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Rolczynski BS, Díaz SA, Kim YC, Mathur D, Klein WP, Medintz IL, Melinger JS. Determining interchromophore effects for energy transport in molecular networks using machine-learning algorithms. Phys Chem Chem Phys 2023; 25:3651-3665. [PMID: 36648290 DOI: 10.1039/d2cp04960k] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Nature uses chromophore networks, with highly optimized structural and energetic characteristics, to perform important chemical functions. Due to its modularity, predictable aggregation characteristics, and established synthetic protocols, structural DNA nanotechnology is a promising medium for arranging chromophore networks with analogous structural and energetic controls. However, this high level of control creates a greater need to know how to optimize the systems precisely. This study uses the system's modularity to produce variations of a coupled 14-Site chromophore network. It uses machine-learning algorithms and spectroscopy measurements to reveal the energy-transport roles of these Sites, paying particular attention to the cooperative and inhibitive effects they impose on each other for transport across the network. The physical significance of these patterns is contextualized, using molecular dynamics simulations and energy-transport modeling. This analysis yields insights about how energy transfers across the Donor-Relay and Relay-Acceptor interfaces, as well as the energy-transport pathways through the homogeneous Relay segment. Overall, this report establishes an approach that uses machine-learning methods to understand, in fine detail, the role that each Site plays in an optoelectronic molecular network.
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Affiliation(s)
- Brian S Rolczynski
- Electronics Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, DC 20375, USA.
| | - Sebastián A Díaz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, USA
| | - Young C Kim
- Materials Science and Technology Division, Code 6300, U.S. Naval Research Laboratory, Washington, DC 20375, USA
| | - Divita Mathur
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | - William P Klein
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, USA
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, USA
| | - Joseph S Melinger
- Electronics Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, DC 20375, USA.
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Chiriboga M, Diaz SA, Mathur D, Hastman DA, Melinger JS, Veneziano R, Medintz IL. Understanding Self-Assembled Pseudoisocyanine Dye Aggregates in DNA Nanostructures and Their Exciton Relay Transfer Capabilities. J Phys Chem B 2021; 126:110-122. [PMID: 34962787 DOI: 10.1021/acs.jpcb.1c09048] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Progress has been made using B-form DNA duplex strands to template chromophores in ordered molecular aggregates known as J-aggregates. These aggregates can exhibit strong electronic coupling, extended coherent lifetimes, and long-range exciton delocalization under appropriate conditions. Certain cyanine dyes such as pseudoisocyanine (PIC) dye have shown a proclivity to form aggregates in specific DNA sequences. In particular, DX-tiles containing nonalternating poly(dA)-poly(dT) dinucleotide tracks (AT-tracks), which template noncovalent PIC dye aggregates, have been demonstrated to exhibit interesting emergent photonic properties. These DNA-based aggregates are referred to as J-bits for their similarity to J-aggregates. Here, we assemble multifluorophore DX-tile scaffolds which template J-bits into both contiguous and noncontiguous linear arrays. Our goal is to understand the relay capability of noncontiguous J-bit arrays and probe the effects that orientation and position have on the energy transfer between them. We find that linearly contiguous J-bits can relay excitons from an initial AlexaFluor 405 donor to a terminal AlexaFluor 647 acceptor across a distance of up to 16.3 nm. We observed a maximum increase in energy transfer of 41% in the shortest scaffold and an 11% increase in energy transfer across the maximum distance. However, in nonlinear arrays, exciton transfer is not detectable, even when off-axis J-bit-to-J-bit transfer distances were <2 nm. These results, in conjunction with the previous work on PIC-DNA systems, suggest that PIC-DNA-based systems may currently be limited to simple 1-D designs, which prevent isolating J-bits for enhanced energy-transfer characteristics until further understanding and improvements to the system can be made.
