Advanced Crystallography: Refinement of Disordered Structures November 13, 2012 Disorder Webinar

This Webinar is being broadcast from our Madison, Wisconsin, USA, facility November 13, 2012 Disorder Webinar

Charles Campana, Ph.D. Senior Applications Scientist at Bruker AXS, Madison, WI, USA BS, Chemistry (1970), Montana State University, Bozeman, Montana PhD (1975), Inorganic Chemistry (with L. F. Dahl), University of Wisconsin, Madison, Wisconsin Assistant Professor (1976 – 1980), University of New Mexico University, Albuquerque, New Mexico Senior Applications Scientist (1980 - present) Single-Crystal X-ray Diffraction, Nicolet, Siemens and Bruker; Crystallographic co-author on several hundred scientific papers. November 13, 2012 Disorder Webinar

Audience Poll Please use your mouse to answer the question on your screen: What is your experience level? I have not done any crystal structures I have done only routine structures I have done problem structures I’m a crystallographer Please use: Boxes with GREY outlines for pictures and text Boxes with RED outlines for text only. FULL GREY boxes for conclusions only. November 13, 2012

Introduction Modern X-ray crystallographic systems with automatic features have made it possible for synthetic chemists with limited crystallographic training to obtain publication-quality crystal structures quickly and easily for routine structures. While the automated structure routines perform well on straight-forward molecular compounds, these routines are not capable of automatically modeling various disorder problems. In these cases, the user must utilize some of the advanced SHELXL/XL instructions involving the use of free variables, constraints and restraints to successfully refine and publish his / her results. All of these techniques involve editing the SHELXL/XL output (*.res) file, with either a text editor or a specialized graphical editor, to produce a new, modified SHELXL/XL input (*.ins) file. November 13, 2012 Disorder Webinar

George Sheldrick Professor of Structural Chemistry and part-time programming technician at the University of Göttingen PhD (1966) University of Cambridge with E.A.V. Ebsworth; thesis entitled "NMR Studies of Inorganic Hydrides" 1966 - 1978: University Lecturer and Fellow of Jesus College, Cambridge Since 1978 Professor at the University of Göttingen Since 2011 Niedersachsen Professor at the University of Göttingen (emeritus) Author of about 800 scientific papers and of a computer program called SHELX (http://shelx.uni-ac.gwdg.de/SHELX/) Sheldrick, GM (2008) A short history of SHELX. Acta Crystallogr., A64:112-122 (open access) This paper is currently the most highly cited scientific paper of the last five years in all subjects. November 13, 2012 Disorder Webinar

SHELX References A short history of SHELX, Sheldrick, GM (2008) (http://journals.iucr.org/a/issues/2008/01/00/sc5010/sc5010.pdf) SHELX Manual (http://shelx.uni-ac.gwdg.de/SHELX/shelx.pdf) Crystal Structure Refinement: A Crystallographer's Guide to SHELXL (International Union of Crystallography Texts on Crystallography) November 13, 2012 Disorder Webinar

SHELXTL vs. SHELX* http://shelx.uni-ac.gwdg.de/SHELX/index.html SHELXTL (Bruker AXS) XPREP XS XM XE XL XPRO XWAT XP XSHELL XCIF SHELX (Public Domain)* None SHELXS SHELXD SHELXE SHELXL SHELXPRO SHELXWAT CIFTAB November 13, 2012 Disorder Webinar

Peter Müller, MIT Director of the Diffraction Facility MIT Department of Chemistry Cambridge, Massachusetts November 13, 2012 Disorder Webinar

Objectives of this presentation Use of text editors or graphical editors to insert additional instructions into SHELXL / XL input instruction (*.ins) files. Introduction to the concepts of constraints and restraints in crystal structure refinement. Introduction to the internal atom connectivity concept and PART n and PART –n instructions. Introduction to the use of free variables in constraints and restraints. Examples of commonly used instructions for applying a variety of constraints and restraints to the refinement of disordered structures. November 13, 2012

