J. Phyr. Chrm. So/i& Vol. 53. I*;o. 4. pp. 529-537, 1992 0022-3697~92 IS.00 + 0.

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THE STRUCTURAL RESPONSE OF THE HOST

FRAMEWORK FOLLOWING REMOVAL OF THE GUEST
MOLECULES FROM A UREA INCLUSION COMPOUND: A
MONTE CARLO SIMULATION STUDY

K. D. M. HARRIS?
Department of Physical Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 IEP, U.K.
and Davy Faraday Research Laboratory, The Royal Institution, 21 Albemarle Street, London WlX 4BS,
U.K.

(Received 17 September 1991; uccepted 24 Seplember 1991)

Abstract-Monte Carlo simulation techniques have been used to investigate, under conditions of constant
temperature and constant pressure, the structural response of the ‘empty’ tunnel-containing urea (host)
structure that is produced by removing the guest molecules from a urea inclusion compound. Over a wide
range of temperatures and pressures, this ‘empty’ urea tunnel structure is unstable and collapses to a more
compact structure. While this vindicates earlier experimental findings, the Monte Carlo simulations
reported here have extended our understanding of this behaviour to new regimes of temperature and
pressure which have not hitherto been investigated experimentally.
Keywordy: Monte Carlo simulation, urea inclusion compounds, structural transformation, host framework
stability.

1. INTRODIJCI’ION the ‘real’ inclusion compound. A comprehensive dis-

Crystalline organic inclusion compounds [I, 2) are of cussion of these concepts, and of the crystallographic
immense interest to the solid state chemist not only properties of urea inclusion compounds in general, is
because they exhibit many important fundamental given in Ref. 3. In the present paper, the distinction
properties that can be utilized in a wide range of between the basic host structure and the host sub-
applications, but also because they represent, in many structure is not of primary importance and, to sim-
respects, structural analogues of microporous inor- plify the discussions here, the general terms ‘host
ganic solids, such as zeolites and aluminophosphates. structure’ and ‘urea tunnel structure’ are used to refer
In the presence of appropriate ‘guest’ molecules (such to the arrangement of urea molecules within a urea
as sufficiently long n-alkanes), urea will crystallize in inclusion compound. However, when making specific
an extensively hydrogen-bonded arrangement (Fig. 1) reference to results from Ref. 3, it is considered
containing linear, parallel, essentially infinite, non- correct to use the more precise terminology (e.g.
intersecting tunnels (channels) which completely ‘basic host structure’) employed in that paper.
enclose the guest molecules (Fig. 2). In the absence of suitable guest molecules, urea
These urea inclusion compounds are conveniently crystallizes in a tetragonal structure [4, 51 which is
considered to consist of two distinct, although not referred to here as ‘pure’ crystalline urea. This struc-
independent, host (urea) and guest substructures. ture differs substantially from the host structure in
Each substructure, in turn, is best considered in terms urea inclusion compounds and, in particular, does nor
of an incommensurately modulated ‘basic structure’. contain ‘empty’ tunnels.
In essence, the ‘basic host structure’, for example, It is generally (although not universally [6]) be-
represents an ‘ideal’ (three-dimensionally periodic) lieved that the guest molecules within a urea inclusion
arrangement of the host molecules; in the ‘real’ compound are always closely packed along the urea
inclusion compound, this ‘ideal’ host structure is tunnels. Single-crystal X-ray diffraction 13, 7-101, for
perturbed as a result of host-guest interaction (this example, has shown that the guest molecules are
perturbation constitutes the incommensurate modu- arranged in a periodic manner along the tunnel with
lation). The term ‘host substructure’ is used to refer a periodic repeat distance that is approximately equal
to the incommensurately modulated basic host struc- to the length of the guest molecule in the type of
ture; i.e. the actual arrangement of host molecules in linear conformation that it must adopt in order to fit
~ .. within the confined space available inside the tunnel.
+Present address; Department of Chemistry, University of Consequently, at a given temperature, the urea in-
St. Andrews, Fife, KY16 9ST, U.K. clusion compound containing a particular type of

