Chem3D Users Manual - CambridgeSoft

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Property Description Error Message Cause Administrator Vapor Pressure (Pa) Water Solubility at 25° C (mg/L) Limitations Property prediction using CS ChemProp Pro has following limitations: • Single molecules with no more than 100 atoms. • Literature values for Partition Coefficients (LogP) and Henry's Law Constant are not available for all molecules. • Some atom arrangements are not parameterized for the fragmentation methods used to calculate the properties. Because of these limitations, the property prediction fails for some molecules. Error Messages The vapor pressure for the structure at 25° C. Prediction of the water solubility of the structure. If ChemProp Pro fails, one of the following error messages appears: Error Message Unparametrized fragment Cause A fragment in the molecule is unrecognized so no parameters exist for the property calculation. Data not in database Bad MDL Molfile format Invalid aggregate Too many molecules The literature values for this property are not in the database. The molecule is too large or complex, causing bad input data to be generated. A fragment in the molecule is unrecognized or there is more than one disjointed molecule or fragment. There is more than one molecule. Too many atoms There are more than 100 atoms. exceeded MDL Molfile size limit The input data generated for this molecule exceeds the maximum size limit. MM2 Server The MM2 server computes property predictions using the methods of molecular mechanics. For more information on MM2, see “Molecular Mechanics Theory in Brief ” on page 135 and ‘MM2 and MM3 Computations” Out of memory failure There is insufficient memory for the calculation. 208•SAR Descriptors <strong>CambridgeSoft</strong> MM2 Server
The MM2 server provides the following property calculations: Property Description Property Bending Energy (kcal/mol) Charge-Charge Energy (kcal/mol) Charge-Dipole Energy (kcal/mol) Dipole Moment (Debye) Dipole-Dipole Energy (kcal/mol) Non-1,4 van der Waals Energy (kcal/mol) Description The sum of the angle-bending terms of the force-field equation. The sum of the electrostatic energy representing the pairwise interaction of charged atoms. The sum of the electrostatic energy terms resulting from interaction of a dipole and charged species. Molecular dipole moment. The sum of the electrostatic energy terms resulting from interaction of two dipoles. The sum of pairwise van der Waals interaction energy terms for atoms separated by more than 3 chemical bonds. Torsion Energy (kcal/mol) Total Energy (kcal/mol) van der Waals Energy (kcal/mol) MOPAC Server The sum of the dihedral bond rotational energy term of the force-field equation. The sum of all terms the the force-field equation. The MOPAC server calculates property predictions based on semi-empirical computational methods. For more information, see “The Semi-empirical Methods” on page 146 and “Running MOPAC Jobs” on page 178 The MOPAC server provides the following property calculations: Property Alpha Coefficients Beta Coefficients The sum of pairwise van der Waals interaction energy terms for atoms separated by exactly 3 chemical bonds. Description First order polarizability coefficients. Second order polarizability coefficients. Stretch-Bend Energy (kcal/mol) The sum of the stretchbend coupling terms of the force-field equation. Dipole (Debye) Molecular dipole moment. ChemOffice 2005/<strong>Chem3D</strong> SAR Descriptors • 209 MOPAC Server
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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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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 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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Administrator density 67 editing 67
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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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