Deducing the conformational space for an octa-proline helix.

A molecular dyad, PY-P8-PER, comprising a proline octamer sandwiched between pyrene and perylene terminals has been synthesized in order to address the dynamics of electronic energy transfer (EET) along the oligo-proline chain. A simple pyrene-based control compound equipped with a bis-proline attachment serves as a reference for spectroscopic studies. The N-H NMR signal at the terminal pyrene allows distinction between cis and trans amides and, although the crystal structure for the control has the trans conformation, temperature-dependent NMR studies provide clear evidence for trans/cis isomerisation in D6-DMSO. Polar solvents tend to stabilise the trans structure for the pyrene amide group, even for longer oligo-proline units. Circular dichroism shows that the proline spacer for PY-P8-PER exists mainly in the all-trans geometry in methanol. Preferential excitation of the pyrene chromophore is possible at wavelengths in the 320-350 nm range and, for the dyad, is followed by efficacious EET to the perylene emitter. The probability for intramolecular EET, obtained from analysis of steady-state spectroscopic data, is ca. 80-90% in solvents of disparate polarity. Comparison with the Förster critical distance suggests the terminals are ca. 18 Å apart. Time-resolved fluorescence spectroscopy, in conjunction with DFT calculations, indicates the dyad exists as a handful of conformers displaying a narrow range of EET rates. Optimisation of a distributive model allows accurate simulation of the EET dynamics in terms of reasonable structures based on isomerisation of certain amide groups.

Origin of intersystem crossing in highly distorted organic molecules: a case study with red light-absorbing N,N,O,O-boron-chelated Bodipys.

To explore the relationship between the twisted π-conjugation framework of aromatic chromophores and the efficacy of intersystem crossing (ISC), we have studied a N,N,O,O-boron-chelated Bodipy derivative possessing a severely distorted molecular structure. Surprisingly, this chromophore is highly fluorescent, showing inefficient ISC (singlet oxygen quantum yield, ΦΔ = 12%). These features differ from those of helical aromatic hydrocarbons, where the twisted framework promotes ISC. We attribute the inefficient ISC to a large singlet-triplet energy gap (ΔES1/T1 = 0.61 eV). This postulate is tested by critical examination of a distorted Bodipy having an anthryl unit at the meso-position, for which ΦΔ is increased to 40%. The improved ISC yield is rationalized by the presence of a T2 state, localized on the anthryl unit, with energy close to that of the S1 state. The electron spin polarization phase pattern of the triplet state is (e, e, e, a, a, a), with the Tz sublevel of the T1 state overpopulated. The small zero-field splitting D parameter (-1470 MHz) indicates that the electron spin density is delocalized over the twisted framework. It is concluded that twisting of π-conjugation framework does not necessarily induce ISC, but S1/Tn energy matching may be a generic feature for increasing ISC for a new-generation of heavy atom-free triplet photosensitizers.

A BF2 Chelate Exhibiting Excimer-like Fluorescence with an Unusually Large Stokes Shift in the Crystalline Phase.

The target mono-BF2 complex is weakly emissive in fluid solution because radiationless decay of the excited-singlet state is promoted through an intramolecular N⋅⋅⋅H-N hydrogen bond. The lack of mirror symmetry for this compound is attributed to vibronic effects, as reported previously for the bis-BF2 complex (BOPHY). Red-shifted fluorescence is observed from single crystals, the emission quantum yield approaching 30 % with a fluorescence lifetime of 2 ns. The large Stokes shift of 5,700 cm-1 helps minimize self-absorption. Crystallography indicates that the internal fold and twist angles are increased substantially in the crystal, but the hydrogen bond is weakened relative to solution. The crystal structure is compiled from pairs of head-to-tail molecules having a shift of ca. 4.1 Šand closest approach of ca. 3.5 Å. These molecular pairs are arranged in columns, which, in turn, assemble into sheets. The proximity favors excitonic coupling between individual molecules, with the coupling strength obtained by analysis of the absorption spectrum reaching ca. 1,000 cm-1 . Both the ideal dipole approximation and the extended dipole methodology seriously overestimate the coupling strength, but the atomic transition charge density procedure leads to good agreement with experiment. Emission is attributed to the closely coupled molecular pair functioning in an excimer-like manner with the exciton trapped in a local minimum. Increasing temperature causes a slight blue shift and loss of fluorescence.

Stereochemical Control of Secondary Benzamide-based BODIPY Emitters.

