ChemWiki - User contributions [en]

01198491Year2CompChemLab

2019-05-10T16:56:28Z

Bbl17:

= Optimisations =

== BH3 Optimisation ==

'''Method and basis set:''' B3LYP/6-31G(d,p)

'''Summary Table: '''[[File:01198491bh3optimisationd3h.PNG|none|thumb]]

'''Item Table:'''
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000023 0.001800 YES
RMS Displacement 0.000015 0.001200 YES
'''Frequency Analysis Log File: '''https://wiki.ch.ic.ac.uk/wiki/images/5/57/01198491BH3FREQUENCY.LOG

'''Low Frequencies:'''

Low frequencies --- -0.9432 -0.8611 -0.0055 5.7455 11.7246 11.7625
Low frequencies --- 1162.9963 1213.1826 1213.1853

'''Jmol Image:'''
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>01198491BH3FREQUENCY.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''Table of Vibrations:'''
{| class="wikitable"
!Frequency (cm-1)
(given to 3sf as error is ± 10 cm-1)
!Intensity (arbitrary units)
(given to nearest integer)
!Symmetry
!IR active?
!Type
|-
|1160
|93
|A2"
|Yes
|Out-of-plane bend
|-
|1210
|14
|E'
|Slightly
|In-plane bend
|-
|1210
|14
|E'
|Slightly
|In-plane bend
|-
|2580
|0
|A1'
|No
|Symmetric stretch
|-
|2720
|126
|E'
|Yes
|Asymmetric stretch
|-
|2720
|126
|E'
|Yes
|Asymmetric stretch
|}

'''IR Spectrum:'''

[[File:01198491bh3frequency.PNG|frameless|675x675px]]

There are only three peaks in the IR spectrum despite there being 6 possible vibrations (from 3N-6). This is because the vibration of frequency 2580 cm-1 is IR inactive (as it is a symmetric stretch which does not result in an overall dipole moment) so does not appear in the spectrum. Meanwhile there are also two sets of degenerate pairs, ie. the in-plane bends and asymmetric stretches with frequencies 1210 cm-1 and 2720 cm-1 respectively, which result in overlapping and therefore indistinguishable peaks in the IR spectrum. Therefore only three distinct peaks can be seen in the IR spectrum.

'''MO Diagram:'''

[[File:01198491bh3finalmo.png|frameless|788x788px]]

LCAO diagram provided by: P. Hunt, ''Lecture 4 Tutorial Notes'', Figure.

The MO diagram above shows the MOs constructed from LCAO qualitative analysis on the left, with the MOs calculated using Gaussian on the right. The 1s AO on B is shown at the bottom, and does not interact with any orbitals on H due to being too low in energy, so is not shown in the LCAO diagram on the right. The real and LCAO MOs appear to be fairly similar for all of the bonding MOs (ie. 2a1' and the doubly degenerate 1e'), the non-bonding MO (a2"), and all the antibonding MOs (3a1' and the doubly degenerate 2e'), although the calculated MOs are more diffuse than those predicted from LCAO . The most significant difference between the real and LCAO MOs seems to be the size of the orbitals of the 3a1' MO, with LCAO predicting more electron density around the B atom, while the real MOs show that the electron density is actually greatest around the H atoms. It's difficult to tell if this discrepancy is also true for 2a1' even when viewing the MO using the mesh setting, because the constructive interference prevents the weighting of the H/B orbitals from being seen without re-running the calculations under different NBO settings. This indicates that qualitative MO theory is both accurate and useful in imaging MOs and arranging them in order of energy, although of course the actual MO energies cannot be found from this technique, and furthermore the size of the AO contributions to the final MO may not be as predicted from their relative energies.

