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Title: 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. 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 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 were obtained bymore » simultaneous 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 dye mutual orientation in the aggregates enabled close comparison of aggregate configurations and the elucidation of the influence of dye angular relationship on excitonic hopping interactions in squaraine aggregates. Furthermore, these results encourage the application of squaraine-based aggregates in next generation systems driven by molecular excitons.« less

Authors:
ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [2]; ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [1]
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  1. Boise State Univ., ID (United States)
  2. SETA BioMedicals, LLC, Urbana, IL (United States)
Publication Date:
Research Org.:
Boise State Univ., ID (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES). Materials Sciences & Engineering Division; National Science Foundation (NSF); National Institute of General Medical Sciences (NIGMS); National Institutes of Health (NIH); MJ Murdock Charitable Trust; Idaho State Board of Education
OSTI Identifier:
1670511
Grant/Contract Number:  
SC0020089; 1648655; P20GM103408; P20GM109095; 0619793; 0923535
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry
Additional Journal Information:
Journal Volume: 124; Journal Issue: 43; Related Information: SUPPORTING INFORMATION Exciton Delocalization in Indolenine Squaraine Aggregates Templated byDNA Holliday Junction Scaffolds1Olga A. Mass; 1Christopher K. Wilson; 1Simon K. Roy; Matthew S. Barclay; 1Lance K. Patten;2Ewald A. Terpetschnig; *1,3Jeunghoon Lee; *1Ryan D. Pensack; *1,4Bernard Yurke;*1,4William B. Knowlton.1Micron School of Materials Science & Engineering, 3Department of Chemistry andBiochemistry, 4Department of Electrical & Computer Engineering, Boise State University, Boise,Idaho 83725, United States2SETA BioMedicals, LLC, 2014 Silver Court East, Urbana, IL 61801, United States; Journal ID: ISSN 1520-6106
Publisher:
American Chemical Society
Country of Publication:
United States
Language:
English
Subject:
77 NANOSCIENCE AND NANOTECHNOLOGY; 36 MATERIALS SCIENCE; 71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS; Exciton delocalization; Indolenine Squaraine dye-DNA aggregates; DNA Holliday junctions; Davydov splitting; H-type packing Scaffolds

Citation Formats

Mass, Olga A., Wilson, Christopher Kimo, Roy, Simon K., Barclay, Matthew S., Patten, Lance K., Terpetschnig, Ewald A., Lee, Jeunghoon, Pensack, Ryan D., Yurke, Bernard, and Knowlton, William B.. Exciton Delocalization in Indolenine Squaraine Aggregates Templated by DNA Holliday Junction Scaffolds. United States: N. p., 2020. Web. doi:10.1021/acs.jpcb.0c06480.
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Mass, Olga A., Wilson, Christopher Kimo, Roy, Simon K., Barclay, Matthew S., Patten, Lance K., Terpetschnig, Ewald A., Lee, Jeunghoon, Pensack, Ryan D., Yurke, Bernard, & Knowlton, William B.. Exciton Delocalization in Indolenine Squaraine Aggregates Templated by DNA Holliday Junction Scaffolds. United States. https://doi.org/10.1021/acs.jpcb.0c06480
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Mass, Olga A., Wilson, Christopher Kimo, Roy, Simon K., Barclay, Matthew S., Patten, Lance K., Terpetschnig, Ewald A., Lee, Jeunghoon, Pensack, Ryan D., Yurke, Bernard, and Knowlton, William B.. Wed . "Exciton Delocalization in Indolenine Squaraine Aggregates Templated by DNA Holliday Junction Scaffolds". United States. https://doi.org/10.1021/acs.jpcb.0c06480. https://www.osti.gov/servlets/purl/1670511.
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@article{osti_1670511,
title = {Exciton Delocalization in Indolenine Squaraine Aggregates Templated by DNA Holliday Junction Scaffolds},
author = {Mass, Olga A. and Wilson, Christopher Kimo and Roy, Simon K. and Barclay, Matthew S. and Patten, Lance K. and Terpetschnig, Ewald A. and Lee, Jeunghoon and Pensack, Ryan D. and Yurke, Bernard and Knowlton, William B.},
abstractNote = {Exciton delocalization plays a prominent role in the photophysics of molecular aggregates, ultimately governing their particular function or application. 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 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 were obtained by simultaneous 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 dye mutual orientation in the aggregates enabled close comparison of aggregate configurations and the elucidation of the influence of dye angular relationship on excitonic hopping interactions in squaraine aggregates. Furthermore, these results encourage the application of squaraine-based aggregates in next generation systems driven by molecular excitons.},
doi = {10.1021/acs.jpcb.0c06480},
journal = {Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry},
number = 43,
volume = 124,
place = {United States},
year = {2020},
month = {10}
}
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journal, April 2018

