Chem3D Users Manual - CambridgeSoft

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DATABASES • Encyclopedic reference for over 10,000 chemicals, drugs, and biologicals • Fully searchable by ChemDraw structure, substructure, names, partial names, synonyms and other data fields • Available in desktop, enterprise and online formats Integrated Information Having The Merck Index in ChemOffice format confers another valuable benefit: integration with other information sources. For example, after locating a substance in The Merck Index, it is a simple matter to copy the name, structure or other data elements to search ChemACX Database to find out whether there are commercial suppliers of the substance. The structures could also be used as input to Chem3D to obtain three-dimensional models and to perform electronic structure and physical property calculations. Information can also be brought into any ChemOffice desktop or enterprise solution, including ChemDraw/Excel, ChemFinder/Word, E-Notebook and Registration System. ChemOffice Formats The Merck Index is available in two ChemOffice compatible formats. The desktop edition is a CD-ROM in a ChemFinder database format, for use by an individual researcher. The enterprise edition, designed for workgroups and larger user communities, is served by ChemOffice WebServer to connected users. The Merck Index thus adds to the growing set of reference databases served by ChemOffice WebServer. Just as ChemOffice integrates the desktop edition of The Merck Index with the scientist’s everyday activities, the enterprise edition becomes an integral part of the applications deployed on ChemOffice WebServer. Web Versions The complete contents of The Merck Index are also available online through your favorite web browser. To meet your specific needs, single user subscriptions, corporate extranet subscriptions and intranet webservers are all available. 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.
CHEMICAL Chemical Databases Reference, Chemicals, Reactions, Patents P and MSDS Databases ChemOffice WebServer provides a full range of compound and reaction databases essential for research. Databases are available at ChemFinder.Com, or over corporate intranets. Reference The Merck Index contains encyclopedic references for over 10,000 chemicals, drugs and biologicals. ChemINDEX includes 100,000 chemicals, public NCI compounds and others. World Drug Index (WDI) from Derwent contains over 58,000 compounds with known biological activity. WDI classifies compounds according to type of biological activity, mechanism, synonyms, trade names, references and more. Chemicals ChemACX and ChemACX-SC, Available Chemicals Xchange, is a large and growing source for information on compound availability. It lists compounds from Alfa Aesar and Aldrich to TCI and Zeneca with hundreds in between, including 500,000 products from 300 catalogs. ChemACX-SC is a library of screening compounds. ISI Reactions Derwent Patents
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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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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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Page 328 and 329: Desktop Software Enterprise Solutio
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Page 340 and 341: SOFTWARE ChemFinder/Word • Search
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Page 346 and 347: SOLUTIONS •Adds chemical data typ
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Page 364 and 365: DATABASES • Fully structure-searc
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Page 370: SERVICES · Business Case Developme
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Chem3D Users Manual - CambridgeSoft

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