The Shift_and_Fix procedure inEXPO: advances for solvingab initiocrystal structures by powder diffraction data

2017 ◽  
Vol 50 (6) ◽  
pp. 1812-1820 ◽  
Author(s):  
Angela Altomare ◽  
Corrado Cuocci ◽  
Anna Moliterni ◽  
Rosanna Rizzi ◽  
Nicola Corriero ◽  
...  
Keyword(s):  
Ab Initio ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Solution Process ◽  
Direct Methods ◽  
Structure Model ◽  
Powder Diffraction Data ◽  
New Approach ◽  
Chemical Content

The Shift_and_Fix procedure is a new method which has been developed for improving the quality of a structure model obtained by theab initiosolution process from powder diffraction data. The main features of the new approach, which is fully automatic, are as follows: (a) the structure model usually attained at the end of the phasing process by direct methods is shifted partly and randomly; (b) a combination of Fourier map calculation and least-squares cycles has been designed for relocating the shifted atoms onto positions which can finally be moved onto the true ones by the standard model optimization approaches; (c) the Fourier map is calculated using coefficients which depend on the chemical content of the compound under study. When the figure of merit for selecting the best set of phases derived by direct methods does not work well, the ALLTRIALS strategy can be applied: it aims to investigate, automatically and sequentially, all the stored direct methods phasing sets and pick up the correct solution. The Shift_and_Fix method has been applied for improving the structure model calculated by each one of the phasing sets processed by ALLTRIALS. It has been implemented in the computer programEXPOand proved to be effective in providing a better ALLTRIALS outcome and increasing the probability of succeeding in theab initiopowder solution.

Ab initio structure determination of monoclinic 2,2-dihydroxymethylbutanoic acid from synchrotron radiation powder diffraction data: combined use of direct methods and the Monte Carlo method

2001 ◽  
Vol 57 (2) ◽  
pp. 184-189 ◽  
Author(s):  
Yusaku Tanahashi ◽  
Hisayoshi Nakamura ◽  
Satoru Yamazaki ◽  
Yuko Kojima ◽  
Hideshi Saito ◽  
...  
Keyword(s):  
Monte Carlo ◽  
Monte Carlo Method ◽  
Synchrotron Radiation ◽  
Ab Initio ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Rietveld Method ◽  
Direct Methods ◽  
Powder Diffraction Data ◽  
The Monte Carlo Method

The crystal structure of 2,2-dihydroxymethylbutanoic acid (C6H12O4) in monoclinic form has been determined ab initio from synchrotron radiation powder diffraction data. Two O and five C atoms were first derived by direct methods. Two missing O atoms and one C atom were found by the Monte Carlo method without applying constraint to their relative positions. Positional and isotropic displacement parameters of these non-H atoms were refined by the Rietveld method. Molecules are linked by hydrogen bonds and they make sheet-like networks running parallel to the (010) plane. The Monte Carlo method is demonstrated to be a powerful tool for finding missing atoms in partially solved structure.

Direct methods and the solution of organic structures from powder data

2007 ◽  
Vol 40 (2) ◽  
pp. 344-348 ◽  
Author(s):  
Angela Altomare ◽  
Mercedes Camalli ◽  
Corrado Cuocci ◽  
Carmelo Giacovazzo ◽  
Anna Grazia Giuseppina Moliterni ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Organic Compounds ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Direct Methods ◽  
Structure Model ◽  
Powder Diffraction Data ◽  
Complete Structure ◽  
Density Map ◽  
Electron Density Map

The electron density map produced after the application of direct methods to powder diffraction data of organic compounds is usually very approximated: some atoms are missed, other atoms are in false positions, some atoms are imperfectly located and the connectivity is quite low. A new procedure able to recover the complete structure model is described. In this procedure, a better interpretation of the map is combined with geometrical techniques for generating new atomic positions. The application of the new procedure may lead to the recovery of the complete crystal structure.

Advances in space-group determination from powder diffraction data

2007 ◽  
Vol 40 (4) ◽  
pp. 743-748 ◽  
Author(s):  
Angela Altomare ◽  
Mercedes Camalli ◽  
Corrado Cuocci ◽  
Carmelo Giacovazzo ◽  
Anna Grazia Giuseppina Moliterni ◽  
...  
Keyword(s):  
Powder Diffraction ◽  
Diffraction Data ◽  
Large Set ◽  
Powder Diffraction Data ◽  
New Approach ◽  
Extinction Group ◽  
Space Group ◽  
Determination Process ◽  
New Algorithms

The space-group determination process by powder diffraction data is not straightforward. The low accuracy of the reflection intensities may invalidate the calculation of the probability associated to each extinction group that is compatible with the crystal system determined in the indexation step. Here the combination of thezstatistics with two new algorithms is reported: the first checks the quality of each 2θ interval in order to omit doubtfulzestimates from the calculations; the second creates a list of reflections with peaks that weakly overlap with any other peak, in order to check if any of them violates the extinction rules of the extinction symbol. The new approach has been applied to a large set of test structures and proved to be much more efficient than the procedure based only on thezstatistics.

