Presentation on theme: "PLATON TUTORIAL A.L.Spek, National Single Crystal Service Facility, Utrecht, The Netherlands."— Presentation transcript:
PLATON TUTORIAL A.L.Spek, National Single Crystal Service Facility, Utrecht, The Netherlands.
What is PLATON A Multipurpose Crystallographic Tool Compatible with and Complementary to P.D. SHELX & Bruker-AXS SHELXTL ‘Public domain’ (I.e. free-of-charge for academics, License Fee for Profit Org.) Available on UNIX/LINUX, MS-Windows & MAC-OSX Platforms
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,
ADDSYM REPORT 2003/1 > > (25 out of 466)
J.A.C.S. 124 (2002) 9052 Communications
IUCR CHECKCIF ALERTS
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
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?
NOT SO HOT AFTER ALL !!
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 -CH3 Moiety Geometry
Validation with PLATON -Details: -Driven by the file CHECK.DEF with criteria, ALERT messages and advice. -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
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
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, POVRAY,RASTER3D, CSD etc. Internal: PLATON Tools: Space Group Det, Abs.Cor., Graphics, ADDSYM etc.
Input for an Exec of System S 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