Richard Cooper

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.]

Programme

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?”

 

May 122011
 

CRYSTALS v14.23c installer is available to download for the Windows platfom.

[Update – patched version 1423c released 27 May, fixes format problem with tiny weights in FCF, CIF input bug]

Selected highlights:

  • Added bond colouring to indicate either element type, or disordered part
  • Improved robustness of weighting scheme 17 (Shelx weights)
  • Output observation weights in FCF CIF
  • Allow omission of Friedel pairs of reflections from Absolute Configuration plots.
  • Fixed crash on ‘Select All’ atoms for large structures.
  • Fixed Hide/Show H button on toolbar.
Apr 212011
 

CRYSTALS v14.21 installer is available to download for the Windows platfom.

Selected highlights:

  • Constraints (List 12), restraints (List 16) and manually omitted reflections (List 28) are appended to the CIF for easy reference.
  • Punch for list 1 is now possible.
  • Included slant 2Fo-Fc maps on the menu.
  • Fixed 2 bugs in #Perhydro: phenyl rings now work again and addition of H to disordered components is fixed.
  • New list 9 stores parameter standard uncertainties from last cycle of least squares.
  • New script for reading general CIFs from diffractometers.
  • New script for centering structures in cells.
  • Reduced number of questions during reading back of Superflip solutions.
  • New script for editing f’ and f”.

 

Mar 302011
 

Rowena ScottIn-situ Diamond RingNot content with showing off the eye-catching brilliance of her new diamond engagement ring, final year Inorganic Chemistry student Rowena Scott wanted to reveal the beautiful symmetry of its atomic structure. She recorded an X-ray diffraction pattern from the diamond using one of the Chemistry Department’s new state of the art, SuperNova dual source X‑ray diffractometers.

Rowena’s current research project with Dr Simon Clarke involves the synthesis of iron chalcogenide superconductors. The structures of these materials are then determined using single crystal X-ray diffraction techniques.

Chemical Crystallography Service manager, Dr Amber Thompson said “We see a wide range of materials of varying crystallinity from many research groups in the Department of Chemistry, usually grown at the bottom of glass schlenks or flasks; it’s not often that such a lovely crystal turns up mounted in a band of gold”.

Diffraction pattern of the diamondThe diffracted X-rays were measured while rotating the diamond in an X-ray beam. The resulting diffraction pattern shows the position and intensity of the beams diffracted by the organised structure of carbon atoms in the crystal. The white rings overlaid on the image indicate the angles at which diamond peaks are expected to occur, which agree with the collected data.

Diamond diffracts X-rays so efficiently that the X-ray generator had to be run at 10% of its usual power in order to avoid overloading the X-ray detector.

Dec 072010
 

Acta Cryst. (2011), A67, 21-34.    [ doi:10.1107/S010876731004287X ]

The practical use of the average and difference intensities of Friedel opposites at different stages of structure analysis has been investigated. It is shown how these values may be properly and practically used at the stage of space-group determination. At the stage of least-squares refinement, it is shown that increasing the weight of the difference intensities does not improve their fit to the model. The correct form of the coefficients for a difference electron-density calculation is given. In the process of structure validation, it is further shown that plots of the observed and model difference intensities provide an objective method to evaluate the fit of the data to the model and to reveal insufficiencies in the intensity measurements. As a further tool for the validation of structure determinations, the use of the Patterson functions of the average and difference intensities has been investigated and their clear advantage demonstrated.

Electronic reprints

Publisher’s copy

Nov 272010
 

J. Appl. Cryst. (2011), 44, 52-59.    [ doi:10.1107/S0021889810042470 ]

One of the requirements for the next generation of small-molecule crystallographers is a mathematical programming infrastructure. It should provide a modelling design process, where the model formulation is kept separate from the optimization process to provide gains in reliability, scalability and extensibility, enabling the application of optimization components in general, and refinement-based applications in particular, as applied to crystallographic problems. A research project has been undertaken to design and implement an innovative toolkit library – a small-molecule toolkit (SMTK) – for crystallographic modelling and refinement. This paper provides an overview of SMTK and its object-oriented implementation. As a practical illustration, it also shows the context of use for a set of classes and discusses how the toolkit enables the user rapidly to develop, maintain and explore the full capabilities of crystallography and so create new applications. SMTK reduces the degree of effort required to construct and develop new algorithms and provides users with an easy and efficient means to test ideas, as well as to build large and maintainable models which can readily be adapted to any new situation.

Publishers copy: