Optimal Difference Fourier Synthesis in Fibre Diffraction

1997 ◽  
Vol 6 (6) ◽  
pp. 14
Author(s):  
R. P. Millane ◽  
S. Baskaran
Keyword(s):  
Fourier Synthesis ◽  
Difference Fourier Synthesis ◽  
Fibre Diffraction ◽  
Difference Fourier

scholarly journals Redetermination of (2,2′-bipyridine-κ2N,N′)dichloridopalladium(II) dichloromethane solvate

2009 ◽  
Vol 65 (6) ◽  
pp. m615-m616 ◽  
Author(s):  
Nam-Ho Kim ◽  
In-Chul Hwang ◽  
Kwang Ha
Keyword(s):  
Hydrogen Bonds ◽  
Structure Refinement ◽  
Chloride Ions ◽  
Fourier Synthesis ◽  
Complex Molecules ◽  
Bipy Ligand ◽  
Π Interactions ◽  
Centroid Distance ◽  
Square Planar ◽  
Difference Fourier

In the title compound, [PdCl2(C10H8N2)]·CH2Cl2, the Pd2+ion is four-coordinated in a slightly distorted square-planar environment by two N atoms of the 2,2′-bipyridine (bipy) ligand and two chloride ions. The compound displays intramolecular C—H...Cl hydrogen bonds and pairs of complex molecules are connected by intermolecular C—H...Cl hydrogen bonds. Intermolecular π–π interactions are present between the pyridine rings of the ligand, the shortest centroid–centroid distance being 4.096 (3) Å. As a result of the electronic nature of the chelate ring, it is possible to create π–π interactions to its symmetry-related counterpart [3.720 (2) Å] and also with a pyridine ring [3.570 (3) Å] of the bipy unit. The present structure is a redetermination of a previous structure [Vicenteet al.(1997). Private communication (refcode PYCXMN02). CCDC, Cambridge, England]. In the new structure refinement all H atoms were located in a difference Fourier synthesis. Their coordinates were refined freely, together with isotropic displacement parameters.

Advances in the VLD algorithm

2011 ◽  
Vol 44 (6) ◽  
pp. 1143-1151 ◽  
Author(s):  
Maria Cristina Burla ◽  
Benedetta Carrozzini ◽  
Giovanni Luca Cascarano ◽  
Carmelo Giacovazzo ◽  
Giampiero Polidori
Keyword(s):  
Least Squares ◽  
Crystal Structures ◽  
Direct Methods ◽  
Fourier Synthesis ◽  
Correct Position ◽  
Random Models ◽  
The Difference ◽  
Difference Fourier ◽  
Additional Phase

The VLD algorithm relies on the properties of the difference Fourier synthesis and is designed for solving crystal structures in the correct space group, starting from random models. The standard approach has been modified by integrating it with the RELAX procedure, for translating to the correct position misplaced but correctly oriented models. A better control of the parameters and additional phase refinement cycles were able to improve the quality of the solutions and to make superfluous, for macromolecules and medium-sized molecules, the least-squares refinement cycles that, in the standard VLD approach, follow the phasing step. As a result, the efficiency of the new VLD algorithm is strongly increased; it has been checked using a wide variety of practical cases and compared with the effectiveness of direct methods.

VLD algorithm and hybrid Fourier syntheses

2012 ◽  
Vol 45 (6) ◽  
pp. 1287-1294 ◽  
Author(s):  
Maria Cristina Burla ◽  
Benedetta Carrozzini ◽  
Giovanni Luca Cascarano ◽  
Carmelo Giacovazzo ◽  
Giampiero Polidori
Keyword(s):  
Electron Density ◽  
Standard Procedure ◽  
Joint Probability ◽  
Distribution Functions ◽  
Medium Size ◽  
Joint Probability Distribution ◽  
Fourier Synthesis ◽  
Acta Cryst ◽  
The Difference ◽  
Difference Fourier

