Complete crystal structure of decafluorocyclohex-1-ene at 4.2 K from original neutron diffraction data

2014 ◽  
Vol 70 (2) ◽  
pp. 395-397
Author(s):  
Leonid A. Solovyov ◽  
Alexandr S. Fedorov ◽  
Aleksandr A. Kuzubov
Keyword(s):  
Crystal Structure ◽  
Diffraction Data ◽  
Molecular Orientation ◽  
State Energy ◽  
Structure Model ◽  
Perfect Agreement ◽  
Acta Cryst ◽  
Difference Density ◽  
Density Analysis ◽  
The Difference

The crystal structure model of decafluorocyclohex-1-ene at 4.2 K derived from simulated powder diffraction data and solid-state energy minimization [Smrčoket al.(2013).Acta Cryst.B69, 395–404] is found to be incomplete. In this study it is completed by an additional alternative molecular orientation revealed from the difference density analysis and direct space search. The structure is refined by the derivative difference method in the rigid-body approximation leading to perfect agreement between observed and calculated neutron powder patterns.

scholarly journals Statistical quality indicators for electron-density maps

2012 ◽  
Vol 68 (4) ◽  
pp. 454-467 ◽  
Author(s):  
Ian J. Tickle
Keyword(s):  
Electron Density ◽  
Statistical Significance ◽  
Significance Test ◽  
Real Space ◽  
Structure Model ◽  
Space Correlation ◽  
The Real ◽  
Difference Density ◽  
Density Maps ◽  
The Difference

The commonly used validation metrics for the local agreement of a structure model with the observed electron density, namely the real-space R (RSR) and the real-space correlation coefficient (RSCC), are reviewed. It is argued that the primary goal of all validation techniques is to verify the accuracy of the model, since precision is an inherent property of the crystal and the data. It is demonstrated that the principal weakness of both of the above metrics is their inability to distinguish the accuracy of the model from its precision. Furthermore, neither of these metrics in their usual implementation indicate the statistical significance of the result. The statistical properties of electron-density maps are reviewed and an improved alternative likelihood-based metric is suggested. This leads naturally to a χ2 significance test of the difference density using the real-space difference density Z score (RSZD). This is a metric purely of the local model accuracy, as required for effective model validation and structure optimization by practising crystallographers prior to submission of a structure model to the PDB. A new real-space observed density Z score (RSZO) is also proposed; this is a metric purely of the model precision, as a substitute for other precision metrics such as the B factor.

scholarly journals Ab-initio crystal structure analysis and refinement approaches of oligo p-benzamides based on electron diffraction data

2012 ◽  
Vol 68 (2) ◽  
pp. 171-181 ◽  
Author(s):  
Tatiana E. Gorelik ◽  
Jacco van de Streek ◽  
Andreas F. M. Kilbinger ◽  
Gunther Brunklaus ◽  
Ute Kolb
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Electron Diffraction ◽  
Ab Initio ◽  
Structure Analysis ◽  
Diffraction Data ◽  
Crystal Structure Analysis ◽  
Electron Diffraction Data ◽  
Perfect Agreement ◽  
Bonding Scheme

Ab-initio crystal structure analysis of organic materials from electron diffraction data is presented. The data were collected using the automated electron diffraction tomography (ADT) technique. The structure solution and refinement route is first validated on the basis of the known crystal structure of tri-p-benzamide. The same procedure is then applied to solve the previously unknown crystal structure of tetra-p-benzamide. In the crystal structure of tetra-p-benzamide, an unusual hydrogen-bonding scheme is realised; the hydrogen-bonding scheme is, however, in perfect agreement with solid-state NMR data.

scholarly journals Crystal structure of incommensurate ηʺ-Cu1.235Sn intermetallic

2020 ◽  
Vol 235 (10) ◽  
pp. 445-457 ◽  
Author(s):  
Andreas Leineweber ◽  
Christian Wieser ◽  
Werner Hügel
Keyword(s):  
Crystal Structure ◽  
Diffraction Data ◽  
Local Level ◽  
Unit Cell ◽  
Spatial Modulation ◽  
Group Symmetry ◽  
Electron Diffraction Data ◽  
Temperature Phase ◽  
Structure Model ◽  
Nias Type

