PLATON A Multipurpose Crystallographic Tool Ton Spek National

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

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.

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.

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)

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

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

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

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

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

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

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

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 Post. Script printer or inspection with ghostview. • We routinely provide this exhaustive listing to the chemist/client along with an ORTEP.

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

BAMYEU Dalton Trans 2003, 134 -140 Cc

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

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.

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

Cg

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

(Pseudo)Merohedral Twinning • Options to handle twinning in L. S. refinement available in SHELXL, CRYSTALS etc. • Problem: Determination of the Twin Law that is in effect. • Partial solution: coset decomposition, try all possibilities (I. e. all symmetry operations of the lattice but not of the structure) • ROTAX (S. Parson et al. (2002) J. Appl. Cryst. , 35, 168. (Based on the analysis of poorly fitting reflections of the type F(obs) >> F(calc) ) • Twin. Rot. Mat Automatic Twinning Analysis as implemented in PLATON (Based on a similar analysis but implemented differently)

Example • Structure refined to R= 20% in P-3 • Run Twin. Rot. Mat on CIF/FCF • Result: Twinlaw with estimate of the twinning fraction and drop in R-value

Absolute Structure • The absolute structure of a compound is normally determined with the refinement of the Flack parameter. • The value of the Flack parameter can be inconclusive in view of a high su. • A detailed scatter-plot may be more conclusive.

BIJVOET PAIR SCATTER PLOT

System S • Automatic structure determination (Space group determination, solution, refinement, analysis) • Build-in in PLATON (Unix only) • Calls external programs including itself for various functions. • Program runs in either guided or noquestions-asked mode

SYSTEM S • 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, Absorption Correction, Graphics, Validation, ADDSYM etc. • Platon –s compound. ins nqa

Finally • • Other features: Structure Tidy (CIF input) Bond Valence Renaming of atoms, cif 2 res, asym-view More Info: ‘www. cryst. chem. uu. nl/platon’ Right mouse clicks > help on menu item

Thanks • • • Thanks to the users for their: Complaints Bug reports (‘undocumented features. . ) Suggestions And you for your attention