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== Computational analysis of NH3 and hydrogen peroxide ==

This page contains a report constituting part of the first year physical chemistry lab course. It aims to provide account of optimization calculations of a range of molecules using gaussian and report on the key features of those optimized structures such as energies of equilibrium states, vibrational modes and their frequencies and visualization of molecular orbitals.

==NH3 ==

<pre>
File Name = FRIST(3)NH3OPTIMIZATION2
Molecule name = NH3
Calculation Method = RB3LYP
Basis Set = 6-31G(d,p)
E(RB3LYP) = -56.55776873 a.u.
RMS Gradient Norm = 0.00000485 a.u.
Point Group = C3V
</pre>

<jmol><jmolApplet>
<script>frame 1.7</script>
<title>NH3 molecule </title>
<color>pink</color>
<size>250</size>
<uploadedFileContents>FRIST(3)NH3OPTIMIZATION2.LOG</uploadedFileContents>
</jmolApplet></jmol> [[File:FrequenciesforNH3(2)dp513.png]]

==== Questions about molecular vibrations ====
#- 6 vibrations are expected as the molecule is formed from 4 atoms.
#- Scisoring of different N-H bonds at 1693 frequency units in  and two assymetric bond stretches at 3589 units, in one of which stretch of the two N-H bonds while position of the other remains fixed, in the second mode all three bonds stretch. Similar pattern occurs with scissoring.
#- Mode numbers 1,2,3 are bending modes while 4,5,6 are stretches.
#- symmetric stretch at 3461 units.
#- symmetric bend at 1089 units. 
#- 4. 

==== Atomic charges ====

According to the NBO analysis atomic charge on N is 1.125e and on H the value is -0.375e 

==== Reaction energies ====

After running an optimization of N2 and H2 the following parameters were determined.
{| class="wikitable" border="1"
|-
! Property
! N2
! H2
|-
| File Name
| n2optimizationdp513
| H2OPTIMIZATION2DP513
|-
| Energy
| -109.52412868
| -1.17853936
|-
| RMS Gradient Norm
| 0.00000060
| 0.00000204
|-
| Frequency
| 2457
| 4466
|}
<pre>
H2
        Item               Value     Threshold  Converged?
 Maximum Force            0.000000     0.000450     YES
 RMS     Force            0.000000     0.000300     YES
 Maximum Displacement     0.000000     0.001800     YES
 RMS     Displacement     0.000001     0.001200     YES
 Predicted change in Energy=-1.167770D-13
 Optimization completed.
</pre>

<pre>
N2
         Item               Value     Threshold  Converged?
 Maximum Force            0.000001     0.000450     YES
 RMS     Force            0.000001     0.000300     YES
 Maximum Displacement     0.000000     0.001800     YES
 RMS     Displacement     0.000000     0.001200     YES
 Predicted change in Energy=-3.383675D-13
 Optimization completed.
</pre>

Calculation 

*E(NH3)=-56.55776873
*2*E(NH3)=-113.1155375
*E(N2)=-109.5241287
*E(H2)=-1.17853936
*3*E(H2)= -3.53561808
*ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -146.4784828 Kjmol<sup>-1</sup>

=== MOs ===
Below are images of the three highest (with HOMO being the MO 7 ) occupied molecular orbitals of N2. There is apparent in phase orbital overlap which shows that all three highest occupied molecular orbitals are bonding.


[[File:BondingMOn2dp513.png]]

==== Reference gaussveiwfiles ====

[[File:FRIST(3)NH3OPTIMIZATION2.LOG]]

[[Media:H2OPTIMIZATION2DP513.LOG]]

[[Media:N2OPTIMIZATIONDP513.LOG]]


== Hydrogen peroxide ==
==== Intro ====
Molecule under investigation in the independent part of the lab was chosen to be O<sub>2</sub>H<sub>2</sub>. The reason + a historical fact(?) was that hydrogen peroxide was used as torpedo propellent in the 1950-60. Then it was decommissioned in most fleets around the world apart from ussr and potentially even there. In 2000 Russian navy dug up those old torpedoes and used them during naval exercises as a cost saving measure. Result - a blown up submarine resting on the oceans floor(partly lifted though) and a few dozen dead personnel. Peroxide leaked and rapid decomposition started catalysed by the rust on the torpedo launch tube resulting in an explosion.   

====Optimization====
<pre>
Hydrogen peroxide optimization
File Name	HYDROGENPEROXIDEOPTIMIZATIONDP513
File Type	.log
Calculation Type	FREQ
Calculation Method	RB3LYP
Basis Set	6-31G(d,p)
Charge	0
Spin	Singlet
E(RB3LYP)	-151.54319153	 a.u.
RMS Gradient Norm	0.00001203	 a.u.
Dipole Moment	1.7585	 Debye
Point Group	C1
Item section of the output file
         Item               Value     Threshold  Converged?
 Maximum Force            0.000033     0.000450     YES
 RMS     Force            0.000017     0.000300     YES
 Maximum Displacement     0.000432     0.001800     YES
 RMS     Displacement     0.000375     0.001200     YES
 Predicted change in Energy=-6.479291D-09
 Optimization completed.
</pre>

==== Jmol ====

<jmol><jmolApplet>
<script>frame 1.27</script>
<title>Hydrogen Peroxide</title>
<color>pink</color>
<size>250</size>
<uploadedFileContents>HYDROGENPEROXIDEOPTIMIZATIONDP513.LOG</uploadedFileContents>
</jmolApplet></jmol> 

==== Charges ====
Optimized structure was found to have charge of 0.478e on oxygen atoms and -0.478 on hydrogens

==== Vibrations ====


[[File:VibrationsofH2O2dp513.png| 250px ]]

2nd vibrational mode is the o-o bond stretch with a very low frequency value of 955 indicating weakness of this bond hence easy decomposition of hydrogen peroxide. 

Modes 5 and 6 are degenerate (within 1 unit of frequency) symmetric and asymmetric stretches of the O-H bonds.

==== MO ====
{| class="wikitable" border="1"
|-
! MO Picture
! MO Energy
! Bonding/antibonding
|-
| [[File:LUMOperoxidedp513.png| 250px ]]
| LUMO
| antibonding
|-
| [[File:HOMOperoxidedp513.png | 250px ]]
| HOMO
| Antibonding
|-
| [[File:2ndHOMOperoxidedp513.png| 250px ]]
| 2nd HOMO
| antibonding
|-
| [[File:3rdHOMOperoxidedp513.png| 250px ]]
| 3rd HOMO
| perhaps bonding as no node in between atom groups(?)
|}

Orbitals in the HOMO/LUMO region are high in energy explaining the instability of the molecule. 
==== Reference gausslogfile ====
[[Media:HYDROGENPEROXIDEOPTIMIZATIONDP513.LOG]]