The many names of crowns

What is the best way to name the structure (a)?

(a)

1,4,7-trioxonane (Hantzsch-Widman) 1,4,7-trioxacyclononane (replacement) cyclo[tri(oxyethylene)] (organic macrocycle) 9-crown-3 (Pedersen) 9<O3coronand-3> (Vögtle-Weber)

The general naming method is skeletal replacement applied to the corresponding carbocyclic parent hydride, in our case cyclononane, thus 1,4,7-trioxacyclononane. Or we can use extended Hantzsch-Widman (H-W) system and call it 1,4,7-trioxonane. For rings with up to ten members, the H-W names are preferred [1, p. 96].

What about the structures (b)—(d) then? Since all of these rings have more than ten members, we cannot use H-W system, so we have to give them replacement names: 1,4,7,10-tetraoxacyclododecane (b), 1,4,7,10,13-pentaoxacyclopentadecane (c), 1,4,7,10,13,16-hexaoxacyclooctadecane (d). Rather long, completely unambiguous, and very boring.

Polyoxomolybdate clusters of Mo/W-storage protein

Five years ago, Schemberg et al. reported the crystal structure of molybdenum/tungsten storage protein from Azotobacter vinelandii complexed with polyoxotungstates [1, 2].

Now Kowalewski et al. report the 1.6 Å X-ray structure of the same protein containing a variety of polyoxomolybdate clusters, from Mo₃ to Mo₈ [3].

Some N₂-fixing bacteria prolong the functionality of nitrogenase in molybdenum starvation by a special Mo storage protein (MoSto) that can store more than 100 Mo atoms. The presented 1.6 Å X-ray structure of MoSto from Azotobacter vinelandii reveals various discrete polyoxomolybdate clusters, three covalently and three noncovalently bound Mo₈, three Mo_5–7, and one Mo₃ clusters, and several low occupied, so far undefinable clusters, which are embedded in specific pockets inside a locked cage-shaped (αβ)₃ protein complex. <...> The formed polyoxomolybdate clusters of MoSto, not detectable in bulk solvent, are the result of an interplay between self- and protein-driven assembly processes that unite inorganic supramolecular and protein chemistry in a host–guest system.

1. Schemberg, J., Schneider, K., Demmer, U., Warkentin, E., Müller, A. and Ermler, U. (2007) Towards biological supramolecular chemistry: a variety of pocket-templated, individual metal oxide cluster nucleations in the cavity of a Mo/W-storage protein. Angewandte Chemie International Edition 46, 2408—2413.
2. PDB:2OGX
3. Kowalewski, B., Poppe, J., Demmer, U., Warkentin, E., Dierks, T., Ermler, U. and Schneider, K. (2012) Nature’s polyoxometalate chemistry: X-ray structure of the Mo storage protein loaded with discrete polynuclear Mo–O clusters. J. Am. Chem. Soc. 134, 9768—9774.

Cucurbituril

“Cucurbituril” may sound as a name of a natural product derived from some plant of Cucurbita genus. Wrong. There is a connection, though. According to this review,

In 1981, the macrocyclic methylene-bridged glycoluril hexamer (CB[6]) was dubbed cucurbituril by Mock and co-workers because of its resemblance to the most prominent member of the cucurbitaceae family of plants — the pumpkin.

My best 2-D representation for cucurbit[5]uril (a) does not look particularly pumpkiney. It is more like a sea urchin skeleton. Granted, its 3-D model (b) may look a bit like cleaned pumpkin devoid of top and bottom, but it still looks like a sea urchin skeleton (c) to me.

(a) cucurbit[5]uril in 2-D

(b) cucurbit[5]uril in 3-D

(c) sea urchin skeleton

Cucurbiturils, pumpkin-like or not, can be as useful as hunny pot that Pooh the Bear presented Eeyore: you can put things in them. For example, the platinum-containing anticancer drug oxaliplatin (d) can be put inside of cucurbit[7]uril to form a stable 1:1 complex (e). Jeon et al. suggest that this can increase the stability of the drug as well as to reduce unwanted side effects of oxaliplatin.

(d) oxaliplatin

(e) cucurbit[7]uril-oxaliplatin