Is there an automatic way to generate conformers for radical like systems (spin multiplicity is doublet)? My system for the study is a substituted fullerene with a missing H atom from the functional group.

I have tried using different conformer generators for this purpose (Baloon, RDKit, Obabel, Fullmonte, CCDC's Conformer_generator) but none of them successfully yielded out any conformers. I do not know how to run MD of such a system for which there is no general force-filed available. I have also tried to go through the AMBER tutorial but was unsuccessful: http://ambermd.org/tutorials/basic/tutorial4b/

I would really appreciate if anyone can suggest something that actually works for the system in consideration.

Thanks in advance.

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    $\begingroup$ Are you sure that a non-reactive MD calculation would be meaningful for a radical system? $\endgroup$ – Greg Jan 22 at 8:01
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    $\begingroup$ I recommend gfn2-xtb from the Grimme group: chemie.uni-bonn.de/pctc/mulliken-center/software/xtb/xtb I have not tried the confscript yet, but the siman option works reasonable well for my systems. $\endgroup$ – Martin - マーチン Jan 25 at 21:10
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    $\begingroup$ RDKit should work. Can you post the code somewhere (e.g. gist.github.com)? This code should also work for you github.com/jensengroup/get_conformations $\endgroup$ – Jan Jensen Jan 26 at 6:54
  • $\begingroup$ Just saw this - can you post the compound? I'm surprised that OB (and others) don't see "conformers" and it's possible that your structure falls beyond the usual rules. I'll post more later. $\endgroup$ – Geoff Hutchison Jan 28 at 21:54

tldr: Manually or script dihedral angle changes, then use a GFN or another DFTB method to find any/all conformers

Without seeing the compound, it's really hard to know the problem. Most programs, including those you mentioned, have a set of rules to identify "rotatable bonds" and suggest likely dihedral angles.

As you might expect, such rules are derived for neutral, ground-state organic molecules.

There are a few options:

  • As suggested by Jan Jensen's comments above, you can use RDKit, Open Babel or another tool to drive your own dihedral angle search.
  • As suggested by Martin's comments above, there are some tools in Grimme's xtb program to sample conformations. These will use the GFN1 or GFN2 approximate density functional (pretty much DFTB + dispersion correction) to evaluate energies.

I'd probably suggest a combination of both. From what I understand of Grimme's conformer search scripts, it calculates the vibrational modes of the molecule and samples geometries along vibrational modes. This is a good idea, although in some molecules it may not sample all minima (e.g., if you have many conformations in a large molecule, you might never "reach" the whole potential energy surface from any given initial geometry).

So you can change the dihedral angles using your program of choice, generate a few initial structures, then use xtb to optimize the geometries and confscript to sample a few more geometries.

I feel pretty confident that in small to medium geometry molecules, this will do a good job.

A few notes:

  • If you're sampling a radical, you definitely want to use a good DFT or quantum method to evaluate the energies. I doubt any current force field will do what you want.
  • We haven't finished our evaluation, but right now, GFN2 is performing better than any current method on conformer energetics for neutral organic molecules. We haven't checked radicals, but I would trust it more than any other current "fast" method.
  • If you don't have the xtb package, the method and conformer sampling scripts are now available as part of ORCA 4.1 too. There's a description of this kind of conformer sampling in the manual when discussing prediction of NMR spectra.
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    $\begingroup$ Your question is a great illustration of why my group is currently working on a "conformer toolbox" - an NSF-funded project to create a set of easy-to-use software for generating many kinds of conformers. I'll come back and revise when we have some better tools for problems like this. $\endgroup$ – Geoff Hutchison Jan 29 at 20:04

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