Constraints and Restraints In crystal structure refinement, there is an important distinction between a 'constraint' and a 'restraint'. A constraint enables one or more least-squares variables to be expressed exactly in terms of other variables or constants, and hence eliminated. A restraint takes the form of additional information which is not exact but is subject to a probability distribution; for example we could restrain two chemically but not crystallographically equivalent bonds to be approximately equal. November 13, 2012 Disorder Webinar

Constraints and Restraints in SHELXL The following general categories of constraints and restraints are available using SHELXL: Constraints for the coordinates and anisotropic displacement parameters for atoms on special positions: these are generated automatically by the program for ALL special positions in ALL space groups, in conventional settings or otherwise. Floating origin restraints: these are generated automatically by the program, so the user should not attempt to fix the origin in such cases by fixing the coordinates of a heavy atom. Two or more atoms sharing the same site: the xyz and Uij parameters may be equated using the EXYZ and EADP constraints respectively (or by using 'free variables'). The occupation factors may be expressed in terms of a 'free variable' so that their sum is constrained to be constant (e.g. 1.0). If more than two different chemical species share a site, a linear free variable restraint (SUMP) is required to restrain the sum of occupation factors. Geometrical constraints: these include rigid-group refinements (AFIX 6), variable-metric rigid-group refinements (AFIX 9) and various riding models (AFIX/HFIX) for hydrogen atom refinement, for example torsional refinement of a methyl group about the local threefold axis. November 13, 2012 Disorder Webinar

Constraints and Restraints in SHELXL Fragments of known geometry may be fitted to target atom, and the coordinates generated for any missing atoms. Four standard groups are available: regular pentagon, regular hexagon, naphthalene and pentamethylcyclopentadienyl. Other groups may be used simply by specifying orthogonal or fractional coordinates in a given cell (AFIX mn with m > 16 and FRAG...FEND). Geometrical restraints: a particularly useful restraint is to make chemically but not crystallographically equivalent distances equal without having to invent a value for this distance (SADI). The SAME instruction can be used to generate such restraints automatically, e.g. when chemically identical molecules or residues are present. This has the same effect as making equivalent bond lengths and angles but not torsion angles equal. The FLAT instruction restrains a group of atoms to lie in a plane (but the plane is free to move and rotate). Restraints on anisotropic displacement parameters: three different types of restraint may be applied to Uij values. DELU applies a 'rigid-bond' restraint to Uij of two bonded (or 1,3) atoms; the anisotropic displacement components of the two atoms along the line joining them are restrained to be equal. Isolated atoms may be restrained to be approximately isotropic (ISOR). Similarly, the assumption of 'similar' Uij values for spatially adjacent atoms (SIMU) is useful for partially overlapping atoms of disordered groups. November 13, 2012 Disorder Webinar

Types of constraints in SHELXL Constraints for special positions: the necessary constraints on co-ordinates, occupancies and Uij are derived automatically. Rigid groups (AFIX 6 … AFIX 0): the 3 positional parameters per atom are replaced by 3 rotations and 3 translations for the whole rigid group. Atoms may not be in more than one rigid group. Riding hydrogen atoms (AFIX mn): xH = xC + x – no extra positional parameters. Fixed parameters: add 10 to x, y, z, occ, U etc. Typically occupancies are fixed at 1.0 by adding 10, i.e. given as 11.0 Free variables: can be used to add extra linear constraints to the usual refinement parameters and also be used instead of restraint target values. This provides a convenient way of getting target values with esd’s for use as restraints in other structures. November 13, 2012 Disorder Webinar

Special position constraints Example: Atom on twofold axis in space group C2. The two positions related by the twofold axis (x,y,z: -x,y,-z) coincide when x = 0 and z = 0. Since we still wish to sum over all symmetry operators in the structure factor calculation, the occupancy is fixed at 0.5. The probability ellipsoid used to describe the anisotropic motion should not be changed by the 180º rotation. [U11, U22, U33, U23, U13, U12]  [U11, U22, U33, -U23, U13, -U12] which is only true if U23 = 0 and U12 = 0. All these constraints are generated automatically by SHELXL for all special positions in all space groups. November 13, 2012 Disorder Webinar

