4.

Solid-State Host-Guest Compounds

The formation of solid-state clathrate, or cage, compounds has been known since the discovery of the
chlorine clathrate hydrate, an inclusion compound between Cl2 gas and water–ice, by Sir Humphrey Davy in
1811. The term clathrate was coined by H. M. Powell in 1945 from the Latin clathratus meaning ‘to fit with
bars’. Originally the term applied to inclusion compounds of hydroquinone and was specific to cases where
the guest is held in a cage-like cavity in the host solid. It has gradually broadened to include most aspects of
molecular solid-state inclusion chemistry and is almost interchangeable with the term ‘solid-state inclusion
compound’. As with many aspects of supramolecular chemistry, it required the advent of modern X-ray
diffraction techniques by which chemists fully understood these inclusion compounds. The realization that
clathrates essentially involve the physical imprisonment of the guest molecule either within a host cavity or,
more commonly, within voids in the crystal in between hosts, has inspired modern supramolecular design of
molecular hosts that can imprison neutral guests in both the solid state and solution and, indeed, carry out
chemistry within the host matrix or cavity. However, there are two crucial differences between the kind of
molecular host-guest chemistry and the more traditional solid-state clathrate chemistry:

1. The host in a clathrate is the entire (usually crystalline) solid and the guest binding cavity does not
need to be an intrinsic property of the individual host molecules.
2. Clathrates can often be non-stoichiometric corresponding to cases in which not all of the voids in the
crystal are filled by guests.

Clathrate Hydrates
Formation
Clathrate hydrates are inclusion compounds formed by the enclosure of a small guest molecule
within a hydrogen bonded cage of solid-state water. Clathrate hydrates are co-crystals and are thus distinct
from ice, which is made of pure water, and hence can have different physical properties to ice such as a
different melting point. The classic example of a clathrate hydrate is the ‘burning snowball’ of methane
clathrate hydrate. The combustion of the methane in the clathrate is self-sustaining, Figure 7.1.

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 Figure 7.1 ‘Burning snowballs’ of methane clathrate hydrate

Compounds such as alcohols, acids and ammonia, which are capable of such stronger interactions,
do not generally form hydrates, although a few examples are known in which anions (e.g. F−) are
incorporated within the host framework without causing its collapse. This type of inclusion is a typical
example of enclathration and is quite distinct from the formation of stoichiometric metal salt hydrates such
as NiCl2·6H2O, which actually contains the discrete octahedral coordination complex [Ni(H2O)6]2+.

Structures and properties

‘Normal’ ice, Ih, does not possess any cavities capable of including guest molecules. However, in the
presence of hydrate-forming species, a template reaction occurs in which polyhedral cavities are formed
about the guest according to guest size. These cavities are composed almost exclusively of fused five- and
six-membered hydrogen-bonded rings (Figure 7.2), and are denoted by superscripts according to the
numbers of each type of ring present in the cage (Figure 7.3).

Almost all clathrate hydrates form one of two basic structures, termed type I and type II. Type I
clathrates arise from the fusion of two 512 and six 51262 cavities (i.e. two cavities comprising twelve 5-
membered rings and six comprising twelve 5-membered rings and two 6-membered rings), while the much
larger type II unit cell (the crystallographic unit cell is the basic structural repeat unit or building block of
the crystal) possesses sixteen 512 and eight 51264 cages. There are only around six exceptions to these two
basic types, out of more than 100 clathrate-forming compounds. These exceptions are bromine, dimethyl
ether, ethanol, ammonium and alkyl amine salt hydrates (low-symmetry structures III–VII) and molecules
approximately the size of methyl cyclohexane or larger (structure H – a material that is now known to be

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naturally occurring and remarkably stable). Structure H is unique in being the only structure to include four-
membered rings of water molecules (a special case is dimethylether which forms ‘structure T’ hydrate which
possesses 51263, 51262 and 4151063 cages). More recently, Udachin and Ripmeester have also reported a very
unusual new ‘complex’ structure containing features related to structure H and structure II (composition:
1.67 choline hydroxide · tetra–n–propylammonium fluoride ·30.33 H2O). The properties of the three main
structural types and cages are summarized in Figure 7.3. The bromine clathrate hydrate is unique in being
the only one to form a 15-hedral cage, 51263, which generally has an unfavorable strain relative to the other
three cavities.

