1
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Rilievo G, Cecconello A, Fouladi Ghareshiran N, Magro M, Simmel FC, Vianello F. Integration of DNA-RNA-triplex-based regulation of transcription into molecular logic gates. FEBS Lett 2023; 597:2461-2472. [PMID: 37591635 DOI: 10.1002/1873-3468.14721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/07/2023] [Accepted: 08/08/2023] [Indexed: 08/19/2023]
Abstract
In recent years, increasing numbers of noncoding RNA molecules were identified as possible components of endogenous DNA-RNA hybrid triplexes involved in gene regulation. Triplexes are potentially involved in complex molecular signaling networks that, if understood, would allow the engineering of biological computing components. Here, by making use of the enhancing and inhibiting effects of such triplexes, we demonstrate in vitro the construction of triplex-based molecular gates: 'exclusive OR' (XOR), 'exclusive NOT-OR' (XNOR), and a threshold gate, via transcription of a fluorogenic RNA aptamer. Precise modulation was displayed by the biomolecular-integrated systems over a wide interval of transcriptional outputs, ranging from drastic inhibition to significant enhancement. The present contribution represents a first example of molecular gates developed using DNA-RNA triplex nanostructures.
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Affiliation(s)
- Graziano Rilievo
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Italy
| | - Alessandro Cecconello
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Italy
| | | | - Massimiliano Magro
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Italy
| | - Friedrich C Simmel
- Physik Department, Technische Universitat München, Garching bei München, Germany
| | - Fabio Vianello
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Italy
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2
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Bruschi M, Bolzonello L, Gallina F, Fresch B. Unifying Nonlinear Response and Incoherent Mixing in Action-2D Electronic Spectroscopy. J Phys Chem Lett 2023; 14:6872-6879. [PMID: 37490770 PMCID: PMC10405272 DOI: 10.1021/acs.jpclett.3c01670] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 07/20/2023] [Indexed: 07/27/2023]
Abstract
Action-detection has expanded the scope and applicability of 2D electronic spectroscopy, while posing new challenges for the unambiguous interpretation of spectral features. In this context, identifying the origin of cross-peaks at early waiting times is not trivial, and incoherent mixing is often invoked as an unwanted contribution masking the nonlinear signal. In this work, we elaborate on the relation between the nonlinear response and the incoherent mixing contribution by analyzing the action signal in terms of one- and two-particle observables. Considering a weakly interacting molecular dimer, we show how cross-peaks at early waiting times, reflecting exciton-exciton annihilation dynamics, can be equivalently interpreted as arising from incoherent mixing. This equivalence, on the one hand, highlights the information content of spectral features related to incoherent mixing and, on the other hand, provides an efficient numerical scheme to simulate the action response of weakly interacting systems.
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Affiliation(s)
- Matteo Bruschi
- Dipartimento
di Scienze Chimiche, Università degli
Studi di Padova, via Marzolo 1, Padua 35131, Italy
| | - Luca Bolzonello
- ICFO
- Institut de Ciencies Fotoniques, The Barcelona
Institute of Science and Technology, Castelldefels, Barcelona 08860, Spain
| | - Federico Gallina
- Dipartimento
di Scienze Chimiche, Università degli
Studi di Padova, via Marzolo 1, Padua 35131, Italy
| | - Barbara Fresch
- Dipartimento
di Scienze Chimiche, Università degli
Studi di Padova, via Marzolo 1, Padua 35131, Italy
- Padua
Quantum Technologies Research Center, Università
degli Studi di Padova, Padua 35131, Italy
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3
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Hart SM, Gorman J, Bathe M, Schlau-Cohen GS. Engineering Exciton Dynamics with Synthetic DNA Scaffolds. Acc Chem Res 2023; 56:2051-2061. [PMID: 37345736 DOI: 10.1021/acs.accounts.3c00086] [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: 06/23/2023]
Abstract