Rigid group constraints In SHELXL, rigid groups are defined by three rotations about the first atom in the group and by three translations of the group as a whole. Special position constraints may be applied to the first atom and restraints and riding hydrogen atoms are allowed on all atoms in the group. Note that the esd’s of bond lengths and angles but not of co-ordinates within a rigid group come out as zero from the L.S. matrix algebra. AFIX 6 rigid group – all AFIX 9 variable metric … bond lengths and … rigid group - angles atoms angles fixed atoms fixed, bond lengths … … multiplied by the AFIX 0 AFIX 0 same factor November 13, 2012 Disorder Webinar

The connectivity list The connectivity list is used for the automatic generation of hydrogen atoms and some restraints. Non-hydrogen atoms i and j are considered to be ‘bonded’ if: dij < ri + rj + 0.5 Å The CONN instruction may be used to modify r and to set a maximum connectivity for an atom (e.g. 0 for water). A shell of symmetry equivalents is generated automatically around the unique atoms. Bonds may be added with BIND or deleted with FREE. PART N controls the generation of bonds for disordered groups. Most atoms have N = 0; multiple conformations have N = 1, 2 etc. Bonds are generated only when the N are equal or one N is zero. If N is negative, bonds are not made to symmetry equivalents. November 13, 2012 Disorder Webinar

Free variables Free variables are an extremely concise but effective way of applying linear constraints to atom parameters (especially occupancies), restraint targets etc. The parameter x is given as (10m+p), which is interpreted as follows: m = 0: refine normally, starting at value p m = 1: fix at value p m > 1: x = p* fv(m) m <-1: x = p* [fv(–m) – 1] e.g., 30.25 (m = 3, p = 0.25) means 0.25*[fv(3)] and –30.25 (m = –3, p = –0.25) means 0.25*[1 – fv(3)], which could be used to constrain two occupancies to add up to 0.25 (only one parameter, free variable #3, is refined). The starting values for the free variables are given on the FVAR instruction (but free variable #1 is the overall scale factor). November 13, 2012 Disorder Webinar

Standard SHELX Instructions TITL YLID in P2(1)2(1)2(1) CELL 0.71073 5.9651 9.0437 18.4047 90.000 90.000 90.000 ZERR 4.00 0.0002 0.0003 0.0006 0.000 0.000 0.000 LATT -1 SYMM 0.5-X, -Y, 0.5+Z SYMM -X, 0.5+Y, 0.5-Z SYMM 0.5+X, 0.5-Y, -Z SFAC C H O S UNIT 44 40 8 4 TEMP 23.000 SIZE 0.32 0.34 0.34 L.S. 4 BOND FMAP 2 PLAN 20 FVAR 1.00000 S1 4 0.19050 0.68120 0.74160 11.00000 0.05000 C1 1 0.36850 0.62830 0.67080 11.00000 0.05000 C2 1 0.31150 0.50160 0.62620 11.00000 0.05000 O1 3 0.16360 0.40830 0.63170 11.00000 0.05000 C3 1 0.49610 0.49860 0.56590 11.00000 0.05000 C4 1 0.52540 0.41640 0.51090 11.00000 0.05000 C5 1 0.70740 0.44010 0.46220 11.00000 0.05000 C6 1 0.84660 0.54890 0.47510 11.00000 0.05000 C7 1 0.82480 0.64010 0.53680 11.00000 0.05000 C8 1 0.65310 0.61620 0.58110 11.00000 0.05000 O2 3 0.66890 0.80130 0.67590 11.00000 0.05000 C9 1 0.56180 0.69740 0.64820 11.00000 0.05000 C10 1 0.16570 0.88170 0.72670 11.00000 0.05000 C11 1 0.34520 0.68260 0.82310 11.00000 0.05000 HKLF 4 November 13, 2012 Disorder Webinar

