Chem3D Users Manual - CambridgeSoft

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Administrator Density surface is calculated from scratch for each molecule. The Total Charge Density is generally more accurate than the Space Filling display. For Total Charge Density surfaces, the properties available for mapping are Molecular Orbital, Spin Density, Electrostatic Potential, and Partial Charges. The color scale uses red for the highest magnitude and blue for the lowest magnitude of the property. Neutral is white. You can choose the orbital to map onto the surface with the Molecular Orbital tool on the Surfaces menu. The orbital number appears in parentheses in the HOMO/LUMO submenu. Total Spin Density The total spin density surface describes the difference in densities between spin-up and spin-down electrons in any given region of a molecule’s space. The larger the difference in a given region, the more that region approximates an unpaired electron. The relative predominance of spin-up or spin-down electrons in regions of the total spin density surface can be visualized by color when total spin density is mapped onto another surface (total charge density). Entirely spin-up (positive value) electrons are red, entirely spin-down (negative) blue, and paired electrons (neutral) are white. The total spin density surface is used to examine the unpaired electrons of a molecule. The surface exists only where unpaired electrons are present. Viewing the total spin density surface requires that both Spin Density and Molecular Surfaces are calculated by MOPAC or Gaussian using an Open Shell Wavefunction. negative values and repulsion is indicated by positive values. Experimental MEP values can be obtained by X-ray diffraction or electron diffraction techniques, and provide insight into which regions of a molecule are more susceptible to electrophilic or nucleophilic attack. You can visualize the relative MEP values by color when MEP is mapped onto another surface (total charge density). The most positive MEP value is red, the most negative blue, and neutral is white. Molecular Orbitals Molecular orbital (MO) surfaces visually represent the various stable electron distributions of a molecule. According to frontier orbital theory, the shapes and symmetries of the highest-occupied and lowest-unoccupied molecular orbitals (HOMO and LUMO) are crucial in predicting the reactivity of a species and the stereochemical and regiochemical outcome of a chemical reaction. To set the molecular orbital being displayed: • From the Surfaces menu, point to Molecular Orbital to see the HOMO/LUMO options. Select the orbital. You can specify the isocontour value for any computed MO surface using the Isocontour tool on the Surfaces menu. The default isocontour value for a newly computed surface is the value you last specified for a previously computed surface. If you have not specified an isocontour value, the default value is 0.01. NOTE: The default isocontour value for an MO surface imported from a cube file is 0.01 regardless of any previously set isocontour value. Molecular Electrostatic Potential The molecular electrostatic potential (MEP) represents the attraction or repulsion between a molecule and a proton. Attraction is represented by 70 •Displaying Models CambridgeSoft Molecular Surface Displays
Visualizing Surfaces from Other Sources You can use files from sources other than Chem3D to visualize surfaces. From Windows sources, you can open a Gaussian Formatted Checkpoint (.fchk) or Cube (.cub) file. From sources other than Windows, create a Gaussian Cube file, which you can open in Chem3D. ChemOffice 2005/Chem3D Displaying Models • 71 Visualizing Surfaces from Other Sources
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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 A variety of other ba
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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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Chem3D Users Manual - CambridgeSoft

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