ChemWiki - User contributions [en]

JoeWiki1

2019-05-24T15:09:51Z

Jh3817:

== Year 2 Inorganic comp labs ==

=== BH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p),
Symmetry= D3h

[[File:BH3_info.PNG]]

Item Value Threshold Converged?

Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

Link to frequency file: [[File:JH_BH3_FREQ.LOG]]

Low frequencies --- -0.4072 -0.1962 -0.0055 25.2514 27.2430 27.2460

Low frequencies --- 1163.1897 1213.3128 1213.3155

<jmol><jmolApplet>
<title>Optimised BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JH_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Vibration Data ====

{| class="wikitable" border="1"
|+ Vibrations table
! Stretch or Bend? !! Intensity !! Symmetry !! IR active? !! Wavenumber(cm-1)
|-
| Bend || 92 || A2" || Yes || 1163
|-
| Bend || 14 || E' || Yes || 1213
|-
| Bend || 14 || E' || Yes || 1213
|-
| Symmetric Stretch || 0 || A1' || No || 2581
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|}

[[File:BH3_vibrations_spectrum_JH.PNG]]

Spectrum shows 3 peaks out of 6 vibrational modes given by BH3 shown in table. 1 is IR in active leaving 5 as it causes no change in dipole in the molecule. Two pairs in the 5 are degenerate meaning they have the same energy and therefore overlap, meaning only 3 peaks show.

[[File:MO_diagram_JH.PNG]] [1]

The LCAOs seem very accurate as they depict AOs which combine to form the real MOs very well. Minor issues arise from the fact that it can be said that the overlapping of the orbitals may not be able to be seen fully and the fact that the sizes of the AOs, which represents contribution isn’t consistent. Hydrogen is more electronegative then boron and is therefore lower in energy. Hydrogen should be contributing more to the bonding orbitals and born should be contributing more to the anti-bonding orbitals but for some of them this might not be able to be seen accurately. This shows that the LCAO is a useful tool for finding what a real MO would look like.

=== NH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:NH3_point_group_summary.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES

Link to frequency file: [[File:NH3_OP_JH.LOG]]

Low frequencies --- -8.5628 -8.5571 -0.0047 0.0454 0.1785 26.4189

Low frequencies --- 1089.7603 1694.1865 1694.1865

<jmol><jmolApplet>
<title>Optimised NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3_OP_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:BH3NH3_point_group_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000514 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

Link to frequency file: [[File:NH3BH3_FREQ_NEW.LOG]]

Low frequencies --- -0.0005 0.0003 0.0014 16.7270 18.7414 42.2600

Low frequencies --- 266.2799 632.3010 639.2486

<jmol><jmolApplet>
<title>Optimised NH3BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3BH3_FREQ_NEW.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Association energies ====
E(NH3)= -56.55776863 a.u.

E(BH3)= -26.61532362 a.u.

E(NH3BH3)= -83.22469031 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)], Therefore ΔE= (-83.22468960) - [(-56.55776863)+(-26.61532362)]= -0.05159806 a.u. (-134 KJ/Mol)

The B-N dative bond is weak and this shown when compared to the Al-N bond which has an energy of 297KJ/Mol [2]

=== NI3 ===
Method= RB3LYP,
Basis set= Gen

[[File:New_NI3_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000102 0.000450 YES
RMS Force 0.000075 0.000300 YES
Maximum Displacement 0.000858 0.001800 YES
RMS Displacement 0.000629 0.001200 YES

Link to frequency file: [[File:NEW_NI3_JH.LOG]]

Low frequencies --- -12.3845 -12.3781 -5.6129 -0.0040 0.0194 0.0711

Low frequencies --- 100.9307 100.9314 147.2333

<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NEW_NI3_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised B-I bond distance is 2.18 angstrom

===Days 2 and 3 Project: Metal carbonyls===
This sections of the wiki page focuses on metal carbonyls, more specifically their bond-lengths and CO bond frequencies. The metal-complexes which will be focused on are [Cr(CO)6], [Mn(CO)6]+ and [Fe(CO)6]2+. These were chosen as they come one after another in the d-block so it would be interesting to see how bond-lengths and bond frequencies vary across the period. 2 of the complexes are charged (positively) while one is neutral and this is something which must be taken into account when analysing bond-lengths and bond frequencies. An initial prediction would be that bond length increases across a period (as the metal complexes are becoming more positive meaning less overlap with the CO pi* and overall less back-donation and since back donation strengths the M-C bond less of this means an increases in bond length) and that bond frequencies increases.

==== [Cr(CO)6] ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Cr

[[File:Cr(CO)6_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000110 0.000450 YES
RMS Force 0.000041 0.000300 YES
Maximum Displacement 0.000705 0.001800 YES
RMS Displacement 0.000334 0.001200 YES

Link to frequency file: [[File:CR(CO)6_JH_2.LOG]]

Low frequencies --- -0.0014 -0.0013 -0.0010 11.7482 11.7482 11.7482

Low frequencies --- 66.6574 66.6574 66.6574

<jmol><jmolApplet>
<title>Optimised Cr(CO)6 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>CR(CO)6_JH_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Mn(CO)6]+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Mn

[[File:-Mn(CO)62+_summary_JH3817.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000430 0.001800 YES
RMS Displacement 0.000204 0.001200 YES

Link to frequency file: [[File:-MN(CO)6-+_OP_FREQ_JH.LOG]]

Low frequencies --- -0.0007 0.0006 0.0009 4.7607 4.7607 4.7607

Low frequencies --- 76.3202 76.3202 76.3202

<jmol><jmolApplet>
<title>Optimised [Mn(CO)6]+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-MN(CO)6-+_OP_FREQ_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Fe(CO)6]2+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Fe

[[File:-Fe(CO)6-2+_freq_op_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000429 0.001800 YES
RMS Displacement 0.000200 0.001200 YES

Link to frequency file: [[File:-FE(CO)6-2+_OP_FREQ.LOG]]

Low frequencies --- -10.5293 -10.5293 -10.5292 -0.0014 -0.0011 -0.0009

Low frequencies --- 82.1285 82.1285 82.1285

<jmol><jmolApplet>
<title>Optimised [FE(CO)6]2+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-FE(CO)6-2+_OP_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Analysing properties ====

{| class="wikitable" border="1"
|+ Bond Length
! Metal complex !! Bond Length(Å)
|-
| [Cr(CO)6] || 1.915
|-
| [Mn(CO)6]+ || 1.908
|-
| [Fe(CO)6]2+ || 1.940
|}

The table above shows the bond metal centre-carbon bond lengths. It shows a decrease moving from Cr to Mn and from Mn to Fe there is an increase. This initial decrease in M-C bond length goes against what was predicted but after speaking to Professor Hunt it turns out a full explanation of this decrease in bond length is too complex for the course and so wont be provided.The later drastic increase is due to a contraction of the d-orbitals causing greater repulsion between the electrons leading to poorer overlap with the CO orbitals meaning less back-bonding and and weaker, so therefore longer, metal-carbon bonds. This agrees with the prediction made earlier.

{| class="wikitable" border="1"
|+ Vibrations table 2
! Metal complex !! Intensity !! Vibration type !! Wavenumber(cm-1)
|-
| [Cr(CO)6] || 1637 || symmetric stretch || 2086
|-
| [Mn(CO)6]+ || 879 || symmetric stretch || 2199
|-
| [Fe(CO)6]2+ || 272 || symmetric stretch || 2297
|}

This table above shows the wave-number and intensity all the IR active symmetric stretches of all the metal complexes CO ligands. As each complex has 13 atoms it is expected to have 3(13)-6= 33 vibrational modes but as shown in the vibrational spectra below many of these modes are IR inactive and have intensities of 0, an example of this is the totally symmetric C-O vibrations meaning they cannot be analysed given the fact that they don't appear. As predicted earlier across the period CO bond frequency would increase and this is due to back donation. Whilst back bonding causes an increase in the M-C bond there is also a increase in the CO bond length. The more positive the metal centre means contraction of the d-orbitals and this means that their is a less overlap between the d-orbital and CO pi* orbital and the less overlap with this orbital the stronger the CO bond.

[[File:Cr_vibrational_spectrum.PNG]] Cr complex Vibrational spectrum

[[File:Mn_vibrational_spectrum.PNG]] Mn complex Vibrational spectrum

[[File:Fe_vibrational_spectrum.PNG]] Fe complex Vibrational spectrum

The images below are three of the molecular orbitals of the [Fe(CO)6]2+ complex with the corresponding LCAO drawn beside them. Also on the diagrams of the LCAOs there are annotations analysing the structure.

[[File:Real_MO_37.PNG]] [[File:LCAO MO 36.PNG || 500px ]]

bonding MO 36 (eg)

[[File:Real_MO_46_take_2.PNG]] [[File:LCAO_MO_46.PNG || 500px ]]

bonding MO 46 (t1g)

[[File:Real_mo_LUMO_take_2.PNG]] [[File:LCAO MO 50 LUMO.PNG || 500px ]]

anti-bonding MO 50 (LUMO/eg)

=== References ===

[1]- Hunt. T, [online] Huntresearchgroup.org.uk, Available at: http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf [Accessed 20 May 2019].

[2]- T. L. Cottrell,The Strengths of Chemical Bonds,2nd ed, Butterworth, London, 1958

File:LCAO MO 46.PNG

2019-05-24T15:09:16Z

Jh3817:

JoeWiki1

2019-05-24T15:03:26Z

Jh3817:

== Year 2 Inorganic comp labs ==

=== BH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p),
Symmetry= D3h

[[File:BH3_info.PNG]]

Item Value Threshold Converged?

Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

Link to frequency file: [[File:JH_BH3_FREQ.LOG]]

Low frequencies --- -0.4072 -0.1962 -0.0055 25.2514 27.2430 27.2460

Low frequencies --- 1163.1897 1213.3128 1213.3155

<jmol><jmolApplet>
<title>Optimised BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JH_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Vibration Data ====

{| class="wikitable" border="1"
|+ Vibrations table
! Stretch or Bend? !! Intensity !! Symmetry !! IR active? !! Wavenumber(cm-1)
|-
| Bend || 92 || A2" || Yes || 1163
|-
| Bend || 14 || E' || Yes || 1213
|-
| Bend || 14 || E' || Yes || 1213
|-
| Symmetric Stretch || 0 || A1' || No || 2581
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|}

[[File:BH3_vibrations_spectrum_JH.PNG]]

Spectrum shows 3 peaks out of 6 vibrational modes given by BH3 shown in table. 1 is IR in active leaving 5 as it causes no change in dipole in the molecule. Two pairs in the 5 are degenerate meaning they have the same energy and therefore overlap, meaning only 3 peaks show.

[[File:MO_diagram_JH.PNG]] [1]

The LCAOs seem very accurate as they depict AOs which combine to form the real MOs very well. Minor issues arise from the fact that it can be said that the overlapping of the orbitals may not be able to be seen fully and the fact that the sizes of the AOs, which represents contribution isn’t consistent. Hydrogen is more electronegative then boron and is therefore lower in energy. Hydrogen should be contributing more to the bonding orbitals and born should be contributing more to the anti-bonding orbitals but for some of them this might not be able to be seen accurately. This shows that the LCAO is a useful tool for finding what a real MO would look like.

=== NH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:NH3_point_group_summary.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES

Link to frequency file: [[File:NH3_OP_JH.LOG]]

Low frequencies --- -8.5628 -8.5571 -0.0047 0.0454 0.1785 26.4189

Low frequencies --- 1089.7603 1694.1865 1694.1865

<jmol><jmolApplet>
<title>Optimised NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3_OP_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:BH3NH3_point_group_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000514 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

Link to frequency file: [[File:NH3BH3_FREQ_NEW.LOG]]

Low frequencies --- -0.0005 0.0003 0.0014 16.7270 18.7414 42.2600

Low frequencies --- 266.2799 632.3010 639.2486

<jmol><jmolApplet>
<title>Optimised NH3BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3BH3_FREQ_NEW.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Association energies ====
E(NH3)= -56.55776863 a.u.

E(BH3)= -26.61532362 a.u.

E(NH3BH3)= -83.22469031 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)], Therefore ΔE= (-83.22468960) - [(-56.55776863)+(-26.61532362)]= -0.05159806 a.u. (-134 KJ/Mol)

The B-N dative bond is weak and this shown when compared to the Al-N bond which has an energy of 297KJ/Mol [2]

=== NI3 ===
Method= RB3LYP,
Basis set= Gen

[[File:New_NI3_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000102 0.000450 YES
RMS Force 0.000075 0.000300 YES
Maximum Displacement 0.000858 0.001800 YES
RMS Displacement 0.000629 0.001200 YES

Link to frequency file: [[File:NEW_NI3_JH.LOG]]

Low frequencies --- -12.3845 -12.3781 -5.6129 -0.0040 0.0194 0.0711

Low frequencies --- 100.9307 100.9314 147.2333

<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NEW_NI3_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised B-I bond distance is 2.18 angstrom

===Days 2 and 3 Project: Metal carbonyls===
This sections of the wiki page focuses on metal carbonyls, more specifically their bond-lengths and CO bond frequencies. The metal-complexes which will be focused on are [Cr(CO)6], [Mn(CO)6]+ and [Fe(CO)6]2+. These were chosen as they come one after another in the d-block so it would be interesting to see how bond-lengths and bond frequencies vary across the period. 2 of the complexes are charged (positively) while one is neutral and this is something which must be taken into account when analysing bond-lengths and bond frequencies. An initial prediction would be that bond length increases across a period (as the metal complexes are becoming more positive meaning less overlap with the CO pi* and overall less back-donation and since back donation strengths the M-C bond less of this means an increases in bond length) and that bond frequencies increases.

==== [Cr(CO)6] ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Cr

[[File:Cr(CO)6_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000110 0.000450 YES
RMS Force 0.000041 0.000300 YES
Maximum Displacement 0.000705 0.001800 YES
RMS Displacement 0.000334 0.001200 YES

Link to frequency file: [[File:CR(CO)6_JH_2.LOG]]

Low frequencies --- -0.0014 -0.0013 -0.0010 11.7482 11.7482 11.7482

Low frequencies --- 66.6574 66.6574 66.6574

<jmol><jmolApplet>
<title>Optimised Cr(CO)6 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>CR(CO)6_JH_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Mn(CO)6]+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Mn

[[File:-Mn(CO)62+_summary_JH3817.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000430 0.001800 YES
RMS Displacement 0.000204 0.001200 YES

Link to frequency file: [[File:-MN(CO)6-+_OP_FREQ_JH.LOG]]

Low frequencies --- -0.0007 0.0006 0.0009 4.7607 4.7607 4.7607

Low frequencies --- 76.3202 76.3202 76.3202

<jmol><jmolApplet>
<title>Optimised [Mn(CO)6]+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-MN(CO)6-+_OP_FREQ_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Fe(CO)6]2+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Fe

[[File:-Fe(CO)6-2+_freq_op_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000429 0.001800 YES
RMS Displacement 0.000200 0.001200 YES

Link to frequency file: [[File:-FE(CO)6-2+_OP_FREQ.LOG]]

Low frequencies --- -10.5293 -10.5293 -10.5292 -0.0014 -0.0011 -0.0009

Low frequencies --- 82.1285 82.1285 82.1285

<jmol><jmolApplet>
<title>Optimised [FE(CO)6]2+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-FE(CO)6-2+_OP_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Analysing properties ====

{| class="wikitable" border="1"
|+ Bond Length
! Metal complex !! Bond Length(Å)
|-
| [Cr(CO)6] || 1.915
|-
| [Mn(CO)6]+ || 1.908
|-
| [Fe(CO)6]2+ || 1.940
|}

The table above shows the bond metal centre-carbon bond lengths. It shows a decrease moving from Cr to Mn and from Mn to Fe there is an increase. This initial decrease in M-C bond length goes against what was predicted but after speaking to Professor Hunt it turns out a full explanation of this decrease in bond length is too complex for the course and so wont be provided.The later drastic increase is due to a contraction of the d-orbitals causing greater repulsion between the electrons leading to poorer overlap with the CO orbitals meaning less back-bonding and and weaker, so therefore longer, metal-carbon bonds. This agrees with the prediction made earlier.

{| class="wikitable" border="1"
|+ Vibrations table 2
! Metal complex !! Intensity !! Vibration type !! Wavenumber(cm-1)
|-
| [Cr(CO)6] || 1637 || symmetric stretch || 2086
|-
| [Mn(CO)6]+ || 879 || symmetric stretch || 2199
|-
| [Fe(CO)6]2+ || 272 || symmetric stretch || 2297
|}

This table above shows the wave-number and intensity all the IR active symmetric stretches of all the metal complexes CO ligands. As each complex has 13 atoms it is expected to have 3(13)-6= 33 vibrational modes but as shown in the vibrational spectra below many of these modes are IR inactive and have intensities of 0, an example of this is the totally symmetric C-O vibrations meaning they cannot be analysed given the fact that they don't appear. As predicted earlier across the period CO bond frequency would increase and this is due to back donation. Whilst back bonding causes an increase in the M-C bond there is also a increase in the CO bond length. The more positive the metal centre means contraction of the d-orbitals and this means that their is a less overlap between the d-orbital and CO pi* orbital and the less overlap with this orbital the stronger the CO bond.

[[File:Cr_vibrational_spectrum.PNG]] Cr complex Vibrational spectrum

[[File:Mn_vibrational_spectrum.PNG]] Mn complex Vibrational spectrum

[[File:Fe_vibrational_spectrum.PNG]] Fe complex Vibrational spectrum

The images below are three of the molecular orbitals of the [Fe(CO)6]2+ complex with the corresponding LCAO drawn beside them. Also on the diagrams of the LCAOs there are annotations analysing the structure.

[[File:Real_MO_37.PNG]] [[File:LCAO MO 36.PNG || 500px ]]

bonding MO 36 (eg)

[[File:Real_MO_46_take_2.PNG]] [[File:MO_46_LCAO.PNG || 500px ]]

bonding MO 46 (t1g)

[[File:Real_mo_LUMO_take_2.PNG]] [[File:LCAO MO 50 LUMO.PNG || 500px ]]

anti-bonding MO 50 (LUMO/eg)

=== References ===

[1]- Hunt. T, [online] Huntresearchgroup.org.uk, Available at: http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf [Accessed 20 May 2019].

[2]- T. L. Cottrell,The Strengths of Chemical Bonds,2nd ed, Butterworth, London, 1958

JoeWiki1

2019-05-24T15:02:50Z

Jh3817: /* Days 2 and 3 Project: Metal carbonyls */

== Year 2 Inorganic comp labs ==

=== BH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p),
Symmetry= D3h

[[File:BH3_info.PNG]]

Item Value Threshold Converged?

Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

Link to frequency file: [[File:JH_BH3_FREQ.LOG]]

Low frequencies --- -0.4072 -0.1962 -0.0055 25.2514 27.2430 27.2460

Low frequencies --- 1163.1897 1213.3128 1213.3155

<jmol><jmolApplet>
<title>Optimised BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JH_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Vibration Data ====

{| class="wikitable" border="1"
|+ Vibrations table
! Stretch or Bend? !! Intensity !! Symmetry !! IR active? !! Wavenumber(cm-1)
|-
| Bend || 92 || A2" || Yes || 1163
|-
| Bend || 14 || E' || Yes || 1213
|-
| Bend || 14 || E' || Yes || 1213
|-
| Symmetric Stretch || 0 || A1' || No || 2581
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|}

[[File:BH3_vibrations_spectrum_JH.PNG]]

Spectrum shows 3 peaks out of 6 vibrational modes given by BH3 shown in table. 1 is IR in active leaving 5 as it causes no change in dipole in the molecule. Two pairs in the 5 are degenerate meaning they have the same energy and therefore overlap, meaning only 3 peaks show.

[[File:MO_diagram_JH.PNG]] [1]

The LCAOs seem very accurate as they depict AOs which combine to form the real MOs very well. Minor issues arise from the fact that it can be said that the overlapping of the orbitals may not be able to be seen fully and the fact that the sizes of the AOs, which represents contribution isn’t consistent. Hydrogen is more electronegative then boron and is therefore lower in energy. Hydrogen should be contributing more to the bonding orbitals and born should be contributing more to the anti-bonding orbitals but for some of them this might not be able to be seen accurately. This shows that the LCAO is a useful tool for finding what a real MO would look like.

=== NH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:NH3_point_group_summary.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES

Link to frequency file: [[File:NH3_OP_JH.LOG]]

Low frequencies --- -8.5628 -8.5571 -0.0047 0.0454 0.1785 26.4189

Low frequencies --- 1089.7603 1694.1865 1694.1865

<jmol><jmolApplet>
<title>Optimised NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3_OP_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:BH3NH3_point_group_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000514 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

Link to frequency file: [[File:NH3BH3_FREQ_NEW.LOG]]

Low frequencies --- -0.0005 0.0003 0.0014 16.7270 18.7414 42.2600

Low frequencies --- 266.2799 632.3010 639.2486

<jmol><jmolApplet>
<title>Optimised NH3BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3BH3_FREQ_NEW.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Association energies ====
E(NH3)= -56.55776863 a.u.

E(BH3)= -26.61532362 a.u.

E(NH3BH3)= -83.22469031 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)], Therefore ΔE= (-83.22468960) - [(-56.55776863)+(-26.61532362)]= -0.05159806 a.u. (-134 KJ/Mol)

The B-N dative bond is weak and this shown when compared to the Al-N bond which has an energy of 297KJ/Mol [2]

=== NI3 ===
Method= RB3LYP,
Basis set= Gen

[[File:New_NI3_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000102 0.000450 YES
RMS Force 0.000075 0.000300 YES
Maximum Displacement 0.000858 0.001800 YES
RMS Displacement 0.000629 0.001200 YES

Link to frequency file: [[File:NEW_NI3_JH.LOG]]

Low frequencies --- -12.3845 -12.3781 -5.6129 -0.0040 0.0194 0.0711

Low frequencies --- 100.9307 100.9314 147.2333

<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NEW_NI3_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised B-I bond distance is 2.18 angstrom

===Days 2 and 3 Project: Metal carbonyls===
This sections of the wiki page focuses on metal carbonyls, more specifically their bond-lengths and CO bond frequencies. The metal-complexes which will be focused on are [Cr(CO)6], [Mn(CO)6]+ and [Fe(CO)6]2+. These were chosen as they come one after another in the d-block so it would be interesting to see how bond-lengths and bond frequencies vary across the period. 2 of the complexes are charged (positively) while one is neutral and this is something which must be taken into account when analysing bond-lengths and bond frequencies. An initial prediction would be that bond length increases across a period (as the metal complexes are becoming more positive meaning less overlap with the CO pi* and overall less back-donation and since back donation strengths the M-C bond less of this means an increases in bond length) and that bond frequencies increases.

==== [Cr(CO)6] ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Cr

[[File:Cr(CO)6_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000110 0.000450 YES
RMS Force 0.000041 0.000300 YES
Maximum Displacement 0.000705 0.001800 YES
RMS Displacement 0.000334 0.001200 YES

Link to frequency file: [[File:CR(CO)6_JH_2.LOG]]

Low frequencies --- -0.0014 -0.0013 -0.0010 11.7482 11.7482 11.7482

Low frequencies --- 66.6574 66.6574 66.6574

<jmol><jmolApplet>
<title>Optimised Cr(CO)6 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>CR(CO)6_JH_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Mn(CO)6]+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Mn

[[File:-Mn(CO)62+_summary_JH3817.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000430 0.001800 YES
RMS Displacement 0.000204 0.001200 YES

Link to frequency file: [[File:-MN(CO)6-+_OP_FREQ_JH.LOG]]

Low frequencies --- -0.0007 0.0006 0.0009 4.7607 4.7607 4.7607

Low frequencies --- 76.3202 76.3202 76.3202

<jmol><jmolApplet>
<title>Optimised [Mn(CO)6]+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-MN(CO)6-+_OP_FREQ_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Fe(CO)6]2+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Fe

[[File:-Fe(CO)6-2+_freq_op_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000429 0.001800 YES
RMS Displacement 0.000200 0.001200 YES

Link to frequency file: [[File:-FE(CO)6-2+_OP_FREQ.LOG]]

Low frequencies --- -10.5293 -10.5293 -10.5292 -0.0014 -0.0011 -0.0009

Low frequencies --- 82.1285 82.1285 82.1285

<jmol><jmolApplet>
<title>Optimised [FE(CO)6]2+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-FE(CO)6-2+_OP_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Analysing properties ====

{| class="wikitable" border="1"
|+ Bond Length
! Metal complex !! Bond Length(Å)
|-
| [Cr(CO)6] || 1.915
|-
| [Mn(CO)6]+ || 1.908
|-
| [Fe(CO)6]2+ || 1.940
|}

The table above shows the bond metal centre-carbon bond lengths. It shows a decrease moving from Cr to Mn and from Mn to Fe there is an increase. This initial decrease in M-C bond length goes against what was predicted but after speaking to Professor Hunt it turns out a full explanation of this decrease in bond length is too complex for the course and so wont be provided.The later drastic increase is due to a contraction of the d-orbitals causing greater repulsion between the electrons leading to poorer overlap with the CO orbitals meaning less back-bonding and and weaker, so therefore longer, metal-carbon bonds. This agrees with the prediction made earlier.

{| class="wikitable" border="1"
|+ Vibrations table 2
! Metal complex !! Intensity !! Vibration type !! Wavenumber(cm-1)
|-
| [Cr(CO)6] || 1637 || symmetric stretch || 2086
|-
| [Mn(CO)6]+ || 879 || symmetric stretch || 2199
|-
| [Fe(CO)6]2+ || 272 || symmetric stretch || 2297
|}

This table above shows the wave-number and intensity all the IR active symmetric stretches of all the metal complexes CO ligands. As each complex has 13 atoms it is expected to have 3(13)-6= 33 vibrational modes but as shown in the vibrational spectra below many of these modes are IR inactive and have intensities of 0, an example of this is the totally symmetric C-O vibrations meaning they cannot be analysed given the fact that they don't appear. As predicted earlier across the period CO bond frequency would increase and this is due to back donation. Whilst back bonding causes an increase in the M-C bond there is also a increase in the CO bond length. The more positive the metal centre means contraction of the d-orbitals and this means that their is a less overlap between the d-orbital and CO pi* orbital and the less overlap with this orbital the stronger the CO bond.

[[File:Cr_vibrational_spectrum.PNG]] Cr complex Vibrational spectrum

[[File:Mn_vibrational_spectrum.PNG]] Mn complex Vibrational spectrum

[[File:Fe_vibrational_spectrum.PNG]] Fe complex Vibrational spectrum

The images below are three of the molecular orbitals of the [Fe(CO)6]2+ complex with the corresponding LCAO drawn beside them. Also on the diagrams of the LCAOs there are annotations analysing the structure.

[[File:Real_MO_37.PNG]] [[File:LCAO MO 36.PNG || 500px ]]

bonding MO 36 (eg)

[[File:Real_MO_46_take_2.PNG]] [[File:MO_46_LCAO.PNG || 500px ]]

bonding MO 46 (t1g)

[[File:Real_mo_LUMO_take_2.PNG] [[File:LCAO MO 50 LUMO.PNG || 500px ]]

anti-bonding MO 50 (LUMO/eg)

=== References ===

[1]- Hunt. T, [online] Huntresearchgroup.org.uk, Available at: http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf [Accessed 20 May 2019].

[2]- T. L. Cottrell,The Strengths of Chemical Bonds,2nd ed, Butterworth, London, 1958

File:Real mo LUMO take 2.PNG

2019-05-24T15:02:12Z

Jh3817:

JoeWiki1

2019-05-24T14:50:49Z

Jh3817: /* Analysing properties */

== Year 2 Inorganic comp labs ==

=== BH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p),
Symmetry= D3h

[[File:BH3_info.PNG]]

Item Value Threshold Converged?

Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

Link to frequency file: [[File:JH_BH3_FREQ.LOG]]

Low frequencies --- -0.4072 -0.1962 -0.0055 25.2514 27.2430 27.2460

Low frequencies --- 1163.1897 1213.3128 1213.3155

<jmol><jmolApplet>
<title>Optimised BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JH_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Vibration Data ====

{| class="wikitable" border="1"
|+ Vibrations table
! Stretch or Bend? !! Intensity !! Symmetry !! IR active? !! Wavenumber(cm-1)
|-
| Bend || 92 || A2" || Yes || 1163
|-
| Bend || 14 || E' || Yes || 1213
|-
| Bend || 14 || E' || Yes || 1213
|-
| Symmetric Stretch || 0 || A1' || No || 2581
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|}

[[File:BH3_vibrations_spectrum_JH.PNG]]

Spectrum shows 3 peaks out of 6 vibrational modes given by BH3 shown in table. 1 is IR in active leaving 5 as it causes no change in dipole in the molecule. Two pairs in the 5 are degenerate meaning they have the same energy and therefore overlap, meaning only 3 peaks show.

[[File:MO_diagram_JH.PNG]] [1]

The LCAOs seem very accurate as they depict AOs which combine to form the real MOs very well. Minor issues arise from the fact that it can be said that the overlapping of the orbitals may not be able to be seen fully and the fact that the sizes of the AOs, which represents contribution isn’t consistent. Hydrogen is more electronegative then boron and is therefore lower in energy. Hydrogen should be contributing more to the bonding orbitals and born should be contributing more to the anti-bonding orbitals but for some of them this might not be able to be seen accurately. This shows that the LCAO is a useful tool for finding what a real MO would look like.

=== NH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:NH3_point_group_summary.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES

Link to frequency file: [[File:NH3_OP_JH.LOG]]

Low frequencies --- -8.5628 -8.5571 -0.0047 0.0454 0.1785 26.4189

Low frequencies --- 1089.7603 1694.1865 1694.1865

<jmol><jmolApplet>
<title>Optimised NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3_OP_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:BH3NH3_point_group_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000514 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

Link to frequency file: [[File:NH3BH3_FREQ_NEW.LOG]]

Low frequencies --- -0.0005 0.0003 0.0014 16.7270 18.7414 42.2600

Low frequencies --- 266.2799 632.3010 639.2486

<jmol><jmolApplet>
<title>Optimised NH3BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3BH3_FREQ_NEW.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Association energies ====
E(NH3)= -56.55776863 a.u.

E(BH3)= -26.61532362 a.u.

E(NH3BH3)= -83.22469031 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)], Therefore ΔE= (-83.22468960) - [(-56.55776863)+(-26.61532362)]= -0.05159806 a.u. (-134 KJ/Mol)

The B-N dative bond is weak and this shown when compared to the Al-N bond which has an energy of 297KJ/Mol [2]

=== NI3 ===
Method= RB3LYP,
Basis set= Gen

[[File:New_NI3_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000102 0.000450 YES
RMS Force 0.000075 0.000300 YES
Maximum Displacement 0.000858 0.001800 YES
RMS Displacement 0.000629 0.001200 YES

Link to frequency file: [[File:NEW_NI3_JH.LOG]]

Low frequencies --- -12.3845 -12.3781 -5.6129 -0.0040 0.0194 0.0711

Low frequencies --- 100.9307 100.9314 147.2333

<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NEW_NI3_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised B-I bond distance is 2.18 angstrom

===Days 2 and 3 Project: Metal carbonyls===
This sections of the wiki page focuses on metal carbonyls, more specifically their bond-lengths and CO bond frequencies. The metal-complexes which will be focused on are [Cr(CO)6], [Mn(CO)6]+ and [Fe(CO)6]2+. These were chosen as they come one after another in the d-block so it would be interesting to see how bond-lengths and bond frequencies vary across the period. 2 of the complexes are charged (positively) while one is neutral and this is something which must be taken into account when analysing bond-lengths and bond frequencies. An initial prediction would be that bond length increases across a period (as the metal complexes are becoming more positive meaning less overlap with the CO pi* and overall less back-donation and since back donation strengths the M-C bond less of this means an increases in bond length) and that bond frequencies increases.

==== [Cr(CO)6] ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Cr

[[File:Cr(CO)6_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000110 0.000450 YES
RMS Force 0.000041 0.000300 YES
Maximum Displacement 0.000705 0.001800 YES
RMS Displacement 0.000334 0.001200 YES

Link to frequency file: [[File:CR(CO)6_JH_2.LOG]]

Low frequencies --- -0.0014 -0.0013 -0.0010 11.7482 11.7482 11.7482

Low frequencies --- 66.6574 66.6574 66.6574

<jmol><jmolApplet>
<title>Optimised Cr(CO)6 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>CR(CO)6_JH_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Mn(CO)6]+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Mn

[[File:-Mn(CO)62+_summary_JH3817.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000430 0.001800 YES
RMS Displacement 0.000204 0.001200 YES

Link to frequency file: [[File:-MN(CO)6-+_OP_FREQ_JH.LOG]]

Low frequencies --- -0.0007 0.0006 0.0009 4.7607 4.7607 4.7607

Low frequencies --- 76.3202 76.3202 76.3202

<jmol><jmolApplet>
<title>Optimised [Mn(CO)6]+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-MN(CO)6-+_OP_FREQ_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Fe(CO)6]2+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Fe

[[File:-Fe(CO)6-2+_freq_op_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000429 0.001800 YES
RMS Displacement 0.000200 0.001200 YES

Link to frequency file: [[File:-FE(CO)6-2+_OP_FREQ.LOG]]

Low frequencies --- -10.5293 -10.5293 -10.5292 -0.0014 -0.0011 -0.0009

Low frequencies --- 82.1285 82.1285 82.1285

<jmol><jmolApplet>
<title>Optimised [FE(CO)6]2+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-FE(CO)6-2+_OP_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Analysing properties ====

{| class="wikitable" border="1"
|+ Bond Length
! Metal complex !! Bond Length(Å)
|-
| [Cr(CO)6] || 1.915
|-
| [Mn(CO)6]+ || 1.908
|-
| [Fe(CO)6]2+ || 1.940
|}

The table above shows the bond metal centre-carbon bond lengths. It shows a decrease moving from Cr to Mn and from Mn to Fe there is an increase. This initial decrease in M-C bond length goes against what was predicted but after speaking to Professor Hunt it turns out a full explanation of this decrease in bond length is too complex for the course and so wont be provided.The later drastic increase is due to a contraction of the d-orbitals causing greater repulsion between the electrons leading to poorer overlap with the CO orbitals meaning less back-bonding and and weaker, so therefore longer, metal-carbon bonds. This agrees with the prediction made earlier.

{| class="wikitable" border="1"
|+ Vibrations table 2
! Metal complex !! Intensity !! Vibration type !! Wavenumber(cm-1)
|-
| [Cr(CO)6] || 1637 || symmetric stretch || 2086
|-
| [Mn(CO)6]+ || 879 || symmetric stretch || 2199
|-
| [Fe(CO)6]2+ || 272 || symmetric stretch || 2297
|}

This table above shows the wave-number and intensity all the IR active symmetric stretches of all the metal complexes CO ligands. As each complex has 13 atoms it is expected to have 3(13)-6= 33 vibrational modes but as shown in the vibrational spectra below many of these modes are IR inactive and have intensities of 0, an example of this is the totally symmetric C-O vibrations meaning they cannot be analysed given the fact that they don't appear. As predicted earlier across the period CO bond frequency would increase and this is due to back donation. Whilst back bonding causes an increase in the M-C bond there is also a increase in the CO bond length. The more positive the metal centre means contraction of the d-orbitals and this means that their is a less overlap between the d-orbital and CO pi* orbital and the less overlap with this orbital the stronger the CO bond.

[[File:Cr_vibrational_spectrum.PNG]] Cr complex Vibrational spectrum

[[File:Mn_vibrational_spectrum.PNG]] Mn complex Vibrational spectrum

[[File:Fe_vibrational_spectrum.PNG]] Fe complex Vibrational spectrum

The images below are three of the molecular orbitals of the [Fe(CO)6]2+ complex with the corresponding LCAO drawn beside them. Also on the diagrams of the LCAOs there are annotations analysing the structure.

[[File:Real_MO_37.PNG]] [[File:LCAO MO 36.PNG || 500px ]]

bonding MO 36 (eg)

[[File:Real_MO_46_take_2.PNG]] [[File:MO_46_LCAO.PNG || 500px ]]

bonding MO 46 (t1g)

[[File:Real MO 50 LUMO.PNG]] [[File:LCAO MO 50 LUMO.PNG || 500px ]]

anti-bonding MO 50 (LUMO/eg)

=== References ===

[1]- Hunt. T, [online] Huntresearchgroup.org.uk, Available at: http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf [Accessed 20 May 2019].

[2]- T. L. Cottrell,The Strengths of Chemical Bonds,2nd ed, Butterworth, London, 1958

File:Real MO 46 take 2.PNG

2019-05-24T14:50:25Z

Jh3817:

JoeWiki1

2019-05-24T14:13:09Z

Jh3817: /* Analysing properties */

== Year 2 Inorganic comp labs ==

=== BH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p),
Symmetry= D3h

[[File:BH3_info.PNG]]

Item Value Threshold Converged?

Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

Link to frequency file: [[File:JH_BH3_FREQ.LOG]]

Low frequencies --- -0.4072 -0.1962 -0.0055 25.2514 27.2430 27.2460

Low frequencies --- 1163.1897 1213.3128 1213.3155

<jmol><jmolApplet>
<title>Optimised BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JH_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Vibration Data ====

{| class="wikitable" border="1"
|+ Vibrations table
! Stretch or Bend? !! Intensity !! Symmetry !! IR active? !! Wavenumber(cm-1)
|-
| Bend || 92 || A2" || Yes || 1163
|-
| Bend || 14 || E' || Yes || 1213
|-
| Bend || 14 || E' || Yes || 1213
|-
| Symmetric Stretch || 0 || A1' || No || 2581
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|}

[[File:BH3_vibrations_spectrum_JH.PNG]]

Spectrum shows 3 peaks out of 6 vibrational modes given by BH3 shown in table. 1 is IR in active leaving 5 as it causes no change in dipole in the molecule. Two pairs in the 5 are degenerate meaning they have the same energy and therefore overlap, meaning only 3 peaks show.

[[File:MO_diagram_JH.PNG]] [1]

The LCAOs seem very accurate as they depict AOs which combine to form the real MOs very well. Minor issues arise from the fact that it can be said that the overlapping of the orbitals may not be able to be seen fully and the fact that the sizes of the AOs, which represents contribution isn’t consistent. Hydrogen is more electronegative then boron and is therefore lower in energy. Hydrogen should be contributing more to the bonding orbitals and born should be contributing more to the anti-bonding orbitals but for some of them this might not be able to be seen accurately. This shows that the LCAO is a useful tool for finding what a real MO would look like.

=== NH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:NH3_point_group_summary.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES

Link to frequency file: [[File:NH3_OP_JH.LOG]]

Low frequencies --- -8.5628 -8.5571 -0.0047 0.0454 0.1785 26.4189

Low frequencies --- 1089.7603 1694.1865 1694.1865

<jmol><jmolApplet>
<title>Optimised NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3_OP_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:BH3NH3_point_group_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000514 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

Link to frequency file: [[File:NH3BH3_FREQ_NEW.LOG]]

Low frequencies --- -0.0005 0.0003 0.0014 16.7270 18.7414 42.2600

Low frequencies --- 266.2799 632.3010 639.2486

<jmol><jmolApplet>
<title>Optimised NH3BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3BH3_FREQ_NEW.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Association energies ====
E(NH3)= -56.55776863 a.u.

E(BH3)= -26.61532362 a.u.

E(NH3BH3)= -83.22469031 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)], Therefore ΔE= (-83.22468960) - [(-56.55776863)+(-26.61532362)]= -0.05159806 a.u. (-134 KJ/Mol)

The B-N dative bond is weak and this shown when compared to the Al-N bond which has an energy of 297KJ/Mol [2]

=== NI3 ===
Method= RB3LYP,
Basis set= Gen

[[File:New_NI3_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000102 0.000450 YES
RMS Force 0.000075 0.000300 YES
Maximum Displacement 0.000858 0.001800 YES
RMS Displacement 0.000629 0.001200 YES

Link to frequency file: [[File:NEW_NI3_JH.LOG]]

Low frequencies --- -12.3845 -12.3781 -5.6129 -0.0040 0.0194 0.0711

Low frequencies --- 100.9307 100.9314 147.2333

<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NEW_NI3_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised B-I bond distance is 2.18 angstrom

===Days 2 and 3 Project: Metal carbonyls===
This sections of the wiki page focuses on metal carbonyls, more specifically their bond-lengths and CO bond frequencies. The metal-complexes which will be focused on are [Cr(CO)6], [Mn(CO)6]+ and [Fe(CO)6]2+. These were chosen as they come one after another in the d-block so it would be interesting to see how bond-lengths and bond frequencies vary across the period. 2 of the complexes are charged (positively) while one is neutral and this is something which must be taken into account when analysing bond-lengths and bond frequencies. An initial prediction would be that bond length increases across a period (as the metal complexes are becoming more positive meaning less overlap with the CO pi* and overall less back-donation and since back donation strengths the M-C bond less of this means an increases in bond length) and that bond frequencies increases.

==== [Cr(CO)6] ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Cr

[[File:Cr(CO)6_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000110 0.000450 YES
RMS Force 0.000041 0.000300 YES
Maximum Displacement 0.000705 0.001800 YES
RMS Displacement 0.000334 0.001200 YES

Link to frequency file: [[File:CR(CO)6_JH_2.LOG]]

Low frequencies --- -0.0014 -0.0013 -0.0010 11.7482 11.7482 11.7482

Low frequencies --- 66.6574 66.6574 66.6574

<jmol><jmolApplet>
<title>Optimised Cr(CO)6 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>CR(CO)6_JH_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Mn(CO)6]+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Mn

[[File:-Mn(CO)62+_summary_JH3817.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000430 0.001800 YES
RMS Displacement 0.000204 0.001200 YES

Link to frequency file: [[File:-MN(CO)6-+_OP_FREQ_JH.LOG]]

Low frequencies --- -0.0007 0.0006 0.0009 4.7607 4.7607 4.7607

Low frequencies --- 76.3202 76.3202 76.3202

<jmol><jmolApplet>
<title>Optimised [Mn(CO)6]+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-MN(CO)6-+_OP_FREQ_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Fe(CO)6]2+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Fe

[[File:-Fe(CO)6-2+_freq_op_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000429 0.001800 YES
RMS Displacement 0.000200 0.001200 YES

Link to frequency file: [[File:-FE(CO)6-2+_OP_FREQ.LOG]]

Low frequencies --- -10.5293 -10.5293 -10.5292 -0.0014 -0.0011 -0.0009

Low frequencies --- 82.1285 82.1285 82.1285

<jmol><jmolApplet>
<title>Optimised [FE(CO)6]2+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-FE(CO)6-2+_OP_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Analysing properties ====

{| class="wikitable" border="1"
|+ Bond Length
! Metal complex !! Bond Length(Å)
|-
| [Cr(CO)6] || 1.915
|-
| [Mn(CO)6]+ || 1.908
|-
| [Fe(CO)6]2+ || 1.940
|}

The table above shows the bond metal centre-carbon bond lengths. It shows a decrease moving from Cr to Mn and from Mn to Fe there is an increase. This initial decrease in M-C bond length goes against what was predicted but after speaking to Professor Hunt it turns out a full explanation of this decrease in bond length is too complex for the course and so wont be provided.The later drastic increase is due to a contraction of the d-orbitals causing greater repulsion between the electrons leading to poorer overlap with the CO orbitals meaning less back-bonding and and weaker, so therefore longer, metal-carbon bonds. This agrees with the prediction made earlier.

{| class="wikitable" border="1"
|+ Vibrations table 2
! Metal complex !! Intensity !! Vibration type !! Wavenumber(cm-1)
|-
| [Cr(CO)6] || 1637 || symmetric stretch || 2086
|-
| [Mn(CO)6]+ || 879 || symmetric stretch || 2199
|-
| [Fe(CO)6]2+ || 272 || symmetric stretch || 2297
|}

This table above shows the wave-number and intensity all the IR active symmetric stretches of all the metal complexes CO ligands. As each complex has 13 atoms it is expected to have 3(13)-6= 33 vibrational modes but as shown in the vibrational spectra below many of these modes are IR inactive and have intensities of 0, an example of this is the totally symmetric C-O vibrations meaning they cannot be analysed given the fact that they don't appear. As predicted earlier across the period CO bond frequency would increase and this is due to back donation. Whilst back bonding causes an increase in the M-C bond there is also a increase in the CO bond length. The more positive the metal centre means contraction of the d-orbitals and this means that their is a less overlap between the d-orbital and CO pi* orbital and the less overlap with this orbital the stronger the CO bond.

[[File:Cr_vibrational_spectrum.PNG]] Cr complex Vibrational spectrum

[[File:Mn_vibrational_spectrum.PNG]] Mn complex Vibrational spectrum

[[File:Fe_vibrational_spectrum.PNG]] Fe complex Vibrational spectrum

The images below are three of the molecular orbitals of the [Fe(CO)6]2+ complex with the corresponding LCAO drawn beside them. Also on the diagrams of the LCAOs there are annotations analysing the structure.

[[File:Real_MO_37.PNG]] [[File:LCAO MO 36.PNG || 500px ]]

bonding MO 36 (eg)

[[File:Real_MO_46.PNG]] [[File:MO_46_LCAO.PNG || 500px ]]

bonding MO 46 (t1g)

[[File:Real MO 50 LUMO.PNG]] [[File:LCAO MO 50 LUMO.PNG || 500px ]]

anti-bonding MO 50 (LUMO/eg)

=== References ===

[1]- Hunt. T, [online] Huntresearchgroup.org.uk, Available at: http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf [Accessed 20 May 2019].

[2]- T. L. Cottrell,The Strengths of Chemical Bonds,2nd ed, Butterworth, London, 1958

JoeWiki1

2019-05-24T14:08:03Z

Jh3817: /* References */

== Year 2 Inorganic comp labs ==

=== BH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p),
Symmetry= D3h

[[File:BH3_info.PNG]]

Item Value Threshold Converged?

Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

Link to frequency file: [[File:JH_BH3_FREQ.LOG]]

Low frequencies --- -0.4072 -0.1962 -0.0055 25.2514 27.2430 27.2460

Low frequencies --- 1163.1897 1213.3128 1213.3155

<jmol><jmolApplet>
<title>Optimised BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JH_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Vibration Data ====

{| class="wikitable" border="1"
|+ Vibrations table
! Stretch or Bend? !! Intensity !! Symmetry !! IR active? !! Wavenumber(cm-1)
|-
| Bend || 92 || A2" || Yes || 1163
|-
| Bend || 14 || E' || Yes || 1213
|-
| Bend || 14 || E' || Yes || 1213
|-
| Symmetric Stretch || 0 || A1' || No || 2581
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|}

[[File:BH3_vibrations_spectrum_JH.PNG]]

Spectrum shows 3 peaks out of 6 vibrational modes given by BH3 shown in table. 1 is IR in active leaving 5 as it causes no change in dipole in the molecule. Two pairs in the 5 are degenerate meaning they have the same energy and therefore overlap, meaning only 3 peaks show.

[[File:MO_diagram_JH.PNG]] [1]

The LCAOs seem very accurate as they depict AOs which combine to form the real MOs very well. Minor issues arise from the fact that it can be said that the overlapping of the orbitals may not be able to be seen fully and the fact that the sizes of the AOs, which represents contribution isn’t consistent. Hydrogen is more electronegative then boron and is therefore lower in energy. Hydrogen should be contributing more to the bonding orbitals and born should be contributing more to the anti-bonding orbitals but for some of them this might not be able to be seen accurately. This shows that the LCAO is a useful tool for finding what a real MO would look like.

=== NH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:NH3_point_group_summary.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES

Link to frequency file: [[File:NH3_OP_JH.LOG]]

Low frequencies --- -8.5628 -8.5571 -0.0047 0.0454 0.1785 26.4189

Low frequencies --- 1089.7603 1694.1865 1694.1865

<jmol><jmolApplet>
<title>Optimised NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3_OP_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:BH3NH3_point_group_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000514 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

Link to frequency file: [[File:NH3BH3_FREQ_NEW.LOG]]

Low frequencies --- -0.0005 0.0003 0.0014 16.7270 18.7414 42.2600

Low frequencies --- 266.2799 632.3010 639.2486

<jmol><jmolApplet>
<title>Optimised NH3BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3BH3_FREQ_NEW.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Association energies ====
E(NH3)= -56.55776863 a.u.

E(BH3)= -26.61532362 a.u.

E(NH3BH3)= -83.22469031 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)], Therefore ΔE= (-83.22468960) - [(-56.55776863)+(-26.61532362)]= -0.05159806 a.u. (-134 KJ/Mol)

The B-N dative bond is weak and this shown when compared to the Al-N bond which has an energy of 297KJ/Mol [2]

=== NI3 ===
Method= RB3LYP,
Basis set= Gen

[[File:New_NI3_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000102 0.000450 YES
RMS Force 0.000075 0.000300 YES
Maximum Displacement 0.000858 0.001800 YES
RMS Displacement 0.000629 0.001200 YES

Link to frequency file: [[File:NEW_NI3_JH.LOG]]

Low frequencies --- -12.3845 -12.3781 -5.6129 -0.0040 0.0194 0.0711

Low frequencies --- 100.9307 100.9314 147.2333

<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NEW_NI3_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised B-I bond distance is 2.18 angstrom

===Days 2 and 3 Project: Metal carbonyls===
This sections of the wiki page focuses on metal carbonyls, more specifically their bond-lengths and CO bond frequencies. The metal-complexes which will be focused on are [Cr(CO)6], [Mn(CO)6]+ and [Fe(CO)6]2+. These were chosen as they come one after another in the d-block so it would be interesting to see how bond-lengths and bond frequencies vary across the period. 2 of the complexes are charged (positively) while one is neutral and this is something which must be taken into account when analysing bond-lengths and bond frequencies. An initial prediction would be that bond length increases across a period (as the metal complexes are becoming more positive meaning less overlap with the CO pi* and overall less back-donation and since back donation strengths the M-C bond less of this means an increases in bond length) and that bond frequencies increases.

==== [Cr(CO)6] ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Cr

[[File:Cr(CO)6_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000110 0.000450 YES
RMS Force 0.000041 0.000300 YES
Maximum Displacement 0.000705 0.001800 YES
RMS Displacement 0.000334 0.001200 YES

Link to frequency file: [[File:CR(CO)6_JH_2.LOG]]

Low frequencies --- -0.0014 -0.0013 -0.0010 11.7482 11.7482 11.7482

Low frequencies --- 66.6574 66.6574 66.6574

<jmol><jmolApplet>
<title>Optimised Cr(CO)6 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>CR(CO)6_JH_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Mn(CO)6]+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Mn

[[File:-Mn(CO)62+_summary_JH3817.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000430 0.001800 YES
RMS Displacement 0.000204 0.001200 YES

Link to frequency file: [[File:-MN(CO)6-+_OP_FREQ_JH.LOG]]

Low frequencies --- -0.0007 0.0006 0.0009 4.7607 4.7607 4.7607

Low frequencies --- 76.3202 76.3202 76.3202

<jmol><jmolApplet>
<title>Optimised [Mn(CO)6]+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-MN(CO)6-+_OP_FREQ_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Fe(CO)6]2+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Fe

[[File:-Fe(CO)6-2+_freq_op_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000429 0.001800 YES
RMS Displacement 0.000200 0.001200 YES

Link to frequency file: [[File:-FE(CO)6-2+_OP_FREQ.LOG]]

Low frequencies --- -10.5293 -10.5293 -10.5292 -0.0014 -0.0011 -0.0009

Low frequencies --- 82.1285 82.1285 82.1285

<jmol><jmolApplet>
<title>Optimised [FE(CO)6]2+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-FE(CO)6-2+_OP_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Analysing properties ====

{| class="wikitable" border="1"
|+ Bond Length
! Metal complex !! Bond Length(Å)
|-
| [Cr(CO)6] || 1.915
|-
| [Mn(CO)6]+ || 1.908
|-
| [Fe(CO)6]2+ || 1.940
|}

The table above shows the bond metal centre-carbon bond lengths. It shows a decrease moving from Cr to Mn and from Mn to Fe there is an increase. This initial decrease in M-C bond length goes against what was predicted but after speaking to Professor Hunt it turns out a full explanation of this decrease in bond length is to complex for the course and so wont be provided.The the later drastic increase is due to a contraction of the d-orbitals causing greater repulsion between the electrons leading to poorer overlap with the CO orbitals meaning less back-bonding and and weaker, so therefore longer, metal-carbon bonds. This agrees with the prediction made earlier.

{| class="wikitable" border="1"
|+ Vibrations table 2
! Metal complex !! Intensity !! Vibration type !! Wavenumber(cm-1)
|-
| [Cr(CO)6] || 1637 || symmetric stretch || 2086
|-
| [Mn(CO)6]+ || 879 || symmetric stretch || 2199
|-
| [Fe(CO)6]2+ || 272 || symmetric stretch || 2297
|}

This table above shows the wave-number and intensity all the IR active symmetric stretches of all the metal complexes CO ligands. As each complex has 13 atoms it is expected to have 3(13)-6= 33 vibrational modes but as shown in the vibrational spectra below many of these modes are IR inactive and have intensities of 0, an example of this is the totally symmetric C-O vibrations meaning they cannot be analysed given the fact that they don't appear. As predicted earlier across the period CO bond frequency would increase and this is due to back donation. Whilst back bonding causes an increase in the M-C bond there is also a increase in the CO bond length. The more positive the metal centre means contraction of the d-orbitals and this means that their is a less overlap between the d-orbital and CO pi* orbital and the less overlap with this orbital the stronger the CO bond.

[[File:Cr_vibrational_spectrum.PNG]] Cr complex Vibrational spectrum

[[File:Mn_vibrational_spectrum.PNG]] Mn complex Vibrational spectrum

[[File:Fe_vibrational_spectrum.PNG]] Fe complex Vibrational spectrum

The images below are three of the molecular orbitals of the [Fe(CO)6]2+ complex with the corresponding LCAO drawn beside them. Also on the diagrams of the LCAOs there are annotations analysing the structure.

[[File:Real_MO_37.PNG]] [[File:LCAO MO 36.PNG || 500px ]]

bonding MO 36 (eg)

[[File:Real_MO_46.PNG]] [[File:MO_46_LCAO.PNG || 500px ]]

bonding MO 46 (t1g)

[[File:Real MO 50 LUMO.PNG]] [[File:LCAO MO 50 LUMO.PNG || 500px ]]

anti-bonding MO 50 (LUMO/eg)

=== References ===

[1]- Hunt. T, [online] Huntresearchgroup.org.uk, Available at: http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf [Accessed 20 May 2019].

[2]- T. L. Cottrell,The Strengths of Chemical Bonds,2nd ed, Butterworth, London, 1958

JoeWiki1

2019-05-24T13:58:44Z

Jh3817: /* Association energies */

== Year 2 Inorganic comp labs ==

=== BH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p),
Symmetry= D3h

[[File:BH3_info.PNG]]

Item Value Threshold Converged?

Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

Link to frequency file: [[File:JH_BH3_FREQ.LOG]]

Low frequencies --- -0.4072 -0.1962 -0.0055 25.2514 27.2430 27.2460

Low frequencies --- 1163.1897 1213.3128 1213.3155

<jmol><jmolApplet>
<title>Optimised BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JH_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Vibration Data ====

{| class="wikitable" border="1"
|+ Vibrations table
! Stretch or Bend? !! Intensity !! Symmetry !! IR active? !! Wavenumber(cm-1)
|-
| Bend || 92 || A2" || Yes || 1163
|-
| Bend || 14 || E' || Yes || 1213
|-
| Bend || 14 || E' || Yes || 1213
|-
| Symmetric Stretch || 0 || A1' || No || 2581
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|}

[[File:BH3_vibrations_spectrum_JH.PNG]]

Spectrum shows 3 peaks out of 6 vibrational modes given by BH3 shown in table. 1 is IR in active leaving 5 as it causes no change in dipole in the molecule. Two pairs in the 5 are degenerate meaning they have the same energy and therefore overlap, meaning only 3 peaks show.

[[File:MO_diagram_JH.PNG]] [1]

The LCAOs seem very accurate as they depict AOs which combine to form the real MOs very well. Minor issues arise from the fact that it can be said that the overlapping of the orbitals may not be able to be seen fully and the fact that the sizes of the AOs, which represents contribution isn’t consistent. Hydrogen is more electronegative then boron and is therefore lower in energy. Hydrogen should be contributing more to the bonding orbitals and born should be contributing more to the anti-bonding orbitals but for some of them this might not be able to be seen accurately. This shows that the LCAO is a useful tool for finding what a real MO would look like.

=== NH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:NH3_point_group_summary.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES

Link to frequency file: [[File:NH3_OP_JH.LOG]]

Low frequencies --- -8.5628 -8.5571 -0.0047 0.0454 0.1785 26.4189

Low frequencies --- 1089.7603 1694.1865 1694.1865

<jmol><jmolApplet>
<title>Optimised NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3_OP_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:BH3NH3_point_group_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000514 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

Link to frequency file: [[File:NH3BH3_FREQ_NEW.LOG]]

Low frequencies --- -0.0005 0.0003 0.0014 16.7270 18.7414 42.2600

Low frequencies --- 266.2799 632.3010 639.2486

<jmol><jmolApplet>
<title>Optimised NH3BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3BH3_FREQ_NEW.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Association energies ====
E(NH3)= -56.55776863 a.u.

E(BH3)= -26.61532362 a.u.

E(NH3BH3)= -83.22469031 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)], Therefore ΔE= (-83.22468960) - [(-56.55776863)+(-26.61532362)]= -0.05159806 a.u. (-134 KJ/Mol)

The B-N dative bond is weak and this shown when compared to the Al-N bond which has an energy of 297KJ/Mol [2]

=== NI3 ===
Method= RB3LYP,
Basis set= Gen

[[File:New_NI3_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000102 0.000450 YES
RMS Force 0.000075 0.000300 YES
Maximum Displacement 0.000858 0.001800 YES
RMS Displacement 0.000629 0.001200 YES

Link to frequency file: [[File:NEW_NI3_JH.LOG]]

Low frequencies --- -12.3845 -12.3781 -5.6129 -0.0040 0.0194 0.0711

Low frequencies --- 100.9307 100.9314 147.2333

<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NEW_NI3_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised B-I bond distance is 2.18 angstrom

===Days 2 and 3 Project: Metal carbonyls===
This sections of the wiki page focuses on metal carbonyls, more specifically their bond-lengths and CO bond frequencies. The metal-complexes which will be focused on are [Cr(CO)6], [Mn(CO)6]+ and [Fe(CO)6]2+. These were chosen as they come one after another in the d-block so it would be interesting to see how bond-lengths and bond frequencies vary across the period. 2 of the complexes are charged (positively) while one is neutral and this is something which must be taken into account when analysing bond-lengths and bond frequencies. An initial prediction would be that bond length increases across a period (as the metal complexes are becoming more positive meaning less overlap with the CO pi* and overall less back-donation and since back donation strengths the M-C bond less of this means an increases in bond length) and that bond frequencies increases.

==== [Cr(CO)6] ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Cr

[[File:Cr(CO)6_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000110 0.000450 YES
RMS Force 0.000041 0.000300 YES
Maximum Displacement 0.000705 0.001800 YES
RMS Displacement 0.000334 0.001200 YES

Link to frequency file: [[File:CR(CO)6_JH_2.LOG]]

Low frequencies --- -0.0014 -0.0013 -0.0010 11.7482 11.7482 11.7482

Low frequencies --- 66.6574 66.6574 66.6574

<jmol><jmolApplet>
<title>Optimised Cr(CO)6 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>CR(CO)6_JH_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Mn(CO)6]+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Mn

[[File:-Mn(CO)62+_summary_JH3817.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000430 0.001800 YES
RMS Displacement 0.000204 0.001200 YES

Link to frequency file: [[File:-MN(CO)6-+_OP_FREQ_JH.LOG]]

Low frequencies --- -0.0007 0.0006 0.0009 4.7607 4.7607 4.7607

Low frequencies --- 76.3202 76.3202 76.3202

<jmol><jmolApplet>
<title>Optimised [Mn(CO)6]+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-MN(CO)6-+_OP_FREQ_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Fe(CO)6]2+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Fe

[[File:-Fe(CO)6-2+_freq_op_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000429 0.001800 YES
RMS Displacement 0.000200 0.001200 YES

Link to frequency file: [[File:-FE(CO)6-2+_OP_FREQ.LOG]]

Low frequencies --- -10.5293 -10.5293 -10.5292 -0.0014 -0.0011 -0.0009

Low frequencies --- 82.1285 82.1285 82.1285

<jmol><jmolApplet>
<title>Optimised [FE(CO)6]2+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-FE(CO)6-2+_OP_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Analysing properties ====

{| class="wikitable" border="1"
|+ Bond Length
! Metal complex !! Bond Length(Å)
|-
| [Cr(CO)6] || 1.915
|-
| [Mn(CO)6]+ || 1.908
|-
| [Fe(CO)6]2+ || 1.940
|}

The table above shows the bond metal centre-carbon bond lengths. It shows a decrease moving from Cr to Mn and from Mn to Fe there is an increase. This initial decrease in M-C bond length goes against what was predicted but after speaking to Professor Hunt it turns out a full explanation of this decrease in bond length is to complex for the course and so wont be provided.The the later drastic increase is due to a contraction of the d-orbitals causing greater repulsion between the electrons leading to poorer overlap with the CO orbitals meaning less back-bonding and and weaker, so therefore longer, metal-carbon bonds. This agrees with the prediction made earlier.

{| class="wikitable" border="1"
|+ Vibrations table 2
! Metal complex !! Intensity !! Vibration type !! Wavenumber(cm-1)
|-
| [Cr(CO)6] || 1637 || symmetric stretch || 2086
|-
| [Mn(CO)6]+ || 879 || symmetric stretch || 2199
|-
| [Fe(CO)6]2+ || 272 || symmetric stretch || 2297
|}

This table above shows the wave-number and intensity all the IR active symmetric stretches of all the metal complexes CO ligands. As each complex has 13 atoms it is expected to have 3(13)-6= 33 vibrational modes but as shown in the vibrational spectra below many of these modes are IR inactive and have intensities of 0, an example of this is the totally symmetric C-O vibrations meaning they cannot be analysed given the fact that they don't appear. As predicted earlier across the period CO bond frequency would increase and this is due to back donation. Whilst back bonding causes an increase in the M-C bond there is also a increase in the CO bond length. The more positive the metal centre means contraction of the d-orbitals and this means that their is a less overlap between the d-orbital and CO pi* orbital and the less overlap with this orbital the stronger the CO bond.

[[File:Cr_vibrational_spectrum.PNG]] Cr complex Vibrational spectrum

[[File:Mn_vibrational_spectrum.PNG]] Mn complex Vibrational spectrum

[[File:Fe_vibrational_spectrum.PNG]] Fe complex Vibrational spectrum

The images below are three of the molecular orbitals of the [Fe(CO)6]2+ complex with the corresponding LCAO drawn beside them. Also on the diagrams of the LCAOs there are annotations analysing the structure.

[[File:Real_MO_37.PNG]] [[File:LCAO MO 36.PNG || 500px ]]

bonding MO 36 (eg)

[[File:Real_MO_46.PNG]] [[File:MO_46_LCAO.PNG || 500px ]]

bonding MO 46 (t1g)

[[File:Real MO 50 LUMO.PNG]] [[File:LCAO MO 50 LUMO.PNG || 500px ]]

anti-bonding MO 50 (LUMO/eg)

=== References ===

[1]- Hunt. T, [online] Huntresearchgroup.org.uk, Available at: http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf [Accessed 20 May 2019].

[2]-

JoeWiki1

2019-05-24T13:53:31Z

Jh3817: /* References */

== Year 2 Inorganic comp labs ==

=== BH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p),
Symmetry= D3h

[[File:BH3_info.PNG]]

Item Value Threshold Converged?

Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

Link to frequency file: [[File:JH_BH3_FREQ.LOG]]

Low frequencies --- -0.4072 -0.1962 -0.0055 25.2514 27.2430 27.2460

Low frequencies --- 1163.1897 1213.3128 1213.3155

<jmol><jmolApplet>
<title>Optimised BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JH_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Vibration Data ====

{| class="wikitable" border="1"
|+ Vibrations table
! Stretch or Bend? !! Intensity !! Symmetry !! IR active? !! Wavenumber(cm-1)
|-
| Bend || 92 || A2" || Yes || 1163
|-
| Bend || 14 || E' || Yes || 1213
|-
| Bend || 14 || E' || Yes || 1213
|-
| Symmetric Stretch || 0 || A1' || No || 2581
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|}

[[File:BH3_vibrations_spectrum_JH.PNG]]

Spectrum shows 3 peaks out of 6 vibrational modes given by BH3 shown in table. 1 is IR in active leaving 5 as it causes no change in dipole in the molecule. Two pairs in the 5 are degenerate meaning they have the same energy and therefore overlap, meaning only 3 peaks show.

[[File:MO_diagram_JH.PNG]] [1]

The LCAOs seem very accurate as they depict AOs which combine to form the real MOs very well. Minor issues arise from the fact that it can be said that the overlapping of the orbitals may not be able to be seen fully and the fact that the sizes of the AOs, which represents contribution isn’t consistent. Hydrogen is more electronegative then boron and is therefore lower in energy. Hydrogen should be contributing more to the bonding orbitals and born should be contributing more to the anti-bonding orbitals but for some of them this might not be able to be seen accurately. This shows that the LCAO is a useful tool for finding what a real MO would look like.

=== NH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:NH3_point_group_summary.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES

Link to frequency file: [[File:NH3_OP_JH.LOG]]

Low frequencies --- -8.5628 -8.5571 -0.0047 0.0454 0.1785 26.4189

Low frequencies --- 1089.7603 1694.1865 1694.1865

<jmol><jmolApplet>
<title>Optimised NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3_OP_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:BH3NH3_point_group_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000514 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

Link to frequency file: [[File:NH3BH3_FREQ_NEW.LOG]]

Low frequencies --- -0.0005 0.0003 0.0014 16.7270 18.7414 42.2600

Low frequencies --- 266.2799 632.3010 639.2486

<jmol><jmolApplet>
<title>Optimised NH3BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3BH3_FREQ_NEW.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Association energies ====
E(NH3)= -56.55776863 a.u.

E(BH3)= -26.61532362 a.u.

E(NH3BH3)= -83.22469031 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)], Therefore ΔE= (-83.22468960) - [(-56.55776863)+(-26.61532362)]= -0.05159806 a.u. (-134 KJ/Mol)

The B-N dative bond is weak and this shown when compared to the Al-N bond which has an energy of 297KJ/Mol (https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf)(22222222222)

=== NI3 ===
Method= RB3LYP,
Basis set= Gen

[[File:New_NI3_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000102 0.000450 YES
RMS Force 0.000075 0.000300 YES
Maximum Displacement 0.000858 0.001800 YES
RMS Displacement 0.000629 0.001200 YES

Link to frequency file: [[File:NEW_NI3_JH.LOG]]

Low frequencies --- -12.3845 -12.3781 -5.6129 -0.0040 0.0194 0.0711

Low frequencies --- 100.9307 100.9314 147.2333

<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NEW_NI3_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised B-I bond distance is 2.18 angstrom

===Days 2 and 3 Project: Metal carbonyls===
This sections of the wiki page focuses on metal carbonyls, more specifically their bond-lengths and CO bond frequencies. The metal-complexes which will be focused on are [Cr(CO)6], [Mn(CO)6]+ and [Fe(CO)6]2+. These were chosen as they come one after another in the d-block so it would be interesting to see how bond-lengths and bond frequencies vary across the period. 2 of the complexes are charged (positively) while one is neutral and this is something which must be taken into account when analysing bond-lengths and bond frequencies. An initial prediction would be that bond length increases across a period (as the metal complexes are becoming more positive meaning less overlap with the CO pi* and overall less back-donation and since back donation strengths the M-C bond less of this means an increases in bond length) and that bond frequencies increases.

==== [Cr(CO)6] ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Cr

[[File:Cr(CO)6_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000110 0.000450 YES
RMS Force 0.000041 0.000300 YES
Maximum Displacement 0.000705 0.001800 YES
RMS Displacement 0.000334 0.001200 YES

Link to frequency file: [[File:CR(CO)6_JH_2.LOG]]

Low frequencies --- -0.0014 -0.0013 -0.0010 11.7482 11.7482 11.7482

Low frequencies --- 66.6574 66.6574 66.6574

<jmol><jmolApplet>
<title>Optimised Cr(CO)6 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>CR(CO)6_JH_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Mn(CO)6]+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Mn

[[File:-Mn(CO)62+_summary_JH3817.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000430 0.001800 YES
RMS Displacement 0.000204 0.001200 YES

Link to frequency file: [[File:-MN(CO)6-+_OP_FREQ_JH.LOG]]

Low frequencies --- -0.0007 0.0006 0.0009 4.7607 4.7607 4.7607

Low frequencies --- 76.3202 76.3202 76.3202

<jmol><jmolApplet>
<title>Optimised [Mn(CO)6]+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-MN(CO)6-+_OP_FREQ_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Fe(CO)6]2+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Fe

[[File:-Fe(CO)6-2+_freq_op_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000429 0.001800 YES
RMS Displacement 0.000200 0.001200 YES

Link to frequency file: [[File:-FE(CO)6-2+_OP_FREQ.LOG]]

Low frequencies --- -10.5293 -10.5293 -10.5292 -0.0014 -0.0011 -0.0009

Low frequencies --- 82.1285 82.1285 82.1285

<jmol><jmolApplet>
<title>Optimised [FE(CO)6]2+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-FE(CO)6-2+_OP_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Analysing properties ====

{| class="wikitable" border="1"
|+ Bond Length
! Metal complex !! Bond Length(Å)
|-
| [Cr(CO)6] || 1.915
|-
| [Mn(CO)6]+ || 1.908
|-
| [Fe(CO)6]2+ || 1.940
|}

The table above shows the bond metal centre-carbon bond lengths. It shows a decrease moving from Cr to Mn and from Mn to Fe there is an increase. This initial decrease in M-C bond length goes against what was predicted but after speaking to Professor Hunt it turns out a full explanation of this decrease in bond length is to complex for the course and so wont be provided.The the later drastic increase is due to a contraction of the d-orbitals causing greater repulsion between the electrons leading to poorer overlap with the CO orbitals meaning less back-bonding and and weaker, so therefore longer, metal-carbon bonds. This agrees with the prediction made earlier.

{| class="wikitable" border="1"
|+ Vibrations table 2
! Metal complex !! Intensity !! Vibration type !! Wavenumber(cm-1)
|-
| [Cr(CO)6] || 1637 || symmetric stretch || 2086
|-
| [Mn(CO)6]+ || 879 || symmetric stretch || 2199
|-
| [Fe(CO)6]2+ || 272 || symmetric stretch || 2297
|}

This table above shows the wave-number and intensity all the IR active symmetric stretches of all the metal complexes CO ligands. As each complex has 13 atoms it is expected to have 3(13)-6= 33 vibrational modes but as shown in the vibrational spectra below many of these modes are IR inactive and have intensities of 0, an example of this is the totally symmetric C-O vibrations meaning they cannot be analysed given the fact that they don't appear. As predicted earlier across the period CO bond frequency would increase and this is due to back donation. Whilst back bonding causes an increase in the M-C bond there is also a increase in the CO bond length. The more positive the metal centre means contraction of the d-orbitals and this means that their is a less overlap between the d-orbital and CO pi* orbital and the less overlap with this orbital the stronger the CO bond.

[[File:Cr_vibrational_spectrum.PNG]] Cr complex Vibrational spectrum

[[File:Mn_vibrational_spectrum.PNG]] Mn complex Vibrational spectrum

[[File:Fe_vibrational_spectrum.PNG]] Fe complex Vibrational spectrum

The images below are three of the molecular orbitals of the [Fe(CO)6]2+ complex with the corresponding LCAO drawn beside them. Also on the diagrams of the LCAOs there are annotations analysing the structure.

[[File:Real_MO_37.PNG]] [[File:LCAO MO 36.PNG || 500px ]]

bonding MO 36 (eg)

[[File:Real_MO_46.PNG]] [[File:MO_46_LCAO.PNG || 500px ]]

bonding MO 46 (t1g)

[[File:Real MO 50 LUMO.PNG]] [[File:LCAO MO 50 LUMO.PNG || 500px ]]

anti-bonding MO 50 (LUMO/eg)

=== References ===

[1]- Hunt. T, [online] Huntresearchgroup.org.uk, Available at: http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf [Accessed 20 May 2019].

[2]-

JoeWiki1

2019-05-24T13:45:25Z

Jh3817:

== Year 2 Inorganic comp labs ==

=== BH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p),
Symmetry= D3h

[[File:BH3_info.PNG]]

Item Value Threshold Converged?

Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

Link to frequency file: [[File:JH_BH3_FREQ.LOG]]

Low frequencies --- -0.4072 -0.1962 -0.0055 25.2514 27.2430 27.2460

Low frequencies --- 1163.1897 1213.3128 1213.3155

<jmol><jmolApplet>
<title>Optimised BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JH_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Vibration Data ====

{| class="wikitable" border="1"
|+ Vibrations table
! Stretch or Bend? !! Intensity !! Symmetry !! IR active? !! Wavenumber(cm-1)
|-
| Bend || 92 || A2" || Yes || 1163
|-
| Bend || 14 || E' || Yes || 1213
|-
| Bend || 14 || E' || Yes || 1213
|-
| Symmetric Stretch || 0 || A1' || No || 2581
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|}

[[File:BH3_vibrations_spectrum_JH.PNG]]

Spectrum shows 3 peaks out of 6 vibrational modes given by BH3 shown in table. 1 is IR in active leaving 5 as it causes no change in dipole in the molecule. Two pairs in the 5 are degenerate meaning they have the same energy and therefore overlap, meaning only 3 peaks show.

