In SEAGrid, how do I build a molecule and run a Gaussian job?

The following will show you how to use NanoCAD to build a new molecule (acetaldehyde) and generate a Gaussian input file.

Building a molecule

  1. To open the NanoCAD editor, from the main menu on the home screen, click Nanocad.
  2. At the top of the "Nanocad" window, read the summary of Nanocad commands. The commands are:
    • Rotate: Drag gray space
    • Translate: Shift-drag gray space
    • Zoom: Ctrl-drag gray space
    • Move atom: Drag atom
    • Add atom: Shift-click gray space
    • Delete atom: Shift-click atom
    • Add bond: Shift-drag atom to atom
    • Delete bond: Ctrl-drag atom to atom
    • Select atom: Ctrl-click atom
    • Add double bond: Shift-drag between bonded atoms
    • Select group: Ctrl-Alt-click atom
  3. If there is an example water structure, to erase it, click Clear at the bottom of the "Nanocad" window.
  4. To build a new structure, at the bottom of the "Nanocad" window, click Structure. The "Import Structure" window will open. Move the "Nanocad" window slightly below the "Import Structure" window so that both are visible.
  5. In the "Import Structure" window, the current element (default element is H) is the atom that you can place in the "Nanocad" window.
  6. To change the current element, in the "Change current element to:" field, enter an element name; for this example, enter C for carbon. Click Select.

    Note:
    Atom names start with uppercase letters. To select barium, for example, enter Ba.
  7. To add a carbon atom, Shift-click in the gray area of "Nanocad" window; a gray carbon atom will appear.
  8. In an area close to (not on top of) your first carbon atom, Shift-click to place a second carbon atom. If the atom is too close, you can delete it by Shift-clicking the atom.
  9. To build a bond between your two atoms, you will Shift-drag from one carbon atom to the other:
    1. Position your cursor over one of the carbon atoms. Hold down Shift and drag your cursor to the second atom. During the operation, you will see a line appear between your atom and your cursor. The two atoms will temporarily change color to match the background, indicating an active operation.
    2. When you move your cursor over the second carbon atom, release (in this order) the mouse button and Shift key. A bond will appear between the two atoms, and their color will change back to deep gray.
  10. To change the current element to oxygen, in the "Import Structure" window, enter O. Click Select.
  11. In the "Nanocad" window, Shift-click near a carbon atom. A red oxygen atom will appear.
  12. To build a carbon-oxygen bond, Shift-drag from one carbon atom to the oxygen atom. Because the carbon-oxygen bond in acetaldehyde is a double bond, you need to repeat this process one more time.

    You will see a double bond between the carbon and oxygen atoms.

  13. You now have all the heavy atoms in acetaldehyde; the only missing atoms are hydrogen. To add hydrogen, at the bottom of the "Nanocad" window, click Add H. NanoCAD will add the four missing hydrogen atoms to your unfinished acetaldehyde molecule.
  14. The last step for building the acetaldehyde molecule is minimizing the current structure. At the bottom of the "Nanocad" window, from the Minimize drop-down menu, choose either the Conj. Grad. (conjugate gradients) method or the Stp. Desc. (steepest descent) method to minimize the current molecule.
    Note:
    Nanocad has many template molecules to choose from. In the "Import Structure" window, click Ion, Function-Group, or Molecule to view them.

The acetaldehyde molecule is complete. You are ready to create a Gaussian input file for this molecule.

Creating your Gaussian input file

  1. At the bottom right in the "Nanocad" window, from the Export drop-down menu, choose Gaussian Input. The "Nanocad" window will disappear, and the the "Gaussian 03 Input GUI" window will open.
  2. From the Methods menu, choose DFTs, then Common Hybrid Functionals, and then B3LYP.
  3. In the "Select Wavefunction Type" window that opens, choose R - Restricted closed-shell.
  4. From the Basis Sets menu, select Frequently-used basis sets, and then 6-31G.
  5. In the "Add Polarization and/or Diffuse Functions" window that appears, choose Yes.
  6. In the "6-31G" window, under "Diffuse Functions", choose 6-31+G (the first option, not 6-31++g).
  7. From the Job Types menu, select Common-Used Types, and then OptFreq.
  8. From the Keywords menu, select Common Keywords, and then Pop (for electronic population analysis).
  9. In the "Pop Options" window that appears, from the "Output File" column, choose Reg (for regular).
  10. In the "Gaussian 03 Input GUI" window, from the Keywords menu, choose Other Keywords.
  11. In the "Additional Keywords" window that appears, select options in the following order:
    1. GFInput
    2. GFPrint
    3. IOp
  12. The last option (IOp) opens an "Options for IOp" window. Set the following values:
    • Op: 6
    • Ov: 7
    • N: 3

    These settings help some post-processing programs.

  13. To close the "Options for IOp" window, click Done. In the "Additional Keywords" window, click Done to add all the keywords to the job.
  14. In the "Gaussian 03 Input GUI" window, set the following parameters:
    • %nproc: 16
    • %lproc: 1
    • %mem (in MB): 300mb
    • Job Name: Acetaldehyde optimization
    • Charge: 0
    • Multiplicity: 1
  15. Click Done & Export. You will be directed to the "Create Experiment" window with the Gaussian input you created.

This is document amtp in the Knowledge Base.
Last modified on 2016-10-17 09:54:21.

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