1、Some Strategies for the Refinement of Disordered Crystal Structures,Ng Seik WengDepartment of Chemistry University of Malaya Kuala Lumpur Malaysia,The assumption of perfect periodicity is a basic assumption of crytallography. However, real crystals are not perfect.,The vibration of some atoms 2 - 3
2、times those of other atoms of the same molecular fragment.Peaks in the difference map that are too close to existing atoms to form plausible bonds. Atoms that are too close to symmetry elements in the space group to produce chemically-reasonable bonding. Anyway, the data are mothballed because the s
3、tructures cannot be published.,SHELXL-97,The mathematics is unstable and some restraints must be used to hold the mathematics together. There will be more variables to be refined. The data must be reasonably good, e.g., I 2 is large and Rint small.Which SHELX commands to use depend on the disorder.
4、And it is very messy to treat disorder.,The energy barrier to rotation of CO2CH2CH3 radical is of the order of kT there is nothing you can do about the data.,Disorder in a CH2CH2CH2CH3 chain,DFIX 1.50 0.01 C1 C2 DFIX 2.45 0.01 C1 C3 EXYZ C1 C1 EADP C1 C1 FVAR,Rings must be separated by more than 0.5
5、 . Pyridyl rings can also be fitted as hexagons.,Fitting phenyl rings,AFIX 66 for phenyl rings,Can be used for non-centric space groups because there are fewer reflections, or if there is a spread of CC distances.,A phenylene ring disordered along the C1C4 axis,As the anion lies on a center-of-inver
6、sion, AFIX 66 cannot be used. DFIX pairs of distances, and FLAT some atoms.,Disorder in a cyclopentyl ring,DFIX the CC to 1.50 and the CCC distance to 2.45 so that the angle is 109.5.,Perchlorate ions are usually disordered: any molecular fragment that is spherical will be disordered.,Look for water
7、 near the ion.,Disorder over a center-of-inversion,Use a PART 1 command to suppress symmetry. Refine the ring with AFIX 66. Some atoms to have full and other half occupancy.,Disorder of 15-crown-5: an odd number of atoms packing in a over a center-of-inversion,Use a PART 1 command to suppress the ca
8、lculation of bonds/angles. Assign occupancies to all atoms. DFIX CC = 1.50, CO = 1.41, CO = CC = 2.37 .,DMF =,Disorder imposed by mm2 symmetry,Disorder imposed by mm2 symmetry,Mirror plane passing through ring. Mirror plane perpendicular to ring. Rotation axis through the mid-points of the 1,2 and 4
9、,5 carbon atoms.Asymmetric unit has 2 aromatic and 1 carboxyl carbon atoms, and 1 oxygen atom only.High R, which is an artifact of the disorder and not because the data are bad.,Disorder in the para substituents, and disorder in the halides,SUMP to tie three p-Cl to 2 site occupancy, along with dist
10、ance restraints. DFIX to separate the Sn-bonded Cl and Br.,More severe disorder,The Sn atom is disordered. The CF3 groups are disordered. The C6H11 ring is disordered with respect to the C6H6 ring.The entire anion is disordered but the Ph2P(CH2)3PPh22Ag cation is ordered.,Refinement of more than two
11、 atoms sharing the same site: The SUMP command,Because total charge is 8, there are should be 1 Cu(II) and 2 Fe(III) for the 3 sites.Refine each site as CuFe.Or, use SUMP to tie the 3 Cu atoms to unit occupancy (0.73, 0.15, 0.12). The 0.12 occupancy M atom is coordinated by water.,Disorder in mixed
12、bis-chelate structures: MLL” = ML2 + ML”2 ?,X = O, S,The acid hydrogen atom on a center-of-inversion,H constrained by symmetry (C2/c, Z = 4)OH = 1.25 H restrained by DFIX (P21/c, Z = 4) OH = 0.85 ,A case of suppressing the symmetry constraint,Two zwitterions connected by an acid H (chemically wrong,
13、 crystallographically right).A pyridinium cation H-bonded to a neutral pyridinone (chemically right, crystallographically wrong).,Disorder in four-atom, pyramidal fragments, e.g., CHCl3 and CH3CH(OH)CO2,The methine CH fragments are above and below the carboxyl plane.,Disorder in the heavy atom only,
14、Ag is 3-coordinate in major component and 4-coordinate in minor component in centric structure.Complicated as two N atoms are disordered with two CH units. The correctly refined structure should not have any AgH interactions.,Twinning Case 1: Monoclinic emulating orthorhombic = 90.05(1),TWIN 1 0 0 0
15、 -1 0 0 0 -1 BASF 0.47The diffraction pattern emulates orthorhombic but is not because the intensities cannot be averaged in orthorhombic (Rint is large).,A simple idea of twinning,A brick with top and bottom indentations, embossed with London Brick on the top only.Point group 2 Point group mmm,Turn
16、ing brick upside down uses an operation of mmm.,Twinning Case 2: Monoclinic with nearly equal a- (12.479 ) and c- (12.597 ) axes,TWIN 0 0 1 0 -1 0 1 0 0 BASF 0.18The twin component is 18%. Another crystal that is not twinned has been found.,Twinning Case 3: Flack parameter of 0.5 for non-centric spa
17、ce groups,TWIN BASF 0.5Heavy atom structure is a racemic twin if organic component is achiral. For light-atom structure, Friedel pairs must be merged, plus ,If a heavy atom is present in a chiral structure, the configuration must agree with the expected configuration.,If not, merge equivalent reflec
18、tions.,230 Space groups and the Flack parameter,230 Space Groups,Centrosymmetric,“Chiral” and Non-centrosymmetric,Non-centrosymmetric,“Chiral”,Enantiomorphous,Friedel pairs are not associated with chirality!,Fixing H atoms of water,Find the H atoms by using the HYDROGEN option in the WinGX suiteFix
19、the positions by adding 10 to x, y, z, and tie U to Ueq of the O atom. Doesnt always work. Need to counter-check the H-bonding distances.,Find the H atoms from a difference Fourier or by using HYDROGEN, and then ,DFIX 0.85 0.01 O1w H1w1 O1w H1w2 DFIX 1.39 0.01 H1w1 H1w2but there are many other ways.
20、,Finding the hydrogen atoms on water may be critical to the oxidation state of Co,CH&N % cannot differentiate oxidation state of Co. Unfortunately, for one water molecule, it is impossible to place one hydrogen anywhere without HH 2.0 .,Mis-assigning space groups because of disorder,K2(C2O4)3Zr.C2H2
21、O4.H2O in CcFlack parameter = 0.07 (Baggio et al., Inorg. Chem., 1997, 36, 737739) The correct space group is C2/c; Zr lies on a twofold axis, and the oxalic acid and water are disordered with respect to each other.,Incorrect space groups: Structures ordered in the lower-symmetry but incorrect space
22、 group, usually non-centric,ExceptionTungstogallate acid, H5GaW12O40 in monoclinic Cm (Niu et al., J. Chem. Cryst., 2003, 39, 799-803)should be described in cubic I-43m (Ng, J. Chem. Cryst., 2004, 39, 000-000),Goodness-of-fit, S,_refine_ls_goodness_of_fit_ref _refine_ls_S_allIf S 1.0 and FVAR 1.0, then refine EXTI.Look out for WGHT!,There is no one definite way to refine disordered structures it depends on the data and the nature of the disorder.,It is my pleasure to thank my collaborators who provided the diffraction data.,
