Optimal structure determination from sub‐optimal diffraction data

2021 ◽  
Author(s):  
Wladek Minor ◽  
Marcin Cymborowski ◽  
Dominika Borek ◽  
David R. Cooper ◽  
Maksymilian Chruszcz ◽  
...  
Keyword(s):  
Diffraction Data ◽  
Structure Determination ◽  
Optimal Structure

Crystal Structure Determination of Glycerol-Containing Lipids from Electron Diffraction Data. Use of Analog Compounds Based upon Configurational Isomers of Cyclopentane-1, 2, 3-TRIOL

1977 ◽  
Vol 35 ◽  
pp. 24-25
Author(s):  
Douglas L. Dorset ◽  
Anthony J. Hancock
Keyword(s):  
Crystal Structure ◽  
Electron Diffraction ◽  
Diffraction Data ◽  
Structure Determination ◽  
Crystal Surface ◽  
Coherent Scattering ◽  
Crystal Structure Determination ◽  
Electron Diffraction Data ◽  
Polar Group ◽  
Axis Orientation

Lipids containing long polymethylene chains were among the first compounds subjected to electron diffraction structure analysis. It was only recently realized, however, that various distortions of thin lipid microcrystal plates, e.g. bends, polar group and methyl end plane disorders, etc. (1-3), restrict coherent scattering to the methylene subcell alone, particularly if undistorted molecular layers have well-defined end planes. Thus, ab initio crystal structure determination on a given single uncharacterized natural lipid using electron diffraction data can only hope to identify the subcell packing and the chain axis orientation with respect to the crystal surface. In lipids based on glycerol, for example, conformations of long chains and polar groups about the C-C bonds of this moiety still would remain unknown.One possible means of surmounting this difficulty is to investigate structural analogs of the material of interest in conjunction with the natural compound itself. Suitable analogs to the glycerol lipids are compounds based on the three configurational isomers of cyclopentane-1,2,3-triol shown in Fig. 1, in which three rotameric forms of the natural glycerol derivatives are fixed by the ring structure (4-7).

Challenging structure determination from powder diffraction data: two pharmaceutical salts and one cocrystal with Z′ = 2

2019 ◽  
Vol 234 (4) ◽  
pp. 257-268 ◽  
Author(s):  
Carina Schlesinger ◽  
Michael Bolte ◽  
Martin U. Schmidt
Keyword(s):  
Single Crystal ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Structure Determination ◽  
Real Space ◽  
Powder Diffraction Data ◽  
The Real ◽  
Pharmaceutical Salts ◽  
Structure Solution ◽  
Space Method

Abstract Structure solution of molecular crystals from powder diffraction data by real-space methods becomes challenging when the total number of degrees of freedom (DoF) for molecular position, orientation and intramolecular torsions exceeds a value of 20. Here we describe the structure determination from powder diffraction data of three pharmaceutical salts or cocrystals, each with four molecules per asymmetric unit on general position: Lamivudine camphorsulfonate (1, P 21, Z=4, Z′=2; 31 DoF), Theophylline benzamide (2, P 41, Z=8, Z′=2; 23 DoF) and Aminoglutethimide camphorsulfonate hemihydrate [3, P 21, Z=4, Z′=2; 31 DoF (if the H2O molecule is ignored)]. In the salts 1 and 3 the cations and anions have two intramolecular DoF each. The molecules in the cocrystal 2 are rigid. The structures of 1 and 2 could be solved without major problems by DASH using simulated annealing. For compound 3, indexing, space group determination and Pawley fit proceeded without problems, but the structure could not be solved by the real-space method, despite extensive trials. By chance, a single crystal of 3 was obtained and the structure was determined by single-crystal X-ray diffraction. A post-analysis revealed that the failure of the real-space method could neither be explained by common sources of error such as incorrect indexing, wrong space group, phase impurities, preferred orientation, spottiness or wrong assumptions on the molecular geometry or other user errors, nor by the real-space method itself. Finally, is turned out that the structure solution failed because of problems in the extraction of the integrated reflection intensities in the Pawley fit. With suitable extracted reflection intensities the structure of 3 could be determined in a routine way.

scholarly journals Procedure and Computer Programs for the Structure Determination of Gaseous Molecules from Electron Diffraction Data.

1969 ◽  
Vol 23 ◽  
pp. 3224-3234 ◽  
Author(s):  
B. Andersen ◽  
H. M. Seip ◽  
T. G. Strand ◽  
R. Stølevik ◽  
Gunner Borch ◽  
...  
Keyword(s):  
Electron Diffraction ◽  
Diffraction Data ◽  
Structure Determination ◽  
Computer Programs ◽  
Electron Diffraction Data
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