如何处理无序(晶体解析).ppt

SomeStrategiesfortheRefinementofDisorderedCrystalStructures NgSeikWengDepartmentofChemistryUniversityofMalayaKualaLumpurMalaysia Theassumptionofperfectperiodicityisabasicassumptionofcrytallography However realcrystalsarenotperfect Thevibrationofsomeatoms2 3timesthoseofotheratomsofthesamemolecularfragment Peaksinthedifferencemapthataretooclosetoexistingatomstoformplausiblebonds Atomsthataretooclosetosymmetryelementsinthespacegrouptoproducechemically reasonablebonding Anyway thedataaremothballedbecausethestructurescannotbepublished SHELXL 97 Themathematicsisunstableandsomerestraintsmustbeusedtoholdthemathematicstogether Therewillbemorevariablestoberefined Thedatamustbereasonablygood e g I 2 islargeandRintsmall WhichSHELXcommandstousedependonthedisorder Anditisverymessytotreatdisorder TheenergybarriertorotationofCO2CH2CH3radicalisoftheorderofkT thereisnothingyoucandoaboutthedata Disorderina CH2CH2CH2CH3chain DFIX1 500 01C1C2DFIX2 450 01C1C3EXYZC1C1 EADPC1C1 FVAR Ringsmustbeseparatedbymorethan0 5 Pyridylringscanalsobefittedashexagons Fittingphenylrings AFIX66 forphenylrings Canbeusedfornon centricspacegroupsbecausetherearefewerreflections orifthereisaspreadofC Cdistances AphenyleneringdisorderedalongtheC1 C4axis Astheanionliesonacenter of inversion AFIX66 cannotbeused DFIXpairsofdistances andFLATsomeatoms Disorderinacyclopentylring DFIXtheC Cto1 50 andtheC C Cdistanceto2 45 sothattheangleis109 5 Perchlorateionsareusuallydisordered anymolecularfragmentthatissphericalwillbedisordered Lookforwaterneartheion Disorderoveracenter of inversion Usea PART 1 commandtosuppresssymmetry Refinetheringwith AFIX66 Someatomstohavefullandotherhalfoccupancy Disorderof15 crown 5 anoddnumberofatomspackinginaoveracenter of inversion Usea PART 1 commandtosuppressthecalculationofbonds angles Assign occupanciestoallatoms DFIXC C 1 50 C O 1 41 C O C C 2 37 DMF Disorderimposedbymm2symmetry Disorderimposedbymm2symmetry Mirrorplanepassingthroughring Mirrorplaneperpendiculartoring Rotationaxisthroughthemid pointsofthe1 2and4 5carbonatoms Asymmetricunithas2aromaticand1carboxylcarbonatoms and1oxygenatomonly HighR whichisanartifactofthedisorderandnotbecausethedataarebad Disorderintheparasubstituents anddisorderinthehalides SUMPtotiethreep Clto2siteoccupancy alongwithdistancerestraints DFIXtoseparatetheSn bondedClandBr Moreseveredisorder TheSnatomisdisordered The CF3groupsaredisordered TheC6H11ringisdisorderedwithrespecttotheC6H6ring Theentireanionisdisorderedbutthe Ph2P CH2 3PPh2 2Agcationisordered Refinementofmorethantwoatomssharingthesamesite TheSUMPcommand Becausetotalchargeis8 thereareshouldbe1Cu II and2Fe III forthe3sites Refineeachsiteas Cu Fe Or useSUMPtotiethe3Cuatomstounitoccupancy 0 73 0 15 0 12 The0 12occupancyMatomiscoordinatedbywater Disorderin mixed bis chelatestructures ML L ML 2 ML 2 X O S The acid hydrogenatomonacenter of inversion Hconstrainedbysymmetry C2 c Z 4 O H 1 25 HrestrainedbyDFIX P21 c Z 4 O H 0 85 Acaseofsuppressingthesymmetryconstraint TwozwitterionsconnectedbyanacidH chemicallywrong crystallographicallyright ApyridiniumcationH bondedtoaneutralpyridinone chemicallyright crystallographicallywrong Disorderinfour atom pyramidalfragments e g CHCl3andCH3CH OH CO2 Themethine CHfragmentsareaboveandbelowthecarboxylplane Disorderintheheavyatomonly Agis3 coordinateinmajorcomponentand4 coordinateinminorcomponentincentricstructure ComplicatedastwoNatomsaredisorderedwithtwoC Hunits ThecorrectlyrefinedstructureshouldnothaveanyAg Hinteractions TwinningCase1 Monoclinicemulatingorthorhombic 90 05 1 TWIN1000 1000 1BASF0 47Thediffractionpatternemulatesorthorhombicbutisnotbecausetheintensitiescannotbeaveragedinorthorhombic Rintislarge Asimpleideaoftwinning Abrickwithtopandbottomindentations embossedwith LondonBrick onthetoponly Pointgroup2Pointgroupmmm Turningbrickupsidedownusesanoperationofmmm TwinningCase2 Monoclinicwithnearlyequala 12 479 andc 12 597 axes TWIN0010 10100BASF0 18Thetwincomponentis18 Anothercrystalthatisnottwinnedhasbeenfound TwinningCase3 Flackparameterof0 5fornon centricspacegroups TWINBASF0 5Heavyatomstructureisaracemictwiniforganiccomponentisachiral Forlight atomstructure Friedelpairsmustbemerged plus Ifaheavyatomispresentinachiralstructure theconfigurationmustagreewiththeexpectedconfiguration Ifnot mergeequivalentreflections 230SpacegroupsandtheFlackparameter 230SpaceGroups Centrosymmetric Chiral andNon centrosymmetric Non centrosymmetric Chiral Enantiomorphous Friedelpairsarenotassociatedwithchirality FixingHatomsofwater FindtheHatomsbyusingtheHYDROGENoptionintheWinGXsuiteFixthepositionsbyadding10tox y z andtieUtoUeqoftheOatom Doesn talwayswork Needtocounter checktheH bondingdistances FindtheHatomsfromadifferenceFourierorbyusingHYDROGEN andthen DFIX0 850 01O1wH1w1O1wH1w2DFIX1 390 01H1w1H1w2buttherearemanyotherways FindingthehydrogenatomsonwatermaybecriticaltotheoxidationstateofCo CH N cannotdifferentiateoxidationstateofCo Unfortunately foronewatermolecule itisimpossibletoplaceonehydrogenanywherewithoutH H 2 0 Mis assigningspacegroupsbecauseofdisorder K2 C2O4 3Zr C2H2O4 H2OinCcFlackparameter 0 07 Baggioetal Inorg Chem 1997 36 737 739 ThecorrectspacegroupisC2 c Zrliesonatwofoldaxis andtheoxalicacidandwateraredisorderedwithrespecttoeachother Incorrectspacegroups Structuresorderedinthelower symmetrybutincorrectspacegroup usuallynon centric ExceptionTungstogallateacid H5GaW12O40inmonoclinicCm Niuetal J Chem Cryst 2003 39 799 803 shouldbedescribedincubicI 43m Ng J Chem Cryst 20