In this post I will show an example where initial molecules are rotated to generate initial conditions for bimolecular collisions. The molecules which are considered are sulfanide and acetone cyanohydrin. These molecules most likely played an important role in the production of origins of life compounds (see B.H. Patel, C. Percivalle, D. J. Ritson, C. D. Duffy & J. D. Sutherland, Nature Chemistry 7, 301–307 (2015))
In Fig. 1, the minimized structure of each molecule is shown.
In Fig. 2, a set of randomly rotated structures of the molecules of Fig. 1 is shown.
With these initial positions and by defining some initial atomic velocities we can run dynamics for bimolecular collisions. Here this was done using TeraChem (http://www.petachem.com/). In the first video here below, I show a set of multiple trajectories (each of these was run separately) where the molecules collide at 300K.
In the second video a single trajectory is shown. From this we can see that the angle at which reactants approach is an important variable in determining whether a reaction will occur. In fact for this trajectory no reaction occurs.