Length Of Polymethine Chain Research Articles

Flavylium Fluorophores as Near-Infrared Emitters.

This theoretical work rationalizes the absorption and fluorescence emission properties of conjugated dyes composed of dimethylamino flavylium heterocycles linked by a polymethine chain, which were recently reported to act as efficient shortwave infrared emitters. Density functional theory is used to characterize the electronic structure of the low-lying excited states as a function of the polymethine chain length. Decomposition of the computed excitations in terms of diabatic states is also performed to deconvolute the excited states wavefunction into charge-transfer intramolecular excitations. Based on these results, chemical substitution patterns consisting in enhancing the electron-withdrawing strength of the polymethine bridge and the electron-donating ability of the lateral flavylium fragments, are proposed to further redshift the photoluminescence of the fluorophores.

Structure and redox properties of polymethine dyes: Electrochemical and DFT/TD-DFT study

The electrochemical properties of 48 cationic, anionic and merocyanine polymethine dyes have been studied using cyclic voltammetry. The effect of structural parameters, viz. the chromophore charge, the donor-acceptor properties of the terminal groups, the polymethine chain length, and the molecular symmetry on the redox-potentials are analyzed. The DFT calculations of all the studied dyes have been performed with three different exchange-correlation functionals (B3LYP, CAM-B3LYP, and B97D3) in both vacuum and acetonitrile using the PCM solvation model; additionally, for selected species the BP86, PBE0 and M06-2X functionals were employed. The HOMO and LUMO energies of the dyes obtained from voltammetry data are compared with those from the DFT calculations to select the best performing theoretical approach for evaluation of the frontier orbital energy levels and energy gap of these π-conjugated compounds. Linear correlation equations obtained from the data for 48 dyes may be employed for credible prediction of the HOMO and LUMO energies in the search for designed molecules with required redox properties. TD-DFT calculations have demonstrated that the pure (non-hybrid) BP86 and B97D3 functionals give a relatively low mean absolute error for excitation energies, proving to perform better than the hybrid functionals applied, especially CAM-B3LYP.

Tracers for Fluorescence-Guided Surgery: How Elongation of the Polymethine Chain in Cyanine Dyes Alters the Pharmacokinetics of a Dual-Modality c[RGDyK] Tracer.

The potential of receptor-mediated fluorescence-based image-guided surgery tracers is generally linked to the near-infrared emission profile and good-manufacturing-production availability of fluorescent dyes. Surprisingly, little is known about the critical interaction between the structural composition of the dyes and the pharmacokinetics of the tracers. In this study, a dual-modality tracer design was used to systematically and quantitatively evaluate the influence of elongation of the polymethine chain in a fluorescent cyanine dye on the imaging potential of a targeted tracer. Methods: As a model system, the integrin marker αvβ3 was targeted using arginylglycylaspartisc acid [RGD]-based vectors functionalized with a 111In-diethylenetriaminepentaacetic acid (DTPA) chelate and a fluorescent dye: (Cy3-(SO3)methyl-COOH [emission wavelength (λem), 580 nm], Cy5-(SO3)methyl-COOH [λem, 680 nm], or Cy7-(SO3)methyl-COOH [λem, 780 nm]). Tracers were analyzed for differences in photophysical properties, serum protein binding, chemical or optical stability, and signal penetration through tissue. Receptor affinities were evaluated using saturation and competition experiments. In vivo biodistribution (SPECT imaging and percentage injected dose per gram of tissue) was assessed in tumor-bearing mice and complemented with in vivo and ex vivo fluorescence images obtained using a clinical-grade multispectral fluorescence laparoscope. Results: Two carbon-atom-step variations in the polymethine chain of the fluorescent cyanine dyes were shown to significantly influence the chemical and photophysical characteristics (e.g., stability, brightness, and tissue penetration) of the hybrid RGD tracers. DTPA-Cy5-(SO3)methyl-COOH-c[RGDyK] structurally outperformed its Cy3 and Cy7 derivatives. Radioactivity-based evaluation of in vivo tracer pharmacokinetics yielded the lowest nonspecific uptake and highest tumor-to-background ratio for DTPA-Cy5-(SO3)methyl-COOH-c[RGDyK] (13.2 ± 1.7), with the Cy3 and Cy7 analogs trailing at respective tumor-to-background ratios of 5.7 ± 0.7 and 4.7 ± 0.7. Fluorescence-based assessment of tumor visibility revealed a similar trend. Conclusion: These findings underline that variations in the polymethine chain lengths of cyanine dyes have a profound influence on the photophysical properties, stability, and in vivo targeting capabilities of fluorescent imaging tracers. In a direct comparison, the intermediate-length dye (Cy5) yielded a superior c[RGDyK] tracer, compared with the shorter (Cy3) and longer (Cy7) analogs.

