Degrees of freedom

The degrees of freedom of a chemical species are the number of independent displacements of the species.

An atom has three degrees of freedom because its instantaneous displacement is defined by three orthogonal directions in the  space. A molecule of atoms is characterised by degrees of freedom, as every atom can be displaced from its equilibrium position in three orthogonal directions. Each of the motion is independent and cannot be expressed as a combination of the others. However, the presence of chemical bonds restrict some of these displacements, resulting in three groups of independent motion: translation, rotation and vibration.

To understand how the restriction of molecular motion by chemical bonds results in three groups of motion, each of which is independent of the others, we consider a diatomic molecule (see diagram above), where the red, purple and brown arrows represent instantaneous displacements of the atoms.

Firstly, we would expect the molecule to have six degrees of freedom since . Next, the motion of the two atoms (red arrows) in the same direction and with the same magnitude, which is equivalent to the motion of the centre of mass of the molecule in the positive -direction, is a translational motion. Similarly, the centre of mass of the molecule can move independently in the -direction and -direction, resulting in another two degrees of translational freedom.

The rotational motion of the molecule around the -axis passing through its centre of mass is described by the two brown arrows that are tangent to the circle of motion. The rotation about the -axis contributes to another degree of freedom. However, the molecule spinning around the -axis is not considered a degree of freedom, as no atomic displacement has occurred. In fact, all linear molecules have two degrees of rotational freedom. One common property of translational motion and rotational motion is that they are both rigid transformations, meaning that the bond length doesn’t change throughout either motion.

When the atoms are displaced in opposite directions (purple arrows), they oscillate about their equilibrium positions because they are restricted by the chemical bond. This is known as vibrational motion.

Combining two degrees of rotational freedom with three degrees of translational freedom, all linear molecules have degrees of vibrational freedom. Since the centre of mass moves during translation, while the position of the centre of mass of a molecule does not change during rotational motion and vibrational motion, translational motion is independent of rotational motion and vibrational motion. Furthermore, rotational motion is independent of vibrational motion because rotational motion is a rigid transformation, whereas vibrational motion is not. In general, the three types of motion are independent of one another and all possible motion of atoms of a molecule are a combination of them.

 

Question

What if the brown arrows represent linear motions, instead of tangents to the circle of motion?

Answer

If that’s the case, the atoms move linearly in the directions of the arrows until they are restricted by the chemical bond. Such a motion is a combination of vibrational and rotational motions and not an independent motion. Therefore, it is not a degree of freedom.

 

Since an arrow on an atom can be expressed as a linear combination of three orthogonal vectors centred on the atom, the degrees of freedom of a molecule with  atoms are often expressed in terms of  orthogonal unit displacement vectors.

For example, when the motion of the water molecule in the above diagram is described only by the three -unit vectors, and the magnitudes of the displacement of all atoms are equal, the molecule is translating in the -direction. Similarly, if the only unit vectors describing the molecule’s motion are  and , and the atoms have equal displacement magnitude, the molecule is rotating around the -axis. We will show, in the next article, that the translational motion of  in the -direction and the rotational motion of around the -axis can be expressed as the symmetry-adapted linear combinations  and  respectively.

 and  can also describe a twisting motion of the molecule (like a gym glider machine). However, such a motion, as explained in the Q&A above, is not a degree of freedom of the molecule. Unlike a linear molecule, a non-linear molecule has three rotational degrees of freedom, and hence,  degrees of vibrational freedom. Group theory allows us to determine which irreducible representation of a point group a particular degree of freedom belongs to, and consequently provides a simple way to predict spectroscopic properties the molecule.

 

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Set and subset

A set is collection of different mathematical objects called elements, which can be numbers, people, colours, matrices, etc. Examples of sets are {4, 20, 83, 1059, …} and {red, blue, cyan, grey}, where the former is an infinite set and the latter is a finite set. Two sets  and are equal if they have the same elements, e.g. and . A set with no element, denoted by , is called an empty set. An element in a set is denoted by .

A subset is an equal or smaller collection of elements of a particular set. With reference to the above diagram, the set is a subset of the set , which is mathematically denoted by . Similarly,  and .

Question

Is  a set.

Answer

No, because a set is defined as a collection of different elements.

 

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Group theory (overview)

Group theory is the study of mathematical structures called groups, which have properties that are used to classify molecules by symmetry.

