Solvent, Temperature, and Excitonic Effects in the Optical Spectra of Pseudoisocyanine Monomer and J-Aggregates

Shortwave infrared polymethine dyes for bioimaging: ultrafast relaxation dynamics and excited-state decay pathways

Excited-state relaxation in two prototypical shortwave infrared (SWIR) polymethine dyes developed for bioimaging, heptamethine chromenylium Chrom7 and flavylium Flav7, is studied by means of femtosecond transient absorption with broadband ultraviolet-to-SWIR probing complemented by steady-state and time-resolved fluorescence and phosphorescence measurements. The relaxation processes of the dyes in dichloromethane are resolved with sub-100 fs temporal resolution using SWIR, near-IR, and visible photoexcitation. Different population members of the ground-state inhomogeneous ensemble are found to equilibrate via skeletal deformation changes with time constants of 90 fs and either 230 fs (Chrom7) and 350 fs (Flav7) followed by slower evolution matching the 1-ps timescale of diffusive solvation dynamics. Molecules excited into high-lying singlet electronic states (Sn) by visible excitation repopulate with time constants of 400 fs (Chrom7) and 450 fs (Flav7) the corresponding first excited singlet S1 states, which decay within several hundreds of picoseconds in dichloromethane and chloroform solvents. Vibrational relaxation in S1 for both Chrom7 and Flav7 in dichloromethane occurs with time constants of 350 and 800 fs for excess of vibrational energy of ∼1000 and 10 000 cm-1 deposited by near-IR and visible excitation, respectively. Two competing non-radiative processes are present in S1: temperature-independent internal conversion, and thermally-activated twisting about a carbon-carbon bond of the conjugated chain, which is substantial at room temperature but essentially nonreactive, producing traces of isomer product. Intersystem crossing in S1, and thus the triplet quantum yield, is minor. The importance of absorption bands from the excited S1 state in applications requiring high-intensity excitation conditions is discussed.

H-Aggregation of Squaraine Dye as Generic Colorimetric Molecules to Detect Cu2

An infrared squaraine dye was utilized to detect Cu2+ in solvents based on H-aggregates of squaraine dye. H-aggregates are a type of aggregation with enhanced photophysical properties compared to monomers. In the presence of a Ca2+ solution, F-Cl offers exceptional H-aggregators that can be transformed into monomers by adding Cu2+. Furthermore, this mode successfully demonstrated fluorescence changes in HeLa cells cultured in vitro after the addition of Ca2+ or Cu2+. A highly specific detection of Cu2+ was achieved using this transformation mode.

Universal Scalings in Two-Dimensional Anisotropic Dipolar Excitonic Systems

Low-dimensional excitonic materials have inspired much interest owing to their novel physical and technological prospects. In particular, those with strong in-plane anisotropy are among the most intriguing but short of general analyses. We establish the universal functional form of the anisotropic dispersion in the small k limit for 2D dipolar excitonic systems. While the energy is linearly dispersed in the direction parallel to the dipole in plane, the perpendicular direction is dispersionless up to linear order, which can be explained by the quantum interference effect of the interaction among the constituents of 1D subsystems. The anisotropic dispersion results in a E^{∼0.5} scaling of the system density of states and predicts unique spectroscopic signatures including: (1) disorder-induced absorption linewidth, W(σ)∼σ^{2.8}, with σ the disorder strength, (2) temperature dependent absorption linewidth, W(T)∼T^{s+1.5}, with s the exponent of the environment spectral density, and (3) the out-of-plane angular θ dependence of the peak splittings in absorption spectra, ΔE(θ)∝sin^{2}θ. These predictions are confirmed quantitatively with numerical simulations of molecular thin films and tubules.

Atomistic simulation studies of ionic cyanine dyes: self-assembly and aggregate formation in aqueous solution

Cyanine dyes are known to form large-scale aggregates of various morphologies via spontaneous self-assembly in aqueous solution, akin to chromonic liquid crystals. Atomistic molecular dynamics simulations have been performed on four cyanine dyes: pseudoisocyanine chloride (PIC), pinacyanol chloride (PCYN), 5,5',6,6'-tetrachloro-1,1',3,3'-tetraethylbenzimidazolylcarbocyanine chloride (TTBC) and 1,1'-disulfopropyl-3,3'-diethyl-5,5',6,6'-tetrachloro-benzimidazolylcarbocyanine sodium salt (BIC). Simulations employed an optimised general AMBER force field and demonstrate the organisation of the dyes into stacked structures at dilute concentrations. The thermodynamics of self-assembly was studied by calculating potentials of mean force for n-mers (n = 2, 3 or 4), from which the free energies of association are determined. We report binding free energies in the range of 8 to 15k_BT for dimerisation, concordant with typical values for ionic chromonics (7 to 14k_BT), and examine the enthalpic and entropic contributions to the aggregation process. The self-assembly of these dyes yields two distinct classes of structures. We observe the formation of H-aggregate stacks for PCYN, with further complexity in these assemblies for PIC; where the aggregates contain shift and Y junction defects. TTBC and BIC associate into a J-aggregate sheet structure of unimolecular thickness, and is composed of a brickwork arrangement between molecules. These sheet structures are characteristic of the smectic chromonic mesophase, and such assemblies provide a route to the emergence of nanoscale tubular architectures.

