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Inorganic Structure Prediction with GRINSP Armel Le Bail

Inorganic Structure Prediction with GRINSP Armel Le Bail Université du Maine, Laboratoire des oxydes et Fluorures, CNRS UMR 6010, Avenue O. Messiaen, 72085 Le Mans Cedex 9, France. Email : alb@cristal.org. CONTENT

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Inorganic Structure Prediction with GRINSP Armel Le Bail

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  1. Inorganic Structure Prediction with GRINSP Armel Le Bail Université du Maine, Laboratoire des oxydes et Fluorures, CNRS UMR 6010, Avenue O. Messiaen, 72085 Le Mans Cedex 9, France. Email : alb@cristal.org

  2. CONTENT • IntroductionGRINSP algorithmGRINSP predictionsOpened doors, and limitationsPrediction confirmationConclusion

  3. I- INTRODUCTION To predict a crystal structure is to be able to announce it before any confirmation by chemical synthesis or discovery in nature. A predicted structure should be sufficiently accurate for the calculation of a predicted powder pattern that would further be used with success in the identification of a real compound not yet characterized.

  4. Where are we with inorganic structure prediction? If the state of the art had dramatically evolved, we should have huge databases of predicted compounds. Not any new crystal structure would surprise us since it would correspond already to an entry in that database. Moreover, we would have obtained in advance the physical properties and we would have preferably synthesized those interesting compounds. Of course, this is absolutely not the case.

  5. Things are changing, maybe : Two databases of hypothetical compounds were built in 2004. >100000 hypothetical zeolites at :http://www.hypotheticalzeolites.net/ >2000 inorganic compounds in PCOD(zeolites as well as other oxides and fluorides) at :http://www.crystallography.net/pcod/ However, inorganic prediction software and methods remain scarce: CASTEP, GULP, G42, SPuDS, AASBU, CERIUS2… Hence the development of a new one : GRINSP

  6. II- GRINSP Algorithm Geometrically Restrained INorganic Structure Prediction Applies the knowledge of the common geometrical characteristics of a well defined group of crystal structures (N-connected 3D nets with N = 3, 4, 5, 6 and combinations of two N values), in a Monte Carlo algorithm, In GRINSP, the quality of a model is established by a cost function depending on the weighted differences between calculated and ideal interatomic first neighbour distances M-X, X-X and M-M in binary MaXb or ternary MaM'bXc compounds. J. Appl. Cryst. 38, 2005, 389-395.

  7. Comparison of a few GRINSP-predicted cell parameters with observed ones Predicted (Å) Observed or idealized (Å) Dense SiO2 a b c R a b cQuartz 4.965 4.965 5.375 0.0009 4.912 4.912 5.404Tridymite 5.073 5.073 8.400 0.0045 5.052 5.052 8.270 Cristobalite 5.024 5.024 6.796 0.0018 4.969 4.969 6.926 Zeolites ABW 9.872 5.229 8.733 0.0056 9.9 5.3 8.8EAB 13.158 13.158 15.034 0.0037 13.2 13.2 15.0EDI 6.919 6.919 6.407 0.0047 6.926 6.926 6.410GIS 9.772 9.772 10.174 0.0027 9.8 9.8 10.2GME 13.609 13.609 9.931 0.0031 13.7 13.7 9.9JBW 5.209 7.983 7.543 0.0066 5.3 8.2 7.5LTA 11.936 11.936 11.936 0.0035 11.9 11.9 11.9RHO 14.926 14.926 14.926 0.0022 14.9 14.9 14.9 Aluminum fluorides-AlF3 10.216 10.216 7.241 0.0162 10.184 10.184 7.174 Na4Ca4Al7F33 10.860 10.860 10.860 0.0333 10.781 10.781 10.781AlF3-pyrochl. 9.668 9.668 9.668 0.0047 9.749 9.749 9.749

  8. More details on the GRINSP algorithm Two steps : 1-Generation of structure candidates First the M/M’ atoms are placed in a box whose dimensions are selected at random, and the model should exactly correspond to the geometrical specifications (exact coordinations, but some tolerance on distances). The cell is progressively filled with M/M’ atoms, up to completely respect the geometrical restraints, if possible. The number of M/M' atoms placed is not predetermined. In this first step, atoms do not move, their possible positions are tested and checked, then they are retained or not.

