entities in morphologically well-defined shapes remains one of the key challenges in the processing of organic molecules1. Among various π-conjugated species, pyrene exhibits a set of unique properties, which make it an attractive compound for the utilization in materials science2. In this contribution we report on properties of self-assembled structures prepared from amphiphilic pyrene trimers (Py3) consisting of phosphodiester-linked pyrenes. Depending on the geometry of a pyrene core substitution (1.6-, 1.8-, or 2.7- type, see Scheme), the thermally-controlled self-assembly allows the preparation of supramolecular architectures of different morphologies in a bottom-up approach: two-dimensional (2D) nanosheets3 are formed in case of 1.6- and 2.7-substitution4 whereas one-dimensional (1D) fibers are built from 1.8- substituted isomers. The morphologies of the assemblies are established by AFM and TEM, and the results are further correlated with spectroscopic and scattering data. Two-dimensional assemblies consist of an inner layer of hydrophobic pyrenes, sandwiched between a net of phosphates. Due to the repulsion of the negative charges, the 2D assemblies exist mostly as free-standing sheets. An internal alignment of pyrenes leads to strong exciton coupling with an unprecedented observation (simultaneous development of J- and H-bands from two different electronic transitions). Despite the similarity in spectroscopic properties, the structural parameters of the 2D aggregates drastically depend on the preparation procedure. Under certain conditions extra-large sheets (thickness of 2 nm, aspect ratio area/thickness ~107) in aqueous solution are formed4B. Finally, one-dimensional assemblies are formed as micrometer-long and nanometer-thick fibers. Both, planar and linear structures are intriguing objects for the creation of conductive nanowires that may find interest for applications in supramolecular electronics.

Benzo(a)pyrene Metabolism and EROD and GST Biotransformation Activity in the Liver of Red- and White-Blooded Antarctic Fish.

Climate change and anthropogenic pollution are of increasing concern in remote areas such as Antarctica. The evolutionary adaptation of Antarctic notothenioid fish to the cold and stable Southern Ocean led to a low plasticity of their physiological functions, what may limit their capacity to deal with altered temperature regimes and pollution in the Antarctic environment. Using a biochemical approach, we aimed to assess the hepatic biotransformation capacities of Antarctic fish species by determining (i) the activities of ethoxyresorufin-O-deethylase (EROD) and glutathione-S-transferase (GST), and (ii) the metabolic clearance of benzo(a)pyrene by hepatic S9 supernatants. In addition, we determined the thermal sensitivity of the xenobiotic biotransformation enzymes. We investigated the xenobiotic metabolism of the red-blooded Gobionotothen gibberifrons and Notothenia rossii, the hemoglobin-less Chaenocephalus aceratus and Champsocephalus gunnari, and the rainbow trout Oncorhynchus mykiss as a reference. Our results revealed similar metabolic enzyme activities and metabolic clearance rates between red- and white-blooded Antarctic fish, but significantly lower rates in comparison to rainbow trout. Therefore, bioaccumulation factors for metabolizable lipophilic contaminants may be higher in Antarctic than in temperate fish. Likewise, the thermal adaptive capacities and flexibilities of the EROD and GST activities in Antarctic fish were significantly lower than in rainbow trout. As a consequence, increasing water temperatures in the Southern Ocean will additionally compromise the already low detoxification capacities of Antarctic fish.

Two-Dimensional Manganese(II) Coordination Polymer Based on Phthalate and Pyrazine Bridges Exhibiting Antiferromagnetic Porperties

Benzodifuran-functionalised pyrene and anthracene fluorophores 1 and 2 were obtained in reasonable yields. Their single crystal structures, electrochemical, optical absorption, and fluorescence characteristics have been described. They show strong luminescence with high quantum yields of 0.53 for 1 and 0.48 for 2. Magnetic measurements for the 2D coordination polymer [Mn(Pht(Pyz(H2O)2]n (1), in which metal centres are linked together by pyrazine (Pyz) and 1,6-bridging o-phthalate ligand (Pht2-), revealed antiferromagnetic interactions between Mn(II) ions.