Graphical Editors for SHELXL/XL files XP (Bruker AXS Inc.) XShell (Bruker AXS Inc.) APEX2 (Bruker AXS Inc.) WinGX (L. Farrugia) Crystals (D. Watkin et al.) X-Seed (L. Barbour) shelXle (C. Hubschle et al.) OLEX2 (O. Dolomanov et al.) November 13, 2012 Disorder Webinar

Two cations sharing the same site The best strategy is to constrain the positions and displacement parameters to be the same, and refine the occupancies so that their sum is constrained to be unity: EXYZ MG CA EADP MG CA FVAR 1.0 0.6 .. PART 1 MG 6 0.37041 0.34874 0.03824 21.0 0.20936 PART 2 CA 7 0.37041 0.34874 0.03824 -21.0 0.20936 PART 0 If the cations were sharing a special position on a twofold axis, their occupancies would be specified as 20.5 and –20.5. For three atoms (or molecules) sharing a site, it is better to tether each occupancy to a free variable (e.g. by 31, 41 and 51) and to restrain the sum of these free variables to unity: SUMP 1.0 0.001 1.0 1 1.0 2 1.0 3 November 13, 2012 Disorder Webinar

DFIX or SADI? The DFIX restraint is able to restrain bond lengths to target values but sometimes the target is uncertain. For example the P―O distance in a phosphate may vary with the pH and the extent of libration. SADI can be very useful in such cases, e.g. SADI P O1 P O2 P O3 P O4 SADI O1 O2 O1 O3 O1 O4 O2 O3 O2 O4 O3 O4 ensures that the phosphate will be a regular tetrahedron, but allow the bond length to refine. The same can however be achieved by an AFIX 9 constraint or by using DFIX with a free variable, e.g. FVAR …… …… 1.55 DFIX 31 P O1 P O2 P O3 P O4 DFIX 31.6330 O1 O2 O1 O3 O1 O4 O2 O3 O2 O4 O3 O4 November 13, 2012 Disorder Webinar

The rigid-bond restraint DELU In SHELXL, the DELU restraint is a strict rigid-bond restraint, i.e. the components of the anisotropic motion of two atoms along the line joining them are restrained to be equal. Although DELU is a reliable restraint and so can be given a small esd, there are not as many DELU restraints as Uij, so it may be necessary to supplement them with the less accurate but more numerous SIMU and ISOR restraints with larger esd’s. November 13, 2012 Disorder Webinar

Restraints on ADP's November 13, 2012 Disorder Webinar

Toluene on an inversion center Toluene is a good solvent for growing crystals because of its long liquid range, but it simply cannot resist inversion centers: This can be handled with one complete toluene molecule with occupancies of 10.5 (fixed at 0.5) and PART -1. Equivalent 1,2- and 1,3-distances can be restrained to be equal with SADI and a FLAT restraint applied to all 7 carbons, or a rigid hexagon can be used for the 6-membered ring (plus two SADI and one CHIV for the CH3). SIMU and DELU are recommended. The hydrogen atoms should be set with HFIX in a later job: HFIX 43 C1 > C5 (generates 5H with occupancies of 0.5) HFIX 123 C7 (generates 6H with occupancies of 0.25) November 13, 2012 Disorder Webinar

Use of PART 1, PART 2 and SAME ISOR DELU WGHT 0.045500 FVAR 0.22187 PART 1 C1A 1 0.42827 0.23894 0.85590 10.50000 0.04467 0.03563 = 0.04915 0.00377 0.01463 -0.00748 . C17A 1 0.42023 0.25662 1.14925 10.50000 0.05042 0.04274 = 0.05014 -0.00305 -0.00756 0.00391 AFIX 43 H17A 2 0.53968 0.31799 1.15025 10.50000 0.05761 AFIX 0 PART 2 SAME C1A > C17A C1B 1 0.47550 0.26048 1.14359 10.50000 0.04169 0.03667 = 0.04839 0.00438 -0.00897 0.00686 C17D 1 0.23382 -0.11832 0.35155 10.50000 0.03704 0.02547 = 0.04522 0.00395 0.00013 -0.00093 H17D 2 0.16654 -0.00313 0.35229 10.50000 0.02412 PART 0 November 13, 2012 Disorder Webinar

