Article
Chemistry, Multidisciplinary
Xiao Wang, Ruojie Sha, William B. Knowlton, Nadrian C. Seeman, James W. Canary, Bernard Yurke
Summary: A chiral dimer of an organic semiconductor was created by assembling an octamer of polyaniline with DNA. The dimer showed easy reconfiguration between its monomeric and dimeric forms. Experimental and theoretical studies were conducted to examine the dimer's geometry and the exciton coupling between its molecules. Protonic doping allowed for easy switching between different electronic states, and the dimer exhibited a Davydov splitting similar to DNA-dye systems with strong transition dipoles. This research provides a possible platform for studying the fundamental properties of organic semiconductors with DNAtemplated assemblies, which have potential applications in artificial light-harvesting systems and excitonic devices.
Article
Biochemistry & Molecular Biology
Shibani Basu, Keitel Cervantes-Salguero, Bernard Yurke, William B. Knowlton, Jeunghoon Lee, Olga A. Mass
Summary: In this study, a DNA Holliday junction scaffold was used to investigate the relative positions of squaraine-labeled thymine modifiers and their correlation with excitonic coupling strength. Photocrosslinking between squaraine-labeled thymine modifiers was carried out, and the outcomes were evaluated. The study found that a combination of adjacent dimer configuration, strong dye-dye interactions, and an A-T neighboring base pair was necessary for high-yield photocrosslinking reactions.
Article
Chemistry, Physical
Olga A. Mass, Christopher K. Wilson, German Barcenas, Ewald A. Terpetschnig, Olena M. Obukhova, Olga S. Kolosova, Anatoliy L. Tatarets, Lan Li, Bernard Yurke, William B. Knowlton, Ryan D. Pensack, Jeunghoon Lee
Summary: This study investigates the influence of dye hydrophobicity on the strength of excitonic coupling in squaraine aggregates templated by DNA Holliday Junction. It shows a strong correlation between squaraine hydrophobicity and the strength of excitonic coupling, with dimers of dichloroindolenine squaraine exhibiting the strongest coupling strength. The research provides insights into how dye structures affect excitonic coupling in dye aggregates templated by DNA, offering guidance for the design of exciton-based materials and devices.
JOURNAL OF PHYSICAL CHEMISTRY C
(2022)
Article
Chemistry, Multidisciplinary
Matthew S. Barclay, Simon K. Roy, Jonathan S. Huff, Olga A. Mass, Daniel B. Turner, Christopher K. Wilson, Donald L. Kellis, Ewald A. Terpetschnig, Jeunghoon Lee, Paul H. Davis, Bernard Yurke, William B. Knowlton, Ryan D. Pensack
Summary: Molecular excitons play a crucial role in various fields such as light harvesting and organic electronics, with their structure and dynamics being influenced by molecular packing. The addition of rotaxane rings to squaraine dyes templated with DNA can result in an oblique packing arrangement with improved optical properties. This method may be beneficial for optimizing excitonic materials for applications ranging from solar energy conversion to quantum information science.
COMMUNICATIONS CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
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, Ryan D. Pensack
Summary: This study investigates the electronic structure and excited-state dynamics of DNA-templated molecular aggregates. The researchers found a new nonradiative decay pathway in the dimers, which may facilitate singlet fission. This is of great significance in the fields of energy conversion and quantum information.
Article
Chemistry, Physical
Yu-Chen Wei, Shin-Wei Shen, Cheng-Ham Wu, Ssu-Yu Ho, Zhiyun Zhang, Chih- Wu, Pi-Tai Chou
Summary: The study elucidates the mechanism of exciton delocalization in HJ aggregates through photophysical measurements and simulations of molecular crystals, providing important clues for further control of exciton delocalization in three-dimensional molecular solids.
JOURNAL OF PHYSICAL CHEMISTRY A
(2021)
Article
Chemistry, Physical
Rizalina Tama Saragi, Marcos Juanes, Cristobal Perez, Pablo Pinacho, Denis S. Tikhonov, Walther Caminati, Melanie Schnell, Alberto Lesarri
Summary: Jet-cooled broadband rotational spectroscopy was used to investigate the balance between pi-stacking and hydrogen-bonding interactions in the self-aggregation of thiophenol. Two different isomers were detected for the thiophenol dimer, with dispersion-controlled pi-stacked structures anchored by a long S-H center dot center dot center dot S sulfur hydrogen bond. The results highlight the relevance of substituent effects in modulating pi-stacking geometries and the role of the sulfur-centered hydrogen bonds.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Biochemistry & Molecular Biology
Austin Biaggne, Lawrence Spear, German Barcenas, Maia Ketteridge, Young C. Kim, Joseph S. Melinger, William B. Knowlton, Bernard Yurke, Lan Li
Summary: A computational workflow using machine learning, density functional theory, time-dependent density functional theory, and molecular dynamics was established to identify dyes with large transition dipole moments (mu) for excitonic applications. The results demonstrate the effectiveness of this workflow in developing new dyes for excitonic applications.
