NCI

N C I

Go to my webpage

Theory

Download NCIPLOT et al.

Exercises

You can donwload the files for this exercises here.

You will see there are two repositories "wfn-files" and "xyz-files". Inside them you will find all the files necessary for these exercises. You will see that there are many extra files with dimers, for your own optional use.

Exercise 1.Looking at non covalent interactionsi

a) Phenol dimer is a good example where all types of interactions are present. Have a look at the interactions from the files PhenolDimer.xyz and PhenolDimer.wfn. Try to identify the different interactions and compare the differences between the promolecular and the SCF approach. You will see that you have to shift the cutoff in order to obtain similar images.

b) Intramolecular interactions are usually more complex in nature, with NCI surfaces that can contain both attractive and repulsive interactions. Work on peptide.xyz and see how the interactions look like.

Exercise 2. Selecting non covalent interactions

Work on PhenolDimer.wfn and try to separate the different types of interactions. Use the range-sign.csh script. Alternatively, you can also try to do it through keywords (CUBE,CUTOFF).

Exercise 3. Selecting the cutoff

Work on the file IL.wfn to visualize its interactions. You will need to appropriately choose the cutoff in order to see the stronger interactions. You can use the OUTPUT option first to see what range would interest you, and then choose the appropriate cutoff with the CUTOFFS and the CUTPLOT keywords.

Exercise 4. Analysing intermolecular interactions

Analyse the interactions in the inclusion complex between the 7-cucurbit and a bicycle derivative (files: cb7.xyz and bcb.xyz). This complex has a binding energy of the order of protein-ligand interactions. What interactions are responsible for the stabilization?

Use the intermolecular keyword and compare the result with the one from a normal run.