1 Intramolecular and intermolecular interactions

Central to our understanding of soft matter systems are the interactions that make it possible for atoms
to form molecules and, on the other hand, forces that hold the various types of molecules together
as condensed phases. The former result in chemical bonds, whereas the latter give rise to so-called
physical bonds. The fundamental difference between these two interactions is that in the formation
of chemical bonds electron clouds of the bonding atoms are significantly redistributed. In the case
of physical bonds, only a slight perturbations of electron distributions takes place. These types of
interactions are commonly referred to as non-covalent interactions.

In soft matter physics the relevant energy scale is thermal energy k B T , where kB is the Boltzmann
constant (≈ 1.381 × 10−23 J/K) and T is “room temperature”, something between 293 and 300 K,
depending on the author. Here we will use the value 298 K, but note that the exact value of the ambient
temperature - when picked from the range above - will not cause a huge quantitative variation in the
interaction energies in terms of kB T . The thermal energy kB T can be taken as a rough measure for the
magnitude of thermal forces in the system. These forces result from the random thermal motion and
subsequent collisions of atoms and molecules in the system. However, a more fundamental reason for
the use of kB T as our energy scale in soft matter physics will become apparent in our review of basic
thermodynamics and statistical mechanics.

In this lecture we will first consider some aspects regarding chemical bonding, introducing the
concepts of purely and polar covalent bonds, and electronegativity (1.1). We then turn our attention
to electrostatic interactions between charges and dipoles, as these serve as useful models when trying
to understand interactions between real molecules (1.2). A special type of electrostatic interaction,
the hydrogen bond, is also introduced due to its immense importance in describing, for example, the
properties of water and three-dimensional structures of biological macromolecules (1.3). We end this
brief review of basic interactions by finally considering the ubiquitous van der Waals forces between
atoms and molecules (1.4).

Clearly, the coverage of the material below is not exhaustive. Instead, we concentrate only on the
issues essential to the later topics of this course. You can seek further insight on the topics at hand in
more specialized textbooks (see the list at the end of this text).

1
 r

Energy

ε
r0 Interatomic spacing

Figure 1: Morse curve for two atoms forming a chemical bond. The equilibrium bond length r 0 is the
interatomic distance where the energy is at minimum, ε.

1.1 Chemical bonding

By chemical bonding we mean the effect that causes the energy of two atoms close to each other
to be significantly lower, 100 kJ/mol or more, than when they are apart. The effect arises from the
sharing of the outer (valence) electrons of these atoms which, in the presence of two or more positively
charged nuclei, rearrange themselves into spatial distributions (orbitals) where the electrons are, on
the average, closer to the nuclei.

It is common to represent the strength and length of a chemical bond (i.e., distance between the
bonding nuclei) with a so-called energy-distance Morse curve, see Fig. 1. The minimum energy
distance is called the equilibrium bond length, around which the nuclei vibrate according to the system
temperature. The bond energy (value of energy at the minimum) is then defined as the amount of
energy required to increase the separation of the atoms forming the bond to infinity. However, what
is lacking from the Morse curves is the fact that chemical bonds, due to the redistributed electron
clouds, have distinct directionality1 . Probably the most widely used model for chemical bonding is
the covalent bond or shared electron model.

Different elements have different tendencies to draw electrons toward their nuclei. This ability is
called electronegativity. Thus, in general the shared electron cloud is not evenly distributed in the
space between the bonding nuclei. Electronegativities cannot be directly measured, but the scale
most often used (developed by Linus Pauling) assigns fluorine the highest value, 4.0. The difference
in the electronegativities of the bonding atoms then quantifies the extent how evenly or unevenly
the bond electrons are shared. A purely covalent bond (i.e., completely evenly shared electrons)
can only be obtained when the bonding atoms are of the same element. When the difference in the
electronegativities is large, the bond is said to posses ionic character or polarity. That is, we can
view part of the electronic charge, −δ, to be associated with the more electronegative atom, 00 X 00 .
The atom with a smaller electronegativity, 00Y 00 , on the other hand, can be viewed as having a partial
1 Thereis a type of interatomic bonding known as the metallic bonding which has very little or even no directionality.
However, this is not a topic of utmost importance to our course on soft matter.

2
positive charge +δ, as the positive charge of its nuclei is not fully screened anymore by the valence
electrons. The polar character of a chemical bond is typically expressed in the form X δ− − Y δ+ . A
useful, though approximative, way of looking at this effect is to think that there is a permanent dipole
associated with the polar bond.

