Mobile adsorbate with TAMkin

[tfjer...@gmail.com]

Dear all, 

I would like to compute the free energy of a zeolite + adsorbate following the methodology described in J.Chem.TheoryComput.2011, 7,1090–1101

I compute a partial Hessian displacing the atoms of the adsorbate (methanol in this case) and the Brønsted acid proton of the zeolite. 

I then do a normal mode analysis on the Hessian treating the methanol molecule as a mobile block, followed by a normal mode analysis where all atoms are moved individually. 

Please the attached python script for the details.

By computing the overlap between the modes resulting from the mobile block treatment (class PHVA_MBH) and the  modes resulting from the partial Hessian (class PHVA), I see that there is one mode of the partial Hessian with a frequency < 100 cm-1 and a large overlap > 0.9 with a mode of the mobile block Hessian. 

When I animate the frequencies with Molden, I see that the frequency corresponds to a rotation. 

I now want to substitute that vibrational mode with a rotational mode as done in J.Chem.TheoryComput.2011, 7,1090–1101.

However, I am not able to understand how this is done in TAMkin. 

I would be very happy if someone could give me some guidelines on how to do this. 

Please find attached the python script for the procedure described above. 

Thanks a lot in advance for your help. 

Regards,

Torstein Fjermestad

 

[Jakob Brauer]

Hi Torstein,

I am attempting a similar approach to get the free adsorption energy of molecules adsorbed in zeolites. Have you by any chance figured out how to remove the identified frequencies from the vibrational partition and how to treat them as rotations?

Thanks in advance and kind regards

Jakob Brauer