Sensitizing of TiO2 with a merocyanine dye in the photocatalytic reduction of methylene blue

Three merocyanine dyes (D) with various polymethine chain lengths were checked for their applicability as sensitizers for TiO2. Based on the absorption data and cyclic voltammetric redox potentials, the lower unoccupied molecular orbital (LUMO) energy was calculated. The LUMO energy was higher than the conductance band edge energy of the anatase-type TiO2 for all the dyes, meaning that they all can act as efficient sensitizers for various functional materials to be used in the wide-zone visible light solar cells, toxic wastes decontamination technologies and other similar applications. Merocyanines applicability as effective sensitizing agents was approved by construction of the heterostructures (HS) D/TiO2 consisting of the merocyanines and acting as photocatalysts in the test reaction of methylene blue (MB) reduction by formaldehyde.

D–π–A–π–D Dyes with a 1,3,2‐Dioxaborine Cycle in the Polymethine Chain: Efficient Long‐Wavelength Fluorophores

The nitrile group in newly synthesized 5‐cyano‐2,2‐difluoro‐4,6‐dimethyl‐1,3,2‐dioxaborine is shown to significantly increase the acidity of the methyl groups. This allows the cyanine condensation with both methyl groups to form D–π–A–π–D dyes in which the dioxaborine cycle is a part of the polymethine chain. There, the reactivity of the remaining methyl group in the semi‐product is reduced enough to perform the reaction stepwise, giving access to nonsymmetric derivatives. The synthesis of dyes with various electron donor termini [indole, benzothiazole, pyran, 4‐(dialkylamino)phenyl] and with different polymethine chain lengths is reported. The obtained compounds show intense absorption and fluorescence in the red and NIR region, their fluorescence brightness (the product of the molar extinction and the fluorescence quantum yield) attaining a value of 200,000 m–1 cm–1. They are characterized by small‐scale positive solvatochromism, yet their fluorescence quantum yield is much more sensitive to ambient polarity. Time‐dependent (TD)DFT calculations have been performed to study the electronic structure of the new dioxaborines and reveal the nature of the long‐wavelength electronic transitions in those molecules.

UV–Vis absorption spectra and electronic structure of merocyanines in the gas phase

Gas-phase absorption spectra of a merocyanine vinylogous series have been studied for the first time. In vapour, their long-wavelength absorption bands were found to be considerably shifted hypsochromically, broader, more symmetrical, less intense, and their vinylene shift much smaller than even in low-polarity n-hexane. This indicates that in the gas phase their electronic structure closely approaches the nonpolar polyene limiting structure. The TDDFT calculations of the long-wavelength electronic transitions in the studied merocyanines in vacuo demonstrated good-to-excellent correlation – depending on the functional used – with the obtained experimental data. For comparison, the solvent effects was accounted for using the polarizable continuum model (PCM) with n-hexane and ethanol as low-polarity and high-polarity media, and compared with the UV–Vis spectral data in these solvents. In this case, the discrepancy between theory and experiment was much greater, increasing at that with the polymethine chain length.

