Molecular partition functions

May 10, 2014

1 Partition functions for polyatomic molecules
For a polyatomic molecule with n atoms, the total number of coordinate degrees
of freedom is 3n, as each atom is free to move in three independent directions
(x, y and z). However, when dealing with molecular motions, it is more useful
to think in terms of internal coordinates - bond lengths, angles, torsional angles,
and external coordinates - translational motion of the molecules centre of mass,
and rotational motion about the molecules centre of mass.
It is pretty clear that all gas phase molecules have three translational degrees
of freedom, as they are all free to move along all three Cartesian (x,y,z) axes.
Happily, the translational partition function for molecules is identical to the
translational partition function for atoms and diatomics, so this expression will
only be reproduced for completeness in this appendix.
For most molecules, there are also three rotational degrees of freedom (because
the molecule can rotate about three mutually perpendicular axes) and therefore
3n 6 vibrational modes. The one exception to this is linear molecules, which
have only two rotational degrees of freedom. Rotation about the axis on which
the atoms are aligned is not meaningful as it does not change anything. Or, in
other words, all rotated congurations are indistinguishable from the original
conguration. Therefore, for a linear molecule, there are two rotational degrees
of freedom and 3n 5 vibrational modes.
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iotation in
plane of page
spinning on lineai axis
- no change
iotation out of
plane of page
in to plane of page
out of plane of page
in-plane benu out-of-plane benu
symmetiic stietch asymmetiic stietch
Figure 1: Rotational and vibrational modes of CO
2
, a linear polyatomic
2
iotation in
plane of page
- boomeiang
style
iotation out of
plane of page - enu
ovei enu flipping
iotation out of
plane of page -
spinning
angle benuing symmetiic stietch
asymmetiic stietch
Figure 2: Rotational and vibrational modes of H
2
O, a non-linear polyatomic
3
2 Translational partition functions
The translational partition function of any discrete particle free to move in three
dimensions is:
q
trans
=
V

3
(1)
where V = volume of container and
=
h

2 m k
B
T
(2)
where m = mass of molecule in kilograms, h = Plancks constant in SI units (J
s

1), k
B
= Boltzmanns constant in SI units (J K
1
) and T = temperature in
Kelvin.
4
3 Rotational partition functions
3.1 Linear molecules
The simplest case we will consider here is a linear polyatomic molecule. In this
case, the energies and degeneracies of the energy levels are the same as for a
diatomic molecule (which must be linear, by denition!). The only dierence
lies in how the moment of inertia is calculated:
For a diatomic molecule:
I = R
2
(3)
For a polyatomic molecule, we must rst nd the molecules centre of mass in
Cartesian coordinates, {x
c
, y
c
, z
c
}:
m
tot
=
n

i=1
m
i
x
c
=
1
m
tot
n

i=1
m
i
x
i
y
c
=
1
m
tot
n

i=1
m
i
y
i
z
c
=
1
m
tot
n

i=1
m
i
z
i
Then its moment of inertia is given by:
I =
n

i=1
m
i
d
2
i
(4)
where d
i
is the distance of the i
th
nucleus from the centre of mass of the molecule.
Now, the usual expressions for the rotational partition function apply. Gen-
erally:
q
rot
=
1

J
(2J + 1)e

h
2
8
2
Ik
B
T
J(J+1)
(5)
where is the symmetry number of the molecule (number of symmetry opera-
tions that result in an identical conguration of the system).
And in the high-temperature / equal distribution among rotational states limit:
q
rot
=
1

8
2
Ik
B
T
h
2
(6)
5
3.2 Non-linear molecules
In the general case, we need to consider how the molecule rotates about its cen-
tre of mass. First, we need to dene the principal axes of inertia of the molecule
- the three directions it naturally rotates about its centre of mass. For an
intuitive understanding of principal axes of inertia, consider the human body.
teitiaiy
piincipal axis is
peipenuiculai
to plane of page
seconuaiy
piincipal axis
piimaiy
piincipal axis
Figure 3: Principal axes of the human body
The centre of mass is easy to nd - near the navel. The longest (or primary)
principal axis runs from middle of the top of the head to between the feet, and
rotation about the axis looks like spinning on your feet (or head, if youre into
that). The next longest principal axis runs from one side of your body to the
other. Rotation about this principal axis looks like somersaulting. The shortest
principal axis goes from the front of your body to the back, and rotation about
this axis looks like cartwheeling. Any other form of rotation looks (and feels)
unnatural.
Mathematically, we can nd the principal axes of inertia for a molecule by trans-
lating the molecule so its centre of mass (see above) lies at the origin (0,0,0)
and then solving the following set of matrix equations:
(I
xx
) I
xy
I
xz
= 0
I
yx
+ (I
yy
) I
yz
= 0
I
zx
I
zy
+ (I
zz
) = 0
6
where
I
xx
=

