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Title: Ordering, flexibility and frustration in arrays of porphyrin nanorings

Abstract

The regular packing of atoms, molecules and nanoparticles provides the basis for the understanding of structural order within condensed phases of matter. Typically the constituent particles are considered to be rigid with a fixed shape. Here we show, through a combined experimental and numerical study of the adsorption of cyclic porphyrin polymers, nanorings, on a graphite surface, that flexible molecules can exhibit a rich and complex packing behaviour. Depending on the number of porphyrin sub-units within the nanoring we observe either a highly ordered hexagonal phase or frustrated packing driven by directional interactions which for some arrangements is combined with the internal deformation of the cyclic polymer. Frustration and deformation occur in arrays of polymers with ten sub-units since close packing and co-alignment of neighbouring groups cannot be simultaneously realised for nanorings with this internal symmetry.

Authors:
 [1];  [2];  [3]; ORCiD logo [3];  [4];  [1];  [1]; ORCiD logo [1]
  1. Univ. of Nottingham (United Kingdom)
  2. Univ. of Nottingham (United Kingdom); CNR-ISMN Bologna (Italy)
  3. Univ. of Oxford (United Kingdom)
  4. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES)
OSTI Identifier:
1559230
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Nature Communications
Additional Journal Information:
Journal Volume: 10; Journal Issue: 1; Journal ID: ISSN 2041-1723
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY

Citation Formats

Summerfield, Alex, Baldoni, Matteo, Kondratuk, Dmitry V., Anderson, Harry L., Whitelam, Stephen, Garrahan, Juan P., Besley, Elena, and Beton, Peter H. Ordering, flexibility and frustration in arrays of porphyrin nanorings. United States: N. p., 2019. Web. https://doi.org/10.1038/s41467-019-11009-y.
Summerfield, Alex, Baldoni, Matteo, Kondratuk, Dmitry V., Anderson, Harry L., Whitelam, Stephen, Garrahan, Juan P., Besley, Elena, & Beton, Peter H. Ordering, flexibility and frustration in arrays of porphyrin nanorings. United States. https://doi.org/10.1038/s41467-019-11009-y
Summerfield, Alex, Baldoni, Matteo, Kondratuk, Dmitry V., Anderson, Harry L., Whitelam, Stephen, Garrahan, Juan P., Besley, Elena, and Beton, Peter H. Wed . "Ordering, flexibility and frustration in arrays of porphyrin nanorings". United States. https://doi.org/10.1038/s41467-019-11009-y. https://www.osti.gov/servlets/purl/1559230.
@article{osti_1559230,
title = {Ordering, flexibility and frustration in arrays of porphyrin nanorings},
author = {Summerfield, Alex and Baldoni, Matteo and Kondratuk, Dmitry V. and Anderson, Harry L. and Whitelam, Stephen and Garrahan, Juan P. and Besley, Elena and Beton, Peter H.},
abstractNote = {The regular packing of atoms, molecules and nanoparticles provides the basis for the understanding of structural order within condensed phases of matter. Typically the constituent particles are considered to be rigid with a fixed shape. Here we show, through a combined experimental and numerical study of the adsorption of cyclic porphyrin polymers, nanorings, on a graphite surface, that flexible molecules can exhibit a rich and complex packing behaviour. Depending on the number of porphyrin sub-units within the nanoring we observe either a highly ordered hexagonal phase or frustrated packing driven by directional interactions which for some arrangements is combined with the internal deformation of the cyclic polymer. Frustration and deformation occur in arrays of polymers with ten sub-units since close packing and co-alignment of neighbouring groups cannot be simultaneously realised for nanorings with this internal symmetry.},
doi = {10.1038/s41467-019-11009-y},
journal = {Nature Communications},
number = 1,
volume = 10,
place = {United States},
year = {2019},
month = {7}
}

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Works referenced in this record:

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Conformation and Packing of Porphyrin Polymer Chains Deposited Using Electrospray on a Gold Surface
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Conformation and Packing of Porphyrin Polymer Chains Deposited Using Electrospray on a Gold Surface
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    Works referencing / citing this record:

    Chromatic Adaptation of Photosynthetic Membranes
    journal, July 2005


    Host–guest chemistry in two-dimensional supramolecular networks
    journal, January 2016

