|The IUCr is an International Scientific Union. Its objectives are to promote international cooperation in crystallography and to contribute to all aspects of crystallography, to promote international publication of crystallographic research, to facilitate standardization of methods, units, nomenclatures and symbols, and to form a focus for the relations of crystallography to other sciences.|
Organic molecules can have a remarkable array of solid forms, including different polymorphs and various multi-component systems, such as salts and co-crystals. The potential diversity of this solid-form landscape presents both opportunities and headaches for the practical use of molecules in solid forms.
Experimental screening of the solid-form landscape can be a time-consuming and expensive process. It’s therefore not surprising that over the past 25 years numerous computational methods have been developed to predict crystal structures, providing an alternative or supplement to experimental screening of solid forms and allowing us to explore the solid state of molecules that have yet to be synthesised.
In the case of organic crystal-structure prediction (CSP), progress over the last 15 years has been charted by a series of blind tests of CSP methods that have been hosted by the Cambridge Crystallographic Data Centre (CCDC).
The blind tests of methods have shown great advances in the ability to generate and rank putative crystal structures and in our understanding of cohesion in the solid state. However, many challenges remain in making CSP a reliable and efficient tool. The computational cost of some methods limits their high-throughput use, and reliability and applicability for the full diversity of organic molecules and solid forms remains an open question.
Following dialogue with the CSP community, the CCDC has decided to host a sixth blind test of organic CSP methods. This test will provide the community with a fair benchmark of the state of the art in CSP methodology. We hope that it will, once again, act as a platform for communicating ongoing progress and challenges in CSP and will spur the continued development of these methods. The invitation to participate is an open one.
This test will run from 1 September 2014 until 31 August 2015.
This is an extract taken from Groom, C.R. & Reilly, A.M. (2014), Acta Cryst. B70, doi:10.1107/S2052520614015923
For further details, or to express interest in taking part in the sixth blind test, please contact Colin Groom (firstname.lastname@example.org) or Anthony Reilly (email@example.com). The blind test website can be found at http://www.ccdc.cam.ac.uk/Community/Initiatives/Pages/CSPBlindTests.aspx, and will be updated over time with details, progress and the results of the blind test.
Nature Milestones in Crystallography has just launched. Produced with support from the IUCr and the worldwide network of neutron and X-ray sources, the supplement has been timed to coincide with the International Year of Crystallography, and features 25 topics that have been specially selected to highlight the breadth of crystallography. Nature Milestones in Crystallography, a collaborative effort between Nature, Nature Materials, Nature Nanotechnology and Nature Structure & Molecular Biology, is the eleventh supplement in the series.
Crystallography is a subject that is practised in almost all of the scientific disciplines including physics, chemistry, biology and materials sciences, and the IUCr’s journals are ideally placed to represent papers from each of these disciplines and many other cross-disciplinary fields. Our new journal, IUCrJ, which launched at the beginning of the year, publishes high-profile articles on all aspects of the sciences and technologies supported by the IUCr via its Commissions.
On 11 and 12 July 2014, Editor-in-Chief of IUCr Journals, Samar Hasnain, chaired the second meeting of the Journals Management Board (JMB), which took place at the historic Gladstone’s Library in Hawarden, North Wales. Attendees were Simon Billinge (Acta A), Sandy Blake (Acta B), Tony Linden (Acta C), Helen Stoeckli-Evans (Acta E), Luc van Meervelt (Acta E), Matthias Weil (Acta E), Howard Einspahr (Acta F), Bill Hunter (Acta F), Mitchell Guss (IUCr Executive Committee), Sine Larsen (IUCrJ), and Andrew Allen (JAC), along with Chester staff.
The IUCr Executive Committee approved the establishment of the JMB comprising the main Editors of each of the journals, the IUCr President (or his/her nominee), the IUCr General Secretary and Treasurer, the Editor-in-Chief and the Executive Managing Editor in 2012. At last week’s meeting, attendees discussed issues relating to the short- to long-term development of the journals, such as journal impact factors, open access and special issues.
