Gaussian has the ability to predict many different kinds of spectra,
and Gaussview can display these results.
In this video, we will examine a variety of spectra displays,
as well as ways of customizing them, along with related features for Gaussview
plots.
We begin with infrared spectra.
Let’s examine the predicted spectrum for C60.
We already opened the checkpoint file from the frequency calculation.
We select vibrations from the results menu in order to view the IR results.
Display the spectrum using the Spectra button at the bottom of the dialog.
By default, the x-axis units are wavenumbers.
In this case, though, we want to compare our results to
some infrared telescope data, which is reported in nanometers.
We can change the units using the properties item from the plots drop down
in the upper left corner of the dialog.
The plot tab allows you to customize many aspects of the X and Y axes.
We will select nanometers as the unit for the x-axis.
We also want to limit the range of the x-axis to the range actually containing data,
so we check fixed range and change the upper limit to 20,000.
Once we close the dialog, the spectrum display updates following our specifications.
GaussView also can also optionally scale the frequencies within the spectrum display
using the field at the very bottom of the dialog.
We next examine Raman spectroscopic results for the topical anesthetic benzocaine.
The mode list in the vibrations dialog contains several additional columns when Raman results
are available.
Clicking on any of the column headers causes the list to be sorted based on that column.
We click on the Raman activity header, which sorts the modes accordingly,
first in ascending order, and then in descending order after a second
click.
The ordering is indicated by the direction of the arrow icon.
The most active Raman modes are now at the top of the list.
We can animate them as usual.
Here we use the displacement amplitude slider to decrease the range of motion.
The items below the start/stop animation button can be used to save a movie
of the molecular motion.
There are also additional controls available in the GaussView movie preferences.
We want to create a high-quality movie, so we move the object quality slider all the
way to realistic.
You can also enlarge the display in the generated movie using the enlargement field below the
slider.
We also change the background color of the generated movie to white.
Note that we have to do this here, even though the current view window has a white background.
There are also choices for the rendering method and the aspect ratio of the generated movie.
We keep the default aspect ratio which is correct for HD format.
The 3 fields in the vibration animations section are the same as those in the vibrations dialog.
Once we return to the vibrations dialog, we can click the save movie button to generate
the movie.
We now open the Spectra window.
The window contains plots of all available spectra for this result set.
In this case, both the IR and Raman spectra are present.
The current spectrum is indicated by a red border.
You can control which ones are visible in the window using various items on the plots
menu.
The top section of the menu contains a list of all available plots.
The ones that are checked are present within the window.
You can turn an individual item on or off by selecting it from this list.
However, we close the selected plot, which is the IR spectrum, using “Hide This Plot”
in the second section of the menu.
Here is the Raman spectrum for our benzocaine molecule.
There are many peaks quite close together, and we would like a more detailed view of
the range above 3000 wavenumbers.
Clicking and dragging a rectangle within any spectrum display zooms in on that portion
of the graph.
You can repeatedly zoom as much as you like.
In order to zoom out, there are two choices available on the context menu.
The undo last zoom item reverses the most recent zoom-in,
while the zoom out item restores the display as it was before you started zooming.
In our next example, we look at GaussView's support for isotopic substitution
in harmonic vibrational frequency analyses.
Remember that the optimized geometry for a molecule is independent of an isotopic composition.
Therefore, reoptimizing the geometry is not required for different isotopologues.
We've already opened the checkpoint file from a frequency calculation on formaldehyde.
We want to examine the frequency analysis for the deuterated form.
In the vibrations dialog, controls related to isotopic substitution are located at the
top.
Specifying alternate isotopes involves two steps:
First, you must define an isotopologue, which is simply a set of isotope specifications;
Second, you must compute the vibrational data for that isotopologue.
By default, isotopologue 0 is defined as a set of isotopes specified for the calculation,
which are usually the most abundant isotopes.
We click the edit isotopologues button to define an additional isotopologue.
