Rational Design of Bright Long Fluorescence Lifetime Dyad Fluorophores for Single Molecule Imaging and Detection.

Increasing demand for detecting single molecules in challenging environments has raised the bar for the fluorophores used. To achieve better resolution and/or contrast in fluorescence microscopy, it is now essential to use bright and stable dyes with tailored photophysical properties. While long fluorescence lifetime fluorophores offer many advantages in time-resolved imaging, their inherently lower molar absorption coefficient has limited applications in single molecule imaging. Here we propose a generic approach to prepare bright, long fluorescence lifetime dyad fluorophores comprising an absorbing antenna chromophore with high absorption coefficient linked to an acceptor emitter with a long fluorescence lifetime. We introduce a dyad consisting of a perylene antenna and a triangulenium emitter with 100% energy transfer from donor to acceptor. The dyad retained the long fluorescence lifetime (∼17 ns) and high quantum yield (75%) of the triangulenium emitter, while the perylene antenna increased the molar absorption coefficient (up to 5 times) in comparison to the free triangulenium dye. These triangulenium based dyads with significantly improved brightness can now be detected at the single molecule level and easily discriminated from bright autofluorescence by time-gated and other lifetime-based detection schemes.

Assessing The Key Photophysical Properties of Triangulenium Dyes for DNA Binding by Alteration of the Fluorescent Core.

Four-stranded G-quadruplex (G4) DNA is a non-canonical DNA topology that has been proposed to form in cells and play key roles in how the genome is read and used by the cellular machinery. Previously, a fluorescent triangulenium probe (DAOTA-M2) was used to visualise G4s in cellulo, thanks to its distinct fluorescence lifetimes when bound to different DNA topologies. Herein, the library of available triangulenium probes is expanded to explore how modifications to the fluorescent core of the molecule affect its photophysical characteristics, interaction with DNA and cellular localisation. The benzo-bridged and isopropyl-bridged diazatriangulenium dyes, BDATA-M2 and CDATA-M2 respectively, featuring ethyl-morpholino substituents, were synthesised and characterised. The interactions of these molecules with different DNA topologies were studied to determine their binding affinity, fluorescence enhancement and fluorescence lifetime response. Finally, the cellular uptake and localisation of these optical probes were investigated. Whilst structural modifications to the triangulenium core only slightly alter the binding affinity to DNA, BDATA-M2 and CDATA-M2 cannot distinguish between DNA topologies through their fluorescence lifetime. It is argued theoretically and experimentally that this is due to reduced effectiveness of photoinduced electron transfer (PET) quenching. This work presents valuable new evidence into the critical role of PET quenching when using the fluorescence lifetime of triangulenium dyes to discriminate G4 DNA from duplex DNA, highlighting the importance of fine tuning redox and spectral properties when developing new triangulenium-based G4 probes.

Extended Triangulenium Ions: Syntheses and Characterization of Benzo-Bridged Dioxa- and Diazatriangulenium Dyes.

The very limited class of fluorophores, with a long fluorescence lifetime (>10 ns) and fluorescence beyond 550 nm, has been expanded with two benzo-fused triangulenium derivatives and two cationic [5]-helicene salts. The syntheses of the benzo-bridged dioxa- and diazatriangulenium derivatives (BDOTA+ and BDATA+, respectively) required two different synthetic approaches, which reflect the structural and physiochemical impact on the reactivity of [5]-helicenium precursors. Spectroscopic investigations show that the introduction of the benzo bridge into the triangulenium chromophore significantly redshifts the absorption and emission while maintaining fluorescence lifetimes above 10 ns. The combination of a high quantum yield, long fluorescence lifetime, and emission above 600 nm is possible only if the structural aspects of the triangulenium framework are perfectly harmonized to secure a low rate of nonradiative deactivation. The new benzo bridge may be a general motif to obtain red-shifted derivatives of other dye classes.

Fluorometric Recognition of Nucleotides within a Water-Soluble Tetrahedral Capsule.