Figure 7.2 Hydrogen bonded rings of water molecules found in clathrate hydrate structures. Four-membered rings are
only found in structure H

In general, small guests occupy the small 512 type cavities. The small difference between the size of
this cavity in structures I and II can have a significant effect on which structural type is adopted. Thus, the
smallest guest, argon (radius 1.92 Å) occupies the smaller 512 cavity of structure II, as do N2 and O2.
Methane and H2S (radii 2.18 and 2.29 Å, respectively), while still small enough to fit within the 512 cavities,
form structure I hydrates. Helium, hydrogen and neon are small enough to diffuse through the hydrogen
bond ‘bars’ of the cage and do not form hydrates. The larger 51262 cage found in structure I hydrates is large
enough to entrap molecules of diameter up to about 6.0 Å (e.g., ethane, CO2) and plays the main structure-
stabilizing role in almost all structure I hydrates, being the preferred site for most guests. The 51264 cavity
will encompass molecules as large as 6.6 Å, such as propane and iso-butane. Even n-butane may be
accommodated over a limited temperature and pressure range if a small co-guest is available to fill the 512
cavities. The range of guest sizes and their effect on structural type adopted is summarized in Figure 7.4.
While it is possible to fill all of the cavities with the appropriately sized guest molecules, in reality some
cages remain empty and real hydrates have more water than the ideal composition. For example, the original
chlorine clathrate hydrate was determined (after some controversy) to have an empirical formula Cl2.10H2O,
compared to the ideal 7⅔ water molecules for a type I structure with only the 51262 cavities occupied. In the
vast majority of cases only a maximum of one guest molecule occupies any given cage. Under high pressure
small guests particularly hydrogen can form hydrates with up to two guest molecules in the small cage and
four in the large cage of hydrate structure II.

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Figure 7.3 Cavity types found in structures I, II and H clathrate hydrates and the numbers of each that goes into each
structure unit cell along with number of water molecules and typical guests. Each vertex denotes a water molecule;
connecting lines represent hydrogen-bonded contacts

Figure 7.4 Comparison of guest sizes and cavities occupied as simple hydrates

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Problems and Applications
The oil and gas industry has developed a number of methods for combating the problems of hydrate
formation, both in terms of treatment of the gas and equipment and in process design, in order to minimize
hydrate-forming conditions and the consequences of hydrate deposition. Indeed, it is estimated that between
5 % and 8 % of the total process cost is in addressing the hydrate problem (about US$1 billion per annum).
Among the most important methods are:
• drying the natural gas;
• heating the gas to temperatures above the hydrate melting point;
• lowering the gas pressure to below the hydrate formation point;
• influencing the hydrate formation phase diagram by injection of large quantities of inhibitors such as
methanol, glycol or salt solutions, although these latter may often be corrosive (these are known as
thermodynamic inhibitors); and
• reducing the rate of hydrate formation through the use of low dosage hydrate inhibitors – small
quantities of polymeric organic materials, which inhibit the nucleation of hydrate crystals (i.e. they
act as kinetic inhibitors) such as PVP (polyvinylpyrrolidinone, 7.1).

In addition to post-extraction problems, the presence of a gas hydrate layer in the earth during
drilling may also have catastrophic effects. Gas hydrates and their decomposition due to sudden changes in
pressure or temperature have been known to cause problems such as casing damage, uncontrolled gas
release, blowouts, fires and gas leakage outside the casing. As a result, extensive geological surveys are
carried out to determine hydrate distribution, volume, reservoir temperature, pore pressures, rock porosities
and permeabilities. Particularly large natural hydrate layers may occur in sediment either below permafrost,
or beneath the ocean floor. Action is generally taken to either prevent hydrate decomposition or promote its
decomposition in a controlled, manageable fashion.