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Affiliation(s)
- Matthew Chiriboga
- Center for Bio/Molecular Science & Engineering Code 6900, U.S. Naval Research Laboratory, 4555 Overlook Avenue S.W., Washington, District of Columbia 20375, United States.,Volgenau School of Engineering, Department of Bioengineering, Institute for Advanced Biomedical Research George Mason University, Manassas, Virginia 22030, United States
| | - Sebastian A Diaz
- Center for Bio/Molecular Science & Engineering Code 6900, U.S. Naval Research Laboratory, 4555 Overlook Avenue S.W., Washington, District of Columbia 20375, United States
| | - Divita Mathur
- Center for Bio/Molecular Science & Engineering Code 6900, U.S. Naval Research Laboratory, 4555 Overlook Avenue S.W., Washington, District of Columbia 20375, United States.,College of Science, George Mason University, Fairfax, Virginia 22030, United States
| | - David A Hastman
- Center for Bio/Molecular Science & Engineering Code 6900, U.S. Naval Research Laboratory, 4555 Overlook Avenue S.W., Washington, District of Columbia 20375, United States.,A. James Clark School of Engineering, Fischell Department of Bioengineering, University of Maryland College Park, College Park, Maryland 20742, United States
| | - Joseph S Melinger
- Electronics Science and Technology Division Code 6800, U.S. Naval Research Laboratory, 4555 Overlook Avenue S.W., Washington, District of Columbia 20375, United States
| | - Remi Veneziano
- Volgenau School of Engineering, Department of Bioengineering, Institute for Advanced Biomedical Research George Mason University, Manassas, Virginia 22030, United States
| | - Igor L Medintz
- Center for Bio/Molecular Science & Engineering Code 6900, U.S. Naval Research Laboratory, 4555 Overlook Avenue S.W., Washington, District of Columbia 20375, United States
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Rolczynski BS, Díaz SA, Kim YC, Medintz IL, Cunningham PD, Melinger JS. Understanding Disorder, Vibronic Structure, and Delocalization in Electronically Coupled Dimers on DNA Duplexes. J Phys Chem A 2021; 125:9632-9644. [PMID: 34709821 DOI: 10.1021/acs.jpca.1c07205] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Structural DNA nanotechnology is a promising approach to create chromophore networks with modular structures and Hamiltonians to control the material's functions. The functional behaviors of these systems depend on the interactions of the chromophores' vibronic states, as well as interactions with their environment. To optimize their functions, it is necessary to characterize the chromophore network's structural and energetic properties, including the electronic delocalization in some cases. In this study, parameters of interest are deduced in DNA-scaffolded Cyanine 3 and Cyanine 5 dimers. The methods include steady-state optical measurements, physical modeling, and a genetic algorithm approach. The parameters include the chromophore network's vibronic Hamiltonian, molecular positions, transition dipole orientations, and environmentally induced energy broadening. Additionally, the study uses temperature-dependent optical measurements to characterize the spectral broadening further. These combined results reveal the quantum mechanical delocalization, which is important for functions like coherent energy transport and quantum information applications.
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Affiliation(s)
- Brian S Rolczynski
- Electronics Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Sebastián A Díaz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Young C Kim
- Materials Science and Technology Division, Code 6300, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Paul D Cunningham
- Electronics Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Joseph S Melinger
- Electronics Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
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Armstrong ZT, Kunz MB, Zanni MT. Ultrafast Fluctuations in PM6 Domains of Binary and Ternary Organic Photovoltaic Thin Films Probed with Two-Dimensional White-Light Spectroscopy. J Phys Chem Lett 2021; 12:8972-8979. [PMID: 34506148 DOI: 10.1021/acs.jpclett.1c02234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We present two-dimensional white-light spectroscopy (2DWL) measurements of binary and ternary bulk heterojunctions of the polymer donor PM6 mixed with state-of-the-art nonfullerene acceptors Y6 or IT4F. The ternary film has a shorter lifetime and faster spectral diffusion than either of the binary films. 2D line shape analysis of the PM6 ground state bleach with a Kubo model determines that all three films have similar amplitudes of fluctuations (Δ = 0.29 fs-1) in their transition frequencies, but different relaxation times (ranging from 102 to 24 fs). The ternary film exhibits faster dynamics than either of the binary films. The short lifetime of the ternary blend is consistent with increased photoexcitation transfer and the fast frequency fluctuations are consistent with structural dynamics of aliphatic side chains. These results suggest that the femtosecond fluctuations of PM6 are impacted by the choice of the acceptor molecules. We hypothesize that those dynamics are either indicative, or perhaps the initial source, of structural dynamics that ultimately contribute to solar cell operation.
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Affiliation(s)
- Zachary T Armstrong
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Miriam Bohlmann Kunz
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Martin T Zanni
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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