View source for ModAGSTest1

== Ammonia Molecule ==
===Optimisation===

Molecular Formula=NH<sub>3<sub>

N-H bond length= 1.01798 Angstroms

H-N-H bond angle=105.7446°

Calculation Method= RB3LYP

Basis Set= 6-31G(d,p)

Final Energy=-56.55776873 a.u.

RMS gradient= 0.00000323 a.u

Point Group= C<sub>3V<sub>
<pre>
Item               Value     Threshold  Converged?
 Maximum Force            0.000006     0.000450     YES
 RMS     Force            0.000004     0.000300     YES
 Maximum Displacement     0.000014     0.001800     YES
 RMS     Displacement     0.000009     0.001200     YES
 </pre>
<jmol><jmolApplet>
  <title>Ammonia</title>
  <color>black</color>
  <size>200</size>
  <uploadedFileContents>ALEXGS NHS OPTM.LOG</uploadedFileContents>
</jmolApplet></jmol>
This optimisation file is linked to [[Media:ALEXGS NHS OPTM.LOG| here]]

===Vibrations===
[[File:Alexgs ammonia vibrations table.png|250px|thumb|left|A table showing the vibrational modes of Ammonia.]]
This is a non-linear molecule so due to the 3N-6 rule, 3 modes would be expected on the IR spectrum. As shown in the table the modes 2&3 are degenerate as well as 4&5. Modes 1,2 &3 are all "bending" vibrations whereas modes 4,5&6 are "bond stretching" vibrations. Mode 6 is highly symmetric and mode 1 is given the term of "umbrella" mode due to its appearance. On experimental spectrum of gaseous ammonia, 4 bands would be expected but 3 may be seen due to merging of 2 modes at around 3500.





















===Charges===

[[File:alexgs_ammonia_charges.png|300px|thumb|left|A Gaussview image showing the charges on the atoms in optimized Ammonia structure]] The charges are distributed in this way mainly because nitrogen is a lot more electronegative than hydrogen so the electrons are placed nearer to it resulting in the nitrogen being negatively charged and the hydrogens being positively charged. The charges on the hydrogens are all the same because they're all in exactly the same environment and they all add up to cancel out the negative charge on the nitrogen because its a molecule with no overall charge.














== Nitrogen Molecule ==
===Optimisation===

Molecular Formula=N<sub>2<sub>

N-N bond length= 1.09200 Angstroms

Calculation Method= RB3LYP

Basis Set= 6-31G(d,p)

Final Energy=-109.52359111 a.u.

RMS gradient= 0.02473091 a.u

Point Group= D<sub>∞h<sub>
<pre>
         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
  </pre>

<jmol><jmolApplet>
  <title>Nitrogen</title>
  <color>black</color>
  <size>200</size>
  <uploadedFileContents>ALEXGS_NITROGEN_OPTM.LOG</uploadedFileContents>
</jmolApplet></jmol>
This optimisation file is linked to [[ALEXGS_NITROGEN_OPTM.LOG| here]]

===Vibrations===
[[File:Alexgs nitrogen vibrations table.png|250px|thumb|left|A table showing the vibrational modes of Nitrogen(N<sub>2</sub>).]]This is a linear molecule so due to the 3N-5 rule, 1 mode would be expected on the IR spectrum. As shown in the table, there is only 1 mode with a frequency of 2457.


























== Hydrogen Molecule ==
===Optimisation===

Molecular Formula=H<sub>2<sub>

H-H bond length= 0.6000000 Angstroms

Calculation Method= RB3LYP

Basis Set= 6-31G(d,p)

Final Energy=-1.19151183 a.u.

RMS gradient= 0.09719500 a.u

Point Group= D<sub>∞h<sub>
<pre>
         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
  </pre>

<jmol><jmolApplet>
  <title>Hydrogen</title>
  <color>black</color>
  <size>200</size>
  <uploadedFileContents>ALEXGS HYDROGEN OPTM.LOG</uploadedFileContents>
</jmolApplet></jmol>
This optimisation file is linked to [[ALEXGS HYDROGEN OPTM.LOG| here]]

===Vibrations===
[[File:Alexgs hydrogen vibrations table.png|250px|thumb|left|A table showing the vibrational modes of Hydrogen(H<sub>2<sub>).]]This is a linear molecule so due to the 3N-5 rule, 1 mode would be expected on the IR spectrum. As shown in the table, there is only 1 mode with a frequency of 4465.68.
