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  • The Journal of Physical Chemistry B, Vol. 122, Issue 19
  • DOI: 10.1021/acs.jpcb.8b02134

Exciton Delocalization and Transport in Photosystem I of Cyanobacteria Synechococcus elongates : Simulation Study of Coherent Two-Dimensional Optical Signals
journal, April 2009

  • Abramavicius, Darius; Mukamel, Shaul
  • The Journal of Physical Chemistry B, Vol. 113, Issue 17
  • DOI: 10.1021/jp811339p

DNA−Dye Conjugates for Controllable H* Aggregation 1
journal, February 2003

  • Asanuma, Hiroyuki; Shirasuka, Kenji; Takarada, Tohru
  • Journal of the American Chemical Society, Vol. 125, Issue 8
  • DOI: 10.1021/ja021153k

Control of aggregation-induced emission by DNA hybridization
journal, January 2013

  • Li, Shaoguang; Langenegger, Simon M.; Häner, Robert
  • Chemical Communications, Vol. 49, Issue 52
  • DOI: 10.1039/c3cc42706d

Interaction of YOYO-3 with Different DNA Templates to Form H-Aggregates
journal, May 2014

  • Ruedas-Rama, Maria J.; Orte, Angel; Martin-Domingo, Maria C.
  • The Journal of Physical Chemistry B, Vol. 118, Issue 23
  • DOI: 10.1021/jp5022888

Coherent Exciton Delocalization in a Two-State DNA-Templated Dye Aggregate System
journal, September 2017

  • Cannon, Brittany L.; Kellis, Donald L.; Patten, Lance K.
  • The Journal of Physical Chemistry A, Vol. 121, Issue 37
  • DOI: 10.1021/acs.jpca.7b04344

Davydov Splitting in Squaraine Dimers
journal, July 2019

  • Zhong, Chuwei; Bialas, David; Collison, Christopher J.
  • The Journal of Physical Chemistry C, Vol. 123, Issue 30
  • DOI: 10.1021/acs.jpcc.9b05297

Lessons from nature about solar light harvesting
journal, September 2011

  • Scholes, Gregory D.; Fleming, Graham R.; Olaya-Castro, Alexandra
  • Nature Chemistry, Vol. 3, Issue 10
  • DOI: 10.1038/nchem.1145

Characterization of Chiral H and J Aggregates of Cyanine Dyes Formed by DNA Templating Using Stark and Fluorescence Spectroscopies
journal, December 2001

  • Chowdhury, Arindam; Wachsmann-Hogiu, Sebastian; Bangal, Prakriti R.
  • The Journal of Physical Chemistry B, Vol. 105, Issue 48
  • DOI: 10.1021/jp012825g

Exciton Transport in Molecular Aggregates - From Natural Antennas to Synthetic Chromophore Systems
journal, July 2017

  • Brixner, Tobias; Hildner, Richard; Köhler, Jürgen
  • Advanced Energy Materials, Vol. 7, Issue 16
  • DOI: 10.1002/aenm.201700236

Stark Spectroscopy of Size-Selected Helical H-Aggregates of a Cyanine Dye Templated by Duplex DNA. Effect of Exciton Coupling on Electronic Polarizabilities †
journal, May 2003

  • Chowdhury, Arindam; Yu, Liping; Raheem, Izzat
  • The Journal of Physical Chemistry A, Vol. 107, Issue 18
  • DOI: 10.1021/jp021866p

Analysis of the UV/Vis and CD Spectral Line Shapes of Carotenoid Assemblies: Spectral Signatures of Chiral H -Aggregates
journal, April 2009

  • Spano, Frank C.
  • Journal of the American Chemical Society, Vol. 131, Issue 12
  • DOI: 10.1021/ja806853v

Determining the spatial coherence of excitons from the photoluminescence spectrum in charge-transfer J-aggregates
journal, December 2016

Molecular, Nematic and Crystal States of I: I-Diethyl--Cyanine Chloride
journal, April 1937

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