The design of aqueous probes and binders for complex, biologically relevant anions presents a key challenge in supramolecular chemistry. Herein, a tetrahedral assembly with cationic faces and corners is reported that is capable of discriminating between anionic and neutral guests in water. Electrostatic repulsion between subcomponents can be overcome by the addition of an anionic template, or generating a robust covalent framework by incorporating tris(2-aminoethyl)amine (TREN). The resultant TREN-capped, water-soluble, fluorescent cage binds mono- and poly-phosphoric esters, including nucleotides. Its covalent skeleton renders it stable at micromolar concentrations in water, enabling the fluorometric detection of biologically relevant guests in an aqueous environment. Selective supramolecular encapsulants, such as 1, could enable new sensing applications, such as recognition of toxins and drugs, under biological conditions.

Synthesis and properties of sulfur-functionalized triarylmethylium, acridinium and triangulenium dyes.

Triangulenium dyes functionalized with one, two or three ethylthiol functionalities were synthesized and their optical properties were studied. The sulfur functionalities were introduced by aromatic nucleophilic substitution of methoxy groups in triarylmethylium cations with ethanethiol followed by partial or full ring closure of the ortho positions with nitrogen or oxygen bridges leading to sulfur-functionalized acridinium, xanthenium or triangulenium dyes. For all the dye classes the sulfur functionalities are found to lead to intensely absorbing dyes in the visible range (470 to 515 nm), quite similar to known analogous dye systems with dialkylamino donor groups in place of the ethylthiol substituents. For the triangulenium derivatives significant fluorescence was observed (Φf = 0.1 to Φf = 0.3).

Thieno-Fused Subporphyrazines: A New Class of Light Harvesters.

Boron subphthalocyanines comprised of three isoindole units bridged by aza-linkages are attractive light harvesters on account of their intense low-energy absorptions. Herein, we present a class of related compounds, in which one or two isoindole units are substituted for thieno[3,4-c]pyrrole units - thieno-fused subporphyrazines. Such changes have remarkable consequences for the optical properties, as was revealed by combined experimental and theoretical studies. Thus, we find that the lowest-energy absorptions cover a much broader region with a significantly redshifted end-absorption and without compromising the absorption intensities. Thieno-fused subporphyrazines also underwent more readily oxidation and reduction, indicating an increased HOMO energy and decreased LUMO energy. In addition, they were found to readily co-crystallize with Buckminsterfullerene, C60 . Altogether, these findings render this new class of chromophores attractive candidates for light-harvesting applications.

Acetylenic scaffolding with subphthalocyanines - synthetic scope and elucidation of electronic interactions in dimeric structures.

Boron subphthalocyanines (SubPcs) are powerful chromophoric heterocycles that can be synthetically modified at both axial and peripheral positions. Acetylenic scaffolding offers the possibility of building large, unsaturated carbon-rich frameworks that can exhibit excellent electron-accepting properties, and when combined with SubPcs it presents a convenient method for preparing interesting chromophore-acceptor architectures. Here we present synthetic methodologies for the post-functionalization of the relatively sensitive SubPc chromophore via acetylenic coupling reactions. By gentle AlCl3-mediated alkynylation at the axial boron position, we managed to anchor two SubPcs to the geminal positions of a tetraethynylethene (TEE) acceptor. Convenient conditions that allow for stepwise desilylations of trimethylsilyl (TMS) and triisopropylsilyl (TIPS) protected SubPc-decorated acetylenes using silver(i) fluoride were developed. The resulting terminal alkynes were successfully used as coupling partners in metal-catalyzed couplings, providing access to larger acetylenic SubPc scaffolds and multiple chromophore systems. Moreover, conditions allowing for the conversion of a terminal alkyne into an iodoalkyne in the presence of SubPc were developed, and the product was subjected to cross-coupling reactions affording unsymmetrical 1,3-butadiynes. The degree of interactions between two SubPc units as a function of the acetylenic bridge was studied by UV-Vis absorption spectroscopy and cyclic voltammetry. A TEE bridging unit was found to strongly influence the reductions and oxidations of the two SubPc units, while a more flexible bridge had no influence.

