View source for Rep:Mod:mm1213

== Wiki page Computational Chemistry ==
=== Michelle Madin 01340133 ===
== NH3 molecule ==
Optimized N-H bond distance = 1.01798 Å

Optimized H-N-H bond angle = 105.741 °

Calculation method = RB3LYP

Basis set = 6-31G(d.p)

Final energy E(RB3LYP) = -56.55776873 a.u.

RMS gradient norm = 0.00000485 a.u.

Point group = C<sub>3V</sub>

===  Final set of forces and displacements for NH<sub>3</sub> Optimization ===

<pre>
         Item             Value        Threshold    Converged?
 Maximum Force            0.000004     0.000450     YES
 RMS     Force            0.000004     0.000300     YES
 Maximum Displacement     0.000072     0.001800     YES
 RMS     Displacement     0.000035     0.001200     YES

</pre>

=== Jmol and File Link ===

<jmol><jmolApplet>
  <title>NH3 Optimisation</title>
  <color>black</color>
  <size>200</size>
  <uploadedFileContents>MMADIN_01340133_NH3_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

[[Media:MMADIN_01340133_NH3_OPTF_POP.LOG|NH<sub>3</sub> Optimization]]

=== NH<sub>3</sub> Vibration Frequencies ===

{| class="wikitable"
|-
! Mode #
! Frequency
! Infrared
|-
| 1
| 1089.54
| 145.3814
|-
| 2
| 1693.95
| 13.5533
|-
| 3
| 1693.95
| 13.5533
|-
| 4
| 3461.29
| 1.0608
|-
| 5
| 3589.82
| 0.2711
|-
| 6
| 3589.82
| 0.2711
|}

''How many modes do you expect from the 3N-6 rule?'' = 6 modes of vibration.

''Which modes are degenerate?'' = 2 and 3 are degenerate and 5 and 6 are degenerate.

''Which modes are "bending" vibrations and which are "bond stretch" vibrations?'' = 1,2,3 are bending and 4,5,6 are bond stretches.

''Which mode is highly symmetric?'' = 4

''Which mode is known as the "umbrella" mode?'' = 1

''How many bands would you expect to see in an experimental spectrum of gaseous ammonia?'' = You would see two peaks in the spectrum , with the most intense vibration being the first. Vibrations 2 and 3 would show as a single peak due to these modes being degenerate. Vibrations 4,5 and 6 are negligible as a result of the noise in the experimental results.

==== Charge Distribution of NH3 ====

[[File:MMadin 01340133 nh3 charge distribution.PNG]]

Nitrogen has the higher electronegativity and therefore has the higher electron density. This will result in nitrogen having a negative charge and the hydrogens having the positive charges, which is confirmed by the charge distribution shown above.

== N2 molecule ==

Optimized N-N bond distance = 1.10550 Å

Optimized N-N bond angle = 180.000 °

Calculation method = RB3LYP

Basis set = 6-31G(d.p)

Final energy E(RB3LYP) = -109.52412868 a.u. 

RMS gradient norm = 0.00000060 a.u.

Point group = D∞H


===  Final set of forces and displacements for N<sub>2</sub> Optimization ===

<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 and File Link ===

<jmol><jmolApplet>
  <title>N2 Optimisation</title>
  <color>black</color>
  <size>200</size>
  <uploadedFileContents>MMADIN 01340133 N2 OPTF POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

[[Media:MMADIN 01340133 N2 OPTF POP.LOG|N<sub>2</sub> Optimization]]

=== N<sub>2</sub> Vibration Frequencies ===
{| class="wikitable"
|-
! Mode #
! Frequency
! Infrared
|-
| 1
| 2457.33
| 0.0000

|}

== H2 molecule ==

Optimized H-H bond distance = 0.74279 Å

Optimized H-H bond angle = 180.000 °

Calculation method = RB3LYP

Basis set = 6-31G(d.p)

Final energy E(RB3LYP) = -1.17853936 a.u. 

RMS gradient norm = 0.00000017 a.u.

Point group = D∞H

===  Final set of forces and displacements for H<sub>2</sub> Optimization ===

<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 and File Link ===

<jmol><jmolApplet>
  <title>H2 Optimisation</title>
  <color>black</color>
  <size>200</size>
  <uploadedFileContents>MMADIN 01340133 H2 OPTF POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

[[Media:MMADIN 01340133 H2 OPTF POP.LOG|H<sub>2</sub> Optimization]]

=== H<sub>2</sub> Vibration Frequencies ===

{| class="wikitable"
|-
! Mode #
! Frequency
! Infrared
|-
| 1
| 4465.68
| 0.0000
|}

== Haber-Bosch reaction energy calculations ==

'''E(NH<sub>3</sub>)''' = -56.55776873 a.u.

'''2*E(NH<sub>3</sub>)''' = -113.11553746 a.u.

'''E(N<sub>2</sub>)''' = -109.52412868 a.u. 

'''E(H<sub>2</sub>)''' =  -1.17853936 a.u. 

'''3*E(H<sub>2</sub>)''' = -3.53561808 a.u.

'''ΔE=2*E(NH<sub>3</sub>) - [E(N<sub>2</sub>) + 3*E(H<sub>2</sub>)]''' = -0.0557907 a.u. = -146.47849401 kJ mol<sup>-1</sup>

== O2 molecule ==

Optimized O-O bond distance = 1.21602 Å

Optimized O-O bond angle = 180.000 °

Calculation method = RB3LYP

Basis set = 6-31G(d.p)

Final energy E(RB3LYP) = -150.25742434 a.u. 

RMS gradient norm = 0.00007502 a.u.