The classification of a molecule according to its symmetry in turn allows us to analyse its molecular properties. In the field of quantum chemistry, group theory simplifies calculations, e.g. in determining if overlap integrals are zero and investigating the degree of degeneracy of a system. Group theory is also useful in predicting spectroscopic transitions, especially in electronic and vibrational transitions.

To fully understand the theory, we need to have some knowledge of abstract algebra and apply it to derive the great orthogonality theorem.

 

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Binary operation

A binary operation is a rule that combines two elements to form another element.

The most basic binary operations are the addition and multiplication of numbers in a set. For example, for  is a binary operation. In general, a binary operation is denoted by , where and are the operands and is the chosen binary operation.

 

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Group

A group is a set, together with a chosen binary operation, that satisfies the properties of closure, identity, inverse and associativity as follows:

    1. Closure: if and  are elements of the group , then  is also an element of .
    2. Identity: there exists an element called the identity, which is denoted by , such that for .
    3. Inverse: every element in  has an inverse , which is itself an element of , such that .
    4. Associativity: for all .

Consider the set  under the binary operation of addition mod 4. It is a group because it satisfies the four properties mentioned above. For example, the element 0 is the identity, since , where . As for inverses, , because gives the identity. Similarly, ,  and . The closure and associativity properties can be easily verified.

Question

What is addition mod 4 for the set ?

Answer

It means that if the sum of two elements of the set is greater than 3, then we divide the result by 4 (called the modulus) and take the remainder as the answer. For example, ,  and .

 

Similarly, the set  under the binary operation of multiplication mod 8 is a group. In this case, if the product of two elements of  is greater than 7, we divide the result by 8 and take the remainder as the answer. All possible binary operations and answers can be presented in the form of a multiplication table as follows:

where the left operand and right operand of the binary operation are listed in the top row and the leftmost column respectively.

Clearly, the multiplication of integers is associative. From the multiplication table, we can validate the closure property of , authenticate that 1 is the identity element and determine that the inverse of an element is the element itself. The associativity property is also easily verified separately.

Question

Is the set under the binary operation of multiplication a group?

Answer

Yes, it is a trivial group with only one element.

 

If the results of all binary operations of a group are independent of the order of the operands (i.e., ), the group is said to be Abelian. Both groups  and  mentioned above are examples of Abelian groups.

The order of a group , denoted by , is the number of elements in . For example,  for both  and . The order of an element  of a group  under the binary operation of multiplication, denoted by , is the smallest value of  such that . For example, the order of the all elements in the group  is 2.

Finally, some useful properties of a group can be inferred from the main properties of closure, identity, inverses and associativity. Two such inferred properties are:

  1. Cancellation

(Statement) If , then  for all  in the group . In other words,  is “cancellable”.

According to the inverses property of a group, if , there exists a unique , where . The proof for the cancellation theorem then involves left-multiplying  by  and using the associativity and identity properties:

Question

Proof the uniqueness of inverses in a group, i.e. for each , there is a unique element such that .

Answer

Suppose has two inverses and . Then or . By cancellation, .

 

  1. Rearrangement theorem

(Statement) Let and . Suppose we multiply each element of  by to form a new group , where . Then, contains each element of once and only once. In other words, .

This theorem is proven by contradiction. Suppose two elements of are equal, where . By cancellation, we have , which contradicts the definition that a group is a set, which is a collection of different elements. However, if , the order of elements in  may not be the same as that in , and thus the term ‘rearrangement’.

 

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Molecular point group

Molecular point groups are point groups to which molecules are assigned according to their inherent symmetries. They are used for analysing and predicting chemical properties of the assigned molecules.

The laborious way to identify the point group of a molecule is to visually determine all the symmetry operations associated with the molecule and compare them with the sets of symmetry operations of all point groups. A less arduous method involves finding key symmetry elements of a molecule and matching them sequentially to the characteristic symmetry operations of a point group. For example, cyclohexane in its twisted boat form (see diagram above) has two  axes perpendicular to the main  axis, while the dihedral groups  and  all have in common, the elements  and . Furthermore, the molecule does not have any mirror plane and hence belongs to the point group . Similarly, a molecule with at least one  axis belongs to either or , while a molecule with two or more , where , belongs to one of the cubic or icosahedral point groups. We can summarise such an identification logic in the following flow chart:

 

 

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Similarity transformation

A similarity transformation of a matrix  to a matrix  is expressed as , where

    1. is an invertible matrix called the change of basis matrix.
    2. is a linear transformation matrix with respect to the basis .
    3. is the transformed representation of , such that  performs the same linear transformation as  but with respect to another basis .

