Basic tutorial 3

In this tutorial we learn how to analyze unknown molecule structure with ChemAdder.


  1. Integration
  2. Spin system
  3. Parameter iteration


  • In this section we have unknown molecule structure. The used solvent is CDCl3 and the reference is TMS.


    Let's start with zooming into the aliphatic region. We can ignore the reference signal and then integrate the other ones by moving the marginals around the signals and clicking integrate button.

    Integrate the signals

    Next we want to normalize the integrals by choosing the least integral value.

    Choose the least integral value

    There appears integral options on the left panel. Edit the value of 'Normalized' to 1.

    Integral options

    Aliphatic region with the integrals will look like this:

    Integrated spectrum

    Let's move to the aromatic region.

    The aromatic region

    The small signal corresponds to residual CHCl3 solvent signal. Let's ignore it and integrate the aromatic signals.

    The integrated aromatic region

    The aromatic region signals seem to be traditional "AA'BB'" system which means the structure is para-substituted benzene. Note the strong 2nd order effect.

    Next we can create the spin system.

  • Spin system and spin particle determination

  • Let's create a spin system with five chemical shifts and move the shifts to correct positions.

    Spectrum after creating spin system

    In the previous tutorial we had also para-substituted benzene so the chemical shifts '1' and '2' are also spin particle type of '1*2*1'.

    Spin particle type

    The shift '3' is clearly spin particle type of '1*1*1' and shift '4' is '1*1*3'. The shift '5' is either type of '2*1*3' or '1*2*3'. Let's investigate what is the difference between these types. Set the type to '2*1*3' and add also a J-coupling of about 6.8 Hz between shifts '3' and '5'. Add some initial guess for molecular weight f.e. 120 g/mol, after that we need to simulate the spectrum and the result will look like this:

    Simulated spectrum

    The spectrum intensity has been changed to show the splitting pattern of the shift '3' more clearly. You can change the intensity by scrolling the mouse wheel. In the simulated spectrum the splitting pattern is quartet but the obserced splitting pattern is septet. Now change the spin particle type of shift '5' from '2*1*3' to '1*2*3' and the result should look like this:

    Simulated spectrum with spin particle type of '1*2*3'

    Now we can move to the aromatic region and add initial guesses for J-couplings:

    J-coupling matrix

    The result should look like this:

    Simulated spectrum of aromatic region
  • Parameter iteration

  • Let's resize the spectrum for full size and iterate the spectrum.

    Iterated spectrum

    Because the integrals aren't totally integers we can enhance the result by going to 'Profile & Control Parameters' and 'Constraints' and changing 'Responses' to 'Unfix all'.

    Change 'Responses' to 'Unfix all'

    Now iterate again. After iteration and cutting the x-axis (Ctrl+A and Shift+X) the spectrum should look like this:

    Iterated spectrum with responses unfixed

    The calculated spectrum is not perfect yet so we can change line shape options now. From 'Profile & Control Parameters' and 'Line Shape' change 'Linewidth Optimized' to 'Release'. Check also the 'Gaussian Optimized' and 'Asymmetry Optimized' options. Now iterate again and the spectrum should look like this:

    Spectrum with almost perfect match

    The calculated spectrum should now look almost a perfect match with the observed one. Now we can deduce the molecule structure. As we already know the signals in aromatic region is caused by protons in para-substituted benzene. The chemical shift '4' seems to be methyl group bonded directly to the benzene group. The chemical shift '5' seems to arise from two methyl groups. The J-coupling value of about 6.9 Hz with the shift '3' is due to vicinal (three-bond) J-coupling. So the shifts '3' and '5' arise from isopropyl group. Then our analyzed molecule structure is p-cymene (p-isopropyltoluene):

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