Chem3D 8.0 Manual - CambridgeSoft

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Administrator116 • Chapter 8: Printing and Exporting Models CambridgeSoftExporting With the Clipboard
Chapter 9: Computation ConceptsComputationalChemistry OverviewComputational chemistry extends beyond thetraditional boundaries separating chemistry fromphysics, biology, and computer science. It allows theexploration of molecules by using a computer whenan actual laboratory investigation may beinappropriate, impractical, or impossible. As anadjunct to experimental chemistry, its significancecontinues to be enhanced by increases in computerspeed and power.Aspects of computational chemistry include:• Molecular modeling.• Computational methods.• Computer-Aided Molecular Design (CAMD).• Chemical databases.• Organic synthesis design.While a number of different definitions have beenproposed, the definition offered by Lipkowitz andBoyd of computational chemistry as “those aspectsof chemical research that are expedited or renderedpractical by computers” is perhaps the mostinclusive.Molecular modeling, while often taken to includecomputational methods, can be thought of as therendering of a 2D or 3D model of a molecule’sstructure and properties. Computational methods,on the other hand, calculate the structure andproperty data necessary to render the model. Withina modeling program, such as Chem3D,computational methods are referred to ascomputation engines, while geometry engines andgraphics engines render the model.Chem3D supports a number of powerfulcomputational chemistry methods and extensivevisualization options.Computational MethodsOverviewComputational chemistry encompasses a variety ofmathematical methods which fall into two broadcategories:• Molecular mechanics—applies the laws ofclassical physics to molecular nuclei withoutexplicit consideration of electrons.• Quantum mechanics—relies on theSchrödinger equation to describe a moleculewith explicit treatment of electronic structure.Quantum mechanical methods can besubdivided into two classes: ab initio andsemiempirical.The generally accepted method classes are shown inthe following chart.Chem3D 8 Chapter 9: Computation Concepts • 115Computational Methods Overview
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ChemOffice.Com®ChemOffice®Chem3D,
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CS Product RegistrationRegistering
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User’s GuideCS Chem3D 8.0for Wind
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CambridgeSoft Software License1. Gr
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No Waiver. The failure of either pa
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The failure of either party to asse
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ContentsIntroduction . . . . . . .
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Rotating Fragments. . . . . . . . .
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Choosing a Hamiltonian . . . . . .
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Appendix D: MM2 . . . . . . . . . .
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Administrator• Faster graphics-3D
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AdministratorInstallation and Syste
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AdministratorModel WindowThe Model
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Table ElementDescriptionObjectDescr
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To specify the rendering type, atom
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AdministratorYou can also build mod
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AdministratorElementBound-to orderS
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Customizing the UserInterfaceAdmini
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AdministratoroptionUse BackBuffer f
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AdministratorExamine the atoms and
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Administrator2. Release the mouse b
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AdministratorReplacing AtomsTo chan
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Change the model display type:Build
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You will also save the frames you c
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Tutorial 4: SearchingFor Conformati
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Administrator3. Click in the model
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Administrator5. In the Theory tab,
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AdministratorFor phenol, the greate
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Creating a Model UsingTemplatesChem
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The Cartesian Coordinates Options d
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Saving a Model with a Different Nam
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Administrator44 • Chapter 3: Crea
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AdministratorThe following table de
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After you have the backbone, you ca
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AdministratorThe interpretation of
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AdministratorTo use a substructure
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AdministratorThe standard measureme
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AdministratorTo change the bond ord
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Administratorvalues are the standar
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AdministratorTo remove the formal c
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AdministratorRefining a ModelAfter
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AdministratorSelecting Atoms in a G
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AdministratorWhen you choose Show A
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AdministratorTo perform a rotation
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To move three atoms to a plane and
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The heat of formation is composed o
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AdministratorComparing Cation Stabi
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Administratormeta>para>ortho, where
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Administrator3. Click in the model
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Form ofglycine∆H(kcal/mole)Solven
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AdministratorThe following table co
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AdministratorThe Message window dis
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AdministratorDescriptionVibrational
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You can create a structure from the
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AdministratorIf you want to …reco
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AdministratorSave a customized job
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Administrator2. Type the full path
