如何处理无序晶体解析

Click to edit Master title style,Click to edit Master text styles,Second level,Third level,Fourth level,Fifth level,*,Click to edit Master title style,Click to edit Master text styles,Second level,Third level,Fourth level,Fifth level,*,Some Strategies for the Refinement of Disordered Crystal Structures,Ng Seik Weng,Department of Chemistry,University of Malaya,Kuala Lumpur,Malaysia,1,The assumption of,perfect,periodicity is a basic assumption of crytallography. However, real crystals are not perfect.,The vibration of some atoms 2 - 3 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 structures cannot be published.,2,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,R,int,small.,Which SHELX commands to use depend on the disorder.,And it is very messy to treat disorder.,3,The energy barrier to rotation of CO,2,CH,2,CH,3,radical is of the order of,kT, there is nothing you can do about the data.,4,Disorder in a CH,2,CH,2,CH,2,CH,3,chain,DFIX 1.50 0.01 C1 C2,DFIX 2.45 0.01 C1 C3,EXYZ C1 C1,EADP C1 C1,FVAR,5,Rings must be separated by more than 0.5 .,Pyridyl rings can also be fitted as hexagons.,Fitting phenyl rings,6,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.,7,A phenylene ring disordered along the,C,1,C,4,axis,As the anion lies on a center-of-inversion, AFIX 66 cannot be used. DFIX pairs of distances, and FLAT some atoms.,8,Disorder in a cyclopentyl ring,DFIX the CC to 1.50 and the C,C,C distance to 2.45 so that the angle is 109.5.,9,Perchlorate ions are usually disordered:,any molecular fragment that is spherical will be disordered.,Look for water near the ion.,10,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.,11,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 calculation of bonds/angles.,Assign occupancies to all atoms.,DFIX CC = 1.50,CO = 1.41, C,O = C,C = 2.37 .,12,DMF =,Disorder imposed by,mm,2 symmetry,13,Disorder imposed by,mm,2 symmetry,Mirror plane passing through ring.,Mirror plane perpendicular to ring.,Rotation axis through the mid-points of the 1,2 and 4,5 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.,14,Disorder in the,para,substituents, and disorder in the halides,SUMP,to tie three,p,-Cl to 2 site occupancy, along with distance restraints.,DFIX,to separate the Sn-bonded Cl and Br.,15,More severe disorder,The Sn atom is disordered.,The CF,3,groups are disordered.,The C,6,H,11,ring is disordered with respect to the C,6,H,6,ring.,The entire anion is disordered but the Ph,2,P(CH,2,),3,PPh,2,2,Ag cation is ordered.,16,Refinement of more than two 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.,17,Disorder in mixed bis-chelate structures: MLL” = ML,2,+ ML”,2,?,X = O, S,18,The acid hydrogen atom on a center-of-inversion,H,constrained,by symmetry (,C,2/,c, Z,= 4),O,H = 1.25 ,H,restrained,by DFIX (,P,2,1,/,c,Z,= 4),OH = 0.85 ,19,A case of suppressing the symmetry constraint,Two zwitterions connected by an acid H (,chemically wrong, crystallographically right,).,A pyridinium cation H-bonded to a neutral pyridinone (,chemically right, crystallographically wrong,).,20,Disorder in four-atom, pyramidal fragments, e.g., CHCl,3,and CH,3,CH(OH)CO,2,The methine,CH fragments are above and below the carboxyl plane.,21,Disorder in the heavy atom only,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 Ag,H interactions.,22,Twinning Case 1:Monoclinic emulating orthorhombic, = 90.05(1),TWIN 1 0 0 0 -1 0 0 0 -1,BASF 0.47,The diffraction pattern,emulates,orthorhombic but is not because the intensities cannot be averaged in orthorhombic (,R,int,is large).,23,A simple idea of twinning,A brick with top and bottom indentations, embossed with London Brick on the top only.,Point group 2Point group,mmm,Turning brick upside down uses an operation of,mmm.,24,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 0.18,The twin component is 18%. Another crystal that is not twinned has been found.,25,Twinning Case 3: Flack parameter of 0.5 for non-centric space groups,TWIN,BASF 0.5,Heavy atom structure is a,racemic,twin if organic component is achiral.,For light-atom structure, Friedel pairs,must,be merged, plus .,26,If a heavy atom is present in a chiral structure, the configuration must agree with the expected configuration.,If not, merge equivalent reflections.,27,230 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!,28,Fixing H atoms of water,Find the H atoms by using the,HYDROGEN,option in the,WinGX,suite,Fix the positions by adding 10 to,x,y,z, and tie,U,to,U,eq,of the O atom.,Doesnt always work.,Need to counter-check the H-bonding distances.,29,Find the H atoms from a difference Fourier or by using,HYDROGEN, and then .,DFIX 0.85 0.01 O1,w,H1,w,1 O1,w,H1,w,2,DFIX 1.39 0.01 H1,w,1 H1,w,2,but there are many other ways.,30,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 H,H 1.0 and,FVAR, 1.0, then refine EXTI.,Look out for WGHT!,34,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.,35,