Rep:Mod:isi17

Inorganic Computational Lab - Iman Safia Ilyas

BH₃ Molecule

Basis Set: 6-31G(d,p)

Method: B3LYP

Summary Table for BH₃ Molecule

B-H Bond Length = $1.192\AA$

H-B-H Bond Angle = $120.0$°

        Item               Value     Threshold  Converged?
Maximum Force            0.000009     0.000450     YES
RMS     Force            0.000004     0.000300     YES
Maximum Displacement     0.000034     0.001800     YES
RMS     Displacement     0.000017     0.001200     YES

File:IMAN BH3 FREQ.LOG

Low frequencies ---   -2.2126   -1.0751   -0.0055    2.2359   10.2633   10.3194
Low frequencies ---   1162.9860 1213.1757 1213.1784

BH3 Molecule

IR Analysis of BH₃

Mode	Vibrations (cm-1)	IR Active?	Intensity (Arbitrary Units)	Symmetry	Bend or Stretch
1	1163	Active	93	A2	Out of Plane Bend
2	1213	Active	14	E'	Bend
3	1213	Active	14	E'	Bend
4	2582	Inactive	0	A1'	Symmetric Stretch
5	2715	Active	126	E'	Asymmetric Stretch
6	2715	Active	126	E'	Asymmetric Stretch

There are less than 6 peaks in the spectrum although there are 6 modes of vibration. This is because not all modes are IR active. To be IR active there must be a change in dipole moment. Mode 4 is a symmetric stretch therefore is not IR active and is therefore not visible on the spectrum. The vibrations of modes 2 and 3 have frequencies very close to each other and therefore overlap showing one prominent peak. The same thing occurs for modes 5 and 6. The third peak is for Mode 1.

MO Analysis of BH₃

(MO Diagram for BH₃, Lecture 4 Tutorial Problem Model Answers, P. Hunt, Accessed 08/05/19 [1])

There are differences between the real MOs and the MOs predicted by LCAO, but they are not significant. Both have areas of high electron density and no electron density. Areas with no electron density represent nodes. By seeing the comparison between the real MOs and those predicted by LCAO, it can be said that MO theory is very accurate and useful. the differences are mainly the shape of the orbitals themselves. These are more distorted in the real MOs computed by gaussian.

Ng611 (talk) 20:50, 20 May 2019 (BST) Describe the differences you see!

NH₃ Molecule

Basis Set: 6-31G(d,p)

Method: B3LYP

Summary Table for NH₃

N-H Bond Length = $1.018\AA$

H-N-H Bond Angle = $105.7$°

        Item               Value     Threshold  Converged?
Maximum Force            0.000005     0.000450     YES
RMS     Force            0.000003     0.000300     YES
Maximum Displacement     0.000012     0.001800     YES
RMS     Displacement     0.000006     0.001200     YES

File:ISI17 NH3 FREQ 631G.LOG

Low frequencies ---  -11.6527  -11.6490   -0.0048    0.0332    0.1312   25.5724
Low frequencies --- 1089.6616 1694.1736 1694.1736

NH3 Molecule

NH₃BH₃ Molecule

Basis Set: 6-31G(d,p)

Method: B3LYP

Summary Table for NH₃BH₃

B-H Bond Length = $1.019\AA$

N-H Bond Length = $1.210\AA$

B-N Bond Length = $1.668\AA$

H-B-H Bond Angle = $107.9$°

H-N-H Bond Angle = $113.9$°

H-B-N Bond Angle = $111.0$°

H-N-B Bond Angle = $104.6$°

        Item               Value     Threshold  Converged?
Maximum Force            0.000139     0.000450     YES
RMS     Force            0.000063     0.000300     YES
Maximum Displacement     0.000771     0.001800     YES
RMS     Displacement     0.000338     0.001200     YES

File:ISI17 NH3BH3 FREQ.LOG

Low frequencies ---   -0.0010   -0.0006    0.0005   19.1023   23.7761   42.9934
Low frequencies ---  266.5969  632.3818  639.5198

NH3BH3 Molecule

Energy Calculations

$E(B{H}_3)=-26.61532363au$

$E(N{H}_3)=-56.55776856au$

$E(B{H}_{3}N{H}_3)=-83.22469009au$

Association Energy: $\mathrm{\Delta }E=E(N{H}_{3}B{H}_3)-(E(N{H}_3)+E(B{H}_3))=-0.0515979au$

Converting from au to kJmol^-1 :

$(-0.0515979)(2625.5)=-135.4702865$

$\mathrm{\Delta }E=-135kJmo{l}^{-1}$

We can see that the N-B bond is relatively weak, especially if we compare this to a C-C bond with bond energy of 346 kJmol^-1. The B-N bond has an energy less than half the bond energy of C-C.

Ng611 (talk) 20:51, 20 May 2019 (BST) Provide a reference for your literature bond value.

NI₃ Molecule

Method: B3LYP

Basis Set: 6-31G(d,p) for Nitrogen, LanL2DZ (Pseudo Potential) for Iodine

My calculation took too long to complete on the SCAN server so I have included the Optimised LOG file and Summary Table from this file instead. Sorry for any inconvenience.

