Aggregation Of Cyanine Dyes Research Articles

Multilayers and multichromic aggregates of anionic and cationic cyanine dyes

The method of formation of multilayers and multichromic 3D-J-aggregates from anionic and cationic cyanines via the sequential recharge of the metal-complexis J-aggregate surface of the anionic dye, the so-called “platform,” by the cationic dye as a result of the matrix synthesis of the J-aggregate of this dye on the surface of the platform and at the subsequent J- aggregation of anionic cyanine on a positively charged surface of the 3D-platform is considered. The conclusion that a similar method offers the possibility of selfassembly of the complex systems of aggregates from the large number of dyes distinguished by both spectral properties and by the position of the electron levels in the aggregates is made.

Specific excitonic interactions in the aggregates of hyaluronic acid and cyanine dyes with different lengths of methine group.

The absorption and circular dichroism (CD) spectra of three types of cyanine dyes with different lengths of methine group (3,3'-diethylthiadicarbocyanine iodide, DTDC; 3,3'-diethylthiacarbocyanine iodide, DTC; and 3,3'-diethylthiacyanine iodide, DTTHC) in an aqueous solution were compared with and without hyaluronic acid (HA), which has a helical structure. DTDC forms chiral H- and J-aggregates, whereas DTC and DTTHC are unable to form any aggregates. DTDC also forms H- and J-aggregates in the presence of sodium polyacrylate (PA) with a random-coil structure; however, the PA-DTDC aggregates exhibit no chirality. These results suggest that the chirality of HA-DTDC aggregates is induced by the helical structure of HA. In 2.4 vol% and 10 vol% methanol, HA-DTDC aggregates displayed different patterns of temperature dependence, whereas no aggregation was observed in 30 vol% methanol. The solubility of DTDC in a mixed solvent of water and methanol is generally improved by the addition of methanol, which prevents the aggregation of DTDC.

Light absorption and plasmon – exciton interaction in three-layer nanorods with a gold core and outer shell composed of molecular J- and H-aggregates of dyes

Optical properties of hybrid rod-like nanoparticles, consisting of a gold core, an intermediate passive organic layer (spacer) and outer layer of ordered molecular cyanine dye aggregates, are experimentally and theoretically investigated. It is shown that these dyes can form not only ordered J-aggregates but also H-aggregates (differing by the packing angle of dye molecules in an aggregate and having other spectral characteristics) in the outer shell of the hybrid nanostructure. Absorption spectra of synthesised three-layer nanorods are recorded, and their sizes are determined. The optical properties of the composite nanostructures under study are found to differ significantly, depending on the type of the molecular aggregate formed in the outer shell. The experimental data are quantitatively explained based on computer simulation using the finite-difference time-domain (FDTD) method, and characteristic features of the plasmon – exciton interaction in the systems under study are revealed.

59 De-aggregation mediated monitoring of protein aggregation through controlled aggregation of cyanine dyes

59 De-aggregation mediated monitoring of protein aggregation through controlled aggregation of cyanine dyes

J-aggregate formation behavior of a cationic cyanine dye on inorganic layered material

Adsorption, aggregation, and photochemical behavior of a cationic cyanine dye (5,5′,6,6′-tetrachloro-1,1′,3,3′-tetraethylbenzimidazolylcarbo-cyanine chloride (JC-1)) on an inorganic layered material were examined. JC-1 formed J-aggregates on the clay surface even at a low loading level. The structure of the J-aggregate was determined through analysis using the extended dipole model proposed by Kuhn et al. Aggregation number and slip angle of the J-aggregate on the clay surface were calculated as more than 8 molecules and 20–22°, respectively. The J-aggregate on the clay sheet exhibited high fluorescence quantum yield (0.4), thus, this complex will be promising to construct photochemical reaction systems such as artificial light harvesting systems.