529
530 K. D. M. HARRIS

(a) (bl

Fig. 1. Two representations (showing nine complete tunnels) of the basic host structure in urea inclusion
compounds [3], viewed along the tunnel axis (c,,). The atomic radii are zero in (a) whereas conventional
van der Waals radii are used in (b). Space group P6,22; k+,i = &,I = 8.227 A; /c,,[ = 11.017 A. Note that
in the complete inclusion compound, the tunnels within this host structure are filled with a dense packing
of guest molecules (not shown).

guest species will form only at one specific host/guest
molar ratio (or a narrow range of host/guest molar
ratios). It might be envisaged that an inclusion com-
pound containing a lower proportion of guest could
be produced by driving guest molecules out of the
tunnels (e.g. at low pressure). This, however, is
thought [IO, 111 to give rise to disproportionation,
resulting in a smaller amount of inclusion compound
containing the mandatory host/guest ratio plus an
amount of urea in its ‘pure’ crystalline phase. This
process can be summarized by the following scheme.
UltimateIy, when all the guest molecules have been
removed (i.e. when z =x), no inclusion compound
will remain and all the urea will be present in its ‘pure’
crystalline phase. Thus, according to this proposed
scheme, it should nut be possible to prepare the
‘empty’ tunnel-containing urea host structure, this
structure being unstable with respect to recrystalliza-
tion as the ‘pure’ crystalline phase of urea. Exper-
imentally, the removal of guest molecules from urea
inclusion compounds (either at sufficiently high tem-
perature [ 12-141 or low pressure [ 151)has indeed been

(G,H,,) - zG + {Gx-,ffyl -+ IG,-,ff-wxJ + {f&,xf

Inclusion Unstable Inclusion ‘Pure’
compound inclusion compound compound crystalline
host/guest ratio = y :x host/guest ratio = y :(x - zf host/guest ratio = y :x form of host

