A rational design of squaraine dyes with lipophilic and zwitterionic groups tunes cell entry, allowing for selective far-red/near-infrared imaging of plasma membrane vs. endoplasmic reticulum. They ...exhibit up to 110-fold fluorescence enhancement in biomembranes and enable cellular imaging at 1 nM concentration, which make them the brightest membrane probes to date.
Control over the strength of excitonic coupling in molecular dye aggregates is a substantial factor for the development of technologies such as light harvesting, optoelectronics, and quantum ...computing. According to the molecular exciton model, the strength of excitonic coupling is inversely proportional to the distance between dyes. Covalent DNA templating was proved to be a versatile tool to control dye spacing on a subnanometer scale. To further expand our ability to control photophysical properties of excitons, here, we investigated the influence of dye hydrophobicity on the strength of excitonic coupling in squaraine aggregates covalently templated by DNA Holliday Junction (DNA HJ). Indolenine squaraines were chosen for their excellent spectral properties, stability, and diversity of chemical modifications. Six squaraines of varying hydrophobicity from highly hydrophobic to highly hydrophilic were assembled in two dimer configurations and a tetramer. In general, the examined squaraines demonstrated a propensity toward face-to-face aggregation behavior observed via steady-state absorption, fluorescence, and circular dichroism spectroscopies. Modeling based on the Kühn–Renger–May approach quantified the strength of excitonic coupling in the squaraine aggregates. The strength of excitonic coupling strongly correlated with squaraine hydrophobic region. Dimer aggregates of dichloroindolenine squaraine were found to exhibit the strongest coupling strength of 132 meV (1065 cm–1). In addition, we identified the sites for dye attachment in the DNA HJ that promote the closest spacing between the dyes in their dimers. The extracted aggregate geometries, and the role of electrostatic and steric effects in squaraine aggregation are also discussed. Taken together, these findings provide a deeper insight into how dye structures influence excitonic coupling in dye aggregates covalently templated via DNA, and guidance in design rules for exciton-based materials and devices.
While only one enantiomer of chiral biomolecules performs a biological function, access to both enantiomers (or enantiomorphs) proved to be advantageous for technology. Using dye covalent attachment ...to a DNA Holliday junction (HJ), we created two pairs of dimers of bis(chloroindolenine)squaraine dye that enabled strongly coupled molecular excitons of opposite chirality in solution. The exciton chirality inversion was achieved by interchanging single covalent linkers of unequal length tethering the dyes of each dimer to the HJ core. Dimers in each pair exhibited profound exciton-coupled circular dichroism (CD) couplets of opposite signs. Dimer geometries, modeled by simultaneous fitting absorption and CD spectra, were related in each pair as nonsuperimposable and nearly exact mirror images. The origin of observed exciton chirality inversion was explained in the view of isomerization of the stacked Holliday junction. This study will open new opportunities for creating excitonic DNA-based materials that rely on programmable system chirality.
Dye molecules that absorb light in the visible region are key components in many applications, including organic photovoltaics, biological fluorescent labeling, super-resolution microscopy, and ...energy transport. One family of dyes, known as squaraines, has received considerable attention recently due to their favorable electronic and photophysical properties. In addition, these dyes have a strong propensity for aggregation, which results in emergent materials properties, such as exciton delocalization. This will be of benefit in charge separation and energy transport along with fundamental studies in quantum information. Given the high structural tunability of squaraine dyes, it is possible that exciton delocalization could be tailored by modifying the substituents attached to the π-conjugated network. To date, limited theoretical studies have explored the role of substituent effects on the electronic and photophysical properties of squaraines in the context of DNA-templated dye aggregates and resultant excitonic behavior. We used
ab initio
theoretical methods to determine the effects of substituents on the electronic and photophysical properties for a series of nine different squaraine dyes. Solvation free energy was also investigated as an insight into changes in hydrophobic behavior from substituents. The role of molecular symmetry on these properties was also explored
via
conformation and substitution. We found that substituent effects are correlated with the empirical Hammett constant, which demonstrates their electron donating or electron withdrawing strength. Electron withdrawing groups were found to impact solvation free energy, transition dipole moment, static dipole difference, and absorbance more than electron donating groups. All substituents showed a redshift in absorption for the squaraine dye. In addition, solvation free energy increases with Hammett constant. This work represents a first step toward establishing design rules for dyes with desired properties for excitonic applications.
