ARCHIVED: In SEAGrid, how do I build a molecule?

The following will show you how to build simple molecules with the NanoCAD tool in SEAGrid, and how to create Gaussian input files using Gaussian Input GUI.

• Logging in
• Launching and using NanoCAD in the SEAGrid client
• Creating your Gaussian input file

Logging in

1. To open the SEAGrid desktop client, find and double-click gridchem.jnlp.
2. Click Sign In. The "Get Access to SEAGrid" window will open.
3. Enter your workshop username (e.g., wrk###) and password, and click LOGIN. You will be authorized to use SEAGrid.
4. To access information about your current job history, in the SEAGrid client, click My CCG.
5. Close the "My CCG" window.

Launching and using NanoCAD in the SEAGrid client

For demonstration purposes, the following steps show you how to use NanoCAD to build an acetaldehyde molecule and generate a Gaussian input file.

1. From the Open NanoCAD menu, choose NanoCAD (not Nanocad3D). The default NanoCAD molecular editor will open.
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. To erase the example water structure, at the bottom of the "Nanocad" window, click Clear.
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.
   Note:

   Nanocad has many template molecules to choose from. To view them, in the "Import Structure" window, click Ion, Function-Group, or Molecule.
5. In the "Import Structure" window, the current element (default element is H) is the atom that you can place in the "Nanocad" window.

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.
6. To add a carbon atom, Shift-click in the gray area of "Nanocad" window; a gray carbon atom will appear.
7. In an area close to (not on top of) your first carbon atom, Shift-click to place a second carbon atom.
   Note:

   To delete an atom, Shift-click the atom.
8. To build a bond between your two atoms:
   1. Position your cursor over one of the carbon atoms. Hold down Shift-click and drag your cursor to the second atom. 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.
9. To change the current element to oxygen, in the "Import Structure" window, enter O. Click Select.
10. In the "Nanocad" window, Shift-click near a carbon atom. A red oxygen atom will appear.
11. To build a carbon-oxygen bond, Shift-drag from one carbon atom to the oxygen atom. Because the carbon-oxygen bond in acetaldehyde is double bond, you must repeat this process one more time.

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

12. You now have all the heavy atoms in acetaldehyde; you are only missing hydrogen atoms. 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.
13. 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.

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 of the "Nanocad" window, from the Export drop-down menu (labeled Input/Output Menu), choose Gaussian Input. The "Nanocad" window will disappear; the "Gaussian 03 Input GUI" window will open.
2. From the Methods menu, choose DFT, 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 (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): 300
• Job Name: Acetaldehyde optimization
• Charge: 0
• Multiplicity: 1
15. Click Done & Export.
16. The "Gaussian 03 Input" window will close, and the "Job Editor" window will open. The "Job Editor" window has the proper Gaussian input file for acetaldehyde in the editing area below "Input file Information", based on the options that you specified.

    From the File menu, select Save as and give the file a meaningful name (e.g., acetaldehyde.inp).

17. The saved file should appear in the "Input File Information" section. If there was a default sample input file, to remove it, select the additional file and click - (minus sign) below. Only the acetaldehyde.inp file should remain.
18. If necessary, change other settings in the "Job Editor" window. For example:
    • Change the default_test job name to acetaldehydeopt.
    • Click View/Edit Structure to open a "Molecular Specification" text view window, which contains the molecule input data.

    You may now submit your Gaussian job for processing.

19. From the File menu, select Save/Displaymol. A graphic representation of the molecule will appear in the "Gaussian 03 Input GUI" window.
20. Change the system that you would like the job to run on.
21. Choose Comet.
22. In the bottom right of the "Job Editor" window, click Submit. This window will disappear and the focus will be on the "Submit Jobs" window with an entry for the job in the "Queued Jobs" list.
23. If the job in the job list is not highlighted, click it.
24. To submit this job, click Submit Selected Jobs To Queue.

    After a small window indicating that your job is being submitted disappears, you will see your job in the "Submitted Jobs" list below.

    You can monitor the submitted job using the "My CCG" window from the SEAGrid client.