skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

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 [2]; ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [3]; ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [1]
  1. Boise State Univ., ID (United States)
  2. (Kimo) [Boise State Univ., ID (United States)
  3. 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
OSTI Identifier:
1670511
Grant/Contract Number:  
SC0020089
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 INFORMATIONExciton 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, Wilson, Christopher, Roy, Simon, Barclay, Matthew, Patten, Lance, Terpetschnig, Ewald, Lee, Jeunghoon, Pensack, Ryan, Yurke, Bernard, and Knowlton, William. Exciton Delocalization in Indolenine Squaraine Aggregates Templated by DNA Holliday Junction Scaffolds. United States: N. p., 2020. Web. https://doi.org/10.1021/acs.jpcb.0c06480.
Mass, Olga, Wilson, Christopher, Roy, Simon, Barclay, Matthew, Patten, Lance, Terpetschnig, Ewald, Lee, Jeunghoon, Pensack, Ryan, Yurke, Bernard, & Knowlton, William. Exciton Delocalization in Indolenine Squaraine Aggregates Templated by DNA Holliday Junction Scaffolds. United States. https://doi.org/10.1021/acs.jpcb.0c06480
Mass, Olga, Wilson, Christopher, Roy, Simon, Barclay, Matthew, Patten, Lance, Terpetschnig, Ewald, Lee, Jeunghoon, Pensack, Ryan, Yurke, Bernard, and Knowlton, William. Thu . "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.
@article{osti_1670511,
title = {Exciton Delocalization in Indolenine Squaraine Aggregates Templated by DNA Holliday Junction Scaffolds},
author = {Mass, Olga and Wilson, Christopher and Roy, Simon and Barclay, Matthew and Patten, Lance and Terpetschnig, Ewald and Lee, Jeunghoon and Pensack, Ryan and Yurke, Bernard and Knowlton, William},
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}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Save / Share:

Works referenced in this record:

Squaraine dyes: a mine of molecular materials
journal, January 2008

  • Sreejith, Sivaramapanicker; Carol, Priya; Chithra, Parayalil
  • J. Mater. Chem., Vol. 18, Issue 3
  • DOI: 10.1039/B707734C

Spontaneous Assembly of Helical Cyanine Dye Aggregates on DNA Nanotemplates
journal, April 1999

  • Seifert, Jennifer L.; Connor, Rebecca E.; Kushon, Stuart A.
  • Journal of the American Chemical Society, Vol. 121, Issue 13
  • DOI: 10.1021/ja984279j

Theory of exciton-vibrational dynamics in molecular dimers
journal, March 1996


Quantum coherence in biological systems
journal, July 2011


Cooperative self-assembly of squaraine dyes
journal, January 2012

  • Mayerhöffer, Ulrich; Würthner, Frank
  • Chemical Science, Vol. 3, Issue 4
  • DOI: 10.1039/c2sc00996j

Exciton dynamics in chromophore aggregates with correlated environment fluctuations
journal, May 2011

  • Abramavicius, Darius; Mukamel, Shaul
  • The Journal of Chemical Physics, Vol. 134, Issue 17
  • DOI: 10.1063/1.3579455

The coming of age of de novo protein design
journal, September 2016

  • Huang, Po-Ssu; Boyken, Scott E.; Baker, David
  • Nature, Vol. 537, Issue 7620
  • DOI: 10.1038/nature19946

Helical Aggregation of Cyanine Dyes on DNA Templates:  Effect of Dye Structure on Formation of Homo- and Heteroaggregates
journal, August 2002

  • Garoff, Rachel A.; Litzinger, Elizabeth A.; Connor, Rebecca E.
  • Langmuir, Vol. 18, Issue 16
  • DOI: 10.1021/la025742f

Quantum entanglement in photosynthetic light-harvesting complexes
journal, April 2010

  • Sarovar, Mohan; Ishizaki, Akihito; Fleming, Graham R.
  • Nature Physics, Vol. 6, Issue 6
  • DOI: 10.1038/nphys1652

Functionalized DNA nanostructures for light harvesting and charge separation
journal, November 2012

