ChemWiki - User contributions [en]

InorganicCompLab yd3717

2019-05-10T16:27:33Z

Yd3717: /* MO analysis of molecule 2 */

== EX3 ==

=== BH3 ===

==== General information ====

B3LYP / 6-31G(d, p) level

[[File:Bh3_summary_yd3717.PNG|center|thumb|Summary table of BH3 molecule.]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000014 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000053 0.001800 YES
RMS Displacement 0.000027 0.001200 YES
</pre>

BH3 frequency file: [[File:YD3717_BH3_FREQ.LOG]]

<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

<jmol><jmolApplet>
<title>Optimized BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>YD3717_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

----

==== Vibrational spectrum ====

{| class="wikitable"
|+
|-
|Wavenumber (cm-1) || Intensity (arbitrary units) || Symmetry || IR active? || Type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|}

[[File:Bh3_ir_yd3717.PNG|center|thumb|800px|Predicted IR spectrum of BH3 molecule.]]

There are clearly 6 vibrations, but only 3 peaks are seen on the IR spectrum. First reason is that there are two sets of degenerate vibrations, at frequency = 1213 cm-1 and 2716 cm-1. Therefore these four vibrations will only show two different peaks on the spectrum. The vibration at frequency = 2582 cm-1 is a symmetric stretch, which has no change in dipole moment. So this vibration is IR inactive and will not show on the spectrum. The other peak shown on the spectrum corresponds to the vibration at 1163 cm-1.

----

==== MO diagram ====

[[File:full_picture3_yd3717.PNG|center|thumb|800px|MO diagram of BH3 molecule.]]

The predicted LCAO MOs look very similar to the real MOs. They have exactly the same distribution of phases and nodes. However there are slight differences in phase orientation. For example, the 7th LCAO MO are predicted to have p orbital horizontal. But the real MO shows the p orbital is push downwards a little bit. Similar for the 8th MO, the vertical p orbital is squeezed in between the other phases.

Therefore MO theory can predict most of the MOs correctly, with slight differences on phase orientations. However it is still very useful in learning orbital bondings as it predicts the MO phases and nodes correctly.

----

=== NH3 ===

==== General information ====

B3LYP / 6-31G(d, p) level

[[File:Nh3_summary3_yd3717.PNG|center|thumb|Summary table of NH3 molecule.]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000040 0.001800 YES
RMS Displacement 0.000013 0.001200 YES
</pre>

NH3 frequency file: [[File:YD3717_NH3_FREQ.LOG]]

<pre>
Low frequencies --- -8.5223 -8.4750 -0.0033 0.0335 0.1919 26.4067
Low frequencies --- 1089.7616 1694.1862 1694.1866
</pre>

<jmol><jmolApplet>
<title>Optimized NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>YD3717_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

----

=== NH3BH3 ===

==== General information ====

B3LYP / 6-31G(d, p) level

[[File:Nh3bh3_summary2_yd3717.PNG|center|thumb|Summary table of NH3BH3 molecule.]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000114 0.000450 YES
RMS Force 0.000063 0.000300 YES
Maximum Displacement 0.000621 0.001800 YES
RMS Displacement 0.000355 0.001200 YES
</pre>

NH3BH3 frequency file: [[File:YD3717_NH3BH3_FREQ.LOG]]

<pre>
Low frequencies --- -0.0614 -0.0457 -0.0065 21.6818 21.6877 40.5522
Low frequencies --- 266.0205 632.3610 640.1375
</pre>

<jmol><jmolApplet>
<title>Optimized NH3BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>YD3717_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

----

=== Energy calculation ===

E(NH3) = -56.55777 a.u.

E(BH3) = -26.61532 a.u.

E(NH3BH3) = -83.22469 a.u.

ΔE = E(NH3BH3)-[E(NH3)+E(BH3)]

= -0.0516 a.u.

= -135 kJ/mol

The normal B-N bond has a strength of 389 kJ/mol [1], while the dative B-N bond strength calculated above is 135 kJ/mol. A very strong bond like N-N triple bond has a energy of 946 kJ/mol [1]. Therefore in comparison, this B-N dative bond is only a weak bond.

----

=== NI3 ===

==== General information ====

B3LYP / 6-31G(d, p) LANL2DZ level

[[File:Ni3_summary_yd3717.PNG|center|thumb|Summary table of NI3 molecule.]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000096 0.000450 YES
RMS Force 0.000050 0.000300 YES
Maximum Displacement 0.001084 0.001800 YES
RMS Displacement 0.000616 0.001200 YES
</pre>

NI3 frequency file: [[File:YD3717_NI3_FREQ.LOG]]

<pre>
Low frequencies --- -12.7232 -12.7172 -6.4215 -0.0039 0.0189 0.0620
Low frequencies --- 101.0767 101.0775 147.4581
</pre>

<jmol><jmolApplet>
<title>Optimized NI3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>YD3717_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

----

==== N-I distance ====

The optimised N-I distance is 2.184 Å.