[[File:MO_diagram_JH.PNG]] [1]

The LCAOs seem very accurate as they depict AOs which combine to form the real MOs very well. Minor issues arise from the fact that it can be said that the overlapping of the orbitals may not be able to be seen fully and the fact that the sizes of the AOs, which represents contribution isn’t consistent. Hydrogen is more electronegative then boron and is therefore lower in energy. Hydrogen should be contributing more to the bonding orbitals and born should be contributing more to the anti-bonding orbitals but for some of them this might not be able to be seen accurately. This shows that the LCAO is a useful tool for finding what a real MO would look like.

=== NH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:NH3_point_group_summary.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES

Link to frequency file: [[File:NH3_OP_JH.LOG]]

Low frequencies --- -8.5628 -8.5571 -0.0047 0.0454 0.1785 26.4189

Low frequencies --- 1089.7603 1694.1865 1694.1865

<jmol><jmolApplet>
<title>Optimised NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3_OP_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:BH3NH3_point_group_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000514 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

Link to frequency file: [[File:NH3BH3_FREQ_NEW.LOG]]

Low frequencies --- -0.0005 0.0003 0.0014 16.7270 18.7414 42.2600

Low frequencies --- 266.2799 632.3010 639.2486

<jmol><jmolApplet>
<title>Optimised NH3BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3BH3_FREQ_NEW.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Association energies ====
E(NH3)= -56.55776863 a.u.

E(BH3)= -26.61532362 a.u.

E(NH3BH3)= -83.22469031 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)], Therefore ΔE= (-83.22468960) - [(-56.55776863)+(-26.61532362)]= -0.05159806 a.u. (-134 KJ/Mol)

The B-N dative bond is weak and this shown when compared to the Al-N bond which has an energy of 297KJ/Mol (https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf)(22222222222)

=== NI3 ===
Method= RB3LYP,
Basis set= Gen

[[File:New_NI3_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000102 0.000450 YES
RMS Force 0.000075 0.000300 YES
Maximum Displacement 0.000858 0.001800 YES
RMS Displacement 0.000629 0.001200 YES

Link to frequency file: [[File:NEW_NI3_JH.LOG]]

Low frequencies --- -12.3845 -12.3781 -5.6129 -0.0040 0.0194 0.0711

Low frequencies --- 100.9307 100.9314 147.2333

<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NEW_NI3_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised B-I bond distance is 2.18 angstrom

===Days 2 and 3 Project: Metal carbonyls===
This sections of the wiki page focuses on metal carbonyls, more specifically their bond-lengths and CO bond frequencies. The metal-complexes which will be focused on are [Cr(CO)6], [Mn(CO)6]+ and [Fe(CO)6]2+. These were chosen as they come one after another in the d-block so it would be interesting to see how bond-lengths and bond frequencies vary across the period. 2 of the complexes are charged (positively) while one is neutral and this is something which must be taken into account when analysing bond-lengths and bond frequencies. An initial prediction would be that bond length increases across a period (as the metal complexes are becoming more positive meaning less overlap with the CO pi* and overall less back-donation and since back donation strengths the M-C bond less of this means an increases in bond length) and that bond frequencies increases.

==== [Cr(CO)6] ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Cr

[[File:Cr(CO)6_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000110 0.000450 YES
RMS Force 0.000041 0.000300 YES
Maximum Displacement 0.000705 0.001800 YES
RMS Displacement 0.000334 0.001200 YES

Link to frequency file: [[File:CR(CO)6_JH_2.LOG]]

Low frequencies --- -0.0014 -0.0013 -0.0010 11.7482 11.7482 11.7482

Low frequencies --- 66.6574 66.6574 66.6574

<jmol><jmolApplet>
<title>Optimised Cr(CO)6 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>CR(CO)6_JH_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Mn(CO)6]+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Mn

[[File:-Mn(CO)62+_summary_JH3817.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000430 0.001800 YES
RMS Displacement 0.000204 0.001200 YES

Link to frequency file: [[File:-MN(CO)6-+_OP_FREQ_JH.LOG]]

Low frequencies --- -0.0007 0.0006 0.0009 4.7607 4.7607 4.7607

Low frequencies --- 76.3202 76.3202 76.3202

<jmol><jmolApplet>
<title>Optimised [Mn(CO)6]+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-MN(CO)6-+_OP_FREQ_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Fe(CO)6]2+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Fe

[[File:-Fe(CO)6-2+_freq_op_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000429 0.001800 YES
RMS Displacement 0.000200 0.001200 YES

Link to frequency file: [[File:-FE(CO)6-2+_OP_FREQ.LOG]]

Low frequencies --- -10.5293 -10.5293 -10.5292 -0.0014 -0.0011 -0.0009

Low frequencies --- 82.1285 82.1285 82.1285

<jmol><jmolApplet>
<title>Optimised [FE(CO)6]2+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-FE(CO)6-2+_OP_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Analysing properties ====

{| class="wikitable" border="1"
|+ Bond Length
! Metal complex !! Bond Length(Å)
|-
| [Cr(CO)6] || 1.915
|-
| [Mn(CO)6]+ || 1.908
|-
| [Fe(CO)6]2+ || 1.940
|}

The table above shows the bond metal centre-carbon bond lengths. It shows a decrease moving from Cr to Mn and from Mn to Fe there is an increase. This initial decrease in M-C bond length goes against what was predicted but after speaking to Professor Hunt it turns out a full explanation of this decrease in bond length is to complex for the course and so wont be provided.The the later drastic increase is due to a contraction of the d-orbitals causing greater repulsion between the electrons leading to poorer overlap with the CO orbitals meaning less back-bonding and and weaker, so therefore longer, metal-carbon bonds. This agrees with the prediction made earlier.

{| class="wikitable" border="1"
|+ Vibrations table 2
! Metal complex !! Intensity !! Vibration type !! Wavenumber(cm-1)
|-
| [Cr(CO)6] || 1637 || symmetric stretch || 2086
|-
| [Mn(CO)6]+ || 879 || symmetric stretch || 2199
|-
| [Fe(CO)6]2+ || 272 || symmetric stretch || 2297
|}

This table above shows the wave-number and intensity all the IR active symmetric stretches of all the metal complexes CO ligands. As each complex has 13 atoms it is expected to have 3(13)-6= 33 vibrational modes but as shown in the vibrational spectra below many of these modes are IR inactive and have intensities of 0, an example of this is the totally symmetric C-O vibrations meaning they cannot be analysed given the fact that they don't appear. As predicted earlier across the period CO bond frequency would increase and this is due to back donation. Whilst back bonding causes an increase in the M-C bond there is also a increase in the CO bond length. The more positive the metal centre means contraction of the d-orbitals and this means that their is a less overlap between the d-orbital and CO pi* orbital and the less overlap with this orbital the stronger the CO bond.

[[File:Cr_vibrational_spectrum.PNG]] Cr complex Vibrational spectrum

[[File:Mn_vibrational_spectrum.PNG]] Mn complex Vibrational spectrum

[[File:Fe_vibrational_spectrum.PNG]] Fe complex Vibrational spectrum

The images below are three of the molecular orbitals of the [Fe(CO)6]2+ complex with the corresponding LCAO drawn beside them. Also on the diagrams of the LCAOs there are annotations analysing the structure.

[[File:Real_MO_37.PNG]] [[File:LCAO MO 36.PNG || 500px ]]

bonding MO 36 (eg)

[[File:Real_MO_46.PNG]] [[File:MO_46_LCAO.PNG || 500px ]]

bonding MO 46 (t1g)

[[File:Real MO 50 LUMO.PNG]] [[File:LCAO MO 50 LUMO.PNG || 500px ]]

anti-bonding MO 50 (LUMO/eg)

=== References ===

JoeWiki1

2019-05-24T13:44:27Z

Jh3817: /* Vibration Data */

== Year 2 Inorganic comp labs ==

=== BH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p),
Symmetry= D3h

[[File:BH3_info.PNG]]

Item Value Threshold Converged?

Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

Link to frequency file: [[File:JH_BH3_FREQ.LOG]]

Low frequencies --- -0.4072 -0.1962 -0.0055 25.2514 27.2430 27.2460

Low frequencies --- 1163.1897 1213.3128 1213.3155

<jmol><jmolApplet>
<title>Optimised BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JH_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Vibration Data ====

{| class="wikitable" border="1"
|+ Vibrations table
! Stretch or Bend? !! Intensity !! Symmetry !! IR active? !! Wavenumber(cm-1)
|-
| Bend || 92 || A2" || Yes || 1163
|-
| Bend || 14 || E' || Yes || 1213
|-
| Bend || 14 || E' || Yes || 1213
|-
| Symmetric Stretch || 0 || A1' || No || 2581
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|}

[[File:BH3_vibrations_spectrum_JH.PNG]]

Spectrum shows 3 peaks out of 6 vibrational modes given by BH3 shown in table. 1 is IR in active leaving 5 as it causes no change in dipole in the molecule. Two pairs in the 5 are degenerate meaning they have the same energy and therefore overlap, meaning only 3 peaks show.

[[File:MO_diagram_JH.PNG]] [1]

The LCAOs seem very accurate as they depict AOs which combine to form the real MOs very well. Minor issues arise from the fact that it can be said that the overlapping of the orbitals may not be able to be seen fully and the fact that the sizes of the AOs, which represents contribution isn’t consistent. Hydrogen is more electronegative then boron and is therefore lower in energy. Hydrogen should be contributing more to the bonding orbitals and born should be contributing more to the anti-bonding orbitals but for some of them this might not be able to be seen accurately. This shows that the LCAO is a useful tool for finding what a real MO would look like.

=== NH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:NH3_point_group_summary.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES

Link to frequency file: [[File:NH3_OP_JH.LOG]]

Low frequencies --- -8.5628 -8.5571 -0.0047 0.0454 0.1785 26.4189

Low frequencies --- 1089.7603 1694.1865 1694.1865

<jmol><jmolApplet>
<title>Optimised NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3_OP_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:BH3NH3_point_group_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000514 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

Link to frequency file: [[File:NH3BH3_FREQ_NEW.LOG]]

Low frequencies --- -0.0005 0.0003 0.0014 16.7270 18.7414 42.2600

Low frequencies --- 266.2799 632.3010 639.2486

<jmol><jmolApplet>
<title>Optimised NH3BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3BH3_FREQ_NEW.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Association energies ====
E(NH3)= -56.55776863 a.u.

E(BH3)= -26.61532362 a.u.

E(NH3BH3)= -83.22469031 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)], Therefore ΔE= (-83.22468960) - [(-56.55776863)+(-26.61532362)]= -0.05159806 a.u. (-134 KJ/Mol)

The B-N dative bond is weak and this shown when compared to the Al-N bond which has an energy of 297KJ/Mol (https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf)(22222222222)

=== NI3 ===
Method= RB3LYP,
Basis set= Gen

[[File:New_NI3_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000102 0.000450 YES
RMS Force 0.000075 0.000300 YES
Maximum Displacement 0.000858 0.001800 YES
RMS Displacement 0.000629 0.001200 YES

Link to frequency file: [[File:NEW_NI3_JH.LOG]]

Low frequencies --- -12.3845 -12.3781 -5.6129 -0.0040 0.0194 0.0711

Low frequencies --- 100.9307 100.9314 147.2333

<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NEW_NI3_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised B-I bond distance is 2.18 angstrom

===Days 2 and 3 Project: Metal carbonyls===
This sections of the wiki page focuses on metal carbonyls, more specifically their bond-lengths and CO bond frequencies. The metal-complexes which will be focused on are [Cr(CO)6], [Mn(CO)6]+ and [Fe(CO)6]2+. These were chosen as they come one after another in the d-block so it would be interesting to see how bond-lengths and bond frequencies vary across the period. 2 of the complexes are charged (positively) while one is neutral and this is something which must be taken into account when analysing bond-lengths and bond frequencies. An initial prediction would be that bond length increases across a period (as the metal complexes are becoming more positive meaning less overlap with the CO pi* and overall less back-donation and since back donation strengths the M-C bond less of this means an increases in bond length) and that bond frequencies increases.

==== [Cr(CO)6] ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Cr

[[File:Cr(CO)6_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000110 0.000450 YES
RMS Force 0.000041 0.000300 YES
Maximum Displacement 0.000705 0.001800 YES
RMS Displacement 0.000334 0.001200 YES

Link to frequency file: [[File:CR(CO)6_JH_2.LOG]]

Low frequencies --- -0.0014 -0.0013 -0.0010 11.7482 11.7482 11.7482

Low frequencies --- 66.6574 66.6574 66.6574

<jmol><jmolApplet>
<title>Optimised Cr(CO)6 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>CR(CO)6_JH_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Mn(CO)6]+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Mn

[[File:-Mn(CO)62+_summary_JH3817.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000430 0.001800 YES
RMS Displacement 0.000204 0.001200 YES

Link to frequency file: [[File:-MN(CO)6-+_OP_FREQ_JH.LOG]]

Low frequencies --- -0.0007 0.0006 0.0009 4.7607 4.7607 4.7607

Low frequencies --- 76.3202 76.3202 76.3202

<jmol><jmolApplet>
<title>Optimised [Mn(CO)6]+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-MN(CO)6-+_OP_FREQ_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Fe(CO)6]2+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Fe

[[File:-Fe(CO)6-2+_freq_op_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000429 0.001800 YES
RMS Displacement 0.000200 0.001200 YES

Link to frequency file: [[File:-FE(CO)6-2+_OP_FREQ.LOG]]

Low frequencies --- -10.5293 -10.5293 -10.5292 -0.0014 -0.0011 -0.0009

Low frequencies --- 82.1285 82.1285 82.1285

<jmol><jmolApplet>
<title>Optimised [FE(CO)6]2+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-FE(CO)6-2+_OP_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Analysing properties ====

{| class="wikitable" border="1"
|+ Bond Length
! Metal complex !! Bond Length(Å)
|-
| [Cr(CO)6] || 1.915
|-
| [Mn(CO)6]+ || 1.908
|-
| [Fe(CO)6]2+ || 1.940
|}

The table above shows the bond metal centre-carbon bond lengths. It shows a decrease moving from Cr to Mn and from Mn to Fe there is an increase. This initial decrease in M-C bond length goes against what was predicted but after speaking to Professor Hunt it turns out a full explanation of this decrease in bond length is to complex for the course and so wont be provided.The the later drastic increase is due to a contraction of the d-orbitals causing greater repulsion between the electrons leading to poorer overlap with the CO orbitals meaning less back-bonding and and weaker, so therefore longer, metal-carbon bonds. This agrees with the prediction made earlier.

{| class="wikitable" border="1"
|+ Vibrations table 2
! Metal complex !! Intensity !! Vibration type !! Wavenumber(cm-1)
|-
| [Cr(CO)6] || 1637 || symmetric stretch || 2086
|-
| [Mn(CO)6]+ || 879 || symmetric stretch || 2199
|-
| [Fe(CO)6]2+ || 272 || symmetric stretch || 2297
|}

This table above shows the wave-number and intensity all the IR active symmetric stretches of all the metal complexes CO ligands. As each complex has 13 atoms it is expected to have 3(13)-6= 33 vibrational modes but as shown in the vibrational spectra below many of these modes are IR inactive and have intensities of 0, an example of this is the totally symmetric C-O vibrations meaning they cannot be analysed given the fact that they don't appear. As predicted earlier across the period CO bond frequency would increase and this is due to back donation. Whilst back bonding causes an increase in the M-C bond there is also a increase in the CO bond length. The more positive the metal centre means contraction of the d-orbitals and this means that their is a less overlap between the d-orbital and CO pi* orbital and the less overlap with this orbital the stronger the CO bond.

[[File:Cr_vibrational_spectrum.PNG]] Cr complex Vibrational spectrum

[[File:Mn_vibrational_spectrum.PNG]] Mn complex Vibrational spectrum

[[File:Fe_vibrational_spectrum.PNG]] Fe complex Vibrational spectrum

The images below are three of the molecular orbitals of the [Fe(CO)6]2+ complex with the corresponding LCAO drawn beside them. Also on the diagrams of the LCAOs there are annotations analysing the structure.

[[File:Real_MO_37.PNG]] [[File:LCAO MO 36.PNG || 500px ]]

bonding MO 36 (eg)

[[File:Real_MO_46.PNG]] [[File:MO_46_LCAO.PNG || 500px ]]

bonding MO 46 (t1g)

[[File:Real MO 50 LUMO.PNG]] [[File:LCAO MO 50 LUMO.PNG || 500px ]]

anti-bonding MO 50 (LUMO/eg)

JoeWiki1

2019-05-24T13:38:42Z

Jh3817: /* Analysing properties */

== Year 2 Inorganic comp labs ==

=== BH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p),
Symmetry= D3h

[[File:BH3_info.PNG]]

Item Value Threshold Converged?

Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

Link to frequency file: [[File:JH_BH3_FREQ.LOG]]

Low frequencies --- -0.4072 -0.1962 -0.0055 25.2514 27.2430 27.2460

Low frequencies --- 1163.1897 1213.3128 1213.3155

<jmol><jmolApplet>
<title>Optimised BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JH_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Vibration Data ====

{| class="wikitable" border="1"
|+ Vibrations table
! Stretch or Bend? !! Intensity !! Symmetry !! IR active? !! Wavenumber(cm-1)
|-
| Bend || 92 || A2" || Yes || 1163
|-
| Bend || 14 || E' || Yes || 1213
|-
| Bend || 14 || E' || Yes || 1213
|-
| Symmetric Stretch || 0 || A1' || No || 2581
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|}

[[File:BH3_vibrations_spectrum_JH.PNG]]

Spectrum shows 3 peaks out of 6 vibrational modes given by BH3 shown in table. 1 is IR in active leaving 5 as it causes no change in dipole in the molecule. Two pairs in the 5 are degenerate meaning they have the same energy and therefore overlap, meaning only 3 peaks show.

[[File:MO_diagram_JH.PNG]] [1111111111111111111111111111111111111111]

The LCAOs seem very accurate as they depict AOs which combine to form the real MOs very well. Minor issues arise from the fact that it can be said that the overlapping of the orbitals may not be able to be seen fully and the fact that the sizes of the AOs, which represents contribution isn’t consistent. Hydrogen is more electronegative then boron and is therefore lower in energy. Hydrogen should be contributing more to the bonding orbitals and born should be contributing more to the anti-bonding orbitals but for some of them this might not be able to be seen accurately. This shows that the LCAO is a useful tool for finding what a real MO would look like.

=== NH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:NH3_point_group_summary.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES

Link to frequency file: [[File:NH3_OP_JH.LOG]]

Low frequencies --- -8.5628 -8.5571 -0.0047 0.0454 0.1785 26.4189

Low frequencies --- 1089.7603 1694.1865 1694.1865

<jmol><jmolApplet>
<title>Optimised NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3_OP_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:BH3NH3_point_group_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000514 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

Link to frequency file: [[File:NH3BH3_FREQ_NEW.LOG]]

Low frequencies --- -0.0005 0.0003 0.0014 16.7270 18.7414 42.2600

Low frequencies --- 266.2799 632.3010 639.2486

<jmol><jmolApplet>
<title>Optimised NH3BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3BH3_FREQ_NEW.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Association energies ====
E(NH3)= -56.55776863 a.u.

E(BH3)= -26.61532362 a.u.

E(NH3BH3)= -83.22469031 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)], Therefore ΔE= (-83.22468960) - [(-56.55776863)+(-26.61532362)]= -0.05159806 a.u. (-134 KJ/Mol)

The B-N dative bond is weak and this shown when compared to the Al-N bond which has an energy of 297KJ/Mol (https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf)(22222222222)

=== NI3 ===
Method= RB3LYP,
Basis set= Gen

[[File:New_NI3_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000102 0.000450 YES
RMS Force 0.000075 0.000300 YES
Maximum Displacement 0.000858 0.001800 YES
RMS Displacement 0.000629 0.001200 YES

Link to frequency file: [[File:NEW_NI3_JH.LOG]]

Low frequencies --- -12.3845 -12.3781 -5.6129 -0.0040 0.0194 0.0711

Low frequencies --- 100.9307 100.9314 147.2333

<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NEW_NI3_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised B-I bond distance is 2.18 angstrom

===Days 2 and 3 Project: Metal carbonyls===
This sections of the wiki page focuses on metal carbonyls, more specifically their bond-lengths and CO bond frequencies. The metal-complexes which will be focused on are [Cr(CO)6], [Mn(CO)6]+ and [Fe(CO)6]2+. These were chosen as they come one after another in the d-block so it would be interesting to see how bond-lengths and bond frequencies vary across the period. 2 of the complexes are charged (positively) while one is neutral and this is something which must be taken into account when analysing bond-lengths and bond frequencies. An initial prediction would be that bond length increases across a period (as the metal complexes are becoming more positive meaning less overlap with the CO pi* and overall less back-donation and since back donation strengths the M-C bond less of this means an increases in bond length) and that bond frequencies increases.

==== [Cr(CO)6] ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Cr

[[File:Cr(CO)6_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000110 0.000450 YES
RMS Force 0.000041 0.000300 YES
Maximum Displacement 0.000705 0.001800 YES
RMS Displacement 0.000334 0.001200 YES

Link to frequency file: [[File:CR(CO)6_JH_2.LOG]]

Low frequencies --- -0.0014 -0.0013 -0.0010 11.7482 11.7482 11.7482

Low frequencies --- 66.6574 66.6574 66.6574

<jmol><jmolApplet>
<title>Optimised Cr(CO)6 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>CR(CO)6_JH_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Mn(CO)6]+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Mn

[[File:-Mn(CO)62+_summary_JH3817.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000430 0.001800 YES
RMS Displacement 0.000204 0.001200 YES

Link to frequency file: [[File:-MN(CO)6-+_OP_FREQ_JH.LOG]]

Low frequencies --- -0.0007 0.0006 0.0009 4.7607 4.7607 4.7607

Low frequencies --- 76.3202 76.3202 76.3202

<jmol><jmolApplet>
<title>Optimised [Mn(CO)6]+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-MN(CO)6-+_OP_FREQ_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Fe(CO)6]2+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Fe

[[File:-Fe(CO)6-2+_freq_op_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000429 0.001800 YES
RMS Displacement 0.000200 0.001200 YES

Link to frequency file: [[File:-FE(CO)6-2+_OP_FREQ.LOG]]

Low frequencies --- -10.5293 -10.5293 -10.5292 -0.0014 -0.0011 -0.0009

Low frequencies --- 82.1285 82.1285 82.1285

<jmol><jmolApplet>
<title>Optimised [FE(CO)6]2+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-FE(CO)6-2+_OP_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Analysing properties ====

{| class="wikitable" border="1"
|+ Bond Length
! Metal complex !! Bond Length(Å)
|-
| [Cr(CO)6] || 1.915
|-
| [Mn(CO)6]+ || 1.908
|-
| [Fe(CO)6]2+ || 1.940
|}

The table above shows the bond metal centre-carbon bond lengths. It shows a decrease moving from Cr to Mn and from Mn to Fe there is an increase. This initial decrease in M-C bond length goes against what was predicted but after speaking to Professor Hunt it turns out a full explanation of this decrease in bond length is to complex for the course and so wont be provided.The the later drastic increase is due to a contraction of the d-orbitals causing greater repulsion between the electrons leading to poorer overlap with the CO orbitals meaning less back-bonding and and weaker, so therefore longer, metal-carbon bonds. This agrees with the prediction made earlier.

{| class="wikitable" border="1"
|+ Vibrations table 2
! Metal complex !! Intensity !! Vibration type !! Wavenumber(cm-1)
|-
| [Cr(CO)6] || 1637 || symmetric stretch || 2086
|-
| [Mn(CO)6]+ || 879 || symmetric stretch || 2199
|-
| [Fe(CO)6]2+ || 272 || symmetric stretch || 2297
|}

This table above shows the wave-number and intensity all the IR active symmetric stretches of all the metal complexes CO ligands. As each complex has 13 atoms it is expected to have 3(13)-6= 33 vibrational modes but as shown in the vibrational spectra below many of these modes are IR inactive and have intensities of 0, an example of this is the totally symmetric C-O vibrations meaning they cannot be analysed given the fact that they don't appear. As predicted earlier across the period CO bond frequency would increase and this is due to back donation. Whilst back bonding causes an increase in the M-C bond there is also a increase in the CO bond length. The more positive the metal centre means contraction of the d-orbitals and this means that their is a less overlap between the d-orbital and CO pi* orbital and the less overlap with this orbital the stronger the CO bond.

[[File:Cr_vibrational_spectrum.PNG]] Cr complex Vibrational spectrum

[[File:Mn_vibrational_spectrum.PNG]] Mn complex Vibrational spectrum

[[File:Fe_vibrational_spectrum.PNG]] Fe complex Vibrational spectrum

The images below are three of the molecular orbitals of the [Fe(CO)6]2+ complex with the corresponding LCAO drawn beside them. Also on the diagrams of the LCAOs there are annotations analysing the structure.

[[File:Real_MO_37.PNG]] [[File:LCAO MO 36.PNG || 500px ]]

bonding MO 36 (eg)

[[File:Real_MO_46.PNG]] [[File:MO_46_LCAO.PNG || 500px ]]

bonding MO 46 (t1g)

[[File:Real MO 50 LUMO.PNG]] [[File:LCAO MO 50 LUMO.PNG || 500px ]]

anti-bonding MO 50 (LUMO/eg)

JoeWiki1

2019-05-24T13:36:31Z

Jh3817: /* Year 2 Inorganic comp labs */

== Year 2 Inorganic comp labs ==

=== BH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p),
Symmetry= D3h

[[File:BH3_info.PNG]]

Item Value Threshold Converged?

Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

Link to frequency file: [[File:JH_BH3_FREQ.LOG]]

Low frequencies --- -0.4072 -0.1962 -0.0055 25.2514 27.2430 27.2460

Low frequencies --- 1163.1897 1213.3128 1213.3155

<jmol><jmolApplet>
<title>Optimised BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JH_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Vibration Data ====

{| class="wikitable" border="1"
|+ Vibrations table
! Stretch or Bend? !! Intensity !! Symmetry !! IR active? !! Wavenumber(cm-1)
|-
| Bend || 92 || A2" || Yes || 1163
|-
| Bend || 14 || E' || Yes || 1213
|-
| Bend || 14 || E' || Yes || 1213
|-
| Symmetric Stretch || 0 || A1' || No || 2581
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|}

[[File:BH3_vibrations_spectrum_JH.PNG]]

Spectrum shows 3 peaks out of 6 vibrational modes given by BH3 shown in table. 1 is IR in active leaving 5 as it causes no change in dipole in the molecule. Two pairs in the 5 are degenerate meaning they have the same energy and therefore overlap, meaning only 3 peaks show.

[[File:MO_diagram_JH.PNG]] [1111111111111111111111111111111111111111]

The LCAOs seem very accurate as they depict AOs which combine to form the real MOs very well. Minor issues arise from the fact that it can be said that the overlapping of the orbitals may not be able to be seen fully and the fact that the sizes of the AOs, which represents contribution isn’t consistent. Hydrogen is more electronegative then boron and is therefore lower in energy. Hydrogen should be contributing more to the bonding orbitals and born should be contributing more to the anti-bonding orbitals but for some of them this might not be able to be seen accurately. This shows that the LCAO is a useful tool for finding what a real MO would look like.

=== NH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:NH3_point_group_summary.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES

Link to frequency file: [[File:NH3_OP_JH.LOG]]

Low frequencies --- -8.5628 -8.5571 -0.0047 0.0454 0.1785 26.4189

Low frequencies --- 1089.7603 1694.1865 1694.1865

<jmol><jmolApplet>
<title>Optimised NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3_OP_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:BH3NH3_point_group_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000514 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

Link to frequency file: [[File:NH3BH3_FREQ_NEW.LOG]]

Low frequencies --- -0.0005 0.0003 0.0014 16.7270 18.7414 42.2600

Low frequencies --- 266.2799 632.3010 639.2486

<jmol><jmolApplet>
<title>Optimised NH3BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3BH3_FREQ_NEW.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Association energies ====
E(NH3)= -56.55776863 a.u.

E(BH3)= -26.61532362 a.u.

E(NH3BH3)= -83.22469031 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)], Therefore ΔE= (-83.22468960) - [(-56.55776863)+(-26.61532362)]= -0.05159806 a.u. (-134 KJ/Mol)

The B-N dative bond is weak and this shown when compared to the Al-N bond which has an energy of 297KJ/Mol (https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf)(22222222222)

=== NI3 ===
Method= RB3LYP,
Basis set= Gen

[[File:New_NI3_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000102 0.000450 YES
RMS Force 0.000075 0.000300 YES
Maximum Displacement 0.000858 0.001800 YES
RMS Displacement 0.000629 0.001200 YES

Link to frequency file: [[File:NEW_NI3_JH.LOG]]

Low frequencies --- -12.3845 -12.3781 -5.6129 -0.0040 0.0194 0.0711

Low frequencies --- 100.9307 100.9314 147.2333

<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NEW_NI3_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised B-I bond distance is 2.18 angstrom

===Days 2 and 3 Project: Metal carbonyls===
This sections of the wiki page focuses on metal carbonyls, more specifically their bond-lengths and CO bond frequencies. The metal-complexes which will be focused on are [Cr(CO)6], [Mn(CO)6]+ and [Fe(CO)6]2+. These were chosen as they come one after another in the d-block so it would be interesting to see how bond-lengths and bond frequencies vary across the period. 2 of the complexes are charged (positively) while one is neutral and this is something which must be taken into account when analysing bond-lengths and bond frequencies. An initial prediction would be that bond length increases across a period (as the metal complexes are becoming more positive meaning less overlap with the CO pi* and overall less back-donation and since back donation strengths the M-C bond less of this means an increases in bond length) and that bond frequencies increases.

==== [Cr(CO)6] ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Cr

[[File:Cr(CO)6_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000110 0.000450 YES
RMS Force 0.000041 0.000300 YES
Maximum Displacement 0.000705 0.001800 YES
RMS Displacement 0.000334 0.001200 YES

Link to frequency file: [[File:CR(CO)6_JH_2.LOG]]

Low frequencies --- -0.0014 -0.0013 -0.0010 11.7482 11.7482 11.7482

Low frequencies --- 66.6574 66.6574 66.6574

<jmol><jmolApplet>
<title>Optimised Cr(CO)6 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>CR(CO)6_JH_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Mn(CO)6]+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Mn

[[File:-Mn(CO)62+_summary_JH3817.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000430 0.001800 YES
RMS Displacement 0.000204 0.001200 YES

Link to frequency file: [[File:-MN(CO)6-+_OP_FREQ_JH.LOG]]

Low frequencies --- -0.0007 0.0006 0.0009 4.7607 4.7607 4.7607

Low frequencies --- 76.3202 76.3202 76.3202

<jmol><jmolApplet>
<title>Optimised [Mn(CO)6]+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-MN(CO)6-+_OP_FREQ_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Fe(CO)6]2+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Fe

[[File:-Fe(CO)6-2+_freq_op_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000429 0.001800 YES
RMS Displacement 0.000200 0.001200 YES

Link to frequency file: [[File:-FE(CO)6-2+_OP_FREQ.LOG]]

Low frequencies --- -10.5293 -10.5293 -10.5292 -0.0014 -0.0011 -0.0009

Low frequencies --- 82.1285 82.1285 82.1285

<jmol><jmolApplet>
<title>Optimised [FE(CO)6]2+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-FE(CO)6-2+_OP_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Analysing properties ====

{| class="wikitable" border="1"
|+ Bond Length
! Metal complex !! Bond Length(Å)
|-
| [Cr(CO)6] || 1.915
|-
| [Mn(CO)6]+ || 1.908
|-
| [Fe(CO)6]2+ || 1.940
|}

The table above shows the bond metal centre-carbon bond lengths. It shows a decrease moving from Cr to Mn and from Mn to Fe there is an increase. This initial decrease in M-C bond length goes against what was predicted but after speaking to Professor Hunt it turns out a full explanation of this decrease in bond length is to complex for the course and so wont be provided.The the later drastic increase is due to a contraction of the d-orbitals causing greater repulsion between the electrons leading to poorer overlap with the CO orbitals meaning less back-bonding and and weaker, so therefore longer, metal-carbon bonds. This agrees with the prediction made earlier.

{| class="wikitable" border="1"
|+ Vibrations table 2
! Metal complex !! Intensity !! Vibration type !! Wavenumber(cm-1)
|-
| [Cr(CO)6] || 1637 || symmetric stretch || 2086
|-
| [Mn(CO)6]+ || 879 || symmetric stretch || 2199
|-
| [Fe(CO)6]2+ || 272 || symmetric stretch || 2297
|}

This table above shows the wave-number and intensity all the IR active symmetric stretches of all the metal complexes CO ligands. As each complex has 13 atoms it is expected to have 3(13)-6= 33 vibrational modes but as shown in the vibrational spectra below many of these modes are IR inactive and have intensities of 0, an example of this is the totally symmetric C-O vibrations meaning they cannot be analysed given the fact that they don't appear. As predicted earlier across the period CO bond frequency would increase and this is due to back donation. Whilst back bonding causes an increase in the M-C bond there is also a increase in the CO bond length. The more positive the metal centre means contraction of the d-orbitals and this means that their is a less overlap between the d-orbital and CO pi* orbital and the less overlap with this orbital the stronger the CO bond.

[[File:Cr_vibrational_spectrum.PNG]] Cr complex Vibrational spectrum

[[File:Mn_vibrational_spectrum.PNG]] Mn complex Vibrational spectrum

[[File:Fe_vibrational_spectrum.PNG]] Fe complex Vibrational spectrum

The images below are three of the molecular orbitals of the [Fe(CO)6]2+ complex with the corresponding LCAO drawn beside them. Also on the diagrams of the LCAOs there are annotations analysing the structure.

[[File:Real_MO_37.PNG]] [[File:LCAO MO 36.PNG || 500px ]]

bonding MO 36 (eg)

[[File:Real_MO_46.PNG]] [[File:MO_46_LCAO.PNG || 500px ]]

bonding MO 46 (t1g)

[[File:Real MO 50 LUMO.PNG]] [[File:LCAO MO 50 LUMO.PNG || 500px ]]

anti-bonding MO 50 (LUMO/eg)

JoeWiki1

2019-05-24T13:19:05Z

Jh3817:

== Year 2 Inorganic comp labs ==

=== BH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p),
Symmetry= D3h

[[File:BH3_info.PNG]]

Item Value Threshold Converged?

Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

Link to frequency file: [[File:JH_BH3_FREQ.LOG]]

Low frequencies --- -0.4072 -0.1962 -0.0055 25.2514 27.2430 27.2460

Low frequencies --- 1163.1897 1213.3128 1213.3155

<jmol><jmolApplet>
<title>Optimised BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JH_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Vibration Data ====

{| class="wikitable" border="1"
|+ Vibrations table
! Stretch or Bend? !! Intensity !! Symmetry !! IR active? !! Wavenumber(cm-1)
|-
| Bend || 92 || A2" || Yes || 1163
|-
| Bend || 14 || E' || Yes || 1213
|-
| Bend || 14 || E' || Yes || 1213
|-
| Symmetric Stretch || 0 || A1' || No || 2581
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|}

[[File:BH3_vibrations_spectrum_JH.PNG]]

Spectrum shows 3 peaks out of 6 shown in table. 1 is IR in active leaving 5. Two pairs in the 5 are degenerate meaning they have the same energy meaning only 3 peaks show.

[[File:MO_diagram_JH.PNG]] [1111111111111111111111111111111111111111]

The LCAOs seem very accurate as they depict AOs which combine to form the real MOs very well. Minor issues arise from the fact that it can be said that the overlapping of the orbitals may not be able to be seen fully and the fact that the sizes of the AOs, which represents contribution isn’t consistent. Hydrogen is more electronegative then boron and is therefore lower in energy. Hydrogen should be contributing more to the bonding orbitals and born should be contributing more to the anti-bonding orbitals but for some of them this might not be able to be seen accurately. This shows that the LCAO is a useful tool for finding what a real MO would look like.

=== NH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:NH3_point_group_summary.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES

Link to frequency file: [[File:NH3_OP_JH.LOG]]

Low frequencies --- -8.5628 -8.5571 -0.0047 0.0454 0.1785 26.4189

Low frequencies --- 1089.7603 1694.1865 1694.1865

<jmol><jmolApplet>
<title>Optimised NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3_OP_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:BH3NH3_point_group_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000514 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

Link to frequency file: [[File:NH3BH3_FREQ_NEW.LOG]]

Low frequencies --- -0.0005 0.0003 0.0014 16.7270 18.7414 42.2600

Low frequencies --- 266.2799 632.3010 639.2486

<jmol><jmolApplet>
<title>Optimised NH3BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3BH3_FREQ_NEW.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Association energies ====
E(NH3)= -56.55776863 a.u.

E(BH3)= -26.61532362 a.u.

