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Kelestemur S, Maity P, Visaveliya NR, Halpern D, Parveen S, Khatoon F, Khalil A, Greenberg M, Jiang Q, Ng K, Eisele DM. Solution-based Supramolecular Hierarchical Assembly of Frenkel Excitonic Nanotubes Driven by Gold Nanoparticle Formation and Temperature. J Phys Chem B 2024; 128:329-339. [PMID: 38157497 DOI: 10.1021/acs.jpcb.3c05681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Translating nature's successful design principle of solution-based supramolecular self-assembling to broad applications─ranging from renewable energy and information technology to nanomedicine─requires a fundamental understanding of supramolecular hierarchical assembly. Though the forces behind self-assembly (e.g., hydrophobicity) are known, the specific mechanism by which monomers form the hierarchical assembly still remains an open question. A crucial step toward formulating a complete mechanism is understanding not only how the monomer's specific molecular structure but also how manifold environmental conditions impact the self-assembling process. Here, we elucidate the complex correlation between the environmental self-assembling conditions and the resulting structural properties by utilizing a well-characterized model system: well-defined supramolecular Frenkel excitonic nanotubes (NTs), self-assembled from cyanine dye molecules in aqueous solution, which further self-assemble into bundled nanotubes (b-NTs). The NTs and b-NTs inhabit distinct spectroscopic signatures, which allows the use of steady-state absorption spectroscopy to monitor the transition from NTs to b-NTs directly. Specifically, we investigate the impact of temperature (ranging from 23 °C, 55 °C, 70 °C, 85 °C, up to 100 °C) during in situ formation of gold nanoparticles to determine their role in the formation of b-NTs. The considered time regime for the self-assembling process ranges from 1 min to 8 days. With our work, we contribute to a basic understanding of how environmental conditions impact solution-based hierarchical supramolecular self-assembly in both the thermodynamic and the kinetic regime.
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Affiliation(s)
- Seda Kelestemur
- Department of Chemistry and Biochemistry, The City College of New York at The City University of New York, New York City, New York 10031, United States
- Biotechnology Department, Institute of Health Sciences, University of Health Sciences, Istanbul, 34668, Turkey
| | - Piyali Maity
- Department of Chemistry and Biochemistry, The City College of New York at The City University of New York, New York City, New York 10031, United States
| | - Nikunjkumar R Visaveliya
- Department of Chemistry and Biochemistry, The City College of New York at The City University of New York, New York City, New York 10031, United States
| | - Damien Halpern
- Department of Chemistry and Biochemistry, The City College of New York at The City University of New York, New York City, New York 10031, United States
| | - Sadiyah Parveen
- Department of Chemistry and Biochemistry, The City College of New York at The City University of New York, New York City, New York 10031, United States
| | - Firdaus Khatoon
- Department of Chemistry and Biochemistry, The City College of New York at The City University of New York, New York City, New York 10031, United States
| | - Ali Khalil
- Department of Chemistry and Biochemistry, The City College of New York at The City University of New York, New York City, New York 10031, United States
| | - Matthew Greenberg
- Department of Chemistry and Biochemistry, The City College of New York at The City University of New York, New York City, New York 10031, United States
| | - Qingrui Jiang
- Department of Chemistry and Biochemistry, The City College of New York at The City University of New York, New York City, New York 10031, United States
| | - Kara Ng
- Department of Chemistry and Biochemistry, The City College of New York at The City University of New York, New York City, New York 10031, United States
- PhD Program in Chemistry, Graduate Center of The City University of New York, New York City, New York 10016, United States
| | - Dorthe M Eisele
- Department of Chemistry and Biochemistry, The City College of New York at The City University of New York, New York City, New York 10031, United States
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Ress L, Malý P, Landgraf JB, Lindorfer D, Hofer M, Selby J, Lambert C, Renger T, Brixner T. Time-resolved circular dichroism of excitonic systems: theory and experiment on an exemplary squaraine polymer. Chem Sci 2023; 14:9328-9349. [PMID: 37712031 PMCID: PMC10498725 DOI: 10.1039/d3sc01674a] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 07/28/2023] [Indexed: 09/16/2023] Open
Abstract
Experimental and theoretical foundations for femtosecond time-resolved circular dichroism (TRCD) spectroscopy of excitonic systems are presented. In this method, the system is pumped with linearly polarized light and the signal is defined as the difference between the transient absorption spectrum probed with left and with right circularly polarized light. We present a new experimental setup with a polarization grating as key element to generate circularly polarized pulses. Herein the positive (negative) first order of the diffracted light is left-(right-)circularly polarized and serves as a probe pulse in a TRCD experiment. The grating is capable of transferring ultrashort broadband pulses ranging from 470 nm to 720 nm into two separate beams with opposite ellipticity. By applying a specific chopping scheme we can switch between left and right circular polarizations and detect transient absorption (TA) and TRCD spectra on a shot-to-shot basis simultaneously. We perform experiments on a squaraine polymer, investigating excitonic dynamics, and we develop a general theory for TRCD experiments of excitonically coupled systems that we then apply to describe the experimental data in this particular example. At a magic angle of 54.7° between the pump-pulse polarization and the propagation direction of the probe pulse, the TRCD and TA signals become particularly simple to analyze, since the orientational average over random orientations of complexes factorizes into that of the interaction with the pump and the probe pulse, and the intrinsic electric quadrupole contributions to the TRCD signal average to zero for isotropic samples. Application of exciton theory to linear absorption and to linear circular dichroism spectra of squaraine polymers reveals the presence of two fractions of polymer conformations, a dominant helical conformation with close interpigment distances that are suggested to lead to short-range contributions to site energy shifts and excitonic couplings of the squaraine molecules, and a fraction of unfolded random coils. Theory demonstrates that TRCD spectra of selectively excited helices can resolve state populations that are practically invisible in TA spectroscopy due to the small dipole strength of these states. A qualitative interpretation of TRCD and TA spectra in the spectral window investigated experimentally is offered. The 1 ps time component found in these spectra is related to the slow part of exciton relaxation obtained between states of the helix in the low-energy half of the exciton manifold. The dominant 140 ps time constant reflects the decay of excited states to the electronic ground state.
