Mount Holyoke College – Gaussian 09 and GaussView Tutorial
Overview Overview Building a m olecule Energy calculation and geometry optimization Result Fetching 1. Summary 2. Molecular orbitals 3. Electrostatic plots 4. Vibration and animations GaussView is an interface that allows users to build molecules, select calculation types, basis sets, molecular features (e.g, charges), submit jobs to Gaussian 09 and obtain results. Gaussian 09 provides users with data about a molecule’s energies, orbitals, electrostatic potential maps as well as predictions and interpretations of spectra (NMR spectra, optical spectra, hyperfine spectra, etc.).
Building a molecule Starting GaussView by clicking on the GaussView icon
on the dock at the bottom of a Mac screen. Two windows will appear (Figure 1). The grey window is the Builder window, where users can select fragments to construct a molecule and the purple one is the Active View window, where the actual molecule is shown. In order to choose different fragments of a molecule, use the three buttons at the top of the grey window (Red box -­‐ Figure 1). Alternatively, users can go to View menu on the Menu bar (Green box -­‐ Figure 1) > select Builder. A separate Builder menu window will appear.
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Select a fragment from the Builder menu and click on the purple window, continue choosing other fragments and click on the end of a bond to attach the new fragment to the existing one. Note: The calculation only “sees” nuclei, basis functions and electrons and the bonds connecting atoms on the Active View window do not really matter. -­‐
Change bond types and bond length by selecting Modify bond button, clicking on the two atoms comprising the bond, a window will appear and users can customize the bond type and bond length (in Å). 1
Mount Holyoke College – Gaussian 09 and GaussView Tutorial
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Change bond angles by selecting Modify Angle and/or Modify dihedral buttons. Delete an atom and a bond by selecting Delete atom button Measure bond length by selecting Inquire button, clicking on two atoms comprising the bond of interest in the purple window, the result appears at the bottom of the window. Tidy the structures by selecting the Clean button. Figure 1. Builder window (top), Active View window (bottom left) and separate Builder menu window (bottom right) 2
Mount Holyoke College – Gaussian 09 and GaussView Tutorial
Energy calculations and Geometry optimization
Under the Menu bar > Calculate > Gaussian Calculation setup, a window will appear and allow users to set up calculations (Figure 2). -­‐ Under Job Type, users can choose from the dropdown menu: Energy (to calculate the energy of the exact structure as specified in the Active View window or Optimization (which will optimize the structure of the molecule) or Opt+Freq to obtain data about geometry optimization and at the same time frequencies of different modes of molecular motions. -­‐ Under Method, users can specify the type of calculations that Gaussian 09 implements, including but not limited to Hatree-­‐Fock method or DFT (Density Functional Theory) and various different Basis sets. Users can also specify the Charge and Spin state of the molecule. After specifying Job type and Method, click on Submit and save the Gaussian input file, which has the .com (Input file) extension. Figure 2. Gaussian calculation setup window 3
Mount Holyoke College – Gaussian 09 and GaussView Tutorial
Result Fetching
Output files will be automatically saved in Thawspace > GaussianOutput. The output comprises of a .chk file (Gaussian checkpoint file) and a .log file (Gaussian Output file).
1. Displaying Summary Opening the .chk file, from the Menu bar, select Result > Summary. A summary window will appear with information on the type of calculations, energy of the molecules, etc (Figure 3). The energy of the molecule is reported in a.u (atomic unit), i.e. hartree (1 hartree = 627.5095 kcal/mol). Figure 3. Summary window
2. Displaying Molecular Orbitals Open the chk. file. Under Menu bar, select Surfaces/Contours. A panel will appear (Figure 4). Select Cube Actions drop-­‐down menu > New Clube > Type > Molecular Orbital > specify the types of orbitals you would like to display > OK and wait for the MO to appear in the Cubes Available box. Next, select Surface Actions drop-­‐down menu > New Surface. The MO will appear in a separate purple window. -­‐ To change the transparency of the display, select GaussView from the Menu bar > Preferences > Display format > Surface > Format: Transparent > set the slide scale to the desired value. Figure 4. Surfaces and Contours window 4
Mount Holyoke College – Gaussian 09 and GaussView Tutorial
-­‐ Multiple MO’s can be displayed simultaneously. To display/hide/remove an MO from the view window, click on the MO listed in the Surfaces Available box, he go to Surface Actions > select Show Surface or Hide Surface or Remove Surface. Alternatively, users can open the .chk file and go to Menu bar > Edit > MOs. A window will appear (Figure 5) and allow users to select the MOs. Select Visualize > Update … and wait for the program to calculate the MOs.
Figure 5. MOs displaying window
3. Displaying Electrostatic potential plot First, similar to Displaying MO’s, go to Menu bar > Surface/Contours > Cube Actions > New Cube > Total density and wait for the Electron density from Total SCF Density bar to appear in the Cubes Available box.
Next, select Surface Actions > New Mapped Surface > Type: ESP. The electrostatic potential map of the molecule will appear in a separate purple window. The map provides an indication of where the negative (red) and positive (blue) regions of the molecule are.
4. Displaying data on vibrations and animation Select Opt+Freq for Job Type (Figure 2) and open the .chk file. Under Menu bar > Results > Vibration. A window will appear (Figure 6) with different modes of vibration and frequencies. Select a mode of vibration, check Show Displacement vectors and Start Animation to observe the motions of the molecule in the purple window. 5
Mount Holyoke College – Gaussian 09 and GaussView Tutorial
Figure 6. Display Vibrations window -­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐*****-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐
Special thanks to Professor Gary J. Snyder for for his advice and suggestions on this tutorial.
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