Symmetry operations molecules

At this point the reader may feel that we have done little in the way of explaining molecular synnnetry. All we have done is to state basic results, nonnally treated in introductory courses on quantum mechanics, connected with the fact that it is possible to find a complete set of simultaneous eigenfiinctions for two or more commuting operators. However, as we shall see in section Al.4.3.2. the fact that the molecular Hamiltonian //coimmites with and F is intimately coimected to the fact that //commutes with (or, equivalently, is invariant to) any rotation of the molecule about a space-fixed axis passing tlirough the centre of mass of the molecule. As stated above, an operation that leaves the Hamiltonian invariant is a symmetry operation of the Hamiltonian. The infinite set of all possible rotations of the... 

Another distinction we make concerning synnnetry operations involves the active and passive pictures. Below we consider translational and rotational symmetry operations. We describe these operations in a space-fixed axis system (X,Y,Z) with axes parallel to the X, Y, Z) axes, but with the origin fixed in space. In the active picture, which we adopt here, a translational symmetry operation displaces all nuclei and electrons in the molecule along a vector, say. 

We now define the effect of a translational synnnetry operation on a fiinction. Figure Al.4.3 shows how a PHg molecule is displaced a distance A X along the X axis by the translational symmetry operation that changes Xq to X = Xq -1- A X. Together with the molecule, we have drawn a sine wave symbolizing the... 

Corresponding to every symmetry element is a symmetry operation which is given the same symbol as the element. For example, C also indicates the actual operation of rotation of the molecule by 2n/n radians about the axis. 

All molecules possess the identity element of symmetry, for which the symbol is / (some authors use E, but this may cause confusion with the E symmetry species see Section 4.3.2). The symmetry operation / consists of doing nothing to the molecule, so that it may seem too trivial to be of importance but it is a necessary element required by the mles of group theory. Since the C operation is a rotation by 2n radians, Ci = I and the symbol is not used. 

The dipole moment vector /i must be totally symmetric, and therefore symmetric to all operations of the point group to which the molecule belongs otherwise the direction of the dipole moment could be reversed by carrying out a symmetry operation, and this clearly cannot happen. The vector /i has components fiy and along the cartesian axes of the molecule. In the examples of NH3 and NF3, shown in Figures 4.18(b) and 4.18(e), respectively, if the C3 axis is the z-axis, 7 0 but = 0. Similarly in H2O and cis-... 

In Section 4.3.f it was shown that there are 3N — 5 normal vibrations in a linear molecule and 3N — 6 in a non-linear molecule, where N is the number of atoms in the molecule. There is a set of fairly simple rules for determining the number of vibrations belonging to each of the symmetry species of the point group to which the molecule belongs. These rules involve the concept of sets of equivalent nuclei. Nuclei form a set if they can be transformed into one another by any of the symmetry operations of the point group. For example, in the C2 point group there can be, as illustrated in Figure 6.18, four kinds of set ... 

These elements of symmetry are best recognized by performing various symmetry operations, which are geometrically defined ways of exchanging equivalent parts of a molecule. The 5 symmetry operations are ... 

The complete set of symmetry operations that can be performed on a molecule is called the symmetry group or point group of the molecule and the order of the point group is the number of symmetry operations it contains. Table A2.1 lists the various point groups, together with their elements of symmetry and with examples of each. 

Figure 6-3. Top Structure of the T6 single crystal unit cell. The a, b, and c crystallographic axes are indicated. Molecule 1 is arbitrarily chosen, whilst the numbering of the other molecules follows the application of the factor group symmetry operations as discussed in the text. Bottom direction cosines between the molecular axes L, M, N and the orthogonal crystal coordinate system a, b, c. The a axis is orthogonal to the b monoclinic axis.

Table 6-1. C2(l molecular poinl group. The electronic stales of the flat T6 molecule are classified according lo the lwo-1 old screw axis (C2). inversion (/). and glide plane reflection (o ) symmetry operations. The A and lt excited slates transform like translations Oi along the molecular axes and are optically allowed. The Ag and Bg stales arc isoniorphous with the polarizability tensor components (u), being therefore one-photon forbidden and Iwo-pholon allowed.

