Topological building blocks of hydrogen bond network in water

M. Matsumoto, A. Baba, and I. Ohmine

Citation: The Journal of Chemical Physics 127, 134504 (2007); doi: 10.1063/1.2772627
View online: http://dx.doi.org/10.1063/1.2772627
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 THE JOURNAL OF CHEMICAL PHYSICS 127, 134504 共2007兲

Topological building blocks of hydrogen bond network in water

M. Matsumoto
Research Center for Materials Science and Chemistry Department, Nagoya University, Furo-cho, Chikusa,
Nagoya 464-8602, Japan
A. Baba
Department of Earth and Planetary Sciences, Faculty of Science, Kobe University, Rokkodai, Nada,
Kobe 657-8501, Japan
I. Ohmine
Department of Chemistry, Faculty of Science, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8602,
Japan
共Received 22 May 2007; accepted 25 July 2007; published online 4 October 2007兲

Basic three-dimensional units of the network, called fragments, are introduced to characterize the
hydrogen bond 共HB兲 network structure of water. Topological differences among normal liquid
water, water at low temperature, and water under high pressure are elucidated by their fragment
statistics. Water at low temperature has almost defect-free network and is filled with stable
fragments with small distortion. It is found that there exists a certain way on how fragments
mutually aggregate. Well-formed aggregates heterogeneously constitute very stable network
structures. HB network rearrangements occur scarcely inside these aggregated domains but take
place in their surface areas. The heterogeneity of HB structure and rearrangement in water is thus
explained in terms of the fragment structure and its rearrangements. The fragment analysis thus
elucidates the intermediate-range order in water HB network. © 2007 American Institute of Physics.
关DOI: 10.1063/1.2772627兴

I. INTRODUCTION of five- and six-membered rings. Such a cagelike structure

Water is a “random” three-dimensional hydrogen bonded
共HB兲 network system where individual water molecules form
the tetrahedral hydrogen bonds with their surrounding water
molecules. There have been many studies to analyze the HB
network structure of water. Great success has been made to
elucidate the origin of water anomalies by characterizing lo-
cal physical quantities of the water HB network, such as
coordination number and tetrahedral order.1,2 It is, however,
expected for water to have certain intermediate-range order
in its HB network structure, which derives, for example, the
distinct heterogeneity of the HB network structures and dy-
namics in water.3,4
If one tries to build tetrahedral network structure of
amorphous water or silicon by using ball and stick model by
hand, numerous trials and errors are required to eliminate
large distortion and “defects” 共not four-coordinated sites; we
use this terminology hereafter兲 because of the constraints on
their structures, that is, the regular tetrahedral coordination
and the bond lengths.5 These local constraints impose a cer-
tain rule to build the intermediate-range order on the random
structure. The structure of amorphous ice has many similari-
ties with tetrahedrally coordinated continuous random net-
work 共CRN兲, which is a structural model for amorphous sili-
con 共a-Si兲.6–9 Recently, the intermediate-range order of a-Si
is detected by fluctuation electron microscopy10 but its struc-
tural origin is still under debate.11,12
In ice phases at low pressure 共hexagonal/cubic ice I兲 and
clathrate hydrates, their HB networks can be decomposed
into few types of “cages,” i.e., polyhedral cavities consisting
can become a cavity to include hydrophobic guest molecules.
It has also been reported that such polyhedral local structures
can be seen in the hydrogen bond network of supercooled
liquid water,13,14 but the actual exhaustive search for them
has not been performed yet.
In the present work, the cagelike structures, i.e., frag-
ments, are systematically searched in HB network of water,
especially, at low temperature. Analysis of these fragments is
found to be useful to elucidate the topological and steric
aspect of the intermediate-range order in water. The tight
relation between the fragment aggregation and the hydrogen
bond rearrangements will be investigated.
Simulation method and fragment perception method are
explained in Sec. II. In Sec. III, the results and discussion of
the fragment analysis for liquid water in various conditions
are given. Section IV presents the conclusions.
II. METHODS
A. Simulation
Replica exchange molecular dynamics simulations are
performed on the system containing 512 water molecules in
the cubic cell with the periodic boundary condition.15 Nada
and van der Eerden’s six-site water model potential16 is used.
