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

BAMYEU

Dalton Trans2003,134-140

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

Cg1 0.946 0.234 0.592

Cg2 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

- 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

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.

STEP #1 – EXCLUDE VOLUME INSIDE THE VAN DER WAALS SPHERE

DEFINE SOLVENT ACCESSIBLE VOID

DEFINE SOLVENT ACCESSIBLE VOID

STEP # 2 – EXCLUDE AN ACCESS RADIAL VOLUMETO 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 WITHIN1.2 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) )• 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.

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 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