Platon, a multipurpose Crystallographic Tool Ton Spek, National Single Crystal Service Facility

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 PostScript 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 

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?

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: 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

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.

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) )

• TwinRotMat 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 TwinRotMat 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.

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

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

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 > help on menu item

Thanks

• Thanks to the users for their:

• Complaints

• Bug reports (‘undocumented features ..)

• Suggestions

• And you for your attention