Dear MS Community,
I came across a research paper,https://pubs.acs.org/doi/10.1021/acs.cgd.7b00163. In this paper, the authors have calculated the binding interaction energy using DFT in Gaussian 09 software. For geometry optimization, they used the B97-D3 Grimme function with the Gaussian-type 6-31(d,p) basis set. And for energy calculations, they used the double hybrid B2PLYP-D3 function with def2-QZVPP as the basis set. They calculated the Interaction Energy (IE) for API with different surfactants (at polar head and non-polar tail positions) using the formula IE= E of complex - (Ea+Eb).
I was trying to replicate the process on Materials Studio using the DMol3 module.
I have several queries in the process. I am describing them step by step:
- Geometry Optimization of Individual molecule: I have taken the .pdb files of API (Carbamazepine in this case) and surfactant (here Sodium Stearate). Then I geometry optimized the individual molecule in DMol3 using Hybrid B3LYP function and DNP as basis set. So query here is I am not able to find the exact function and basis set used by the authors. Please suggest the best possible combination that is available on MS.
- Making a complex: In this step, I am copying and pasting one molecule into the xsd file of geometrically optimized another molecule, let's say copying and pasting CBZ in the sodium stearate xsd file. I am placing CBZ at varying distances from the polar head of sodium stearate (ranging from 1.5-3Å). Is this methodology correct?
- Geometry Optimization of complex: Then, I am optimizing the geometry of these different complexes using Dmol3.
Single Point Energy Calculation: Next, I am calculating the Single Point energy of the complex and individual molecules (that are frozen in this complex). Here I am using the same function and basis set as used during optimization. Since I am varying the distance, I am getting different final interaction binding energies for each complex, whereas authors have reported a single value without mentioning the distance. Please throw some light on this
Also, please let me know if the workflow that I have adopted is correct. Suggest some tutorials or documentation to further my understanding.
I have attached a screenshot from the concerned research paper (Figure 8).
