The System-S Approach to Automated Structure

Determination:Problems and Solutions

Ton Spek

National Single Crystal Service

Utrecht University, The Netherlands

Is a Fully Automatic Structure Determination Possible ?

• Yes, in many cases given good quality low temperature reflection data and correct prior knowledge of the chemical composition.

• Good examples are light atom structures with no disorder and with no unknown solvent of crystallization.

• No, in all cases needing an experienced crystallographer (I.e. when no automated methods are available yet for the problem at hand)

e.g.: many/most coordination complexes.

Current Setup in Utrecht

KappaCCD/Rotating Anode/LNT

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Collect, DENZO or EVAL-CCD (Not AUTO!)

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import.cif (includes Formula & Unit Cell)

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Silent System-S Auto-Mode: platon -F import.cif

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Result files -> ORTEP/PLUTON Plots

Typical Import CIF Filter Job

Unix Command Line Instruction:

platon –F import.cif

….. Wait 0.5 minute …..

Standard Console Output:

Tentative Result on: /mnt/spea/import_s.cif

and: /mnt/spea/import_s.res

Validation Report: /mnt/spea/import_s.chk

Details may be found in: /mnt/s/import

0.5 Min. from import.cif to ORTEP (3GHz Linux Box)

System-S Approach

• Crystallographic Shell around public domain tools (SHELX, SIR, PLATON etc.)

• Two Modes of operation:• Guided Mode: Suggests/Executes next step in the

structure determination (handles I/O)• Automatic Mode: (NQA-Mode) Executes

automatically all default steps• Build-in Structure Validation• System-S is included in the UNIX PLATON exe.

Standard System-S Example

• Two files: name.ins & name.hkl

• Content name.hkl : SHELX style HKLF 3/4

• Content name.ins: TITL, CELL, CELLSD, SFAC, UNIT, HKLF 4 (or 3)

• Note: No Spacegroup Info Needed

• Run: s name.ins NQA.

• 18 Seconds later for C16H20NO3P ….

Problems and Solutions

• There are still many interesting ‘Real World’ problems to be solved for a full proof automatic replacement of an experienced crystallographer.

• Already the use of the Guided Mode to quickly try multiple approaches to solve a structure is a big help (even for the experienced crystallographer)

• System-S stores all relevant I/O files in a hierarchic directory structure for inspection when problems arise.

Problem #0 – Complete Failure

• Example: The chemist provides us with crystals labeled to be a Zn-coordination complex requiring

human ‘Expert Forensic Crystallography’ to tell us that the inorganic salt MnK2(SO4)2 gives us a perfect fit with the experimental data.

Partial Solution: Check with databases (I.e. CELL or simulated powder patterns) and stop.

Failure #1 – Space group

• The space group can not always be determined uniquely from systematic absences (e.g Cc or C2/c).

• Some structures solve only in lower than the actual space group symmetry (sometimes only in P1)

• Solution: loop over the various space group candidates to solve the structure and use ADDSYM to find out about the correct symmetry of the model (implemented in S).

Failure #2 – Phase Problem

- Attempts to automatically solve a structure with a single solution package might fail.

- Solution: loop over all available packages and approaches until a solution is found.

- System-S: SHELX86, SHELXS97, SHELXD, SIR97, SIR2002, DIRDIF99

- ‘Workup’ with EXOR – Example next …

Raw Output from SHELXS86

Result of the EXOR workup

Failure #3 – Incorrect Atom Type Assignment

• Automatic atom type assignment is not always straightforward.

• A large variation in displacement parameters often hampers a correct atom type assignment

• Solution: detailed analysis of intra- and intermolecular geometry and ADP’s

• Example next …

Misassigned Atom Types (S & P)

Atom Type Assignment

Assignment Methods (can be) based on:

1 - An analysis of the Peak heights & Shapes

2 - the value of the displacement parameters

3 - Population parameter refinement (S)

4 - Refinement of each site with alternative

scattering types (E.g. C,N,O)

5 - Chemistry (& CSD knowledge, Mogul)

Failure #4 - Disorder

• Type 1 – Orientational, Conformational or Substitutional disorder of (part of) the structure.

Solution: (Expert) Crystallographer

• Type 2 – Voids filled with unknown (mixtures of) solvents.

Solution: PLATON/SQUEEZE

Failure #5 - Twinning

• (Pseudo) Merohedral Twinning may lead to refined structures with unexpectedly high final R-values and high residual peaks in a difference Fourier Map.

• Solution: Software to detect the applicable twin law.

E.g. Rotax (Simon Parsons & Bob Gould) available in WINGX and CRYSTALS or

PLATON/TwinRotMat Example next ….

Space group P-3 – R = 20 %

3 independent molecules

Problem #6 – Wrong Structure

• Sometimes automatic procedures can come up with ‘reasonably looking’ but wrong structures.

• Structure validation software should send out proper ALERTS (e.g. IUCr Checkcif)

• Example: The chemist expects a Cu-complex, so that is what he gets … (confirmed by X-ray crystallography !) …. and tries to publish … and caught by a knowledgeable referee … on the bases of Checkcif ALERTS.

ORTEP of the False Structure

R < 7 %Cu not Coordinated =>

Ortep of the Correct Structure

R < 6 %

CONCLUDING REMARKS• SYSTEM-S can be used easily for the re-

examination of structures with CIF + FCF data taken from the Acta Cryst Archives or for refereeing purposes to investigate unclear details of the analysis.

• Future implementation:C,N,O etc. discrimination in difficult casesMore chemical knowledgeExtension of the already available procedures for structure determination without any Content Information.

End