This water model is originally designed to deal with solid-
liquid coexistence. It is found to also well reproduce various
thermodynamic properties in the ambient and supercooled
conditions. We have surveyed P共
, T兲 surface by using this
potential at wide temperature range between supercooled and
ambient states and density range between stretched

0021-9606/2007/127共13兲/134504/9/$23.00 127, 134504-1 © 2007 American Institute of Physics

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 134504-2 Matsumoto, Baba, and Ohmine
共0.95 g / cm3兲 and compressed 共1.15 g / cm3兲 states. It under-
estimates the pressure 共about 25%兲 at high-density end, and
shifts the isobaric contour at zero pressure about 15 K higher
from the experimental values, but still reproduces overall
phase space quite well. Its long-range interaction is truncated
at 1 nm using quadratic smooth function in the same manner
as their study.16 The simulation time step is set to be 1 fs.
Pressure is kept constant at zero with Andersen’s barostat.17
With Nada and van der Eerden’s water model, the density
decreases monotonically below its temperature at maximal
density 共estimated value of 284 K兲 toward 230 K. The den-
sity change is found to be continuous and there is no first
order phase transition intercept at this zero pressure in the
present calculation. Below 230 K, the molecular mobility be-
comes very small and it is difficult to cover sufficient num-
ber of the water configurations by a standard trajectory
method. The replica exchange molecular dynamics method is
thus employed. Tens of different temperatures between 200
and 280 K are assigned to replicas. The molecular dynamics
simulations are also performed at several temperatures under
3000 atm, where water is expected to be in high-density liq-
uid 共HDL兲 water state. Normal isobaric-isothermal molecular
dynamics simulations are also performed at 290, 260, and
230 K for time-dependent analyses.
In the present work, two water molecules are regarded as
hydrogen bonded when their nearest intermolecular O–H dis-
tance is less than 0.25 nm.18 The topological properties of
the HB network are analyzed in terms of the inherent struc-
tures to eliminate the ambiguity over the hydrogen bond cri-
teria. Inherent structures are obtained by applying the conju-
gate gradient method to the instantaneous structures along
the trajectories.19
B. Fragment analysis
The hydrogen bond network of water is covered with
rings 共cyclic paths along the network兲.1 A pair of nearby
rings share edges 共hydrogen bonds兲 and vertices 共water mol-
ecules兲. The directionality of the hydrogen bond will be ig-
nored hereafter for simplicity, so that the HB network is
treated as an undirected graph in the present work. The ring
perception algorithm utilized here is described in Appendix
A.
A fragment, a three-dimensional network block, is de-
fined for an undirected graph satisfying the following condi-
tions:
共1兲 All the edges in the graph must be shared by two rings
in it.
共2兲 The graph must satisfy the following extended Euler
equation:
V − E + R = 2,
where V, E, and R are number of vertices, edges, and
rings in the graph, respectively.
共3兲 Each vertex of the graph must be two or three con-
nected, i.e., has two or three edges.
The first two conditions prescribe the cagelike structure cov-
ered by surface rings and the total shape is isomorphic to a
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J. Chem. Phys. 127, 134504 共2007兲
sphere. The last condition comes from the characteristics of
the tetrahedral network structure; only two or three surface
rings meet at a vertex. A fragment is not a polyhedron13
because a polyhedron is defined as wrapped with flat sur-
faces. So it should be called as “quasipolyhedron” or “vit-
rite” 共named by contrast with the term “crystallite”兲. There
are a large variety of fragments found in the HB network of
liquid water and amorphous ice. In this study, the largest ring
size in a fragment is limited to 8. The larger-sized rings are
very rare in the supercooled state and form a big hole of the
cage. Fragment structures are common not only in water but
also in tetrahedral semiconductors.20
All fragments satisfying the above conditions are
searched over HB network of the system and stored in a
topology database.21 A typical network structure around a
water molecule at low temperature, elucidated by using frag-
ments, is illustrated in Fig. 1共d兲. Fragments in the HB net-
work structure at 200 K are illustrated in Fig. 1共e兲. The HB
network at low temperature is almost free from network “de-
fects” 共vertices having more or less than four edges兲 and the
whole network can be fully and uniquely tessellated into
fragments.
At higher temperature or under higher pressure, on the
other hand, HB network of liquid water is not fully covered
by such fragments. There are many nine- and ten-membered
rings and some water molecules having only one hydrogen
bond, in the network and some parts of HB network form
highly complicated network structures having interstitial wa-
ter molecules.