Aggregation Control of Hemicyanine Fluorescent Dye by Using of Cucurbit[7]uril and Pillar[6]arene

AbstractThe aggregation of cyanine‐based fluorescent dyes easily results in the fluorescence quenching, which limits the applications in biological science and materials science. So developing an efficient method to adjust the aggregation of cyanine dyes is very significant. In this work, we employ two different macrocyclic hosts pillar[6]arene (DEP[6]) and cucurbit[7]uril (CB[7]) to investigate their effects towards fluorescence spectra of dye 1. The result indicates that both of them can disrupt the aggregation of dye 1, resulting in the enhancement of its fluorescence intensity. Interestingly, investigation on the corresponding titration experiments of 1H NMR and density functional theory calculations shows that CB[7] and DEP[6] play different roles in the process of disaggregation.

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.

First-Principles Calculation of the Optical Properties of an Amphiphilic Cyanine Dye Aggregate

Using a first-principles approach, we calculate electronic and optical properties of molecular aggregates of the dye amphi-pseudoisocyanine, whose structures we obtained from molecular dynamics (MD) simulations of the self-aggregation process. Using quantum chemistry methods, we translate the structural information into an effective time-dependent Frenkel exciton Hamiltonian for the dominant optical transitions in the aggregate. This Hamiltonian is used to calculate the absorption spectrum. Detailed analysis of the dynamic fluctuations in the molecular transition energies and intermolecular excitation transfer interactions in this Hamiltonian allows us to elucidate the origin of the relevant time scales; short time scales, on the order of up to a few hundreds of femtoseconds, result from internal motions of the dye molecules, while the longer (a few picosecond) time scales we ascribe to environmental motions. The absorption spectra of the aggregate structures obtained from MD feature a blue-shifted peak compared to that of the monomer; thus, our aggregates can be classified as H-aggregates, although considerable oscillator strength is carried by states along the entire exciton band. Comparison to the experimental absorption spectrum of amphi-PIC aggregates shows that the simulated line shape is too wide, pointing to too much disorder in the internal structure of the simulated aggregates.

A near-infrared fluorescent probe for selective detection of HClO based on Se-sensitized aggregation of heptamethine cyanine dye

A Se-containing heptamethine cyanine dye based fluorescent probe was successfully developed and used for HClO detection with rapid response and high selectivity based on aggregation behavior. The probe could react with HClO with significant change in its fluorescence profile, which makes it practical for detecting HClO in fetal bovine serum and in living mice.

Quantification of the Na+/K+ ratio based on the different response of a newly identified G-quadruplex to Na+ and K+

A G-quadruplex is identified which can exhibit two different motifs, respectively, corresponding to Na(+) and K(+). The relative amount of each motif is related to the Na(+)/K(+) ratio. Based on selective recognition of the G-quadruplex motifs by a cyanine dye aggregate, a method for both colorimetric and quantitative measurements of Na(+)/K(+) ratios is constructed.

Induced Optical Activity of DNA-Templated Cyanine Dye Aggregates: Exciton Coupling Theory and TD-DFT Studies

Certain cyanine dye molecules have been observed to self-assemble in DNA templates to form large chiral aggregates, which exhibit induced circular dichroism. The structure and circular dichroism (CD) of one such system, aggregates of a cationic DiSC2(5) cyanine dye, are investigated using the time-dependent Kohn-Sham density functional theory (TD-DFT) and exciton coupling model. A series of TD-DFT calculations on the aggregates with one, two, and four dye molecules clearly shows the onset of CD induced by the helically twisted structure compatible with the minor groove of DNA templates. More simplified exciton coupling model analysis successfully reproduces the major positive Cotton effect observed in the experiment as well as the TD-DFT calculations, but it is unable to capture minor features of the CD spectrum that are closely related to absolute configurations of constituent dyes in the complex. We assess the performance of various methods used for evaluation of the electronic coupling energies between interacting chromophores. Our results confirm that the interchromophore interactions in cyanine dye aggregates are primarily electrostatic in nature and indicate that the exciton coupling model is adequate for studying induced CD of self-assembled aggregates of cyanine dye molecules.

