晶体学结构的解析Xray粉末衍射法Topas软件

晶体学结构的解析

X-ray粉末衍射法

Topas软件李国宝北京大学化学学院2006晶体学结构晶体学结构一种描述简单原则三斜合理原则讨论内容基本处理(结构解析(一))结构解析(二)结构精修一般性问题结构解析(一):基本处理样品的准备和数据的采集数据的处理(衍射图)一般步骤数据的读入寻峰(峰形拟合)指标化空间群的判断结构解析数据的读入布鲁克衍射仪的数据(*.raw)理学衍射仪的数据中子衍射的数据程序的启用可读入数据的格式布鲁克衍射仪的数据(*.raw)BrukerAXSbinaries(DIFFRACATandDIFFRACplus)*.DATSeveralASCIIfileformatsincludingLHPM/RIET7/CSRIET,GSAS("std-const","alt-ralf")andFullProf.*.XDD/*.CALASCIIfileformat.*.XY,*XYEASCIIfileformats.Canbeusedfornon-equidistantx-axissteps.岛津衍射仪的ASCII数据*Group:YSH*Data:Ti-c1*FileName:Ti-c1.RAW*Comment:10.00000.02000120.00202200238188236210210208220198218224198192210190210222192218196186196216186

*Group:YSH*Data:Ti-c1*FileName:Ti-c1.RAW*Comment:*550110.00000.02000202200238188236210210208220198218224198192210190210222192218

理学衍射仪的ASCII数据GSAS数据格式5.0000.020120.0000501047.3.2006BANK15751575CONST500200STD

137412941388136813421366135013641400136013601410137213381330130813181372137413141414134613401348134213181290131413841348129413161358128013361294137812681324137412761356132012801388130013961386128213061332133612821328129813741392135012621310*.XY格式050104OriginalData5751513725.0213845.0413705.0613885.0813845.113345.1213785.1413525.1613725.1813685.21378

513725.0213845.0413705.0613885.0813845.113345.121378

界面简介（userinterface）•MenubarContainsthenamesofsubmenus,whichprovidelistsofallcommandsavailabletogetherwiththeirshortcutsrespectivelytoolbaricons,ifexisting.•ToolbarDisplaysthemostimportantcommandsinformoficonsforfastaccess.•WorkingAreaContainsallelementsneededforprofilefittingsuchasobservedandcalculateddata,fitparameters,andfitresults,whicharedisplayedinseparatedviews.•StatusBarDisplayssomecontextsensitivehelpinformationandthex-andy-coordinatesofthedatacursorintheactiveScanWindow,whichisdescribedinsection2.2.数据的处理数据的组成背底峰位置

峰形Globalitem(全域项)Background(section2.3.2.4)Instrument(section2.3.2.5)Corrections(section2.3.2.6)Miscellaneous(section2.3.2.7)Display•AllPeaks(section2.3.2.8)AllStructures/hklPhases(section2.3.2.11)BackgroundTwobackgroundfunctionsareprovided1.aChebychevpolynomialofanyorder2.a1/Xfunction.TheChebychevCoefficientspagecontainsthecoefficientsofthepolynomial.Emissionprofile

(光源的信息)GivestheabilitytoaddanddeleteemissionlineswhichformtheemissionprofileoftheX-raysource.TheOptionspagecontainsthefollowingoptions:Option:Remarks:•YminonYmaxDeterminesthex-axisextenttowhichpeaktailsarecalculated(cutoff)•NoThdependenceDefinesanemissionprofilethatis2θindependent.Allowstheuseofnon-X-raydataorfittingtonegative2θvalues.•ForLAMcursorSwitchesthemousecursortoamulti-linecursorrepresentingthedifferentemissionlinesofthecurrentemissionprofile(Fig.2-14)•LamforBraggangleOnlyforexpertusers,refertotheTechnicalReferencemanual•CalculateLamOnlyforexpertusers,refertotheTechnicalReferencemanual*.lam文件的内容普通衍射仪：lamymin_on_ymax0.0001la0.653817lo1.540596lh0.501844la0.346183lo1.544493lh0.626579布鲁克的D8Advance：