Let a vector be with respect to the basis  and  with respect to the basis . Let another vector be with respect to the basis  and with respect to the basis . Consider the transformation of these vectors as follows:

where the first two equations describe change of basis transformations and the last equation is a linear transformation of  to in the same basis .

Combining the three equation, we have . If  is invertible, we can multiply  by  on the left to give , where . Comparing and ,  is the transformed representation of , where  performs the same linear transformation as  but with respect to another basis . We say that  is similar to  because  has properties that are similar to . For example, the trace of , which is defined as , is the same as the trace of .

To show that , we have,

where  is the identity matrix and where we have used the identity for the second equality.

Question

Proof that .

Answer

 

The common properties of similar matrices are useful for explaining certain group theory concepts, such as why there are exactly 32 crystallographic point groups.

One of the most common applications of similarity transformations is to transform a matrix to a diagonal matrix . Consider the eigenvalue problem  and let the eigenvectors of  be the columns of :

Since , where , we have

If the eigenvectors of  are linearly independent, then  is non-singular (i.e. invertible). This allows us to multiply  on the left by  to give , with the diagonal entries of  being the eigenvalues of .

Question

Why is  non-singular if the eigenvectors of  are linearly independent?

Answer

The eigenvectors  are linearly independent if the only solution to is when  for all . In other words,

or simply .

We need to show that the only solution to  is  and this is possible if  is invertible such that

 

Using the same eigenvalue problem, we can show that Hermitian operators  are diagonalisable, i.e.  (see this article for details).

Question

Show that a Hermitian matrix  can be diagonalised by , i.e. , where is a unitary matrix, and that is also Hermitian.

Answer

A unitary matrix has the property: . If a complete set of orthonormal eigenvectors of  are the columns of , we have  and  because orthonormal eigenvectors are linearly independent. The remaining step is to show that .

For example, . Since  is non-singular, multiplying  on the right of  gives . So, .

To show that  is also Hermitian, we have

.

 

As mentioned above, . The -th column  of is , while the -th column of  is . So, , where  is an eigenvector of  and  is the corresponding eigenvalue. Therefore, the order of the columns of the change of basis matrix corresponds to the order of the diagonal entries in the diagonal matrix.

 

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Symmetry element and symmetry operation

A symmetry element (not to be confused with a group element) is a point, a line, a plane or an axis with respect to which a symmetry operation is carried out. For three-dimensional objects, there are only 5 types of symmetry elements that need to be considered:

Question

Is  a unique symmetry operation?

Answer

Yes, because an object with an  symmetry element may not have a symmetry element of the same . For example, a tetragonal disphenoid has an symmetry element but only a symmetry element.

 

If an object has more than one symmetry axis of rotation, the one with the highest  is called the principal axis, which is conventionally coincident with the -axis.

Consider an equilateral triangle in a three-dimensional real vector space (see figure I). It has a  axis of symmetry and three planes of reflection. Figure II has a  axis of symmetry, while figure III has an  axis of symmetry and a centre of inversion . All objects have the identity symmetry element.

A symmetry operation is a geometric transformation of an object with respect to a symmetry element in a real vector space such that the object looks the same after the transformation. However, the labelling of components of the object may be different post-transformation. For example, a reflection of the equilateral triangle in the -plane results in the triangle looking the same but the labels  and  being swapped.

Question

Why do we need to label the corners of the equilateral triangle?

Answer

Since the object is defined in a real vector space, each point on the object, and hence each label, is represented by a position vector. A symmetry operation preserves the magnitude of the position vector but changes its direction. For example, a reflection  in the -plane results in the triangle looking the same but transforms vector  to vector  (see diagram below). If we carry out two consecutive symmetry operations of  on the original triangle, vector  transforms into itself. This is equivalent to performing the symmetry operation  on the original triangle. Consequently, we are able to form mathematical groups, whose elements are symmetry operators, and use them to analyse the properties of objects like molecules.

 

In total, there are 6 symmetry elements and 6 associated symmetry operations for the equilateral triangle:

Question

What does the notation  mean and why is the reflection in the -plane not included in the set of symmetry operations for the equilateral triangle?

Answer

The angle of rotation is regarded as positive if the rotation is counter-clockwise when we look down the axis of rotation towards the origin (and hence the notation ).  and  can also be denoted as  and respectively, where  is counter-clockwise by default and  is the double application of . The reflection in the -plane is a symmetry operation for the equilateral triangle but has the same effect as  and hence not included in the set.