== NH3 Optimisation ==
'''Method and basis set:''' B3LYP/6-31G(d,p)

'''Summary Table: '''
[[File:01198491nh3optimisation.PNG|none|thumb]]
'''Item Table:'''
Item Value Threshold Converged?
Maximum Force 0.000084 0.000450 YES
RMS Force 0.000054 0.000300 YES
Maximum Displacement 0.000771 0.001800 YES
RMS Displacement 0.000454 0.001200 YES
'''Frequency Analysis Log File: '''https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:01198491NH3OPTIMISATION3.LOG

'''Low Frequencies:'''
Low frequencies --- -12.3035 -12.3002 -2.9634 -0.0046 0.0318 0.1242
Low frequencies --- 1092.1833 1694.3583 1694.3584
'''Jmol Image:'''
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>01198491NH3OPTIMISATION3.LOG</uploadedFileContents>
</jmolApplet></jmol>

== NH3BH3 Optimisation ==
'''Summary Table:'''
[[File:01198491nh3bh3optimisation.PNG|none|thumb]]
'''Item Table:'''
Item Value Threshold Converged?
Maximum Force 0.000191 0.000450 YES
RMS Force 0.000053 0.000300 YES
Maximum Displacement 0.001016 0.001800 YES
RMS Displacement 0.000409 0.001200 YES
'''Frequency Analysis Log File: '''https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:01198491NH3BH3OPTIMISATION2.LOG

'''Low Frequencies:'''
Low frequencies --- -0.0010 -0.0008 -0.0004 4.9684 15.7491 30.4833
Low frequencies --- 264.7685 632.4434 637.6342
'''Jmol Image:'''
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>01198491NH3BH3OPTIMISATION2.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''NH3BH3 N-B Bond Dissociation Energy:'''
* E(BH3)= -26.615 AU (3dp as ±0.002)
* E(NH3)= -56.558 AU
* E(NH3BH3)= -83.225 AU

* ΔE = E(NH3BH3)-[E(NH3)+E(BH3)] = -83.225 - (-56.558 - 26.615) AU = -0.052 AU

(= -0.051598/3.8088x10-4 kJ/mol) = -135 kJ/mol (0dp as ± 5 kJ/mol)

Based on my energy calculations, the B-N dative bond is weak, because it has a bond dissociation energy which is much lower than the N-N covalent bond (BDE = 945 kJ/mol), B-B covalent bond (BDE = 297 kJ/mol), N-C covalent bond (BDE = 770 kJ/mol), or the B-C covalent bond (BDE = 448 kJ/mol). Bond dissociation values are from https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf. This means that little energy is required to break the B-N bond, so it is weak.

== NI3 Optimisation ==
'''Method and basis set: '''B3LYP/6-31G(d,p)LANL2DZ

'''Summary Table:'''
[[File:01198491ni3optimisation.PNG|none|thumb]]
'''Item Table:'''
Item Value Threshold Converged?
Maximum Force 0.000071 0.000450 YES
RMS Force 0.000047 0.000300 YES
Maximum Displacement 0.000534 0.001800 YES
RMS Displacement 0.000354 0.001200 YES
'''Frequency Analysis Log File: '''https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:01198491NH1OPTIMISATION.LOG

'''Low Frequencies:'''
Low frequencies --- -62.3258 -62.3226 -62.0183 -0.0147 -0.0079 -0.0074
Low frequencies --- 134.1619 134.1653 196.3662
'''Jmol Image:'''
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>01198491NH1OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

The N-I bond length is 2.184 Å (3dp as ± 0.001 Å).

= Mini-Project: Ionic Liquids =

== N(CH3)4+ Optimisation ==
With Td symmetry imposed

'''Method and Basis Set:''' B3LYP/6-31G(d,p)

'''Summary Table:'''
[[File:01198491n(ch3)4+optimisation1.PNG|none|thumb]]
'''Item Table:'''
Item Value Threshold Converged?
Maximum Force 0.000147 0.000450 YES
RMS Force 0.000060 0.000300 YES
Maximum Displacement 0.001642 0.001800 YES
RMS Displacement 0.000639 0.001200 YES
'''Low Frequencies:'''
Low frequencies --- -0.0008 -0.0007 -0.0004 33.5608 33.5608 33.5608
Low frequencies --- 215.9246 315.5855 315.5855
'''Frequency Analysis Log File: '''https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:01198491NCH34OPTIMISATION2.LOG

