Chem3D Users Manual - CambridgeSoft

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Administrator • Bond Angles—Displays bond angles in the Measurements Table. The Actual values come from the model and the Optimal values come from Angle Bending Parameters and other external tables. • Dihedral Angles—Displays dihedral angles in the Measurements Table. The Actual values come from the model and the Optimal values come from Angle Bending Parameters and other external tables. • Clear—Clears the entire Measurement table. If you only want to clear part of the table, select the portion you want to clear, and choose Delete from the right-click menu. The Model Position submenu • Center Model on Origin—Resizes and centers the model in the model window after a change to the model is made. • Center Selection on Origin—Resizes and centers the selected portion of the model in the model window. • Align Model With X Axis—When two atoms are selected, moves them to the X- axis. • Align Model With Y-axis—When two atoms are selected, moves them to the Y- axis. • Align Model With Z-axis—When two atoms are selected, moves them to the Z- axis. • Align Model With XY Plane—When three atoms are selected, moves them to the XY-plane. • Align Model With XZ Plane—When three atoms are selected, moves them to the XZ-plane. • Align Model With YZ Plane—When three atoms are selected, moves them to the YZ-plane. The Reflect Model submenu • Through XY Plane—Reflects the model through the XY plane by negating Z coordinates. If the model contains any chiral centers this will change the model into its enantiomer. Pro-R positioned atoms will become Pro-S and Pro-S positioned atoms will become Pro-R. All dihedral angles used to position atoms will also be negated. • Through XZ Plane—Reflects the model through the XZ plane by negating Y coordinates. If the model contains any chiral centers this will change the model into its enantiomer. Pro-R positioned atoms will become Pro-S and Pro-S positioned atoms will become Pro-R. All dihedral angles used to position atoms will also be negated. • Through YZ Plane—Reflects the model through the YZ plane by negating X coordinates. If the model contains any chiral centers this will change the model into its enantiomer. Pro-R positioned atoms will become Pro-S and Pro-S positioned atoms will become Pro-R. All dihedral angles used to position atoms will also be negated. • Invert Through Origin—Reflects the model through the origin, negating all Cartesian coordinates. If the model contains any chiral centers this will change the model into its enantiomer. Pro-R positioned atoms will become Pro-S and Pro-S positioned atoms will become Pro-R. All dihedral angles used to position atoms will also be negated. The Set Z-Matrix submenu • Set Origin Atom(s) file—Sets the selected atom(s) as the origin of the internal coordinates. Up to three atoms may be selected. “Setting Measurements” on page 85 18 •Chem3D Basics CambridgeSoft The Graphical User Interface
• Position by Dihedrals—Positions an atom relative to three previously positioned atoms using a bond distance, a bond angle, and a dihedral angle. For more information on changing the internal coordinates see “Setting Dihedral Angles” on page 86. • Position by Bond Angles—Positions an atom relative to three previously positioned atoms using a bond distance and two bond angles. For more information on changing the internal coordinates see “Setting Bond Angles” on page 86. • Detect Stereochemistry—Scans the model and lists the stereocenters in the Output box. • Invert—Inverts the isomeric form. For example, to invert a model from the cis- form to the trans- form, select one of the stereo centers and use the Invert command. • Deviation from Plane—When you select four or more atoms, outputs the RMS deviation from the plane to the Output window. • Add Centroid—Adds a centroid to a selected model or fragment. At least two atoms must be selected. The centroid and “bonds” to the selected atoms are displayed, and “bond” lengths can be viewed in the tool tips. To delete a centroid, select it and press the Delete or Backspace key. • Rectify—Fills the open valences for an atom, usually with hydrogen atoms. This command is only useful if the default automatic rectification is turned off in the Model Settings dialog box. • Clean Up—Corrects unrealistic bond lengths and bond angles that may occur when building models, especially when you build strained ring systems. • Overlay—The Overlay submenu provides all of the commands to enable you to compare fragments by superimposing one fragment in a model window over a second fragment. Two types of overlay are possible: quick, and minimization. See “Tutorial 6: Overlaying Models” on page 43, and “Comparing Models by Overlay” on page 109 for information on each overlay type. • Dock—The Dock command enables you to position a fragment into a desired orientation and proximity relative to a second fragment. Each fragment remains rigid during the docking computation. The Standard Toolbar The Standard toolbar contains tools for standard Windows functions, including up to 20 steps of Undo and Redo. New File Open File Save File Copy Cut Paste Undo Redo Print About Chem3D ChemOffice 2005/Chem3D Chem3D Basics • 19 The Graphical User Interface
Page 1: ChemOffice.Com ® ChemOffice ® Che
Page 4 and 5: License Information ChemOffice, Che
Page 6 and 7: · Licensed users of ChemOffice Ent
Page 8 and 9: computer, except as provided below.
Page 10 and 11: Q: IS IT OK TO COPY MY COLLEAGUE’
Page 12 and 13: A Guide to CambridgeSoft Manuals An
Page 14 and 15: Administrator Setting Molecular Sur
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Page 18 and 19: Administrator Defining Atom Types.
