Oligothiophene isothiocyanates as a new class of fluorescent markers for biopolymers

Iodine-catalyzed three-component annulation: access to highly fluorescent trisubstituted thiophenes

An efficient synthesis of highly fluorescent trisubstituted thiophenes was achieved via iodine-catalyzed, base-promoted annulation employing elemental sulfur as a sulfur source. The compounds exhibit excellent photophysical properties like solid-state fluorescence, high quantum yield and solvatochromism. As these thiophene derivatives have potential application in the development of optoelectronic devices, gram-scale synthesis of the desired heterocycles was demonstrated.

Synthesis of Glycodendrimers with Antiviral and Antibacterial Activity

Glycodendrimers are an important class of synthetic macromolecules that can be used to mimic many structural and functional features of cell-surface glycoconjugates. Their carbohydrate moieties perform key important functions in bacterial and viral infections, often regulated by carbohydrate-protein interactions. Several studies have shown that the molecular structure, valency and spatial organisation of carbohydrate epitopes in glycoconjugates are key factors in the specificity and avidity of carbohydrate-protein interactions. Choosing the right glycodendrimers almost always helps to interfere with such interactions and blocks bacterial or viral adhesion and entry into host cells as an effective strategy to inhibit bacterial or viral infections. Herein, the state of the art in the design and synthesis of glycodendrimers employed for the development of anti-adhesion therapy against bacterial and viral infections is described.

Oligoprolines guide the self-assembly of quaterthiophenes

Oligoprolines of differing lengths control the self-assembly of quaterthiophenes into mono-layered or double-layered sheets, or helically twisted ribbons.

Control over the molecular organization of π-conjugated oligothiophenes into different types of supramolecular assemblies is key to their use in organic electronics but difficult to achieve as these chromophores have a pronounced tendency to aggregate. Herein we show that oligoprolines, which do not self-assemble on their own, control the self-assembly of quaterthiophenes. Spectroscopic, microscopic, and diffraction studies with quaterthiophene–oligoproline conjugates revealed the formation of mono- or double-layered sheets or, alternatively, helically twisted ribbons – depending on the length of the oligoproline. The dimensions of the nanoscopic objects, which extend into the micrometer regime, correlate with the molecular dimensions of the quaterthiophene–oligoproline building blocks.

A solid phase-assisted approach for the facile synthesis of a highly water-soluble zirconium-89 chelator for radiopharmaceutical development

The solid-phase synthesis of a water-soluble bifunctional chelator for ⁸⁹Zr is reported.

Fluorescent thiophene-based materials and their outlook for emissive applications

An overview of fluorescent thiophene-based materials and their applications, highlighting in particular the various methods employed to achieve highly emissive materials.

The geometry relaxation and intersystem crossing of quaterthiophene studied by femtosecond spectroscopy

The geometry relaxation in the singlet state and the intersystem crossing from relaxed singlet to triplet state are 70 and 398 ps, respectively.

Multivalent glycoconjugate syntheses and applications using aromatic scaffolds

Glycan-protein interactions are of utmost importance in several biological phenomena. Although the variety of carbohydrate residues in mammalian cells is limited to less than a dozen different sugars, their spatial topographical presentation in what is now associated as the "glycocodes" provides the fundamental keys for specific and high affinity "lock-in" recognition events associated with a wide range of pathologies. Toward deciphering our understanding of these glycocodes, chemists have developed new creative tools that included dendrimer chemistry in order to provide monodisperse multivalent glycoconjugates. This review provides a survey of the numerous aromatic architectures generated for the multivalent presentation of relevant carbohydrates using covalent attachment or supramolecular self-assemblies. The basic concepts toward their controlled syntheses will be described using modern synthetic procedures with a particular emphasis on powerful organometallic methodologies. The large variety of dendritic aromatic scaffolds, together with a brief survey of their unique biophysical and biological properties will be critically reviewed. The distinctiveness of the resulting multivalent glycoarchitectures, encompassing glycoclusters, glycodendrimers and molecularly defined self-assemblies, in forming well organized cross-linked lattices with multivalent carbohydrate binding proteins (lectins) together with their photophysical, medical, and imaging properties will also be briefly highlighted. The topic will be presented in increasing order of aromatic backbone complexities and will end with fullerenes together with self-assembled nanostructures, thus complementing the various scaffolds described in this special thematic issue dedicated to multivalent glycoscience.

Polymer coated inorganic nanoparticles: tailoring the nanocrystal surface for designing nanoprobes with biological implications

The use of inorganic nanoparticles in biomedicine, in particular in the field of diagnosis and therapy of human diseases, has rapidly grown in the last few decades. Water solubilisation of the nanoparticles, especially for particles synthesized in non-polar solvents, is an essential prerequisite for their biological exploitation. The encapsulation of surfactant coated nanoparticles into polymer shells represents one of the most suitable and most popular methods to make them water soluble. Herein we provide an overview of the amphiphilic polymer molecules used and the efforts undertaken to further tailor the surface of polymer coated nanoparticles with fluorescent dyes, chemical sensor molecules and small or large biomolecules for the preparation of bio-functional nanoprobes. Their biological implications, highlighting limitations and challenges, are also discussed.