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Affiliation(s)
- Lea Ress
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg Am Hubland 97074 Würzburg Germany
| | - Pavel Malý
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg Am Hubland 97074 Würzburg Germany
- Faculty of Mathematics and Physics, Charles University Ke Karlovu 5 121 16 Praha 2 Czech Republic
| | - Jann B Landgraf
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg Am Hubland 97074 Würzburg Germany
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), Universität Freiburg Georges-Köhler-Allee 105 79110 Freiburg Germany
| | - Dominik Lindorfer
- Institut für Theoretische Physik, Johannes Kepler Universität Linz Altenberger Str. 69 4040 Linz Austria
| | - Michael Hofer
- Institut für Theoretische Physik, Johannes Kepler Universität Linz Altenberger Str. 69 4040 Linz Austria
| | - Joshua Selby
- Institut für Organische Chemie, Universität Würzburg Am Hubland 97074 Würzburg Germany
| | - Christoph Lambert
- Institut für Organische Chemie, Universität Würzburg Am Hubland 97074 Würzburg Germany
| | - Thomas Renger
- Institut für Theoretische Physik, Johannes Kepler Universität Linz Altenberger Str. 69 4040 Linz Austria
| | - Tobias Brixner
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg Am Hubland 97074 Würzburg Germany
- Center for Nanosystems Chemistry (CNC), Universität Würzburg Theodor-Boveri-Weg 97074 Würzburg Germany
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3
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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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Fiedler J, Berland K, Borchert JW, Corkery RW, Eisfeld A, Gelbwaser-Klimovsky D, Greve MM, Holst B, Jacobs K, Krüger M, Parsons DF, Persson C, Presselt M, Reisinger T, Scheel S, Stienkemeier F, Tømterud M, Walter M, Weitz RT, Zalieckas J. Perspectives on weak interactions in complex materials at different length scales. Phys Chem Chem Phys 2023; 25:2671-2705. [PMID: 36637007 DOI: 10.1039/d2cp03349f] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Nanocomposite materials consist of nanometer-sized quantum objects such as atoms, molecules, voids or nanoparticles embedded in a host material. These quantum objects can be exploited as a super-structure, which can be designed to create material properties targeted for specific applications. For electromagnetism, such targeted properties include field enhancements around the bandgap of a semiconductor used for solar cells, directional decay in topological insulators, high kinetic inductance in superconducting circuits, and many more. Despite very different application areas, all of these properties are united by the common aim of exploiting collective interaction effects between quantum objects. The literature on the topic spreads over very many different disciplines and scientific communities. In this review, we present a cross-disciplinary overview of different approaches for the creation, analysis and theoretical description of nanocomposites with applications related to electromagnetic properties.
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Affiliation(s)
- J Fiedler
- Department of Physics and Technology, University of Bergen, Allégaten 55, 5007 Bergen, Norway.
| | - K Berland
- Department of Mechanical Engineering and Technology Management, Norwegian University of Life Sciences, Campus Ås Universitetstunet 3, 1430 Ås, Norway
| | - J W Borchert
- 1st Institute of Physics, Georg-August-University, Göttingen, Germany
| | - R W Corkery
- Surface and Corrosion Science, Department of Chemistry, KTH Royal Institute of Technology, SE 100 44 Stockholm, Sweden
| | - A Eisfeld
- Max-Planck-Institut für Physik komplexer Systeme, Nöthnitzer Strasse 38, 01187 Dresden, Germany
| | - D Gelbwaser-Klimovsky
- Schulich Faculty of Chemistry and Helen Diller Quantum Center, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - M M Greve
- Department of Physics and Technology, University of Bergen, Allégaten 55, 5007 Bergen, Norway.
| | - B Holst
- Department of Physics and Technology, University of Bergen, Allégaten 55, 5007 Bergen, Norway.
| | - K Jacobs
- Experimental Physics, Saarland University, Center for Biophysics, 66123 Saarbrücken, Germany.,Max Planck School Matter to Life, 69120 Heidelberg, Germany
| | - M Krüger
- Institute for Theoretical Physics, Georg-August-Universität Göttingen, 37073 Göttingen, Germany
| | - D F Parsons
- Department of Chemical and Geological Sciences, University of Cagliari, Cittadella Universitaria, 09042 Monserrato, CA, Italy
| | - C Persson
- Centre for Materials Science and Nanotechnology, University of Oslo, P. O. Box 1048 Blindern, 0316 Oslo, Norway.,Department of Materials Science and Engineering, KTH Royal Institute of Technology, 100 44 Stockholm, Sweden
| | - M Presselt
- Leibniz Institute of Photonic Technology (IPHT), Albert-Einstein-Str. 9, 07745 Jena, Germany
| | - T Reisinger
- Institute for Quantum Materials and Technologies, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany
| | - S Scheel
- Institute of Physics, University of Rostock, Albert-Einstein-Str. 23-24, 18059 Rostock, Germany
| | - F Stienkemeier
- Institute of Physics, University of Freiburg, Hermann-Herder-Str. 3, 79104 Freiburg, Germany
| | - M Tømterud
- Department of Physics and Technology, University of Bergen, Allégaten 55, 5007 Bergen, Norway.
| | - M Walter
- Institute of Physics, University of Freiburg, Hermann-Herder-Str. 3, 79104 Freiburg, Germany
| | - R T Weitz
- 1st Institute of Physics, Georg-August-University, Göttingen, Germany
| | - J Zalieckas
- Department of Physics and Technology, University of Bergen, Allégaten 55, 5007 Bergen, Norway.
