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

Vibronic coupling and ultrafast relaxation dynamics in the first five excited singlet electronic states of bithiophene

The vibronic structure and nuclear dynamics in the first five excited singlet electronic states of bithiophene (2T) are investigated here. Specifically, considerations are given to comprehend the first two structureless and broad electronic absorption bands and the role of nonadiabatic coupling in the excited state relaxation mechanism of 2T in the gas phase. Associated potential energy surfaces (PESs) are established by constructing a model vibronic coupling Hamiltonian using 18 vibrational degrees of freedom and extensive ab initio electronic structure calculations. The topographies of these PESs are critically examined, and multiple conical intersections are established. The nuclear dynamics calculations are performed by propagating wave packets on the coupled electronic manifold. The present theoretical results are in good agreement with the experimental observations. It is found that strong nonadiabatic coupling between the S1-S4 and S1-S5 states along totally symmetric modes is predominantly responsible for the structureless and broad first absorption band, and overlapping S2, S3, S4, and S5 states form the second absorption band. Photorelaxation from the highly excited S5 to the lowest S1 state takes place through a cascade of diabatic population transfers among the S1-S4-S5 electronic manifold within the first ∼100 fs. Totally symmetric C=C stretching, C-S stretching, C-H wagging, ring puckering, and inter-ring bending modes collectively drive such relaxation dynamics.

Targeting Human CD22/Siglec-2 with Dimeric Sialosides as Novel Oligosaccharide Mimetics

Significant interest in the development of high-affinity ligands for Siglecs exists due to the various therapeutically relevant functions of these proteins. Here, we report a new strategy to develop and design Siglec ligands as disialyl-oligosaccharide mimetics exemplified on Siglec-2 (CD22). We report insights into development of dimeric ligands with high affinity and avidity to cell surface-expressed CD22, assay development, tool compounds, structure activity relationships, and biological data on calcium flux regulation in B-cells. The binding modes of selected ligands have been modeled based on state-of-the-art molecular dynamics simulations on the microsecond timescale, providing detailed views on ligand binding and opening a new perspective on drug design efforts for Siglecs. High-avidity dimeric ligands containing a linker opening the way towards bispecifics are presented as well.

Ab initio molecular dynamics of thiophene: the interplay of internal conversion and intersystem crossing

Ab initio on-the-fly molecular dynamics reveals that excited thiophene decays via low lying conical intersections and via intersystem crossing. Open-ring structures are responsible for the observed long life times.

1-Phenylethynylpyrene (PEPy) as a novel blue-emitting dye for qPCR assay

An alkyl azide derivative of 1-phenylethynylpyrene (PEPy) dye was prepared and used in the functionalization of oligonucleotides via click chemistry. Spectral and photo-physical properties of the PEPy-modified oligonucleotides as a single strand, and in perfect or mismatched duplexes, have been studied. A series of PEPy-Dabcyl fluorogenic TaqMan probes were synthesized and tested in qPCR. PEPy proved to be a superior substitute for AMCA as a short wavelength fluorescent dye for qPCR probes. PEPy probes were shown to significantly reduce Cq (a fractional PCR cycle used for quantification) vs. AMCA labeled probes, thus improving on the reliability of detection. Moreover, a larger increase of fluorescence during amplification was observed in the case of PEPy probes that makes this dye very suitable for an end-point PCR technique. This study broadens the panel of fluorescent dyes suitable for the use in probes for quantitative real-time PCR.

Deactivation pathways of thiophene and oligothiophenes: internal conversion versus intersystem crossing

Quantum chemical calculations reveal that excited thiophene decays via a low lying conical intersection seam. In oligothiophenes barriers inhibit this passage while deactivation pathways via intersystem crossing channels open.

Self-assembling oligothiophene–bolaamphiphiles for loading and controlled release of doxorubicin into living cells

Symmetric mannose-functionalized oligothiophenes for efficient transport and release of the anti-tumour drug doxorubicin.

New biocompatible polymeric micelles designed for efficient intracellular uptake and delivery

New amphiphilic block copolymers are easily synthesised by post-polymerisation modifications of poly(glycidyl methacrylate) chain derivatives. The obtained material, upon dispersion in water, is capable of self-assembling into robust micelles. These nanoparticles, which are also characterised by adaptable stability, were loaded with different thiophene based fluorophores. The photoluminescent micelles were administered to cultured cells revealing a high and rapid internalisation of structurally different fluorescent molecules by the same internalisation pathway. Appropriate pairs of chromophores were selected and loaded into the micelles to induce Förster resonance energy transfer (FRET). The disappearing of the FRET phenomenon, after cell uptaking, demonstrated the intracellular release of the nanoparticle contents. The studied nanomaterial and the loaded chromophores have also shown to be biocompatible and non toxic towards the tested cells.