Aromatic amides can be used to construct light-harvesting materials with valuable optical properties. The amide bond is formed using well-known coupling agents in near quantitative yield, as illustrated here through the synthesis of two boron dipyrromethene derivatives bearing an amide linkage. The primary concern with acyl amides is rotation around the C-N bond, leading to cis and trans isomers. Using NMR spectroscopy, quantum chemical calculations and critical comparison to simpler benzamides, the stereochemistry of the target compounds has been addressed. The N-cyclohexyl derivative gave diffraction quality crystals that established a trans geometry for the amide bond. Quantum chemical calculations support the trans geometry as being the lowest-energy structure in solution but indicate that inversion of the aryl ring is an important structural feature. Indeed, rotation around the C(sp2 )-C(aryl) bond has a strong influence on the solution-phase NMR spectra. The amide connection has minimal effect on the photophysical properties.

Light-Harvesting Crystals Formed from BODIPY-Proline Biohybrid Conjugates: Antenna Effects and Excitonic Coupling.

A boron dipyrromethene (BODIPY) derivative bearing a cis-proline residue at the meso-position crystallizes in the form of platelets with strong (i.e., ΦF = 0.34) red fluorescence, but the absorption and emission spectra differ markedly from those for dilute solutions. A key building block for the crystal is a pseudo-dimer where hydrogen bonding aligns the proline groups and separates the terminal chromophores by ca. 25 Å. Comparison with a covalently linked bichromophore suggests that one-dimensional (1D) excitonic coupling between the terminals is too small to perturb the optical properties. However, accretion of the pseudo-dimer forms narrow channels possessing a high density of chromophores. The resultant absorption spectrum exhibits strong excitonic splitting, which can be explained quantitatively using the extended dipole approach and allowing for coupling between ca. 30 BODIPY units. Fluorescence, which decays with a lifetime of 2.2 ns, is assigned to a delocalized and (slightly) super-radiant BODIPY dimer situated at the interface and populated via electronic energy transfer from the interior.

Pulse Radiolysis Investigation of Radicals Derived from Water-Soluble Cyanine Dyes: Implications for Super-resolution Microscopy.

Light-induced blinking, an inherent feature of many forms of super-resolution microscopy, has been linked to transient reduction of the fluorescent cyanine dye used as an imaging agent. There is, however, only scant literature information related to one-electron reduced cyanine dyes, especially in an aqueous environment. Here, we examine a small series of cyanine dyes, possessing disparate π-conjugation lengths, under selective reducing or oxidizing conditions. The experiment allows recording of both differential absorption spectra and decay kinetics of the resultant one-electron reduced or oxidized transient species in water. Relative to the ground state, absorption transitions for the various radicals are weak and somewhat broadened but do allow correlation with the π-conjugation length. In all cases, absorption maxima lie to the blue of the main ground-state transition. Under anaerobic conditions, the transient species decay on the microsecond to millisecond time scale, with the mean lifetime depending on molecular structure, radiation dose, and dye concentration. The experimental absorption spectra recorded for the one-electron reduced radicals and the presumed dimer cation radical compare well to spectra obtained from time-dependent density functional theory calculations. The results allow conclusions to be drawn regarding the plausibility of the reduced species being responsible for light-induced blinking in direct stochastic optical reconstruction microscopy.

Singlet Exciton Fission and Associated Enthalpy Changes with a Covalently Linked Bichromophore Comprising TIPS-Pentacenes Held in an Open Conformation.

A covalently linked bichromophore, embracing 6,13-bis(triisopropylsilylethinyl)pentacene (TIPS-pentacene) terminals bridged by a rigid fluorene spacer, generates a relatively high yield (i.e., 65 ± 6%) of the spin-correlated, triplet biexciton upon illumination in toluene. Under the same conditions, the extent of fluorescence quenching relative to the parent TIPS-pentacene approaches 97% and is insensitive to temperature. The biexciton, having overall singlet spin multiplicity, undergoes internal conversion in competition to spin decorrelation. These latter processes occur on the relatively slow time scale of a hundred or so nanoseconds, possibly reflecting the restricted level of electronic communication between the terminals. Spin decorrelation leads to evolution of an independent triplet pair with an overall quantum yield of 0.50 ± 0.06 and a lifetime of 8 ± 2 µs in deaerated toluene. Photoacoustic calorimetry (PAC) indicates three separate enthalpy changes: a very fast step associated with intramolecular singlet exciton fission to form the correlated triplet biexciton, a fast step essentially reflecting spin decorrelation, and a slow step associated with relaxation of the independent triplet pair. Analysis of the PAC data, in conjunction with the transient absorption results, establishes excitation energies for both spin-correlated and independent triplet pairs. Polar solvent enhances both fluorescence quenching and triplet formation at the expense of radiationless decay while temperature effects have been recorded for all important intermediate species.

