Combining aminocyanine dyes with polyamide dendrons: a promising strategy for imaging in the near-infrared region

Cyanine dyes are known for their fluorescence in the near-IR (NIR) region, which is desirable for biological applications. We report the synthesis of a series of aminocyanine dyes containing terminal functional groups such as acid, azide, and cyclooctyne groups for further functionalization through, for example, click chemistry. These aminocyanine dyes can be attached to polyfunctional dendrons by copper-catalyzed azide alkyne cycloaddition (CuAAC), strain-promoted azide alkyne cycloaddition (SPAAC), peptide coupling, or direct S(NR)1 reactions. The resulting dendron-dye conjugates were obtained in high yields and displayed high chemical stability and photostability. The optical properties of the new compounds were studied by UV/Vis and fluorescence spectroscopy. All compounds show large Stokes shifts and strong fluorescence in the NIR region with high quantum yields, which are optimal properties for in vivo optical imaging.     

Chromo- and fluororeactands: indicators for detection of neutral analytes by using reversible covalent-bond chemistry

Chromo- and fluororeactands are indicator dyes that allow the optical detection of electrically neutral analytes. Unlike complexing agents such as calixarenes, cyclodextrines or cyclophanes, reactands form a reversible covalent bond with the analyte molecule. This chemical reaction causes strong changes in absorbance or fluorescence. In this article reactands for analytes such as amines, alcohols, aldehydes, saccharides, carbon dioxide and sulfur dioxide are presented. Methods to enhance the sensitivity of the reactands as well as the operational and shelf lives of the corresponding optical sensors are discussed.     

Isolation and Characterization of Precise Dye/Dendrimer Ratios

Fluorescent dyes are commonly conjugated to nanomaterials for imaging applications using stochastic synthesis conditions that result in a Poisson distribution of dye/particle ratios and therefore a broad range of photophysical and biodistribution properties. We report the isolation and characterization of generation 5 poly(amidoamine) (G5 PAMAM) dendrimer samples containing 1, 2, 3, and 4 fluorescein (FC) or 6‐carboxytetramethylrhodamine succinimidyl ester (TAMRA) dyes per polymer particle. For the fluorescein case, this was achieved by stochastically functionalizing dendrimer with a cyclooctyne “click” ligand, separation into sample containing precisely defined “click” ligand/particle ratios using reverse‐phase high performance liquid chromatography (RP‐HPLC), followed by reaction with excess azide‐functionalized fluorescein dye. For the TAMRA samples, stochastically functionalized dendrimer was directly separated into precise dye/particle ratios using RP‐HPLC. These materials were characterized using ¹H and ¹⁹F NMR spectroscopy, RP‐HPLC, UV/Vis and fluorescence spectroscopy, lifetime measurements, and MALDI.     

Synthesis and Optical Properties of Water‐Soluble Polyglycerol‐Dendronized Rylene Bisimide Dyes

Four new water‐soluble polyglycerol‐dendronized perylene, terrylene, and quaterrylene bisimides have been synthesized and characterized with respect to their optical properties in polar organic solvents and water by using UV/Vis and fluorescence spectroscopy. All of these dyes were highly soluble in water, but the size of the chosen polyglycerol dendron was only sufficient to completely suppress dye aggregation for the core‐unsubstituted perylene derivative. Their high solubility in water and their absorption and emission wavelengths up to the NIR region make the core‐unsubstituted perylene and terrylene bisimides ideal candidates for applications in bioimaging, whilst the lack of fluorescence for quaterrylene bisimide in all polar solvents does not warrant further investigation of this chromophore in fluorescence and imaging applications. Likewise, tuning of the emission of rylene bisimides towards longer wavelengths by employing electron‐donating bay substituents is not a promising strategy, owing to the lower fluorescence quantum yields in polar solvents and, in particular, in water.     

Chemiluminescence imaging for microRNA detection based on cascade exponential isothermal amplification machinery

A novel G-quadruplex DNAzyme-driven chemiluminescence (CL) imaging method was developed for ultrasensitive and specific detection of miRNA based on the cascade exponential isothermal amplification reaction (EXPAR) machinery. A structurally tailored hairpin probe switch was designed to selectively recognise miRNA and form hybridisation products to trigger polymerase and nicking enzyme machinery, resulting in the generation of product I, which was complementary to a region of the functional linear template. Then, the response of the functional linear template to the generated product I further activated the exponential isothermal amplification machinery, leading to synthesis of numerous horseradish peroxidase mimicking DNAzyme units for CL signal transduction. The amplification paradigm generated a linear response from 10 fM to 100 pM, with a low detection limit of 2.91 fM, and enabled discrimination of target miRNA from a single-base mismatched target. The developed biosensing platform demonstrated the advantages of isothermal, homogeneous, visual detection for miRNA assays, offering a promising tool for clinical diagnosis.     