Molecular Arrangements in Two-Dimensional J-Aggregate Monolayers of Cyanine Dyes

Atomic force microscopy was used for the study of two-dimensional J-aggregates monolayer structures of two cyanine dyes with a high-resolution. Two coexisting morphologically different types (i.e. the bilayer rectangular stripes and monolayer curve shaped leaves) were observed for 3,3’-di(γ-sulfopropyl)-4,4’,5,5’-dibenzo-9-ethylthiacarbocyanine betaine pyridinium (dye D-1). The morphological diversity, the crystallographic peculiarities and the monolayer height ~ 1.35 nm are selfconsistently explained by the difference in the molecular packing arrangements, i.e. the ladder for stripes and the staircase for leaves. A building unit of both J-aggregate types is a symmetric monolayer with the same height and slip angle ~ 15o, composed of all-trans monomers with anti-parallel up-down orientation. For the two-dimensional sheets of the second cyanine dye (5,5'-dichloro-3,3'-disulfopropyl thiacyanine sodium salt) Dye-2 the fine substructure formed by close packed parallel narrow threads was resolved. The stripes were inclined at the angle ~30o to the J-aggregates long side providing for the first time the direct microscopic support for the probable staircase molecular arrangement. It is speculated that the quazi-one-dimensional staircase-type and ladder-type units are building blocks of the two-dimensional aggregates of various cyanine dyes.

Visual detection of potassium by a cyanine dye supramolecular aggregate responsive to G-quadruplex motif transition

A supramolecular probe is designed for visual detection of potassium based on a novel cyanine dye aggregate recognizing the motif transition of telomeric G-quadruplexes under the Na(+) background. The practical application for colorimetric measurement of urine potassium has been tested.

ハロゲン化物モノレヤーで修飾されたAg(111)表面を吸着場としたシアニン色素凝集体のSTM観察-H-凝集体とJ-凝集体の比較

ハロゲン化物モノレヤーで修飾されたAg(111)表面を吸着場としたシアニン色素凝集体のSTM観察-H-凝集体とJ-凝集体の比較

Investigation of the Effect of Concentration on Molecular Aggregation of Cyanine Dyes in Aqueous Solution

The aggregation of the cyanine dye, 3,3’-disulfobutyl-5,5’-dichloro thiacarbocyanine triethylamine, (NK-3796) in aqueous solution was investigated using absorption and emission spectroscopy. The equilibrium, n(monomer) ⇆ n(dimer) ⇆ (H-aggregate)n , was observed over a series of dye concentrations ranging from 10-4 mM to 0.1mM. At concentrations <10-3 mM, the dye exists in solution mostly in the monomeric form. However, dimers become more significant when the concentration of the dye exceeds 10-2 mM. Unlike the substituted dye in the 9th position, the NK-3796 dye tends to form H-aggregates at higher concentration (>10-1 mM). Monomers and dimers exhibit strong emission in the visible region. Also notable, is that the emission from the H-aggregates was very weak due to self quenching.

Substituent Effects on the Assembly of Helical Cyanine Dye Aggregates in the Minor Groove of a DNA Template

Double-helical DNA was used as a template for the assembly of helical cyanine dye aggregates. The aggregates consist of cofacial dimers aligned end-to-end in the minor groove of the DNA. The effect of methoxy or fluoro substituents placed on the periphery of the cyanine dye heterocycles on aggregation both in water and on the DNA template was studied by UV-vis and circular dichroism spectroscopy. Methoxy groups were found to be stronger promoters of aggregation than fluoro, and a dimethoxy dye exhibited a higher propensity to aggregate compared with an unsymmetrical methoxy/fluoro dye. Semiempirical calculations supported the experimental observation of methoxy substitution favoring aggregation. These results indicate that dispersion and hydrophobic effects contribute more to dimerization/aggregation than do electron donor-acceptor effects.

