StructureEditorWindow

ToopentheStructureEditorwindow:

clicktheStructureEditorbuttononthemaintoolbar.

orchoosetheTools|StructureEditormenuitem.

oropenastructurebychoosingtheFile|Open|StructuremenuitemandStructureEditorwillstartautomatically.

OnlyoneStructureEditorwindowcanbeopenedatanyonetimeintheprogram.IfyouclicktheStructureEditorbutton,oryouchoosetheTools|StructureEditormenu,andtheStructureEditorisalreadyopened,thiswindowbecomesactive.

TobegindrawingachemicalstructureinStructureEditor,clickoneofthebuttonsontheverticalbar.Everytimeyouclickoneofthesebuttonstheshapeofthecursorwillchangetovisuallyrepresenttheengageddrawingmode.Theverticalbuttons,incontrasttothehorizontalbuttons,arenotrepresentedinthemenu.Ifthefunctionofabuttonisnotapparentfromitsappearance,simplypointthecursoratthisbuttonusingthemouseandahintwillbedisplayed.Werecommendtryingoutallthevariousfeaturesonateststructure.

ReducedSizeofStructureEditorWindow

WhenyoureducethesizeoftheStructureEditorwindowthebuttonarrayonyourdesktopchanges.ThereducedStructureEditorwindowismorecompact,butretainsallthebuttonsonthebuttonbars.Asmallerwindowmayproveadvantageousifyourprogramdesktopisfilledwithothermodules.

RestoringDefaults

IntheStructureEditor'sdefaultstateallbuttonsareswitchedoffandnoatomorbondisselected.TheplainarrowcursorindicatesthattheStructureEditorisindefaultstate.Torestorethedefaultstateoftheeditor,chooseanyofthesemethods:

ClicktheDefaultmodebuttonintheupperleftcornerintheStructureEditorwindow.

Presstherightmousebottom.

Switchofftheactivatedbuttonanddeselectallatoms.

OpeningandSavingStructures

Toopenorsaveastructure:

ClickontheOpenStructureorSaveStructurebuttonintheStructureEditorwindow.

ChoosetheFile|Open|StructureortheFile|Save|Structuremenuitem.

Ifyouareopeningafilewhichcontainsmorethenonestructure(*.sdffile),onlythefirststructureinthefilewillbeloadedintoStructureeditor.

MassFrontierisa32-bitapplication,soyoucanuselongnamestosavestructures.Youcanevensavestructuresbytheiractualnames(e.g.1-Amino-2-hydroxyindane.mol).

StructureDataFormats

StructureEditorsupportstwokindsofstructureformats:MDLMOL-files(SDF-files),withthe*.mol(*.sdf)extension,andHighChemMCSformat(MaximalCompressedStructure),withthe*.mcsextension.TheseformatsarealsosupportedintheDatabaseManagermodule.

Templates

arestoredinMCS-format,usingtheextension*.tml.

OneofMassFrontier'sparticularlyusefulfeaturesistheabilitytorestrictasearchbyasetofstructuralconstraints,thesocalled

"Good-Bad"

list.Forexample,youcaninstructtheprogramtoconductalibrarysearchcomparinganunknownspectrumonlywiththespectraofketons.Thisfeatureprovidesanendlessrangeofpossibilitiestotargetyoursearchresultswith.The“Good-Bad”structuresarestoredinthedirectory..\Constraints,andthestructuresaresavedinMSC-format(*.mcs).TheprogramautomaticallyretrievesallMCS-structuresfrom..\Constraintsdirectoryandputsthemina“Good-Bad”listboxintheConstraintsdialogbox.

StructureLayout

MassFrontierisalayoutpowerhouse.Forstructures,aswellasforotherobjects,youcanchangealmostanythingthatitispossibletochange.Everylayoutsettingchangealsoaffectsprintingand

copying

intoClipboard,exceptbackgroundcolor,whichaffectsonlyscreendisplayintheMassFrontierprogram.Thevariouslayoutitemsallowyoutotailorthegraphicstoyourindividualreportorpublicationneeds.

ToopenStructureLayoutdialogwindow,

ClickontheStructureLayoutbuttonintheStructureEditorwindow.

ChoosetheOptions|StructureLayoutmenuitem.

