Tools for Molecular Simulation

Question

I am a high school student and I don't know a whole lot about molecular simulation. I wish to view different conformers of cyclohexane and the changes that occur when substituents are attached (for example cis-1,4-di-tertbutylcyclohexane attains a twist boat shape) through molecular simulation.

The only easy-to-use tool I could find was MolView, but I can't see the above molecule getting into a twist boat shape when I ran an energy minimization because it swapped the cis to a trans form (which is in a chair conformation). Couldn't find the molecule through PubChem as well, so that I could import it.

I would also like to try out ortho effect on substituted benzene rings. Basically, I want to see a few simple molecules, (not anything like proteins and other macromolecules) and run an energy minimization on them.

So, is there any easy-to-use, free molecular energy minimization simulation program that can help me achieve this?

Answer 1

A very simple way is using molecular mechanics: it only applies to very simple molecules, but it should be enough for your purpose. Avogadro is a free software which allows you to build structures and to minimize them via molecular mechanics, through a variety of "methods" (force fields). The software outputs an estimate of the energy of your geometry, which you can compare to that if other geometries (for instance, boat vs chair cyclohexane).

Note that these results are very approximate, the methods work properly only in the case of neutral and covalent molecules, but anyway they provide good results for a qualitative analysis.

More accurate methods, capable of working with more complex molecules (in order of accuracy: semiempirical methods, like PM3, PM6, AM1... << Ab initio methods like HF and DFT methods like B3LYP, M06, PBE...) exist in other software packages, but this is a good starting point for learning.

Molecular mechanics works by treating angles, bonds, etc. as subject to forces (Imagine them as springs) which constrain them to an "optimal" conformation, as seen in sets of typical and simple molecules.

The other methods work by solving quantum-mechanical equations, with or without some approximations, and thus can treat "atypical" geometries which don't work with molecular mechanics.

To make a example, molecular mechanics works well for whole sets of typical molecules like our amino acids, but fails to predict the geometry of strange molecules, like tetrahedrane, which shows very atypical angles.

Within these limits, you can use molecular mechanics for free and with not much computational and software hassle