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Zhou X, Lin S, Yan H. Interfacing DNA nanotechnology and biomimetic photonic complexes: advances and prospects in energy and biomedicine. J Nanobiotechnology 2022; 20:257. [PMID: 35658974 PMCID: PMC9164479 DOI: 10.1186/s12951-022-01449-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 05/05/2022] [Indexed: 11/16/2022] Open
Abstract
Self-assembled photonic systems with well-organized spatial arrangement and engineered optical properties can be used as efficient energy materials and as effective biomedical agents. The lessons learned from natural light-harvesting antennas have inspired the design and synthesis of a series of biomimetic photonic complexes, including those containing strongly coupled dye aggregates with dense molecular packing and unique spectroscopic features. These photoactive components provide excellent features that could be coupled to multiple applications including light-harvesting, energy transfer, biosensing, bioimaging, and cancer therapy. Meanwhile, nanoscale DNA assemblies have been employed as programmable and addressable templates to guide the formation of DNA-directed multi-pigment complexes, which can be used to enhance the complexity and precision of artificial photonic systems and show the potential for energy and biomedical applications. This review focuses on the interface of DNA nanotechnology and biomimetic photonic systems. We summarized the recent progress in the design, synthesis, and applications of bioinspired photonic systems, highlighted the advantages of the utilization of DNA nanostructures, and discussed the challenges and opportunities they provide.
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Affiliation(s)
- Xu Zhou
- Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA
| | - Su Lin
- Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Hao Yan
- Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA. .,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA.
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Grebenko AK, Motovilov KA, Bubis AV, Nasibulin AG. Gentle Patterning Approaches toward Compatibility with Bio-Organic Materials and Their Environmental Aspects. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2200476. [PMID: 35315215 DOI: 10.1002/smll.202200476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/06/2022] [Indexed: 06/14/2023]
Abstract
Advances in material science, bioelectronic, and implantable medicine combined with recent requests for eco-friendly materials and technologies inevitably formulate new challenges for nano- and micropatterning techniques. Overall, the importance of creating micro- and nanostructures is motivated by a large manifold of fundamental and applied properties accessible only at the nanoscale. Lithography is a crucial family of fabrication methods to create prototypes and produce devices on an industrial scale. The pure trend in the miniaturization of critical electronic semiconducting components has been recently enhanced by implementing bio-organic systems in electronics. So far, significant efforts have been made to find novel lithographic approaches and develop old ones to reach compatibility with delicate bio-organic systems and minimize the impact on the environment. Herein, such delicate materials and sophisticated patterning techniques are briefly reviewed.
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Affiliation(s)
- Artem K Grebenko
- Skolkovo Institute of Science and Technology, Nobel str. 3, Moscow, 121205, Russia
- Center for Photonics and 2D Materials, Moscow Institute of Physics and Technology, Institute Lane 9, Dolgoprudny, 141701, Russia
| | - Konstantin A Motovilov
- Center for Photonics and 2D Materials, Moscow Institute of Physics and Technology, Institute Lane 9, Dolgoprudny, 141701, Russia
| | - Anton V Bubis
- Skolkovo Institute of Science and Technology, Nobel str. 3, Moscow, 121205, Russia
- Institute of Solid State Physics, Russian Academy of Sciences, 2 Academician Ossipyan str., Chernogolovka, 142432, Russia
| | - Albert G Nasibulin
- Skolkovo Institute of Science and Technology, Nobel str. 3, Moscow, 121205, Russia
- Department of Chemistry and Materials Science, Aalto University, P.O. Box 16100, Aalto, FI-00076, Finland
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Abstract
Numerous linear and non-linear spectroscopic techniques have been developed to elucidate structural and functional information of complex systems ranging from natural systems, such as proteins and light-harvesting systems, to synthetic systems, such as solar cell materials and light-emitting diodes. The obtained experimental data can be challenging to interpret due to the complexity and potential overlapping spectral signatures. Therefore, computational spectroscopy plays a crucial role in the interpretation and understanding of spectral observables of complex systems. Computational modeling of various spectroscopic techniques has seen significant developments in the past decade, when it comes to the systems that can be addressed, the size and complexity of the sample types, the accuracy of the methods, and the spectroscopic techniques that can be addressed. In this Perspective, I will review the computational spectroscopy methods that have been developed and applied for infrared and visible spectroscopies in the condensed phase. I will discuss some of the questions that this has allowed answering. Finally, I will discuss current and future challenges and how these may be addressed.
