H-NMR spectrum with spin-spin coupling¶

Logfile: AMStail¶

You can follow the progress of the calculation by clicking SCM → Logfile (AMStail). The chemical shifts will be calculated first, followed by the couplings constants for the perturbing and responding atoms.

When the calculation has finished the end of your logfile will look something like this:

View the ¹ H-NMR spectrum¶

Use AMSspectra to visualize the calculated spectrum

Select SCM → Spectra

In AMSspectra, set the “Width” to 0.01

By default only the chemical shifts are visualized using plain singlets. To switch on the visualization of couplings:

Click on the coupling checkbox

This switches on the spin-spin coupling (default machine frequency at 200 Mhz). An additional section in the table will appear which displays additional information for any selected atom or peak in the spectrum. For example:

Click on the quartet in the spectrum

Average chemical shifts and couplings for equivalent atoms¶

As you may have noticed, there are a lot of splittings in the simulated spectrum. This is because all the chemical shifts and coupling constants are calculated at fixed geometry, which means that there is no rotation which would create magnetically equivalent groups.

You can resolve this issue by either flagging chemically equivalent atoms manually or have AMSspectra guess them for you. To manually supply the information:

Select groups of chemically equivalent atoms and

Hold down the SHIFT key on your keyboard

Use the left key of the mouse to select several atoms

Press CTRL+G or go to Regions → New Region From Selected Atoms

The atoms should now be surrounded by a colored sphere. Continue with all remaining atoms. Your spectrum should look as follows now:

Alternatively, to have AMSspectra guess chemically equivalent regions for you, go to

Click on NMR → Chemical Equivalent Regions**

Comparison of calculated and experimental spectrum¶

A good source for experimental spectra is the SDBS database: http://sdbs.db.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi

These are the peak data for the ¹ H-NMR spectrum of ethyl acetate (CAS = 141-78-6) from the SDBS database (the three columns are Hz, ppm and Intensity):

379.88   4.242     52
372.75   4.163    171
365.56   4.082    180
358.50   4.003     62
182.56   2.039   1000
119.69   1.337    245
112.63   1.258    560
105.38   1.177    214

Select the peak data above (three columns, all lines with peaks) and copy it ot clipboard (ctrl+c)

Now we switch back to AMSspectra where we can paste the contents from the clipboard directly:

Activate the AMSspectra window showing the calculated ethanol spectrum

Edit → Paste

AMSspectra will ask which columns to use for X and Y, and offer to rescale the data:

Enter 2 to use the second column as X values (that column contains the chemical shift in ppm) and click OK

Enter 3 to use the third columns as Y vales and click OK

You now should see both the experimental and the calculated spectrum in one graph. The experimental spectrum (at least the one used to create this tutorial) was measured at 89.56 MHz. So adjust the frequency (default at 200 MHz) of the calculated spectrum:

Change the frequency (next to the Coupling check box) from 200 MHz to 89.56 MHz

This should give you something like this:

Sometimes it makes sense to change one of the spectra to a stick spectrum, showing only sticks for the calculated positions and heights, not applying the broadening. As an example lets do that here for the calculated peak positions:

Double click below the X-axes to show the Graph options dialog

Click on the Curves tab

Select the NMR curve (not the Clipboard one) in the menu on the left

For this curve, on the right side: Show the Sticks, and do NOT show the Curve itself

Click OK

Now you should get the experimental spectrum as a broadened curve, with sticks for the calculated positions: