Exciton transport in thin-film cyanine dye J-aggregates
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Second-order spectra of symmetric cyanine dyes.
Second order absorption spectra of symmetric cyanine dyes in methanol solution using spectrophotometer
SPECTROPHOTOMETER↗
Molecular engineering of cyanine dyes to design a panchromatic response in Co-sensitized dye-sensitized solar cells
Cyanines are optically tunable dyes with high molar extinction coefficients, suitable for applications in co-sensitized dye-sensitized solar cells (DSCs); yet, barely thus applied. This might be due to the lack of a rational molecular design strategy that efficiently exploits cyanine properties. This study computationally re-designs these dyes, to broaden their optical absorption spectrum and create dye···TiO 2 binding and co-sensitization functionality. This is achieved via a stepwise molecular engineering approach. Firstly, the structural and optical properties of four parent dyes are experimentally and computationally investigated: 3,3’-diethyloxacarbocyanine iodide, 3,3’-diethylthiacarbocyanine iodide, 3,3’-diethylthiadicarbocyanine iodide and 3,3’-diethylthiatricarbocyanine iodide. Secondly, the molecules are theoretically modified and their energetics are analyzed and compared to the parent dyes. A dye···TiO 2 anchoring group (carboxylic or cyanoacrylic acid), absent from the parent dyes, is chemically substituted at different molecular positions to investigate changes in optical absorption. We find that cyanoacrylic acid substitution at the para-quinoidal position affects the absorption wavelength of all parent dyes, with an optimal bathochromic shift of ca. 40 nm. The theoretical lengthening of the polymethine chain is also shown to effect dye absorption. Two molecularly engineered dyes are proposed as promising co-sensitizers. Finally, corresponding dye···TiO 2 adsorption energy calculations corroborate their applicability, demonstrating the potential of cyanine dyes in DSC research.
14 SOLAR ENERGY↗
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. Furthermore, 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.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Optical and photoelectric properties of multichromic cyanine dye J-aggregates
We report the results of investigation of spectra and kinetics of photoluminescence as well as of photoabsorption and photoelectric properties for multichromic molecular crystals consisting of J-aggregates of three cyanine dyes with various structures. An original ‘self-assembly’ method is used for fabricating such prolate ordered structures with a thickness of 5 – 100 nm, width of 0.1 – 5 μm, and length of 50 – 300 μm. The method is based on the formation of the anionic platform in a water solution, which absorbs light in the blue spectrum range and comprises J-aggregates of magnesium complexes of anionic cyanine dye. Then the ‘matrix synthesis’ is used for coating its surface with J-aggregates of the two cationic dyes that have the absorption maxima in the green and red spectral ranges. It is shown that each of the multichromic organic crystals produced in this way is a multilayer photoelement, which possesses photoconductivity in three excitonic absorption maxima (in the blue, green, and red spectral ranges) with the external quantum efficiency varying from 2.7 % to 6.1 %. The results obtained provide a basis for technological development of highly-ordered molecular structures, which are promising for using in organic and hybrid photonics and optoelectronics including thin-film photo-converters operating in wide spectral ranges.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Probing DNA structural heterogeneity by identifying conformational subensembles of a bicovalently bound cyanine dye
DNA is a re-configurable, biological information-storage unit, and much remains to be learned about its heterogeneous structural dynamics. For example, while it is known that molecular dyes templated onto DNA exhibit increased photostability, the mechanism by which the structural dynamics of DNA affect the dye photophysics remains unknown. Here, we use femtosecond, two-dimensional electronic spectroscopy measurements of a cyanine dye, Cy5, to probe local conformations in samples of single-stranded DNA (ssDNA–Cy5), double-stranded DNA (dsDNA–Cy5), and Holliday junction DNA (HJ–DNA–Cy5). A line shape analysis of the 2D spectra reveals a strong excitation–emission correlation present in only the dsDNA–Cy5 complex, which is a signature of inhomogeneous broadening. Molecular dynamics simulations support the conclusion that this inhomogeneous broadening arises from a nearly degenerate conformer found only in the dsDNA–Cy5 complex. These insights will support future studies on DNA’s structural heterogeneity.