  • Albinsson, Bo; Hannestad, Jonas K.; Börjesson, Karl
  • Coordination Chemistry Reviews, Vol. 256, Issue 21-22
  • DOI: 10.1016/j.ccr.2012.02.024

Physics of life: The dawn of quantum biology
journal, June 2011


Formation of Stable BOBO-3 H-Aggregate Complexes Hinders DNA Hybridization
journal, June 2010

  • Ruedas-Rama, Maria J.; Alvarez-Pez, Jose M.; Orte, Angel
  • The Journal of Physical Chemistry B, Vol. 114, Issue 27
  • DOI: 10.1021/jp103131r

Spectral Absorption and Fluorescence of Dyes in the Molecular State
journal, December 1936


An immobile nucleic acid junction constructed from oligonucleotides
journal, October 1983

  • Kallenbach, Neville R.; Ma, Rong-Ine; Seeman, Nadrian C.
  • Nature, Vol. 305, Issue 5937
  • DOI: 10.1038/305829a0

Coherent interactions of dyes assembled on DNA
journal, June 2012

  • Asanuma, Hiroyuki; Fujii, Taiga; Kato, Tomohiro
  • Journal of Photochemistry and Photobiology C: Photochemistry Reviews, Vol. 13, Issue 2
  • DOI: 10.1016/j.jphotochemrev.2012.04.002

Folding DNA to create nanoscale shapes and patterns
journal, March 2006


DNA-Templated Aggregates of Strongly Coupled Cyanine Dyes: Nonradiative Decay Governs Exciton Lifetimes
journal, April 2019

  • Huff, Jonathan S.; Davis, Paul H.; Christy, Allison
  • The Journal of Physical Chemistry Letters, Vol. 10, Issue 10
  • DOI: 10.1021/acs.jpclett.9b00404

Excitons in Photosynthetic Purple Bacteria:  Wavelike Motion or Incoherent Hopping?
journal, September 1997

  • Chachisvilis, Mirianas; Kühn, Oliver; Pullerits, Tõnu
  • The Journal of Physical Chemistry B, Vol. 101, Issue 37
  • DOI: 10.1021/jp963360a

Optical properties of disordered molecular aggregates: A numerical study
journal, December 1991

  • Fidder, Henk; Knoester, Jasper; Wiersma, Douwe A.
  • The Journal of Chemical Physics, Vol. 95, Issue 11
  • DOI: 10.1063/1.461317

Explicit Correlated Exciton-Vibrational Dynamics of the FMO Complex
journal, May 2015


Organic Optoelectronic Materials: Mechanisms and Applications
journal, October 2016


Evidence for wavelike energy transfer through quantum coherence in photosynthetic systems
journal, April 2007

  • Engel, Gregory S.; Calhoun, Tessa R.; Read, Elizabeth L.
  • Nature, Vol. 446, Issue 7137
  • DOI: 10.1038/nature05678

Light Absorption and Energy Transfer in the Antenna Complexes of Photosynthetic Organisms
journal, March 2016


Exciton Interactions in Nonconjugated Squaraine Dimers. Mechanisms for Coupling and Consequences for Photophysics and Photochemistry
journal, January 1997

  • Liang, Kangning; Farahat, Mohammad S.; Perlstein, Jerry
  • Journal of the American Chemical Society, Vol. 119, Issue 4
  • DOI: 10.1021/ja962091z

Coherently and fluorescence-detected two-dimensional electronic spectroscopy: direct comparison on squaraine dimers
journal, January 2020

  • Malý, Pavel; Lüttig, Julian; Mueller, Stefan
  • Physical Chemistry Chemical Physics, Vol. 22, Issue 37
  • DOI: 10.1039/D0CP03218B

Energy Transfer Mechanisms and the Molecular Exciton Model for Molecular Aggregates
journal, September 1963


Photobleaching of organic fluorophores: quantitative characterization, mechanisms, protection
journal, February 2020


Molecular Recognition of PNA-Containing Hybrids:  Spontaneous Assembly of Helical Cyanine Dye Aggregates on PNA Templates
journal, March 1999

  • Smith, Jeffrey O.; Olson, Darren A.; Armitage, Bruce A.
  • Journal of the American Chemical Society, Vol. 121, Issue 12
  • DOI: 10.1021/ja9837553