The formation of one or more chemical bonds allows atoms to form energetically stable molecules
which are characterized by their structure and composition. By stable we mean that the molecules
remain intact despite thermal collisions with other atoms and molecules. Since chemical bonds result
in increased localized electron densities, it can be assumed that the spatial regions associated with
different chemical bonds repel each other electrostatically. This way of thinking, known as the
“valence shell electron repulsion” (VSEPR) model is quite good at explaining the shapes of various
molecules2 .

1.2 Electrostatic interactions

As became apparent from our discussion on chemical bonds above, many molecules contain polar
chemical bonds that can be associated with electic dipoles, comprising of atomic “partial charges”
±δ. The molecules, in turn, as collections of these partial charges, can be associated with electric
dipoles, quadrupoles, and higher multipoles. On the other hand, solvation of salt in an aqueous
environment introduces ionized atoms, such as Na+ and Cl− , into the system. Many chemical groups
in molecules may also be charged (e.g., protonated and de-protonated) at certain values of pH of the
host medium.

All in all, we see that electrostatic effects are important in a wide range of molecular systems 3 . It
turns out that relating the intricate intermolecular forces to simple electrostatic interactions between
charges, dipoles, and higher multipoles works surprisingly well in understanding the strcuture and
dynamics of condensed matter systems. In particular, in soft matter even the weakest intermolecular
forces are comparable to kB T , and may play an important role in the behavior of the system studied.
Hence, in the following we will review the very basic electrostatic interactions between groups of
charged particles.

1.2.1 Charge-charge interaction

The simplest, as well as the strongest, electrostatic interaction we will study is the one between two
charges Q1 and Q2 . From basic electrostatics we recall the interaction energy to be

Q1 Q2 z1 z2 e 2
U (r) = = , (1)
4πε0 εr r 4πε0 εr r
2 As a final note on chemical bonds, you may think that orbitals, the spatial representations of the atomic and molecular
electron distributions, are only useful “tools” for carrying out quantum-mechanical calculations. However, a number
of recent experimental studies using weak laser pulses have allowed researchers to “map” the electron distributions of
different molecules. And yes, the obtained spatial electron probability distributions are in excellent agreement with the
orbital model.
3 All intramolecular and intermolecular effects are ultimately electronic effects!

3
where r is the distance between the charges, ε0 permittivity of vacuum (= 8.854 × 10−12 F/m), and
εr is the relative permittivity or dielectric constant of the medium where the charges are located in.
For example, in vacuum εr = 1, in hydrocarbons typically εr = 2 − 5, and in water εr ≈ 78 at room
temperature. (Note that polar media, such as water, screen charge-charge interactions very efficiently,
whereas apolar media do not.) In the right-hand side equation we have introduced the notation Q i =
zi e, where the integer zi is called the ionic valency of charge i. This is usually used when describing
systems with ionized atoms, e.g., dissolved salt. For cationic ions we have z = +1 for Na + , z = +2
for Ca2+ and so forth. For anionic Cl− we correspondingly have z = −1. The electrostatic force
(Coulomb force) between the charges is

dU (r) z1 z2 e 2
Fc (r) = − = , (2)
dr 4πε0 εr r2
and, as you well know, is repulsive for like charges and attractive for unlike charges.

The important characteristics of charge-charge interactions is that they are non-directional (depending
only on the radial distance between the charges), long-ranged (∝ r −1 ) and strong. The last point is
shown by considering two isolated monovalent ions, Na+ and Cl− , in contact. In vacuum, their
interaction energy at a distance corresponding to the sum of their van der Waals radii 4 , 0.276 nm, is

(1.602 × 10−19 )2
U (r) = − J = −503 kJ/mol,
4π(8.854 × 10−12 )(0.276 × 10−9)

which translates to 200 kB T at 298 K. However, since electrostatic interactions are screened by a factor
εr in different media, in many cases it is useful to define a characteristic length at which the magnitude
of the electrostatic interaction between two elementary charges is equal to the corresponding thermal
energy. This distance is called the Bjerrum length,

e2
λB ≡ . (3)
4πε0 εr kB T
For example, in water at 298 K the Bjerrum length is 0.71 nm.

In solutions the strong charge-charge interaction leads to the situation where ions of one type
are surrounded by other ions with charges of opposite sign. That is, positively charged ions are
surrounded by negatively charged ones and vice versa. This leads to an effective shielding of the bare
charge-charge interactions, reducing the apparent range of the Coulomb forces.

1.2.2 Charge-dipole interaction

We then consider a slightly more complex situation: interaction between a charged particle and an
electric dipole, u = ql (see Fig. 2). An example of such case is the interaction between a solvated ion,
say Na+ , with a molecule that has a permanent dipole moment, such as H 2 O. The interaction energy
4 The distance of closest approach between two non-bonded atoms. This minimum distance is due to the repulsion of
the atom electron clouds, as dictated by the Pauli exclusion principle, and also, to some extent, the electrostatic repulsion
between the positively charged nuclei.