AbstractThe crystallographic parameters of the incommensurately ordered phase ηʺ of the composition Cu1.235Sn are reported. This phase belongs to the group of ordered Ni2In/NiAs-type phases, with a NiAs-type arrangement Cu(1)Sn and additional Cu(2) atoms partially occupying trigonal-bipyramidal interstices in an ordered fashion, leading to the formula Cu(1)Cu(2)0.235Sn = Cu1.235Sn. The structure model, afterward refined on the basis of powder X-ray diffraction data, has been derived on the basis of the slightly Cu-poorer commensurately ordered η′-Cu6Sn5 (=Cu1.2Sn) phase but also on previously reported commensurate structure models η8-Cu1.25Sn and η4+1-Cu1.243Sn derived from selected area electron diffraction data. In line with a recent work (Leineweber, Wieser & Hügel, Scr. Mater. 2020, 183, 66–70), the incommensurate ηʺ phase is regarded as a metastable phase formed upon partitionless ordering of the η high-temperature phase with absent long-range ordering of the Cu(2) atoms. The previously described η8 and η4+1 superstructure are actually of the same phase, and the corresponding superstructure models can be regarded as approximant structures of the ηʺ phase.The refined structure model is described in 3+1 dimensional superspace group symmetry C2/c(q10-q3)00 with a unit cell of the average structure with lattice parameters of aav = 4.21866(3) Å, bav = 7.31425(5) Å, cav = 5.11137(3) Å and bav = 90.2205(5)° and a unit cell volume V = 157.717(2) Å3. The modulation vector is with q1 = 0.76390(4), q3 = 1.51135(5), and governs the spatial modulation of the occupancy of the Cu(2) atoms described by a Crenel function. The occupational ordering is accompanied by displacive modulations of the atoms constituting the crystal structure, ensuring reasonable interatomic distances on a local level. In particular, the spatial requirements of pairs of edge-sharing Cu(2)Sn5 trigonal bipyramids (Cu(2)2Sn8) lead to a measurable splitting of some fundamental reflections in the powder diffraction data. This splitting is considerable smaller in η′-Cu1.20Sn, which lacks such pairs due to the lower Cu content.

scholarly journals A second polymorph of sodium dihydrogen citrate, NaH2C6H5O7: structure solution from powder diffraction data and DFT comparison

2016 ◽  
Vol 72 (6) ◽  
pp. 854-857 ◽  
Author(s):  
Alagappa Rammohan ◽  
James A. Kaduk
Keyword(s):  
Crystal Structure ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Density Functional ◽  
Powder Diffraction Data ◽  
Commercial Sample ◽  
Acta Cryst ◽  
Coordination Polyhedra ◽  
Structure Solution ◽  
Sodium Dihydrogen

The crystal structure of a second polymorph of sodium dihydrogen citrate, Na+·H2C6H5O7−, has been solved and refined using laboratory X-ray powder diffraction data, and optimized using density functional techniques. The powder pattern of the commercial sample used in this study did not match that corresponding to the known crystal structure [Gluskeret al.(1965).Acta Cryst.19, 561–572; refcode NAHCIT]. In this polymorph, the [NaO7] coordination polyhedra form edge-sharing chains propagating along theaaxis, while in NAHCIT the octahedral [NaO6] groups form edge-sharing pairs bridged by two hydroxy groups. The most notable difference is that in this polymorph one of the terminal carboxyl groups is deprotonated, while in NAHCIT the central carboxylate group is deprotonated, as is more typical.

