1 / 28

Structure Solution in Direct Space The State of the Art

Structure Solution in Direct Space The State of the Art. Yuri G. Andreev University of St. Andrews, Scotland. OTHER METHODS OF STRUCTURE DETERMINATION FROM POWDERS. Direct Methods Patterson Methods Maximum Entropy and Likelihood.

jane-pollard
Download Presentation

Structure Solution in Direct Space The State of the Art

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Structure Solution in Direct Space The State of the Art Yuri G. Andreev University of St. Andrews, Scotland

  2. OTHER METHODS OF STRUCTURE DETERMINATION FROM POWDERS • Direct Methods • Patterson Methods • Maximum Entropy and Likelihood Baerlocher, Bricogne, David, Estermann, Giacovazzo, Gilmore, McCusker, Peschar, Rius, Schenk, Shankland

  3. 15. K. Shankland, W.I.F. David: Global optimisation strategies 16. P.G. Bruce, Y.G. Andreev: Solution of flexible molecular structures by simulated annealing

  4. In the beginning there was the Word, and the Word was with Newsam, Deem and Freeman NIST Spec. Publ., 1992, 80-91, and the Word was Simulated Annealing

  5. Newsam,DeemandFreeman “The PXD profile simulated based on the known crystal structure was used as a target”

  6. From Refinement to Ab Initio Structure Determination Structural model Experimental powder pattern Space group Cell parameters Atomic coordinates Profile parameters Stereochemical descriptors Calculate powder pattern. Calculate figure-of-merit. 2 Calculate parameter increments using gradient least-squares. simulated annealing The structure

  7. Simulated AnnealingvsRefinement RefinementSimulated annealing Pnew = Pold + D P Iterative procedure D P= D Pmax·R D P=f (2/ P) R -random number[-1,1] Downhill if2new< 2old Directional change in2value after each iteration Downhill only: Uphill if2new>2oldand exp[-(2new- 2old)/ 2]>r r-random number[0,1] 2new< 2old  2- ‘Temperature’

  8. Transitional Period 1993-1995 Solovyov and Kirik.Materials Science Forum 133-136, 195 (1993) Application of SA method to finding the positions of heavy atoms in several previously known structures using experimental integrated intensities of diffraction peaks. Harris, Tremayne, Lightfoot and Bruce.J. Am. Chem. Soc. 116, 3543 (1994) Ramprasad, Pez, Toby, Markley and Pearlstein.J. Am. Chem. Soc. 117, 10694 (1995) Structure solution of previously unknown structures with rigid-body molecules using full-profile fitting to the experimental pattern. Monte Carlo method - randomised search using Metropolis sampling. Not a global optimisation approach.

  9. The Methods are Born 1996 -1998 Andreev, Lightfoot and Bruce.Chem. Commun, 2169 (1996) Andreev, Lightfoot and Bruce.J. Appl. Cryst. 30, 294 (1997) The first previously unknown molecular structure solved using global optimisation (SA) of full-profile 2. Detailed account of the algorithm and of the geometrical description of the molecules. Shankland, David and Czoka.Z. Krist. 212, 550 (1997) Solution of previously known molecular structures using genetic algorithm (GA). FoM based on experimental integrated intensities. Harris, Johnston, Kariuki and Tremayne.J. Chem. Res., 390 (1998) Solution of previously known molecular structures using GA and full- profile fitting to the experimental pattern. David, Shankland and Shankland.Chem. Commun., 931 (1998) Solution of previously unknown molecular structures. SA. FoM based on experimental integrated intensities.

  10. Modern Times 1999 - 2002 A number of methods and computer programs have been developed. QUESTIONNAIRE 1. Program name 2. Authors 3. Institution 4. Method of minimisation 5. Experimental data (full-profile or integrated intensities) 6. Literature reference to the method/algorithm of solution 7. Literature reference to the solution of the most complex or typical previously unknown structure using the program 8. Program availability Other groups/authors developing direct-space methods of structure solution

  11. ENDEAVOURK. Brandenburg and H. Putz, Crystal Impact, Bonn, Germany Combined global optimization of R-factor and potential energy using SA Integrated intensities J.Appl.Cryst.32, 864 (1999) Ag2NiO2- typical structure Schreyer and Jansen,Sol. State Sci.3(1-2), 25, (2001). 15 atoms in the a.u. of P1. 45 DoF. Available from Crystal Impact at reduced price for academic users.