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5
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Li X, Buda F, de Groot HJ, Sevink GJA. The role of chirality and plastic crystallinity in the optical and mechanical properties of chlorosomes. iScience 2022; 25:103618. [PMID: 35005556 PMCID: PMC8719020 DOI: 10.1016/j.isci.2021.103618] [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: 08/17/2021] [Revised: 11/15/2021] [Accepted: 12/08/2021] [Indexed: 11/26/2022] Open
Abstract
The most efficient light-harvesting antennae found in nature, chlorosomes, are molecular tubular aggregates (TMAs) assembled by pigments without protein scaffolds. Here, we discuss a classification of chlorosomes as a unique tubular plastic crystal and we attribute the robust energy transfer in chlorosomes to this unique nature. To systematically study the role of supramolecular tube chirality by molecular simulation, a role that has remained unresolved, we share a protocol for generating realistic tubes at atomic resolution. We find that both the optical and the mechanical behavior are strongly dependent on chirality. The optical-chirality relation enables a direct interpretation of experimental spectra in terms of overall tube chirality. The mechanical response shows that the overall chirality regulates the hardness of the tube and provides a new characteristic for relating chlorosomes to distinct chirality. Our protocol also applies to other TMA systems and will inspire other systematic studies beyond lattice models. Classifies chlorosomes in terms of a tubular plastic crystal phase Clarifies the unique strategy of chlorosomes for harvesting and transporting energy Presents a protocol for building atom-resolved helical tube structures Maps tube chirality directly to measurable optical and mechanical responses
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Affiliation(s)
- Xinmeng Li
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, South Holland, the Netherlands
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, P.O.Box 1033, Blindern, Oslo, 0315 Oslo, Norway
- Corresponding author
| | - Francesco Buda
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, South Holland, the Netherlands
| | - Huub J.M. de Groot
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, South Holland, the Netherlands
| | - G. J. Agur Sevink
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, South Holland, the Netherlands
- Corresponding author
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6
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Yu G, Wilson MR. Molecular simulation studies of self-assembly for a chromonic perylene dye: All-atom studies and new approaches to coarse-graining. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118210] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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7
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Singh AK, Schade B, Wycisk V, Böttcher C, Haag R, von Berlepsch H. Aggregation of Amphiphilic Carbocyanines: Fluorination Favors Cylindrical Micelles over Bilayered Tubes. J Phys Chem B 2021; 125:10538-10550. [PMID: 34505509 DOI: 10.1021/acs.jpcb.1c05128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The synthesis of a new amphiphilic 5,5',6,6'-tetrachlorobenzimidacarbocyanine dye derivative with -(CH2)2-(CF2)5-CF3 chains attached to the nitrogen atoms in the 1,1'-position, CF8O3, is reported. Depending on the dye concentration and the addition of MeOH, CF8O3 forms J- and H-aggregates in aqueous solutions. The aggregation behavior was investigated using steady-state absorption, linear dichroism, and fluorescence spectroscopy, as well as by cryogenic transmission electron microscopy (cryo-TEM). The J-band of the MeOH-free solution is monomer-like, rather broad, and less red-shifted with respect to the monomer absorption, indicating weak excitonic coupling and disorder effects. Cryo-TEM reveals a diversity of supramolecular structures, wherein linear and branched cylindrical micelles dominate. It is concluded that the high stiffness of fluoroalkyl chains does not allow the chains to splay and completely fill up the hydrophobic gap between opposing chromophores. This destabilizes the bilayers and favors the micellar structure motifs instead. The aggregates appearing at 30% MeOH show a split absorption spectrum consisting of a broad blue-shifted H-band and an accompanying sharp red-shifted J-band with perpendicular polarizations. These HJ-type aggregates are also composed of micellar fibers, but these bundle into rope-like strands. For 10% MeOH, a narrow bilayered tube is the dominating morphology. The observed MeOH dependence of aggregation reveals a clear cosolvent effect.
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Affiliation(s)
- Abhishek Kumar Singh
- Institut für Chemie und Biochemie, Organische Chemie, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
| | - Boris Schade
- Forschungszentrum für Elektronenmikroskopie, Institut für Chemie und Biochemie, Freie Universität Berlin, Fabeckstraße 36a, 14195 Berlin, Germany.,Core Facility BioSupraMol, Institut für Chemie und Biochemie, Freie Universität Berlin, Fabeckstraße 36a, 14195 Berlin, Germany
| | - Virginia Wycisk
- Institut für Chemie und Biochemie, Organische Chemie, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
| | - Christoph Böttcher
- Forschungszentrum für Elektronenmikroskopie, Institut für Chemie und Biochemie, Freie Universität Berlin, Fabeckstraße 36a, 14195 Berlin, Germany
| | - Rainer Haag
- Institut für Chemie und Biochemie, Organische Chemie, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
| | - Hans von Berlepsch
- Core Facility BioSupraMol, Institut für Chemie und Biochemie, Freie Universität Berlin, Fabeckstraße 36a, 14195 Berlin, Germany
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8
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Rizvi A, Mulvey JT, Carpenter BP, Talosig R, Patterson JP. A Close Look at Molecular Self-Assembly with the Transmission Electron Microscope. Chem Rev 2021; 121:14232-14280. [PMID: 34329552 DOI: 10.1021/acs.chemrev.1c00189] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Molecular self-assembly is pervasive in the formation of living and synthetic materials. Knowledge gained from research into the principles of molecular self-assembly drives innovation in the biological, chemical, and materials sciences. Self-assembly processes span a wide range of temporal and spatial domains and are often unintuitive and complex. Studying such complex processes requires an arsenal of analytical and computational tools. Within this arsenal, the transmission electron microscope stands out for its unique ability to visualize and quantify self-assembly structures and processes. This review describes the contribution that the transmission electron microscope has made to the field of molecular self-assembly. An emphasis is placed on which TEM methods are applicable to different structures and processes and how TEM can be used in combination with other experimental or computational methods. Finally, we provide an outlook on the current challenges to, and opportunities for, increasing the impact that the transmission electron microscope can have on molecular self-assembly.