Diazaoxatriangulenium: synthesis of reactive derivatives and conjugation to bovine serum albumin.

The azaoxa-triangulenium dyes are characterised by emission in the red and a long fluorescence lifetime (up to 25 ns). These properties have been widely explored for the azadioxatrianguelnium (ADOTA) dye. Here, the syntheses of reactive maleimide and NHS-ester forms of the diazaoxatriangulenium (DAOTA) system are reported. The DAOTA fluorophore was conjugated to bovine serum albumin (BSA) and investigated in comparison to the corresponding ADOTA-BSA conjugate. It was found that the fluorescence of DAOTA experienced a significantly higher degree of solvent quenching if compared to ADOTA as non-conjugated dyes in aqueous solution, while the fluorescence quenching observed upon conjugation to BSA was significantly reduced for DAOTA when compared to ADOTA. The differences in observed quenching for the conjugates can be explained by the different electronic structures of the dyes, which renders DAOTA significantly less prone to reductive photoinduced electron transfer (PET) quenching from e.g. tryptophan. We conclude that DAOTA, with emission in the red and inherent resistance to PET quenching, is an ideal platform for the development of long fluorescence lifetime probes for time-resolved imaging and fluorescence polarisation assay.

Emissive Photoconversion Products of an Amino-triangulenium Dye.

Upon prolonged exposure to intense blue light, the tris(diethylamino)-trioxatriangulenium (A3-TOTA(+)) fluorophore can undergo a photochemical reaction to form either a blue-shifted or a red-shifted fluorescent photoproduct. The formation of the latter depends on the amount of oxygen present during the photoconversion. The A3-TOTA(+) fluorophore is structurally similar to rhodamine, with peripheral amino groups on a cationic aromatic system. The photoconversion products were identified by UV-vis absorption and steady-state and time-resolved fluorescence spectroscopy, and further characterized by HPLC, LC-MS, and (1)H NMR. Two reaction pathways were identified: a dealkylation reaction and an oxidation leading to formation of one or more amide groups on the peripheral donor groups. The photoconversion is controlled by the experimental conditions, in particular the presence of oxygen and water, and the choice of solvent. The results highlight the need to characterize the formation of fluorescent photoproducts of commonly used fluorescent probes, since these could give rise to false positives in multicolor/multilabel imaging, colocalization studies, and FRET based assays. Finally, an improved understanding of the photochemical reaction leading to bleaching of fluorescent dyes can lead to the creation of specific probes for fluorescence based monitoring of chemical reactions.

Azadioxatriangulenium: Synthesis and Photophysical Properties of Reactive Dyes for Bioconjugation.

Azadioxatriangulenium (ADOTA) is a fluorescent triangulenium dye with a long fluorescence lifetime, highly polarized transitions and emission in the red part of the visible spectrum. These properties make the chromophore suited for application in fluorescence polarization/anisotropy assay. To be useful for these applications, reactive forms of the dyes must be available in significant quantities. Here, the synthesis and photophysical properties of amine-reactive NHS esters and a thiol-reactive maleimide derivate of ADOTA are reported. The synthesis involves two steps of nucleophilic bridge forming reactions starting from tris(2,6-dimethoxyphenyl) methylium tetrafluoroborate, which can readily be made on 100 gram scale. In the third and final step the reactive NHS or maleimide groups are formed. The beneficial photophysical properties of the ADOTA chromophore are maintained in these derivatives, and we conclude that these systems are ideal to study protein motion and protein-protein interactions for systems of up towards 1000 kDa.

A comprehensive study of extended tetrathiafulvalene cruciform molecules for molecular electronics: synthesis and electrical transport measurements.

