Hostname: page-component-cd9895bd7-jkksz Total loading time: 0 Render date: 2024-12-26T08:15:53.956Z Has data issue: false hasContentIssue false
  • English
  • Français

FOX: A friendly tool to solve nonmolecular structures from powder diffraction

Published online by Cambridge University Press:  01 March 2012

Radovan Černý  and
Vincent Favre-Nicolin
Radovan Černý*
Affiliation:
Laboratoire de Cristallographie, Université de Genève, 24, quai Ernest-Ansermet, CH-1211 Genève 4, Switzerland
Vincent Favre-Nicolin
Affiliation:
Université Joseph Fourier and CEA, DRFMC∕SP2M∕NRS, 17, rue des Martyrs, F-38054 Grenoble Cedex 9, France
*
a)Electronic mail: radovan.cerny@cryst.unige.ch
Get access Rights & Permissions [Opens in a new window]

Abstract

Structural characterization from powder diffraction of compounds not containing isolated molecules but three-dimensional infinite structure (alloys, intermetallics, framework compounds, extended solids) by direct space methods has been largely improved in the last 15 years. The success of the method depends very much on a proper modeling of the structure from building blocks. The modeling from larger building blocks improves the convergence of the global optimization algorithm by a factor of up to 10. However, care must be taken about the correctness of the building block, like its rigidity, deformation, bonding distances, and ligand identity. Dynamical occupancy correction implemented in the direct space program FOX has shown to be useful when merging excess atoms, and even larger building blocks like coordination polyhedra. It also allows joining smaller blocks into larger ones in the case when the connectivity was not a priori evident from the structural model. We will show in several examples of nonmolecular structures the effect of the modeling by correct structural units.

Keywords

powder diffractionstructure solutiondirect space methodsimulated annealing
Type
Invited Articles
Information
Powder Diffraction , Volume 20 , Issue 4 , December 2005 , pp. 359 - 365
Copyright
Copyright © Cambridge University Press 2005

