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The most stable cyclohexane form is the chair conformation but on the other hand, the bigger the side-chain of the cyclohexane is, its hydrogen atoms become more equatorial rather than axial, which brings them closer to the cyclohexane's hydrogens. Shouldn't they arrange in a less energetic, but a more stable conformation?

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    $\begingroup$ The general rule is that larger substituents prefer the equatorial positions. I'm not sure I understand what you're asking here, which hydrogens do you mean? $\endgroup$ – Mad Scientist Apr 29 '12 at 12:05
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    $\begingroup$ ""Shouldn't they arrange in a less energetic, but a more stable conformation?"" The "but" is nonsense. $\endgroup$ – Georg Apr 29 '12 at 12:25
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    $\begingroup$ Consider rewriting your question and choosing a more appropriate title, as both are a bit confusing. Also, @MadScientist, he seems to be talking about the side-chain's hydrogen atoms. $\endgroup$ – CHM Apr 29 '12 at 15:50
  • $\begingroup$ @CHM: but then "equatorial" is not exactly an appropriate adjective for those hydrogens, seeing that they're not attached to cyclohexane... yes? $\endgroup$ – user95 Apr 30 '12 at 12:39
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It's not exactly clear from your question what distances you consider, but I have taken snapshots of a methylcyclohexane with the methyl group in the equatorial and axial positions:

enter image description here      (equatorial)

enter image description here    (axial)

The distance of the methyl $\ce{H}$ atoms to the nearest cyclohexane $\ce{H}$ atoms are displayed, and you'll see that indeed the axial position has a shorted $\ce{H–H}$ distance of ~ 2 Å, while equatorial position has longer $\ce{H–H}$ distances.

Also, as others have remarked in the comments: only the groups (and $\ce{H}$ atoms) directly on the cyclohexane ring are said to be in axial or equatorial position. Atoms of side chains do not follow this terminology, in particular for side chains that can rotate freely as it means nothing there.

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