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Affiliation(s)
- Aoon Rizvi
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Justin T Mulvey
- Department of Materials Science and Engineering, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Brooke P Carpenter
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Rain Talosig
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Joseph P Patterson
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
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Yu G, Walker M, Wilson MR. Atomistic simulation studies of ionic cyanine dyes: self-assembly and aggregate formation in aqueous solution. Phys Chem Chem Phys 2021; 23:6408-6421. [PMID: 33705506 DOI: 10.1039/d0cp06205g] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Cyanine dyes are known to form large-scale aggregates of various morphologies via spontaneous self-assembly in aqueous solution, akin to chromonic liquid crystals. Atomistic molecular dynamics simulations have been performed on four cyanine dyes: pseudoisocyanine chloride (PIC), pinacyanol chloride (PCYN), 5,5',6,6'-tetrachloro-1,1',3,3'-tetraethylbenzimidazolylcarbocyanine chloride (TTBC) and 1,1'-disulfopropyl-3,3'-diethyl-5,5',6,6'-tetrachloro-benzimidazolylcarbocyanine sodium salt (BIC). Simulations employed an optimised general AMBER force field and demonstrate the organisation of the dyes into stacked structures at dilute concentrations. The thermodynamics of self-assembly was studied by calculating potentials of mean force for n-mers (n = 2, 3 or 4), from which the free energies of association are determined. We report binding free energies in the range of 8 to 15kBT for dimerisation, concordant with typical values for ionic chromonics (7 to 14kBT), and examine the enthalpic and entropic contributions to the aggregation process. The self-assembly of these dyes yields two distinct classes of structures. We observe the formation of H-aggregate stacks for PCYN, with further complexity in these assemblies for PIC; where the aggregates contain shift and Y junction defects. TTBC and BIC associate into a J-aggregate sheet structure of unimolecular thickness, and is composed of a brickwork arrangement between molecules. These sheet structures are characteristic of the smectic chromonic mesophase, and such assemblies provide a route to the emergence of nanoscale tubular architectures.
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Affiliation(s)
- Gary Yu
- Department of Chemistry, Durham University, Lower Mountjoy, Stockton Road, Durham, UK.
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10
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Sahu A, Kurian JS, Tiwari V. Vibronic resonance is inadequately described by one-particle basis sets. J Chem Phys 2020; 153:224114. [DOI: 10.1063/5.0029027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Affiliation(s)
- Amitav Sahu
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Jo Sony Kurian
- Department of Chemistry, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh 462066, India
| | - Vivek Tiwari
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
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11
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Kunsel T, Löhner A, Mayo JJ, Köhler J, Jansen TLC, Knoester J. Unraveling intra-aggregate structural disorder using single-molecule spectroscopy. J Chem Phys 2020; 153:134304. [PMID: 33032400 DOI: 10.1063/5.0023551] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Structural disorder within self-assembled molecular aggregates may have strong effects on their optical functionality. Such disorder, however, is hard to explore using standard ensemble measurements. In this paper, we report on the characterization of intra-aggregate structural disorder through a linewidth analysis of fluorescence excitation experiments on individual zinc-chlorin (ZnChl) nanotubular molecular aggregates. Recent experiments suggest an anomaly in the linewidths of the two absorption bands that dominate the spectra: the higher-energy bands on average show a smaller linewidth than the lower-energy bands. This anomaly is explored in this paper by analyzing and modeling the correlation of the two linewidths for each aggregate. We exploit a Frenkel exciton model to show that the experimentally observed correlation of linewidths and other statistical properties of the single-aggregate spectra can be explained from small variations of the molecular orientations within individual aggregates.
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Affiliation(s)
- T Kunsel
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - A Löhner
- Spectroscopy of Soft Matter, University of Bayreuth, Universitätsstraße 30, 94557 Bayreuth, Germany
| | - J J Mayo
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - J Köhler
- Spectroscopy of Soft Matter, University of Bayreuth, Universitätsstraße 30, 94557 Bayreuth, Germany
| | - T L C Jansen
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - J Knoester
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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12
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Patmanidis I, de Vries AH, Wassenaar TA, Wang W, Portale G, Marrink SJ. Structural characterization of supramolecular hollow nanotubes with atomistic simulations and SAXS. Phys Chem Chem Phys 2020; 22:21083-21093. [PMID: 32945311 DOI: 10.1039/d0cp03282d] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Self-assembled nanostructures arise when building blocks spontaneously organize into ordered aggregates that exhibit different properties compared to the disorganized monomers. Here, we study an amphiphilic cyanine dye (C8S3) that is known to self-assemble into double-walled, hollow, nanotubes with interesting optical properties. The molecular packing of the dyes inside the nanotubes, however, remains elusive. To reveal the structural features of the C8S3 nanotubes, we performed atomistic Molecular Dynamics simulations of preformed bilayers and nanotubes. We find that different packing arrangements lead to stable structures, in which the tails of the C8S3 molecules are interdigitated. Our results are verified by SAXS experiments. Together our data provide a detailed structural characterization of the C8S3 nanotubes. Furthermore, our approach was able to resolve the ambiguity inherent from cryo-TEM measurements in calculating the wall thickness of similar systems. The insights obtained are expected to be generally useful for understanding and designing other supramolecular assemblies.
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Affiliation(s)
- Ilias Patmanidis
- Groningen Biomolecular Science and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands.
