Unraveling Excited State Dynamics of a Single-Stranded DNA-Assembled Conjugated Polyelectrolyte.

Conformational templating of conjugated polyelectrolytes with single-stranded DNAs (ssDNAs) has the prospect of tailoring excited state dynamics for specific optoelectronic applications. We use ultrafast time-resolved infrared spectroscopy to study the photophysics of a cationic polythiophene assembled with different ssDNAs, inducing distinct conformations (flexible disordered structures vs more rigid complexes with increased backbone planarity). Intrachain polarons are always produced upon selective excitation of the polymer, the extent being dependent on backbone torsional order. Polaron formation and decay were monitored through evolution of IR-active vibrational modes that interfere with mid-IR polaron electronic absorption giving rise to Fano-antiresonances. Selective UV excitation of ssDNAs revealed that stacking interactions between thiophene rings and nucleic acid bases can promote the formation of an intermolecular charge transfer complex. The findings inform designers of functional conjugated polymers by identifying that involvement of the scaffold in the photophysics needs to be considered when developing such structures for optoelectronic applications.

Gaining Insights on the Interactions of a Class of Decorated (2-([2,2'-Bipyridin]-6-yl)phenyl)platinum Compounds with c-Myc Oncogene Promoter G-Quadruplex and Other DNA Structures.

Organometallic molecules offer some of the most promising scaffolds for interaction with G-quadruplex nucleic acids. We report the efficient synthesis of a family of organoplatinum(II) complexes, featuring a 2-([2,2'-bipyridin]-6-yl)phenyl tridentate (N∧ N∧ C) ligand, that incorporates peripheral side-chains aiming at enhancing and diversifying its interaction capabilities. These include a di-isopropyl carbamoyl amide, a morpholine ethylenamide, two enantiomeric proline imides and an oxazole. The binding affinities of the Pt-complexes were evaluated via UV-vis and fluorescence titrations, against 5 topologically-distinct DNA structures, including c-myc G-quadruplex, two telomeric (22AG) G-quadruplexes, a duplex (ds26) and a single-stranded (polyT) DNA. All compounds exhibited binding selectivity in favour of c-myc, with association constants (Ka ) in the range of 2-5×105  M-1 , lower affinity for both folds of 22AG and for ds26 and negligible affinity for polyT. Remarkable emission enhancements (up to 200-fold) upon addition of excess DNA were demonstrated by a subset of the compounds with c-myc, providing a basis for optical selectivity, since optical response to all other tested DNAs was low. A c-myc DNA-melting experiment showed significant stabilizing abilities for all compounds, with the most potent binder, the morpholine-Pt-complex, exhibiting a ΔTm >30 °C, at 1 : 5 DNA-to-ligand molar ratio. The same study implied contributions of the diverse side-chains to helix stabilization. To gain direct evidence of the nature of the interactions, mixtures of c-myc with the four most promising compounds were studied via UV Resonance Raman (UVRR) spectroscopy, which revealed end-stacking binding mode, combined with interactions of side-chains with loop nucleobase residues. Docking simulations were conducted to provide insights into the binding modes for the same four Pt-compounds, suggesting that the binding preference for two alternative orientations of the c-myc G-quadruplex thymine 'cap' ('open' vs. 'closed'), as well as the relative contributions to affinity from end-stacking and H-bonding, are highly dependent on the nature of the interacting Pt-complex side-chain.

Structural and Photophysical Templating of Conjugated Polyelectrolytes with Single-Stranded DNA.

A promising approach to influence and control the photophysical properties of conjugated polymers is directing their molecular conformation by templating. We explore here the templating effect of single-stranded DNA oligomers (ssDNAs) on cationic polythiophenes with the goal to uncover the intermolecular interactions that direct the polymer backbone conformation. We have comprehensively characterized the optical behavior and structure of the polythiophenes in conformationally distinct complexes depending on the sequence of nucleic bases and addressed the effect on the ultrafast excited-state relaxation. This, in combination with molecular dynamics simulations, allowed us a detailed atomistic-level understanding of the structure-property correlations. We find that electrostatic and other noncovalent interactions direct the assembly with the polymer, and we identify that optimal templating is achieved with (ideally 10-20) consecutive cytosine bases through numerous π-stacking interactions with the thiophene rings and side groups of the polymer, leading to a rigid assembly with ssDNA, with highly ordered chains and unique optical signatures. Our insights are an important step forward in an effective approach to structural templating and optoelectronic control of conjugated polymers and organic materials in general.

