Structure determination of molecular materials from powder diffraction data

Structure determination of molecular materials from powder diffraction data

Current Opinion in Solid State and Materials Science 6 (2002) 125–130 Structure determination of molecular materials from powder diffraction data Ken...

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Current Opinion in Solid State and Materials Science 6 (2002) 125–130

Structure determination of molecular materials from powder diffraction data Kenneth D.M. Harris* School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2 TT, UK

Abstract Many solids can be prepared only as microcrystalline powders and are not suitable for structural characterization by single crystal diffraction techniques. In such cases, it is necessary to carry out structure determination using powder diffraction data. There has been considerable recent interest in this field, and considerable progress has been achieved both in the development of new techniques and in the application of these techniques to tackle a wide range of structural problems. This article highlights recent developments of techniques in this field, and their application in the field of molecular solid state chemistry.  2002 Elsevier Science Ltd. All rights reserved. Keywords: Structure determination; Molecular materials; Powder diffraction

1. Introduction Although single crystal X-ray diffraction is the most powerful and routinely applied technique for determining crystal structures, an intrinsic limitation of this technique is the requirement to prepare a crystal of sufficient size, quality and stability. When appropriate single crystals cannot be obtained, it is necessary instead to tackle structure determination using powder diffraction data. Crystal structure determination from diffraction data (single crystal or powder data) comprises the following stages: (i) unit cell determination (‘indexing’) and symmetry determination (space group assignment), (ii) structure solution, and (iii) structure refinement. Determination of the unit cell requires consideration of the positions of peaks in the powder diffraction pattern, whereas space group assignment, structure solution and structure refinement also require consideration of the relative intensities of the peaks. Structure solution starts from no knowledge of the arrangement of atoms or molecules within the unit cell, and aims to derive a good approximation to the crystal structure from analysis of the experimental diffraction data. If a sufficiently good structure solution is obtained, a high quality structure may then be obtained by refinement of this structural model in the structure refinement stage. For powder diffraction data, refinement of crystal struc*Tel.: 144-121-414-7474; fax: 144-121-414-7473. E-mail address: [email protected] (K.D.M. Harris).

tures can be carried out fairly routinely using the Rietveld refinement technique. In general, however, structure solution from powder diffraction data is a significantly greater challenge than structure refinement, and consequently, the main emphasis of fundamental developments in recent years has focused on the structure solution stage of the structure determination process. There are two general strategies for structure solution from powder diffraction data—the ‘traditional’ approach and the ‘direct-space’ approach. In the traditional approach, the aim is to extract the intensities I(hkl) of individual reflections directly from the experimental powder diffraction pattern, and then to use these I(hkl) data in the types of structure solution calculation that have been developed for single crystal diffraction data (for example, direct methods and Patterson methods). However, as a consequence of peak overlap in the powder diffraction pattern, it is often difficult to obtain reliable values of the intensities I(hkl) of the individual diffraction maxima from the experimental powder diffraction pattern, and much fundamental work on the development of the traditional approach has been devoted to improving the reliability of the procedures for peak extraction. In the direct-space approach, trial structures are generated in direct space, independently of the experimental powder diffraction data, and the suitability of each trial structure is assessed by comparing the powder diffraction pattern calculated for the trial structure and the experimental powder diffraction pattern. This comparison is quantified using an appropriate R-factor (often the weighted

1359-0286 / 02 / $ – see front matter  2002 Elsevier Science Ltd. All rights reserved. PII: S1359-0286( 02 )00045-1

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powder profile R-factor R wp is used, as in Rietveld refinement). The direct-space strategy for structure solution aims to find the trial crystal structure that has the lowest possible R-factor, and the approach is equivalent to exploring a hypersurface R(G ) to find the global minimum on the hypersurface, where G represents the set of variables that defines the structure. In principle, any technique for global optimization (e.g., Monte Carlo, simulated annealing, genetic algorithms, etc.) may be used to locate the lowest point on the R(G ) hypersurface, and a wide variety of different global optimization strategies have been employed in this regard. The field of structure determination from powder diffraction data has experienced a period of considerable development in recent years, and the aim of this article is to survey the developments and progress published in the literature during 2001 and the early part of 2002. The article is focused on applications of such techniques in the specific case of molecular crystal structures, although the developments of fundamentals and methodology described in this article clearly have much wider applicability to other classes of materials. In continuation of recent trends, the majority of applications of powder diffraction techniques to determine the structures of molecular crystals have employed direct-space techniques for structure solution, although some examples employing traditional techniques have also been reported. The article gives emphasis to those applications involving complete structure determination from powder diffraction data, as opposed to cases in which structural models have been obtained from other sources and then refined using powder diffraction data. Furthermore, with regard to fundamental aspects of the development of methodology, focus is given to developments of structure solution techniques, partly in recognition of the fact that this remains, in general, the most challenging stage of the structure determination process. There have been a number of review articles on structure determination from powder diffraction data, including two comprehensive reviews [1,2] covering essentially all aspects of the field, as well as a number of shorter reviews [3,4] of a general nature. Other review articles have tended to focus on the work of specific research groups, covering the development of direct-space methodology [5], the combination of Monte-Carlo / simulated annealing techniques with first principles density functional theory calculations [6], the use of a grid-search technique [7], applications of genetic algorithm methods [8,9], a simulated annealing approach [10], and a Monte Carlo program [11].

