PLATON, A Multipurpose Crystallographic Tool

1. PLATON, A Multipurpose Crystallographic Tool Ton Spek, National Single Crystal Service Facility, Utrecht, The Netherlands.

2. What is PLATON • A Multipurpose Crystallographic Tool. • A Program Developed in, and Addressing the needs of, a Single Crystal Service Environment. • Compatible with and Complementary to the Public Domain SHELX & Bruker-AXS SHELXTL Software. (.res,.hkl,.cif,.fcf) • ‘Semi Public domain’ (I.e. free-of-charge for academics, but with a License Fee for For Profit Organizations). • Developed on UNIX/LINUX and available on MS-Windows & MAC-OSX Platforms.

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

4. EXAMPLE • Input Shelx Style: sucrose.res • Alternatively: .cif, .pdb, .fdat, .spf style files • Invoke PLATON: UNIX: platon sucrose.res MS-Windows: via ‘Farrugia’ task menu • Opening Menu (4 areas) 

6. EXAMPLE • Input Shelx Style: sucrose.res • (Alternatively: .cif,.pdb,.dat,.spf style) • Automatic ORTEP style PLOT 

9. EXAMPLE • Input Shelx Style: sucrose.res • (Alternatively: .cif,.pdb,.dat,.spf style) • Automatic PLUTON style PLOT 

11. EXAMPLE • Input Shelx Style: sucrose.res • (Alternatively: .cif,.pdb,.dat,.spf style) • NEWMAN Plots 

13. EXAMPLE • Input Shelx Style: sucrose.res • (Alternatively: .cif,.pdb,.dat,.spf style) • Simulated Powder Pattern (hkl or coord) • from coordinates 

15. Intra-molecular Geometry • Atom list sort. • Detection of residues (connected set) and derivation of the Moiety formula, Z and Z’. • Bond distances, Bond Angles, Torsion Angles. • Automatic ring search,automatic seach of planar parts in the structure

16. Intra-Molecular (Continued) • Determination of the hybridization, R/S assignments and ‘topology numbers’. • Listing of the plane-plane and bond-plane angles. • Ring puckering analysis (Cremer & Pople) Example 

18. Inter-Molecular • Hydrogen Bonds (linear, bi- and trifurcated) • Automatic analysis in terms of 1, 2 and 3-D networks (aggregates or cooperative) • Search for pi-pi and C-H..pi interactions • Example H-Bond Table 

20. CALC ALL GEOMETRY LISTING • With CALC ALL an exhaustive listing of derived intra-, inter- and coordination geometry etc. is produced, including a structure validation report. • Two ‘content 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 exhaustive listing to the chemist/client along with an ORTEP.

21. PLATON/ADDSYM ANALYSIS • Example of a missed symmetry case from the CSD 

22. BAMYEU Dalton Trans 2003,134-140 Cc

25. 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.

28. 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

30. QUATERNION FIT

31. Cg1 0.946 0.234 0.592 Cg2 0.441 0.253 0.581

34. 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?

35. 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

36. 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

37. 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

38. 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

39. Example of Misplaced Hydrogen Atom

40. Two ALERTS related to the misplaced Hydrogen Atom

41. Unsatisfactory Hydrogen Bond Network

44. Satisfactory Hydrogen Bond Network with new H-position

46. 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 are defined as 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.

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

48. DEFINE SOLVENT ACCESSIBLE VOID STEP # 2 – EXCLUDE AN ACCESS RADIAL VOLUME TO FIND THE LOCATION OF ATOMS WITH THEIR CENTRE AT LEAST 1.2 ANGSTROM AWAY

49. DEFINE SOLVENT ACCESSIBLE VOID STEP # 3 – EXTEND INNER VOLUME WITH POINTS WITHIN 1.2 ANGSTROM FROM ITS OUTER BOUNDS

50. Cg