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13
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Bondarenko AS, Patmanidis I, Alessandri R, Souza PCT, Jansen TLC, de Vries AH, Marrink SJ, Knoester J. Multiscale modeling of molecular structure and optical properties of complex supramolecular aggregates. Chem Sci 2020; 11:11514-11524. [PMID: 34094396 PMCID: PMC8162738 DOI: 10.1039/d0sc03110k] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Supramolecular aggregates of synthetic dye molecules offer great perspectives to prepare biomimetic functional materials for light-harvesting and energy transport. The design is complicated by the fact that structure–property relationships are hard to establish, because the molecular packing results from a delicate balance of interactions and the excitonic properties that dictate the optics and excited state dynamics, in turn sensitively depend on this packing. Here we show how an iterative multiscale approach combining molecular dynamics and quantum mechanical exciton modeling can be used to obtain accurate insight into the packing of thousands of cyanine dye molecules in a complex double-walled tubular aggregate in close interaction with its solvent environment. Our approach allows us to answer open questions not only on the structure of these prototypical aggregates, but also about their molecular-scale structural and energetic heterogeneity, as well as on the microscopic origin of their photophysical properties. This opens the route to accurate predictions of energy transport and other functional properties. Multiscale modeling resolves the molecular structure of a synthetic light-harvesting complex, unraveling the microscopic origin of its photophysical properties.![]()
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Affiliation(s)
- Anna S Bondarenko
- University of Groningen, Zernike Institute for Advanced Materials Groningen The Netherlands
| | - Ilias Patmanidis
- University of Groningen, Zernike Institute for Advanced Materials Groningen The Netherlands .,University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute Groningen The Netherlands
| | - Riccardo Alessandri
- University of Groningen, Zernike Institute for Advanced Materials Groningen The Netherlands .,University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute Groningen The Netherlands
| | - Paulo C T Souza
- University of Groningen, Zernike Institute for Advanced Materials Groningen The Netherlands .,University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute Groningen The Netherlands
| | - Thomas L C Jansen
- University of Groningen, Zernike Institute for Advanced Materials Groningen The Netherlands
| | - Alex H de Vries
- University of Groningen, Zernike Institute for Advanced Materials Groningen The Netherlands .,University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute Groningen The Netherlands
| | - Siewert J Marrink
- University of Groningen, Zernike Institute for Advanced Materials Groningen The Netherlands .,University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute Groningen The Netherlands
| | - Jasper Knoester
- University of Groningen, Zernike Institute for Advanced Materials Groningen The Netherlands
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14
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Schade B, Singh AK, Wycisk V, Cuellar‐Camacho JL, von Berlepsch H, Haag R, Böttcher C. Stereochemistry-Controlled Supramolecular Architectures of New Tetrahydroxy-Functionalised Amphiphilic Carbocyanine Dyes. Chemistry 2020; 26:6919-6934. [PMID: 32027069 PMCID: PMC7317399 DOI: 10.1002/chem.201905745] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Indexed: 11/28/2022]
Abstract
The syntheses of novel amphiphilic 5,5',6,6'-tetrachlorobenzimidacarbocyanine (TBC) dye derivatives with aminopropanediol head groups, which only differ in stereochemistry (chiral enantiomers, meso form and conformer), are reported. For the achiral meso form, a new synthetic route towards asymmetric cyanine dyes was established. All compounds form J aggregates in water, the optical properties of which were characterised by means of spectroscopic methods. The supramolecular structure of the aggregates is investigated by means of cryo-transmission electron microscopy, cryo-electron tomography and AFM, revealing extended sheet-like aggregates for chiral enantiomers and nanotubes for the mesomer, respectively, whereas the conformer forms predominately needle-like crystals. The experiments demonstrate that the aggregation behaviour of compounds can be controlled solely by head group stereochemistry, which in the case of enantiomers enables the formation of extended hydrogen-bond chains by the hydroxyl functionalities. In case of the achiral meso form, however, such chains turned out to be sterically excluded.
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Affiliation(s)
- Boris Schade
- Forschungszentrum für Elektronenmikroskopie und Gerätezentrum BioSupraMolInstitut für Chemie und BiochemieFreie Universität BerlinFabeckstraße 36a14195BerlinGermany
| | - Abhishek Kumar Singh
- Institut für Chemie und BiochemieOrganische ChemieFreie Universität BerlinTakustrasse 314195BerlinGermany
| | - Virginia Wycisk
- Institut für Chemie und BiochemieOrganische ChemieFreie Universität BerlinTakustrasse 314195BerlinGermany
| | - Jose Luis Cuellar‐Camacho
- Institut für Chemie und BiochemieOrganische ChemieFreie Universität BerlinTakustrasse 314195BerlinGermany
| | - Hans von Berlepsch
- Forschungszentrum für Elektronenmikroskopie und Gerätezentrum BioSupraMolInstitut für Chemie und BiochemieFreie Universität BerlinFabeckstraße 36a14195BerlinGermany
| | - Rainer Haag
- Institut für Chemie und BiochemieOrganische ChemieFreie Universität BerlinTakustrasse 314195BerlinGermany
| | - Christoph Böttcher
- Forschungszentrum für Elektronenmikroskopie und Gerätezentrum BioSupraMolInstitut für Chemie und BiochemieFreie Universität BerlinFabeckstraße 36a14195BerlinGermany
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15