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Page 26 and 27: Administrator The following table d
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Page 44 and 45: Administrator 2. Click the ChemDraw
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Administrator 2. Adjust the slider
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Administrator Density surface is ca
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Administrator 72 •Displaying Mode
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Administrator The following table d
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Administrator When Correct Atom Typ
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Administrator To use the same text
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Administrator Example 2. Building a
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Administrator copied into blank tab
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Administrator 3. Type the atom type
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Administrator Clean Up Structure or
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Setting Serial Numbers this step, y
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Administrator Refining a Model Afte
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Administrator Selecting Multiple At
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Administrator New in Chem3D version
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Administrator Dragging moves atoms
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Administrator 3. Hold down the Shif
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To position a plane in your model p
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Administrator • Second Positioned
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Administrator For example, consider
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Administrator If you want to displa
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Administrator Example: To examine t
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Administrator Chem3D provides two o
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Administrator change a property. By
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Administrator To add to a group: 1.
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To stop spinning: • On the Movie
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Administrator If you want to … Th
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Administrator EPS The PostScript fi
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If you want the file to … Then cl
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Molecular Design Limited MolFile (.
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Administrator 7. Leave the last lin
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Administrator 128•Printing and Ex
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Administrator • Semiempirical Ext
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Method Type Advantages Disadvantage
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Administrator • A single point ca
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Administrator • Molecular mechani
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Administrator constant), while θ 0
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Administrator The van der Waals int
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Administrator 6. The modified value
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the same wave function and a consta
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Administrator A variety of other ba
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Administrator Molecular wave functi
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Administrator activation barriers.
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3. From the Calculations menu, poin
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minimizing a second model, the mini
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Administrator move to lower the ene
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. Administrator Molecular Dynamics
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Administrator If you want to … Th
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Administrator The Compute Propertie
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Administrator To run a previously c
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Administrator The procedures assume
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Administrator improvements in each
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Administrator • Overall errors in
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Administrator The following table c
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Administrator TRIPLET QUARTET QUINT
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Administrator Chemical symbol ++ ba
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Administrator 4. Click Run. A new m
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Administrator Minimizing Energy Min
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Administrator criteria, to optimize
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Administrator 6. Hold down the S ke
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Administrator Dipole Moment The dip
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Administrator Molecular Surfaces Mo
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The following table contains the ke
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Administrator 3. Click in the model
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Keyword Description 7. On the Prope
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Administrator Hyperfine Coupling Co
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Administrator 198•MOPAC Computati
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Administrator If you want to … re
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Administrator In the Results In tex
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Administrator Repeating a Gaussian
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Property Description Property Descr
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Property Description Error Message
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Administrator Property Electronic E
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Administrator To specify the calcul
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Administrator 3. Click Open. The ap
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Administrator • Server—limits t
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Administrator To perform property c
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The Step 4 of 4 dialog box appears.
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Administrator • From the ChemOffi
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Administrator Accessing the Online
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Administrator To find a structure t
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Administrator 228• Accessing the
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Administrator Performance Below are
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Administrator Defining Substructure
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Administrator If an atom can be ass
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Key Drag Shift+Drag Administrator Q
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Administrator 238• Keyboard Modif
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Administrator Example 3 In Example
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Administrator 14 13 H 2.197 -0.8229
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Administrator Connection tables by
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Administrator FORTRAN Formats The F
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5 6 1.11606 3 109.41 5 109.41 -1 21
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Administrator 41 4 1 0 0 0 0 0 0 0
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Administrator 32 3 12 1 0 0 0 33 3
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Administrator 13 * 3D displacement
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Administrator The field value for C
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Administrator Line 4e: C 1.53597 1
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Administrator CONECT 4 2 9 10 11 CO
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Administrator COMPND ATOM HETATM CO
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Administrator Line 56 -2794 21139 6
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Administrator 7 2 10 1 8 3 6 1 9 3
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Administrator Line 16 6 C -0.559 1.
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Administrator 12. Line 30, “@BOND
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Parameter Table Use Parameter Table
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Administrator 3. Type the informati
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Administrator Geometry The geometry
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Administrator KS The KS, or bond st
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Administrator one attached hydrogen
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Administrator bond length between t
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Administrator R* The R* field is th
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Administrator The V1 torsional cons
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Administrator VDW Interactions The
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Administrator Editing Parameters Yo
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Administrator 6. The pi molecular o
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Administrator Adding Parameters to
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Administrator fragments 84 paramete
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Administrator CC1 see Cartesian coo
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Administrator Copy As Bitmap comman
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Administrator Examining angles, tut
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Administrator density 67 editing 67
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Administrator editing 107 non-bonde
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Administrator repeating jobs 178 RH
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Administrator Rectification, when d
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Administrator all atoms 95 atoms or
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Administrator Translucent surface t
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Desktop Software Enterprise Solutio
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SOLUTIONS Enterprise Solutions APPL
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Desktop to Enterprise Solutions Che
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SOFTWARE E-Notebook Ultra Ultimate
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SOFTWARE ChemDraw Ultra Ultimate Dr
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SOFTWARE Chem3D Ultra Ultimate Mode
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SOFTWARE ChemFinder/Word • Search
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SOFTWARE The Merck Index • Encycl
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SOLUTIONS •Development and deploy
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SOLUTIONS •Adds chemical data typ
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MANAGEMENT •Custom organization o
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MANAGEMENT • Indexes chemical str
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MANAGEMENT • E-Notebook Enterpris
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DISCOVERY • Accessed through your
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DISCOVERY • Integrated with Regis
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DISCOVERY • Reagent lists can be
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DISCOVERY •Effectively manages da
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DISCOVERY • Catalog driven data m
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DATABASES • Fully structure-searc
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DATABASES • Encyclopedic referenc
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DATABASES • Extensive collection
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SERVICES · Business Case Developme
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CS ChemOffice ® Desktop to Enterpr
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Chem3D Users Manual - CambridgeSoft

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