Temperature-dependent conformations of exciton-coupled Cy3 dimers in double-stranded DNA
journal, February 2018

  • Kringle, Loni; Sawaya, Nicolas P. D.; Widom, Julia
  • The Journal of Chemical Physics, Vol. 148, Issue 8
  • DOI: 10.1063/1.5020084

Proximity-Induced H-Aggregation of Cyanine Dyes on DNA-Duplexes
journal, December 2016

  • Nicoli, Francesca; Roos, Matthias K.; Hemmig, Elisa A.
  • The Journal of Physical Chemistry A, Vol. 120, Issue 50
  • DOI: 10.1021/acs.jpca.6b10939

UCSF Chimera?A visualization system for exploratory research and analysis
journal, January 2004

  • Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C.
  • Journal of Computational Chemistry, Vol. 25, Issue 13
  • DOI: 10.1002/jcc.20084

Programmed coherent coupling in a synthetic DNA-based excitonic circuit
journal, November 2017

  • Boulais, Étienne; Sawaya, Nicolas P. D.; Veneziano, Rémi
  • Nature Materials, Vol. 17, Issue 2
  • DOI: 10.1038/nmat5033

Three-Dimensional Structures Self-Assembled from DNA Bricks
journal, November 2012


Architecture and mechanism of the light-harvesting apparatus of purple bacteria
journal, May 1998

  • Hu, X.; Damjanovic, A.; Ritz, T.
  • Proceedings of the National Academy of Sciences, Vol. 95, Issue 11
  • DOI: 10.1073/pnas.95.11.5935

J- vs. H-type assembly: pentamethine cyanine (Cy5) as a near-IR chiroptical reporter
journal, January 2013

  • Markova, Larysa I.; Malinovskii, Vladimir L.; Patsenker, Leonid D.
  • Chemical Communications, Vol. 49, Issue 46
  • DOI: 10.1039/c3cc42103a

Ultrafast Excitation Transfer in Cy5 DNA Photonic Wires Displays Dye Conjugation and Excitation Energy Dependency
journal, May 2020

  • Mazuski, Richard J.; Díaz, Sebastián A.; Wood, Ryan E.
  • The Journal of Physical Chemistry Letters, Vol. 11, Issue 10
  • DOI: 10.1021/acs.jpclett.0c01020

Spectroscopic Studies of Cryptophyte Light Harvesting Proteins: Vibrations and Coherent Oscillations
journal, July 2015

  • Arpin, Paul C.; Turner, Daniel B.; McClure, Scott D.
  • The Journal of Physical Chemistry B, Vol. 119, Issue 31
  • DOI: 10.1021/acs.jpcb.5b04704

Synthesis and properties of squaraine-modified DNA
journal, January 2012

  • Markova, Larysa I.; Malinovskii, Vladimir L.; Patsenker, Leonid D.
  • Organic & Biomolecular Chemistry, Vol. 10, Issue 45
  • DOI: 10.1039/c2ob26787j

Squaraine Dyes: Molecular Design for Different Applications and Remaining Challenges
journal, July 2019


Covalent Incorporation of Methyl Red Dyes into Double-Stranded DNA for Their Ordered Clustering
journal, January 2006

  • Kashida, Hiromu; Tanaka, Masayuki; Baba, Seiki
  • Chemistry - A European Journal, Vol. 12, Issue 3
  • DOI: 10.1002/chem.200500111

Exchange narrowing of the J band of molecular dye aggregates
journal, January 2008

  • Walczak, P. B.; Eisfeld, A.; Briggs, J. S.
  • The Journal of Chemical Physics, Vol. 128, Issue 4
  • DOI: 10.1063/1.2823730

Anomalous strong exchange narrowing in excitonic systems
journal, January 2011

  • Roden, Jan; Eisfeld, Alexander
  • The Journal of Chemical Physics, Vol. 134, Issue 3
  • DOI: 10.1063/1.3528718

Analysis of Coherent Heteroclustering of Different Dyes by Use of Threoninol Nucleotides for Comparison with the Molecular Exciton Theory
journal, October 2009

