Electronic Structure and Excited-State Dynamics of DNA-Templated Monomers and Aggregates of Asymmetric Polymethine Dyes

Duncan, Katelyn M.; Byers, Hannah M.; Houdek, Madaline E.; Roy, Simon K.; Biaggne, Austin; Barclay, Matthew S.; Patten, Lance K.; Huff, Jonathan S.; Kellis, Donald L.; Wilson, Christopher K.; Lee, Jeunghoon; Davis, Paul H.; Mass, Olga A.; Li, Lan; Turner, Daniel B.; Hall, John A.; Knowlton, William B.; Yurke, Bernard; Pensack, Ryan D.

doi:10.1021/acs.jpca.3c00562

Title: Electronic Structure and Excited-State Dynamics of DNA-Templated Monomers and Aggregates of Asymmetric Polymethine Dyes

Journal Article · Thu Jun 01 00:00:00 EDT 2023 · Journal of Physical Chemistry. A, Molecules, Spectroscopy, Kinetics, Environment, and General Theory

DOI:https://doi.org/10.1021/acs.jpca.3c00562· OSTI ID:1975990

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Center for Advanced Energy Studies, Idaho Falls, Idaho 83401, United States

Aggregates of conjugated organic molecules (i.e., dyes) may exhibit relatively large one- and two-exciton interaction energies, which has motivated theoretical studies on their potential use in quantum information science (QIS). In practice, one way of realizing large one- and two-exciton interaction energies is by maximizing the transition dipole moment (μ) and difference static dipole moment (Δd) of the constituent dyes. In this work, we characterized the electronic structure and excited-state dynamics of monomers and aggregates of four asymmetric polymethine dyes templated via DNA. Using steady-state and time-resolved absorption and fluorescence spectroscopy along with quantum-chemical calculations, we found the asymmetric polymethine dye monomers exhibited a large μ, an appreciable Δd, and a long excited-state lifetime (τp). We formed dimers of all four dyes and observed that one dye, Dy 754, displayed the strongest propensity for aggregation and exciton delocalization. Motivated by these results, we undertook a more comprehensive survey of Dy 754 dimer and tetramer aggregates using steady-state absorption and circular dichroism spectroscopy. Modeling these spectra revealed an appreciable excitonic hopping parameter (J). Lastly, we used femtosecond transient absorption spectroscopy to characterize τp of the dimer and tetramer, which we observed to be exceedingly short. This work revealed that asymmetric polymethine dyes exhibited μ, Δd, monomer τp, and J values promising for QIS; however, further work is needed to overcome excited-state quenching and achieve long aggregate τp.

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Research Organization:: Boise State Univ., ID (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES); US Department of the Navy, Office of Naval Research (ONR)

Grant/Contract Number:: SC0020089; N00014-19-1-2615

OSTI ID:: 1975990

Alternate ID(s):: OSTI ID: 1985643; OSTI ID: 1992624

Journal Information:: Journal of Physical Chemistry. A, Molecules, Spectroscopy, Kinetics, Environment, and General Theory, Journal Name: Journal of Physical Chemistry. A, Molecules, Spectroscopy, Kinetics, Environment, and General Theory Vol. 127 Journal Issue: 23; ISSN 1089-5639

Publisher:: American Chemical SocietyCopyright Statement

Country of Publication:: United States

Language:: English

References (140)