lamymin_on_ymax0.0001la1lo1.540596lh0.401844Instrument

（仪器参数）Bragg-BrentanogeometryAdditionalConvolutionsBragg-BrentanogeometryCorrectionsMiscellaneousFitmethodConstraintsandkeywords1)SPF:SinglepeakfittingNoconstraintsbydefault.Optionallyallprofileparameterscanbeconstrained(e.g.sameshape,samewidth,relativeintensity,...)Keywords:"xo_I","d_I"WPPF:WholePowderpatternfitting.•Noconstraintsbydefault.Optionallyallprofileparameterscanbeconstrained(e.g.sameshape,samewidth,relativeintensity,...)•Profileparametersconstrainedtobesmoothlyvaryingfunctionsof2θKeywords:"xo_I","d_I"WPPD:WholepowderpatterndecompositionPawleyandLeBailmethodNumberofpeaksandtheirpositionsconstrainedbycrystalsystem/spacegrouppluslatticeparametersKeyword:"hkl_I"Rietveld:Rietveldstructurerefinement,ab-initiostructuredeterminationPeakintensitiesconstrainedbythecrystalstructureKeyword:"str"1)FordetailsrefertotheTechnicalReferencemanual寻峰单谱线拟合步骤峰形函数TopasUsersManual.pdfTOPAS提供的两类峰形拟合方法1.AnalyticalProfileFitting:analyticalpeakshapefunctions(PSF)

Gaussian,Lorentzian,sumsofGaussiansorLorentzians,Voigt,pseudo-VoigtandPearsonVIIfunctions2.DirectConvolutionApproach:Y(2θ)=W⊗F1(2θ)⊗F2(2θ)⊗...⊗Fi(2θ)⊗...⊗Fn(2θ)

Y(2θ)istheobservedlineprofileshape,Wisthesourceemissionprofile,and⊗denotestheconvolutionprocess.Sourceemissionprofiles

（衍射源谱线的描述）单色器对峰形的影响Directconvolutionapproach

Empiricalparameterisation

（直接卷积法：实验参数法）经验函数Directconvolutionapproach:Fundamentalparameters

（基本参数法）DiffractometerconfigurationsandtheirgeometricalaberrationsDivergentBeamLaboratoryDiffractometersParallelBeamDiffractometersDivergentBeamLaboratoryDiffractometersPositionsensitivedetectors(PSDs)ParallelBeamDiffractometersPositionsensitivedetectors(PSDs)Treatmentofsatellitepeaksandtubetails全谱拟合如何指标化LSILP-SearchAdvancesin

IndexingofPowderDiffractionPatterns:

IterativeUseofLeastSquares(LSI)

and

Monte-CarloBased

WholePowderPatternDecompositionArntKern

TOPASV3

TOtalPatternAnalysisSolutionsIntensityExtractionLeBail,PawleyStructureDeterminationusingF2(obs)StructureRefinementusingyi(obs)"Profiling"LeBail,PawleyStructureDetermination

ANDRefinement

usingyi(obs)PeakFindingIndexingTOPASApproach

Coelho(2000)QuantitativeRietveldAnalysisNewTOPASV3

LSIandLP-SearchLSIIterativeuseofleastsquaresOperatesond-valuesextractedfromreasonablequalitypowderdiffractiondataLP-SearchMonte-CarloBasedWholePowderPatternDecompositionIndependentofd-spacingextractionandlineprofileshapeandthereforesuitedforindexingofpoorqualitypowderdata!Nod-valuesrequired!TOPASV3

LSIMethod1.LSIIterativeProcesshklsassignedusingpresent(random)latticeparametersReciprocallatticerelationshipsolvedusingleastsquaresforallhkl