The “volume” of each fragment can be introduced. The
detailed definition of the volume is given in Appendix B. For
example, the volume of a cubic ice fragment 关Fig. 1共c兲兴 is 1,
that is, a fragment of cubic ice covers one water molecule,
and a crystal consisting of N water molecules contains N
fragments. Generally, large fragments have large volume.
The total volume summed over the whole fragments is equal
to the number of molecules in the system when each water
molecule has four hydrogen bonds and the network is fully
covered by the fragments. Although this is a rough estima-
tion, it is useful to understand how much portion of the net-
work is covered by the fragments.
III. RESULTS AND DISCUSSION
Under zero pressure, the number of the network defects
共molecules not having four HB兲 in water decreases rapidly
when the temperature becomes lower. Number of rings, ratio
of network defects, and liquid density all change rapidly be-
tween 240 and 260 K, reflecting the transition to a so-called
low density liquid 共LDL兲 state 共see Fig. 2兲.
The numbers of six- and seven-membered rings increase
monotonically, while the numbers of four- and eight-
membered rings decrease, when the number of defects de-
creases. HB network structure of LDL water is then mostly
covered by five- to seven-membered rings at very low tem-
perature, and becomes much alike that of CRN, whose ring
elements are indicated with the triangles at the left end of
 134504-3 Topology of hydrogen bond networks in water
FIG. 1. 共Color兲 Quasipolyhedra, fragments building the hexagonal ice, are
shown in 共a兲 and 共b兲. Their volume per fragment is 1.5 and 0.5, respectively.
Cubic ice is built of a single kind of fragment shown in 共c兲. Its volume per
a fragment is 1. See Appendix B for the definition of volume of a fragment.
In 共d兲, a typical configuration of seven fragments surrounding a water mol-
ecule 共circle兲 is exemplified, where fragments are drawn by different colors.
A snapshot of all the fragments found in the hydrogen bond network at
200 K is illustrated in 共e兲, where water molecules and hydrogen bonds are
not drawn and fragments are depicted by translucent hulls. The fragments
are separated by a small gap in order to show the internal structure. The
network is totally tessellated into fragments.
Fig. 2.12 Under 3000 atm, on the other hand, the number of
rings changes only a little even when the system is cooled
down to 200 K.
A. Temperature dependence of fragment distribution
We have performed the fragment analyses on water HB
network structures at various temperatures. Figure 3 plots
how often individual types of fragments appear in HB net-
work. We can see in the figure that the ratios of their appear-
ance change mostly monotonically with the temperature. At
280 K, the total portion of the network covered by fragments
is 57%. Other portion of the network is unclassifiable be-
cause its network topology is much entangled. At 200 K, on
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FIG. 2. Density, number of network “defects,” and number of rings in the
HB network are plotted against temperature with dotted, dashed, and solid
lines, respectively, at 共a兲 0 atm and 共b兲 3000 atm. Ring sizes are indicated in
the graph. At lower pressure, there is a clear and continuous transition from
low- to high-density liquid state between 240 and 270 K while these prop-
erties are kept constant within the whole range of temperature at 3000 atm.
Triangles indicate the number of rings for CRN taken from Ref. 12.
the other hand, 91% of the network is covered by the frag-
ments. The fragments can be classified into two categories,
of the cryophile type 共whose number increases by cooling兲
and of the thermophile type 共whose number decreases by
cooling兲. We can see in Fig. 3 that the network is indeed
covered almost fully by cryophiles at 200 K, whereas cryo-
philes cover only 25% of the network at 280 K. Topological
variety of cryophiles is much smaller than that of thermo-
philes. The topologies of major 11 fragments 共all of them are
cryophiles and consist of five- to seven-membered rings兲
dominating in the low temperature water are illustrated in
Fig. 4.
Histograms of the fragment sizes, i.e., the number of
rings in individual fragments, are plotted in Fig. 5 for various
temperatures. We can see in the figure that the distributions
of all fragment sizes increase when the temperature de-
creases. Below 250 K under zero pressure, 6- to 12-hedral
fragments, especially 6- and 7-hedra significantly increase in
number, yielding a shoulder in the distribution, while the
fragments larger than 12-hedra are rare even at the lowest
temperature. There exists no distinct peak in the histogram
distribution, that is, there is no magic number.