Immobilization of Cyanines in DNA Produces Systematic Increases in Fluorescence Intensity Pace, Natalie A.; Hennelly, Scott P.; Goodwin, Peter M. The Journal of Physical Chemistry Letters, Vol. 12, Issue 37 https://doi.org/10.1021/acs.jpclett.1c02022	journal	September 2021
Glotaran : A Java -Based Graphical User Interface for the R Package TIMP Snellenburg, Joris J.; Laptenok, Sergey P.; Seger, Ralf Journal of Statistical Software, Vol. 49, Issue 3 https://doi.org/10.18637/jss.v049.i03	journal	January 2012
An addressable quantum dot qubit with fault-tolerant control-fidelity Veldhorst, M.; Hwang, J. C. C.; Yang, C. H. Nature Nanotechnology, Vol. 9, Issue 12 https://doi.org/10.1038/nnano.2014.216	journal	October 2014
Reduction of the Fluorescence Transition Dipole Moment by Excitation Localization in a Vibronically Coupled Squaraine Dimer Marciniak, Henning; Auerhammer, Nina; Ricker, Sophie The Journal of Physical Chemistry C, Vol. 123, Issue 6 https://doi.org/10.1021/acs.jpcc.8b11957	journal	January 2019
An Optically Modulated Self-Assembled Resonance Energy Transfer Pass Gate LaBoda, Craig D.; Lebeck, Alvin R.; Dwyer, Chris L. Nano Letters, Vol. 17, Issue 6 https://doi.org/10.1021/acs.nanolett.7b01112	journal	May 2017
Expanding molecular logic capabilities in DNA-scaffolded multiFRET triads Buckhout-White, Susan; Brown III, Carl W.; Hastman, David A. RSC Advances, Vol. 6, Issue 100 https://doi.org/10.1039/C6RA23079B	journal	January 2016
An Assessment of RASSCF and TDDFT Energies and Gradients on an Organic Donor–Acceptor Dye Assisted by Resonance Raman Spectroscopy Kupfer, Stephan; Guthmuller, Julien; González, Leticia Journal of Chemical Theory and Computation, Vol. 9, Issue 1 https://doi.org/10.1021/ct3009057	journal	December 2012
Spontaneous Assembly of Helical Cyanine Dye Aggregates on DNA Nanotemplates Seifert, Jennifer L.; Connor, Rebecca E.; Kushon, Stuart A. Journal of the American Chemical Society, Vol. 121, Issue 13 https://doi.org/10.1021/ja984279j	journal	April 1999
Theory of exciton-vibrational dynamics in molecular dimers Kühn, Oliver; Renger, Thomas; May, Volkhard Chemical Physics, Vol. 204, Issue 1 https://doi.org/10.1016/0301-0104(95)00448-3	journal	March 1996
Design and self-assembly of two-dimensional DNA crystals Winfree, Erik; Liu, Furong; Wenzler, Lisa A. Nature, Vol. 394, Issue 6693 https://doi.org/10.1038/28998	journal	August 1998
Failure of the IDA in FRET Systems at Close Inter-Dye Distances Is Moderated by Frequent Low κ ² Values Spiegel, J. Dominik; Fulle, Simone; Kleinschmidt, Martin The Journal of Physical Chemistry B, Vol. 120, Issue 34 https://doi.org/10.1021/acs.jpcb.6b05754	journal	August 2016
Designing excitonic circuits for the Deutsch–Jozsa algorithm: mitigating fidelity loss by merging gate operations Castellanos, Maria A.; Willard, Adam P. Physical Chemistry Chemical Physics, Vol. 23, Issue 28 https://doi.org/10.1039/D1CP01643A	journal	January 2021
STARK SPECTROSCOPY: Applications in Chemistry, Biology, and Materials Science Bublitz, Gerold U.; Boxer, Steven G. Annual Review of Physical Chemistry, Vol. 48, Issue 1 https://doi.org/10.1146/annurev.physchem.48.1.213	journal	October 1997
The coming of age of de novo protein design Huang, Po-Ssu; Boyken, Scott E.; Baker, David Nature, Vol. 537, Issue 7620 https://doi.org/10.1038/nature19946	journal	September 2016
Essential States Model for Merocyanine Dye Stacks: Bridging Electronic and Optical Absorption Properties Bialas, David; Zhong, Chuwei; Würthner, F. The Journal of Physical Chemistry C, Vol. 123, Issue 30 https://doi.org/10.1021/acs.jpcc.9b04430	journal	July 2019
Spectral Absorption and Fluorescence of Dyes in the Molecular State Jelley, Edwin E. Nature, Vol. 138, Issue 3502 https://doi.org/10.1038/1381009a0	journal	December 1936
Exciton coupling effects on the two-photon absorption of squaraine homodimers with varying bridge units Michail, Evripidis; Schreck, Maximilian H.; Holzapfel, Marco Physical Chemistry Chemical Physics, Vol. 22, Issue 33 https://doi.org/10.1039/D0CP03410J	journal	January 2020
Coherent Dynamics of Coupled Electron and Nuclear Spin Qubits in Diamond Childress, L.; Gurudev Dutt, M. V.; Taylor, J. M. Science, Vol. 314, Issue 5797 https://doi.org/10.1126/science.1131871	journal	October 2006
A dressed spin qubit in silicon Laucht, Arne; Kalra, Rachpon; Simmons, Stephanie Nature Nanotechnology, Vol. 12, Issue 1 https://doi.org/10.1038/nnano.2016.178	journal	October 2016
DNA-Templated Aggregates of Strongly Coupled Cyanine Dyes: Nonradiative Decay Governs Exciton Lifetimes Huff, Jonathan S.; Davis, Paul H.; Christy, Allison The Journal of Physical Chemistry Letters, Vol. 10, Issue 10 https://doi.org/10.1021/acs.jpclett.9b00404	journal	April 2019
