View source for Chl2118 comp

==NH3 molecule==

The full optimisation file can be found [[Media:CHL2118_NH3_OPTIMISATION.LOG| here]].

===Interactive molecule (Jmol file)===

<jmol><jmolApplet>
   <title>Interactive NH3 structure</title>
   <size>200</size>
   <color>white</color>
   <uploadedFileContents>CHL2118_NH3_OPTIMISATION.LOG</uploadedFileContents>
   <script>frame 1.22</script>
 </jmolApplet></jmol>

===Summary information===

{| class="wikitable" border="1"

|+ Summary information

| <b>Calculation method</b> || RB3LYP

|- 

| <b>Basis set</b> || 6-31G(d,p) 

|- 

| <b>Final energy</b> (au) || -56.5577687299

|- 

| <b>RMS gradient</b> (au) || 0.000045

|-

| <b>Point group</b> || C3V

|}

===Structural information===

{| class="wikitable" border="1"

|+ Bond lengths and angles

| <b>N-H bond length</b> (Å) || 1.02 ± 0.01

|- 

| <b>H-N-H bond angle</b> (°) || 106 ± 1 

|}

In literature the bond length of N-H in NH3 is 1.019 ± 0.001Å and the bond angle is 109.1 ± 0.1° <ref name="NH3_Lit" />. This value was found from an isolated molecule ie not part of a complex, which was also the case for the Gaussian calculation, suggesting that, despite Gaussian being theoretical, it is relatively accurate -- although it has a higher uncertainty.

===Conversion of molecule forces=== 

{| class="wikitable" border="1" 

|+ Forces and displacements 

! 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 

|} 


===Vibrations and intensities===

[[File:Chl2118_nh3_vibrations.PNG|thumb|center|Screenshot of vibrations table in Gaussian.]]

{| class="wikitable" border="1" 

|+ Vibration information

| <b>Wavenumber</b> cm^-1 || 1090 || 1694 || 1694 || 3461 || 3590 || 3590

|- 

| <b>Symmetry</b> || A1 || E || E || A1 || E || E 

|- 

| '''Intensity''' || 145 || 14 || 14 || 1 || 0 || 0

|- 

| '''Image''' || [[File:Chl2118_nh3_vib1.PNG|200px]] || [[File:Chl2118_nh3_vib2.PNG|200px]] || [[File:Chl2118_nh3_vib3.PNG|200px]] || [[File:Chl2118_nh3_vib4.PNG|200px]] || [[File:Chl2118_nh3_vib5.PNG|200px]] || [[File:Chl2118_nh3_vib6.PNG|200px]]

|} 

From the 3N-6 rule, 6 modes of vibration are expected. Two modes are degenerate (four different energies in total). There are three bending vibrations and three stretching vibrations. The fourth mode is highly symmetric -- both 1090cm-1 mode and the 3461cm-1 are symmetric, but with 3461cm-1, the point group doesn't change. The 1090cm-1 mode is known as the 'umbrella mode' (the bends are in the same direction at the same time). Two main bands would be seen in an IR spectrum of gaseous ammonia, as the intensity at 3590cm-1 is 0, and the peak at 3461cm-1 is so small it would be very difficult to see.

===NBO charges===

[[File:Chl2118_nh3_chargedis.PNG|thumb|center|Screenshot of NBO charge distribution on NH3.]]

The charge on the central nitrogen atom is -1.125, and the charge on the H-atoms is +0.375. A negative charge would be expected for nitrogen as it is more electronegative than hydrogen and therefore would have a higher electron density (negative ion); a positive charge would be expected for the hydrogen atoms for the same reasoning.

==N2==

The optimisation file can be found [[Media:CHL2118_N2_OPTIMISATION.LOG| here]].

===Interactive molecule (Jmol file)===

<jmol><jmolApplet>
   <title>Interactive N2 structure</title>
   <color>white</color>
   <size>200</size>
   <uploadedFileContents>CHL2118_N2_OPTIMISATION.LOG</uploadedFileContents>
   <script>frame 1.11</script>
 </jmolApplet></jmol>

===Summary information===

{| class="wikitable" border="1"

|+ Summary information

| <b>Calculation method</b> || RB3LYP

|- 

| <b>Basis set</b> || 6-31G(d,p) 

|- 

| <b>Final energy</b> (au) || -109.52412878

|- 

| <b>RMS gradient</b> (au) || 0.00000060

|-

| <b>Point group</b> || D*H

|}

===Structural information===

{| class="wikitable" border="1"

|+ Bond lengths and angles

| <b>N-N bond length</b> (Å) || 1.11 ± 0.01

|- 

| <b>N-N bond angle</b> (°) || 180

|}

===Conversion of molecule forces===

{| class="wikitable" border="1" 

|+ N2 forces and displacements 

! 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 

|} 

===Vibrations and intensities===

[[File:Chl2118_N2_vibrations.PNG|thumb|center|Screenshot of vibrations table in Gaussian.]]

