晶體學(xué)結(jié)構(gòu)的解析Xray粉末衍射法Topas軟件

晶體學(xué)結(jié)構(gòu)的解析

X-ray粉末衍射法

Topas軟件李國寶北京大學(xué)化學(xué)學(xué)院2006晶體學(xué)結(jié)構(gòu)晶體學(xué)結(jié)構(gòu)一種描述簡單原則三斜合理原則討論內(nèi)容基本處理(結(jié)構(gòu)解析(一))結(jié)構(gòu)解析(二)結(jié)構(gòu)精修一般性問題結(jié)構(gòu)解析(一):基本處理樣品的準(zhǔn)備和數(shù)據(jù)的采集數(shù)據(jù)的處理(衍射圖)一般步驟數(shù)據(jù)的讀入尋峰(峰形擬合)指標(biāo)化空間群的判斷結(jié)構(gòu)解析數(shù)據(jù)的讀入布魯克衍射儀的數(shù)據(jù)(*.raw)理學(xué)衍射儀的數(shù)據(jù)中子衍射的數(shù)據(jù)程序的啟用可讀入數(shù)據(jù)的格式布魯克衍射儀的數(shù)據(jù)(*.raw)BrukerAXSbinaries(DIFFRACATandDIFFRACplus)*.DATSeveralASCIIfileformatsincludingLHPM/RIET7/CSRIET,GSAS("std-const","alt-ralf")andFullProf.*.XDD/*.CALASCIIfileformat.*.XY,*XYEASCIIfileformats.Canbeusedfornon-equidistantx-axissteps.島津衍射儀的ASCII數(shù)據(jù)*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

理學(xué)衍射儀的ASCII數(shù)據(jù)GSAS數(shù)據(jù)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

界面簡介（userinterface）?MenubarContainsthenamesofsubmenus,whichprovidelistsofallcommandsavailabletogetherwiththeirshortcutsrespectivelytoolbaricons,ifexisting.?ToolbarDisplaysthemostimportantcommandsinformoficonsforfastaccess.?WorkingAreaContainsallelementsneededforprofilefittingsuchasobservedandcalculateddata,fitparameters,andfitresults,whicharedisplayedinseparatedviews.?StatusBarDisplayssomecontextsensitivehelpinformationandthex-andy-coordinatesofthedatacursorintheactiveScanWindow,whichisdescribedinsection2.2.數(shù)據(jù)的處理數(shù)據(jù)的組成背底峰位置

峰形Globalitem(全域項(xiàng))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文件的內(nèi)容普通衍射儀：lamymin_on_ymax0.0001la0.653817lo1.540596lh0.501844la0.346183lo1.544493lh0.626579布魯克的D8Advance：

lamymin_on_ymax0.0001la1lo1.540596lh0.401844Instrument

（儀器參數(shù)）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尋峰單譜線擬合步驟峰形函數(shù)TopasUsersManual.pdfTOPAS提供的兩類峰形擬合方法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

（衍射源譜線的描述）單色器對峰形的影響Directconvolutionapproach

Empiricalparameterisation

（直接卷積法：實(shí)驗(yàn)參數(shù)法）經(jīng)驗(yàn)函數(shù)Directconvolutionapproach:Fundamentalparameters

（基本參數(shù)法）DiffractometerconfigurationsandtheirgeometricalaberrationsDivergentBeamLaboratoryDiffractometersParallelBeamDiffractometersDivergentBeamLaboratoryDiffractometersPositionsensitivedetectors(PSDs)ParallelBeamDiffractometersPositionsensitivedetectors(PSDs)Treatmentofsatellitepeaksandtubetails全譜擬合如何指標(biāo)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=5.879?

b=7.329?

c=9.130?

D8ADVANCE,Ka1

Allenetal.(2003)FinalPawleyfittakinganisotropiclinebroadeningintoaccountSphericalharmonicsfunctionusedtomodelexcessbroadeningLT-ZrMo2O8

a=5.879?

b=7.329?

c=9.130?

D8ADVANCE,Ka1

Allenetal.(2003)TOPASV3

LP-Search:LT-ZrMo2O8具體操作存儲峰位置文件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中國科學(xué)院物理研究所董成研究員如何確定空間群消光規(guī)律簡單嘗試Im-3P23使用Sir97程序結(jié)構(gòu)解析GUI模式Lauch模式添加Structure項(xiàng)設(shè)定相關(guān)參數(shù)*.cif格式的變換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一般特點(diǎn)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的來源GUI模式的輸出文件已有的模版r_exp2.186r_exp_dash4.660r_wp2.922r_wp_dash6.227r_p2.275r_p_dash6.184weighted_Durbin_Watson1.333gof1.336iters1000chi2_convergence_criteria0.001xddD:\北京青少年科技后備人才培養(yǎng)計(jì)劃\杜喬羽\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精修的參數(shù)*.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)數(shù)據(jù)文件名及背底函數(shù)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)關(guān)于單晶數(shù)據(jù)Shelxl,ShelxssiteO1num_posns2occO-21beq1x0.0000y0.000z0.000RigidbodiesandbondlengthrestraintsPenaltiesusedinstructuredetermination擬合因子結(jié)構(gòu)精修

兩相的精修物相鑒定尋峰數(shù)據(jù)庫的使用結(jié)構(gòu)解析(二)真實(shí)結(jié)構(gòu)與結(jié)構(gòu)的可表征性有關(guān)物理性質(zhì)與結(jié)構(gòu)的相關(guān)性電子衍射等電鏡技術(shù)中子衍射有關(guān)物理性質(zhì)與結(jié)構(gòu)的相關(guān)性對稱中心二階非線性光學(xué)系數(shù)鐵電性壓電系數(shù)發(fā)光Ba1-xLaxTi1-xCrxO3的相關(guān)系示意圖0x1x2x3