Exciton Delocalization in Indolenine Squaraine Aggregates Templated by DNA Holliday Junction Scaffolds

Abstract

Exciton delocalization plays a prominent role in the photophysics of molecular aggregates, ultimately governing their particular function or application. Deoxyribonucleic acid (DNA) is a compelling scaffold in which to template molecular aggregates and promote exciton delocalization. As individual dye molecules are the basis of exciton delocalization in molecular aggregates, their judicious selection is important. Motivated by their excellent photostability and spectral properties, here, we examine the ability of squaraine dyes to undergo exciton delocalization when aggregated via a DNA Holliday junction (HJ) template. A commercially available indolenine squaraine dye was chosen for the study given its strong structural resemblance to Cy5, a commercially available cyanine dye previously shown to undergo exciton delocalization in DNA HJs. Three types of DNA–dye aggregate configurationstransverse dimer, adjacent dimer, and tetramerwere investigated. Signatures of exciton delocalization were observed in all squaraine–DNA aggregates. Specifically, strong blue shift and Davydov splitting were observed in steady-state absorption spectroscopy and exciton-induced features were evident in circular dichroism (CD) spectroscopy. Strongly suppressed fluorescence emission provided additional, indirect evidence for exciton delocalization in the DNA-templated squaraine dye aggregates. To quantitatively evaluate and directly compare the excitonic Coulombic coupling responsible for exciton delocalization, the strength of excitonic hopping interactions between the dyes was obtained by simultaneously fitting the experimental steady-state absorption and CD spectra via a Holstein-like Hamiltonian, in which, following the theoretical approach of Kühn, Renger, and May, the dominant vibrational mode is explicitly considered. The excitonic hopping strength within indolenine squaraines was found to be comparable to that of the analogous Cy5 DNA-templated aggregate. The squaraine aggregates adopted primarily an H-type (dyes oriented parallel to each other) spatial arrangement. Extracted geometric details of the dye mutual orientation in the aggregates enabled a close comparison of aggregate configurations and the elucidation of the influence of dye angular relationship on excitonic hopping interactions in squaraine aggregates. These results encourage the application of squaraine-based aggregates in next-generation systems driven by molecular excitons.

Excited-State Lifetimes of DNA-Templated Cyanine Dimer, Trimer, and Tetramer Aggregates: The Role of Exciton Delocalization, Dye Separation, and DNA Heterogeneity

“…In the case of our DNA-templated Cy5 aggregates, insights into dye separation can be gleaned by simulating the optical properties of the materials, namely, the absorbance and circular dichroism spectra, via an approach based on Kühn–Renger–May (KRM) theory. 47 , 49 , 58 Figure 9 displays the orientation of the TDMs that result from modeling the optical properties of the duplex dimer, the transverse dimer, and type 2 tetramer, highlighting the separation between TDMs in these aggregates.…”

“…The optical properties of selected DNA-dye constructs were modeled using in-house software based on the Kühn–Renger–May method (version 13.7). 47 , 49 , 58 The software simultaneously fits absorbance and circular dichroism data by constructing and diagonalizing a Holstein Hamiltonian 19 that includes a single dominant vibronic mode. The fitting procedure begins with a user input dye configuration and performs a stochastic search by randomly perturbing the dye configuration and checking the fit quality.…”

First-principles studies of substituent effects on squaraine dyes

“…DNA was found to negligibly affect the absorbance data of a monomer. 18,35 Atomic structures were optimized using a tight root mean square residual force of 1 Â (10) À5 Hartree/Bohr and an ultra-ne integration grid of 99 radial shells and 590 angular points per shell. The ground-state optimization of these molecules was veried by ground-state frequency calculations to ensure that no imaginary frequencies were present, because imaginary frequencies represent unstable geometry.…”

“…DNA is an attractive choice for dye templating due to its customization at the nanoscale and an ability to promote the exciton delocalization of dyes. [17][18][19][20][21][22][23][24][25][26][27][28][29][30][31][32][33][34] DNA has been shown to negligibly change the electronic properties of visible-light absorbing dye monomers. 35 As such, the electronic properties of the dye monomers can be evaluated as free-dyes to screen their potential utility as DNA-templated dyes.…”

“…52 The photophysical features and extensive structural tunability make squaraines well-suited candidates for the investigation of exciton delocalization when assembled. 18,24,28,55 Although the dipole-dipole coulombic coupling between dyes must be considered to accurately predict aggregate absorption spectra, monomer transition dipole moments provide estimates of the strength of exciton delocalization for various dye congurations via the extended dipole approximation, which can be used as a guide for exciton applications. 15,56 There is also a robust body of work demonstrating the customizability of squaraine dyes, offering opportunities for the tunability of dye properties through the engineering of functional groups to yield desired properties.…”