E(NH3BH3)= -83.22469031 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)], Therefore ΔE= (-83.22468960) - [(-56.55776863)+(-26.61532362)]= -0.05159806 a.u. (-134 KJ/Mol)

The B-N dative bond is weak and this shown when compared to the Al-N bond which has an energy of 297KJ/Mol (https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf)(22222222222)

=== NI3 ===
Method= RB3LYP,
Basis set= Gen

[[File:New_NI3_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000102 0.000450 YES
RMS Force 0.000075 0.000300 YES
Maximum Displacement 0.000858 0.001800 YES
RMS Displacement 0.000629 0.001200 YES

Link to frequency file: [[File:NEW_NI3_JH.LOG]]

Low frequencies --- -12.3845 -12.3781 -5.6129 -0.0040 0.0194 0.0711

Low frequencies --- 100.9307 100.9314 147.2333

<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NEW_NI3_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised B-I bond distance is 2.18 angstrom

===Days 2 and 3 Project: Metal carbonyls===
This sections of the wiki page focuses on metal carbonyls, more specifically their bond-lengths and CO bond frequencies. The metal-complexes which will be focused on are [Cr(CO)6], [Mn(CO)6]+ and [Fe(CO)6]2+. These were chosen as they come one after another in the d-block so it would be interesting to see how bond-lengths and bond frequencies vary across the period. 2 of the complexes are charged (positively) while one is neutral and this is something which must be taken into account when analysing bond-lengths and bond frequencies. An initial prediction would be that bond length increases across a period (as the metal complexes are becoming more positive meaning less overlap with the CO pi* and overall less back-donation and since back donation strengths the M-C bond less of this means an increases in bond length) and that bond frequencies increases.

==== [Cr(CO)6] ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Cr

[[File:Cr(CO)6_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000110 0.000450 YES
RMS Force 0.000041 0.000300 YES
Maximum Displacement 0.000705 0.001800 YES
RMS Displacement 0.000334 0.001200 YES

Link to frequency file: [[File:CR(CO)6_JH_2.LOG]]

Low frequencies --- -0.0014 -0.0013 -0.0010 11.7482 11.7482 11.7482

Low frequencies --- 66.6574 66.6574 66.6574

<jmol><jmolApplet>
<title>Optimised Cr(CO)6 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>CR(CO)6_JH_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Mn(CO)6]+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Mn

[[File:-Mn(CO)62+_summary_JH3817.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000430 0.001800 YES
RMS Displacement 0.000204 0.001200 YES

Link to frequency file: [[File:-MN(CO)6-+_OP_FREQ_JH.LOG]]

Low frequencies --- -0.0007 0.0006 0.0009 4.7607 4.7607 4.7607

Low frequencies --- 76.3202 76.3202 76.3202

<jmol><jmolApplet>
<title>Optimised Mn(CO)6+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-MN(CO)6-+_OP_FREQ_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Fe(CO)6]2+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Fe

[[File:-Fe(CO)6-2+_freq_op_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000429 0.001800 YES
RMS Displacement 0.000200 0.001200 YES

Link to frequency file: [[File:-FE(CO)6-2+_OP_FREQ.LOG]]

Low frequencies --- -10.5293 -10.5293 -10.5292 -0.0014 -0.0011 -0.0009

Low frequencies --- 82.1285 82.1285 82.1285

<jmol><jmolApplet>
<title>Optimised [FE(CO)6]2+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-FE(CO)6-2+_OP_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Analysing properties ====

{| class="wikitable" border="1"
|+ Bond Length
! Metal complex !! Bond Length(Å)
|-
| [Cr(CO)6] || 1.915
|-
| [Mn(CO)6]+ || 1.908
|-
| [Fe(CO)6]2+ || 1.940
|}

The table above shows the bond metal centre-carbon bond lengths. It shows a decrease moving from Cr to Mn and from Mn to Fe there is an increase. This initial decrease in M-C bond length goes against what was predicted but after speaking to Professor Hunt it turns out a full explanation of this decrease in bond length is to complex for the course and so wont be provided.The the later drastic increase is due to a contraction of the d-orbitals causing greater repulsion between the electrons leading to poorer overlap with the CO orbitals meaning less back-bonding and and weaker, so therefore longer, metal-carbon bonds. This agrees with the prediction made earlier.

{| class="wikitable" border="1"
|+ Vibrations table 2
! Metal complex !! Intensity !! Vibration type !! Wavenumber(cm-1)
|-
| Cr(CO)6 || 1637 || symmetric stretch || 2086
|-
| [Mn(CO)6]+ || 879 || symmetric stretch || 2199
|-
| [Fe(CO)6]2+ || 272 || symmetric stretch || 2297
|}

This table above shows the wave-number and intensity all the IR active symmetric stretches of all the metal complexes CO ligands. As each complex has 13 atoms it is expected to have 3(13)-6= 33 vibrational modes but as shown in the vibrational spectra below many of these modes are IR inactive and have intensities of 0, an example of this is the totally symmetric C-O vibrations meaning they cannot be analysed given the fact that they don't appear. As predicted earlier across the period CO bond frequency would increase and this is due to back donation. Whilst back bonding causes an increase in the M-C bond there is also a increase in the CO bond length. The more positive the metal centre means contraction of the d-orbitals and this means that their is a less overlap between the d-orbital and CO pi* orbital and the less overlap with this orbital the stronger the CO bond.

[[File:Cr_vibrational_spectrum.PNG]] Cr complex Vibrational spectrum

[[File:Mn_vibrational_spectrum.PNG]] Mn complex Vibrational spectrum

[[File:Fe_vibrational_spectrum.PNG]] Fe complex Vibrational spectrum

The images below are three of the molecular orbitals of the [Fe(CO)6]2+ complex with the corresponding LCAO drawn beside them. Also on the diagrams of the LCAOs there are annotations analysing the structure.

[[File:Real_MO_37.PNG]] [[File:LCAO MO 36.PNG || 500px ]]

bonding MO 36 (eg)

[[File:Real_MO_46.PNG]] [[File:MO_46_LCAO.PNG || 500px ]]

bonding MO 46 (t1g)

[[File:Real MO 50 LUMO.PNG]] [[File:LCAO MO 50 LUMO.PNG || 500px ]]

anti-bonding MO 50 (LUMO/eg)

File:MO 46 LCAO.PNG

2019-05-24T13:18:46Z

Jh3817:

JoeWiki1

2019-05-23T21:31:41Z

Jh3817:

== Year 2 Inorganic comp labs ==

=== BH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p),
Symmetry= D3h

[[File:BH3_info.PNG]]

Item Value Threshold Converged?

Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

Link to frequency file: [[File:JH_BH3_FREQ.LOG]]

Low frequencies --- -0.4072 -0.1962 -0.0055 25.2514 27.2430 27.2460

Low frequencies --- 1163.1897 1213.3128 1213.3155

<jmol><jmolApplet>
<title>Optimised BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JH_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Vibration Data ====

{| class="wikitable" border="1"
|+ Vibrations table
! Stretch or Bend? !! Intensity !! Symmetry !! IR active? !! Wavenumber(cm-1)
|-
| Bend || 92 || A2" || Yes || 1163
|-
| Bend || 14 || E' || Yes || 1213
|-
| Bend || 14 || E' || Yes || 1213
|-
| Symmetric Stretch || 0 || A1' || No || 2581
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|}

[[File:BH3_vibrations_spectrum_JH.PNG]]

Spectrum shows 3 peaks out of 6 shown in table. 1 is IR in active leaving 5. Two pairs in the 5 are degenerate meaning they have the same energy meaning only 3 peaks show.

[[File:MO_diagram_JH.PNG]] [1111111111111111111111111111111111111111]

The LCAOs seem very accurate as they depict AOs which combine to form the real MOs very well. Minor issues arise from the fact that it can be said that the overlapping of the orbitals may not be able to be seen fully and the fact that the sizes of the AOs, which represents contribution isn’t consistent. Hydrogen is more electronegative then boron and is therefore lower in energy. Hydrogen should be contributing more to the bonding orbitals and born should be contributing more to the anti-bonding orbitals but for some of them this might not be able to be seen accurately. This shows that the LCAO is a useful tool for finding what a real MO would look like.

=== NH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:NH3_point_group_summary.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES

Link to frequency file: [[File:NH3_OP_JH.LOG]]

Low frequencies --- -8.5628 -8.5571 -0.0047 0.0454 0.1785 26.4189

Low frequencies --- 1089.7603 1694.1865 1694.1865

<jmol><jmolApplet>
<title>Optimised NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3_OP_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:BH3NH3_point_group_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000514 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

Link to frequency file: [[File:NH3BH3_FREQ_NEW.LOG]]

Low frequencies --- -0.0005 0.0003 0.0014 16.7270 18.7414 42.2600

Low frequencies --- 266.2799 632.3010 639.2486

<jmol><jmolApplet>
<title>Optimised NH3BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3BH3_FREQ_NEW.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Association energies ====
E(NH3)= -56.55776863 a.u.

E(BH3)= -26.61532362 a.u.

E(NH3BH3)= -83.22469031 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)], Therefore ΔE= (-83.22468960) - [(-56.55776863)+(-26.61532362)]= -0.05159806 a.u. (-134 KJ/Mol)

The B-N dative bond is weak and this shown when compared to the Al-N bond which has an energy of 297KJ/Mol (https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf)(22222222222)

=== NI3 ===
Method= RB3LYP,
Basis set= Gen

[[File:New_NI3_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000102 0.000450 YES
RMS Force 0.000075 0.000300 YES
Maximum Displacement 0.000858 0.001800 YES
RMS Displacement 0.000629 0.001200 YES

Link to frequency file: [[File:NEW_NI3_JH.LOG]]

Low frequencies --- -12.3845 -12.3781 -5.6129 -0.0040 0.0194 0.0711

Low frequencies --- 100.9307 100.9314 147.2333

<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NEW_NI3_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised B-I bond distance is 2.18 angstrom

===Days 2 and 3 Project: Metal carbonyls===
This sections of the wiki page focuses on metal carbonyls, more specifically their bond-lengths and CO bond frequencies. The metal-complexes which will be focused on are [Cr(CO)6], [Mn(CO)6]+ and [Fe(CO)6]2+. These were chosen as they come one after another in the d-block so it would be interesting to see how bond-lengths and bond frequencies vary across the period. 2 of the complexes are charged (positively) while one is neutral and this is something which must be taken into account when analysing bond-lengths and bond frequencies. An initial prediction would be that bond length increases across a period (as the metal complexes are becoming more positive meaning less overlap with the CO pi* and overall less back-donation and since back donation strengths the M-C bond less of this means an increases in bond length) and that bond frequencies increases.

==== [Cr(CO)6] ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Cr

[[File:Cr(CO)6_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000110 0.000450 YES
RMS Force 0.000041 0.000300 YES
Maximum Displacement 0.000705 0.001800 YES
RMS Displacement 0.000334 0.001200 YES

Link to frequency file: [[File:CR(CO)6_JH_2.LOG]]

Low frequencies --- -0.0014 -0.0013 -0.0010 11.7482 11.7482 11.7482

Low frequencies --- 66.6574 66.6574 66.6574

<jmol><jmolApplet>
<title>Optimised Cr(CO)6 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>CR(CO)6_JH_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Mn(CO)6]+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Mn

[[File:-Mn(CO)62+_summary_JH3817.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000430 0.001800 YES
RMS Displacement 0.000204 0.001200 YES

Link to frequency file: [[File:-MN(CO)6-+_OP_FREQ_JH.LOG]]

Low frequencies --- -0.0007 0.0006 0.0009 4.7607 4.7607 4.7607

Low frequencies --- 76.3202 76.3202 76.3202

<jmol><jmolApplet>
<title>Optimised Mn(CO)6+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-MN(CO)6-+_OP_FREQ_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Fe(CO)6]2+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Fe

[[File:-Fe(CO)6-2+_freq_op_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000429 0.001800 YES
RMS Displacement 0.000200 0.001200 YES

Link to frequency file: [[File:-FE(CO)6-2+_OP_FREQ.LOG]]

Low frequencies --- -10.5293 -10.5293 -10.5292 -0.0014 -0.0011 -0.0009

Low frequencies --- 82.1285 82.1285 82.1285

<jmol><jmolApplet>
<title>Optimised [FE(CO)6]2+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-FE(CO)6-2+_OP_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Analysing properties ====

{| class="wikitable" border="1"
|+ Bond Length
! Metal complex !! Bond Length(Å)
|-
| [Cr(CO)6] || 1.915
|-
| [Mn(CO)6]+ || 1.908
|-
| [Fe(CO)6]2+ || 1.940
|}

The table above shows the bond metal centre-carbon bond lengths. It shows a decrease moving from Cr to Mn and from Mn to Fe there is an increase. This initial decrease in M-C bond length goes against what was predicted but after speaking to Professor Hunt it turns out a full explanation of this decrease in bond length is to complex for the course and so wont be provided.The the later drastic increase is due to a contraction of the d-orbitals causing greater repulsion between the electrons leading to poorer overlap with the CO orbitals meaning less back-bonding and and weaker, so therefore longer, metal-carbon bonds. This agrees with the prediction made earlier.

{| class="wikitable" border="1"
|+ Vibrations table 2
! Metal complex !! Intensity !! Vibration type !! Wavenumber(cm-1)
|-
| Cr(CO)6 || 1637 || symmetric stretch || 2086
|-
| [Mn(CO)6]+ || 879 || symmetric stretch || 2199
|-
| [Fe(CO)6]2+ || 272 || symmetric stretch || 2297
|}

This table above shows the wave-number and intensity all the IR active symmetric stretches of all the metal complexes CO ligands. As each complex has 13 atoms it is expected to have 3(13)-6= 33 vibrational modes but as shown in the vibrational spectra below many of these modes are IR inactive and have intensities of 0, an example of this is the totally symmetric C-O vibrations meaning they cannot be analysed given the fact that they don't appear. As predicted earlier across the period CO bond frequency would increase and this is due to back donation. Whilst back bonding causes an increase in the M-C bond there is also a increase in the CO bond length. The more positive the metal centre means contraction of the d-orbitals and this means that their is a less overlap between the d-orbital and CO pi* orbital and the less overlap with this orbital the stronger the CO bond.

[[File:Cr_vibrational_spectrum.PNG]] Cr complex Vibrational spectrum

[[File:Mn_vibrational_spectrum.PNG]] Mn complex Vibrational spectrum

[[File:Fe_vibrational_spectrum.PNG]] Fe complex Vibrational spectrum

The images below are three of the molecular orbitals of the [Fe(CO)6]2+ complex with the corresponding LCAO drawn beside them. Also on the diagrams of the LCAOs there are annotations analysing the structure.

[[File:Real_MO_37.PNG]] [[File:LCAO MO 36.PNG || 500px ]]

bonding MO 36 (eg)

[[File:Real_MO_46.PNG]] [[File: || 500px ]]

bonding MO 46 (t1g)

[[File:Real MO 50 LUMO.PNG]] [[File:LCAO MO 50 LUMO.PNG || 500px ]]

anti-bonding MO 50 (LUMO/eg)

File:Real MO 46.PNG

2019-05-23T21:30:39Z

Jh3817:

JoeWiki1

2019-05-23T21:25:16Z

Jh3817:

== Year 2 Inorganic comp labs ==

=== BH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p),
Symmetry= D3h

[[File:BH3_info.PNG]]

Item Value Threshold Converged?

Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

Link to frequency file: [[File:JH_BH3_FREQ.LOG]]

Low frequencies --- -0.4072 -0.1962 -0.0055 25.2514 27.2430 27.2460

Low frequencies --- 1163.1897 1213.3128 1213.3155

<jmol><jmolApplet>
<title>Optimised BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JH_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Vibration Data ====

{| class="wikitable" border="1"
|+ Vibrations table
! Stretch or Bend? !! Intensity !! Symmetry !! IR active? !! Wavenumber(cm-1)
|-
| Bend || 92 || A2" || Yes || 1163
|-
| Bend || 14 || E' || Yes || 1213
|-
| Bend || 14 || E' || Yes || 1213
|-
| Symmetric Stretch || 0 || A1' || No || 2581
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|}

[[File:BH3_vibrations_spectrum_JH.PNG]]

Spectrum shows 3 peaks out of 6 shown in table. 1 is IR in active leaving 5. Two pairs in the 5 are degenerate meaning they have the same energy meaning only 3 peaks show.

[[File:MO_diagram_JH.PNG]] [1111111111111111111111111111111111111111]

The LCAOs seem very accurate as they depict AOs which combine to form the real MOs very well. Minor issues arise from the fact that it can be said that the overlapping of the orbitals may not be able to be seen fully and the fact that the sizes of the AOs, which represents contribution isn’t consistent. Hydrogen is more electronegative then boron and is therefore lower in energy. Hydrogen should be contributing more to the bonding orbitals and born should be contributing more to the anti-bonding orbitals but for some of them this might not be able to be seen accurately. This shows that the LCAO is a useful tool for finding what a real MO would look like.

=== NH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:NH3_point_group_summary.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES

Link to frequency file: [[File:NH3_OP_JH.LOG]]

Low frequencies --- -8.5628 -8.5571 -0.0047 0.0454 0.1785 26.4189

Low frequencies --- 1089.7603 1694.1865 1694.1865

<jmol><jmolApplet>
<title>Optimised NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3_OP_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:BH3NH3_point_group_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000514 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

Link to frequency file: [[File:NH3BH3_FREQ_NEW.LOG]]

Low frequencies --- -0.0005 0.0003 0.0014 16.7270 18.7414 42.2600

Low frequencies --- 266.2799 632.3010 639.2486

<jmol><jmolApplet>
<title>Optimised NH3BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3BH3_FREQ_NEW.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Association energies ====
E(NH3)= -56.55776863 a.u.

E(BH3)= -26.61532362 a.u.

E(NH3BH3)= -83.22469031 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)], Therefore ΔE= (-83.22468960) - [(-56.55776863)+(-26.61532362)]= -0.05159806 a.u. (-134 KJ/Mol)

The B-N dative bond is weak and this shown when compared to the Al-N bond which has an energy of 297KJ/Mol (https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf)(22222222222)

=== NI3 ===
Method= RB3LYP,
Basis set= Gen

[[File:New_NI3_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000102 0.000450 YES
RMS Force 0.000075 0.000300 YES
Maximum Displacement 0.000858 0.001800 YES
RMS Displacement 0.000629 0.001200 YES

Link to frequency file: [[File:NEW_NI3_JH.LOG]]

Low frequencies --- -12.3845 -12.3781 -5.6129 -0.0040 0.0194 0.0711

Low frequencies --- 100.9307 100.9314 147.2333

<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NEW_NI3_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised B-I bond distance is 2.18 angstrom

===Days 2 and 3 Project: Metal carbonyls===
This sections of the wiki page focuses on metal carbonyls, more specifically their bond-lengths and CO bond frequencies. The metal-complexes which will be focused on are [Cr(CO)6], [Mn(CO)6]+ and [Fe(CO)6]2+. These were chosen as they come one after another in the d-block so it would be interesting to see how bond-lengths and bond frequencies vary across the period. 2 of the complexes are charged (positively) while one is neutral and this is something which must be taken into account when analysing bond-lengths and bond frequencies. An initial prediction would be that bond length increases across a period (as the metal complexes are becoming more positive meaning less overlap with the CO pi* and overall less back-donation and since back donation strengths the M-C bond less of this means an increases in bond length) and that bond frequencies increases.

==== [Cr(CO)6] ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Cr

[[File:Cr(CO)6_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000110 0.000450 YES
RMS Force 0.000041 0.000300 YES
Maximum Displacement 0.000705 0.001800 YES
RMS Displacement 0.000334 0.001200 YES

Link to frequency file: [[File:CR(CO)6_JH_2.LOG]]

Low frequencies --- -0.0014 -0.0013 -0.0010 11.7482 11.7482 11.7482

Low frequencies --- 66.6574 66.6574 66.6574

<jmol><jmolApplet>
<title>Optimised Cr(CO)6 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>CR(CO)6_JH_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Mn(CO)6]+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Mn

[[File:-Mn(CO)62+_summary_JH3817.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000430 0.001800 YES
RMS Displacement 0.000204 0.001200 YES

Link to frequency file: [[File:-MN(CO)6-+_OP_FREQ_JH.LOG]]

Low frequencies --- -0.0007 0.0006 0.0009 4.7607 4.7607 4.7607

Low frequencies --- 76.3202 76.3202 76.3202

<jmol><jmolApplet>
<title>Optimised Mn(CO)6+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-MN(CO)6-+_OP_FREQ_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Fe(CO)6]2+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Fe

[[File:-Fe(CO)6-2+_freq_op_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000429 0.001800 YES
RMS Displacement 0.000200 0.001200 YES

Link to frequency file: [[File:-FE(CO)6-2+_OP_FREQ.LOG]]

Low frequencies --- -10.5293 -10.5293 -10.5292 -0.0014 -0.0011 -0.0009

Low frequencies --- 82.1285 82.1285 82.1285

<jmol><jmolApplet>
<title>Optimised [FE(CO)6]2+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-FE(CO)6-2+_OP_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Analysing properties ====

{| class="wikitable" border="1"
|+ Bond Length
! Metal complex !! Bond Length(Å)
|-
| [Cr(CO)6] || 1.915
|-
| [Mn(CO)6]+ || 1.908
|-
| [Fe(CO)6]2+ || 1.940
|}

The table above shows the bond metal centre-carbon bond lengths. It shows a decrease moving from Cr to Mn and from Mn to Fe there is an increase. This initial decrease in M-C bond length goes against what was predicted but after speaking to Professor Hunt it turns out a full explanation of this decrease in bond length is to complex for the course and so wont be provided.The the later drastic increase is due to a contraction of the d-orbitals causing greater repulsion between the electrons leading to poorer overlap with the CO orbitals meaning less back-bonding and and weaker, so therefore longer, metal-carbon bonds. This agrees with the prediction made earlier.

{| class="wikitable" border="1"
|+ Vibrations table 2
! Metal complex !! Intensity !! Vibration type !! Wavenumber(cm-1)
|-
| Cr(CO)6 || 1637 || symmetric stretch || 2086
|-
| [Mn(CO)6]+ || 879 || symmetric stretch || 2199
|-
| [Fe(CO)6]2+ || 272 || symmetric stretch || 2297
|}

This table above shows the wave-number and intensity all the IR active symmetric stretches of all the metal complexes CO ligands. As each complex has 13 atoms it is expected to have 3(13)-6= 33 vibrational modes but as shown in the vibrational spectra below many of these modes are IR inactive and have intensities of 0, an example of this is the totally symmetric C-O vibrations meaning they cannot be analysed given the fact that they don't appear. As predicted earlier across the period CO bond frequency would increase and this is due to back donation. Whilst back bonding causes an increase in the M-C bond there is also a increase in the CO bond length. The more positive the metal centre means contraction of the d-orbitals and this means that their is a less overlap between the d-orbital and CO pi* orbital and the less overlap with this orbital the stronger the CO bond.

[[File:Cr_vibrational_spectrum.PNG]] Cr complex Vibrational spectrum

[[File:Mn_vibrational_spectrum.PNG]] Mn complex Vibrational spectrum

[[File:Fe_vibrational_spectrum.PNG]] Fe complex Vibrational spectrum

The images below are three of the molecular orbitals of the [Fe(CO)6]2+ complex with the corresponding LCAO drawn beside them. Also on the diagrams of the LCAOs there are annotations analysing the structure.

[[File:Real_MO_37.PNG]] [[File:LCAO MO 36.PNG || 500px ]]

bonding MO 36 (eg)

[[File:]] [[File: || 500px ]]

bonding MO 49 (HOMO/t2g)

[[File:Real MO 50 LUMO.PNG]] [[File:LCAO MO 50 LUMO.PNG || 500px ]]

anti-bonding MO 50 (LUMO/eg)

JoeWiki1

2019-05-23T21:24:15Z

Jh3817:

== Year 2 Inorganic comp labs ==

=== BH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p),
Symmetry= D3h

[[File:BH3_info.PNG]]

Item Value Threshold Converged?

Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

Link to frequency file: [[File:JH_BH3_FREQ.LOG]]

Low frequencies --- -0.4072 -0.1962 -0.0055 25.2514 27.2430 27.2460

Low frequencies --- 1163.1897 1213.3128 1213.3155

<jmol><jmolApplet>
<title>Optimised BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JH_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Vibration Data ====

{| class="wikitable" border="1"
|+ Vibrations table
! Stretch or Bend? !! Intensity !! Symmetry !! IR active? !! Wavenumber(cm-1)
|-
| Bend || 92 || A2" || Yes || 1163
|-
| Bend || 14 || E' || Yes || 1213
|-
| Bend || 14 || E' || Yes || 1213
|-
| Symmetric Stretch || 0 || A1' || No || 2581
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|}

[[File:BH3_vibrations_spectrum_JH.PNG]]

Spectrum shows 3 peaks out of 6 shown in table. 1 is IR in active leaving 5. Two pairs in the 5 are degenerate meaning they have the same energy meaning only 3 peaks show.

[[File:MO_diagram_JH.PNG]] [1111111111111111111111111111111111111111]

The LCAOs seem very accurate as they depict AOs which combine to form the real MOs very well. Minor issues arise from the fact that it can be said that the overlapping of the orbitals may not be able to be seen fully and the fact that the sizes of the AOs, which represents contribution isn’t consistent. Hydrogen is more electronegative then boron and is therefore lower in energy. Hydrogen should be contributing more to the bonding orbitals and born should be contributing more to the anti-bonding orbitals but for some of them this might not be able to be seen accurately. This shows that the LCAO is a useful tool for finding what a real MO would look like.

=== NH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:NH3_point_group_summary.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES

Link to frequency file: [[File:NH3_OP_JH.LOG]]

Low frequencies --- -8.5628 -8.5571 -0.0047 0.0454 0.1785 26.4189

Low frequencies --- 1089.7603 1694.1865 1694.1865

<jmol><jmolApplet>
<title>Optimised NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3_OP_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:BH3NH3_point_group_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000514 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

Link to frequency file: [[File:NH3BH3_FREQ_NEW.LOG]]

Low frequencies --- -0.0005 0.0003 0.0014 16.7270 18.7414 42.2600

Low frequencies --- 266.2799 632.3010 639.2486

<jmol><jmolApplet>
<title>Optimised NH3BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3BH3_FREQ_NEW.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Association energies ====
E(NH3)= -56.55776863 a.u.

E(BH3)= -26.61532362 a.u.

E(NH3BH3)= -83.22469031 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)], Therefore ΔE= (-83.22468960) - [(-56.55776863)+(-26.61532362)]= -0.05159806 a.u. (-134 KJ/Mol)

The B-N dative bond is weak and this shown when compared to the Al-N bond which has an energy of 297KJ/Mol (https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf)(22222222222)

=== NI3 ===
Method= RB3LYP,
Basis set= Gen

[[File:New_NI3_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000102 0.000450 YES
RMS Force 0.000075 0.000300 YES
Maximum Displacement 0.000858 0.001800 YES
RMS Displacement 0.000629 0.001200 YES

Link to frequency file: [[File:NEW_NI3_JH.LOG]]

Low frequencies --- -12.3845 -12.3781 -5.6129 -0.0040 0.0194 0.0711

Low frequencies --- 100.9307 100.9314 147.2333

<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NEW_NI3_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised B-I bond distance is 2.18 angstrom

===Days 2 and 3 Project: Metal carbonyls===
This sections of the wiki page focuses on metal carbonyls, more specifically their bond-lengths and CO bond frequencies. The metal-complexes which will be focused on are [Cr(CO)6], [Mn(CO)6]+ and [Fe(CO)6]2+. These were chosen as they come one after another in the d-block so it would be interesting to see how bond-lengths and bond frequencies vary across the period. 2 of the complexes are charged (positively) while one is neutral and this is something which must be taken into account when analysing bond-lengths and bond frequencies. An initial prediction would be that bond length increases across a period (as the metal complexes are becoming more positive meaning less overlap with the CO pi* and overall less back-donation and since back donation strengths the M-C bond less of this means an increases in bond length) and that bond frequencies increases.

==== [Cr(CO)6] ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Cr

[[File:Cr(CO)6_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000110 0.000450 YES
RMS Force 0.000041 0.000300 YES
Maximum Displacement 0.000705 0.001800 YES
RMS Displacement 0.000334 0.001200 YES

Link to frequency file: [[File:CR(CO)6_JH_2.LOG]]

Low frequencies --- -0.0014 -0.0013 -0.0010 11.7482 11.7482 11.7482

Low frequencies --- 66.6574 66.6574 66.6574

<jmol><jmolApplet>
<title>Optimised Cr(CO)6 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>CR(CO)6_JH_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Mn(CO)6]+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Mn

[[File:-Mn(CO)62+_summary_JH3817.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000430 0.001800 YES
RMS Displacement 0.000204 0.001200 YES

Link to frequency file: [[File:-MN(CO)6-+_OP_FREQ_JH.LOG]]

Low frequencies --- -0.0007 0.0006 0.0009 4.7607 4.7607 4.7607

Low frequencies --- 76.3202 76.3202 76.3202

<jmol><jmolApplet>
<title>Optimised Mn(CO)6+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-MN(CO)6-+_OP_FREQ_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Fe(CO)6]2+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Fe

[[File:-Fe(CO)6-2+_freq_op_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000429 0.001800 YES
RMS Displacement 0.000200 0.001200 YES

Link to frequency file: [[File:-FE(CO)6-2+_OP_FREQ.LOG]]

Low frequencies --- -10.5293 -10.5293 -10.5292 -0.0014 -0.0011 -0.0009

Low frequencies --- 82.1285 82.1285 82.1285

<jmol><jmolApplet>
<title>Optimised [FE(CO)6]2+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-FE(CO)6-2+_OP_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Analysing properties ====

{| class="wikitable" border="1"
|+ Bond Length
! Metal complex !! Bond Length(Å)
|-
| [Cr(CO)6] || 1.915
|-
| [Mn(CO)6]+ || 1.908
|-
| [Fe(CO)6]2+ || 1.940
|}

The table above shows the bond metal centre-carbon bond lengths. It shows a decrease moving from Cr to Mn and from Mn to Fe there is an increase. This initial decrease in M-C bond length goes against what was predicted but after speaking to Professor Hunt it turns out a full explanation of this decrease in bond length is to complex for the course and so wont be provided.The the later drastic increase is due to a contraction of the d-orbitals causing greater repulsion between the electrons leading to poorer overlap with the CO orbitals meaning less back-bonding and and weaker, so therefore longer, metal-carbon bonds. This agrees with the prediction made earlier.

{| class="wikitable" border="1"
|+ Vibrations table 2
! Metal complex !! Intensity !! Vibration type !! Wavenumber(cm-1)
|-
| Cr(CO)6 || 1637 || symmetric stretch || 2086
|-
| [Mn(CO)6]+ || 879 || symmetric stretch || 2199
|-
| [Fe(CO)6]2+ || 272 || symmetric stretch || 2297
|}

This table above shows the wave-number and intensity all the IR active symmetric stretches of all the metal complexes CO ligands. As each complex has 13 atoms it is expected to have 3(13)-6= 33 vibrational modes but as shown in the vibrational spectra below many of these modes are IR inactive and have intensities of 0, an example of this is the totally symmetric C-O vibrations meaning they cannot be analysed given the fact that they don't appear. As predicted earlier across the period CO bond frequency would increase and this is due to back donation. Whilst back bonding causes an increase in the M-C bond there is also a increase in the CO bond length. The more positive the metal centre means contraction of the d-orbitals and this means that their is a less overlap between the d-orbital and CO pi* orbital and the less overlap with this orbital the stronger the CO bond.

[[File:Cr_vibrational_spectrum.PNG]] Cr complex Vibrational spectrum

[[File:Mn_vibrational_spectrum.PNG]] Mn complex Vibrational spectrum

[[File:Fe_vibrational_spectrum.PNG]] Fe complex Vibrational spectrum

The images below are three of the molecular orbitals of the [Fe(CO)6]2+ complex with the corresponding LCAO drawn beside them. Also on the diagrams of the LCAOs there are annotations analysing the structure.

[[File:Real_MO_37.PNG]] [[File:LCAO MO 36.PNG || 500px ]]

bonding MO 36 (eg)

[[File:]] [[File: || 500px ]]

bonding MO 49 (HOMO/t2g)

[[File:LCAO MO 50 LUMO.PNG]] [[File: || 500px ]]

anti-bonding MO 50 (LUMO/eg)

File:LCAO MO 50 LUMO.PNG

2019-05-23T21:23:48Z

Jh3817:

File:Real MO 50 LUMO.PNG

2019-05-23T21:19:14Z

Jh3817:

JoeWiki1

2019-05-23T20:41:07Z

Jh3817: /* Days 2 and 3 Project: Metal carbonyls */

JoeWiki1

2019-05-23T20:37:13Z

Jh3817: /* Analysing properties */

== Year 2 Inorganic comp labs ==

=== BH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p),
Symmetry= D3h

[[File:BH3_info.PNG]]

Item Value Threshold Converged?

Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

Link to frequency file: [[File:JH_BH3_FREQ.LOG]]

Low frequencies --- -0.4072 -0.1962 -0.0055 25.2514 27.2430 27.2460

Low frequencies --- 1163.1897 1213.3128 1213.3155

<jmol><jmolApplet>
<title>Optimised BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JH_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Vibration Data ====

{| class="wikitable" border="1"
|+ Vibrations table
! Stretch or Bend? !! Intensity !! Symmetry !! IR active? !! Wavenumber(cm-1)
|-
| Bend || 92 || A2" || Yes || 1163
|-
| Bend || 14 || E' || Yes || 1213
|-
| Bend || 14 || E' || Yes || 1213
|-
| Symmetric Stretch || 0 || A1' || No || 2581
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|}

[[File:BH3_vibrations_spectrum_JH.PNG]]

Spectrum shows 3 peaks out of 6 shown in table. 1 is IR in active leaving 5. Two pairs in the 5 are degenerate meaning they have the same energy meaning only 3 peaks show.

[[File:MO_diagram_JH.PNG]] [1111111111111111111111111111111111111111]

The LCAOs seem very accurate as they depict AOs which combine to form the real MOs very well. Minor issues arise from the fact that it can be said that the overlapping of the orbitals may not be able to be seen fully and the fact that the sizes of the AOs, which represents contribution isn’t consistent. Hydrogen is more electronegative then boron and is therefore lower in energy. Hydrogen should be contributing more to the bonding orbitals and born should be contributing more to the anti-bonding orbitals but for some of them this might not be able to be seen accurately. This shows that the LCAO is a useful tool for finding what a real MO would look like.

=== NH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:NH3_point_group_summary.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES

Link to frequency file: [[File:NH3_OP_JH.LOG]]

Low frequencies --- -8.5628 -8.5571 -0.0047 0.0454 0.1785 26.4189

Low frequencies --- 1089.7603 1694.1865 1694.1865

<jmol><jmolApplet>
<title>Optimised NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3_OP_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:BH3NH3_point_group_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000514 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

Link to frequency file: [[File:NH3BH3_FREQ_NEW.LOG]]

Low frequencies --- -0.0005 0.0003 0.0014 16.7270 18.7414 42.2600

Low frequencies --- 266.2799 632.3010 639.2486

<jmol><jmolApplet>
<title>Optimised NH3BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3BH3_FREQ_NEW.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Association energies ====
E(NH3)= -56.55776863 a.u.

E(BH3)= -26.61532362 a.u.

E(NH3BH3)= -83.22469031 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)], Therefore ΔE= (-83.22468960) - [(-56.55776863)+(-26.61532362)]= -0.05159806 a.u. (-134 KJ/Mol)

The B-N dative bond is weak and this shown when compared to the Al-N bond which has an energy of 297KJ/Mol (https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf)(22222222222)

=== NI3 ===
Method= RB3LYP,
Basis set= Gen

[[File:New_NI3_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000102 0.000450 YES
RMS Force 0.000075 0.000300 YES
Maximum Displacement 0.000858 0.001800 YES
RMS Displacement 0.000629 0.001200 YES

Link to frequency file: [[File:NEW_NI3_JH.LOG]]

Low frequencies --- -12.3845 -12.3781 -5.6129 -0.0040 0.0194 0.0711

Low frequencies --- 100.9307 100.9314 147.2333

<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NEW_NI3_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised B-I bond distance is 2.18 angstrom

===Days 2 and 3 Project: Metal carbonyls===
This sections of the wiki page focuses on metal carbonyls, more specifically their bond-lengths and CO bond frequencies. The metal-complexes which will be focused on are [Cr(CO)6], [Mn(CO)6]+ and [Fe(CO)6]2+. These were chosen as they come one after another in the d-block so it would be interesting to see how bond-lengths and bond frequencies vary across the period. 2 of the complexes are charged (positively) while one is neutral and this is something which must be taken into account when analysing bond-lengths and bond frequencies. An initial prediction would be that bond length increases across a period (as the metal complexes are becoming more positive meaning less overlap with the CO pi* and overall less back-donation and since back donation strengths the M-C bond less of this means an increases in bond length) and that bond frequencies increases.