Excitons are the molecular-scale currency of electronic energy. Control over excitons enables energy to be directed and harnessed for light harvesting, electronics, and sensing. Excitonic circuits achieve such control by arranging electronically active molecules to prescribe desired spatiotemporal dynamics. Photosynthetic solar energy conversion is a canonical example of the power of excitonic circuits, where chromophores are positioned in a protein scaffold to perform efficient light capture, energy transport, and charge separation. Synthetic systems that aim to emulate this functionality include self-assembled aggregates, molecular crystals, and chromophore-modified proteins. While the potential of this approach is clear, these systems lack the structural precision to control excitons or even test the limits of their power. In recent years, DNA origami has emerged as a designer material that exploits biological building blocks to construct nanoscale architectures. The structural precision afforded by DNA origami has enabled the pursuit of naturally inspired organizational principles in a highly precise and scalable manner. In this Account, we describe recent developments in DNA-based platforms that spatially organize chromophores to construct tunable excitonic systems. The high fidelity of DNA base pairing enables the formation of programmable nanoscale architectures, and sequence-specific placement allows for the precise positioning of chromophores within the DNA structure. The integration of a wide range of chromophores across the visible spectrum introduces spectral tunability. These excitonic DNA-chromophore assemblies not only serve as model systems for light harvesting, solar conversion, and sensing but also lay the groundwork for the integration of coupled chromophores into larger-scale nucleic acid architectures.We have used this approach to generate DNA-chromophore assemblies of strongly coupled delocalized excited states through both sequence-specific self-assembly and the covalent attachment of chromophores. These strategies have been leveraged to independently control excitonic coupling and system-bath interaction, which together control energy transfer. We then extended this framework to identify how scaffold configurations can steer the formation of symmetry-breaking charge transfer states, paving the way toward the design of dual light-harvesting and charge separation DNA machinery. In an orthogonal application, we used the programmability of DNA chromophore assemblies to change the optical emission properties of strongly coupled dimers, generating a series of fluorophore-modified constructs with separable emission properties for fluorescence assays. Upcoming advances in the chemical modification of nucleotides, design of large-scale DNA origami, and predictive computational methods will aid in constructing excitonic assemblies for optical and computing applications. Collectively, the development of DNA-chromophore assemblies as a platform for excitonic circuitry offers a pathway to identifying and applying design principles for light harvesting and molecular electronics.
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Affiliation(s)
- Stephanie M Hart
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jeffrey Gorman
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Gabriela S Schlau-Cohen
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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4
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Nandi S, Coane C, Villegas AE, Ray A, Di Felice R. The impact of G-quadruplex dynamics on inter-tetrad electronic couplings: a hybrid computational study. Phys Chem Chem Phys 2022; 24:22513-22522. [PMID: 36106845 DOI: 10.1039/d2cp03505g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The G-quadruplex is a fascinating nucleic acid motif with implications in biology, medicine, and nanotechnologies. G-quadruplexes can form in the telomeres at the edges of chromosomes and in other guanine-rich regions of the genome. They can also be engineered for exploitation as biological materials for nanodevices. Their higher stiffness and higher charge transfer rates make them better candidates in nanodevices than duplex DNA. For the development of molecular nanowires, it is important to optimize electron transport along the wire axis. One powerful basis to do so is by manipulating the structure, based on known effects that structural changes have on electron transport. Here, we investigate such effects, by a combination of classical simulations of the structure and dynamics and quantum calculations of electronic couplings. We find that this structure-function relationship is complex. A single helix shape parameter alone does not embody such complexity, but rather a combination of distances and angles between stacked bases influences charge transfer efficiency. By analyzing linear combinations of shape descriptors for different topologies, we identify the structural features that most affect charge transfer efficiency. We discuss the transferability of the proposed model and the limiting effects of inherent flexibility.
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Affiliation(s)
- Samprita Nandi
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089, USA.
| | - Colin Coane
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089, USA.
| | - Angel-Emilio Villegas
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089, USA.
| | - Angana Ray
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089, USA.
| | - Rosa Di Felice
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089, USA. .,Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.,CNR Institute of Nanoscience, 41125 Modena, Italy
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5
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Lu SY, Zuehlsdorff TJ, Hong H, Aguirre VP, Isborn CM, Shi L. The Influence of Electronic Polarization on Nonlinear Optical Spectroscopy. J Phys Chem B 2021; 125:12214-12227. [PMID: 34726915 DOI: 10.1021/acs.jpcb.1c05914] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The environment surrounding a chromophore can dramatically affect the energy absorption and relaxation process, as manifested in optical spectra. Simulations of nonlinear optical spectroscopy, such as two-dimensional electronic spectroscopy (2DES) and transient absorption (TA), will be influenced by the computational model of the environment. We here compare a fixed point charge molecular mechanics model and a quantum mechanical (QM) model of the environment in computed 2DES and TA spectra of Nile red in water and the chromophore of photoactive yellow protein (PYP) in water and protein environments. In addition to simulating these nonlinear optical spectra, we directly juxtapose the computed excitation energy correlation function to the dynamic Stokes shift function often used to analyze environment dynamics. Overall, we find that for the three systems studied here the mutual electronic polarization provided by the QM environment manifests in broader 2DES signals, as well as a larger reorganization energy and a larger static Stokes shift due to stronger coupling between the chromophore and the environment.
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Affiliation(s)
- Shao-Yu Lu
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Tim J Zuehlsdorff
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, United States
| | - Hanbo Hong
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Vincent P Aguirre
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Christine M Isborn
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Liang Shi
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
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6
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Dovzhenko D, Lednev M, Mochalov K, Vaskan I, Rakovich Y, Karaulov A, Nabiev I. Polariton-assisted manipulation of energy relaxation pathways: donor-acceptor role reversal in a tuneable microcavity. Chem Sci 2021; 12:12794-12805. [PMID: 34703566 PMCID: PMC8494027 DOI: 10.1039/d1sc02026a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 08/29/2021] [Indexed: 11/21/2022] Open
Abstract
Resonant interaction between excitonic transitions of molecules and localized electromagnetic field allows the formation of hybrid light-matter polaritonic states. This hybridization of the light and the matter states has been shown to significantly alter the intrinsic properties of molecular ensembles placed inside the optical cavity. Here, we have observed strong coupling of excitonic transition in a pair of closely located organic dye molecules demonstrating an efficient donor-to-acceptor resonance energy transfer with the mode of a tuneable open-access cavity. Analysing the dependence of the relaxation pathways between energy states in this system on the cavity detuning, we have demonstrated that predominant strong coupling of the cavity photon to the exciton transition in the donor dye molecule can lead not only to an increase in the donor-acceptor energy transfer, but also to an energy shift large enough to cause inversion between the energy states of the acceptor and the mainly donor lower polariton energy state. Furthermore, we have shown that the polariton-assisted donor-acceptor chromophores' role reversal or "carnival effect" not only changes the relative energy levels of the donor-acceptor pair, but also makes it possible to manipulate the energy flow in the systems with resonant dipole-dipole interaction and direct energy transfer from the acceptor to the mainly donor lower polariton state. Our experimental data are the first confirmation of the theoretically predicted possibility of polariton-assisted energy transfer reversal in FRET systems, thus paving the way to new avenues in FRET-imaging, remote-controlled chemistry, and all-optical switching.