Molecular Engineering of a Donor-Acceptor Polymer To Realize Single Band Absorption toward a Red-Selective Thin-Film Organic Photodiode

Herein, we explore the strategy of realizing a red-selective thin-film organic photodiode (OPD) by synthesizing a new copolymer with a highly selective red-absorption feature. PCZ-Th-DPP, with phenanthrocarbazole (PCZ) and diketopyrrolopyrrole (DPP) as donor and acceptor units, respectively, was strategically designed/synthesized based on a time-dependent density functional theory calculation, which predicted the significant suppression of the band II absorption of PCZ-Th-DPP due to the extremely efficient intramolecular charge transfer. We demonstrate that the synthesized PCZ-Th-DPP exhibits not only a high absorption coefficient within the red-selective band I region, as theoretically predicted, but also a preferential face-on intermolecular structure in the thin-film state, which is beneficial for vertical charge extraction as an outcome of a glancing incidence X-ray diffraction study. By employing PCZ-Th-DPP as a photoactive layer of Schottky OPD, to fully match its absorption characteristic to the spectral response of the red-selective OPD, we demonstrate a genuine red-selective specific detectivity in the order of 10¹² Jones while maintaining a thin active layer thickness of ∼300 nm. This work demonstrates the possibility of realizing a full color image sensor with a synthetic approach to the constituting active layers without optical manipulation.

M13 Virus-Based Framework for High Fluorescence Enhancement

Fluorescence imaging is a powerful tool for studying biologically relevant macromolecules, but its applicability is often limited by the fluorescent probe, which must demonstrate both high site-specificity and emission efficiency. In this regard, M13 virus, a versatile biological scaffold, has previously been used to both assemble fluorophores on its viral capsid with molecular precision and to also target a variety of cells. Although M13-fluorophore systems are highly selective, these complexes typically suffer from poor molecular detection limits due to low absorption cross-sections and moderate quantum yields. To overcome these challenges, a coassembly of the M13 virus, cyanine 3 dye, and silver nanoparticles is developed to create a fluorescent tag capable of binding with molecular precision with high emissivity. Enhanced emission of cyanine 3 of up to 24-fold is achieved by varying nanoparticle size and particle-fluorophore separation. In addition, it is found that the fluorescence enhancement increases with increasing dye surface density on the viral capsid. Finally, this highly fluorescent probe is applied for in vitro staining of E. coli. These results demonstrate an inexpensive framework for achieving tuned fluorescence enhancements. The methodology developed in this work is potentially amendable to fluorescent detection of a wide range of M13/cell combinations.

Hierarchical self-assembly of squaraine and silica nanoparticle functionalized with cationic coordination sites for near infrared detection of ATP

Optical activity of hierarchical supramolecular assemblies based on organic dyes would create multiple functional architectures. In this work, three kinds of silica nanoparticles with or without functional groups were synthesized. For the first time, silica nanoparticles can induce positively charged squaraine (SQ) to aggregate to form supramolecular assemblies. Adenosine-5'-triphosphate (ATP) as building blocks was absorbed on the surface of silica nanoparticles through metal-anion coordination and electrostatic interactions, in which the aggregates of SQ was transferred to monomer. The thickness being composed of ATP and SQ on the outside of nanoparticles is about 5 nm. These supramolecular assemblies showed selective turn-on fluorescence response to ATP in near infrared (NIR) region over other ions through metal-anion coordination and electrostatic interactions. These functional silica nanoparticles possessing many advantages provide proof-of-principle "seed crystals" for construction of supramolecular assemblies and platforms for sensing with facile performance.

Proximity-Induced H-Aggregation of Cyanine Dyes on DNA-Duplexes

A wide variety of organic dyes form, under certain conditions, clusters know as J- and H-aggregates. Cyanine dyes are such a class of molecules where the spatial proximity of several dyes leads to overlapping electron orbitals and thus to the creation of a new energy landscape compared to that of the individual units. In this work, we create artificial H-aggregates of exactly two Cyanine 3 (Cy3) dyes by covalently linking them to a DNA molecule with controlled subnanometer distances. The absorption spectra of these coupled systems exhibit a blue-shifted peak, whose intensity varies depending on the distance between the dyes and the rigidity of the DNA template. Simulated vibrational resolved spectra, based on molecular orbital theory, excellently reproduce the experimentally observed features. Circular dichroism spectroscopy additionally reveals distinct signals, which indicates a chiral arrangement of the dye molecules. Molecular dynamic simulations of a Cy3-Cy3 construct including a 14-base pair DNA sequence verified chiral stacking of the dye molecules.

