Chem3D Users Manual - CambridgeSoft

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Administrator If you want to … record each iteration as a frame in a movie for later replay view the value of each measurement in the Measurement table Then select … Record Every Iteration Copy Measurements to Output The Theory Tab Use the Theory tab to specify the combination of basis set and particular electronic structure theory referred to in Gaussian documentation as the model chemistry. By default, this tab is optimized for setting up ab initio computations. calculate the second derivative matrix determined from atomic radii and a simple valence force field. This is the Gaussian default initial guess. Do Not Calculate Force Constants calculate the initial force constant at the current level of theory. Corresponds to the Gaussian keyword Opt = CalcFC Calculate Initial Force Constants To set the Theory specifications: 1. Select the appropriate Method. calculate a new force constant at every point in the minimization. Corresponds to the Gaussian keyword Opt=CalcAll. Calculate Force Constants At Each Point NOTE: To use a Method or Basis Set that is not on the list, type it in the Additional Keywords section on the General page. For more information, see “The General Tab” on page 201. 2. Select the wave function to use: Closed Shell (Restricted), Open Shell (Unrestricted), or Restricted Open Shell. calculate using the equivalent to the Gaussian keyword Opt=Tight Use Tight Convergence Criteria 3. Select the Basis Set. 4. Select the Diffuse function to add to the basis set. 5. Select the Polarization Heavy Atom. If you select a Heavy Atom function, also choose an H option. 200•Gaussian Computations <strong>CambridgeSoft</strong> Minimize Energy
6. Select a Spin Multiplicity value between one and 10. The Properties Tab The Properties tab allows you to select the properties and charges to calculate from the minimized structure. To specify the general settings: To set the properties and charges: 7. From the Properties list, select the properties to calculate. 8. From the Population Analysis list, select the method to compute atomic charges: • Mulliken population analysis • Electrostatic potential-derived charges according to the CHelp, CHelpG, and Merz- Singh-Kollman schemes • Natural Bond Order analysis (NBO) • Analysis according to the Theory of atoms in molecules by Bader et al. (Atoms In Molecules). The General Tab The General tab allows you to customize the calculation for the model. 1. From the Solvation Model list, choose a solvation model: • Gas Phase • Onsager Model (Dipole & Sphere) • Tomasi’s PCM Model (PCM Model) • Isodensity Model (I-PCM Model) • Self-consistent Isodensity Model (SCI-PCM Model) 2. Enter values for: • Dielectric Constant, ε, for the solvent • Solute Radius • Points per Sphere • Isodensity as appropriate NOTE: No value entry boxes appear for gas-phase computations. 3. Type Gaussian keywords in the Additional Keywords text box for access to less common or more advanced functionality. ChemOffice 2005/<strong>Chem3D</strong> Gaussian Computations • 201 Minimize Energy
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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 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 modes and color setti
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Administrator 30 •Chem3D Basics C
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Administrator In the Measurements t
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Administrator Tutorial 7: Docking M
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Administrator To save the iteration
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Administrator Determine the raw spi
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Administrator atoms are relatively
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Administrator When sizing by partia
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Administrator Surface Type Solid De
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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 Example: To examine t
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Method Type Advantages Disadvantage
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Administrator Molecular wave functi
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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 bond length between t
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Administrator R* The R* field is th
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Administrator Adding Parameters to
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Administrator density 67 editing 67
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Administrator repeating jobs 178 RH
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Administrator Rectification, when d
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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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