Chem3D Users Manual - CambridgeSoft

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Desktop to Enterprise Solutions ChemOffice Ultra includes it all, providing ChemDraw Ultra, Chem3D Ultra, E-Notebook Ultra, ChemFinder, CombiChem, BioAssay and The Merck Index, for a seamlessly integrated suite for chemists.Use ChemDraw/Excel and ChemFinder/ Word for Microsoft Office integration. Predict spectra, use Name=Struct, and visualize 3D molecular surfaces and orbitals with MOPAC. Use the ChemDraw and Chem3D Plugins to publish your work or to query databases on the web. ChemOffice WebServer enterprise solutions and databases help organizations collaborate on shared information with ChemDraw webbased interface and Oracle Cartridge security. Knowledge Management with E-Notebook Enterprise streamlines daily record-keeping with rigorous security and efficient archiving. Document Manager indexes chemical structure content of documents and folders. Research & Discovery efforts are improved with Registration System by organizing new compound information, while Inventory Manager works with chemical databases for complete management of chemical inventories. Applied BioInformatics scientists use BioAssay HTS and BioSAR Browser to set up biological models and visualize information, to generate spreadsheets correlating structure and activity, and to search by structure. Chemical Databases include the ChemACX Database of commercially available chemicals, The Merck Index 13th edition, and other databases. Consulting & Services includes consulting development, technical support, and education training for pharmaceutical, biotechnology, and chemical customers, including government and education, by CambridgeSoft’s experienced staff. ChemOffice WebServer Enterprise Solutions & Databases • Oracle Cartridge & Database Webserver Knowledge Management • E-Notebook Enterprise, Document Mgr, Discovery LIMS & 21CFR11 Compliance Research & Discovery • Registration System, Formulations & Mixtures, Inventory Manager & CombiChem Enterprise Applied BioInformatics • BioAssay HTS & BioSAR Browser Chemical Databases • The Merck Index, ChemACX & ChemSAR Properties ChemOffice Ultra Ultimate Drawing, Modeling & Information • Adds The Merck Index, E-Notebook, CombiChem, MOPAC, BioAssay & ChemACX to Office Pro ChemOffice Pro Premier Drawing, Modeling & Information • Includes ChemDraw Ultra, Chem3D Pro, ChemSAR/Excel, ChemFinder Pro, ChemINDEX & ChemRXN databases Also Available Separately… ChemDraw Ultra Ultimate Drawing, Query & Analysis • Adds ChemDraw/Excel, ChemNMR, Name=Struct, AutoNom & ChemFinder /Word to ChemDraw Pro • ChemNMR, Stereochemistry, Polymers & BioArt ChemDraw Pro Premier Drawing & Database Query • Define complex database queries • ISIS/Draw & Base compatible via copy/paste • Structure CleanUp and Chemical Intelligence Chem3D Ultra Ultimate Modeling, Visualization & Analysis • Adds MOPAC, CLogP, Tinker, ChemProp, ChemSAR & Chem3D Plugin to Chem3D Pro • Advanced modeling & molecular analysis tool E-Notebook Ultra Ultimate Journaling & Information • E-Notebook, ChemDraw Std, Chem3D Std, ChemDraw/Excel & CombiChem/Excel • Includes ChemFinder, ChemFinder/Word, ChemINDEX & ChemRXN databases Some features are Windows only. All specifications subject to change without notice.
DESKTOP CS E-Notebook Electronic Journal J and Information E-Notebook Ultra streamlines daily record keeping tasks of research scientists, maintains live chemical structures and data, and saves time documenting work and retrieving chemical information. E-Notebook combines all of your notebooks into one and sets up as many project notebooks as you need, organized the way you work. Notebook pages include ChemDraw documents, Excel spreadsheets, Word documents and spectral data. E-Notebook automatically performs stoichiometry calculations on ChemDraw reaction pages. Search by structure, keyword, dates and other types of data. Maintain required hardcopy archives by printing out pages. Information cannot be accidentally modified. Spectral controls from Thermo Galactic are available. CombiChem/Excel builds combinatorial libraries with embedded ChemDraw structures using ChemDraw/Excel for Windows. Find reagents with ChemFinder and design experiments. BioAssay Pro, available in ChemOffice Ultra, allows for flexible storage and retrieval of biological data. It is designed for complex lead optimization experiments and supports almost any biological model. Automatic Stoichiometric Calculations Scanned Images in Notebook Pages
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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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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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Page 328 and 329: Desktop Software Enterprise Solutio
Page 330 and 331: SOLUTIONS Enterprise Solutions APPL
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
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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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Chem3D Users Manual - CambridgeSoft

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