Cruciform-like molecules with two orthogonally placed π-conjugated systems have in recent years attracted significant interest for their potential use as molecular wires in molecular electronics. Here we present synthetic protocols for a large selection of cruciform molecules based on oligo(phenyleneethynylene) (OPE) and tetrathiafulvalene (TTF) scaffolds, end-capped with acetyl-protected thiolates as electrode anchoring groups. The molecules were subjected to a comprehensive study of their conducting properties as well as their photophysical and electrochemical properties in solution. The complex nature of the molecules and their possible binding in different configurations in junctions called for different techniques of conductance measurements: (1) conducting-probe atomic force microscopy (CP-AFM) measurements on self-assembled monolayers (SAMs), (2) mechanically controlled break-junction (MCBJ) measurements, and (3) scanning tunneling microscopy break-junction (STM-BJ) measurements. The CP-AFM measurements showed structure-property relationships from SAMs of series of OPE3 and OPE5 cruciform molecules; the conductance of the SAM increased with the number of dithiafulvene (DTF) units (0, 1, 2) along the wire, and it increased when substituting two arylethynyl end groups of the OPE3 backbone with two DTF units. The MCBJ and STM-BJ studies on single molecules both showed that DTFs decreased the junction formation probability, but, in contrast, no significant influence on the single-molecule conductance was observed. We suggest that the origins of the difference between SAM and single-molecule measurements lie in the nature of the molecule-electrode interface as well as in effects arising from molecular packing in the SAMs. This comprehensive study shows that for complex molecules care should be taken when directly comparing single-molecule measurements and measurements of SAMs and solid-state devices thereof.

Triazatriangulene as binding group for molecular electronics.

The triazatriangulene (TATA) ring system was investigated as a binding group for tunnel junctions of molecular wires on gold surfaces. Self-assembled monolayers (SAMs) of TATA platforms with three different lengths of phenylene wires were fabricated, and their electrical conductance was recorded by both conducting probe-atomic force microscopy (CP-AFM) and scanning tunneling microscopy (STM). Similar measurements were performed for phenylene SAMs with thiol anchoring groups as references. It was found that, despite the presence of a sp(3) hybridized carbon atom in the conduction path, the TATA platform displays a contact resistance only slightly larger than the thiols. This surprising finding has not been reported before and was analyzed by theoretical computations of the transmission functions of the TATA anchored molecular wires. The relatively low contact resistance of the TATA platform along with its high stability and directionality make this binding group very attractive for molecular electronic measurements and devices.

Molecular junctions based on SAMs of cruciform oligo(phenylene ethynylene)s.

Cruciform oligo(phenylene ethynylene)s (OPEs) with an extended tetrathiafulvalene (TTF) donor moiety (OPE5-TTF and OPE3-TTF) and their simple analogues (OPE5-S and OPE3) without conjugated substituents were used to form high-quality self-assembled monolayers (SAMs) on ultraflat gold substrates. Molecular junctions based on these SAMs were investigated using conducting-probe atomic force microscopy (CP-AFM). The TTF substituent changes the molecular orbital energy levels and decreases the HOMO-LUMO energy gap, resulting in a 9-fold increase in conductance for both TTF cruciform OPEs compared to the unsubstituted analogues. The difference in electrical transport properties of the SAMs was reproduced by the theoretical transport calculations for the single molecules.

Dihydroazulene-buckminsterfullerene conjugates.

The dihydroazulene (DHA)/vinylheptafulvene (VHF) photo/thermoswitch has recently attracted interest as a molecular switch for molecular electronics. In this field, Buckminsterfullerene, C(60), has been shown to be a useful anchoring group for adhering a molecular wire to an electrode. Here we have combined the two units with the overall aim to elucidate how C(60) influences the DHA-VHF switching events. Efficient synthetic protocols for making covalently linked DHA-C(60) conjugates were developed, using Prato, Sonogashira, Hay, and Cadiot-Chodkiewicz reactions. These syntheses provide as well a variety of potentially useful DHA and C(60) building blocks for acetylenic scaffolding. The two units were separated by bridges of various lengths, such as oligo(phenyleneethynylene) (OPE2 and OPE3) wires. The distance of separation was found to influence strongly the light-induced ring-opening reaction of DHA to its corresponding VHF. Thus, C(60) was found to significantly quench this conversion when situated closely to the DHA unit.