Fluorescent DNA probes at liquid/liquid interfaces studied by surface second harmonic generation

The excited-state properties of oxazole yellow DNA probes change substantially when going from bulk water to the dodecane/water interface.

Forcing aggregation of cyanine dyes with salts: a fine line between dimers and higher ordered aggregates

It is uncommon to read about cyanine dyes in the literature and not have their aggregation discussed. They are of high interest considering their propensity to undergo self-organization in aqueous solution, leading to interesting photophysical properties resulting from the formation of their dimers and higher ordered aggregates. Currently, the study of their aggregation is in high demand due to their diverse application range including dye-sensitized solar cells. However, their aggregation in high salt solutions is under studied, and the effect on aggregation in congruence with high ionic strength is often overlooked. In a previous study, our group established the role of specific ion effects and in particular the necessity of matching water affinity to induce aggregation of a cationic cyanine dye, thiazole orange. In order to advance the understanding of this topic, we present in this article the diverse aggregation of cyanine dyes, as a single monovalent salt can cause different aggregation responses in a variety of these dyes. We established via absorption spectroscopy combined with chemometric analyses that the inherent monomer-dimer equilibrium of a dye depends on its geometry. More interestingly, experimental data coupled with DFT calculations reveal that not only the geometry of a dye but also its charge location plays a role in the aggregate morphology formed by the interaction of a cationic cyanine dye and an anion. It is thought that contact ion pair formation and effective charge screening generated within that ion pair are responsible for aggregates with a greater order.

Strong plasmon-exciton coupling in a hybrid system of gold nanostars and J-aggregates

Hybrid materials formed by plasmonic nanostructures and J-aggregates provide a unique combination of highly localized and enhanced electromagnetic field in metal constituent with large oscillator strength and extremely narrow exciton band of the organic component. The coherent coupling of localized plasmons of the multispiked gold nanoparticles (nanostars) and excitons of JC1 dye J-aggregates results in a Rabi splitting reaching 260 meV. Importantly, broad absorption features of nanostars extending over a visible and near-infrared spectral range allowed us to demonstrate double Rabi splitting resulting from the simultaneous coherent coupling between plasmons of the nanostars and excitons of J-aggregates of two different cyanine dyes.

Influence of complex exciton-phonon coupling on optical absorption and energy transfer of quantum aggregates

We present a theory that efficiently describes the quantum dynamics of an electronic excitation that is coupled to a continuous, highly structured phonon environment. Based on a stochastic approach to non-Markovian open quantum systems, we develop a dynamical framework that allows us to handle realistic systems where a fully quantum treatment is desired yet the usual approximation schemes fail. The capability of the method is demonstrated by calculating spectra and energy transfer dynamics of mesoscopic molecular aggregates, elucidating the transition from fully coherent to incoherent transfer.

Solvation effect of bacteriochlorophyll excitons in light-harvesting complex LH2

We have characterized the influence of the protein environment on the spectral properties of the bacteriochlorophyll (Bchl) molecules of the peripheral light-harvesting (or LH2) complex from Rhodobacter sphaeroides. The spectral density functions of the pigments responsible for the 800 and 850 nm electronic transitions were determined from the temperature dependence of the Bchl absorption spectra in different environments (detergent micelles and native membranes). The spectral density function is virtually independent of the hydrophobic support that the protein experiences. The reorganization energy for the B850 Bchls is 220 cm(-1), which is almost twice that of the B800 Bchls, and its Huang-Rhys factor reaches 8.4. Around the transition point temperature, and at higher temperatures, both the static spectral inhomogeneity and the resonance interactions become temperature-dependent. The inhomogeneous distribution function of the transitions exhibits less temperature dependence when LH2 is embedded in membranes, suggesting that the lipid phase protects the protein. However, the temperature dependence of the fluorescence spectra of LH2 cannot be fitted using the same parameters determined from the analysis of the absorption spectra. Correct fitting requires the lowest exciton states to be additionally shifted to the red, suggesting the reorganization of the exciton spectrum.

