Materials Studio: Modules Tutorials

1 MODULESTUTORIALSMATERIALSSTUDIO2017 CopyrightNotice 2016 DassaultSyst ,theCompassiconandthe3 DSlogo,CATIA,SOLIDWORKS,ENOVIA,DELMIA,SI MULIA,GEOVIA,EXALEAD,3 DVIA,BIOVIAandNETVIBES arecommercialtrademarksorregisteredtrade marksofDassaultSyst (figuresand/ordata)obtainedusingBIOVIA software, :"Computationalresultsobtainedusingsoftw areprogramsfromDassaultSyst ,andgraphicaldisplaysgeneratedwithBIOVIA |Page1 AdsorptionLocatortutorialsThefollowingtu torialsillustratehowtoutilizetheAdsorpti onLocator' (111)surfacewithAdsorptionLocatorModelin ginhibitoradsorptionontoaPigmentRedcryst alfaceDeterminingthelocationofSO2ontheNi (111) :MaterialsVisualizer,AdsorptionLocator,F orciteTime:Prerequisites: SketchingabenzamidemoleculeVisualizerTut orialBackgroundThistutorialisinspiredbya paperon"Densityfunctionaltheoryinvestiga tionofthestructureofSO2andSO3onCu(111)an dNi(111)"byHarrisonetal.(2006). :togenerateadsorbedconfigurationsautomat ically, , (111),andcovers:GettingstartedTopreparet hestructuresTosetuptheAdsorptionLocatorc alculationToanalyzetheresultsSummaryNote :Inordertoensurethatyoucanfollowthistuto rialexactlyasintended, , |MaterialsStudio (111) | , ,buildanSO2moleculedefiningbothS-Obondsa sdoublebonds, | |Forcite| , (111) | |Surfaces| (hkl) , |Symmetry| , ,adistanceof15 |Page3 SelectBuild|Crystals| | ,changetheDisplaystyletoBallandstick, , (111).

2 , , , , , |MaterialsStudio ModulesTutorialsNi(111)afterdefiningtheT argetAtomssetThefixedenergywindowisusedt oselectwhichconfigurationsarereported,so allconfigurationswhichdifferfromthelowes tconfigurationbylessthan100 , (111) , (111) , (111). | :Toimprovetheviewoftheenergyfieldsoverth eNisurface,selectallofthenon-surfaceNiat omsand,ontheAtomtaboftheDisplayStyledial og, ,itisnecessarytorunlonger, ,thebridgesitewasfoundtobethelowestonein energy, "Densityfunctionaltheoryinvestigationoft hestructureofSO2andSO3onCu(111)andNi(111 )" , , ,SurfaceScience,600,1827,(2006)Page6|Mat erialsStudio :MaterialsVisualizer,AdsorptionLocator,F orcite,COMPASSTime:Prerequisites: ,including:Dissolutionrateofchemicalsand biologicalavailabilityofdrugsHandling,pa ckaging,andstorageofcrystallineproductsS lurryhandling,caking,andfiltrationduring processingMilling,grinding,fragmentation ,anddustingDensityandtextureoptimization WaxandscaleformationinpetrochemicalsTher elationshipbetweenthecrystalmorphologyan dtheinternalarrangementofatomsinthecryst alisthereforeofgreatinteresttochemists,c hemicalengineers, ,thedevelopmentoftailor-madeadditives, (adiphenylderivativeof1,4-diketopyrrolo( 3,4-c)pyrrole,DPP)isahighqualityheterocy clicpigment,offeringgoodheatstability,hi ghcoloringstrengthandhidingpower, ,youwillstudythedistancesbetweenfunction algroupsonsurfaces,theresultssuggestthat anaminoacidderivativethatcouldactasagrow thinhibitor, :GettingstartedToprepareacrystalsurfaceT ocreateanadditiveTostudyinteractionsbetw eenthesurfaceandtheadditiveAdsorptionLoc atortutorials |Page7 Note.