A New Highly Selective and Sensitive Assay for Fluorescence Imaging of .OH in Living Cells: Effectively Avoiding the Interference of Peroxynitrite

A new nonredox fluorescent probe to realize the imaging of hydroxyl radicals (^.OH) in living cells was designed and synthesized. The structure comprised the fluorescent dye boron dipyrromethene (BDP) and a 2,2,6,6‐tetramethyl‐1‐piperidinoxyl (TEMPO) unit. This probe could rapidly respond to ^.OH with a detection limit of 18 pM , and it possessed superior photostability and pH insensitivity. Other reactive oxygen species (ROS) and relevant intracellular components did not interfere. In particular, the important problem of ONOO^? interference was efficiently avoided. An MTT assay proved that the probe was not very cytotoxic. The probe could penetrate into intact cell membranes to selectively detect intracellular ^.OH without causing cellular damage in living mice macrophages, normal human liver cells. and human hepatoma cells. These advantageous characteristics make the fluorescent probe potentially useful as a new candidate to detect ^.OH in broad biosystems.     

A mesoporous 3D hybrid material with dual functionality for Hg2+ detection and adsorption

Dual-function hybrid material U1 was designed for simultaneous chromofluorogenic detection and removal of Hg(2+) in an aqueous environment. Mesoporous material UVM-7 (MCM41 type) with homogeneously distributed pores of about 2-3 nm in size, a large specific surface area exceeding 1000 m(2) g(-1), and nanoscale particles was used as an inorganic support. The mesoporous solid is decorated with thiol groups that were treated with squaraine dye III to give a 2,4-bis(4-dialkylaminophenyl)-3-hydroxy-4-alkylsulfanylcyclobut-2-enone (APC) derivative that is covalently anchored to the inorganic silica matrix. The solid was characterised by various techniques including X-ray diffraction, transmission electron microscopy, Raman spectroscopy, and nitrogen adsorption. This hybrid solid is the chemodosimeter for Hg(2+) detection. Hg(2+) reacts with the APC fragment in U1 with release of the squaraine dye into the solution, which turns deep blue and fluoresces strongly. Naked-eye Hg(2+) detection is thus accomplished in an easy-to-use procedure. In contrast, U1 remains silent in the presence of other thiophilic transition metal ions, alkali and alkaline earth metal ions, or anions ubiquitously present in water such as chloride, carbonate, sulfate, and phosphate. Material U1 acts not only as chemodosimeter that signals the presence of Hg(2+) down to parts-per-billion concentrations, but at the same time is also an excellent adsorbent for the removal of mercury cations from aqueous solutions. The amount of adsorbed mercury ranges from 0.7 to 1.7 mmol g(-1), depending on the degree of functionalisation. In addition, hybrid material U1 can be regenerated for both sensing and removal purposes. As far as we know, U1 is the first example of a promising new class of polyfunctional hybrid supports that can be used as both remediation and alarm systems by selective signalling and removal of target species of environmental importance. Model compounds based on silica gel (G1), fumed silica (F1), and micrometre-sized MCM-41 scaffolds (M1) were also prepared and studied for comparative purposes.     

Synthesis of a peptide-linked chlorin dyad as a model compound for the photosynthetic reaction centre

The enantiomerically pure chlorins 19 and 21 were synthesised from tripyrrolic nickel complex rac-17 and pyrrole building blocks 12 and 16. The pyrroles are annelated with norbornane moieties which contain the chiral information as well as two different functionalities. The functional groups, namely a carboxylic acid ester and a carbonitrile group, of chlorin 21 finally allowed the formation of an amino acid functionality at the periphery of the macrotetracycle. By using principles of peptide chemistry, the two chlorin subunits were joined to form the peptide-linked chlorin-chlorin dyad 24, which mimics the molecular parts of the natural photosynthetic reaction centre.     

