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Li Y, Castillo HD, Dobscha JR, Morgan AR, Tait SL, Flood AH. Breaking Radial Dipole Symmetry in Planar Macrocycles Modulates Edge-to-Edge Packing and Disrupts Cofacial Stacking. Chemistry 2024; 30:e202302946. [PMID: 37950681 DOI: 10.1002/chem.202302946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 11/13/2023]
Abstract
Dipolar interactions are ever-present in supramolecular architectures, though their impact is typically revealed by making dipoles stronger. While it is also possible to assess the role of dipoles by altering their orientations by using synthetic design, doing so without altering the molecular shape is not straightforward. We have now done this by flipping one triazole unit in a rigid macrocycle, tricarb. The macrocycle is composed of three carbazoles (2 Debye) and three triazoles (5 Debye) defining an array of dipoles aligned radially but organized alternately in and out. These dipoles are believed to dictate edge-to-edge tiling and face-to-face stacking. We modified our synthesis to prepare isosteric macrocycles with the orientation of one triazole dipole rotated 40°. The new dipole orientation guides edge-to-edge contacts to reorder the stability of two surface-bound 2D polymorphs. The impact on dipole-enhanced π stacking, however, was unexpected. Our stacking model identified an unchanged set of short-range (3.4 Å) anti-parallel dipole contacts. Despite this situation, the reduction in self-association was attributed to long-range (~6.4 Å) dipolar repulsions between π-stacked macrocycles. This work highlights our ability to control the build-up and symmetry of macrocyclic skeletons by synthetic design, and the work needed to further our understanding of how dipoles control self-assembly.
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Affiliation(s)
- Yan Li
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, IN, 47405, USA
| | - Henry D Castillo
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, IN, 47405, USA
| | - James R Dobscha
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, IN, 47405, USA
| | - Amanda R Morgan
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, IN, 47405, USA
| | - Steven L Tait
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, IN, 47405, USA
| | - Amar H Flood
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, IN, 47405, USA
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Freibert A, Dieterich JM, Hartke B. Exploring self-organization of molecular tether molecules on a gold surface by global structure optimization. J Comput Chem 2019; 40:1978-1989. [PMID: 31069834 DOI: 10.1002/jcc.25853] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 04/16/2019] [Accepted: 04/22/2019] [Indexed: 11/11/2022]
Abstract
We employ nondeterministic global cluster structure optimization, based on the evolutionary algorithms paradigm, to model the self-assembly of complex molecules on a surface. As a real-life application example directly related to many recent experiments, we use this approach for the assembly of triazatriangulene "platform" molecules on the Au(111) surface. Without additional restrictions like spatial discretizations, coarse-graining or precalculated adsorption poses, and despite the proof-of-principle character of this study, we achieve satisfactory qualitative agreement with several experimental observations and can provide answers to questions that experiments on these species had left open so far. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Antonia Freibert
- Institute for Physical Chemistry, Christian-Albrechts-University, Olshausenstr. 40, 24098, Kiel, Germany.,Department of Chemistry, University College London, Gower Street, London, WC1E 6BT, United Kingdom
| | - Johannnes M Dieterich
- Institute for Physical Chemistry, Christian-Albrechts-University, Olshausenstr. 40, 24098, Kiel, Germany
| | - Bernd Hartke
- Institute for Physical Chemistry, Christian-Albrechts-University, Olshausenstr. 40, 24098, Kiel, Germany
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Vu TH, Wandlowski T. Self-assembly of 8-; 5- and 2-hydroxylquinolines on Au(111) single crystal in perchloric acid. J Electroanal Chem (Lausanne) 2019. [DOI: 10.1016/j.jelechem.2019.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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De Marchi F, Galeotti G, Simenas M, Ji P, Chi L, Tornau EE, Pezzella A, MacLeod J, Ebrahimi M, Rosei F. Self-assembly of 5,6-dihydroxyindole-2-carboxylic acid: polymorphism of a eumelanin building block on Au(111). NANOSCALE 2019; 11:5422-5428. [PMID: 30855042 DOI: 10.1039/c8nr09810g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Investigating two-dimensional (2D) self-assembled structures of biological monomers governed by intermolecular interactions is a prerequisite to understand the self-assembly of more complex biomolecular systems. 5,6-Dihydroxyindole carboxylic acid (DHICA) is one of the building blocks of eumelanin - an irregular heteropolymer and the most common form of melanin which has potential applications in organic electronics and bioelectronics. By means of scanning tunneling microscopy, density functional theory and Monte Carlo calculations, we investigate DHICA molecular configurations and interactions underlying the multiple 2D patterns formed on Au(111). While DHICA self-assembled molecular networks (SAMNs) are dominated by the hydrogen bonding of carboxylic acid dimers, a variety of 2D architectures are formed due to the multiple weak interactions of the catechol group. The hydroxyl group also allows for redox reactions, caused by oxidation via O2 exposure, resulting in molecular rearrangement. The susceptibility of the molecules to oxidation is affected by their SAMNs architectures, giving insights on the reactivity of indoles as well as highlighting non-covalent assembly as an approach to guide selective oxidation reactions.