3 Inordertoensurethatyoucanfollowthistutor ialexactlyasintended, , , , ,youwillbuildaslab(asurfacewitharegionof vacuum)fromthe(010) |Symmetry| |Crystals| ,changetheVacuumthicknessto50 , , , ,thethicknessofthe(010)surfaceisabout20 ,soavacuumregionthicknessof50 |SaveProjectfromthemenubar,followedbyWin dow| ,2-phenylglycine, |MaterialsStudio , (shownbelow) , |Forcite| , , , | (010)surfaceandoptimizedthestructureofth einhibitor, , |Page9 Youwillrunanadsorptioncalculationtoexplo rethelikelybindingsiteandtheorientationo ftheinhibitormoleculeonthesurface, |AdsorptionLocator| , , :TheEwaldsummationmethodismoreaccuratefo rnon-bondenergycalculations, , + |MaterialsStudio , , , , | :theenergyofadsorbingthesorbateontothesu rfaceinitsinputconformation,listedincolu mnDandasmalldeformationenergyduetorelaxa tionofthesorbateinthepresenceofthesurfac e, , , , (010)facehaspreviouslybeencalculatedasar ound-27 (010)face, ,2-phenylglycineisagoodcandidatetoinhibi tthegrowthofthefastgrowing(010)faceofPig mentRedcrystals, |SaveProjectfromthemenubar,followedbyWin dow| ,P.

4 ;Perdok, ,8,521(1955).Bennema, ,166,17(1996).Page12|MaterialsStudio ModulesTutorialsAmorphousCelltutorialsTh efollowingtutorialillustrateshowtoutiliz eAmorphousCell' :Demonstrateshowtopackmoleculesintoexist ingstructuresusingAmorphousCellModules:M aterialsVisualizer,AmorphousCellTime:Pre requisites: Sketchingorganometallicstructures,Usingt hepolymerbuilder, , , :GettingstartedTocreatethenanotubeTosoak thenanotubewithwaterTosetupthestructures andisosurfacesTopackintoisosurfaceenclos edvolumesNote:Inordertoensurethatyoucanf ollowthistutorialexactlyasintended, , |Page13 SelectBuild|BuildNanostructure| |Symmetry| , , | , , |AmorphousCell| |MaterialsStudio ,inthiscase, , , ,inthiscase, ,youcancontrolhowtorsionsaredefined,theb uildingsteps, , , , , , , , , , | ,inthePropertiesExplorer, g cm-3, , ,youwillfindthatthecalculationterminates withtheerror:"Thedensityintheisosurfacee nclosedvolumeisgreaterthantherequestedde nsity.

5 "ToenablethepackingintoaConnollysurface, , :IfyouareusingMaterialsScript, , , ,inthePropertiesExplorer, g |SaveProjectfollowedbyWindow| , |MaterialsStudio , , ,unchecktheConnollySurface,Segregate1, |Page17 Nanotubewithsegregatedisosurfacescolored greenandblueNote:Asthesegregatedisosurfa cesshowvolumesoffreespace, (theorderisnotimportant).However, > , , , |MaterialsStudio ModulesTutorialsMakeSWNT_ ,uncheckSegregate2->Isosurface1andcheckS egregate1-> , :Ifyouaredoingamultisteppackingasinthise xerciseandyougeneratemultipleframesforth efirstpack, , , |Page19 BlendstutorialsThefollowingtutorialillus trateshowtoutilizeBlends' :MaterialsVisualizer,Blends,Forcite(opti onal)Time:Prerequisites: ,solvents, ,thegoalistoproduceablendedproductwithop timizedphysicalorchemicalproperties, , ,bywhichpoint, ,moreimportantly, , (oxyethylene),polypropylene,andpoly(acry licacid).YouwillthensetupaBlendscalculat iontoexaminethecompatibilityofpoly(oxyet hylene)withbothpolypropyleneandpoly(acry licacid).

