Adsorption of molecule on surfaces
The adsorption is the process of adhesion of any atom, ion or molecule from a generic phase (such as gas, liquid or solid) to a surface. This is a surface phenomenon and it is strictly related to the surface energy of a specific material: differently from a bulk structure, the surface atoms are under-coordinated, thus enabling the attraction of adsorbent. The adsorption of molecules can be divided in two main categories: physisorption, which is usually related to weak van der Waals interaction, and chemisorption, in which covalent bonding arises between the surface and the adsorbate. With this definition, chemisorption is usually stronger than physisorption.
Adsorption is present in a variety of natural processes and is involved in many research field (such as physics, chemistry and biology). Moreover, it is of paramount importance in many industrial and technological applications such as the creation heterogeneous catalysts, the addition of lubricant additives in base oils, the use of molecular inhibitors to reduce corrosion, and so on.
In the following sections, you will find a quick guide on how to compute the adsorption energy of molecules on a generic surface. This guide is completely independent on the code you are using, so it can be used as a general overview.
Creating the surface
The first step in computing the adsorption energy is to create the proper surface on which you will adsorb the molecule. This choice depends on the system you want to study. Usually, you have to choose the proper surface orientation (i.e., the proper Miller index, such as (100) or (111)) and model the system using a supercell with a specific number of layers and in-plane size of the surface (such as 1x1 or 2x2). In this way, you can change the coverage of your adsorbate, check if this can affect the adsorption energy and analyse different configurations useful for your study. Moreover, depending on the code you are using, you could add also a vacuum region along the vertical direction in order to avoid the self interaction of the system with its replicas (when periodic boundary conditions are applied).
Select the proper adsorption site
After you have decided which surface you want to use in your system, you have to choose the adsorption sites of your molecule. In principle, you can put your molecule in any point of the surface. However, it is well known that a surface has specific high symmetry points in which usually the adsorption of atoms and molecule reach a minimum (or a maximum). This is due to the fact that the surface atoms in these specific points have a higher (or lower) coordination, thus favouring a higher (or lower) adsorption of the molecule.
In the picture, you can see an example of a water molecule adsorbed on an aluminium (100) surface. As you can see, there are 3 high symmetry points in this surface. When you change the position of the water molecule over the surface, you can find different values of the adsorption energy, which can give you some hints of the nature of the adsorption process. If you don’t have any previous knowledge of which is the most favourable adsorption site, you can run separate calculations in order to find it.
To detect the high symmetry points of a surface, you can check the literature since these points have been already identify for any possible surface orientation and add manually the molecule over a specific site. Another possible approach is to use computational codes that can automatically check where are these points in a specific surface and that can add automatically the molecule over the surface. To do that, you can use the adsorption code written in python which is present in the repository.
Computing the adsorption energy
Once you have completed the previous steps, you can run the calculation and optimise (i.e., find the structure with the minimum energy) of you adsorbed system. To compute the adsorption energy , you can simply use the following formula:
where is the energy of the surface covered by molecules, is the energy of the isolated molecule and is the energy of the isolated surface. Therefore, to compute properly the adsorption energy, you should run 3 separate calculation: the first one in which you compute the energy of the complete system with the adsorbed molecule over the surface, and the following two with the calculation of the energy of the isolated surface and the isolated molecule. You can notice that when you use this formula, the adsorption will be energetically favourable when it is lower than 0.