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Affiliation(s)
- F De Marchi
- Centre Energie, Materiaux et Telecommunications, Institut National de la Recherche Scientifique, 1650 Boulevard Lionel-Boulet, Varennes, QC, Canada J3X 1S2.
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Kim S, Castillo HD, Lee M, Mortensen RD, Tait SL, Lee D. From Foldable Open Chains to Shape-Persistent Macrocycles: Synthesis, Impact on 2D Ordering, and Stimulated Self-Assembly. J Am Chem Soc 2018. [DOI: 10.1021/jacs.8b01805] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Soobin Kim
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Henry D. Castillo
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Milim Lee
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Riley D. Mortensen
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Steven L. Tait
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Dongwhan Lee
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
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Castillo HD, Espinosa-Duran JM, Dobscha JR, Ashley DC, Debnath S, Hirsch BE, Schrecke SR, Baik MH, Ortoleva PJ, Raghavachari K, Flood AH, Tait SL. Amphiphile self-assembly dynamics at the solution-solid interface reveal asymmetry in head/tail desorption. Chem Commun (Camb) 2018; 54:10076-10079. [DOI: 10.1039/c8cc04465a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Asymmetric dynamics in fundamental adsorption and desorption steps drive self-assembly at solution/solid interface.
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Affiliation(s)
| | | | | | | | | | | | | | - Mu-Hyun Baik
- Department of Chemistry
- Indiana University
- Bloomington
- USA
| | | | | | - Amar H. Flood
- Department of Chemistry
- Indiana University
- Bloomington
- USA
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Amabilino DB, Tait SL. Complex molecular surfaces and interfaces: concluding remarks. Faraday Discuss 2017; 204:487-502. [PMID: 29028066 DOI: 10.1039/c7fd90075a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This paper is derived from our concluding remarks presentation and the ensuing conversations at the Faraday Discussions meeting on Complex Molecular Surfaces and Interfaces, Sheffield, UK, 24th-26th July 2017. This meeting was comprised of sessions on understanding the interaction of molecules with surfaces and their subsequent organisation, reactivity or properties from both experimental and theoretical perspectives. This paper attempts to put these presentations in the wider context and focuses on topics that were debated during the meeting and where we feel that opportunities lie for the future development of this interdisciplinary research area.
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Affiliation(s)
- David B Amabilino
- School of Chemistry, The University of Nottingham, NG7 2RD Nottingham, UK.
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Brown RD, Quardokus RC, Wasio NA, Petersen JP, Silski AM, Corcelli SA, Kandel SA. Non-intuitive clustering of 9,10-phenanthrenequinone on Au(111). BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2017; 8:1801-1807. [PMID: 28904841 PMCID: PMC5588540 DOI: 10.3762/bjnano.8.181] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 08/11/2017] [Indexed: 06/07/2023]
Abstract
The direct injection of a 9,10-phenanthrenequinone in tetrahydrofuran solution on a Au(111) substrate in high vacuum results in the formation of metastable clusters with a non-intuitive structure. Metastable, rectangular tetramers of this molecule form in which the net molecular dipoles all orient toward the center of the cluster. This structure does not allow for additional hydrogen bonding and thus the origin of its metastability is not clear. We compare this feature to other structures observed on this surface, as well as those formed during the deposition of 9-fluorenone, which does not exhibit this anomalous clustering behavior.
