ORIGEN DE LAS ESPECIES 4.1 Modos de especiación.

DFT calculations were used to generate PES landscapes for all the intramolecular degrees of freedom within the cage fragment. These were obtained using B3LYP calculations with a 6-31G(d,p) basis set within the Gaussian09 package.59

2.7.2. DL_POLY_2.20 MD package

All MD simulations simulations were carried out using DL_POLY 2.20; Smith, Forester and Todorov developed this at Daresbury Laboratory.60 _{DL_POLY_prep,}

developed by David Willock,61 _{was used to convert the starting configurations into}

the correct file formats. Analyse_hist61 _{was used to examine the MD trajectories;}

this calculated the relative energies, deviations of the intramolecular degrees of freedom, mean squared displacement of gas molecules and from this their diffusion coefficients.

2.7.3. Accelrys materials studio 5.0

Materials Studio was used to visualise the structures as well as calculate both the surface areas. Both the Forcite and Discover modules were used to minimise any structures; here CSFF was implemented. The Atom Volumes and Surfaces module was used as one method to generate the calculated surfaces.18

2.7.4. Visual molecular dynamics

The Visual Molecular Dynamics, VMD, was used to display and analyse the trajectories of all MD calculations.62 _{It was also used in combination with Zeo}++ _to

generate both the connectivity pore topologies as well as accessible surface area plots.21

2.7.5. Zeo++

Zeo++_{, developed by Haranczyk, was used in combination with VMD to visualise}

both the connectivity and pore topologies of the systems. In addition to this, Zeo++ _{was used to generate binary cube files that were in turn read into the}

VISIT software package,63 _{so that any dynamic connectivity could be studied.}

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