This opens the atom list editor with the isotopes feature active.
GaussView automatically adds a column for an additional isotopologue, here isotopologue
1.
We specify an atomic weight of 2, for both hydrogen atoms using the pop-up menu in each
cell.
Additional isotopologues can also be defined directly
by enabling another item on the columns-mass submenu.
Here we demonstrate setting up isotopologue 2
which substitutes tritium for one hydrogen atom.
We close the atom list editor and return to the vibrations dialog.
When examining the items in the active data drop-down,
the only available data set is for isotopologue 0.
We still need to generate the vibrational analysis for the deuterated form.
Do this by clicking the new data button and then specifying isotopologue 1.
This causes GaussView to run the freqchk utility.
It finishes almost immediately for this molecule, but can take a bit of time for larger molecules.
Once freqchk finishes, we can set Data 1 as the active data set.
The reported frequencies and intensities as well as the spectrum
now correspond to the deuterated form of formaldehyde.
We can also view the spectra for both isotopologues at the same time
via the mixture spectra feature.
The green line corresponding to the deuterated form
shows significant shifts in the peak locations compared to the standard isotopes.
Camphor is a compound found in evergreen trees in the Laurel family,
and it is a significant ingredient in the herb Rosemary.
Camphor is a chiral molecule with two chiral centers.
This slide illustrates the full molecule in the (R,R) enantiomer above,
with backbone versions of both enantiomers below.
We optimized the structure of the (S,S) enantiomer and then performed
a frequency calculation for which we also requested calculation of
the Vibrational Circular Dichroism (VCD) spectrum with the Freq=VCD option.
When VCD results are available, the vibrational modes list contains an additional column reporting
the VCD rotational strength.
The VCD spectrum is also included in the spectra display.
This is the experimental VCD spectrum to which we will compare our results
in order to determine the absolute configuration of the experimental camphor sample.
GaussView's plot presents the predicted spectrum in a different format,
but we can modify the display to match what the instrument produced.
Open the plot properties dialog and match the X axis range to that of the spectrometer.
Also reverse the ordering of the x-axis using the invert axis checkbox.
We can now compare the two spectra.
As we can see, the spectra are quite different, in fact, almost exact opposites.
Since the spectrum of the (R,R) enantiomer is always
the mirror-image of the one for the (S,S) enantiomer,
there is no need to calculate it separately.
Rather, we can simply invert the y-axis in order to compare
the R,R spectrum to experiment.
The computed spectrum matches the observed one very well.
We want to prepare a publication quality image for the predicted spectrum.
To do so, we will need to change a few of its display properties.
First, we specify a more descriptive title for the figure.
We also change the label for the x-axis.
GaussView automatically adds the units to both axes’ labels.
If you want to include special characters within any of the text on the plot,
you can use the format shown for the Y axis title here:
enclose the text in opening and closing HTML tags,
and use the HTML entities corresponding to the desired characters.
You can also use HTML superscript and subscript tags within any text.
Our next modification is to specify a range for the y-axis which takes maximum advantage
of the available space.
Finally, we use controls on the appearance tab
to turn off the current peak marker and sticks within the spectrum
and also to make the plotted line thicker.
We also change the color of the background and the canvas
from GaussView's usual light gray colors to white, which works better in print.
Finally, we turn off the background grid.
We can then save the customized spectrum to an image file in the usual way.
Our next example examines the Raman optical activity, ROA, spectrum of the small chiral
molecule R-epichlorohydrin.
The ROA calculations were performed in cyclohexane solution.
This molecule has three conformations, corresponding to different values of the chlorine-carbon-carbon-oxygen
dihedral angle: an anti form and two gauche forms.
We opened the three checkpoint files into a single molecule group.
Change the view to a single molecule and open the vibrations dialog.
When ROA data is available, there will be many additional columns in the modes list.
There are several sets labeled ROA which correspond to different instrument configurations.
