Chem3D Users Manual - CambridgeSoft

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SOFTWARE ChemFinder/Word • Search structures in documents & folders ChemDraw/Excel • Add chemical intelligence to spreadsheets Purchase/Excel •Organize chemical purchasing information ChemFinder Pro Premier Searching & Information • Advanced search and structure query features • Stores structures and reactions along with calculated data and associated information • Search by substructure including stereochemistry using ChemDraw • Import/export MDL SD and RD files • Integration with ChemDraw and Chem3D ChemFinder/Word Searching Word, Excel & More • Searches documents for embedded structures • Indexes structures and source locations • Searches specified folders and whole hard drives ChemDraw/Excel Searching & Calculating in Excel • Displays ChemDraw structures in spreadsheet cells • Adds chemical calculations to Excel functions • Useful for graphing and analyzing chemical data Purchase/Excel High Throughput Purchasing • Finds vendor and price information from ChemACX Database or ChemACX.Com • Search for suppliers and purchase online • Maintains lists of compounds CombiChem/Excel Combinatorial Chemistry in Excel • Generate combinatorial libraries •Choose starting materials and reaction schemes •View structures and track plate/well assignments SYSTEMS & LANGUAGES English & Japanese Windows: 95, 98, Me, NT, 2000, XP This software is Windows only. All specifications subject to change without notice. EMAIL info@cambridgesoft.com WWW www.cambridgesoft.com TEL 1 800 315–7300 INT’L 1 617 588–9300 FAX 1 617 588–9390 MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, MA 02140 USA ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft ©2002. All other trademarks are the property of their respective holders. All specifications subject to change without notice.
DESKTOP CS ChemInfo Reference and Chemical Databases The Merck Index is an encyclopedia of chemicals, drugs, and biologicals, with over 10,000 monographs covering names, synonyms, physical properties, preparations, patents, literature references, therapeutic uses and more. ChemACX Pro includes 500,000 chemical products from 300 supplier catalogs, searchable with a single query by structure, substructure, name, synonym, partial name, and other text and numeric criteria. ChemACX-SC is a compilation of searchable catalogs from leading screening compound suppliers. ChemACX.Com is the ChemACX web site with full search capabilities and convenient online ordering from major suppliers. ChemINDEX includes 100,000 chemicals, public NCI compounds, and more. ChemRXN is a collection of 30,000 fully atom-mapped reactions selected and refined from the chemical literature. It includes reactions from InfoChem’s ChemSelect database and ISI’s ChemPrep database. ChemMSDX provides material safety data sheets for 7,000 pure compounds. ChemFinder.Com is the award-winning web site with information and WWW links for over 100,000 chemicals. Search by name or partial name, view structure drawings, or use the ChemDraw Plugin for structure and substructure searches. View live ChemDraw files on Windows and Macintosh clients. ChemRXN database on CD-ROM ChemINDEX database on ChemFinder.Com
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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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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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Page 328 and 329: Desktop Software Enterprise Solutio
Page 330 and 331: SOLUTIONS Enterprise Solutions APPL
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Page 338 and 339: SOFTWARE Chem3D Ultra Ultimate Mode
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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Chem3D Users Manual - CambridgeSoft

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