Research: Science and Education

Modeling the Hydrogen Bond within Molecular Dynamics

Peter Lykos
Chemistry Division, Illinois Institute of Technology, Chicago, IL 60616; lykos@iit.edu

The kinetic molecular theory of gases is the traditional

first application of classical mechanics in general chemistry.
The model assumes a dilute gas to be made up of a large
number of particles moving randomly in a container with
no interparticle forces operating. Furthermore all collisions
of the particles with the container walls are assumed to be
elastic. The result of that analysis, based on Newtons laws of
motion, is compared with the equation of state of an ideal
gas, that is, with the empirical Charles and Boyles laws to
which is added Avogadros hypothesis. Via that comparison
we find the average kinetic energy of many particles comprising a gas at equilibrium to be proportional to the absolute temperature of that gas. Thus we do introduce the
concept of temperature into a mechanical many-particle
model of matter.
Real gases do not follow the equation of state for the
perfect gas well at low temperatures and high pressures. Indeed at sufficiently low temperatures, on compression, real
gases undergo a change in state to a liquid. Further the resulting liquid is essentially incompressible.
A Nobel Prize was awarded to van der Waals for extending the equation of state for an ideal gas. He recognized that
there must be forces of attraction operating between particles
for condensation to take place and also that the particles must
have finite extension in space or, put another way, experience strong repulsive forces when in close proximity. Thus
an important refinement was introduced using bulk variables
but reasoning from a molecular model of gases. In the process, the van der Waals equation of state introduced two parameters that, unlike the ideal gas model, particularized it to
the specific gas of interest.
The advent of the electronic digital computer made it
feasible to extend the kinetic molecular theory of gases. Numerical solution of Newtons laws applied to conservative systems made up of many particles, including provision for
intermolecular forces, led to the development of molecular
dynamics. Initially that was done for spherically symmetrical
rare gas atoms such as argon. But once that method was well
developed, Rahman and Stillinger (R-S) extended it to their
landmark and comprehensive treatment of liquid water (1).
Waters physical properties1 required the introduction of
the concept of the hydrogen bond (H-bond) to rationalize
the trends observed for similar compounds made up of elements in the periodic chart in the column beginning with
oxygen (similarly for nitrogen and fluorine). Thus, even for
a fairly simple model of water, provision had to be made for
the H-bond, a bond with a dissociation energy about one
twentieth the dissociation energy of ordinary covalent bonds.
The H-bond of course is essential to us as living beings.
The rungs in the twisted ladder model of DNA are just representations of the hydrogen bonds that hold the two strands
together. However a simple yet revealing and easily accessible
quantitative mechanical model of the ubiquitous hydrogen
bond is not customarily developed in any of the usual underwww.JCE.DivCHED.org

graduate courses in biology, chemistry, or physics. Thus we

took the initiative to extract from the R-S liquid water model
how they accommodated hydrogen bonding in the context
of molecular dynamics and to incorporate that treatment in
undergraduate physical chemistry together with the entire subject of molecular mechanics applied to liquid water. In that
manner we hoped to reveal the anatomy of a hydrogen bond.
In class we review the general chemistry treatment of the
kinetic molecular theory of gases, its features listed in a column, and then go on to systematically refine that model, in
a parallel column, until we arrive at the R-S model for liquid water. We then append their treatment of the water dimer
as a separate example of their two-body interaction. As an
extension of the R-S article, we assign as a problem for the
class calculation of the two body potential for the vibration
of the two rigid water molecules comprising the water dimer
model using the given R-S potential.
The Rahman and Stillinger Molecular Dynamics
Model of Liquid Water
The R-S model for liquid water, limited in scope by the
size and speed of the IBM 36075 available at Argonne National Laboratory in the late 1960s, had these specifications:
The container selected is a mathematical cube containing 216
(6 6 6) molecules with a volume corresponding to the
actual density of liquid water at room temperature. Each of
the faces, sides, and corners of that cube are shared with other
similar cubes forming a stack of 27 cubes (3 3 3 or three
cubes on each edge) such that periodic boundary conditions
could be imposed. What that means is that as a molecule approaches one of the walls in the central cube, instead of colliding with the wall and bouncing back it is allowed to pass
through the wall and its mirror image molecule enters the central cube through the opposite wall. That feature was introduced to offset the very large ratio of surface to volume that
would have dominated the trajectories of the molecules.
The geometry of the water molecule, as well as the isotopes
of hydrogen and oxygen, need to be specified so that the principal components of the molecular moment of inertia could
be determined (needed for the rotational kinetic energy expression) as well as computation of the intermolecular potential as a function of intermolecular distance and relative
orientation. As the model is approximate, R-S assumed that
it was sufficient to take the water molecule as a regular tetrahedron with the oxygen at the center, a proton at each of two
vertices, and a lone pair of electrons at each of the remaining
two vertices. Net partial charges of equal magnitude (0.19 e),
with appropriate sign at each vertex are selected, presumably
to replicate the permanent electric dipole moment of the water molecule. Of course as an additional exercise this may be
checked by actual computation of the electric dipole moment
from the model.

