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.

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.

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.

The crystal structure of sarmientite, Fe23+ (AsO4)(SO4)(OH)·5H2O, solved ab initio from laboratory powder diffraction data

2014 ◽  
Vol 78 (2) ◽  
pp. 347-360 ◽  
Author(s):  
F. Colombo ◽  
J. Rius ◽  
O. Vallcorba ◽  
E. V. Pannunzio Miner
Keyword(s):  
Crystal Structure ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Rietveld Method ◽  
Direct Methods ◽  
Hydroxyl Group ◽  
Monoclinic Space Group ◽  
Powder Diffraction Data ◽  
Patterson Function ◽  
Unit Cell Dimensions

AbstractThe crystal structure of sarmientite, Fe23+ (AsO4)(SO4)(OH)·5H2O, from the type locality (Santa Elena mine, San Juan Province, Argentina), was solved and refined from in-house powder diffraction data (CuKα1,2 radiation). It is monoclinic, space group P21/n, with unit-cell dimensions a = 6.5298(1), b = 18.5228(4), c = 9.6344(3) Å, β = 97.444(2)º, V = 1155.5(5) Å3, and Z = 4. The structure model was derived from cluster-based Patterson-function direct methods and refined by means of the Rietveld method to Rwp = 0.0733 (X2 = 2.20). The structure consists of pairs of octahedral-tetrahedral (Fe−As) chains at (y,z) = (0,0) and (½,½), running along a. There are two symmetry-independent octahedral Fe sites. The Fe1 octahedra share two corners with the neighbouring arsenate groups. Both individual chains are related by a symmetry centre and joined by two symmetry-related Fe2 octahedra. Each Fe2 octahedron shares three corners with double-chain polyhedra (O3, O4 with arsenate groups; the O8 hydroxyl group with the Fe1 octahedron) and one corner (O11) with the monodentate sulfate group. The coordination of the Fe2 octahedron is completed by two H2O molecules (O9 and O10). There is also a complex network of H bonds that connects polyhedra within and among chains. Raman and infrared spectra show that (SO4)2− tetrahedra are strongly distorted.

XLENS, a direct methods program based on the modulus sum function: Its application to powder data

1999 ◽  
Vol 14 (4) ◽  
pp. 267-273 ◽  
Author(s):  
Jordi Rius
Keyword(s):  
Crystal Structure ◽  
Powder Diffraction ◽  
Distinctive Feature ◽  
Diffraction Data ◽  
Target Function ◽  
Direct Methods ◽  
Real Space ◽  
Control Parameters ◽  
Powder Diffraction Data ◽  
Mathematical Basis

XLENS is a traditional direct methods program working exclusively in reciprocal space. The distinctive feature of XLENS is the use of the modulus sum function as target function for the phase refinement. Due to its efficiency, robustness, and no need of weighting schemes, this function is specially well suited for treating powder diffraction data. The mathematical basis as well as the significance of the most important control parameters of the program will be described here. To illustrate how XLENS works, three different examples will be shown. Due to its simplicity, the modulus sum function can be easily combined with real-space filtering procedures to produce even more efficient crystal structure solving strategies.

Crystal Structure of the Ternary Compound Sc6Cu24.1Al11.9

2016 ◽  
Vol 257 ◽  
pp. 26-29 ◽  
Author(s):  
Nastasia Klymentiy ◽  
Nataliya Semuso ◽  
Svitlana Pukas ◽  
Yaroslav O. Tokaychuk ◽  
Lev Akselrud ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Direct Methods ◽  
The Body ◽  
Powder Diffraction Data ◽  
Coordination Polyhedra ◽  
X Ray ◽  
Pearson Symbol ◽  
Icosahedral Clusters

The crystal structure of a new ternary aluminide of refined composition Sc6Cu24.1(2)Al11.9(2) was solved by direct methods from X-ray powder diffraction data. It belongs to the cubic space group Im-3, Pearson symbol cI176-8, a = 13.5337(5) Å. The structure of Sc6Cu24.1Al11.9 may be described as a packing of 16-vertex coordination polyhedra of the Sc atoms, which form icosahedral clusters around the origin and the center of the body-centered unit cell. The voids at the centers of the clusters are filled by Cu4 tetrahedra, disordered between two possible orientations. The structure is closely related to the structure types Ru3Be17 and Ce6Au27.6Sn6.8.

Structure of the novel ternary hydrides Li4 Tt 2D (Tt = Si and Ge)

2007 ◽  
Vol 63 (1) ◽  
pp. 63-68 ◽  
Author(s):  
Hui Wu ◽  
Michael R. Hartman ◽  
Terrence J. Udovic ◽  
John J. Rush ◽  
Wei Zhou ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Direct Methods ◽  
Neutron Powder Diffraction ◽  
The Novel ◽  
Powder Diffraction Data ◽  
Hydrogen Atoms ◽  
Neutron Powder Diffraction Data ◽  
Orthorhombic Cell

The crystal structures of newly discovered Li4Ge2D and Li4Si2D ternary phases were solved by direct methods using neutron powder diffraction data. Both structures can be described using a Cmmm orthorhombic cell with all hydrogen atoms occupying Li6-octahedral interstices. The overall crystal structure and the geometry of these interstices are compared with those of other related phases, and the stabilization of this novel class of ternary hydrides is discussed.

scholarly journals Crystal Structure Solution of Organic Compounds from X-ray Powder Diffraction Data

2007 ◽  
Vol 65 (12) ◽  
pp. 1203-1212 ◽  
Author(s):  
Hirohito Tsue ◽  
Masahiro Horiguchi ◽  
Rui Tamura ◽  
Kotaro Fujii ◽  
Hidehiro Uekusa
Keyword(s):  
Crystal Structure ◽  
Organic Compounds ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Powder Diffraction Data ◽  
X Ray ◽  
Structure Solution
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