Summary Table of NI₃

        Item               Value     Threshold  Converged?
Maximum Force            0.000067     0.000450     YES
RMS     Force            0.000044     0.000300     YES
Maximum Displacement     0.000492     0.001800     YES
RMS     Displacement     0.000333     0.001200     YES

File:Isi17 NI3 OPT SCAN pps.log

Optimised N-I distance: $2.187\AA$

NI3 Molecule

Ng611 (talk) 20:52, 20 May 2019 (BST) Your bond length is out by .004 A. Otherwise, good calculation.

Project: Ionic Liquids

[N(CH₃)₄]⁺ Molecule

Basis Set: 6-31G(d,p)

Method: B3LYP

Summary Table of [N(CH₃)₄]⁺

        Item               Value     Threshold  Converged?
Maximum Force            0.000072     0.000450     YES
RMS     Force            0.000029     0.000300     YES
Maximum Displacement     0.000178     0.001800     YES
RMS     Displacement     0.000079     0.001200     YES

File:ISI17 -N(CH3)4- FREQ 01333599.LOG

Low frequencies ---   -0.0011   -0.0007   -0.0007   35.5217   35.5217   35.5217
Low frequencies ---  217.0556  316.2155  316.2155

[N(CH3)4]+ Molecule

[P(CH₃)₄]⁺ Molecule

Basis Set: 6-31G(d,p)

Method: B3LYP

Summary Table of [P(CH₃)₄]⁺

        Item               Value     Threshold  Converged?
Maximum Force            0.000095     0.000450     YES
RMS     Force            0.000032     0.000300     YES
Maximum Displacement     0.001541     0.001800     YES
RMS     Displacement     0.000494     0.001200     YES

File:ISI17 -P(CH3)4- FREQ 01333599.LOG

Low frequencies ---   -0.0003    0.0018    0.0026   13.7497   22.4514   35.0103
Low frequencies ---  162.9535  193.8816  195.5982

[P(CH3)4]+ Molecule

Comparison of Charge Distributions of [N(CH₃)₄]⁺ and [P(CH₃)₄]⁺

Image 1: Shows Charge Distribution of [N(CH₃)₄]⁺

Image 2: Shows Charge Distribution of [P(CH₃)₄]⁺

The Charges of the Individual Atoms in [N(CH₃)₄]⁺ are:

Charge on the Nitrogen atom = -0.295

Charge on each Carbon atom = -0.484

Charge on each Hydrogen atom = +0.269

The sum of the partial charges is: +0.997

The Charges of the Individual Atoms in [P(CH₃)₄]⁺ are:

Charge on the Phosphorous atom = +1.667

Charge on each Carbon atom = -1.060

Charge on each Hydrogen atom = +0.298

The sum of the partial charges is: + 1.003

The colour range used was from -1.667 to +1.667, where green represents a positive charge and the red represents a negative charge. This was due to the fact that Phosphorous held the highest charge of +1.667 out of any atom in either of the systems. This range was kept constant for both cations, so that direct comparisons of the charges on each atom could be made. It can be seen that the Phosphorous atom holds a much more positive charge than the nitrogen in their respective cations. This can be explained as Nitrogen (3.04) is a much more electronegative element than Phosphorous (2.19) on the Pauling scale. this means that Nitrogen is more likely to pull the electron density towards itself in the N-C bond thus having a more negative charge on the atom. The charge is also more negative on the carbon atoms in [P(CH₃)₄]⁺ than in [N(CH₃)₄]⁺ as the carbons (2.55) in [P(CH₃)₄]⁺ are the most electronegative atoms in the cation therefore hold more of the negative charge, whereas in [N(CH₃)₄]⁺ they are bonded to an even more electronegative atom, nitrogen, which withdraws some electron density. [P(CH₃)₄]⁺ has a higher overall positive charge (+1.003) than [N(CH₃)₄]⁺ (+0.997) but they both round to +1.00 if we take them at 2 decimal places.

Ng611 (talk) 20:55, 20 May 2019 (BST) Good! A discussion about symmetry and perhaps some discussion about the hydrogen partial charge.

Validity of Traditional Description of [N(CH₃)₄]⁺

If we look at the traditional description, the formal charge is said to be localised solely on the nitrogen atom, however, it can be seen that it actually holds part of a negative charge. The positive charge is spread around the outside of the molecule as it is delocalised around the hydrogen atoms. The Hydrogen atoms are where the actual positive charge is located for this molecule.

Ng611 (talk) 20:58, 20 May 2019 (BST) Why is this the case?

Occupied Valence MOs Showing Bonding and Anti-bonding Character

Valence MO 6

This is a bonding MO and has 2 nodes, one between the nitrogen and carbon and one between the carbon above and the hydrogen atoms attached to it. We can see sigma bonding here as 2 lobes are interacting in phase alone the bond.

Valence MO 15

This MO has 1 node which can be seen as the area with no electron density between the large green and red lobes. This MO is an anti bonding orbital.

Valence MO 21

This MO has 1 node, which can be seen as the area with no electron density between the large red and green lobes, which are out of phase with each other. This MO is an anti bonding orbital.

Ng611 (talk) 20:56, 20 May 2019 (BST) You're missing LCAO analyses for MOs 16/21 (which look fairly similar to one and other). A detailed MO analysis for all orbitals (highlighting key interactions) would have improved this answer significantly.