While natural gas hydrate formation is currently regarded as an expensive nuisance by the petroleum
industry, as natural fossil fuels run out it may be that hydrates of methane could become a valuable fuel
source. Calculation of density of methane within methane hydrate, CH4·6H2O, suggests that the hydrate
corresponds with a highly compressed form of the gas (184 times the amount of methane is stored by
hydrates than the equivalent gas volume at standard temperature and pressure), despite its stability at
relatively low pressures. The lattice energy of methane hydrate is such that about only 10 % of the energy
available from combustion of the methane would be required to decompose the hydrate. This is illustrated
strikingly by the fact that methane hydrate will support its own combustion (Figure 7.1).
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In addition to the use of existing hydrates, it has also been suggested that clathrate hydrates could find
applications in storage and separation technology. Bardhun showed in 1962 the viable application of
hydrates in desalination of sea water, while hydrates have also been investigated as a method for the storage
and transport of methane without the use of high-pressure containers.

The use of hydrates in synthetic systems is in the separation of gases by the differences in the
formation conditions of their respective hydrates. For example, it is possible to separate hydrofluorocarbons
and nitrogen in this manner. Pollutant streams can also be cleared up in a similar fashion and it has been
shown that hydrates are able to recover carbon dioxide from a mixture of CO2, O2 and N2 in high yields.
Perhaps the most striking recent results in the promise of clathrate hydrates in hydrogen storage applications.
Up to 4 % by weight hydrogen can be included at modest pressures by tuning clathrate hydrate composition
to allow the hydrogen guests to enter both larger and smaller cages using water-soluble hydrate promoters
and various small gaseous guests.

Urea and Thiourea Clathrates

Structure
The common organic molecule, urea (7.2), and its sulfur analogue, thiourea (7.3), both form solid-
state clathrates with long-chain hydrocarbons such as n-alkanes. Urea is able to act as a host by virtue of
strong intermolecular hydrogen bonding interactions between the acidic protons of the NH2 groups and the
oxygen or sulfur atoms of adjacent molecules. This results in the formation of a chiral, helical hollow tube of
urea molecules of minimum van der Waals diameter 5.5–5.8 Å, into which guests of small cross-section can
fit. This helical arrangement, termed hexagonal- or β-urea, allows each urea molecule to hydrogen bond with
all of its NH protons, maximizing intermolecular interactions. This means that each oxygen (or sulfur) atom
must accept a total of four hydrogen bonds. The thiourea channels are similar but larger and with more
variation in their diameter, allowing inclusion of branched hydrocarbons although not small n-alkanes
(Figure 7.5). While hexagonal urea may generally be regarded as comprising fairly smooth tunnel-like
channels, the thiourea host channels are more ‘cage-like’.

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Figure 7.5 (a) Stereoview of one urea host channel. The chiral ribbons are defined by the anti-N—H … O hydrogen
bonds and are interlinked by the syn-N—H … O hydrogen bonds. (b) Van der Waals cross-section of the cavity in the
urea channel compared with the size of n-octane (left), benzene (top), 3-methylheptane (right) and 2,2,4-
trimethylpentane (bottom), (c) chemical structures of urea and thiourea, (d) packing of urea channels to give the
honeycomb-like structure of hexagonal urea.

Guest Order and Disorder

One of the main interests in urea inclusion compounds is their potential application in the separation
of linear and branched hydrocarbons in the petroleum industry. Because the channel diameter is only slightly
larger than the van der Waals diameter of a linear hydrocarbon, only a small amount of branching can be
tolerated. Whether a particular urea inclusion compound will form or not may be assessed simply by
comparison of the channel size with the diameter of the guest. For example, benzene is found to be
marginally wider than the channel, and inclusion is quite difficult (Figure 7.5b). Interestingly however,
increasing chain lengths allow the toleration of larger, more branching end groups. Thus, 1-phenyloctane
does not form an inclusion compound, but the much longer 1-phenyleicosane does. Equilibrium vapor-phase
measurements suggest that the enthalpy of complexation increases by approximately 10.0 kJ mol−1 for each
−CH2− group added to a linear chain, and hence the additional stabilization gained upon complexation of the
longer guest outweighs the unfavorable steric interactions with the phenyl end group. In general, alkane
guest molecules display one-dimensional ordering in urea channels. They are ordered along the urea channel
direction in the sense that they all have the same orientation, but the line of guests in one channel may freely
slip along the channel axis relative to the guests in another. This one-dimensional ordering is characterized
by the observation of diffuse scattering lines in the X-ray diffraction pattern instead of discrete Bragg peaks.
If the guests have a more anisotropic shape, then they can distort the urea channels and give rise to two-
dimensional ordering. The example of the p-didecylbenzene inclusion compound of urea was studied by T.
CHE 0531 5244 (Supramolecular Chemistry)/Chapter 4 Page 7
R. Welberry of the Australian National University. This compound gives remarkable circular X-ray diffuse
scattering features that arise from partial two-dimensional ordering. The elongated shape profile of the
aromatic guest viewed along the channel axis (Figure 7.7b) slightly distorts the urea channels such that they
pack best when orientated in the same direction (Figure 7.7c). This distortion results in domains within the
crystal in which all of the guests are aligned along with interfaces where stacking faults occur giving a
domain with a different orientation. The hexagonal shape of the channel means that three possible
orientations are possible (Figure 7.7d). Using this model, a calculated diffraction pattern can be derived that
agrees closely with experiment (Figure 7.7e).

