by the way, i want it to be free preferably.i have two organic molecular structures that they are so much the same, i just want to know little differences between them and a software which can overlay them and show me the differences ... thank you so much for your attention.
You can use vmd program (www.ks.uiuc.edu/Research/vmd/). RMSD tools available there for analyzing structures will do what you are looking for.
I think Gaussian 09 software can help you in this case. This software is useful for prediction of molecular stability .
I think Gaussian 09 software can help you in this case. This software is useful for prediction of molecular optimization, molecular structure, and pictures of Homo and Lumo orbitals and overlaid structures and etc. of properties related to molecular structures such as natural charge, stability energies, geometry bond lengths and bond angles.
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