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Re^2: Calculation of complexation constant in water using firefly

Enrico
e.chiavazza@gmail.com


thx jim for having replied..
the anwer is..no, anything scientifically speaking... probably the main reason is that i don't have much experience on MD, asking about my work to some colleague they also suggested me to use MD to find the correct initial solvatation state for the reagent/product. So i performed some MD/MM for the aquo complex and for the ligand prior and after the complexation, in order to obtain the initial explicit water molecules positions.
I have to check the codes you cited.
thanks again
EC
 
On Mon Feb 9 '15 7:57am, Jim Kress wrote
----------------------------------------
>Is there any particular reason you are not doing this calculation with a Molecular Dynamics (e.g. gromacs) or Quantum Molecular Dynamics (e.g. Cp2K) code?

>I would think they would be better suited to your needs.

>Jim

>On Mon Jan 19 '15 2:12pm, Enrico wrote
>--------------------------------------
>>Hello to everyone,
>>I'm trying to estimate a trend in the complexation constant of sodium ion with several polycarboxylic ligand in water, i know that i should calculate the dG value of the complex from the G value of the reagents, i read several paper on which they explain the need of corrections that account for the solvatation contribution and for the thermal factor (in order to bring the system from 0 K to 298 K and 1 bar). In order to do that I've found the optimized structure of the participant molecule under PCM solvent modeling and than i run an hessian calculation to obtain the thermochemistry at RT but if i use the gibbs energy that i obtained from the thermochemistry i obtain a positive dG for the complex that do not reflect at all the experimental behavior so now i have some question to which i couldn't find an answer elsewhere:

>>- what is the correct energy value that i have to consider from the firefly output?
>>- what are the correct correction factor (Ezpe,Hcorr,Scorr,solvent) that i need to get a formally correct dG for the complexation reaction?

>>solved these basic issues, in your opinion is it better to take into account explicitly the first solvatation sphere of the sodium ion (6 water molecules)?

>>you can find attached a set of output file for the smaller complex of my serie,
>>thank you

>>EC


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