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How is the absolute configuration of chiral molecular knots determined? What rules should be applied? For centrochiral compounds, the CIP rules are applied, for axially chiral is described here and for planar chiral here. I can't find the system for assigning R/S (or possibly some other stereodescriptors) for molecular knots, e.g the attached knot doesn't contain an Sn improper axis, therefore it is chiral.

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  • $\begingroup$ I edited your question to improve it, but it would be still nice if you elaborated. $\endgroup$ – Mithoron Jun 12 '16 at 14:00
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    $\begingroup$ This is where topology\mathematics meets chemistry and becomes fairly complex fairly quickly. Mislow, one of the great, modern-day stereochemists, got the ball rolling. If you google "Mislow, trefoil chirality" you'll get a number of useful links, but again, it's involved. $\endgroup$ – ron Jun 13 '16 at 0:33
  • $\begingroup$ I've read it a bit and encountered this interesting question: could these compounds be resolved? $\endgroup$ – Marko Jun 13 '16 at 8:58
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The nomenclature of knot-like structures is not yet developed in IUPAC, let alone their stereochemistry.

However, there are some attempts in chemistry literature to describe the knots, drawing inspiration from math knot theory (however, even the detection of chiral knot is not yet completely resolved problem, apparently).

And sometimes there are contradictions. In TAUBER, Stephen J. Absolute Configuration and Chemical Topology. J. Res. Nat. Bur. Stand. A, 1963, 67: 591-599., you example knot's (let us just rotate him slightly in the paper plane by 60° clockwise or anticlockwise, does not matter, for "compatibility") intersection points are, according with the rule:

plus minus rule scheme

designated with plus signs at the intersection points:

knot plus

and the enantiomeric one with minuses:

knot minus

This notation is mentioned elsewhere, e.g. in SCHILL, Gottfried. Catenanes, rotaxanes, and knots. Elsevier, 2013.

However, in SAUVAGE, Jean-Pierre; DIETRICH-BUCHECKER, Christiane (ed.). Molecular catenanes, rotaxanes and knots: a journey through the world of molecular topology. John Wiley & Sons, 2008., in the chapter DNA Knots, your example knot is denoted in the opposite sense with minus signs,

enter image description here

and named "TREFOIL KNOT (−), 31", and the opposite one as "TREFOIL KNOT (+), 31+".

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I guess that the IUPAC Gold Book rules for helicity apply here.

The chirality of a helical, propeller or screw-shaped molecular entity. A right-handed helix is described as P (or plus), a left-handed one as M (or minus).

The above knotane is right-handed, so it should be P.

For more complex molecular knots such simple rules most likely will fail.

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    $\begingroup$ I agree that this system is applicable, but I would argue that the helicity here is left handed (M). Do you have any source applying the this system trefoil knot? Btw, here is knots helicity boosted one level above :) $\endgroup$ – mykhal May 7 '17 at 14:10
  • $\begingroup$ From both the image in the IUPAC Golden Book and from applying the right hand rule to the propeller (en.wikipedia.org/wiki/Right-hand_rule) I concluded that it should be P. However, I don't know any source where the system is applied to the molecular trefoil knot. Mathematically the trefoil knots are classified the other way round. So I might be wrong. $\endgroup$ – aventurin May 7 '17 at 18:38
  • $\begingroup$ i think it could be designated P using both the knot intersection points method in my answer and helicity nomenclature when focusing on fan lobes, or in opposite sense M when focusing on the interior – the knot it can be threaded on the "anti-screw" (levorotatory helix) $\endgroup$ – mykhal Sep 11 '17 at 2:02

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