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Affiliation(s)
- Dmitriy Dovzhenko
- National Research Nuclear University MEPhI (Moscow Engineering Physics Institute) 115409 Moscow Russia .,Department of Physics and Astronomy, University of Southampton Southampton SO17 1BJ UK
| | - Maksim Lednev
- National Research Nuclear University MEPhI (Moscow Engineering Physics Institute) 115409 Moscow Russia
| | - Konstantin Mochalov
- National Research Nuclear University MEPhI (Moscow Engineering Physics Institute) 115409 Moscow Russia .,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences 117997 Moscow Russia
| | - Ivan Vaskan
- National Research Nuclear University MEPhI (Moscow Engineering Physics Institute) 115409 Moscow Russia .,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences 117997 Moscow Russia.,Moscow Institute of Physics and Technology Dolgoprudny 141701 Moscow Russia
| | - Yury Rakovich
- IKERBASQUE, Basque Foundation for Science 48009 Bilbao Spain.,Donostia International Physics Center, Polímeros y Materiales Avanzados: Física, Química y Tecnología, UPV-EHU, Centro de Física de Materiales (MPC, CSIC-UPV/EHU) 20018 Donostia - San Sebastian Spain
| | - Alexander Karaulov
- Sechenov First Moscow State Medical University (Sechenov University) 119146 Moscow Russia
| | - Igor Nabiev
- National Research Nuclear University MEPhI (Moscow Engineering Physics Institute) 115409 Moscow Russia .,Sechenov First Moscow State Medical University (Sechenov University) 119146 Moscow Russia.,Laboratoire de Recherche en Nanosciences, LRN-EA4682, Université de Reims Champagne-Ardenne 51100 Reims France
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7
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Trapani M, Castriciano MA, Collini E, Bella G, Cordaro M. Supramolecular BODIPY based dimers: synthesis, computational and spectroscopic studies. Org Biomol Chem 2021; 19:8118-8127. [PMID: 34473180 DOI: 10.1039/d1ob01433a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synthetic procedures for the preparation of supramolecular BODIPY dimers decorated with complementary patterns able to induce the formation of a triple hydrogen bond through mutual interactions are here reported. The BODIPY and styryl-equipped BODIPY species have been suitably functionalized in meso position with 2,6-diacetamido-4-pyridyl and 1-butyl-6-uracyl moieties. Dimers and monomers have been subjected to computational and photophysical investigations in solvent media. Various peculiarities concerning the effects of the interaction geometry on the stability of the H-bonded systems have also been investigated. The combination of modelling and experimental data provides a paradigm for improving and refining the BODIPY synthetic pathway to have chromophoric architectures with a programmable supramolecular identity. Furthermore, the possibility of assembling dimers of different dyes through H-bonds could be appealing for a systematic investigation of the principal factors affecting the dynamics of the energy migration and possibly driving coherent transfer mechanisms. Our work highlights how the chemical versatility of these dyes can be exploited to design new BODIPY-based supramolecular architectures.
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Affiliation(s)
- Mariachiara Trapani
- CNR-ISMN, Istituto per lo Studio dei Materiali Nanostrutturati, c/o Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, V.le F. Stagno D'Alcontres 31, 98166, University of Messina, Messina, Italy
| | - Maria Angela Castriciano
- CNR-ISMN, Istituto per lo Studio dei Materiali Nanostrutturati, c/o Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, V.le F. Stagno D'Alcontres 31, 98166, University of Messina, Messina, Italy
| | - Elisabetta Collini
- Dipartimento di Scienze Chimiche, Università di Padova, via Marzolo 1, 35131 Padova, Italy
| | - Giovanni Bella
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, V.le F. Stagno D'Alcontres 31, 98166, University of Messina, Messina, Italy.
| | - Massimiliano Cordaro
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, V.le F. Stagno D'Alcontres 31, 98166, University of Messina, Messina, Italy.
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8
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Collini E. 2D Electronic Spectroscopic Techniques for Quantum Technology Applications. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2021; 125:13096-13108. [PMID: 34276867 PMCID: PMC8282191 DOI: 10.1021/acs.jpcc.1c02693] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/22/2021] [Indexed: 05/14/2023]
Abstract
2D electronic spectroscopy (2DES) techniques have gained particular interest given their capability of following ultrafast coherent and noncoherent processes in real-time. Although the fame of 2DES is still majorly linked to the investigation of energy and charge transport in biological light-harvesting complexes, 2DES is now starting to be recognized as a particularly valuable tool for studying transport processes in artificial nanomaterials and nanodevices. Particularly meaningful is the possibility of assessing coherent mechanisms active in the transport of excitation energy in these materials toward possible quantum technology applications. The diverse nature of these new target samples poses significant challenges and calls for a critical rethinking of the technique and its different realizations. With the confluence of promising new applications and rapidly developing technical capabilities, the enormous potential of 2DES techniques to impact the field of nanosystems, quantum technologies, and quantum devices is here delineated.