CYP2J19 mediates carotenoid colour introgression across a natural avian hybrid zone.

It has long been of interest to identify the phenotypic traits that mediate reproductive isolation between related species, and more recently, the genes that underpin them. Much work has focused on identifying genes associated with animal colour, with the candidate gene CYP2J19 identified in laboratory studies as the ketolase converting yellow dietary carotenoids to red ketocarotenoids in birds with red pigments. However, evidence that CYP2J19 explains variation between red and yellow feather coloration in wild populations of birds is lacking. Hybrid zones provide the opportunity to identify genes associated with specific traits. Here we investigate genomic regions associated with colour in red-fronted and yellow-fronted tinkerbirds across a hybrid zone in southern Africa. We sampled 85 individuals, measuring spectral reflectance of forecrown feathers and scoring colours from photographs, while testing for carotenoid presence with Raman spectroscopy. We performed a genome-wide association study to identify associations with carotenoid-based coloration, using double-digest RAD sequencing aligned to a short-read whole genome of a Pogoniulus tinkerbird. Admixture mapping using 104,933 single nucleotide polymorphisms (SNPs) identified a region of chromosome 8 that includes CYP2J19 as the only locus with more than two SNPs significantly associated with both crown hue and crown score, while Raman spectra provided evidence of ketocarotenoids in red feathers. Asymmetric backcrossing in the hybrid zone suggests that yellow-fronted females mate more often with red-fronted males than vice versa. Female red-fronted tinkerbirds mating assortatively with red-crowned males is consistent with the hypothesis that converted carotenoids are an honest signal of quality.

Resonance Raman study of the J-type aggregation process of a water soluble perylene bisimide.

Perylene bisimides (PBIs) are dyes known for combining high absorption and emission in the visible region with thermal and photochemical stability. H-bond-directed aggregation driven by free imide groups has been reported to promote the uncommon J-type aggregate formation of PBIs. J-aggregates are highly desired thanks to their bathochromically shifted narrow absorption and fluorescence due to excitonic coupling, together with hyperchromicity and superradiance compared to the monomer. Herein we present the water soluble MEG-PBI showing interesting aggregation in water and in the solid state. Unlike its hydrophobic counterparts, MEG-PBI aggregates in water with increasing temperature, indicating entropy-driven self-assembly. Temperature-dependent Resonance Raman (RR) spectroscopy was employed for the structural characterization of MEG-PBI in aqueous solution versus toluene and in aggregated thin films, employing excitation at different wavelengths to probe the contribution of various chromophores to the supramolecular structure of the aggregate. We find that the perylene core distorts upon aggregation, where the bonds along the perylene long N-N axis lengthen and the ones perpendicular to that shorten, suggesting a head-to-tail arrangement due to H-bonding between neighboring units.

Salt-induced thermochromism of a conjugated polyelectrolyte.

We report here the photophysical properties of a water-soluble conjugated polythiophene with cationic side-chains. When dissolved in aqueous buffer solution (PBS, phosphate buffered saline), there is ordering of the polymer chains due to the presence of the salts, in contrast to pure water, where a random-coil conformation is adopted at room temperature. The ordering leads to a pronounced colour change of the solution (the absorption maximum shifts from 400 nm to 525 nm). Combining resonance Raman spectroscopy with density functional theory computations, we show a significant backbone planarization in the ordered phase. Moreover, the ratio of ordered phase to random-coil phase in PBS solution, as well as the extent of intermolecular interactions in the ordered phase, can be tuned by varying the temperature. Femtosecond transient absorption spectroscopy reveals that the excited-state behaviour of the polyelectrolyte is strongly affected by the degree of ordering. While triplet state formation is favoured in the random-coil chains, the ordered chains show a weak yield of polarons, related to interchain interactions. The investigated polyelectrolyte has been previously used as a biological DNA sensor, based on optical transduction when the conformation of the polyelectrolyte changes during assembly with the biomolecule. Therefore, our results, by correlating the photophysical properties of the polyelectrolyte to backbone and intermolecular conformation in a biologically relevant buffer, provide a significant step forward in understanding the mechanism of the biological sensing.

