High-resolution electron microscopy of molecular crystals. II. Image simulation

Abstract

Computer-simulated electron-microscope images have been produced for several different aromatic hydrocarbons, as well as the organometaUic compound chlorinated copper phthalocyanine. Weak-phase-object images are compared with full multislice imaging calculations that include the resolution-limiting effects of limited spatial and temporal coherence; the comparisons indicate a considerable range of focus and thickness where intuitive image interpretation is possible. This favourable situation arises directly from the low atomic numbers of the atoms comprising the molecules and the almost monotonic fall-off with scattering angle of those structure factors within the resolution limit of the microscope. The occurrence and nature of both first-and second-order resolutionlimiting effects on typical 100 and 500 kV images is also discussed.

Electron crystallography

“…Even 2.3 A images of copper perchlorophthalocyanine, where only the molecular quatrefoil outline is seen (O'Keefe, Fryer & Smith, 1983), have been found useful as a starting point for phase extension via the Sayre equation or the tangent formula (Dorset, McCourt, Fryer, Tivol & Turner, 1994;Dorset, Kopp, Fryer & Tivol, 1995). Even 2.3 A images of copper perchlorophthalocyanine, where only the molecular quatrefoil outline is seen (O'Keefe, Fryer & Smith, 1983), have been found useful as a starting point for phase extension via the Sayre equation or the tangent formula (Dorset, McCourt, Fryer, Tivol & Turner, 1994;Dorset, Kopp, Fryer & Tivol, 1995).…”

High resolution electron microscopy of interfaces in chlorinated phthalocyanine molecular crystals

“…Perfect areas of the crystal provided images that could be filtered and processed such that the chlorine atomic columns were visible (Saxton & Koch, 1982) but such averaging techniques could obviously not be applied to nonperiodic regions. However, the quatrefoil shape of the molecule in all suitably oriented areas was clearly resolved so that, on the basis of previously published images (O'Keefe et al, 1983) the position and alignment of each molecular stack was unambiguous right up to, and including, the interface.…”

The Accurate Electron Crystallographic Refinement of Organic Structures Containing Heavy Atoms

“…Phase determination by symbolic addition was sufficient to generate a map with a few identifiable atomic positions and, eventually, after Fourier refinement, the complete structure could be visualised (Dorset, Tivol & Turner, 1991). Other starting phase sets derived from the Fourier transform of electron micrographs (Uyeda, Kobayashi, Ishizuka & Fujiyoshi, 1978-1979O'Keefe, Fryer & Smith, 1983) were also useful for the direct analysis after phase extension via the tangent formula or the Sayre equation (Fan, Xiang, Li, Pan, Uyeda & Fujiyoshi, 1991;Dorset, McCourt, Fryer, Tivol & Turner, 1994;Dorset, Kopp, Fryer & Tivol, 1995). When constraints were imposed on the refinements, chemical bonding parameters in the final model were in good agreement with those found in X-ray determinations of other metal-containing phthalocyanines (Brown, 1968), even though the final kinematical R factor was somewhat higher than expected for typical electron crystallographic determinations.…”