'''Jmol Image:'''
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>01198491NCH34OPTIMISATION2.LOG</uploadedFileContents>
</jmolApplet></jmol>

== P(CH3)4+ Optimisation ==
With Td symmetry imposed

'''Method and Basis Set:''' B3LYP/6-31G(d,p)

'''Summary Table:'''
[[File:01198491pch34optimisation.PNG|none|thumb]]

'''Item Table:'''
Item Value Threshold Converged?
Maximum Force 0.000052 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000121 0.001800 YES
RMS Displacement 0.000089 0.001200 YES
'''Low Frequencies:'''
Low frequencies --- -0.0022 -0.0021 -0.0019 50.6234 50.6234 50.6234
Low frequencies --- 187.9337 213.0177 213.0177
'''Frequency Analysis Log File:''' https://wiki.ch.ic.ac.uk/wiki/index.php?title=File:01198491PCH34OPTIMISATION1.LOG

'''Jmol Image:'''
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>01198491PCH34OPTIMISATION1.LOG</uploadedFileContents>
</jmolApplet></jmol>

== NBO Charge Analysis ==
[[File:01198491Nch34colour.PNG|none|thumb|N(CH3)4+ NBO Charge Distribution]]
[[File:01198491Pch34colour.PNG|none|thumb|P(CH3)4+ NBO Charge Distribution]]
The NBO Charge Distributions for both N(CH3)4+ and P(CH3)4+ are shown above, with the depth of colour showing the extent of the charge on each atom. Red indicates a negative charge, while green indicates a postive charge.

In N(CH3)4+ the NBO Charges: N=-0.295, C=-0.483, H=0.269.

N (electronegativity of 3.04) is more electronegative than C (electronegativity of 2.55), so has a negative charge in the N(CH3)4+ NBO due to the covalent N-C bonds being polarised so that there is more electron density near the nitrogen nucleus (which has a higher effective nuclear charge, so that this polarisation makes the system lower energy and therefore more stable). This negative charge is not very high as it is offset by its cationic charge. Meanwhile, H (electronegativity of 2.20) is less electronegative than C, so the C-H covalent bonds are polarised towards C, giving H a positive charge in the N(CH3)4+ NBO. The C/H electronegativity difference is smaller than the N/C electronegativity difference, however H still has a significant NBO charge due to having no electron shielding (as all its electrons are in the C-H bond) so it has a very high effective nuclear charge.

In P(CH3)4+ the NBO Charges: P=1.667, C=-1.060, H=0.298

P (electronegativity of 2.19) has a lower electronegativity than N due to its extra shell of screening electrons, and is also less electronegative than C. This gives it a positive charge in the P(CH3)4+ NBO due to the covalent N-C bonds being polarised so that there is more electron density near the carbon nuclei (which have a higher effective nuclear charge, so that this polarisation makes the system lower energy and therefore more stable). Unlike in N(CH3)4+, this polarisation is enforced by the cationic charge, so the positive charge is to a great extent. The same electronegativity difference exists between C and H, so that the C-H covalent bonds are polarised towards the more electronegative C, giving H a positive charge in the P(CH3)4+ NBO, and C a negative charge, as in the N(CH3)4+ NBO. However, in the P(CH3)4+ NBO the C-H and P-C polarisations reinforce each other so result in C having a very negative charge, while in the N(CH3)4+ NBO the C-H and N-C polarisations oppose each other, so lead to charges being 'cancelled out' so that the atom charges are less extreme - the exception of course being the H atoms, which have largely the same charges in both structures due to having identical bonding.

== [NR4]+ ==
[NR4]+ (R=alkyl) is often drawn as a tetrahedral structure, with the positive cationic charge localised on the nitrogen centre. This successfully represents one of N's 5 valence electrons having to be removed in order for it to form four bonds to carbon atoms and achieve a full (but not expanded) octet, ie. N is oxidised in the formation of this structure from N in an atomic state. Furthermore, the representation of [NR4]+ with a tetrahedral structure is shown to be accurate by the N(CH3)4+ Td symmetry.