Simulation of interaction of oriented J aggregates with resonance laser radiation

The interaction of laser radiation with single J aggregates of cyanine dyes is theoretically analyzed and numerically simulated. The quantum-mechanical calculations of the equilibrium geometry and the energies and intensities of the lowest singlet electronic transitions in pseudoisocyanine chloride and its linear (chain) oligomers are fulfilled. The data of these calculations can serve as parameters of the analyzed model of interaction of J aggregates with radiation in the one-particle density matrix approximation. This model takes into account relaxation processes, the annihilation of excitations at neighboring molecules, and inhomogeneous broadening. Assuming that the inhomogeneous broadening is absent, calculations demonstrate the existence of spatial bistability, molecular switching waves, and dissipative solitons. The effect of the inhomogeneous broadening and the radiation intensity on the effective coherence length in linear (chain) J aggregates is analyzed.

Peptide Adsorption to Cyanine Dye Aggregates Revealed by Cryo-Transmission Electron Microscopy

The binding interaction between aggregates of the 5-chloro-2-[[5-chloro-3-(3-sulfopropyl)-3H-benzothiazol-2-ylidene]methyl]-3-(3-sulfopropyl)benzothiazolium hydroxide inner salt ammonium salt (CD-1) and alpha-helix, as well as beta-sheet forming de novo designed peptides, was investigated by absorption spectroscopy, circular dichroism spectroscopy, and cryogenic transmission electron microscopy. Both pure dye and pure peptides self-assembled into well-defined supramolecular assemblies in acetate buffer at pH = 4. The dye formed sheetlike and tubular H- and J-aggregates and the peptides alpha-helical coiled-coil assemblies or beta-sheet rich fibrils. After mixing dye and peptide solutions, tubular aggregates with an unusual ultrastructure were found, most likely due to the decoration of dye tubes with monolayers of peptide assemblies based on the strong electrostatic attraction between the oppositely charged species. There was neither indication of a transfer of chirality from the peptides to the dye aggregates nor the opposite effect of a structural transfer from dye aggregates onto the peptides secondary structure.

Excitonic couplings and interband energy transfer in a double-wall molecular aggregate imaged by coherent two-dimensional electronic spectroscopy

The early stage of molecular excitonics and its quantum-kinetic dynamics in the multiband, bitubular cyanine dye aggregate C(8)O(3) at room temperature are revealed by employing two-dimensional (2D) coherent electronic spectroscopy in the visible spectral region. The sub-20 fs measurements provide a direct look into the details of elementary electronic couplings by spreading spectroscopic transitions into two frequency axes. Correlation spectra of rephasing (k(I) = -k(1) + k(2) + k(3)) and nonrephasing (k(II) = +k(1) - k(2) + k(3)) data in emission (omega(3))-absorption (omega(1)) 2D-frequency space image interband excitons into cross-peak signals and unveil the quantum-dissipative regime of exciton relaxation. Spectral streaking of cross peaks directly reveals interband dephasing and exciton population relaxation on the road to tube-to-tube energy transfer without making recourse to an a priori model. Theory and simulations, based on an effective multilevel scheme and a quantum-dissipative model with experimental pulse envelopes, explain the origin of the cross peaks, reveal the underlying sequences of electronic transitions, recover the streaking patterns of relaxing cross peaks along omega(1), and reconstruct the space-energy pathways of electronic excitation flow.

Chiral Transformation of Cyanine Dye Aggregates Induced by Small Peptides

Three small peptides (K4, K5, and K6) with different length were designed to induce the transformation of the assembled state and the chirality of cyanine dye supramolecule. The absorption and circular dichroism (CD) results indicated that, the peptides tend to induce cyanine dye to H-aggregation, competed with Na(+) in PBS, which would induce dye to J-aggregation. Meanwhile, all three peptides could influence the chirality of both J-aggregates induced by Na(+) and H-aggregates, among which K6 could induce chiral reversion of J-aggregates. Furthermore, molecular modeling and energy calculation results have shown that the peptides with different chain length have different conformations. This might be the reason for cyanine dye to form the different chiral assembly induced by these oligo-peptide templates.