Exploring the origin of high optical absorption in conjugated polymers.

The specific optical absorption of an organic semiconductor is critical to the performance of organic optoelectronic devices. For example, higher light-harvesting efficiency can lead to higher photocurrent in solar cells that are limited by sub-optimal electrical transport. Here, we compare over 40 conjugated polymers, and find that many different chemical structures share an apparent maximum in their extinction coefficients. However, a diketopyrrolopyrrole-thienothiophene copolymer shows remarkably high optical absorption at relatively low photon energies. By investigating its backbone structure and conformation with measurements and quantum chemical calculations, we find that the high optical absorption can be explained by the high persistence length of the polymer. Accordingly, we demonstrate high absorption in other polymers with high theoretical persistence length. Visible light harvesting may be enhanced in other conjugated polymers through judicious design of the structure.

Oxidation of Tetraphenylhexaazaanthracene: Accessing a Scissor Dimer of a 16π Biscyanine.

Tetraphenylhexaazaanthracene (TPHA), a fluorescent zwitterionic biscyanine with a closed-shell singlet ground state, on treatment with manganese dioxide or phenyliodine bis(trifluoroacetate) (PIFA), undergoes oxidative dimerization to give a near-zero dipole scissor 5,5'-dimer DI-TPHA. Both acene components of the new dimer DI-TPHA maintain their biscyanine closed-shell singlet ground state motifs, as judged by analysis of both single crystal X-ray crystallographic and density functional theory computational studies; however, unlike TPHA, DI-TPHA is only very weakly fluorescent.

Tetraphenylhexaazaanthracenes: 16π Weakly Antiaromatic Species with Singlet Ground States.

Tetraphenylhexaazaanthracene, TPHA-1, is a fluorescent zwitterionic biscyanine with a closed-shell singlet ground state. TPHA-1 overcomes its weak 16π antiaromaticity by partitioning its π system into 6π positive and 10π negative cyanines. The synthesis of TPHA-1 is low yielding and accompanied by two analogous TPHA isomers: the deep red, non-charge-separated, quinoidal TPHA-2, and the deep green TPHA-3 that partitions into two equal but oppositely charged 8π cyanines. The three TPHA isomers are compared.

Direct observation of ultrafast long-range charge separation at polymer-fullerene heterojunctions.

In polymeric semiconductors, charge carriers are polarons, which means that the excess charge deforms the molecular structure of the polymer chain that hosts it. This results in distinctive signatures in the vibrational modes of the polymer. Here, we probe polaron photogeneration dynamics at polymer:fullerene heterojunctions by monitoring its time-resolved resonance-Raman spectrum following ultrafast photoexcitation. We conclude that polarons emerge within 300 fs. Surprisingly, further structural evolution on ≲ 50-ps timescales is modest, indicating that the polymer conformation hosting nascent polarons is not significantly different from that near equilibrium. We interpret this as suggestive that charges are free from their mutual Coulomb potential because we would expect rich vibrational dynamics associated with charge-pair relaxation. We address current debates on the photocarrier generation mechanism at molecular heterojunctions, and our work is, to our knowledge, the first direct probe of molecular conformation dynamics during this fundamentally important process in these materials.

Analysis of depolarization ratios of ClNO(2) dissolved in methanol.

