GMMX Conformer Tutorial
The following tutorial illustrates how to perform a conformational search and predict their Boltzmann-weighted spectra. It has three parts:
1-1 Open or build one conformation of the molecule whose spectrum you want to analyze. We chose desflurane because of its simplicity and ease of illustration. You can find our starting file, desflurane_start, in the gmmx-tut subfolder of the help folder in the main GaussView installation directory.
1-2 Choose , and the GMMX Conformer Calculation window will appear.
1-3 We want to use the defaults for this calculation, so simply click .
1-4 GaussView will prompt you to save a .GMMX file before it runs the conformational search. Click , and the standard Save window will open.
1-5 Provice a file name and then click . You will be prompted to submit the job to GMMX. Choose .
1-6 When the conformation search completes, a dialog will appear, asking you which results file to open. Open the .SDF file:
The Open .SDF File Dialog
1-7 The resulting dialog contains a list of the conformers the calculation found. Typically, there will be many duplicates (see below).
The Reading .SDF File Dialog
Use this window to select the conformations to examine. The selected ones will be
opened in a
new molecule group. The list will probably contain potential duplicates (e.g., conformers 1-5 above).
1-8 We select all of the conformers initially and open them by clicking and then . Then from the menu, we choose , which opens the Energy Plot window:
The Energy Plot Window
Use this window to determine which conformations should be retained.
The graph shows the energy (Y-axis) for each conformation (X-axis). This plot makes it easy to identify conformations with nearly the same energy. By stepping through the resulting plot, we can compare the structures and identify the physically distinct ones. For the purposes of this tutorial, we will work with the following conformations:
1-9 Once we have selected the conformations for which we want to run additional calculations, we close the .SDF file and reopen it by selecting its name from the list. Be sure that the drop-down is set to . The following molecule group will result (which we've annotated here with conformer identifications):
Conformations of Desflurane
2-1 We now need to optimize the structures of the various conformation with a more accurate model chemistry and then predict their VCD spectra. Set up an Optimization+Frequency calculation using GaussView to do this, using the APFD/6-311+G(2d,p) model chemistry (or a different one of your choice). Check the button on the panel.
The Gaussian Calculation Setup Window
This window sets the parameters for the Gaussian calculation.
The button applies them to the whole molecule group.
2-2 You can specify the job’s parameters by hand or by using a scheme.
2-3 Assign the job to the whole molecule group by clicking the button at the bottom right of the dialog.
2-4 Press , and you will be prompted to save the input files in the subsequent window.
2-5 Click in order to open the Advanced Save dialog. This will allow us to save the input files for all 6 conformations in a single step.
Accessing the Advanced Save Dialog
Click on the button in the Basic Save dialog.
2-6 Set to .
2-7 Right click and then choose in order to designate the base file name and directory location for the files. We used the base name desflurane.
2-8 Select . This will add a number to the base file name for each conformer, making them unique. This process is shown below.
Adding Molecule Numbers to the File Names
2-9 Be sure that the checkbox in the first column of each row is checked. This tells GaussView whether to save the corresponding file. Then click .
2-10 Once the files are saved, GaussView will prompt you to submit to each job. If you choose to do so, the resulting dialogs will differ depending on whether you are using the SC Job Manager (specified in the Job Setup Preferences).
However, for the purposes of this tutorial, do not actually submit the jobs. We have provided the log files in the help/gmmx-tut subfolder of the main GaussView installation location (help\gmmx-tut under Windows systems).
3-1 Open the log files. They are in the gmmx-tut subfolder of the help folder under the GaussView installation directory:
Opening the Results Files
Be sure that the
is set to . This allows you to open all the files as a single molecule group.3-2 Select , which will open the following window. In the Vibrations window, click on the button, then choose .
The Vibrations Window
Opening the composite spectrum window.
3-3 The Vibrational Spectra of Mixture window will appear. Close the IR Spectrum plot by clicking in the upper left and deselecting from the list. The VCD spectrum plot is displayed below.
The Vibrational Spectra of Mixture Window
The spectra defaults to curve and stick representation, resulting in a "busy" plot.
Note that each conformer’s data appears twice: as both a curve plot and as a stick plot. Thus, this display is busy and hard to interpret.
3-4 To make the plot easier to understand, we changed the field of each spectrum to (the default is ). Set in the Combination area to .
Modifying the Plot Type
This produces the following spectra graph, which is much simpler to read. It is also zoomed to show the relevant parts of the spectra.
VCD Spectrum of Desflurane
We have removed the sticks plot for each conformer.
3-6 Go back to Mixture Editor. Click on the column header in order to select the entire column. Then right click, and choose . The weight values will be changed to their population fraction.
Applying Boltzmann Weighting
3-7 For demonstration purposes, we will remove most of the curves from the spectrum. Set the to for all but the first two conformations.
3-8 Add the Boltzmann-averaged combination plot by selecting in the Combination area. Then click . Set the curve pen to be thicker, dotted and its color to be red, as shown below.
Modifing the Curve Appearance
Click Mixture Editor. These changes produce the following plot.
to close the
Final Spectra Display
The composite spectrum is shown as a dotted red curve.
This spectrum display can be saved, customized, and printed as usual.
3-9 Close the spectrum display and the Vibrations dialog. Select from the menu. This opens a window where you can view the key calculation results in a tabular form:
Default Molecule Group Table Display
It is possible to customize this table; the exact options depend on the job type. Here, we have added the
column and changed the magnification and orientation for each conformation:
The Customized Molecule Group Table Window
Experiment with different options within the Molecule Group Table to acquaint yourself with its features.