Protein and lipid binding parameters in rainbow trout (Oncorhynchus mykiss) blood and liver fractions to extrapolate from an in vitro metabolic degradation assay to in vivo bioaccumulation potential of hydrophobic organic chemicals

Binding of hydrophobic chemicals to colloids such as proteins or lipids is difficult to measure using classical microdialysis methods due to low aqueous concentrations, adsorption to dialysis membranes and test vessels, and slow kinetics of equilibration. Here, we employed a three-phase partitioning system where silicone (polydimethylsiloxane, PDMS) serves as a third phase to determine partitioning between water and colloids and acts at the same time as a dosing device for hydrophobic chemicals. The applicability of this method was demonstrated with bovine serum albumin (BSA). Measured binding constants (K(BSAw)) for chlorpyrifos, methoxychlor, nonylphenol, and pyrene were in good agreement with an established quantitative structure-activity relationship (QSAR). A fifth compound, fluoxypyr-methyl-heptyl ester, was excluded from the analysis because of apparent abiotic degradation. The PDMS depletion method was then used to determine partition coefficients for test chemicals in rainbow trout (Oncorhynchus mykiss) liver S9 fractions (K(S9w)) and blood plasma (K(bloodw)). Measured K(S9w) and K(bloodw) values were consistent with predictions obtained using a mass-balance model that employs the octanol-water partition coefficient (K(ow)) as a surrogate for lipid partitioning and K(BSAw) to represent protein binding. For each compound, K(bloodw) was substantially greater than K(S9w), primarily because blood contains more lipid than liver S9 fractions (1.84% of wet weight vs 0.051%). Measured liver S9 and blood plasma binding parameters were subsequently implemented in an in vitro to in vivo extrapolation model to link the in vitro liver S9 metabolic degradation assay to in vivo metabolism in fish. Apparent volumes of distribution (V(d)) calculated from the experimental data were similar to literature estimates. However, the calculated binding ratios (f(u)) used to relate in vitro metabolic clearance to clearance by the intact liver were 10 to 100 times lower than values used in previous modeling efforts. Bioconcentration factors (BCF) predicted using the experimental binding data were substantially higher than the predicted values obtained in earlier studies and correlated poorly with measured BCF values in fish. One possible explanation for this finding is that chemicals bound to proteins can desorb rapidly and thus contribute to metabolic turnover of the chemicals. This hypothesis remains to be investigated in future studies, ideally with chemicals of higher hydrophobicity.

Cooperative and Noncooperative Assembly of Oligopyrenotides Resolved by Atomic Force Microscopy

The supramolecular assembly of amphiphilic oligopyrenotide building blocks (covalently linked heptapyrene, Py7) is studied by atomic force microscopy (AFM) in combination with optical spectroscopy. The assembly process is triggered in a controlled manner by increasing the ionic strength of the aqueous oligomer solution. Cooperative noncovalent interactions between individual oligomeric units lead to the formation of DNA-like supramolecular polymers. We also show that the terminal attachment of a single cytidine nucleotide to the heptapyrenotide (Py7-C) changes the association process from a cooperative (nucleation−elongation) to a noncooperative (isodesmic) regime, suggesting a structure misfit between the cytidine and the pyrene units. We also demonstrate that AFM enables the identification and characterization of minute concentrations of the supramolecular products, which was not accessible by conventional optical spectroscopy.

Tissue-specific induction of EROD activity and CYP1A protein in Sparus aurata exposed to B(a)P and TCDD

The purpose of this study was to compare xenobiotic CYP1A induction in liver, gills, and excretory kidney of gilthead seabream, Sparus aurata. Fishes were exposed via water for 20 days to different concentrations of benzo(a)pyrene (B(a)P) or 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). CYP1A was measured at the enzyme activity level as 7-ethoxyresorufin-O-deethylase (EROD) activity, and at the protein level by means of ELISA. The liver displayed the highest absolute levels of EROD activity, both under non-exposed and exposed conditions. Organ- or inducer-related differences in the time course of CYP1A induction were moderate; however, the magnitude of the induction response varied between the organs and between B(a)P and TCDD. In the case of TCDD, liver, and kidney yielded a comparable induction response, whereas in the case of B(a)P, the kidney showed a substantially higher maximum induction factor than the liver. In the gills, the two xenobiotics resulted in similar maximum induction factors. In B(a)P-exposed seabream, EROD activities and CYP1A protein levels showed a good correlation in all three organs, whereas with TCDD as inducer the correlation was poor, what was mainly due to a decrease of EROD activities at the higher concentrations of TCDD, while CYP1A protein levels showed no concomitant decline. Overall, the study revealed both similarities and differences in the time-, concentration-, and inducer-dependent CYP1A responses of the three target organs, liver, kidney, and gills. Although, the findings of this study principally confirm the notion of the liver as the major metabolic organ in fish, they also provide evidence for substantial metabolic potential in gills and particularly in the kidney.

