H-NMR spectrum with spin-spin coupling
**************************************

ADF Spectroscopy Nuclear magnetic resonance (NMR) nuclear spin-spin
coupling constants (NSSCCs) Chemical shift SimIR

In this tutorial, you will learn how to:

* use the GUI to set up the calculation of NMR chemical shifts and
  nuclear spin-spin coupling constants (NSSCCs)

* use the AMSspectra module to inspect the results and compare the
  simulated and experimental NMR spectra directly

[image]

See also:

  * Don't miss this **must-read** FAQ entry  on NMR settings based on
    the work done by the group of Jochen Autschbach

  * The NMR part of the ADF manual  contains a neat summary of the
    science behind spin-spin coupling calculations as well as some
    additional advice.

  * The advanced tutorial on relativistic NMR calculations .


Start AMSinput and copy the molecule
====================================

   **1.** Start **AMSinput**
   **2.** Obtain a pre-optimized ethyl acetate structure by copy-pasting the following coordinates into AMSinput:

   O       1.48603879      -1.49561627       0.00000000
   C       1.29751002      -0.30552432       0.00000000
   O       0.07403584       0.25228979       0.00000000
   C      -1.02449892      -0.67494471       0.00000000
   C      -2.30056502       0.12358769       0.00000000
   C       2.36905363       0.74347075       0.00000000
   H      -0.94187587      -1.31519741       0.88039373
   H      -0.94187587      -1.31519741      -0.88039373
   H      -2.36617127       0.75820872       0.88525259
   H      -3.15628689      -0.55419212       0.00000000
   H      -2.36617127       0.75820872      -0.88525259
   H       3.34355252       0.26293272       0.00000000
   H       2.26362714       1.38098693       0.87932777
   H       2.26362714       1.38098693      -0.87932777

The above structure was optimized with the following settings:

* Hybrid XC: PBE0

* Basis: TZP

* Frozen core: None

* Numerical Quality: Good

In case you want to run the geometry optimization yourself, take a
look at the GUI tutorial on geometry optimizations.


Setting up the NMR calculation
==============================

Select the following settings in AMSinput

   XC functional: **GGA → OPBE**
   Basis set: **J → TZ2P-J**
   Frozen core: **None**
   Numerical quality: **Good**
 [image]

Note:

  The basis sets in "J", including TZ2P-J, have been especially
  designed for ESR hyperfine and NMR spin-spin coupling calculations.

Next, instruct the program to calculate the shieldings for all
hydrogen atoms.

   **1.** In the panel bar, select **Properties → NMR**
   **2.** Click checkbox **H atoms** next to **Shielding for all**
   **3.** Click checkbox **H atoms** next to **Perturbing / responding all**
 [image]

Note:

  In some cases, e.g. when dealing with alcohol groups, you might want
  to exclude atoms from the list of perturbing and responding atoms.
  To do so, just select the atoms you want to calculate the splittings
  for, and use the **+** button to add to the list of perturbing and
  responding atoms manually.

You have now finished the setup of the calculation and are ready to
run it.

   **1.** Select **File → Save As** and give it an appropriate name (e.g. 'Ethyl_acetate_NMR')
   **2.** Select **File → Run**
   **3.** Wait for the calculation to finish (this can take 5 minutes up to several hours, that highly depends on your hardware)


Results of your calculations
============================


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:

   [image]


View the ^1H-NMR spectrum
-------------------------

Use AMSspectra to visualize the calculated spectrum

   Select **SCM → Spectra**
   In AMSspectra, set the "Width" to 0.01
 [image]

The NMR chemical shift \delta_i is defined as the difference of the
isotropic NMR chemical shielding of a reference compound \sigma_{ref}
minus that of the interesting compound \sigma_i:

   \delta_i = \sigma_{ref} - \sigma_i

The NMR program calculates NMR chemical shieldings \sigma_i.
AMSspectra uses as ^1H reference (TMS) shielding \sigma_{ref} = 31.7
ppm.

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

   Click on the **coupling** checkbox
 [image]

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:

   Select H(8) and click on the quartet in the spectrum
 [image]


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**
 [image]

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

[image]

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

   Click on **NMR** → **Chemical Equivalent Regions**

Tip:

  In the **NMR** menu you can adjust the thresholds that are used by
  the algorithm to identify equivalent regions.


Comparison of calculated and experimental spectrum
--------------------------------------------------

A good source for experimental spectra is the SDBS database:
https://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 ethyl acetate 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:

[image]

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:

[image]


Spectrum overlap
================

If you have an (experimental) spectrum in xy format with the same
units as your calculated spectrum, you can calculate and optimize the
overlap. The method used to calculate the overlap is SimIR/VCD from J.
Shen et al. Spectrochimica Acta Part A 76 (2010) 418-422. First, we
start with a clean AMSspectra window with our NMR calculation and
apply the previous NMR options:

   **1.** Open a **new** AMSspectra window: Select **SCM → Spectra**
   **2.** In AMSspectra, set the "Width" to 0.01
   **3.** Tick the Coupling checkbox
   **4.** Change the frequency from 200 MHz to  "89.56" MHz
   **5.** Click on **Chemical Equivalent Regions** in the **NMR** menu

Now we will add an experimental spectrum that has the same units as
our calculated spectrum:

   **1.** Click "here" to download the .xy file **Ethyl_acetate.xy**
   **2.** Add the spectrum: **File →  Add**
   **3.** Answer 'Yes' when asked to put the spectrum on the left axis

Tip:

  If your spectrum has different units you will want to put it on the
  right axis, so you can scale it separately. In that case you cannot
  calculate or optimize the overlap.

We will now optimize the overlap. The peak width, standard reference
(or offset in general), and scaling will be optimized to maximize the
overlap between the spectra.

Important to note is that only the current horizontal range is used to
optimize the overlap. Specific areas of the spectrum can be optimized
this way by limiting the range. The results are immediately applied to
the calculated spectrum. If the spectra are too dissimilar the
automatic optimization will fail, therefore first the calculated
spectrum is shifted by changing the reference chemical shift, such
that the largest peak at around 2 ppm almost coincides.

   In AMSspectra, set the "Standard" to 31.8
   Optimize the overlap: **Tools →  Optimize SimIR Spectra Overlap**
 [image]

The automatic optimization is sensitive to numerical noise, thus the
results of the automatic optimization may be different than the shown
results. Instead of the automatic optimizing of the overlap, just the
overlap can be shown and updated on the fly when the width, standard,
scale or horizontal range are changed.

   Show the overlap: **Tools →  Show SimIR Spectra Overlap**
