Post on 16-Jul-2020
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ThePLATONcheckCIFandSQUEEZETools
TonSpekUtrechtUniversity,NL
Rigaku/OxfordDiffracIonUsermeeIngWroclaw,june20,2016
QUESTION:IsthisStructureCorrect?TheAug.2015IUCr/checkCIFreportsnoseriousALERTS
NoVoidsNoUnusualContactsNormal?DifferenceDensityRange
R1=0.0111wR2=0.0339S=1.042Rhomin-0.43Rhomax0.47
No,TheStructurewasDeliberatelyINVENTEDThisdeviousstructurewascleverycreatedbyNatalieJohnsonetal.,Newcastle,UK,aimingtobeatcheckCIF.ItwaspresentedasanexcellentPosterduringthe2015ECMCongressinRovinj,CroaIa.But:Everycrimeleavesitstraces…..
UnusualActualdifferencemapDensity
Cleartracesofthe‘Crime’areintheDifferenceDensityMap
DifferencemapintheCH2planeTheCH2HydrogenatomsatcalculatedposiIonsaredefinitelynotinF(obs)
Expectedtypeofdifferencemap
NATALIE
YLID
HowwasStructure‘Natalie’created?
YLID
‘StarIngMaterial’(Bruker)
Chemicalissue:Se+
NoexampleintheCSDforthe6-memberedringSystemMogul:Se–Coutlier
í
ë
NoH-density
NoDensityonBonds
CURRENTPLATON/CHECKCIFVALIDATIONREPORTFOR‘NATALIE’
WhatisPLATON
• AcollecIonofSHELXcompaIbletoolsbundledinasingleprogram
• TheToolsetincludes:– CheckCIF (StructureValidaIon)– SQUEEZE (HandlingDisorderedSolvents)– ADDSYM (MissedSymmetry)– TwinRotMat (TwinningDetecIon)– Bijvoet (AbsoluteStructure–Hoom(y))
PLATON/CHECKCIF• IscurrentlythemajorvalidaIonenginebehindtheIUCrdrivencheckCIFvalidaIonprojectofcrystalstructures.
• ItChecksandReportson(withALERTS)– CompletenessofthesuppliedinformaIon– Problemswiththeexperimentaldata– ProblemswiththeinterpretaIonofthedata– Problemswiththereportedstructuremodel– Unusualstructuralfeatures
StructureValidaIonnowover20Years
• TheintroducIonoftheCIFstandardfordataarchivalmadeautomaIcstructurecheckingpossible.
• StructurevalidaIonprovidesauthors,refereesandreaderswithalistofpossiblyinteresIngissueswithastructurereportthatmightneedtobeaddressed.
• Currentlyabout500testshavebeenimplementedincheckCIFandthatnumberissIllincreasingonthebasisofnewlydetectedissueswithsuppliedCIF’s.
• ALERTSarenotnecessarilyerrors.TheyomenpointatinteresIngstructuralfeaturestobediscussed.
SomeValidaIonIssues• ACIFessenIallyarchivestheauthorsinterpretaIonof
theunderlyingexperimentaldiffracIondata.• ArchivedreflecIondataareneededforameaningful
evaluaIonofunusualresultsandfortestcalculaIons.• ArchivalofFo/Fcdata(FCF)alreadysolvespartofthis
issue(sideeffectofitsavailability:detecIonandproveofcasesofafewhundredseriouslyfraudedstructuresinActaCryst.E)
• Recently:embeddingofrefinementinstrucIons(res)andunmergedreflecIondata(hkl)intheCIFurged.
• Theembeddingofthe.res&.hklintotheCIFwithSHELXL2014currentlyvoidstheneedtosupplyanFCF.
• IUCr/checkCIFandhkldeposiIonarenowalsopartoftheCSDdeposiIonandarchivalprocedures.
FCF-ValidaIonadds:
• Analysisofthequalityoftherefinement• Analysisofthedifferencemap(peaks)• DetecIonofvoidcontent(SQUEEZE)• DetecIonofmissingreflecIons• DetecIonofoutliers• DetecIonofmissedtwinning• Checkoftheabsolutestructure
BenefitsoftheSHELXL2014standardembeddingof.res,.hkl(&.fab)
• NoneedtosupplyanFCFfilealongwiththeCIFaspartofadatadeposiIon.TheFCFcanbecreatedfromtheembeddeddata.
• Whensupplied,theFCFshouldbe‘LIST4’or‘LIST8’type• SHELXL2014CIF+FCFaretherecommendedfilestoruntheSQUEEZEtoolsincetheoriginalreflecIondataareretainedintheCIF
STATISTICSPREPAREDBYTHECCDCONSQUEEZEdorOLEX2-MASKdSTRUCTURESintheCSD
TheSQUEEZETool
PLATON/SQUEEZE• ThecurrentimplementaIonoftheSQUEEZEtooltohandledisorderedsolventsisthethirdgeneraIonofamethodpublishedbyusmorethan25yearsago.