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Affiliation(s)
- Elisabetta Collini
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131 Padova, Italy
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9
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Zuehlsdorff TJ, Shedge SV, Lu SY, Hong H, Aguirre VP, Shi L, Isborn CM. Vibronic and Environmental Effects in Simulations of Optical Spectroscopy. Annu Rev Phys Chem 2021; 72:165-188. [DOI: 10.1146/annurev-physchem-090419-051350] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Including both environmental and vibronic effects is important for accurate simulation of optical spectra, but combining these effects remains computationally challenging. We outline two approaches that consider both the explicit atomistic environment and the vibronic transitions. Both phenomena are responsible for spectral shapes in linear spectroscopy and the electronic evolution measured in nonlinear spectroscopy. The first approach utilizes snapshots of chromophore-environment configurations for which chromophore normal modes are determined. We outline various approximations for this static approach that assumes harmonic potentials and ignores dynamic system-environment coupling. The second approach obtains excitation energies for a series of time-correlated snapshots. This dynamic approach relies on the accurate truncation of the cumulant expansion but treats the dynamics of the chromophore and the environment on equal footing. Both approaches show significant potential for making strides toward more accurate optical spectroscopy simulations of complex condensed phase systems.
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Affiliation(s)
- Tim J. Zuehlsdorff
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
| | - Sapana V. Shedge
- Department of Chemistry and Chemical Biology, University of California, Merced, California 95343, USA
| | - Shao-Yu Lu
- Department of Chemistry and Chemical Biology, University of California, Merced, California 95343, USA
| | - Hanbo Hong
- Department of Chemistry and Chemical Biology, University of California, Merced, California 95343, USA
| | - Vincent P. Aguirre
- Department of Chemistry and Chemical Biology, University of California, Merced, California 95343, USA
| | - Liang Shi
- Department of Chemistry and Chemical Biology, University of California, Merced, California 95343, USA
| | - Christine M. Isborn
- Department of Chemistry and Chemical Biology, University of California, Merced, California 95343, USA
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10
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Hart SM, Chen WJ, Banal JL, Bricker WP, Dodin A, Markova L, Vyborna Y, Willard AP, Häner R, Bathe M, Schlau-Cohen GS. Engineering couplings for exciton transport using synthetic DNA scaffolds. Chem 2021. [DOI: 10.1016/j.chempr.2020.12.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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11
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Cunningham PD, Díaz SA, Yurke B, Medintz IL, Melinger JS. Delocalized Two-Exciton States in DNA Scaffolded Cyanine Dimers. J Phys Chem B 2020; 124:8042-8049. [PMID: 32706583 DOI: 10.1021/acs.jpcb.0c06732] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The engineering and manipulation of delocalized molecular exciton states is a key component for artificial biomimetic light harvesting complexes as well as alternative circuitry platforms based on exciton propagation. Here we examine the consequences of strong electronic coupling in cyanine homodimers on DNA duplex scaffolds. The most closely spaced dyes, attached to positions directly across the double-helix from one another, exhibit pronounced Davydov splitting due to strong electronic coupling. We demonstrate that the DNA scaffold is sufficiently robust to support observation of the transition from the lowest energy (J-like) one-exciton state to the nonlocal two-exciton state, where each cyanine dye is in the excited state. This transition proceeds via sequential photon absorption and persists for the lifetime of the exciton, establishing this as a controlled method for creating two-exciton states. Our observations suggest that DNA-organized dye networks have potential as platforms for molecular logic gates and entangled photon emission based on delocalized two-exciton states.