    • Teyssandier, Joan; Feyter, Steven De; Mali, Kunal S.
    • Chemical Communications, Vol. 52, Issue 77
    • DOI: 10.1039/c6cc05256h

    cp2k: atomistic simulations of condensed matter systems
    journal, June 2013

    • Hutter, Jürg; Iannuzzi, Marcella; Schiffmann, Florian
    • Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 4, Issue 1
    • DOI: 10.1002/wcms.1159

    Template-Directed Synthesis of a π-Conjugated Porphyrin Nanoring
    journal, April 2007

    • Hoffmann, Markus; Wilson, Craig J.; Odell, Barbara
    • Angewandte Chemie International Edition, Vol. 46, Issue 17
    • DOI: 10.1002/anie.200604601

    Conformation and Packing of Porphyrin Polymer Chains Deposited Using Electrospray on a Gold Surface
    journal, October 2010

    • Saywell, Alex; Sprafke, Johannes K.; Esdaile, Louisa J.
    • Angewandte Chemie International Edition, Vol. 49, Issue 48
    • DOI: 10.1002/anie.201004896

    Elementary Structural Motifs in a Random Network of Cytosine Adsorbed on a Gold(111) Surface
    journal, January 2008


    Quasicrystallinity expressed in two-dimensional coordination networks
    journal, May 2016

    • Urgel, José I.; Écija, David; Lyu, Guoqing
    • Nature Chemistry, Vol. 8, Issue 7
    • DOI: 10.1038/nchem.2507

    Random two-dimensional string networks based on divergent coordination assembly
    journal, January 2010

    • Marschall, Matthias; Reichert, Joachim; Weber-Bargioni, Alexander
    • Nature Chemistry, Vol. 2, Issue 2
    • DOI: 10.1038/nchem.503

    Building molecular wires from the colours of life: conjugated porphyrin oligomers
    journal, January 1999


    Vernier templating and synthesis of a 12-porphyrin nano-ring
    journal, January 2011

    • O’Sullivan, Melanie C.; Sprafke, Johannes K.; Kondratuk, Dmitry V.
    • Nature, Vol. 469, Issue 7328
    • DOI: 10.1038/nature09683

    Frontiers of supramolecular chemistry at solid surfaces
    journal, January 2017

    • Mali, Kunal S.; Pearce, Nicholas; De Feyter, Steven
    • Chemical Society Reviews, Vol. 46, Issue 9
    • DOI: 10.1039/c7cs00113d

    Hard-disk equation of state: First-order liquid-hexatic transition in two dimensions with three simulation methods
    journal, April 2013


    Mechanical Stiffening of Porphyrin Nanorings through Supramolecular Columnar Stacking
    journal, June 2013

    • Svatek, Simon A.; Perdigão, Luis M. A.; Stannard, Andrew
    • Nano Letters, Vol. 13, Issue 7
    • DOI: 10.1021/nl4017557

    A molecular overlayer with the Fibonacci square grid structure
    journal, August 2018


    Random Tiling and Topological Defects in a Two-Dimensional Molecular Network
    journal, November 2008


    Self-assembly of hydrogen-bonded two-dimensional quasicrystals
    journal, March 2014

    • Wasio, Natalie A.; Quardokus, Rebecca C.; Forrest, Ryan P.
    • Nature, Vol. 507, Issue 7490
    • DOI: 10.1038/nature12993

    Ultrafast delocalization of excitation in synthetic light-harvesting nanorings
    journal, January 2015

    • Yong, Chaw-Keong; Parkinson, Patrick; Kondratuk, Dmitry V.
    • Chemical Science, Vol. 6, Issue 1
    • DOI: 10.1039/c4sc02424a

    Broken symmetry and the variation of critical properties in the phase behaviour of supramolecular rhombus tilings
    journal, November 2011

    • Stannard, Andrew; Russell, James C.; Blunt, Matthew O.
    • Nature Chemistry, Vol. 4, Issue 2
    • DOI: 10.1038/nchem.1199

    Fast Parallel Algorithms for Short-Range Molecular Dynamics
    journal, March 1995


    The architecture and function of the light-harvesting apparatus of purple bacteria: from single molecules to in vivo membranes
    journal, August 2006