== Project: Lewis acids and bases ==

=== Five possible structures and symmetry ===

Determine the five possible isomers and identify the symmetry of each isomer of Al2Cl4Br2.

[[File:Structures_yd3717.PNG|center|thumb|600px|Five possible structures and their symmetries of Al2Cl4Br2 molecule.]]

----

=== Two bridging Br ions (Molecule 1) ===

B3LYP / 6-31G(d, p) LANL2DZ level

[[File:molecule1_summary2_yd3717.PNG|center|thumb|Summary table of molecule 1.]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000034 0.000450 YES
RMS Force 0.000016 0.000300 YES
Maximum Displacement 0.000687 0.001800 YES
RMS Displacement 0.000394 0.001200 YES
</pre>

Molecule 1 frequency file: [[File:YD3717_MOLECULE1_FREQ.LOG]]

<pre>
Low frequencies --- -4.9368 -4.7940 -3.2374 0.0019 0.0028 0.0031
Low frequencies --- 14.9456 63.3281 86.1024
</pre>

<jmol><jmolApplet>
<title>Optimized molecule 1</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>YD3717_MOLECULE1_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

----

=== Bridging Cl ions and trans terminal Br ions (Molecule 2) ===

B3LYP / 6-31G(d, p) LANL2DZ level

[[File:molecule2_summary_yd3717.PNG|center|thumb|Summary table of molecule 2.]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000039 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.001287 0.001800 YES
RMS Displacement 0.000438 0.001200 YES
</pre>

Molecule 2 frequency file: [[File:YD3717_MOLECULE2_FREQ.LOG]]

<pre>
Low frequencies --- -4.2020 -2.2652 0.0037 0.0041 0.0042 1.1849
Low frequencies --- 17.7423 48.9741 72.9606
</pre>

<jmol><jmolApplet>
<title>Optimized molecule 2</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>YD3717_MOLECULE2_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

----

=== Energy and stability analysis ===

E (molecule 1) = -2352.40631 a.u. = -6175067 kJ/mol

E (molecule 2) = -2352.41629 a.u. = -6175093 kJ/mol

ΔE = E(molecule 1) - E(molecule 2)

= 0.00998 a.u.

= 26 kJ/mol

Molecule 1 with two Br ions bridging has higher energy than molecule 2 with two Cl ions bridging. The energy difference is about 26 kJ/mol.

This is because both Al and Cl are in row 3, while Br is in row 4. The 3p orbitals are similar in energy and sizes, therefore 3p-3p overlap of Al-Cl is better than the 3p-4p overlap of Al-Br.

Better overlap results in lower energy, which means molecule 2 with Cl bridging is more stable than molecule 1.

----

=== AlCl2Br ===

B3LYP / 6-31G(d, p) LANL2DZ level

[[File:alcl2br_summary_yd3717.PNG|center|thumb|Summary table of AlCl2Br molecule.]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000081 0.000450 YES
RMS Force 0.000042 0.000300 YES
Maximum Displacement 0.001588 0.001800 YES
RMS Displacement 0.000974 0.001200 YES
</pre>

AlCl2Br frequency file: [[File:YD3717_ALCL2BR_FREQ.LOG]]

<pre>
Low frequencies --- 0.0045 0.0048 0.0053 1.3569 3.6367 4.2604
Low frequencies --- 120.5042 133.9178 185.8950
</pre>

<jmol><jmolApplet>
<title>Optimized AlCl2Br</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>YD3717_ALCL2BR_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

----

=== Dissociation energy analysis ===

E (molecule 2) = -2352.41629 a.u. = -6175093 kJ/mol

E (AlCl2Br) = -1176.19014 a.u. = -3087499 kJ/mol

ΔE = 2 * E(AlCl2Br) - E(molecule 2)

= 0.03601 a.u.

= 95 kJ/mol

The reaction of molecule 2 dissociate into 2AlCl2Br takes in energy, which means this is an endothermic reaction. The product, i.e. AlCl2Br, is higher in energy than the reactant molecule 2.

Therefore, AlCl2Br is less stable.

----

=== MO analysis of molecule 2===

==== 40th MO ====

[[File:40MO_full_yd3717.PNG|center|thumb|600px|40th MO of molecule 2.]]