  12. DASHW.I.F. David and K. Shankland Rutherford Appleton Laboratory, further developed by J. Cole and J. van de Streek CCDC, UK SA Correlated integrated intensities Chem. Commun. 931 (1998) Capsaicin - most complex structure in terms of number of variables Chem. Commun. 931 (1998) 10 torsions and 6 external DoF. Telmisartan forms A and B - fairly typical structure J. Pharm. Sci.89, 1465 (2000) 7 torsions and 6 external DoF. Academics receive a 95% discount

  13. ESPOIRA. Le Bail, Universite du Maine, France Reverse Monte Carlo and pseudo SA Integrated intensities or full profile on a pseudo powder pattern regenerated from extracted |Fobs| Mat. Sci. Forum378-381, 65 (2001). Souzalite/Gormanite Le Bail, Stephens and Hubert, submitted to European J. Mineralogy 19 atoms in the a.u. of P-1. Fe at 0,0,0 54 DoF. Free and Open - all available : executable as well as Fortran and Visual C++ source code (GPL - GNU Public Licence).Web site: http://www.cristal.org/sdpd/espoir/

  14. TOPASA.A. Coelho, R.W.Cheary, A. Kern, T. Taut. Bruker AXS GmbH, Karlsruhe, Germany SA (together with user definable penalty functions, rigid bodies, various bond length restraints and lattice energy minimization techniques including user definable force fields) Caffeine Anhydrous C8H10N4O2 Stowasser and Lehmann,Abstract submitted to the XIX IUCr Congress 5 molecules in the a.u. 93 DoF. Full-profile or integrated intensities J.Appl.Cryst.33, 899 (2000) Discounted price for academic users.

  15. POWDERSOLVE (part of Reflex Plus integrated package) G. Engel, S. Wilke, D. Brown, F. Leusen, O. Koenig, M. Neumann, C. Conesa-Morarilla Accelrys Ltd., Cambridge, UK Monte Carlo SA and Monte Carlo parallel tempering (Falcioni and Deem. J. Chem. Phys. 110, 1754 (1999)) Full profile J.Appl.Cryst.32, 1169 (1999) Docetaxel (C43H53NO14·3H2O) - most complex structure L. Zaske, M.-A. Perrin and F. Leveiller, J. Phys. IV, Pr10, 221 (2001) 29 DoF including 3 rotations, 12 translations and 14 torsion angles. Can be purchased from Accelrys Inc., generous discounts given to academic researchers

  16. FOXV. Favre-Nicolin and R. Cerny, University of Geneva, Switzerland (Free Objects for Xtallography) Parallel Tempering or SA. Automatic correction of special positions and of sharing of atoms between polyhedra, without any a priori knowledge; multi-pattern Full profile, integrated intensities, partial integrated intensities Submitted to J.Appl.Cryst. Aluminium methylphosphonate Al2(CH3PO3)3- most complex structure Edgar et al.Chem. Commun. 808, (2002). 3 molecules and 2 Al atoms in the a.u. 24 DoF including bond lengths and bond angles. Free, open-source published under the GPL license http://objcryst.sourceforge.net

  17. EAGER K.D.M. Harris, R.L. Johnston, D. Albesa Jové, M.H. Chao, E.Y. Cheung, S. Habershon, B.M. Kariuki, O.J. Lanning, E. Tedesco, G.W. Turner University of Birmingham, UK Genetic Algorithm Full profile Acta Cryst.A, 54, 632 (1998) Heptamethylene-1,7-bis(diphenylphosphane oxide) Ph2P(O)(CH2)7P(O)Ph2 - typical structure. B.M. Kariuki, P. Calcagno, K.D.M. Harris, D. Philp, R.L. Johnston.Angew. Chem. Int. Ed.38, 831 (1999). 35 non-H atoms in the a.u. 18 DoF including 12 torsion angles. Under active development