Crystal fragments 关Fig. 1共a兲 and 1共b兲兴 are subsidiary in
LDL water because they are highly symmetrical. The frag-
ment of hexagonal ice I has, for example, the very large
symmetry number, 12. Such highly symmetrical structures
appear much less than asymmetrical ones. In the random
 134504-4 Matsumoto, Baba, and Ohmine
FIG. 3. 共Color兲 Total coverage by fragments is plotted against the tempera-
ture under 共a兲 0 atm and 共b兲 3000 atm. Coverage by each fragment type is
indicated by the bandwidth between the lines. Cryophiles, i.e., fragments
which increase by cooling, are plotted with red lines, and thermophiles, i.e.,
fragments that increase by heating, are plotted with blue lines. Under zero
pressure, each fragment increases/decreases monotonically and the cryo-
philes are supposed to fill the whole network at low temperature limit.
Shapes of the major fragments, indicated by capitals, are illustrated
in Fig. 4.
network structure, the binding energy of an ice fragment is
comparable to that of other major fragments. Unless ice frag-
ments aggregate to form larger ice block, it cannot become
very stable. Crystal fragments are thus not abundant. Al-
though it has been repeatedly anticipated that the empty cage
structures of the clathrate-hydrate type might be spontane-
ously constructed in liquid water at low temperature,13,14,22,23
such a large-size 共consisting of 12 or more rings兲 and sym-
metric fragment has never been observed in simulations.
Under pressure of 3000 atm, the composition of the frag-
ments changes only slightly by cooling down from
280 to 200 K. It should be noted that the total coverage by
fragments 共i.e., the abscissa of the Fig. 3兲 is not well defined
at high pressure because the network is strongly distorted by
strain. The fragment composition under pressure is found to
be similar to that at room temperature; their networks have
mutually common topological elements 共at least for the do-
main covered by fragments.兲 We can see in Fig. 5共b兲 that the
size distributions under 3000 atm are similar to those at
room temperature under zero pressure. Coverage by small
fragments between 3- to 5-hedra increases monotonically by
cooling under both zero and 3000 atm. Under 3000 atm,
however, no significant increase of large fragments consist-
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FIG. 4. Topologies of the major 11 fragments in LDL water are illustrated.
Residual distortion 共RD兲 values of individual fragments are indicated. Types
C and K are the same as 共b兲 and 共c兲 in Fig. 1.
ing of more than five surface rings is observed by cooling;
the distribution is unchanged. The distinct topological differ-
ence between LDL and HDL waters thus resides in the dis-
tribution of these larger fragments, composed of more than
five surface rings. Typical 10-hedral fragments are illustrated
in Fig. 6. Their shape is not spherical, contrary to those in
clathrate hydrate, but rather ellipsoidal.
B. Frustration in fragments
A fragment built of a couple of four-membered rings has
large distortion in their bond angles. A fragment even built
only of 5- to 7-membered rings might have large distortion in
case their combination is inappropriate. Such a distortion
cannot be relieved unless the network connectivity is
changed. Thus, the total network connectivity in a fragment
involves the intrinsic frustration. Here, we define a quantity
that quantifies the intrinsic frustration of each fragment. For
simplicity, it is assumed that the hydrogen bond network of
water can be characterized by the distorted network with
almost fixed bond length and a variety of containing angles
between adjacent hydrogen bonds. Water molecules prefer
regular tetrahedral configurations so that every angle ␪ be-
tween two adjacent hydrogen bonds tends to become 109.5°,
 134504-5 Topology of hydrogen bond networks in water
FIG. 5. Volume coverage by fragments is plotted against the fragment size,
that is, the number of rings in the fragment. Pressure is 共a兲 0 atm and 共b兲
3000 atm. Temperatures are indicated in the graph. Large fragments which
have six or more rings increase below 260 K under zero pressure, while the
shape of the distribution is almost constant under 3000 atm. Much larger
fragments having more than 12 rings are very rare even at low temperature.
cos ␪ ⬃ −1 / 3, if the network topology is ideal. The frustra-
tion, however, exists in a real system because of the topo-
logical constrain of the network. Each fragment has its own
lowest bound of frustration. Only when the network topology
has small frustration, large portion of the nodes 共i.e., water
molecules兲 can simultaneously yield the regular tetrahedral
HBs. In other words, when every node of the system seeks
the regular tetrahedral configuration, the system forms the
network topology with small frustration preferentially.
We introduce the residual distribution 共RD兲 to evaluate
the frustration as follows.