Folding DNA to create nanoscale shapes and patterns Rothemund, Paul W. K. Nature, Vol. 440, Issue 7082, p. 297-302 https://doi.org/10.1038/nature04586	journal	March 2006
Influence of Hydrophobicity on Excitonic Coupling in DNA-Templated Indolenine Squaraine Dye Aggregates Mass, Olga A.; Wilson, Christopher K.; Barcenas, German The Journal of Physical Chemistry C, Vol. 126, Issue 7 https://doi.org/10.1021/acs.jpcc.1c08981	journal	February 2022
Exciton Delocalization Drives Rapid Singlet Fission in Nanoparticles of Acene Derivatives Pensack, Ryan D.; Tilley, Andrew J.; Parkin, Sean R. Journal of the American Chemical Society, Vol. 137, Issue 21 https://doi.org/10.1021/ja512668r	journal	May 2015
AM1 Study of the Ground and Excited State Potential Energy Surfaces of Symmetric Carbocyanines Rodríguez, Javier; Scherlis, Damián; Estrin, Darío The Journal of Physical Chemistry A, Vol. 101, Issue 37 https://doi.org/10.1021/jp9713569	journal	September 1997
Organic Optoelectronic Materials: Mechanisms and Applications Ostroverkhova, Oksana Chemical Reviews, Vol. 116, Issue 22 https://doi.org/10.1021/acs.chemrev.6b00127	journal	October 2016
CNOT gate operation on a photogenerated molecular electron spin-qubit pair Nelson, Jordan N.; Zhang, Jinyuan; Zhou, Jiawang The Journal of Chemical Physics, Vol. 152, Issue 1 https://doi.org/10.1063/1.5128132	journal	January 2020
50 years of DNA ‘Breathing’: Reflections on old and new approaches [For special issue of biopolymers on 50 years of nucleic acids research] von Hippel, Peter H.; Johnson, Neil P.; Marcus, Andrew H. Biopolymers https://doi.org/10.1002/bip.22347	journal	July 2013
Light Absorption and Energy Transfer in the Antenna Complexes of Photosynthetic Organisms Mirkovic, Tihana; Ostroumov, Evgeny E.; Anna, Jessica M. Chemical Reviews, Vol. 117, Issue 2 https://doi.org/10.1021/acs.chemrev.6b00002	journal	March 2016
Universal Computation by Multiparticle Quantum Walk Childs, A. M.; Gosset, D.; Webb, Z. Science, Vol. 339, Issue 6121 https://doi.org/10.1126/science.1229957	journal	February 2013
The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals Zhao, Yan; Truhlar, Donald G. Theoretical Chemistry Accounts, Vol. 120, Issue 1-3 https://doi.org/10.1007/s00214-007-0310-x	journal	July 2007
Exciton Interactions in Nonconjugated Squaraine Dimers. Mechanisms for Coupling and Consequences for Photophysics and Photochemistry Liang, Kangning; Farahat, Mohammad S.; Perlstein, Jerry Journal of the American Chemical Society, Vol. 119, Issue 4 https://doi.org/10.1021/ja962091z	journal	January 1997
Molecular Understanding of Organic Solar Cells: The Challenges Brédas, Jean-Luc; Norton, Joseph E.; Cornil, Jérôme Accounts of Chemical Research, Vol. 42, Issue 11 https://doi.org/10.1021/ar900099h	journal	November 2009
Fluorescence Properties and Photophysics of the Sulfoindocyanine Cy3 Linked Covalently to DNA Sanborn, Matthew E.; Connolly, Brian K.; Gurunathan, Kaushik The Journal of Physical Chemistry B, Vol. 111, Issue 37 https://doi.org/10.1021/jp072912u	journal	September 2007
Probing DNA structural heterogeneity by identifying conformational subensembles of a bicovalently bound cyanine dye Barclay, Matthew S.; Chowdhury, Azhad U.; Biaggne, Austin The Journal of Chemical Physics, Vol. 158, Issue 3 https://doi.org/10.1063/5.0131795	journal	January 2023
Energy Transfer Mechanisms and the Molecular Exciton Model for Molecular Aggregates Kasha, Michael Radiation Research, Vol. 20, Issue 1 https://doi.org/10.2307/3571331	journal	September 1963
Josephson Persistent-Current Qubit Mooij, J. E. Science, Vol. 285, Issue 5430 https://doi.org/10.1126/science.285.5430.1036	journal	August 1999
Organic Dye Bearing Asymmetric Double Donor-π-Acceptor Chains for Dye-Sensitized Solar Cells Hong, Yanping; Liao, Jin-Yun; Cao, Derong The Journal of Organic Chemistry, Vol. 76, Issue 19 https://doi.org/10.1021/jo201057b	journal	October 2011
Excited state dynamics and photophysics of aggregated dye chromophores in solution Sundström, Villy; Gillbro, Tomas The Journal of Chemical Physics, Vol. 83, Issue 6 https://doi.org/10.1063/1.449275	journal	September 1985
Temperature-dependent conformations of exciton-coupled Cy3 dimers in double-stranded DNA Kringle, Loni; Sawaya, Nicolas P. D.; Widom, Julia The Journal of Chemical Physics, Vol. 148, Issue 8 https://doi.org/10.1063/1.5020084	journal	February 2018
TD-DFT benchmarks: A review Laurent, Adèle D.; Jacquemin, Denis International Journal of Quantum Chemistry, Vol. 113, Issue 17 https://doi.org/10.1002/qua.24438	journal	April 2013
Photoisomerization of Cyanines. A Comparative Study of Oxygen- and Sulfur-Containing Species Awad, M. M.; McCarthy, P. K.; Blanchard, G. J. The Journal of Physical Chemistry, Vol. 98, Issue 5 https://doi.org/10.1021/j100056a014	journal	February 1994
