The Accurate Electron Crystallographic Refinement of Organic Structures Containing Heavy Atoms

Abstract

Prospects for the accurate structure determination of heavy-atom-containing organic crystals were evaluated with electron diffraction data from perchloro and perbromo derivatives of copper phthalocyanine. While the extensive overlap of experimental Patterson maps (from 1200kV intensities) with respective crystal autocorrelation functions explains the success of previous direct structure analyses, it is clear that multiple-scattering perturbations still evident at high voltage will frustrate the determination of accurate bond distances and angles. If, however, the result obtained after direct structure analysis and Fourier refinement is used to position an idealized molecular model (i.e. with chemically reasonable bonding parameters), the correct structure can then be justified by a rotational search coupled with a multislice dynamical calculation. Even though dynamical scattering is not the only major perturbation to such data sets, the resolution-limited correction is still sufficient to identify the correct molecular orientation in the unit cell. Alternatively, an acceptable unconstrained structure refinement can be carried out via a procedure proposed by Huang, Liu, Gu, Xiong, Fan & Li [Acta Cryst. (1996), A52, 152-157]. A phenomenological adjustment of observed intensities, based initially on the heavy-atom positions found in a high-resolution electron micrograph, will permit all light atoms to be observed near their ideal positions in the ensuing Fourier refinement.

Stability Due to Peripheral Halogenation in Phthalocyanine Complexes

“…The V unit is estimated based on accepted statistical sources in the literature~Uyeda et al, 1972bliterature~Uyeda et al, , 1979Kobayashi et al, 1980Kobayashi et al, , 2003Ziolo et al, 1980;Moxon et al, 1981;Isoda et al, 1994;Dorset, 1997;McKeown, 1998;Hashimoto et al, 1999;Schlettwein et al, 2000;Hoshino et al, 2003!. It is also estimated from the density~d ! measurement, according to the equation V unit ϭ M/d{N 0 {10 21~n m 3 !, where M is the molecular mass and N 0 is the Avogadro constant.…”

Fluorescence anisotropy and transient absorption of halogenated silicon(IV) phthalocyanines with axial poly(ethylene-glycol) substituents

“…For biomedical applications, these compounds are also highly desirable because of their hydrophilic and bio-compatible nature. Although halogenated phthalocyanines are well-documented [15][16][17][18], studies of their photophysical properties remain extremely rare [17][18][19]. …”