PLATON TUTORIAL A L Spek National Single Crystal

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). • (Bruker)Nonius Kappa. CCD 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)

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

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.

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…….

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

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

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

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

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

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

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.

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

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

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

IUCR CHECKCIF ALERTS Data From Supplementary Material

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.

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

QUATERNION FIT

Cg 1 0. 946 0. 234 0. 592 Cg 2 0. 441 0. 253 0. 581

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?

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

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

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 CH 3 Moiety Geometry

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

Example of Misplaced Hydrogen Atom

Two ALERTS related to the misplaced Hydrogen Atom

Unsatisfactory Hydrogen Bond Network

Satisfactory Hydrogen Bond Network with new H-position

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.

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.

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

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

DEFINE SOLVENT ACCESSIBLE VOID STEP # 3 – EXTEND INNER VOLUME WITH POINTS WITHIN 1. 2 ANGSTROM FROM ITS OUTER BOUNDS

SQUEEZE • Takes the contribution of disordered solvents into account by back-Fourier transformation of density found in the ‘solvent accessible volume’ outside the ordered part of the structure. • Filter: Input shelxl. res & shelxl. hkl Output: ‘solvent free’ shelxl. hkl

SQUEEZE PROCEDURE • Refine structure including H-atoms • Use. res and. hkl for the SQUEEZE calculation • Continue refinement using the reflection file produced by SQUEEZE • Calculate a final. fcf using the latest. res and. hkl (from SQUEEZE) using PLATON/FCF • Append the. fsq file to the final. cif for publication.

Twinning • Twinning results in overlap of reflections with different hkl • Twinning can be detected during the data collection experiment • Cases of (Pseudo) Merohedral twinning are generally detected during the structure determination

TWINNING - SYMPTOMS • Spots that do not fit in the proposed lattice • Strange extinctions • Laue symmetry higher than consistent with the systematic extinctions. • E-statistics • Unexpected high R-value • Ghost peaks in the difference map • A Significant # of reflections with Fobs >> Fcalc

TWIN DETECTION • SOFTWARE: ROTAX & PLATON/TWINROTMAT • ANALYSIS BASED ON (CIF &) FCF FILES • PROPOSALS FOR TWIN-OPERATION

SYSTEM S • Guided or Automatic Crystallographic Shell for Structure Determination from diffraction data to refined structure. • INPUT: HKL, CELL & CONTENT data • Interface to SHELX(S/L), DIRDIF, SIR 97, SIR 2002, POVRAY, RASTER 3 D etc. • Internal: PLATON Tools: Space Group Det, Abs. Cor. , Graphics, ADDSYM etc.

Input for an Exec of System S • System S is available for LINUX only • Kappa. CCD/DENZO: platon –s import. cif • Comp. hkl + comp. ins (= title, cell, sfac, unit, hklf 4) platon –s comp. ins • Comp. cif + comp. fcf (Acta): platon –s comp. cif • Default: suggestions for next step (can be overruled by the user) • Automatic Mode: add ‘nqa’: platon –s comp. ins nqa

Finally • • • Other features: Renaming of atoms, cif 2 res, asym-view More Info: ‘www. cryst. chem. uu. nl/platon’ Right mouse clicks > help on menu item DEMO