Figure 7.7 (a) Space-filling model of the p-didecylbenzene molecule. (b) Urea channel containing the ‘footprint’ of an
n-alkane molecule, together with a comparison of the ‘footprints’ of an n-alkane and the more elongated
didecylbenzene molecule. (c) Exaggerated schematic view of three different orientations of the distorted urea network
when containing the didecylbenzene molecules. (d) Portion of distribution of three ‘footprint’ orientations as
calculated from Monte Carlo simulation. The three shades of grey represent the three orientations shown in (c). (e)
Diffraction pattern calculated from the distribution shown in (d) and strongly resembling the experimental one.

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 The ordering effects of inclusion compound formation on guest behavior are best illustrated by the
case of long-chain alkanones and alkanediones (7.6 and 7.7). In general, a study of more than 100 such
guests suggests that, unlike alkane analogues, many of them display an X-ray diffraction pattern that
suggests significant three-dimensional ordering, as opposed to order along the channel axis only. This
observation implies both inter-channel interactions between the guests, and regular head-to-head or head-to-
tail packing along the channel axis. However, calculations suggest that the dipole–dipole interactions of
Cδ+= Oδ−…C δ+= Oδ− type are too weak to effect such an inter-channel ordering, and indeed in some cases
(e.g. 7.6b and 7.6c) only one-dimensional ordering is found by X-ray diffraction and solid-state 13C-NMR
spectroscopic measurements.

Applications of Urea Inclusion Compounds

We have already mentioned the linear channel of urea inclusion compounds which makes them
applicable in the separation of linear and branched hydrocarbons. The larger channels in thiourea are suited
to the intriguing application of these inclusion compounds in carrying out chemical reactions within the host
matrix. The rigorous steric constraints of the host impose a great deal of stereo- and regioselectivity on the
course of the reaction, which might otherwise be difficult to control under normal conditions. The channel
structure of urea compounds immediately suggests their suitability for the selective formation of long,
straight-chain polymers. In particular, as early as 1960, Brown and White published the inclusion
polymerization of 2,3-butadiene, 2,3-dichlorobutadiene, cyclohexadiene and related compounds. In most
cases, crystalline polymers with high melting points were isolated, suggesting long-chain materials with a
narrow molecular weight band, clearly formed in a highly controlled fashion.

Recently the ability of urea inclusion compounds to line up molecules in their channels has also
suggested their possible application as X-ray dichroic filters. Visible light dichroic filters (polaroid sheets)
are commonplace. The dichroic filter selectively attenuates (reduces the intensity of) radiation with
polarization parallel to a certain axis in the filter material while allowing radiation with perpendicular
polarization to pass through with much less absorption. Dichroic filters for X-rays are difficult to achieve
but have technological applications in areas such as magnetic X-ray scattering. X-rays are absorbed strongly
by heavy, multi-electron atoms such as bromine and a urea inclusion compound of 1,10-dibromodecane has
been shown to act as an X-ray dichroic filter. X-ray radiation polarized parallel to the C–Br bond is absorbed
preferentially over radiation polarized perpendicular to it. However, the efficiency is reduced by the
tendency of the C–Br bonds to undergo reorientation under ambient conditions (cf. gauche 7.5). A much

CHE 0531 5244 (Supramolecular Chemistry)/Chapter 4 Page 9

more efficient material is the designer thiourea inclusion compound of 1-bromoadamantane. In this material
all of the C–Br bonds are aligned with the channel axis and do not reorientate under ambient conditions. The
compound achieves almost the theoretical maximum X-ray attenuation ratio.

