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Excitons in Molecular Aggregates

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A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Physical Chemistry".

Deadline for manuscript submissions: closed (28 February 2023) | Viewed by 9489

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Dr. Daniel B. Turner

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Guest Editor

Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA
Interests: femtosecond time-resolved spectroscopy; nonadiabatic dynamics; many-body interactions; molecular excitons

Dr. Lan Li

E-Mail Website
Guest Editor

Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA
Interests: computational materials science; machine learning development and applications; organic molecules; electronic and energy applications
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Special Issue Information

Dear Colleagues,

A molecular aggregate is a collection of organic dye molecules held in close proximity. In many cases, chromophores are strongly bound to a macromolecular scaffold such as a protein via covalent bonds, and in other cases, molecules are bound by weaker van der Waals forces. Electronic interactions among chromophores often lead to excitons, which are collective excitations delocalized over multiple chromophores. The same electronic interactions can lead to electronic energy transfer. These characteristics have made excitons in molecular aggregates attractive for potential application in quantum-information and solar-energy devices. Nonetheless, fundamental questions remain about how tight synthetic control of the molecular or supramolecular structures can be used to tailor the electronic and vibrational environment of the excitons.

This Special Issue explores how computational, theoretical, and laboratory measurement studies can be used to yield a comprehensive understanding of excitons in molecular aggregates, including natural biological complexes and tailored synthetic systems. Both original research articles and reviews in the field are welcome.

Dr. Daniel B. Turner
Dr. Lan Li
Guest Editors

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Keywords

Molecular aggregate
Photosynthetic complex
Frenkel exciton
Electronic energy transfer
H-aggregate and J-aggregate

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Published Papers (4 papers)

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Research

12 pages, 3461 KiB

Open AccessArticle

Multifaceted Excited State Dynamics of Coumarin Dyes Anchored on Al₂O₃ Film

by Hyun Seok Lee, Yun Jeong Na, Chul Hoon Kim and Jae Yoon Shin

Molecules 2023, 28(1), 111; https://doi.org/10.3390/molecules28010111 - 23 Dec 2022

Cited by 1 | Viewed by 1375

Abstract

The co-facially stacked dyes on semiconductor films serve as an alternative model to elucidate the photo-driven exciton dynamics occurring in a molecular assembly. In this study, we report the unique emission properties of coumarin dye adsorbed on the surface of the semiconductor film, measured by ultrafast time-resolved fluorescence. When a rigid coumarin derivative, 7-hydroxycoumarin-3-carboxylic acid (OHCCA), is anchored on the Al₂O₃ film, the dye manifests dual emissions from the two lowest excited states. Various anchoring modes of a carboxylic acid group on the Al₂O₃ surface are invoked to account for the unusual emission process. Additionally, we identified characteristic transition dipole interactions in the well-stacked dye aggregates, which leads to discernible excitonic splitting in the electronic transitions. Femtosecond time-resolved fluorescence reveals that the excimer formation in the aggregate occurs with the time constant of 550 fs. Picosecond time-resolved emission spectra confirm the subsequent structural relaxations of the nascent excimer. The enhanced transition dipole via the electronic coupling between OHCCA and metal oxide can be responsible for the dual emission and the ultrafast excimer formation. Full article

(This article belongs to the Special Issue Excitons in Molecular Aggregates)

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18 pages, 2670 KiB

Open AccessFeature PaperArticle

Symmetry Breaking Charge Transfer in DNA-Templated Perylene Dimer Aggregates

by Katelyn M. Duncan, Donald L. Kellis, Jonathan S. Huff, Matthew S. Barclay, Jeunghoon Lee, Daniel B. Turner, Paul H. Davis, Bernard Yurke, William B. Knowlton and Ryan D. Pensack

Molecules 2022, 27(19), 6612; https://doi.org/10.3390/molecules27196612 - 5 Oct 2022

Cited by 5 | Viewed by 2511

Abstract

Molecular aggregates are of interest to a broad range of fields including light harvesting, organic optoelectronics, and nanoscale computing. In molecular aggregates, nonradiative decay pathways may emerge that were not present in the constituent molecules. Such nonradiative decay pathways may include singlet fission, excimer relaxation, and symmetry-breaking charge transfer. Singlet fission, sometimes referred to as excitation multiplication, is of great interest to the fields of energy conversion and quantum information. For example, endothermic singlet fission, which avoids energy loss, has been observed in covalently bound, linear perylene trimers and tetramers. In this work, the electronic structure and excited-state dynamics of dimers of a perylene derivative templated using DNA were investigated. Specifically, DNA Holliday junctions were used to template the aggregation of two perylene molecules covalently linked to a modified uracil nucleobase through an ethynyl group. The perylenes were templated in the form of monomer, transverse dimer, and adjacent dimer configurations. The electronic structure of the perylene monomers and dimers were characterized via steady-state absorption and fluorescence spectroscopy. Initial insights into their excited-state dynamics were gleaned from relative fluorescence intensity measurements, which indicated that a new nonradiative decay pathway emerges in the dimers. Femtosecond visible transient absorption spectroscopy was subsequently used to elucidate the excited-state dynamics. A new excited-state absorption feature grows in on the tens of picosecond timescale in the dimers, which is attributed to the formation of perylene anions and cations resulting from symmetry-breaking charge transfer. Given the close proximity required for symmetry-breaking charge transfer, the results shed promising light on the prospect of singlet fission in DNA-templated molecular aggregates. Full article

