Chem3D Users Manual - CambridgeSoft

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Administrator The field value for Carbon 6 from the example file is included in parentheses for reference: 1. Line 1 is a standard header line for MSI MolFile format files. 2. Line 2 normally indicates the application which created the file. 3. Line 3 is the header for the File format version number section. 4. Line 4 indicates the file format version number. The format for this field is YY.MMDD. 5. Line 5 is the header for the File update version number section. 6. Line 6 indicates the file update version number. The format for this field is YY.MMDD. 7. Line 7 is the header for the molecule name section. 8. Line 8 contains the field molecule name. This field contains either the file name, or “Undefined Name”. 9. Line 9 is the header for the empirical formula. 10. Line 10 contains the empirical formula field. This field contains either the empirical formula or “Undefined Empirical Formula”. 11. Lines 11–24 each contains information concerning conversions from 3D to 2D. 12. Line 25 is the header for the Global display attributes section. 13. Line 26 contains 5 fields describing the global display attributes: Line thickness (1), font style (0), type face (1), type size (12), font (256). These values are specific to the platform that is generating the file. 14. .Line 27 contains the header for the Atom Lists section. 15. Line 28 contains a listing of all the possible fields for the atom list section. When the file is created using Chem3D Pro the following fields are used: Atom#,Lbl, Type, and x,y,z. 16. Lines 29–47 each contains 28 fields describing information about each of the atoms in the structure: the first field is the atom number (6), the second field is the atom label (C), the third field is the atom type (10), the fourth field and fifth fields contain 2D coordinates, and contain zeros when the file is created using Chem3D Pro, the sixth field is the X coordinate (-0.113) and the fifth field is the Y coordinate (1.005), the sixth field is the Z coordinate (-0.675), the seventh through fifteenth fields are ignored and contain zeros when the file is created by Chem3D Pro, the sixteenth field is, again, the atom label (C), the eighteenth field is, again, the atom number (6), the nineteenth field is the segment field, the twentieth field is the coordination field, the twenty first field is ignored, the twenty-second field is called the saturation field: if the atom is attached to any single, double or delocalized bonds this field is 1 (not saturated) otherwise this field is 0. The twenty-third through the twenty-sixth fields are ignored and contain zeros when the file is created using Chem3D Pro, the twentyseventh field is, again, the atom label (C). NOTE: Atom types in the Molecular Simulations MolFile format are user-definable. For more information, see “Editing File Format Atom Types” on page 241. 17. Line 48 contains the header for the Bond List section. 18. Line 49 contains a listing of all the possible fields for the bond list section. When the file is created by Chem3D Pro the following fields are used: Bond#, Bond_type, atom 1, atom 2 and cis/trans and Qorder. 19. Lines 50–68 each contain 4 fields describing information about each of the bonds in the structure: the first field is the internal bond number (6), the second field is the bond type (1), the third and fourth fields are the atom 256• File Formats CambridgeSoft MSI MolFile
serial numbers for the atoms involved in the bond [atom 1 (2), atom 2 (16)], the fifth field is the cis/trans designator (this is 0 if it does not apply), the sixth through tenth fields are ignored, and contain zeros if the file is created using Chem3D Pro, the eleventh field contains the bond order ([S] meaning single), the twelfth and thirteenth fields are ignored and contain zeros if the file is created using Chem3D Pro. 20. Lines 69–73 are each a section header for 3D conversion use. This section only contains the header name only (as shown) when the file is created using Chem3D Pro. 21. Line 74 is a header for the section User data area. This section contains the header name only (as shown) when the file is created using Chem3D Pro. 22. Line 75 is a header that indicates the End of File. FORTRAN Formats The FORTRAN format for each record of the Molecular Simulations MolFile format is as follows: 29-47 atom list, field value 50-68 bond list, field values MOPAC I,1X,A,3(1X,I),3F9. 3,1X,I,F4.1,7(1X,I), 1X,A,I,8(1X,I), “[“,A, “] “ I,4(1X,I),F9.3,4(2X ,I),1X, “[“,A1, “] “,2(1X,I) The specific format of the MOPAC files used by Chem3D is the MOPAC Data-File format. This format is described on pages 1-5 through 1-7 of the “Description of MOPAC” section and page 3-5 of the “Geometry Specification” section in the MOPAC Manual (fifth edition). For further details about the MOPAC Data-File format, please refer to the above publication. The following is a sample MOPAC output file from Chem3D for cyclohexanol: Line Number Description FORTRAN Format Line 1: Line 2: Cyclohexanol Line 3: Line 4a: C 0 0 0 0 0 0 0 0 0 Line 4b: C 1.54152 1 0 0 0 0 1 0 0 Line 4c: C 1.53523 1 111.7747 1 0 0 2 1 0 Line 4d: C 1.53973 1 109.7114 1 -55.6959 1 1 2 3 Appendices ChemOffice 2005/Appendix File Formats • 257 MSI MolFile
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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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Page 284 and 285: Parameter Table Use Parameter Table
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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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