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I want to estimate mean Gibbs free energy of formation of glucose and for that purpose I think conformers of ring flip should be taken into account. Do you know if some free program can find those structures automatically? (for example Balloon).

The following image shows the conformers I need to get. I am trying to avoid the possibility of drawing it.

ring flip by Jawero from Wikipedia

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    $\begingroup$ I use RDKit for conformation searching. More info here proteinsandwavefunctions.blogspot.dk/2016/08/… $\endgroup$ – Jan Jensen Sep 28 '17 at 7:44
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    $\begingroup$ I'm sorry (new to chemistry here, but your question is interesting to me and I would like some clarification.) Are you asking for software that will generate conformers for you? (Just thought it was a cool question and wanted clarity.) $\endgroup$ – Melanie Shebel Oct 12 '17 at 18:36
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    $\begingroup$ @MelanieShebel yes, some free programs that can do that are: balloon and RDkit, you can download them in the web. Also avogadro can do that, although I never try it :).. $\endgroup$ – santimirandarp Oct 12 '17 at 18:41
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Use RDKit

It sounds like you're only considering free or open source conformer generation tools. In that case, I highly recommend using RDKit, since the distance-geometry (and in turn ETKDG) methods will intrinsically generate all possible ring geometries. That includes not just the two chair forms you indicate, but all possible ring-puckering forms.

There are other free tools which do this, but RDKit has been repeatedly shown to be the best or among the best free conformer generation tools. (Based on current benchmarks.)

I'd advocate the newer ETKDG method with RDKit, since it seems to produce somewhat better geometries.

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  • $\begingroup$ Hi, thanks for the reply. As far as I know RDkit doesn't move B-A-O-H diedrals(doesn't see hydrogens), and also doesn't find conformers for ciclohexane. Have you tried that? $\endgroup$ – santimirandarp Oct 12 '17 at 19:37
  • $\begingroup$ With most conformer programs, the hydrogens are added at the end. As for cyclohexane, yes RDKit can generate multiple different conformers. $\endgroup$ – Geoff Hutchison Oct 12 '17 at 19:52
  • $\begingroup$ Is it possible to add hydrogens to oxygen and nitrogen before the conf search for those programs? Otherwise, I think some relevant structures will be missed, mainly in sugars. $\endgroup$ – santimirandarp May 31 at 14:32
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I am not aware of a program that does that, unless you want to run a PMF yourself, but, on the side, here is a systematic study of the energetics of monosaccharide sugar puckering: Heather B. Mayes, Linda J. Broadbelt, and Gregg T. Beckham, J. Am. Chem. Soc. 2014, 136 (3), 1008–1022. DOI: 10.1021/ja410264d. You may find here the info you are looking for.

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    $\begingroup$ Welcome to Chemistry.SE! Take the tour to get familiar with this site. We prefer to use human-readable references and non-pdf links, I have edited your post accordingly. $\endgroup$ – Martin - マーチン Sep 28 '17 at 11:52
  • $\begingroup$ great!Thanks Elisa. Would you clarify PMF? $\endgroup$ – santimirandarp Sep 28 '17 at 12:52
  • $\begingroup$ PMF stands for potential of mean force. Here is a review you may find interesting, sciencedirect.com/science/article/pii/001046559500053I $\endgroup$ – Elisa Fadda Sep 29 '17 at 13:31

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