Point group = D∞H

===  Final set of forces and displacements for O<sub>2</sub> Optimization ===

<pre>

         Item             Value        Threshold    Converged?
 Maximum Force            0.000130     0.000450     YES
 RMS     Force            0.000130     0.000300     YES
 Maximum Displacement     0.000080     0.001800     YES
 RMS     Displacement     0.000113     0.001200     YES

</pre>

=== Jmol and File Link ===

<jmol><jmolApplet>
  <title>O2 Optimisation</title>
  <color>black</color>
  <size>200</size>
  <uploadedFileContents>MMADIN 01340133 O2 OPTF POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

[[Media:MMADIN 01340133 O2 OPTF POP.LOG|O<sub>2</sub> Optimization]]

=== O<sub>2</sub> Vibration Frequencies ===

{| class="wikitable"
|-
! Mode #
! Frequency
! Infrared
|-
| 1
| 1642.74
| 0.0000
|}

=== MO's of Optimized O<sub>2</sub> ===

[[File:MMadin 01340133 MO 3.PNG]]

'''Energy''' = -1.27663 a.u.

'''Is the MO occupied or unoccupied?''' = Occupied. 

'''Is the MO bonding or antibonding?''' = Bonding 2σ<sub>g</sub>

'''What AO's contribute to the MO?''' = Two 2s AO's, one from each oxygen atom.

'''What effect does the MO have on bonding?''' = This MO has no contribution on the bonding between the two oxygen atoms.
 
[[File:MMadin 01340133 MO 5.PNG]]

'''Energy''' = -0.53151 a.u.

'''Is the MO occupied or unoccupied?''' = Occupied. 

'''Is the MO bonding or antibonding?''' = Bonding 3σ<sub>g</sub>

'''What AO's contribute to the MO?''' = Two  2p<sub>z</sub> AO's, one from each oxygen atom.

'''What effect does the MO have on bonding?''' = This MO has no contribution on the bonding between the two oxygen atoms.

[[File:MMadin 01340133 MO 6.PNG]]

'''Energy''' = -0.51526 a.u.

'''Is the MO occupied or unoccupied?''' = Occupied. 

'''Is the MO bonding or antibonding?''' = Bonding 1π<sub>u</sub>

'''What AO's contribute to the MO?''' = Two  2p<sub>x</sub> AO's or two 2p<sub>y</sub> AO's, one from each oxygen atom.

'''What effect does the MO have on bonding?''' = This MO forms the sigma bond between the two oxygen atoms.

[[File:MMadin 01340133 MO 8.PNG]]

'''Energy''' = -0.25018 a.u.

'''Is the MO occupied or unoccupied?''' = Occupied. 

'''Is the MO bonding or antibonding?''' = Antibonding 1π*<sub>g</sub>

'''What AO's contribute to the MO?''' = Two  2p<sub>x</sub> AO's or two 2p<sub>y</sub> AO's, one from each oxygen atom.

'''What effect does the MO have on bonding?''' = This MO has no contribution on the bonding between the two oxygen atoms.

Gauss View shows this MO as being filled with 2 electrons of opposite spin, therefore identifying it as the HOMO. However the  1π*<sub>g</sub> is made of two degenerate energy levels, therefore the two electrons are actually unpaired, making this MO the SOMO. As a result of this, oxygen is para magnetic.

[[File:MMadin 01340133 MO 9.PNG]]

'''Energy''' = -0.17928 a.u.

'''Is the MO occupied or unoccupied?''' = Unoccupied. 

'''Is the MO bonding or antibonding?''' = Anti bonding 1π*<sub>g</sub>, this MO is the LUMO

'''What AO's contribute to the MO?''' = Two  2p<sub>x</sub> AO's or two 2p<sub>y</sub> AO's, one from each oxygen atom.

'''What effect does the MO have on bonding?''' = This MO has no contribution on the bonding between the two oxygen atoms.

== CF4 molecule ==

Optimized C-F bond distance = 1.32939 Å

Optimized F-C-F bond angle = 109.471 °

Calculation method = RB3LYP

Basis set = 6-31G(d.p)

Final energy E(RB3LYP) = -437.47627267 a.u.

RMS gradient norm = 0.00004049 a.u.

Point group = TD

===  Final set of forces and displacements for CF<sub>4</sub> Optimization ===

<pre>

         Item             Value        Threshold    Converged?
 Maximum Force            0.000078     0.000450     YES
 RMS     Force            0.000042     0.000300     YES
 Maximum Displacement     0.000133     0.001800     YES
 RMS     Displacement     0.000071     0.001200     YES

</pre>

=== Jmol and File Link ===

<jmol><jmolApplet>
  <title>CF4 Optimisation</title>
  <color>black</color>
  <size>200</size>
  <uploadedFileContents>MMADIN_01340133_CF4_OPTF_POP.LOG</uploadedFileContents>
</jmolApplet></jmol>

[[Media:MMADIN_01340133_CF4_OPTF_POP.LOG|CF<sub>4</sub> Optimization]]

=== CF<sub>4</sub> Vibration Frequencies ===

{| class="wikitable"
|-
! Mode #
! Frequency
! Infrared
|-
| 1
| 424.00
| 0.0000
|-
| 2
| 424.00
| 0.0000
|-
| 3
| 616.80
| 4.5048
|-
| 4
| 616.80
| 4.5048
|-
| 5
| 616.80
| 4.5048
|-
| 6
| 906.23
| 0.0000
|-
| 7
| 1305.80
| 387.1737
|-
| 8
| 1305.80
| 387.1737
|-
| 9
| 1305.80
| 387.1737
|}

==== Charge Distribution of CF4 ====

[[File:MMadin 01340133 cf4 charge distribution.PNG]]

The fluorine's are more electronegative than the carbon, therefore will withdraw electron density from the carbon atom. As a result of this, the fluorine's will be negatively charged and the carbon will be positive, which is confirmed by the charge distribution shown above.