shown, by powder X-ray diffraction, to lead to the

Fig. 2. Computer graphics representation (using van der
Waals radii) of a single tunnel of a urea inclusion compound
containing n-hexadecane as the guest molecule. Note that
urea inclusion compounds do not consist of single, isolated
tunnels, but comprise a regular array (see Fig. 1) of parallel
tunnels of the type shown.
production of ‘pure’ crystalline urea.
The instability of the ‘empty’ urea tunnel structure
signifies a major difference between urea inclusion
compounds on the one hand and the topologically-
similar zeolitic systems (such as theta-l, mordenite
and zeolite L, all of which contain uni-dimensional
tunnel structures) on the other. In general, the
‘empty’ zeolites can exist as stable structures
(although this is not necessarily the case under ex-
tremes of pressure and temperature [ 161)and a range
of guest concentrations can therefore be applied,
ranging from zero (‘empty’ host) to some maximum
value (saturation). As discussed above, however, any
particular type of urea inclusion compound is known
 The structural response of the host framework
at only one specific host/guest ratio (corresponding,
in principle, to saturation). Therefore, at any specific
temperature, the host/guest ratio in the urea inclusion
compounds is nor an experimental variable.
In this paper, we report computer simulation stud-
ies, employing Monte Carlo (MC) methods [ 17, 181,
which have probed the structural response of the
‘empty’ urea tunnel structure (produced by removing
the guest molecules from a urea inclusion com-
pound). These constant temperature-constant press-
ure simulations were carried out firstly under ambient
conditions (room temperature (300 K) and atmos-
pheric pressure (I 0’ Pa)) using, as the initial ‘configur-
ation’ of the system, the basic host structure
determined from our room temperature
diffraction investigations of n-hexadecanelurea
X-ray
(31.
Simulations probing the behaviour of this structure
were also carried out under conditions of extreme
temperature and pressure. In this regard, it is relevant
to note that computer simulation often represents the
most viable approach for investigating the properties
of systems under conditions which may be difficult or
impossible to attain experimentally.
We have previously [19] investigated both the
liquid and ‘pure’ solid phases of urea using MC
simulation techniques, and these previous studies
have served, in part, to vindicate the validity of the
potential energy parameterization used in the present
work (see section 2). It is important to note here that
the informative stage of the simulation of the ‘empty’
urea tunnel structure is nor that after equilibration
has been attained since, if the experimental obser-
vations are indeed reproduced, this would simply
repeat our earlier simulations on the ‘pure’ crystalline
phase of urea [ 191.Instead, in the present simulations,
we are interested in the structural evolution of the
system as it approaches the equilibrium distribution
from the initial configuration (the ‘empty’ urea tunnel
structure). It is essential to stress that studying the
evolution of a system as it approaches equilibrium
under a Monte Carlo algorithm gives only one of a
large number of possible trajectories of the system
through configuration space; and furthermore, as a
result of the uncorrelated nature of Monte Carlo
movements, there is no certainty that the actual
trajectory observed in the simulation will necessarily
represent a realistic pathway between the initial and
final states of the corresponding experimental system.
Despite these limitations of the Monte Carlo method,
there is nevertheless some value in considering, in
detail, the structural evolution of the system as it
approaches equilibrium in the simulation, in-so-far
as we cannot rule out the possibility that these
structural changes may indeed represent a probable
pathway for the structural transformation in the
531
experimental system. This issue is discussed further in
section 3.
2. COMPUTATIONAL DETAILS
MC simulations were carried out in the isother-
mal-isobaric (NpT) ensemble [20,21] using the stan-
dard techniques of Metropolis importance sampling
[22] and periodic boundary conditions [18]. The total
potential energy E(X) of the system in a particular
configuration X (specifying the positions of all mol-
ecules within the simulation cell) was calculated via
the following atom-atom summation:
aw = i
,-2,-l
‘2M,,(r,)
x [-4,(r,J6 + Mr,,)-‘* + Cq,q,(r,,)-‘I,
where
(1) there are n atomic ‘interaction sites’ in the
structure. each assigned a unique label from 1
to n.
(2)M,(r, 1= 0 if atoms i and i are in the same
molecule;
M,,(r,) = 0 if atoms i and j are in different
molecules with the distance be-
tween the centres of mass of these
molecules greater than a cut-off
distance r,;
M,,(r,) = 1 if atoms i and i are in different
molecules with the distance be-
tween the centres of mass of these
molecules less than or equal to r,.
(3) I and J denote the ‘types’ (i.e. 0, C, N or H)
of atoms i and i, respectively.
(4) ri, is the distance between atoms i and i.
(5) A,, and B,, are Lennard-Jones parameters, the
values of which depend on the atom types (I
and J, respectively) of atoms i and i.
(6) q, and q, are the charges associated with atoms
i and j, respectively.
(7) C is a constant which establishes the correct
units for the final term in the summation.
The Lennard-Jones potential parameters (A,, and
B,,) for homoatomic atom-atom interactions (e.g.
0.. .o, c.. . C, etc.) and the atomic charges (qi)
were taken from the work of Hagler et al. (see Table
IV in Ref. 23). The Lennard-Jones parameters (A,,
and B,,; I #J) for heteroatomic atom-atom inter-
actions (e.g. 0. . . C, N . . . 0, etc.) were derived from
the homoatomic parameters by applying the follow-
ing combination rules: A,_, = dwJ, and
B,,= ,/m.
532 K. D. M. HARRIS

The MC simulation program used in this work (a) NUMBER OF MONTE CARLO MOVES E 0

was essentially the same as that used in our previous

studies of the ‘pure’ solid and liquid phases of
urea [ 191, and can calculate the same average proper-
ties, energy-related distribution functions, and
structure-related distribution functions for the
system, from a series of configurations generated
in the simulation. However, since the system did
not reach equilibrium in the simulations described
here, these properties are not of primary relevance
in the current work, although some of the structure-
related distribution functions are mentioned briefly
in section 3.
MC simulations were carried out under the follow- @I
NUMBER OF MONTE CARLO MOVES I 1000
ing conditions:

(a) Simulation I: T=300K;p = lOsPa

(b) Simulation II: Z’=77K;p = lO*Pa
(c) Simulation III: T = 77 K;p = 10m2Pa.

