Exercise 5 Molecular Orbital Representation

Theoretical Organic Chemistry, 2013

Anastazija Ristovska
The purpose of this exercise is to examine the topological properties of molecules and learn how
to create a topological matrix of carbohydrates.
The properties of a molecule depend on several factors, among which are the geometry of the
molecule such as cis/trans geometric isomerism, the individual properties of the atoms forming a
molecule, and, most importantly, the topology of a molecule. If two molecules are geometric
isomers and have the same topology they will have same or nearly same chemical properties,
however, even if two molecules have the same geometry but different topology, they will have
very different chemical and physical properties. Even molecules built of different atoms that
have the same topology will exhibit similar properties, particularly similar physical properties.
The molecule we will be examining is shown in figure 1. It has 10 carbon atoms, 10 pi electrons,
5 double bonds, and 4 single bonds. For our calculations and explanation we used the molecular
carbon atom numbering shown on the molecule 3-methylene-4-ethenyl-hept-1,4,6-triene on the
left in figure 1.

10

10

4
5

6
1

Figure 1

Adjacency (Huckel) matrix

1
2
3
4
5
6
7
8
9
10

1
x
0
0
0
1
0
0
0
0
0

2
0
x
0
0
0
1
0
0
0
0

3
0
0
x
1
1
0
0
0
0
0

4
0
0
1
x
0
0
1
0
1
0

5
1
0
1
0
x
0
0
0
0
0

6
0
1
0
0
0
x
1
0
0
0

7
0
0
0
1
0
1
x
1
0
0

8
0
0
0
0
0
0
1
x
0
0

9
0
0
0
1
0
0
0
0
x
1

10
0
0
0
0
0
0
0
0
1
x

Table 1

I fill in the Huckel matrix. Every field containing 1 indicates that the atoms, given by atom
numbers as the x and y coordinates of the field, are two neighbouring atoms. Since C1-C1, C2C2, etc. cannot form neighbouring atom pairs, these fields are left out. The empty fields are
automatically filled with zeros by the program.
Energies
Orbital
MO 10
MO 9
MO 8
MO 7
MO 6
MO 5
MO 4
MO 3
MO 2
MO 1
Total Energy

Energy (B)
-2.151
-1.505
-1.221
-0.699
-0.362
0.362
0.699
1.221
1.505
2.151
11.875

Electrons
0
0
0
0
0
2
2
2
2
2

Table 2

Table 2 displays the energies of the molecular orbitals and the number of electrons that fill in
each orbital. This table is discussed in the conclusion, and is the main focus of this lab.

Conclusion: The pi energies are expressed in Beta. The table and diagram above display the
energy (in beta) of all molecular orbitals, and gives the number of electrons found in each
molecular orbital. Alpha is the ground state of the atomic orbitals, whereas the Beta coefficient
fits into the following formula: E=-c. For the first molecular orbital, MO 1, E1=-2.151.
There are two electrons in this orbital. Whenever the total energy is lower than the value i.e.
the ground state energy, as is in the case of MO 1, the molecular orbital is bonding and pi
electrons are likely to be found in it. Whenever the total energy is higher than , the molecular
orbital is anti-bonding and it is strongly preferred that electrons are not located in it or otherwise
the molecule will lose on stability. The energy of the second molecular orbital, MO 2, is E2=1.505 which is lower than the ground state energy , meaning MO 2 is a bonding molecular
orbital and two pi electrons are located in it. The third molecular orbital has an energy of E3=1.221, meaning E3< , thus MO 3 is a bonding molecular orbital filled by two pi electrons. The
fourth molecular orbital has an energy of E4=-0.699, and again E4< , which means MO 4 is a
bonding molecular orbital. The last bonding molecular orbital is MO 5, with E5= -0.362 and
thus E5> , and the last remaining pi electrons are placed in it, for a total of 10 pi electrons
placed in 5 bonding molecular orbitals.
The sixth molecular orbital is of energy E6= +0.362, E6> , implying that this ought to be an
anti-bonding molecular orbital - for every electron placed in it there will be a decrease in the
stability of the molecule. Fortunately, the 10 pi electrons have been outsourced and already
placed in the first five binding molecular orbitals, with no pi electrons needing to be placed in an
anti-bonding molecular orbital. The seventh molecular orbital has E7=+0.699, E7> , antibonding; MO 8 is anti-bonding with E8=+1.221, E8> ; MO 9 is also anti-bonding with
E9=+1.505 and thus E9> ; and, finally, the tenth molecular orbital, which is most antibonding, has E10=+2.151 and thus E10> .

