SYSTEM-S The Challenge of Automated Structure Determination Ton Spek National Single Crystal Service Utrecht University, The Netherlands

The Challenge Early 1990’s, with a serial detector TurboCAD4 on rotating anode producing about one data set per day ==> need for: 1-Automated data collection 2-Automated structure determination Ad1: Argus (Schreurs/Duisenberg) Ad2: System-S (Spek, 1991-)

Routine Structure Determination Single Crystal I Data collection (CAD4/Argus: GO) I Formula I Autosolve, Refine and Validate (S: NQA) I ORTEP

Current Setup KappaCCD/Rotating Anode/LNT I Collect, DENZO or EVAL-CCD (Not AUTO!) I Import.cif (includes Formula) I System-S Auto-Mode: platon -F import.cif I ORTEP/PLUTON Plots

Standard System-S Example Two files: name.ins & name.hkl Content name.hkl : SHELX style HKLF 3/4 Content name.ins: TITL, CELL, SFAC, UNIT, HKLF 3 or 4 Note: No Spacegroup Info Needed Run: s name.ins NQA.

Example: with shelx.ins & shelx.hkl Structure solved/refined in 18 seconds

Critical Points of Failure Formula - Can be either incomplete or completely wrong (Example later). Space group - Often not uniquely determined when not P-1, P21/c or Pbca (e.g. Cc or C2/c) Phase Problem - Multiple methods (Shelxs/Sir etc) Atom type assignment Non-ideal crystal: Disorder, Twinning Voids with disordered (unknown) content (solvent mixture, charges)

Misassigned Atom Types (S & P)

Atom Type Assignment Assignment Methods (can be) based on: 1 - the analysis of Peak heights 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)

Raw Output from SHELXS86

Result of the EXOR workup

Space-group Determination Use LePage Algorithm for the Metrical Symmetry Determination of the Lattice Get Laue averages for each of the proposed (Sub)Lattices and Laue group. Select tentative Lattice (e.g. tP, 4/m) Get systematic absences Select tentative space-group

Phase Determination Primary: SHELXS86 & SHELXS97 SIR97 & SIR2002 DIRDIF PATTY & ORIENT ‘WORKUP’ of Approximate Solutions: EXOR(cise)

SYSTEM-S DESIGN FEATURES EASY USE OF THE BEST PUBLIC DOMAIN TOOLS (NO LOCAL MODIFICATION) DIRECTORY TREE STRUCTURE FOR THE ARCHIVAL OF INTERMEDIATE FILES MANAGEMENT OF MULTIPLE SPACE GROUP & STRUCTURE DETERMINATION ATTEMPTS (SHELXS, SIR, DIRDIF) AUTOMATIC, GUIDED AND COMMAND LINE MODES OF OPERATION BUILD-IN VALIDATION

Special Features Automatic Spacegroup determination EXOR: Automatic workup of raw Direct Methods results (population refinement) Automatic H-atom assignments Automatic numbering scheme Missed symmetry handling Automatic (weighted) refinement Validation

Horror Story Example: Paper submitted for publication in Acta Cryst. C Supposedly coordination complex with composition Cu(2+) Ligand(2-), at least that was what the chemist wanted to see confirmed with a routine X-ray study That is what he got …. With R < 7% using SHELXTL software

False Structure, R < 7% Cu NOT coordinated !

Correct Structure Cu(2+) --> Br(1-) [HBr was used during the synthesis/crystallisation] Additional H-atoms needed/found on sp3-N and -CO2 (short intermolecular acid bridge. Thus NOT Cu(2+) L(2-) but Br(1-)L(1+) Problems clearly indicated with validation ALERTS

Correct Structure, R < 6%

What about the ORTEPS ? Surprisingly, the ORTEPS of the false and correct structure are very similar Ellipsoids are as expected for room- temperature data

Ortep of the False Structure

Ortep of the Correct Structure

Redetermination with System-S System-S / Guided Mode Using original Room-temperature data and expected formula (CuL) Result: Direct Methods (SIR etc) reproduce results largely consistent with the expected composition apart from some C,N & O miss-assignments, not uncommon for RT data and easy to correct.

Raw Result with SIR97 O O C N N Br

EXPERIENCE AUTOMATIC STRUCTURE DETERMINATION SYSTEM-S WORKS CURRENTLY BEST FOR : - LIGHT ATOM STRUCTURES - BASED ON LOW TEMPERTURE DATA - WITH NO DISORDER - WITH CORRECT FORMULE Otherwise: The Manual GUIDED-Mode appears to be the more appropriate protocol.

CONCLUDING REMARKS SYSTEM-S can be used easily for the re- examination of structures with CIF + FCF data taken from the Acta Cryst Archives. Future implementation: - (C,N,O) etc. L.S. Refinement - More chemical knowledge - Extention of the already available procedures for Structure determination without any Content Information.