Bydefaultthesymbolsforhydrogenatomsattachedtocarbonatomsarenotdisplayed(examplea).IfyouwishtodisplaythemselectShowCarbonSymbols(exampleb)intheStructureLayoutdialogbox.

HydrogenatomsareonlydisplayedforcarbonsiftheShowCarbonSymbolscheckboxisclicked.Otherwisecorrespondinghydrogensaredisplayedforheteroatomsonly.

Note:

Ifyoudrawnonisotopicexplicithydrogenatoms(examplec)theseareremovedintheFragments&Mechanismswindow,astheycanmakethemechanismnetworkunclear,especiallyforcomplexhydrogenrearrangementsteps.Asubstructuresearchignoresthenumberandpositionsofhydrogenatoms.

ThestructurelayoutsettingsapplytoallstructuresinMassFrontiersimultaneously.Thismeansthatifyouchangeastructurelayoutitem,allstructuresinthe

StructureEditor

,

DatabaseManager

,

Fragments&Mechanisms

,

FragmentationLibrary

,and

FragmentsComparator

modulesareaffected.

Note:

Ifyoudonothaveacolorprinterandareprintinginblackandwhite,andyouhavesetbrightcolorsforbondsoratoms,thelinesandfontsmayappearindistinct.Toavoidthisproblem,specifydarkercolorsforallstructuralitems,includingspectra,chromatograms,andmechanisms.

StructureTextNote

StructureEditoroffersthepossibilityoflabelingastructureordisplayingatextnoteonthescreenorontheprintout.

Toenteratextnote:

ClickontheTextbuttonintheStructureEditorwindow.

Clickanywhereinthedrawingareatoplacethetext.

Typethedesiredtext.

ConfirmthetextbyclickingoutsidethetextareaorpressanybuttoninStructureEditor..

Itispossibletocreateupto127separatetextnotes.Ifyouwanttochangethefont,color,size,orbackgroundofthetextnotesyoucandothisinthe

StructureLayout

dialogwindowintheTexttab.

Note:

Textnotesarenotassociatedwithstructures.Asaresult

Open

,

Save

,

Copy

,and

Paste

actionsapplytostructure(s)only.Whentheseactionsareappliedthetextnotesareignoredevenifastructureisselectedtogetherwithatext.Additionallystructurehandlingroutinessuchas

resizing

,

rotating

,or

mirroring

canbeperformedonlyonstructures.

Templates

WhenyouclicktheTemplatesbuttonintheStructureEditorwindow,theTemplatedialogwindowappears.MassFrontiercomeswithmorethen200predefinedtemplates.ToinsertatemplatestructureintoStructureEditor:

Selectagroupoftemplatesinthedirectorylistbox.Youcandothisusingthearrowkeysonthekeyboardorclickingtheappropriatenameofthegroup.

Clickanyatomorbond,dependingonwhetheryouwanttoattachthetemplatetoanatomorabondofastructureinStructureEditor.

TheTemplatedialogwindowwillthendisappearandyoucanplaceorattachthechosentemplate.

Switchoffthetemplatebuttonorrestorethe

defaultstate

oftheEditor.

MassFrontiermakesiteasyforyoutocreateyourowngroupoftemplatesoraddastructuretoanexistinggroup.Thetemplatesareorganizedbydirectory.Thetemplaterootdirectoryis..\Templates.Everygroupoftemplatesisstoredinaseparatesubdirectoryofthetemplaterootdirectory.Subdirectoriesarenamedaftercompoundgroups(e.g.Steroids).Thefileswithineachsubdirectoryarenamedafteractualstructuresusingtheextension

*.tml

(e.g.Cholesterol.tml).WhenyousaveastructurefortemplatepurposesselectTemplate(*.tml)formatintheSaveasTypescrollboxintheSaveStructuredialogbox.

Tobuildyourowntemplates,followthesesteps:

Drawatemplatestructure.

ClickontheSaveStructurebuttonintheStructureEditorwindoworchoosetheFile|Save|Structuremenuitem.

SelectTemplate(*.tml)formatintheFilesoftype:comboboxintheSaveStructuredialogwindow.

Createorselectasubdirectoryinthedirectory..\HighChem\MassFrontier4.0\Templatesforyournewtemplate.

TypenameofyournewtemplatestructureandclickOK.

