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1/57 CRYSTALS 2000 Most of the infra-structure needed to enable enhanced functionality to be added was in place for The Millennium. Since then the underlying.

Published byTylor Tillie Modified over 4 years ago


Presentation on theme: "1/57 CRYSTALS 2000 Most of the infra-structure needed to enable enhanced functionality to be added was in place for The Millennium. Since then the underlying."— Presentation transcript:

1 1/57 CRYSTALS 2000 Most of the infra-structure needed to enable enhanced functionality to be added was in place for The Millennium. Since then the underlying FORTRAN and user accessible features have continued to be developed in response to the communities needs. Publicity material, 2003

2 2/57 OLEX2: a complete structure solution, refinement and analysis program Oleg V. Dolomanov, Luc J. Bourhis, Richard J. Gildea, Judith A. K. Howard and Horst Puschmann Age Concern As part of the EPSRC Age Concern project the group in Durham has shared complete access to CRYSTALS source code and SCRIPTS to help them develop their own user interface.

3 3/57 Age Concern smtbx/cctbx focusing on those key computational details which have been the treasures of the classic programs CRYSTALS or SHELX. ACA 2010: 07.26.4 Solution and Refinement with the cctbx and smtbx Luc Bourhis, Oleg Dolomanov, Richard Gildea, Judith Howard, Horst Puschmann SMTK/cctbx provide a modelling design process, where the model formulation is kept separate from the optimization process. SMTK – a small-molecule toolkit library for crystallographic modelling and refinement Mustapha Sadki* and David J. Watkin J. Appl. Cryst. (2011). 44, 52–59 The project has also given rise to two refinement sub-systems.

4 4/57 Age Concern Regression to the 1990s The speed of instruments and computers is such that crystallographers have become the slowest link. Once again, we are trying to teach computers some chemistry. Dave Brown is working on a project to use chemical information in the form of SMILES strings to help analyse proposed structure solutions and unpick disorder. O=S(c1Ncc(C)cc1)(NC(COC(C2=NC=CC=C2)=O)C(OC)=O)=F

5 5/57 X-Ray Structure Analysis The Gold Standard

6 6/57 Why was X-ray Structure Analysis a Gold Standard? The materials were carefully chosen. The materials were already well characterised There were no other techniques to compete with it The people who did it knew what they were doing

7 7/57 Early Structures J Chem Soc, 1926, 2944 habit & polymorphism twinning pseudosymmetry hydrogen bond dimerisation

8 8/57 The unavailability of computers forced workers to think about problems Hexachlorobenzene, 1931

9 9/57 Hexachlorobenzene - Rigid Body Refinement Lonsdale, 1931 From the distribution of the h0l intensities, Lonsdale argued that the 6 (x0z) coordinates of the three Cl atoms could be replaced by a rigid body with only its orientation and radius ( and R) to be determined The structure factor expression can be simplified to contain only two variables.

10 10/57 Film methods gave views of large swathes of reciprocal space alerted the crystallographer to potential problems Data Collection Serial diffractometers were about to change that Apparatus for Measuring Complete Single-Crystal X-Ray Diffraction Data by Means of a Geiger Counter Diffractometer Thomas c. Furnas, jr., and David Harker The Review of Scientific Instruments, volume 26, number 5 May, 1955

11 11/57 Royal Institution Automated Analogue Diffractometer Hilger & Watts Y190 Stepping motors moved across a layer of reciprocal space. One or two layers of data could be measured in 24 hours. Hilger & Watts Y290 Fully Automated Digital Diffractometer The computer is a first generation PDP8, built with discrete transistors and a ferrite core. It became know as the Straight 8 Two Nonius Kccd instruments. 8am-2pm Booking:2pm-6pm 6pm-8am Chemical Crystallography Laboratory, Oxford 2000

12 12/57 Chemical Crystallography Laboratory, Oxford In 2011, data collection from fair crystals is no longer an issue. Agilent Supernova

13 13/57 Digital Computing Digital computers have revolutionised crystallography. Has computing replaced thinking? Bob Sparks matrix-accumulation benchmark: Microvax 3800 (1989)1,824 secs 1.8Ghz Athlon, (2005)3secs 3.0Ghz Intel Duo (2010)1sec We can now do in one day what would have taken three days in 2005, and almost five years in 1990

14 14/57 Crystallography 2011 In 2011 we have diffractometers of great sensitivity, we have low-energy laboratory sources and we have immensely powerful synchrotron sources. Work at 100K is routine, and 10K reasonably feasible. Diamond Anvil Cells enable samples to be examined at pressures up to 10 GPa Computers work at breath-taking speeds. In effect, we have amazing technology available. What science can we do with it?

15 15/57 Whats Happening to Crystallography? The age of intramolecular structural chemistry is declining for small molecules. There is very little that can be added to the average intramolecular geometrical data collected by use of the Cambridge Structural Database; anything at variance with these well-established averages is most probably wrong. Gavezzotti & Flack, 2005 http://www.iucr.org/iucr-top/comm/cteach/pamphlets/21/21.html

16 16/57 Just Stamp-Collecting?

17 17/57 The Journals of Squeaky-Clean Structures On a one-by-one basis, perfect structures probably have a very limited crystallographic interest. Rint2.8% R12.9% wR26.8% 94% with I>2σ(I) X-ray crystallography unequivocally confirmed the stereochemistry of the 2-C-methyl group. 3,4-O-Isopropylidene-2-C-methyl-D-galactonolactone N. Dai, S. F. Jenkinson, G. W. J. Fleet and D. J. Watkin

18 18/57 The Journal of Rotten Structures Much more interesting are the careful but imperfect analyses, where the analyst has had real problems which he is happy to share with the community.

