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== Molecular Modelling 2 - Oana Popescu ==

=== NH3 Molecule ===

'''Molecule Type''': NH3

'''Calculation Method:''' RB3LYP

'''Basis Set:''' 6-31G(D,P)

'''Final Energy (au):''' -56.55776873

'''Point Group:''' None

<b>Item Table:</b>

<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
 Predicted change in Energy=-5.986286D-10
 Optimization completed.
    -- Stationary point found.</pre>

<b>JMol Simulation</b>:<br>
<jmol><jmolApplet>
  <title>NH3 molecule</title>
  <color>black</color>
  <size>200</size>
  <uploadedFileContents>oana_NH3_OPTIMISATION_INITIAL_THIRDTRY.LOG</uploadedFileContents>
</jmolApplet></jmol>
<br>The above optimisation file is linked [[Media:Oana_NH3_OPTIMISATION_INITIAL_THIRDTRY.LOG| here.]]
<br>
<b>Vibrations</b>:<br>
[[File:Oana_NH3_vibrations_short.PNG]]

<br><b>Questions</b><br><br>
<i>how many modes do you expect from the 3N-6 rule?</i>
<br> The molecule has 4 atoms; thus, (3*4)-6 is 6 vibrational modes, in line with results.<br><br>
<i>which modes are degenerate (ie have the same energy)?</i>
<br> Modes 2-3 and 5-6 respectively, in the above image.<br><br>
<i>which modes are "bending" vibrations and which are "bond stretch" vibrations?</i><br>
1,2,3 - bend, 4, 5, 6 - stretch<br><br>
<i>which mode is highly symmetric?</i><br>
Mode 4 (symmetrical stretches in all directions)<br><br>
<i>one mode is known as the "umbrella" mode, which one is this?</i><br>
Mode 1 - symmetrical bend of all 3 molecules<br><br>
<i>how many bands would you expect to see in an experimental spectrum of gaseous ammonia?</i>
<br>2 Bands - Due to the degeneracy of results 2 and 3, and the last 3 results being too small to record on an infrared spectrum.

<br><br>
<b>Charges</b>
<br><i>Expectation:</i> The H-atoms are positive and the N-atom is negative, due to the high electronegativity of Nitrogen and the Electropositivity of Hydrogen.

<br>[[File:Oana_NH3_charges.PNG]]<br>
<i>Calculated Charges:</i> Hydrogen: 0.375; Nitrogen: -1.125

<br><br><br>

=== N2 Molecule ===

'''Molecule Type''': N2

'''Calculation Method:''' RB3LYP

'''Basis Set:''' 6-31G(D,P)

'''Final Energy (au):''' -109.52412868

'''Point Group:''' None


<b>Item Table:</b>

<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
 Predicted change in Energy=-3.401066D-13
 Optimization completed.
    -- Stationary point found.</pre>

<b>JMol Simulation</b>:<br>
<jmol><jmolApplet>
  <title>N2 molecule</title>
  <color>black</color>
  <size>200</size>
  <uploadedFileContents>OANA_N2_OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>
<br>The above optimisation file is linked [[Media:OANA_N2_OPTIMISATION.LOG| here.]]

<b>Vibrations:</b> One vibration at frequency 2457.33, infrared 0

<b>Charges</b>: Molecule is 100% covalent. No dipole found.


=== H2 Molecule ===

'''Molecule Type''': H2

'''Calculation Method:''' RB3LYP

'''Basis Set:''' 6-31G(D,P)

'''Final Energy (au):''' -1.17853936

'''Point Group:''' None

<b>Item Table:</b>

<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
 Predicted change in Energy=-1.164080D-13
 Optimization completed.
    -- Stationary point found.</pre>


<b>JMol Simulation</b>:<br>
<jmol><jmolApplet>
  <title>H2 molecule</title>
  <color>black</color>
  <size>200</size>
  <uploadedFileContents>OANA_H2_OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>
<br>The above optimisation file is linked [[Media:OANA_H2_OPTIMISATION.LOG| here.]]