  • Fujii, Taiga; Kashida, Hiromu; Asanuma, Hiroyuki
  • Chemistry - A European Journal, Vol. 15, Issue 39
  • DOI: 10.1002/chem.200900962

A DNA-Based Light-Harvesting Antenna
journal, December 2011

  • Garo, Florian; Häner, Robert
  • Angewandte Chemie International Edition, Vol. 51, Issue 4
  • DOI: 10.1002/anie.201103295

Preparation of supramolecular chromophoric assemblies using a DNA duplex
journal, January 2012

  • Kashida, Hiromu; Asanuma, Hiroyuki
  • Physical Chemistry Chemical Physics, Vol. 14, Issue 20
  • DOI: 10.1039/c2cp40520b

Coherent Multidimensional Optical Spectroscopy of Excitons in Molecular Aggregates; Quasiparticle versus Supermolecule Perspectives
journal, June 2009

  • Abramavicius, Darius; Palmieri, Benoit; Voronine, Dmitri V.
  • Chemical Reviews, Vol. 109, Issue 6
  • DOI: 10.1021/cr800268n

Hybridization-Sensitive On–Off DNA Probe: Application of the Exciton Coupling Effect to Effective Fluorescence Quenching
journal, June 2008


A modular LHC built on the DNA three-way junction
journal, January 2014

  • Probst, Markus; Langenegger, Simon M.; Häner, Robert
  • Chem. Commun., Vol. 50, Issue 2
  • DOI: 10.1039/C3CC47490A

Synthesis and characterization of unsymmetrical squaraines: a new class of cyanine dyes
journal, January 1993


Ultrafast excitation energy transfer dynamics in photosynthetic pigment–protein complexes
journal, March 2001


Pump−Probe Polarization Anisotropy Study of Femtosecond Energy Transfer within the Photosynthetic Reaction Center of Rhodobacter sphaeroides R26
journal, January 1996

  • Jonas, David M.; Lang, Matthew J.; Nagasawa, Yutaka
  • The Journal of Physical Chemistry, Vol. 100, Issue 30
  • DOI: 10.1021/jp960708t

Nucleic acid junctions and lattices
journal, November 1982


J-Aggregates: From Serendipitous Discovery to Supramolecular Engineering of Functional Dye Materials
journal, March 2011

  • Würthner, Frank; Kaiser, Theo E.; Saha-Möller, Chantu R.
  • Angewandte Chemie International Edition, Vol. 50, Issue 15
  • DOI: 10.1002/anie.201002307

Expanded Theory of H- and J-Molecular Aggregates: The Effects of Vibronic Coupling and Intermolecular Charge Transfer
journal, April 2018


Coherent Quenching of a Fluorophore for the Design of a Highly Sensitive In-Stem Molecular Beacon
journal, July 2010

  • Hara, Yuichi; Fujii, Taiga; Kashida, Hiromu
  • Angewandte Chemie International Edition, Vol. 49, Issue 32
  • DOI: 10.1002/anie.201001459

The Structure and Dynamics of Molecular Excitons
journal, April 2014


Nanoscale Resonance Energy Transfer-Based Devices for Probabilistic Computing
journal, September 2015

  • Wang, Siyang; Lebeck, Alvin R.; Dwyer, Chris
  • IEEE Micro, Vol. 35, Issue 5
  • DOI: 10.1109/MM.2015.124

Photon harvesting by excimer-forming multichromophores
journal, January 2012

  • Adeyemi, Oliver O.; Malinovskii, Vladimir L.; Biner, Sarah M.
  • Chemical Communications, Vol. 48, Issue 77
  • DOI: 10.1039/c2cc34183b

Synthesis, spectral properties and photostabilities of symmetrical and unsymmetrical squarines; a new class of flourophores with long-wavelength exiciation and emmision
journal, October 1993


Squaraine dyes: The hierarchical synthesis and its application in optical detection
journal, June 2017


Nucleic acid-guided assembly of aromatic chromophores
journal, January 2010

  • Malinovskii, Vladimir L.; Wenger, Daniel; Häner, Robert
  • Chem. Soc. Rev., Vol. 39, Issue 2
  • DOI: 10.1039/B910030J

Synthesis, photophysical properties and applications of NIR absorbing unsymmetrical squaraines: A review
journal, November 2019