  18. OCTOPUS K.D.M. Harris, M. Tremayne and B.M. Kariuki University of Birmingham, UK Monte Carlo Full profile J. Am. Chem. Soc.116, 3543 (1994). Red fluorescein - typical structure. Tremayne, Kariuki and Harris.Angew. Chem. Int. Ed.36, 770 (1997). 25 non-H atoms in the a.u. 7 DoF including 1 torsion angle. Under active development

  19. PSSPP. Stephens and S. Pagola State University of New York, Stony Brook, (Powder Structure Solution Program) USA SA Integrated intensities (Le Bail) with novel handling of peak overlap Submitted to J.Appl.Cryst.Preprint available on http://powder.physics.sunysb.edu Malaria Pigment Beta Haematin - most complex structure. Pagola, Stephens, Bohle, Kosar, and Madsen. Nature404307(2000) 43 non-H atoms in the a.u. 14 DoF. Free, including open source. Available athttp://powder.physics.sunysb.edu

  20. FOCUSR.W. Grosse-Kunstleve, L.B. McCusker and Ch. Baerlocher ETH Zentrum, Zurich, Switzerland Combined atomatic Fourier recycling algorithm with a specialised framework search. Rubidium zincosilicate VPI-9 - one of the most complex structures. McCusker, Grosse-Kunstleve, Baerlocher, Yoshikawa and Davis. Microporous Materials6, 295(1996) 7 Si/Zn atoms and 15 O atoms at the solution stage. Integrated intensities J.Appl.Cryst.32,536 (1999) Free. Available over the internet

  21. SAFES. Brenner, L.B. McCusker and Ch. Baerlocher ETH Zentrum, Zurich, Switzerland (Simulated Annealingand Fragment search within an Envelope) SA + option of using a structure envelope. Tri--peptide C32N3O6H53 - the most complex structure. Brenner, McCusker and Baerlocher J.Appl.Cryst.35,243 (2002) 17 torsion angles and 6 positional and orientational DoF. Full-profile J.Appl.Cryst.35,243 (2002) Not ready for general distribution but will be in public domain.

  22. Simulated AnnealingY. G. Andreev and P. G. Bruce, University of St. Andrews SA Full-profile J.Appl.Cryst. 30, 294 (1997) Free, very user unfriendly. Requires changing of the code for each new structure determination. Customised molecular description without Z-matrix input. (CH2CH2O)6:LiAsF6 - most complex structure. MacGlashan, Andreev, and Bruce Nature398792(1999) 26 non-H atoms in the a.u. 79 DoF including 15 torsion angles.

  23. PEO6:LiPF6 PEO6:LiAsF6 PEO6:LiSbF6

  24. Diglyme2:LiSbF6 (CH3O(CH2CH2O)2CH3) structure from single crystal diffraction R. Frech et al. PEO6:LiSbF6 (CH3O(CH2CH2O)22÷2200CH3) structure from powder diffraction The structures of PEO6:LiXF6 opened a new avenue in polymer electrolyte research.

  25. Polymer Electrolytes • Salts, e.g. LiPF6, dissolved in solid, high molecular • weight, polymers, e.g. PEO (CH2CH2O)n. Cations • co-ordinated by ether oxygens and anions. • Unique class of ionic conductors with conductivities • comparable to liquids but processable as thin • flexible films • Many applications in devices.

  26. Polymer Electrolytes: Misconceptions After 25 years of intensive research: Only amorphous polymer electrolytes conduct and above Tg - ions move due to polymer chain motion Structure is largely retained on passing to amorphous state Crystal structure Amorphous structure Understand structural chemistry of polymer electrolytes Design higher ionic conductivity

  27. Better conductivity in static crystalline environment! Crystalline Amorphous • Double non-helical chains • Cation coordinated by 5 • ether oxygens from 2 chains • ‘Spare’ ether oxygen • No coordination of • cationsby anions Gadjourova, Andreev, Tunstall and Bruce. Nature, 412, 520 (2001).

  28. Acknowledgements Peter Bruce Holger Putz, Crystal Impact Kenneth Shankland, ISIS Armel Le Bail, Universite du Maine Arnt Kern, Bruker AXS GmbH Frank Leusen, Accelrys Ltd Vincent Favre-Nicolin, currently ESRF Kenneth Harris, University of Birmingham Peter Stephens, State University of New York Lynne McCusker, ETH Zentrum

More Related