19 19/57 Theta Halogen-bond Templated Rotaxane (R1 = 15.0%) Even low temperature synchrotron data were weak and the sample suffered radiation damage Final refinement had a data to parameter ratio of 3.6 :1 and required 4401 restraints Completeness vs Theta

20 20/57 The Cambridge Structural Database The CCDC grew out of the activities of the crystallography group led by Dr Olga Kennard OBE FRS in 1965. Building a database is now an easy technology. The scientific contribution from CCDC is the expertise to devise products to turn data into knowledge. Museum? Grave Yard? Gold Mine?

21 21/57 The CSD and Validation PLATON may let us know if there is something wrong with the physics. The CSD may let us know that there is something wrong with the chemistry. Simple frequency distributions of bond lengths are meaningless. In MOGUL, bond lengths have been classified according to their local environment.

22 22/57 CRYSTALS interface to MOGUL

23 23/57 Just Stamp-Collecting? Not entirely Structure determination by X-ray crystallography has become a vital tool for modern preparative chemistry. This form of crystallography is certainly a technology, but the technology is immature. The scientific challenge now is to make the total systems robust when used by informally trained chemists.

24 24/57 Automatic Structure Solution and Refinement Direct methods and charge flipping are now very powerful procedures for phasing a Fourier map to the level that the atomic skeleton of the structure can be seen. However, physics alone cannot always make automatic unambiguous assignment of atomic sites. Worse than that, some molecules refuse to fit into normal space groups - they are disordered.

25 25/57 Disorder Disorder is a bottomless pit into which crystallographers throw time, effort and money. When disorder is eventually resolved, it is often clear that the resolution has added nothing significant to the scientific value of the structure. Was it worth the effort?

26 26/57 Number of Structures What is the cost of an X-ray Structure Analysis? About ½ of the structures going through a laboratory could be made ready for publication in one working day.

27 27/57 What is the cost of an X-ray Structure Analysis? However, most of these cost continue even if the instruments are turned off. The recoverable cost of not doing an analysis is perhaps only $30.

28 28/57 Bringing Down the Cost 1.Put more samples on the instruments each day. This increases the burden on the analyst, and may even require additional analysts 2.Provide better automation for the treatment of disorder. 3.Have a clear strategy to limit the amount of time spent on each structure. A number of things can be done to bring down the unit cost:

29 29/57 Cost-benefit Analysis In the UK, research funding is not so generous that we can be wasteful of resources. Before starting an analysis it is important to declare what the analysis will be used for. It is important to agree with the customer if/how the work will be published. The experiment and data processing can then be tailored to those aims.

30 30/57 Cost-benefit Analysis Occasionally the analysis proves to be much more important than was foreseen. In general, it is a better use of resources to re-measure a few data sets than to collect everything to the highest standards first time around.

31 31/57 The Gold Standard We do not use a micrometer to measure the timber for a chicken house. Crystallography can still be the Gold Standard, but a gold standard is not needed for all work. The analyst simply needs to demonstrate fitness-for- purpose. If the customer changes the purpose later, that is a separate issue.

32 32/57 The Gold Standard The problem for journals is to understand the purpose of the work, and see if it is satisfied. The purpose cannot be evident from the information currently included in a cif, therefore it is unlikely that a program can make this decision. checkCIF may help the referee decide if the analysis is good enough for the purpose described in the text. In the future, cifs may also need to record what the analysis was good enough for.

33 33/57 Where Next? Why does Nature choose to use space groups? Does Nature use space groups? What are Z>1 structures? What are modulated structures? How do molecules share information about each other? How can I get this ****** material to crystallise nicely? The molecular solid state has become interesting in its own right.

34 34/57 The Molecular Solid State Structure Prediction Progress is painfully slow. Morphology Prediction Even when the crystal structure in known, reliable morphology predictions fall a long way short of experimental observations. Growth of x-ray quality crystals. Still a black art. Even in a single laboratory, some people have better luck than others.

35 35/57 KpenV, P1, Z'=4 This chiral molecule in the non-centrosymmetric space group P1 would just love to pack in P-1. Why cant these molecules get their act together, and crystallise with Z=2? Carol Brock calls this Frustrated symmetry

36 36/57 VONVUP, P2 1, Z'=2 Another enantiopure material in a non-centrosymmetric space group. There is no pseudo-symmetry. The blue molecules assume an L shape. The green molecules assume an S shape

37 37/57 Where Next? Worrying about whether completeness is 89% or 98% is almost irrelevant. Understanding molecular crystals is a New Frontier for crystallographers Most modern technology depends upon second or third order effects. Molecular Structure Determination is a done-deal

38 38/57 I would like to thank the American Crystallographic Association for this opportunity to have shared some of my ideas with its members, and thank the dozens of colleagues who helped form those ideas.
 Copyright © Cengage Learning. All rights reserved. Chapter 12 Decision Support Systems Author: Julia Richards and R. Scott Hawley STATISTICS Random Variables and Distribution Functions UNITED NATIONS Shipment Details Report – January 2006. Writing Pseudocode And Making a Flow Chart A Number Guessing Game What gas makes up 78% of our atmosphere? Chapter 7 Sampling and Sampling Distributions