FIG. 6. Four typical quasi-10-hedral fragments are illustrated. All of them
consist of five- to seven-membered rings.
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The structure of a fragment or a ring can be optimized
by fixing the bond length and changing their bond angles to
minimize the following d value:
冉 冊
N 2
1 1
d= 兺 cos ␪i + 3
N i
, 共1兲
where the summation sums over all N contained angles ␪i
between adjacent edges of a fragment. Note that
cos 共109.5°兲 is −1 / 3, where 109.5° is the angle forming the
exact regular tetrahedral structure. The minimal value of d is
called the “residual distortion” of the network structure. Re-
sidual distortions of four- and five-membered rings are 1 / 9
and 0.0006, respectively. Residual distortion of six- and
seven-membered rings are zero when they are in boat or
chair conformation.24 Rings larger than seven member have
many stable conformations with zero residual distortion. Re-
sidual distortion of a fragment is always larger than the av-
erage of residual distortions of its component rings because
of the steric constraints, except for ice I fragment where d
values of the fragment itself and its component rings are all
zero 关Fig. 1共a兲–1共c兲兴.
It is found that 90% of the hydrogen bond network at
200 K under zero pressure is covered by the fragments
whose RD values are less than 0.03. RDs of major 11 frag-
ments in LDL water, illustrated in Fig. 4, are at most 0.016
共for type F兲. In Fig. 7共a兲, averaged binding energy of water
molecules belonging to each type of fragment is plotted
against RD. There is a correlation between the RD value and
the stability of a fragment. Fragments with small RD are
more stable than the average at all temperatures.
Hydrogen bond rearrangement in liquid water leads to
the change in the network topology and molecular configu-
rations. If the water molecules are in the stable structure like
ice, its hydrogen bond decays slower and the lifetime of the
structure itself also becomes longer. Hence we here evaluate
the decay time of each fragment type.
Decay time of hydrogen bond is defined by the decay of
冓 冔
time correlation function C共t兲 as follows:
兩NHB兩t=0
C共t兲 = 兺ij ␦ij共0兲 · ␦ij共t兲 , 共2兲
where
␦ij共t兲 = 1, if molecules i and j that are hydrogen-bonded
at t = 0 are still hydrogen-bonded at time t = 0, otherwise, and
the summation sums over all existing HB pairs at time t = 0.
Angle brackets express the time average.
Decay time of hydrogen bond in a fragment or a ring,
say, A structure, is also defined in a same manner. In this
case, time correlation function CA共t兲 is used instead,
CA共t兲 = 冓兺 兺
k ij苸兩Ak兩t=0
␦ij共0兲 · ␦ij共t兲 ,冔 共3兲
where the first summation sums over all existing A structure
at time t = 0. In order to define the decay time ␶, we assume
here that these correlation functions decay exponentially in
time, such as
 134504-6 Matsumoto, Baba, and Ohmine
FIG. 7. 共a兲 Binding energy of water molecules and 共b兲 decay times of the
hydrogen bonds covered by various kinds of fragment are plotted against its
residual distortion. Temperature is 260 K and pressure is 0 atm. Averaged
binding energy of a water molecule is −107.15 kJ/ mol, indicated by the
horizontal line in panel 共a兲, as a reference. In panel 共b兲, horizontal line
indicates the average decay time of all the hydrogen bonds 共48.5 ps兲. Filled
triangles for small fragments 共number of rings ⬍6兲 and open circles for
large fragments 共otherwise兲. Large fragments are more stable in general. HB
of fragments with small RD survives longer. HB in larger fragments sur-
vives longer in general. The decay times of hydrogen bonds in four-, five-,
six-, seven-, and eight-membered rings are 33, 48, 53, 51, and 45 ps,
respectively.
C共␶0兲
␶ = − ␶0/log , of the probability of actually being adjacent to the simple
C共0兲
where the observation time ␶0 is chosen arbitrarily as 20 ps
for 260 K. Although actual decay curve involves slower
components, we here employ rough approximation of fitting
by single exponential decay, because we only pay attention
to relative slowing down of bond rearrangements when the
network is in a particular topology.
In Fig. 7共b兲, the decay time of each fragment is plotted
against its RD. It clearly shows that fragments with smaller
residual distortion survive longer. The decay time of a hy-
drogen bond in a large fragment becomes much longer than
the average when RD is small. That is, a large network with
small distortion keeps its structure living longer.
