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

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.