6 , :GettingstartedTopreparetheinputstructur esTosetupandruntheBlendscalculationToana lyzetheresultsNote:Inordertoensurethatyo ucanfollowthistutorialexactlyasintended, |MaterialsStudio ModulesTutorialsOpentheNewProjectdialoga ndenterPolyoxyethyleneastheprojectname, ,youaregoingtoscreenpoly(oxyethylene)aga instpolypropyleneandpoly(acrylicacid).Se lectFile| , ,youcanscreenforpolymer-polymer,polymer- solvent, , , |Forcite| , , ,oxyethyleneForciteGeomOpt, , | |SaveProjectfromthemenubarandthenWindow| , , , ,choosingthetask, , , |MaterialsStudio , +Screen,Base, ,thatis,poly(oxyethylene)-poly(oxyethyle ne),poly(oxyethylene)-polypropylene,poly (oxyethylene)-poly(acrylicacid),polyprop ylene-polypropylene,polypropylene-poly(a crylicacid),andpoly(acrylicacid)-poly(ac rylicacid),youwouldneedtoassignallthreei nputstructuresaBase+ + , ,interactionenergy, , ,theenergybinwidth, , , , :Ifyouwishtodefinemorethantwoatomsasnon- contact, ,BlendswillreturnthreeBlendstutorials |Page23trajectorydocumentscontainingthec onfigurationsofthebase-base,base-screen, , , , , , , ,thisfolderwillcontainthefollowingdocume nts: ,Blendsreturnsthreetrajectorydocumentsco ntainingtheconfigurationsofthebase-base, base-screen, , ,containsasummaryofthescreeningresults.

7 DuetothenatureofBlendscalculations, , |MaterialsStudio ,base-screen, ,minimum, (Ebb),base-screen(Ebs),andscreen-screen( Ess)combinationshaveverysimilardistribut ions, ,shownbelow,indicatethatpoly(oxyethylene )shouldbemisciblewithpoly(acrylicacid), |Page25A (chi)valueclosetozeroindicatesmiscibilit y, andEmixvaluesincrease, (oxyethylene)willbemisciblewithpoly(acry licacid), , , |Blends| ,Chiparameter, , ,isdisplayedshowingthetemperaturedepende nceof forpoly(oxyethylene)mixedwithpoly(acryli cacid).Youcanalsoperformanalysisonmoreth anonestudytablerowatatime, , , ,thechartshowsthetemperaturedependenceof , ,theseshowthatpoly(oxyethylene)willbemis ciblewithpoly(acrylicacid),butnotwithpol ypropylene, , |Toolbars| , ,alongwithrelatedtimeandenergydata, |MaterialsStudio ModulesTutorialsoftheenergyvaluesarealso zeroasbonds,angles,andsoon, , , , , , , ,therearetwomaininteractionsitesandtheya renotasspreadoutaroundthemoleculeastheyw ereforthepoly(oxyethylene)-poly(acrylica cid) |Page27 CASTEP tutorialsThefollowingtutorialsillustrate howtoutilizeCASTEP' (110)SurfaceCalculatingelasticconstantsf orBNPredictingthethermodynamicproperties ofgermaniumCalculatingphononspectraforfe rromagneticFeAssigningthe17 ONMR spectrumofL-alanineChargedensitydifferen ceofCOonPd(110)SimulatingtheSTMprofileof COonPd(110) :MaterialsVisualizer,CASTEPTime:Prerequi sites.