Article
Chemistry, Physical
Jonathan S. Huff, Sebastian A. Diaz, Matthew S. Barclay, Azhad U. Chowdhury, Matthew Chiriboga, Gregory A. Ellis, Divita Mathur, Lance K. Patten, Simon K. Roy, Aaron Sup, Austin Biaggne, Brian S. Rolczynski, Paul D. Cunningham, Lan Li, Jeunghoon Lee, Paul H. Davis, Bernard Yurke, William B. Knowlton, Igor L. Medintz, Daniel B. Turner, Joseph S. Melinger, Ryan D. Pensack
Summary: In this study, DNA Holliday junctions were used to assemble aggregates of different ratios of cyanine dyes Cy5 and Cy5.5, allowing control over the energy position of the absorption features. The assembled aggregates exhibited shorter excited-state lifetimes and quenched emission compared to the monomeric dyes. A purely electronic exciton theory model was used to describe the properties of the aggregates, and the potential advantages of an idealized J-aggregate based on Förster resonance energy transfer (FRET) were discussed.
JOURNAL OF PHYSICAL CHEMISTRY C
(2022)
Article
Chemistry, Multidisciplinary
German Barcenas, Austin Biaggne, Olga A. Mass, Christopher K. Wilson, Olena M. Obukhova, Olga S. Kolosova, Anatoliy L. Tatarets, Ewald Terpetschnig, Ryan D. Pensack, Jeunghoon Lee, William B. Knowlton, Bernard Yurke, Lan Li
Summary: Squaraine dyes, with their favorable electronic and photophysical properties, have attracted considerable attention recently. The impact of substituents on these properties can be studied through both experimental and theoretical methods, potentially providing a foundation for designing rules for excitonic applications.
Article
Chemistry, Multidisciplinary
Robin Bernhardt, Marick Manrho, Jennifer Zablocki, Lukas Rieland, Arne Lutzen, Manuela Schiek, Klaus Meerholz, Jingyi Zhu, Thomas L. C. Jansen, Jasper Knoester, Paul H. M. van Loosdrecht
Summary: By studying aggregated n-butyl anilino squaraines, we found that structural disorder affects the generation of red- and blue-shifted peaks, as well as the absence of photoluminescence in the aggregates.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Multidisciplinary
Sebastian A. Diaz, Gissela Pascual, Lance K. Patten, Simon K. Roy, Adam Meares, Matthew Chiriboga, Kimihiro Susumu, William B. Knowlton, Paul D. Cunningham, Divita Mathur, Bernard Yurke, Igor L. Medintz, Jeunghoon Lee, Joseph S. Melinger
Summary: Understanding and controlling exciton coupling in dye aggregates is important for potential applications such as coherent exciton devices, nanophotonics, and biosensing. DNA nanostructure templates provide a powerful modular approach. In this study, Cy5-R dyes were used to examine the formation and properties of 30 unique DNA templated homodimers, revealing the role of sterics and hydrophobicity in determining the orientation and coupling strength of the dimers.
Article
Chemistry, Physical
Ander Camiruaga, Rizalina Tama Saragi, Fernando Torres-Hernandez, Marcos Juanes, Imanol Usabiaga, Alberto Lesarri, Jose A. Fernandez
Summary: Gas-phase spectroscopic studies of alcohol clusters are important for understanding the influence of non-covalent interactions on molecular recognition and modeling supramolecular and biological chemical processes. In this study, a multi-methodological gas-phase approach combining microwave spectroscopy and mass-resolved electronic and vibrational laser spectroscopy was used to examine the role of the aliphatic side chain in the self-aggregation of aromatic alcohols. The results show that the conformational landscape of the clusters is shallow and multiple competing isomers are present, indicating a tendency for cyclic hydrogen bond structures during cluster growth.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Polymer Science
Hyuk Gu Yun, Hak-Won Nho, Se Gyo Han, Jun Sang Cho, Jieun Bang, Tae Woong Yoon, Jungho Mun, Jaebum Noh, Minyoung Jeong, Dong Hyeon Kim, Bora Kim, Hyeongjin Hwang, Mun Seok Jeong, Hansol Lee, Junsuk Rho, Boseok Kang, Jaehong Park, Joon I. Jang, Kilwon Cho, Oh-Hoon Kwon, Dongki Lee
Summary: This study investigates the effects of chain length and fluorination on the photophysics of push-pull conjugated polymer aggregates. It reveals that J-type excitons are induced more in ordered domains and provides insights into the formation of localized chain cross-linked points in the PBDB-T aggregates and the enhanced H-type excitonic couplings in the PM6 aggregates.