C. Fragment aggregation and compatibility
Almost-unstrained fragments must be covered by
almost-unstrained rings such as five-membered flat rings,
six- and seven-membered rings in boat or chair conforma-
tions, etc. Actually, major fragments in the hydrogen bond
network of LDL water consist of these almost-unstrained
rings. This restriction on the size and shape of surface rings
leads to a certain correlation 共“compatibility”兲 between a pair
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FIG. 8. Compatibilities c共i , j兲 between major 11 fragments 共A-K in Fig. 4兲
are plotted. Box height indicates the compatibility 共see Appendix C for
definition兲. Gray boxes indicate that the corresponding fragments have com-
mon rings which are chair-shaped six-membered ring, boat-shaped six-
membered ring, boat-shaped seven-membered ring, or flat five-membered
ring. Black boxes indicate that both fragments have six-membered rings but
their conformation is incompatible 共boat vs chair兲 or the fragments do not
have the rings of the same size. Adjacency between other combinations of
fragments 共indicated in white boxes兲 is achieved by imposing certain distor-
tion to the fragments.
of adjacent fragments. Here, we define two fragments to be
adjacent when they share one complete ring. The conforma-
tion of the rings is also an important factor. For example, the
fragment of hexagonal ice 共type C in Fig. 4兲 consisting of
six-membered rings in the boat-type conformation is not
compatible with the fragment of cubic ice 共type K in Fig. 4兲
which consists of six-membered rings in the chair-type con-
formation, unless both the fragments are highly distorted to
be adjacent. Indeed, the probability of these fragments being
adjacent is one-fiftieth of the product of their appearance
probabilities 共the simple joint probability兲. We call this ratio
joint probability the compatibility c. 共See Appendix C for
details.兲 Compatibilities between major fragments are shown
in Fig. 8. The conformation and size of the surface rings
have significant effects on the compatibility among the adja-
cent fragments. The fact that there exists strong tendency of
certain pairs of fragments being adjacent imposes the lower
conformational entropy of LDL water.
D. Hydrogen bond network and fragment
rearrangements
At low temperature, fragments occupy large part of the
HB network to form aggregates. Surface and body rings of a
fragment aggregate are defined as the rings in the aggregate
which belongs to one and two fragments, respectively. Other
rings are the surface rings of isolated fragment or rings that
do not compose any fragment. Under zero pressure, numbers
of body, surface, and other rings per molecule are
0.71:0.74:0.18, 0.95:0.64:0.10, and 1.48:0.28:0.01 at 290,
260, and 230 K, respectively, showing that body rings domi-
nate at low temperature.
The hydrogen bond rearrangements take place very het-
erogeneously in space, especially at low temperature. At
 134504-7 Topology of hydrogen bond networks in water
FIG. 9. 共Color兲 Positions of the surface rings of the fragment aggregates are
drawn by translucent flakes. Red and blue lines and black dots indicate the
created and annihilated hydrogen bonds and network defects observed dur-
ing 10 ps, respectively. Temperature is 230 K and pressure is 0 atm. Water
molecules are omitted. All ten snapshots during 10 ps are overlaid in the
picture, so the dark area of flakes corresponds to the high probability of
finding a surface ring. Top-right region, where no flakes, lines or dots are
drawn, indicates that the space is filled by the fragment aggregates without
defects and no HB rearrangements happen there.
230 K, for example, while 39% of total hydrogen bonds be-
long to the surface rings, 71% of total HB rearrangements
are found to occur at those surface rings. Here, we define the
frequency of the HB rearrangements as the total number of
hydrogen bonds changed within 2 ps. That is, the HB rear-
rangements occur about four times more frequently on the
surface than in the body of the aggregate. On the other hand,
the inside of the aggregate is very stable against HB rear-
rangement 共Fig. 9兲.
The existence of network defects is always associated
with the network distortion. When fragments aggregate, they
tend to minimize the distortion by expelling the defects from
their region and the defects localize to the surface area.
These defects at the surface can move around by rearranging
the HB network; a sequential creation and annihilation of
hydrogen bonds transport a defect. We can indeed see in Fig.
9 that the time-averaged spatial distribution of network de-
fects is very heterogeneous localizing on surface rings. Frag-
ment aggregates can be regarded as pure low density amor-
phous domains and the surface rings are the grain boundary
of them.