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Affiliation(s)
- Thomas L C Jansen
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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Li X, Buda F, de Groot HJ, Sevink GJA. Contrasting Modes of Self-Assembly and Hydrogen-Bonding Heterogeneity in Chlorosomes of Chlorobaculum tepidum. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2018; 122:14877-14888. [PMID: 30258522 PMCID: PMC6150686 DOI: 10.1021/acs.jpcc.8b01790] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 05/30/2018] [Indexed: 06/08/2023]
Abstract
Chlorosome antennae form an interesting class of materials for studying the role of structural motifs and dynamics in nonadiabatic energy transfer. They perform robust and highly quantum-efficient transfer of excitonic energy while allowing for compositional variation and completely lacking the usual regulatory proteins. Here, we first cast the geometrical analysis for ideal tubular scaffolding models into a formal framework, to relate effective helical properties of the assembly structures to established characterization data for various types of chlorosomes. This analysis shows that helicity is uniquely defined for chlorosomes composed of bacteriochlorophyll (BChl) d and that three chiral angles are consistent with the nuclear magnetic resonance (NMR) and electron microscope data for BChl c, including two novel ones that are at variance with current interpretations of optical data based on perfect cylindrical symmetry. We use this information as a starting point for investigating dynamic and static heterogeneity at the molecular level by unconstrained molecular dynamics. We first identify a rotational degree of freedom, along the Mg-OH coordination bond, that alternates along the syn-anti stacks and underlies the (flexible) curvature on a larger scale. Because rotation directly relates to the formation or breaking of interstack hydrogen bonds of the O-H···O=C structural motif along the syn-anti stacks, we analyzed the relative fractions of hydrogen-bonded and the nonbonded regions, forming stripe domains in otherwise spectroscopically homogeneous curved slabs. The ratios 7:3 for BChl c and 9:1 for BChl d for the two distinct structural components agree well with the signal intensities determined by NMR. In addition, rotation with curvature-independent formation of stripe domains offers a viable explanation for the localization and dispersion of exciton states over two fractions, as observed in single chlorosome fluorescence decay studies.
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Gelbwaser-Klimovsky D, Aspuru-Guzik A. On thermodynamic inconsistencies in several photosynthetic and solar cell models and how to fix them. Chem Sci 2017; 8:1008-1014. [PMID: 28451238 PMCID: PMC5354066 DOI: 10.1039/c6sc04350j] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 10/21/2016] [Indexed: 12/20/2022] Open
Abstract
We analyze standard theoretical models of solar energy conversion developed to study solar cells and photosynthetic systems. We show that assuming the energy transfer to the reaction center/electric circuit is through a decay rate or "sink", contradicts the second law of thermodynamics. We put forward a thermodynamically consistent alternative by explicitly considering parts of the reaction center/electric circuit and by employing a Hamiltonian transfer. The predicted energy transfer by the new scheme differs from the one found using a decay rate, casting doubts on the validity of the conclusions obtained by models which include the latter.
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Affiliation(s)
| | - Alán Aspuru-Guzik
- Department of Chemistry and Chemical Biology , Cambridge , MA 02138 , USA .