----

==== 41st MO ====

[[File:41MO_full_yd3717.PNG|center|thumb|600px|41st MO of molecule 2.]]

----

==== 43rd MO ====

[[File:43MO_full_yd3717.PNG|center|thumb|600px|43rd MO of molecule 2.]]

== Reference ==

[1] Bond strength https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf

File:43MO full yd3717.PNG

2019-05-10T16:24:48Z

Yd3717:

File:41MO full yd3717.PNG

2019-05-10T16:24:30Z

Yd3717:

2019-05-10T13:35:59Z

Yd3717: /* AlCl2Br */

== EX3 ==

=== BH3 ===

==== General information ====

B3LYP / 6-31G(d, p) level

[[File:Bh3_summary_yd3717.PNG|center|thumb|Summary table of BH3 molecule.]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000014 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000053 0.001800 YES
RMS Displacement 0.000027 0.001200 YES
</pre>

BH3 frequency file: [[File:YD3717_BH3_FREQ.LOG]]

<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

<jmol><jmolApplet>
<title>Optimized BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>YD3717_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

----

==== Vibrational spectrum ====

{| class="wikitable"
|+
|-
|Wavenumber (cm-1) || Intensity (arbitrary units) || Symmetry || IR active? || Type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|}

[[File:Bh3_ir_yd3717.PNG|center|thumb|800px|Predicted IR spectrum of BH3 molecule.]]

There are clearly 6 vibrations, but only 3 peaks are seen on the IR spectrum. First reason is that there are two sets of degenerate vibrations, at frequency = 1213 cm-1 and 2716 cm-1. Therefore these four vibrations will only show two different peaks on the spectrum. The vibration at frequency = 2582 cm-1 is a symmetric stretch, which has no change in dipole moment. So this vibration is IR inactive and will not show on the spectrum. The other peak shown on the spectrum corresponds to the vibration at 1163 cm-1.

----

==== MO diagram ====

[[File:full_picture3_yd3717.PNG|center|thumb|800px|MO diagram of BH3 molecule.]]

The predicted LCAO MOs look very similar to the real MOs. They have exactly the same distribution of phases and nodes. However there are slight differences in phase orientation. For example, the 7th LCAO MO are predicted to have p orbital horizontal. But the real MO shows the p orbital is push downwards a little bit. Similar for the 8th MO, the vertical p orbital is squeezed in between the other phases.

Therefore MO theory can predict most of the MOs correctly, with slight differences on phase orientations. However it is still very useful in learning orbital bondings as it predicts the MO phases and nodes correctly.

----

=== NH3 ===

==== General information ====

B3LYP / 6-31G(d, p) level

[[File:Nh3_summary3_yd3717.PNG|center|thumb|Summary table of NH3 molecule.]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000040 0.001800 YES
RMS Displacement 0.000013 0.001200 YES
</pre>

NH3 frequency file: [[File:YD3717_NH3_FREQ.LOG]]

<pre>
Low frequencies --- -8.5223 -8.4750 -0.0033 0.0335 0.1919 26.4067
Low frequencies --- 1089.7616 1694.1862 1694.1866
</pre>

<jmol><jmolApplet>
<title>Optimized NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>YD3717_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

----

=== NH3BH3 ===

==== General information ====

B3LYP / 6-31G(d, p) level

[[File:Nh3bh3_summary2_yd3717.PNG|center|thumb|Summary table of NH3BH3 molecule.]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000114 0.000450 YES
RMS Force 0.000063 0.000300 YES
Maximum Displacement 0.000621 0.001800 YES
RMS Displacement 0.000355 0.001200 YES
</pre>

NH3BH3 frequency file: [[File:YD3717_NH3BH3_FREQ.LOG]]

<pre>
Low frequencies --- -0.0614 -0.0457 -0.0065 21.6818 21.6877 40.5522
Low frequencies --- 266.0205 632.3610 640.1375
</pre>

<jmol><jmolApplet>
<title>Optimized NH3BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>YD3717_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

----

=== Energy calculation ===

E(NH3) = -56.55777 a.u.

E(BH3) = -26.61532 a.u.

E(NH3BH3) = -83.22469 a.u.

ΔE = E(NH3BH3)-[E(NH3)+E(BH3)]

= -0.0516 a.u.

= -135 kJ/mol

The normal B-N bond has a strength of 389 kJ/mol [1], while the dative B-N bond strength calculated above is 135 kJ/mol. A very strong bond like N-N triple bond has a energy of 946 kJ/mol [1]. Therefore in comparison, this B-N dative bond is only a weak bond.