Surface functionalization of aluminosilicate nanotubes with organic molecules

The surface functionalization of inorganic nanostructures is an effective approach for enriching the potential applications of existing nanomaterials. Inorganic nanotubes attract great research interest due to their one-dimensional structure and reactive surfaces. In this review paper, recent developments in surface functionalization of an aluminosilicate nanotube, "imogolite", are introduced. The functionalization processes are based on the robust affinity between phosphate groups of organic molecules and the aluminol (AlOH) surface of imogolite nanotubes. An aqueous modification process employing a water soluble ammonium salt of alkyl phosphate led to chemisorption of molecules on imogolite at the nanotube level. Polymer-chain-grafted imogolite nanotubes were prepared through surface-initiated polymerization. In addition, the assembly of conjugated molecules, 2-(5''-hexyl-2,2':5',2''-terthiophen-5-yl)ethylphosphonic acid (HT3P) and 2-(5''-hexyl-2,2':5',2''-terthiophen-5-yl)ethylphosphonic acid 1,1-dioxide (HT3OP), on the imogolite nanotube surface was achieved by introducing a phosphonic acid group to the corresponding molecules. The optical and photophysical properties of these conjugated-molecule-decorated imogolite nanotubes were characterized. Moreover, poly(3-hexylthiophene) (P3HT) chains were further hybridized with HT3P modified imogolite to form a nanofiber hybrid.

Oligothiophenes as fluorescent markers for biological applications

This paper summarizes some of our results on the application of oligothiophenes as fluorescent markers for biological studies. The oligomers of thiophene, widely known for their semiconductor properties in organic electronics, are also fluorescent compounds characterized by chemical and optical stability, high absorbance and quantum yield. Their fluorescent emission can be easily modulated via organic synthesis by changing the number of thiophene rings and the nature of side-chains. This review shows how oligothiophenes can be derivatized with active groups such as phosphoramidite, N-hydroxysuccinimidyl and 4-sulfotetrafluorophenyl esters, isothiocyanate and azide by which the (bio)molecules of interest can be covalently bound. This paper also describes how molecules such as oligonucleotides, proteins and even nanoparticles, tagged with oligothiophenes, can be used in experiments ranging from hybridization studies to imaging of fixed and living cells. Finally, a few multilabeling experiments are described.

Photochemical stabilization of terthiophene and its utilization as a new sensing element in the fabrication of monolayer-chemistry-based fluorescent sensing films

To improve the photochemical stability of α-terthiophene (3T) in air, we purposely introduced a naphthalene unit into its conjugated backbone, resulting in a fluorescent compound, 5-(1-naphthyl)-2,2':5',2''-terthiophene (NA-3T). The compound was further employed as a sensing element for the fabrication of a monolayer-chemistry based fluorescent sensing film. It was demonstrated that the fabricated film is highly sensitive and selective to the presence of picric acid (PA). The detection limit was found to be 3.2 × 10(-7) mol/L. The high sensitivity of the film to PA has been attributed to the specific binding of the film to the analyte because of proton transfer from PA to the amino group in the spacer, which is in accordance with the static nature of the quenching as revealed by fluorescence lifetime measurements. Further experiments demonstrated that the sensing process is fully reversible and free of interference from common organic solvents, acids and bases, etc. In addition, the film is stable, at least, within half a year provided it is properly preserved. More importantly, the present work makes it possible to use oligothiophenes as a new class of sensing elements, which may combine the advantages of conjugated polymers or oligomers and those of fluorescent compounds of low-molecular masses. This effort enlarges, definitely, the applications of oligothiophenes and the space for creating monolayer-chemistry based fluorescent sensing films.

Microwave-assisted synthesis of thiophene fluorophores, labeling and multilabeling of monoclonal antibodies, and long lasting staining of fixed cells

We report the expedient microwave-assisted synthesis of thiophene based 4-sulfo-2,3,5,6,-tetrafluorophenyl esters whose molecular structure was engineered to achieve blue to red bright fluorescence. The reactivity toward monoclonal antibodies of the newly synthesized fluorophores was analyzed in comparison with that of the corresponding N-succinimidyl esters. Single-fluorophore and multiple-fluorophore labeled antibodies were easily prepared with both types of esters. Multiple-fluorophore labeling with blue and orange emitting fluorophores resulted in white fluorescent antibodies. Thiophene based fluorophores displayed unprecedented fluorescence stability in immunostaining experiments. First-principles TD-DFT theoretical calculations helped us to interpret the behavior of fluorescence emission in different environments.

