Richard Cooper

Dec 202012

J. Sync. Rad (2013). 20, 200–204. [ doi:10.1107/S0909049512044007 ]

Overlapping absorption edges will occur when an element is present in multiple oxidation states within a material. DetOx is a program for partitioning overlapping X-ray absorption spectra into contributions from individual atomic species and computing the dependence of the anomalous scattering factors on X-ray energy. It is demonstrated how these results can be used in combination with X-ray diffraction data to determine the oxidation state of ions at specific sites in a mixed-valance material, GaCl2 .

Electronic reprints

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Sep 212012

J. Appl. Cryst. (2012). 45, 1057–1060. [ doi:10.1107/S0021889812035790 ]

The traditional Waser distance restraint, the rigid-bond restraint and atomic displacement parameter (ADP) similarity restraints have an equal influence on both atoms involved in the restraint. This may be inappropriate in cases where it can reasonably be expected that the precision of the determination of the positional parameters and ADPs is not equal, e.g. towards the extremities of a librating structure or where one atom is a significantly stronger scatterer than the other. In these cases, the traditional restraint feeds information from the poorly defined atom to the better defined atom, with the possibility that its characteristics become degraded. The modified restraint described here feeds information from the better defined atom to the more poorly defined atom with minimal feedback.

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Aug 022012

Congratulations to Karim Sutton, who has been awarded a Margaret C. Etter Student Lecturer Award at the recent American Crystallographic Association annual meeting in Boston.

He presented his recent research determining oxidation states in mixed-valent materials using tunable synchrotron radiation on Diamond beamline I19.

The awards were established to honour the memory of Professor Etter (1943-1992), who was a major contributor to the field of organic solid-state chemistry.

Apr 302012

J Appl. Cryst. (2012), 45, 417-429. [ doi:10.1107/S0021889812015191 ]

Leverages measure the influence that observations (intensity data and restraints) have on the fit obtained in crystal structure refinement. Further analysis enables the influence that observations have on specific parameters to be measured. The results of leverage analyses are discussed in the context of the amino acid alanine and an incomplete high-pressure data set of the complex bis(salicylaldoximato)copper(II). Leverage analysis can reveal situations where weak data are influential and allows an assessment of the influence of restraints. Analysis of the high-pressure refinement of the copper complex shows that the influence of the highest-leverage intensity observations increases when completeness is reduced, but low leverages stay low. The influence of restraints, notably those applying the Hirshfeld rigid-bond criterion, also increases dramatically. In alanine the precision of the Flack parameter is determined by medium-resolution data with moderate intensities. The results of a leverage analysis can be incorporated into a weighting scheme designed to optimize the precision of a selected parameter. This was applied to absolute structure refinement of light-atom crystal structures. The standard uncertainty of the Flack parameter could be reduced to around 0.1 even for a hydrocarbon.

Electronic reprints

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Jan 062012

The CRYSTALS v14.40b installer is now available to download for the Windows platfom.

[Update: 14.40b fixes failure when importing reflections from Agilent cif_od files]

Selected highlights include:

  • New data import tools for most diffractometer types.
  • Asymmetric distance, Uij and adp vibration restraints.
  • Automatic lookup of neutron scattering factors.
  • Calculation of s.u’s on torsion angles in #TORSION.
  • Consistent updating of weights when importing and re-importing reflection data.
  • Punch of lists 2, 3, 4, 13, 23, 25, 28, 29, 31 is now possible (missing generalised 6 & 30 still).
  • SQUEEZE: Fix compatibility with recent versions of Platon.
  • Command line users from France will be please to learn that you can now use ampersand (&) as well as # or \ to prefix a command. This symbol can be generated on French keyboards without using shift.
  • Numerous other bug fixes…
Oct 282011

The Nobel prize for chemistry has been awarded to Daniel Shechtman, from Technion – the Israel Institute of Technology in Haifa, for his discovery of the structure of quasicrystals. Until 1982, it was thought that only two-, three-, four- or six-fold rotational symmetry were possible, however Dr. Schechtman’s discovery changed all that when his electron diffraction studies of an Al-Mn alloy crystallised from the melt showed “five-fold symmetry”. Since pentagons don’t tessellate, two or more shapes are necessary to form a close packed structure. Thus, although invented long before they were discovered, 3D-Penrose tiling can be used very effectively to describe the diffraction pattern from the Al-Mn quasicrystal by putting atoms at the vertices and calculating the Fourier Transform. Since 1982, dozens of other quasicrystals have been discovered and a new and beautiful branch of structural science was born. Links:

  • Announcement of the 2011 Nobel Prize in Chemistry [video]
  • BBC News Online [Report]
Electron diffraction of Zn-Mg-Ho alloy (left) with a 2D Penrose Tiling (right).

Electron diffraction of Zn-Mg-Ho alloy (left) with a 2D Penrose Tiling (right).