Supramolecular Organization of Heptapyrenotide Oligomers—An in Depth Investigation by Molecular Dynamics Simulations

We present a molecular modeling study based on ab initio and classical molecular dynamics calculations, for the investigation of the tridimensional structure and supramolecular assembly formation of heptapyrenotide oligomers in water solution. Our calculations show that free oligomers self-assemble in helical structures characterized by an inner core formed by π- stacked pyrene units, and external grooves formed by the linker moieties. The coiling of the linkers has high ordering, dominated by hydrogen-bond interactions among the phosphate and amide groups. Our models support a mechanism of longitudinal supramolecular oligomerization based on interstrand pyrene intercalation. Only a minimal number of pyrene units intercalate at one end, favoring formation of very extended longitudinal chains, as also detected by AFM experiment. Our results provide a structural explanation of the mechanism of chirality amplification in 1:1 mixtures of standard heptapyrenotides and modified oligomers with covalently linked deoxycytidine, based on selective molecular recognition and binding of the nucleotide to the groove of the left-wound helix.

Combinatorial chromophore assembly inside a DNA four-way junction

In 1964 first proposed by Robin Holliday as a mechanistic model to solve the mystery of how genetic information is exchanged in yeast, the DNA four-way junction or Holliday junction (HJ) was proofed to be the key in- termediate in homologous recombination and became an important tool in the field of DNA origami, computation and nanomachines. Herein we use the assembly of four modified nucleic acid strands into the planar square conformation of this higher order DNA structure to demonstrate in a proof of principle manner the cumulative effect of pyrene moieties interacting inside the junction.[1][2]

Polycyclic aromatic compounds (PAHs and oxygenated PAHs) and trace metals in fish species from Ghana (West Africa): Bioaccumulation and health risk assessment

We report the concentrations of 28 PAHs, 15 oxygenated PAHs (OPAHs) and 11 trace metals/metalloids (As, Cd, Co, Cr, Cu, Fe, Mn, Ni, Pb, Se, and Zn) in muscle and gut + gill tissues of demersal fishes (Drapane africana, Cynoglossus senegalensis and Pomadasys peroteti) from three locations along the coast of the Gulf of Guinea (Ghana). The concentrations of ∑ 28PAHs in muscle tissues averaged 192 ng g− 1 dw (range: 71–481 ng g− 1 dw) and were not statistically different between locations. The concentrations of ∑ 28 PAHs were higher in guts + gills than in muscles. The PAH composition pattern was dominated by low molecular weight compounds (naphthalene, alkyl-naphthalenes and phenanthrene). All fish tissues had benzo[a]pyrene concentrations lower than the EU limit for food safety. Excess cancer risk from consumption of some fish was higher than the guideline value of 1 × 10− 6. The concentrations of ∑ 15 OPAHs in fish muscles averaged 422 ng g− 1 dw (range: 28–1715 ng g− 1dw). The ∑ 15 OPAHs/∑ 16 US-EPA PAHs concentration ratio was > 1 in 68% of the fish muscles and 100% of guts + gills. The log-transformed concentrations of PAHs and OPAHs in muscles, guts + gills were significantly (p < 0.05) correlated with their octanol–water partitioning coefficients, strongly suggesting that equilibrium partitioning from water/sediment into fish tissue was the main mechanism of bioaccumulation. The trace metal concentrations in the fish tissues were in the medium range when compared to fish from other parts of the world. The concentrations of some trace metals (Cd, Cu, Fe, Mn, Zn) were higher in guts + gills than in muscle tissues. The target hazard quotients for metals were < 1 and did not indicate a danger to the local population. We conclude that the health risk arising from the consumption of the studied fish (due to their PAHs and trace metals content) is minimal.