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Wu W, Wang C, Xu H, Wang J, Zhong Y, Zhang L, Chen Z, Sui X, Mao Z. Study of the aggregation behaviour of three primary reactive dyes via molecular dynamics simulations. MOLECULAR SIMULATION 2020. [DOI: 10.1080/08927022.2020.1755037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Wei Wu
- Key Lab of Science and Technology of Eco-textile, Ministry of Education, National Engineering Research Center for Dyeing and Finishing of Textiles, College of Chemistry, Chemical Engineering and Biotechnology, Innovation Centre for Textile Science and Technology, Donghua University, Shanghai, People’s Republic of China
| | - Chunyi Wang
- Key Lab of Science and Technology of Eco-textile, Ministry of Education, National Engineering Research Center for Dyeing and Finishing of Textiles, College of Chemistry, Chemical Engineering and Biotechnology, Innovation Centre for Textile Science and Technology, Donghua University, Shanghai, People’s Republic of China
| | - Hong Xu
- Key Lab of Science and Technology of Eco-textile, Ministry of Education, National Engineering Research Center for Dyeing and Finishing of Textiles, College of Chemistry, Chemical Engineering and Biotechnology, Innovation Centre for Textile Science and Technology, Donghua University, Shanghai, People’s Republic of China
| | - Jian Wang
- Jifa Group Co. Ltd, Qingdao, People’s Republic of China
| | - Yi Zhong
- Key Lab of Science and Technology of Eco-textile, Ministry of Education, National Engineering Research Center for Dyeing and Finishing of Textiles, College of Chemistry, Chemical Engineering and Biotechnology, Innovation Centre for Textile Science and Technology, Donghua University, Shanghai, People’s Republic of China
| | - Linping Zhang
- Key Lab of Science and Technology of Eco-textile, Ministry of Education, National Engineering Research Center for Dyeing and Finishing of Textiles, College of Chemistry, Chemical Engineering and Biotechnology, Innovation Centre for Textile Science and Technology, Donghua University, Shanghai, People’s Republic of China
| | - Zhize Chen
- Key Lab of Science and Technology of Eco-textile, Ministry of Education, National Engineering Research Center for Dyeing and Finishing of Textiles, College of Chemistry, Chemical Engineering and Biotechnology, Innovation Centre for Textile Science and Technology, Donghua University, Shanghai, People’s Republic of China
| | - Xiaofeng Sui
- Key Lab of Science and Technology of Eco-textile, Ministry of Education, National Engineering Research Center for Dyeing and Finishing of Textiles, College of Chemistry, Chemical Engineering and Biotechnology, Innovation Centre for Textile Science and Technology, Donghua University, Shanghai, People’s Republic of China
| | - Zhiping Mao
- Key Lab of Science and Technology of Eco-textile, Ministry of Education, National Engineering Research Center for Dyeing and Finishing of Textiles, College of Chemistry, Chemical Engineering and Biotechnology, Innovation Centre for Textile Science and Technology, Donghua University, Shanghai, People’s Republic of China
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16
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Sun X, Li HJ, Ou N, Lyu B, Gui B, Tian S, Qian D, Wang X, Yang J. Visible-Light Driven TiO₂ Photocatalyst Coated with Graphene Quantum Dots of Tunable Nitrogen Doping. Molecules 2019; 24:E344. [PMID: 30669386 PMCID: PMC6359080 DOI: 10.3390/molecules24020344] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 01/16/2019] [Accepted: 01/17/2019] [Indexed: 01/20/2023] Open
Abstract
Nitrogen doped graphene quantum dots (NGQDs) were successfully prepared via a hydrothermal method using citric acid and urea as the carbon and nitrogen precursors, respectively. Due to different post-treatment processes, the obtained NGQDs with different surface modifications exhibited blue light emission, while their visible-light absorption was obviously different. To further understand the roles of nitrogen dopants and N-containing surface groups of NGQDs in the photocatalytic performance, their corresponding composites with TiO₂ were utilized to degrade RhB solutions under visible-light irradiation. A series of characterization and photocatalytic performance tests were carried out, which demonstrated that NGQDs play a significant role in enhancing visible-light driven photocatalytic activity and the carrier separation process. The enhanced photocatalytic activity of the NGQDs/TiO₂ composites can possibly be attributed to an enhanced visible light absorption ability, and an improved separation and transfer rate of photogenerated carriers.
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Affiliation(s)
- Xiong Sun
- School of Materials Science and Technology, University of Shanghai for Science and Technology, No. 516 Jungong Rd., Shanghai 200093, China.
| | - Hui-Jun Li
- School of Materials Science and Technology, University of Shanghai for Science and Technology, No. 516 Jungong Rd., Shanghai 200093, China.
| | - Nanquan Ou
- School of Materials Science and Technology, University of Shanghai for Science and Technology, No. 516 Jungong Rd., Shanghai 200093, China.
| | - Bowen Lyu
- School of Materials Science and Technology, University of Shanghai for Science and Technology, No. 516 Jungong Rd., Shanghai 200093, China.
| | - Bojie Gui
- School of Materials Science and Technology, University of Shanghai for Science and Technology, No. 516 Jungong Rd., Shanghai 200093, China.
| | - Shiwei Tian
- School of Materials Science and Technology, University of Shanghai for Science and Technology, No. 516 Jungong Rd., Shanghai 200093, China.
| | - Dongjin Qian
- Department of Chemistry, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, No. 220 Handan Rd., Shanghai 200433, China.
| | - Xianying Wang
- School of Materials Science and Technology, University of Shanghai for Science and Technology, No. 516 Jungong Rd., Shanghai 200093, China.
| | - Junhe Yang
- School of Materials Science and Technology, University of Shanghai for Science and Technology, No. 516 Jungong Rd., Shanghai 200093, China.