4
Figure 2: Schematic presentation of (a) charge-dipole and (b) dipole-dipole electrostatic interactions.

can be constructed from the Coulomb interactions between the bare charge Q and the dipolar charges
±q  
Qq 1 1
U (r) = − , (4)
4πε0 εr r0 r00
q q
0 l
where r = (r + 2 cos θ) + ( 2 sin θ) and r = (r − 2l cos θ)2 + ( 2l sin θ)2 . We ignore here the
2 l 2 00

self-energy of the dipole and assume that the distance between the dipole charges is held fixed. When
the dipole is sufficiently far away from the charge (i.e., r is large enough in comparison to l), we can
approximate r0 ≈ r + 2l cos θ and r00 ≈ r − 2l cos θ. The interaction energy is then
! !
Qq 1 1 Qq l cos θ
U (r, θ) = − =−
4πε0 εr r + 2 cos θ r − 2 cos θ
l l 4πε0 εr r − l 2 cos2 θ
2
4
Qu cos θ
≈ − . (5)
4πε0 εr r2
Note that since Q/4πε0 εr r2 is the magnitude of the electric field ~E due to the charge Q, eq. (5) can
also be written as
U (r, θ) = −uE cos θ = −~u · ~E. (6)

When deriving eqs. (5) and (6) we assumed the dipole to be sufficiently far from the charge. But how
far is sufficiently far? Comparing the interaction energy from the approximate expressions above with
the explicit calculation of the Coulomb interactions, it can be shown that only at about r < 2l does
our approximation deviate more than 10% from the exact result. Taking into account the finite size of
atoms and molecules, eq. (5) is actually an excellent approximation for interactions between ions and
small polar molecules at all physically relevant distances. In the case of larger molecules, where the
charges comprising the dipole may be several ångströms apart, we need to exercise good judgement
whether to use eq. (5) or not.

1.2.3 Dipole-dipole interaction

Similar to the charge-dipole case, the interaction between two dipoles u 1 and u2 can be constructed
from the explicit Coulombic interactions of the charges ±Q and ±q of the dipoles. Again, provided
the dipole-dipole distance r is sufficiently large in comparison with the size of the dipoles, the
interaction energy can be shown5 to be
u1 u2
U (r, θ1 , θ2 , φ) = − (2 cos θ1 cos θ2 − sin θ1 sin θ2 cos φ), (7)
4πε0 εr r3
5 You get to show this in the first exercise!

5
where θ1 and θ2 are the polar orientation angles of u1 and u2 , respectively, and φ is the azimuthal
orientation angle of u2 in reference to u1 .

1.3 Hydrogen bond

Consider a hydrogen atom covalently bonded to a highly electronegative atom, say “D” (not to be
confused with the chemical symbol of deuterium, a heavier isotope of hydrogen 1 H). Due to its low
electronegativity, the hydrogen atom will be positively polarized. Furthermore, since it has only one
electron, the positively charged H nucleus (proton) is exposed to the region of space away from D.

Now, suppose another electronegative atom, “A”, approaches the D-H group. Since the lone electron
of the hydrogen atom is attracted by D, there will be an electrostatic interaction between the negatively
polarized A and the positively polarized H. This interaction is called hydrogen bonding. In general,
hydrogen bond can be represented as

Dδ− − Hδ+ · · ·δ− A,

or simply
D − H· · ·A,
where D denotes a donor, to which the H atom is covalently bonded, and A an acceptor that has a
lone pair of electrons (hence our strange choice of element symbols D and A). Common donor and
acceptor atoms are N, O, and F.

A typical H· · ·A distance is at least 0.05 nm shorter than the van der Waals distance between the
bonding atoms (see 1.2.1). For example, in water the H· · ·O distance is 0.18 nm, and clearly differs
both from the H-O covalent distance (0.1 nm) as well as the H-O van der Waals distance (0.26 nm).
Hydrogen bond energies are usually between 10 and 40 kJ/mol. For example in water the bond energy
O-H· · ·O is about 20 kJ/mol or 8 kB T . Thus, although not as strong as bare charge-charge interactions,
hydrogen bonds still dominate over thermal energy kB T . In fact, both the strength and the shortness
of the hydrogen bond led researchers at first to presume it to be some sort of a quasi-covalent bond.
The modern view of hydrogen bonds, however, is that they are mainly of electrostatic origin, with
only about 10% of covalent character.

Hydrogen bonding is largely responsible of the anomalous properties of water (e.g., high boiling point,
high viscosity, and high surface tension). In addition, most biological macromolecules have many
hydrogen bonding sites, the most notable ones being DNA 6 and different proteins. The formation of
many hydrogen bonds provides the three-dimensional structures of these molecules with stability and
also affects their intermolecular associations.

