Clathrate Compound¶
A guest-containing inclusion compound whose host molecule or host-molecule arrangement forms a cage enclosing a guest molecule.
Core Idea¶
A clathrate compound is a guest-containing inclusion compound. A host molecule or arrangement of host molecules forms a cage, and a guest molecule sits inside it. Those four parts—host, cage, guest and inclusion—define this entry. Water cages around CO2 are one example, but clathrates need not have water hosts or a fixed cage-filling fraction.[ref-8f54920c2ed1][ref-ec77f2fc026c][^ref-46efc31d861a]
Both original positive examples here are crystals. IUPAC permits a cage formed by one host molecule as well as a host-molecule arrangement, so their crystallinity is not made a universal requirement. This packet does not claim an observed noncrystalline example.[ref-8f54920c2ed1][ref-ec77f2fc026c][^ref-46efc31d861a]
Scope of Application¶
The definition applies to guest-containing host-cage inclusion compounds, not to every hollow material or open-channel inclusion. Water-hydrate and organic hydroquinone structures are unlike chemical examples. Preparation pressure, cage size, guest occupancy, weak contacts and host survival are measured or conditional properties of particular materials, not all-instance rules.[ref-8f54920c2ed1][ref-5a7af08a796c][ref-ec77f2fc026c][ref-46efc31d861a]
The empty-framework comparison is limited. Publisher abstracts report guest-free Ge136 and nearly empty sodium–silicon cages; materials nomenclature can call them clathrate frameworks, but an actually guest-free framework does not pass this entry's IUPAC guest-containing test. The silicon sample still reports residual sodium.[ref-b5c6970bf518][ref-764fd110371f][^ref-8f54920c2ed1]
Clarity¶
For a proposed specimen, name the molecular host, show the enclosure it forms, identify a guest actually inside it, and explain the inclusion relation. A partly occupied set of cages can qualify. An open passage alone or an empty cage framework does not supply all four roles.[ref-8f54920c2ed1][ref-5a7af08a796c][ref-ec77f2fc026c][ref-46efc31d861a][^ref-764fd110371f]
Manages Complexity¶
This test separates what the compound is from how it formed and how much guest it contains. It prevents one measured water-hydrate filling fraction or one hydroquinone contact analysis from becoming a universal law. It also keeps the selected hydrate from standing in for every host chemistry.[ref-8f54920c2ed1][ref-ec77f2fc026c][^ref-46efc31d861a]
Abstract Reasoning¶
- Find a host molecule or host-molecule arrangement and the cage it makes.[^ref-8f54920c2ed1]
- Check that a molecular guest occupies the cage; distinguish a cage from an open channel.[ref-8f54920c2ed1][ref-5a7af08a796c]
- Describe measured occupancy or interaction only for the actual case. If no guest is present, report a framework boundary rather than this inclusion-compound positive.[ref-ec77f2fc026c][ref-46efc31d861a][^ref-764fd110371f]
Knowledge Transfer¶
Water and hydroquinone provide unlike hosts while preserving the same host–cage–guest–inclusion relation. This comparison transfers a chemical classification test, not a crystal-lattice requirement, a universal pressure recipe, or a substrate-neutral Prime. The reviewed DAG placement is an approved unparented root with zero strict edges.[ref-8f54920c2ed1][ref-ec77f2fc026c][^ref-46efc31d861a]
Example¶
CO2 water hydrate. Hartmann and colleagues study structure-I hydrogen-bonded water cages with CO2 guests. Their reported H2O specimen, prepared at 268.15 K and 15 bar, has refined small-cage occupancy 59.4(5)% and large-cage occupancy 99.2(2)%. This fills the host, cage, guest and inclusion roles; the percentages belong to that specimen.[^ref-ec77f2fc026c]
CO2–hydroquinone compound. Kleemiss and colleagues study hydroquinone host rings enclosing CO2 and report guest-site occupancy 0.854(2). Its organic host differs from water, while the same four roles remain. Their weak-contact inference is case-specific, and neither example proves a noncrystalline specimen.[^ref-46efc31d861a]
Neighborhood in Abstraction Space¶
Clathrate Compound sits in a sparse region of the domain-specific corpus (98th percentile for distinctiveness): few abstractions share its structure, so a faithful description tends to retrieve it precisely.
Family — Molecular & Cellular Biology Mechanisms (13 abstractions)
Nearest neighbors
- Regulation of gene expression — 0.77
- Protein quinary structure — 0.77
- Crystal structure prediction — 0.76
- Biological pathway — 0.76
- Chemical space — 0.75
Computed from structural-signature embeddings · 2026-10-08
Not to Be Confused With¶
- Clathrate hydrate: it is the water-host subclass, not the whole IUPAC class.[ref-8f54920c2ed1][ref-ec77f2fc026c]
- Open-channel inclusion: without enclosure it does not meet the cage test.[^ref-5a7af08a796c]
- Guest-free cage framework: “clathrate” may survive as materials terminology, but the guest-containing role does not.[ref-8f54920c2ed1][ref-764fd110371f]
- Universal occupancy or stability: the reported measurements and abstract-only near-empty case do not establish one.[ref-ec77f2fc026c][ref-46efc31d861a][^ref-b5c6970bf518]
References¶
[^ref-8f54920c2ed1]: International Union of Pure and Applied Chemistry, Gold Book, clathrates, term C01097, DOI 10.1351/goldbook.C01097, Definition. Authoritative definition; direct page retrieval can be intermittent. [^ref-5a7af08a796c]: International Union of Pure and Applied Chemistry, Gold Book, inclusion compound (inclusion complex), term I02998, DOI 10.1351/goldbook.I02998, Definition. The general inclusion entry distinguishes enclosure from an open channel; its interaction language is qualified. [^ref-ec77f2fc026c]: Christiane D. Hartmann, Susanne Hemes, Andrzej Falenty, and Werner F. Kuhs (2011), The Structure and Cage Filling of Gas Hydrates as Established by Synchrotron Powder Diffraction Data, Proceedings of the 7th International Conference on Gas Hydrates, Edinburgh; author manuscript posted to arXiv in 2015. PDF p.1 Introduction, p.3 Experimental Methods, pp.6–7 Results and Table 1. Full original conference study; sample occupancies are not universal. [^ref-46efc31d861a]: Florian Kleemiss and coauthors (2021), Accurate crystal structures and chemical properties from NoSpherA2, Chemical Science 12, 1675–1692, DOI 10.1039/D0SC05526C, §1.5.1 and §4.1.1, Fig. 4(a),(b). Full original methods paper; CO2–hydroquinone measurements are one case. [^ref-b5c6970bf518]: Abdelaziz Ammar and coauthors (2004), On the clathrate form of elemental silicon, Si136, preparation and characterisation of NaxSi136 (x→0), Solid State Sciences 6, 393–400, DOI 10.1016/j.solidstatesciences.2004.02.006, publisher abstract only. The printed original uses a colon before “preparation”; comma here retains a complete citation-work title. Reported residual sodium is about 35 ppm, so this is nearly empty, not guest-free. [^ref-764fd110371f]: Arnold M. Guloy and coauthors (2006), A guest-free germanium clathrate, Nature 443, 320–323, DOI 10.1038/nature05145, publisher abstract/title only. A materials-framework terminology boundary, not an IUPAC guest-containing positive.