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17
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Lincoln CN, Block M, Baudisch B, Malevich P, von Berlepsch H, Riedle E, Hauer J. Exciton-Exciton Annihilation as a Mechanism for Uphill Transfer in a Molecular Excitonic System. EPJ WEB OF CONFERENCES 2019. [DOI: 10.1051/epjconf/201920506017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Exciton dynamics in a HJ-aggregate of cyanine dye TTBC are investigated by transient absorption with a time resolution of <60 fs and power-dependent emission spectroscopies. Both measurements are consistent with an exciton delocalization length of ~28 monomers. A model assuming diffusive exciton motion reveals that the exciton mobility is at least bimodal and restricted to one spatial dimension. J-band diffusion rates of 2.69 and 2.79e-3 cm2s-1 are found, leading to maximal diffusion lengths of 449 and 14.5 nm. The findings indicate that exciton-exciton annihilation is the origin of effective uphill transfer. This mechanism, if present under solar radiation, maybe useful for organic photovoltaic systems.
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18
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Fothergill JW, Hernandez AC, Knowlton WB, Yurke B, Li L. Ab Initio Studies of Exciton Interactions of Cy5 Dyes. J Phys Chem A 2018; 122:8989-8997. [PMID: 30380862 DOI: 10.1021/acs.jpca.8b05237] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The excited state properties of cyanine dyes and the orientations of their aggregates were studied using density functional theory (DFT). The effects of exchange-correlation functional and solvent model on the absorption spectrum of Cy5 was investigated. Using the 6-31+G(d,p) basis set and B3LYP exchange-correlation functional with IEF-PCM (water) solvent, the predicted spectrum achieved a maximum absorbance within 0.007 eV of experiment. An in-house program based on the theoretical model of Kühn, Renger, and May (KRM), which predicts the orientation of dyes within an aggregate from its absorbance and circular dichroism (CD) spectra or vice versa, was used to investigate the orientation of an experimentally observed dimer. The absorbance spectrum predicted using the KRM model of the dimer structure optimized with the 6-31+G(d,p) basis set, ωB97XD exchange-correlation functional, and IEF-PCM solvent agrees with experimental data.
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Affiliation(s)
- Jenny W Fothergill
- Micron School of Materials Science and Engineering , Boise State University , Boise , Idaho 83725 , United States
| | - Andres C Hernandez
- Micron School of Materials Science and Engineering , Boise State University , Boise , Idaho 83725 , United States
| | - William B Knowlton
- Micron School of Materials Science and Engineering , Boise State University , Boise , Idaho 83725 , United States.,Department of Electrical and Computer Engineering , Boise State University , Boise , Idaho 83725 , United States
| | - Bernard Yurke
- Micron School of Materials Science and Engineering , Boise State University , Boise , Idaho 83725 , United States.,Department of Electrical and Computer Engineering , Boise State University , Boise , Idaho 83725 , United States
| | - Lan Li
- Micron School of Materials Science and Engineering , Boise State University , Boise , Idaho 83725 , United States.,Center for Advanced Energy Studies , Idaho Falls , Idaho 83401 , United States
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19
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Frederix PWJM, Patmanidis I, Marrink SJ. Molecular simulations of self-assembling bio-inspired supramolecular systems and their connection to experiments. Chem Soc Rev 2018; 47:3470-3489. [PMID: 29688238 PMCID: PMC5961611 DOI: 10.1039/c8cs00040a] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Indexed: 01/01/2023]
Abstract
In bionanotechnology, the field of creating functional materials consisting of bio-inspired molecules, the function and shape of a nanostructure only appear through the assembly of many small molecules together. The large number of building blocks required to define a nanostructure combined with the many degrees of freedom in packing small molecules has long precluded molecular simulations, but recent advances in computational hardware as well as software have made classical simulations available to this strongly expanding field. Here, we review the state of the art in simulations of self-assembling bio-inspired supramolecular systems. We will first discuss progress in force fields, simulation protocols and enhanced sampling techniques using recent examples. Secondly, we will focus on efforts to enable the comparison of experimentally accessible observables and computational results. Experimental quantities that can be measured by microscopy, spectroscopy and scattering can be linked to simulation output either directly or indirectly, via quantum mechanical or semi-empirical techniques. Overall, we aim to provide an overview of the various computational approaches to understand not only the molecular architecture of nanostructures, but also the mechanism of their formation.
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Affiliation(s)
- Pim W. J. M. Frederix
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials , University of Groningen , Groningen , The Netherlands . ;
| | - Ilias Patmanidis
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials , University of Groningen , Groningen , The Netherlands . ;
| | - Siewert J. Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials , University of Groningen , Groningen , The Netherlands . ;
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20
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Prokhorov VV, Pozin SI, Perelygina OM, Mal'tsev EI. Crystallography and Molecular Arrangement of Polymorphic Monolayer J-Aggregates of a Cyanine Dye: Multiangle Polarized Light Fluorescence Optical Microscopy Study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:4803-4810. [PMID: 29601203 DOI: 10.1021/acs.langmuir.8b01008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The molecular orientation in monolayer J-aggregates of 3,3-di(γ-sulfopropyl)-5,5-dichlorotiamonomethinecyanine dye has been precisely estimated using improved linear polarization measurements in the fluorescence microscope in which a multiangle set of polarization data is obtained using sample rotation. The estimated molecular orientation supplemented with the previously established crystallographic constraints based on the analysis of the well-developed two-dimensional J-aggregate shapes unambiguously indicate the staircase type of molecular arrangement for striplike J-aggregates with the staircases oriented along strips. The molecular transition dipoles are inclined at an angle of ∼25° to the strip direction, whereas the characteristic strip vertex angle ∼45° is formed by the [100] and [1-10] directions of the monoclinic unit cell. Measurements of the geometry of partially unwound tubes and their polarization properties support the model of tube formation by close-packed helical winding of flexible monolayer strips. In the tubes, the long molecular axes are oriented at a small angle in the range of 5-15° to the normal to the tube axis providing low bending energy. At a nanoscale, high-resolution atomic force microscopy imaging of J-aggregate monolayers reveals a complex quasi-one-dimensional organization.