SelectingAtomsandBonds

AnymodificationthatyoumaketoastructureappliesonlytotheselectedatomsorbondsInaddition,whena

(Sub)Structure

searchisinitiated,theprogramautomaticallyusestheselected(sub)structureinStructure.Beforeyouselectoneormoreatomsyoushouldrestorethe

defaultstate

oftheeditor.Toselectagroupofatomsthatarenexttoeachother:

Holddownthemousebuttonanddragarectanglearoundtheatomsyouwanttoselect.

TheusualWindowsconventionforselectingmultipleitemsapplies.Toselectatomsatdifferentlocations,youshouldusethekeyboardSHIFTkey.Youcanselectagroupofatomsthatarenotadjacentinoneoftwoways:

Clicktheatomsyouwanttoselect,whileholdingdowntheSHIFTkey.

Orholddownthemousebuttonanddragarectanglearoundtheatomsyouwanttoselect,whileholdingdowntheSHIFTkey.

Ifyouwanttoselectalloftheatomsandbondsinthestructure:

ClicktheSelectAllbuttonintheStructureEditorwindoworchoosetheStructure|SelectAllmenuitem.

OrdoubleclickanywhereinthedrawareawithinStructureEditor,exceptonatomsandbonds.

StructureEditorofferstwoselectionmodes:RectangleSelectionandLassoSelection.Tochoosetheselectionmodethatfitsyourneeds:

ClickwiththerightmousebuttonontheDefaultModebuttonandchoosetheappropriateselectionmodefromthepopupmenu.

OrclickwiththerightmousebuttonanywhereinthedrawareawithinStructureEditor,andclicktheRectangleorLassoSelectionmenuitemonthepop-upmenuthatwillappearinthedrawarea.

AtomProperties

Tochangethechargestateorisotopeofanatom,ortochangetheelemententirely,usetheAtomPropertiesdialogbox.

ToopentheAtomPropertieswindow,useoneofthefollowingmethods:

SelecttheAtomPropertiesbuttonintheStructureEditorwindowandthenclicktheatomyouwanttochange.

Or

restoredefaults

,andthendouble-clickontheatomyouwanttochange.

IntheAtomPropertiesdialogwindow,youcanmakethechangesbyclickingtheappropriateelementbutton,chargeandradicalcheckbox,ornucleonnumbereditbox.

Note:

AllchangescarriedoutintheAtomPropertiesdialogwindowwillonlyaffectasingleatom.

Ifyouwishtochangeanelementthathasasinglecharactersymbol,i.e.C,H,N,O,B,F,K,P,S,I,V,W,Y,UandR;afastermethodisavailable:

Selectalltheatomsthatyouwanttochangeandpresstheappropriatekeyonthekeyboard.Alltheselectedatomswillbetransformedintotheelementyouhavechosen.

Chlorine(Cl)orbromine(Br)atomscanbesetinasimilarmanner:

SelectalltheatomsthatyouwanttochangeandpresseithertheC(forchlorine)keyorB(forbromine)keyonthekeyboard,whileholdingdowntheSHIFTkey.

Itispossibletousea

substituent

insteadofaspecificelement.Thesymbol”R”representsasubstituent.Asubstituentcanbewithorwithoutindex.

Substructuresearch

and

fragmentsgeneration

algorithmsconsidersubstituentswithidenticalindexesasequalandsubstituentswithdifferentindexesasnotequal.Whensearchingstructureswithsubstituents,pleasenotethe

searchrules

thatapply.

BondProperties

BondPropertiesincludebondmultiplicity,bondstyleandbondcolor.

Tochangethemultiplicityofabond,

Clickthe,or,orbuttonintheStructureEditorwindowandthenclickthebondyouwanttochange.

Tochangethecolororopticalorientationofabond,usetheBondPropertiesdialogwindow.

ToopentheBondPropertieswindow:

ClicktheBondPropertiesbuttoninStructureEditorandthenclickthebondyouwanttochange.TheBondPropertiesdialogwindowwillthenappear.

Or

restoredefaults

,andthendouble-clickonthebondyouwanttochange.TheBondPropertiesdialogwindowwillthenappear.

MassFrontierautomaticallyrecognizesaromaticbondsinanappropriatesix-memberedringorinpolyaromaticstructures.However,ifunusualsemiaromaticoraromaticresonancestructuresarerequired,thearomaticbondcanbeforcedtoselectedbond(s)bycheckingtheForceAromaticitycheckbox.