Coefficients

Figure 2

Figure 3

Bond Orders

Figure 4

Figure 5

The bond order is given of all nine molecular bonds. The order of the bond between atom C1
and atom C5 is 0.857, indicating a double bond, whereas the bond between atom C5 and atom
C3 has a bond order of 0.505, indicating a single bond. The bond orders of all the bond
molecules are given in this table:
Atom Pair
C1-C5
C3-C4
C2-C6
C3-C5
C4-C7
C6-C7
C4-C9
C7-C8
C9-C10

Bond Order
0.857
0.717
0.908
0.505
0.397
0.410
0.441
0.813
0.888

Type of Bond
Double
Double
Double
Single
Single
Single
Single
Double
Double

Table 2

We arrange this table in decreasing bond order to see if we can find a pattern:
1
2
3
4
5
6
7
8
9

Atom Pair
C2-C6
C9-C10
C1-C5
C7-C8
C3-C4
C3-C5
C4-C9
C6-C7
C4-C7

Bond Order
0.908
0.888
0.857
0.813
0.717
0.505
0.441
0.410
0.397

Type of Bond
Double
Double
Double
Double
Double
Single
Single
Single
Single

Table 3

Figure 6

All double bonds in this molecule are conjugated. The double bond between atoms C6 and C2,
as well as the double bond between atoms C9 and C10 are in an s-cis arrangement only, and have
a pi electron conjugation with only one other adjacent pi bond. The double bond formed by
atoms C1 and C5 is likewise conjugated to only one other double bond in this system, however,
its arrangement is s-trans relative to the double bond of atoms C3 and C4. The double bond
between atoms C7 and C8 is conjugated to two other double bonds, via an s-cis bond to one and
via an s-trans bond to the other. However, this double bond has both the s-cis as well as the strans conjugations on the same carbon atom C7. The higher the bond order of the bond, the
greater the double bond character of the bond and the greater the electron density of the pi
electron cloud. The C3-C4 double bond has the least double-bond character, given that it is
conjugated with two other double bonds via both sides of the bond, i.e. it has double-bond
conjugation via both atom C3 as well as atom C4, in an s-trans and s-cis arrangement,
respectively.
There are a total of 9 bonds, 5 of which are double, and 4 are single. The bond between
atoms C3 and C5 exhibits the lowest single-bond character, followed by C4-C9, C6-C7, and C4C7. The bond between atoms C4-C7 exhibits the highest single-bond character. Presumably the
reason behind this is the fact that atoms C7 and C4 have the longest carbon chains bonded to
them, with multiple double bonds. In the C6 -C7 bond even though there is a long carbon chain
bonded to atom C7, there is only one carbon atom bonded to C6 (short chain); this same
observation applies to the single bond C4-C9 both C6-C7 as well as C4-C9 have an s-cis
conformation, and this is the only difference between these two bonds and the C3-C5 single
bond that participates in an s-trans double bond conjugation which is supposedly the reason
behind its increased double-bond character.

The e-densities of all 10 carbon atoms were 1.000, unity.

Energy
(beta)
-2.151
-1.505
-1.221
-0.699
-0.362
0.362
0.699
1.221
1.505
2.151

MO

Electrons

10
9
8
7
6
5
4
3
2
1

0
0
0
0
0
2
2
2
2
2

Table 4

All calculations were conducted using the Huckel Molecular Orbitals (HMO) Calculations
computer program, Copyright 1993 by David R. Anderson, Department of Chemistry,
University of Colorado, Colorado Springs, CO 80933.