Use of PART 1, PART 2 and SAME Part 1 Part 2 Parts 1 & 2 November 13, 2012 Disorder Webinar

Ethyl acetate disordered about a 2-fold axis FVAR 0.07920 0.57624 C1 1 1.056270 0.672587 0.015161 11.00000 0.07754 0.17320 = 0.19702 -0.03184 0.00034 0.03626 . O6 3 0.793446 0.479760 0.011891 11.00000 0.07630 0.08652 = 0.06854 -0.00308 -0.00415 0.05024 SAME C1 > O6 PART -1 C1' 1 0.122354 -0.092142 0.016919 20.50000 0.16721 0.13875 = 0.20344 0.02675 -0.02623 0.07727 AFIX 0 O6' 3 0.167969 0.159420 0.007654 20.50000 0.08280 0.06135 = 0.12535 0.00968 -0.00772 0.03937 PART 0 November 13, 2012 Disorder Webinar

Disordered t-butyl group November 13, 2012

Disorder between Cl and C November 13, 2012

Disorder of a cyclopentadienyl ring November 13, 2012

November 13, 2012 Disorder Webinar

Disorder of a chloroform molecule on a mirror plane November 13, 2012 Disorder Webinar

DMSO disordered over three positions November 13, 2012 Disorder Webinar

Example 1 - Os3(CO)10(PPh2~PPh2) Background Sample from UCSD Summer School Prof. Michael Richmond et al. (U. of North Texas) NMR indicated dynamic equilibrium between two isomers Structure was easily ‘solved’, but could not be refined R1 = 16% Many NPD atoms Three very large difference peaks (‘Star of David’) November 13, 2012

Example 1 - Os3(CO)10(PPh2~PPh2) preliminary structure – chelating phosphine ligand November 13, 2012

Example 1 - Os3(CO)10(PPh2~PPh2) L.S. 4 BOND FMAP 2 PLAN 99 WGHT 0.040000 FVAR 0.15477 0.8500 ANIS 3 OS1 5 1.38180 0.36327 0.23664 21.00000 0.01306 OS2 5 1.16037 0.44356 0.29321 21.00000 0.01737 OS3 5 1.22802 0.46498 0.16310 21.00000 0.01676 C1A 1 1.22737 0.29544 0.22637 21.00000 0.01424 O1A 3 1.14724 0.25371 0.21696 21.00000 0.01327 C2A 1 1.53166 0.43473 0.24515 21.00000 0.02705 O2A 3 1.61483 0.47245 0.24881 21.00000 0.01637 C3A 1 1.00907 0.38885 0.25481 21.00000 0.02644 O3A 3 0.91212 0.35992 0.23556 21.00000 0.03082 C4A 1 1.33420 0.49045 0.32785 21.00000 0.02520 O4A 3 1.42200 0.51620 0.35349 21.00000 0.02519 C5A 1 1.13429 0.40796 0.37402 21.00000 0.01968 O5A 3 1.11507 0.38537 0.42076 21.00000 0.04168 C6A 1 1.03019 0.51972 0.29063 21.00000 0.02206 O6A 3 0.94876 0.56097 0.28462 21.00000 0.04682 C7A 1 1.12667 0.38230 0.13189 21.00000 0.02768 O7A 3 1.06313 0.34129 0.11120 21.00000 0.02261 C8A 1 1.33629 0.53964 0.20167 21.00000 0.02088 O8A 3 1.39946 0.58535 0.21995 21.00000 0.02206 C9A 1 1.34144 0.46478 0.08771 21.00000 0.02607 O9A 3 1.39311 0.47459 0.04379 21.00000 0.02768 C10A 1 1.07098 0.52231 0.13931 21.00000 0.02470 O10A 3 0.98114 0.55458 0.12305 21.00000 0.04529 ANIS 2 P1 4 1.49269 0.30401 0.31810 11.00000 0.01685 P2 4 1.51235 0.30162 0.16667 11.00000 0.02253 C1 1 1.64848 0.25992 0.21803 11.00000 0.02086 C2 1 1.64668 0.26068 0.28099 11.00000 0.02963 C3 1 1.77319 0.22528 0.30686 11.00000 0.03008 November 13, 2012