==== [Cr(CO)6] ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Cr

[[File:Cr(CO)6_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000110 0.000450 YES
RMS Force 0.000041 0.000300 YES
Maximum Displacement 0.000705 0.001800 YES
RMS Displacement 0.000334 0.001200 YES

Link to frequency file: [[File:CR(CO)6_JH_2.LOG]]

Low frequencies --- -0.0014 -0.0013 -0.0010 11.7482 11.7482 11.7482

Low frequencies --- 66.6574 66.6574 66.6574

<jmol><jmolApplet>
<title>Optimised Cr(CO)6 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>CR(CO)6_JH_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Mn(CO)6]+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Mn

[[File:-Mn(CO)62+_summary_JH3817.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000430 0.001800 YES
RMS Displacement 0.000204 0.001200 YES

Link to frequency file: [[File:-MN(CO)6-+_OP_FREQ_JH.LOG]]

Low frequencies --- -0.0007 0.0006 0.0009 4.7607 4.7607 4.7607

Low frequencies --- 76.3202 76.3202 76.3202

<jmol><jmolApplet>
<title>Optimised Mn(CO)6+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-MN(CO)6-+_OP_FREQ_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Fe(CO)6]2+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Fe

[[File:-Fe(CO)6-2+_freq_op_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000429 0.001800 YES
RMS Displacement 0.000200 0.001200 YES

Link to frequency file: [[File:-FE(CO)6-2+_OP_FREQ.LOG]]

Low frequencies --- -10.5293 -10.5293 -10.5292 -0.0014 -0.0011 -0.0009

Low frequencies --- 82.1285 82.1285 82.1285

<jmol><jmolApplet>
<title>Optimised [FE(CO)6]2+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-FE(CO)6-2+_OP_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Analysing properties ====

{| class="wikitable" border="1"
|+ Bond Length
! Metal complex !! Bond Length(Å)
|-
| [Cr(CO)6] || 1.915
|-
| [Mn(CO)6]+ || 1.908
|-
| [Fe(CO)6]2+ || 1.940
|}

The table above shows the bond metal centre-carbon bond lengths. It shows a decrease moving from Cr to Mn and from Mn to Fe there is an increase. This initial decrease in M-C bond length goes against what was predicted but after speaking to Professor Hunt it turns out a full explanation of this decrease in bond length is to complex for the course and so wont be provided.The the later drastic increase is due to a contraction of the d-orbitals causing greater repulsion between the electrons leading to poorer overlap with the CO orbitals meaning less back-bonding and and weaker, so therefore longer, metal-carbon bonds. This agrees with the prediction made earlier.

{| class="wikitable" border="1"
|+ Vibrations table 2
! Metal complex !! Intensity !! Vibration type !! Wavenumber(cm-1)
|-
| Cr(CO)6 || 1637 || symmetric stretch || 2086
|-
| [Mn(CO)6]+ || 879 || symmetric stretch || 2199
|-
| [Fe(CO)6]2+ || 272 || symmetric stretch || 2297
|}

This table above shows the wave-number and intensity all the IR active symmetric stretches of all the metal complexes CO ligands. As each complex has 13 atoms it is expected to have 3(13)-6= 33 vibrational modes but as shown in the vibrational spectra below many of these modes are IR inactive and have intensities of 0, an example of this is the totally symmetric C-O vibrations meaning they cannot be analysed given the fact that they don't appear. As predicted earlier across the period CO bond frequency would increase and this is due to back donation. Whilst back bonding causes an increase in the M-C bond there is also a increase in the CO bond length. The more positive the metal centre means contraction of the d-orbitals and this means that their is a less overlap between the d-orbital and CO pi* orbital and the less overlap with this orbital the stronger the CO bond.

[[File:Cr_vibrational_spectrum.PNG]] Cr complex Vibrational spectrum

[[File:Mn_vibrational_spectrum.PNG]] Mn complex Vibrational spectrum

[[File:Fe_vibrational_spectrum.PNG]] Fe complex Vibrational spectrum

The images below are three of the molecular orbitals of the [Fe(CO)6]2+ complex with the corresponding LCAO drawn beside them

[[File:Real_MO_37.PNG]] [[File:LCAO MO 36.PNG || 500px ]]

bonding MO 36 (eg)

JoeWiki1

2019-05-23T20:36:40Z

Jh3817: /* Analysing properties */

== Year 2 Inorganic comp labs ==

=== BH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p),
Symmetry= D3h

[[File:BH3_info.PNG]]

Item Value Threshold Converged?

Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

Link to frequency file: [[File:JH_BH3_FREQ.LOG]]

Low frequencies --- -0.4072 -0.1962 -0.0055 25.2514 27.2430 27.2460

Low frequencies --- 1163.1897 1213.3128 1213.3155

<jmol><jmolApplet>
<title>Optimised BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JH_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Vibration Data ====

{| class="wikitable" border="1"
|+ Vibrations table
! Stretch or Bend? !! Intensity !! Symmetry !! IR active? !! Wavenumber(cm-1)
|-
| Bend || 92 || A2" || Yes || 1163
|-
| Bend || 14 || E' || Yes || 1213
|-
| Bend || 14 || E' || Yes || 1213
|-
| Symmetric Stretch || 0 || A1' || No || 2581
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|}

[[File:BH3_vibrations_spectrum_JH.PNG]]

Spectrum shows 3 peaks out of 6 shown in table. 1 is IR in active leaving 5. Two pairs in the 5 are degenerate meaning they have the same energy meaning only 3 peaks show.

[[File:MO_diagram_JH.PNG]] [1111111111111111111111111111111111111111]

The LCAOs seem very accurate as they depict AOs which combine to form the real MOs very well. Minor issues arise from the fact that it can be said that the overlapping of the orbitals may not be able to be seen fully and the fact that the sizes of the AOs, which represents contribution isn’t consistent. Hydrogen is more electronegative then boron and is therefore lower in energy. Hydrogen should be contributing more to the bonding orbitals and born should be contributing more to the anti-bonding orbitals but for some of them this might not be able to be seen accurately. This shows that the LCAO is a useful tool for finding what a real MO would look like.

=== NH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:NH3_point_group_summary.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES

Link to frequency file: [[File:NH3_OP_JH.LOG]]

Low frequencies --- -8.5628 -8.5571 -0.0047 0.0454 0.1785 26.4189

Low frequencies --- 1089.7603 1694.1865 1694.1865

<jmol><jmolApplet>
<title>Optimised NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3_OP_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:BH3NH3_point_group_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000514 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

Link to frequency file: [[File:NH3BH3_FREQ_NEW.LOG]]

Low frequencies --- -0.0005 0.0003 0.0014 16.7270 18.7414 42.2600

Low frequencies --- 266.2799 632.3010 639.2486

<jmol><jmolApplet>
<title>Optimised NH3BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3BH3_FREQ_NEW.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Association energies ====
E(NH3)= -56.55776863 a.u.

E(BH3)= -26.61532362 a.u.

E(NH3BH3)= -83.22469031 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)], Therefore ΔE= (-83.22468960) - [(-56.55776863)+(-26.61532362)]= -0.05159806 a.u. (-134 KJ/Mol)

The B-N dative bond is weak and this shown when compared to the Al-N bond which has an energy of 297KJ/Mol (https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf)(22222222222)

=== NI3 ===
Method= RB3LYP,
Basis set= Gen

[[File:New_NI3_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000102 0.000450 YES
RMS Force 0.000075 0.000300 YES
Maximum Displacement 0.000858 0.001800 YES
RMS Displacement 0.000629 0.001200 YES

Link to frequency file: [[File:NEW_NI3_JH.LOG]]

Low frequencies --- -12.3845 -12.3781 -5.6129 -0.0040 0.0194 0.0711

Low frequencies --- 100.9307 100.9314 147.2333

<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NEW_NI3_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised B-I bond distance is 2.18 angstrom

===Days 2 and 3 Project: Metal carbonyls===
This sections of the wiki page focuses on metal carbonyls, more specifically their bond-lengths and CO bond frequencies. The metal-complexes which will be focused on are [Cr(CO)6], [Mn(CO)6]+ and [Fe(CO)6]2+. These were chosen as they come one after another in the d-block so it would be interesting to see how bond-lengths and bond frequencies vary across the period. 2 of the complexes are charged (positively) while one is neutral and this is something which must be taken into account when analysing bond-lengths and bond frequencies. An initial prediction would be that bond length increases across a period (as the metal complexes are becoming more positive meaning less overlap with the CO pi* and overall less back-donation and since back donation strengths the M-C bond less of this means an increases in bond length) and that bond frequencies increases.

==== [Cr(CO)6] ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Cr

[[File:Cr(CO)6_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000110 0.000450 YES
RMS Force 0.000041 0.000300 YES
Maximum Displacement 0.000705 0.001800 YES
RMS Displacement 0.000334 0.001200 YES

Link to frequency file: [[File:CR(CO)6_JH_2.LOG]]

Low frequencies --- -0.0014 -0.0013 -0.0010 11.7482 11.7482 11.7482

Low frequencies --- 66.6574 66.6574 66.6574

<jmol><jmolApplet>
<title>Optimised Cr(CO)6 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>CR(CO)6_JH_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Mn(CO)6]+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Mn

[[File:-Mn(CO)62+_summary_JH3817.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000430 0.001800 YES
RMS Displacement 0.000204 0.001200 YES

Link to frequency file: [[File:-MN(CO)6-+_OP_FREQ_JH.LOG]]

Low frequencies --- -0.0007 0.0006 0.0009 4.7607 4.7607 4.7607

Low frequencies --- 76.3202 76.3202 76.3202

<jmol><jmolApplet>
<title>Optimised Mn(CO)6+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-MN(CO)6-+_OP_FREQ_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Fe(CO)6]2+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Fe

[[File:-Fe(CO)6-2+_freq_op_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000429 0.001800 YES
RMS Displacement 0.000200 0.001200 YES

Link to frequency file: [[File:-FE(CO)6-2+_OP_FREQ.LOG]]

Low frequencies --- -10.5293 -10.5293 -10.5292 -0.0014 -0.0011 -0.0009

Low frequencies --- 82.1285 82.1285 82.1285

<jmol><jmolApplet>
<title>Optimised [FE(CO)6]2+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-FE(CO)6-2+_OP_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Analysing properties ====

{| class="wikitable" border="1"
|+ Bond Length
! Metal complex !! Bond Length(Å)
|-
| [Cr(CO)6] || 1.915
|-
| [Mn(CO)6]+ || 1.908
|-
| [Fe(CO)6]2+ || 1.940
|}

The table above shows the bond metal centre-carbon bond lengths. It shows a decrease moving from Cr to Mn and from Mn to Fe there is an increase. This initial decrease in M-C bond length goes against what was predicted but after speaking to Professor Hunt it turns out a full explanation of this decrease in bond length is to complex for the course and so wont be provided.The the later drastic increase is due to a contraction of the d-orbitals causing greater repulsion between the electrons leading to poorer overlap with the CO orbitals meaning less back-bonding and and weaker, so therefore longer, metal-carbon bonds. This agrees with the prediction made earlier.

{| class="wikitable" border="1"
|+ Vibrations table 2
! Metal complex !! Intensity !! Vibration type !! Wavenumber(cm-1)
|-
| Cr(CO)6 || 1637 || symmetric stretch || 2086
|-
| [Mn(CO)6]+ || 879 || symmetric stretch || 2199
|-
| [Fe(CO)6]2+ || 272 || symmetric stretch || 2297
|}

This table above shows the wave-number and intensity all the IR active symmetric stretches of all the metal complexes CO ligands. As each complex has 13 atoms it is expected to have 3(13)-6= 33 vibrational modes but as shown in the vibrational spectra below many of these modes are IR inactive and have intensities of 0, an example of this is the totally symmetric C-O vibrations meaning they cannot be analysed given the fact that they don't appear. As predicted earlier across the period CO bond frequency would increase and this is due to back donation. Whilst back bonding causes an increase in the M-C bond there is also a increase in the CO bond length. The more positive the metal centre means contraction of the d-orbitals and this means that their is a less overlap between the d-orbital and CO pi* orbital and the less overlap with this orbital the stronger the CO bond.

[[File:Cr_vibrational_spectrum.PNG]] Cr complex Vibrational spectrum

[[File:Mn_vibrational_spectrum.PNG]] Mn complex Vibrational spectrum

[[File:Fe_vibrational_spectrum.PNG]] Fe complex Vibrational spectrum

The images below are three of the molecular orbitals of the [Fe(CO)6]2+ complex with the corresponding LCAO drawn beside them

[[File:Real_MO_37.PNG]] [[File:LCAO MO 36.PNG || 400px ]]

bonding MO 36 (eg)

JoeWiki1

2019-05-23T20:36:22Z

Jh3817: /* Analysing properties */

== Year 2 Inorganic comp labs ==

=== BH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p),
Symmetry= D3h

[[File:BH3_info.PNG]]

Item Value Threshold Converged?

Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

Link to frequency file: [[File:JH_BH3_FREQ.LOG]]

Low frequencies --- -0.4072 -0.1962 -0.0055 25.2514 27.2430 27.2460

Low frequencies --- 1163.1897 1213.3128 1213.3155

<jmol><jmolApplet>
<title>Optimised BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JH_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Vibration Data ====

{| class="wikitable" border="1"
|+ Vibrations table
! Stretch or Bend? !! Intensity !! Symmetry !! IR active? !! Wavenumber(cm-1)
|-
| Bend || 92 || A2" || Yes || 1163
|-
| Bend || 14 || E' || Yes || 1213
|-
| Bend || 14 || E' || Yes || 1213
|-
| Symmetric Stretch || 0 || A1' || No || 2581
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|}

[[File:BH3_vibrations_spectrum_JH.PNG]]

Spectrum shows 3 peaks out of 6 shown in table. 1 is IR in active leaving 5. Two pairs in the 5 are degenerate meaning they have the same energy meaning only 3 peaks show.

[[File:MO_diagram_JH.PNG]] [1111111111111111111111111111111111111111]

The LCAOs seem very accurate as they depict AOs which combine to form the real MOs very well. Minor issues arise from the fact that it can be said that the overlapping of the orbitals may not be able to be seen fully and the fact that the sizes of the AOs, which represents contribution isn’t consistent. Hydrogen is more electronegative then boron and is therefore lower in energy. Hydrogen should be contributing more to the bonding orbitals and born should be contributing more to the anti-bonding orbitals but for some of them this might not be able to be seen accurately. This shows that the LCAO is a useful tool for finding what a real MO would look like.

=== NH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:NH3_point_group_summary.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES

Link to frequency file: [[File:NH3_OP_JH.LOG]]

Low frequencies --- -8.5628 -8.5571 -0.0047 0.0454 0.1785 26.4189

Low frequencies --- 1089.7603 1694.1865 1694.1865

<jmol><jmolApplet>
<title>Optimised NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3_OP_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:BH3NH3_point_group_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000514 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

Link to frequency file: [[File:NH3BH3_FREQ_NEW.LOG]]

Low frequencies --- -0.0005 0.0003 0.0014 16.7270 18.7414 42.2600

Low frequencies --- 266.2799 632.3010 639.2486

<jmol><jmolApplet>
<title>Optimised NH3BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3BH3_FREQ_NEW.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Association energies ====
E(NH3)= -56.55776863 a.u.

E(BH3)= -26.61532362 a.u.

E(NH3BH3)= -83.22469031 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)], Therefore ΔE= (-83.22468960) - [(-56.55776863)+(-26.61532362)]= -0.05159806 a.u. (-134 KJ/Mol)

The B-N dative bond is weak and this shown when compared to the Al-N bond which has an energy of 297KJ/Mol (https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf)(22222222222)

=== NI3 ===
Method= RB3LYP,
Basis set= Gen

[[File:New_NI3_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000102 0.000450 YES
RMS Force 0.000075 0.000300 YES
Maximum Displacement 0.000858 0.001800 YES
RMS Displacement 0.000629 0.001200 YES

Link to frequency file: [[File:NEW_NI3_JH.LOG]]

Low frequencies --- -12.3845 -12.3781 -5.6129 -0.0040 0.0194 0.0711

Low frequencies --- 100.9307 100.9314 147.2333

<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NEW_NI3_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised B-I bond distance is 2.18 angstrom

===Days 2 and 3 Project: Metal carbonyls===
This sections of the wiki page focuses on metal carbonyls, more specifically their bond-lengths and CO bond frequencies. The metal-complexes which will be focused on are [Cr(CO)6], [Mn(CO)6]+ and [Fe(CO)6]2+. These were chosen as they come one after another in the d-block so it would be interesting to see how bond-lengths and bond frequencies vary across the period. 2 of the complexes are charged (positively) while one is neutral and this is something which must be taken into account when analysing bond-lengths and bond frequencies. An initial prediction would be that bond length increases across a period (as the metal complexes are becoming more positive meaning less overlap with the CO pi* and overall less back-donation and since back donation strengths the M-C bond less of this means an increases in bond length) and that bond frequencies increases.

==== [Cr(CO)6] ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Cr

[[File:Cr(CO)6_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000110 0.000450 YES
RMS Force 0.000041 0.000300 YES
Maximum Displacement 0.000705 0.001800 YES
RMS Displacement 0.000334 0.001200 YES

Link to frequency file: [[File:CR(CO)6_JH_2.LOG]]

Low frequencies --- -0.0014 -0.0013 -0.0010 11.7482 11.7482 11.7482

Low frequencies --- 66.6574 66.6574 66.6574

<jmol><jmolApplet>
<title>Optimised Cr(CO)6 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>CR(CO)6_JH_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Mn(CO)6]+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Mn

[[File:-Mn(CO)62+_summary_JH3817.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000430 0.001800 YES
RMS Displacement 0.000204 0.001200 YES

Link to frequency file: [[File:-MN(CO)6-+_OP_FREQ_JH.LOG]]

Low frequencies --- -0.0007 0.0006 0.0009 4.7607 4.7607 4.7607

Low frequencies --- 76.3202 76.3202 76.3202

<jmol><jmolApplet>
<title>Optimised Mn(CO)6+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-MN(CO)6-+_OP_FREQ_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Fe(CO)6]2+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Fe

[[File:-Fe(CO)6-2+_freq_op_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000429 0.001800 YES
RMS Displacement 0.000200 0.001200 YES

Link to frequency file: [[File:-FE(CO)6-2+_OP_FREQ.LOG]]

Low frequencies --- -10.5293 -10.5293 -10.5292 -0.0014 -0.0011 -0.0009

Low frequencies --- 82.1285 82.1285 82.1285

<jmol><jmolApplet>
<title>Optimised [FE(CO)6]2+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-FE(CO)6-2+_OP_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Analysing properties ====

{| class="wikitable" border="1"
|+ Bond Length
! Metal complex !! Bond Length(Å)
|-
| [Cr(CO)6] || 1.915
|-
| [Mn(CO)6]+ || 1.908
|-
| [Fe(CO)6]2+ || 1.940
|}

The table above shows the bond metal centre-carbon bond lengths. It shows a decrease moving from Cr to Mn and from Mn to Fe there is an increase. This initial decrease in M-C bond length goes against what was predicted but after speaking to Professor Hunt it turns out a full explanation of this decrease in bond length is to complex for the course and so wont be provided.The the later drastic increase is due to a contraction of the d-orbitals causing greater repulsion between the electrons leading to poorer overlap with the CO orbitals meaning less back-bonding and and weaker, so therefore longer, metal-carbon bonds. This agrees with the prediction made earlier.

{| class="wikitable" border="1"
|+ Vibrations table 2
! Metal complex !! Intensity !! Vibration type !! Wavenumber(cm-1)
|-
| Cr(CO)6 || 1637 || symmetric stretch || 2086
|-
| [Mn(CO)6]+ || 879 || symmetric stretch || 2199
|-
| [Fe(CO)6]2+ || 272 || symmetric stretch || 2297
|}

This table above shows the wave-number and intensity all the IR active symmetric stretches of all the metal complexes CO ligands. As each complex has 13 atoms it is expected to have 3(13)-6= 33 vibrational modes but as shown in the vibrational spectra below many of these modes are IR inactive and have intensities of 0, an example of this is the totally symmetric C-O vibrations meaning they cannot be analysed given the fact that they don't appear. As predicted earlier across the period CO bond frequency would increase and this is due to back donation. Whilst back bonding causes an increase in the M-C bond there is also a increase in the CO bond length. The more positive the metal centre means contraction of the d-orbitals and this means that their is a less overlap between the d-orbital and CO pi* orbital and the less overlap with this orbital the stronger the CO bond.

[[File:Cr_vibrational_spectrum.PNG]] Cr complex Vibrational spectrum

[[File:Mn_vibrational_spectrum.PNG]] Mn complex Vibrational spectrum

[[File:Fe_vibrational_spectrum.PNG]] Fe complex Vibrational spectrum

The images below are three of the molecular orbitals of the [Fe(CO)6]2+ complex with the corresponding LCAO drawn beside them

[[File:Real_MO_37.PNG]] [[File:LCAO MO 36.PNG || 450px ]]

bonding MO 36 (eg)

JoeWiki1

2019-05-23T20:36:03Z

Jh3817: /* Analysing properties */

== Year 2 Inorganic comp labs ==

=== BH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p),
Symmetry= D3h

[[File:BH3_info.PNG]]

Item Value Threshold Converged?

Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

Link to frequency file: [[File:JH_BH3_FREQ.LOG]]

Low frequencies --- -0.4072 -0.1962 -0.0055 25.2514 27.2430 27.2460

Low frequencies --- 1163.1897 1213.3128 1213.3155

<jmol><jmolApplet>
<title>Optimised BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JH_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Vibration Data ====

{| class="wikitable" border="1"
|+ Vibrations table
! Stretch or Bend? !! Intensity !! Symmetry !! IR active? !! Wavenumber(cm-1)
|-
| Bend || 92 || A2" || Yes || 1163
|-
| Bend || 14 || E' || Yes || 1213
|-
| Bend || 14 || E' || Yes || 1213
|-
| Symmetric Stretch || 0 || A1' || No || 2581
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|}

[[File:BH3_vibrations_spectrum_JH.PNG]]

Spectrum shows 3 peaks out of 6 shown in table. 1 is IR in active leaving 5. Two pairs in the 5 are degenerate meaning they have the same energy meaning only 3 peaks show.

[[File:MO_diagram_JH.PNG]] [1111111111111111111111111111111111111111]

The LCAOs seem very accurate as they depict AOs which combine to form the real MOs very well. Minor issues arise from the fact that it can be said that the overlapping of the orbitals may not be able to be seen fully and the fact that the sizes of the AOs, which represents contribution isn’t consistent. Hydrogen is more electronegative then boron and is therefore lower in energy. Hydrogen should be contributing more to the bonding orbitals and born should be contributing more to the anti-bonding orbitals but for some of them this might not be able to be seen accurately. This shows that the LCAO is a useful tool for finding what a real MO would look like.

=== NH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:NH3_point_group_summary.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES

Link to frequency file: [[File:NH3_OP_JH.LOG]]

Low frequencies --- -8.5628 -8.5571 -0.0047 0.0454 0.1785 26.4189

Low frequencies --- 1089.7603 1694.1865 1694.1865

<jmol><jmolApplet>
<title>Optimised NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3_OP_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:BH3NH3_point_group_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000514 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

Link to frequency file: [[File:NH3BH3_FREQ_NEW.LOG]]

Low frequencies --- -0.0005 0.0003 0.0014 16.7270 18.7414 42.2600

Low frequencies --- 266.2799 632.3010 639.2486

<jmol><jmolApplet>
<title>Optimised NH3BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3BH3_FREQ_NEW.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Association energies ====
E(NH3)= -56.55776863 a.u.

E(BH3)= -26.61532362 a.u.

E(NH3BH3)= -83.22469031 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)], Therefore ΔE= (-83.22468960) - [(-56.55776863)+(-26.61532362)]= -0.05159806 a.u. (-134 KJ/Mol)

The B-N dative bond is weak and this shown when compared to the Al-N bond which has an energy of 297KJ/Mol (https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf)(22222222222)

=== NI3 ===
Method= RB3LYP,
Basis set= Gen

[[File:New_NI3_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000102 0.000450 YES
RMS Force 0.000075 0.000300 YES
Maximum Displacement 0.000858 0.001800 YES
RMS Displacement 0.000629 0.001200 YES

Link to frequency file: [[File:NEW_NI3_JH.LOG]]

Low frequencies --- -12.3845 -12.3781 -5.6129 -0.0040 0.0194 0.0711

Low frequencies --- 100.9307 100.9314 147.2333

<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NEW_NI3_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised B-I bond distance is 2.18 angstrom

===Days 2 and 3 Project: Metal carbonyls===
This sections of the wiki page focuses on metal carbonyls, more specifically their bond-lengths and CO bond frequencies. The metal-complexes which will be focused on are [Cr(CO)6], [Mn(CO)6]+ and [Fe(CO)6]2+. These were chosen as they come one after another in the d-block so it would be interesting to see how bond-lengths and bond frequencies vary across the period. 2 of the complexes are charged (positively) while one is neutral and this is something which must be taken into account when analysing bond-lengths and bond frequencies. An initial prediction would be that bond length increases across a period (as the metal complexes are becoming more positive meaning less overlap with the CO pi* and overall less back-donation and since back donation strengths the M-C bond less of this means an increases in bond length) and that bond frequencies increases.

==== [Cr(CO)6] ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Cr

[[File:Cr(CO)6_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000110 0.000450 YES
RMS Force 0.000041 0.000300 YES
Maximum Displacement 0.000705 0.001800 YES
RMS Displacement 0.000334 0.001200 YES

Link to frequency file: [[File:CR(CO)6_JH_2.LOG]]

Low frequencies --- -0.0014 -0.0013 -0.0010 11.7482 11.7482 11.7482

Low frequencies --- 66.6574 66.6574 66.6574

<jmol><jmolApplet>
<title>Optimised Cr(CO)6 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>CR(CO)6_JH_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Mn(CO)6]+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Mn

[[File:-Mn(CO)62+_summary_JH3817.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000430 0.001800 YES
RMS Displacement 0.000204 0.001200 YES

Link to frequency file: [[File:-MN(CO)6-+_OP_FREQ_JH.LOG]]

Low frequencies --- -0.0007 0.0006 0.0009 4.7607 4.7607 4.7607

Low frequencies --- 76.3202 76.3202 76.3202

<jmol><jmolApplet>
<title>Optimised Mn(CO)6+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-MN(CO)6-+_OP_FREQ_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Fe(CO)6]2+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Fe

[[File:-Fe(CO)6-2+_freq_op_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000429 0.001800 YES
RMS Displacement 0.000200 0.001200 YES

Link to frequency file: [[File:-FE(CO)6-2+_OP_FREQ.LOG]]

Low frequencies --- -10.5293 -10.5293 -10.5292 -0.0014 -0.0011 -0.0009

Low frequencies --- 82.1285 82.1285 82.1285

<jmol><jmolApplet>
<title>Optimised [FE(CO)6]2+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-FE(CO)6-2+_OP_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Analysing properties ====

{| class="wikitable" border="1"
|+ Bond Length
! Metal complex !! Bond Length(Å)
|-
| [Cr(CO)6] || 1.915
|-
| [Mn(CO)6]+ || 1.908
|-
| [Fe(CO)6]2+ || 1.940
|}

The table above shows the bond metal centre-carbon bond lengths. It shows a decrease moving from Cr to Mn and from Mn to Fe there is an increase. This initial decrease in M-C bond length goes against what was predicted but after speaking to Professor Hunt it turns out a full explanation of this decrease in bond length is to complex for the course and so wont be provided.The the later drastic increase is due to a contraction of the d-orbitals causing greater repulsion between the electrons leading to poorer overlap with the CO orbitals meaning less back-bonding and and weaker, so therefore longer, metal-carbon bonds. This agrees with the prediction made earlier.

{| class="wikitable" border="1"
|+ Vibrations table 2
! Metal complex !! Intensity !! Vibration type !! Wavenumber(cm-1)
|-
| Cr(CO)6 || 1637 || symmetric stretch || 2086
|-
| [Mn(CO)6]+ || 879 || symmetric stretch || 2199
|-
| [Fe(CO)6]2+ || 272 || symmetric stretch || 2297
|}

This table above shows the wave-number and intensity all the IR active symmetric stretches of all the metal complexes CO ligands. As each complex has 13 atoms it is expected to have 3(13)-6= 33 vibrational modes but as shown in the vibrational spectra below many of these modes are IR inactive and have intensities of 0, an example of this is the totally symmetric C-O vibrations meaning they cannot be analysed given the fact that they don't appear. As predicted earlier across the period CO bond frequency would increase and this is due to back donation. Whilst back bonding causes an increase in the M-C bond there is also a increase in the CO bond length. The more positive the metal centre means contraction of the d-orbitals and this means that their is a less overlap between the d-orbital and CO pi* orbital and the less overlap with this orbital the stronger the CO bond.

[[File:Cr_vibrational_spectrum.PNG]] Cr complex Vibrational spectrum

[[File:Mn_vibrational_spectrum.PNG]] Mn complex Vibrational spectrum

[[File:Fe_vibrational_spectrum.PNG]] Fe complex Vibrational spectrum

The images below are three of the molecular orbitals of the [Fe(CO)6]2+ complex with the corresponding LCAO drawn beside them

[[File:Real_MO_37.PNG]] [[File:LCAO MO 36.PNG || 250px ]]
bonding MO 36 (eg)

JoeWiki1

2019-05-23T20:35:21Z

Jh3817: /* Analysing properties */

== Year 2 Inorganic comp labs ==

=== BH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p),
Symmetry= D3h

[[File:BH3_info.PNG]]

Item Value Threshold Converged?

Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

Link to frequency file: [[File:JH_BH3_FREQ.LOG]]

Low frequencies --- -0.4072 -0.1962 -0.0055 25.2514 27.2430 27.2460

Low frequencies --- 1163.1897 1213.3128 1213.3155

<jmol><jmolApplet>
<title>Optimised BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JH_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Vibration Data ====

{| class="wikitable" border="1"
|+ Vibrations table
! Stretch or Bend? !! Intensity !! Symmetry !! IR active? !! Wavenumber(cm-1)
|-
| Bend || 92 || A2" || Yes || 1163
|-
| Bend || 14 || E' || Yes || 1213
|-
| Bend || 14 || E' || Yes || 1213
|-
| Symmetric Stretch || 0 || A1' || No || 2581
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|}

[[File:BH3_vibrations_spectrum_JH.PNG]]

Spectrum shows 3 peaks out of 6 shown in table. 1 is IR in active leaving 5. Two pairs in the 5 are degenerate meaning they have the same energy meaning only 3 peaks show.

[[File:MO_diagram_JH.PNG]] [1111111111111111111111111111111111111111]

The LCAOs seem very accurate as they depict AOs which combine to form the real MOs very well. Minor issues arise from the fact that it can be said that the overlapping of the orbitals may not be able to be seen fully and the fact that the sizes of the AOs, which represents contribution isn’t consistent. Hydrogen is more electronegative then boron and is therefore lower in energy. Hydrogen should be contributing more to the bonding orbitals and born should be contributing more to the anti-bonding orbitals but for some of them this might not be able to be seen accurately. This shows that the LCAO is a useful tool for finding what a real MO would look like.

=== NH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:NH3_point_group_summary.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES

Link to frequency file: [[File:NH3_OP_JH.LOG]]

Low frequencies --- -8.5628 -8.5571 -0.0047 0.0454 0.1785 26.4189

Low frequencies --- 1089.7603 1694.1865 1694.1865

<jmol><jmolApplet>
<title>Optimised NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3_OP_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:BH3NH3_point_group_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000514 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

Link to frequency file: [[File:NH3BH3_FREQ_NEW.LOG]]

Low frequencies --- -0.0005 0.0003 0.0014 16.7270 18.7414 42.2600

Low frequencies --- 266.2799 632.3010 639.2486

<jmol><jmolApplet>
<title>Optimised NH3BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3BH3_FREQ_NEW.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Association energies ====
E(NH3)= -56.55776863 a.u.

E(BH3)= -26.61532362 a.u.

E(NH3BH3)= -83.22469031 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)], Therefore ΔE= (-83.22468960) - [(-56.55776863)+(-26.61532362)]= -0.05159806 a.u. (-134 KJ/Mol)

The B-N dative bond is weak and this shown when compared to the Al-N bond which has an energy of 297KJ/Mol (https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf)(22222222222)

=== NI3 ===
Method= RB3LYP,
Basis set= Gen

[[File:New_NI3_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000102 0.000450 YES
RMS Force 0.000075 0.000300 YES
Maximum Displacement 0.000858 0.001800 YES
RMS Displacement 0.000629 0.001200 YES

Link to frequency file: [[File:NEW_NI3_JH.LOG]]

Low frequencies --- -12.3845 -12.3781 -5.6129 -0.0040 0.0194 0.0711

Low frequencies --- 100.9307 100.9314 147.2333

<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NEW_NI3_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised B-I bond distance is 2.18 angstrom

===Days 2 and 3 Project: Metal carbonyls===
This sections of the wiki page focuses on metal carbonyls, more specifically their bond-lengths and CO bond frequencies. The metal-complexes which will be focused on are [Cr(CO)6], [Mn(CO)6]+ and [Fe(CO)6]2+. These were chosen as they come one after another in the d-block so it would be interesting to see how bond-lengths and bond frequencies vary across the period. 2 of the complexes are charged (positively) while one is neutral and this is something which must be taken into account when analysing bond-lengths and bond frequencies. An initial prediction would be that bond length increases across a period (as the metal complexes are becoming more positive meaning less overlap with the CO pi* and overall less back-donation and since back donation strengths the M-C bond less of this means an increases in bond length) and that bond frequencies increases.

==== [Cr(CO)6] ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Cr

[[File:Cr(CO)6_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000110 0.000450 YES
RMS Force 0.000041 0.000300 YES
Maximum Displacement 0.000705 0.001800 YES
RMS Displacement 0.000334 0.001200 YES

Link to frequency file: [[File:CR(CO)6_JH_2.LOG]]

Low frequencies --- -0.0014 -0.0013 -0.0010 11.7482 11.7482 11.7482

Low frequencies --- 66.6574 66.6574 66.6574

<jmol><jmolApplet>
<title>Optimised Cr(CO)6 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>CR(CO)6_JH_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Mn(CO)6]+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Mn

[[File:-Mn(CO)62+_summary_JH3817.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000430 0.001800 YES
RMS Displacement 0.000204 0.001200 YES

Link to frequency file: [[File:-MN(CO)6-+_OP_FREQ_JH.LOG]]

Low frequencies --- -0.0007 0.0006 0.0009 4.7607 4.7607 4.7607

Low frequencies --- 76.3202 76.3202 76.3202

<jmol><jmolApplet>
<title>Optimised Mn(CO)6+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-MN(CO)6-+_OP_FREQ_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Fe(CO)6]2+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Fe

[[File:-Fe(CO)6-2+_freq_op_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000429 0.001800 YES
RMS Displacement 0.000200 0.001200 YES

Link to frequency file: [[File:-FE(CO)6-2+_OP_FREQ.LOG]]

Low frequencies --- -10.5293 -10.5293 -10.5292 -0.0014 -0.0011 -0.0009

Low frequencies --- 82.1285 82.1285 82.1285

<jmol><jmolApplet>
<title>Optimised [FE(CO)6]2+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-FE(CO)6-2+_OP_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Analysing properties ====

{| class="wikitable" border="1"
|+ Bond Length
! Metal complex !! Bond Length(Å)
|-
| [Cr(CO)6] || 1.915
|-
| [Mn(CO)6]+ || 1.908
|-
| [Fe(CO)6]2+ || 1.940
|}

The table above shows the bond metal centre-carbon bond lengths. It shows a decrease moving from Cr to Mn and from Mn to Fe there is an increase. This initial decrease in M-C bond length goes against what was predicted but after speaking to Professor Hunt it turns out a full explanation of this decrease in bond length is to complex for the course and so wont be provided.The the later drastic increase is due to a contraction of the d-orbitals causing greater repulsion between the electrons leading to poorer overlap with the CO orbitals meaning less back-bonding and and weaker, so therefore longer, metal-carbon bonds. This agrees with the prediction made earlier.

{| class="wikitable" border="1"
|+ Vibrations table 2
! Metal complex !! Intensity !! Vibration type !! Wavenumber(cm-1)
|-
| Cr(CO)6 || 1637 || symmetric stretch || 2086
|-
| [Mn(CO)6]+ || 879 || symmetric stretch || 2199
|-
| [Fe(CO)6]2+ || 272 || symmetric stretch || 2297
|}

This table above shows the wave-number and intensity all the IR active symmetric stretches of all the metal complexes CO ligands. As each complex has 13 atoms it is expected to have 3(13)-6= 33 vibrational modes but as shown in the vibrational spectra below many of these modes are IR inactive and have intensities of 0, an example of this is the totally symmetric C-O vibrations meaning they cannot be analysed given the fact that they don't appear. As predicted earlier across the period CO bond frequency would increase and this is due to back donation. Whilst back bonding causes an increase in the M-C bond there is also a increase in the CO bond length. The more positive the metal centre means contraction of the d-orbitals and this means that their is a less overlap between the d-orbital and CO pi* orbital and the less overlap with this orbital the stronger the CO bond.

[[File:Cr_vibrational_spectrum.PNG]] Cr complex Vibrational spectrum

[[File:Mn_vibrational_spectrum.PNG]] Mn complex Vibrational spectrum

[[File:Fe_vibrational_spectrum.PNG]] Fe complex Vibrational spectrum

The images below are three of the molecular orbitals of the [Fe(CO)6]2+ complex with the corresponding LCAO drawn beside them

[[File:Real_MO_37.PNG]] [[File:LCAO MO 36.PNG]]
bonding MO 36 (eg)

File:LCAO MO 36.PNG

2019-05-23T20:34:49Z

Jh3817: Jh3817 uploaded a new version of File:LCAO MO 36.PNG

File:LCAO MO 36.PNG

2019-05-23T20:34:26Z

Jh3817:

File:Real MO 37.PNG

2019-05-23T20:29:55Z

Jh3817:

JoeWiki1

2019-05-23T18:23:11Z

Jh3817: /* Analysing properties */

JoeWiki1

2019-05-23T18:22:17Z

Jh3817: /* Analysing properties */

== Year 2 Inorganic comp labs ==

=== BH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p),
Symmetry= D3h

[[File:BH3_info.PNG]]

Item Value Threshold Converged?

Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

Link to frequency file: [[File:JH_BH3_FREQ.LOG]]

Low frequencies --- -0.4072 -0.1962 -0.0055 25.2514 27.2430 27.2460

Low frequencies --- 1163.1897 1213.3128 1213.3155

<jmol><jmolApplet>
<title>Optimised BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JH_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Vibration Data ====

{| class="wikitable" border="1"
|+ Vibrations table
! Stretch or Bend? !! Intensity !! Symmetry !! IR active? !! Wavenumber(cm-1)
|-
| Bend || 92 || A2" || Yes || 1163
|-
| Bend || 14 || E' || Yes || 1213
|-
| Bend || 14 || E' || Yes || 1213
|-
| Symmetric Stretch || 0 || A1' || No || 2581
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|}

[[File:BH3_vibrations_spectrum_JH.PNG]]

Spectrum shows 3 peaks out of 6 shown in table. 1 is IR in active leaving 5. Two pairs in the 5 are degenerate meaning they have the same energy meaning only 3 peaks show.

[[File:MO_diagram_JH.PNG]] [1111111111111111111111111111111111111111]

The LCAOs seem very accurate as they depict AOs which combine to form the real MOs very well. Minor issues arise from the fact that it can be said that the overlapping of the orbitals may not be able to be seen fully and the fact that the sizes of the AOs, which represents contribution isn’t consistent. Hydrogen is more electronegative then boron and is therefore lower in energy. Hydrogen should be contributing more to the bonding orbitals and born should be contributing more to the anti-bonding orbitals but for some of them this might not be able to be seen accurately. This shows that the LCAO is a useful tool for finding what a real MO would look like.

=== NH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:NH3_point_group_summary.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES

Link to frequency file: [[File:NH3_OP_JH.LOG]]

Low frequencies --- -8.5628 -8.5571 -0.0047 0.0454 0.1785 26.4189

Low frequencies --- 1089.7603 1694.1865 1694.1865

<jmol><jmolApplet>
<title>Optimised NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3_OP_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:BH3NH3_point_group_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000514 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

Link to frequency file: [[File:NH3BH3_FREQ_NEW.LOG]]

Low frequencies --- -0.0005 0.0003 0.0014 16.7270 18.7414 42.2600

Low frequencies --- 266.2799 632.3010 639.2486

<jmol><jmolApplet>
<title>Optimised NH3BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3BH3_FREQ_NEW.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Association energies ====
E(NH3)= -56.55776863 a.u.

E(BH3)= -26.61532362 a.u.

E(NH3BH3)= -83.22469031 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)], Therefore ΔE= (-83.22468960) - [(-56.55776863)+(-26.61532362)]= -0.05159806 a.u. (-134 KJ/Mol)

The B-N dative bond is weak and this shown when compared to the Al-N bond which has an energy of 297KJ/Mol (https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf)(22222222222)

=== NI3 ===
Method= RB3LYP,
Basis set= Gen

[[File:New_NI3_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000102 0.000450 YES
RMS Force 0.000075 0.000300 YES
Maximum Displacement 0.000858 0.001800 YES
RMS Displacement 0.000629 0.001200 YES

Link to frequency file: [[File:NEW_NI3_JH.LOG]]

Low frequencies --- -12.3845 -12.3781 -5.6129 -0.0040 0.0194 0.0711

Low frequencies --- 100.9307 100.9314 147.2333

<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NEW_NI3_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised B-I bond distance is 2.18 angstrom

===Days 2 and 3 Project: Metal carbonyls===
This sections of the wiki page focuses on metal carbonyls, more specifically their bond-lengths and CO bond frequencies. The metal-complexes which will be focused on are [Cr(CO)6], [Mn(CO)6]+ and [Fe(CO)6]2+. These were chosen as they come one after another in the d-block so it would be interesting to see how bond-lengths and bond frequencies vary across the period. 2 of the complexes are charged (positively) while one is neutral and this is something which must be taken into account when analysing bond-lengths and bond frequencies. An initial prediction would be that bond length increases across a period (as the metal complexes are becoming more positive meaning less overlap with the CO pi* and overall less back-donation and since back donation strengths the M-C bond less of this means an increases in bond length) and that bond frequencies increases.

==== [Cr(CO)6] ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Cr

[[File:Cr(CO)6_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000110 0.000450 YES
RMS Force 0.000041 0.000300 YES
Maximum Displacement 0.000705 0.001800 YES
RMS Displacement 0.000334 0.001200 YES

Link to frequency file: [[File:CR(CO)6_JH_2.LOG]]

Low frequencies --- -0.0014 -0.0013 -0.0010 11.7482 11.7482 11.7482

Low frequencies --- 66.6574 66.6574 66.6574

<jmol><jmolApplet>
<title>Optimised Cr(CO)6 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>CR(CO)6_JH_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Mn(CO)6]+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Mn

[[File:-Mn(CO)62+_summary_JH3817.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000430 0.001800 YES
RMS Displacement 0.000204 0.001200 YES

Link to frequency file: [[File:-MN(CO)6-+_OP_FREQ_JH.LOG]]

Low frequencies --- -0.0007 0.0006 0.0009 4.7607 4.7607 4.7607

Low frequencies --- 76.3202 76.3202 76.3202

<jmol><jmolApplet>
<title>Optimised Mn(CO)6+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-MN(CO)6-+_OP_FREQ_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Fe(CO)6]2+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Fe

[[File:-Fe(CO)6-2+_freq_op_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000429 0.001800 YES
RMS Displacement 0.000200 0.001200 YES

Link to frequency file: [[File:-FE(CO)6-2+_OP_FREQ.LOG]]

Low frequencies --- -10.5293 -10.5293 -10.5292 -0.0014 -0.0011 -0.0009

Low frequencies --- 82.1285 82.1285 82.1285

<jmol><jmolApplet>
<title>Optimised [FE(CO)6]2+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-FE(CO)6-2+_OP_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Analysing properties ====

{| class="wikitable" border="1"
|+ Bond Length
! Metal complex !! Bond Length(Å)
|-
| [Cr(CO)6] || 1.915
|-
| [Mn(CO)6]+ || 1.908
|-
| [Fe(CO)6]2+ || 1.940
|}

The table above shows the bond metal centre-carbon bond lengths. It shows a decrease moving from Cr to Mn and from Mn to Fe there is an increase. This initial decrease in M-C bond length goes against what was predicted but after speaking to Professor Hunt it turns out a full explanation of this decrease in bond length is to complex for the course.The the later drastic increase is due to a contraction of the d-orbitals causing greater repulsion between the electrons leading to poorer overlap with the CO orbitals meaning less back-bonding and and weaker, so therefore longer, metal-carbon bonds. This agrees with the prediction made earlier.

{| class="wikitable" border="1"
|+ Vibrations table 2
! Metal complex !! Intensity !! Vibration type !! Wavenumber(cm-1)
|-
| Cr(CO)6 || 1637 || symmetric stretch || 2086
|-
| [Mn(CO)6]+ || 879 || symmetric stretch || 2199
|-
| [Fe(CO)6]2+ || 272 || symmetric stretch || 2297
|}

This table above shows the wave-number and intensity all the IR active symmetric stretches of all the metal complexes CO ligands. As each complex has 13 atoms it is expected to have 3(13)-6= 33 vibrational modes but as shown in the vibrational spectra below many of these modes are IR inactive and have intensities of 0, an example of this is the totally symmetric C-O vibrations meaning they cannot be analysed given the fact that they don't appear. As predicted earlier across the period CO bond frequency would increase and this is due to back donation. Whilst back bonding causes an increase in the M-C bond there is also a increase in the CO bond length. The more positive the metal centre means contraction of the d-orbitals and this means that their is a less overlap between the d-orbital and CO pi* orbital and the less overlap with this orbital the stronger the CO bond.

[[File:Cr_vibrational_spectrum.PNG]] Cr complex Vibrational spectrum

[[File:Mn_vibrational_spectrum.PNG]] Mn complex Vibrational spectrum

[[File:Fe_vibrational_spectrum.PNG]] Fe complex Vibrational spectrum

JoeWiki1

2019-05-23T18:07:42Z

Jh3817: /* Days 2 and 3 Project: Metal carbonyls */

== Year 2 Inorganic comp labs ==

=== BH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p),
Symmetry= D3h

[[File:BH3_info.PNG]]

Item Value Threshold Converged?

Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

Link to frequency file: [[File:JH_BH3_FREQ.LOG]]

Low frequencies --- -0.4072 -0.1962 -0.0055 25.2514 27.2430 27.2460

Low frequencies --- 1163.1897 1213.3128 1213.3155

<jmol><jmolApplet>
<title>Optimised BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JH_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Vibration Data ====

{| class="wikitable" border="1"
|+ Vibrations table
! Stretch or Bend? !! Intensity !! Symmetry !! IR active? !! Wavenumber(cm-1)
|-
| Bend || 92 || A2" || Yes || 1163
|-
| Bend || 14 || E' || Yes || 1213
|-
| Bend || 14 || E' || Yes || 1213
|-
| Symmetric Stretch || 0 || A1' || No || 2581
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|}

[[File:BH3_vibrations_spectrum_JH.PNG]]

Spectrum shows 3 peaks out of 6 shown in table. 1 is IR in active leaving 5. Two pairs in the 5 are degenerate meaning they have the same energy meaning only 3 peaks show.

[[File:MO_diagram_JH.PNG]] [1111111111111111111111111111111111111111]

The LCAOs seem very accurate as they depict AOs which combine to form the real MOs very well. Minor issues arise from the fact that it can be said that the overlapping of the orbitals may not be able to be seen fully and the fact that the sizes of the AOs, which represents contribution isn’t consistent. Hydrogen is more electronegative then boron and is therefore lower in energy. Hydrogen should be contributing more to the bonding orbitals and born should be contributing more to the anti-bonding orbitals but for some of them this might not be able to be seen accurately. This shows that the LCAO is a useful tool for finding what a real MO would look like.

=== NH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:NH3_point_group_summary.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES

Link to frequency file: [[File:NH3_OP_JH.LOG]]

Low frequencies --- -8.5628 -8.5571 -0.0047 0.0454 0.1785 26.4189

Low frequencies --- 1089.7603 1694.1865 1694.1865

<jmol><jmolApplet>
<title>Optimised NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3_OP_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:BH3NH3_point_group_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000514 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

Link to frequency file: [[File:NH3BH3_FREQ_NEW.LOG]]

Low frequencies --- -0.0005 0.0003 0.0014 16.7270 18.7414 42.2600

Low frequencies --- 266.2799 632.3010 639.2486

<jmol><jmolApplet>
<title>Optimised NH3BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3BH3_FREQ_NEW.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Association energies ====
E(NH3)= -56.55776863 a.u.

E(BH3)= -26.61532362 a.u.

E(NH3BH3)= -83.22469031 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)], Therefore ΔE= (-83.22468960) - [(-56.55776863)+(-26.61532362)]= -0.05159806 a.u. (-134 KJ/Mol)

The B-N dative bond is weak and this shown when compared to the Al-N bond which has an energy of 297KJ/Mol (https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf)(22222222222)

=== NI3 ===
Method= RB3LYP,
Basis set= Gen

[[File:New_NI3_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000102 0.000450 YES
RMS Force 0.000075 0.000300 YES
Maximum Displacement 0.000858 0.001800 YES
RMS Displacement 0.000629 0.001200 YES

Link to frequency file: [[File:NEW_NI3_JH.LOG]]

Low frequencies --- -12.3845 -12.3781 -5.6129 -0.0040 0.0194 0.0711

Low frequencies --- 100.9307 100.9314 147.2333

<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NEW_NI3_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised B-I bond distance is 2.18 angstrom

===Days 2 and 3 Project: Metal carbonyls===
This sections of the wiki page focuses on metal carbonyls, more specifically their bond-lengths and CO bond frequencies. The metal-complexes which will be focused on are [Cr(CO)6], [Mn(CO)6]+ and [Fe(CO)6]2+. These were chosen as they come one after another in the d-block so it would be interesting to see how bond-lengths and bond frequencies vary across the period. 2 of the complexes are charged (positively) while one is neutral and this is something which must be taken into account when analysing bond-lengths and bond frequencies. An initial prediction would be that bond length increases across a period (as the metal complexes are becoming more positive meaning less overlap with the CO pi* and overall less back-donation and since back donation strengths the M-C bond less of this means an increases in bond length) and that bond frequencies increases.

==== [Cr(CO)6] ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Cr

[[File:Cr(CO)6_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000110 0.000450 YES
RMS Force 0.000041 0.000300 YES
Maximum Displacement 0.000705 0.001800 YES
RMS Displacement 0.000334 0.001200 YES

Link to frequency file: [[File:CR(CO)6_JH_2.LOG]]

Low frequencies --- -0.0014 -0.0013 -0.0010 11.7482 11.7482 11.7482

Low frequencies --- 66.6574 66.6574 66.6574

<jmol><jmolApplet>
<title>Optimised Cr(CO)6 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>CR(CO)6_JH_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Mn(CO)6]+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Mn

[[File:-Mn(CO)62+_summary_JH3817.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000430 0.001800 YES
RMS Displacement 0.000204 0.001200 YES

Link to frequency file: [[File:-MN(CO)6-+_OP_FREQ_JH.LOG]]

Low frequencies --- -0.0007 0.0006 0.0009 4.7607 4.7607 4.7607

Low frequencies --- 76.3202 76.3202 76.3202

<jmol><jmolApplet>
<title>Optimised Mn(CO)6+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-MN(CO)6-+_OP_FREQ_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Fe(CO)6]2+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Fe

[[File:-Fe(CO)6-2+_freq_op_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000429 0.001800 YES
RMS Displacement 0.000200 0.001200 YES

Link to frequency file: [[File:-FE(CO)6-2+_OP_FREQ.LOG]]

Low frequencies --- -10.5293 -10.5293 -10.5292 -0.0014 -0.0011 -0.0009

Low frequencies --- 82.1285 82.1285 82.1285

<jmol><jmolApplet>
<title>Optimised [FE(CO)6]2+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-FE(CO)6-2+_OP_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Analysing properties ====

{| class="wikitable" border="1"
|+ Bond Length
! Metal complex !! Bond Length(Å)
|-
| [Cr(CO)6] || 1.915
|-
| [Mn(CO)6]+ || 1.908
|-
| [Fe(CO)6]2+ || 1.940
|}

The table above shows the bond metal centre-carbon bond lengths. It shows a decrease moving from Cr to Mn and from Mn to Fe there is an increase. The initial decrease is due to a contraction of the d-orbitals causing greater repulsion between the electrons leading to poorer overlap with the CO orbitals meaning less back-bonding and and weaker, so therefore longer, metal-carbon bonds.

This initial decrease in M-C bond length goes against what was predicted earlier. As predicted moving across a period causes the bond length to decrease for the first two but when looking at iron there is an unexpected increase. The decrease between the first two likely due to an increase in oxidation state as increasing oxidation state leads to an increase in bond strength and the sudden increase in the bond length for the iron complex is due to the contraction of the d-orbitals greater repulsion between the electrons leading to poorer overlap with the CO orbitals but after speaking to professor Hunt it turns out a full explanation of this increase in bond length is to complex for the course.

{| class="wikitable" border="1"
|+ Vibrations table 2
! Metal complex !! Intensity !! Vibration type !! Wavenumber(cm-1)
|-
| Cr(CO)6 || 1637 || symmetric stretch || 2086
|-
| [Mn(CO)6]+ || 879 || symmetric stretch || 2199
|-
| [Fe(CO)6]2+ || 272 || symmetric stretch || 2297
|}

This table above shows the wave-number and intensity all the IR active symmetric stretches of all the metal complexes CO ligands. As each complex has 13 atoms it is expected to have 3(13)-6= 33 vibrational modes but as shown in the vibrational spectra below many of these modes are IR inactive and have intensities of 0, an example of this is the totally symmetric C-O vibrations meaning they cannot be analysed given the fact that they don't appear. As predicted earlier across the period CO bond frequency would increase and this is due to back donation. Whilst back bonding causes an increase in the M-C bond there is also a increase in the CO bond length. The more positive the metal centre means contraction of the d-orbitals and this means that their is a less overlap between the d-orbital and CO pi* orbital and the less overlap with this orbital the stronger the CO bond.

[[File:Cr_vibrational_spectrum.PNG]] Cr complex Vibrational spectrum

[[File:Mn_vibrational_spectrum.PNG]] Mn complex Vibrational spectrum

[[File:Fe_vibrational_spectrum.PNG]] Fe complex Vibrational spectrum

JoeWiki1

2019-05-23T17:58:45Z

Jh3817: /* Analysing properties */

== Year 2 Inorganic comp labs ==

=== BH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p),
Symmetry= D3h

[[File:BH3_info.PNG]]

Item Value Threshold Converged?

Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

Link to frequency file: [[File:JH_BH3_FREQ.LOG]]

Low frequencies --- -0.4072 -0.1962 -0.0055 25.2514 27.2430 27.2460

Low frequencies --- 1163.1897 1213.3128 1213.3155

<jmol><jmolApplet>
<title>Optimised BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JH_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Vibration Data ====

{| class="wikitable" border="1"
|+ Vibrations table
! Stretch or Bend? !! Intensity !! Symmetry !! IR active? !! Wavenumber(cm-1)
|-
| Bend || 92 || A2" || Yes || 1163
|-
| Bend || 14 || E' || Yes || 1213
|-
| Bend || 14 || E' || Yes || 1213
|-
| Symmetric Stretch || 0 || A1' || No || 2581
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|}

[[File:BH3_vibrations_spectrum_JH.PNG]]

Spectrum shows 3 peaks out of 6 shown in table. 1 is IR in active leaving 5. Two pairs in the 5 are degenerate meaning they have the same energy meaning only 3 peaks show.

[[File:MO_diagram_JH.PNG]] [1111111111111111111111111111111111111111]

The LCAOs seem very accurate as they depict AOs which combine to form the real MOs very well. Minor issues arise from the fact that it can be said that the overlapping of the orbitals may not be able to be seen fully and the fact that the sizes of the AOs, which represents contribution isn’t consistent. Hydrogen is more electronegative then boron and is therefore lower in energy. Hydrogen should be contributing more to the bonding orbitals and born should be contributing more to the anti-bonding orbitals but for some of them this might not be able to be seen accurately. This shows that the LCAO is a useful tool for finding what a real MO would look like.

=== NH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:NH3_point_group_summary.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES

Link to frequency file: [[File:NH3_OP_JH.LOG]]

Low frequencies --- -8.5628 -8.5571 -0.0047 0.0454 0.1785 26.4189

Low frequencies --- 1089.7603 1694.1865 1694.1865

<jmol><jmolApplet>
<title>Optimised NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3_OP_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:BH3NH3_point_group_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000514 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

Link to frequency file: [[File:NH3BH3_FREQ_NEW.LOG]]

Low frequencies --- -0.0005 0.0003 0.0014 16.7270 18.7414 42.2600

Low frequencies --- 266.2799 632.3010 639.2486

<jmol><jmolApplet>
<title>Optimised NH3BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3BH3_FREQ_NEW.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Association energies ====
E(NH3)= -56.55776863 a.u.

E(BH3)= -26.61532362 a.u.

E(NH3BH3)= -83.22469031 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)], Therefore ΔE= (-83.22468960) - [(-56.55776863)+(-26.61532362)]= -0.05159806 a.u. (-134 KJ/Mol)

The B-N dative bond is weak and this shown when compared to the Al-N bond which has an energy of 297KJ/Mol (https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf)(22222222222)

=== NI3 ===
Method= RB3LYP,
Basis set= Gen

[[File:New_NI3_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000102 0.000450 YES
RMS Force 0.000075 0.000300 YES
Maximum Displacement 0.000858 0.001800 YES
RMS Displacement 0.000629 0.001200 YES

Link to frequency file: [[File:NEW_NI3_JH.LOG]]

Low frequencies --- -12.3845 -12.3781 -5.6129 -0.0040 0.0194 0.0711

Low frequencies --- 100.9307 100.9314 147.2333

<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NEW_NI3_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised B-I bond distance is 2.18 angstrom

===Days 2 and 3 Project: Metal carbonyls===
This sections of the wiki page focuses on metal carbonyls, more specifically their bond-lengths and CO bond frequencies. The metal-complexes which will be focused on are [Cr(CO)6], [Mn(CO)6]+ and [Fe(CO)6]2+. These were chosen as they come one after another in the d-block so it would be interesting to see how bond-lengths and bond frequencies vary across the period. 2 of the complexes are charged (positively) while one is neutral and this is something which must be taken into account when analysing bond-lengths and bond frequencies. An initial prediction would be that bond length decreases across a period and that bond frequencies increases.

==== [Cr(CO)6] ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Cr

[[File:Cr(CO)6_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000110 0.000450 YES
RMS Force 0.000041 0.000300 YES
Maximum Displacement 0.000705 0.001800 YES
RMS Displacement 0.000334 0.001200 YES

Link to frequency file: [[File:CR(CO)6_JH_2.LOG]]

Low frequencies --- -0.0014 -0.0013 -0.0010 11.7482 11.7482 11.7482

Low frequencies --- 66.6574 66.6574 66.6574

<jmol><jmolApplet>
<title>Optimised Cr(CO)6 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>CR(CO)6_JH_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Mn(CO)6]+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Mn

[[File:-Mn(CO)62+_summary_JH3817.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000430 0.001800 YES
RMS Displacement 0.000204 0.001200 YES

Link to frequency file: [[File:-MN(CO)6-+_OP_FREQ_JH.LOG]]

Low frequencies --- -0.0007 0.0006 0.0009 4.7607 4.7607 4.7607

Low frequencies --- 76.3202 76.3202 76.3202

<jmol><jmolApplet>
<title>Optimised Mn(CO)6+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-MN(CO)6-+_OP_FREQ_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Fe(CO)6]2+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Fe

[[File:-Fe(CO)6-2+_freq_op_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000429 0.001800 YES
RMS Displacement 0.000200 0.001200 YES

Link to frequency file: [[File:-FE(CO)6-2+_OP_FREQ.LOG]]

Low frequencies --- -10.5293 -10.5293 -10.5292 -0.0014 -0.0011 -0.0009

Low frequencies --- 82.1285 82.1285 82.1285

<jmol><jmolApplet>
<title>Optimised [FE(CO)6]2+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-FE(CO)6-2+_OP_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Analysing properties ====

{| class="wikitable" border="1"
|+ Bond Length
! Metal complex !! Bond Length(Å)
|-
| [Cr(CO)6] || 1.915
|-
| [Mn(CO)6]+ || 1.908
|-
| [Fe(CO)6]2+ || 1.940
|}

The table above shows the bond metal centre-carbon bond lengths. Electrons from a d-orbital on the metal centres is partially donated into the pi* orbital of the CO ligand. This strengthens the M-C bond. As predicted moving across a period causes the bond length to decrease for the first two but when looking at iron there is an unexpected increase. The decrease between the first two likely due to an increase in oxidation state as increasing oxidation state leads to an increase in bond strength and the sudden increase in the bond length for the iron complex is due to the contraction of the d-orbitals greater repulsion between the electrons leading to poorer overlap with the CO orbitals but after speaking to professor Hunt it turns out a full explanation of this increase in bond length is to complex for the course.

{| class="wikitable" border="1"
|+ Vibrations table 2
! Metal complex !! Intensity !! Vibration type !! Wavenumber(cm-1)
|-
| Cr(CO)6 || 1637 || symmetric stretch || 2086
|-
| [Mn(CO)6]+ || 879 || symmetric stretch || 2199
|-
| [Fe(CO)6]2+ || 272 || symmetric stretch || 2297
|}

This table above shows the wave-number and intensity all the IR active symmetric stretches of all the metal complexes CO ligands. As each complex has 13 atoms it is expected to have 3(13)-6= 33 vibrational modes but as shown in the vibrational spectra below many of these modes are IR inactive and have intensities of 0, an example of this is the totally symmetric C-O vibrations meaning they cannot be analysed given the fact that they don't appear. As predicted earlier across the period CO bond frequency would increase and this is due to back donation. Whilst back bonding causes an increase in the M-C bond there is also a increase in the CO bond length. The more positive the metal centre means contraction of the d-orbitals and this means that their is a less overlap between the d-orbital and CO pi* orbital and the less overlap with this orbital the stronger the CO bond.

[[File:Cr_vibrational_spectrum.PNG]] Cr complex Vibrational spectrum

[[File:Mn_vibrational_spectrum.PNG]] Mn complex Vibrational spectrum

[[File:Fe_vibrational_spectrum.PNG]] Fe complex Vibrational spectrum

JoeWiki1

2019-05-23T17:41:28Z

Jh3817: /* Analysing properties */

== Year 2 Inorganic comp labs ==

=== BH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p),
Symmetry= D3h

[[File:BH3_info.PNG]]

Item Value Threshold Converged?

Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

Link to frequency file: [[File:JH_BH3_FREQ.LOG]]

Low frequencies --- -0.4072 -0.1962 -0.0055 25.2514 27.2430 27.2460

Low frequencies --- 1163.1897 1213.3128 1213.3155

<jmol><jmolApplet>
<title>Optimised BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JH_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Vibration Data ====

{| class="wikitable" border="1"
|+ Vibrations table
! Stretch or Bend? !! Intensity !! Symmetry !! IR active? !! Wavenumber(cm-1)
|-
| Bend || 92 || A2" || Yes || 1163
|-
| Bend || 14 || E' || Yes || 1213
|-
| Bend || 14 || E' || Yes || 1213
|-
| Symmetric Stretch || 0 || A1' || No || 2581
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|}

[[File:BH3_vibrations_spectrum_JH.PNG]]

Spectrum shows 3 peaks out of 6 shown in table. 1 is IR in active leaving 5. Two pairs in the 5 are degenerate meaning they have the same energy meaning only 3 peaks show.

[[File:MO_diagram_JH.PNG]] [1111111111111111111111111111111111111111]

The LCAOs seem very accurate as they depict AOs which combine to form the real MOs very well. Minor issues arise from the fact that it can be said that the overlapping of the orbitals may not be able to be seen fully and the fact that the sizes of the AOs, which represents contribution isn’t consistent. Hydrogen is more electronegative then boron and is therefore lower in energy. Hydrogen should be contributing more to the bonding orbitals and born should be contributing more to the anti-bonding orbitals but for some of them this might not be able to be seen accurately. This shows that the LCAO is a useful tool for finding what a real MO would look like.

=== NH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:NH3_point_group_summary.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES

Link to frequency file: [[File:NH3_OP_JH.LOG]]

Low frequencies --- -8.5628 -8.5571 -0.0047 0.0454 0.1785 26.4189

Low frequencies --- 1089.7603 1694.1865 1694.1865

<jmol><jmolApplet>
<title>Optimised NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3_OP_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:BH3NH3_point_group_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000514 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

Link to frequency file: [[File:NH3BH3_FREQ_NEW.LOG]]

Low frequencies --- -0.0005 0.0003 0.0014 16.7270 18.7414 42.2600

Low frequencies --- 266.2799 632.3010 639.2486

<jmol><jmolApplet>
<title>Optimised NH3BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3BH3_FREQ_NEW.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Association energies ====
E(NH3)= -56.55776863 a.u.

E(BH3)= -26.61532362 a.u.

E(NH3BH3)= -83.22469031 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)], Therefore ΔE= (-83.22468960) - [(-56.55776863)+(-26.61532362)]= -0.05159806 a.u. (-134 KJ/Mol)

The B-N dative bond is weak and this shown when compared to the Al-N bond which has an energy of 297KJ/Mol (https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf)(22222222222)

=== NI3 ===
Method= RB3LYP,
Basis set= Gen

[[File:New_NI3_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000102 0.000450 YES
RMS Force 0.000075 0.000300 YES
Maximum Displacement 0.000858 0.001800 YES
RMS Displacement 0.000629 0.001200 YES

Link to frequency file: [[File:NEW_NI3_JH.LOG]]

Low frequencies --- -12.3845 -12.3781 -5.6129 -0.0040 0.0194 0.0711

Low frequencies --- 100.9307 100.9314 147.2333

<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NEW_NI3_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised B-I bond distance is 2.18 angstrom

===Days 2 and 3 Project: Metal carbonyls===
This sections of the wiki page focuses on metal carbonyls, more specifically their bond-lengths and CO bond frequencies. The metal-complexes which will be focused on are [Cr(CO)6], [Mn(CO)6]+ and [Fe(CO)6]2+. These were chosen as they come one after another in the d-block so it would be interesting to see how bond-lengths and bond frequencies vary across the period. 2 of the complexes are charged (positively) while one is neutral and this is something which must be taken into account when analysing bond-lengths and bond frequencies. An initial prediction would be that bond length decreases across a period and that bond frequencies increases.

==== [Cr(CO)6] ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Cr

[[File:Cr(CO)6_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000110 0.000450 YES
RMS Force 0.000041 0.000300 YES
Maximum Displacement 0.000705 0.001800 YES
RMS Displacement 0.000334 0.001200 YES

Link to frequency file: [[File:CR(CO)6_JH_2.LOG]]

Low frequencies --- -0.0014 -0.0013 -0.0010 11.7482 11.7482 11.7482

Low frequencies --- 66.6574 66.6574 66.6574

<jmol><jmolApplet>
<title>Optimised Cr(CO)6 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>CR(CO)6_JH_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Mn(CO)6]+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Mn

[[File:-Mn(CO)62+_summary_JH3817.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000430 0.001800 YES
RMS Displacement 0.000204 0.001200 YES

Link to frequency file: [[File:-MN(CO)6-+_OP_FREQ_JH.LOG]]

Low frequencies --- -0.0007 0.0006 0.0009 4.7607 4.7607 4.7607

Low frequencies --- 76.3202 76.3202 76.3202

<jmol><jmolApplet>
<title>Optimised Mn(CO)6+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-MN(CO)6-+_OP_FREQ_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Fe(CO)6]2+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Fe

[[File:-Fe(CO)6-2+_freq_op_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000429 0.001800 YES
RMS Displacement 0.000200 0.001200 YES

Link to frequency file: [[File:-FE(CO)6-2+_OP_FREQ.LOG]]

Low frequencies --- -10.5293 -10.5293 -10.5292 -0.0014 -0.0011 -0.0009

Low frequencies --- 82.1285 82.1285 82.1285

<jmol><jmolApplet>
<title>Optimised [FE(CO)6]2+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-FE(CO)6-2+_OP_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Analysing properties ====

{| class="wikitable" border="1"
|+ Bond Length
! Metal complex !! Bond Length(Å)
|-
| [Cr(CO)6] || 1.915
|-
| [Mn(CO)6]+ || 1.908
|-
| [Fe(CO)6]2+ || 1.940
|}

The table above shows the bond metal centre-carbon bond lengths. Electrons from a d-orbital on the metal centres is partially donated into the pi* orbital of the CO ligand. This strengthens the M-C bond. As predicted moving across a period causes the bond length to decrease for the first two but when looking at iron there is an unexpected increase. The decrease between the first two likely due to back bonding and increase in oxidation state as increasing oxidation state leads to an increase in bond strength and the sudden increase in the bond length for the iron complex is due to the contraction of the d-orbitals greater repulsion between the electrons leading to poorer overlap with the CO orbitals but after speaking to professor Hunt it turns out a full explanation of this increase in bond length is to complex for the course.

{| class="wikitable" border="1"
|+ Vibrations table 2
! Metal complex !! Intensity !! Vibration type !! Wavenumber(cm-1)
|-
| Cr(CO)6 || 1637 || symmetric stretch || 2086
|-
| [Mn(CO)6]+ || 879 || symmetric stretch || 2199
|-
| [Fe(CO)6]2+ || 272 || symmetric stretch || 2297
|}

This table above shows the wave-number and intensity all the IR active symmetric stretches of all the metal complexes CO ligands. As each complex has 13 atoms it is expected to have 3(13)-6= 33 vibrational modes but as shown in the vibrational spectra below many of these modes are IR inactive and have intensities of 0, an example of this is the totally symmetric C-O vibrations meaning they cannot be analysed given the fact that they don't appear. As predicted earlier across the period CO bond frequency would increase and this is due to back donation. Whilst back bonding causes an increase in the M-C bond there is also a increase in the CO bond length. The more positive the metal centre means contraction of the d-orbitals and this means that their is a less overlap between the d-orbital and CO pi* orbital and the less overlap with this orbital the stronger the CO bond.

[[File:Cr_vibrational_spectrum.PNG]] Cr complex Vibrational spectrum

[[File:Mn_vibrational_spectrum.PNG]] Mn complex Vibrational spectrum

[[File:Fe_vibrational_spectrum.PNG]] Fe complex Vibrational spectrum

JoeWiki1

2019-05-23T17:30:58Z

Jh3817: /* Analysing properties */

== Year 2 Inorganic comp labs ==

=== BH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p),
Symmetry= D3h

[[File:BH3_info.PNG]]

Item Value Threshold Converged?

Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

Link to frequency file: [[File:JH_BH3_FREQ.LOG]]

Low frequencies --- -0.4072 -0.1962 -0.0055 25.2514 27.2430 27.2460

Low frequencies --- 1163.1897 1213.3128 1213.3155

<jmol><jmolApplet>
<title>Optimised BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JH_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Vibration Data ====

{| class="wikitable" border="1"
|+ Vibrations table
! Stretch or Bend? !! Intensity !! Symmetry !! IR active? !! Wavenumber(cm-1)
|-
| Bend || 92 || A2" || Yes || 1163
|-
| Bend || 14 || E' || Yes || 1213
|-
| Bend || 14 || E' || Yes || 1213
|-
| Symmetric Stretch || 0 || A1' || No || 2581
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|}

[[File:BH3_vibrations_spectrum_JH.PNG]]

Spectrum shows 3 peaks out of 6 shown in table. 1 is IR in active leaving 5. Two pairs in the 5 are degenerate meaning they have the same energy meaning only 3 peaks show.

[[File:MO_diagram_JH.PNG]] [1111111111111111111111111111111111111111]

The LCAOs seem very accurate as they depict AOs which combine to form the real MOs very well. Minor issues arise from the fact that it can be said that the overlapping of the orbitals may not be able to be seen fully and the fact that the sizes of the AOs, which represents contribution isn’t consistent. Hydrogen is more electronegative then boron and is therefore lower in energy. Hydrogen should be contributing more to the bonding orbitals and born should be contributing more to the anti-bonding orbitals but for some of them this might not be able to be seen accurately. This shows that the LCAO is a useful tool for finding what a real MO would look like.

=== NH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:NH3_point_group_summary.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES

Link to frequency file: [[File:NH3_OP_JH.LOG]]

Low frequencies --- -8.5628 -8.5571 -0.0047 0.0454 0.1785 26.4189

Low frequencies --- 1089.7603 1694.1865 1694.1865

<jmol><jmolApplet>
<title>Optimised NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3_OP_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:BH3NH3_point_group_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000514 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

Link to frequency file: [[File:NH3BH3_FREQ_NEW.LOG]]

Low frequencies --- -0.0005 0.0003 0.0014 16.7270 18.7414 42.2600

Low frequencies --- 266.2799 632.3010 639.2486

<jmol><jmolApplet>
<title>Optimised NH3BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3BH3_FREQ_NEW.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Association energies ====
E(NH3)= -56.55776863 a.u.

E(BH3)= -26.61532362 a.u.

E(NH3BH3)= -83.22469031 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)], Therefore ΔE= (-83.22468960) - [(-56.55776863)+(-26.61532362)]= -0.05159806 a.u. (-134 KJ/Mol)

The B-N dative bond is weak and this shown when compared to the Al-N bond which has an energy of 297KJ/Mol (https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf)(22222222222)

=== NI3 ===
Method= RB3LYP,
Basis set= Gen

[[File:New_NI3_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000102 0.000450 YES
RMS Force 0.000075 0.000300 YES
Maximum Displacement 0.000858 0.001800 YES
RMS Displacement 0.000629 0.001200 YES

Link to frequency file: [[File:NEW_NI3_JH.LOG]]

Low frequencies --- -12.3845 -12.3781 -5.6129 -0.0040 0.0194 0.0711

Low frequencies --- 100.9307 100.9314 147.2333

<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NEW_NI3_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised B-I bond distance is 2.18 angstrom

===Days 2 and 3 Project: Metal carbonyls===
This sections of the wiki page focuses on metal carbonyls, more specifically their bond-lengths and CO bond frequencies. The metal-complexes which will be focused on are [Cr(CO)6], [Mn(CO)6]+ and [Fe(CO)6]2+. These were chosen as they come one after another in the d-block so it would be interesting to see how bond-lengths and bond frequencies vary across the period. 2 of the complexes are charged (positively) while one is neutral and this is something which must be taken into account when analysing bond-lengths and bond frequencies. An initial prediction would be that bond length decreases across a period and that bond frequencies increases.