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Research: Science and Education

Twelve parameters need to be specified for each molecule at the time the simulation is started: three Cartesian
coordinates and their time derivatives for linear velocity; and
three Eulerian angles and their time derivatives for angular
velocity. The molecules are assumed to be rigid rotors. The
potential is assumed to be a sum over all unique water molecule pairs of an effective two-body potential. The two body
potential itself is a sum of two contributions from the interacting pair of molecules as follows:
(i)

(ii)

Lennard-Jones (L-J) potential taken to be the neonneon

L-J potential (1) as Ne is the isoelectronic united atom
limit for water (as are each in the series methane, ammonia, water, hydrogen fluoride, and of course neon itself ). The L-J potential accounts primarily for the
repulsion at small intermolecular distances (hence the incompressibility of liquid water).
The electrostatic potential arising from the Coulomb attraction and repulsion between the four partial charges
on one rigid molecule and the four partial charges on
the other molecule for a total of 16 attractions and repulsions (1). This component would be a point dipole
point dipole interaction at large distances but not at the
intermolecular distances encountered here. R-S introduced as a precaution a multiplicative switch factor,
changing smoothly from zero at small distances to one
at larger distances. That was done because use of a finite
increment of time to numerically solve the second-order
ordinary differential equations might project a next step
to nearly superpose two point charges and thus lead to
an enormous nonphysical Coulombic interaction. More
specifically, the switching function is zero from zero distance to 2.0379 and becomes one at R = 3.1877 .2
Between those two values of R the function is S-shaped
rising from zero (initially with zero slope) to one, again
with zero slope at that point. The students were asked to
verify the switch function properties of being continuous as well as having a continuous first derivative needed
for a conservative system.

The Hydrogen Bond According to R-S

The minimum energy configuration for the two rigid
water molecule hydrogen-bonded dimer is displayed in Figure 1. The dimer has a distance of 0.76 between the hydrogen of one water molecule and the lone pair of the other
of the water molecules (1). As is displayed in Figure 1 each
of the four vertices in a tetrahedral water molecule is 1
from the oxygen and each bears a charge of appropriate sign

O
1.00

0.76

O
1.00

H
H

Figure 1. The water dimer at its equilibrium configuration according to the R-S model.

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Journal of Chemical Education

of +0.19 e at each proton and 0.19 e at each lone pair. Thus

the distance between the two oxygen atoms is 1.00 + 0.76 +
1.00 .
There are three equivalent planes of symmetry in the
water dimer model, each of which contain the pair of oxygen atoms, and one hydrogen atom and one lone pair between them, all in a straight line. For example, the plane of
symmetry in the plane of the paper has a hydrogen atom
above the first oxygen that is contributing a hydrogen atom
to the H-bond and a lone pair above the second oxygen that
is contributing a lone pair to the H-bond.
Where physical chemistry has calculus-based physics as
a prerequisite it is reasonable to pose the following problem
to physical chemistry students:
For the water dimer described in Figure 1:
(a) Find the four unique intercharge (intermolecular)
distances at 2.76 .
(b) Increase (stretch) and decrease (compress) the Hbond by 0.1 and find the corresponding unique
intercharge distances between the two sets of four
charges.
(c) Find the values for the total Coulomb energy at each
of the three intermolecular distances (0.75, 0.76,
0.77 ).
(d) Find the values of the switching function at the three
intermolecular distances.
(e) Find the value of the L-J energy at each of the three
distances.
(f )

Find the potential energy of the dimer at the three

distances. Note the increase in potential energy
when the H-bond is both stretched and compressed
from the equilibrium geometry.

(g) Assuming the potential is a quadratic in the displacement find the force constant for vibration of two
rigid water molecules as a pseudo diatomic molecule.
(h)

Check the value of the equilibrium H-bond distance.

(i)

To more fully explicate the several contributions to

the total potential energy as a function of separation, examine separately the effects each of the parts.

The potential energy at the equilibrium configuration

gives 6.5 kcalmole-pair for the dissociation energy of the
dimer. Of course that result, based on use of classical mechanics, does not include the zero-point energy correction
one would get using quantum mechanics. A more recent and
more sophisticated determination of the water pair potential
energy per se, estimated from spectroscopic data, gives 5.40
kcalmole-pair and 1.74 kcal for the zero-point correction
for a net dissociation energy of 3.66 kcalmole-pair (2). Thus
the relatively crude model used by R-S captures the dissociation energy of the water dimer (and hence the energy of that
H-bond) reasonably well.
The question remains as to why the H-bond is linear in
this model? There are two aspects to that question; namely,
rotation about the linear H-bond and bending of the H-bond
in any of the planes of symmetry. In both aspects the L-J
potential energy is independent of both rotation and bend-