Even if there is no defect, the HB rearrangements may
take place. In Fig. 10, a typical HB rearrangement inside the
fragment aggregate is illustrated. The snapshots of the local
HB network before and after the rearrangement at 230 K are
shown. In the snapshots, all fragments participated in the HB
rearrangement are shown. Inside the aggregate, there are
only a few network defects 共water molecules having more or
less than four hydrogen bonds兲 and, also, RD is small. In
such a condition, possible routes to change the network to-
pology are very limited. In this rearrangement, two hydrogen
bonds are exchanged at a time in order to avoid creation of
the defects. This kind of cyclic network rearrangement is
well known for ordered systems such as the formation of 5
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FIG. 10. Two snapshots of the HB network around the rearrangement inside
the fragment aggregate. The time interval is 1 ps. The nodes concerning the
rearrangement are pointed by the arrows. Water molecules are omitted and
all the fragments adjacent to the two nodes are drawn. The influence area of
a single rearrangement contains six fragments, 51 water molecules, and 35
rings. By the rearrangement, two five-membered and three seven-membered
rings appear, and six six-membered and two eight-membered rings disap-
pear, while no four-membered rings are included in both structures. Total
RD slightly increases from 0.0230 to 0.0237, but still small.
+ 7 defects in ice,25 Stones-Wales process on the buckyball,26
and formation of topological defect in Si.27 Also, a rear-
rangement always causes topological changes to all the frag-
ments adjacent to the hydrogen bonds, leading to the changes
in RD. At low temperature, structure changes inducing small
frustration are preferred. In the figure, both structures do not
include any four-membered rings or fragments with high
RD.
Rearrangements at the surface rings cause the changes of
the network topology at the surface of the aggregate, leading
to the growth and decay of the fragment aggregation domain.
At very low temperature, where the network defects almost
vanish, it is expected that the whole network is filled with
percolated aggregate of fragments. In such a network, sur-
face rings form scattered very small domains. HB network
rearrangements are thus very limited.
IV. CONCLUSION
The fragment analyses were performed on water HB net-
work structure and its rearrangement in water. The fragments
are the basic compact three-dimensional structure units. The
HB network of water at low temperature was found to be
almost fully tessellated with these fragments. It was found
that the fragments with small strains mutually aggregate by
sharing their common surface rings and form large stable
domains, i.e., fragments aggregates. There exist, therefore,
strong correlations among the types of the neighboring frag-
ments. It is found that the compatibility of a fragment inside
the aggregates is strongly influenced by its neighboring frag-
ments, that is, whether a fragment structural rearrangement
does occur or not depends on the types of surface rings
shared and on the topologies of the neighboring fragments.
The hydrogen bond network rearrangement is thus very re-
stricted inside the fragment aggregates and, instead, they
take places mostly in the surface areas of the aggregate do-
mains. The origins of structural and dynamical heterogeneity
in water HB network were therefore explained systematically
in terms of the fragment distributions and their rearrange-
ments. The existence of the fragment-fragment correlation
set the intermediate-range order in HB network and its dy-
namics in water.
 134504-8 Matsumoto, Baba, and Ohmine
The present fragment analysis might also be applied to
elucidate the mechanisms of the initial seed formation and its
growth in the nucleation process of ice and clathrate
hydrates,28–30 liquid-liquid coexistence in a-Si,31 and the HB
structures at interface and in the vicinity of a hydrophobic
solute.32–34 In the nucleation process, an initial nucleus is
created and then grown to the crystalline structure, where the
intermediate-range order transforms and grows to the long-
range order.28
ACKNOWLEDGMENTS
This work is partially supported by the Grant-in-Aid for
Scientific Research on “Meso-timescale Dynamics of Crys-
tallization” 共Grant No. 14,077,210兲, “Chemistry on Homoge-
neous Nucleation” 共Grant No. 15,685,002兲, and “Water Dy-
namics” 共Grant No. 1,400,100兲 from the Ministry of
Education, Science and Culture. Calculations were carried
out partly by using the supercomputers at Nagoya University
Information Technology Center and at Research Center for
Computational Science of Okazaki National Institute.
APPENDIX A: RING PERCEPTION ALGORITHM
In the analyses of network-forming materials such as
water, silicon, silica, and CRN, ring content is often dis-
cussed, while the ring perception algorithm is not always
explained in detail. It must be stressed that there are so many
different ways of perceiving them, and different methods
may give different numbers of rings in a given network.35
In the present work, we introduce the following ring
perception algorithm. Here the network is treated as an un-
directed graph. First of all, all the triplets of successive ver-
tices along the edges in the graph are listed. Second, for each
triplet, all the cyclic paths containing the triplet are searched.