Complex shapes self-assembled from single-stranded DNA tiles
journal, May 2012


Studies of polaron motion
journal, November 1959


Aggregation of Dyes in Aqueous Solution
journal, March 1946

  • Vickerstaff, T.; Lemin, D. R.
  • Nature, Vol. 157, Issue 3986
  • DOI: 10.1038/157373a0

Accurate design of megadalton-scale two-component icosahedral protein complexes
journal, July 2016


Cyclotrimethine Dyes Derived from Squaric Acid
journal, August 1965

  • Treibs, A.; Jacob, K.
  • Angewandte Chemie International Edition in English, Vol. 4, Issue 8
  • DOI: 10.1002/anie.196506941

The aggregation of cyanine dyes in aqueous solution
journal, January 1947


Alternating Hetero H Aggregation of Different Dyes by Interstrand Stacking from Two DNA-Dye Conjugates
journal, December 2004

  • Kashida, Hiromu; Asanuma, Hiroyuki; Komiyama, Makoto
  • Angewandte Chemie International Edition, Vol. 43, Issue 47
  • DOI: 10.1002/anie.200460870

The Spectral Signatures of Frenkel Polarons in H- and J-Aggregates
journal, March 2010

  • Spano, Frank C.
  • Accounts of Chemical Research, Vol. 43, Issue 3
  • DOI: 10.1021/ar900233v

Excitonic AND Logic Gates on DNA Brick Nanobreadboards
journal, February 2015

  • Cannon, Brittany L.; Kellis, Donald L.; Davis, Paul H.
  • ACS Photonics, Vol. 2, Issue 3
  • DOI: 10.1021/ph500444d

Theory of excitation transfer in coupled nanostructures – from quantum dots to light harvesting complexes
journal, August 2006

  • Richter, Marten; Ahn, Kwang Jun; Knorr, Andreas
  • physica status solidi (b), Vol. 243, Issue 10
  • DOI: 10.1002/pssb.200668053

Entanglement dynamics of J-aggregate systems
journal, March 2011


Red Chlorophylls in the Exciton Model of Photosystem I
journal, November 2005

  • Vaitekonis, Sarunas; Trinkunas, Gediminas; Valkunas, Leonas
  • Photosynthesis Research, Vol. 86, Issue 1-2
  • DOI: 10.1007/s11120-005-2747-x

Coherence Dynamics in Photosynthesis: Protein Protection of Excitonic Coherence
journal, June 2007


Density Matrix Analysis and Simulation of Electronic Excitations in Conjugated and Aggregated Molecules
journal, September 2002

  • Tretiak, Sergei; Mukamel, Shaul
  • Chemical Reviews, Vol. 102, Issue 9
  • DOI: 10.1021/cr0101252

Extracting single and two-exciton couplings in photosynthetic complexes by coherent two-dimensional electronic spectra
journal, February 2009


Photosynthetic light harvesting: excitons and coherence
journal, March 2014

  • Fassioli, Francesca; Dinshaw, Rayomond; Arpin, Paul C.
  • Journal of The Royal Society Interface, Vol. 11, Issue 92
  • DOI: 10.1098/rsif.2013.0901

The DNA three-way junction as a mould for tripartite chromophore assembly
journal, January 2012

  • Probst, Markus; Wenger, Daniel; Biner, Sarah M.
  • Org. Biomol. Chem., Vol. 10, Issue 4
  • DOI: 10.1039/C1OB06400B

DNA in a material world
journal, January 2003


The crystal structure of the light-harvesting complex II (B800–850) from Rhodospirillum molischianum
journal, May 1996


The J-band of organic dyes: lineshape and coherence length
journal, July 2002


DNA-Templated Formation of a Helical Cyanine Dye J-Aggregate
journal, October 2000

  • Wang, Miaomiao; Silva, Gloria L.; Armitage, Bruce A.
  • Journal of the American Chemical Society, Vol. 122, Issue 41
  • DOI: 10.1021/ja002184n

Coherence in photosynthesis
journal, June 2011


Large Davydov Splitting and Strong Fluorescence Suppression: An Investigation of Exciton Delocalization in DNA-Templated Holliday Junction Dye Aggregates
journal, February 2018