A detailed analysis of the resonance Raman depolarization ratio dispersion curve for the N-O symmetric stretch of nitryl chloride in methanol at excitation wavelengths spanning the D absorption band is presented. The depolarization ratios are modeled using the time-dependent formalism for Raman scattering with contributions from two excited states (2(1)A1 and 3(1)B1), which are taken as linearly dissociative along the Cl-N coordinate. The analysis focuses on the interplay between different types of broadening revealing the importance of inhomogenous broadening in determining the relative contributions of the two electronic transitions. We find that the transition dipole moment (M) for 2(1)A1 is greater than for 3(1)B1, in agreement with gas phase calculations in the literature [A. Lesar, M. Hdoscek, M. Muhlhauser, and S. D. Peyerimhoff, Chem. Phys. Lett. 383, 84 (2004)]. However, we find that the polarity of the solvent influences the excited state energetics, leading to a reversal in the ordering of these two states with 3(1)B1 shifting to lower energies. Molecular dynamics simulations along with linear response and ab initio calculations support the evidence extracted from resonance Raman intensity analysis, providing insights on ClNO2 electronic structure, solvation effects in methanol, and the source of broadening, emphasizing the importance of a contribution from inhomogeneous linewidth.

Resonance Raman investigation of ß-cyclodextrin-encapsulated π-conjugated polymers.

Resonance Raman (RR) spectroscopy is used to investigate the effect of ß-cyclodextrin encapsulation on the structural and photophysical properties of poly(4,4'-diphenylenevinylene). We especially focus on the thermal stability of the polymer. We find that within the range of 10-55 °C the uninsulated polymer exhibits decreased Raman intensity in all the vibrational bands with temperature, along with changes in the relative intensity of the C-C inter-ring stretch mode at 1270 cm(-1) with respect to the ring C-H in-plane symmetric bend at 1187 cm(-1), which provides evidence for conformational changes as a function of temperature. No changes are observed in the intensity of the in-phase CH out-of-plane wag of the vinylene group at 968 cm(-1). Therefore, the conformational changes involve mainly dihedral angle modification between the adjacent phenyl rings toward planarization, and little or no change in the planarity of the trans-vinylene group. The decrease of the optical absorption at 55 °C with respect to that at room temperature and the appearance of a new absorption band at lower energies explain the decrease in the RR intensities and the wavelength dependence of the relative intensities of the Raman band. We note that the conformational change into a more planar geometry, which affects a significant portion of the polymer population, is irreversible and consistent with thermally induced aggregation. Such a planarization is unexpected in view of the usually observed thermochromic behavior of conjugated polymers, which leads to an increase of the energy gap for increasing temperature, as the average dihedral angles are increased due to excitation of a larger number of vibrational modes. Interestingly, the higher threading ratio polymers are resistant to any conformational changes within this temperature range, as reflected by their unchanged RR spectra, due to the rotaxane's ability to suppress intermolecular interactions and aggregation. Interestingly, the conformation of the uninsulated polymer at room temperature appears to be the same as that in the threaded analogues, which suggests that the cyclodextrin cavity hosts the polymer without physically interacting with it.

Resonance Raman intensity analysis of ClNO(2) dissolved in methanol.

Halogens such as chlorine are converted from halides, including ClNO(2), to reactive radicals by UV solar radiation. These radicals can affect ozone production and destruction in the stratosphere. Recently, it became clear that halogen radicals can also play a significant role in the chemistry of the troposphere. The photochemistry of ClNO(2) has been the subject of several studies in the gas and solid state that demonstrated a clear phase-dependent reactivity. Here, we report our initial studies of nitryl chloride in solution. Resonance Raman (RR) spectra of ClNO(2) dissolved in methanol after excitation within the 1(1)A(1)-2(1)A(1) absorption band (D band) in the region 200-240 nm are presented. RR intensity along the NO symmetric stretch coordinate (v(1)) at 1291 cm(-1) is observed at all excitation wavelengths, whereas limited intensity corresponding to the transition of the N-Cl symmetric stretch (v(3)) was only observed at 199.8 nm, whereas no intensity corresponding to the O-N-O symmetric bend (v(2)) was observed. Depolarization ratios and absolute resonance Raman cross sections for v(1) were obtained at several excitation wavelengths spanning the D band. Depolarization ratios were found to deviate significantly from 1/3, consistent with more than a single dipole-allowed electronic transition contributing to the scattering. RR intensity analysis (RRIA) reveals that two closely spaced excited electronic states contribute to the scattering, which are dissociative along the Cl-N coordinate. In this study the role the solvent environment plays in ClNO(2) state energetics and excited structural evolution along fundamental coordinates is discussed.