<b>Vibrations:</b> One vibration at frequency 4465.68, infrared 0

<b>Charges</b>: Molecule is 100% covalent. No dipole found.


=== Reaction Energy Calculations ===

E(NH3)= -56.55776873au <br>
2*E(NH3)= -113.11553746au <br>
E(N2)= -109.52412868au <br>
E(H2)= -1.17853936au <br>
3*E(H2)= -3.53561808au <br>
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= <b>-0.0557907au = -146.48kJ/mol</b><br>

Since the energy change is negative, the reaction is exothermic; thus, the products have a lower energy than the reactants, and are more stable.


=== Molecule of Choice: Methane (CH4) ===

'''Molecule Type''': CH4

'''Calculation Method:''' RB3LYP

'''Basis Set:''' 6-31G(D,P)

'''Final Energy (au):''' -40.52401404

'''Point Group:''' None

<b>Item Table:</b>
<pre> Item               Value     Threshold  Converged?
 Maximum Force            0.000063     0.000450     YES
 RMS     Force            0.000034     0.000300     YES
 Maximum Displacement     0.000179     0.001800     YES
 RMS     Displacement     0.000095     0.001200     YES
 Predicted change in Energy=-2.256034D-08
 Optimization completed. 
 -- Stationary point found.</pre>

<b>JMol Simulation</b>:<br>
<jmol><jmolApplet>
  <title>CH4 molecule</title>
  <color>black</color>
  <size>200</size>
  <uploadedFileContents>OANA_CH4_OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>
<br>The above optimisation file is linked [[Media:OANA_CH4_OPTIMISATION.LOG| here.]]

<b>Vibrations</b>:<br>
[[File:Oana_CH4_vibrations.PNG]]

The Molecule has 9 vibrations 4 stretches (6-9) and 5 bends (1-5); 6 show a change in dipole moment and are infrared-active, whilst the other three are symmetrical from a dipole perspective and are not visible on an IR spectrum. Of the ones that are IR-active, bends 1-3 and stretches 7-9 vibrate at the same frequency; thus, they would show up as one band each on an IR spectrum, creating a final spectrum with 2 bands. 

<b>Charges</b>:<br>
[[File:Oana_CH4_charges.PNG]]<br>
The molecule itself isn't charged, but has a slight dipole, with the carbon being slightly electronegative at -0.930, and the hydrogens all slightly electropositive at 0.233.

<b>Some Molecular Orbitals</b><br><br>
[[File:Oana_orbital_1.PNG]]<br>
<i>Orbital 1</i> - A low orbital that is very deep in energy; it stays close to the carbon and does not appear to be involved in bonding, most likely being the Carbon 1s orbital.<br><br>
[[File:Oana_orbital_2.PNG]]<br>
<i>Orbital 2</i> - A lot higher in energy than the previous orbital, this encompasses both the Carbon and the Hydrogens, and is thus the first carbon-hydrogen bonding obrital, composed of the 2s orbital from Carbon and 1s orbital from Hydrogen, forming a sigma s-s bond. This can be seen in its round shape.<br><br>
[[File:Oana_orbital_3.PNG]]<br>
<i>Orbital 3</i> - Another Carbon-Hydrogen Bonding Orbital, it consists of one of the Carbon p-orbitals and the Hydrogen 1s orbital; this can be seen from the 2 major "lobes" of the orbital, which suggest a p-orbital being involed. <br><br>
[[File:Oana_orbital_4.PNG]]<br>
<i>Orbital 4</i> - This is the HOMO; similar to the previous MO, it is another S-P bond between Carbon and Hydrogen, using a different pi orbital from the carbon.<br><br>
[[File:Oana_orbital_5.PNG]]<br>
<i>Orbital 5</i> - This is the LUMO; as seen in the picture, it has a different structure within the outside orbital, and thus appears to be an antibonding orbital. It is most likely the antibonding orbital of the aforementioned s-s bonding orbital, due to its round structure which does not suggest p-orbitals being involved.<br><br>