Nucleobase-Specific Enhancement of Cy3 Fluorescence Harvey, Billie J.; Levitus, Marcia Journal of Fluorescence, Vol. 19, Issue 3 https://doi.org/10.1007/s10895-008-0431-1	journal	October 2008
Design of immobile nucleic acid junctions Seeman, N. C.; Kallenbach, N. R. Biophysical Journal, Vol. 44, Issue 2 https://doi.org/10.1016/S0006-3495(83)84292-1	journal	November 1983
Proximity-Induced H-Aggregation of Cyanine Dyes on DNA-Duplexes Nicoli, Francesca; Roos, Matthias K.; Hemmig, Elisa A. The Journal of Physical Chemistry A, Vol. 120, Issue 50 https://doi.org/10.1021/acs.jpca.6b10939	journal	December 2016
Understanding Disorder, Vibronic Structure, and Delocalization in Electronically Coupled Dimers on DNA Duplexes Rolczynski, Brian S.; Díaz, Sebastián A.; Kim, Young C. The Journal of Physical Chemistry A, Vol. 125, Issue 44 https://doi.org/10.1021/acs.jpca.1c07205	journal	October 2021
Quantum Mechanical Continuum Solvation Models Tomasi, Jacopo; Mennucci, Benedetta; Cammi, Roberto Chemical Reviews, Vol. 105, Issue 8 https://doi.org/10.1021/cr9904009	journal	August 2005
Ultrafast Photophysical Investigation of Cresyl Violet Aggregates Adsorbed onto Nanometer-Sized Particles of SnO ₂ and SiO ₂ Martini, Ignacio; Hartland, Gregory V.; Kamat, Prashant V. The Journal of Physical Chemistry B, Vol. 101, Issue 24 https://doi.org/10.1021/jp9702964	journal	June 1997
Excited-State Lifetimes of DNA-Templated Cyanine Dimer, Trimer, and Tetramer Aggregates: The Role of Exciton Delocalization, Dye Separation, and DNA Heterogeneity Huff, Jonathan S.; Turner, Daniel B.; Mass, Olga A. The Journal of Physical Chemistry B, Vol. 125, Issue 36 https://doi.org/10.1021/acs.jpcb.1c04517	journal	September 2021
Stark Spectroscopy of Donor/Acceptor Substituted Polyenes Bublitz, Gerold U.; Ortiz, Rafael; Marder, Seth R. Journal of the American Chemical Society, Vol. 119, Issue 14 https://doi.org/10.1021/ja9640814	journal	April 1997
A Novel Preparation Method of Organic Microcrystals Kasai, Hitoshi; Nalwa, Hari Singh; Oikawa, Hidetoshi Japanese Journal of Applied Physics, Vol. 31, Issue 8A https://doi.org/10.1143/JJAP.31.L1132	journal	August 1992
Solar Fuels via Artificial Photosynthesis Gust, Devens; Moore, Thomas A.; Moore, Ana L. Accounts of Chemical Research, Vol. 42, Issue 12 https://doi.org/10.1021/ar900209b	journal	December 2009
Self-Assembly Strategies for Integrating Light Harvesting and Charge Separation in Artificial Photosynthetic Systems Wasielewski, Michael R. Accounts of Chemical Research, Vol. 42, Issue 12 https://doi.org/10.1021/ar9001735	journal	December 2009
Photogenerated Spin-Entangled Qubit (Radical) Pairs in DNA Hairpins: Observation of Spin Delocalization and Coherence Olshansky, Jacob H.; Krzyaniak, Matthew D.; Young, Ryan M. Journal of the American Chemical Society, Vol. 141, Issue 5 https://doi.org/10.1021/jacs.8b13155	journal	January 2019
Three-Dimensional Structures Self-Assembled from DNA Bricks Ke, Y.; Ong, L. L.; Shih, W. M. Science, Vol. 338, Issue 6111 https://doi.org/10.1126/science.1227268	journal	November 2012
DFT study of the effect of substituents on the absorption and emission spectra of Indigo Cervantes-Navarro, Francisco; Glossman-Mitnik, Daniel Chemistry Central Journal, Vol. 6, Issue 1 https://doi.org/10.1186/1752-153X-6-70	journal	July 2012
Data-Driven and Multiscale Modeling of DNA-Templated Dye Aggregates Biaggne, Austin; Spear, Lawrence; Barcenas, German Molecules, Vol. 27, Issue 11 https://doi.org/10.3390/molecules27113456	journal	May 2022
Ultrafast Excitation Transfer in Cy5 DNA Photonic Wires Displays Dye Conjugation and Excitation Energy Dependency Mazuski, Richard J.; Díaz, Sebastián A.; Wood, Ryan E. The Journal of Physical Chemistry Letters, Vol. 11, Issue 10 https://doi.org/10.1021/acs.jpclett.0c01020	journal	May 2020
Natural strategies for photosynthetic light harvesting Croce, Roberta; van Amerongen, Herbert Nature Chemical Biology, Vol. 10, Issue 7 https://doi.org/10.1038/nchembio.1555	journal	June 2014
Synthesis and properties of squaraine-modified DNA Markova, Larysa I.; Malinovskii, Vladimir L.; Patsenker, Leonid D. Organic & Biomolecular Chemistry, Vol. 10, Issue 45 https://doi.org/10.1039/c2ob26787j	journal	January 2012
Exciton Delocalization in Indolenine Squaraine Aggregates Templated by DNA Holliday Junction Scaffolds Mass, Olga A.; Wilson, Christopher K.; Roy, Simon K. The Journal of Physical Chemistry B, Vol. 124, Issue 43 https://doi.org/10.1021/acs.jpcb.0c06480	journal	October 2020