Analysis of the excited-state absorption spectral bandshape of oligofluorenes.

We present ultrafast transient absorption spectra of two oligofluorene derivatives in dilute solution. These spectra display a photoinduced absorption band with clear vibronic structure, which we analyze rigorously using a time-dependent formalism of absorption to extract the principal excited-state vibrational normal-mode frequencies that couple to the electronic transition, the configurational displacement of the higher-lying excited state, and the reorganization energies. We can model the excited-state absorption spectrum using two totally symmetric vibrational modes with frequencies 450 (dimer) or 400 cm(-1) (trimer), and 1666 cm(-1). The reorganization energy of the ground-state absorption is rather insensitive to the oligomer length at 230 meV. However, that of the excited-state absorption evolves from 58 to 166 meV between the oligofluorene dimer and trimer. Based on previous theoretical work [A. Shukla et al., Phys. Rev. B 67, 245203 (2003)], we assign the absorption spectra to a transition from the 1B(u) excited state to a higher-lying mA(g) state, and find that the energy of the excited-state transition with respect to the ground-state transition energy is in excellent agreement with the theoretical predictions for both oligomers studied here. These results and analysis permit profound understanding of the nature of excited-state absorption in pi-conjugated polymers, which are the subject of general interest as organic semiconductors in the solid state.

UV resonance Raman spectroscopy of TTR(105-115): determination of the pKa of tyrosine.

The 11-residue peptide fragment from transthyretin (TTR(105-115)) has been investigated using UV resonance Raman spectroscopy. Excitation at 239.5 nm reveals selective enhancement of scattering from two Tyr residues. The titrating behavior of the tyrosines is followed through the change in the Y8a band (1617 cm(-1)) frequency as a function of pH, and a pK(a) = 10.2 +/- 0.2 is obtained. This is compared to the value of 9.1 +/- 0.2 for the pK(a) of aqueous Tyr also obtained in the present study. The pK(a) difference observed here, along with observations in the nu(OH) region, suggest that the two Tyr residues in the peptide probe two distinct microenvironments.

Time resolved infrared absorption studies of geminate recombination and vibrational relaxation in OClO photochemistry.

Ultrafast time-resolved infrared absorption studies of aqueous chlorine dioxide (OClO) photochemistry are reported. Following photoexcitation at 401 nm, the evolution in optical density at frequencies between 1000 to 1100 cm(-1) is monitored to investigate vibrational energy deposition and relaxation along the asymmetric-stretch coordinate following the reformation of ground-state OClO via geminate recombination of the primary photofragments. The measured kinetics are compared to two proposed models for the vibrational-relaxation dynamics along the asymmetric-stretch coordinate. This comparison demonstrates that the perturbation model derived from molecular dynamics studies is capable of qualitatively reproducing the observed kinetics, where the collisional model employed in previous UV-pump, visible probe experiments demonstrates poor agreement with experiment. The ability of the perturbation model to reproduce the optical-density evolution observed in these studies demonstrates that for aqueous OClO, frequency dependence of the solvent-solute coupling is important in defining the level-dependent vibrational relaxation rates along the asymmetric-stretch coordinate. The absence of optical-density evolution corresponding to the population of higher vibrational levels (n>8) along the asymmetric-stretch coordinate suggests that following geminate recombination, energy is initially deposited into a local Cl-O stretch, with the relaxation of vibrational energy from this coordinate providing for delayed vibrational excitation of the asymmetric- and symmetric-stretch coordinates relative to geminate recombination, as previously observed.