In all cases, the initial configuration was taken as the

basic host structure determined from our room tem-
perature single-crystal X-ray diffraction data for the
n -hexadecane/urea inclusion compoundt[3] (see also
Fig. 1). The simulation cell (represented by basis
vectors {as, b,, c,}) comprised 48 crystallographic
unit cells (represented by basis lattice vectors {a,, , b,,, (cl
q,}) of this hexagonal basic host structure as follows: NUMBER OF MONTE CARLO MOVES q 2000

a,=4a,; b,=4b,; cs=3c,,. (Note that Iahl=lbhl=

8.227& lc,,l = 11.017A.) Since there are six urea
molecules in the crystallographic unit cell, the simu-
lation cell contained 288 urea molecules. The centre
of mass-to-centre of mass cut-off distance for con-
sideration of intermolecular interactions was taken as
rc = 1OA for all calculations. This value was justified
by the fact that the energy calculated for the exper-
imentally-determined structure of ‘pure’ crystalline
urea [4,5] using the above potential energy parame-
terization together with this value of r, was in accept-
able agreement with the experimental lattice energy
of ‘pure’ urea [23]. (4
NUMBER OF MONTE CARLO MOVES I 3000
One ‘Monte Carlo move’ consisted of moving each
molecule, in turn, to a trial position by displacing the
centre of mass of the molecule by a random amount
in a randomly chosen direction and rotating the
molecule by a random amount about a randomly
selected axis passing through the centre of mass of the
molecule (full details are given elsewhere [24]). The
maximum values for these random displacements and

tit was not possible to refine the positions of the urea H

atoms in a satisfactory manner from these X-ray diffraction
data and, for the MC simulations, H atoms were ‘added’ to
the refined positions of the 0, C and N atoms of the urea
molecule in positions which generate a standard geometry
for the -NH, group. Fig. 3 (a-d)
 The structural response of the host framework 533

(e) NUMBER OF MONTE CARLO MOVES q 4000 (0 NUMBER OF MONTE CARLO MOVES z 5000

@I NUMBER OF MONTE CARLO MOVES I 7600

(is9 NUMBER OF MONTE CARLO MOVES = 6000

(9 (j)
NUMBER OF MONTE CARLO MOVES = 10000
NUMBER OF MONTE CARLO MOVES = 8500

Fig. 3 (e-j)
Fig. 3. Plots of the simulation cell contents, viewed along the original tunnel axis, at different stages during
the MC simulation (Simulation I) of the ‘empty’ urea tunnel structure under ambient conditions
(T = 300 K, p = 10s Pa). (a) the ‘empty’ urea tunnel structure at the start of the simulation; (b)-(j) show
the structure after the following numbers of MC moves: (b) 1000, (c) 2000, (d) 3000, (e) 400, (f) 5000,
(g) 6000, (h) 7600, (i) 8500, (j) 10,000.

rotations were chosen such that about 40% of trial
moves were accepted [25] on application of the
Metropolis algorithm.
In every seventh MC move, a trial change was also
made in the volume and shape of the simulation cell.
This involved a random ‘displacement’ of the six
unconstrained components (h,, , h,*, IJ,~,h12,h,, and
/z,~) of the matrix &’ which establishes the relation-
ship between the simulation cell {a,, b,, q} and a
space-fixed orthogonal reference frame (represented
by basis vectors {q, b,, c,}),
i.e.
[%4c,l= b,~rcrIJf’,
534 K. D. M. HARRIS