The molecules shown in Fig. 1 are planar thus, the paper on which they are drawn is an element of symmetry and the reflection of all points through the plane yields an equivalent (congruent) structure. The process of carrying out the reflection is referred to as the symmetry operation a. However, as the atoms of these molecules are essentially point masses, the reflection operations are in each case simply the inversion of the coordinate perpendicular to the plane of symmetry. Following certain conventions, the reflection operation corresponds to z + z for BF3 and benzene, as it is the z axis that is chq ep perpendicular to die plane, while it is jc —> —x for water. It should be evident that the symmetry operation has an effect on the chosen coordinate systems, but not on the molecule itself. 

To illustrate the application of Eq. (37), consider the ammonia molecule with the system of 12 Cartesian displacement coordinates given by Eq. (19) as the basis. The reducible representation for the identity operation then corresponds to the unit matrix of order 12, whose character is obviously equal to 12. The symmetry operation A = Cj of Eq. (18) is represented by the matrix of Eq. (20) whore character is equal to zero. Hie same result is of course obtained for die operation , as it belongs to the same class. For the class 3av the character is equal to two, as exemplified by the matrices given by Eqs. (21) and (22) for the operations C and Z), respectively. The representation of the operation F is analogous to D (problem 12). 

The molecule LaBe occupies a cubic site in the crystal. Find the 48 symmetry operations and thus the point group of the molecule. 

The term inversion is used here to refer to a feasible physical phenomenon, whioh in this case is similar to an umbrella that turns inside-out in the wind. The word has already been used twice in different senses (i) the inversion of coordinates, e.g. the passage from a right-handed system to a left-handed one and (ii) a traditional symmetry operation applied to a molecule with a center of invmioa. Accordingly, this term must be used with care ... 

Although all molecules are in constant thermal motion, when all of their atoms are at their equilibrium positions, a specific geometrical structure can usually be assigned to a given molecule. In this sense these molecules are said to be rigid. The first step in the analysis of the structure of a molecule is the determination of the group of operations that characterizes its symmetry. Each symmetry operation (aside from the trivial one, E) is associated with an element of symmetry. Thus for example, certain molecules are said to be planar. Well known examples are water, boron trifluoride and benzene, whose structures can be drawn on paper in the forms shown in Fig. 1. 

The effect of the symmetry operations on the Cartesian displacement coordinates of the two hydrogen atoms in die water molecule. The sharp ( ) indicates the inversion of a coordinate axis, resulting in a change in handedness of the Cartesian coordinate system. 

The four operations which form the symmetry group for the water molecule are represented in Fig. 2. It can be easily verified that the multiplication table for these symmetry operations is that already developed (Table 2). Thus, the symmetry group of the water molecule is isomorphic with the four-group. 

The internal coordinates for the water molecule are chosen as changes in the structural parameters defined in Fig. 3. The effect of each symmetry operation of the symmetry group ( 2 on these internal coordinates is specified in Table 2. Clearly, the internal coordinate Ace is totally symmetric, as the characters xy(Aa) correspond to those given for the irreducible representation (IR) Ai. On die other hand, the characters x/(Ar), as shown, can not be identified with a specific IR. By inspection of Table 2, however, it is apparent that the direct sum Ai B2 corresponds to the correct symmetry of these coordinates. In more complicated cases the magic formula can always be employed to achieve the correct reduction of the representation in question. 

Excited states formed by light absorption are governed by (dipole) selection rules. Two selection rules derive from parity and spin considerations. Atoms and molecules with a center of symmetry must have wavefunctions that are either symmetric (g) or antisymmetric (u). Since the dipole moment operator is of odd parity, allowed transitions must relate states of different parity thus, u—g is allowed, but not u—u or g—g. Similarly, allowed transitions must connect states of the same multiplicity—that is, singlet—singlet, triplet-triplet, and so on. The parity selection rule is strictly obeyed for atoms and molecules of high symmetry. In molecules of low symmetry, it tends to break down gradually however,... 

First, it is apparent that reflection through the xz plane, indicated by transforms H into H". More precisely, we could say that H and H" are interchanged by reflection. Because the z-axis contains a C2 rotation axis, rotation about the z-axis of the molecule by 180° will take H into H" and H" into H, but with the "halves" of each interchanged with respect to the yz plane. The same result would follow from reflection through the xz plane followed by reflection through the yz plane. Therefore, we can represent this series of symmetry operations in the following way ... 