An enolisable barbiturate with adjustable hydrogen-bonding structure for UV/Vis detection of nucleic acid bases and related compounds

The use of hydrogen-bonding patterns in the same way as is known from DNA building blocks is a challenge for the construction of novel types of suitable chromophoric probes. This feature has been utilised for the construction of a novel type of UV/Vis probe for detection of supramolecular AAD or DAD sequences (A=hydrogen bond acceptor, D=hydrogen bond donor). Here we report on the structure of the enolisable chromophore 1-n-butyl-5-(4-nitrophenyl)barbituric acid (1), which has an adjustable hydrogen-bonding pattern. The position of the keto-enol equilibrium of this dye is strongly influenced both by the solvent polarity and by the chemical environment. Furthermore, the recognition properties of the barbiturate were examined by the use of seven artificial receptors: the pyridine bases 2,6-diaminopyridine (DAP), 2,6-diacetamidopyridine (DAC) and 2,6-bis(trifluoroacetamido)pyridine (TFA), as well as the nucleic acid bases 9-ethyladenine (EtAd), 9-ethylguanine (EtGu), 1-n-butylcytosine (BuCy) and 1-n-butylthymine (BuTy). It was found that 1 can interact with these bases either through acid-base interaction or by hydrogen-bonding complexation. The balance between the interactions is dependent both on the basicity strength and on the presence of a suitable recognition sequence in the base. The induced formation of the enol form of 1 thus causes a significant UV/Vis shift as function of the nature of the base.     

Clathrate formation from octaazaphthalocyanines possessing bulky phenoxyl substituents: a new cubic crystal containing solvent-filled, nanoscale voids

The synthesis of octaazaphthalocyanine (AzaPc) derivatives, with bulky phenoxyl substituents placed at eight peripheral positions and containing either H(+), Ni(2+) or Zn(2+) ions in their central cavity, is described. The required precursors, derivatives of pyrazine-2,3-dicarbonitrile, were prepared using a nucleophilic aromatic substitution reaction between 2,6-diisopropylphenol or 2,6-diphenylphenol and 5,6-dichloropyrazine-2,3-dicarbonitrile. Analysis of the resulting AzaPcs by UV/Visible and (1)H NMR spectroscopy confirms that steric isolation of the AzaPc cores was enforced both in solution and in the solid state. X-ray diffraction studies of single crystals of the AzaPcs reveal that solvent inclusion takes place in each case. Of particular significance is the finding that the zinc derivative of 2,3,9,10,16,17,23,24-octa-(2,6-diisopropylphenoxy)octaazaphthalocyanine provides nanoporous cubic crystals, containing massive (8 nm(3)) solvent-filled voids, similar to those of the analogous phthalocyanine derivative. Exchange of the included solvent within the voids can be readily achieved by using a number of alternative solvents including water. Based on the observed loading of included water, the internal volume of this nanoporous cubic crystal appears to be more hydrophilic than its phthalocyanine counterpart.     

Ultrafast Internal Conversion in a Model Anthocyanin–Polyphenol Complex: Implications for the Biological Role of Anthocyanins in Vegetative Tissues of Plants

The red flavylium cations of anthocyanins form ground‐state charge‐transfer complexes with several naturally occurring electron‐donor copigments, such as hydroxylated flavones and hydroxycinnamic or benzoic acids. Excitation of the 7‐methoxy‐4‐methyl‐flavylium–protocatechuic acid complex results in ultrafast (240 fs) internal conversion to the ground state of the complex by way of a low‐lying charge‐transfer state. Thus, both uncomplexed anthocyanins, whose excited state decays by fast (5–20 ps) excited‐state proton transfer, and anthocyanin–copigment complexes have highly efficient mechanisms of deactivation that are consistent with the proposed protective role of anthocyanins against excess solar radiation in the vegetative tissues of plants.     

Tetraazaperopyrenes: a new class of multifunctional chromophores

Tetraazaperopyrene and a range of derivatives have been synthesised and their photophysical and redox-chemical properties studied. The parent compound, 1,3,8,10-tetraazaperopyrene (1), was prepared by treating 4,9-diamino-3,10-perylenequinone diimine with triethyl orthoformate, whereas the 2,9-disubstituted derivatives of 1 were obtained after treatment with the corresponding carboxylic acid chloride or anhydride (2 mol equiv). The 1,3,8,10-tetraazaperopyrene core structure was established by X-ray diffraction of 2,9-bis(2-bromophenyl)-1,3,8,10-tetraazaperopyrene (6). The UV-visible absorption spectra of the compounds have a characteristic visible pi(*)<--pi absorption band at 440 nm (log epsilon(max)=4.80) with a strong vibrational progression (Delta nu approximately 1450 cm(-1)). Diprotonation of the nitrogen atoms induces a bathochromic shift of this band from 430-440 to 470-480 nm and all four nitrogen atoms are protonated when pure H(2)SO(4) is used as the solvent. The first and second as well as the third and fourth protonations occur concomitantly, which implies that they have very similar pK(a) values and, consequently, similar proton affinities. A theoretical study of the proton affinities in the gas phase and in solution attributes this behaviour to the effects of polar solvents, which dampen the charge of a protonated site at the other end of the molecule and thus effectively decouple the two opposite pyrimidine units in the polycondensed aromatic compound. The photophysical data were modelled in a time-dependent DFT study of 1, 1H(2)(2+) and 1H(4)(4+) in both the gas phase and in a polar solvent. All the dyes show weak fluorescence in organic solvents, however, their protonated conjugate acids show dramatically increased fluorescence intensity. All of the dyes undergo two electrochemically reversible one-electron reductions with cyclovoltammetric half-wave potentials at E(red1) approximately -0.9 V and E(red2) approximately -1.3 V (vs. SCE), which are associated with characteristic spectral changes.     