Cyanine Dye Coupling Mediates Self‐assembly of a pH Sensitive Peptide into Novel 3D Architectures Fernandes, Rita; Chowdhary, Suvrat; Mikula, Natalia Angewandte Chemie International Edition, Vol. 61, Issue 48 https://doi.org/10.1002/anie.202208647	journal	October 2022
Phototheranostic DNA micelles from the self-assembly of DNA-BODIPY amphiphiles for the thermal ablation of cancer cells Atchimnaidu, Siriki; Perumal, Devanathan; Harikrishanan, Kaloor S. Nanoscale, Vol. 12, Issue 22 https://doi.org/10.1039/D0NR02622K	journal	January 2020
Ultrafast Symmetry-Breaking Charge Separation in a Perylene Bisimide Dimer Enabled by Vibronic Coupling and Breakdown of Adiabaticity Hong, Yongseok; Schlosser, Felix; Kim, Woojae Journal of the American Chemical Society, Vol. 144, Issue 34 https://doi.org/10.1021/jacs.2c03916	journal	August 2022
Molecular dynamics simulations of cyanine dimers attached to DNA Holliday junctions Biaggne, Austin; Kim, Young C.; Melinger, Joseph. S. RSC Advances, Vol. 12, Issue 43 https://doi.org/10.1039/D2RA05045E	journal	January 2022
Implementation of a Frenkel exciton-based controlled phase shifter Yurke, Bernard; Elliott, Richard; Sup, Aaron Physical Review A, Vol. 107, Issue 1 https://doi.org/10.1103/PhysRevA.107.012603	journal	January 2023
Quantum computation with quantum dots Loss, Daniel; DiVincenzo, David P. Physical Review A, Vol. 57, Issue 1 https://doi.org/10.1103/PhysRevA.57.120	journal	January 1998
Photogenerated Spin-Correlated Radical Pairs: From Photosynthetic Energy Transduction to Quantum Information Science Harvey, Samantha M.; Wasielewski, Michael R. Journal of the American Chemical Society, Vol. 143, Issue 38 https://doi.org/10.1021/jacs.1c07706	journal	September 2021
Substituent Effects on the Solubility and Electronic Properties of the Cyanine Dye Cy5: Density Functional and Time-Dependent Density Functional Theory Calculations Biaggne, Austin; Knowlton, William B.; Yurke, Bernard Molecules, Vol. 26, Issue 3 https://doi.org/10.3390/molecules26030524	journal	January 2021
DNA-Enabled Integrated Molecular Systems for Computation and Sensing LaBoda, Craig; Duschl, Heather; Dwyer, Chris L. Accounts of Chemical Research, Vol. 47, Issue 6 https://doi.org/10.1021/ar500054u	journal	May 2014
The Appeal of Small Molecules for Practical Nonlinear Optics Biaggio, Ivan Chemistry – A European Journal, Vol. 28, Issue 6 https://doi.org/10.1002/chem.202103168	journal	December 2021
Exciton Coupling of Merocyanine Dyes from H- to J-type in the Solid State by Crystal Engineering Liess, Andreas; Lv, Aifeng; Arjona-Esteban, Alhama Nano Letters, Vol. 17, Issue 3 https://doi.org/10.1021/acs.nanolett.6b04995	journal	February 2017
Quantum supremacy using a programmable superconducting processor Arute, Frank; Arya, Kunal; Babbush, Ryan Nature, Vol. 574, Issue 7779 https://doi.org/10.1038/s41586-019-1666-5	journal	October 2019
TD-DFT Assessment of Functionals for Optical 0–0 Transitions in Solvated Dyes Jacquemin, Denis; Planchat, Aurélien; Adamo, Carlo Journal of Chemical Theory and Computation, Vol. 8, Issue 7 https://doi.org/10.1021/ct300326f	journal	June 2012
Introduction to Fluorescence Lakowicz, Joseph R. Principles of Fluorescence Spectroscopy https://doi.org/10.1007/978-0-387-46312-4_1	book	January 2006
Asymmetric Squaraine Dyes: Spectroscopic and Theoretical Investigation Shafeekh, K. M.; Das, Suresh; Sissa, Cristina The Journal of Physical Chemistry B, Vol. 117, Issue 28 https://doi.org/10.1021/jp401099g	journal	July 2013
Solvatochromism and Solvation Dynamics of Structurally Related Cyanine Dyes Yu, Anchi; Tolbert, Catherine A.; Farrow, Darcie A. The Journal of Physical Chemistry A, Vol. 106, Issue 41 https://doi.org/10.1021/jp0205867	journal	October 2002
Nucleic acid junctions and lattices Seeman, Nadrian C. Journal of Theoretical Biology, Vol. 99, Issue 2 https://doi.org/10.1016/0022-5193(82)90002-9	journal	November 1982
Design of NIR-Absorbing Simple Asymmetric Squaraine Dyes Carrying Indoline Moieties for Use in Dye-Sensitized Solar Cells with Pt-Free Electrodes Funabiki, Kazumasa; Mase, Hiroyoshi; Saito, Yasuteru Organic Letters, Vol. 14, Issue 5 https://doi.org/10.1021/ol300054a	journal	February 2012
Time dependent correlations of entangled states with nondegenerate branches and possible experimental realization using singlet fission Bardeen, Christopher J. The Journal of Chemical Physics, Vol. 151, Issue 12 https://doi.org/10.1063/1.5117155	journal	September 2019
Protein Structure Prediction and Structural Genomics Baker, D. Science, Vol. 294, Issue 5540 https://doi.org/10.1126/science.1065659	journal	October 2001
Electrically poled vapor-deposited organic glasses for integrated electro-optics Dallachiesa, Lauren; Biaggio, Ivan Optics Letters, Vol. 47, Issue 8 https://doi.org/10.1364/OL.452742	journal	April 2022