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Altomare, A., Caliandro, R., Camalli, M., Cuocci, C., Giacovazzo, C., Moliternia, A. G. G., and Rizzi, R. (2004). “Automatic structure determination from powder data with EXPO2004,” J. Appl. Crystallogr.JACGAR 37, 1025–1028.Google Scholar
Anokhina, E. V. and Jacobson, A. J. (2004). “[Ni2O(L‐ASP)(H2O)2].4H2O: A homochiral 1D helical chain hybrid compound with extended Ni–O–Ni bonding,” J. Am. Chem. Soc.JACSAT 126, 3044–3045.CrossRefGoogle Scholar
Barbier, J., Penin, N. and Cranswick, L. M. (2005). “Melilite-type borates Bi2ZnB2O7 and CaBiGaB2O7,” Chem. Mater.CMATEX 17, 3130–3136.CrossRefGoogle Scholar
Brinks, H. W. and Hauback, B. C. (2003). “The structure of Li3AlD6,” J. Alloys Compd.JALCEU10.1016/S0925-8388(02)01348-8 354, 143–147.CrossRefGoogle Scholar
Bulychev, B. M., Shpanchenko, R. V., Antipov, E. V., Sheptyakov, D. V., Bushmeleva, S. N., and Balagurov, A. M. (2004). “Synthesis and crystal structure of lithium beryllium deuteride Li2BeD4,” Inorg. Chem.INOCAJ 43, 6371–6376.CrossRefGoogle ScholarPubMed
Černý, R., Favre-Nicolin, V., and Bertheville, B. (2002). “A tetragonal polymorph of caesium hydroxide monohydrate, CsOH.H2O, from X-ray powder data,” Acta Crystallogr., Sect. A: Found. Crystallogr.ACACEQ 58, i31–i32.Google Scholar
Černý, R., Renaudin, G., Favre-Nicolin, V., Hlukhyy, V., and Pöttgen, R. (2004). “Mg1+xIr1−x (x=0, 0.037 and 0.054), a binary intermetallic compound with a new orthorhombic structure type determined from powder and single-crystal X-ray diffraction,” Acta Crystallogr., Sect. B: Struct. Sci.ASBSDK 60, 272–281.CrossRefGoogle ScholarPubMed
Černý, R., Renaudin, G., Tokaychuk, Ya., and Favre-Nicolin, V. (2005). “Complex intermetallic compounds in the Mg–Ir system solved by powder diffraction,” Z. Kristallogr.ZEKRDZ (in press).Google Scholar
Chernaya, V. V., Mitiaev, A. S., Chizhov, P. S., Dikarev, E. V., Shpanchenko, R. V., Antipov, E. V., Korolenko, M. V., and Fabritchnyi, P. B. (2005). “Synthesis and investigation of tin(II) pyrophosphate Sn2P2O7,” Chem. Mater.CMATEX 17, 284–290.CrossRefGoogle Scholar
Chi, L., Swainson, I., Cranswick, L., Her, J.-H., Stephens, P., and Knop, O. (2005). “The ordered phase of methylammonium lead chloride CH3ND3PbCl3,” J. Solid State Chem.JSSCBI 178, 1376–1385.CrossRefGoogle Scholar
David, W. I. F., Shankland, K., McCusker, L. B., and Baerlocher, Ch. (2002). Structure Determination from Powder Diffraction Data (Oxford University Press, Oxford) IUCr. Monographs on Crystallography 13.Google Scholar
Edgar, M., Carter, V. J., Tunstall, D. P., Grewal, P., Favre-Nicolin, V., Cox, P. A., Lightfoot, P., and Wright, P. A. (2002). “Structure solution of a novel aluminum methylphosphonate using a new simulated annealing program and powder X-ray diffraction data,” Chem. Commun. (Cambridge) 8, 808–809. Emald, P. P. (1921). Ann. Phys 64, 253.CrossRefGoogle Scholar
Favre-Nicolin, V. and Černý, R. (2002). “FOX, ‘Free Objects for Crystallography:’ A modular approach to ab initio structure determination from powder diffraction,” J. Appl. Crystallogr.JACGAR 35, 734–743.Google Scholar
Favre-Nicolin, V. and Černý, R. (2004). “A better FOX: Using flexible modelling and maximum likelihood to improve direct-space ab initio structure determination from powder diffraction,” Z. Kristallogr.ZEKRDZ 219, 847–856.CrossRefGoogle Scholar
Grzechnik, A., Dmitriev, V., Weber, H. P., Gesland, J. Y., and van Smaalen, S. (2004a). “The crystal structures of pressure-induced LiSrAlF6‐II and LiCaAlF6‐II,” J. Phys.: Condens. MatterJCOMEL10.1088/0953-8984/16/7/003 16, 1033–1043.Google Scholar
Grzechnik, A., Dmitriev, V., Weber, H. P., Gesland, J. Y., and van Smaalen, S. (2004b). “LiSrAlF6 with the LiBaCrF6-type structure,” J. Phys.: Condens. MatterJCOMEL10.1088/0953-8984/16/18/001 16, 3005–3013.Google Scholar
Grzechnik, A., Friese, K., Dmitriev, V., Weber, H. P., Gesland, J. Y., and Crichton, W. A. (2005). “Pressure-induced tricritical phase transition from the scheelite structure to the fergusonite structure in LiLuF4,” J. Phys.: Condens. MatterJCOMEL10.1088/0953-8984/17/4/018 17, 763–770.Google Scholar
Guénée, L., Favre-Nicolin, V., and Yvon, K. (2003). “Synthesis, crystal structure and hydrogenation properties of the ternary compounds LaNi4Mg and NdNi4Mg,” J. Alloys Compd.JALCEU 348, 129–137.Google Scholar