Fluorescent oligo and poly-thiophenes and their utilization for recording biological events of diverse origin-when organic chemistry meets biology

The technique of using luminescent oligo-thiophenes and luminescent conjugated poly-thiophenes to monitor biological processes has gained increased interest from scientists within different research areas, ranging from organic chemistry and photo-physics to biology since its introduction. The technique is generally straightforward and requires only standard equipment, and the result is available within minutes from sample preparation. In this review, the syntheses of oligo and polythiophenes developed over the last decades are discussed. Furthermore, the utilization of these molecular agents for exploring biological events, e.g., DNA hybridization or protein misfolding events, are covered.

The role of intrachain and interchain interactions of regioregular poly(3-octylthiophene) chains on the optical properties of a new amphiphilic conjugated random copolymer in solution

The synthesis of a random copolymer through free radical copolymerization of a properly vinyl monofunctionalized regioregular poly(3-octylthiophene) (rrP3OT) macromonomer and N,N'-dimethylacrylamide (DMAM) is presented. The optical properties of the copolymer in water and in several organic solvents of varying polarity, as well as in THF/water and THF/methanol mixtures, were explored using UV-vis and photoluminescence spectroscopy. It is demonstrated that the rrP3OT chains adopt a coil conformation in solvents such as tetrahydrofuran (THF) and chloroform with the appearance of the absorption and emission maxima at 439 and 565 nm, respectively. On the contrary, the rrP3OT chains are organized on a single chain packing form (intrachain interactions) in polar solvents such as ethanol and methanol, as it is verified with the observation of the characteristic three vibronic features of the absorption spectra of the copolymer with maxima at 513, 550, and 603 nm and emission maxima at 560 nm. However, when water is used as solvent, the rrP3OT chains self-assemble into a stacklike structure due to the increased interchain interactions, as confirmed by the different aggregation process of the rrP3OT chains in the THF/water mixture, the broader absorption spectrum in water compared to those recorded in ethanol and methanol, and the 80 nm red-shifted emission maximum, centered at 640 nm.

Optical detection of DNA and proteins with cationic polythiophenes

In recent years, intense research has been carried out worldwide with the goal of developing simple, sensitive, and specific detection tools for biomedical applications. Along these lines, we reported in 2002 on cationic polythiophene derivatives able to provide ultrasensitive detection levels and the capability to distinguish perfect matches from oligonucleotides having as little as a single base mismatch. It was shown that the intrinsic fluorescence of the random-coil polymers quenches as a result of the planar, highly conjugated conformation adopted by the polymers when complexed with a single-strand DNA (ssDNA) capture probe but increases again after hybridization with the perfectly matched complementary strand. This change in fluorescence intensity is mainly due to a modification in the delocalization of pi electrons along the carbon chain backbone that occurs when switching between the two conformations. Thus, by monitoring, via the change in fluorescence intensity, the hybridization of the complementary ssDNA target with the "duplex", one could detect as little as 220 complementary target molecules in a 150 microL sample volume (0.36 zmol) in less than 1 hour. Building on this initial concept, we then reported that tagging the DNA probe with a suitable fluorophore dramatically increases the detection sensitivity. This novel molecular system involves the self-assembly of aggregates of duplexes in solution, prior to the introduction of the target, which allows a highly efficient resonance energy transfer (RET) between a "donor" (being the complex formed of the DNA double helix and the polymer chain wrapped around it) and a large number of neighboring "acceptors" (the fluorophores attached to the DNA probes). The massive intrinsic signal amplification (fluorescence chain reaction or FCR) provided by this novel integrated molecular system allows the specific detection of as little as five dsDNA copies in a 3 mL sample volume in only 5 minutes, without the need for prior amplification of the target. Clearly, direct and reliable detection of DNA hybridization without prior PCR amplification or chemical tagging of the genetic target is now possible with this methodology. We have also shown that proteins can be detected following a similar strategy. Impressive results have also been reported by direct and specific staining of targeted proteins. All these features have recently allowed the development of responsive polymeric supports for the detection of DNA and proteins. All these assays that do not require any chemical manipulation of the biological targets or sophisticated experimental procedures should soon lead to major advances in genomics and proteomics.

Synthesis of self-organizing mesogenic materials containing a sulfur-based five-membered heterocyclic core

The majority of low molar mass calamitic mesogenic systems in the literature contain linear cores based on the 1,4-disubstituted phenyl ring. Heterocyclic cores such as thiophene impart unique physical properties as their slightly bent structure leads to features including a reduced packing ability (generally giving rise to lower melting points than their phenyl counterparts), a medium to strong lateral dipole, high anisotropy of the polarizability, low viscosity etc. This critical review describes the most recent synthetic methodology that has been used to prepare thiophene, 1,3-thiazole, and 1,3,4-thiadiazole-based mesogenic materials.

