I like to draw a molecule in different conformations in a) website or b) freeware and

  1. Calculate its relative energy difference (for example to the lowest global energy conformation)

  2. Display the lowest energy conformation

I'm particularly interested in the calculation of diaxial interactions, gauche interactions, double gauche pentane interactions (and less in ring strain, like chair / half-chair / twisted rings).

I know there are plenty of tools for modelling conformational and electrostacic properties. Most of those are not freely available. Do you an easy solution? It does not must to be the most precise one, relative energy differences in steps of 0.1 kcal/mol between two drawn conformations would be fine for me.

May be this question is off-topic, because it's a software request, but I didn't know where else I could ask this question.

  • 4
    $\begingroup$ 0.1 kcal/mol is very precise $\endgroup$ – pH13 - Yet another Philipp Aug 27 '15 at 10:29
  • 2
    $\begingroup$ I agree with @PH13 that 1 kcal/mol, much less 0.1 kcal/mol is extremely precise based on existing computational methods. $\endgroup$ – Geoff Hutchison Aug 27 '15 at 14:14
  • 1
    $\begingroup$ @GeoffHutchison Geoff, I started playing around a bit with Avogadro + Gaussian and had a question. Since you are one of its authors, could you please answer me: what exactly does the conformer energy obtained from Molecular Mechanics -> Calculate Energy signify? Is this enthalpy of formation or energy relative to some standard form or w/e? I tried searching the Wiki first, but it's not really helpful as most articles either don't exist or are only half written. Thanks in advance! $\endgroup$ – Jori Aug 27 '15 at 18:34
  • 1
    $\begingroup$ @Jori If you are using MMFF94, it loosely corresponds to a heat of formation, but relative comparisons are best. Using molecular mechanics for an absolute heat of formation is unreliable at best. $\endgroup$ – Geoff Hutchison Aug 27 '15 at 20:26

Avogadro can do a lot of this for you. It might not be precisely what you want but the molecular mechanics from Open Babel integrated into it can do at least some of the tasks you mentioned. It's free and has a very intuitive and smooth user interface. A real pleasure. The downside is that it's poorly documented.

To play around with conformations, go to Extensions -> Molecular Mechanics. To view the generated conformers (from the Conformer Search option) go to View -> Properties -> Conformer Properties...

  • $\begingroup$ I've drawn methylcyclohexane and then clicked: Extension -> Optimize Geometry. Now I get a planar molecule, whats only from symmetrical point of view optimized. I want now to see that Avogadro changes the conformation (global energy minimization) with the chair and with Me equatorially placed. How can I do this? (Afterwards I'd like to put the Me axially calculate the energy and then see if the energy calculation approximately gives the A value of Me of 1.74 kcal/mol.) $\endgroup$ – laminin Aug 27 '15 at 20:50
  • $\begingroup$ @laminin Just follow my instructions :) . I didn't say to use Extension -> Optimize Geometry! $\endgroup$ – Jori Aug 27 '15 at 20:58
  • $\begingroup$ I have to add that conformer search doesn't work in Avogadro for cyclic parts of the molecules (as I've read and experienced). $\endgroup$ – Jori Aug 27 '15 at 21:10
  • $\begingroup$ When I "draw a molecule, click Extension -> Molecular Mechanics -> Conformer Search -> Systematic rotor search -> OK", I also get a planar methyl-cyclopropane :( $\endgroup$ – laminin Aug 27 '15 at 21:15
  • 1
    $\begingroup$ I'll point out that there's now a manual which covers conformer searching. $\endgroup$ – Geoff Hutchison Nov 25 '15 at 16:23

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.