Chem3D Users Manual - CambridgeSoft

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The following table contains the keywords automatically sent to MOPAC and those you can use to affect this property. A model of formaldehyde appears. Administrator Keyword ESR Description Automatically sent to MOPAC to specify RHF spin density calculation. GEO-OK MMOK Example 1 Automatically sent to MOPAC to override checking of the Z-matrix. Automatically sent to MOPAC to specify Molecular Mechanics correction for amide bonds. Use the additional keyword NOMM to turn this keyword off. The Dipole Moment of Formaldehyde To calculate the dipole moment of formaldehyde: 1. From the File menu, choose New Model. 2. Click the Text Building tool. 3. Click in the model window. A text box appears. 4. Type H2CO and press the Enter key. 5. From the MOPAC Interface menu of the Calculations menu, choose Minimize Energy. 6. On the Theory tab, choose AM1. 7. On the Properties tab, select Dipole. 8. Click Run. The results shown in the Messages window indicate the electron distribution is skewed in the direction of the oxygen atom. Dipole (vector Debye) X Y Z Total -2.317 0.000 -0.000 2.317 If you rotate your model, the X,Y, and Z components of the dipole differ. However, the total dipole does not. In this example, the model is oriented so that the significant component of the dipole lies along the X-axis. 190•MOPAC Computations <strong>CambridgeSoft</strong> Computing Properties
Example 2 Comparing Cation Stabilities in a Homologous Series of Molecules To build the model: 1. From the File menu, choose New Model. 2. Click the Text Building tool. 3. Click in the model window. A text box appears. 4. For tri-chloro, type CCl3 and press the Enter key. 5. Repeat step 1 through step 4 for the other cations: type CHCl2 for di-chloro; type CH2Cl for mono-chloro and CH3 for methyl cation. NOTE: The cations in this example are even electron closed shell systems and are assumed to have Singlet ground state. No modifications through additional keywords are necessary. The default RHF computation is used. 6. For each model, click the central carbon, type “+” and press the Enter key. The model changes to a cation and insures that the charge is sent to MOPAC. To perform the computation: 1. From the MOPAC Interface submenu of the Calculations menu, choose Minimize Energy. 2. On the Theory tab, choose AM1. 3. On the Properties tab, select Charges in the Properties list. 4. Select Wang-Ford from the Charges list. 5. Click Run. The results for the model appear in the Message window when the computation is complete. The molecules are now planar, reflecting sp 2 hybridization of the central carbon. The following table shows the results: tri-chloro cation di-chloro cation mono-chloro cation methyl cation C(1) 0.03660 C(1) 0.11255 C(1) 0.32463 C(1) 0.72465 Cl(2) 0.31828 Cl(2) 0.33189 Cl(2) 0.35852 H(2) 0.08722 Cl(3) 0.32260 Cl(3) 0.33171 H(3) 0.15844 H(3) 0.09406 Cl(4) 0.32253 H(4) 0.22384 H(4) 0.15841 H(4) 0.09406 From these simple computations, you can reason that the charge of the cation is not localized to the central carbon, but is rather distributed to different extents by the other atoms attached to the charged carbon. The general trend for this group of cations is that the more chlorine atoms attached to the charged carbon, the more stable the cation (the decreasing order of stability is tri-chloro >di-chloro > mono-chloro > methyl). Example 3 Analyzing Charge Distribution in a Series Of Mono-substituted Phenoxy Ions 1. From the File menu, choose New Model. 2. Click the Text Building tool. ChemOffice 2005/<strong>Chem3D</strong> MOPAC Computations • 191 Computing Properties
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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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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 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 The following table d
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Administrator 3. Type the atom type
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Setting Serial Numbers this step, y
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Administrator New in Chem3D version
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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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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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