Cyclotriveratrylene
Cyclotriveratrylene (CTV, 7.37) has proved to be both a highly versatile host in its own right and a
key bowl-shaped, or shallow saucer-shaped, building block for the construction of a large range of hosts
capable of complexing neutral molecules and even anions in solution as well as in the solid state. The utility
of CTV arises from the significant conformational preference of the central nine-membered cyclononatriene-
derived ring for a crown conformation, which causes the three aryl rings to all point ‘up’ in the same
direction. Variable-temperature 1H-NMR spectroscopic studies have shown that conformational inversion
(via a saddle intermediate with one aryl ring ‘up’ and two ‘down’) is slow on the NMR time scale. The
conformational immobility is observed clearly in the inequivalence of the geminal (attached to the same
carbon atom) protons of the methylene bridge, which appear as an AB quartet. The slow rate of inversion
has also been established by measurement of the racemization rate of the chiral CTV-d9 derivative 7.38,
which gave an energy barrier to inversion of 110.9 kJ mol−1. This means that the inversion half-life is around
one month at 20 ºC, but less than 0.1 s at 200 ºC. The bowl or crown conformation is common to almost all
CTV-related compounds except for 7.39, in which the metastable saddle conformation is a consequence of
the peculiar synthesis of the molecule, and the 2,5-dimethylthiophene derivative 7.40, in which unfavorable
steric interactions between adjacent methyl groups force the adoption of a saddle (C2 symmetric)
conformation (Figure 7.27).

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Figure 7.27 (a) Bowl-shaped conformation of CTV (7.37) and (b) saddle conformation of the related 7.40 which
arises from unfavorable steric interactions between the methyl substituents.

Synthesis
Cyclotriveratrylene was first prepared by Gertrude Robinson in 1915 (Scheme 7.2). Robinson was
interested in following up earlier work on the synthesis of anthracene derivatives and concluded that her
product (empirical formula, C7H10O2, was 2,3,6,7-tetramethoxy-9,10-dihydroanthracene (7.43), the dimer of
the intermediate veratryl cation (7.42). During the 1950s, CTV was again reformulated erroneously as a
hexamer (7.44) and it was not until 1963 that the onset of a variety of modern techniques established a
trimeric formula.

Cyclotriveratrylene is formed in over 70 % yield by the condensation of the veratryl cation (7.42),
whether it is produced from veratryl alcohol (7.41) or directly from veratrole (1,2-dimethoxybenzene) and
rmaldehyde in aqueous acid. In organic solvents such as acetic acid in the presence of a Lewis acid such as
SnCl4 or nzene/BF3/ether, significant amounts of the analogous tetramer cyclotetraveratrylene (CTTV, 7.45)
are produced. CTTV does not possess a bowl conformation and adopts a saddle shape, although it is capable
of forming a limited range of lattice inclusion compounds involving hydrogen bonding to the methoxy
substituents.

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Scheme 7.2 Robinson’s synthesis of CTV, initially assumed to be the dimer (7.43), and later hexamer (7.44). While
neither of these compounds is formed, manipulation of the reaction conditions, e.g. using a Lewis acid such as SnCl4,
does give the tetramer, CTTV (7.45).

Inclusion Chemistry
It was recognized relatively early on that CTV forms solid-state inclusion compounds with a wide
variety of small neutral molecules such as benzene, toluene, water, acetone and CS2. Based on the
correlation of IR spectroscopic data and crystallographic unit-cell parameters, CTV clathrates are divided
into two distinct phases, designated α and β with small differences in their solid-state properties. Early X-ray
crystallographic work showed that in the α phase at least, CTV molecules stack one within the other, rather
like a pile of saucers, to give a characteristic crystallographic b unit cell dimension (9.6–9.7 Å for the α-
phase and 8.1–8.3 Å for the β-phase). It is this characteristic ‘self-inclusion’ that makes the attractive saucer-
shape of the cavity unusable for the inclusion of guests, and all CTV inclusion compounds isolated up until
1994 possess guest species only in channels running between stacks of CTV molecules. The structural
characterization of two β-phase complexes finally resolved the nature of the difference between the two
classes of compound. The differences in the spectroscopic parameters were found to result from a twist of
one of the methoxy groups in response to the hydrogen bond donor/acceptor properties of the guest. In the
language of modern crystal engineering, CTV is solely a hydrogen-bond acceptor, with little donor ability.
In the presence of hydrogen-bond donor guests (even weak hydrogen-bond acids such as benzene), the guest
protons hydrogen bond with the methoxy oxygen atoms. If the guest is incapable of acting as a hydrogen-
bond acid in this way, however, the CTV molecule distorts in order to present the weakly hydrogen-bond
donating OCH3 protons in order to interact with the guest acceptor.

