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Tutorials: Shielding

We now start running castep calculations by looking at two small systems, and examining the issue of "convergence".

Start by copying the input files into your home directory ie

cp /home/jr_yates/jryates/WORKSHOP/workshop_nmr_intro.tgz ./
unpack it
tar -zxvf workshop_nmr_intro.tgz

Example 1 - Ethanol CH3CH2OH


Fig1. Proton spectrum of ethanol

The discovery that one could actually see chemical shifts in hydrogen spectra was made in 1951 at Stanford University by Packard, Arnold, Dharmatti (shown in Fig 1). We will try to reproduce this result.

FILES:

OBJECTIVES:

  1. Examine the convergence of the chemical shieldings with planewave cutoff
  2. Compare to experiment.

INSTRUCTIONS:

A suitable σref for 1H is 30.97ppm.


Fig1. Proton spectrum of liquid ethanol.

Example 2 - Diamond

FILES:

OBJECTIVES:

  1. Examine the convergence of the chemical shielding as the sampling of the electronic Brillouin zone (BZ) is increased.

INSTRUCTIONS:

kpoints_mp_grid 4 4 4

The computational cost scales linearly with the number of kpoints (ie the number of points in the irreducible Brillouin Zone). For a large unit cell (ie a small BZ) it may be possible to get converged results using a single k-point. But which kpoint should we choose?

For diamond we will look at 3 different k-points (0,0,0), (,,) (,,). Specify the kpoint in the cell file using
%BLOCK KPOINTS_LIST
0.25 0.25 0.25 1.0
%ENDBLOCK KPOINTS_LIST

Which gives a result closest to the converged answer? (as the diamond unit cell is rather small the 1 kpoint answer is not too close to converged. However, the observation holds true for all orthorhombic cells)

PART 3

We now look at some more realistic examples.

Oxygen-17

Oxygen is a component of many geological materials. Oxygen is also important element in organic and biological molecules since it is often intimately involved in hydrogen bonding. Solid State 17O NMR should be a uniquely valuable probe as the chemical shift range of 17O covers almost 1000 ppm in organic molecules. Furthermore 17O has spin I = 5/2 and hence a net quadrupole moment. As a consequence of this the solid state NMR spectrum is strongly affected by the electric field gradient at the nucleus.

Because the isotopic abundance of 17O is very low (0.037%) and the NMR linewidths due to the electric field gradient relatively large, only limited Solid State NMR data is available. This is particularly true for organic materials. First principles calculations of 17O NMR parameters have played a vital role in assigning experimental spectra, and developing empirical rules between NMR parameters and local atomic structure.

Example 3 - Alanine, a simple amino acid

FILES:

OBJECTIVES:

  1. Compute the chemical shift and Electric field gradient for alanine
  2. Assign the 17 NMR spectrum


Fig3. Solid-State O17 NMR spectrum of L-alanine. (b) is from MAS (magicangle- spinning) (c) is from DOR (double-orientation rotation)

INSTRUCTIONS:

δ(A)-δ (B) (ppm)23.5
CQ (A) (MHz)7.86
ηQ (A)0.28
CQ(A) (MHz)6.53
ηQ(A)0.70

Table 1: Experimental 17O NMR parameters for alanine. The two resonances are labeled A and B. Isotropic chemical shift δ , quadrupolar coupling CQ, and EFG asymmetry ηQ.

Example 4 - Silicates Quartz and Cristoballite

FILES:

OBJECTIVES:

  1. Compute the chemical shift and Electric field gradient for two silicates.
  2. Assign the 17O NMR spectrum

INSTRUCTIONS:

 δ (ppm)CQ (MHz)ηQ
Material A37.25.210.13
Material B40.85.190.19

Table 2: Experimental 17O NMR parameters for two silicates. Isotropic chemical shift δ , quadrupolar coupling CQ, and EFG asymmetry ηQ.

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Page last modified on August 18, 2015, at 01:49 PM