PLATON TUTORIAL

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 ORTEP style PLOT• Automatic PLUTON style PLOT• Automatic 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

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

CALC ALL GEOMETRY LISTING

• 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

>

>

(25 out of 466)

J.A.C.S. 124 (2002) 9052

Communications

IUCR CHECKCIF ALERTSData From Supplementary Material

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

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.

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 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.

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

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

• Spots that do not fit in the proposed lattice• 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