The VLD (vive la difference) phasing algorithm combines the model electron density with the difference electron densityviareciprocal space relationships to obtain new phase values and drive them to the correct values. The process is iterative and has been applied to small and medium-size structures and to proteins. Hybrid Fourier syntheses show properties that are intermediate between those of the observed synthesis (whose peaks should correspond to the most probable atomic positions) and those of the difference synthesis (whose positive and negative peaks should correspond to missed atomic positions and to false atoms of the model, respectively). Thanks to these properties some hybrid syntheses can be used in the phase extension and refinement step, to reduce the model bias and more rapidly move to the target structure. They have been recently revisitedviathe method of joint probability distribution functions [Burla, Carrozzini, Cascarano, Giacovazzo & Polidori (2011).Acta. Cryst. A67, 447–455]. The results suggested that VLD could be usefully combined, forab initiophasing, with the hybrid rather than with the difference Fourier synthesis. This paper explores the feasibility of such a combination and shows that the original VLD algorithm is only one of several variants, all with relevant phasing capacity. The study explores the role of several parameters in order to design a standard procedure with optimized phasing power.

scholarly journals Crystal structures of egg-white lysozyme of hen in acetate-free medium and of lysozyme complexes with N-acetylglucosamine and β-methyl N-acetylglucosaminide

1978 ◽  
Vol 173 (2) ◽  
pp. 607-616 ◽  
Author(s):  
S J Perkins ◽  
L N Johnson ◽  
P A Machin ◽  
D C Phillips
Keyword(s):  
Conformational Changes ◽  
Crystal Form ◽  
Egg White ◽  
Real Space ◽  
X Ray Diffraction ◽  
Fourier Synthesis ◽  
X Ray ◽  
Egg White Lysozyme ◽  
Tetragonal Crystal ◽  
Difference Fourier

The binding of beta-methyl N-acetylglucosaminide (betaMeGlcNAc) to egg-white lysozyme of hen in the tetragonal crystal form was studied by X-ray diffraction techniques to a resolution of 0.25 nm. The binding of the beta-methyl glycoside is almost identical with the binding of beta-N-acetylglucosamine (betaGlcNAc). Real-space refinement of the lysozyme-alpha/beta GlcNAc and lysozyme-betaMeGlcNAc complexes allowed preliminary analysis of the conformational changes observed on binding monosaccharide inhibitors, specially in the region involving tryptophan-62 and residues 70–76. Tetagonal lysozyme crystals, grown in the absence of acetate ions, were examined by X-ray diffraction to 0.25nm resolution. The resulting difference Fourier synthesis shows no firm evidence for bound acetate ions and indicates only minor conformational changes in the side-chain positions of aspartic acid-101 and asparagine-103. The close similarity of the lysozyme structures in the presence and absence of acetate is contrary to expectations from previous n.m.r. studies.

scholarly journals The Crystal Structure of Defect KBB’O6 Pyrochlores (B,B’: Nb,W,Sb,Te) Revisited from Neutron Diffraction Data

Crystals ◽  
2018 ◽  
Vol 8 (10) ◽  
pp. 368 ◽  
Author(s):  
Sergio Mayer ◽  
Horacio Falcón ◽  
María Fernández-Díaz ◽  
José Alonso
Keyword(s):  
Pyrochlore Structure ◽  
Structural Features ◽  
Neutron Powder Diffraction ◽  
The Other ◽  
Group Symmetry ◽  
Neutron Diffraction Data ◽  
Fourier Synthesis ◽  
Crystallization Water ◽  
Defect Pyrochlore ◽  
Difference Fourier

Three defect pyrochlores KNbWO6·xH2O, KNbTeO6 and KSbWO6 were synthesized by solid state reaction at 750 °C, from stoichiometric mixtures of K2C2O4, Sb2O3, Nb2O5, WO3 and 20% excess TeO2. A neutron powder diffraction (NPD) data analysis allowed unveiling some structural features. They are all defined in the cubic F d 3 ¯ m space group symmetry, with α = 10.5068(1) Å, 10.2466(1) Å and 10.2377(1) Å, respectively. Difference Fourier synthesis for KNbWO6·xH2O clearly showed the presence of crystallization water, with extra O’ oxygen and H+ atoms that were located from NPD data. These O’ oxygen atoms are placed at 32e Wyckoff sites, conforming a K2O’ sublattice interpenetrated with the covalent framework constituted by (Nb,W)O6 octahedra. The H+ ions coordinate the O’ atoms at partially occupied 96g Wyckoff sites while K+ ions shift also along 32e sites, but closer to the 16c special site (0,0,0). By contrast, extra H2O molecules are absent in the other two pyrochlores: in KNbTeO6 and KSbWO6 K+ ions are shifted along 32e (x,x,x) sites further away from the origin than for the previous material, and the higher covalency of the octahedral network determines more compact structures, with shorter B–O distances and narrower B–O–B angles in the proposed AB2O6 defect pyrochlore structure.

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