PLATON TUTORIAL

transcript

PLATON TUTORIALA.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

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-CHECKCIFIUCR-TESTS:- MISSING DATA, PROPER PROCEDURE, QUALITYPLATON TESTS:- SYMMETRY, GEOMETRY, DISPLACEMENT

PARAMETERSALERT 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

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

PLATON TUTORIAL

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