  9. 2- Local optimization The X atoms are added at the midpoints of the (M/M')-(M/M') first neighbours. It is verified by distance and cell improvements (Monte Carlo moves) that regular (M/M’)Xn polyhedra can really be built. The cost function is based on the verification of the provided ideal distances M-M, M-X and X-X first neighbours. A total R factor is defined as : R =  [(R1+R2+R3)/ (R01+R02+R03)], where Rn and R0n for n = 1, 2, 3 are defined as : Rn =  [wn(d0n-dn)]2, R0n =  [wnd0n]2, where d0n are the ideal first interatomic distances M-X (n=1), X-X (n=2) and M-M (n=3), whereas dn are the observed distances in the structural model. The weights retained (wn) are those used in the DLS software for calculating idealized zeolite framework data (w1= 2.0, w2 = 0.61 and w3 = 0.23).

  10. Minimizing the Difference of Distances with Ideal distancesis a very basic approach… The ideal distances are to be provided by the user for pairs of atoms supposed to form polyhedra (for instance in the case of SiO4 tetrahedra, one expects to have d1 = 1.61 Å, d2 = 2.629 Å and d3 = 3.07 Å). For ternary compounds, the M-M' ideal distances are calculated by GRINSP as being the average of the M-M and M'-M' distances. It is clear that this R factor considers only the X-X intra-polyhedra distances, neglecting any X-X inter-polyhedra distances This cost function R could possibly be better defined differently, for instance by using the bond valence sum rules (this is in project for the next GRINSP version). This basic approach can work only for regular polyhedra

  11. More on the optimization second step During this second step, the atoms are moving, but no jump is allowed because a jump would break the coordinations established at the first step. This is a simple routine for local optimization. The change in the cell parameters from the structure candidate to the final model may be quite considerable (up to 30%), During the optimization, the original space group used for placing the M/M' atoms may change after adding the X atoms, so that the final structure is always proposed in the P1 space group, and presented in a CIF. The final choice of the real symmetry has to be done by using a program like PLATON.

  12. How GRINSP works : 1- Create a small datafile corresponding to your desire Example for such a datafile: TiO6/VO5 Pbam - 55 ! Title P B A M ! Space group 4 2 0 2 ! Nsym (symmetry code), Npol, etc 6 5 ! Coordinations of these npol polyhedron-type Ti O ! Definition of the elements for the first polyhedron V O ! Definition of the elements for the second polyhedron 3. 16. 3. 16. 3. 16. ! Min and max a, b, c 90. 90. 90. 90. 90. 90. ! Min and max angles 5. 35. ! Min and max framework density 200000 300000 0.02 0.25 ! Nruns, MCmax, Rmax saving, optimizing 20000 1 ! number of MC optimization cycles, refinement code 9550000 ! first filename (will be 9550000.cif, .xtl, .dat, etc)

  13. 2 – Verify if your atom-pairs are already defined : See into the distgrinsp.txt file : V O 5 3.050 4.050 3.550 1.526 2.126 1.826 2.282 2.882 2.582 4.20 7.00 Ti O 6 3.300 4.300 3.800 1.650 2.250 1.950 2.458 3.057 2.758 4.45 6.95 These are minimal, maximal and ideal distances for V-V, V-O and O-O in VO5 square pyramids, and for Ti-Ti, Ti-O and O-O in TiO6 octahedra.

  14. 3- Run GRINSP

  15. 4- Wait a bit (one day…) and, when finished, see the summary file :

  16. 5 – See the results (here using Diamond from a CIF) :

  17. GRINSP is Open Source, GNU Public Licence Download it at : http://www.cristal.org/grinsp/

  18. III- GRINSP Predictions Binary compounds Formulations M2X3, MX2, M2X5 and MX3 were examined Zeolites More than a thousand models (not >100000) were built with R < 0.01 and cell parameters < 16 Å and placed into the PCOD database. The way GRINSP recognizes a zeotype is by comparing the coordination sequence (CS) of any model with a list of previously established ones (as well as with the other CS already stored during the current run). The CIFs can be obtained by consulting the PCOD database, giving the entry number provided with the figure caption (for instance PCOD1010026, etc).