==== [Cr(CO)6] ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Cr

[[File:Cr(CO)6_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000110 0.000450 YES
RMS Force 0.000041 0.000300 YES
Maximum Displacement 0.000705 0.001800 YES
RMS Displacement 0.000334 0.001200 YES

Link to frequency file: [[File:CR(CO)6_JH_2.LOG]]

Low frequencies --- -0.0014 -0.0013 -0.0010 11.7482 11.7482 11.7482

Low frequencies --- 66.6574 66.6574 66.6574

<jmol><jmolApplet>
<title>Optimised Cr(CO)6 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>CR(CO)6_JH_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Mn(CO)6]+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Mn

[[File:-Mn(CO)62+_summary_JH3817.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000430 0.001800 YES
RMS Displacement 0.000204 0.001200 YES

Link to frequency file: [[File:-MN(CO)6-+_OP_FREQ_JH.LOG]]

Low frequencies --- -0.0007 0.0006 0.0009 4.7607 4.7607 4.7607

Low frequencies --- 76.3202 76.3202 76.3202

<jmol><jmolApplet>
<title>Optimised Mn(CO)6+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-MN(CO)6-+_OP_FREQ_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Fe(CO)6]2+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Fe

[[File:-Fe(CO)6-2+_freq_op_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000429 0.001800 YES
RMS Displacement 0.000200 0.001200 YES

Link to frequency file: [[File:-FE(CO)6-2+_OP_FREQ.LOG]]

Low frequencies --- -10.5293 -10.5293 -10.5292 -0.0014 -0.0011 -0.0009

Low frequencies --- 82.1285 82.1285 82.1285

<jmol><jmolApplet>
<title>Optimised [FE(CO)6]2+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-FE(CO)6-2+_OP_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Analysing properties ====

{| class="wikitable" border="1"
|+ Bond Length
! Metal complex !! Bond Length(Å)
|-
| [Cr(CO)6] || 1.915
|-
| [Mn(CO)6]+ || 1.908
|-
| [Fe(CO)6]2+ || 1.940
|}

The table above shows the bond metal centre-carbon bond lengths. Electrons from a d-orbital on the metal centres is partially donated into the pi* orbital of the CO ligand. This strengthens the M-C bond. As predicted moving across a period causes the bond length to decrease for the first two but when looking at iron there is an unexpected increase. The decrease between the first two likely due to back bonding and increase in oxidation state as increasing oxidation state leads to an increase in bond strength and the sudden increase in the bond length for the iron complex is due to the contraction of the d-orbitals leading to poorer overlap with the CO orbitals but after speaking to professor Hunt it turns out a full explanation of this increase in bond length is to complex for the course.

{| class="wikitable" border="1"
|+ Vibrations table 2
! Metal complex !! Intensity !! Vibration type !! Wavenumber(cm-1)
|-
| Cr(CO)6 || 1637 || symmetric stretch || 2086
|-
| [Mn(CO)6]+ || 879 || symmetric stretch || 2199
|-
| [Fe(CO)6]2+ || 272 || symmetric stretch || 2297
|}

This table above shows the wave-number and intensity all the IR active symmetric stretches of all the metal complexes CO ligands. As each complex has 13 atoms it is expected to have 3(13)-6= 33 vibrational modes but as shown in the vibrational spectra below many of these modes are IR inactive and have intensities of 0, an example of this is the totally symmetric C-O vibrations meaning they cannot be analysed given the fact that they don't appear. As predicted earlier across the period CO bond frequency would increase and this is due to back donation. Whilst back bonding causes an increase in the M-C bond there is also a increase in the CO bond length. The more positive the metal centre means contraction of the d-orbitals and this means that their is a less overlap between the d-orbital and CO pi* orbital and the less overlap with this orbital the stronger the CO bond.

[[File:Cr_vibrational_spectrum.PNG]] Cr complex Vibrational spectrum

[[File:Mn_vibrational_spectrum.PNG]] Mn complex Vibrational spectrum

[[File:Fe_vibrational_spectrum.PNG]] Fe complex Vibrational spectrum

JoeWiki1

2019-05-23T17:30:38Z

Jh3817: /* Analysing properties */

== Year 2 Inorganic comp labs ==

=== BH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p),
Symmetry= D3h

[[File:BH3_info.PNG]]

Item Value Threshold Converged?

Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

Link to frequency file: [[File:JH_BH3_FREQ.LOG]]

Low frequencies --- -0.4072 -0.1962 -0.0055 25.2514 27.2430 27.2460

Low frequencies --- 1163.1897 1213.3128 1213.3155

<jmol><jmolApplet>
<title>Optimised BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JH_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Vibration Data ====

{| class="wikitable" border="1"
|+ Vibrations table
! Stretch or Bend? !! Intensity !! Symmetry !! IR active? !! Wavenumber(cm-1)
|-
| Bend || 92 || A2" || Yes || 1163
|-
| Bend || 14 || E' || Yes || 1213
|-
| Bend || 14 || E' || Yes || 1213
|-
| Symmetric Stretch || 0 || A1' || No || 2581
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|}

[[File:BH3_vibrations_spectrum_JH.PNG]]

Spectrum shows 3 peaks out of 6 shown in table. 1 is IR in active leaving 5. Two pairs in the 5 are degenerate meaning they have the same energy meaning only 3 peaks show.

[[File:MO_diagram_JH.PNG]] [1111111111111111111111111111111111111111]

The LCAOs seem very accurate as they depict AOs which combine to form the real MOs very well. Minor issues arise from the fact that it can be said that the overlapping of the orbitals may not be able to be seen fully and the fact that the sizes of the AOs, which represents contribution isn’t consistent. Hydrogen is more electronegative then boron and is therefore lower in energy. Hydrogen should be contributing more to the bonding orbitals and born should be contributing more to the anti-bonding orbitals but for some of them this might not be able to be seen accurately. This shows that the LCAO is a useful tool for finding what a real MO would look like.

=== NH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:NH3_point_group_summary.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES

Link to frequency file: [[File:NH3_OP_JH.LOG]]

Low frequencies --- -8.5628 -8.5571 -0.0047 0.0454 0.1785 26.4189

Low frequencies --- 1089.7603 1694.1865 1694.1865

<jmol><jmolApplet>
<title>Optimised NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3_OP_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:BH3NH3_point_group_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000514 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

Link to frequency file: [[File:NH3BH3_FREQ_NEW.LOG]]

Low frequencies --- -0.0005 0.0003 0.0014 16.7270 18.7414 42.2600

Low frequencies --- 266.2799 632.3010 639.2486

<jmol><jmolApplet>
<title>Optimised NH3BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3BH3_FREQ_NEW.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Association energies ====
E(NH3)= -56.55776863 a.u.

E(BH3)= -26.61532362 a.u.

E(NH3BH3)= -83.22469031 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)], Therefore ΔE= (-83.22468960) - [(-56.55776863)+(-26.61532362)]= -0.05159806 a.u. (-134 KJ/Mol)

The B-N dative bond is weak and this shown when compared to the Al-N bond which has an energy of 297KJ/Mol (https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf)(22222222222)

=== NI3 ===
Method= RB3LYP,
Basis set= Gen

[[File:New_NI3_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000102 0.000450 YES
RMS Force 0.000075 0.000300 YES
Maximum Displacement 0.000858 0.001800 YES
RMS Displacement 0.000629 0.001200 YES

Link to frequency file: [[File:NEW_NI3_JH.LOG]]

Low frequencies --- -12.3845 -12.3781 -5.6129 -0.0040 0.0194 0.0711

Low frequencies --- 100.9307 100.9314 147.2333

<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NEW_NI3_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised B-I bond distance is 2.18 angstrom

===Days 2 and 3 Project: Metal carbonyls===
This sections of the wiki page focuses on metal carbonyls, more specifically their bond-lengths and CO bond frequencies. The metal-complexes which will be focused on are [Cr(CO)6], [Mn(CO)6]+ and [Fe(CO)6]2+. These were chosen as they come one after another in the d-block so it would be interesting to see how bond-lengths and bond frequencies vary across the period. 2 of the complexes are charged (positively) while one is neutral and this is something which must be taken into account when analysing bond-lengths and bond frequencies. An initial prediction would be that bond length decreases across a period and that bond frequencies increases.

==== [Cr(CO)6] ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Cr

[[File:Cr(CO)6_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000110 0.000450 YES
RMS Force 0.000041 0.000300 YES
Maximum Displacement 0.000705 0.001800 YES
RMS Displacement 0.000334 0.001200 YES

Link to frequency file: [[File:CR(CO)6_JH_2.LOG]]

Low frequencies --- -0.0014 -0.0013 -0.0010 11.7482 11.7482 11.7482

Low frequencies --- 66.6574 66.6574 66.6574

<jmol><jmolApplet>
<title>Optimised Cr(CO)6 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>CR(CO)6_JH_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Mn(CO)6]+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Mn

[[File:-Mn(CO)62+_summary_JH3817.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000430 0.001800 YES
RMS Displacement 0.000204 0.001200 YES

Link to frequency file: [[File:-MN(CO)6-+_OP_FREQ_JH.LOG]]

Low frequencies --- -0.0007 0.0006 0.0009 4.7607 4.7607 4.7607

Low frequencies --- 76.3202 76.3202 76.3202

<jmol><jmolApplet>
<title>Optimised Mn(CO)6+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-MN(CO)6-+_OP_FREQ_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Fe(CO)6]2+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Fe

[[File:-Fe(CO)6-2+_freq_op_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000429 0.001800 YES
RMS Displacement 0.000200 0.001200 YES

Link to frequency file: [[File:-FE(CO)6-2+_OP_FREQ.LOG]]

Low frequencies --- -10.5293 -10.5293 -10.5292 -0.0014 -0.0011 -0.0009

Low frequencies --- 82.1285 82.1285 82.1285

<jmol><jmolApplet>
<title>Optimised [FE(CO)6]2+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-FE(CO)6-2+_OP_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Analysing properties ====

{| class="wikitable" border="1"
|+ Bond Length
! Metal complex !! Bond Length(Å)
|-
| [Cr(CO)6] || 1.915
|-
| [Mn(CO)6]+ || 1.908
|-
| [Fe(CO)6]2+ || 1.940
|}

The table above shows the bond metal centre-carbon bond lengths. Electrons from a d-orbital on the metal centres is partially donated into the pi* orbital of the CO ligand. This strengthens the M-C bond. As predicted moving across a period causes the bond length to decrease for the first two but when looking at iron there is an unexpected increase. The decrease between the first two likely due to back bonding and increase in oxidation state as increasing oxidation state leads to an increase in bond strength and the sudden increase in the bond length for the iron complex is due to the contraction of the d-orbitals leading to poorer overlap with the CO orbitals but after speaking to professor Hunt it turns out a full explanation of this increase in bond length is to complex for the course.

{| class="wikitable" border="1"
|+ Vibrations table 2
! Metal complex !! Intensity !! Vibration type !! Wavenumber(cm-1)
|-
| Cr(CO)6 || 1637 || symmetric stretch || 2086
|-
| [Mn(CO)6]+ || 879 || symmetric stretch || 2199
|-
| [Fe(CO)6]2+ || 272 || symmetric stretch || 2297
|}

This table above shows the wave-number and intensity all the IR active symmetric stretches of all the metal complexes CO ligands. As each complex has 13 atoms it is expected to have 3(13)-6= 33 vibrational modes but as shown in the vibrational spectra below many of these modes are IR inactive and have intensities of 0, an example of this is the totally symmetric C-O vibrations meaning they cannot be analysed given the fact that they don't appear. As predicted earlier across the period CO bond frequency would increase and this is due to back donation. Whilst back bonding causes an increase in the M-C bond there is also a increase in the CO bond length. The more positive the metal centre means contraction of the d-orbitals and this means that their is a less overlap between the d-orbital and CO pi* orbital and the less overlap with this orbital the stronger the CO bond.

[[File:Cr_vibrational_spectrum.PNG]]Cr complex Vibrational spectrum

[[File:Mn_vibrational_spectrum.PNG]]Mn complex Vibrational spectrum

[[File:Fe_vibrational_spectrum.PNG]]Fe complex Vibrational spectrum

File:Fe vibrational spectrum.PNG

2019-05-23T17:30:20Z

Jh3817:

File:Mn vibrational spectrum.PNG

2019-05-23T17:28:30Z

Jh3817:

JoeWiki1

2019-05-23T17:28:08Z

Jh3817: /* Analysing properties */

== Year 2 Inorganic comp labs ==

=== BH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p),
Symmetry= D3h

[[File:BH3_info.PNG]]

Item Value Threshold Converged?

Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

Link to frequency file: [[File:JH_BH3_FREQ.LOG]]

Low frequencies --- -0.4072 -0.1962 -0.0055 25.2514 27.2430 27.2460

Low frequencies --- 1163.1897 1213.3128 1213.3155

<jmol><jmolApplet>
<title>Optimised BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JH_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Vibration Data ====

{| class="wikitable" border="1"
|+ Vibrations table
! Stretch or Bend? !! Intensity !! Symmetry !! IR active? !! Wavenumber(cm-1)
|-
| Bend || 92 || A2" || Yes || 1163
|-
| Bend || 14 || E' || Yes || 1213
|-
| Bend || 14 || E' || Yes || 1213
|-
| Symmetric Stretch || 0 || A1' || No || 2581
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|}

[[File:BH3_vibrations_spectrum_JH.PNG]]

Spectrum shows 3 peaks out of 6 shown in table. 1 is IR in active leaving 5. Two pairs in the 5 are degenerate meaning they have the same energy meaning only 3 peaks show.

[[File:MO_diagram_JH.PNG]] [1111111111111111111111111111111111111111]

The LCAOs seem very accurate as they depict AOs which combine to form the real MOs very well. Minor issues arise from the fact that it can be said that the overlapping of the orbitals may not be able to be seen fully and the fact that the sizes of the AOs, which represents contribution isn’t consistent. Hydrogen is more electronegative then boron and is therefore lower in energy. Hydrogen should be contributing more to the bonding orbitals and born should be contributing more to the anti-bonding orbitals but for some of them this might not be able to be seen accurately. This shows that the LCAO is a useful tool for finding what a real MO would look like.

=== NH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:NH3_point_group_summary.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES

Link to frequency file: [[File:NH3_OP_JH.LOG]]

Low frequencies --- -8.5628 -8.5571 -0.0047 0.0454 0.1785 26.4189

Low frequencies --- 1089.7603 1694.1865 1694.1865

<jmol><jmolApplet>
<title>Optimised NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3_OP_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:BH3NH3_point_group_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000514 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

Link to frequency file: [[File:NH3BH3_FREQ_NEW.LOG]]

Low frequencies --- -0.0005 0.0003 0.0014 16.7270 18.7414 42.2600

Low frequencies --- 266.2799 632.3010 639.2486

<jmol><jmolApplet>
<title>Optimised NH3BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3BH3_FREQ_NEW.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Association energies ====
E(NH3)= -56.55776863 a.u.

E(BH3)= -26.61532362 a.u.

E(NH3BH3)= -83.22469031 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)], Therefore ΔE= (-83.22468960) - [(-56.55776863)+(-26.61532362)]= -0.05159806 a.u. (-134 KJ/Mol)

The B-N dative bond is weak and this shown when compared to the Al-N bond which has an energy of 297KJ/Mol (https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf)(22222222222)

=== NI3 ===
Method= RB3LYP,
Basis set= Gen

[[File:New_NI3_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000102 0.000450 YES
RMS Force 0.000075 0.000300 YES
Maximum Displacement 0.000858 0.001800 YES
RMS Displacement 0.000629 0.001200 YES

Link to frequency file: [[File:NEW_NI3_JH.LOG]]

Low frequencies --- -12.3845 -12.3781 -5.6129 -0.0040 0.0194 0.0711

Low frequencies --- 100.9307 100.9314 147.2333

<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NEW_NI3_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised B-I bond distance is 2.18 angstrom

===Days 2 and 3 Project: Metal carbonyls===
This sections of the wiki page focuses on metal carbonyls, more specifically their bond-lengths and CO bond frequencies. The metal-complexes which will be focused on are [Cr(CO)6], [Mn(CO)6]+ and [Fe(CO)6]2+. These were chosen as they come one after another in the d-block so it would be interesting to see how bond-lengths and bond frequencies vary across the period. 2 of the complexes are charged (positively) while one is neutral and this is something which must be taken into account when analysing bond-lengths and bond frequencies. An initial prediction would be that bond length decreases across a period and that bond frequencies increases.

==== [Cr(CO)6] ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Cr

[[File:Cr(CO)6_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000110 0.000450 YES
RMS Force 0.000041 0.000300 YES
Maximum Displacement 0.000705 0.001800 YES
RMS Displacement 0.000334 0.001200 YES

Link to frequency file: [[File:CR(CO)6_JH_2.LOG]]

Low frequencies --- -0.0014 -0.0013 -0.0010 11.7482 11.7482 11.7482

Low frequencies --- 66.6574 66.6574 66.6574

<jmol><jmolApplet>
<title>Optimised Cr(CO)6 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>CR(CO)6_JH_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Mn(CO)6]+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Mn

[[File:-Mn(CO)62+_summary_JH3817.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000430 0.001800 YES
RMS Displacement 0.000204 0.001200 YES

Link to frequency file: [[File:-MN(CO)6-+_OP_FREQ_JH.LOG]]

Low frequencies --- -0.0007 0.0006 0.0009 4.7607 4.7607 4.7607

Low frequencies --- 76.3202 76.3202 76.3202

<jmol><jmolApplet>
<title>Optimised Mn(CO)6+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-MN(CO)6-+_OP_FREQ_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Fe(CO)6]2+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Fe

[[File:-Fe(CO)6-2+_freq_op_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000429 0.001800 YES
RMS Displacement 0.000200 0.001200 YES

Link to frequency file: [[File:-FE(CO)6-2+_OP_FREQ.LOG]]

Low frequencies --- -10.5293 -10.5293 -10.5292 -0.0014 -0.0011 -0.0009

Low frequencies --- 82.1285 82.1285 82.1285

<jmol><jmolApplet>
<title>Optimised [FE(CO)6]2+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-FE(CO)6-2+_OP_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Analysing properties ====

{| class="wikitable" border="1"
|+ Bond Length
! Metal complex !! Bond Length(Å)
|-
| [Cr(CO)6] || 1.915
|-
| [Mn(CO)6]+ || 1.908
|-
| [Fe(CO)6]2+ || 1.940
|}

The table above shows the bond metal centre-carbon bond lengths. Electrons from a d-orbital on the metal centres is partially donated into the pi* orbital of the CO ligand. This strengthens the M-C bond. As predicted moving across a period causes the bond length to decrease for the first two but when looking at iron there is an unexpected increase. The decrease between the first two likely due to back bonding and increase in oxidation state as increasing oxidation state leads to an increase in bond strength and the sudden increase in the bond length for the iron complex is due to the contraction of the d-orbitals leading to poorer overlap with the CO orbitals but after speaking to professor Hunt it turns out a full explanation of this increase in bond length is to complex for the course.

{| class="wikitable" border="1"
|+ Vibrations table 2
! Metal complex !! Intensity !! Vibration type !! Wavenumber(cm-1)
|-
| Cr(CO)6 || 1637 || symmetric stretch || 2086
|-
| [Mn(CO)6]+ || 879 || symmetric stretch || 2199
|-
| [Fe(CO)6]2+ || 272 || symmetric stretch || 2297
|}

This table above shows the wave-number and intensity all the IR active symmetric stretches of all the metal complexes CO ligands. As each complex has 13 atoms it is expected to have 3(13)-6= 33 vibrational modes but as shown in the vibrational spectra below many of these modes are IR inactive and have intensities of 0, an example of this is the totally symmetric C-O vibrations meaning they cannot be analysed given the fact that they don't appear. As predicted earlier across the period CO bond frequency would increase and this is due to back donation. Whilst back bonding causes an increase in the M-C bond there is also a increase in the CO bond length. The more positive the metal centre means contraction of the d-orbitals and this means that their is a less overlap between the d-orbital and CO pi* orbital and the less overlap with this orbital the stronger the CO bond.

[[File:Cr_vibrational_spectrum.PNG]]Cr complex Vibrational spectrum

[[File:-MN(CO)6-+_OP_FREQ_JH.LOG]]Mn complex Vibrational spectrum

[[File:-MN(CO)6-+_OP_FREQ_JH.LOG]]Fe complex Vibrational spectrum

JoeWiki1

2019-05-23T17:25:37Z

Jh3817:

== Year 2 Inorganic comp labs ==

=== BH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p),
Symmetry= D3h

[[File:BH3_info.PNG]]

Item Value Threshold Converged?

Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

Link to frequency file: [[File:JH_BH3_FREQ.LOG]]

Low frequencies --- -0.4072 -0.1962 -0.0055 25.2514 27.2430 27.2460

Low frequencies --- 1163.1897 1213.3128 1213.3155

<jmol><jmolApplet>
<title>Optimised BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JH_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Vibration Data ====

{| class="wikitable" border="1"
|+ Vibrations table
! Stretch or Bend? !! Intensity !! Symmetry !! IR active? !! Wavenumber(cm-1)
|-
| Bend || 92 || A2" || Yes || 1163
|-
| Bend || 14 || E' || Yes || 1213
|-
| Bend || 14 || E' || Yes || 1213
|-
| Symmetric Stretch || 0 || A1' || No || 2581
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|}

[[File:BH3_vibrations_spectrum_JH.PNG]]

Spectrum shows 3 peaks out of 6 shown in table. 1 is IR in active leaving 5. Two pairs in the 5 are degenerate meaning they have the same energy meaning only 3 peaks show.

[[File:MO_diagram_JH.PNG]] [1111111111111111111111111111111111111111]

The LCAOs seem very accurate as they depict AOs which combine to form the real MOs very well. Minor issues arise from the fact that it can be said that the overlapping of the orbitals may not be able to be seen fully and the fact that the sizes of the AOs, which represents contribution isn’t consistent. Hydrogen is more electronegative then boron and is therefore lower in energy. Hydrogen should be contributing more to the bonding orbitals and born should be contributing more to the anti-bonding orbitals but for some of them this might not be able to be seen accurately. This shows that the LCAO is a useful tool for finding what a real MO would look like.

=== NH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:NH3_point_group_summary.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES

Link to frequency file: [[File:NH3_OP_JH.LOG]]

Low frequencies --- -8.5628 -8.5571 -0.0047 0.0454 0.1785 26.4189

Low frequencies --- 1089.7603 1694.1865 1694.1865

<jmol><jmolApplet>
<title>Optimised NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3_OP_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:BH3NH3_point_group_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000514 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

Link to frequency file: [[File:NH3BH3_FREQ_NEW.LOG]]

Low frequencies --- -0.0005 0.0003 0.0014 16.7270 18.7414 42.2600

Low frequencies --- 266.2799 632.3010 639.2486

<jmol><jmolApplet>
<title>Optimised NH3BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3BH3_FREQ_NEW.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Association energies ====
E(NH3)= -56.55776863 a.u.

E(BH3)= -26.61532362 a.u.

E(NH3BH3)= -83.22469031 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)], Therefore ΔE= (-83.22468960) - [(-56.55776863)+(-26.61532362)]= -0.05159806 a.u. (-134 KJ/Mol)

The B-N dative bond is weak and this shown when compared to the Al-N bond which has an energy of 297KJ/Mol (https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf)(22222222222)

=== NI3 ===
Method= RB3LYP,
Basis set= Gen

[[File:New_NI3_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000102 0.000450 YES
RMS Force 0.000075 0.000300 YES
Maximum Displacement 0.000858 0.001800 YES
RMS Displacement 0.000629 0.001200 YES

Link to frequency file: [[File:NEW_NI3_JH.LOG]]

Low frequencies --- -12.3845 -12.3781 -5.6129 -0.0040 0.0194 0.0711

Low frequencies --- 100.9307 100.9314 147.2333

<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NEW_NI3_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised B-I bond distance is 2.18 angstrom

===Days 2 and 3 Project: Metal carbonyls===
This sections of the wiki page focuses on metal carbonyls, more specifically their bond-lengths and CO bond frequencies. The metal-complexes which will be focused on are [Cr(CO)6], [Mn(CO)6]+ and [Fe(CO)6]2+. These were chosen as they come one after another in the d-block so it would be interesting to see how bond-lengths and bond frequencies vary across the period. 2 of the complexes are charged (positively) while one is neutral and this is something which must be taken into account when analysing bond-lengths and bond frequencies. An initial prediction would be that bond length decreases across a period and that bond frequencies increases.

==== [Cr(CO)6] ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Cr

[[File:Cr(CO)6_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000110 0.000450 YES
RMS Force 0.000041 0.000300 YES
Maximum Displacement 0.000705 0.001800 YES
RMS Displacement 0.000334 0.001200 YES

Link to frequency file: [[File:CR(CO)6_JH_2.LOG]]

Low frequencies --- -0.0014 -0.0013 -0.0010 11.7482 11.7482 11.7482

Low frequencies --- 66.6574 66.6574 66.6574

<jmol><jmolApplet>
<title>Optimised Cr(CO)6 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>CR(CO)6_JH_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Mn(CO)6]+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Mn

[[File:-Mn(CO)62+_summary_JH3817.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000430 0.001800 YES
RMS Displacement 0.000204 0.001200 YES

Link to frequency file: [[File:-MN(CO)6-+_OP_FREQ_JH.LOG]]

Low frequencies --- -0.0007 0.0006 0.0009 4.7607 4.7607 4.7607

Low frequencies --- 76.3202 76.3202 76.3202

<jmol><jmolApplet>
<title>Optimised Mn(CO)6+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-MN(CO)6-+_OP_FREQ_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Fe(CO)6]2+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Fe

[[File:-Fe(CO)6-2+_freq_op_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000429 0.001800 YES
RMS Displacement 0.000200 0.001200 YES

Link to frequency file: [[File:-FE(CO)6-2+_OP_FREQ.LOG]]

Low frequencies --- -10.5293 -10.5293 -10.5292 -0.0014 -0.0011 -0.0009

Low frequencies --- 82.1285 82.1285 82.1285

<jmol><jmolApplet>
<title>Optimised [FE(CO)6]2+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-FE(CO)6-2+_OP_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Analysing properties ====

{| class="wikitable" border="1"
|+ Bond Length
! Metal complex !! Bond Length(Å)
|-
| [Cr(CO)6] || 1.915
|-
| [Mn(CO)6]+ || 1.908
|-
| [Fe(CO)6]2+ || 1.940
|}

The table above shows the bond metal centre-carbon bond lengths. Electrons from a d-orbital on the metal centres is partially donated into the pi* orbital of the CO ligand. This strengthens the M-C bond. As predicted moving across a period causes the bond length to decrease for the first two but when looking at iron there is an unexpected increase. The decrease between the first two likely due to back bonding and increase in oxidation state as increasing oxidation state leads to an increase in bond strength and the sudden increase in the bond length for the iron complex is due to the contraction of the d-orbitals leading to poorer overlap with the CO orbitals but after speaking to professor Hunt it turns out a full explanation of this increase in bond length is to complex for the course.

{| class="wikitable" border="1"
|+ Vibrations table 2
! Metal complex !! Intensity !! Vibration type !! Wavenumber(cm-1)
|-
| Cr(CO)6 || 1637 || symmetric stretch || 2086
|-
| [Mn(CO)6]+ || 879 || symmetric stretch || 2199
|-
| [Fe(CO)6]2+ || 272 || symmetric stretch || 2297
|}

This table above shows the wave-number and intensity all the IR active symmetric stretches of all the metal complexes CO ligands. As each complex has 13 atoms it is expected to have 3(13)-6= 33 vibrational modes but as shown in the vibrational spectra below many of these modes are IR inactive and have intensities of 0, an example of this is the totally symmetric C-O vibrations meaning they cannot be analysed given the fact that they don't appear. As predicted earlier across the period CO bond frequency would increase and this is due to back donation. Whilst back bonding causes an increase in the M-C bond there is also a increase in the CO bond length. The more positive the metal centre means contraction of the d-orbitals and this means that their is a less overlap between the d-orbital and CO pi* orbital and the less overlap with this orbital the stronger the CO bond.

Link to frequency file: [[File:Cr_vibrational_spectrum.PNG]]

Link to frequency file: [[File:-MN(CO)6-+_OP_FREQ_JH.LOG]]

Link to frequency file: [[File:-MN(CO)6-+_OP_FREQ_JH.LOG]]

File:Cr vibrational spectrum.PNG

2019-05-23T17:25:15Z

Jh3817:

JoeWiki1

2019-05-23T17:16:28Z

Jh3817: /* Vibration Data */

== Year 2 Inorganic comp labs ==

=== BH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p),
Symmetry= D3h

[[File:BH3_info.PNG]]

Item Value Threshold Converged?

Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

Link to frequency file: [[File:JH_BH3_FREQ.LOG]]

Low frequencies --- -0.4072 -0.1962 -0.0055 25.2514 27.2430 27.2460

Low frequencies --- 1163.1897 1213.3128 1213.3155

<jmol><jmolApplet>
<title>Optimised BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JH_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Vibration Data ====

{| class="wikitable" border="1"
|+ Vibrations table
! Stretch or Bend? !! Intensity !! Symmetry !! IR active? !! Wavenumber(cm-1)
|-
| Bend || 92 || A2" || Yes || 1163
|-
| Bend || 14 || E' || Yes || 1213
|-
| Bend || 14 || E' || Yes || 1213
|-
| Symmetric Stretch || 0 || A1' || No || 2581
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|}

[[File:BH3_vibrations_spectrum_JH.PNG]]

Spectrum shows 3 peaks out of 6 shown in table. 1 is IR in active leaving 5. Two pairs in the 5 are degenerate meaning they have the same energy meaning only 3 peaks show.

[[File:MO_diagram_JH.PNG]] [1111111111111111111111111111111111111111]

The LCAOs seem very accurate as they depict AOs which combine to form the real MOs very well. Minor issues arise from the fact that it can be said that the overlapping of the orbitals may not be able to be seen fully and the fact that the sizes of the AOs, which represents contribution isn’t consistent. Hydrogen is more electronegative then boron and is therefore lower in energy. Hydrogen should be contributing more to the bonding orbitals and born should be contributing more to the anti-bonding orbitals but for some of them this might not be able to be seen accurately. This shows that the LCAO is a useful tool for finding what a real MO would look like.

=== NH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:NH3_point_group_summary.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES

Link to frequency file: [[File:NH3_OP_JH.LOG]]

Low frequencies --- -8.5628 -8.5571 -0.0047 0.0454 0.1785 26.4189

Low frequencies --- 1089.7603 1694.1865 1694.1865

<jmol><jmolApplet>
<title>Optimised NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3_OP_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:BH3NH3_point_group_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000514 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

Link to frequency file: [[File:NH3BH3_FREQ_NEW.LOG]]

Low frequencies --- -0.0005 0.0003 0.0014 16.7270 18.7414 42.2600

Low frequencies --- 266.2799 632.3010 639.2486

<jmol><jmolApplet>
<title>Optimised NH3BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3BH3_FREQ_NEW.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Association energies ====
E(NH3)= -56.55776863 a.u.

E(BH3)= -26.61532362 a.u.

E(NH3BH3)= -83.22469031 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)], Therefore ΔE= (-83.22468960) - [(-56.55776863)+(-26.61532362)]= -0.05159806 a.u. (-134 KJ/Mol)

The B-N dative bond is weak and this shown when compared to the Al-N bond which has an energy of 297KJ/Mol (https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf)(22222222222)

=== NI3 ===
Method= RB3LYP,
Basis set= Gen

[[File:New_NI3_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000102 0.000450 YES
RMS Force 0.000075 0.000300 YES
Maximum Displacement 0.000858 0.001800 YES
RMS Displacement 0.000629 0.001200 YES

Link to frequency file: [[File:NEW_NI3_JH.LOG]]

Low frequencies --- -12.3845 -12.3781 -5.6129 -0.0040 0.0194 0.0711

Low frequencies --- 100.9307 100.9314 147.2333

<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NEW_NI3_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised B-I bond distance is 2.18 angstrom

===Days 2 and 3 Project: Metal carbonyls===
This sections of the wiki page focuses on metal carbonyls, more specifically their bond-lengths and CO bond frequencies. The metal-complexes which will be focused on are [Cr(CO)6], [Mn(CO)6]+ and [Fe(CO)6]2+. These were chosen as they come one after another in the d-block so it would be interesting to see how bond-lengths and bond frequencies vary across the period. 2 of the complexes are charged (positively) while one is neutral and this is something which must be taken into account when analysing bond-lengths and bond frequencies. An initial prediction would be that bond length decreases across a period and that bond frequencies increases.

==== [Cr(CO)6] ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Cr

[[File:Cr(CO)6_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000110 0.000450 YES
RMS Force 0.000041 0.000300 YES
Maximum Displacement 0.000705 0.001800 YES
RMS Displacement 0.000334 0.001200 YES

Link to frequency file: [[File:CR(CO)6_JH_2.LOG]]

Low frequencies --- -0.0014 -0.0013 -0.0010 11.7482 11.7482 11.7482

Low frequencies --- 66.6574 66.6574 66.6574

<jmol><jmolApplet>
<title>Optimised Cr(CO)6 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>CR(CO)6_JH_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Mn(CO)6]+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Mn

[[File:-Mn(CO)62+_summary_JH3817.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000430 0.001800 YES
RMS Displacement 0.000204 0.001200 YES

Link to frequency file: [[File:-MN(CO)6-+_OP_FREQ_JH.LOG]]

Low frequencies --- -0.0007 0.0006 0.0009 4.7607 4.7607 4.7607

Low frequencies --- 76.3202 76.3202 76.3202

<jmol><jmolApplet>
<title>Optimised Mn(CO)6+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-MN(CO)6-+_OP_FREQ_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Fe(CO)6]2+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Fe

[[File:-Fe(CO)6-2+_freq_op_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000429 0.001800 YES
RMS Displacement 0.000200 0.001200 YES

Link to frequency file: [[File:-FE(CO)6-2+_OP_FREQ.LOG]]

Low frequencies --- -10.5293 -10.5293 -10.5292 -0.0014 -0.0011 -0.0009

Low frequencies --- 82.1285 82.1285 82.1285

<jmol><jmolApplet>
<title>Optimised [FE(CO)6]2+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-FE(CO)6-2+_OP_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Analysing properties ====

{| class="wikitable" border="1"
|+ Bond Length
! Metal complex !! Bond Length(Å)
|-
| [Cr(CO)6] || 1.915
|-
| [Mn(CO)6]+ || 1.908
|-
| [Fe(CO)6]2+ || 1.940
|}

The table above shows the bond metal centre-carbon bond lengths. Electrons from a d-orbital on the metal centres is partially donated into the pi* orbital of the CO ligand. This strengthens the M-C bond. As predicted moving across a period causes the bond length to decrease for the first two but when looking at iron there is an unexpected increase. The decrease between the first two likely due to back bonding and increase in oxidation state as increasing oxidation state leads to an increase in bond strength and the sudden increase in the bond length for the iron complex is due to the contraction of the d-orbitals leading to poorer overlap with the CO orbitals but after speaking to professor Hunt it turns out a full explanation of this increase in bond length is to complex for the course.

{| class="wikitable" border="1"
|+ Vibrations table 2
! Metal complex !! Intensity !! Vibration type !! Wavenumber(cm-1)
|-
| Cr(CO)6 || 1637 || symmetric stretch || 2086
|-
| [Mn(CO)6]+ || 879 || symmetric stretch || 2199
|-
| [Fe(CO)6]2+ || 272 || symmetric stretch || 2297
|}

This table above shows the wave-number and intensity all the IR active symmetric stretches of all the metal complexes CO ligands. As each complex has 13 atoms it is expected to have 3(13)-6= 33 vibrational modes but as shown in the vibrational spectra below many of these modes are IR inactive and have intensities of 0, an example of this is the totally symmetric C-O vibrations meaning they cannot be analysed given the fact that they don't appear. As predicted earlier across the period CO bond frequency would increase and this is due to back donation. Whilst back bonding causes an increase in the M-C bond there is also a increase in the CO bond length. The more positive the metal centre means contraction of the d-orbitals and this means that their is a less overlap between the d-orbital and CO pi* orbital and the less overlap with this orbital the stronger the CO bond.

JoeWiki1

2019-05-23T17:14:17Z

Jh3817: /* Analysing properties */

== Year 2 Inorganic comp labs ==

=== BH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p),
Symmetry= D3h

[[File:BH3_info.PNG]]

Item Value Threshold Converged?

Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

Link to frequency file: [[File:JH_BH3_FREQ.LOG]]

Low frequencies --- -0.4072 -0.1962 -0.0055 25.2514 27.2430 27.2460

Low frequencies --- 1163.1897 1213.3128 1213.3155

<jmol><jmolApplet>
<title>Optimised BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JH_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Vibration Data ====

{| class="wikitable" border="1"
|+ Vibrations table
! Stretch or Bend? !! Intensity !! Symmetry !! IR active? !! Wavenumber(cm)
|-
| Bend || 92 || A2" || Yes || 1163
|-
| Bend || 14 || E' || Yes || 1213
|-
| Bend || 14 || E' || Yes || 1213
|-
| Symmetric Stretch || 0 || A1' || No || 2581
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|}

[[File:BH3_vibrations_spectrum_JH.PNG]]

Spectrum shows 3 peaks out of 6 shown in table. 1 is IR in active leaving 5. Two pairs in the 5 are degenerate meaning they have the same energy meaning only 3 peaks show.