Completion of Crystal Structure with Polyhedral Coordination: A New Procedure

2004 ◽  
Vol 443-444 ◽  
pp. 23-26
Author(s):  
Angela Altomare ◽  
Corrado Cuocci ◽  
Carmelo Giacovazzo ◽  
Anna Grazia ◽  
Anna Grazia Giuseppina Moliterni ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Prior Information ◽  
Direct Methods ◽  
Structure Model ◽  
Powder Diffraction Data ◽  
Partial Structure ◽  
Structure Solution ◽  
Cation Coordination

The ab-initio crystal structure solution via powder diffraction data is often uncomplete. A recent procedure POLPO [1] aims at completing a partial structure model provided by Direct Methods by exploiting the prior information on the polyhedral coordination of the located atoms (tetrahedral or octahedral) and their connectivity has been developed. The POLPO procedure requires that all the cations are correctly labelled and rightly located. This condition does not always occur, particularly when the data quality is poor. A new method is described which is able to locate missing cations and surrounding anions when the cation coordination is tetrahedral or octahedral.

Test of maximum-entropy methods to solve a small structure ab initio from powder diffraction data

1995 ◽  
Vol 10 (1) ◽  
pp. 34-39 ◽  
Author(s):  
Naoaki Sudo ◽  
Hiroo Hashizume ◽  
Carlos A. M. Carvalho
Keyword(s):  
Ab Initio ◽  
Maximum Entropy ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Direct Methods ◽  
Basis Set ◽  
Powder Diffraction Data ◽  
Minimum Entropy ◽  
Entropy Maximization ◽  
Factor Data

Detailed procedures for solving small crystal structures ab initio with the maximum-entropy (ME) methods using X-ray powder diffraction data are described by determining the structure of the low-pressure phase of magnesium boron nitride, Mg3BN3(L), which was previously solved by one of the authors and co-workers using the Patterson method and the direct methods. The simple ME method devised by Gull, Livesey, and Sivia failed to correctly phase the structure-factor data, leading to noninterpretable electron-density maps. This method, maximizing the entropy under the constraints of the observed structure factors with subsequent incorporation of strong extrapolates in the basis set, trapped the solution in a local entropy maximum, from which there is no way to move. The multisolution method of phase determination by entropy maximization and likelihood evaluation, developed by Bricogne and Gilmore, successfully located all the Mg, B, and N atoms in one cycle of phase extension. The correct solution had a highest log-likelihood gain, but a minimum entropy, among the multisolutions generated by phase permutation.

Completion of crystal structure by powder diffraction data: a new method for locating atoms with polyhedral coordination

2002 ◽  
Vol 35 (4) ◽  
pp. 422-429 ◽  
Author(s):  
Carmelo Giacovazzo ◽  
Angela Altomare ◽  
Corrado Cuocci ◽  
Anna Grazia Giuseppina Moliterni ◽  
Rosanna Rizzi
Keyword(s):  
Crystal Structure ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Direct Methods ◽  
New Method ◽  
Structure Model ◽  
Powder Diffraction Data ◽  
Heavy Atoms ◽  
Structure Solution ◽  
Cation Coordination

Ab initiocrystal structure solutionviapowder diffraction data is often incomplete: frequently, the heavy atoms are correctly located but the light-atom positions are usually unreliable. The recently developed procedurePOLPO[Altomareet al.(2000).J. Appl. Cryst.33, 1305–1310], implemented in theEXPOprogram [Altomareet al.(1999).J. Appl. Cryst.32, 339–340], aims at completing a partial structure model provided by direct methods by exploiting the prior information on the polyhedral coordination of the located atoms (tetrahedral or octahedral) and their connectivity. ThePOLPOprocedure requires that all the cations are correctly labelled and rightly located. This condition does not always occur, particularly when the data quality is poor. A new method is described which is able to locate missing cations and surrounding anions when the cation coordination is tetrahedral or octahedral. The procedure has been successfully checked on different test structures.

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