Example 1 - Os3(CO)10(PPh2~PPh2) three large difference peaks November 13, 2012

Example 1 - Os3(CO)10(PPh2~PPh2) L.S. 4 BOND FMAP 2 PLAN 99 WGHT 0.040000 FVAR 0.14765 0.84986 PART 1 ANIS 3 OS1 5 1.381809 0.363269 0.236644 21.00000 0.01398 OS2 5 1.160375 0.443563 0.293216 21.00000 0.01832 OS3 5 1.228021 0.464972 0.163111 21.00000 0.01769 PART 2 OS4 5 1.279201 0.372329 0.290337 -21.00000 0.01897 OS5 5 1.356916 0.404339 0.165486 -21.00000 0.01516 OS6 5 1.132255 0.478575 0.221611 -21.00000 0.02121 C1A 1 1.227149 0.295498 0.226379 21.00000 0.01463 O1A 3 1.147208 0.253766 0.216857 21.00000 0.01437 C2A 1 1.531363 0.434503 0.245167 21.00000 0.02786 O2A 3 1.614757 0.472385 0.248824 21.00000 0.01766 ... C9A 1 1.341290 0.464934 0.087821 21.00000 0.02657 O9A 3 1.392650 0.474727 0.043766 21.00000 0.02908 C10A 1 1.071073 0.522226 0.139298 21.00000 0.02516 O10A 3 0.981357 0.554645 0.123065 21.00000 0.04658 PART 0 ANIS 2 P1 4 1.492683 0.304015 0.318087 11.00000 0.01777 P2 4 1.512382 0.301606 0.166718 11.00000 0.02357 C1 1 1.648401 0.259913 0.218106 11.00000 0.02206 C2 1 1.646876 0.260442 0.280954 11.00000 0.03039 November 13, 2012

Example 1 - Os3(CO)10(PPh2~PPh2) remaining carbonyl atoms revealed in difference map November 13, 2012

Example 1 - Os3(CO)10(PPh2~PPh2) superposition of both isomers November 13, 2012

Example 1 - Os3(CO)10(PPh2RPPh2) chelating phosphine ligand (85%) bridging phosphine ligand (15%) November 13, 2012 Disorder Webinar

Example 1 - Os3(CO)10(PPh2~PPh2) Crystallographic restraints (SADI, ISOR, SIMU, EADP) were used in initial refinement Final refinement converged at R1 = 5.2% Kandala, S.; Yang, L.; Campana, C. F.; Nesterov, V.; Wang, X.; Richmond, M. G. (2010) Isomerization of the diphosphine ligand 3,4-bis(diphenylphosphino)-5-methoxy-2(5H)-furanone (bmf) at a triosmium cluster and P-C bond cleavage in the unsaturated cluster 1,1-Os3(CO)9(bmf): Synthesis and x-ray diffraction structures of the isomeric Os3(CO)10(bmf) clusters and HOs3(CO)8(μ-C6H4)[μ-PhPC:C(Ph2P)CH(OMe)OC(O)]. Polyhedron, 29, 2814-2821. November 13, 2012 Disorder Webinar

Example 2 – Urea Host : Guest Complex Background Prof. Mark Hollingsworth et al. (Kansas State U.) Urea host lattice with long-chain carboxylic acid in channels Structure of urea lattice was ‘solved’, but carboxylic acid molecules could not be located Apparent unit cell Orthorhombic P212121 a = 8.3096 Å , b = 10.9591 Å , c = 13.6330 Å 12 Urea molecules, 4 carboxylic acid molecules per cell November 13, 2012

