Voltage dependence of the electron diffraction amplitudes in the ab initio analysis of copper perchlorophthalocyanine

Copper perchlorophthalocyanine has become a model compound for exploring the application of electron microscopic and diffraction methods in high resolution molecular structure research. Because of the scattering contrast between the Cu and Cl heavy atoms and the lighter C and N atoms, it was not possible to determine the structure with electron diffraction data obtained at 100 kV a number of years ago. Dynamical scattering all but obscures the detail in the diffraction data due to the unit cell Fourier transform. Studies at 500 kV had also determined that the electron microscopic images were influenced by dynamic scattering. Since our HVEM can be operated from 100 kV to 1.2 MV in 100 kV steps, we are studying the influence of accelerating voltage on our ability to determine atomic-level molecular structure.We recorded electron diffraction patterns from crystals epitaxially oriented on KCl and tilted 26.5° relative to the beam in order to align the c-axis of the unit cell along the beam direction.

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EDIFF: a program for automated unit-cell determination and indexing of electron diffraction data

Journal of Applied Crystallography ◽

10.1107/s0021889811030731 ◽

2011 ◽

Vol 44 (5) ◽

pp. 1132-1136 ◽

Cited By ~ 5

Author(s):

Linhua Jiang ◽

Dilyana Georgieva ◽

Jan Pieter Abrahams

Keyword(s):

Electron Diffraction ◽

Diffraction Data ◽

Three Dimensional ◽

Unit Cell ◽

Electron Diffraction Data ◽

Cell Determination ◽

Diffraction Patterns ◽

Inorganic Molecules ◽

User Friendly

EDIFFis a new user-friendly software suite for unit-cell determination of three-dimensional nanocrystals from randomly oriented electron diffraction patterns with unknown independent orientations. It can also be used for three-dimensional cell reconstruction from diffraction tilt series. In neither case is exact knowledge of the angular relationship between the patterns required. The unit cell can be validated and the crystal system assigned.EDIFFcan index the reflections in electron diffraction patterns. Thus,EDIFFcan be employed as a first step in reconstructing the three-dimensional atomic structure of organic and inorganic molecules and of proteins from diffraction data. An example illustrates the viability of theEDIFFapproach.

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Molecular Structure of Pyrazinamide: a Critical Assessment of Modern Gas Electron Diffraction Data from Three Laboratories

10.26434/chemrxiv.12254393 ◽

2020 ◽

Author(s):

Arseniy A. Otlyotov ◽

Georgiy V. Girichev ◽

Anatolii N. Rykov ◽

Timo Glodde ◽

Yury Vishnevskiy

Keyword(s):

Molecular Structure ◽

Electron Diffraction ◽

Structure Refinement ◽

Diffraction Method ◽

Detailed Examination ◽

Gas Electron Diffraction ◽

Electron Diffraction Data ◽

Data Sets ◽

Background Elimination ◽

Diffraction Patterns

<div><div>Accuracy and precision of molecular parameters determined by modern gas electron diffraction method</div><div>have been investigated. Diffraction patterns of gaseous pyrazinamide have been measured independently in three laboratories, in Bielefeld (Germany), Ivanovo (Russia) and Moscow (Russia). All data sets have been analysed in equal manner using highly controlled background elimination procedure and flexible restraints in molecular structure refinement. In detailed examination and comparison of the obtained results we have determined the average experimental precision of 0.004 Å for bond lengths and 0.2 degrees for angles. The corresponding average deviations of the refined parameters from the ae-CCSD(T)/ccpwCVTZ theoretical values were 0.003 Å and 0.2 degrees. The average precision for refined amplitudes of interatomic vibrations was determined to be 0.005 Å. It is recommended to take into account these values in calculations of total errors for refined parameters of other molecules with comparable complexity.</div></div><div><br></div>

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