I have a very long pathway to map using DFT. There are approximately 15 intermediates. I am using Gaussian to capture the reactants, intermediates, transitions states and the products.
I have so far managed to successfully isolate my first five transition states. From going from one transition state to the other, the product of one which essentially becomes the reactant of the next, needs some changing e.g., a change in number of water molecules. Now I fin that the DeltaG (also the DeltaH, DeltaE and DeltaSCF) are way off.
For examples:
Re(+16.54kcal/mol)TS1(+16.10kcal/mol)Int1 This involved two water molecules.
The next step only involves one water molecule on the other side of this long fragment. So I took Int1 (from above) and added a new water molecule on the other side. Note: I took out the first two water molecules, as they are not directly involved at this stage of the reaction mechanism.
Int2(+42.27kcal/mol)TS2(+30.29kcal/mol)Int3.
Unfortunately, the problem occurs when I try and compare any of the energy measurements (enthalpy, gibbs free, SCF, ZPE, etc..) between In1 (product 2 water molecules) with Int2 (the reactant, only one water molecule). There is a huge +401037.58 kcal/mol difference. So in total....
Re(+16.54kcal/mol)TS1(+16.10kcal/mol)Int1 (+401037.58kcal/mol) Int2(+42.27kcal/mol)TS2(+30.29kcal/mol)Int3.
I am now certain that it is because I took out the first two water molecules. But I thought DeltaG was a state function, so in theory, that reaction would/could happen even without those two water molecules present from the previous reaction.
Would really appreciate some assistance with this one.
Thanks
Anthony
Dear Anthony,
I suggest that you add one water molecule to the optimized structure having only one molecule of water and place the new water molecule about 4 Angstrom from the structure and run optimization. Using this strategy you can compare the two intermediates since they have the same number of atoms.
Hoping this will be helpful,
Rafik
Thanks Rafik for the explanation. I will try that suggestion.
However, if I were to be measuring Gibbs Free Energy, which is a state function, would I be able to add the Free energy of separate water molecules to my system instead? i.e., reaction A has happened with two water molecules, and it releases one water from the system, reaction B only requires one water moles, so the two others water molecule are accounted for separately as it in theory has nothing to do with the second reaction. e.g.,
Re(molecule+2H2O) -> TS -> IntA(Molecule+3HO)
IntB(Molecule+1H2O) -> TS IntC(Molecule+1H2O)
........
For the free energy (G):
G(intA) = G(Molecule+3 water)
G(intB) = G(Molecule+1 water) + G(2 water)
Although, when I do this, I now find there is a DeltaG of 37 kcal/mol, which although it is a lot smaller than 401037.58kcal/mol, it is still quite large.
Thanks
Dear Jonathan,
If you add the Free energy of separate water molecule you will end with incorrect value.
The best way is to add the water molecule to the structure with less water molecule and to optimize by DFT. By this way you balance the number of atoms.
Doing the calculation as it is shown below will lead to false result.
G(intA) = G(Molecule+3 water)
G(intB) = G(Molecule+1 water) + G(2 water)
Rafik
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