Article
Multidisciplinary Sciences
Tomas Malina, Rob Koehorst, David Bina, Jakub Psencik, Herbert van Amerongen
Summary: Chlorosomes, the main light-harvesting complexes of green photosynthetic bacteria adapted to low-light conditions, exhibit excitonic interactions and superradiance, enhancing the probability of excitation energy transfer.
SCIENTIFIC REPORTS
(2021)
Article
Chemistry, Physical
Matthew S. Barclay, Azhad U. Chowdhury, Austin Biaggne, Jonathan S. Huff, Nicholas D. Wright, Paul H. Davis, Lan Li, William B. Knowlton, Bernard Yurke, Ryan D. Pensack, Daniel B. Turner
Summary: DNA is a re-configurable, biological information-storage unit, but there is still much to learn about its heterogeneous structural dynamics. In this study, femtosecond, two-dimensional electronic spectroscopy is used to probe local conformations in different DNA samples. The analysis reveals a strong excitation-emission correlation in only the double-stranded DNA-Cy5 complex, indicating inhomogeneous broadening. Molecular dynamics simulations support the conclusion that this broadening is caused by a specific conformer found only in the double-stranded DNA-Cy5 complex. These insights will contribute to future studies on DNA's structural heterogeneity.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Sebastian A. Diaz, Gissela Pascual, Lance K. Patten, Simon K. Roy, Adam Meares, Matthew Chiriboga, Kimihiro Susumu, William B. Knowlton, Paul D. Cunningham, Divita Mathur, Bernard Yurke, Igor L. Medintz, Jeunghoon Lee, Joseph S. Melinger
Summary: Understanding and controlling exciton coupling in dye aggregates is important for potential applications such as coherent exciton devices, nanophotonics, and biosensing. DNA nanostructure templates provide a powerful modular approach. In this study, Cy5-R dyes were used to examine the formation and properties of 30 unique DNA templated homodimers, revealing the role of sterics and hydrophobicity in determining the orientation and coupling strength of the dimers.
Article
Biochemistry & Molecular Biology
German Barcenas, Austin Biaggne, Olga A. A. Mass, William B. B. Knowlton, Bernard Yurke, Lan Li
Summary: This study investigates the effects of dye-DNA interactions on excitonic coupling through molecular dynamics simulations. The results reveal that adjacent dimers exhibit stronger excitonic coupling and weaker dye-DNA interactions compared to transverse dimers. Furthermore, certain dyes with specific functional groups facilitate aggregate packing via hydrophobic effects, leading to enhanced excitonic coupling. This work provides a fundamental understanding of the impacts of dye-DNA interactions on aggregate orientation and excitonic coupling.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Physical
KatelynM. Duncan, Hannah M. Byers, Madaline E. Houdek, Simon K. Roy, Austin Biaggne, Matthew S. Barclay, Lance K. Patten, Jonathan S. Huff, Donald L. Kellis, Christopher K. Wilson, Jeunghoon Lee, Paul H. Davis, Olga A. Mass, Lan Li, Daniel B. Turner, John A. Hall, William B. Knowlton, Bernard Yurke, Ryan D. Pensack
Summary: In this study, the electronic structure and excited-state dynamics of monomers and aggregates of four asymmetric polymethine dyes templated via DNA were characterized. The asymmetric polymethine dye monomers exhibited large transition dipole moments (mu), appreciable static dipole moment differences (Delta d), and long excited-state lifetimes (tau(p)). Dye Dy 754 displayed the strongest propensity for aggregation and exciton delocalization, with promising values of the excitonic hopping parameter (J).
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Biochemistry & Molecular Biology
Maia Ketteridge, Austin Biaggne, Ryan Rau, German Barcenas, Olga A. Mass, William B. Knowlton, Bernard Yurke, Lan Li
Summary: Aggregates of organic dyes with excitonic coupling have wide applications in medical imaging, organic photovoltaics, and quantum information devices. This study investigates the effects of substituent location on the properties of squaraine (SQ) dye aggregates using density functional theory (DFT) and time-dependent density functional theory (TD-DFT). The results provide insights into the structure-property relationships and guide the design of dye monomers for desired performance.