Tuning the p Ka of a pH Responsive Fluorophore and the Consequences for Calibration of Optical Sensors Based on a Single Fluorophore but Multiple Receptors.

Since Sørensen and Bjerrum defined the pH scale, we have relied on two methods for determining pH, the colorimetric or the electrochemical. For pH electrodes, calibration is easy as a linear response is observed in the interesting pH range from 1 to ∼12. For colorimetric sensors, the response follows the sigmoidal Bjerrum diagram of an acid-base equilibrium. Thus, calibration of colorimetric sensors is more complex. Here, seven pH responsive fluorescent dyes based on the same diazaoxatriangulenium (DAOTA) fluorophore linked to varying receptor groups were prepared. Photoinduced electron transfer (PeT) quenching from appended aniline or phenol receptors generated the pH response of the DAOTA dyes, and the position of the p Ka value of the dye was tuned using the Hammett relationship as a guideline. The fluorescence intensity of the dyes in a sol-gel matrix environment was measured as a function of pH in universal buffer, and it was found that the dyes behave as perfect pH responsive probes under these conditions. The response of optical pH sensors is nonlinear and was found to be limited to 2-3 pH units for a precision of 0.01 pH unit. As sensors with a broader sensitivity range can be achieved by mixing multiple dyes with different p Ka values, mixtures of dyes in solution were investigated, and a broad range pH sensor with a precision of 0.006 pH units over a range of 3.6 pH units was demonstrated. Further, approximating the sensor response as linear was considered, and a limiting precision for this approach was determined. As the responses of the pH responsive DAOTA dyes were found to be ideally sigmoidal and as the six dyes were shown to have p Ka values scattered over a range from ∼2 to ∼9, this allows for design of a broad range optical pH sensor in the pH range from 1 to 10. This hypothesis was tested using quaternary mixtures of the different DAOTA dyes, and these were found to behave as a direct sum of the individual components. Thus, while linear calibration is limited to a precision of 0.02 in a range of 2-3 pH units, calibration using ideal sigmoidal functions is possible in the range of 1-10 with a precision better than 0.01, and as good as 0.002 pH units.

Subphthalocyanine-radiaannulene scaffold - a multi-electron acceptor and strong chromophore.

Two subphthalocyanine (SubPc) units and a perethynylated, alkyne-expanded radiaannulene (RA) were fused together by a four-fold Sonogashira reaction to give a compound exhibiting: (i) four reversible one-electron reductions, the first signalling good acceptor strength of the RA core itself, while the following three are a consequence of the entire scaffold, and (ii) intense light absorption that spans a remarkably broad region.

Human reach-to-grasp compensation with object pose uncertainty.

This paper examined how humans alter reach-to-grasp behavior to compensate for environmentally-induced object orientation uncertainty. We used a novel motion tracking framework to capture hand-object interactions, as well as a custom cylindrical object to detect contacts. Subjects were instructed to reach, grasp, and lift the object with or without vision. The orientation of the object was randomly changed on each trial. We hypothesized subjects would use a reach-to-grasp strategy that minimizes post-contact adjustments. However, our results indicate that (1) subjects are more likely to use the hand as a sensing apparatus prior to contact, and (2) the reach-to-grasp kinematics may be optimized for efficient sensing of object orientation. Our findings could provide potential solution to efficient tactile sensing for robotic hand in unstructured environment.

A new class of extended tetrathiafulvalene cruciform molecules for molecular electronics with dithiafulvene-4,5-dithiolate anchoring groups.

Cruciform motifs with two orthogonally oriented π-extended tetrathiafulvalenes and with differently protected thiolate end-groups are synthesized by stepwise coupling reactions. The molecules are subjected to single-molecule conductivity studies in a break-junction and to conducting probe atomic force microscopy studies in a self-assembled monolayer on gold.