1.4 van der Waals interactions

Finally, we consider short-ranged and weak interactions existing between all types of atoms and
molecules, known as the van der Waals interactions. These ever-present forces are named after
6 It is in fact a myriad of hydrogen bonds that hold the two strands of DNA together in the famous double helix form.

6
the Dutch scientist Johannes Diderik van der Waals (1837 - 1923), who was one of the first to
add considerations of attractive interactions between molecules into the macroscopic description of
gases7 .

All atoms and molecules, even non-polar and uncharged ones, exert attractive forces on each other.
This is a result of the atomic polarizability α0 of atoms. The constant motion of electrons in atoms
results in the fact that at any given instant in time, any atom actually has a finite electric dipole
moment. Despite the quantum-mechanical uncertainty of position, even particles as light as electrons
have to occupy some region of space at a given time. In the absence of an external influence, the
average dipole moment of an atom nevertheless is zero.

However, if an atom is affected by an electric field, such as one due to an ionized atom or a polar
molecule, there will be an induced dipole moment on the atom, u ind = α0 E, resulting in a finite net
force. In general, the van der Waals forces arise from three different contributions: (1) orientation or
Keesom interaction; (2) induction or Debye interaction; and (3) dispersion or London interaction. The
first of these is nothing but the interaction between two permanent dipoles, averaged over different
orientations due to the thermal motion of the molecules. The average is in fact a weighted average,
with the weight of each orientation given by the so-called Boltzmann factor exp(−U (r, θ)/k BT ). We
will return to this issue as we review basic thermodynamics and statistical mechanics. (But yes, it is
just that thermal energy term kB T in the Boltzmann factor that sets the convenient energy scale in soft
matter physics.) The result of this weighted averaging is that the dipole-dipole interaction is of the
form,
u21 u22
UKeesom = − , (8)
3(4πε0 εr )2 kB T r6
where you should note the dependence of this van der Waals component on the thermal energy k B T .
The Debye interaction is one between a permanent and an induced dipole (again, via Boltzmann-
factor-weighted averaging),
u21 α2
UDebye = − . (9)
(4πε0 εr )2 r6
Finally, the London dispersion interaction is of purely quantum-mechanical origin. We will not
venture further to the rigorous derivation of the interaction energy, but simply note that it is
α1 α2
ULondon ∝ − . (10)
r6

Thus, in general the total van der Waals energy is given by UvdW = UKeesom + UDebye + ULondon . The
dispersion term is the most important of the three contributions, as it is always present, regardless
whether permanent dipoles take part in the interaction or not. Moreover, usually the dispersion term
is also the strongest, contributing around 80 - 100% to the total van der Waals interaction energy. A
notable exception to this is water, where in fact the Keesom interaction dominates (about 70% of the
total interaction energy).
7
Actually, van der Waals himself had no idea at first where these attractive forces result from. But his famous equation
of state was, for the first time, able to describe liquid-gas phase transitions and the existence of a critical point in the phase
diagram.

7
1.5 Summary

Below is a table summarizing various of properties of different basic interactions. Since the
electrostatic interactions depend highly on the intermolecular spacing r, the values in the table are
calculated for Na+ ions (“charges”) and water molecules (“dipoles”; cos θ = 1) in vacuum. The
intermolecular distances r in the electrostatic interactions are further taken as equal to the sums of the
respective van der Waals radii (rNa+ = 0.095 nm, rH2 O ≈ 0.14 nm). Hence, the exact values should
not be taken too strictly, but simply as rough orders of magnitude (remember that the electrostatic
interactions are screeened by εr in different media!)

Interaction type Range Directional Energy (kJ/mol) Energy (kB T )

Covalent very short yes 100 - 900 40 - 360
Hydrogen bond very short yes 10 - 40 4 - 16
Charge-charge ∝ r−1 no 503 200
Charge-dipole ∝ r−2 yes 97 39
Dipole-dipole ∝ r−3 yes 19 7.5
van der Waals ∝r −6 no 0.5 - 5 0.2 - 2

Literature
Regarding any aspects of intermolecular forces, a good book to start out with is the excellent
monograph by Jacob Israelachvili, Intermolecular & Surface Forces (2nd edition, Academic Press,
1992).

General biochemistry textbooks, such as the voluminous Biochemistry (3rd edition, John Wiley
& Sons, 2003) by Donald Voet and Judith G. Voet, contain a fair bit of information on basic
intermolecular interactions, along with examples related to biomolecular systems.

A more in-depth treatment of electrostatic effects in biological systems can be found in Dielectric and
Electronic Properties of Biological Materials (John Wiley & Sons, 1979) by Ronald Pethig.