Hi I want to model the adsorption of molecule on surface. Is it possible to change the orientation of molecule and to calculate adsorption energy for different position? How to change a ring from vertical to planar?
The orientation of a molecule adsorbed on the surface can be characterized by its center of mass and the three Euler angles. Given the atomic positions of your molecule in the molecule fixed system, you can recalculate the atomic positions in the surface fixed coordinate system by an appropriate shift of its center of mass, and the appropriate multiplication with rotation matrices containing the Euler angles.
However, especially in the case of chemisorption, the internal geometry of a molecule (bond lengths, bond angles) could also depend on the orientation and the distance relative to the surface.
I think, as a first approximation the quantum-chemical method can help
A program for the quantum-chemical calculations should be available (for example, Gaussian). It is necessary to optimize the system "surface - molecule". The program will display the most favorable location of the molecule concerning the surface. Different variants of bonds of "surface - molecule" should be calculated; the system with the lowest energy is the most preferred.