Novel tools for visualizing and exploring intermolecular interactions in molecular crystals

Abstract

A new way of exploring packing modes and intermolecular interactions in molecular crystals is described, using Hirshfeld surfaces to partition crystal space. These molecular Hirshfeld surfaces, so named because they derive from Hirshfeld's stockholder partitioning, divide the crystal into regions where the electron distribution of a sum of spherical atoms for the molecule (the promolecule) dominates the corresponding sum over the crystal (the procrystal). These surfaces reflect intermolecular interactions in a novel visual manner, offering a previously unseen picture of molecular shape in a crystalline environment. Surface features characteristic of different types of intermolecular interactions can be identified, and such features can be revealed by colour coding distances from the surface to the nearest atom exterior or interior to the surface, or by functions of the principal surface curvatures. These simple devices provide a striking and immediate picture of the types of interactions present, and even reflect their relative strengths from molecule to molecule. A complementary two-dimensional mapping is also presented, which summarizes quantitatively the types of intermolecular contacts experienced by molecules in the bulk and presents this information in a convenient colour plot. This paper describes the use of these tools in the compilation of a pictorial glossary of intermolecular interactions, using identifiable patterns of interaction between small molecules to rationalize the often complex mix of interactions displayed by large molecules.

Preparation and characterisation of novel chlorothiazide potassium solid-state salt forms: Intermolecular self assembly suprastructures

“…The crystallographic data was analysed using: Mercury 2.2 (Blessing, 1995), Ortep-3 (Faruggia, 1997) and Platon (Spek, 2003) whereas the program Crystal Explorer 2.1 (McKinnon et al, 2004) was used to visualise and analyse Hirshfeld surfaces of molecules (Hirshfeld, 1977). The enhancement factor of 100% was used in all fingerprint plots to improve visualisation of interactions.…”

In situ crystallization and crystal structure determination of chlorobenzene

“…The Hirshfeld surface analysis [26][27][28] provides a quantitative measure of intermolecular contacts in a crystal structure that can be conveniently visualized as three-dimensional contour plots and two-dimensional fingerprint plots. where r i vdW and r e vdW represents Van der Waals radii of the nearest atoms inside and outside the surface, respectively.…”

Solid-state structures of peapod bearings composed of finite single-wall carbon nanotube and fullerene molecules

“…We show that, even in the solid state, the belt-persistent tubular molecule allows the dynamic motion of the encapsulated C 60 molecule. An inflection-free, smooth surface inside the tube was revealed by a combination of diffraction analysis using a high-flux X-ray beam (18) and graphical inspection using the Hirshfeld surface of the encapsulated C 60 probe (19). The atomic-level structural information at the tube-sphere interface should be valuable and useful for the in-depth understanding of curved π-systems, for the discussion of peapods in the solid state, and for the design of peapod molecular machines in the future.…”