Testo.pdf

COMMISSION ON POWDER DIFFRACTION
INTERNATIONAL UNION OF CRYSTALLOGRAPHY
http://www.iucr.org/iucr-top/comm/cpd/
NEWSLETTER No. 25, July 2001
http://www.iucr.org/iucr-top/comm/cpd/Newsletters/ .
IN THIS ISSUE
Structure Determination from Powder Diffraction Data
(Bill David, Editor)
CPD chairman’s message, Paolo Scardi
Ab-initio structure determination of oligopeptides
from powder diffraction data
Editor’s message, Bill David
K D M Harris, R L Johnston, E Tedesco and G W Turner CPD projects:
Correlating crystal structure with the physical
Quantitative Phase Analysis RR, Ian Madsen
properties of pharmaceutical compounds
Size-Strain RR, Davor Balzar
N Shankland, W I F David, K Shankland, A Kennedy, CS Frampton and A Florence WWW sites related to Powder Diffraction
EXPO: New developments
IUCr Commission on Powder Diffraction
A Altomare, C Giacovazzo, A G G Moliterni and R Rizzi Structure determination from powder diffraction data
News from ICDD and IXAS 26
Revisiting the 1998 SDPD Round Robin
Computer Corner, L M D Cranswick
What’s On
A 117-atom structure from powder diffraction data
L B McCusker, Ch Baerlocher and T Wessels Companies
Drug polymorphism and powder diffraction
How to receive the CPD Newsletter
P Sieger, R Dinnebier, K Shankland and W I F David Calls for contributions to CPD newsletter 26
Malaria, synchrotron radiation and Monte Carlo
P W Stephens, S Pagola, D S Bohle and A D Kosar A case of mistaken identity: metastable Me2SBr2
A N Fitch, G B M Vaughan and A J Mora Combined Rietveld and stereochemical- restraint
refinement with high resolution powder diffraction
offers a new approach for obtaining protein-drug
structures
On the reliablility of Rwp in structure prediction
Revisiting the 1998 SDPD Round Robin
published now proving that a solution was obtainable frompowder data [5].
Armel Le Bail (1) and Lachlan M.D. Cranswick (2) PARTICIPANTS
1. Université du Maine, Laboratoire des Fluorures, The 70 people who downloaded data may be considered CNRS ESA 6010, Avenue O. Messiaen, 72085 Le to be subscribers to this Round Robin. The possibility was Mans cedex 9, France - E-mail: [email protected] given for either anonymous download or filling a Web 2. Lamont-Doherty Earth Observatory of Columbia form asking for details about which methods and software University PO Box 1000, 61 Route 9W Palisades, New will be used for 3 main steps : structure factors extraction, structure solution and structure completion and refinement.
E-mail: [email protected] 31 subscribers filled in the Web form, more or less INTRODUCTION
completely, indicating that they intended to use some of In the middle of 1998, the number of structure the best known programs such as GSAS, FULLPROF, determinations by powder diffractometry (SDPD) was SHELX and SIRPOW. 11 participants gave explicit close to 300 of which 250 were published in the period answers to all the 3 main steps, simultaneously. One expert 1992-1997 [1]. At that time, a huge number of methods indicated after the deadline that he would have participated and computer programs had already proven, at least once, if the molecular shape had been given for sample 2.
their efficiency in succeeding in the various steps of the RESULTS AND DISCUSSION
process of solving structures from powder diffraction data.
In the end, we received 5 full questionnaires from 4 final The word "routine" was pronounced more and more participants; one questionnaire for sample 1 and four for frequently, so that it was considered timely to organize a sample 2. Participant 1 made a very rapid reply but was Round Robin, in order to try to clarify the various claims unable to provide coordinates. By a search in the about the ease or otherwise in performing SDPDs. Data Cambridge Structural Database, he easily found the and questionnaires were made available from a Web site reference for the pharmaceutical compound as being the starting from May 18, 1998 and the deadline was the last tetracycline (alias achromycin) hydrochloride. He then day of June. The competition was spammingly announced suggested that the coordinates should be found in this at many Newsgroups and Mailing lists related to reference. Unfortunately, however, the coordinates were crystallography and material science. Mails were sent also not available in this paper or in the Cambridge Structural to some chemistry lists (Chemweb and CCL), trying to Database. Only the molecular formula was available.
interest structure predictors to undertake first principles or Participant 2 was the only regular subscriber to have sent a semi-empirical calculations. Moreover, personal e-mails successful questionnaire. He focused his attention were sent to a number of well-known experts. As a exclusively on sample 2 and solved its structure, including consequence of this campaign, more than 800 visitors had the hydrogen atom positions by the global optimization a link to the homepage, which is still available [2]. 70 of method. A model for the molecule was taken from the the 800 visitors downloaded the data.