  • Cannon, Brittany L.; Patten, Lance K.; Kellis, Donald L.
  • The Journal of Physical Chemistry A, Vol. 122, Issue 8
  • DOI: 10.1021/acs.jpca.7b12668

Comparison of a series of hydrophilic squaraine and cyanine dyes for use as biological labels
journal, December 2013


Molecular Aggregate Photophysics beyond the Kasha Model: Novel Design Principles for Organic Materials
journal, January 2017


A unified theory of radiative and radiationless molecular energy transfer
journal, August 1989


Excitonics: A Set of Gates for Molecular Exciton Processing and Signaling
journal, June 2018

  • Sawaya, Nicolas P. D.; Rappoport, Dmitrij; Tabor, Daniel P.
  • ACS Nano, Vol. 12, Issue 7
  • DOI: 10.1021/acsnano.8b00584

The Protein-Folding Problem, 50 Years On
journal, November 2012


A structural model for cyanine dyes templated into the minor groove of DNA
journal, June 2006


Photophysics of J-Aggregate-Mediated Energy Transfer on DNA
journal, November 2017

  • Banal, James L.; Kondo, Toru; Veneziano, Rémi
  • The Journal of Physical Chemistry Letters, Vol. 8, Issue 23
  • DOI: 10.1021/acs.jpclett.7b01898

Exciton Dynamics from Strong to Weak Coupling Limit Illustrated on a Series of Squaraine Dimers
journal, March 2018

  • Röhr, Merle I. S.; Marciniak, Henning; Hoche, Joscha
  • The Journal of Physical Chemistry C, Vol. 122, Issue 15
  • DOI: 10.1021/acs.jpcc.8b00847

DNA-Assisted Self-Assembly of Pyrene Foldamers
journal, June 2009

  • Häner, Robert; Samain, Florent; Malinovskii, Vladimir L.
  • Chemistry - A European Journal, Vol. 15, Issue 23
  • DOI: 10.1002/chem.200900369

Extended dipole model for aggregates of dye molecules
journal, August 1970


Squaraines as light-capturing materials in photovoltaic cells
journal, January 2014

  • Jiang, Jian-Qiao; Sun, Chun-Lin; Shi, Zi-Fa
  • RSC Adv., Vol. 4, Issue 62
  • DOI: 10.1039/C4RA03972F

Substituent Effects on the Assembly of Helical Cyanine Dye Aggregates in the Minor Groove of a DNA Template
journal, February 2011

  • Stadler, Andrea L.; Renikuntla, Babu Rao; Yaron, David
  • Langmuir, Vol. 27, Issue 4
  • DOI: 10.1021/la104329c

DNA-mediated excitonic upconversion FRET switching
journal, November 2015


Photophysical processes in single molecule organic fluorescent probes
journal, January 2014

  • Stennett, Elana M. S.; Ciuba, Monika A.; Levitus, Marcia
  • Chem. Soc. Rev., Vol. 43, Issue 4
  • DOI: 10.1039/C3CS60211G

Geometric Principles for Designing Highly Symmetric Self-Assembling Protein Nanomaterials
journal, May 2017


DNA-Templated Assembly of Helical Cyanine Dye Aggregates:  A Supramolecular Chain Polymerization
journal, November 2004

  • Hannah, Kristen C.; Armitage, Bruce A.
  • Accounts of Chemical Research, Vol. 37, Issue 11
  • DOI: 10.1021/ar030257c

DNA-Controlled Excitonic Switches
journal, January 2012

  • Graugnard, Elton; Kellis, Donald L.; Bui, Hieu
  • Nano Letters, Vol. 12, Issue 4
  • DOI: 10.1021/nl3004336

Optical Properties of Vibronically Coupled Cy3 Dimers on DNA Scaffolds
journal, April 2018

  • Cunningham, Paul D.; Kim, Young C.; Díaz, Sebastián A.
  • 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

Self-assembly of organic dyes in supramolecular aggregates
journal, January 2016

  • Heyne, Belinda
  • Photochemical & Photobiological Sciences, Vol. 15, Issue 9
  • DOI: 10.1039/C6PP00221H

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