== Haber-Bosch Reaction ==
Reaction Equation: N<sub>2</sub> + 3H<sub>2</sub> --> 2NH<sub>3</sub>

===Energy Calculation===

In atomic units:    
    E(NH<sub>3</sub>)= -56.55776873 
    E(N<sub>2</sub>)= -109.52359111
    E(H<sub>2</sub>)= -1.19151183 
    ΔE=2*E(NH<sub>3</sub>)-[E(N<sub>2</sub>)+3*E(H<sub>2</sub>)]=-0.01741086
In kJ/mol:
    ΔE= -45.71221641
As this reaction is exothermic, this means that the ammonia product is more stable than the gaseous reactants.

== Hydrogen Chloride ==
===Optimisation===

Molecular Formula=HCl

H-Cl bond length= 1.2900000 angstroms 

Calculation Method= RB3LYP

Basis Set= 6-31G(d,p)

Final Energy= -460.80077017 a.u.

RMS gradient= 0.00135233 a.u

Point Group= C<sub>∞v<sub>
<pre>
Item               Value     Threshold  Converged?
 Maximum Force            0.000090     0.000450     YES
 RMS     Force            0.000090     0.000300     YES
 Maximum Displacement     0.000139     0.001800     YES
 RMS     Displacement     0.000197     0.001200     YES
 </pre>
<jmol><jmolApplet>
  <title>Hydrogen Chloride molecule</title>
  <color>black</color>
  <size>200</size>
  <uploadedFileContents>ALEXGS HCL OPTM.LOG</uploadedFileContents>
</jmolApplet></jmol>
This optimisation file is linked to [[Media:ALEXGS HCL OPTM.LOG| here]]
===Vibrations===
[[File:Alexgs hcl vibrations table.png|250px|thumb|left|A table showing the vibrational modes of Hydrogen Chloride.]]
This is a linear molecule so due to the 3N-5 rule, 1 mode would be expected on the IR spectrum.






















===Charges===

[[File:Alexgs hcl charges.png|400px|thumb|left|A Gaussview image showing the charges on the atoms in optimized Hydrogen Chloride structure]]The charges are distributed in this way because chloride is a lot more electronegative than hydrogen so it places a greater force on the electrons which pulls them closer to it resulting in the chlorine being negatively charged and the hydrogen being positively charged. 




















===Molecular Orbitals===

[[File:Alexgs hcl mo3.png|thumb|left|Third Molecular Orbital of Hydrogen Chloride]]
[[File:Alexgs hcl mo4.png|thumb|left|Fourth Molecular Orbital of Hydrogen Chloride]]
Hydrogen has a electronic configuration of 1s<sup>2</sup> whereas chlorine has an electronic configuration of 1s<sup>2</sup>2s<sup>2</sup>2p<sup>6</sup>3s<sup>2</sup>3p<sup>5</sup>. The third and fourth molecular orbitals (shown on left) are occupied and non-bonding and they are both formed just from the 2p atomic orbitals on the Chlorine (third one is from 2p<sub>x</sub> and the fourth one is from the 2p<sub>z</sub> orbital). They are both equivalent in energy as shown in the table on the right hand side and this energy level is very deep compared to other molecular orbitals so they're not involved in bonding as the energy gap is too large. The eighth and ninth molecular orbitals are also degenerate, occupied and are non-bonding. They are formed out of just the 3p atomic orbitals on the Chlorine and are the highest occupied molecular orbital. Finally, the tenth molecular orbital has been contributed to by the 1s orbital on hydrogen and a 3p orbital on Chlorine (any direction) and it is the lowest unoccupied molecular orbital. It is called σ<sup>*</sup><sub>3pz</sub> and is non-bonding.
[[File:Alexgs hcl mo energies.png|thumb|right|Table showing Energies of the first 12 Molecule Orbitals of Hydrogen Chloride in atomic units]]
[[File:Alexgs hcl mo8.png|thumb|left|Eighth Molecular Orbital of Hydrogen Chloride]]
[[File:Alexgs hcl mo9.png|thumb|left|Ninth Molecular Orbital of Hydrogen Chloride]]
[[File:Alexgs hcl mo10.png|thumb|left|Tenth Molecular Orbital of Hydrogen Chloride]]