Photodriven quantum teleportation of an electron spin state in a covalent donor–acceptor–radical system Rugg, Brandon K.; Krzyaniak, Matthew D.; Phelan, Brian T. Nature Chemistry, Vol. 11, Issue 11 https://doi.org/10.1038/s41557-019-0332-8	journal	September 2019
Bis(merocyanine) Hetero‐Folda‐Dimers: Evaluation of Exciton Coupling between Different Types of π‐Stacked Chromphores Kirchner, Eva; Bialas, David; Würthner, Frank Chemistry – A European Journal https://doi.org/10.1002/chem.201901757	journal	August 2019
Programmable Transformations of DNA Origami Made of Small Modular Dynamic Units Wang, Dongfang; Yu, Lei; Huang, Chao-Min Journal of the American Chemical Society, Vol. 143, Issue 5 https://doi.org/10.1021/jacs.0c10576	journal	February 2021
Exciton Delocalization and Scaffold Stability in Bridged Nucleotide-Substituted, DNA Duplex-Templated Cyanine Aggregates Roy, Simon K.; Mass, Olga A.; Kellis, Donald L. The Journal of Physical Chemistry B, Vol. 125, Issue 50 https://doi.org/10.1021/acs.jpcb.1c07602	journal	December 2021
Excitons in nanoscale systems Scholes, Gregory D.; Rumbles, Garry Nature Materials, Vol. 5, Issue 9 https://doi.org/10.1038/nmat1710	journal	September 2006
Synthesis, photophysical properties and applications of NIR absorbing unsymmetrical squaraines: A review Khopkar, Sushil; Shankarling, Ganapati Dyes and Pigments, Vol. 170 https://doi.org/10.1016/j.dyepig.2019.107645	journal	November 2019
Excited State Electronic Structures of 5,10-Methenyltetrahydrofolate and 5,10-Methylenetetrahydrofolate Determined by Stark Spectroscopy Pauszek, Raymond F.; Kodali, Goutham; Stanley, Robert J. The Journal of Physical Chemistry A, Vol. 118, Issue 37 https://doi.org/10.1021/jp501143u	journal	May 2014
Photocrosslinking Probes Proximity of Thymine Modifiers Tethering Excitonically Coupled Dye Aggregates to DNA Holliday Junction Basu, Shibani; Cervantes-Salguero, Keitel; Yurke, Bernard Molecules, Vol. 27, Issue 13 https://doi.org/10.3390/molecules27134006	journal	June 2022
Principles of Fluorescence Spectroscopy Lakowicz, Joseph R. Springer New York, NY https://doi.org/10.1007/978-0-387-46312-4	book	January 2006
Exciton Chirality Inversion in Dye Dimers Templated by DNA Holliday Junction Mass, Olga A.; Basu, Shibani; Patten, Lance K. The Journal of Physical Chemistry Letters, Vol. 13, Issue 46 https://doi.org/10.1021/acs.jpclett.2c02721	journal	November 2022
The Spectral Signatures of Frenkel Polarons in H- and J-Aggregates Spano, Frank C. Accounts of Chemical Research, Vol. 43, Issue 3 https://doi.org/10.1021/ar900233v	journal	March 2010
Excitonic AND Logic Gates on DNA Brick Nanobreadboards Cannon, Brittany L.; Kellis, Donald L.; Davis, Paul H. ACS Photonics, Vol. 2, Issue 3 https://doi.org/10.1021/ph500444d	journal	February 2015
Near-Infrared Heptamethine Cyanine Dyes for Nanoparticle-Based Photoacoustic Imaging and Photothermal Therapy St. Lorenz, Anna; Buabeng, Emmanuel Ramsey; Taratula, Oleh Journal of Medicinal Chemistry, Vol. 64, Issue 12 https://doi.org/10.1021/acs.jmedchem.1c00771	journal	June 2021
Charge Photogeneration in Organic Solar Cells Clarke, Tracey M.; Durrant, James R. Chemical Reviews, Vol. 110, Issue 11, p. 6736-6767 https://doi.org/10.1021/cr900271s	journal	November 2010
Rotaxane rings promote oblique packing and extended lifetimes in DNA-templated molecular dye aggregates Barclay, Matthew S.; Roy, Simon K.; Huff, Jonathan S. Communications Chemistry, Vol. 4, Issue 1 https://doi.org/10.1038/s42004-021-00456-8	journal	February 2021
Stark Realities ^† Boxer, Steven G. The Journal of Physical Chemistry B, Vol. 113, Issue 10 https://doi.org/10.1021/jp8067393	journal	March 2009
A new integral equation formalism for the polarizable continuum model: Theoretical background and applications to isotropic and anisotropic dielectrics Cancès, E.; Mennucci, B.; Tomasi, J. The Journal of Chemical Physics, Vol. 107, Issue 8 https://doi.org/10.1063/1.474659	journal	August 1997
Extracting single and two-exciton couplings in photosynthetic complexes by coherent two-dimensional electronic spectra Abramavicius, Darius; Palmieri, Benoit; Mukamel, Shaul Chemical Physics, Vol. 357, Issue 1-3 https://doi.org/10.1016/j.chemphys.2008.10.010	journal	February 2009
Laser action and photoisomerisation of 3,3′-diethyl oxadicarbocyanine iodide (DODCI): Influence of temperature and concentration Rullière, C. Chemical Physics Letters, Vol. 43, Issue 2 https://doi.org/10.1016/0009-2614(76)85308-0	journal	October 1976
Density-difference maps in quantum chemistry Steiner, E. Theoretica Chimica Acta, Vol. 60, Issue 6 https://doi.org/10.1007/BF00549611	journal	January 1982