Synthesis, Structure and Photophysical Properties of a New Class of Inherently Chiral Boron(III) Chelates-The tert-Leucine Complexes.

A new family of boron(III) chelates is introduced whereby molecular chirality, confirmed by circular dichroism, is imported during synthesis such that isolation of the diastereoisomers does not require separation procedures. The photophysical properties of two members of the family have been examined: the N,O,O-salicylaldehyde-based derivative shows pronounced intramolecular charge-transfer character in fluid solution and is weakly fluorescent, with a large Stokes shift. The corresponding 2-methylamino-benzaldehyde-derived N,N,O-chelate absorbs and fluoresces in the visible region with a much smaller Stokes shift. Orange fluorescence is also observed for this compound as a cast film. Temperature-dependence studies show that decay of the fluorescent state is weakly activated but emission is less than quantitative at 77 K. Quite rare for boron(III)-based chelates, this derivative undergoes intersystem crossing to form a meta-stable triplet-excited state. X-ray crystal structures are reported for both compounds, along with simulated ECD spectra.

Triplet Distribution in a Symmetrical Zinc(II) Porphyrin-BODIPY Pentameric Array.

A symmetrical molecular array has been synthesized comprising a central zinc(II) 5,10,15,20-tetraphenylporphyrin with identical boron dipyrromethene (BODIPY) units appended at each of the meso sites. Excitation of any subunit causes a cascade of electronic energy-transfer steps, ultimately leading to the BODIPY triplet-excited state in high yield. Coincidentally, the triplet energy levels of the zinc(II) porphyrin and BODIPY appendage are closely balanced such that an equilibrium is established at both 77 K and room temperature. This fast equilibration allows global distribution of the triplet exciton around the array, leading to a significantly increased capture volume for bimolecular quenching and a substantial increase in the rate constant for bimolecular triplet-triplet annihilation. The corresponding free-base porphyrin analogue does not favor triplet exciton decentralization because of the large disparity in the electronic energy levels.

Origin of Fluorescence from Boranils in the Crystalline Phase.

A small series of boranil complexes has been studied by fluorescence spectroscopy. Weakly fluorescent in most organic solvents at room temperature, the target compounds display bright emission in the crystalline phase. X-ray diffraction patterns obtained for single crystals indicate a distorted tetrahedral geometry around the O-B-N center with the boron atom being displaced from the plane of the heterobicyclic ring. Consideration of the various bond lengths in comparison with those of reference compounds indicates that the ancillary phenyl ring, bearing different para-substituents, does not make a prominent contribution to the molecular dipole moment in the solid state. Absorption and fluorescence spectra recorded for the crystals remain remarkably similar to those for liquid solutions and display large Stokes shifts. Proximity broadening is observed in one case. The nitrophenyl derivative exhibits additional absorption and emission bands unique to the solid state and could be indicative of an intermolecular charge-transfer transition. The optical properties are discussed in terms of the crystal packing diagrams.

Photocatalysed decolouration of indigo in solution via in situ generation of an organic hydroperoxide.

Indigo, an emblematic violet dye used for thousands of years to colour fabric, is resistant to fading on exposure to sunlight. Prior work has indicated that indigo is reactive towards both hydroperoxyl radicals and superoxide anions in solution. In order to promote photobleaching of indigo, we have utilised a BOPHY-based (BOPHY = aryl fused symmetrical pyrrole-BF2 complex) chromophore known to form both superoxide ions and a stable alkyl hydroperoxide under illumination in aerated solution. Selective irradiation of the photocatalyst causes relatively fast fading of indigo, with the rate increasing gently with increasing concentration of indigo. Molecular oxygen and light are essential for effective bleaching. One molecule of photocatalyst can bleach more than 40 molecules of indigo. An active component of the photocatalyst is a butylated hydroxytoluene (BHT) residue which itself quenches the triplet excited state of indigo. This provides an ancillary mechanism for effecting photofading of indigo but, because the triplet is formed in very low yield, this route is less practical.

Solid-State Emission from Mono- and Bichromophoric Boron Dipyrromethene (BODIPY) Derivatives and Comparison with Fluid Solution.

The syntheses and crystal structures of sterically crowded mono- and bichromophoric BODIPY-based dyes are reported. The "monomeric" compound is weakly fluorescent in the liquid phase due to fast internal conversion associated with rotation of aryl rings at the boron atom. The side-by-side "dimer" exhibits weak excitonic coupling between the dipyrrin units and is much more emissive in fluid solution. Solid samples of both molecular entities are strongly fluorescent under near-UV illumination. Thus, the mono-chromophore exhibits dual fluorescence from what appears to be a mixture of crystalline and possibly amorphous (or interfacial regions) distributions. The bi-chromophore packs in the crystal as pairs of chromophores with each unit being provided by a different molecule. This leads to excitonic splitting and the formation of a strong H-band in the absorption spectrum. Fluorescence occurs from the corresponding J-species and also from what appears to be an aggregated state associated with interfacial areas. Both bulk and interface-bound states show relatively long-lived fluorescence while the crystal structures indicate the likelihood for fast electronic energy migration between molecules.