2. Fundamentals As discussed above, fundamental developments of methodology have mainly concerned the structure solution stage of the structure determination process.

Developments within the domain of the traditional approach for structure solution have included a method [12] for pattern decomposition (i.e., the extraction of the intensities of individual reflections from the powder diffraction pattern) based on utilising preferred orientation in textured samples. Improved procedures for extraction of accurate integrated intensities from overlapped reflections, implemented within the EXPO program, have been described [13] and are shown to reduce the phase error in the phasing process of direct methods structure solution calculations. The EXPO program has also been extended [14] to include the implementation of real-space techniques for phase extension and refinement, as applied previously to structure solution of protein structures. Clearly this strategy introduces aspects of direct-space information within the framework of a traditional structure solution approach. Another development in the same general direction concerns the use of direct-space information to assist in the assignment of peaks in electron density maps produced from direct methods structure solution calculations [15]. An interesting development, with potentially wide applicability, concerns the use of structure envelopes in structure solution from powder diffraction data [16]. The structure envelope essentially defines regions of high electron density in the structure, and can be estimated by considering a small number of strong low-angle reflections in the powder diffraction pattern. Structure envelopes have been used in structure solution of a number of examples, including a tri-b-peptide. In this case, a simulated annealing program was used to locate the correct position of the molecule within the structure envelope. Clearly the use of structure envelopes in this manner can serve to reduce significantly the amount of structural space that requires to be explored in direct-space structure solution calculations. Within direct-space techniques, one factor that can aid future progress is to be able to visualise and understand the multi-dimensional R-factor hypersurfaces that are explored using such techniques. In this regard, a method for determining general sections through such hypersurfaces has been described [17], in which the values of all the variables that define the hypersurface are allowed to vary simultaneously. New methods have also been developed [18] for analysing the evolutionary events that occur during genetic algorithm structure solution calculations, including methods for probing the R-factor distribution within the population and for analysis of the evolutionary trajectory that leads to the correct structure solution. This method allows an understanding of the specific evolutionary events that are important in progressing towards the correct structure solution, and may clearly be exploited in the further development of the genetic algorithm methodology. A detailed analysis of simulated annealing strategies, applied in the field of structure determination from diffraction data (single crystal or powder), has been described

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[19]. The findings in this paper provide important new aspects of fundamental understanding, which may lead towards improvements in direct-space methods for structure solution based on simulated annealing strategies. In another development of direct-space methodology, a technique based on a differential evolution strategy has been described [20], and has been applied successfully to solve the structure of a triclinic polymorph of adipamide. Other fundamental developments have included an approach, based on probability theory, for determination of space group from powder diffraction data [21], and a modified Rietveld refinement procedure, developed within the context of Bayesian probability theory, that is shown to be robust even when the powder diffraction data contains peaks due to impurity phases [22].

3. Applications Techniques for structure determination of molecular materials from powder diffraction data have been applied to a broad range of examples from different areas of structural science, and have involved the application of each of the strategies for structure solution described above. In some cases, combinations of different techniques have been employed, involving either the use of different structure solution strategies, or the use of structure solution techniques in tandem with other sources of information (e.g., energy calculations or spectroscopic information). The traditional approach for structure solution has been applied in a number of cases, including the structure determination of 3,5-diisopropyl-4-nitropyrazole by employing a Patterson search method [23]. Direct methods, on the other hand, have been employed in structure determination of norbornene [24] and R-thiocamphor [25]. In an interesting series of papers, traditional techniques and direct-space techniques have been used in combination, by using a direct-space calculation (Monte Carlo method) to locate ‘missing atoms’ in electron density maps produced from structure solution calculations using a traditional approach (direct methods). This strategy has been applied in the structure determination of 2,2dihydroxymethylbutanoic acid [26], for which two oxygen and five carbon atoms were found by direct methods and the positions of the remaining two oxygen and one carbon atoms in the structure were found subsequently by the Monte Carlo calculation. This strategy has also been applied to find calcium atoms and water molecules in a zeolitic material [27], and to find missing atoms in the partially solved structures of a-SiO 2 and Mg 2 SiO 4 [28]. The genetic algorithm technique for structure solution has been applied in a number of cases, including structure determination of 4,49-trimethylenedipyridine [29], 2(methylsulfonyl)ethyl succinimidyl carbonate [30] and 2,5bis(trimethylsilyl)thiophene-S,S-dioxide [31]. The latter material is of interest with regard to its photoluminescence