Squaraine dyes are candidates for DNA-templated excitonic interactions. This work presents substituent effects on the electronic and photophysicalproperties of squaraine dyes and a correlation between empirical Hammettconstant and those properties.
Molecular aggregates exhibit emergent properties, including the collective sharing of electronic excitation energy known as exciton delocalization, that can be leveraged in applications such as ...quantum computing, optical information processing, and light harvesting. In a previous study, we found unexpectedly large excitonic interactions (quantified by the excitonic hopping parameter
J
m
,
n
) in DNA-templated aggregates of squaraine (SQ) dyes with hydrophilic-imparting sulfo and butylsulfo substituents. Here, we characterize DNA Holliday junction (DNA-HJ) templated aggregates of an expanded set of SQs and evaluate their optical properties in the context of structural heterogeneity. Specifically, we characterized the orientation of and
J
m
,
n
between dyes in dimer aggregates of non-chlorinated and chlorinated SQs. Three new chlorinated SQs that feature a varying number of butylsulfo substituents were synthesized and attached to a DNA-HJ
via
a covalent linker to form adjacent and transverse dimers. Various characteristics of the dye, including its hydrophilicity (in terms of log
P
o/w
) and surface area, and of the substituents, including their local bulkiness and electron withdrawing capacity, were quantified computationally. The orientation of and
J
m
,
n
between the dyes were estimated using a model based on Kühn-Renger-May theory to fit the absorption and circular dichroism spectra. The results suggested that adjacent dimer aggregates of all the non-chlorinated and of the most hydrophilic chlorinated SQ dyes exhibit heterogeneity; that is, they form a mixture of dimers subpopulations. A key finding of this work is that dyes with a higher hydrophilicity (lower log
P
o/w
) formed dimers with smaller
J
m
,
n
and large center-to-center dye distance (
R
m
,
n
). Also, the results revealed that the position of the dye in the DNA-HJ template, that is, adjacent or transverse, impacted
J
m
,
n
. Lastly, we found that
J
m
,
n
between symmetrically substituted dyes was reduced by increasing the local bulkiness of the substituent. This work provides insights into how to maintain strong excitonic coupling and identifies challenges associated with heterogeneity, which will help to improve control of these dye aggregates and move forward their potential application as quantum information systems.
Molecular aggregates exhibit collective sharing of electronic excitation energy known as exciton delocalization, that can be leveraged in applications such as quantum computing, optical information processing, and light harvesting.
Molecular (dye) aggregates are a materials platform of interest in light harvesting, organic optoelectronics, and nanoscale computing, including quantum information science (QIS). Strong excitonic ...interactions between dyes are key to their use in QIS; critically, properties of the individual dyes govern the extent of these interactions. In this work, the electronic structure and excited-state dynamics of a series of indolenine-based squaraine dyes incorporating dimethylamino (electron donating) and/or nitro (electron withdrawing) substituents, so-called asymmetric dyes, were characterized. The dyes were covalently tethered to DNA Holliday junctions to suppress aggregation and permit characterization of their monomer photophysics. A combination of density functional theory and steady-state absorption spectroscopy shows that the difference static dipole moment (Δd) successively increases with the addition of these substituents while simultaneously maintaining a large transition dipole moment (μ). Steady-state fluorescence and time-resolved absorption and fluorescence spectroscopies uncover a significant nonradiative decay pathway in the asymmetrically substituted dyes that drastically reduces their excited-state lifetime (τ). This work indicates that Δd can indeed be increased by functionalizing dyes with electron donating and withdrawing substituents and that, in certain classes of dyes such as these asymmetric squaraines, strategies may be needed to ensure long τ, e.g., by rigidifying the π-conjugated network.
