Chem3D Users Manual - CambridgeSoft

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Desktop Software Enterprise Solutions Research & Discovery Applied BioInformatics Knowledge Management Chemical Databases
CAMBRIDGESOFT ChemOffice Desktop to KNOWLEDGE MANAGEMENT RESEARCH & DISCOVERY Desktop E-Notebook Enterprise Discovery LIMS Registration System Inventory Manager Document Manager 21CFR11 Compliance Formulations & Mixtures Enterprise WebServer DESKTOP SOFTWARE ChemOffice E-Notebook ChemDraw <strong>Chem3D</strong> ChemFinder ChemInfo ChemOffice WebServer Oracle Cartridge Success begins at the desktop, where scientists use ChemDraw and ChemOffice to pursue their ideas and communicate with colleagues using the natural language of chemical structures, models, and information. In the lab, scientists capture their results by organizing chemical information, documents, and data with E-Notebook. <strong>Chem3D</strong> modeling and ChemFinder information retrieval integrate smoothly with ChemOffice and Microsoft Office to speed day-to-day research tasks. ENTERPRISE SOLUTIONS Just as ChemOffice supports the daily work of the individual scientist, enterprise solutions and databases, built on ChemOffice WebServer, and Oracle Cartridge help organizations collaborate and share information. KNOWLEDGE MANAGEMENT E-Notebook Enterprise Document Manager Discovery LIMS 21CFR11 Compliance Research organizations thrive when information is easily captured, well organized, and available to others who need it. E-Notebook Enterprise streamlines daily record keeping with rigorous security and efficient archiving, and facilitates searches by text and structure. Document Manager organizes procedures and reports for archiving and chemically-intelligent data mining. Discovery LIMS tracks laboratory requests, and 21CFR11 Compliance implements an organization’s regulatory compliance processes.
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ChemOffice.Com ® ChemOffice ® Che
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License Information ChemOffice, Che
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· Licensed users of ChemOffice Ent
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computer, except as provided below.
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Q: IS IT OK TO COPY MY COLLEAGUE’
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A Guide to CambridgeSoft Manuals An
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Administrator Setting Molecular Sur
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Administrator Methods Available in
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Administrator Defining Atom Types.
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Administrator • CambridgeSoft
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Administrator provides a balance be
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Administrator the activation each t
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Administrator The following table d
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Administrator • Stereo Pairs—A
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Administrator • Bond Angles—Dis
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Administrator The Building Toolbar
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Administrator The Calculation Toolb
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Administrator 1. Right-click in the
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Administrator • In the Model Sett
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Administrator modes and color setti
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Administrator 30 •Chem3D Basics C
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Administrator 2. Click the ChemDraw
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3. Move the pointer over the C-C bo
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Administrator Add serial numbers an
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Administrator 5. Press the Enter ke
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. Administrator b. From the Structu
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Administrator In the Measurements t
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A molecule of Epinephrine appears.
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Administrator Tutorial 7: Docking M
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Administrator To save the iteration
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The allyl radical, CH 2 =CHCH 2·,
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Administrator Determine the raw spi
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Administrator atoms are relatively
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To change the structural display ty
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Administrator When sizing by partia
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Administrator Depth Fading3D enhanc
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• Select Parallel to rotate the r
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Administrator • From the Computat
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Administrator Surface Type Solid De
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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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Page 280 and 281: Administrator Line 16 6 C -0.559 1.
Page 282 and 283: Administrator 12. Line 30, “@BOND
Page 284 and 285: Parameter Table Use Parameter Table
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Page 288 and 289: Administrator Geometry The geometry
Page 290 and 291: Administrator KS The KS, or bond st
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Page 294 and 295: Administrator bond length between t
Page 296 and 297: Administrator R* The R* field is th
Page 298 and 299: Administrator The V1 torsional cons
Page 300 and 301: Administrator VDW Interactions The
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Page 304 and 305: Administrator 6. The pi molecular o
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Page 310 and 311: Administrator CC1 see Cartesian coo
Page 312 and 313: Administrator Copy As Bitmap comman
Page 314 and 315: Administrator Examining angles, tut
Page 316 and 317: Administrator density 67 editing 67
Page 318 and 319: Administrator editing 107 non-bonde
Page 320 and 321: Administrator repeating jobs 178 RH
Page 322 and 323: Administrator Rectification, when d
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Page 330 and 331: SOLUTIONS Enterprise Solutions APPL
Page 332 and 333: Desktop to Enterprise Solutions Che
Page 334 and 335: SOFTWARE E-Notebook Ultra Ultimate
Page 336 and 337: SOFTWARE ChemDraw Ultra Ultimate Dr
Page 338 and 339: SOFTWARE Chem3D Ultra Ultimate Mode
Page 340 and 341: SOFTWARE ChemFinder/Word • Search
Page 342 and 343: SOFTWARE The Merck Index • Encycl
Page 344 and 345: SOLUTIONS •Development and deploy
Page 346 and 347: SOLUTIONS •Adds chemical data typ
Page 348 and 349: MANAGEMENT •Custom organization o
Page 350 and 351: MANAGEMENT • Indexes chemical str
Page 352 and 353: MANAGEMENT • E-Notebook Enterpris
Page 354 and 355: DISCOVERY • Accessed through your
Page 356 and 357: DISCOVERY • Integrated with Regis
Page 358 and 359: DISCOVERY • Reagent lists can be
Page 360 and 361: DISCOVERY •Effectively manages da
Page 362 and 363: DISCOVERY • Catalog driven data m
Page 364 and 365: DATABASES • Fully structure-searc
Page 366 and 367: DATABASES • Encyclopedic referenc
Page 368 and 369: DATABASES • Extensive collection
Page 370: SERVICES · Business Case Developme
Page 375: CS ChemOffice ® Desktop to Enterpr
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