Guénée, L. and Yvon, K. (2003). “Synthesis, crystal structure and hydrogenation properties of the novel metal compound LaNi2Mn3,” J. Alloys Compd.JALCEU 348, 176–183.CrossRefGoogle Scholar
Kavečanský, V., Mihalik, M., Mitróová, Z., and Lukáčová, M. (2004). “Neutron diffraction study of crystal and magnetic structure of Dy[Fe(CN)6].4D2O,” Czech. J. Phys.CZLIA6 54, D571–D574.CrossRefGoogle Scholar
Lin, J., Sheptyakov, D., Wang, Y., and Allenspach, P. (2004). “Structures and phase transition of vaterite-type rare earth orthoborates: A neutron diffraction study, [Y0.92Er0.08)BO3,” Chem. Mater.CMATEX 16, 2418–2424.Google Scholar
Mahé, N. and Bataille, T. (2004). “Synthesis, crystal structure from single-crystal and powder X-ray diffraction data, and thermal behavior of mixed potassium lanthanide squarates: Thermal transformations of layered [Ln(H2O)6]K(H2C4O4)(C4O4)2 into pillared LnK(C4O4)2 (Ln=Y,La,Gd,Er),” Inorg. Chem.INOCAJ 43, 8379–8386.CrossRefGoogle Scholar
Newsam, J. W., Deem, M. W., and Freeman, C. M. (1992). “Direct space methods of structure solution from powder diffraction data,” NIST Spec. Publ.NSPUE2 846, 80–91.Google Scholar
Pannetier, J., Bassas-Alsina, J., Rodriguez-Carvajal, J., and Caignaert, V. (1990). “Prediction of crystal structures from crystal chemistry rules by simulated annealing,” Nature (London)NATUAS10.1038/346343a0 346, 343–345.CrossRefGoogle Scholar
Paul-Boncour, V., Filipek, S. M., Marchuk, I., André, G., Bourée, F., Wiesinger, G., and Percheron-Guégan, A. (2003). “Structural and magnetic properties of ErFe2D5 studied by neutron diffraction and Mössbauer spectroscopy,” J. Phys.: Condens. MatterJCOMEL10.1088/0953-8984/15/25/306 15, 4349–4359.Google Scholar
Renaudin, G., Bertheville, B., and Yvon, K. (2003a). “Synthesis and structure of an orthorhombic low-pressure polymorph of caesium magnesium hydride, CsMgH3,” J. Alloys Compd.JALCEU 353, 175–179.CrossRefGoogle Scholar
Renaudin, G., Guénée, L., and Yvon, K. (2003b). “LaMg2NiH7, a novel quaternary metal hydride containing tetrahedral [NiH4]4− complexes and hydride anions,” J. Alloys Compd.JALCEU10.1016/S0925-8388(02)00963-5 350, 145–150.Google Scholar
Salvadó, M. A., Pertierra, P., Bortun, A. I., Trobajo, C., and García, J. R. (2005). “New hydrothermal synthesis and structure of Th2(PO4)2(HPO4)∙H2O: The first structurally characterized thorium hydrogenphosphate,” Inorg. Chem.INOCAJ 44, 3512–3517.Google Scholar
Sarp, H. and Černý, R. (2005). “Yazganite, NaFe23+(Mg,Mn)(AsO4)3.H2O, a new mineral: Its description and crystal structure,” Eur. J. Mineral.EJMIER 17, 367–373.Google Scholar
Shankland, K. (2004). “Whole molecule constraints—the Z-matrix unraveled,” Newsletter of the Commission on Crystallographic Computing of the International Union of Crystallography, No. 4, pp. 46–51, see also: http://www.iucr.org/iucrtop/comm/ccom/newsletters/2004aug/index.htmlGoogle Scholar
Shankland, K., David, W. I. F., and Csoka, T. (1997). “Crystal structure determination from powder diffraction data by the application of a genetic algorithm,” Z. Kristallogr.ZEKRDZ 212, 550–552.CrossRefGoogle Scholar
Smrčok, L. and Matěj, Z. (2005). Private communication.Google Scholar
Soulié, J.-Ph., Renaudin, G., Černý, R., and Yvon, K. (2002). “Lithium boro-hydride, LiBH4: I. Crystal structure,” J. Alloys Compd.JALCEU10.1016/S0925-8388(02)00521-2 346, 200–205.Google Scholar
Vivani, R., Costantino, F., Nocchetti, M., and Gatta, G. D. (2004). “Structural homologies in benzylamino- N,N-bis methylphosphonic acid and its layered zirconium derivative,” J. Solid State Chem.JSSCBI 177, 4013–4022.CrossRefGoogle Scholar
Zavalij, I. Yu., Černý, R., Koval’chuck, I. V., Riabov, A. B., and Denys, R. V. (2005). “Synthesis and crystal structure of κ‐Zr9V4SH23.5 hydride,” J. Alloys Compd.JALCEU. (in press).Google Scholar
Zavalij, I. Yu., Černý, R., Koval’chuck, I. V., and Saldan, I. V. (2003). “Hydrogenation of oxygen-stabilized Zr3NiOx compounds,” J. Alloys Compd.JALCEU 360, 173–182.Google Scholar
Zavalij, P. Yu., Yang, S., and Whittingham, M. S. (2003). “Structures of potassium, sodium and lithium bis(oxalato)borate salts from powder diffraction data,” Acta Crystallogr., Sect. B: Struct. Sci.ASBSDK10.1107/S0108768103022602 59, 753–759.CrossRefGoogle ScholarPubMed