4.3.4 Visualizing the PQS job output

Step 8
Capture the {19}F NMR spectrum of perfluoroanthracene.

Note: Make sure you are in the directory where the files from the TUTORIAL/EXAMPLE3 directory were copied.

To view the output of the perfluoroanthracene job, start PQSMOL in View mode by typing pqsview F-anthracene.out at the command prompt, Figure [*].

Image t3-11-5
View window - perfluoroanthracene job visualization

We are going to visualize and capture an image of the NMR spectrum. Press the NMR button Image button-nmr in the toolbar at the bottom of the View window
. This will initially display the $^{13}$C NMR spectrum (carbon being the first atom listed). To display the {19}F NMR spectrum you can either select a fluorine atom, e.g., F9, from the NMR spectrum window, or click on one of the fluorine atoms of perfluoroanthracene in the View window. The resulting NMR spectrum is shown in Figure [*] (Note the red arrow below the peak corresponding to the selected fluorine atom, F9.)

Image e3-1
NMR window - Initial {19}F NMR spectrum of perfluoroanthracene

The halfwidth of the peaks can be controlled using the slider bar; sliding this all the way to the left reduces the half width to zero and simply displays a vertical line, [*].

Image e3-2
NMR window - {19}F NMR spectrum with zero halfwidth

The NMR spectra shown in Figures {19}F NMR spectra is the {19}F signal in CF3Cl. This can be taken to be 179.42 (see M. Muir and J. Baker, J. Fluorine Chem. 126 (2005) 727) and typing this value into the Reference Shift entry in the bottom left corner of the NMR window results in the spectrum shown in Figure [*].

Image e3-3
NMR window - {19}F NMR spectrum using CF$_3$
Cl as reference

Using a non-zero reference of course changes the relative chemical shift values and thus the spectrum range. In order to directly compare different NMR spectra, i.e., in this case the {19}F spectra of perfluoroanthracene with its methoxy-substituted derivatives, it is helpful if the different spectra cover the same spectral range. To facilitate this, we are going to change the Range End entry to 160 ppm and the Range Start entry to 110 ppm. This changes the starting and ending values on the X-axis of the NMR spectrum, as shown in Figure [*].

Image e3-4
NMR window - {19}F NMR spectrum with modified range

Changing the range in this way has the effect of slightly compressing the spectrum.

Finally, we are going to capture an image of the NMR spectrum. Position the mouse pointer anywhere inside the NMR spectrum graph and press the right mouse button; this will produce a popup menu with a single menu item labeled Capture (see Figure [*]).

Image e3-5
NMR window - Capturing an image of the {19}F NMR spectrum

Note: The spectrum image captured in this example has a white NMR plot line on a black background. This color combination may not be the suitable for printed media. You can change the background color of the spectrum with the OptionsrightarrowGraph Background menu item and the plot color with OptionsGraph Plot.

Activating the Capture menu item will cause the Save Image As dialog shown in Figure [*] to appear, prompting you for a file name to save a JPEG image. As shown, the default name is nmr_capture1.jpg. Change this to, e.g., F-anthracene.jpg and press the OK button to save the image.

Image t3-12-1
Save dialog - naming the NMR spectrum image

This completes the first part of this tutorial. At this point we have obtained and saved as a JPEG image the simulated {19}F NMR spectrum of perfluoroanthracene. We will now build the various methoxy-substituted derivatives and obtain their NMR spectra.