Quantum crystallography: The structure of [18]-annulene.

DOI: 10.14469/hpc/15681 Metadata

Created: 2026-02-01 10:06

Last modified: 2026-02-02 08:00

Author: Henry Rzepa

License: Creative Commons: Public Domain Dedication 1.0

Funding: (none given)

Description

The structure of [18]annulene (CCDC refcode ANULEN03[cite]10.5517/ccdc.csd.cc2gzmz2[/cite]) was re-refined using modern quantum crystallography (NoSpherA2[cite]10.1107/S0021889808042726[/cite],[cite],[cite]10.1039/d0sc05526c[/cite]). To do this, we used Def2-SVP as the basis set and wB97X-V for the method, with a multiplicity of 2 in the settings for the OLEX2 program. The published structure has the molecule sitting across a centre of symmetry so only half of it is unique, and it was found to be disordered with a second orientation of the complete molecule (effectively the macrocycle rotated in plane by ca. 30°) in a ca. 84:16 ratio. This caused trouble with the quantum crystallography refinements as allowing all of the hydrogen atoms to be positionally free (i.e. removing the AFIX commands) and anisotropic at the same time caused 6 of the 8 hydrogen atoms of the minor occupancy component to “wander off” into chemically nonsensical positions, and 4 of the major occupancy plus all 8 of the minor occupancy hydrogen atoms went non positive definite (one of the thermal ellipsoid radii refined to a negative length). However, we discovered that doing the refinement in stages allowed a more settled structure. Starting with the published structure and allowing all of the hydrogen atoms to be positionally free gave a nice stable result. Allowing the hydrogens to go anisotropic afterwards did result in 1 of the major occupancy and all 8 of the minor occupancy hydrogen atoms going non positive definite (n.p.d.), but the positions of the hydrogen atoms remained sensible. Subsequently reverting all 8 hydrogen atoms of the minor occupancy component to be isotropic resulted in a stable and sensible refinement where the sole non positive definite atom of the major occupancy component corrected itself into being normal (i.e. no longer non positive definite). This is the version of the structure we used for further analysis.

Files

FilenameSizeTypeDescription
anulen03-qc-aniso-iso-major-occ-nospherA2.cif 71KB chemical/x-cif CIF file
doceo.out 7MB application/octet-stream ORCA output
doceo_fake.log 634KB chemical/x-gaussian-log Fake Gaussian output

Member of collection / collaboration

DOIDescription
10.14469/hpc/177 Computation data for Henry Rzepa's blog

Associated DOIs

Current dataset ...DOIDescription
References 10.1039/d0sc05526c Accurate crystal structures and chemical properties from NoSpherA2
References 10.1107/S0021889808042726 OLEX2: a complete structure solution, refinement and analysis program

Subject Keywords

KeywordValue
inchi InChI=1S/C8H8.CH/c1-3-5-7-8-6-4-2;/h1-8H;1H/b7-5-,8-6+;
inchi InChI=1S/C35H15F15/c36-31(37,38)26-6-16-1-17(7-26)19-3-21(11-28(9-19)33(42,43)44)23-5-25(15-30(13-23)35(48,49)50)24-4-22(12-29(14-24)34(45,46)47)20-2-18(16)8-27(10-20)32(39,40)41/h1-15H
inchikey VGUAGMSOIQFSPO-KHCQPJBVSA-N
inchikey IDQGTHSVRXASEJ-UHFFFAOYSA-N

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