PLATON, A Multipurpose Crystallographic Tool

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PLATON, A Multipurpose Crystallographic Tool

• Ton Spek,
• National Single Crystal Service Facility,
• Utrecht, The Netherlands.

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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.

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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.

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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) ?

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EXAMPLE

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

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EXAMPLE

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

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EXAMPLE

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

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EXAMPLE

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

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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

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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 ?

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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 ?

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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.

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PLATON/ADDSYM ANALYSIS

• Example of a missed symmetry case from the CSD ?

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BAMYEU Dalton Trans 2003,134-140 Cc
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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.

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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

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QUATERNION FIT
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Cg1 0.946 0.234 0.592 Cg2 0.441 0.253 0.581
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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?

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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

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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

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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

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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 CIFs and CCDC-FDAT
• FCF-Valid platon V structure.cif

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Example of Misplaced Hydrogen Atom
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Two ALERTS related to the misplaced Hydrogen Atom
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Unsatisfactory Hydrogen Bond Network
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Satisfactory Hydrogen Bond Network with new
H-position
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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.

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DEFINE SOLVENT ACCESSIBLE VOID
STEP 1 EXCLUDE VOLUME INSIDE THE VAN DER
WAALS SPHERE
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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
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DEFINE SOLVENT ACCESSIBLE VOID
STEP 3 EXTEND INNER VOLUME WITH POINTS
WITHIN 1.2 ANGSTROM FROM ITS OUTER BOUNDS
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Cg
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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

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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.

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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

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(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) gtgt F(calc) )
• TwinRotMat Automatic Twinning Analysis as
  implemented in PLATON (Based on a similar
  analysis but implemented differently)

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Example

• Structure refined to R 20 in P-3
• Run TwinRotMat on CIF/FCF
• Result Twinlaw with estimate of the twinning
  fraction and drop in R-value

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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.

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BIJVOET PAIR SCATTER PLOT
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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
  no-questions-asked mode

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SYSTEM S

• INPUT HKL, CELL CONTENT data
• Interface to SHELX(S/L), DIRDIF,SIR97, SIR2002,
  POVRAY,RASTER3D etc.
• Internal PLATON Tools Space Group Det,
  Absorption Correction, Graphics, Validation,
  ADDSYM etc.
• Platon s compound.ins nqa

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Finally

• Other features
• Structure Tidy (CIF input)
• Bond Valence
• Renaming of atoms, cif2res, asym-view
• More Info
• www.cryst.chem.uu.nl/platon
• Right mouse clicks gt help on menu item

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Thanks

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

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