77 NANOSCIENCE AND NANOTECHNOLOGY↗
Decay kinetics of the excited S{sub 1} state of the cyanine dye Cy{sup +}I{sup -} (thiacarbocyanine iodide): The computation of quantum yields for different pathways
This work explains the unordinary solvent effect which was observed in the photochemical decay kinetics for the cyanine dye thiacarbocyanine iodide (Cy{sup +}I{sup -}) in binary solvent mixtures toluene/dimethylsulfoxide. The interpretation is formulated in terms of the probability density F(R) describing the distribution of interionic distances R in the ion pair Cy{sup +}I{sup -} and depending on the solvent composition. The proper normalization of this distribution is expressed via the degree of association {alpha} for the ion pair in a given solvent mixture. The {alpha} values are, in turn, extracted by means of the mass action law from the ionic association constants computed in a separate publication. The detailed kinetic scheme includes the empirical parametrization of the R-dependent kinetic constants for different decay channels. The multiparameter fitting procedure represents, with the reasonable parameter values, the dependence of the observed quantum yields on the solvent composition.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Enhancement of Fluorescence and Raman Scattering in Cyanine-Dye Molecules on the Surface of Silicon-Coated Silver Nanoparticles
A method of formation of a composite structure based on silver nanoparticles and a thin protective silicon film (AgNPs/Si) is developed. Enhancement of the fluorescence and Raman scattering in cyaninedye molecules deposited onto the formed nanostructure is observed. The optical properties and morphology stability of particles that are in contact with cyanine-dye solutions in organic solvents are studied. It is shown that the AgNPs/Si composite structure can be multiply used as an SERS-active surface.
77 NANOSCIENCE AND NANOTECHNOLOGY↗
DNA-Templated Aggregates of Strongly Coupled Cyanine Dyes: Nonradiative Decay Governs Exciton Lifetimes
Molecular excitons are used in a variety of applications including light harvesting, optoelectronics, and nanoscale computing. Controlled aggregation via covalent attachment of dyes to DNA templates is a promising aggregate assembly technique that enables the design of extended dye networks. Yet, there are few studies of exciton dynamics in DNA-templated dye aggregates. Here we report time-resolved excited-state dynamics measurements of two cyanine-based dye aggregates, a J-like dimer and an H-like tetramer, formed through DNA-templating of covalently attached dyes. Time-resolved fluorescence and transient absorption indicate that nonradiative decay, in the form of internal conversion, dominates the aggregate ground state recovery dynamics, with singlet exciton lifetimes on the order of tens of picoseconds for the aggregates versus nanoseconds for the monomer. These results highlight the importance of circumventing nonradiative decay pathways in the future design of DNA-templated dye aggregates.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Tunable Electronic Structure via DNA-Templated Heteroaggregates of Two Distinct Cyanine Dyes
Not Available
77 NANOSCIENCE AND NANOTECHNOLOGY↗
Identification of Absorption Bands of Monomers and Aggregates in a Layer of Cyanine Dye and Determination of the Orientation of Molecules
The problem of allocating bands of individual monomers or aggregates of the absorption spectrum of a multicomponent structure arises in the study of molecular layers or organic thin films. Not counting the concentrations of the components, the optical properties of this kind of samples are determined by the tilt of the molecules relative to the substrate surface. Molecular orientation can be determined from the dichroic ratio spectra recorded with the tilt probing of samples. Using the example of the tricarbocyanine dye layers, the following two independent methods for the identification of the spectra of the components from the absorption spectrum of a layer are compared: by comparing the spectra of layers of different thicknesses and based on the dichroic ratio spectra. The effect of laser radiation on the samples, which leads to a change in the dichroic ratio, is studied. Photoinduced changes of the orientation angles of molecules are calculated, which allows one to refine the range of possible values of these angles.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Extending Infrared Emission via Energy Transfer in a CsPbI 3 –Cyanine Dye Hybrid
Not provided.