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Research: Science and Education

ing. Also note that the R-S model of the dimer is isomorphic with ethane. In ethane the set of three protons at one
carbon is staggered with respect to the other set of three protons at the other carbon to minimize the Coulomb repulsion of the positive charges. In the case of the R-S model,
the point charges are eclipsed as the alignment of positive
charges at the protons (subtended by one oxygen) with the
negative charges due to the lone pairs (subtended by the second oxygen) maximizes the Coulomb attraction. The electrostatic interaction is such that rotation around the H-bond
increases the distance between opposite charges and decreases
the distance between like charges so the Coulombic energy
increases. Similarly bending in one of the symmetry planes
decreases the distance between one pair of opposite charges
but increases the distance between two pairs of opposite
charges leading to a net increase in Coulomb energy. The
switching function acts in such a manner as to exaggerate
slightly those trends. Thus the linear configuration, with
eclipsed opposite point charges at the given equilibrium inter-oxygen distance, is the lowest energy configuration.
For those people interested in an introductory treatment
of the solution of the differential equations in the context of
molecular dynamics, a good resource is the Saiz and Tarazona
article, Molecular Dynamics and the Water Molecule (3).
Conclusion
In chemistry, experiment and computer-based modeling are progressing hand in hand to elucidate the structure
and other properties of molecules, as well as the properties
of bulk matter modeled as assemblages of molecules near
equilibrium or even significantly away from equilibrium.
Where chemical bonds are made or broken, or where other
quantum effects are operating, one needs to apply quantum
mechanics. However, where the molecules remain intact, often classical mechanics is sufficient and much simpler to apply to both complicated individual molecules with many
internal degrees of freedom as well as to assemblages of molecules such as in liquid water.
In this brief introduction to the seminal Rahman and
Stillinger article, only the model is explored in the context
of using it as a vehicle to introduce undergraduates in physical chemistry to the power and ease of application of classical mechanics to bulk matter from a molecular perspective.
Rahman and Stillinger, however, went on to analyze their results from their extensive and carefully done simulation. They
took great care to explicate thoroughly and exhaustively, not
only the features of the model itself, but also the range of
liquid water physical properties that could be assessed with
good fidelity. Subsequently they published three additional
articles examining the effect on their model of varying the
pressure, varying the temperature, and varying the time increment used in solution of the ordinary second-order differential equations (46).
Thus the article used as the basis of this work, together
with the immediately following three sequels, provide a pow-

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erful tutorial framework within which students can be shown

the power of classical physics when joined with the modern
digital computer and applied to the familiar and, even today, challenging sample of matterliquid water. Today derivative versions of these methods are being used widely,
especially in molecular biochemistry. A recent example appeared in Science (7). A nearly complete treatment of hydrogen bonds appears in Jeffreys remarkable book on hydrogen
bonding (8). A very recent article (9), Ultrafast HydrogenBond Dynamics in the Infrared Spectroscopy of Water, describes an analysis of femtosecond infrared spectroscopic
studies of the OH-stretching frequency of HOD in D2O
that reveals rearrangements of the hydrogen-bonded network
in water. That distinguishes intra hydrogen bond changes that
happen over shorter times (170 femtoseconds) from collective structural changes that happen over longer times (1.2
picoseconds). Finally we should note the vibrational potential of the OH stretch shows extreme anharmonicity arising from the H-bond interaction in OHH as reported
in Science (10).
Note
1. The Web site http://www.sbu.ac.uk/water (accessed Aug,
2003), provided and maintained by Martin Chaplin, contains a rich
and varied display of data and information about water from many
perspectives. The site includes experimental information, critiques
of various models, and an extensive (over 500 references) bibliography.
2. As the 1971 Rahman and Stillinger article may not be conveniently available to some readers, a referee has urged us to write
down the explicit expression for the switching function as it is
the only formula that is not common knowledge. The expression is,
S(rij) = 0

for 0 < rij < RL

S(rij) = (rij RL)2(3RU RL 2rij)(RU RL)3 for (RL < rij < RU)
S(rij) = 1

for RU < rij

where RL = 2.0379 and RU = 3.1877 . One may ask students to

verify that the switching function varies continuously and differentially between zero and one as rij grows from zero to infinity.

Literature Cited
1. Rahman, A.; Stillinger, F. J. Chem. Phys. 1971, 55, 3336.
2. Fellers, R.; Leforestier, S. C.; Braly, L. B.; Brown, M. G.;
Saykally, R. J. Science 1999, 284, 945.
3. Saiz, E.; Tarazona, M. P. J. Chem. Educ. 1997, 74, 1350.
4. Stillinger, F.; Rahman, A. J. Chem. Phys. 1972, 57, 1281.
5. Stillinger, F.; Rahman, A. J. Chem. Phys. 1974, 60, 1545.
6. Stillinger, F.; Rahman, A. J. Chem. Phys. 1974, 61, 4973.
7. de Groot, B. L.; Grubmueller, H. Science 2001, 294, 2353.
8. Jeffrey, G. A. An Introduction to Hydrogen Bonding; Oxford
University Press: Oxford, United Kingdom, 1997.
9. Fecko, C. J.; Eaves, J. D.; Loparo, J. J.; Tokmakoff, A.; Geissler,
P. L. Science 2003, 301, 1698.
10. Bakker, H. J.; Nienhuys, H.-K. Science 2002, 297, 587.

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