Basic tutorial 2

In this tutorial we learn how to create spin systems from molecule structure. We also use another type of spin particle than previous tutorial.


  1. Nmr prediction from structure
  2. Spectrum simulation
  3. Parameter iteration

Nmr prediction from structure

  • In this section we will learn how to create spin system from molecule strucure. In this tutorial we have a simple aromatic molecule p-bromochlorobenzene.


    As we can see the spectrum is very simple. To create spin system and chemical shifts from the molecule structure right click the structure and 'Nmr prediction...'.

    Nmr prediction

    The default options are usually suitable as in this case.

    Nmr prediction window

    Nmr predictor created spin system with two chemical shifts. There seems to be some systematic error so the chemical shifts should be dragged to correct positions.

    Predicted spin system

    Note also that the 'spin particle' type is 1*2*1 for both shifts. This allows different J-couplings between each coupled proton. In the picture below there are marked the possible J-couplings of particle 'A'.

    J-couplings of particle 'A'

    There is also J-coupling between protons 'B' and "B'" so all the couplings of this molecule can be defined with four coupling constants. The initial J-coupling matrix looks like this:

    The initial J-coupling matrix

    The shift '4_5' corresponds to protons 'A' and "A'" in the earlier picture.

    Next we can simulate the spectrum.

  • Spectrum simulation

  • Zoom into the region where the chemical shifts are and then simulate with ctrl+R. If you dragged the shift labels approximately on the observed shifts the result should be almost like this:

    Simulated spectrum

    The initial guesses for the J-couplings looks pretty fine. Now we can match the calculated shifts more accurately with the observed shifts by dragging the labels. Note the appearing stick spectrum when shift is selected. With the help of it we can match the calculated spectrum to the observed one.

    Stick spectrum

    After simulation the spectrum should look like this.

    Simulated spectrum after peak matching

    Now we are ready to iterate the parameters.

  • Parameter iteration

  • Iterate the spectrum with ctrl+T. The result should look like this:

    Iterated spectrum

    And we are ready with this analysis!

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