Effect of donor terminal group and polymethine chain length on structure of merocyanine dyes in the crystal state

X-ray diffraction study of the merocyanine series with different sign of solvatochromism but of the same structural type revealed the effects of donor-acceptor properties of terminal groups and polymethine chain length on their electronic structure in the solid state. The bond length alternation in the negatively solvatochromic dyes corresponds to the dipolar polyene limiting structure, contribution of which, in contrast to solutions, increases for higher vinylogues. Conversely, the nonpolar polyene structure prevails for the positively solvatochromic merocyanines, its contribution increases for higher vinylogues in both solid state and solutions. The DFT (in vacuo and PCM) calculations reproduce tendencies observed for the positively solvatochromic merocyanines but do not reflect the dipolarity growth in higher vinylogues of the negatively solvatochromic ones. The calculations results can be improved taking explicitly into account intermolecular interactions in the crystal.

Study of photophysical properties of a series of polymethine dyes by femtosecond laser photolysis

The excited-state dynamics of 12 symmetric polymethine dyes in acetone was studied with femtosecond pump–probe spectroscopy. Four groups of compounds with different terminal heterocycles were studied: indoles, indoles with cyclic group attached to the nitrogen atom, benzimidazoles and benzo[cd] indoles. Within each group, the length of polymethine chain between the terminal groups was varied. The influence of electron-donating ability of the terminal groups and the length of the polymethine chain on the excited-state dynamics of the compounds was evaluated. The length of the polymethine chain was found to have an obvious effect both on the distance between the S1 ← S0 and Sn ← S1 transition bands and the lifetime of the excited state. The latter parameter is largely affected by the nature of terminal groups, most importantly, their electron-donating ability. In addition to experimental results, quantum chemical calculations were performed to provide with complementary insights on the excited states of investigated compounds.

Selective G-Quadruplex DNA Recognition by a New Class of Designed Cyanines

A variety of cyanines provide versatile and sensitive agents acting as DNA stains and sensors and have been structurally modified to bind in the DNA minor groove in a sequence dependent manner. Similarly, we are developing a new set of cyanines that have been designed to achieve highly selective binding to DNA G-quadruplexes with much weaker binding to DNA duplexes. A systematic set of structurally analogous trimethine cyanines has been synthesized and evaluated for quadruplex targeting. The results reveal that elevated quadruplex binding and specificity are highly sensitive to the polymethine chain length, heterocyclic structure and intrinsic charge of the compound. Biophysical experiments show that the compounds display significant selectivity for quadruplex binding with a higher preference for parallel stranded quadruplexes, such as cMYC. NMR studies revealed the primary binding through an end-stacking mode and SPR studies showed the strongest compounds have primary KD values below 100 nM that are nearly 100-fold weaker for duplexes. The high selectivity of these newly designed trimethine cyanines for quadruplexes as well as their ability to discriminate between different quadruplexes are extremely promising features to develop them as novel probes for targeting quadruplexes in vivo.

Effect of electronic asymmetry and the polymethine chain length on photoprocesses in merocyanine dyes

Abstract The photophysical properties as well as photoisomerization of a series of malononitrile based merocyanines with various electron donating groups and polymethine chain length were studied by ns-laser photolysis. The absorption spectra and the kinetics of cis–trans backward conversion of the photoisomers were investigated in air-saturated solutions upon direct photoexcitation. The T–T absorption of merocyanines was recorded upon sensitized excitation with benzophenone or anthracene as the triplet energy donor and kinetics of the triplet state decay was measured. The obtained results together with the data of DFT/B3LYP quantum-chemical calculation allowed revealing the influence of the merocyanines electronic structure on the spectral properties and the lifetimes of the photoisomers. The long-wavelength absorption bands of photoisomers of the dyes with 3H-indole and benzimidazole electron donating groups were shifted bathochromically whereas the bands of the benzo[cd]indole derivatives were shifted hypsochromically with respect to the corresponding bands of the initial all-trans isomers. The interpretation of the results obtained is given.

Photophysical Properties of Self-assembled Cyanine-dye Dimmer Formation Assisted by Cyclodextrin Inclusion Complexation

We investigated a series of carbocyanine dye dimers formed in a cyclodextrin (CD) nanocavity by analyzing their steady-state absorption spectra in aqueous solution. As increasing CD concentrations, a blue-shifted additional peak was enhanced in several dye/CD combinations. This blue-shifted peak indicates that a ‘sandwich-type’ dimer is formed in CD. In order to obtain dimer-formation constants, we fitted dimer/monomer absorbance ratio to a theoretical equilibrium equation and the dimer structure was estimated on the basis of observed energy splittings in the absorption spectra. These values are significantly influenced by steric factors (poly-methine chain length, bulkiness of the end-group, CD cavity-size, etc.).

Quantum-chemical study of relation of spectral and luminescent properties of positively solvatochromic malononitrile-based merocyanine dyes with their structure

The electronic structure, the spectra, and the efficiency of photophysical processes of energy deactivation are calculated by a semiempirical method for three positively solvatochromic merocyanine dyes with different polymethine chain lengths. The electronic structure and spectra calculated by different modifications of the INDO method at different molecular geometries are compared, and the optimum geometry of the isolated molecule is chosen. The absorption spectra of dyes are interpreted, including the short-wave-length bands related to transitions to highest excited states. The possibility of a specific electrophilic solvation of these compounds in the ground and fluorescent states, as well as the contribution of specific intermolecular interactions to the total interaction with the medium, is estimated. The role played by the trans-cis isomerization of isolated merocyanine molecules in the deactivation of their excited states is considered.

Merocyanines based on 1,3‐indanedione: electronic structure and solvatochromism

AbstractA series of merocyanines derived from 1,3‐indanedione and heterocycles of various electron‐donating properties was studied in detail. Their solvatochromic properties were explored in a wide range of solvent polarities to reveal the dependences of their chromacity and electronic structure on the key structural parameters – the properties of a donor heterocycle and the polymethine chain length. Also the dyes were studied by NMR spectroscopy and by quantum chemical calculations, both with the semiempirical AM1 and the non‐empirical density functional theory/B3LYP method. The solvatochromic properties of the explored dyes are rather close to those of merocyanines derived from malononitrile as acceptor group. Appreciable distinctions were observed only in protic ethanol; obviously, they are connected with the formation of solvent–solute H‐bonds in the case of 1,3‐indanedione derivatives. The electron‐acceptor properties of 1,3‐indanedione were found to be somewhat stronger in comparison with those of malononitrile even in aprotic solvents, contrary to the known literature data. Analysis of the merocyanines' molecular orbitals and simulation of their electronic spectra were carried out both in vacuum and in the solvent matrix, and the absorption electronic transitions were analyzed. Static nonlinear optical properties were calculated for both the new merocyanines and the corresponding cationic and anionic cyanine dyes. Copyright © 2010 John Wiley & Sons, Ltd.

A theoretical study on the ground and excited state behaviors of TTBC related carbocyanine dyes

The effects of functional groups on the benzimidazole rings, length of the conjugated chain and alkyl groups bonded to the nitrogen atoms on the ground and excited state behaviors of the 1,1′,3,3′-tetraethyl-5,5′,6,6′-tetrachlorobenzimidazolocarbocyanine (TTBC or JC-1) have been analyzed via quantum chemical methods. DFT and TDDFT with B3LYP/6-31G(d,p) level of theory were used for the ground and excited state calculations, respectively. It has been found that TTBC has a very rigid geometry; no significant effect of functional groups has been predicted either as donor or acceptor on its optimum structure. However, the length of alkyl groups changes the structure of the molecule. It is possible to increase λ max of TTBC based carbocyanine dye with NH 2, butyl/propyl and increasing polymethine chain length.