Chemistry↗
Structural Insight into a Sixteen Cyanine Dye Construct via Exciton–Exciton Annihilation
Molecular (dye) aggregates play a prominent role in light harvesting and are of interest in quantum information science; however, there are limited reports hat programmably assemble many (>4) dye aggregates featuring strong coupling and exciton delocalization. Using oligonucleotides with four Cy5s covalently linked in series along the phosphate backbone, we bring four, eight, and sixteen Cy5s in close proximity by assembling four-armed junctions. We elucidate their structure via gel electrophoresis and steady-state and transient optical spectroscopy. We find that Cy5 has a strong propensity to form tetramer clusters, where the exciton is delocalized over all four Cy5s, that the exciton is not delocalized beyond tetramer clusters in the eight and sixteen Cy5 constructs, and that the sixteen Cy5 construct may consist of pairs of tetramer clusters that are isolated from one another. Many-dye aggregates such as these may serve useful as antennae for their intense light absorption and spatially directed energy transfer.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
“Turn-On” Protein Fluorescence: In Situ Formation of Cyanine Dyes
Protein reengineering of cellular retinoic acid binding protein II (CRABPII) has yielded a genetically addressable system, capable of binding a profluorophoric chromophore that results in fluorescent protein/chromophore complexes. These complexes exhibit far-red emission, with high quantum efficiencies and brightness and also exhibit excellent pH stability spanning the range of 2$-$11. In the course of this study, it became evident that single mutations of L121E and R59W were most effective in improving the fluorescent characteristics of CRABPII mutants as well as the kinetics of complex formation. The readily crystallizable nature of these proteins was invaluable to provide clues for the observed spectroscopic behavior that results from single mutation of key residues.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Simplified Microarray Technique for Identifying mRNA in Rare Samples
Two simplified methods of identifying messenger ribonucleic acid (mRNA), and compact, low-power apparatuses to implement the methods, are at the proof-of-concept stage of development. These methods are related to traditional methods based on hybridization of nucleic acid, but whereas the traditional methods must be practiced in laboratory settings, these methods could be practiced in field settings. Hybridization of nucleic acid is a powerful technique for detection of specific complementary nucleic acid sequences, and is increasingly being used for detection of changes in gene expression in microarrays containing thousands of gene probes. A traditional microarray study entails at least the following six steps: 1. Purification of cellular RNA, 2. Amplification of complementary deoxyribonucleic acid [cDNA] by polymerase chain reaction (PCR), 3. Labeling of cDNA with fluorophores of Cy3 (a green cyanine dye) and Cy5 (a red cyanine dye), 4. Hybridization to a microarray chip, 5. Fluorescence scanning the array(s) with dual excitation wavelengths, and 6. Analysis of the resulting images. This six-step procedure must be performed in a laboratory because it requires bulky equipment.
Almeida, Eduardo↗
Efficient Long-range, Directional Energy Transfer through DNA-Templated Dye Aggregates
The benzothiazole cyanine dye, K21, forms dye aggregates on double stranded DNA (dsDNA) templates. These aggregates exhibit a red-shifted absorption band, enhanced fluorescence emission and an increased fluorescence lifetime, all indicating strong excitonic coupling among the dye molecules. K21 aggregate formation on dsDNA is only weakly sequence dependent, providing a flexible approach that is adaptable to many different DNA nanostructures. Donor (D) – bridge (B) – Acceptor (A) complexes consisting of Alexa Fluor 350 as the donor, a 30 bp (9.7 nm) DNA templated K21 aggregate as the bridge and Alexa Fluor 555 as the acceptor show an overall donor to acceptor energy transfer efficiency of ~60%, with the loss of excitation energy being almost exclusively at the donor-bridge junction (63%). There was almost no excitation energy loss due to transfer through the aggregate bridge and the transfer efficiency from the aggregate to the acceptor was about 96%. By comparing the energy transfer in templated aggregates at several lengths up to 32 nm, the loss of energy per nanometer through the K21 aggregate bridge was determined to be <1%, suggesting that it should be possible to construct structures that use much longer energy transfer “wires” for light-harvesting applications in photonic systems.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