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Do molecules with bridges through rings (in a manner illustrated by this) exist?

example diagram

I sometimes get results like this when doing Energy Minimization on molview.org. For example:

molview.org Jmol result

Is this actually a thing?

EDIT: As a slightly more realistic example, consider this:

slightly larger molecule as example

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    $\begingroup$ When a lactone is synthesized, a small proportion of the chains close their rings when the chain is passing through a ring previously made. There are no bridges between the two rings, and they cannot get separated. But, who knows. May be in a later step, some bridges may be synthesized between the two rings. $\endgroup$
    – Maurice
    Feb 29, 2020 at 22:31
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    $\begingroup$ This earlier Q&A entitled, Interlocked cyclic compounds, may be helpful. $\endgroup$
    – ron
    Feb 29, 2020 at 22:48
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    $\begingroup$ Bad examples - these are non-existent. $\endgroup$
    – Mithoron
    Feb 29, 2020 at 23:09
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    $\begingroup$ You seem to be asking whether such molecules can exist in general. But are you implicitly asking whether the compound you modeled makes sense? Because what you're seeing is a common artifact of energy minimization that has nothing to do with chemistry. I've seen it referred to as "ring punch" but I can't find much more about it... $\endgroup$
    – Calimo
    Mar 1, 2020 at 14:27
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    $\begingroup$ Not unless you rewrote question. Even your "more realistic example" is not realistic at all. $\endgroup$
    – Mithoron
    Mar 1, 2020 at 22:07

3 Answers 3

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I'm not sure about the existence of molecules with bridges through rings. However, there are several publications of synthesis of molecules mimicking wheels and axles ([2]rotaxanes; The “[2]” refers to the number of interlocked components) as one shown below (Ref. 1):

Wheel & Axle in OC (The diagram is from Reference 1)

This specific molecule (8; an “impossible” [2]rotaxane) represents a macro-cycle with a straight-chain molecule with bulky end groups going through its center. The inclusion of two bulky end groups prevents the straight-chain molecule leaving the macro-cycle (mechanically interlocked) as depicted in the diagram (See Ref. 2 for the total synthesis of the molecule).

Note that Ref. 1 also cited articles for the synthesis of [2]catenanes, which contain two interlocked rings (instead of one axle and one macrocycle). Keep in mind that there are some advanced catenanes and rotaxanes that exist (e.g., [3]catenanes and [3]rotaxanes).

catenanes (The structures are from Reference 1)

References:

  1. Edward A. Neal, Stephen M. Goldup, "Chemical consequences of mechanical bonding in catenanes and rotaxanes: isomerism, modification, catalysis and molecular machines for synthesis," Chem. Commun. 2014, 50(40), 5128-5142 (https://doi.org/10.1039/C3CC47842D).
  2. Jeffrey S. Hannam, Stephen M. Lacy, David A. Leigh, Carlos G. Saiz, Alexandra M. Z. Slawin, Sheila G. Stitchell, "Controlled Submolecular Translational Motion in Synthesis: A Mechanically Interlocking Auxiliary," Angew. Chem., Intl. Fd. 2004, 43(25), 3260-3264 (https://doi.org/10.1002/anie.200353606).
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    $\begingroup$ The examples look pretty much like the catenane chemistry pushed forward by Sauvage (en.wikipedia.org/wiki/Jean-Pierre_Sauvage). The motif of cyclic polyethers / crown ethers, as well as the guiding «pre-orientation» of a chain into an already existing ring by weak coordination (including transition metal complexation) often occured in Lehn's publications, too. $\endgroup$
    – Buttonwood
    Mar 1, 2020 at 22:11
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    $\begingroup$ Catenanes can also be found in biology: the capsid of the bacteriophage HK97 contains 71 rings that pass through each other to form "protein chainmail". ( science.sciencemag.org/content/289/5487/2129.long ) $\endgroup$
    – timeskull
    Mar 2, 2020 at 15:56
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A variation on this theme is Ice VII, in which two cubic ice structures are intertwined with hydrogen bonds from each component structure passing through the hydrogen-bonded rings formed by the other component. Known to occur naturally on Earth as a high-pressure phase trapped in diamonds, Ice VII is a stepping-stone to the macromolecular and superionic ices believed to exist in some giant planets.

enter image description here

Source

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Ring-opening polymerization, in particular using olefin metathesis which keeps growing closed rings in the absence of linear olefins, will produce macrocycles that are intertwined to form a pseudo cross-linked network, globally insoluble polymer. This can be later "un-crosslinked" by resuming the metathesis reaction with linear olefins.

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