Hello, I've been investigating a bunch of monomers which spontaneously react in water to form a polymer. I would like to know how to calculate the thermodynamics of such a system. On the surface, this seems like a straight-forward question, however, I've only seen implementations of thermodynamic integration, free energy perturbation, or umbrella sampling for the most part. Unfortunately, my system is not simply A + A = B, it's A + A + A + A + A + A(n) = B(n). i.e. it's 10 monomers linking together to form a single polymeric molecule. Now in TI, FEP, or US most implementations are simply atom 1 of molecule A and atom 2 of molecule B are constraint and bonded/broken. However, for a many reaction system, how much one achieve Gibbs energy and entropy? I would ideally like to compare the Gibbs energy of state 1 (only monomers in solvent) and state 2 (polymer in solvent). And then also look at solvation energy by obtaining state 3 (only solvent). Is there a way to obtain JUST the thermodynamics of a single set of trajectories or from a single simulation? Why do we need to use two separate simulations which are compared? How would I obtain G and S for my hypothetical system?
Thank you!
Ab-initio calculations are able to converge just for small molecular systems. For big models (>~10 atoms) you should use first principals (DFT) or molecular dynamics methods (MD), probably PM7 semiempirical as a good option.
Once molecular energy of the first monomer is known, you are able to calculate its thermodynamic functions, such us enthalpy, entropy and gibbs free energy (the three are required). Remember, molecular energy does not depend on the tempetarure and pressure but thermodynamic functions yes, so you have to do your thermo functions calculations at T and P you think your system is going to proceed. At this point you are able to calculate them computationally (same level of theory and basis sets as molecular energy trought harmonical frequencies calculation) or with an spreadsheet. For spreadsheet option calculations, apart from math models, you will need the molecular energy, T and P, the rotational constants (A, B and C) and harmonical frequencies (remember these will depend on the degrees of freedom of your molecular system and if it is linear or not). Once thermodynamic functions for one monomer are known, you must calculate them for a) A1+A2 and for b) B. Then Hreact=HB-(HA+HA); Sreact=SB-(SA+SA) and Greact=GB-(GA+GA). If Hreact is negative your reaction is exothermic and if Greact is negative will be exergonic. To proceed that reaction step in cold conditions both are required, and for hot conditions, just exergonic. Now the transition state or minima among A1 and A2 must be calculated, as well as their associated thermofunctions. They will define the barriers to overcome or if it is a barrierless reaction. Remember, before finising this step, you have to proceed with a IRC (or a simmilar method as single or double ending method) in order to assure your reaction flows in the correct direction (from reactants to products) on their potential energy surface (PES). The same for B+A3=C.... and so one.
I hope this helps.
For a fairly small system (something like a dimerization) you can use quantum espresso which comes with the meta-dynamics PLUMED plugin. https://sites.google.com/site/plumedweb/home
This is well known and works most of the time for sufficiently small system. Since, at the end, its PWDFT required for MD, the cost is high to you should not expect to deal with > 500 atoms (that too with very generous computational time !) .
- Badges
- Science topic
- Similar topics
- Chemistry
- Theoretical Chemistry
- Computational Chemistry
- Molecular Dynamics