A better FOX: using flexible modelling and maximum likelihood to improve direct-space ab initio structure determination from powder diffraction

Abstract Ab initio structure determination using direct-space methods, although relying on an essentially brute-force approach, can be greatly improved through smarter algorithms. The most basic improvement involves the use of prior information to reduce the number of configurations evaluated to find the structure solution. It is however vitally important that the parametrization used to incorporate this prior information does not reduce the efficiency with which the configuration space is explored. We will show that this can be achieved by defining molecules and polyhedra through a set of restraints associated to dedicated random changes, allowing to solve structures up to three times as fast as with the ‘standard’ approach where atomic positions are parametrized directly from bond lengths, bond angles and dihedral angles. To further enhance the efficiency of the algorithm, it is also possible to ‘tune’ the convergence criterion used to compare the structural model to the observed diffraction data (usually χ2 or Rwp). By using Maximum Likelihood principles, it is shown that incorporating the fact that the model is approximate in the χ2 evaluation can improve the algorithm convergence towards the structure solution.

[1]  Brian H. Toby,et al.  EXPGUI, a graphical user interface for GSAS , 2001 .

[2]  V. Luzzati,et al.  Traitement statistique des erreurs dans la determination des structures cristallines , 1952 .

[3]  Kenneth D. M. Harris,et al.  PowderSolve – a complete package for crystal structure solution from powder diffraction patterns , 1999 .

[4]  M. Deem,et al.  A biased Monte Carlo scheme for zeolite structure solution , 1998, cond-mat/9809085.

[5]  Roy L. Johnston,et al.  Implementation of Lamarckian concepts in a Genetic Algorithm for structure solution from powder diffraction data , 2000 .

[6]  Peter G. Bruce,et al.  A General Monte Carlo Approach to Structure Solution from Powder Diffraction Data: Application to Poly(ethylene oxide)3:LiN(SO3CF3)2 , 1997 .

[7]  G. Murshudov,et al.  Refinement of macromolecular structures by the maximum-likelihood method. , 1997, Acta crystallographica. Section D, Biological crystallography.

[8]  L. McCusker,et al.  The application of structure envelopes in structure determination from powder diffraction data , 2002 .

[9]  J. Cole,et al.  The use of restraints in Rietveld refinement of molecular compounds; a case study using the crystal structure determination of tryptamine free base. , 2002, Acta crystallographica. Section B, Structural science.

[10]  Anthony K. Cheetham,et al.  The structure of cimetidine (C10H16N6S) solved from synchrotron-radiation x-ray powder diffraction data , 1991 .

[11]  J K Stalick,et al.  Accuracy in powder diffraction II , 1992 .

[12]  Armel Le Bail,et al.  ESPOIR: A Program for Solving Structures by Monte Carlo Analysis of Powder Diffraction Data , 2001 .

[13]  J. Karle,et al.  The calculation of ε associated with normalized structure factors, E , 1976 .

[14]  Lynne B. McCusker,et al.  Rietveld refinement guidelines , 1999 .

[15]  William I. F. David,et al.  Routine determination of molecular crystal structures from powder diffraction data , 1998 .

[16]  R. Blessing,et al.  The first protein crystal structure determined from high-resolution X-ray powder diffraction data: a variant of T3R3 human insulin-zinc complex produced by grinding. , 2000, Acta crystallographica. Section D, Biological crystallography.

[17]  J. C. Schön,et al.  Combined method for ab initio structure solution from powder diffraction data , 1999 .

[18]  R. Read Structure-factor probabilities for related structures , 1990 .

[19]  L. McCusker,et al.  Using a structure envelope to facilitate structure solution from powder diffraction data , 1997 .

[20]  Kenneth D. M. Harris,et al.  CRYSTAL STRUCTURE DETERMINATION FROM POWDER DIFFRACTION DATA BY MONTE CARLO METHODS , 1994 .

[21]  William I. F. David,et al.  Crystal structure determination from powder diffraction data by the application of a genetic algorithm , 1997 .

[22]  J. Sussman,et al.  Protein Model Building by the Use of a Constrained-Restrained Least-Squares Procedure , 1977 .

[23]  A. Markvardsen,et al.  A hybrid Monte Carlo method for crystal structure determination from powder diffraction data. , 2002, Acta crystallographica. Section A, Foundations of crystallography.

[24]  V. Favre-Nicolin,et al.  FOX, `free objects for crystallography': a modular approach to ab initio structure determination from powder diffraction , 2002 .

[25]  Roy L. Johnston,et al.  The genetic algorithm : Foundations and applications in structure solution from powder diffraction data , 1998 .

[26]  P. Bruce,et al.  Ab initio solution of a complex crystal structure from powder-diffraction data using simulated-annealing method and a high degree of molecular flexibility , 1997 .

[27]  Michael S. Chapman,et al.  Restrained real-space macromolecular atomic refinement using a new resolution-dependent electron-density function , 1995 .

[28]  R. Dinnebier Rigid bodies in powder diffraction. A practical guide , 1999, Powder Diffraction.

[29]  R. V. Von Dreele Binding of N-acetylglucosamine to chicken egg lysozyme: a powder diffraction study. , 2001, Acta Crystallographica Section D: Biological Crystallography.

[30]  G. Bricogne A multisolution method of phase determination by combined maximization of entropy and likelihood. III. Extension to powder diffraction data , 1991 .

[31]  H. Schenk,et al.  A grid search procedure of positioning a known molecule in an unknown crystal structure with the use of powder diffraction data , 1998 .

[32]  R. Read,et al.  Improved Structure Refinement Through Maximum Likelihood , 1996 .

[33]  Peter W. Stephens,et al.  The structure of malaria pigment β-haematin , 2000, Nature.

[34]  K. Harris,et al.  The application of a genetic algorithm for solving crystal structures from powder diffraction data , 1997 .

[35]  A. Antoniadis,et al.  Maximum-likelihood methods in powder diffraction refinements , 1990 .

[36]  R J Read,et al.  Pushing the boundaries of molecular replacement with maximum likelihood. , 2003, Acta crystallographica. Section D, Biological crystallography.

[37]  K. Shankland,et al.  Molecular, crystallographic and algorithmic factors in structure determination from powder diffraction data by simulated annealing , 2002 .

[38]  V. Favre-Nicolin,et al.  Mg(1 + x)Ir(1 - 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. , 2004, Acta crystallographica. Section B, Structural science.

[39]  A. Markvardsen,et al.  A maximum-likelihood method for global-optimization-based structure determination from powder diffraction data. , 2002, Acta crystallographica. Section A, Foundations of crystallography.

[40]  V. Favre-Nicolin,et al.  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 , 2004 .