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.

scholarly journals Deciphering the hydrogen-bonding scheme in the crystal structure of triphenylmethanol: a tribute to George Ferguson and co-workers

2019 ◽  
Vol 75 (9) ◽  
pp. 1266-1273
Author(s):  
Tomasa Rodríguez Tzompantzi ◽  
Aldo Guillermo Amaro Hernández ◽  
Rosa Luisa Meza-León ◽  
Sylvain Bernès
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Diffraction Data ◽  
Racemic Mixture ◽  
Asymmetric Unit ◽  
Acta Cryst ◽  
Reliable Determination ◽  
Space Group ◽  
Positional Disorder ◽  
Bonding Scheme

The crystal structure of triphenylmethanol, C19H16O, has been redetermined using data collected at 295 and 153 K, and is compared to the model published by Ferguson et al. over 25 years ago [Ferguson et al. (1992). Acta Cryst. C48, 1272–1275] and that published by Serrano-González et al., using neutron and X-ray diffraction data [Serrano-González et al. (1999). J. Phys. Chem. B, 103, 6215–6223]. As predicted by these authors, the hydroxy groups are involved in weak intermolecular hydrogen bonds in the crystal, forming tetrahedral tetramers based on the two independent molecules in the asymmetric unit, one of which is placed on the threefold symmetry axis of the R\overline{3} space group. However, the reliable determination of the hydroxy H-atom positions is difficult to achieve, for two reasons. Firstly, a positional disorder affects the full asymmetric unit, which is split over two sets of positions, with occupancy factors of ca 0.74 and 0.26. Secondly, all hydroxy H atoms are further disordered, either by symmetry, or through a positional disorder in the case of parts placed in general positions. We show that the correct description of the hydrogen-bonding scheme is possible only if diffraction data are collected at low temperature. The prochiral character of the hydrogen-bonded tetrameric supramolecular clusters leads to enantiomorphic three-dimensional graphs in each tetramer. The crystal is thus a racemic mixture of sup S and sup R motifs, consistent with the centrosymmetric nature of the R\overline{3} space group.

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.

scholarly journals Crystal structure of strontium perchlorate anhydrate, Sr(ClO4)2, from laboratory powder X-ray diffraction data

2019 ◽  
Vol 75 (4) ◽  
pp. 447-450
Author(s):  
Jooeun Hyoung ◽  
Hyeon Woo Lee ◽  
So Jin Kim ◽  
Hong Rim Shin ◽  
Seung-Tae Hong
Keyword(s):  
Crystal Structure ◽  
Diffraction Data ◽  
Bond Valence ◽  
Structure Model ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
Orthorhombic Space Group ◽  
Space Group ◽  
X Ray ◽  
Wyckoff Position

The crystal structure of strontium perchlorate anhydrate, Sr(ClO4)2, was determined and refined from laboratory powder X-ray diffraction data. The material was obtained by dehydration of Sr(ClO4)2·3H2O at 523 K for two weeks. It crystallizes in the orthorhombic space group Pbca and is isotypic with Ca(AlD4)2 and Ca(ClO4)2. The asymmetric unit contains one Sr, two Cl and eight O sites, all on general positions (Wyckoff position 8c). The crystal structure consists of Sr2+ cations and isolated ClO4 − tetrahedra. The Sr2+ cation is coordinated by eight O atoms from eight ClO4 − tetrahedra. The validity of the crystal structure model for Sr(ClO4)2 anhydrate was confirmed by the bond valence method.

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.

Revision of the Mg(ClO4)2·4H2O crystal structure

2012 ◽  
Vol 68 (1) ◽  
pp. 89-90 ◽  
Author(s):  
Leonid A. Solovyov
Keyword(s):  
Crystal Structure ◽  
Difference Method ◽  
Rietveld Analysis ◽  
Structure Model ◽  
Magnesium Perchlorate ◽  
Acta Cryst

A revision is presented of the restrained Rietveld analysis of the crystal structure of magnesium perchlorate tetrahydrate, Mg(ClO4)2·4H2O, recently published by Robertson & Bish [(2010), Acta Cryst. B66, 579–584]. The actual symmetry of the material is shown to be C2/m. The corrected structure model is refined by the derivative difference method [Solovyov (2004). J. Appl. Cryst. 37, 743–749], anisotropically for all non-H atoms and isotropically for two independent H atoms without restraints.

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