You should select the one that is appropriate for the experimental data to which you are
comparing.
Open the Spectra display and navigate to the appropriate ROA spectrum.
This spectrum corresponds to the current molecule, which is the anti form.
If we compare the predicted spectra for all three conformations,
We see significant differences between them.
However, we are interested in the conformationally-averaged spectrum
rather than the ones for the individual conformations.
We open the Mixture Spectrum, and and close all of the plots except the ROA
spectrum of interest.
We modify the plot properties to invert the X axis,
limit the reported data range, and specify an informative title.
Then open the mixture editor, and disable all of the individual plots.
Our goal is to plot the conformationally-averaged ROA spectrum.
We apply weights to the individual spectra corresponding to their Boltzmann populations
by selecting the corresponding item on the right click context menu.
Finally, we add a customized combination line to the graph
using the controls at the top of the dialog.
Previously, we generated the combination spectrum for the same compound
from calculations in solution with acetonitrile.
We can compare the two Spectra and determine the effect of the more polar solvent on the
results.
For this molecule, different solvent environments yield small differences in the observed spectrum.
GaussView can also display the results from Gaussian calculations of optical rotations,
which predict the optical rotatory dispersion, ORD, at various incident light wavelengths.
We will consider ORD results for a small group of substituted oxirane compounds.
We opened the checkpoint files for the five optical rotation calculations
into a single molecule group.
The molecules differ in the substituent bonded to the three membered ring:
Ethynyl, Chloride, Cyano, Fluoride, and Methyl.
We change the view to the single molecule format,
and then choose ORD from the results menu.
This plot shows the ORD curve for the current molecule, methyloxirane.
Note that part of the curve lies below the x-axis;
GaussView occasionally misjudges the appropriate data range.
If you zoom in on the curve and extend the zoom box below the x-axis,
the entire curve becomes visible.
Opening the mixture Spectra shows the results for all five molecules on the same graph.
For three of the substituents, the ABSOLUTE VALUE of the specific rotation
decreases with increasing incident light wavelength.
For the other two substituents, there is much less variation.
GaussView includes a full-featured facility for examining the results of NMR calculations.
We will demonstrate them for 2-nitroaniline.
We've already opened the checkpoint file from the NMR calculation.
Selecting NMR from the results menu opens the NMR spectrum.
By default, the graph plots the predicted shielding values for all of the atoms in the
molecule.
Clicking on either a peak in the plot, or an atom in the molecule
displays the numeric shielding value in the bottom part of the spectrum window.
You can also label each atom in the view window with its shielding value
by selecting “show shieldings in view” from the plots menu.
You can limit the displays to a single element by selecting it from the element drop down
below the spectrum.
Here, we focus on the carbon atoms within the molecule.
If you are interested in chemical shifts rather than raw shieldings,
you can compute them by selecting an item from the reference drop down.
Here, we select a DFT calculation on TMS as the reference,
and the values in the plot and atom labels change to the carbon shift with respect to
TMS.
Clicking on a peak now displays the predicted chemical shift in the information area.
The shielding value for the reference molecule appears in the Shielding field.
Of course, you need to use the same model chemistry for the reference calculation
and for the NMR calculation on the molecule of interest.
It is quite easy to add additional items to the set of available references.
This data is stored in a text file named NMR.data which is located in the data folder under
the main GaussView directory location.
Its format is intuitive.
Each line consists of the element, the shielding value,
and a description enclosed in double quotation marks.
Generally, the description includes at least the name of the reference molecule
and the model chemistry used to compute the value.
We will add values for carbon and hydrogen from an NMR on TMS
using the APFD functional and the 6-311+G(2d,p) basis set.
When adding values to this file, be sure to include sufficient significant figures.
Once we have added our two lines, we save the file.
We recommend saving a copy of the original, unmodified file as a backup before making
any changes.
You will need to restart GaussView in order to use the newly added reference data.