----

=== NI3 ===

==== General information ====

B3LYP / 6-31G(d, p) LANL2DZ level

[[File:Ni3_summary_yd3717.PNG|center|thumb|Summary table of NI3 molecule.]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000096 0.000450 YES
RMS Force 0.000050 0.000300 YES
Maximum Displacement 0.001084 0.001800 YES
RMS Displacement 0.000616 0.001200 YES
</pre>

NI3 frequency file: [[File:YD3717_NI3_FREQ.LOG]]

<pre>
Low frequencies --- -12.7232 -12.7172 -6.4215 -0.0039 0.0189 0.0620
Low frequencies --- 101.0767 101.0775 147.4581
</pre>

<jmol><jmolApplet>
<title>Optimized NI3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>YD3717_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

----

==== N-I distance ====

The optimised N-I distance is 2.184 Å.

== Project: Lewis acids and bases ==

=== Five possible structures and symmetry ===

Determine the five possible isomers and identify the symmetry of each isomer of Al2Cl4Br2.

[[File:Structures_yd3717.PNG|center|thumb|600px|Five possible structures and their symmetries of Al2Cl4Br2 molecule.]]

----

=== Two bridging Br ions (Molecule 1) ===

B3LYP / 6-31G(d, p) LANL2DZ level

[[File:molecule1_summary2_yd3717.PNG|center|thumb|Summary table of molecule 1.]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000034 0.000450 YES
RMS Force 0.000016 0.000300 YES
Maximum Displacement 0.000687 0.001800 YES
RMS Displacement 0.000394 0.001200 YES
</pre>

Molecule 1 frequency file: [[File:YD3717_MOLECULE1_FREQ.LOG]]

<pre>
Low frequencies --- -4.9368 -4.7940 -3.2374 0.0019 0.0028 0.0031
Low frequencies --- 14.9456 63.3281 86.1024
</pre>

<jmol><jmolApplet>
<title>Optimized molecule 1</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>YD3717_MOLECULE1_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

----

=== Bridging Cl ions and trans terminal Br ions (Molecule 2) ===

B3LYP / 6-31G(d, p) LANL2DZ level

[[File:molecule2_summary_yd3717.PNG|center|thumb|Summary table of molecule 2.]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000039 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.001287 0.001800 YES
RMS Displacement 0.000438 0.001200 YES
</pre>

Molecule 2 frequency file: [[File:YD3717_MOLECULE2_FREQ.LOG]]

<pre>
Low frequencies --- -4.2020 -2.2652 0.0037 0.0041 0.0042 1.1849
Low frequencies --- 17.7423 48.9741 72.9606
</pre>

<jmol><jmolApplet>
<title>Optimized molecule 2</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>YD3717_MOLECULE2_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

----

=== Energy and stability analysis ===

E (molecule 1) = -2352.40631 a.u. = -6175067 kJ/mol

E (molecule 2) = -2352.41629 a.u. = -6175093 kJ/mol

ΔE = E(molecule 1) - E(molecule 2)

= 0.00998 a.u.

= 26 kJ/mol

Molecule 1 with two Br ions bridging has higher energy than molecule 2 with two Cl ions bridging. The energy difference is about 26 kJ/mol.

This is because both Al and Cl are in row 3, while Br is in row 4. The 3p orbitals are similar in energy and sizes, therefore 3p-3p overlap of Al-Cl is better than the 3p-4p overlap of Al-Br.

Better overlap results in lower energy, which means molecule 2 with Cl bridging is more stable than molecule 1.

----

=== AlCl2Br ===

B3LYP / 6-31G(d, p) LANL2DZ level

[[File:alcl2br_summary_yd3717.PNG|center|thumb|Summary table of AlCl2Br molecule.]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000081 0.000450 YES
RMS Force 0.000042 0.000300 YES
Maximum Displacement 0.001588 0.001800 YES
RMS Displacement 0.000974 0.001200 YES
</pre>

AlCl2Br frequency file: [[File:YD3717_ALCL2BR_FREQ.LOG]]

<pre>
Low frequencies --- 0.0045 0.0048 0.0053 1.3569 3.6367 4.2604
Low frequencies --- 120.5042 133.9178 185.8950
</pre>

<jmol><jmolApplet>
<title>Optimized AlCl2Br</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>YD3717_ALCL2BR_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

----

=== Dissociation energy analysis ===

== Reference ==

[1] Bond strength https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf

File:YD3717 ALCL2BR FREQ.LOG

2019-05-10T13:34:51Z

Yd3717:

2019-05-10T12:47:53Z

InorganicCompLab yd3717

2019-05-09T14:26:40Z

Yd3717: /* Reference */

InorganicCompLab yd3717

2019-05-09T14:26:12Z

Yd3717: /* Project */