i
m
i
(y
2
i
+ z
2
i
) I
xy
= I
yx
=

i
m
i
x
i
y
i
I
yy
=

i
m
i
(x
2
i
+ z
2
i
) I
xz
= I
zx
=

i
m
i
x
i
z
i
I
zz
=

i
m
i
(x
2
i
+ y
2
i
) I
yz
= I
zy
=

i
m
i
y
i
z
i
Once we have solved these equations to nd , , and , it is easy to rotate
the molecule so that its principal axes of rotation align with the Cartesian x, y
and z axes. Then we can recalculate I
xx
, I
yy
and I
zz
, which are the moments
of inertia for rotation about each axis (subsequently labelled I
A
, I
B
and I
C
).
The results that generally conrm what we would intuitively expect (that one
principal axis aligns itself along the longest part of the molecule, another with
the shortest, and the third is perpendicular to both of these).
teitiaiy piincipal
axis is
peipenuiculai to
plane of page
piimaiy
piincipal axis
seconuaiy
piincipal axis
Figure 4: Principal axes of the water molecule
It is much harder to solve the rotational Schrodinger equation for arbitrary
molecules than diatomics, and the results get quite messy, without providing
any additional insight. So, we will simply skip straight to the expression for the
partition function of an arbitrary asymmetric molecule:
q
rot
=

1/2

8
2
I
A
k
B
T
h
2

1/2

8
2
I
B
k
B
T
h
2

1/2

8
2
I
C
k
B
T
h
2

1/2
(7)
Molecules generally have quite nely spaced rotational energy levels (as their
rotational mass is larger, so the spacing between energy levels is smaller, anal-
ogous to the particle-in-a-box model). Therefore, the high-temperature approx-
imation is practically always valid for molecules.
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4 Vibrational partition functions
Before we start thinking about polyatomic vibrational partition functions, we
must rst answer the simpler question how do we describe (mathematically)
and visualize (schematically) the ways molecules vibrate?
In general, this is already quite a hard problem. However, it is possible to
choose a set of coordinates (made up of dierent linear combinations of atomic
displacements in Cartesian coordinates) such that, for small vibrations around
the lowest energy structure, each vibrational mode may be considered indepen-
dent of all others. These are known as the normal coordinates of the molecule.
Further information on how to determine the normal coordinates of an arbitrary
molecule may be found in the book Molecular Vibrations by Wilson, Decius
and Cross or in a white paper entitled Vibrational Analysis in Gaussian by
Joseph Ochterski (available via the gaussian.com website).
The standard way of illustrating of normal mode coordinates is to show the
vibrational modes of the water molecule:
angle benuing symmetiic stietch
asymmetiic stietch
Figure 5: Normal modes of vibration of the water molecule
The net result is that, by choosing to describe the vibrations of the molecule
using independent normal mode coordinates, the vibrational energy levels of
the molecule may simply be written as a sum over all the vibrational modes
of the molecule (treating each mode as though it experiences a harmonic force
restoring the atoms to their original positions):

vib
=
n
vib

i=1
(n
i
+
1
2
) h
i
(8)
where n
vib
is the number of vibrational modes (3n
atom
6 generally or 3n
atom
5
for a linear polyatomic), n
i
is the quantum number indexing the energy levels
8
of the i
th
vibrational mode (=0,1,2,...), and
i
is the vibrational frequency as-
sociated with the i
th
vibrational mode.
Recalling that if the total energy can be expressed as a sum of independent
contributions, then the total partition function can be expressed as a product
of separate partition functions, it is pretty easy to write down the expression
for the vibrational partition function for a polyatomic molecule, based upon the
diatomic expression:
q
vib
=
n
vib

i=1
1
1 e

h
i
k
B
T
(9)
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