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Affiliation(s)
- Paul D Cunningham
- U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Sebastián A Díaz
- U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Bernard Yurke
- Boise State University, Boise, Idaho 83725, United States
| | - Igor L Medintz
- U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Joseph S Melinger
- U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
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12
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Sohail SH, Otto JP, Cunningham PD, Kim YC, Wood RE, Allodi MA, Higgins JS, Melinger JS, Engel GS. DNA scaffold supports long-lived vibronic coherence in an indodicarbocyanine (Cy5) dimer. Chem Sci 2020; 11:8546-8557. [PMID: 34123114 PMCID: PMC8163443 DOI: 10.1039/d0sc01127d] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Vibronic coupling between pigment molecules is believed to prolong coherences in photosynthetic pigment–protein complexes. Reproducing long-lived coherences using vibronically coupled chromophores in synthetic DNA constructs presents a biomimetic route to efficient artificial light harvesting. Here, we present two-dimensional (2D) electronic spectra of one monomeric Cy5 construct and two dimeric Cy5 constructs (0 bp and 1 bp between dyes) on a DNA scaffold and perform beating frequency analysis to interpret observed coherences. Power spectra of quantum beating signals of the dimers reveal high frequency oscillations that correspond to coherences between vibronic exciton states. Beating frequency maps confirm that these oscillations, 1270 cm−1 and 1545 cm−1 for the 0-bp dimer and 1100 cm−1 for the 1-bp dimer, are coherences between vibronic exciton states and that these coherences persist for ∼300 fs. Our observations are well described by a vibronic exciton model, which predicts the excitonic coupling strength in the dimers and the resulting molecular exciton states. The energy spacing between those states closely corresponds to the observed beat frequencies. MD simulations indicate that the dyes in our constructs lie largely internal to the DNA base stacking region, similar to the native design of biological light harvesting complexes. Observed coherences persist on the timescale of photosynthetic energy transfer yielding further parallels to observed biological coherences, establishing DNA as an attractive scaffold for synthetic light harvesting applications. Dyes coupled to DNA display distance-dependent vibronic couplings that prolongs quantum coherences detected with 2D spectroscopy.![]()
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Affiliation(s)
- Sara H Sohail
- Department of Chemistry, The Institute for Biophysical Dynamics, The James Franck Institute, The University of Chicago Chicago IL 60637 USA +1-773-834-0818
| | - John P Otto
- Department of Chemistry, The Institute for Biophysical Dynamics, The James Franck Institute, The University of Chicago Chicago IL 60637 USA +1-773-834-0818
| | - Paul D Cunningham
- U.S. Naval Research Laboratory 4555 Overlook Avenue SW Washington DC 20375 USA
| | - Young C Kim
- U.S. Naval Research Laboratory 4555 Overlook Avenue SW Washington DC 20375 USA
| | - Ryan E Wood
- Department of Chemistry, The Institute for Biophysical Dynamics, The James Franck Institute, The University of Chicago Chicago IL 60637 USA +1-773-834-0818
| | - Marco A Allodi
- Department of Chemistry, The Institute for Biophysical Dynamics, The James Franck Institute, The University of Chicago Chicago IL 60637 USA +1-773-834-0818
| | - Jacob S Higgins
- Department of Chemistry, The Institute for Biophysical Dynamics, The James Franck Institute, The University of Chicago Chicago IL 60637 USA +1-773-834-0818
| | - Joseph S Melinger
- U.S. Naval Research Laboratory 4555 Overlook Avenue SW Washington DC 20375 USA
| | - Gregory S Engel
- Department of Chemistry, The Institute for Biophysical Dynamics, The James Franck Institute, The University of Chicago Chicago IL 60637 USA +1-773-834-0818
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13
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Rukin PS, Komarova KG, Fresch B, Collini E, Remacle F. Chirality of a rhodamine heterodimer linked to a DNA scaffold: an experimental and computational study. Phys Chem Chem Phys 2020; 22:7516-7523. [PMID: 32219241 DOI: 10.1039/d0cp00223b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The chiroptical properties of multi-chromophoric systems are governed by the intermolecular arrangement of the monomeric units. We report on a computational and experimental study of the linear optical properties and supramolecular structure of a rhodamine heterodimer assembled on a DNA scaffold. The experimental absorption and circular dichroism (CD) profiles confirm the dimer formation. Computationally, starting from low-cost DFT/TDDFT simulations of the bare dimer we attribute the measured -/+ CD sign sequence of the S1/S2 bands to a specific chiral conformation of the heterodimer. In the monomers, as typical for rhodamine