• InterfacingwithSHELXL2014refinementsolvesmanyearlierissueswithSHELX76&SHELXL97using.res&.hkldata.[e.g.ModificaIonoftheobserveddata]
• DocumentaIonoftherecommendedprocedure:A.L.Spek(2015)ActaCryst.C71,9-18
• htp://www.platonsom.nl/PLATON_HOW_TO.pdf
TheDisorderedSolventProblem• ThecalculatedstructurefactorFccanbespitintotwoparts:Fc=Fc(model)+Fc(solvent)
• Fc(solvent)canbeparametrizedwithan(elaborate)disordermodelandrefinedalongwiththeothermodelparameters.
• Fc(solvent)canalsobeapproximatedwiththeSQUEEZEtoolandusedasafixedcontribuIontothestructurefactorsintherefinement.
• Insimplecases,thefirstapproachispreferred
ThePLATON/SQUEEZETool• SQUEEZE,asimplementedinPLATON,analysesthecontentofsolventaccessibleVOID(s)inacrystalstructure.(Q:arethevoidsempty?).
• TheVOIDcontentwillgenerallyinvolve(heavily)disorderedsolvent(s)thatmightbedifficulttoparameterizemeaningfully(e.g.unknownsolvents).
• ThesolventcontribuIontothecalculatedstructurefactorsisapproximatedbyFouriertransformaIonofthedensityintheVOID(s)aspartoftheleast-squaresrefinementofthemodelparameters.(.fab)
• SQUEEZEdoesnotrefinetheFc(model)
TheProperuseofSQUEEZE• ItisimportantthatthefinalCIFarchivesboththedetailsoftheSQUEEZEcalculaIonandtheunmergedreflecIondata.Inthatway,thecalculaIonscanbereconstructedand/oralternaIverefinementmodelsatempted.
• SHELXL2014offersallwhatisneededforthat.• SQUEEZEusesthemodelparameterstakenfrom.cifandmergedobservedstructurefactorsfromtheLIST4orLIST8.fcftocalculatesolventF(calc)on.fab.
• FinalSHELXLrefinementwillbebasedontheCIFembedded.res,.hklfilesalongwiththe.fabfile.
HowtoSQUEEZEwithSHELXL2014
1. Refineanon-solventmodelwithname.ins&name.hkl(IncludeACTArecord,NOLIST6).
2. RunPLATON/SQUEEZE,basedonname.cif&name.fcffrom1as‘platon–qname.cif’.
3. ConInueSHELXLrefinementwiththefilesname_sq.ins,name_sq.hkl&name_sq.fabfrom2as‘shelxlname_sq’
4. Inspectthe.lis&.lstfilesandValidate
SQUEEZEDisorderedSolvent+Twinning
• Step1:SHELXLrefinementbasedaname.ins(thatshouldinclude‘ACTA’,‘LIST8’,‘BASF’and‘HKLF5’[or‘TWIN’]records)andaname.hklfile
• Step2:RunSQUEEZEwiththename.cifandname.fcffilesproducedinStep1(i.e.run:platon–qname.cif)
• Step3:ConInueSHELXLrefinementwiththefilesname_sq.ins,name_sq.hklandname_sq.fabproducedbyPLATONinstep2èname_sq.cif&name_sq.fcf
• Note:Thename_sq.fabfilecontainsthesolventcontribuIontotheSFandthedetailsofSQUEEZE.
SQUEEZE-2016Example:CoordinaIonCompound
SpaceGroupP21Z=4,Z’=260:40TwinTwinaxis:(001)150KTWINABShklf5dataAcetonitrilsolvateStep1(SHELXL2014)èR1=0.047,wR2=0.1445Step2(SQUEEZE)è177electronsfoundinunitcellStep3(SHELXL2014)èR1=0.0275,wR2=0.0679,S=1.064
AcetonitrilModel:R=0.0323,wR2=0.0889,rho(max)=1.34e/A-3
EffectofonR(F)beforeandamerSQUEEZEasafuncIonofsin(theta)/lambda
Requirements• Thereshouldbenoresidualunresolveddensityinthediscretemodelregionofthestructurebecauseofitsimpactonthedifferencemapinthesolventregion.
• ThedatasetshouldbereasonablycompleteandwithsufficientresoluIon[i.e.sin(theta)/lambda>0.6].
• Thereshouldbenounresolvedchargebalanceissuesthatmighteffectthechemistryinvolved(e.g.Thevalencyofametalintheorderedpartofthestructure)
LimitaIons• ThereportedelectroncountinthesolventregionismeaningfulonlywiththesupplyofacompleteandreliablereflecIondataset.• TheSQUEEZEtechniquecannothandleproperlycasesofcoupleddisordereffecIngboththemodelandthesolventregion.• Thesolventregionisassumednottocontainsignificantanomalousscaterers(Friedelsaveraged)
Thankyou!
a.l.spek@uu.nlMoreinfo:www.platonsom.nl(includingthispowerpointpresentaIon)
PleasesendsuggesIonsandexamples(withdata)of(annoying)issuesto: