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PLATON TUTORIAL

PLATON TUTORIAL. A.L.Spek, National Single Crystal Service Facility, Utrecht, The Netherlands. Who Are We ?. We, a small group of 3 to 4 people run a National Single Crystal Service in the Netherlands since 1971 (Utrecht University).

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PLATON TUTORIAL

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  1. PLATON TUTORIAL A.L.Spek, National Single Crystal Service Facility, Utrecht, The Netherlands.

  2. Who Are We ? • We, a small group of 3 to 4 people run a National Single Crystal Service in the Netherlands since 1971 (Utrecht University). • (Bruker)Nonius KappaCCD on Rotating Anode + Oxford LNT + UNIX/LINUX Computers. • Over 3000 structures studied so far, about 1800 published in over 1100 papers. • Mainly organometallic and coordination chemistry • Main Software: P.D. SHELX + PLATON • Co-Editor Acta Cryst. C (> 850 papers handled)

  3. Tutorial Program • 1 PLATON Overview Presentation • 2 Life PLATON Demonstration (Linux) • 3 Hands-on Exercises (MS-WINDOWS) • 4 Lecture on Structure Validation

  4. What is PLATON • A Multipurpose Crystallographic Tool. • Developed in a Single Xtal Service Environment. • Compatible with and Complementary to the Public Domain SHELX & Bruker-AXS SHELXTL Software. • ‘Public domain’ (I.e. free-of-charge for academics, License Fee for For Profit Organizations). • Available on UNIX/LINUX, MS-Windows & MAC-OSX Platforms.

  5. Multipurpose Crystallographic Tool • Automatic Geometry Analysis & Listing. • Molecular Graphics (PLUTON, ORTEP, Contour) • Absorption Correction Tools(MULABS,TOMPA) • ADDSYM - Check for Missed Symmetry. • SQUEEZE – Disordered Solvent Handling. • Generation of Powder Patterns. • Structure Validation (part of IUCr CHECKCIF). • Analysis of Fo/Fc data including Bijvoet Pairs. • System-S, Automated Structure Determination. • Etc…….

  6. EXAMPLE • Input Shelx Style: sucrose.res • (Alternatively: .cif,.pdb,.fdat,.spf style) • Invoke PLATON (UNIX: platon sucrose.res) • Opening Menu (4 areas) • Automatic ORTEP style PLOT • Automatic PLUTON style PLOT • Automatic NEWMAN PLOTS • Simulated Powder Pattern • H-Bond Table

  7. EXAMPLE • Input Shelx Style: sucrose.res • (Alternatively: .cif,.pdb,.dat,.spf style) • Invoke PLATON (UNIX: Platon sucrose.res) • Opening Menu (4 areas) • Automatic ORTEP style PLOT • Automatic PLUTON style PLOT • NEWMAN PLOTS • Simulated Powder Pattern • H-Bond Table

  8. EXAMPLE • Input Shelx Style: sucrose.res • (Alternatively: .cif,.pdb,.dat,.spf style) • Invoke PLATON (UNIX: Platon sucrose.res) • Opening Menu (4 areas) • Automatic ORTEP style PLOT • Automatic PLUTON style PLOT • NEWMAN Plots • Simulated Powder Pattern • H-Bond Table

  9. EXAMPLE • Input Shelx Style: sucrose.res • (Alternatively: .cif,.pdb,.dat,.spf style) • Invoke PLATON (UNIX: Platon sucrose.res) • Opening Menu (4 areas) • Automatic ORTEP style PLOT • Automatic PLUTON style PLOT • NEWMAN Plots • Simulated Powder Pattern • H-Bond Table

  10. EXAMPLE • Input Shelx Style: sucrose.res • (Alternatively: .cif,.pdb,.dat,.spf style) • Invoke PLATON (UNIX: Platon sucrose.res) • Opening Menu (4 areas) • Automatic ORTEP style PLOT • Automatic PLUTON style PLOT • NEWMAN Plots • Simulated Powder Pattern • H-Bond Table

  11. EXAMPLE • Input Shelx Style: sucrose.res • (Alternatively: .cif,.pdb,.dat,.spf style) • Invoke PLATON (UNIX: Platon sucrose.res) • Opening Menu (4 areas) • Automatic ORTEP style PLOT • Automatic PLUTON style PLOT • NEWMAN Plots • Simulated Powder Pattern • H-Bond Table

  12. CALC ALL GEOMETRY LISTING • With CALC ALL an exhaustive listing of derived intra-, inter- and coordination geometry etc. is produced. • Two ‘identical’ files are produced. ‘.lis’ and ‘lps’. The first is lineprinter style, the latter is suitable for either a postscript printer or inspection with ghostview. • We routinely provide this listing to the client along with an ORTEP.