Novel indolenine based norsquaraine dyes, wherein the oxygen of the squaric acid bridge was substituted with a barbituric or a dicyanomethylene group, were synthesized and their molecular structure, ...spectral and luminescent properties were compared to those of analogous squaraine dyes. The molecular structure was investigated using X-ray analysis, NMR spectroscopy and ab initio DFT B3LYP/6-311G (d, p) simulations. The calculated populations of possible conformers and the barriers of internal rotations were found to be in good agreement with the experimental data. Norsquaraines absorb and emitt light within the same long-wavelength spectral range as the corresponding squaraines but due to intramolecular H-bonds and increased conformational rigidity they were less sensitive to solvent polarity and the presence of protein (BSA).
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•Novel, norsquaraine dyes were synthesized and compared to analogous squaraines.•Squaric oxygen was substituted with a barbituric and dicyanomethylene group.•The molecular structures were investigated using X-ray, NMR and ab initio.•Norsquaraine molecules are more flat, rigid and polar compared to squaraines.•Both dye classes are suitable for fluorescence based sensing applications.
Novel pH-sensitive, water-soluble, long-wavelength fluorescent norsquaraine dyes and their barbituric and dicyanomethylene derivatives were synthesized and investigated. Some of these dyes contain a ...carboxylic functionality that was converted into an NHS ester to facilitate bio-conjugation. The absorption and emission spectra, fluorescence quantum yields, lifetimes, polarization, and photostabilities were measured free in solution and after binding to bovine serum albumin (BSA) and compared to those of conventional squaraines and the norcyanine dye CypHer5. Contrary to squaraines, norsquaraines are pH-sensitive but almost unaffected by the interaction with proteins. These dyes can potentially be used as fluorescent labels for biomedical applications, in particular for protein labeling, polarization-based assays, cell-based and pH-sensing measurements.
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•Novel pH-sensitive, water-soluble, fluorescent norsquaraine dyes were synthesized.•Squaric oxygen was substituted with a barbituric and dicyanomethylene group.•NHS esters of some of these dyes were synthesized to facilitate bio-conjugation.•Spectral and protolytic properties were investigated and compared to squaraines.•The dyes are suitable for protein labeling, polarization and pH-sensing assays.
A series of new symmetrical and asymmetrical squaraines were synthesised and efficiency of their use as fluorescent probes for the specific detection of proteins was studied. Spectral-luminescent ...properties of the squaraines were measured in presence of bovine serum albumin (BSA), human serum albumin (HSA), ovalbumin, avidin from hen egg white (AVI), lysozyme, and trypsin. All investigated squaraines show considerable (in 24–190 times) emission increase in the presence of BSA. At the same time the fluorescent response of the studied dyes in the presence of other albumins is significantly lower – emission enhances up to 24 times. The 3-oxo-substituted indolenine dye
9(74) demonstrates sufficient fluorescence increasing value and emission intensity level in the presence of BSA as well as of HSA and ovalbumin. Dyes containing
N-carboxyalkyl group demonstrate sufficient emission enhancement (up to 16 times) and noticeable fluorescent signal in the presence of avidin from hen egg white. Squaraines slightly increase or even decrease their emission intensity in the presence of hydrolases lysozyme or trypsin.
We investigate the reactions of mono-substituted squaraines with CH-acidic nucleophiles, heterocyclic methylene bases and thionating reagents. The reactions of mono-substituted squaraines with ...malononitrile, cyano- and nitroacetic esters, barbituric acid, 1,3-indanedione, NaHS and P
4S
10 lead to ring-substituted mono-squaraines. These intermediates are useful for the synthesis of novel squaraine dyes with interesting photophysical properties.
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