To provide further illustrations of the use of symmetry elements and operations, the ammonia molecule, NH3, will be considered (Figure 5.6). Figure 5.6 shows that the NH3 molecule has a C3 axis through the nitrogen atom and three mirror planes containing that C3 axis. The identity operation, E, and the C32 operation complete the list of symmetry operations for the NH3 molecule. It should be apparent that... 

This process could be continued so that all the combinations of symmetry operations would be worked out. Table 5.3 shows the multiplication table for the C3 point group, which is the point group to which a pyramidal molecule such as NH3 belongs. 

For a given molecule belonging to a particular point group, it is possible to consider the various symmetry species as indicating the behavior of the molecule under symmetry operations. As will be shown later, these species also determine the ways in which the atomic orbitals can combine to produce molecular orbitals because the combinations of atomic orbitals must satisfy the character table of the group. We need to give some meaning that is related to molecular structure for the species A1( B, and so on. 

If we now consider a planar molecule like BF3 (D3f, symmetry), the z-axis is defined as the C3 axis. One of the B-F bonds lies along the x-axis as shown in Figure 5.9. The symmetry elements present for this molecule include the C3 axis, three C2 axes (coincident with the B-F bonds and perpendicular to the C3 axis), three mirror planes each containing a C2 axis and the C3 axis, and the identity. Thus, there are 12 symmetry operations that can be performed with this molecule. It can be shown that the px and py orbitals both transform as E and the pz orbital transforms as A, ". The s orbital is A/ (the prime indicating symmetry with respect to ah). Similarly, we could find that the fluorine pz orbitals are Av Ev and E1. The qualitative molecular orbital diagram can then be constructed as shown in Figure 5.10. 

Of particular importance in the physical sciences is the fact that the symmetry operations of any symmetrical system constitute a group under the operators that effect symmetry transformations, such as rotations or reflections. A symmetry transformation is an operation that leaves a physical system invariant. Thus any rotation of a circle about the perpendicular axis through its centre is a symmetry transformation for the circle. The permutation of any two identical atoms in a molecule is a symmetry transformation... 

Each symmetry operation of a group has the effect of turning the symmetrical object (molecule) into itself. An alternative statement of this observation is that each symmetry operation on the molecule is equivalent to multiplication by unity, as shown below for the operators of point group Civ, using H2O as example. 

The unit cell considered here is a primitive (P) unit cell that is, each unit cell has one lattice point. Nonprimitive cells contain two or more lattice points per unit cell. If the unit cell is centered in the (010) planes, this cell becomes a B unit cell for the (100) planes, an A cell for the (001) planes a C cell. Body-centered unit cells are designated I, and face-centered cells are called F. Regular packing of molecules into a crystal lattice often leads to symmetry relationships between the molecules. Common symmetry operations are two- or three-fold screw (rotation) axes, mirror planes, inversion centers (centers of symmetry), and rotation followed by inversion. There are 230 different ways to combine allowed symmetry operations in a crystal leading to 230 space groups.12 Not all of these are allowed for protein crystals because of amino acid asymmetry (only L-amino acids are found in proteins). Only those space groups without symmetry (triclinic) or with rotation or screw axes are allowed. However, mirror lines and inversion centers may occur in protein structures along an axis. 

Seven crystal systems as described in Table 3.2 occur in the 32 point groups that can be assigned to protein crystals. For crystals with symmetry higher than triclinic, particles within the cell are repeated as a consequence of symmetry operations. The number of asymmetric units within the unit cell is related but not necessarily equal to the number of molecules in a unit cell, depending on how the molecules are related by symmetry operations. From the symmetry in the X-ray diffraction pattern and the systematic absence of specific reflections in the pattern, it is possible to deduce the space group to which the crystal belongs. 

As a particular example of materials with high spatial symmetry, we consider first an isotropic chiral bulk medium. Such a medium is, for example, an isotropic solution of enantiomerically pure molecules. Such material has arbitrary rotations in three dimensions as symmetry operations. Under rotations, the electric and magnetic quantities transform similarly. As a consequence, the nonvanishing components of y(2),eee, y 2)-een and y,2)jnee are the same. Due to the isotropy of the medium, each tensor has only one independent component of the xyz type ... 

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