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Administrator3. From the Basis Set
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AdministratorA new model window is
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PropertyDescriptionPropertyDescript
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PropertyDescriptionError MessageCau
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PropertyDescriptionThe GAMESS serve
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The property filters are:Administra
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AdministratorTo perform property ca
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The Select Descriptors dialog box a
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Administrator• Sum• Standard de
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To access Browse ChemStore.com:The
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AdministratorTo access the ChemOffi
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AdministratorDefining Substructures
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AdministratorA4 • CambridgeSoftDe
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AdministratorIf an atom can be assi
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AdministratorExample 3In Example 3,
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AdministratorEditing ParametersYou
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Administrator5. A matrix called the
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AdministratorAdding Parameters toMO
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AdministratorParameter Table UseEle
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AdministratorThe ElementsThe Elemen
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AdministratorTo view the menu of ge
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AdministratorFinally, the 1-19 bond
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AdministratorPi AtomsThe Pi Atoms t
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AdministratorCubic and Quartic Stre
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potential well increases, as does t
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AdministratorThe counterintuitive f
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Administratorcorrespondence between
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AdministratorAlchemy FileThe follow
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Administrator2. The first line of a
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H 102 2.127594 1.865631 1.48999 21
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Administrator6 1 1.40195 2 107.6989
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41 3 1 0 0 0 0 0 0 0 0 0 0 1.222366
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Administrator21 -1.2615 2.1277 0.01
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Administrator24-42 Bond id, fromato
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Administrator51 2 1 1 6 0 0.000 0 0
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Administrator18. Line 49 contains a
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AdministratorFORTRAN FormatsThe des
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22 Chain Identifier No12-16 Serial
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AdministratorLine 18 H 0 0 0Line 19
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Administratorof hydrogens attached
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AdministratorNumberof AtomsNumberof
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AdministratorLine 30 @BONDLine 31 1
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11-29 Atom type, name,coordinates a
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AdministratorA66 • CambridgeSoftW
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AdministratorTroubleshootingThis se
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4. If the problem still occurs, Fax
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AdministratorAtom typesassigning au
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Administratorchem3d.h 17chem3d.tlb
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AdministratorDisplay Stereo View 80
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AdministratorFont 16Font size 16For
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Administratorjdt file format 114, 1
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AdministratorMolecular Surfacescalc
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AdministratorParameters 12bond angl
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AdministratorSelect Fragment comman
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AdministratorTools palette 6, 44Too
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Administratorxx • IndexCambridgeS
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CAMBRIDGESOFTChemOffice Desktop toK
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CS ChemOfficeSoftware SuitesChemOff
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DESKTOPCS E-NotebookElectronic Jour
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DESKTOPCS ChemDrawChemical Structur
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DESKTOPCS Chem3DMolecular Modeling
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DESKTOPCS ChemFinderSearching and I
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DESKTOPCS ChemInfoReference and Che
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ENTERPRISEChemOffice WebServerEnter
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ENTERPRISEOracle CartridgeEnterpris
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KNOWLEDGEE-Notebook EnterpriseDeskt
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KNOWLEDGEDocument ManagerDesktop to
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KNOWLEDGE21CFR11 ComplianceElectron
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RESEARCH&Registration SystemChemica
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RESEARCH&Inventory ManagerChemical
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RESEARCH&CombiChem EnterpriseDeskto
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RESEARCH&BioAssay HTSBiological Ass
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RESEARCH&BioSAR BrowserBiological a
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CHEMICALChemACX DatabaseAvailable C
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CHEMICALThe Merck IndexChemistry’
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CHEMICALChemical DatabasesReference
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CONSULTING &Consulting & ServicesDe
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Administrator
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MENUSCreate a new model window.Open
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WORKING WITH SELECTIONSIf you want
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CS ChemOffice®Desktop to Enterpris
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