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 Shortly after the first β-phase structures, a third clathrate phase, termed the γ-phase, was reported by
Ibragimov et al. The compound is of formula (CTV)4·acetone, and contains an acetone molecule
sandwiched between a pair of CTV bowls facing each another in order to create a capsule-like space. As
with the β-phase clathrates, the nature of the host–guest interaction involves OCH3 … OCMe2 hydrogen
bonds (Figure 7.28). The solid-state structure of (CTV)4 · acetone is remarkable since it both demonstrates
intracavity inclusion and represents a noncovalent analogue of the capsular CTV-based cryptophanes. More
recently a further example CTV·0.25EtOH has been reported. These intrabowl inclusion compound with
simple, small molecule guests are relatively unusual for CTV, with CTV·(DMSO)2·(H2O)2 which contains
an intra-cavity DMSO molecule being the only other known example. However, for more unusual spherical
guests such as buckminsterfullerene (C60) and 1,2-dicarbadodecaborane (12) (o-carborane, 7.47),
intracavity ‘ball-and-socket’ inclusion compounds have been known since 1994. Intra-cavity inclusion is
also observed extensively in CTV-based coordination networks, as we will see in the next section. In the
case of C60, there is both a steric and electronic complementarity between host and guest. The radius of
curvature of the wide CTV cavity is similar to that of the large fullerene sphere. In addition, the CTV aryl
rings are very electron-rich as a consequence of the electron-donating effect of the methoxy substituents.
This complements the electron-deficient nature of C60, allowing the formation of solution charge-transfer
complexes. The solution interaction can be monitored by UV–visible spectroscopy which indicates the
formation of micelle-like aggregates. Confirmation of the intracavity inclusion has been demonstrated for
both carborane and fullerene complexes by X-ray crystallography in the solid state. In the case of C60, a six-
membered ring is positioned directly above the CTV three-fold rotation axis, giving a good symmetry match.
For the carborane complex the compound is stabilized by C—H … π interactions of 2.18 and 2.56 Å from
the acidic carborane C— H protons to the CTV rings. Significantly, the much more electron-rich B— H
hydrogen atoms are repelled by the CTV aryl rings (shortest B—H … π distance, 2.77 Å) (Figure 7.29).

Figure 7.28 (a) Stacking in the α-phase of CTV; (b) stereoview of the X-ray crystal structure of the γ-phase
CTV clathrate, (CTV)4 · acetone (acetone guest disordered).

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 Figure 7.29 X-ray crystal structure of the 1,2-dicarbadodecaborane(12) cavity inclusion complex with CTV

In addition to these complementary species, the electron-rich nature of the CTV veratrole rings
enable it to form a range of unusual inclusion complexes with cyclopentadienyl-arene iron(II) cations.
Generally, the smaller C5H5 ring sits within the CTV cavity and the acidic protons of the coordinated ring
engage in C−H … π hydrogen bonds with the electron-rich CTV aryl moieties. The principal interaction is
of a charge transfer type, with face-to-face stacking of the C5H5 ring with one of the CTV aryl residues. This
results in the formation of noncentrosymmetric two-dimensional polar frameworks in the solid state. A
variety of CTV derivatives have been synthesised using both standard and solventless methodologies with
other substituents at the rim of the CTV bowl (e.g. ethyl, propyl, allyl or propargyl) Crystal structures of the
hexa(ethyl), tri(ethyl) and tri(propargyl) analogues have been determined, and show either intra-cavity host-
guest binding or self-stacking motifs.

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