Article
Multidisciplinary Sciences
Franky Djutanta, Peter T. Brown, Bonfilio Nainggolan, Alexis Coullomb, Sritharini Radhakrishnan, Jason Sentosa, Bernard Yurke, Rizal F. Hariadi, Douglas P. Shepherd
Summary: The hydrodynamic properties of bacteria's helical-shaped propellers, which drive their complex motility, have never been directly measured. To solve this problem, a dual statistical viewpoint is adopted, connecting to the hydrodynamics through the fluctuation-dissipation theorem (FDT). By regarding the propellers as colloidal particles, their Brownian fluctuations are characterized, and a measurement is performed using high-resolution oblique plane microscopy. The results provide a direct measurement of the propulsion matrix of a microhelix, revealing the inefficiency of the flagella as propellers.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Shibani Basu, Simon K. Roy, German Barcenas, Lan Li, Bernard Yurke, William B. Knowlton, Jeunghoon Lee
Summary: Programmable self-assembly of dyes using DNA templates to promote exciton delocalization in dye aggregates is gaining interest. This study focuses on improving the stability of DNA-scaffolded dye aggregates through photo-cross-linking reactions between thymines. By evaluating the cross-linking yield of dye-DNA aggregates with different linker lengths, it is found that shorter interstrand distances between thymines result in higher cross-linking yield. This method has the potential to enhance the stability of DNA-scaffolded dye aggregates for various exciton-based applications.
Article
Instruments & Instrumentation
J. S. Huff, K. M. Duncan, C. J. van Galen, M. S. Barclay, W. B. Knowlton, B. Yurke, P. H. Davis, D. B. Turner, R. J. Stanley, R. D. Pensack
Summary: Developmental details of a high-sensitivity Stark absorption spectrometer with a laser-driven light source are reported. The spectrometer exhibits minimal intensity fluctuations, drift, and 1/f noise, with additional features of balanced detection and multiplex sampling. Measurements show low noise amplitudes.
REVIEW OF SCIENTIFIC INSTRUMENTS
(2023)
Article
Optics
Bernard Yurke, Richard Elliott, Aaron Sup
Summary: Frenkel excitons are of interest for ultrafast switching applications due to their femtosecond timescale coherent excitation transfer between chromophores. The Frenkel Hamiltonian, which governs the exciton dynamics, belongs to a class of Hamiltonians that enable universal quantum computation. Therefore, it is important to determine how a complete set of exciton-based gates can be constructed using chromophore aggregates.
Article
Chemistry, Physical
Olga A. Mass, Devan R. Watt, Lance K. Patten, Ryan D. Pensack, Jeunghoon Lee, Daniel B. Turner, Bernard Yurke, William B. Knowlton
Summary: Exciton delocalization can be achieved in a synthetic bacteriochlorin (BC) dimer covalently templated by DNA, demonstrating the potential for facile engineering of exciton-based systems. The synthesized BC dimer showed similar spectral properties to the natural Bchla dimer, indicating successful exciton delocalization.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Olga A. Mass, Devan R. Watt, Lance K. Patten, Ryan D. Pensack, Jeunghoon Lee, Daniel B. Turner, Bernard Yurke, William B. Knowlton
Summary: We demonstrate exciton delocalization in a synthetic bacteriochlorin dimer covalently templated by DNA, which lacks the pigment-protein interactions critical for natural Bchla dimer. The synthetic dimer shows spectral properties similar to natural Bchla and has potential applications in exciton-based systems.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Nicholas D. Wright, Jonathan S. Huff, Matthew S. Barclay, Christopher K. Wilson, German Barcenas, Katelyn M. Duncan, Maia Ketteridge, Olena M. Obukhova, Alexander I. Krivoshey, Anatoliy L. Tatarets, Ewald A. Terpetschnig, Jacob C. Dean, William B. Knowlton, Bernard Yurke, Lan Li, Olga A. Mass, Paul H. Davis, Jeunghoo Lee, Daniel B. Turner, Ryan D. Pensack
Summary: Molecular (dye) aggregates are a materials platform of interest in various fields, and this study characterizes the properties of certain asymmetric squaraine dyes and suggests strategies to enhance their interaction.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Review
Chemistry, Multidisciplinary
Divita Mathur, Sebastian A. Diaz, Niko Hildebrandt, Ryan D. Pensack, Bernard Yurke, Austin Biaggne, Lan Li, Joseph S. Melinger, Mario G. Ancona, William B. Knowlton, Igor L. Medintz
Summary: DNA nanotechnology enables the self-assembly of 3D nanoscale structures, with potential applications in various fields. These structures can be modified and used as optical substrates. Dynamic DNA structures have the ability to reconfigure and change their properties, allowing for multiple applications.
CHEMICAL SOCIETY REVIEWS
(2023)