Hello all.
I am working on aqueous adsorption of pharmaceuticals with MOF, COF, and generally nano materials.
I am a bit familiar with the above tools most especially Chemdraw.
I wish to calculate Binding/Adsorption energies via DFT calculations. But first of all, I must need simulate the binding of the adsorbent-adsorbate. Please how can I use either of the above software tools to bind molecules together OR better still, what is the modus-operandi to simulate the binding of the adsorbent-adsorbate in order to calculate E(adsorbent_adsorbate).
NOTE: As for E(adsorbent) or E(adsorbate) alone, I guess I can sort them out myself.
Thanks in advance for your kind response.
This topic falls in the more general investigation on the interaction of a molecule (whatever its application) on a surface.
According to my experience, two main theoretical approaches can be tested:
1) Using plane wave DFT. A portion of the assemble surface+molecule is repeated following the symmetry rules of (and hence the periodicity) of the crystal. Software suites such as Quantum Espresso (https://www.scm.com/product/quantum-espresso/) can be used.
2) Cutting a portion of the surface (also including a portion of the bulk) of not lesse than 100-300 atoms with the interacting molecule disposed as far as possible from sides and corners. The assemble is relaxed with the positions of the surface kept frozen. This can be done with several QM software suites. An example is Gaussian (http://www.gaussian.com).
I recently worked on the application of the second approach in investigating restoration/consolidation materials for carbonate stones (see DOI:10.1039/C8NJ01714J on New J Chem).
As far as the design of the model is concerned, in any case you probably want to start from crystallographic data of the solid phase, and you can use Mercury (https://www.ccdc.cam.ac.uk/solutions/csd-system/components/mercury/) to elaborate the cif data, from which the orthogonal Cartesian coordinates of the atoms you select can be saved.
In a second step, you can add the interacting molecule with Molden (free: http://cheminf.cmbi.ru.nl/molden/) or GaussView (commercial: http://gaussian.com/gaussview6/).
This topic falls in the more general investigation on the interaction of a molecule (whatever its application) on a surface.
According to my experience, two main theoretical approaches can be tested:
1) Using plane wave DFT. A portion of the assemble surface+molecule is repeated following the symmetry rules of (and hence the periodicity) of the crystal. Software suites such as Quantum Espresso (https://www.scm.com/product/quantum-espresso/) can be used.
2) Cutting a portion of the surface (also including a portion of the bulk) of not lesse than 100-300 atoms with the interacting molecule disposed as far as possible from sides and corners. The assemble is relaxed with the positions of the surface kept frozen. This can be done with several QM software suites. An example is Gaussian (http://www.gaussian.com).
I recently worked on the application of the second approach in investigating restoration/consolidation materials for carbonate stones (see DOI:10.1039/C8NJ01714J on New J Chem).
As far as the design of the model is concerned, in any case you probably want to start from crystallographic data of the solid phase, and you can use Mercury (https://www.ccdc.cam.ac.uk/solutions/csd-system/components/mercury/) to elaborate the cif data, from which the orthogonal Cartesian coordinates of the atoms you select can be saved.
In a second step, you can add the interacting molecule with Molden (free: http://cheminf.cmbi.ru.nl/molden/) or GaussView (commercial: http://gaussian.com/gaussview6/).
Thanks Prof. Massimiliano Arca for your elaborate explanation. I think I will give the last suggestion a try, since I'm already familiar with GaussView.
Thanks again.
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