{| class="wikitable" border="1" 

|+ Vibration information

| <b>Wavenumber</b> cm^-1 || 2457

|- 

| <b>Symmetry</b> || SGG

|- 

| <b>Intensity</b> || 0.0000

|- 

| <b>Image</b> || [[File:Chl2118_n2_vib.PNG]] 

|}

===NBO charges===

[[File:Chl2118_n2_chargedis.PNG|thumb|center|Screenshot of NBO charge distribution on N2.]]

As N2 is a homonuclear diatomic molecule, the charge distribution on each atom is 0.

==H2==

The optimisation file can be found [[Media:CHL2118_H2_OPTIMISATION.LOG | here]].

===Interactive molecule (Jmol file)===

<jmol><jmolApplet>
   <title>Interactive H2 structure</title>
   <color>white</color>
   <size>200</size>
   <uploadedFileContents>CHL2118_H2_OPTIMISATION.LOG</uploadedFileContents>
   <script>frame 1.13</script>
 </jmolApplet></jmol> 

===Summary information===

{| class="wikitable" border="1"

|+ Summary information

| <b>Calculation method</b> || RB3LYP

|- 

| <b>Basis set</b> || 6-31G(d,p) 

|- 

| <b>Final energy</b> (au) || -1.17853935735

|- 

| <b>RMS gradient</b> (au) || 0.00000017

|-

| <b>Point group</b> || D*H

|}

===Structural information===

{| class="wikitable" border="1"

|+ Bond lengths and angles

| <b>H-H bond length</b> (Å) || 0.74 ± 0.01

|- 

| <b>H-H bond angle</b> (°) || 180

|}

===Conversion of molecule forces===

{| class="wikitable" border="1" 

|+ H2 Forces and Displacements 

! Item !! Value !! Threshold !! Converged? 

|- 

| Maximum force || 0.168347 || 0.000450 || YES 

|- 

| RMS force || 0.168347 || 0.000300 || YES 

|- 

| Maximum displacement || 0.119698 || 0.001800 || YES 

|- 

| RMS displacement || 0.169278 || 0.001200 || YES 

|} 

===Vibrations and intensities===

[[File:Chl2118_h2_vib.PNG|thumb|center|Screenshot of vibrations table in Gaussian.]]

{| class="wikitable" border="1" 

|+ Vibration Information

| <b>Wavenumber</b> cm^-1 || 4466

|- 

| <b>Symmetry</b> || SGG

|- 

| <b>Intensity</b> || 0.0000

|- 

| <b>Image</b> || [[File:Chl2118_h2_vector.PNG]] 

|}

===NBO charges===

[[File:Chl2118_h2_chargedis.PNG|thumb|center|Screenshot of NBO charge distribution on H2.]]

As H2 is a homonuclear diatomic molecule, the charge distribution on each atom is 0.

==Mono-metallic transition metal complex with N2 coordinate==

The link to the page can be found [https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=CANKEK&DatabaseToSearch=Published here].

{| class="wikitable" border="1" |thumb|right
|+ Mono-metallic TM complex information
|-
! colspan="3" style="text-align: left;"|Structure
|-
| colspan="3" align="center"|[[File:Chl2118_cankek.PNG | 300px]]
|-
! colspan="3" style="text-align: left;"|3D crystalline structure
|-
| colspan="3" align="center"|[[File:Chl2118_cankek_3d.png|300px]]
|-
! colspan="3" style="text-align: left;"|More Info
|-
| style="text-align: center;"|<b>Unique identifier</b>
| style="text-align: center;"|CANKEK
|-
| rowspan="2" style="text-align: center;" | <b>N-N bond length (Å)</b>
| colspan="2" style="text-align: center;" | 1.37 ± 0.01
|-
|}

In N2, the Gaussian bond length is 1.11 ± 0.01Å, but in the above compound it is 1.37 ± 0.01Å<ref name="CANKEK" />. This increase in bond length could be due to the decrease in bond order - from three (triple bond) to one (single bond). Also, the nitrogen connected to the copper atom has a charge of +1 whereas the other nitrogen in the N-N bond has a neutral charge. As a result, the N-N may be weaker. Another possible reason is a difference between theoretical bond distances (Gaussian) and values found from experimental results -- this would suggest that the Gaussian bond length is less accurate than the experimentally found value.

==The Haber-Bosch process==

<b>N2 + 3H2 → 2NH3</b>

E(NH3) = -56.5577687299 au

2 * E(NH3) = -113.1155374598 au

E(N2) = -109.524128676 au

E(H2) = -1.17853935735 au

3 * E(H2) = -3.53561807205 au

ΔE = 2 * E(NH3) - [E(N2) + 3 * E(H2)]

ΔE = -0.05573652015 au

0.000038 au = 0.1 kJ/mol

-0.05573652015 au = -146.7 kJ/mol

<u>ΔE = -146.7 kJ/mol</u>

As the energy difference is a negative value, the reaction is exothermic and the product (ammonia) is more stable.

