DORI reveals the influence of non-covalent interactions on covalent bonding patterns in molecular crystals under pressure

Authors: Benjamin Meyer1, Senja Barthel2, Amber Mace3, Laurent Vannay4, Benoit Guillot5, Berend Smit2, Clémence Corminboeuf1*

  1. Laboratory for Computational Molecular Design (LCMD), Institute of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, (Switzerland) and National Center for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, (Switzerland)
  2. Laboratory of Molecular Simulation (LSMO), Institute of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne (EPFL Valais), CH-1951 Sion, (Switzerland) and National Center for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, (Switzerland)
  3. Laboratory of Molecular Simulation (LSMO), Institute of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne (EPFL Valais), CH-1951 Sion, (Switzerland) and National Center for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, (Switzerland) and Department of Materials and Environmental Chemistry, Stockholm University, SE-10691 Stockholm, (Sweden)
  4. Laboratory for Computational Molecular Design (LCMD), Institute of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, (Switzerland)
  5. Laboratoire CRM2, UMR 7036, Université de Lorraine, F-54506 Vandoeuvre-lès-Nancy, (France)
  • Corresponding author email: clemence.corminboeuf@epfl.ch

DOI10.24435/materialscloud:2019.0006/v1 (version v1, submitted on 06 February 2019)

How to cite this entry

Benjamin Meyer, Senja Barthel, Amber Mace, Laurent Vannay, Benoit Guillot, Berend Smit, Clémence Corminboeuf, DORI reveals the influence of non-covalent interactions on covalent bonding patterns in molecular crystals under pressure, Materials Cloud Archive (2019), doi: 10.24435/materialscloud:2019.0006/v1.

Description

The study of organic molecular crystals under high pressure provides fundamental insight into crystal packing distortions and reveals mechanisms of phase transitions and the crystallization of polymorphs. These solid state transformations can be monitored directly by analyzing electron charge densities that are experimentally obtained at high pressure. However, restricting the analysis to the featureless electron density does not reveal the chemical bonding nature and the existence of intermolecular interactions. This shortcoming can be resolved by the use of the DORI (Density Overlap Region Indicator) descriptor, which is capable of detecting simultaneously both covalent patterns and non-covalent interactions from electron density and its derivatives. Using the biscarbonyl[14]annulene crystal under pressure as an example, we demonstrate how DORI can be exploited on experimental electron densities to reveal and monitor changes in electronic structure patterns resulting from molecular compression. A novel approach based on a flood fill type algorithm is proposed for analyzing the topology of the DORI isosurface. This approach avoids the arbitrarily selection of DORI isovalues and provides an intuitive way to assess how compression packing affects covalent bonding in organic solids.

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Files

File name Size Description
Crystals_Information.tar.gz
MD5MD5: aed6107987ae6cdd77f9644c3651c951
107.6 MiB This file contains the crystal information files of the BCA unit cell at ambient pressure (AP) and at high pressure (HP), the refined experimental electron densities and the computed DORI molecular scalar fields.

License

Files and data are licensed under the terms of the following license: Creative Commons Attribution 4.0 International.

External references

Journal reference
Benjamin Meyer, Senja Barthel, Amber Mace, Laurent Vannay, Benoit Guillot, Berend Smit and Clémence Corminboeuf. Submitted.

Keywords

Molecular scalar fields Organic crystals Topology High pressure

Version history

06 February 2019 [This version]