Photo-isomerization of the Cyanine Dye Alexa-Fluor 647 (AF-647) in the Context of dSTORM Super-Resolution Microscopy.

Cyanine dyes, as used in super-resolution fluorescence microscopy, undergo light-induced "blinking", enabling localization of fluorophores with spatial resolution beyond the optical diffraction limit. Despite a plethora of studies, the molecular origins of this blinking are not well understood. Here, we examine the photophysical properties of a bio-conjugate cyanine dye (AF-647), used extensively in dSTORM imaging. In the absence of a potent sacrificial reductant, light-induced electron transfer and intermediates formed via the metastable, triplet excited state are considered unlikely to play a significant role in the blinking events. Instead, it is found that, under conditions appropriate to dSTORM microscopy, AF-647 undergoes reversible photo-induced isomerization to at least two long-lived dark species. These photo-isomers are characterized spectroscopically and their interconversion probed by computational means. The first-formed isomer is light sensitive and transforms to a longer-lived species in modest yield that could be involved in dSTORM related blinking. Permanent photobleaching of AF-647 occurs with very low quantum yield and is partially suppressed by the anaerobic redox buffer.

Optical spectroscopic properties recorded for simple BOPHY dyes in condensed media: The mirror-symmetry factor.

The BOPHY structural scaffold provides opportunities for the synthesis of innumerable derivatives with linear geometries and well-controlled π-conjugation pathways. The simpler BOPHY chromophores are highly fluorescent but exhibit poor mirror symmetry between absorption and fluorescence spectra at ambient temperature. In particular, the absorption (and excitation) spectra are broad and appear as two overlapping bands of comparable intensity. In constrained media, such as low-temperature rigid glasses or stretched poly(ethylene) films, mirror symmetry is restored. Analysis of the temperature dependence recorded for simple BOPHY derivatives indicates that the vibronic envelope accompanying the electronic transitions can be well described in terms of low- and medium-frequency modes. Whereas the fluorescence spectral profile is only weakly dependent on temperature, the excitation spectrum is far more affected. The magnitude of the low-frequency mode, and the associated electron-phonon coupling, increase substantially with increasing temperature and is responsible for temperature broadening and distortion of the excitation spectrum in solution. This critical low-frequency vibronic mode is associated with out-of-plane torsional bending of the BOPHY unit. Variable temperature NMR studies failed to provide unequivocal evidence for conformational changes of one of the derivatives over the temperature range 193-353 K.

Nonradiative Decay Channels for a Structurally-Distorted, Monostrapped BODIPY Derivative.

A boron dipyrromethene (BODIPY) derivative has been synthesized whereby a phenoxyl ring attached at the 3-position is bound through the oxygen atom to the boron center. This compound is structurally distorted, with the molecular surface being curved, and undergoes further geometrical perturbation at the excited singlet state level. Fluorescence is readily observed in solution at ambient temperature, with the quantum yield rising with increasing viscosity of the surrounding solvent. Dual-exponential decay kinetics are observed, corresponding to E-type delayed fluorescence. In solution, the emission yield falls with increasing temperature, but the opposite situation is found for the same compound dispersed in an amorphous sugar. These results are considered in terms of two radiationless decay channels. A viscosity-dependent avenue allows the fluorophore to function as a conventional fluorescent rotor for tracking changes in local rheology. A temperature-dependent channel leads to trapping within a new conformation, which is weakly coupled to the ground state but is able to repopulate the emitting state on a relatively slow time scale. Analysis of the experimental data allows estimation of some of the key kinetic parameters as a function of temperature.

Pulse Radiolysis of TIPS-Pentacene and a Fluorene-bridged Bis(pentacene): Evidence for Intramolecular Singlet-Exciton Fission.

Exposing TIPS-pentacene in deaerated benzene to ionizing radiation generates a mixture of singlet- and triplet-excited states of the solute. The singlet undergoes radiative decay without spin conversion whereas the triplet undergoes radiationless decay on the microsecond time scale. The concentration of each species was established by dosimetry. The excited-singlet state is not observed on the nanosecond-time scale for a related fluorene-bridged bis(pentacene), but the triplet is present in high concentration. Failure to detect the excited-singlet state is attributed to fast intramolecular singlet-exciton fission (iSEF) which is found to produce two triplet species. A short-lived intermediate (τT = 145 ns) is identified as the species (T_T) having both pentacene units present as triplet states. The second transient is longer lived (τT = 7.5 µs) and is assigned to the corresponding species (T_G) with a single pentacene promoted to the triplet level. Dosimetry is used to conclude that iSEF partitions overwhelmingly in favor of T_G (70%) relative to T_T (25%). The total triplet yield from iSEF, therefore, is ca. 120% in this system, where the pentacene terminals are weakly coupled.

Photocatalysis and self-catalyzed photobleaching with covalently-linked chromophore-quencher conjugates built around BOPHY.

Two Chromophore-Quencher Conjugates (CQCs) have been synthesized by covalent attachment of the anti-oxidant dibutylated-hydroxytoluene (BHT) to a pyrrole-BF2 chromophore (BOPHY) in an effort to protect the latter against photofading. In fluid solution, light-induced intramolecular charge transfer is favoured in polar solvents and helps to inhibit photo-bleaching of the chromophore. The rate of photo-fading, which scales with the number of BHT residues, is zero-order in polar solvents but shows a linear dependence on the number of absorbed photons. The zero-order rate constant shows an inverse correlation with the fluorescence quantum yield measured in the same solvent. Photo-bleaching in benzonitrile involves autocatalysis while reaction in cyclohexane shows an unexpected stoichiometry. NMR spectroscopy indicates initial damage takes place at the BHT unit and allows identification of a reactive hydroperoxide as being the primary product. In the presence of an adventitious substrate, this hydroperoxide is a photocatalyst for amide formation under mild conditions.

Ultrafast Through-Space Electronic Energy Transfer in Molecular Dyads Built around Dynamic Spacer Units.

A pair of complementary molecular dyads have been synthesized around a 1,2-diaminocyclohexyl spacer that itself undergoes ring inversion. Despite these conformational exchange processes, the donor and acceptor occupy quite restricted spatial regions, and they are not interchangeable. The donor and acceptor pair comprise disparate boron dipyrromethene dyes selected to display favorable electronic energy transfer (EET). Steady-state emission spectroscopy confirms that through-space EET from donor to acceptor is almost quantitative, aided by the relatively short separations. Ultrafast time-resolved fluorescence spectroscopy has allowed determination of the rates of EET for both dyads. Surprisingly, in view of the close proximity of donor and acceptor (center-to-center separations less than 20 Å), the EET dynamics are well-accounted for in terms of the computed molecular conformations and conventional Förster theory. One dyad appears as a single family of conformations, but EET for the second dyad corresponds to dual-exponential kinetics. In this latter case, an intramolecular hydrogen bond helps stabilize an open geometry, wherein EET is relatively slow.

Cyanine dyes as ratiometric fluorescence standards for the far-red spectral region.

Most quantitative fluorescence measurements report emission quantum yields by referring the integrated fluorescence profile to that of a well-known standard compound measured under carefully controlled conditions. This simple protocol works well provided an appropriate standard fluorophore is available and that the experimental conditions used for reference and unknown are closely comparable. Commercial fluorescence spectrophotometers tend to perform very well at wavelengths between 250 and 650 nm but are less responsive at longer wavelengths. There are no recognized emission standards for the far-red region. We now report fluorescence quantum yields for a series of commercially available cyanine dyes in methanol solution at room temperature. The compounds are selected to span the wavelength region from 600 to 850 nm, with absolute emission quantum yields being determined by thermal blooming spectrometry. Calibration of the instrument is made by reference to aluminium(iii) phthalocyanine tetrasulfonate and aza-BODIPY in methanol.

Effects of Temperature and Concentration on the Rate of Photobleaching of Erythrosine in Water.

Erythrosine, a popular food dye, undergoes fast O2-sensitive bleaching in water when subjected to visible light illumination. In dilute solution, erythrosine undergoes photobleaching via first-order kinetics, where the rate of bleaching depends critically on the rate of photon absorption and on the concentration of dissolved oxygen. Kinetic studies indicate that this inherent bleaching is augmented by self-catalysis at higher concentrations of erythrosine and on long exposure times. Under the conditions used, bleaching occurs by way of geminate attack of singlet molecular oxygen on the chromophore. Despite the complexity of the overall photobleaching process, the rate constants associated with both inherent and self-catalytic bleaching reactions follow Arrhenius-type behavior, allowing the activation parameters to be resolved. Bleaching remains reasonably efficient in the solid state, especially if the sample is damp, and provides a convenient means by which to construct a simple chemical actinometer.