==Project molecule - [MnO4]– ==

The full optimisation file can be found [[Media:CHL2118_MNO4_OPTIMISATION.LOG| here]].

===Interactive molecule (Jmol file)===

<jmol><jmolApplet>
   <title>Interactive MNO4- structure</title>
   <size>200</size>
   <color>white</color>
   <uploadedFileContents>CHL2118_MNO4_OPTIMISATION.LOG</uploadedFileContents>
   <script>frame 1.5</script>
 </jmolApplet></jmol>

===Summary Information===

{| class="wikitable" border="1"

|+ Summary information

| <b>Calculation method</b> || RB3LYP

|- 

| <b>Basis set</b> || 6-31G(d,p) 

|- 

| <b>Final energy</b> (au) || -1451.84084417

|- 

| <b>RMS gradient</b> (au) || 0.00002308

|-

| <b>Point group</b> || TD

|}

===Structural information===

{| class="wikitable" border="1"

|+ Bond lengths and angles

| <b>Mn-O bond length</b> (Å) || 1.59 ± 0.01

|- 

| <b>O-Mn-O bond angle</b> (°) || 109 ± 1

|}

The Gaussian Mn-O bond length is 1.59 ± 0.01Å, but this is 0.02Å different from the literature value<ref name="MnO_Lit" />, which gave a value of 1.61 ± 0.01Å as the Mn-O bond length. This difference in values could be due to the fact that the bond length from the literature value is from an Mn-O bond in a complex, which would affect the bond distance. Another explanation for the difference could be due to the Gaussian value being theoretical, whereas the literature value was found from an experimental process. As a result, the literature value is likely more accurate than the Gaussian bond length.

===Conversion of molecule forces=== 

{| class="wikitable" border="1" 

|+ Forces and displacements 

! Item !! Value !! Threshold !! Converged? 

|- 

| Maximum force || 0.000045 || 0.000450 || YES 

|- 

| RMS force || 0.000024 || 0.000300 || YES 

|- 

| Maximum displacement || 0.000081 || 0.001800 || YES 

|- 

| RMS displacement || 0.000043 || 0.001200 || YES 

|} 


===Vibrations and intensities===

[[File:Chl2118_mno4_vibrations.PNG|thumb|center|Screenshot of vibrations table in Gaussian.]]


In the following table, in some images the Mn-O bonds have been removed to show more fully the displacement vectors for vibrations.

{| class="wikitable" border="1" 

|+ Vibration information

| <b>Wavenumber</b> cm^-1 || 378 || 378 || 426 || 426 || 426 || 957 || 1018 || 1018 || 1018

|- 

| <b>Symmetry</b> || E || E || T2 || T2 || T2 || A1 ||  T2 || T2 || T2 

|- 

| '''Intensity''' || 0.00 || 0.00 || 6 || 6 || 6 || 0.00 || 213 || 213 || 213 

|- 

| '''Image''' || [[File:Chl2118_mno4_vib1.png|180px]] || [[File:Chl2118_mno4_vib2.png|180px]] || [[File:Chl2118_mno4_vib3.png|180px]] || [[File:Chl2118_mno4_vib4.png|180px]] || [[File:Chl2118_mno4_vib5.png|180px]] || [[File:Chl2118_mno4_vib6.png|180px]] || [[File:Chl2118_mno4_vib7.png|180px]] || [[File:Chl2118_mno4_vib8.png|180px]] || [[File:Chl2118_mno4_vib9.png|180px]] 

|}

===NBO charges===

[[File:Chl2118_mno4_chargedis.PNG|thumb|center|Screenshot of NBO charge distribution on MNO4-.]]

===Molecular orbitals===

{| class="wikitable" border="1" 

|+ Select molecule orbitals

| <b>Molecular orbital number</b> || 1 || 18 || 23 || 29 || 30

|- 

| <b>Orbital energy</b> (kJ/mol) || -235.48687 || -0.24210 || -0.16333 || -0.08537 || -0.06959

|- 

| <b>Orbital image</b> || [[File:Chl2118_mno4_mo1.PNG|200px]] || [[File:Chl2118_mno4_mo18.PNG|200px]] || [[File:Chl2118_mno4_mo23.PNG|200px]] || [[File:Chl2118_mno4_mo29.PNG|200px]] || [[File:Chl2118_mno4_mo30.PNG|200px]]

|- 

| <b>Orbital character</b> || This first orbital is comprised mostly of the 1s AO of the manganese atom and therefore is very small, which is why it is invisible in the above image. This is a bonding orbital and is the deepest in energy and most stable as a core orbital. It is fully occupied by two electrons, and has very little effect on bonding -- in an MO diagram, this orbital would be omitted as it is so low in energy and relatively uninteresting. || The eighteenth orbital is comprised of a d orbital from the manganese atom, and four total p orbitals (one from each oxygen atom). Its energy is shared with three other orbitals (19 and 20) -- they are degenerate. As the p orbitals seem to be in phase with the d orbital (they combine), this orbital is likely bonding and not anti-bonding. This orbital is also occupied and not very high in energy, though much higher than the 1s orbital. It may have an effect on bonding, but the effect would likely be very slight as it still has 11 occupied orbitals above it. || Orbital 23 is likely made of one central, large s orbital from the manganese atom, and p orbitals from the four oxygen atoms. This is evidenced by the large circular center and the nodes formed at the oxygen atoms. The size of the s orbital indicates a high energy level, possibly 3s or 4s. There are no other orbitals with the same energy as there is only one s orbital of each level. This orbital is relatively high in energy but still occupied fully. As a result, it would have a greater effect on bonding. This is likely a bonding orbital as the p orbitals match with the central s orbital and combine. || This orbital is formed of p orbitals from the oxygen atoms with no visible AOs from manganese, which could mean it is a very small orbital, though this is unlikely as it is very high in energy, and represents the HOMO of the molecule. There are another two degenerate orbitals with the same shape (three degenerate in total). It is still fully occupied with two electrons of parallel spin, and likely has a large effect on bonding. || Orbital thirty is the LUMO of the molecule and is fully unoccupied. It is much higher in energy than the other listed MOs, and its orbital energy is positive. Being the LUMO, its effect on bonding is likely very great. It appears to be comprised of a dz**2 orbital on the manganese and out of phase p orbitals on the oxygen atoms, suggesting an anti-bonding orbital. There is one other orbital (31) with the same energy, containing a different d orbital from the manganese atom.

|}

==References==

<ref name="NH3_Lit">H. J. Freund, in <i>Landolt-Börnstein - Group III Condensed Matter</i>, ed. A. Goldmann, E. E. Koch, vol. 23A, 1989, ch. 2.3.8, pp. 204-206</ref>

<ref name="CANKEK">The page for the quoted bond length value for N2 can be found at [https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=CANKEK&DatabaseToSearch=Published CCDC].</ref>

<ref name="MnO_Lit">The page for the quoted literature value can be found at [https://www.ccdc.cam.ac.uk/structures/search?pid=ccdc:1285645&sid=IUCr CCDC].</ref>

=Marking=

Note: All grades and comments are provisional and subject to change until your grades are officially returned via blackboard. Please do not contact anyone about anything to do with the marking of this lab until you have received your grade from blackboard.

==Wiki structure and presentation 1/1 ==

Is your wiki page clear and easy to follow, with consistent formatting?

YES

Do you effectively use tables, figures and subheadings to communicate your work?

YES

==NH3 1/1 ==

Have you completed the calculation and given a link to the file?

YES

Have you included summary and item tables in your wiki?

YES

Have you included a 3d jmol file or an image of the finished structure?

YES

Have you included the bond lengths and angles asked for?

YES

Have you included the “display vibrations” table?

YES

Have you added a table to your wiki listing the wavenumber and intensity of each vibration?

YES

Did you do the optional extra of adding images of the vibrations?

YES

Have you included answers to the questions about vibrations and charges in the lab script?

YES

== N2 and H2 0/0.5 ==

Have you completed the calculations and included all relevant information? (summary, item table, structural information, jmol image, vibrations and charges)

YES, however you have given a bond angle of 180 for N2 and H2, there are no bond angles in diatomic molecules. Bond angles involve exactly 3 atoms.

==Crystal structure comparison 0.5/0.5 ==

Have you included a link to a structure from the CCDC that includes a coordinated N2 or H2 molecule?

YES

Have you compared your optimised bond distance to the crystal structure bond distance?

YES

==Haber-Bosch reaction energy calculation 1/1==

Have you correctly calculated the energies asked for? ΔE=2*E(NH3)-[E(N2)+3*E(H2)]

YES

Have you reported your answers to the correct number of decimal places?

YES

Do your energies have the correct +/- sign?

YES

Have you answered the question, Identify which is more stable the gaseous reactants or the ammonia product?

YES

== Your choice of small molecule 4.5/5 ==

Have you completed the calculation and included all relevant information?

YES

Have you added information about MOs and charges on atoms?

YES - good explanations overall well done! You could have attempted to explain the charge values you presented.

== Independence 1/1 ==

If you have finished everything else and have spare time in the lab you could:

Check one of your results against the literature, or

YES - Well done

Do an extra calculation on another small molecule, or

Do some deeper analysis on your results so far