Influence of perylenediimide–pyrene supramolecular interactions on the stability of DNA-based hybrids: Importance of electrostatic complementarity

Aromatic pi–pi stacking interactions are ubiquitous in nature, medicinal chemistry and materials sciences. They play a crucial role in the stacking of nucleobases, thus stabilising the DNA double helix. The following paper describes a series of chimeric DNA–polycyclic aromatic hydrocarbon (PAH) hybrids. The PAH building blocks are electron-rich pyrene and electron-poor perylenediimide (PDI), and were incorporated into complementary DNA strands. The hybrids contain different numbers of pyrene–PDI interactions that were found to directly influence duplex stability. As the pyrene–PDI ratio approaches 1:1, the stability of the duplexes increases with an average value of 7.5 °C per pyrene–PDI supramolecular interaction indicating the importance of electrostatic complementarity for aromatic pi–pi stacking interactions.

Diversity of morphological patterns in supramolecular polymers formed from the amphiphilic oligomers of pyrenes

Very important aspects of the modern nanotechnology are control and prediction of arraying patterns of opto- and electroactive molecules in discrete objects on nanoscale level both on surface and solution. Consequqntly, a self-assembly of small molucules provides such an opportunity.For example, oligopyrenotides (OPs, short amphiphilic pyrene oligomers) represent a novel class of amphiphilic molecules which tend to aggegate in aqueous phase. As has been already shown, OPs are able to form 1D supramolecular polymer only under high salt concentration. Since programmed arraying of polyaromatic hydrocarbons in structurally defined objects could offer enhanced performance over the individual components, prediction and controlling of their spatial arrangement remains challenging. Herein we demonstrate that substitution type of the pyrene is crutial, and it determines a morphology of the assemblies. Thus, a 1.6-linkage causes a formation of large, free-standing 2D supromolecular polymers with a thickness 2 nm. These assemblies possess a high degree of an internal order: the interior consists of hydrophobic pyrenes and alkyl chains, whereas the exterior exists as a net of hydrophilic negatively charged phosphates. Contrary, a 1.8-linkage exclusiveley leads to a formation of long (up to a few micrometer), nanometer thick helical supramolecular polymers. These structures tend to form even more complex structures (bundles, superhelixes). Moreover for both molecules, the polymerizations occurs via a nucleation-elongation mechanism. To study Py3 self-assembly, we carried out whole set of spectroscopic (UV/vis, fluorescence, DLS) and microscopic experiments (AFM).

Hierarchical self-assembly of nucleotide-appended oligopyrenotides into defined supramolecular objects

Supramolecular DNA assembly blends DNA building blocks with synthetic organic and inorganic molecules giving structural and functional advantages both to the initial self-assembly process and to the final construct. Synthetic molecules can bring a number of additional interactions into DNA nanotechnology. Incorporating extended aromatic molecules as connectors of DNA strands allows folding of these strands through π-π stacking (DNA “foldamers”). In previous work it was shown that short oligopyrenotides (phosphodiester-linked pyrene oligomers) behave as staircase-like foldamers, which cooperatively self-assemble into two-dimensional supramolecular polymers in aqueous medium. Herein, we demonstrate that a 10-mer DNA-sequence modified with 7 pyrene units (see illustration) forms dimensionally-defined supramolecular polymers under thermodynamic conditions in water. We present the self-assembly behavior, morphological studies, and the spectroscopic properties of the investigated DNA-sequences (illustrative AFM picture shown below).

Diversity of morphological patterns in supramolecular polymers formed from the amphiphilic oligomers of pyrenes

Herein we demonstrate that a substitution type of the pyrene in short amphiphilic oligomers determines a morphology of the assemblies formed. Thus, 1.6- and 2.7-linkages lead to a formation of micrometer-sized 2D supromolecular polymers with a constant thickness 2 nm (pictures A and B). These assemblies possess a high degree of an internal order: the interior consists of hydrophobic pyrenes and alkyl chains, whereas the exterior exists as a net of hydrophilic negatively charged phosphates. Contrary, a 1.8-linkage exclusiveley leads to a formation of long nanometer thick helical supramolecular polymers (picturee C). These structures tend to form even more complex assemblies (bundles, superhelixes). Moreover, for all samples the polymerization process occurs via a nucleation-elongation mechanism. To study Py3 self-assembly, we carried out whole set of spectroscopic (UV/vis, fluorescence, DLS) and microscopic experiments (AFM).