Since the first Nobel Prize for Physics was awarded in 1901 to Wilhelm Conrad Röntgen for the discovery of X-rays, advances in (or key to) structural science have been recognised many times, including:

  • Venkatraman Ramakrishnan, Thomas A. Steitz and Ada E. Yonath “for studies of the structure and function of the ribosome” (Chemistry, 2009)
  • Walter Kohn “for his development of the density-functional theory” and John A. Pople “for his development of computational methods in quantum chemistry” (Chemistry, 1998)
  • Robert F. Curl Jr., Sir Harold W. Kroto and Richard E. Smalley “for their discovery of fullerenes” (Chemistry, 1996)
  • Herbert A. Hauptman and Jerome Karle “for their outstanding achievements in the development of direct methods for the determination of crystal structures” (Chemistry, 1985)
  • Dorothy Crowfoot Hodgkin “for her determinations by X-ray techniques of the structures of important biochemical substances” (Chemistry, 1964)
  • Max Ferdinand Perutz and John Cowdery Kendrew “for their studies of the structures of globular proteins” (Chemistry, 1962)
  • Francis Harry Compton Crick, James Dewey Watson and Maurice Hugh Frederick Wilkins “for their discoveries concerning the molecular structure of nucleic acids and its significance for information transfer in living material” (Medicine, 1962)
  • Linus Pauling “for his research into the nature of the chemical bond and its application to the elucidation of the structure of complex substances” (Chemistry, 1954)
  • Petrus (Peter) Josephus Wilhelmus Debye “for his contributions to our knowledge of molecular structure through his investigations on dipole moments and on the diffraction of X-rays and electrons in gases” (Chemistry, 1936)
  • James Chadwick “for the discovery of the neutron” (Physics, 1935)
  • Prince Louis-Victor Pierre Raymond de Broglie “for his discovery of the wave nature of electrons” (Physics, 1929)
  • Niels Henrik David Bohr “for his services in the investigation of the structure of atoms and of the radiation emanating from them” (Physics, 1922)
  • Sir William Henry Bragg and William Lawrence Bragg “for their services in the analysis of crystal structure by means of X-rays” (Physics, 1915)
  • Max von Laue “for his discovery of the diffraction of X-rays by crystals” (Physics, 1914)
  • Marie Curie, née Sklodowska “in recognition of her services to the advancement of chemistry by the discovery of the elements radium and polonium, by the isolation of radium and the study of the nature and compounds of this remarkable element” (Chemistry, 1911)
  • Ernest Rutherford “for his investigations into the disintegration of the elements, and the chemistry of radioactive substances” (Chemistry, 1908)
  • Antoine Henri Becquerel “in recognition of the extraordinary services he has rendered by his discovery of spontaneous radioactivity”, with Pierre Curie and Marie Curie, née Sklodowska “in recognition of the extraordinary services they have rendered by their joint researches on the radiation phenomena discovered by Professor Henri Becquerel” (Physics, 1903)
  • Hendrik Antoon Lorentz and Pieter Zeeman “in recognition of the extraordinary service they rendered by their researches into the influence of magnetism upon radiation phenomena” (Physics, 1902)
  • Wilhelm Conrad Röntgen “in recognition of the extraordinary services he has rendered by the discovery of the remarkable rays subsequently named after him” (Physics, 1901)
Aug 312011

Chemical Crystallography: Reflections and Predictions
A symposium to mark the retirement of David J. Watkin
Friday 9th September 2011

[Update: Thanks to all the speakers and everyone who attended this event in honour of DJW.]


10.00   Refreshments in the Lecture Theatre Foyer, Inorganic Chemistry Laboratory

10.50   Dr. Richard Cooper (University of Oxford, UK)
Welcome and Introduction

11.10   Prof. Howard Flack (University of Geneva, Switzerland)
Working with a Difference

11.40   Dr. Matthias Meyer (Agilent Technologies, Poland)
Oxford D(diffraction) – some notes…

12.10   Buffet Lunch (University Club, Mansfield Road)

13.40   Dr. Alison Edwards (ANSTO, Australia)
Chemical Crystallography with Neutrons: Laue diffraction in the 21st century!

14.10   Dr. George Tranter (Chiralabs, Oxford)
Giving Molecules a Hand

14.40   Prof. Simon Parsons (University of Edinburgh, UK)
Applications of Leverage Analysis in Chemical Crystallography

15.10   Refreshments in the Lecture Theatre Foyer, Inorganic Chemistry Laboratory

15.30   Dr. Luc Bourhis (Bruker, Paris)
A Toolbox for Programmer Crystallographers

16.00   Prof. Bruce Foxman (Brandeis University, USA)
Secrets from the Oxford Crypt: Old Problems from Keith Prout and John Rollett: Solved!

16.30   Dr. Richard Cooper
Closing Remarks

16.45   Drinks at the University Club

Many thanks to Agilent Technologies for supporting this meeting. Continue reading »

May 202011

David Watkin was presented with his ACA Fankuchen Award at the ACA 2011 meeting. He gave a plenary lecture entitled “X-ray Crystallography. Is the Gold Standard becoming Tarnished?”