On the occasion of the International Year of Crystallography, Samar Hasnain and the University of Liverpool, UK organized a full-day symposium dedicated to crystallography. The speakers in the morning session were Professor Andy Cooper, University of Liverpool; Professor Stephen Pennycook, Oak Ridge, USA; and Nobel Prize Laureate Professor Dan Shechtman, Technion-Israel Institute of Technology. Sessions in the afternoon included presentations from Patience Thomson, daughter of Sir Lawrence Bragg; Vivien Perutz, daughter of Max Perutz; The Barkla Lecture by Professor Gautam Desiraju, President of the IUCr; and the Bragg Lecture by Professor Sir Tom Blundell. The event celebrated the University’s award of an honorary degree to Professor Shechtman and the contributions of Charles Barkla. Charles Barkla graduated from the University of Liverpool and as an active staff member played a key role in establishing the university’s involvement in the development of X-ray crystallography.
A group of scientists from Spain, the UK and the United States has revealed the structure of a protein complex involved in liver and colon cancers. Both of these types of cancer are of significant social and clinical relevance as in 2012 alone, liver cancer was responsible for the second highest mortality rate worldwide, with colon cancer appearing third in the list.
The international team from CIC bioGUNE, the University of Liverpool and the US research centre USC-UCLA has successfully unravelled the mechanism by which two proteins, MATα2 and MATβ, bind to each other, thereby promoting the reproduction of tumour cells in liver and colon cancers. The study was announced in the latest issue of the open access journal IUCrJ published by the IUCr [Murray et al. (2014). IUCrJ 1, 240-249; doi: 10.1107/S2052252514012585]
This structural data discovery opens up additional research opportunities into drugs that can act on the binding of these proteins, thereby possibly inhibiting cancer cell growth.
As a result of this discovery, it is now known which part of their respective structures can be blocked to prevent these proteins from joining together. This is very important as when these proteins bind to each other, the production of a molecule known as SAMe, which plays a role in uncontrolled tumour cell growth, increases considerably. Though the relationship between SAMe and tumour growth has been known for some time, this molecule also has other important functions inside the cell that cannot be altered and there is currently no way of acting against it without affecting these other life-sustaining functions.
The good news is that MATα2 and MATβ are only overexpressed in adults with tumours therefore representing an excellent therapeutic target which could open the door to the creation of highly targeted drugs that act exclusively by blocking those regions that allow their mutual binding rather than attacking other regions of the body.
The CIC bioGUNE researcher Adriana Rojas, who led this study, mentioned during interview “Many years have passed since it was first understood which proteins produce SAMe and how the levels of this molecule affect cancer cell growth, and we have now shown that the complex between MATα2 and MATβ is a possible therapeutic target”.
The research involved X-ray crystallography and solution X-ray scattering techniques utilizing some of Europe’s most powerful X-ray synchrotron sources, ALBA in Spain and SOLEIL and DIAMOND in France and the UK.
The International Year of Crystallography 2014 Symposium is fast approaching; join us at the University of Liverpool on 17 July for a full-day symposium dedicated to the science examining the arrangement of atoms in solids. Three separate sessions (you can attend all or just one or two) will celebrate the University’s award of an honorary degree to Professor Dan Shechtman (Nobel Prize in Chemistry 2011) as well as the contributions of Charles Barkla and Sir Lawrence Bragg. Charles Barkla, a Liverpool graduate and a staff member of the University, played a key role in establishing X-ray crystallography (Nobel Prize in Physics 1917) while Lawrence Bragg established its fundamental basis (Nobel Prize in Physics 1915). Only a few seats remain; book your place to attend this historic event by following this link.
The Royal Society of Chemistry and the International Union of Crystallography announce the Global Experiment 2014 “The art of crystallization”. Aimed at school children between the ages of 7 and 16 years, entrants will try and find the best conditions for growing crystals; find out more here.
The IUCr-UNESCO OpenFactory in partnership with STOE, DECTRIS and Xenocs will take place from 10 to 19 September 2014 in Darmstadt and Grenoble. Delegates will receive seven days of intensive training by STOE, DECTRIS and Xenocs staff and guest scientists in cooperation with the IUCr. The training will focus on teaching participants the relevant theoretical skillset as well as include practical hands-on training. The President of the IUCr, Professor Gautam R. Desiraju, said of this landmark event, “we believe this is a unique opportunity for young scientists to be trained and build up their network in the crystallographic community”. Interest in attending the course was overwhelming. The 21 chosen delegates from 19 nations have now been announced; more details can be found here. Registrations for the Anton Paar OpenFactory taking place on 22 and 23 September 2014 are still open; further information can be found here.