Tetramethoxy‐Aminorhodamine (TMARh): A Bichromophore,an Improved Fluorophore,and a pH Switch

Rhodamine is one of the most widely used fluorescent dyes. Here, a new synthetic pathway to the popular dyes is reported and the effect of adding four methoxy groups to the molecular structure is investigated. Tetramethoxy‐aminorhodamine ( TMARh ) is found to show superior pH switching compared to the rhodamine without the four methoxy groups, owing to changed properties of the dark “off” state and increased fluorescence intensity in the protonated “on” state.     

Antibody-catalyzed benzoin oxidation as a mechanistic probe for nucleophilic catalysis by an active site lysine

Aldolase antibody 24H6, which was obtained by reactive immunization against a 1,3-diketone hapten, is shown to catalyze additional reactions, including H/D exchange and oxidation reactions. Comparison of the H/D exchange reaction at the alpha-position of a wide range of aldehydes and ketones by 24H6 and by other aldolase antibodies, such as 38C2, pointed at the significantly larger size of the 24H6 active site. This property allowed for the catalysis of the oxidation of substituted benzoins to benzils by potassium ferricyanide. This reaction was used as a mechanistic probe to learn about the initial steps of the 24H6-catalyzed aldol condensation reaction. The Hammett correlation (rho=4.7) of log(k(cat)) versus the substituent constant, sigma, revealed that the reaction involves rapid formation of a Schiff base intermediate from the ketone and an active site lysine residue. The rate-limiting step in this oxidation reaction is the conversion of the Schiff base to an enamine intermediate. In addition, linear correlation (rho=3.13) was found between log(K(M)) and sigma, indicating that electronic rather than steric factors are dominant in the antibody-substrate binding phenomenon and confirming that the reversible formation of a Schiff base intermediate comprises part of the substrate-binding mechanism.     

Boron-diindomethene (BDI) dyes and their tetrahydrobicyclo precursors--en route to a new class of highly emissive fluorophores for the red spectral range

The X-ray crystallographic, optical spectroscopic, and electrochemical properties of a newly synthesized class of boron-diindomethene (BDI) dyes and their tetrahydrobicyclo precursors (bc-BDP) are presented. The BDI chromophore was designed to show intensive absorption and strong fluorescence in an applicationary advantageous spectral range. Its modular architecture permits fusion of a second subunit, for example, a receptor moiety to the dye's core to yield directly linked yet perpendicularly prearranged composite systems. The synthesis was developed to allow facile tuning of the chromophore platform and to thus adjust its redox properties. X-ray analysis revealed a pronounced planarity of the chromophore in the case of the BDIs, which led to a remarkable close packing in the crystal of the simplest derivative. On the other hand, deviation from planarity was found for the diester-substituted bc-BDP benzocrown that exhibits a "butterfly"-like conformation in the crystal. Both families of dyes show charge- or electron-transfer-type fluorescence-quenching characteristics in polar solvents when equipped with a strong donor in the meso-position of the core. These processes can be utilized for signaling purposes if an appropriate receptor is introduced. Further modification of the chromophore can invoke such a guest-responsive intramolecular quenching process, also for receptor groups of low electron density, for example, benzocrowns. In addition to the design of various prototype molecules, a promising fluoroionophore for Na+ was obtained that absorbs and emits in the 650 nm region and shows a strong fluorescence enhancement upon analyte binding. Furthermore, investigation of the remarkable solvatokinetic fluorescence properties of the "butterfly"-like bc-BDP derivatives suggested that a second intrinsic nonradiative deactivation channel can play a role in the photophysics of boron-dipyrromethene dyes.