tetracycline hydrate in the Cambridge Structural Database SELECTION OF SAMPLES FOR ANALYSIS
(TETCYH10 entry) and the water was removed. The There is a clear distinction between compounds for which tetracycline fragment and the Cl atom were positioned at prior knowledge is available (molecular formula) or not.
random in the unit cell and an optimum position was This difference may lead to one choosing quite different searched (Fig. 1) by simulated annealing using the DRUID methods for solving the crystal structures. It was thus program against the 100 first structure factors extracted by decided to propose two samples that fulfilled these the Pawley method from the synchrotron data. The final conditions. We restricted the scope of this Round Robin to Rietveld refinement plot is shown on the Figure 2. There is the structure solution part by providing the cell and space something curious between the starting and final model.
group information. The first sample was inorganic, a The main move is that O2 and N1 in the TETCYH10 carbonatocobalt(III)pentamine nitrate hydrate; the second model have rotated by 180° along the C2-C3 axis. The H sample was organic, the pharmaceutical compoundtetracycline hydrochloride. A medium resolutionsynchrotron pattern was provided for the latter, as well as aconventional X-ray powder pattern with similar resolution.
The organic sample was especially selected for modellocation methods; the molecular shape, however, was notgiven. We considered that the shape could have been veryeasily obtained from various sources. During the RoundRobin course, one of the participants gave a very accuratestructure for tetracycline hydrochloride that even includedhydrogen positions. Thus for validation purposes, it wasfound necessary to record a data set from a very smallsingle crystal (40x30x20µ) selected in the powder, usingthe Daresbury 9.8 station equipped with the SMARTSiemens system [3]. The subsequent structure wasdetermined easily (SHELXS) and refined without any Fig. 1 Comparison of the molecular structures of tetracycline
constraint, including the hydrogen atoms [4]. This raises hydrochloride obtained from global optimization and the question of what constitutes a powder and what a from the final Rietveld refinement (Participant 2) single crystal sample. The inorganic structure is also Fig. 3 Final conventional X-ray diffraction Rietveld plot for
Fig. 2 Final synchrotron X-ray diffraction Rietveld plot
flood of results? The solving of sample 2 structure from Patterson is not really the way that most crystallographers atoms did not moved much between the initial and final would have expected. Preconceived ideas would have model. An additional hydrogen atom should have been prevailed that the unique Cl atom would not have been so found for building the complete sample 2 structure, O2 in heavy that a Patterson would have easily disclosed it.
the hydrate becoming an OH. This hydrogen was not Participant 4 obtained RF=0.57 with the Cl atom.
included by participant 2. Interviewed on this question, Remember that putting anything at any place gives you participant 2 commented that the exclusion of the already RF=0.5 or 0.6. In fact, the structure solution as hydrogen atom was an oversight caused by no sleep on the described by participant 4 appears disarmingly simple, but previous night. The diffraction pattern had been it is not that straightforward. Here is why. Let us examine downloaded and the structure solved the day after a trans- the Fourier difference as Participant 4 provided it. The 2 Atlantic flight. The total time for solution was two hours.
main first peaks are not atoms, neither is the fourth, the Participant 3 did not have easy Web access and obtained seventh nor the ninth. Many standard crystallographers the data by e-mail. He thought that sample 2 would be would have given up at this stage, but not Participant 4. He unsolvable without the molecule connectivity and asked was able to recognize a connected chain of 6 atoms. Here for it. We had anticipated that we would reply positively to is the importance of skill, and experience. Most people such a request, as the connectivity could normally be would have stopped, rejecting this Fourier synthesis independently determined by a chemist using other because of the two first intense peaks do not correspond to methods such as magnetic resonance. Participant 3 sent anything, or perhaps would have attempted a refinement of filled questionnaires for samples 1 and 2, estimating finally the coordinates, which would have failed. Many would not that both of them were unsolvable. We are forced to even have believed that a Fourier synthesis with only the conclude that the remaining participants found the Cl atom would have a chance to be successful. The structures either non-routine, non-solvable or too organizers did not try the Patterson method because they had the preconceived idea that it was impossible (in factwe continue to think that way). Because the SDPDRR is Participant 4 downloaded the data anonymously and mainly a YES/NO Round Robin (i.e. you win or not), we solved the sample 2 structure from the conventional X-ray should take all those lacking questionnaires for 68x2 as a data by using the CSD package. 158 structure factors were failure to solve. Perhaps, we should not count the 70 data extracted by using the CSD-PROFAN program. Using the downloaded but only the 31 regular subscribers.
CSD-MAIN program, the chlorine atom was located by Anonymous downloaders never formally declared their Patterson methods. The first Fourier map produced the intention to solve the problems. However, it should be coordinates of ten of the other atoms. Several cycles of noted that if single crystal data had have been provided, Rietveld and Fourier syntheses were required to complete structure solving would have been “routine” using all the structure (Figs. 3 and 4). According to participant 4, the freely and commonly available single crystal structure full time needed for solution and refinement was only 3hours, 2 cups of coffee and 5 cigarettes by using a low-endIntel PC. Participant 4 wrote also that "the structure of theinorganic complex is very simple and that is why it is notinteresting." It should be stated that participant 2 had provided the most accurate results with mean displacements relative tothe single crystal data lower by a factor 2 than those fromparticipant 4 and from the organisers [2]. Even thehydrogen atom positions were well located with a meanerror of 0.2 angstroms.
