Thanks John:

I mean how to do encapsulation computationally, eg. by Gaussian or any other method.

There have been several publications of MD (molecular dynamics) studies of the encapsulation of different kind of molecules within cyclodextrins, here are some of them:

1) Rodriguez, J.; Elola, M. D. J. Phys. Chem. B 2009, 113, 1423.

2) Cai, W.; Sun, T.; Liu, P.; Chipot, C.; Shao X. J. Phys. Chem. B 2009, 113, 7836.

3)  Yu, Y.; Chipot, C.; Sun, T.; Shao X. J. Phys. Chem. B 2008, 112, 5268.

4)  Yu, Y.; Chipot, C.; Cai,W.; Shao X. J. Phys. Chem. B 2006, 110, 6372.

5) He, J.; Chipot, C. J.; Shao, X.; Cai, W. J. Phys. Chem. C 2013, 177, 11750.

They use the ABF (adaptive biasing force) methodology within the NAMD simulation package. Details on the technique can be found at:

6) Darve, E.; Pohorille, A. J. Chem. Phys. 2001, 115, 9169.

7) Henin, J.; Chipot, C. J. Chem. Phys. 2004, 121, 2904.

8) Rodriguez-Gomez, D.; Darve, E.; Pohorille, A. J. Chem. Phys. 2004, 120, 3563.

The ABF tutorial at NAMD website is very good:

http://www.ks.uiuc.edu/Training/Tutorials/namd/ABF/ABF-tutorial-files/