2
$\begingroup$

I am trying to calculate the total energies for a particular organic molecule that undergoes radical decomposition. I was able to calculate the neutral molecule with the exact results of a paper I found. My trouble is obtaining the correctly calculated energies for the radical molecules. I am new to computational chemistry and am looking for a bit of guidance on this.

$\endgroup$
10
  • 2
    $\begingroup$ The question is too broad. You did not mention neither the molecule in question, nor the level of theory. Anyway, reproducing someone's results is usually a tough task; in many cases it requires the use of exact same program. But since you was able to reproduce the results for the neutral molecule, then presumably you use exact same level of theory (and maybe even the same program). For radical the first thing to check is which formalism was used in the published work: restricted open-shell or unrestricted. $\endgroup$ – Wildcat Jul 14 '15 at 17:09
  • 2
    $\begingroup$ The best way to make the discussion much more meaningful is: 1) to provide the reference to the published work you're aiming to reproduce; 2) to provide the details of your attempts to reproduce it (i.e. input files). $\endgroup$ – Wildcat Jul 14 '15 at 17:15
  • 1
    $\begingroup$ True. Then, presumably, the default, i.e. unrestricted, formalism was used for radical species. That is fine, since it is the default option in (almost?) all programs; at least it is also default in Q-Chem (according to the manual). What I don't understand is that in the referenced paper Mo6-2x was not used; ωB97X-D was used instead. How then you was able to reproduce the total energy for the neutral molecule using a different functional? $\endgroup$ – Wildcat Jul 14 '15 at 20:09
  • 1
    $\begingroup$ I skimmed through the paper (as well as the supporting materials), and I couldn't see any total energies out there, but only relative total energies. If you reproduced relative total energies for the neutral molecule, then how good the reproducibility was? You've said it was "exact", but what do you actually mean by this? Do you have exact same relative total energy in kcal/mol for neutral molecule? And what is the difference for radical then? $\endgroup$ – Wildcat Jul 14 '15 at 20:16
  • 1
    $\begingroup$ @EdwardHD I suggest you edit the details you provided in the comments into the body of your question. Right now it is in the close queue. I would also like to encourage you to follow wildcats advise and provide as much context as you can. Only this way, we will be able to help you. $\endgroup$ – Martin - マーチン Jul 15 '15 at 6:59
3
$\begingroup$

Disclaimer: this is a preliminary answer based on the current state of the discussion with OP; it might be the subject to major changes in the near future.

So.

  1. OP (original poster) is trying to reproduce some relative energies previously computed at ωB97X-D/6-31+G(d,p) at a different M06-2X/6-31G(d,p) level of theory. OP has exact same results for closed-shell molecular species in question, the meaning of which is probably that the resulting M06-2X/6-31G(d,p) relative energies in kcal/mol or kJ/mol are exactly equal to the previously published ωB97X-D/6-31+G(d,p).
  2. OP also mentioned that he has some troubles in reproducing the relative energies for open-shell species, by which he probably means that for open-shell species M06-2X/6-31G(d,p) spits out different numbers in kcal/mol or kJ/mol than ωB97X-D/6-31+G(d,p).

Before we have some numbers let me say few things which hold in generality.

  1. The difference in few kJ/mol in relative energies computed using two different functionals is pretty normal (even at exact same geometry). One should not even expect exactly same relative energies with any two different functionals in the first place.
  2. OP presumably run geometry optimization at M06-2X/6-31G(d,p) but did not mention how different are the equilibrium geometries obtained at this level from those at ωB97X-D/6-31+G(d,p) level published previously. In fact, this would be difficult to do, because I could not find the Cartesian coordinates of the species in question in the Supporting Information for the work published previously. But at least some quick visual comparison has to be done to make sure that equilibrium geometries are at least not totally different.
  3. OP did not mention why M06-2X functional was chosen. Even if the ultimate goal is not just to reproduce the previously published work, it is mentioned there that:

    ωB97X-D, a range-separated double-hybrid functional, has been shown to describe reaction energies accurately.45

    But, first of all, ωB97X-D is not a double-hybrid functional. And secondly, the paper quoted there is fairly well-known benchmark of density functional methods done by Lars Goerigkab and Stefan Grimme, and in fact, Goerigkab and Grimme found M062X-D3 and not ωB97X-D to be "statistically the best of all hybrids". Note though that M062X-D3 differs from M062X: the former includes the empirical dispersion correction while the later does not.

  4. With respect to the empirical dispersion correction, today it is usually recommended to include it in DFT calculations, since it is available at almost no (computational) cost but can substantially improve the results. Note also that dispersion correction is already included in case of ωB97X-D functional but has to be "manually" added for the case of M06-2X. In fact, the absence of it might explain some differences in equilibrium geometries and relative energies.

$\endgroup$

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