DNA in a material world Seeman, Nadrian C. Nature, Vol. 421, Issue 6921 https://doi.org/10.1038/nature01406	journal	January 2003
An All-Optical Excitonic Switch Operated in the Liquid and Solid Phases Kellis, Donald L.; Sarter, Christopher; Cannon, Brittany L. ACS Nano, Vol. 13, Issue 3 https://doi.org/10.1021/acsnano.8b07504	journal	February 2019
Large Davydov Splitting and Strong Fluorescence Suppression: An Investigation of Exciton Delocalization in DNA-Templated Holliday Junction Dye Aggregates Cannon, Brittany L.; Patten, Lance K.; Kellis, Donald L. The Journal of Physical Chemistry A, Vol. 122, Issue 8 https://doi.org/10.1021/acs.jpca.7b12668	journal	February 2018
The exciton model in molecular spectroscopy Kasha, M.; Rawls, H. R.; Ashraf El-Bayoumi, M. Pure and Applied Chemistry, Vol. 11, Issue 3-4 https://doi.org/10.1351/pac196511030371	journal	January 1965
Tuning between Quenching and Energy Transfer in DNA-Templated Heterodimer Aggregates Chowdhury, Azhad U.; Díaz, Sebastián A.; Huff, Jonathan S. The Journal of Physical Chemistry Letters, Vol. 13, Issue 12 https://doi.org/10.1021/acs.jpclett.2c00017	journal	March 2022
Determining a fluorophore’s transition dipole moment from fluorescence lifetime measurements in solvents of varying refractive index Chung, Pei-Hua; Tregidgo, Carolyn; Suhling, Klaus Methods and Applications in Fluorescence, Vol. 4, Issue 4 https://doi.org/10.1088/2050-6120/4/4/045001	journal	November 2016
Electronic structure and nonlinear optical properties of push-pull polyenes: theoretical investigation of benzodithia polyenals and dithiolene polyenals Meyers, F.; Bredas, J. L.; Zyss, J. Journal of the American Chemical Society, Vol. 114, Issue 8 https://doi.org/10.1021/ja00034a024	journal	April 1992
Low band gap polymers for organic photovoltaics Bundgaard, Eva; Krebs, Frederik C. Solar Energy Materials and Solar Cells, Vol. 91, Issue 11, p. 954-985 https://doi.org/10.1016/j.solmat.2007.01.015	journal	July 2007
Symmetric vs. asymmetric: Which one is the better molecular configuration for achieving robust NLO response? Muhammad, Shabbir Journal of Molecular Graphics and Modelling, Vol. 114 https://doi.org/10.1016/j.jmgm.2022.108209	journal	July 2022
Molecular Aggregate Photophysics beyond the Kasha Model: Novel Design Principles for Organic Materials Hestand, Nicholas J.; Spano, Frank C. Accounts of Chemical Research, Vol. 50, Issue 2 https://doi.org/10.1021/acs.accounts.6b00576	journal	January 2017
Influence of Excitonic Interactions on the Transient Absorption and Two-Photon Absorption Spectra of Porphyrin J-Aggregates in the NIR Region Collini, Elisabetta; Ferrante, Camilla; Bozio, Renato The Journal of Physical Chemistry C, Vol. 111, Issue 50 https://doi.org/10.1021/jp074974q	journal	November 2007
Absolute comparison of simulated and experimental protein-folding dynamics Snow, Christopher D.; Nguyen, Houbi; Pande, Vijay S. Nature, Vol. 420, Issue 6911 https://doi.org/10.1038/nature01160	journal	October 2002
Excitonics: A Set of Gates for Molecular Exciton Processing and Signaling Sawaya, Nicolas P. D.; Rappoport, Dmitrij; Tabor, Daniel P. ACS Nano, Vol. 12, Issue 7 https://doi.org/10.1021/acsnano.8b00584	journal	June 2018
Ultrafast Exciton Dynamics of J- and H-Aggregates of the Porphyrin-Catechol in Aqueous Solution Verma, Sandeep; Ghosh, Amrita; Das, Amitava The Journal of Physical Chemistry B, Vol. 114, Issue 25 https://doi.org/10.1021/jp101643c	journal	July 2010
The Protein-Folding Problem, 50 Years On Dill, K. A.; MacCallum, J. L. Science, Vol. 338, Issue 6110 https://doi.org/10.1126/science.1219021	journal	November 2012
Large Molecular Third-Order Optical Nonlinearities in Polarized Carotenoids Marder, S. R. Science, Vol. 276, Issue 5316 https://doi.org/10.1126/science.276.5316.1233	journal	May 1997
Methylene Blue Exciton States Steer Nonradiative Relaxation: Ultrafast Spectroscopy of Methylene Blue Dimer Dean, Jacob C.; Oblinsky, Daniel G.; Rafiq, Shahnawaz The Journal of Physical Chemistry B, Vol. 120, Issue 3 https://doi.org/10.1021/acs.jpcb.5b11847	journal	January 2016
Tailoring the acceptor moiety of novel thiophene-based chromophores: Conjoined experimental and theoretical study on the nonlinear optical properties Popczyk, Anna; Grabarz, Anna; Cheret, Yohan Dyes and Pigments, Vol. 196 https://doi.org/10.1016/j.dyepig.2021.109789	journal	December 2021
On the (uninteresting) dependence of the absorption and emission transition moments of coumarin 153 on solvent Lewis, J. E.; Maroncelli, M. Chemical Physics Letters, Vol. 282, Issue 2 https://doi.org/10.1016/S0009-2614(97)01270-0	journal	January 1998
Oblique Packing and Tunable Excitonic Coupling in DNA‐Templated Squaraine Rotaxane Dimer Aggregates Barclay, Matthew S.; Wilson, Christopher K.; Roy, Simon K. ChemPhotoChem, Vol. 6, Issue 7 https://doi.org/10.1002/cptc.202200039	journal	May 2022