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Prokhorov VV, Perelygina OM, Pozin SI, Mal’tsev EI, Vannikov AV. Polymorphism of Two-Dimensional Cyanine Dye J-Aggregates and Its Genesis: Fluorescence Microscopy and Atomic Force Microscopy Study. J Phys Chem B 2015; 119:15046-53. [DOI: 10.1021/acs.jpcb.5b07821] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Valery V. Prokhorov
- A. N. Frumkin Institute of Physical Chemistry and Electrochemistry, RAS, Leninsky prospect 31, Moscow, 199071, Russia
| | - Olga M. Perelygina
- A. N. Frumkin Institute of Physical Chemistry and Electrochemistry, RAS, Leninsky prospect 31, Moscow, 199071, Russia
| | - Sergey I. Pozin
- A. N. Frumkin Institute of Physical Chemistry and Electrochemistry, RAS, Leninsky prospect 31, Moscow, 199071, Russia
| | - Eugene I. Mal’tsev
- A. N. Frumkin Institute of Physical Chemistry and Electrochemistry, RAS, Leninsky prospect 31, Moscow, 199071, Russia
| | - Anatoly V. Vannikov
- A. N. Frumkin Institute of Physical Chemistry and Electrochemistry, RAS, Leninsky prospect 31, Moscow, 199071, Russia
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Duque S, Brumer P, Pachón LA. Classical approach to multichromophoric resonance energy transfer. PHYSICAL REVIEW LETTERS 2015; 115:110402. [PMID: 26406811 DOI: 10.1103/physrevlett.115.110402] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Indexed: 06/05/2023]
Abstract
A classical formulation of the quantum multichromophoric theory of resonance energy transfer is developed on the basis of classical electrodynamics. The theory allows for the identification of a variety of processes of different order in the interactions that contribute to the energy transfer in molecular aggregates with intracoupling in donors and acceptor chromophores. Enhanced rates in multichromophoric resonance energy transfer are shown to be well described by this theory. Specifically, in a coupling configuration between N_{A} acceptors and N_{D} donors, the theory correctly predicts an enhancement of the energy transfer rate dependent on the total number of donor-acceptor pairs. As an example, the theory, applied to the transfer rate in light harvesting II, gives results in excellent agreement with experiment. Finally, it is explicitly shown that as long as linear response theory holds, the classical multichromophoric theory formally coincides with the quantum formulation.
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Affiliation(s)
- Sebastián Duque
- Grupo de Física Atómica y Molecular, Instituto de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia UdeA; Calle 70 No. 52-21, Medellín, Colombia
| | - Paul Brumer
- Chemical Physics Theory Group, Department of Chemistry and Center for Quantum Information and Quantum Control, University of Toronto, Toronto, Canada M5S 3H6
| | - Leonardo A Pachón
- Grupo de Física Atómica y Molecular, Instituto de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia UdeA; Calle 70 No. 52-21, Medellín, Colombia
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Sawaya NPD, Huh J, Fujita T, Saikin SK, Aspuru-Guzik A. Fast delocalization leads to robust long-range excitonic transfer in a large quantum chlorosome model. NANO LETTERS 2015; 15:1722-1729. [PMID: 25694170 DOI: 10.1021/nl504399d] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Chlorosomes are efficient light-harvesting antennas containing up to hundreds of thousands of bacteriochlorophyll molecules. With massively parallel computer hardware, we use a nonperturbative stochastic Schrödinger equation, while including an atomistically derived spectral density, to study excitonic energy transfer in a realistically sized chlorosome model. We find that fast short-range delocalization leads to robust long-range transfer due to the antennae's concentric-roll structure. Additionally, we discover anomalous behavior arising from different initial conditions, and outline general considerations for simulating excitonic systems on the nanometer to micrometer scale.
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Affiliation(s)
- Nicolas P D Sawaya
- Department of Chemistry and Chemical Biology, Harvard University , 12 Oxford Street, Cambridge, Massachusetts 02138, United States
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Liu X, Qiu J. Recent advances in energy transfer in bulk and nanoscale luminescent materials: from spectroscopy to applications. Chem Soc Rev 2015; 44:8714-46. [DOI: 10.1039/c5cs00067j] [Citation(s) in RCA: 147] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We discuss optical energy transfer involving ions, QDs, molecules etc., together with the relevant applications in different areas.
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Affiliation(s)
- Xiaofeng Liu
- State Key Laboratory of Modern Optical Instrumentation
- School of Materials Science and Engineering
- Zhejiang University
- Hangzhou 310027
- China
| | - Jianrong Qiu
- State Key Laboratory of Modern Optical Instrumentation
- School of Materials Science and Engineering
- Zhejiang University
- Hangzhou 310027
- China
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Tamiaki H, Kuno M, Ohata M. Self-aggregation of Synthetic Zinc Chlorophyll Derivatives Possessing 31-Hydroxy or Methoxy Group and 131-Mono- or Dicyanomethylene Moiety in Nonpolar Organic Solvents as Models of Chlorosomal Bacteriochlorophyll-dAggregates. Photochem Photobiol 2014; 90:1277-86. [DOI: 10.1111/php.12327] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 08/01/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Hitoshi Tamiaki
- Graduate School of Life Sciences; Ritsumeikan University; Kusatsu Shiga Japan
| | - Masaki Kuno
- Graduate School of Life Sciences; Ritsumeikan University; Kusatsu Shiga Japan
| | - Masaki Ohata
- Graduate School of Life Sciences; Ritsumeikan University; Kusatsu Shiga Japan
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