Dear Chandra,

The question is vague. As you know isomers can be if many different kind ex. Geometric, structural, conformational, etc.

Then there are a multitude of properties that could be measured using dft. So it would help the question to identify which compound, isomer and the property you are looking at to obtain an adequate answer.

Thanks for reply. I have cis &trans stilbene interacting with graphene. Although trans binds more. I want to know apart from binding energy is their any way that explains this phenomena.

I'm assuming you have already looked at the output model? Orientation might be one reason. In the cis formation seems more compact. I would even go farther to say that it might even be a smaller isomer in size due to such high localisation of pi-orbitals. The trans conformation does not appear to be so and may simply be a little larger. Have you seen how well each isomer stacks on graphene? I wonder if there is a way to quantify alignment.