dyes, the electric transition dipole of the lowest π-π* transition is parallel to the long axis of the xanthene planes. We show that in the heterodimer the sign sequence of the two CD bands is related to the orientation of these long axes. To account explicitly for environment effects, we use molecular dynamics (MD) simulations for characterizing the supramolecular structure of the two optical isomers tethered on DNA. Average absorption and CD-profiles were modeled using ab initio TDDFT calculations at the geometries sampled along a few nanosecond MD run. The absorption profiles computed for both optical isomers are in good agreement with the experimental absorption spectrum and do not allow one to discriminate between them. The computed averaged CD profiles provide the orientation of monomers in the enantiomer that is dominant under the experimental conditions.
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Affiliation(s)
- P S Rukin
- Theoretical Physical Chemistry, UR MolSys B6c, University of Liege, B4000, Liege, Belgium.
| | - K G Komarova
- Theoretical Physical Chemistry, UR MolSys B6c, University of Liege, B4000, Liege, Belgium.
| | - B Fresch
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131 Padova, Italy
| | - E Collini
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131 Padova, Italy
| | - F Remacle
- Theoretical Physical Chemistry, UR MolSys B6c, University of Liege, B4000, Liege, Belgium.
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Silori Y, De AK. Controlling balance between homo-FRET and hetero-FRET within hetero-chromophoric systems by tuning nature of solvent. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2019.112093] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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15
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Silori Y, De AK. Tuning effect of local environment to control mechanism of fluorescence depolarization: Rotational diffusion and resonance energy transfer within homo-aggregates of xanthenes. J Photochem Photobiol A Chem 2019. [DOI: 10.1016/j.jphotochem.2019.04.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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16
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Volpato A, Collini E. Optimization and selection of time-frequency transforms for wave-packet analysis in ultrafast spectroscopy. OPTICS EXPRESS 2019; 27:2975-2987. [PMID: 30732326 DOI: 10.1364/oe.27.002975] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 12/19/2018] [Indexed: 06/09/2023]
Abstract
The analysis of quantum beats in time-resolved spectroscopic signals is becoming a task of primary importance because it is now clear that they bring crucial information about chemical reactivity, transport, and relaxation processes. Here we describe how to exploit the wide family of time-frequency transform methodologies to obtain information not only about the frequency but also about the dynamics of the oscillating components contributing to the overall beating signal. Several linear and bilinear transforms have been considered, and a general and easy procedure to judge in a non-arbitrary way the performances of different transforms has been outlined.
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17
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Raman and 2D electronic spectroscopies: A fruitful alliance for the investigation of ground and excited state vibrations in chlorophyll a. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.03.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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18
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Abstract
The subtle details of the mechanism of energy flow from carotenoids to chlorophylls in biological light-harvesting complexes are still not fully understood, especially in the ultrafast regime. Here we focus on the antenna complex peridinin–chlorophyll a–protein (PCP), known for its remarkable efficiency of excitation energy transfer from carotenoids—peridinins—to chlorophylls. PCP solutions are studied by means of 2D electronic spectroscopy in different experimental conditions. Together with a global kinetic analysis and multiscale quantum chemical calculations, these data allow us to comprehensively address the contribution of the potential pathways of energy flow in PCP. These data support dominant energy transfer from peridinin S2 to chlorophyll Qy state via an ultrafast coherent mechanism. The coherent superposition of the two states is functional to drive population to the final acceptor state, adding an important piece of information in the quest for connections between coherent phenomena and biological functions. Energy transfer from carotenoids to chlorophylls in light-harvesting is still not fully understood, especially in the ultrafast regime. Here, the authors investigate the coherent dynamics of this process in peridinin-chlorophyll a-protein complex via 2D electronic spectroscopy and quantum chemical calculations.