COMMENTS
If the structure was in fact quite simple to solve using Fig. 4 Tetracycline hydrochloride model built from Patterson
Patterson - doesn't it say something t hat there was not a and Fourier recycling (Participant 4).
solution packages; e.g.; SHELXS, SIR, DIRDIF, CRUNCH.
approaching 500, and the proportion of organic compoundsslightly increases, but remains lower than 20%. New CONCLUDING REMARKS AND RECOMMENDATIONS
programs for molecule location have been made available The conclusion from this 1998 Round Robin is that [8]: POWDERSOLVE (having proposed a post-deadline solving structures “on demand” from powder diffraction is contribution [9]), PSSP, ENDEAVOUR, TOPAS, ESPOIR, non-routine and non-trivial, requiring much skill and etc, or new options of old programs (the upcoming version tenacity on the part of practitioners (though this should be of EXPO2000 and the renamed DASH, which was formally tempered by the fact that no molecule location program DRUID. Alas a good number of these programs are was easily available for free from any website in 1998).
commercial. Moreover, the use of the Internet has grown Publications stating that structure solution using powder since 1998 so that if the Round Robin had been proposed diffraction data is now “routine” (especially from the in 2001, more participants would have had a chance to perspective of single crystal practitioners attempting succeed with both samples. Nevertheless, confirming this powder diffraction based structure solution) could be hypothesis needs a new Round Robin to be organized.
considered misleading. Providing inaccurate, rosy reviews can be counter productive with respect to bringing the field REFERENCES
into disrepute as being one populated by thecrystallographic equivalent of snake-oil salesmen. The crystallographic definition of “routine” structure solution is presently based on the single crystal experience, of one 3. CLRC Daresbury Synchrotron, Station 9.8.
where structures literally solve to near completion at the click of a button. At present much work can be done to 4. Clegg, W. & Teat, S.J. (2000). Acta Cryst. C56, 1343-
enhance powder diffraction based software to give them single crystal quality automation and robustness to help 5. Zhu, J.H., Wu, H.X. & Le Bail, A. (1999). Solid State make structure solution from powder diffraction more an Science 1, 56-62.
attractive method than it is at present.
6. http://www.cristal.org/iniref/ecm18/ecm18sdpdrr.html7. http://www.chemweb.com/alchem/alchem98/catalyst/cto A report on the SDPD Round Robin delivered at the ECM- 8. http://www.cristal.org/iniref/progmeth.html#n7 18 congress is still available [6], as well as one written by a 9. http://www.msi.com/materials/cases/an_roundrobin.html scientific journalist, David Bradley [7]. The number ofdetermined structures using powder diffraction data is now A 117-Atom Structure from Powder
information about the relative intensities of reflections thatoverlap in 2θ.
Diffraction Data
Lynne B. McCusker, Christian Baerlocher Consider the three types of samples (single crystal, "ideal" powder and textured powder) sketched in two Laboratory of Crystallography, ETH, Zurich, Switzerland dimensions in Fig. 1a-c. The textured sample is intuitively INTRODUCTION
intermediate between a perfectly oriented single crystal, This is the story of how the structure of the very complex and a powder with crystallites oriented in all directions, zeolite UTD-1F, with 117 atoms in the asymmetric unit, and the corresponding two-dimensional diffraction patterns could be solved from powder diffraction data[1]. The support this view. The three reflections highlighted in (a), structure solution was the culmination of a long period ofmethod development that required not only new dataanalysis software, but also a new way of collecting data [2].
But let us begin at the beginning.
Our research group has a long-standing interest in zeolite structure analysis, and, because zeolites are rarely availablein the form of single crystals, this has always includeddevelopment of powder diffraction methodology. In oursearch for more powerful approaches to zeolite structuresolution, model calculations reported by Hedel et al.[3]prompted us to consider the possibility of exploitingtexture (preferred orientation of the crystallites). Usually,powder diffractionists go to great lengths to avoid any Fig 1 Two-dimensional schematic drawings of a specimen
preferred orientation in their samples, because it can and its diffraction pattern for (a) a single crystal, (b) a severely distort the intensities in the measured diffraction powder with randomly oriented crystallites, and (c) a pattern. However, if the data are collected appropriately, textured powder. The arrows highlight three reflections this distortion, which is a function function of the with similar diffraction angles that are separated in thesingle-crystal pattern, but overlap in the normal powder orientation of the crystallites in the sample and of the pattern. The diffraction angle 2θ increases radially sample in the X-ray beam, can provide additional from the center of each diffraction pattern.

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