Example 2 – Urea Host : Guest Complex projection down b-axis November 13, 2012

Example 2 – Urea Host : Guest Complex Projection down a-axis November 13, 2012

Example 2 – Urea Host : Guest Complex analysis of Q-peaks November 13, 2012

Example 2 – Urea Host : Guest Complex analysis of Q-peaks November 13, 2012

Example 2 – Urea Host : Guest Complex N2C 3 0.662814 0.937759 0.024542 11.00000 0.02028 AFIX 93 H2CA 2 0.626060 1.006875 0.048581 11.00000 0.05118 H2CB 2 0.753628 0.936746 -0.008654 11.00000 0.05692 AFIX 0 PART -1 C1S 1 0.047758 0.093743 0.256429 10.33333 0.02221 O1S 4 -0.065938 0.059457 0.208123 10.33333 0.03123 O2S 4 0.147213 0.019479 0.303494 10.33333 0.03285 AFIX 3 H2S 2 0.117603 -0.055411 0.292184 10.33333 0.05883 C2S 1 0.090446 0.226023 0.271096 10.33333 0.02369 AFIX 23 H2SA 2 0.196427 0.240424 0.240008 10.33333 0.03582 H2SB 2 0.103898 0.240028 0.342366 10.33333 0.05245 .... C10S 1 0.080032 1.122110 0.284898 10.33333 0.02266 H10A 2 0.095393 1.108073 0.356020 10.33333 0.03019 H10B 2 0.185537 1.108980 0.252859 10.33333 0.07844 C11S 1 0.034726 1.252421 0.270929 10.33333 0.02477 O3S 4 -0.087391 1.287204 0.233376 10.33333 0.03143 O4S 4 0.147522 1.327757 0.305089 10.33333 0.03101 H4S 2 0.123082 1.402847 0.301909 10.33333 0.66676 PART 0 November 13, 2012

Example 2 – Urea Host : Guest Complex Anisotropic refinement of dicarboxylic acid Final refinement R1 = 3.83% Temperature factors on hydrogen atoms refined November 13, 2012

Example 3 - Fe3(CO)12 Crystallographic Problem Space group is P21/n with Z = 2 Each molecule must lie on a crystallographic center of symmetry Successful refinement is difficult because it requires two half-weighted molecules superimposed on the center of symmetry

Example 3 - Fe3(CO)12 Refinement Results 100K Data Resolution – 0.40Å R1 = 3.82% wR2 = 9.14% 12633 Ind. Refl. 298K Data Resolution – 0.65Å R1 = 5.11% wR2 = 13.45% 2989 Ind. Refl.

Example 3 - Fe3(CO)12 November 13, 2012 Disorder Webinar PART -1 0.01192 -0.00304 0.00029 0.00180 FE2 3 0.178487 -0.013488 0.072272 10.50000 0.01366 0.03072 = 0.01623 -0.00211 0.00057 0.00456 FE3 3 -0.113197 0.044515 0.114740 10.50000 0.01190 0.02706 = 0.01485 -0.00692 0.00156 0.00141 C1 1 0.081260 0.147371 0.115557 10.50000 0.01956 0.02010 = 0.01724 -0.00283 0.00109 -0.00231 O1 2 0.126014 0.245819 0.134149 10.50000 0.04116 0.01783 = 0.02873 -0.00442 0.00366 -0.00946 C2 1 0.021315 -0.103724 0.184318 10.50000 0.02054 0.01953 = 0.01435 -0.00137 0.00099 0.00160 O2 2 0.008896 -0.191357 0.252741 10.50000 0.04893 0.02094 = 0.02342 0.00376 0.00923 0.00349 C3 1 -0.081841 -0.177419 -0.115438 10.50000 0.01853 0.01948 = 0.01636 -0.00508 0.00216 -0.00150 O3 2 -0.103377 -0.276377 -0.093423 10.50000 0.03593 0.02098 = 0.03320 -0.00557 0.00597 -0.00602 . C11 1 -0.287792 -0.062646 0.088306 10.50000 0.02252 0.03041 = 0.02577 -0.00620 0.00431 -0.00036 O11 2 -0.394246 -0.123109 0.074063 10.50000 0.02464 0.04749 = 0.05354 -0.01977 0.00761 -0.00933 C12 1 -0.225303 0.177277 0.034806 10.50000 0.01673 0.03692 = 0.02324 -0.00162 0.00748 -0.00024 O12 2 -0.293440 0.264375 0.000260 10.50000 0.02529 0.04527 = 0.03472 -0.00706 0.01154 -0.00290 PART 0 November 13, 2012 Disorder Webinar