(This article belongs to the Special Issue Excitons in Molecular Aggregates)

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15 pages, 2380 KiB

Open AccessArticle

Photocrosslinking Probes Proximity of Thymine Modifiers Tethering Excitonically Coupled Dye Aggregates to DNA Holliday Junction

by Shibani Basu, Keitel Cervantes-Salguero, Bernard Yurke, William B. Knowlton, Jeunghoon Lee and Olga A. Mass

Molecules 2022, 27(13), 4006; https://doi.org/10.3390/molecules27134006 - 22 Jun 2022

Cited by 6 | Viewed by 2130

Abstract

A DNA Holliday junction (HJ) has been used as a versatile scaffold to create a variety of covalently templated molecular dye aggregates exhibiting strong excitonic coupling. In these dye-DNA constructs, one way to attach dyes to DNA is to tether them via single long linkers to thymine modifiers incorporated in the core of the HJ. Here, using photoinduced [2 + 2] cycloaddition (photocrosslinking) between thymines, we investigated the relative positions of squaraine-labeled thymine modifiers in the core of the HJ, and whether the proximity of thymine modifiers correlated with the excitonic coupling strength in squaraine dimers. Photocrosslinking between squaraine-labeled thymine modifiers was carried out in two distinct types of configurations: adjacent dimer and transverse dimer. The outcomes of the reactions in terms of relative photocrosslinking yields were evaluated by denaturing polyacrylamide electrophoresis. We found that for photocrosslinking to occur at a high yield, a synergetic combination of three parameters was necessary: adjacent dimer configuration, strong attractive dye–dye interactions that led to excitonic coupling, and an A-T neighboring base pair. The insight into the proximity of dye-labeled thymines in adjacent and transverse configurations correlated with the strength of excitonic coupling in the corresponding dimers. To demonstrate a utility of photocrosslinking, we created a squaraine tetramer templated by a doubly crosslinked HJ with increased thermal stability. These findings provide guidance for the design of HJ-templated dye aggregates exhibiting strong excitonic coupling for exciton-based applications such as organic optoelectronics and quantum computing. Full article

(This article belongs to the Special Issue Excitons in Molecular Aggregates)

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20 pages, 4231 KiB

Open AccessArticle

Data-Driven and Multiscale Modeling of DNA-Templated Dye Aggregates

by Austin Biaggne, Lawrence Spear, German Barcenas, Maia Ketteridge, Young C. Kim, Joseph S. Melinger, William B. Knowlton, Bernard Yurke and Lan Li

Molecules 2022, 27(11), 3456; https://doi.org/10.3390/molecules27113456 - 27 May 2022

Cited by 7 | Viewed by 2538

Abstract

Dye aggregates are of interest for excitonic applications, including biomedical imaging, organic photovoltaics, and quantum information systems. Dyes with large transition dipole moments (

μ

) are necessary to optimize coupling within dye aggregates. Extinction coefficients (

ε

) can be used to [...] Read more.

Dye aggregates are of interest for excitonic applications, including biomedical imaging, organic photovoltaics, and quantum information systems. Dyes with large transition dipole moments (

μ

) are necessary to optimize coupling within dye aggregates. Extinction coefficients (

ε

) can be used to determine the

μ

of dyes, and so dyes with a large

ε

(>150,000 M⁻¹cm⁻¹) should be engineered or identified. However, dye properties leading to a large

ε

are not fully understood, and low-throughput methods of dye screening, such as experimental measurements or density functional theory (DFT) calculations, can be time-consuming. In order to screen large datasets of molecules for desirable properties (i.e., large

ε

and

μ

), a computational workflow was established using machine learning (ML), DFT, time-dependent (TD-) DFT, and molecular dynamics (MD). ML models were developed through training and validation on a dataset of 8802 dyes using structural features. A Classifier was developed with an accuracy of 97% and a Regressor was constructed with an

R^{2}

of above 0.9, comparing between experiment and ML prediction. Using the Regressor, the

ε

values of over 18,000 dyes were predicted. The top 100 dyes were further screened using DFT and TD-DFT to identify 15 dyes with a

μ

relative to a reference dye, pentamethine indocyanine dye Cy5. Two benchmark MD simulations were performed on Cy5 and Cy5.5 dimers, and it was found that MD could accurately capture experimental results. The results of this study exhibit that our computational workflow for identifying dyes with a large

μ

for excitonic applications is effective and can be used as a tool to develop new dyes for excitonic applications. Full article

(This article belongs to the Special Issue Excitons in Molecular Aggregates)

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