The cyclic path must not have shortcut paths. Searching
starts from three-membered rings and develop the ring size
until at least one cyclic path is found. When a cyclic path is
found, all the different cyclic paths of the same size contain-
ing the triplet are looked up and set in a stack. The same
process is repeated for all the triplets in the network. In the
postprocess, identical rings are eliminated from the stack,
and, finally, the list of all distinguishable rings is obtained in
the stack.
APPENDIX B: DEFINITION OF “COVERAGE” BY A
FRAGMENT
Here, we define a “coverage” of fragment to find how
much volume the fragments cover. As the graph is purely a
topological concept, it is not possible to define the “volume”
of a graph by itself.
In case of HB network of water at low temperature, geo-
metrical information can be obtained from molecular con-
figuration. Suppose all vertices have exactly four edges,
which are almost in regular tetrahedral directions. Every trip-
let among the four edges at a vertex makes a solid angle that
is approximately a quarter of entire sphere. In other words, a
quarter of a vertex is cropped by the triplet. Now, let us
consider the volume of a graph. When all the vertices of a
graph have four edges, the total number of the triplets is four
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J. Chem. Phys. 127, 134504 共2007兲
times the number of vertices. If a value 1 / 4 is given as the
“partial” volume for a triplet, the total number of vertices is
recovered by the sum of the partial volume.
The same procedure can be applied for a subgraph, cut
from a larger graph in which every vertex has four edges.
This subgraph has vertices not having four edges as in gen-
eral. We therefore give different partial volume for a vertex
according to the number of edges. Based on the consider-
ation of solid angles, partial volume of a vertex having four
edges is regarded as 1. Partial volume of a vertex having
three edges is 1 / 4. Partial volume of a vertex having less
than three edges are determined to be 0 because at least three
edges are required to involve the solid angle. Partial volume
for each vertex is determined by the rules above and the total
volume of a subgraph is defined as the sum of partial vol-
umes of vertices in the subgraph. Then we can define the
volume coverage by a given fragment as follows: First, pick
up all the fragments by graph matching technique and mark
those hydrogen bonds covered by the fragments. Marked hy-
drogen bonds construct a subgraph. Volume coverage is ex-
pressed by the ratio of the total subgraph volume to the total
system volume, i.e., the number of molecules.
A good example for this method is ice. A crystallite of
cubic ice 关Fig. 1共c兲兴 has four triplets and six vertices having
two edges so that its partial volume is 1. Hexagonal ice con-
sists of two kinds of crystallites 关Fig. 1共a兲 and 1共b兲兴. The
former has six three-connected vertices and six two-
connected vertices and the partial volume is 6 ⫻ 1 / 4 + 6 ⫻ 0
= 3 / 2. The latter has two three-connected vertices and six
two-connected vertices and its partial volume is 1 / 2. Sum-
mation of partial volume recovers the number of vertices in
the crystal exactly. In this sense, coverage is a “volumetric”
measure and more useful than other indices such as the total
number of rings or fragments.
This approximation is expected to work well at low tem-
perature. In hydrogen bond network at high temperature,
however, it might be inaccurate because there are many wa-
ter molecules not having four hydrogen bonds or having dis-
torted local configurations.
APPENDIX C: PROBABILITY OF FINDING A PAIR OF
ADJACENT FRAGMENTS
Suppose that the total number of type i fragment found
in a snapshot structure is n共i兲, and there are m共i , j兲 pairs of
adjacencies between types i and j fragments. Let type i frag-
ment consist of r共i兲 surface rings. The total surface rings of
the fragments, say, R, is calculated by
R = 兺 n共i兲r共i兲.
When the fragment distribution is homogeneous, the
probability of finding the case that types i and j fragments
are adjacent is approximately proportional to the number of
surface rings of both types of fragments, so the number of
adjacencies between types i and j fragments is expected to be
m0共i, j兲 = Nr共i兲n共i兲r共j兲n共j兲/R2 ,
where N is the total number of adjacencies in the structure.
In the actual configuration, m共i , j兲 may be different from
 134504-9 Topology of hydrogen bond networks in water J. Chem. Phys. 127, 134504 共2007兲

20
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