8 UsingthecrystalbuilderVisualizerTutorial BackgroundRecentdevelopmentsindensityfun ctionaltheory(DFT) , , :GettingstartedTobuildanAlAscrystalstruc tureTosetupandruntheCASTEP calculationToanalyzetheresultsTocomparet hestructurewithexperimentaldataVisualizi ngthechargedensityDensityofstatesandband structurePage28|MaterialsStudio , :Inordertoensurethatyoucanfollowthistuto rialexactlyasintended, , ,right-clickontherootandselectNew| ,youneedtoknowthespacegroup,latticeparam eters, ,thespacegroupisF-43m, ,AlandAswithfractionalcoordinatesof(0,0, 0)and( , , ), . |Crystals| ,SpaceGrouptabCASTEP Tutorials |Page29 ClickintheEntergroupboxandtype216, , | ,AtomstabUsingthisdialog, , , , ,b, |Crystals| |MaterialsStudio , , ,containing2atomsperunitcell,canbeused,a sopposedtotheconventionalcell, ,bonddistances,andtotalenergyperatomwill allbethesamenomatterhowtheunitcellisdefi ned, |Symmetry| |CASTEP| |Page31 CASTEPC alculationdialog, ,inthiscase, , , |MaterialsStudio , , , , ,showingupdatesofthemodelduringoptimizat ion,astatusdocumenttorelayinformationabo utthejobsetupparametersandruninformation ,andchartsofthetotalenergy,andconvergenc einenergy,forces,stress, , ,youshouldhaveseveraldocuments, , |Page33 IntheAlAsstructure,theforcesarezerobysym metry, ,toensurethatthecalculationhascompletedp roperly, | , , |Symmetry| , ,givinganerrorofabout1%.

9 Thisiswithinthe1-2% , , |SaveProjectonthemenubar,thenWindow| |CASTEP| , , |MaterialsStudio , |Symmetry| |Page35 DisplayStyledialog, , , , , , | |MaterialsStudio ,DOS, , , , ,containslimitedbandstructureandDOSinfor mation, , ,youcanchoosetodisplayboththebandstructu reanddensityofstatesinformationonthesame chartdocumentandcontroltheDOS DOS Analysisdialog, | :Youcanexportanychartdocumentasacomma-se paratedvariablefilewhichcanthenbereadina nyspreadsheetpackage,forexample, , |MaterialsStudio ModulesTutorialsAdsorptionofCOontoaPd(11 0) :MaterialsVisualizer,CASTEPTime:Prerequi sites: UsingthecrystalbuilderVisualizerTutorial BackgroundInthistutorialyouwillexamineth eadsorptionofCOonPd(110). ,DFTsimulationscancontributetothisunders tandingbyaddressingthefollowingquestions :Wheredoesthemoleculewanttoadsorb?Howman ymoleculeswillsticktothesurface?Whatisth eadsorptionenergy?Whatdoesthestructurelo oklike?Whatarethemechanismsofadsorption?

10 Youwillfocusononeadsorptionsite,theshort bridgesite, (1 1)and(2 1) (110) (110) , |Page39 IntroductionInthistutorial, ,youwillbeabletocalculatethechemisorptio nenergyforCOonPd(110).Thistutorialcovers :GettingstartedTooptimizebulkPdTobuildan doptimizeCOTobuildthePd(110)surfaceTorel axthePd(110)surfaceToaddCOtothe1 1Pd(110)surfaceandoptimizethestructureTo setupandoptimizethe2 1Pd(110)surfaceToanalyzetheenergiesToana lyzethedensityofstates(DOS)Note:Inordert oensurethatyoucanfollowthistutorialexact lyasintended, , , |Folder, ,Pd(110),COmolecule,(1x1)COonPd(110)and( 2x1)COonPd(110). , , |CASTEP| |MaterialsStudio ModulesTutorialsCASTEPC alculationdialog, , ,youmustconverttheprimitivecellresultbac ktoaconventionalcellrepresentationinorde rtoproceedwithbuildingthePd(110) , |Symmetry| |Page41 SelectFile|SaveProject,thenWindow| , , . , ,right-clickontheCOmoleculefolderandsele ctNew| |Crystals| ,b, | . , , |MaterialsStudio , (110) (110) |SaveProject,thenWindow| |Surfaces| (hkl) ,CASTEP requiresa3 Dperiodicsystemasinput, |Crystals| , , , :CASTEP Tutorials |Page43 ThePdatomwiththelargestz-coordinatewillb ecalled"theuppermostPdlayer".