2.Monte-CarloapproachtosearchingparameterspaceRandomizelatticeparametersExecutionoftheLSIiterativeprocessuntilconvergenceTOPASV3

LSIReciprocallatticerelationship:Modifiedtoincludeazeroerrorandaweightingfunction:Objectivefunction:Forlarged-spacingsaswellasforhigh2qerrorsweightingsareincreasedautomaticallyTOPASV3

LSILSIisappliedconsecutivelywithhklscorrespondingtominimumsymmetryBravaislatticesfromeachcrystalsystemandindecreasingorderofsymmetry.MonocliniclatticesaretreateddifferentlywhereasearchisperformedusingthesixuniquesetsofhklscorrespondingtothespacegroupsP2,P21,Pc,P21/c,

C2,andCc

andnotjusttheBravaislattices.OnpresentpersonalcomputersLSIsearchesallcrystalssystemsdowntothetricliniclatticeinlessthanthreeminutes.TOPASV3

LSIMostimportantfeatures:SeamlessintegrationintoTOPASV3Zero-pointerrorconsiderationAutomaticdeterminationofpossiblespacegroupsHighlytoleranttoimpuritypeaks,missinghighd-spacings,extremelatticeparameterratiosaswellaslarged-spacingandzeropointerrors(>0.05°2q)Particularilystronginindexingofverylargecells(>>100.000A3)anddominantzoneproblemsWeightingofreflectionsusingobservedpeakintensitiesoruser-definedweightsFullyautomatedPawleyorLeBailfittingofalloruser-selectedsolutionsGoodness-of-fitversusvolumeplotsTOPASV3

LSIPowderpatternoverlaidwithbothobserved(blue)andcalculated(red)peakpositionsDetailedindexingresults

forallsolutionsTOPASV3

LSIGoodness-of-fitversusvolumedisplayEasyidentificationoffractionalandmultiplevolumesFullyautomaticPawleyor

LeBailfittingofalloruserselectedsolutionsTOPASV3

LSIReferenceIndexingofpowderdiffractionpatternsbyiterativeuseofsingularvaluedecompositionA.A.CoelhoJ.Appl.Cryst.(2003),36,86–95TOPASV3

LP-SearchLP-SearchisaMonte-CarlobasedWholePowderPatternDecompositionapproachItminimizesonanewfigureofmeritfunctionthatgivesameasureofcorrectnessforaparticularsetoflatticeparametersThefigureofmeritfunctionassignspartsofthediffractionpatterntocalculatedpeakpositionsandthensumstheabsolutevaluesoftheproductsofthediffractionintensitiesmultipliedbythedistancetothecalculatedpeakpositionsLP-Searchavoidsdifficultiesassociatedwithextractingd-spacingsfromcomplexpatternscomprisingheavilyoverlappedlinesTOPASV3

LP-SearchPoorsolution,highR-valueGoodsolution,lowR-valueGeneratesetsoflatticeparametersandcalculated-valuesForeachsolution,foreachcalculatedd-valuedefinepatternsegmentssumtheabsolutevaluesof(stepintensities*distancetothed-value)RefinethebestsolutionReiterateTOPASV3

LP-SearchMostimportantfeatures:SeamlessintegrationintoTOPASV3Independentof2qord-spacingextractionIndependentoflineprofileshapeZero-pointerrorconsideration,highlytoleranttolargezeropointerrors(>0.05°2q)Particularysuitedforindexingofpoorqualitypowderdata,wherereliable2qord-spacingextractionisdifficultorevenimpossibleTOPASV3

LP-SearchDirectPawleyorLeBailfittingofrandomlatticeparameterstothepowderpattern!Nod-valuesrequired!TOPASV3

LP-Search:LT-ZrMo2O8Particularysuitedforindexingofpoorqualitypowderdata:

Howmanypeaksarethere?Peakoverlap?2+phases?Anisotropiclinebroadening?TOPASV3

LP-Search:LT-ZrMo2O8DataareeasilyindexedwithLP-SearchLP-SearchprofilefitrevealsstronganisotropiclinebroadeningLT-ZrMo2O8

a=5.879Ǻ

b=7.329Ǻ

c=9.130Ǻ

D8ADVANCE,Ka1

Allenetal.(2003)FinalPawleyfittakinganisotropiclinebroadeningintoaccountSphericalharmonicsfunctionusedtomodelexcessbroadeningLT-ZrMo2O8

a=5.879Ǻ

b=7.329Ǻ

c=9.130Ǻ

D8ADVANCE,Ka1

Allenetal.(2003)TOPASV3

LP-Search:LT-ZrMo2O8具体操作存储峰位置文件TypeUsePositionAreaCrySizeL(nm)CrySizeG(nm)StrainLStrainGSPVII116.9066617.46451200.0200.00.10.1SPVII123.95561134.764200.0200.00.10.1SPVII127.249244.839198200.0200.00.10.116.90666,17.4645123.95561,134.76427.24924,4.839198CopytheDatatoClipboardLP-Search方法其他方法Powder-X中国科学院物理研究所董成研究员如何确定空间群消光规律简单尝试Im-3P23使用Sir97程序结构解析GUI模式Lauch模式添加Structure项设定相关参数*.cif格式的变换data__chemical_name_mineral'Structure'_cell_length_a7.438554_cell_length_b7.438554_cell_length_c7.438554_cell_angle_alpha90_cell_angle_beta90_cell_angle_gamma90_cell_volume411.5907loop__symmetry_equiv_pos_as_xyz '-x,-y,-z' '-x,-y,z' '-x,y,-z' '-x,y,z' '-y,-z,-x'data__chemical_name_mineral'Structure'_symmetry_cell_setting?_symmetry_space_group_name_H-MIm-3loop__symmetry_equiv_pos_as_xyz '-x,-y,-z'_cell_length_a7.438554_cell_length_b7.438554_cell_length_c7.438554_cell_angle_alpha90_cell_angle_beta90_cell_angle_gamma90_cell_volume411.5907GUIandLaunch一般特点FeaturesavailableinGUIandLaunchModeFiletypesandformatsTheScanWindowChartOptionsDialogPeakSearchDialogPeakDetailsDialogOptionsDialogFitWindowTheParametersWindowGlobalitemRangeitem(s)PeakPhasehklPhaseStructureStructures/hklPhasesGlobalitem•Background(section2.3.2.4)•Instrument(section2.3.2.5)•Corrections(section2.3.2.6)•Miscellaneous(section2.3.2.7)•DisplayAdditionallythefollowingitemsmaybedisplayedaswell:•AllPeaks(section2.3.2.8)•AllStructures/hklPhases(section2.3.2.11)Rangeitem(s)EmissionprofilePeakPhasehklPhaseStructureStructures/hklPhasesPrintingandreportingOperationinGUIandLaunchModeLauch模式SetINPfile*.inp的来源GUI模式的输出文件已有的模版r_exp2.186r_exp_dash4.660r_wp2.922r_wp_dash6.227r_p2.275r_p_dash6.184weighted_Durbin_Watson1.333gof1.336iters1000chi2_convergence_criteria0.001xddD:\北京青少年科技后备人才培养计划\杜乔羽\CaTaTi\d11\d11s.dat r_exp2.186r_exp_dash4.660r_wp2.922r_wp_dash6.227r_p2.275r_p_dash6.184weighted_Durbin_Watson1.333gof1.336 bkg@1215.64401208.701692-188.17575298.679653-151.78017159.956008-87.398948439.269390516.2762255 One_on_X(@,6118.28199) Zero_Error(@,-0.20911) Specimen_Displacement(@,-0.00575) LP_Factor(26.4) Rp217.5 Rs217.5 Cylindrical_2Th_Correction(@,0.63346) Absorption(@,31.40650) Specimen_Tilt(@,0.37208) lam ymin_on_ymax0.001 la0.653817lo1.540596lh0.501844 la0.346183lo1.544493lh0.626579 str CS_L(@,120.54707) PVII_Peak_Type(@,0.03757,@,0.00372,@,0.12792,@,0.00010,@,1.56236,@,0.39528) r_bragg0.490306945 phase_nameStructure MVW(1680.577,411.7866,100.000) scale@0.0001260772 space_group"I_m_-3" Phase_LAC_1_on_cm(725.41115) Phase_Density_g_on_cm3(6.77697) Cubic(@7.43973) siteCu1num_posns6occCu+21beq1x0y0.5z0.5 siteO2num_posns24occO-21beq1x0y@0.29392z@0.22710 siteTi1num_posns8occTi+40.5beq1x0.25y0.25z0.25 siteta2num_posns8occTa+50.5beq1x0.25y0.25z0.25 xo_Is xo@16.9550599 I@13.078614 CS_L(@,216.24903) peak_typefp"keywords"and"macros"

*.inpr_exp2.186r_exp_dash4.660r_wp2.922r_wp_dash6.227r_p2.275r_p_dash6.185weighted_Durbin_Watson1.333gof1.336iters1000chi2_convergence_criteria0.001精修的参数*.inpxddD:\北\杜\CaTaTi\d11\d11s.dat r_exp2.186r_exp_dash4.660r_wp2.922r_wp_dash6.227r_p2.275r_p_dash6.185weighted_Durbin_Watson1.333gof1.336

bkg

@1215.64267208.70024-188.175586298.679649-151.78075759.9557014-87.399097439.269385216.2758868

One_on_X(@,6118.28036)数据文件名及背底函数Backgroundfunctionsusingfit_objects*.inp

Zero_Error(@,-0.20911) Specimen_Displacement(@,-0.00575)

LP_Factor(26.4)

Rp217.5 Rs217.5

Specimen_Tilt(@,0.37208)Cylindrical_2Th_Correction(@,0.63346)

Absorption(@,31.40664) lam ymin_on_ymax0.001 la0.653817lo1.540596lh0.501844 la0.346183lo1.544493lh0.626579lam ymin_on_ymax0.001 la0.653817lo1.540596lh0.501844 la0.346183lo1.544493lh0.626579CuKa5(0.001)*.inp str CS_L(@,120.54619) PVII_Peak_Type(@,0.03757,@,0.00372,@,0.12792,@,0.00010,@,1.56236,@,0.39524) r_bragg0.489677278 phase_nameStructure MVW(1680.577,411.7860,100.000) scale@0.0001260781 space_group"I_m_-3"SampleconvolutionsQuantitativeanalysis*.inpPhase_LAC_1_on_cm(725.41213) Phase_Density_g_on_cm3(6.77698) Cubic(@7.43973) siteCu1num_posns6occCu+21beq1x0y0.5z0.5 siteO2num_posns24occO-21beq1x0y@0.29393z@0.22710 siteTi1num_posns8occTi+40.5beq1x0.25y0.25z0.25 siteta2num_posns8occTa+50.5beq1x0.25y0.25z0.25 xo_Is xo@16.9550654 I@13.0775354 CS_L(@,216.31479)关于单晶数据Shelxl,ShelxssiteO1num_posns2occO-21beq1x0.0000y0.000z0.000RigidbodiesandbondlengthrestraintsPenaltiesusedinstructuredetermination拟合因子结构精修

两相的精修物相鉴定寻峰数据库的使用结构解析(二)真实结构与结构的可表征性有关物理性质与结构的相关性电子衍射等电镜技术中子衍射有关物理性质与结构的相关性对称中心二阶非线性光学系数铁电性压电系数发光Ba1-xLaxTi1-xCrxO3的相关系示意图0x1x2x3