CRYSTALS Enhancements: Dealing with Hydrogen Atoms in Refinement

Jun 292010
 

J. Appl. Cryst. (2010), 43, 1100-1107.    [ doi:10.1107/S0021889810025598 ]

Because they scatter X-rays weakly, H atoms are often abused or neglected during structure refinement. The reasons why the H atoms should be included in the refinement and some of the consequences of mistreatment are discussed along with selected real examples demonstrating some of the features for hydrogen treatment that can be found in the software suite CRYSTALS.

Hydrogen addition in CRYSTALS

Hydrogen addition in CRYSTALS

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ECM 25

Aug 212009
 

The 25th European Crystallographic Meeting was held in the Harbiye Museum and Cultural Centre in the beautiful city of Istanbul.  It was a very eventful week, and contributions to the conference made by Chem. Cryst. include:

N. David Brown, James Haestier, Mustapha Sadki, Amber L. Thompson & David J. Watkin
A Further Improved Structure Matching Algorithm (Poster)

James Haestier
Handling of Cell Errors and their Effect on Derived Parameters (Poster)

Mustapha Sadki
New Modelling for Disordered Atoms in Free-form Based Hybrid Refinement and Visual Representation (Poster)

Mustapha Sadki
The Application of Novel Modelling and Refinement Strategies to Crystallography (Presentation)

Amber L. Thompson & David J. Watkin
Absolute Configuration Determination – Is there More Information in the Data? (Poster)

David J. Watkin, Richard I. Cooper & Amber L. Thompson
CRYSTALS:  Refinement and Validation Tools (Poster)

David Watkin
The Future of Small Molecule Software (Session Chair)

Handling Cell-Parameter Errors in Crystallographic Data

Aug 012009
 

J. Appl. Cryst. (2009), 42, 798-809.    [ doi:10.1107/S0021889809024376 ]

A new method is presented for handling errors on crystallographic data. In single-crystal diffraction experiments, two variance-covariance matrices are present, one for the cell parameters and the second for the refined parameters (atomic coordinates and anisotropic displacement parameters). These two matrices can be combined so that errors on derived parameters, such as bond distances, bond angles and TLS tensors, may be calculated more simply. The new method works for all space groups but there are limitations on its application to triclinic space groups. The method allows errors to be transformed between space groups.

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BCA Spring Meeting 2009

Apr 212009
 

The 2009 British Crystallographic Association Spring Meeting was held at the University of Loughborough.  Contributions from Chem. Cryst. included:

N. David Brown, James Haestier, Mustapha Sadki, David J. Watkin & Amber L. Thompson
A Further Improved Structure Matching Algorithm (Poster)

James Haestier
Effects of Cell Errors on Derived Parameters (YC Presentation)

James Haestier
Computation of Cell Errors Effects on Derived Parameters (Poster)

Mustapha Sadki & David J. Watkin
New Framework for Reliable Refinement Data Types (Presentation)

Error Estimates on Bond-length and Angle Corrections from TLS Analysis

Apr 082008
 

J. Appl. Cryst. (2008), 41, 531-536.    [ doi:10.1107/S0021889808005463 ]

Librational motion within a crystal structure distorts the measured bond distances and angles from their physical values. TLS analysis of a rigid molecule or a rigid part of a molecule allows the calculation of bond-length and angle corrections. Until now, no estimate of the error on these corrections has been available. A method is presented for propagating the errors on the anisotropic displacement parameters (ADPs) to the bond-length and angle corrections which are a function of the libration tensor. The numerical significance of approximations made during the calculation is discussed.

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Retrieval of Crystallographically-Derived Molecular Geometry Information

Oct 132004
 

J. Chem. Inf. Comput. Sci. (2004), 44, 2133-2144. [ doi:10.1021/ci049780b ]

The crystallographically determined bond length, valence angle, and torsion angle information in the Cambridge Structural Database (CSD) has been made accessible by development of a new program (Mogul) for automated retrieval of molecular geometry data from the CSD. The program uses a system of keys to encode the chemical environments of fragments (bonds, valence angles, and acyclic torsions) from CSD structures. Fragments with identical keys are deemed to be chemically identical and are grouped together, and the distribution of the appropriate geometrical parameter (bond length, valence angle, or torsion angle) is computed and stored. Validation experiments indicate that, with rare exceptions, search results afford precise and unbiased estimates of molecular geometrical preferences. Such estimates may be used, for example, to validate the geometries of libraries of modeled molecules or of newly determined crystal structures or to assist structure solution from low-resolution (e.g. powder diffraction) X-ray data.

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CRYSTALS Enhancements: Refinement of Atoms Continuously Disordered Along a Line, on a Ring or on the Surface of a Sphere

Apr 222004
 

J. Appl. Cryst. (2004), 37, 545-550.    [ doi:10.1107/S0021889804009847 ]

A Cp* fragment consisting of partial atoms embedded in annuliThe program CRYSTALS [Betteridge, Carruthers, Cooper, Prout & Watkin (2003). J. Appl. Cryst. 36, 1487] has been extended to include an option for the refinement of a continuous electron density distribution lying along a line, a ring or on the surface of a sphere. These additional non-atomic electron distributions can be refined in any combination with traditional anisotropically distributed spherical atoms, including the refinement of `partial’ atoms overlapping with the special electron distributions.

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CRYSTALS Version 12: Software for Guided Crystal Structure Analysis

Dec 012003
 

J. Appl. Cryst. (2003), 36, 1487.    [ doi:10.1107/S0021889803021800 ]

CRYSTALS version 12 contains a modern crystallographic user interface, and novel strategies that incorporate chemical knowledge and crystallographic guidance into the crystal structure analysis software.

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The Control of Difficult Refinements

Jul 011994
 

Acta Cryst.  (1994), A50, 411-437.    [ doi:10.1107/S0108767393012784 ]

Each year, many single-crystal structure analyses are reported that show evidence of over- or under-refinement. Often, the refinement strategies have been naive or over-complex and alternative strategies might have been more effective. The many descriptions of crystallographic and numerical techniques suitable for assisting with the control of difficult refinements are distributed widely in the literature and so are not always easily accessible. Without being a review of these procedures (which would require a substantial book), this article attempts to list readily available procedures, together with a brief outline of their backgrounds and examples of their applications to organic and organometallic compounds. The analysis of extended-lattice materials (usually inorganic materials) often raises problems in addition to those covered here. The particular aim of this article is to remind the reader that X-ray structure analysis is a modelling process and that, while standard models may be adequate for most analyses, more care and imagination must be applied to the treatment of difficult cases. Principles of methods are described without detailed mathematical derivations, although sufficient references to the literature are provided to permit careful study. Future requirements for refinement processes are outlined, including the use of new machine architectures, applications of sparse-matrix methods and the development of expert systems.

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  • Oxford University Research Archive [direct pdf]

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A Weighting Scheme for Least-Squares Structure Refinement

Jul 171979
 

Acta Cryst. (1979), A35, 698-699.    [ doi:10.1107/S0567739479001613 ]

The truncated Chebyshev polynomial provides a reliable scheme for the automatic determination of empirical weights for least-squares structure refinement when the errors are a function of |Fo|.

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