0-0 Energies Using Hybrid Schemes: Benchmarks of TD-DFT, CIS(D), ADC(2), CC2, and BSE/GW formalisms for 80 Real-Life Compounds

The 0-0 energies of 80 medium and large molecules have been computed with a large panel of theoretical formalisms. We have used an approach computationally tractable for large molecules, that is, the structural and vibrational parameters are obtained with TD-DFT, the solvent effects are accounted for with the PCM model, whereas the total and transition energies have been determined with TD-DFT and with five wave function approaches accounting for contributions from double excitations, namely, CIS(D), ADC(2), CC2, SCS-CC2, and SOS-CC2, as well as Green's function based BSE/GW approach. Atomic basis sets including diffuse functions have been systematically applied, and several variations of the PCM have been evaluated. Using solvent corrections obtained with corrected linear-response approach, we found that three schemes, namely, ADC(2), CC2, and BSE/GW allow one to reach a mean absolute deviation smaller than 0.15 eV compared to the measurements, the two former yielding slightly better correlation with experiments than the latter. CIS(D), SCS-CC2, and SOS-CC2 provide significantly larger deviations, though the latter approach delivers highly consistent transition energies. In addition, we show that (i) ADC(2) and CC2 values are extremely close to each other but for systems absorbing at low energies; (ii) the linear-response PCM scheme tends to overestimate solvation effects; and that (iii) the average impact of nonequilibrium correction on 0-0 energies is negligible.

Supramolecular oligothiophene microfibers spontaneously assembled on surfaces or coassembled with proteins inside live cells

During the last few decades, multifunctional nano- and microfibers made of semiconducting π-conjugated oligomers and polymers have generated much interest because of a broad range of applications extending from sensing to bioelectronic devices and (opto)electronics. The simplest technique for the fabrication of these anisotropic supramolecular structures is to let the molecules do the work by spontaneous organization driven by the information encoded in their molecular structure. Oligothiophenes-semiconducting and fluorescent compounds that have been extensively investigated for applications in thin-film field-effect transistors and solar cells and to a lesser extent as dyes for fluorescent labeling of proteins, DNA, and live cells-are particularly suited as building blocks for supramolecular architectures because of the peculiar properties of the thiophene ring. Because of the great polarizability of sulfur outer-shell electrons and the consequent facile geometric deformability and adaptability of the ring to the environment, thiophene can generate multiple nonbonding interactions to promote non-covalent connections between blocks. Furthermore, sulfur can be hypervalent, i.e., it can accommodate more than the eight electrons normally associated with s and p shells. Hypervalent oligothiophene-S,S-dioxides whose oxygen atoms can be involved in hydrogen bonding have been synthesized. These compounds are amphiphilic, and some of them are able to spontaneously cross the membrane of live cells. Hypervalent nonbonding interactions of divalent sulfur, defined as weak coordination to a proximate nitrogen or oxygen, have also been invoked in the solid-state packing of many organic molecules and in the architecture of proteins. In this Account, we describe two different types of thiophene-based building blocks that can induce the spontaneous formation of nanostructured microfibers in very different environments. The first, based on the synthesis of "sulfur-overrich" hexamers and octamers, leads to surface-independent self-assembly of microfibers-helical or rodlike depending on the groups attached to the same identical inner core-that are crystalline, fluorescent, and conductive and display chirality despite the lack of chiral carbon atoms on the building blocks. Supramolecular polymorphic microfibers are also formed, and they are characterized by very different functional properties. The second, based on a rigid oligothiophene-S,S-dioxide, leads to coassembled protein-oligothiophene microfibers that are physiologically formed inside live cells. The oligothiophene-S,S-dioxide can indeed spontaneously cross the membrane of live cells and be directed toward the perinuclear region, where it is recognized and incorporated by specific peptides during the formation of fibrillar proteins without being harmful to the cells. Coassembled oligothiophene-protein microfibers are progressively formed through a cell-mediated physiological process. Thanks to the oligothiophene blocks, the microfibers possess fluorescence and charge-conduction properties. By means of fluorescence imaging, we demonstrated that various types of live cells seeded on these microfibers were able to internalize and degrade them, experiencing in turn different effects on their morphology and viability, suggesting a possible use of the microfibers as multiscale biomaterials to direct cell behavior. On the whole, our results show the great versatility of oligothiophene building blocks and allow us to foresee that their capabilities of spontaneous assembly in the most different environments could be exploited in much more exciting research fields than those explored to date.

Palladium-catalyzed direct C–H arylations of dioxythiophenes bearing reactive functional groups: a step-economical approach for functional π-conjugated oligoarenes

A phosphine-free C–H arylation of dioxythiophenes bearing unprotected functional groups affords oligoarenes with good yields.

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.

