Biophysical Chemistry Lab report 2

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Practical Report 2
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Aim:
To illustrate chemical bonding concepts and molecular orbital, with applications to organic
molecules
Done by:
Name Matriculation
Number
Tutorial Group Date

BS1002 Biophysical Chemistry
Biophysical Chemistry Lab report 2
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1. Introduction
Spartan software enables electron densities to be illustrated in different form, such as, space
filling model, electron density surface, bond density surface. Also, it enables distribution of
charges to be illustrated in electrostatic potential maps. In addition, electrophilic and
nucleophilic reactivity are illustrated using LUMO maps. Spartan also provide users with
useful calculated information of the molecules, such bond distance, bond angle, total energy,
dipole moment and even solvation. In the LUMO map, the red coloured region would
indicate the electron rich regions while the blue coloured region would indicate the electron
deficient regions.
LUMO (Lowest Unoccupied Molecular Orbital) is an unoccupied orbital which is electron
deficient which make it susceptible to be attacked by a nucleophile species. The degree of
nucleophilic attack will be determined by the size of LUMO. A large region of LUMO will
render a better nucleophilic reaction than a smaller sized LUMO.
HOMO (Highest Occupied Molecular Orbital) is an occupied orbital which is electron rich
which will make it susceptible to attack upon an electrophilic species. The degree of
electrophilic attack will be determined by the size of LUMO. A large region of HOMO will
render a better electrophilic reaction than a smaller sized HOMO.

2. Result and Discussion
Exercise 1: Acrylonitrile

Picture 1

1. Give all the bond distance in the molecule
Bond distance between H
1
and C
1
atom 1.087
Bond distance between H
2
and C
1
atom 1.086
Bond distance between H
3
and C
2
atom 1.084
Bond distance between C
1
and C
2
atom 1.339
Bond distance between C
2
and C
3
atom 1.421
Bond distance between C
3
and N atom 1.160
Table 1
The bond distance between H atom and C atom has a bond distance of 1.08 which is
comparatively shorter as compared with the bond distance between C atom and C atom and
bond distance between C atom and N atom. A shorter bond distance would imply that there is
a stronger attractive force between both atoms. C atom has a proton number of 6 and energy
level of 2. H atom has a proton number of 1, energy level of 1 and valence electron of 1.
There will be a greater attractive force than repulsive force between them since both atoms
have electrons residing in different energy level and different proton number. There will be
repulsive force presence between electrons of same energy level. But overall, attractive force
N atom
C
3
carbon atom
C
2
carbon atom C
1
carbon atom
H
1
hydrogen atom
H
2
hydrogen atom
H
3
hydrogen atom
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will be higher than repulsive force; hence the high net effective nuclear charge between C
atom and H atom will cause the bond distance to be short.
C atom has a proton number of 6 and shell number of 2. When one C atom moves close to C
atom, there will be greater repulsive force than attractive force between them since both
atoms have same energy level and proton number. Hence, this greater in repulsive force will
cause the bond distance between C atom and C atom to be larger as compared to C atom and
H atom.
N atom has a proton number of 5 and shell number of 2. When the N atom moves close to C
3

atom, there will be only be lower net effective charge as compare to the bonding between H
atom and C atom since both atoms have electrons residing in same energy level and is only
different by 1 proton number. This will cause the bond distance between C
3
atom and N atom
to be larger as compared to C atom and H atom.
There is a double bond between C
3
atom and N atom and between C atom and C atom.
However, bond distance between C
3
atom and N atom is shorter than bond distance between
C atom and C atom. This is due to the greater repulsive force present between C atom and C
atom than the repulsive force present between C
3
atom and N atom.

2. Give the total energy and the dipole moment
Total energy = -168.8204 au = -443153.55 KJ/mol
The amount of total heat needed to form acrylonitrile from the combining of separated nuclei
and electrons will be the total energy. Since a negative value is reflected, hence it would
mean that the molecule would give off heat during reaction

Dipole moment = 4.03 Debye
Since dipole moment is resulted by the differences in electronegativity of the opposite partial
charges of 2 atoms, hence the negative end of dipole lies on the more electronegative atom
while positive end of dipole lies on the less electronegative atom. Therefore, in this structure,
the negative end will be N atom since it is more electronegative than C atom and H atom
while the positive end will be H
2
atom since it is the least electronegative and is positioned
furthest from the electronegative N.

3. Given the value of 2 selected bond angle
Bond angle between C
1
,C
2
and C
3
122.48
o

Bond angle between C
2
, C
3
and H
3
117.15
o

Table 2
The bond angle between C
1
, C
2
and C
3
is 122.48
o
, which is different from regular tetrahedron
angle of 109.5. Hence, this would meant that the lone pair repulsion is more than bonding
pair repulsion. This lone pair repulsion is exerted from the neighbouring N atom. Similarly,
the Bond angle between C
2
, C
3
and H
3
is 117.15
o
, which is different from regular tetrahedron
angle of 109.5. This would also mean that the lone pair repulsion is more than bonding pair
repulsion.

Exercise 2: Cyclohexanone
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Picture 2
1. Give the total energy and the dipole moment
Total energy = -345.001066 au = -905627.79825KJ/mol
The amount of total heat needed to form cyclohexanone from the combining of separated
nuclei and electrons will be the total energy. Since a negative value is reflected, hence it
would mean that the molecule would give off heat during reaction.

Dipole moment = 3.34 Debye
The negative end will be O atom since it is more electronegative than C atom and H
1
atom
while the positive end will be H
1
atom since it is the least electronegative and is positioned
furthest from the electronegative O.

2. Attach a figure of the LUMO orbital

Picture 3

3. Comment the result with respect to reactivity
Orbital is the region where the probability of locating an electron is. LUMO is the orbital that
is unoccupied, hence making the orbital electron deficient, which will make it susceptible to
nucleophilic attack. The degree of nucleophilic attack will be determined by the size of
LUMO. A large region of LUMO will render a better nucleophilic reaction than a smaller
sized LUMO.
Observing from picture 3, C
1
atom has a larger region of LUMO than O atom. This would
mean C
1
atom would render better nucleophilic reaction than O atom, making C
1
atom a
C
1
Carbon atom
Oxygen atom
H
1
hydrogen atom
Oxygen atom
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better electron withdrawing group and O atom will be comparatively a better electron
donating group. This is further explained by the VSEPR theory (Valence Shell Electron Pair
Repulsion), such that O atom has electron configuration 1s
2
2s
2
2p
4
of O atom meant it has 6
valence atoms while C
1
atom has electron configuration meant it has 4 valence atoms. This
would clearly shows that that O atom is more electron rich while C
1
atom is comparatively
more electron deficient.
Hence, C
1
atom has a larger sized LUMO than O atom, hence it will be more reactive
towards nucleophilic reaction.

Exercise 3: Ethanol

Picture 4
1. Give the total energy
Total energy = -153.22268 au = -402209.535KJ/mol
The amount of total heat needed to form ethanol from the combining of separated nuclei and
electrons will be the total energy. Since a negative value is reflected, hence it would mean
that the molecule would give off heat during reaction.

2. Account for some additional feature from the calculation of your own choice
Solvation = -18.62 KJ/mol
A negative value in solvation would mean that ethanol is able to dissolve in water

Heat = -235.30KJ/mol
A negative value in enthalpy would mean that the molecule would give off heat during
reaction


Oxygen atom
Carbon atom
Carbon atom
Hydrogen atom