gaussview and gaussian tutorial for computational chemistry

start GaussView

Launch GaussView. Initially two or three windows will be displayed: the main window, a blue or purple View window, and possibly a small GaussView Tips window. Open the Builder window by selecting Builder in the main-window View menu.

Build a molecule of toluene.

This toluene description and the suggestions follow Taras Pogorelov's tutorial.

  1. Start a new molecule from the Main window: File→New→Create Molecule Group.
  2. In the Builder window, click the ring button. (It looks like benzene.) The Ring Fragments window will appear.
  3. Select benzene (the top left button) and it appears in the main window. Note that the main window's Builder Fragment button also displays "benzene." Click anywhere in the View window and benzene will be added to the View window. Should you want to move (translate) the benzene molecule in the View window, hold down the shift key while dragging with the left mouse button.
  4. Click on the Element button (it displays 6C) on the Builder panel. The "Elements Fragments" panel will appear. Select Carbon and Tetrahedral. CH4 will appear in the main window. The C atom of CH4 is colored light blue, indicating that it is the "hot" atom. In the View window, click on any H atom; it will be changed to CH3, completing toluene.
  5. Use molecular-mechanics energy minimization to quickly, albeit approximately, improve toluene's geometry: In the Builder panel, click the Clean button (the broom icon). GaussView will run a classical-mechanical energy optimization of the toluene structure in the View window.
  6. Save the toluene molecule as toluene.com.
  7. Change toluene to phenol by replacing the CH3 group with OH. This can be done as follows: Open Builder's Element Fragments window, select O and "tetravalent." Water with the O atom "hot" will appear in the main window. Then in the View window click on the methyl C atom. It will be replaced with OH.
  8. Let us try to convert phenol to the phenoxide anion. To do this, delete the H atom that is attached to the O atom, as follows. On the Builder menu, the atom deletion tool has the icon . After selecting the atom-deletion tool, click on the H atom to be removed, in the View window. Then save the C6OH5 molecular fragment as "phenoxide.gif". (In this context, "gif" stands for Gaussian input file.)

    Changing the molecular charge from 0 (for the radical) to -1 (for the anion) cannot be done at the molecular-drawing or clean-up stage. Rather, charge is set when preparing to run a quantum-mechanical calculation, as follows:
    1. In the main window, choose "Gaussian Calculation Setup" from the Calculate menu.
    2. Click on the Method tab. Type -1 in the Charge box.
      If one clicks on any other tab (e.g., the Title tab) the View window updates, showing the new -1 charge.
    3. Clicking on Submit will run a Gaussian calculation on the phenoxide anion. (Gaussview will first prompt for re-saving the Gaussian input file, which one should do.)

 

diatomic molecules

This part of the tutorial uses diatomic molecules to try out computational methods, basis-set selection, and spin specification. Clicking New in the main-window File menu will create a new View window.

  1. O2
    1. Use double-bonded O from Builder's Element Fragments window to create O2.
    2. Save the O2 molecule as a Gaussian input file.
    3. Open the Gaussian Calculations Setup window from the main window's Calculate menu. The following choices will set up a triplet-state geometry optimization using density functional theory and the 6-31g(d) basis set.
      tab box value
      Job Type   Optimization
      Method Method DFT Unrestricted B3LYP
      Method Basis Set 6-31G (d )
      Method Spin Triplet
    4. Submit the calculation.
    5. When the calculation is complete, GaussView will suggest opening the results (the "chk" file). Do open it. In the main window, click on the Results menu and select Summary.
    6. Use the Builder window's Inquire button ( ) to measure the O=O bond length. It should be 1.214 Angstroms.
    7. Repeat the O2 calculation for the singlet state. The only setting to change is the Spin, from triplet to singlet. The calculation results should show that the singlet bond length is 1.216 Angstroms and the total energy (Results Summary window) is -150.2574 au. The energy unit "au" stands for the atomic unit of energy, which is Hartrees. The singlet lies (-150.2574 - - 150.3200) = 0.0626 Hartree = 1.7 eV above the triplet, at this level of theory.
  2. CO
    1. Create a CO molecule in the View window. Save it.
    2. Set up a Gaussian calculation that will optimize the bond length and calculate the vibration frequency.
      tab box value
      Job Type   Opt+Freq
      Method Method MP2
      Method Basis Set 6-31G (2d)
    3. Submit the job.
    4. The Results summary will show total energy = -113.05314 au. The bond length is 1.144 Angsroms.
    5. Selecting Vibrations from the main-window Results menu will calculate and then display the vibration frequency, plus a calculated IR spectrum.
  3. N2
    1. Create a nitrogen molecule in the View window. Run Builder's Clean. The bond length will be 1.092 Angstroms. Save the N2 molecule..
    2. Set up a Gaussian calculation using the defaults.
      tab box value
      Job Type   Energy
      Method Method Hartree-Fock
      Method Basis Set 3-21G
    3. Submit the job. After it finishes, accept GaussView's offer to open the output chk file.
    4. The Results summary will show total energy = -108.3007 Hartree.
    5. To view molecular orbitals, choose Surfaces/Contours from the main-window Results menu. The Surfaces and Contours window will open, but will not list any available surfaces. Begin by generating "cube" files for the HOMO and LUMO.
      Choosing Cube Actions / New Cube will open the Generate Cube window. In the Generate Cube window, choose
            Type: Molecular Orbital
            Orbitals: HOMO (orbital number 7)
      and Click OK. MO 7, the HOMO, will be added to the list of available cubes.
      Also create the cube for the LUMO, MO 8.

      Go to the Surfaces and Contours Window. Select (click on) the MO 7 cube. Then choose Surface Actions / New Surface.
      MO 7 will appear in the Surfaces Available list and will appear in the View window.


      MO8, the LUMO, can be displayed by first hiding MO 7 and then choosing New Surface for MO 8.

 

building larger molecules

Work the Gaussview tutorials "Building Pyridine" and "Building Phenylpyridine." These tutorials may be accessed through the GaussView Help menu. (Help/GaussView Help/Tutorials)

 



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