However, the placing of the positive charge in the traditional interpretation of [NR4]+ is disputed by the NBO charge distribution (whose results are shown above). This is because the traditional structure with a formal positive charge on the N suggests that N had a charge of +1.000 - while the NBO charge distribution assigns the N atom a charge of -0.295 due to the N-C bond polarisation, giving C a more positive charge (although it is still negative it is less negative!), and making the H atoms the only positively charged atoms in the structure.

== N(CH3)4+ Valence MOs ==

[[File:01198491mo10.PNG|none|thumb|MO 10]]MO 10 occurs at -0.80746, and has both antibonding character between the N and C atoms, and bonding character between the C and H atoms. It is made from the out of phase overlap of the N s-orbital with four s-type fragment orbitals. [[File:01198491mo15.PNG|none|thumb|MO 15]]MO 15 occurs at -0.62251 and is made from the overlap of the fragment p-type orbitals, destructive in the x direction, and constructive in the y direction. [[File:01198491mo18.PNG|none|thumb|MO 18]]MOs 16, 17, 18 are degenerate at -0.58038 and have a large amount of antibonding character. They appear to be made from the destructive interference of the CH3 fragment p-orbitals, all of which are out of phase, and the MOs differ from each other due to using different x/y/z alignments for each specific methyl group.

I'm really sorry, my version of ChemDraw just kept crashing on me, and I've run out of time, so I've draw my LCAO representations by hand and taken a photo (below) - I'm also sorry it's so messy and done in a rush!
[[File:01198491modiag.jpeg]]

File:01198491modiag.jpeg

2019-05-10T16:54:00Z

Bbl17:

2019-05-10T16:09:13Z

Bbl17:

File:01198491mo15.PNG

2019-05-10T16:08:59Z

Bbl17:

2019-05-10T13:49:11Z

Bbl17:

File:01198491Nch34colour.PNG

2019-05-10T13:31:25Z

Bbl17:

File:01198491Pch34colour.PNG

2019-05-10T13:31:08Z

Bbl17:

01198491Year2CompChemLab

2019-05-10T12:34:22Z

Bbl17:

01198491spares

2019-05-10T12:33:14Z

Bbl17:

BH3:
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>01198491BH3FREQUENCY.LOG</uploadedFileContents>
</jmolApplet></jmol>

NH3:
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>01198491NH3OPTIMISATION3.LOG</uploadedFileContents>
</jmolApplet></jmol>

NH3BH3:
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>01198491NH3BH3OPTIMISATION2.LOG</uploadedFileContents>
</jmolApplet></jmol>

NI3:
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>01198491NH1OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

N(CH3)4+:
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>01198491NCH34OPTIMISATION2.LOG</uploadedFileContents>
</jmolApplet></jmol>

P(CH3)4+:
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>01198491PCH34OPTIMISATION1.LOG</uploadedFileContents>
</jmolApplet></jmol>

File:01198491NCH34OPTIMISATION2.LOG

2019-05-10T12:32:39Z

Bbl17: for jmol

for jmol

01198491spares

2019-05-10T12:31:22Z

Bbl17:

BH3:
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>01198491BH3FREQUENCY.LOG</uploadedFileContents>
</jmolApplet></jmol>

NH3:
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>01198491NH3OPTIMISATION3.LOG</uploadedFileContents>
</jmolApplet></jmol>

NH3BH3:
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>01198491NH3BH3OPTIMISATION2.LOG</uploadedFileContents>
</jmolApplet></jmol>

NI3:
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>01198491NH1OPTIMISATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

N(CH3)4+:
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>01198491N%28CH3%294%2BOPTIMISATION2.LOG</uploadedFileContents>
</jmolApplet></jmol>

P(CH3)4+:
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>01198491PCH34OPTIMISATION1.LOG</uploadedFileContents>
</jmolApplet></jmol>

01198491Year2CompChemLab

2019-05-10T12:28:35Z

Bbl17:

01198491spares

2019-05-10T12:19:35Z

2019-05-10T11:58:45Z