  19. Hypothetical zeolite PCOD1010026SG : P432, a = 14.623 Å, FD = 11.51

  20. Hypothetical zeolite PCOD1030081SG : P6/m, a = 15.60 Å, c = 7.13Å, FD = 16.0. Estimated number of zeolite models proposed by GRINSP : > 2000

  21. Hypothetical aluminosilicate PCOD1010038SG : P432, a = 14.70 Å - FD = 11.32 formulation : [Si2AlO6]-1 Estimated number of aluminosilicates proposed by GRINSP : > 2000

  22. Hypothetical aluminophosphateSG : Pma2, a = 15.81 Å, b = 8.06 Å, c = 5.64 Å - FD = 13.9 formulation : [Al4PO10]-3 Estimated number of aluminophosphates proposed by GRINSP : > 2000

  23. Can GRINSP predict > 100000 zeolites as well ? Yes, if Rmax fixed at 0.02 instead of 0.01, if the cell parameters maximum limits (16Å) are enlarged, and if multi-redundant solutions in various space groups are all kept. I prefer not. Is there any sense to predict > 100000 zeolites when less than 200 are known ?

  24. B2O3 polymorphs predicted by GRINSP Not a lot of crystalline varieties are known for this B2O3 composition. Too many are proposed by GRINSP. Hypothetical B2O3 PCOD1062004.

  25. Hypothetical B2O3 PCOD1051002 Estimated number of B2O3 models proposed by GRINSP : > 3000

  26. M2X5 compounds Example : unknown V2O5, SG: Pbam, a = 13.78 Å, b = 14.55 Å, c = 7.25 Å, FD = 16.5, R = 0.0056, VO5 square pyramids : Estimated number of V2O5 models proposed by GRINSP : > 200

  27. AlF3 polymorphs yet to be synthesized,predicted by GRINSP All the known structure-types (5) were retrieved, Two other structure types existing with stuffed MX3 formulations were proposed. Five unknown, “yet to be synthesized" AlF3 polymorphs were predicted That time, the total number is small : 12 models only with R < 0.02.

  28. Classification of the 12 AlF3 polymorphs proposed by GRINSP (identified as known or unknown) according to increasing values of the distance quality factor R < 0.02 Structure-type FD a b c  SG Z N R HTB 19.68 6.99 6.99 7.21 90.0 90. 120.0 P63/mmc 6 1 0.0035TlCa2Ta5O1520.67 7.00 7.23 9.56 90.0 90.0 90.0 Pmmm 10 2 0.0040U-1 (AlF3) 21.27 6.99 7.22 13.5 90.0 105. 90.0 P21/m 14 3 0.0042Pyrochlore 17.71 9.67 9.67 9.67 90.0 90.0 90.0 Fd-3m 16 1 0.0046U-2 (AlF3) 20.43 6.88 6.89 8.25 90.0 90.0 90.0 P-4m2 8 2 0.0057Perovskite 21.16 3.62 3.62 3.62 90.0 90.0 90.0 Pm-3m 1 1 0.0063Ba4CoTa10O30 21.15 9.45 13.8 7.22 90.0 90.0 90.0 Iba2 20 2 0.0095TTB 20.78 11.5 11.5 7.22 90.0 90.0 90.0 P42/mbc 20 2 0.0099U-3 (AlF3) 22.37 6.96 7.40 5.21 90.0 90.0 90.0 Pnc2 6 2 0.0160-AlF3 21.17 10.2 10.2 7.24 90.0 90.0 90.0 P4/nmm 16 3 0.0162U-4 (AlF3) 21.71 10.5 10.5 6.68 90.0 90.0 90.0 I41/a 16 1 0.0181U-5 (AlF3) 19.74 7.12 7.12 11.98 90.0 90.0 90.0 P42/mmc 12 2 0.0191 FD = framework density (number of Al atoms for a volume of 1000Å3). SG = higher symmetry spage group in which the initial model of Al-only atoms was obtained (not being necessarily the true final space group obtained after including the F atoms). Z = number of AlF3 formula per cell. N = number of Al atoms with different coordination sequences. R = quality factor regarding the ideal Al-F, F-F and Al-Al first neighbour interatomic distances.

