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. 2021 Apr 27;54(Pt 3):1006-1011.
doi: 10.1107/S1600576721002910. eCollection 2021 Jun 1.

CrystalExplorer: a program for Hirshfeld surface analysis, visualization and quantitative analysis of molecular crystals

Peter R Spackman  1 , Michael J Turner  2 , Joshua J McKinnon  2 , Stephen K Wolff  2 , Daniel J Grimwood  2 , Dylan Jayatilaka  2 , Mark A Spackman  2
Affiliations

CrystalExplorer: a program for Hirshfeld surface analysis, visualization and quantitative analysis of molecular crystals

Peter R Spackman et al. J Appl Crystallogr. .

Abstract

CrystalExplorer is a native cross-platform program supported on Windows, MacOS and Linux with the primary function of visualization and investigation of molecular crystal structures, especially through the decorated Hirshfeld surface and its corresponding two-dimensional fingerprint, and through the visualization of void spaces in the crystal via isosurfaces of the promolecule electron density. Over the past decade, significant changes and enhancements have been incorporated into the program, such as the capacity to accurately and quickly calculate and visualize quantitative intermolecular interactions and, perhaps most importantly, the ability to interface with the Gaussian and NWChem programs to calculate quantum-mechanical properties of molecules. The current version, CrystalExplorer21, incorporates these and other changes, and the software can be downloaded and used free of charge for academic research.

Keywords: CrystalExplorer; Hirshfeld surfaces; computer programs; fingerprints; intermolecular interactions; quantum-mechanical properties; visualization.

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Figures

Figure 1
Figure 1
An ensemble of molecular surfaces available in CrystalExplorer, displayed using acetic acid (CSD refcode ACETAC01) as an example structure. HOMO refers to highest occupied molecular orbital. All density plots are calculated at the isovalue of 0.002 a.u., while the electrostatic potential surface is calculated at 0.05 a.u. A B3LYP/6-31G(d,p) wavefunction was used.
Figure 2
Figure 2
An ensemble of HSs for the saccharin molecule (CSD refcode SCCHRN02; Wardell, Low & Glidewell, 2005 ▸) decorated with different properties available in CrystalExplorer. Quantum-mechanical properties were calculated using B3LYP/6-31G(d,p) wavefunctions.
Figure 3
Figure 3
The CrystalExplorer21 graphical window, showcasing an HS (transparent) surrounding a urea molecule in its crystal environment (CSD refcode UREAXX01), alongside its corresponding fingerprint plot. Neighbouring molecules, corresponding to the highlighted interactions, are also present in the view. O⋯H and H⋯O contacts have been highlighted, demonstrating the link between the regions of the HS and the corresponding values on the two-dimensional fingerprint plot. The coloured fragment patch is decorated with the d norm property, and the vectors joining the oxygen atom inside the surface to the two hydrogen atoms outside of it are seen to go through the centre of the red-coloured d norm spot.
Figure 4
Figure 4
Interaction energies for acetic acid (CSD refcode ACETAC01) calculated with the CE-B3LYP model. It can be seen from the interaction-energies table that the catamer hydrogen-bonding motif between the central molecule (highlighted in yellow mesh) and the −x + 1/2, y + 1/2, z + 1/2 symmetry-related molecule (lime green) is by far the strongest interaction among near neighbours, with an interaction energy of −41.2 kJ mol−1.
Figure 5
Figure 5
Energy frameworks for a 3 × 3 × 1 supercell, viewed down the crystallographic b axis for the fivefold interpenetrated adamantane tetracarboxylic acid (CSD refcode GEJVEW) crystal structure. Despite being a hydrogen-bonded organic framework structure, as demonstrated through the electrostatic framework, we can see a tight cohesive framework of dispersion interactions which also underpin the structure of the crystal.
See this image and copyright information in PMC

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