 

If we conduct all 6 symmetry operations on the triangle, we find one ordered triple invariant: the origin. The significance of the invariant point and the two definitions above, together with the definition of a group, leads to an important mathematical group – the point group – which we’ll discussed in the next article.

 

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Point group

A point group consists of geometric transformations known as symmetry operations, which preserve a single common point while transforming an object defined in a real vector space into physically indistinguishable replicas of itself.

Although an object undergoing a symmetry operation ends up looking the same after the transformation, the labelling of similar components of the object may change. In other words, to form a point group, all symmetry operations for an object must:

    1. Send the object into physically indistinguishable copies of itself.
    2. Combine with one another through binary operations such that the results are consistent with the 4 properties of a group.
    3. Leave one point invariant.

Point groups are determined by considering symmetry operations for different objects, beginning with simple shapes and moving on to more complex ones. According to the three abovementioned requirements, we start by inspecting the chosen object visually and finding all the symmetry elements (not to be confused with group elements) and their associated symmetry operations. For example, the only symmetry elements for the object in figure I, which is made up of two equally spaced right-angled triangles on a circle, are the identity symmetry element  and a 2-fold rotation axis . The corresponding symmetry operations are  and .

Next, we select a position vector  (see figure II) and perform the symmetry operations  and consecutively on the position vector. The results, in relation to the transformation of the position vector, are summarised in the multiplication table i:

Note that we have omitted the carets – i.e. – for simplicity. From the table, we can easily verify all four properties of the group, e.g. the identity element is and the inverse of an element of the group is the element itself. Therefore, the set of symmetry operations for the object forms a point group of order 2 under the binary operation of multiplication. We call this group the  point group. Similarly, the set of symmetry operations  for the object in figure III forms the point group  of order 3 (see multiplication table ii). In general, we have an infinite number of uniaxial point groups , each of which is called a cyclic group, whose elements are . For a cyclic group where is even, one of its elements is equivalent to the symmetry operation .

Let’s suppose the object in figure I have complete arrow heads (see figure IV). Other than  and , the object has a plane of symmetry perpendicular to the axis of rotation (the horizontal plane is denoted by ) and a centre of inversion at the origin. The set of symmetry operations  forms the Abelian point group  (see multiplication table iii). The object in figure IVa belongs to the  point group (see multiplication table iv) with the set of elements , where . Similar to the point groups, if we apply the same logic to other related objects, we have an infinite number of point groups, each with symmetry operations of if  is even (one of the  symmetry operations is equivalent to ) and if is odd.

Question

Why aren’t and elements of the group ?

Answer

They are not unique elements, as they are equivalent to other ‘simpler’ elements of the group:

 

For an object that is made up of two equally spaced equilateral (or isosceles) triangles on a circle (see figure V above), we have the Abelian point group , whose elements are the symmetry operations , ,  and , where the symmetry elements for  and  are the vertical planes: -plane and -plane respectively. The multiplication table for this point group is shown in table v above. As before, we have an infinite number of  point groups. The cone depicted in figure VI is an example of an object that belongs to the  point group, where , i.e. the  point group, with the set of symmetry operations: .

Question

Are and point groups?

Answer

is a trivial point group whose sole element is the symmetry operation . An object of this group is considered to have no rotational symmetry.

and  have the same set of symmetry operations: . Since objects of both point groups have no rotational symmetry, the symbol for the reflection symmetry operation does not have a subscript. In fact, these point groups are so unique that they are collectively known as the point group (for Spiegel, the German word for mirror).

Another unique point group not mentioned above is , whose elements are the symmetry operations and .  and  are known as the non-axial point groups.

 

The next few related point groups are and (for dihedral). They are related in the sense that they have in common the elements  and , which serve as identifiers in categorising molecules by point groups.

Example

Symbol

Object Group elements

Notes

The object is cyclohexane in its twisted boat form. A rhombic disphenoid (tetrahedron with scalene triangles as its faces) also belong to this point group.
 

 

The object is a tetragonal disphenoid (faces are isosceles triangles). is a dihedral plane, i.e. a vertical plane that bisects the angle between two  axes.
1)   axis to screen and bisects .
2)    axes, i) bisects  and ; ii) bisects  and .
3)   planes to screen, i) through ; ii) though .

The  and point groups are identical to the  and point groups respectively in non-standard orientation, i.e. the principal axis is along the -axis. A dumbbell has symmetry elements that are associated with the symmetry operations of

which is a special point group like .