  29. Yet to be synthesized U-3 (AlF3).

  30. Known : -AlF3 - tetrahedra and chains of octahedra

  31. Unknown : U-4 (AlF3), dense packing of tetrahedra of octahedra, exclusively

  32. Model 13 : U-6 (AlF3), R > 0.02, not viable due to a too high level of octahedra distortion and short F-F distances

  33. By-products of the search with GRINSP Irregular polyhedra can be produced… For instance, sixfold polyhedra other than octahedra can be produced: trigonal prisms or pentagonal based pyramids. Since they do not correspond to one unique ideal X-M distance or M-X distance, they are ranked with high R-values.

  34. Octahedra + pentagonal based pyramids :

  35. Octahedra + trigonal prisms :

  36. Chimeric compound mixing trigonal prisms with distorted trigonal bipyramids

  37. Two- and one-dimensionnal compounds can be formed. Nanotubes with B2O3 formulation for instance :

  38. Ternary MaM’bXc compounds with corner-sharing 3D nets M/M’ with same coordination but different ionic radii or different coordination The built ternary compound will not always be electrically neutral.

  39. Borosilicates PCOD2050102, Si5B2O13, R = 0.0055. SiO4 tetrahedraandBO3triangles Estimated number of models built by GRINSP : > 3000

  40. Aluminoborates Example : [AlB4O9]-2, cubic, SG : Pn-3, a = 15.31 Å, R = 0.0051: AlO6octahedraandBO3triangles Estimated number of models built by GRINSP : >2000

  41. Titanosilicates [Si2TiO7]2-, R = 0.0044, SG : P42/mmc, a = 7.73 Å, c = 10.50 Å, FD = 19.1. TiO6octahedraandSiO4tetrahedra Estimated number of models built by GRINSP : > 500

  42. Fluoroaluminates Known as Na4Ca4Al7F33 : PCOD1000015 - [Ca4Al7F33]4-. AlF6and CaF6 octahedra

  43. Unknown : PCOD1010005 - [Ca3Al4F21]3-. Estimated number of fluoroaluminates models built by GRINSP : ???

  44. A satellite software (GRINS) can build isostructural compounds faster than running again GRINSP However, changing the atomic radius may lead to different structures… Automatization is essential for the fast feeding of the PCOD, unfortunately, human eyes looking at the predicted structure is still essential : 5 minutes at least are needed for an evaluation before adding the CIF into the database. With zeolites, identification is easy because the coordination sequences of the known phases helps to recognize if the prediction leads to a new model or is already known But this is less easy with non-zeolites because there is no general extension of structure-types descriptors

  45. IV - Opened doors and limitations Limitation : corner-sharing polyhedra Potentially already > 50 or 100.000 hypothetical compounds in PCOD(only 2000 added yet) Scheduled improvements Make appear corner-, edge-, and face-sharing polyhedra, altogether. Propose an automatic way to obtain an electrical neutrality by the detection of holes and the filling of these holes by large cations. Use of bond valence rules at the optimization step, or/and energy calculations. Extension to quaternary compounds. Etc.

  46. With a few modifications, GRINSP could Predict structures for ice H2O (on the basis of distorted OH4 tetrahedra): or predict alloys MxM’y characterized by MM’4 and M’M4 tetrahedra,or predict fullerene structures, or predict structures for series of organic compounds provided they can be described by common geometrical features, etc. You are limited only by your own imagination…

  47. GRINSP can already predict structures deriving from perovskite by oxygen vacancies : Octahedra and square pyramids : > 500 predictions

  48. Brownmillerite A problem with ICSD is the difficulty to identify if a predicted structure-type is already described in the database. Generalized topology descriptors are lacking…

  49. V- Prediction confirmation More difficult even is the prediction of the synthesis conditions for making to appear these predicted crystal structures. However, if the chemical composition involves at least 3 elements or more, one may try the battery of classical synthesis methods. If an interesting model is predicted having the [Ca3Al4F21]3- formulation, may be it could be really synthesized as Na3Ca3Al4F21 or Li3Ca3Al4F21, or may be not. We can already be sure that most predictions will be vain, never confirmed, because the synthesis route may depend on a precursor (organometallic, hydrate, amorphous compound) which itself is yet unknown, or because the prediction is simply false.

  50. The more the predicted inorganic formula is complex,the more easy classical and direct synthesis routes can be tested,but metastable compounds will mostly occur from indirect routes. The [Ca4Al7F33]4- network proposed by GRINSP really exists with the Na4Ca4Al7F33 formulation.

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