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Affiliation(s)
- Ryan D Brown
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556 USA
| | | | - Natalie A Wasio
- Department of Chemistry, Tufts University, Medford, MA 02155 USA
| | - Jacob P Petersen
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556 USA
| | - Angela M Silski
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556 USA
| | - Steven A Corcelli
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556 USA
| | - S Alex Kandel
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556 USA
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Hirsch BE, McDonald KP, Tait SL, Flood AH. Physical and chemical model of ion stability and movement within the dynamic and voltage-gated STM tip–surface tunneling junction. Faraday Discuss 2017; 204:159-172. [DOI: 10.1039/c7fd00104e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The interaction and mobility of ions in complex systems are fundamental to processes throughout chemistry, biology, and physics. However, nanoscale characterization of ion stability and migration remains poorly understood. Here, we examine ion movements to and from physisorbed molecular receptors at solution–graphite interfaces by developing a theoretical model alongside experimental scanning tunneling microscopy (STM) results. The model includes van der Waals forces and electrostatic interactions originating from the surface, tip, and physisorbed receptors, as well as a tip–surface electric field arising from the STM bias voltage (Vb). Our model reveals how both the electric field and tip–surface distance, dtip, can influence anion stability at the receptor binding sites on the surface or at the STM tip, as well as the size of the barrier for anion transitions between those locations. These predictions agree well with prior and new STM results from the interactions of anions with aryl-triazole receptors that order into functional monolayers on graphite. Scanning produces clear resolution at large magnitude negative surface biases (−0.8 V) while resolution degrades at small negative surface biases (−0.4 V). The loss in resolution arises from frequent tip retractions assigned to anion migration within the tip–surface tunneling region. This experimental evidence in combination with support from the model demonstrates a local voltage gating of anions with the STM tip inside physisorbed receptors. This generalized model and experimental evidence may help to provide a basis to understand the nanoscale details of related chemical transformations and their underlying thermodynamic and kinetic preferences.
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Affiliation(s)
| | | | | | - Amar H. Flood
- Department of Chemistry
- Indiana University
- Bloomington
- USA
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Abstract
Organic (opto)electronic materials have received considerable attention due to their applications in thin-film-transistors, light-emitting diodes, solar cells, sensors, photorefractive devices, and many others. The technological promises include low cost of these materials and the possibility of their room-temperature deposition from solution on large-area and/or flexible substrates. The article reviews the current understanding of the physical mechanisms that determine the (opto)electronic properties of high-performance organic materials. The focus of the review is on photoinduced processes and on electronic properties important for optoelectronic applications relying on charge carrier photogeneration. Additionally, it highlights the capabilities of various experimental techniques for characterization of these materials, summarizes top-of-the-line device performance, and outlines recent trends in the further development of the field. The properties of materials based both on small molecules and on conjugated polymers are considered, and their applications in organic solar cells, photodetectors, and photorefractive devices are discussed.
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Affiliation(s)
- Oksana Ostroverkhova
- Department of Physics, Oregon State University , Corvallis, Oregon 97331, United States
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Flood AH. Creating molecular macrocycles for anion recognition. Beilstein J Org Chem 2016; 12:611-27. [PMID: 27340452 PMCID: PMC4902025 DOI: 10.3762/bjoc.12.60] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 03/07/2016] [Indexed: 11/23/2022] Open
Abstract
The creation and functionality of new classes of macrocycles that are shape persistent and can bind anions is described. The genesis of triazolophane macrocycles emerges out of activity surrounding 1,2,3-triazoles made using click chemistry; and the same triazoles are responsible for anion capture. Mistakes made and lessons learnt in anion recognition provide deeper understanding that, together with theory, now provides for computer-aided receptor design. The lessons are acted upon in the creation of two new macrocycles. First, cyanostars are larger and like to capture large anions. Second is tricarb, which also favors large anions but shows a propensity to self-assemble in an orderly and stable manner, laying a foundation for future designs of hierarchical nanostructures.
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Affiliation(s)
- Amar H Flood
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
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