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patonlab / GoodVibes

Calculate quasi-harmonic free energies from Gaussian output files with temperature and other corrections
http://www.patonlab.colostate.edu
MIT License
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Media keyword #33

Closed medvedev-m closed 4 years ago

medvedev-m commented 4 years ago

Hello!

Could you, please, explain, what is the "entropy correction to calculations done on solvent molecules calculated from their standard concentration", which is requested with --media keyword? Is there any reference to it?

Best regards, Michael G. Medvedev

luchini18 commented 4 years ago

Hi Michael, When calculating standard state free energies (Go), the IUPAC specifies that the standard concentration used (co) should be 1M for calculations of reagents in solution and 1 atm (L mol-1) for gas phase (see doi.org/10.1351/goldbook.S05925). Use of standard state thermodynamic values for computational studies is emphasized in doi.org/10.1021/jp802665d. GoodVibes can calculate standard concentrations for different media specified in the readme, provided an output calculation file for the solvent. Hope this is helpful! Guilian Luchini

bobbypaton commented 4 years ago

With media keyword, we have some solvents for which we have coded the concentration based on their density (eg water is 55 mol/l). The effect on the free energy appears in the translational entropy term. I believe the recent review from Harvey, himo, maseras, Perrin in acs catalysis talks about making such corrections.

medvedev-m commented 4 years ago

Thank you for the explanation!

It seems that "--media" only works correctly when "-p 1" is set (or assumed). So it is impossible to use it along with "-c" which could be important when working with several files simultaneously (e.g. GoodVibes.py -q -c 1 --media h2o *.log). This is likely because --media just adds an appropriate constant for getting from "-p 1" to "-c 55.5", exactly as shown in 10.1021/acscatal.9b01537.

Perhaps, it could prove useful to just switch Solvent concentration to the appropriate value, ignoring the "-c" keyword for it, while using the input concentration for all other entries.

Best regards, Michael G. Medvedev

luchini18 commented 4 years ago

Thanks for the input, the --media keyword will now apply to specifically the solvent molecule, and if the -c option is specified, the specified concentration will apply to all other molecules.