Finally, see this month’s editorial in IUCrJ, Crystallography, materials and computation [Catlow (2014). IUCrJ 1, 200-201; doi:10.1107/S2052252514014122] where Richard discusses the growing interest of structural studies in materials science and the important role of computation, “which now permeates all aspects of crystallography”; let us know what you think.
Alicia Boole Stott, the third daughter of mathematician George Boole, is probably best known for establishing the term "polytope" for a convex solid in four dimensions. Alicia was also a long time collaborator of HSM Coxeter, one of the greatest geometers of the 20th Century.
Platonic solids are regular bodies in three dimensions, such as the cube and icosahedron, and have been known for millennia. They feature prominently in the natural world wherever geometry and symmetry are important, for instance in lattices and quasi-crystals, as well as fullerenes and viruses (see the recent paper by Pierre-Philippe Dechant from Durham University and Reidun Twarock's group in York [Dechant et al. (2014). Acta Cryst. A70, 162-167; doi: 10.1107/S2053273313034220].
Platonic solids have counterparts in four dimensions, and the Swiss mathematician Ludwig Schlaefli and Alicia Boole Stott showed that there are six of them, five of which have very strange symmetries. Stott had a unique intuition into the geometry of four dimensions, which she visualised via three-dimensional cross-sections.
A paper by Dechant published in Acta Crystallographica Section A: Foundations and Advances [Dechant (2013). Acta Cryst. A69, 592-602; doi: 10.1107/S0108767313021442] shows how regular convex 4-polytopes, the analogues of the Platonic solids in four dimensions, can be constructed from three-dimensional considerations concerning the Platonic solids alone. The rotations of the Platonic solids can be interpreted naturally as four-dimensional objects, known as spinors.
These in turn generate symmetry (Coxeter) groups in four dimensions, and yield the analogues of the Platonic solids in four dimensions. In particular, this spinorial construction works for any three-dimensional symmetry (Coxeter) group, such that these cases explain all "exceptional objects" in four dimensions, i.e. those four-dimensional phenomena that do not have counterparts in arbitrary higher dimensions. This also has connections to other "exceptional phenomena" via Arnold's trinities and the McKay correspondence. This spinorial understanding of four-dimensional geometry explains for the first time the strange symmetries that these four dimensional objects have.
This connection between the geometry of four dimension and that of three dimensions via rotations/spinors has not been noticed for centuries despite many of the great mathematicians working on Platonic solids and their symmetries, and is very different from Alicia Boole Stott's way of visualizing three-dimensional sections. It sheds new light on both sides, from real three-dimensional systems with polyhedral symmetries such as (quasi) crystals, viruses and fullerenes to four-dimensional geometries arising for instance in Grand Unified Theories and string and M-theory.
A frequent assumption in refinement models used in conventional crystal-structure determination at cryogenic temperatures is that hydrogen-atom displacements change as much with temperature as the atom they are bonded to. Fixed multipliers of 1.2 and 1.5 of the ratio of hydrogen- and parent-atom displacements are used in most refinement programs in the so-called 'riding-hydrogen' description.
Scientists have found [Lübben et al. (2014). Acta Cryst. A70; doi:10.1107/S2053273314010626] that a physically better description of hydrogen-atom displacements in a structural model should take a temperature dependence of this ratio into account, thereby eliminating a model inaccuracy that potentially leads to small systematic errors in the results.
The researchers' findings have the potential to affect a large number of structure determinations, especially results based on diffraction data measured at cryogenic temperatures around and below 100 Kelvin (-173 °Celsius) which employ the riding-hydrogen model for refinement.
Since the actual effect is small, it can best be detected when 'invarioms', non-spherical scattering factors, are used in refinement of multi-temperature data. When conventional scattering factors are used as implemented in most refinement programs in wide distribution, e.g. SHELXL, OLEX2 or CRYSTALS, differences are within the experimental error. Temperature-dependent multipliers (e.g. 2.2/2.5 at 100 K and 3.2/3.5 below 50 K) are not the optimal solution.
Lübben and the team are currently testing the combination of segmented rigid-body (or 'TLS' for translation, vibration and screw) motion - as obtained from a fit to well determined non-hydrogen displacements - with displacements from frequency computations of model compounds for a particular chemical environment from the invariom database. This will allow assignment of the respective environment, takes temperature dependence of hydrogen atoms into account correctly and also allows an estimation of the anisotropy of hydrogen-atom motion of organic crystal structures.