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  • Videos and Demos

    • Predicting bond angles via Energy Minimization (oleic acid in MMFF94)

    • Presenter: Jesse Gordon , Company: PerkinElmer Informatics
    • Duration: 3 min
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  • This video demonstrates using MMFF94 to predict oleic acid's bond angle, and compares MMFF94's predicted bond angle with the prediction of other computational chemistry packages in ChemBio3D.

    ChemBio3D offers two commonly accepted force field calculation methods, MM2 and MMFF94. These methods are designed so that you can calculate molecular properties of your models. Each of these methods enable you to calculate a variety of steric energy, thermal energy, and other values. In an MMFF94 energy minimization calculation, ChemBio3D examines your model and identifies its various atom types. It then calculates a new position of each atom so that the cumulative potential energy for your model is minimized. Having calculated each new position, ChemBio3D moves each atom in your model so that the total energy is at a minimum. MM2 and MMFF94 may be viewed as different calculation techniques you use to arrive at a specified result. Which technique you use depends on your type of model and the property you want to calculate.

    This video demonstrates:

    • Running an MMFF94 energy minimization on oleic acid, a fatty acid with one double bond.
    • The MMFF94 minimization changes the double-bond angle from 120 degrees (the geometric default) to 124.1 degrees.
    • Compare the MMFF94 angle to an MM2 bond angle prediction of 123.5 degrees, and a GAMESS bond angle prediction of 123.3 degrees.

    You can perform a minimization using either of the force fields: MMFF94 or MM2. To perform an MMFF94 minimization:

    • Go to Calculations>MMFF94>Do MMFF94 Minimization. The Do MMF94 Minimization dialog box appears.
    • Under Preferences tab in the "Do MMFF94 Minimization" dialog box, select any of the following options:
      • "Display Every Iteration"-Select this option to view the model during the calculation. Remember that displaying or recording each iteration may increase the time required to minimize the structure.
      • "Copy Measurements to Output Box"-View each measurement in the Output window.
      • If you want, you can minimize several models simultaneously. If a computation is in progress when you begin minimizing a second model, the minimization of the second model is delayed until the first one stops.
      • You can perform any action in Chem3D that does not move, add, or delete any part of the model. For example, you can move windows around during minimization, change settings, or scale your model.

    This video compares the oleic acid bond angle produced in each of ChemBio3D's computational chemistry packages. Those include:

    • MM2: force field
    • MMFF94: force field
    • GAMESS: ab initio
    • Gaussian: ab initio
    • Jaguar: ab initio
    • MOPAC: semi-empirical

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