Example 3 - Fe3(CO)12 - shelXle diagrams November 13, 2012 Disorder Webinar

50% Thermal Ellipsoids 100K 298K

Example 3 - Fe3(CO)12 Bond Lengths 100K Fe(1) -Fe(2) 2.6932(3) Å Fe(2)- Fe(3) 2.6993(3) Å Fe(2)-Fe(3) 2.5591(4) Å Fe(2)-C(1) 2.013(4) Å Fe(2)-C(2) 1.985(4) Å Fe(3)-C(1) 1.989(4) Å Fe(3)-C(2) 2.020(4) Å 298K Fe(1) -Fe(2) 2.6766 (11) Å Fe(2)- Fe(3) 2.6806 (11) Å Fe(2)-Fe(3) 2.5547 (12) Å Fe(2)-C(1) 2.095(8) Å Fe(2)-C(2) 2.042(8) Å Fe(3)-C(1) 2.063(8) Å Fe(3)-C(2) 2.129(8) Å

Example 3 - Fe3(CO)12 Bond Lengths 100K Fe(1) -Fe(2) 2.6932(3) Å Fe(2)- Fe(3) 2.6993(3) Å Fe(2)-Fe(3) 2.5591(4) Å Fe(2)-C(1) 2.013(4) Å Fe(2)-C(2) 1.985(4) Å Fe(3)-C(1) 1.989(4) Å Fe(3)-C(2) 2.020(4) Å C(1)-O1) 1.161(3) Å C(2)-O(2) 1.163(3) Å 298K Fe(1) -Fe(2) 2.6766 (11) Å Fe(2)- Fe(3) 2.6806 (11) Å Fe(2)-Fe(3) 2.5547 (12) Å Fe(2)-C(1) 2.095(8) Å Fe(2)-C(2) 2.042(8) Å Fe(3)-C(1) 2.063(8) Å Fe(3)-C(2) 2.129(8) Å C(1)-O1) 1.088(6) Å C(2)-O(2) 1.112(6) Å

Example 3 - Fe3(CO)12 Comparison of 100K and 298K Structures

Example 3 - Fe3(CO)12 Conclusions Collection of low temperature (100K) data to high resolution (0.40 Å) facilitates the separation of overlapped peaks in the disordered structure. The refinement of the structure using the PART -1 instruction in SHELX(TL) allows a stable refinement of the Fe3(CO)12 structure with no restraints. The final structure a 100K exhibits only minor deviations from idealized C2v molecular symmetry with symmetrically bridging carbonyl ligands. Although the results of the lower resolution (0.65 Å) dataset collected at room temperature are not as precise, both structures are nearly superimposable with the 100K structure.

Review and Conclusions Use of text editors or graphical editors to insert additional instructions into SHELXL / XL input instruction (*.ins) files. Introduction to the concepts of constraints and restraints in crystal structure refinement. Introduction to the internal atom connectivity concept and PART n and PART –n instructions. Introduction to the use of free variables in constraints and restraints. Examples on commonly used instructions for applying a variety of constraints and restraints to the refinement of disordered structures. November 13, 2012

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Available at www. bruker Available at www.bruker.com/service/education- training/webinars/sc-xrd.html November 13, 2012

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