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properties, and exhibits high efficiency blue fluorescence emission. The genetic algorithm technique has also been applied in the structure determination of a series of peptides, including Piv-Pro-Gly-NHMe [32] and Piv-Prog-Abu-NHMe [33]. Interest in the latter structure includes the fact that it contains an analogue of a b-turn, but constructed via an intramolecular C–H? ? ?O hydrogen bond. The Monte Carlo / simulated annealing strategy has been applied to solve several crystal structures, including structure determination of a number of pharmaceutical materials (some of significant conformational flexibility) [34], structural characterisation of four polymorphic forms of fananserine [35], and structure determination of tetracaine hydrochloride (a local anaesthetic) [36]. Among other examples, structure determination of a material containing one-dimensional spin chains obtained from 2,5bis(pyrazol-1-yl)-l,4-dihydroxybenzene and CuBr 2 in aqueous ammonia (comprising the purple coloured coordination polymer [1Cu] n ) has been reported [37]. Simulated Annealing has also been used to solve the structures of triphenyl phosphite [38], several polymorphs (with different colours) of 5-methyl-2-[(2-nitro-4methylphenyl)amino]-3-thiophenecarbonitrite [39], the low temperature (100 K) structure of S-camphor [40], and a number of other molecular crystal structures [41], and has also been used in combination with structure prediction (energy simulation) methods in the structure determination of metallo–organic complexes containing Zn, Cu and Ni [42]. The Monte Carlo method has been applied as part of a structural investigation of 5-bromonicotinic acid and solvates of 5-bromonicotinic acid [43], and in structure determination of 2,4,6-triisopropylbenzene sulfonamide and the 1:1 hydrogen-bonded adduct of hexamethylenetetramine and 1,2,3-trihydroxybenzene [44]. Finally, an interesting and challenging example [45] concerns the application of a simulated annealing approach to solve the structure of an organic:inorganic layered material containing 4-(4-dimethylamino-phenylazo)-1-methyl pyridinium as the guest component within a metal oxalate host structure. This material, which is of interest with regard to its non-linear optical properties, has 61 independent atoms in the asymmetric unit. The structure determined from the powder diffraction data provides a basis for rationalizing the properties of this material. Grid-search techniques have been applied to solve a number of structures, including several organometallic complexes [46–48] from laboratory and synchrotron X-ray powder diffraction data, and the molecular material 6phenyl - 5 - phenylsulfonyl - 1,2,3,4 - tetrahydropyrimidine - 2thione [49] from neutron powder diffraction data. Grid search methodology has also been employed, in combination with energy calculations and solid state NMR data, in order to determine the structure of anhydrous theophylline [50]. Other materials for which the crystal structures have

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been determined directly from powder diffraction data include decafluoroquaterphenyl [51], pentamethylcyclopentadienylsodium [52], a rigid ferrocenebased macrocycle [53], potassium and rubidium salicylate [54], caesium hydroxide monohydrate [55], pigment orange 2 [56], 8-hydroxy-5-nitroquinoline and 8-hydroxy5-nitroquinolinium chloride [57], and sodium 4-(2pyridinyl diazenyl)-resorcinolate monohydrate and ammonium 2,4-dinitro-1-naphthanenolate [58]. Structure determination from powder diffraction data has also led to an understanding of the thermal isomerisation pathway of 1 - (4 - nitrophenyl) - 2 - phenylimino - 2,5 - dihydro - 1H - pyrido[3,2,-b]indole-3-carbonitrite [59], and has been applied in studies of charge transfer complexes of metal dithiolenes [60]. Among several examples from the pharmaceutical field, powder diffraction has been used in characterization of the hydration properties of docetaxel [61].

4. Concluding remarks The wide-ranging examples of successful structure solution of molecular materials from powder diffraction data that have been reported in recent years, including those highlighted in this article, provide a clear demonstration of the increasing power, scope and applicability of the techniques available in this field. Through the application of these techniques, the option to determine molecular crystal structures directly from powder diffraction data is now a very real opportunity. Nevertheless, there remains considerable scope for further development and optimization of the techniques and strategies in this field, and it may be predicted with some confidence that the progress that has taken place in recent years will be maintained, with much vigour, in the years to come.

Acknowledgements I am grateful to Dr. Eugene Cheung for helpful discussions.

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