    • Cogdell, Richard J.; Gall, Andrew; Köhler, Jürgen
    • Quarterly Reviews of Biophysics, Vol. 39, Issue 3
    • DOI: 10.1017/s0033583506004434

    Vernier-Templated Synthesis, Crystal Structure, and Supramolecular Chemistry of a 12-Porphyrin Nanoring
    journal, August 2014

    • Kondratuk, Dmitry V.; Sprafke, Johannes K.; O'Sullivan, Melanie C.
    • Chemistry - A European Journal, Vol. 20, Issue 40
    • DOI: 10.1002/chem.201403714

    A Multivalent Hexapod: Conformational Dynamics of Six-Legged Molecules in Self-Assembled Monolayers at a Solid−Liquid Interface
    journal, March 2009

    • Xu, Hong; Minoia, Andrea; Tomović, Željko
    • ACS Nano, Vol. 3, Issue 4
    • DOI: 10.1021/nn900131k

    Anisotropy of building blocks and their assembly into complex structures
    journal, August 2007

    • Glotzer, Sharon C.; Solomon, Michael J.
    • Nature Materials, Vol. 6, Issue 8, p. 557-562
    • DOI: 10.1038/nmat1949

    Supramolecular Assemblies on Surfaces: Nanopatterning, Functionality, and Reactivity
    journal, June 2018


    Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids
    journal, January 1996

    • Jorgensen, William L.; Maxwell, David S.; Tirado-Rives, Julian
    • Journal of the American Chemical Society, Vol. 118, Issue 45
    • DOI: 10.1021/ja9621760

    Assembling molecular Sierpiński triangle fractals
    journal, March 2015

    • Shang, Jian; Wang, Yongfeng; Chen, Min
    • Nature Chemistry, Vol. 7, Issue 5
    • DOI: 10.1038/nchem.2211

    Shape change in crystallization of biological macromolecules
    journal, May 2016

    • Vekilov, Peter G.; Chung, Sungwook; Olafson, Katy N.
    • MRS Bulletin, Vol. 41, Issue 5
    • DOI: 10.1557/mrs.2016.87

    Perspective on the Martini model
    journal, January 2013

    • Marrink, Siewert J.; Tieleman, D. Peter
    • Chemical Society Reviews, Vol. 42, Issue 16
    • DOI: 10.1039/c3cs60093a

    Lanthanide-Directed Assembly of Interfacial Coordination Architectures–From Complex Networks to Functional Nanosystems
    journal, January 2018


    MARTINI Model for Physisorption of Organic Molecules on Graphite
    journal, July 2013

    • Gobbo, Cristian; Beurroies, Isabelle; de Ridder, David
    • The Journal of Physical Chemistry C, Vol. 117, Issue 30
    • DOI: 10.1021/jp402615p

    Five-vertex Archimedean surface tessellation by lanthanide-directed molecular self-assembly
    journal, April 2013

    • Ecija, D.; Urgel, J. I.; Papageorgiou, A. C.
    • Proceedings of the National Academy of Sciences, Vol. 110, Issue 17
    • DOI: 10.1073/pnas.1222713110

    Linear and Cyclic Porphyrin Hexamers as Near-Infrared Emitters in Organic Light-Emitting Diodes
    journal, June 2011

    • Fenwick, Oliver; Sprafke, Johannes K.; Binas, Jonathan
    • Nano Letters, Vol. 11, Issue 6
    • DOI: 10.1021/nl2008778

    Emergent Rhombus Tilings from Molecular Interactions with M -fold Rotational Symmetry
    journal, March 2015


    Supramolecular nesting of cyclic polymers
    journal, February 2015

    • Kondratuk, Dmitry V.; Perdigão, Luís M. A.; Esmail, Ayad M. S.
    • Nature Chemistry, Vol. 7, Issue 4
    • DOI: 10.1038/nchem.2182

    Conformational flexibility facilitates self-assembly of complex DNA nanostructures
    journal, July 2008

    • Zhang, C.; Su, M.; He, Y.
    • Proceedings of the National Academy of Sciences, Vol. 105, Issue 31
    • DOI: 10.1073/pnas.0803841105

    Assembly of Molecular Building Blocks into Integrated Complex Functional Molecular Systems: Structuring Matter Made to Order
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    • Hassan, Zahid; Matt, Yannick; Begum, Salma
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    • DOI: 10.1002/adfm.201907625