Geometric Principles for Designing Highly Symmetric Self-Assembling Protein Nanomaterials Yeates, Todd O. Annual Review of Biophysics, Vol. 46, Issue 1 https://doi.org/10.1146/annurev-biophys-070816-033928	journal	May 2017
DNA-Controlled Excitonic Switches Graugnard, Elton; Kellis, Donald L.; Bui, Hieu Nano Letters, Vol. 12, Issue 4 https://doi.org/10.1021/nl3004336	journal	January 2012
The Nature of Excimer Formation in Crystalline Pyrene Nanoparticles Pensack, Ryan D.; Ashmore, Rachel J.; Paoletta, Angela L. The Journal of Physical Chemistry C, Vol. 122, Issue 36 https://doi.org/10.1021/acs.jpcc.8b03963	journal	August 2018
Optical Properties of Vibronically Coupled Cy3 Dimers on DNA Scaffolds Cunningham, Paul D.; Kim, Young C.; Díaz, Sebastián A. The Journal of Physical Chemistry B, Vol. 122, Issue 19 https://doi.org/10.1021/acs.jpcb.8b02134	journal	April 2018
The DNA Duplex as an Aqueous One-Dimensional Soft Crystal Scaffold for Photochemistry Asanuma, Hiroyuki; Murayama, Keiji; Kamiya, Yukiko Bulletin of the Chemical Society of Japan, Vol. 91, Issue 12 https://doi.org/10.1246/bcsj.20180278	journal	December 2018
Passive linear nanoscale optical and molecular electronics device synthesis from nanoparticles Yurke, Bernard; Kuang, Wan Physical Review A, Vol. 81, Issue 3 https://doi.org/10.1103/PhysRevA.81.033814	journal	March 2010
Stark Spectroscopy of Donor−Acceptor Polyenes: Correlation with Nonlinear Optical Measurements Bublitz, Gerold U.; Ortiz, Rafael; Runser, Claude Journal of the American Chemical Society, Vol. 119, Issue 9 https://doi.org/10.1021/ja963672r	journal	March 1997
Aqueous Colloidal Acene Nanoparticles: A New Platform for Studying Singlet Fission Mastron, Joseph N.; Roberts, Sean T.; McAnally, R. Eric The Journal of Physical Chemistry B, Vol. 117, Issue 49 https://doi.org/10.1021/jp4057972	journal	July 2013
Tunable Electronic Structure via DNA-Templated Heteroaggregates of Two Distinct Cyanine Dyes Huff, Jonathan S.; Díaz, Sebastián A.; Barclay, Matthew S. The Journal of Physical Chemistry C, Vol. 126, Issue 40 https://doi.org/10.1021/acs.jpcc.2c04336	journal	September 2022
Coherent Exciton Delocalization in a Two-State DNA-Templated Dye Aggregate System Cannon, Brittany L.; Kellis, Donald L.; Patten, Lance K. The Journal of Physical Chemistry A, Vol. 121, Issue 37 https://doi.org/10.1021/acs.jpca.7b04344	journal	September 2017
Time-Gated FRET and DNA-Based Photonic Molecular Logic Gates: AND, OR, NAND, and NOR Massey, Melissa; Medintz, Igor L.; Ancona, Mario G. ACS Sensors, Vol. 2, Issue 8 https://doi.org/10.1021/acssensors.7b00355	journal	August 2017
Superconducting Circuits for Quantum Information: An Outlook Devoret, M. H.; Schoelkopf, R. J. Science, Vol. 339, Issue 6124 https://doi.org/10.1126/science.1231930	journal	March 2013
Lessons from nature about solar light harvesting Scholes, Gregory D.; Fleming, Graham R.; Olaya-Castro, Alexandra Nature Chemistry, Vol. 3, Issue 10 https://doi.org/10.1038/nchem.1145	journal	September 2011
Programmable self-assembly of three-dimensional nanostructures from 10,000 unique components Ong, Luvena L.; Hanikel, Nikita; Yaghi, Omar K. Nature, Vol. 552, Issue 7683 https://doi.org/10.1038/nature24648	journal	December 2017
Exciton Transport in Molecular Aggregates - From Natural Antennas to Synthetic Chromophore Systems Brixner, Tobias; Hildner, Richard; Köhler, Jürgen Advanced Energy Materials, Vol. 7, Issue 16 https://doi.org/10.1002/aenm.201700236	journal	July 2017
Intramolecular Charge Transfer and Ultrafast Nonradiative Decay in DNA-Tethered Asymmetric Nitro- and Dimethylamino-Substituted Squaraines Wright, Nicholas D.; Huff, Jonathan S.; Barclay, Matthew S. The Journal of Physical Chemistry A, Vol. 127, Issue 5 https://doi.org/10.1021/acs.jpca.2c06442	journal	January 2023
Tuning Exciton Coupling of Merocyanine Nucleoside Dimers by RNA, DNA and GNA Double Helix Conformations Dietzsch, Julia; Bialas, David; Bandorf, Johannes Angewandte Chemie International Edition, Vol. 61, Issue 9 https://doi.org/10.1002/anie.202116783	journal	January 2022
Molecular, Nematic and Crystal States of I: I-Diethyl--Cyanine Chloride Jelley, Edwin E. Nature, Vol. 139, Issue 3519 https://doi.org/10.1038/139631b0	journal	April 1937
Symmetric and asymmetric charge transfer process of twophoton absorbing chromophores: bisdonor substituted stilbenes, and substituted styrylquinolinium and styrylpyridinium derivatives Wang, XiaoMei; Wang, Dong; Zhou, GuangYong Journal of Materials Chemistry, Vol. 11, Issue 6 https://doi.org/10.1039/b009769l	journal	January 2001

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