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 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)
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 PLUTON style PLOT Automatic NEWMAN PLOTS 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
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
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 C) Manual picking of a few atom pairs
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 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 CH3 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
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.
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.
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 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,SIR97, SIR2002, POVRAY,RASTER3D 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 KappaCCD/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, cif2res, asym-view More Info: ‘www.cryst.chem.uu.nl/platon’ Right mouse clicks > help on menu item DEMO
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