Synthesis and Antimalarial Properties of Streptocyanine Dyes

Several streptocyanine dyes were synthesized that contain polymethine chains of varying length. Their in vitro antimalarial activities were evaluated against the virulent P. falciparum parasite. In addition to the influence of polymethine chain length, the effects of structural modifications at nitrogen end groups, para substitution of the phenyl groups, and counter-anions were studied. The most potent antimalarial activities were found for heptacarbon chain streptocyanines, with an IC(50) value of 60 nM. Interestingly, most of the compounds were less cytotoxic toward the mammalian cells tested. The best selective toxicity profiles were found for pentacarbon chain streptocyanines, which have a good in vitro specificity index.

Influence of Cationic Symmetric Polymethine Dyes on Radical Polymerization of Methylmethacrylate in Solution

The polymerization ability of methylmethacrylate solutions in DMF and toluene in the process of their radical thermoinitiated homopolymerization in presence of polymethine dyes is investigated, utilizing dilatometry method. Conformities to the law of influencing of these dyes, depending on length of polymethine chain and concentrations are obtained.

Block building of polymethine dye aggregates

Formation of J-aggregates of polymethine dyes in solutions and in a heterogeneous system of AgHal grains is considered. A new mechanism of formation of polymethine dye J-aggregates from dimers is proposed on the basis of the equilibrium between dimers and J-aggregates in solution. It was concluded that “block building” of J-aggregates from dimers is most preferable for constructing perfect J-aggregates of the same size (mono-structural J-aggregates). Mixed J-aggregates and “heterocontact dimers” of polymethine dyes with various polymethine chain lengths are obtained using the block building technique.

Series of polymethine dyes derived from 2,2-difluoro-1,3,2-(2 H)-dioxaborine of 3-acetyl-7-diethylamino-4-hydroxycoumarin

A series of symmetrical and unsymmetrical dyes with different polymethine chain lengths based on the 2,2-difluoro-1,3,2-(2 H)-dioxaborine of 3-aceto-4-hydroxy-7-diethylaminocoumarin were obtained. It was shown that anionic symmetrical dyes are deeply coloured and highly intense dyes with good fluorescence properties and photostability. Spectral characteristics of the unsymmetrical dyes can be modified in a wide range by changing the electron-donating properties of the second terminal nucleus.

Electronic structure and solvatochromism of merocyanines based on N, N-diethylthiobarbituric acid

A series of merocyanines based on N, N-diethylthiobarbituric acid containing heterocycles of various electron-donating properties have been synthesized. With the aim of studying the dependence of their electronic structure on the main structural factors (i.e. change of the terminal groups and the length of polymethine chain), and also on the solvation, their solvatochromism has been investigated in a wide range of solvents with different polarity. Moreover, their electronic structure has been studied by NMR spectroscopy and quantum-chemical calculations. It has been found a rather significant influence of the polymethine chain length on the electronic structure of merocyanines in solvents in which the condition close to the ideal polymethine state is not achieved. By analysis of the UV/vis absorption spectra in non-polar n-hexane and low-polar toluene the important role of solvation for achievement of the cyanine limit is also shown. Only for dyes with the strong electron-donating group – the benzimidazole end group – a uniformity of bond orders in the chromophore is achieved even in n-hexane with minimum participation of the solvent. These conclusions are confirmed by the data of 1H and 13C NMR spectroscopy. Attempts of correlations of the data observed with the results of quantum-chemical calculations appeared unsatisfactory, which seems to be connected to both, the lack of suitable calculation methods, and the neglect of the solvent influence.

Solvent effect on indocyanine dyes: A computational approach

The solvatochromic behaviour of a series of indocyanine dyes (Dyes I–VIII) was investigated by quantum chemical calculations. The effect of the polymethine chain length and of the indolenine structure has been satisfactorily reproduced by semiempirical Pariser–Parr–Pople (PPP) calculations. The solvatochromism of 3,3,3′,3′-tetramethyl- N, N′-diethylindocarbocyanine iodide (Dye I) has been deeply investigated within the ab initio time-dependent density functional theory (TD-DFT) approach. Dye I undergoes non-polar solvation and a linear correlation has been individuated between absorption shifts and refractive index. Computed absorption λ max and oscillator strengths obtained by TD-DFT are in good agreement with the experimental data.