  13. PLATON/ADDSYM ANALYSIS • Example run on 9163 Z’ = 2 Organic structures present in the in CSD. • ADDSYM  466 Hits (Missed or Pseudo Symmetry Cases) • Some Missed Symmetry Cases already corrected by Dick Marsh et al. • Recent Example of Missed Symmetry in J.A.C.S (2002) 124,11846-11847

  14. ADDSYM REPORT 2003/1 (25 out of 466) > >

  15. J.A.C.S. 124 (2002) 9052 Communications

  16. IUCR CHECKCIF ALERTS Data From Supplementary Material

  17. NEWSYM • Companion to ADDSYM Analysis • Structure factors calculated from current cell, symmetry and coordinate info. • Determination of the Space Group from the systematic absences in F(calc) • Extinctions in F(calc) may differ from those in F(obs) due to poor data.

  18. QUATERNION FIT • In many cases, an automatic molecule fit can be performed • A) Identical atom numbering • B) Sufficient Unique Atoms • C) Manual picking of a few atom pairs

  19. QUATERNION FIT

  20. Cg1 0.946 0.234 0.592 Cg2 0.441 0.253 0.581

  21. STRUCTURE VALIDATION Single crystal structure validation addresses three important questions: 1 – Is the reported information complete? 2 – What is the quality of the analysis? 3 – Is the Structure Correct?

  22. IUCR-CHECKCIF IUCR-TESTS: • MISSING DATA, PROPER PROCEDURE, QUALITY PLATON TESTS: • SYMMETRY, GEOMETRY, DISPLACEMENT PARAMETERS ALERT LEVELS: • ALERT A - SERIOUS PROBLEM • ALERT B - POTENTIALLY SERIOUS PROBLEM • ALERT C - CHECK & EXPLAIN

  23. Problems Addressed by PLATON • Missed Higher Space Group Symmetry • Solvent Accessible Voids in the Structure • Unusual Displacement Parameters • Hirshfeld Rigid Bond test • Miss-assigned Atom Type • Population/Occupancy Parameters • Mono Coordinated/Bonded Metals • Isolated Atoms

  24. Problems Addressed by PLATON • Too Many Hydrogen Atoms on an Atom • Missing Hydrogen Atoms • Valence & Hybridization • Short Intra/Inter-Molecular Contacts • O-H without Acceptor • Unusual Bond Length/Angle • CH3 Moiety Geometry

  25. Validation with PLATON - Details: www.cryst.chem.uu.nl/platon • Driven by the file CHECK.DEF with criteria, ALERT messages and advice. • Button VALIDATION on PLATON MAIN Menu • Use: platon –u structure.cif • Result on file: structure.chk • Applicable on CIF’s and CCDC-FDAT • FCF-Valid: platon –V structure.cif

  26. Example of Misplaced Hydrogen Atom

  27. Two ALERTS related to the misplaced Hydrogen Atom

  28. Unsatisfactory Hydrogen Bond Network

  29. Satisfactory Hydrogen Bond Network with new H-position

  30. ARU-Definition • Molecules (or unique asymmetric parts of a molecule) are assigned in PLATON an ARU value. • npqr.s where n = symmetry number and pqr translations and s the residue # e.g. 2655.02 Used to address symmetry related molecules in packing diagrams and intermolecular contacts.

  31. Solvent Accessible Voids • A typical crystal structure has only 65% of the available space filled. • The remainder volume is in voids in-between atoms (to small to accommodate an H-atom) • Solvent accessible voids defined are regions in the structure that can accommodate at least a sphere with radius 1.2 Angstrom without intersecting with any of the van der Waals spheres assigned to each atom in the structure.

  32. DEFINE SOLVENT ACCESSIBLE VOID STEP #1 – EXCLUDE VOLUME INSIDE THE VAN DER WAALS SPHERE

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