Watching Ultrafast Barrierless Excited-State Isomerization of Pseudocyanine in Real Time

The photoinduced excited-state processes in 1,1'-diethyl-2,2'-cyanine iodine are investigated using femtosecond time-resolved pump-probe spectroscopy. Using a broad range of probe wavelengths, the relaxation of the initially prepared excited-state wavepacket can be followed down to the sink region. The data directly visualize the directed downhill motion along the torsional reaction coordinate and suggest a barrierless excited-state isomerization in the short chain cyanine dye. Additionally, ultrafast ground-state hole and excited-state hole replica broadening is observed. While the narrow excited-state wavepacket broadens during pump-probe overlap, the ground-state hole burning dynamics takes place on a significantly longer time-scale. The experiment reported can be considered as a direct monitoring of the shape and the position of the photoprepared wavepacket on the excited-state potential energy surface.

Two-Photon Fluorescence Spectroscopy of Individually Trapped Pseudoisocyanine J-Aggregates in Aqueous Solution

We have investigated a pseudoisocyanine dye aqueous solution including nanometer-sized J-aggregates by combining optical trapping and two-photon fluorescence spectroscopy. By focusing an intense near-infrared laser into an 8 x 10(-3) M solution, the intense fluorescence from J-aggregates for a few to tens of seconds is observed intermittently, indicating that individual J-aggregates are trapped in and diffuse out from a focal spot. The peak position and full width at half-maximum of the J-band are different from each other. By measuring 171 J-aggregates, it was found that J-aggregates can be classified largely into two groups. The existence of two kinds of groups of J-aggregates could be attributed to the difference in the nucleation process, which is affected by the substrate. J-aggregates possessing a J-band of a narrower bandwidth in a shorter wavelength region are trapped for a longer period of time, indicating that highly ordered J-aggregates are trapped for a longer period of time because of their high polarizability.

Decoherence of excitons in multichromophore systems: thermal line broadening and destruction of superradiant emission

We study the temperature-dependent dephasing rate of excitons in chains of chromophores, accounting for scattering on static disorder as well as acoustic phonons in the host matrix. From this we find a power-law temperature dependence of the absorption linewidth, in excellent quantitative agreement with experiments on dye aggregates. We also propose a relation between the linewidth and the exciton coherence length imposed by the phonons. The results indicate that the much debated steep rise of the fluorescence lifetime of pseudoisocyanine aggregates above 40 K results from the fact that this coherence length drops below the localization length imposed by static disorder.

Thermal broadening of the J-band in disordered linear molecular aggregates: A theoretical study

We theoretically study the temperature dependence of the J-band width in disordered linear molecular aggregates, caused by dephasing of the exciton states due to scattering on vibrations of the host matrix. In particular, we consider inelastic one- and two-phonon scatterings between different exciton states (energy-relaxation-induced dephasing), as well as the elastic two-phonon scattering of the excitons (pure dephasing). The exciton states follow from numerical diagonalization of a Frenkel exciton Hamiltonian with diagonal disorder; the scattering rates between them are obtained using the Fermi golden rule. A Debye-type model for the one- and two-phonon spectral densities is used in the calculations. We find that, owing to the disorder, the dephasing rates of the individual exciton states are distributed over a wide range of values. We also demonstrate that the dominant channel of two-phonon scattering is not the elastic one, as is often tacitly assumed, but rather comes from a similar two-phonon inelastic scattering process. In order to study the temperature dependence of the J-band width, we simulate the absorption spectrum, accounting for the dephasing-induced broadening of the exciton states. We find a power-law (T(p)) temperature scaling of the effective homogeneous width, with an exponent p that depends on the shape of the spectral density of the host vibrations. In particular, for a Debye model of vibrations, we find p approximately 4, which is in good agreement with the experimental data on J aggregates of pseudoisocyanine [I. Renge and U. P. Wild, J. Phys. Chem. A, 101, 7977 (1997)].

Solvent-Dependent Vibrational Frequencies and Reorganization Energies of Two Merocyanine Chromophores

Absorption and resonance Raman spectra have been measured over a wide range of solvents for two merocyanine dyes containing the indoline ("Fischer" base) electron donor group with different accepting groups. One appears to be near the cyanine limit (equal contributions of the neutral and zwitterionic resonance forms to both ground- and excited-state structures) based on electrooptic absorption data showing a very small dipole moment change upon electronic excitation. The resonance Raman spectra of both molecules show significant frequency shifts and intensity redistributions that evolve monotonically with increasing solvent polarity and are consistent with increasing zwitterionic character of the ground-state structure. The vibrational reorganization energies of both molecules, obtained by simulating the absorption band shapes, are smaller in polar solvents than in nonpolar or weakly polar ones, consistent with a more cyanine-like structure at higher solvent polarities. However, the vibrational reorganization energies of both molecules exceed 700 cm(-1) in all solvents, larger than in many true cyanine dyes, and the optical absorption maxima do not correlate well with either solvent polarity or vibrational reorganization energy. This indicates some limitations to the structural conclusions that can be reached from the two-state model for pi-conjugated donor-acceptor systems.