Synthesis of Photostable Amine-Reactive Fluorescent Dyes by Postsynthetic Conversion of Bromide Dithienothiophene Derivatives

The synthesis, purification, and spectral properties of new dithienothiophene-based fluorescent dyes with a terminal alkyl bromide group are described. The bromides were easily converted to isothiocyanates and N-succinimidyl esters by appropriate chemical transformations with sodium thiocyanate or N-hydroxysuccinimide. The new fluorophores exhibited intense fluorescence emission and high photostability. Their suitability for bioanalytical applications was evaluated through conjugation with amine-reactive polystyrene microspheres and IgG anti-CD3 monoclonal antibody.

An Effective Strategy to Tune Supramolecular Interaction via a Spiro-Bridged Spacer in Oligothiophene-S,S-dioxides and Their Anomalous Photoluminescent Behavior

[structure: see text] We demonstrate that incorporating nonplanar spiro-bridged structures is an effective strategy for tuning supramolecular interactions of optoelectronic functional moieties. In the model compounds spiro-bridged oligothiophene-S,S-dioxides (BSiSDTFO), unusual dimers constructed by spiro-bridged spacers do not form excimers, which is confirmed by crystallographic data and fluorescent emission spectra.

Testing Oligothiophene Fluorophores under Physiological Conditions. Preparation and Optical Characterization of the Conjugates of Bovine Serum Albumin with Oligothiophene N-Hydroxysuccinimidyl Esters

Bovine serum albumin (BSA) was reacted with linear and newly synthesized branched oligothiophene N-hydroxysuccinimidyl ester fluorophores (TSEs) in moderately basic carbonate buffer solution. Optically stable BSA-TSE conjugates were obtained with a degree of labeling depending on experimental conditions. Conjugates with high fluorophore to BSA ratios (F/BSA = 8) displayed fluorescence quantum yields in the range of 10-30% in water at pH = 7.2, comparable to the quantum yield (25%) of the BSA-FITC conjugate prepared under the same conditions and with the same degree of labeling.

Oligothiophene molecular beacons

Oligomers of thiophene are widely studied compounds for their electronic and optoelectronic properties. Despite their strong fluorescence, their use as markers for biomolecules, especially for oligonucleotides (ONs), is still largely unexplored. Here, we describe the synthesis of a series of ON molecular beacons employing different oligothiophenes as fluorescent probes and discuss their fluorescence emissions in comparative experiments with and without dabcyl as a quencher, in their hairpin and linear conformations, and as duplexes after hybridization with a complementary target.

Bright oligothiophene N-succinimidyl esters for efficient fluorescent labeling of proteins and oligonucleotides

The synthesis of multicolor fluorescent oligothiophene N-succinimidyl esters (TSEs) is reported, and their optical properties are discussed with the aid of ab initio calculations. The esters were coupled to proteins and to 3'-amino-modified oligonucleotides in mild conditions and with similar modalities. A comparative study of the bioconjugate of IgG1 anti-CD3 antibody labeled with a blue fluorescent TSE and with fluorescein isothiocyanate (FITC) is reported, showing that the former achieves higher photoluminescence intensity and optical stability than the latter. Fluorescence resonance energy transfer experiments with TSE-labeled oligonucleotides and examples of cellular imaging via TSE-labeled proteins are reported.

Optical Properties of N-Succinimidyl Bithiophene and the Effects of the Binding to Biomolecules: Comparison between Coupled-Cluster and Time-Dependent Density Functional Theory Calculations and Experiments

We report a joint theoretical-experimental study on the optical properties of 5-N-succinimidyl-2,2'-bithiophene (NS-2T), a prototype system for a new class of biomarkers. Time-dependent density functional theory (TD-DFT) and approximate coupled-cluster single and doubles (CC2) calculations are performed in the ground and excited states. Theoretical results are compared with absorption, photoluminescence (PL), time-resolved PL, and PL quantum efficiency measurements. The excited state of NS-2T has a larger dipole moment as compared to that of the ground state, explaining the experimental shift of the PL peak in solvents of different polarity, and a smaller intersystem crossing (ISC) rate as compared to that of isolated bithiophene (2T), explaining the increased PL quantum efficiency. We also studied two model systems to describe the effects of the covalent binding of NS-2T to biomolecules and proteins with the epsilon-NH(2) lysine groups. These model systems show optical properties closer to 2T, as the PL quantum efficiency is reduced due to the increased ISC rate. Theoretical calculations and experimental results show that covalent binding of NS-2T to a biomolecule will blue-shift the absorption but not the photoluminescence. CC2 and TD-DFT can very well describe the absorption and photoluminescence energies of all three systems, but the presence of several charge-transfer transitions in the TD-DFT spectrum of NS-2T required the use of a correlated method to validate the TD-DFT results.