-66 ‘~(11’1,1”,,,~“,,,‘,(‘,’
i sumed in Simulation I was therefore about 25 h.
7
-70
z 3. RESULTS AND DISCUSSION
E
3
. -72 I”’
2 ber of MC moves in Simulation I (T = 300 K;
iz
-74
-76 ,,,,,,,,.,,,,,,,,,,,,,,,,, I
0 2000 4000 6000 6000 10000
MONTE CARLO MOVE NUMBER
Fig. 4. Total potential energy E(X) per mole of urea
molecules, as a function of the number of MC moves in
Simulation I.
where
(Note that constraining the matrix components hsl,
h3, and h,, to equal zero ensures that the simulation
cell does not rotate in space during the simulation.)
Again, the maximum values for the random shifts in
the components of X were chosen such that the
acceptance ratio for trial changes in the volume and
shape of the simulation cell was about 40%.
Simulation I was run for 10,000 MC moves with
properties of the system averaged over the final 1500
moves (although it is stressed again that equilibration
was not in fact attained during this simulation (see
section 3)). Simulations II and III were run for 2600
MC moves and 2475 MC moves, respectively. All
calculations were performed on the Cray COSlM
computer at the University of London Computer
Centre. The typical requirement of CPU time was
16 min for 100 MC moves (without accumulation of
averages) and the total amount of CPU time con-
A series of ‘snapshots’ of the configuration (viewed
k
down the original tunnel axis) after a differing num-
p = lo5 Pa) is shown in Fig. 3. The variation in the
i-
total potential energy (per mole of urea molecules)
and simulation cell volume during this simulation are
shown in Figs 4 and 5, respectively. From Figs 3 and
5, it is clear that the ‘empty’ urea tunnel structure has
begun to collapse to a more compact structure, and
from Fig. 4 it is clear that the system has not
equilibrated by the end of the simulation. The
configuration after 10,000 MC moves represents a
poorly crystalline, although not molten, phase; this
fact has been assessed? by comparing structure-
related distribution functions calculated for this
configuration with those characteristic of the liquid
and ‘pure’ crystalline phases of urea. As an illus-
tration, Fig. 6 contains representative results for: (a)
the ‘pure’ crystalline phase of urea (T = 300 K;
p = lOsPa); (b) the collapsing urea tunnel structure
(T = 300 K; p = 10’ Pa); and (c) liquid urea
(T = 450 K; p = lo5 Pa). The results for (a) and (c)
are taken from Ref. 19. The distribution functions
represented in each case are: (i) radial distribution
function g(r) for the distance between molecular
centres of mass; (ii) radial distribution function g(r)
for the distance between 0 atoms; and (iii)
dipole-dipole correlation function$ d(r).
The results from these MC simulations clearly
vindicate experimental findings [12-151 which suggest
that the ‘empty’ urea tunnel structure is unstable; and
2
. 33000 " " " " u--y

tin view of the cautionary comments at the end of section

1, we do not aim to imply that these distribution functions
necessarily represent an accurate description of the corre-
sponding functions for the real experimental system at an
intermediate stage during the structural transformation.

,,,‘i_i
§The urea molecule possesses a permanent dipole mo-
ment, and the dipoledipole correlation function allows an
assessment of the degree to which the relative orientation of
a pair of these molecular dipoles is correlated with inter-
molecular distance. In particular, a unit vector is defined
1_I,,,,,,,,,,,,
parallel to the dipole moment of each molecule, and the
scalar product of these unit vectors is calculated for each
pair of molecules in the structure. The dipoldipole corre- 0 2000 4000 6000 6000 10000
lation function d(r) represents the sum of these scalar MONTE CARLO MOVE NUMBER
products (normalized in the same way as radial distribution
functions 1181) for all pairs of molecules with centre of Fig. 5. Simulation cell volume as a function of the number
mass-to-centre of mass separation equal to r. of MC moves in Simulation I.
The structural response of the host framework