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Green D, V A Camargo F, Heisler IA, Dijkstra AG, Jones GA. Spectral Filtering as a Tool for Two-Dimensional Spectroscopy: A Theoretical Model. J Phys Chem A 2018; 122:6206-6213. [PMID: 29985004 DOI: 10.1021/acs.jpca.8b03339] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Two-dimensional optical spectroscopy is a powerful technique for the probing of coherent quantum superpositions. Recently, the finite width of the laser spectrum has been employed to selectively tune experiments for the study of particular coherences. This involves the exclusion of certain transition frequencies, which results in the elimination of specific Liouville pathways. The rigorous analysis of such experiments requires the use of ever more sophisticated theoretical models for the optical spectroscopy of electronic and vibronic systems. Here we develop a nonimpulsive and non-Markovian model, which combines an explicit definition of the laser spectrum, via the equation of motion-phase matching approach (EOM-PMA), with the hierarchical equations of motion (HEOM). This theoretical framework is capable of simulating the 2D spectroscopy of vibronic systems with low frequency modes, coupled to environments of intermediate and slower time scales. In order to demonstrate the spectral filtering of vibronic coherences, we examine the elimination of lower energy peaks from the 2D spectra of a zinc porphyrin monomer upon blue-shifting the laser spectrum. The filtering of Liouville pathways is revealed through the disappearance of peaks from the amplitude spectra for a coupled vibrational mode.
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Affiliation(s)
- Dale Green
- School of Chemistry , University of East Anglia , Norwich Research Park, Norwich NR4 7TJ , U.K
| | - Franco V A Camargo
- School of Chemistry , University of East Anglia , Norwich Research Park, Norwich NR4 7TJ , U.K.,CAPES Foundation , Ministry of Education of Brazil , Brasilia DF 70040-202 , Brazil
| | - Ismael A Heisler
- School of Chemistry , University of East Anglia , Norwich Research Park, Norwich NR4 7TJ , U.K
| | | | - Garth A Jones
- School of Chemistry , University of East Anglia , Norwich Research Park, Norwich NR4 7TJ , U.K
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Righetto M, Bolzonello L, Volpato A, Amoruso G, Panniello A, Fanizza E, Striccoli M, Collini E. Deciphering hot- and multi-exciton dynamics in core-shell QDs by 2D electronic spectroscopies. Phys Chem Chem Phys 2018; 20:18176-18183. [PMID: 29961782 PMCID: PMC6044327 DOI: 10.1039/c8cp02574f] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
2D electronic spectroscopy maps acquired in different configurations unveil intraband hot carrier cooling and interband multi-exciton recombination dynamics.
Although the harnessing of multiple and hot excitons is a prerequisite for many of the groundbreaking applications of semiconductor quantum dots (QDs), the characterization of their dynamics through conventional spectroscopic techniques is cumbersome. Here, we show how a careful analysis of 2DES maps acquired in different configurations (BOXCARS and pump–probe geometry) allows the tracking and visualization of intraband Auger relaxation mechanisms, driving the hot carrier cooling, and interband bi- and tri-exciton recombination dynamics. The results obtained on archetypal core–shell CdSe/ZnS QDs suggest that, given the global analysis of the resulting datasets, 2D electronic spectroscopy techniques can successfully and efficiently dispel the intertwined dynamics of fast and ultrafast recombination processes in nanomaterials. Hence, we propose this analysis scheme to be used in future research on novel quantum confined systems.
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Affiliation(s)
- Marcello Righetto
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, I-35131 Padova, Italy.
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