Live cell cytoplasm staining and selective labeling of intracellular proteins by non-toxic cell-permeant thiophene fluorophores

A structurally correlated series of cell-permeant thiophene fluorophores, characterized by intense green or red fluorescence inside live mouse embryonic fibroblasts, was developed. The fluorophores displayed rapid internalization, excellent retention inside the cells, and high optical stability in the cytosolic environment and did not alter cell viability and reproducibility. Depending on the molecular structure, they experienced distinct fate inside the cells: from bright and lasting staining of the cytoplasm to selective tagging of a small set of globular proteins.

Performance of an Optimally Tuned Range-Separated Hybrid Functional for 0-0 Electronic Excitation Energies

Using a set of 40 conjugated molecules, we assess the performance of an "optimally tuned" range-separated hybrid functional in reproducing the experimental 0-0 energies. The selected protocol accounts for the impact of solvation using a corrected linear-response continuum approach and vibrational corrections through calculations of the zero-point energies of both ground and excited-states and provides basis set converged data thanks to the systematic use of diffuse-containing atomic basis sets at all computational steps. It turns out that an optimally tuned long-range corrected hybrid form of the Perdew-Burke-Ernzerhof functional, LC-PBE*, delivers both the smallest mean absolute error (0.20 eV) and standard deviation (0.15 eV) of all tested approaches, while the obtained correlation (0.93) is large but remains slightly smaller than its M06-2X counterpart (0.95). In addition, the efficiency of two other recently developed exchange-correlation functionals, namely SOGGA11-X and ωB97X-D, has been determined in order to allow more complete comparisons with previously published data.

TD-DFT Assessment of Functionals for Optical 0-0 Transitions in Solvated Dyes

Using TD-DFT, we performed simulations of the adiabatic energies of 40 fluorescent molecules for which the experimental 0-0 energies in condensed phase are available. We used six hybrid functionals (B3LYP, PBE0, M06, M06-2X, CAM-B3LYP, and LC-PBE) that have been shown to provide accurate transition energies in previous TD-DFT assessments, selected two diffuse-containing basis sets, and applied the most recent models for estimating bulk solvation effects. In each case, the correction arising from the difference of zero-point vibrational energies between the ground and the excited states has been consistently determined. Basis set effects have also been carefully studied. It turned out that PBE0 and M06 are the most effective functionals in terms of average deviation (mean absolute error of 0.22-0.23 eV). However, both the M06-2X global hybrid that contains more exact exchange and the CAM-B3LYP range-separated hybrid significantly improve the consistency of the prediction for a relatively negligible degradation of the average error. In addition, we assessed (1) the cross-structure/spectra relationships, (2) the importance of solvent effects, and (3) the differences between adiabatic and vertical energies.

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.

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.

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.

Oligothiophene-5-labeled deoxyuridines for the detection of single nucleotide polymorphisms

We report the synthesis of four oligothiophene-5-labeled deoxyuridines. These modified fluorescent nucleosides have been incorporated into oligodeoxynucleotides designed to be used as probes to discriminate, through changes in fluorescence emission, between hybridization with a perfectly complementary strand and that with a single nucleotide mismatch facing the modified uridines. Upon hybridization, remarkable differences (up to 47%) of the emitted light, depending on the uridine facing base, were observed.

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.

Single cell fluorescence imaging using metal plasmon-coupled probe

This work constitutes the first fluorescent imaging of cells using metal plasmon-coupled probes (PCPs) at single cell resolution. N-(2-Mercapto-propionyl)glycine-coated silver nanoparticles were synthesized by reduction of silver nitrate using sodium borohyride and then succinimidylated via ligand exchange. Alexa Fluor 647-labeled concanavalin A (con A) was chemically bound to the silver particles to make the fluorescent metal plasmon-coupled probes. The fluorescence images were collected using a scanning confocal microscopy. The fluorescence intensity was observed to enhance 7-fold when binding the labeled con A on a single silver particle. PCPs were conjugated on HEK 293 A cells. Imaging results demonstrate that cells labeled by PCPs were 20-fold brighter than those by free labeled con A.

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.

Local CC2 electronic excitation energies for large molecules with density fitting

A new local method for the computation of electronic excitation energies of singlet states in extended molecular systems is presented. It is based on the CC2 model and local approximations to the wave functions. In the proposed method the singles excitations are treated nonlocally and local restrictions are imposed on doubles amplitudes only. The accuracy of the new method was tested by calculating several lowest excited states for 14 molecules and comparing them with canonical CC2 values. Deviations of the local excitation energies from the canonical reference values do not exceed 0.05 eV for all test molecules and all states in the lower energy range investigated in this work. The method uses the density-fitting approximation for all two-electron integrals, which considerably simplifies the computational complexity of the individual diagrams. A combination of the local approximations and the powerful density-fitting technique leads to a low-scaling method, capable to treat molecular systems comprised of 100 atoms and more in a basis of a polarized double zeta quality. A test calculation for a system consisting of 127 atoms and 370 active electrons without symmetry is presented to show the efficiency of the new method.

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.