h
\i-
536 K. D. M. HARRIS

presumably if each simulation had been allowed to 4. CONCLUDING REMARKS

run for a sufficiently long time (allowing equilibrium

to be established), the system, in the simulation, In conclusion, the ‘empty’ urea tunnel structure,
would again reproduce the experimental observations obtained by removing the guest molecules from a
by crystallizing in the tetragonal structure of ‘pure’ urea inclusion compound, is unstable under each set
urea. of conditions of temperature and pressure investi-
Although, as noted in section I, the structural gated. While this has both confirmed previous exper-
evolution of the system in the Monte Carlo method imental findings and extended our understanding of
will not necessarily represent a trajectory through the behaviour of this system to new regimes of
configuration space that is representative of the corre- temperature and pressure, the results described here
sponding change in the real experimental system, a demonstrate the important role that computer simu-
detailed consideration of the progression of configur- lation may serve in revealing, at a microscopic level,
ations generated in Simulation I is nevertheless inter- details of the structural evolution of unstable crys-
esting, since the possibility that it MU_Vprovide some talline phases. Whereas, as noted in section 1, the
insight into the mechanism of the structural trans- Monte Carlo method has some important limitations
formation cannot be ruled out. It is clear, for in this regard, there is considerably greater potential
example, that the tunnel structure in the simulation for obtaining detailed information of this type via
has a tendency to shear in directions parallel to the molecular dynamics simulation techniques [ 17, 18).
{ 100) form of lattice planes (referred to the crystallo- For this reason, molecular dynamics simulations
graphic axes defined in Fig. 1). This can be seen from aimed towards investigating a wide range of struc-
the plots shown in Fig. 3 (consider, for example, the tural and dynamic properties of urea inclusion
vertical set of three tunnels at the left hand-side of the compounds are currently in progress [26].
simulation cell in Fig. 3(d)). The structural collapse of the ‘empty’ urea tunnel
Although there is an overall decrease in volume structure highlights one crucial difference between
during the simulation (see Fig. 5). the volume initially urea inclusion compounds on the one hand and their
increases in a manner akin to a positive ‘volume topologically-similar zeolitic analogues on the other.
change of activation’. Recrystallization to the com- This instability of the ‘empty’ urea tunnels imposes a
pact tetragonal structure of ‘pure’ urea would be severe limitation on the feasibility of using urea
expected to be thermodynamically feasible at all inclusion compounds as a medium within which
temperatures, and the ‘empty’ urea tunnel structure chemical transformations (of the guest molecules)
should therefore remain intact only under conditions might be carried outt, since removal of product
which render it kinetically stable with respect to this molecules would be expected, in general, to result in
transformation. Kinetic stability will generally be the collapse of the tunnel structure before further
promoted by decreasing temperature and, if there is reactant molecules could be inserted.
a positive ‘volume change of activation’, the kinetic Finally, while the simulations described here reveal
stability is enhanced by increasing pressure (since the clearly the very different structural responses of the
pAV* term in the enthalpy change of activation will urea host structure when comparing the situations
become more positive with increasing pressure (where with guest molecules present (host structure stable)
A V: denotes the volume change of activation)). In the and absent (host structure unstable), it is pertinent
light of these comments, the behaviour of the ‘empty’ to contemplate the more subtle ways in which the
urea tunnel structure at low temperature (T = 77 K) host structure might be perturbed in the presence of
and high pressure (p = IO* Pa) was considered (in different types of included guest molecule. X-ray
Simulation II) in order to investigate whether the diffraction (which indicates that the average basic
structural collapse is indeed suppressed under these host structure is remarkably invariant in urea in-
conditions. In Simulation II, however, collapse of the clusion compounds containing a diverse range of
‘empty’ urea tunnel structure was again apparent. guest species) reveals only a space-averaged and
This behaviour was also observed in Simulation III, time-averaged representation of the true structure,
which was carried out at low temperature (T = 77 K) and we must turn to other techniques to gain an
and low pressure (p = IO-‘Pa). insight into the distribution of local structural
--__ --- -. ..-_ -- features about this average. Computer simulation
tSuch an application wou/d, however, be feasible if it were studies, aimed towards probing details of the way in
possible to feed reactant molecules in at one end of the which the host structure in urea inclusion com-
crystal and to extract product molecules from the other end, pounds ‘relaxes’ in response to the presence of
since there would then always be, at any instant, a dense
packing of guest molecules (reactant and/or product) within different types of guest molecule within it, are in
the tunnels. progress.
 The structural response of the host framework
Acknowledgements-1 am indebted to Professor Sir John
Thomas and Dr S. Yashonath for many valuable discus-
sions in connection with this work, and to Dr Yashonath for
collaborating in writing the Monte Carlo simulation pro-
gram used here. I am grateful to the University of London
Computer Centre for a generous allocation of computer
time, and to British Petroleum for financial support in the
form of a BP Research Studentship.
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