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Affiliation(s)
- Valery V Prokhorov
- 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
| | - Olga M Perelygina
- 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
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21
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Hestand NJ, Spano FC. Expanded Theory of H- and J-Molecular Aggregates: The Effects of Vibronic Coupling and Intermolecular Charge Transfer. Chem Rev 2018; 118:7069-7163. [PMID: 29664617 DOI: 10.1021/acs.chemrev.7b00581] [Citation(s) in RCA: 742] [Impact Index Per Article: 123.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The electronic excited states of molecular aggregates and their photophysical signatures have long fascinated spectroscopists and theoreticians alike since the advent of Frenkel exciton theory almost 90 years ago. The influence of molecular packing on basic optical probes like absorption and photoluminescence was originally worked out by Kasha for aggregates dominated by Coulombic intermolecular interactions, eventually leading to the classification of J- and H-aggregates. This review outlines advances made in understanding the relationship between aggregate structure and photophysics when vibronic coupling and intermolecular charge transfer are incorporated. An assortment of packing geometries is considered from the humble molecular dimer to more exotic structures including linear and bent aggregates, two-dimensional herringbone and "HJ" aggregates, and chiral aggregates. The interplay between long-range Coulomb coupling and short-range charge-transfer-mediated coupling strongly depends on the aggregate architecture leading to a wide array of photophysical behaviors.
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Affiliation(s)
- Nicholas J Hestand
- Department of Chemistry , Temple University , Philadelphia , Pennsylvania 19122 , United States
| | - Frank C Spano
- Department of Chemistry , Temple University , Philadelphia , Pennsylvania 19122 , United States
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22
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Lindorfer D, Renger T. Theory of Anisotropic Circular Dichroism of Excitonically Coupled Systems: Application to the Baseplate of Green Sulfur Bacteria. J Phys Chem B 2018; 122:2747-2756. [PMID: 29420888 DOI: 10.1021/acs.jpcb.7b12832] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A simple exciton theory for the description of anisotropic circular dichroism (ACD) spectra of multichromophoric systems is presented that is expected to be of general use for the analysis of structure-function relationships of molecular aggregates such as photosynthetic light-harvesting antennae. The theory is applied to the baseplate of green sulfur bacteria. It is demonstrated that only the combined analysis of ACD and circular dichroism (CD) spectra for the present baseplate bacteriochlorophyll (BChl) a dimer allows for an unambiguous determination of the parameters of the exciton Hamiltonian from experimental data. The analysis of experimental absorption and linear dichroism spectra suggests that either the NMR structure has to be refined or in addition to the dimers seen in the NMR structure and in the CD and ACD spectra, BChl a monomers are present in the baseplate carotenosome sample. A refined dimer structure is presented, explaining all four optical spectra.
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Affiliation(s)
- Dominik Lindorfer
- Institut für Theoretische Physik , Johannes Kepler Universität Linz , Altenberger Str. 69 , 4040 Linz , Austria
| | - Thomas Renger
- Institut für Theoretische Physik , Johannes Kepler Universität Linz , Altenberger Str. 69 , 4040 Linz , Austria
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23
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Tiwari V, Jonas DM. Electronic energy transfer through non-adiabatic vibrational-electronic resonance. II. 1D spectra for a dimer. J Chem Phys 2018; 148:084308. [DOI: 10.1063/1.5003193] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Vivek Tiwari
- Department of Chemistry and Biochemistry, University of Colorado, 215 UCB, Boulder, Colorado 80309, USA
| | - David M. Jonas
- Department of Chemistry and Biochemistry, University of Colorado, 215 UCB, Boulder, Colorado 80309, USA
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24
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Berlepsch HV, Böttcher C. Tubular J-aggregates of a new thiacarbocyanine Cy5 dye for the far-red spectral region – a spectroscopic and cryo-transmission electron microscopy study. Phys Chem Chem Phys 2018; 20:18969-18977. [DOI: 10.1039/c8cp03378a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A new phenol-substituted Cy5 dye forms tubular J-aggregates that are active in the far-red spectral region.
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Affiliation(s)
- Hans v. Berlepsch
- Forschungszentrum für Elektronenmikroskopie
- Institut für Chemie und Biochemie
- Freie Universität Berlin
- D-14195 Berlin
- Germany
| | - Christoph Böttcher
- Forschungszentrum für Elektronenmikroskopie
- Institut für Chemie und Biochemie
- Freie Universität Berlin
- D-14195 Berlin
- Germany
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25
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Kriete B, Bondarenko AS, Jumde VR, Franken LE, Minnaard AJ, Jansen TLC, Knoester J, Pshenichnikov MS. Steering Self-Assembly of Amphiphilic Molecular Nanostructures via Halogen Exchange. J Phys Chem Lett 2017; 8:2895-2901. [PMID: 28594561 PMCID: PMC5502413 DOI: 10.1021/acs.jpclett.7b00967] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 06/08/2017] [Indexed: 05/31/2023]
Abstract
In the field of self-assembly, the quest for gaining control over the supramolecular architecture without affecting the functionality of the individual molecular building blocks is intrinsically challenging. By using a combination of synthetic chemistry, cryogenic transmission electron microscopy, optical absorption measurements, and exciton theory, we demonstrate that halogen exchange in carbocyanine dye molecules allows for fine-tuning the diameter of the self-assembled nanotubes formed by these molecules, while hardly affecting the molecular packing determined by hydrophobic/hydrophilic interactions. Our findings open a unique way to study size effects on the optical properties and exciton dynamics of self-assembled systems under well-controlled conditions.
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Affiliation(s)
- Björn Kriete
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
| | - Anna S. Bondarenko
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
| | - Varsha R. Jumde
- Stratingh
Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Linda E. Franken
- Groningen
Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Adriaan J. Minnaard
- Stratingh
Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Thomas L. C. Jansen
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
| | - Jasper Knoester
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
| | - Maxim S. Pshenichnikov
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
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