Next, we have the  point group, which is in general associated with the symmetry operations . When , we have the point group , which is the same as the point group . When , the point group  is identical to the point group . For , we need to analyse the point group  with odd and even  separately.

Consider an  point group . When  is odd, the symmetry operation . If , then we have or (according to the closure property of a group). Since , then . Moreover, , which implies that . We can rewrite the symmetry operations of the  point group ( is odd) as

which is equivalent to the set of elements of the point group . For example, the object in figure IVa belongs to the point group and hence to the point group .

When is even, the symmetry operation . Since , we have or . Similarly, or . This implies that . The elements of can be denoted by , where can be odd or even. If is even, then . For example,  and . If is odd, then . We can therefore express the symmetry operations for the  point group (when  is even) as . Figure VII depicts an object that belongs to the  point group.

Taking into account the above characteristics of the  point group, it is possible to relabel it as the  point group, where .

The rest of the point groups are the tetrahedral groups , the octahedral groups , the icosahedral groups  and the special orthogonal group in 3-dimensions  (also known as the full rotation group). The tetrahedral and octahedral groups are collectively called the cubic groups.

Symbol Object Group elements Notes
Each of the three  axes passes perpendicularly through the centre of one of the three depicted faces, e.g. . Each of the four  axes passes through one of four body diagonals, e.g. .

or simply

Same rotation axes as . Three  axes (each with 2 symmetry operations: ) coincident with the  axes. Each of the six  passes through two diagonally opposite edges of the cube.
Same rotation axes as . Four axes (each with 2 symmetry operations: ) coincident with the  axes. A centre of symmetry  and three : i) bisecting  and , ii) bisecting  and , iii) bisecting  and .

or simply

Same as , but the  axes are now  axes (each with 3 symmetry operations: ). Six  axes through mid-points of diagonal edges, e.g.  and .
Same as , but includes centre of inversion ,  axes of  and mirror planes of  and .
The object is a snub dodecahedron with 92 faces (12 pentagons, 80 equilateral triangles), 150 edges and 60 vertices.

The object is a truncated icosahedron with 32 faces (12 pentagons, 20 hexagons), 90 edges and 60 vertices. Same symmetry elements as  with the addition of a centre of inversion, improper axes and mirror planes.

, all possible rotations The object is a sphere with an infinite number of rotation axes, each with all possible values of .

 

Question

Why are  and  called tetrahedral point group and octahedral point group respectively?

Answer

A regular tetrahedron and a regular octahedron have all the same symmetry elements as those used to derive the  point group and the  point group respectively. A tetrahedron with reduced symmetry (e.g. with figure IVa attached to its faces) belongs to the  point group. Similarly, an octahedron with attachments to its vertices belong to the  point group.

 

 

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Crystallographic point groups

Crystallographic point groups are point groups to which crystals are assigned according to their inherent symmetries. They are used for analysing and predicting physical properties of the assigned crystals.

Although there are an infinite number of three-dimensional point groups, only 32 of them are crystallographic point groups. This is due to the crystallographic restriction theorem, which can be proven with trigonometry or linear algebra. The linear algebra proof is as follows:

In crystallography, a lattice point in a three dimensional vector space is described by the position vector  in the form:

where the components , ,  are integers and , , are primitive translation vectors or basis vectors.

A symmetry operation , e.g. a rotation by , maps  to , where the components of  are again integers. Such an operation is always possible only if all the entries of are integers.

Hence, the trace of , i.e. , is also an integer. If we perform a similarity transformation on the rotation matrix , i.e. , such that  is with respect to an orthonormal basis for , is represented by the following matrices:

Since  is invariant under a similarity transformation,  must also be an integer. As we know, , and so, , which implies that . In other words, the rotational symmetry operations of a crystal are restricted to . This is known as the crystallographic restriction theorem.

To derive the 32 crystallographic point groups, we also need to consider the symmetry operation , as it has rotation components. Applying the same logic as above, the entries of the matrix  in the primitive translation vector basis must be integers. An example of the transformed matrix  with respect to an orthonormal basis for is:

Once again,  is an integer. We have, , which allows us to conclude that the  symmetry operations of a crystal are restricted to .

If we disregard point groups whose elements include , we are left with the following 32 crystallographic point groups:

    1. in non-standard orientation
    2. in non-standard orientation
    3. is an element of
    4. is an element of

Question

Are the symmetry operations  and affected by the crystallographic restriction theorem?

Answer

and the trace of a mirror plane is an integer, e.g. .

 

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