Tutorials

Jcoupling

Start by copying the input files into your home directory ie

cp /home/jr_yates/jryates/WORKSHOP/workshop_nmr_jc.tgz ./

Example 1 - Ethene C2H4

FILES:

  • c2h4.cell
  • c2h4.param

OBJECTIVES:

  1. Compute C-C C-H and H-H couplings
  2. Compare to experiment.

INSTRUCTIONS:

  • Look at the param file. task = magres and magres_task = jcoupling .
  • Look at the cell file. Note the line jcoupling_site : C 1. This sets the perturbing atom. We will be computing the J-couplings between this site and all others in the calculation.
  • Run castep. (castepsub ethanol) Look at the output file. At the end the isotropic J-coupling is reported, listed in order of distance from the perturbing atom.
  • Change the perturbing atom and re-run the calculation. How many calculations are needed to compute all the coupling? Some couplings can be computed in two ways - how do they compare?
  • Compare with experiment - J(C1-C1)=67.5Hz, J(C1-H1)=156.3Hz, J(C1-H3)=2.4Hz, J(H1-H2)=2.2Hz , J(H1-H2)=11.6Hz, J(H1-H2)=19Hz
  • What is the effect of using a GGA functional?

Example 2 - Ethyne C2H2

Repeat the above calculations for C2H2

%block POSITIONS_ABS
bohr
C -0.001000 -0.001000 -0.001000
C 2.266671 -0.001000 -0.001000
H 4.269781 -0.001000 -0.001000
H -2.004110 -0.001000 -0.001000
%endblock POSITIONS_ABS
  • Compare with experiment. J(C1-C2)=184Hz, , J(C1-H2)=242Hz, , J(C1-H1)=53, , J(H1-H2)=10Hz.

Example 3 - Alanine

Look at J-couplings in the molecular crystal Alanine (take the cell file from the shielding example).

A calculation on the primitive cell is too small to give converged results - but you can get an idea of the couplings. Note any spurious couplings which arise from interactions of periodic images (eg when the 1st and 2nd distances are roughly equal).