[[File:MO_diagram_JH.PNG]] [1111111111111111111111111111111111111111]

The LCAOs seem very accurate as they depict AOs which combine to form the real MOs very well. Minor issues arise from the fact that it can be said that the overlapping of the orbitals may not be able to be seen fully and the fact that the sizes of the AOs, which represents contribution isn’t consistent. Hydrogen is more electronegative then boron and is therefore lower in energy. Hydrogen should be contributing more to the bonding orbitals and born should be contributing more to the anti-bonding orbitals but for some of them this might not be able to be seen accurately. This shows that the LCAO is a useful tool for finding what a real MO would look like.

=== NH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:NH3_point_group_summary.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES

Link to frequency file: [[File:NH3_OP_JH.LOG]]

Low frequencies --- -8.5628 -8.5571 -0.0047 0.0454 0.1785 26.4189

Low frequencies --- 1089.7603 1694.1865 1694.1865

<jmol><jmolApplet>
<title>Optimised NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3_OP_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:BH3NH3_point_group_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000514 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

Link to frequency file: [[File:NH3BH3_FREQ_NEW.LOG]]

Low frequencies --- -0.0005 0.0003 0.0014 16.7270 18.7414 42.2600

Low frequencies --- 266.2799 632.3010 639.2486

<jmol><jmolApplet>
<title>Optimised NH3BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3BH3_FREQ_NEW.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Association energies ====
E(NH3)= -56.55776863 a.u.

E(BH3)= -26.61532362 a.u.

E(NH3BH3)= -83.22469031 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)], Therefore ΔE= (-83.22468960) - [(-56.55776863)+(-26.61532362)]= -0.05159806 a.u. (-134 KJ/Mol)

The B-N dative bond is weak and this shown when compared to the Al-N bond which has an energy of 297KJ/Mol (https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf)(22222222222)

=== NI3 ===
Method= RB3LYP,
Basis set= Gen

[[File:New_NI3_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000102 0.000450 YES
RMS Force 0.000075 0.000300 YES
Maximum Displacement 0.000858 0.001800 YES
RMS Displacement 0.000629 0.001200 YES

Link to frequency file: [[File:NEW_NI3_JH.LOG]]

Low frequencies --- -12.3845 -12.3781 -5.6129 -0.0040 0.0194 0.0711

Low frequencies --- 100.9307 100.9314 147.2333

<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NEW_NI3_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised B-I bond distance is 2.18 angstrom

===Days 2 and 3 Project: Metal carbonyls===
This sections of the wiki page focuses on metal carbonyls, more specifically their bond-lengths and CO bond frequencies. The metal-complexes which will be focused on are [Cr(CO)6], [Mn(CO)6]+ and [Fe(CO)6]2+. These were chosen as they come one after another in the d-block so it would be interesting to see how bond-lengths and bond frequencies vary across the period. 2 of the complexes are charged (positively) while one is neutral and this is something which must be taken into account when analysing bond-lengths and bond frequencies. An initial prediction would be that bond length decreases across a period and that bond frequencies increases.

==== [Cr(CO)6] ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Cr

[[File:Cr(CO)6_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000110 0.000450 YES
RMS Force 0.000041 0.000300 YES
Maximum Displacement 0.000705 0.001800 YES
RMS Displacement 0.000334 0.001200 YES

Link to frequency file: [[File:CR(CO)6_JH_2.LOG]]

Low frequencies --- -0.0014 -0.0013 -0.0010 11.7482 11.7482 11.7482

Low frequencies --- 66.6574 66.6574 66.6574

<jmol><jmolApplet>
<title>Optimised Cr(CO)6 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>CR(CO)6_JH_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Mn(CO)6]+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Mn

[[File:-Mn(CO)62+_summary_JH3817.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000430 0.001800 YES
RMS Displacement 0.000204 0.001200 YES

Link to frequency file: [[File:-MN(CO)6-+_OP_FREQ_JH.LOG]]

Low frequencies --- -0.0007 0.0006 0.0009 4.7607 4.7607 4.7607

Low frequencies --- 76.3202 76.3202 76.3202

<jmol><jmolApplet>
<title>Optimised Mn(CO)6+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-MN(CO)6-+_OP_FREQ_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Fe(CO)6]2+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Fe

[[File:-Fe(CO)6-2+_freq_op_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000429 0.001800 YES
RMS Displacement 0.000200 0.001200 YES

Link to frequency file: [[File:-FE(CO)6-2+_OP_FREQ.LOG]]

Low frequencies --- -10.5293 -10.5293 -10.5292 -0.0014 -0.0011 -0.0009

Low frequencies --- 82.1285 82.1285 82.1285

<jmol><jmolApplet>
<title>Optimised [FE(CO)6]2+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-FE(CO)6-2+_OP_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Analysing properties ====

{| class="wikitable" border="1"
|+ Bond Length
! Metal complex !! Bond Length(Å)
|-
| [Cr(CO)6] || 1.915
|-
| [Mn(CO)6]+ || 1.908
|-
| [Fe(CO)6]2+ || 1.940
|}

The table above shows the bond metal centre-carbon bond lengths. Electrons from a d-orbital on the metal centres is partially donated into the pi* orbital of the CO ligand. This strengthens the M-C bond. As predicted moving across a period causes the bond length to decrease for the first two but when looking at iron there is an unexpected increase. The decrease between the first two likely due to back bonding and increase in oxidation state as increasing oxidation state leads to an increase in bond strength and the sudden increase in the bond length for the iron complex is due to the contraction of the d-orbitals leading to poorer overlap with the CO orbitals but after speaking to professor Hunt it turns out a full explanation of this increase in bond length is to complex for the course.

{| class="wikitable" border="1"
|+ Vibrations table 2
! Metal complex !! Intensity !! Vibration type !! Wavenumber(cm-1)
|-
| Cr(CO)6 || 1637 || symmetric stretch || 2086
|-
| [Mn(CO)6]+ || 879 || symmetric stretch || 2199
|-
| [Fe(CO)6]2+ || 272 || symmetric stretch || 2297
|}

This table above shows the wave-number and intensity all the IR active symmetric stretches of all the metal complexes CO ligands. As each complex has 13 atoms it is expected to have 3(13)-6= 33 vibrational modes but as shown in the vibrational spectra below many of these modes are IR inactive and have intensities of 0, an example of this is the totally symmetric C-O vibrations meaning they cannot be analysed given the fact that they don't appear. As predicted earlier across the period CO bond frequency would increase and this is due to back donation. Whilst back bonding causes an increase in the M-C bond there is also a increase in the CO bond length. The more positive the metal centre means contraction of the d-orbitals and this means that their is a less overlap between the d-orbital and CO pi* orbital and the less overlap with this orbital the stronger the CO bond.

JoeWiki1

2019-05-23T17:05:57Z

Jh3817: /* Analysing properties */

== Year 2 Inorganic comp labs ==

=== BH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p),
Symmetry= D3h

[[File:BH3_info.PNG]]

Item Value Threshold Converged?

Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

Link to frequency file: [[File:JH_BH3_FREQ.LOG]]

Low frequencies --- -0.4072 -0.1962 -0.0055 25.2514 27.2430 27.2460

Low frequencies --- 1163.1897 1213.3128 1213.3155

<jmol><jmolApplet>
<title>Optimised BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JH_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Vibration Data ====

{| class="wikitable" border="1"
|+ Vibrations table
! Stretch or Bend? !! Intensity !! Symmetry !! IR active? !! Wavenumber(cm)
|-
| Bend || 92 || A2" || Yes || 1163
|-
| Bend || 14 || E' || Yes || 1213
|-
| Bend || 14 || E' || Yes || 1213
|-
| Symmetric Stretch || 0 || A1' || No || 2581
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|}

[[File:BH3_vibrations_spectrum_JH.PNG]]

Spectrum shows 3 peaks out of 6 shown in table. 1 is IR in active leaving 5. Two pairs in the 5 are degenerate meaning they have the same energy meaning only 3 peaks show.

[[File:MO_diagram_JH.PNG]] [1111111111111111111111111111111111111111]

The LCAOs seem very accurate as they depict AOs which combine to form the real MOs very well. Minor issues arise from the fact that it can be said that the overlapping of the orbitals may not be able to be seen fully and the fact that the sizes of the AOs, which represents contribution isn’t consistent. Hydrogen is more electronegative then boron and is therefore lower in energy. Hydrogen should be contributing more to the bonding orbitals and born should be contributing more to the anti-bonding orbitals but for some of them this might not be able to be seen accurately. This shows that the LCAO is a useful tool for finding what a real MO would look like.

=== NH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:NH3_point_group_summary.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES

Link to frequency file: [[File:NH3_OP_JH.LOG]]

Low frequencies --- -8.5628 -8.5571 -0.0047 0.0454 0.1785 26.4189

Low frequencies --- 1089.7603 1694.1865 1694.1865

<jmol><jmolApplet>
<title>Optimised NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3_OP_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:BH3NH3_point_group_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000514 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

Link to frequency file: [[File:NH3BH3_FREQ_NEW.LOG]]

Low frequencies --- -0.0005 0.0003 0.0014 16.7270 18.7414 42.2600

Low frequencies --- 266.2799 632.3010 639.2486

<jmol><jmolApplet>
<title>Optimised NH3BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3BH3_FREQ_NEW.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Association energies ====
E(NH3)= -56.55776863 a.u.

E(BH3)= -26.61532362 a.u.

E(NH3BH3)= -83.22469031 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)], Therefore ΔE= (-83.22468960) - [(-56.55776863)+(-26.61532362)]= -0.05159806 a.u. (-134 KJ/Mol)

The B-N dative bond is weak and this shown when compared to the Al-N bond which has an energy of 297KJ/Mol (https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf)(22222222222)

=== NI3 ===
Method= RB3LYP,
Basis set= Gen

[[File:New_NI3_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000102 0.000450 YES
RMS Force 0.000075 0.000300 YES
Maximum Displacement 0.000858 0.001800 YES
RMS Displacement 0.000629 0.001200 YES

Link to frequency file: [[File:NEW_NI3_JH.LOG]]

Low frequencies --- -12.3845 -12.3781 -5.6129 -0.0040 0.0194 0.0711

Low frequencies --- 100.9307 100.9314 147.2333

<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NEW_NI3_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised B-I bond distance is 2.18 angstrom

===Days 2 and 3 Project: Metal carbonyls===
This sections of the wiki page focuses on metal carbonyls, more specifically their bond-lengths and CO bond frequencies. The metal-complexes which will be focused on are [Cr(CO)6], [Mn(CO)6]+ and [Fe(CO)6]2+. These were chosen as they come one after another in the d-block so it would be interesting to see how bond-lengths and bond frequencies vary across the period. 2 of the complexes are charged (positively) while one is neutral and this is something which must be taken into account when analysing bond-lengths and bond frequencies. An initial prediction would be that bond length decreases across a period and that bond frequencies increases.

==== [Cr(CO)6] ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Cr

[[File:Cr(CO)6_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000110 0.000450 YES
RMS Force 0.000041 0.000300 YES
Maximum Displacement 0.000705 0.001800 YES
RMS Displacement 0.000334 0.001200 YES

Link to frequency file: [[File:CR(CO)6_JH_2.LOG]]

Low frequencies --- -0.0014 -0.0013 -0.0010 11.7482 11.7482 11.7482

Low frequencies --- 66.6574 66.6574 66.6574

<jmol><jmolApplet>
<title>Optimised Cr(CO)6 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>CR(CO)6_JH_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Mn(CO)6]+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Mn

[[File:-Mn(CO)62+_summary_JH3817.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000430 0.001800 YES
RMS Displacement 0.000204 0.001200 YES

Link to frequency file: [[File:-MN(CO)6-+_OP_FREQ_JH.LOG]]

Low frequencies --- -0.0007 0.0006 0.0009 4.7607 4.7607 4.7607

Low frequencies --- 76.3202 76.3202 76.3202

<jmol><jmolApplet>
<title>Optimised Mn(CO)6+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-MN(CO)6-+_OP_FREQ_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Fe(CO)6]2+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Fe

[[File:-Fe(CO)6-2+_freq_op_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000429 0.001800 YES
RMS Displacement 0.000200 0.001200 YES

Link to frequency file: [[File:-FE(CO)6-2+_OP_FREQ.LOG]]

Low frequencies --- -10.5293 -10.5293 -10.5292 -0.0014 -0.0011 -0.0009

Low frequencies --- 82.1285 82.1285 82.1285

<jmol><jmolApplet>
<title>Optimised [FE(CO)6]2+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-FE(CO)6-2+_OP_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Analysing properties ====

{| class="wikitable" border="1"
|+ Bond Length
! Metal complex !! Bond Length(Å)
|-
| [Cr(CO)6] || 1.915
|-
| [Mn(CO)6]+ || 1.908
|-
| [Fe(CO)6]2+ || 1.940
|}

The table above shows the bond metal centre-carbon bond lengths. Electrons from a d-orbital on the metal centres is partially donated into the pi* orbital of the CO ligand. This strengthens the M-C bond. As predicted moving across a period causes the bond length to decrease for the first two but when looking at iron there is an unexpected increase. The decrease between the first two likely due to back bonding and increase in oxidation state as increasing oxidation state leads to an increase in bond strength and the sudden increase in the bond length for the iron complex is due to the contraction of the d-orbitals leading to poorer overlap with the CO orbitals but after speaking to professor Hunt it turns out a full explanation of this increase in bond length is to complex for the course.

{| class="wikitable" border="1"
|+ Vibrations table 2
! Metal complex !! Intensity !! Vibration type !! Wavenumber(cm-1)
|-
| Cr(CO)6 || 1637 || symmetric stretch || 2086
|-
| [Mn(CO)6]+ || 879 || symmetric stretch || 2199
|-
| [Fe(CO)6]2+ || 272 || symmetric stretch || 2297
|}

This table above shows the wave-number and intensity all the IR active symmetric stretches of all the metal complexes. As predicted earlier across the period CO bond frequency would increase and this is due to back donation. Whilst back bonding causes an increase in the M-C bond there is also a increase in the CO bond length. The more positive the metal centre means contraction of the d-orbitals and this means that their is a less overlap between the d-orbital and CO pi* orbital and the less overlap with this orbital the stronger the CO bond.

JoeWiki1

2019-05-23T17:00:04Z

Jh3817: /* Days 2 and 3 Project: Metal carbonyls */

== Year 2 Inorganic comp labs ==

=== BH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p),
Symmetry= D3h

[[File:BH3_info.PNG]]

Item Value Threshold Converged?

Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

Link to frequency file: [[File:JH_BH3_FREQ.LOG]]

Low frequencies --- -0.4072 -0.1962 -0.0055 25.2514 27.2430 27.2460

Low frequencies --- 1163.1897 1213.3128 1213.3155

<jmol><jmolApplet>
<title>Optimised BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JH_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Vibration Data ====

{| class="wikitable" border="1"
|+ Vibrations table
! Stretch or Bend? !! Intensity !! Symmetry !! IR active? !! Wavenumber(cm)
|-
| Bend || 92 || A2" || Yes || 1163
|-
| Bend || 14 || E' || Yes || 1213
|-
| Bend || 14 || E' || Yes || 1213
|-
| Symmetric Stretch || 0 || A1' || No || 2581
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|}

[[File:BH3_vibrations_spectrum_JH.PNG]]

Spectrum shows 3 peaks out of 6 shown in table. 1 is IR in active leaving 5. Two pairs in the 5 are degenerate meaning they have the same energy meaning only 3 peaks show.

[[File:MO_diagram_JH.PNG]] [1111111111111111111111111111111111111111]

The LCAOs seem very accurate as they depict AOs which combine to form the real MOs very well. Minor issues arise from the fact that it can be said that the overlapping of the orbitals may not be able to be seen fully and the fact that the sizes of the AOs, which represents contribution isn’t consistent. Hydrogen is more electronegative then boron and is therefore lower in energy. Hydrogen should be contributing more to the bonding orbitals and born should be contributing more to the anti-bonding orbitals but for some of them this might not be able to be seen accurately. This shows that the LCAO is a useful tool for finding what a real MO would look like.

=== NH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:NH3_point_group_summary.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES

Link to frequency file: [[File:NH3_OP_JH.LOG]]

Low frequencies --- -8.5628 -8.5571 -0.0047 0.0454 0.1785 26.4189

Low frequencies --- 1089.7603 1694.1865 1694.1865

<jmol><jmolApplet>
<title>Optimised NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3_OP_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:BH3NH3_point_group_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000514 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

Link to frequency file: [[File:NH3BH3_FREQ_NEW.LOG]]

Low frequencies --- -0.0005 0.0003 0.0014 16.7270 18.7414 42.2600

Low frequencies --- 266.2799 632.3010 639.2486

<jmol><jmolApplet>
<title>Optimised NH3BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3BH3_FREQ_NEW.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Association energies ====
E(NH3)= -56.55776863 a.u.

E(BH3)= -26.61532362 a.u.

E(NH3BH3)= -83.22469031 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)], Therefore ΔE= (-83.22468960) - [(-56.55776863)+(-26.61532362)]= -0.05159806 a.u. (-134 KJ/Mol)

The B-N dative bond is weak and this shown when compared to the Al-N bond which has an energy of 297KJ/Mol (https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf)(22222222222)

=== NI3 ===
Method= RB3LYP,
Basis set= Gen

[[File:New_NI3_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000102 0.000450 YES
RMS Force 0.000075 0.000300 YES
Maximum Displacement 0.000858 0.001800 YES
RMS Displacement 0.000629 0.001200 YES

Link to frequency file: [[File:NEW_NI3_JH.LOG]]

Low frequencies --- -12.3845 -12.3781 -5.6129 -0.0040 0.0194 0.0711

Low frequencies --- 100.9307 100.9314 147.2333

<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NEW_NI3_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised B-I bond distance is 2.18 angstrom

===Days 2 and 3 Project: Metal carbonyls===
This sections of the wiki page focuses on metal carbonyls, more specifically their bond-lengths and CO bond frequencies. The metal-complexes which will be focused on are [Cr(CO)6], [Mn(CO)6]+ and [Fe(CO)6]2+. These were chosen as they come one after another in the d-block so it would be interesting to see how bond-lengths and bond frequencies vary across the period. 2 of the complexes are charged (positively) while one is neutral and this is something which must be taken into account when analysing bond-lengths and bond frequencies. An initial prediction would be that bond length decreases across a period and that bond frequencies increases.

==== [Cr(CO)6] ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Cr

[[File:Cr(CO)6_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000110 0.000450 YES
RMS Force 0.000041 0.000300 YES
Maximum Displacement 0.000705 0.001800 YES
RMS Displacement 0.000334 0.001200 YES

Link to frequency file: [[File:CR(CO)6_JH_2.LOG]]

Low frequencies --- -0.0014 -0.0013 -0.0010 11.7482 11.7482 11.7482

Low frequencies --- 66.6574 66.6574 66.6574

<jmol><jmolApplet>
<title>Optimised Cr(CO)6 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>CR(CO)6_JH_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Mn(CO)6]+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Mn

[[File:-Mn(CO)62+_summary_JH3817.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000430 0.001800 YES
RMS Displacement 0.000204 0.001200 YES

Link to frequency file: [[File:-MN(CO)6-+_OP_FREQ_JH.LOG]]

Low frequencies --- -0.0007 0.0006 0.0009 4.7607 4.7607 4.7607

Low frequencies --- 76.3202 76.3202 76.3202

<jmol><jmolApplet>
<title>Optimised Mn(CO)6+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-MN(CO)6-+_OP_FREQ_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Fe(CO)6]2+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Fe

[[File:-Fe(CO)6-2+_freq_op_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000429 0.001800 YES
RMS Displacement 0.000200 0.001200 YES

Link to frequency file: [[File:-FE(CO)6-2+_OP_FREQ.LOG]]

Low frequencies --- -10.5293 -10.5293 -10.5292 -0.0014 -0.0011 -0.0009

Low frequencies --- 82.1285 82.1285 82.1285

<jmol><jmolApplet>
<title>Optimised [FE(CO)6]2+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-FE(CO)6-2+_OP_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Analysing properties ====

{| class="wikitable" border="1"
|+ Bond Length
! Metal complex !! Bond Length(Å)
|-
| [Cr(CO)6] || 1.915
|-
| [Mn(CO)6]+ || 1.908
|-
| [Fe(CO)6]2+ || 1.940
|}

The table above shows the bond metal centre-carbon bond lengths. Electrons from a d-orbital on the metal centres is partially donated into the pi* orbital of the CO ligand. This strengthens the M-C bond. As predicted moving across a period causes the bond length to decrease for the first two but when looking at iron there is an unexpected increase. The decrease between the first two likely due to back bonding and increase in oxidation state as increasing oxidation state leads to an increase in bond strength and the sudden increase in the bond length for the iron complex is due to the contraction of the d-orbitals leading to poorer overlap with the CO orbitals but after speaking to professor Hunt it turns out a full explanation of this increase in bond length is to complex for the course.

{| class="wikitable" border="1"
|+ Vibrations table 2
! Metal complex !! Intensity !! Vibration type !! Wavenumber(cm)
|-
| Cr(CO)6 || 1637 || symmetric stretch || 2086
|-
| [Mn(CO)6]+ || 879 || symmetric stretch || 2199
|-
| [Fe(CO)6]2+ || 272 || symmetric stretch || 2297
|}

Whilst back bonding causes an increase in the M-C bond there is also a increase in the CO bond length. The more positive the metal centre means contraction of the d-orbitals and this means that their is a less overlap between the d-orbital and CO pi* orbital and the less overlap with this orbital the stronger the CO bond.

JoeWiki1

2019-05-23T16:51:04Z

Jh3817: /* Analysing properties */

== Year 2 Inorganic comp labs ==

=== BH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p),
Symmetry= D3h

[[File:BH3_info.PNG]]

Item Value Threshold Converged?

Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

Link to frequency file: [[File:JH_BH3_FREQ.LOG]]

Low frequencies --- -0.4072 -0.1962 -0.0055 25.2514 27.2430 27.2460

Low frequencies --- 1163.1897 1213.3128 1213.3155

<jmol><jmolApplet>
<title>Optimised BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JH_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Vibration Data ====

{| class="wikitable" border="1"
|+ Vibrations table
! Stretch or Bend? !! Intensity !! Symmetry !! IR active? !! Wavenumber(cm)
|-
| Bend || 92 || A2" || Yes || 1163
|-
| Bend || 14 || E' || Yes || 1213
|-
| Bend || 14 || E' || Yes || 1213
|-
| Symmetric Stretch || 0 || A1' || No || 2581
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|}

[[File:BH3_vibrations_spectrum_JH.PNG]]

Spectrum shows 3 peaks out of 6 shown in table. 1 is IR in active leaving 5. Two pairs in the 5 are degenerate meaning they have the same energy meaning only 3 peaks show.

[[File:MO_diagram_JH.PNG]] [1111111111111111111111111111111111111111]

The LCAOs seem very accurate as they depict AOs which combine to form the real MOs very well. Minor issues arise from the fact that it can be said that the overlapping of the orbitals may not be able to be seen fully and the fact that the sizes of the AOs, which represents contribution isn’t consistent. Hydrogen is more electronegative then boron and is therefore lower in energy. Hydrogen should be contributing more to the bonding orbitals and born should be contributing more to the anti-bonding orbitals but for some of them this might not be able to be seen accurately. This shows that the LCAO is a useful tool for finding what a real MO would look like.

=== NH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:NH3_point_group_summary.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES

Link to frequency file: [[File:NH3_OP_JH.LOG]]

Low frequencies --- -8.5628 -8.5571 -0.0047 0.0454 0.1785 26.4189

Low frequencies --- 1089.7603 1694.1865 1694.1865

<jmol><jmolApplet>
<title>Optimised NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3_OP_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:BH3NH3_point_group_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000514 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

Link to frequency file: [[File:NH3BH3_FREQ_NEW.LOG]]

Low frequencies --- -0.0005 0.0003 0.0014 16.7270 18.7414 42.2600

Low frequencies --- 266.2799 632.3010 639.2486

<jmol><jmolApplet>
<title>Optimised NH3BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3BH3_FREQ_NEW.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Association energies ====
E(NH3)= -56.55776863 a.u.

E(BH3)= -26.61532362 a.u.

E(NH3BH3)= -83.22469031 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)], Therefore ΔE= (-83.22468960) - [(-56.55776863)+(-26.61532362)]= -0.05159806 a.u. (-134 KJ/Mol)

The B-N dative bond is weak and this shown when compared to the Al-N bond which has an energy of 297KJ/Mol (https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf)(22222222222)

=== NI3 ===
Method= RB3LYP,
Basis set= Gen

[[File:New_NI3_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000102 0.000450 YES
RMS Force 0.000075 0.000300 YES
Maximum Displacement 0.000858 0.001800 YES
RMS Displacement 0.000629 0.001200 YES

Link to frequency file: [[File:NEW_NI3_JH.LOG]]

Low frequencies --- -12.3845 -12.3781 -5.6129 -0.0040 0.0194 0.0711

Low frequencies --- 100.9307 100.9314 147.2333

<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NEW_NI3_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised B-I bond distance is 2.18 angstrom

===Days 2 and 3 Project: Metal carbonyls===
This sections of the wiki page focuses on metal carbonyls, more specifically their bond-lengths and MO energies. The metal-complexes which will be focused on are [Cr(CO)6], [Mn(CO)6]+ and [Fe(CO)6]2+. These were chosen as they come one after another in the d-block so it would be interesting to see how bond-lengths and MO energies vary across the period. 2 of the complexes are charged (positively) while one is neutral and this is something which must be taken into account when analysing bond-lengths and MO energies. An initial prediction would be that bond length decreases across a period as the oxidation state increases and that MO energies decreases.

==== [Cr(CO)6] ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Cr

[[File:Cr(CO)6_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000110 0.000450 YES
RMS Force 0.000041 0.000300 YES
Maximum Displacement 0.000705 0.001800 YES
RMS Displacement 0.000334 0.001200 YES

Link to frequency file: [[File:CR(CO)6_JH_2.LOG]]

Low frequencies --- -0.0014 -0.0013 -0.0010 11.7482 11.7482 11.7482

Low frequencies --- 66.6574 66.6574 66.6574

<jmol><jmolApplet>
<title>Optimised Cr(CO)6 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>CR(CO)6_JH_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Mn(CO)6]+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Mn

[[File:-Mn(CO)62+_summary_JH3817.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000430 0.001800 YES
RMS Displacement 0.000204 0.001200 YES

Link to frequency file: [[File:-MN(CO)6-+_OP_FREQ_JH.LOG]]

Low frequencies --- -0.0007 0.0006 0.0009 4.7607 4.7607 4.7607

Low frequencies --- 76.3202 76.3202 76.3202

<jmol><jmolApplet>
<title>Optimised Mn(CO)6+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-MN(CO)6-+_OP_FREQ_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Fe(CO)6]2+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Fe

[[File:-Fe(CO)6-2+_freq_op_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000429 0.001800 YES
RMS Displacement 0.000200 0.001200 YES

Link to frequency file: [[File:-FE(CO)6-2+_OP_FREQ.LOG]]

Low frequencies --- -10.5293 -10.5293 -10.5292 -0.0014 -0.0011 -0.0009

Low frequencies --- 82.1285 82.1285 82.1285

<jmol><jmolApplet>
<title>Optimised [FE(CO)6]2+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-FE(CO)6-2+_OP_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Analysing properties ====

{| class="wikitable" border="1"
|+ Bond Length
! Metal complex !! Bond Length(Å)
|-
| [Cr(CO)6] || 1.915
|-
| [Mn(CO)6]+ || 1.908
|-
| [Fe(CO)6]2+ || 1.940
|}

The table above shows the bond metal centre-carbon bond lengths. Electrons from a d-orbital on the metal centres is partially donated into the pi* orbital of the CO ligand. This strengthens the M-C bond. As predicted moving across a period causes the bond length to decrease for the first two but when looking at iron there is an unexpected increase. The decrease between the first two likely due to back bonding and increase in oxidation state as increasing oxidation state leads to an increase in bond strength and the sudden increase in the bond length for the iron complex is due to the contraction of the d-orbitals leading to poorer overlap with the CO orbitals but after speaking to professor Hunt it turns out a full explanation of this increase in bond length is to complex for the course. Whilst back bonding causes an increase in the M-C bond there is also a increase in the CO bond length. The more positive the metal centre means contraction of the d-orbitals and this means that their is a less overlap between the d-orbital and CO pi* orbital and the less overlap with this orbital the stronger the CO bond. The process of back bonding strengths the M-C bond but can cause the CO bond to decrease.

{| class="wikitable" border="1"
|+ Vibrations table 2
! Metal complex !! Intensity !! Vibration type !! Wavenumber(cm)
|-
| Cr(CO)6 || 1637 || symmetric stretch || 2086
|-
| [Mn(CO)6]+ || 879 || symmetric stretch || 2199
|-
| [Fe(CO)6]2+ || 272 || symmetric stretch || 2297
|}

JoeWiki1

2019-05-23T14:49:59Z

Jh3817: /* Analysing properties */

== Year 2 Inorganic comp labs ==

=== BH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p),
Symmetry= D3h

[[File:BH3_info.PNG]]

Item Value Threshold Converged?

Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

Link to frequency file: [[File:JH_BH3_FREQ.LOG]]

Low frequencies --- -0.4072 -0.1962 -0.0055 25.2514 27.2430 27.2460

Low frequencies --- 1163.1897 1213.3128 1213.3155

<jmol><jmolApplet>
<title>Optimised BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JH_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Vibration Data ====

{| class="wikitable" border="1"
|+ Vibrations table
! Stretch or Bend? !! Intensity !! Symmetry !! IR active? !! Wavenumber(cm)
|-
| Bend || 92 || A2" || Yes || 1163
|-
| Bend || 14 || E' || Yes || 1213
|-
| Bend || 14 || E' || Yes || 1213
|-
| Symmetric Stretch || 0 || A1' || No || 2581
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|-
| Asymmetric Stretch || 126 || E' || Yes || 2714
|}

[[File:BH3_vibrations_spectrum_JH.PNG]]

Spectrum shows 3 peaks out of 6 shown in table. 1 is IR in active leaving 5. Two pairs in the 5 are degenerate meaning they have the same energy meaning only 3 peaks show.

[[File:MO_diagram_JH.PNG]] [1111111111111111111111111111111111111111]

The LCAOs seem very accurate as they depict AOs which combine to form the real MOs very well. Minor issues arise from the fact that it can be said that the overlapping of the orbitals may not be able to be seen fully and the fact that the sizes of the AOs, which represents contribution isn’t consistent. Hydrogen is more electronegative then boron and is therefore lower in energy. Hydrogen should be contributing more to the bonding orbitals and born should be contributing more to the anti-bonding orbitals but for some of them this might not be able to be seen accurately. This shows that the LCAO is a useful tool for finding what a real MO would look like.

=== NH3 ===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:NH3_point_group_summary.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES

Link to frequency file: [[File:NH3_OP_JH.LOG]]

Low frequencies --- -8.5628 -8.5571 -0.0047 0.0454 0.1785 26.4189

Low frequencies --- 1089.7603 1694.1865 1694.1865

<jmol><jmolApplet>
<title>Optimised NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3_OP_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3===

Method= RB3LYP,
Basis set= 6-31G(d,p)

[[File:BH3NH3_point_group_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000514 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

Link to frequency file: [[File:NH3BH3_FREQ_NEW.LOG]]

Low frequencies --- -0.0005 0.0003 0.0014 16.7270 18.7414 42.2600

Low frequencies --- 266.2799 632.3010 639.2486

<jmol><jmolApplet>
<title>Optimised NH3BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NH3BH3_FREQ_NEW.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Association energies ====
E(NH3)= -56.55776863 a.u.

E(BH3)= -26.61532362 a.u.

E(NH3BH3)= -83.22469031 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)], Therefore ΔE= (-83.22468960) - [(-56.55776863)+(-26.61532362)]= -0.05159806 a.u. (-134 KJ/Mol)

The B-N dative bond is weak and this shown when compared to the Al-N bond which has an energy of 297KJ/Mol (https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf)(22222222222)

=== NI3 ===
Method= RB3LYP,
Basis set= Gen

[[File:New_NI3_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000102 0.000450 YES
RMS Force 0.000075 0.000300 YES
Maximum Displacement 0.000858 0.001800 YES
RMS Displacement 0.000629 0.001200 YES

Link to frequency file: [[File:NEW_NI3_JH.LOG]]

Low frequencies --- -12.3845 -12.3781 -5.6129 -0.0040 0.0194 0.0711

Low frequencies --- 100.9307 100.9314 147.2333

<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NEW_NI3_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised B-I bond distance is 2.18 angstrom

===Days 2 and 3 Project: Metal carbonyls===
This sections of the wiki page focuses on metal carbonyls, more specifically their bond-lengths and MO energies. The metal-complexes which will be focused on are [Cr(CO)6], [Mn(CO)6]+ and [Fe(CO)6]2+. These were chosen as they come one after another in the d-block so it would be interesting to see how bond-lengths and MO energies vary across the period. 2 of the complexes are charged (positively) while one is neutral and this is something which must be taken into account when analysing bond-lengths and MO energies. An initial prediction would be that bond length decreases across a period as the oxidation state increases and that MO energies decreases.

==== [Cr(CO)6] ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Cr

[[File:Cr(CO)6_summary_JH.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000110 0.000450 YES
RMS Force 0.000041 0.000300 YES
Maximum Displacement 0.000705 0.001800 YES
RMS Displacement 0.000334 0.001200 YES

Link to frequency file: [[File:CR(CO)6_JH_2.LOG]]

Low frequencies --- -0.0014 -0.0013 -0.0010 11.7482 11.7482 11.7482

Low frequencies --- 66.6574 66.6574 66.6574

<jmol><jmolApplet>
<title>Optimised Cr(CO)6 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>CR(CO)6_JH_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Mn(CO)6]+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Mn

[[File:-Mn(CO)62+_summary_JH3817.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000430 0.001800 YES
RMS Displacement 0.000204 0.001200 YES

Link to frequency file: [[File:-MN(CO)6-+_OP_FREQ_JH.LOG]]

Low frequencies --- -0.0007 0.0006 0.0009 4.7607 4.7607 4.7607

Low frequencies --- 76.3202 76.3202 76.3202

<jmol><jmolApplet>
<title>Optimised Mn(CO)6+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-MN(CO)6-+_OP_FREQ_JH.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== [Fe(CO)6]2+ ====

Method= RB3LYP, Basis set= 6-31G(d,p) CO and LanL2DZ for Fe

[[File:-Fe(CO)6-2+_freq_op_summary_table.PNG]]

Item Value Threshold Converged?
Maximum Force 0.000054 0.000450 YES
RMS Force 0.000024 0.000300 YES
Maximum Displacement 0.000429 0.001800 YES
RMS Displacement 0.000200 0.001200 YES

Link to frequency file: [[File:-FE(CO)6-2+_OP_FREQ.LOG]]

Low frequencies --- -10.5293 -10.5293 -10.5292 -0.0014 -0.0011 -0.0009

Low frequencies --- 82.1285 82.1285 82.1285

<jmol><jmolApplet>
<title>Optimised [FE(CO)6]2+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-FE(CO)6-2+_OP_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Analysing properties ====

{| class="wikitable" border="1"
|+ Bond Length
! Metal complex !! Bond Length(Å)
|-
| [Cr(CO)6] || 1.915
|-
| [Mn(CO)6]+ || 1.908
|-
| [Fe(CO)6]2+ || 1.940
|}

The table above shows the bond metal centre-carbon bond lengths. Electrons from a d-orbital on the metal centres is partially donated into the pi* orbital of the CO ligand. This strengthens the M-C bond. As predicted moving across a period causes the bond length to decrease for the first two but when looking at iron there is an unexpected increase. The decrease between the first two likely due to back bonding and increase in oxidation state as increasing oxidation state leads to an increase in bond strength and the sudden increase in the bond length for the iron complex is due to the contraction of the d-orbitals leading to poorer overlap with the CO orbitals but after speaking to professor Hunt it turns out a full explanation of this increase in bond length is to complex for the course. Whilst back bonding causes an increase in the M-C bond there is also a increase in the CO bond length. The more positive the metal centre means contraction of the d-orbitals and this means that their is a less overlap between the d-orbital and CO pi* orbital and the less overlap with this orbital the stronger the CO bond. The process of back bonding strengths the M-C bond but can cause the CO bond to decrease.

{| class="wikitable" border="1"
|+ Vibrations table 2
! Metal complex !! Intensity !! Vibration type !! Wavenumber(cm)
|-
| Cr(CO)6 || 1637 || symmetric stretch || 2086
|-
| [Mn(CO)6]+ || 879 || symmetric stretch || 2199
|-
| [Fe(CO)6]2+ || || symmetric stretch ||
|}