CopyingStructure

MassFrontiersupportsextensiveuseoftheWindowsClipboardfortheexchangeofstructuralinformationbetweenmodules.Inaddition,copyandpastefunctionsmaybeusedinsideStructureeditor.Todrawlargerstructuresefficiently,werecommendedtakingadvantageofthecopyandpastefunctions.

TocopyastructureorpartofastructureintotheClipboard:

Selectthestructureorpartofstructure

youwanttocopy.

ClicktheCopybuttonintheStructureEditororchooseCopyfromtheEditmenu.

Note:

Onlythe

selectedatomsandtheirassociatedbonds

willbecopied!

Inadditiontostructureexchangebetweenmodules,MassFrontierallowsstructureexporttootherprogramsthatdealwithstructuralinformation.Whenyoucopyastructure,MassFrontierautomaticallycopiestwodifferentformatsintoclipboard:structuralinformationin

MOLformat

andgraphicsinWindowsMetafileFormat(wmf).IfyoupasteastructureintothestructureeditingsoftwaretheMOLformatwillbeused.Ifyoupastethestructureintoanytexteditor,spreadsheetoranyotherprogramthatworkswithgraphics,thegraphicalinformationwillbeused.Alltheseactionsoccurautomaticallysotheuserneednotworrywhichformatisused.

StructureExchangeviaCopy&Pastecommands.

PastingStructure

Ifyouhavecopiedastructureorfragmentanywhereintheprogramorinathirdpartystructuredrawingtool,youcanpasteittoStructureEditor.Ifnecessary,thestructurecanbechangedorcorrectedandthenreturnedtowhereitoriginated.Thisisespeciallyusefulforstructureelucidation.Forexample,youcancopyastructurefromthe

DatabaseManager

window,pasteittoStructureEditor,makeappropriatechanges,andthenmoveitbacktoDatabaseManager.Ifthespectrumandthestructuralproposalarenotconsistent,theprocesscanberepeated.

TopasteastructuretoStructureEditor:

ClickthePastebuttonintheStructureEditor.

OrchoosethePasteitemfromtheEditmenu.

IfyouhavecopiedastructureorfragmentinaprogramotherthanMassFrontier,youcanonlypastethisstructureiftheexternalstructuredrawingsoftwaresupports

MOLformat

andthisformatisactivated.ThemajorityofstructuredrawingtoolssupportMOLformatandusuallyhavethisformatactivatedbydefault.IfyoupasteastructurefromanexternalsourceitmaysometimesappearlargerinMassFrontierthanintheoriginalsoftware.Ifthisshouldhappen,youcansimplymakethestructuresmallerusingthe

Resize

tool.

StructureExchangeviaCopy&Pastecommands.

MovingStructure

TomoveastructureintheStructureEditor:

Selecttheatomsorbonds

youwishtomove.

Pointthemousecursoratanyselectedatomorbond.

Holddownthemousebuttonanddragtheselectedstructuretothenewlocation.

Releasethemousebuttontodroptheselectedstructureatthenewlocation.

ResizingStructure

ToresizeastructureintheStructureEditor:

Selectthestructure/orpartofstructure

youwishtoresize.

ClicktheResizebutton,orselecttheStructure|Resizemenuitem.

Dragoneofthesmallrectanglesonthestructureedgeuntilthenewsizeisachieved.

Releasethemousebutton.

Note:

Ifyoudragoneofthediagonalrectanglestheaspectratiowillbekeptconstantduringstructureresizing.

RotatingStructure

TheRotateStructureoptionallowsyoutotwistastructureinanydirection.Thecenterofrotation,indicatedbyasmallcirclewithacrossinthemiddle,canbemovedtoanylocation.

TorotateastructureintheStructureEditor:

Selectthestructure/orpartofstructure

youwanttorotate.

ClicktheRotatebutton,orselecttheStructure|Rotateitem.

Movethecenterofrotationtothedesiredpositionbydraggingthecirclewithacross.

Draganyofthesmallrectanglesonthestructureedgetoachievethenewangularposition.

CleaningStructure

TheCleanfunctionallowsyoutoachieveaprofessionallooktoyourstructures.Incontrasttoothercommercialstructuredrawingprograms,withMassFrontieryoucanevencleanupanindividualpartofastructure.Forexample,youcanrestrictcleaningtocertain