1、Some Strategies for the Refinement of Disordered Crystal StructuresNg Seik WengDepartment of ChemistryUniversity of MalayaKuala LumpurMalaysia1The assumption of perfect periodicity is a basic assumption of crytallography. However, real crystals are not perfect.The vibration of some atoms 2 - 3 times

2、 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 struct

3、ures cannot be published.2SHELXL-97The 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. And it i

4、s very messy to treat disorder.3The energy barrier to rotation of CO2CH2CH3 radical is of the order of kT there is nothing you can do about the data. 4Disorder in a CH2CH2CH2CH3 chainDFIX 1.50 0.01 C1 C2 DFIX 2.45 0.01 C1 C3 EXYZ C1 C1EADP C1 C1 FVAR5Rings must be separated by more than 0.5 .Pyridyl

5、 rings can also be fitted as hexagons.Fitting phenyl rings6AFIX 66 for phenyl ringsCan be used for non-centric space groups because there are fewer reflections, or if there is a spread of CC distances.7A phenylene ring disordered along the C1C4 axisAs the anion lies on a center-of-inversion, AFIX 66

6、 cannot be used. DFIX pairs of distances, and FLAT some atoms.8Disorder in a cyclopentyl ringDFIX the CC to 1.50 and the CCC distance to 2.45 so that the angle is 109.5.9Perchlorate ions are usually disordered: any molecular fragment that is spherical will be disordered.Look for water near the ion.1

7、0Disorder over a center-of-inversionUse a PART 1 command to suppress symmetry.Refine the ring with AFIX 66.Some atoms to have full and other half occupancy.11Disorder of 15-crown-5: an odd number of atoms packing in a over a center-of-inversionUse a PART 1 command to suppress the calculation of bond

8、s/angles.Assign occupancies to all atoms.DFIX CC = 1.50, CO = 1.41, CO = CC = 2.37 .12DMF =Disorder imposed by mm2 symmetry13Disorder imposed by mm2 symmetryMirror plane passing through ring.Mirror plane perpendicular to ring.Rotation axis through the mid-points of the 1,2 and 4,5 carbon atoms.Asymm

9、etric 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.14Disorder in the para substituents, and disorder in the halidesSUMP to tie three p-Cl to 2 site occupancy, along with distance restraints. DFIX

10、 to separate the Sn-bonded Cl and Br.15More severe disorderThe 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.16Refinement of more than two atoms sharing the sam

11、e site: The SUMP commandBecause 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.17Disorder in mixed bis-chelate structure

12、s: MLL” = ML2 + ML”2 ?X = O, S18The acid hydrogen atom on a center-of-inversionH constrained by symmetry (C2/c, Z = 4)OH = 1.25 H restrained by DFIX (P21/c, Z = 4) OH = 0.85 19A case of suppressing the symmetry constraintTwo zwitterions connected by an acid H (chemically wrong, crystallographically

13、right).A pyridinium cation H-bonded to a neutral pyridinone (chemically right, crystallographically wrong).20Disorder in four-atom, pyramidal fragments, e.g., CHCl3 and CH3CH(OH)CO2 The methine CH fragments are above and below the carboxyl plane.21Disorder in the heavy atom onlyAg is 3-coordinate in

14、 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.22Twinning Case 1:Monoclinic emulating orthorhombic = 90.05(1)TWIN 1 0 0 0 -1 0 0 0 -1BASF 0.47T

15、he diffraction pattern emulates orthorhombic but is not because the intensities cannot be averaged in orthorhombic (Rint is large). 23A simple idea of twinningA brick with top and bottom indentations, embossed with London Brick on the top only.Point group 2Point group mmm Turning brick upside down u

16、ses an operation of mmm.24Twinning 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. 25Twinning Case 3: Flack parameter of 0.5 for non-centric space groups TWIN BASF

17、0.5Heavy atom structure is a racemic twin if organic component is achiral.For light-atom structure, Friedel pairs must be merged, plus . 26If a heavy atom is present in a chiral structure, the configuration must agree with the expected configuration.If not, merge equivalent reflections.27230 Space g

18、roups and the Flack parameter230 Space GroupsCentrosymmetric “Chiral” and Non-centrosymmetric Non-centrosymmetric“Chiral”EnantiomorphousFriedel pairs are not associated with chirality!28Fixing H atoms of waterFind the H atoms by using the HYDROGEN option in the WinGX suiteFix 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.29Find the H atoms from a diff