Step 5 - Structure Factors

Time to create some isotopologues for our system and calculate the structure factors.

Isotopologues

We need a partly-deuteriated isotopologue for the cation where the alkyl groups are fully deuteriated but the imidazole ring hydrogens remain as protons.

Go to the   EMIM   species tab, Isotopologues section

Select the Isotopologues section to create a new isotopologue definition

Click Add to create a new isotopologue definition

Right-click on the name of the new isotopologue and choose Set hydrogens to ⇨ Deuteriated from the context menu to set all hydrogen types to deuterium

Change the isotopes for the HCW and HCR atom types back to to Natural (bc = -3.739 fm)

Double-click the name of the isotopologue and change it to H3D8

For the anion we need a fully deuteriated version:

Go to the   Acetate   species tab, Isotopologues section

Click Add to create a new isotopologue definition

Change the isotope for the HCA atom type to 2 (bc = 6.671 fm)

Double-click the name of the isotopologue and change it to D3

Structure Factors

Now we can create a new layer to calculate the RDF and structure factors:

Layer ⇨ Create ⇨ Correlations ⇨ RDF and Neutron S(Q)

Our reference datasets are listed in the following table - we’ll refer to them in the form X-Y where X is the isotopologue of the cation and anion respectively:

	Cation	Anion	ID	Datafile
1	Natural	Natural	H-H	SLS39546-H_H.mint01
2	Natural	D3	H-D3	SLS39548-H_D.mint01
3	H3D8	Natural	H3D8-H	SLS39549-H3D8_H.mint01
4	H3D8	D3	H3D8-D3	SLS39550-H3D8_D.mint01
5	Natural	H:D3 50:50	H-50	SLS39567-H_50.mint01
6	H:H3D8 50:50	H:D3 50:50	50-50	SLS39568-50_50.mint01

Note that there are no exchangeable hydrogen atoms in this system.

The existing NeutronSQ represents sample 1 in the table since it will default to use the natural isotopologues for the cation and anion, so all that remains to do for that one is to set its identifying name and the reference datafile:

Click on the first NeutronSQ module to select it

Double-click on its name and change it to H-H

Find the Reference Data settings group, and for the Reference keyword select the file SLS39546-H_H.mint01 and set the format of the data to mint

For the remaining datasets you need to drag a new NeutronSQ into the layer from the module palette (click the Show Avaliable Modules button if you can’t already see it) and set the relevant isotopologues, short name, and datafile as listed above.

Finally, we need to set the instrumental broadening in the SQ module first:

Click on the SQ module to select it

Set the QBroadening to OmegaDependentGaussian with a FWHM of 0.02

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