Hayalex1

lab 2 marking

You did a great job especially with the formatting. It would be good if you gave a chart title in you report quality PES graph. It would be good if you explained the answer more precisely for project molecule. If you have any queries, please contact Prof. Hunt.

BH₃

Calculation Data

Optimisation of BH₃ was performed using the following parameters:

Log file	AH_bh3_opt.log
Molecule	BH3
Method	RB3LYP
Basis set	6-31G(d,p)
Final energy	-26.61532 au
RMS gradient	0.000002
Point group	D3h

Log File

Media:AH_BH3_OPT.LOG

Convergence data

The following data was collected from the log file, confirming convergence.

Item table

         Item               Value     Threshold  Converged?
 Maximum Force            0.000004     0.000015     YES
 RMS     Force            0.000003     0.000010     YES
 Maximum Displacement     0.000017     0.000060     YES
 RMS     Displacement     0.000011     0.000040     YES

Low frequencies

 Low frequencies ---  -11.6940  -11.6861   -6.5543    0.0007    0.0280    0.4289
 Low frequencies --- 1162.9745 1213.1390 1213.1392

Rounded to accurate significant figures:

 Low frequencies ---  -12  -12   -7    0    0    0
 Low frequencies --- 1163 1213 1213

Optimised molecule

Molecule parameters

• r(B-H): 1.192Â
• θ(H-B-H): 120.0°

Molecular structure

BH₃ 2D view

BH₃ 3D view

NH₃BH₃

Calculation Data

Optimisation of NH₃BH₃ was performed using the following parameters:

Log file	AH_bh3_opt.log
Molecule	BH3
Method	RB3LYP
Basis set	6-31G(d,p)
Final energy	-83.22469 au
RMS gradient	0.000001
Point group	C3v

Log File

Media:AH_NH3BH3_OPTF.LOG

Convergence data

The following data was collected from the log file, confirming convergence.

Item table

         Item               Value     Threshold  Converged?
 Maximum Force            0.000002     0.000015     YES
 RMS     Force            0.000001     0.000010     YES
 Maximum Displacement     0.000017     0.000060     YES
 RMS     Displacement     0.000008     0.000040     YES

Low frequencies

 Low frequencies ---   -5.4185   -0.3223   -0.0476   -0.0003    1.1368    1.2200
 Low frequencies ---  263.2927  632.9711  638.4651

Rounded to accurate significant figures:

 Low frequencies ---   -5    0    0    0    1    1
 Low frequencies ---  263  633  638

Optimised molecule

Molecule parameters

• r(B-H): 1.210Â
• r(N-H): 1.018Â
• r(B-N): 1.668Â
• θ(H-B-H): 113.9°
• θ(H-N-H): 107.9°
• θ(N-B-H): 104.6°
• θ(B-N-H): 111.0°
• θ(H-B-N-H): 60.0°

Molecular structure

BH₃ 2D view

BH₃ 3D view

NH₃-BH₃ association energy

The energies of NH₃BH₃ and its substituent fragments are as follows:

Molecule	E (AU)
NH3	-56.55777
BH3	-26.61532
NH3BH3	-83.22469

From this, we find the association energy: ΔE = E(NH₃BH₃) - E(NH₃) - E(BH₃) = -0.05160 AU = -135kJ/mol

Me₃NHCl

Calculation Data

Optimisation of Me₃NHCl was performed using the following parameters:

Log file	AH_Me3NHCl_optf.log
Molecule	Me3NHCl
Method	RB3LYP
Basis set	3-21G
Final energy	-632.16208
RMS gradient	0.000007
Point group	C1

Log File

Media:AH_ME3NHCL_OPTF.LOG

Convergence data

The following data was collected from the log file, confirming convergence.

Item table

         Item               Value     Threshold  Converged?
 Maximum Force            0.000020     0.000450     YES
 RMS     Force            0.000004     0.000300     YES
 Maximum Displacement     0.001396     0.001800     YES
 RMS     Displacement     0.000356     0.001200     YES

Low frequencies

 Low frequencies ---   -3.8137   -1.4370   -0.0040   -0.0040   -0.0031    6.6293
 Low frequencies ---   55.9908   57.0177  190.1670

Rounded to accurate significant figures:

 Low frequencies ---   -4   -1    0    0    0    7
 Low frequencies ---   56   57  190

Optimised molecule

Molecule parameters

• r(N-H): 1.164Â
• r(N-C): 1.504Â
• r(C-H): 1.091Â
• r(N-Cl): 2.902Â
• θ(H-N-C): 106.3°
• θ(N-C-H): 108.1°
• θ(H-C-H): 109.1°

Molecular structure

Me₃NHCl view

Me₃NHCl 3D view

Rigid scan

A rigid scan was performed, measuring the potential energy curve produced by increasing the N-H bond length from 0.8Â to 2.1Â in 0.1Â steps.

The following potential energy surface was generated:

Ionic liquids: HMim-Cl

Method data

Molecule/ion	HMim-Cl (a)	HMim-Cl (b)	HMim-Cl (c)	HMim+ (a/b)	HMim+ (c)	Cl-
Log file	Log	Log	Log	Log	Log	Log
Method	RB3LYP
Basis set	3-21G
Final energy (au)	-722.687898	-722.666201	-761.779525	-264.455119	-303.559223	-458.057087
RMS gradient	0.000015	0.000012	0.000006	0.000011	0.000002	0.000000
Point group	C1					Oh

Convergence data

HMim-Cl (a)

Item Table

         Item               Value     Threshold  Converged?
 Maximum Force            0.000050     0.000450     YES
 RMS     Force            0.000009     0.000300     YES
 Maximum Displacement     0.006960     0.001800     NO 
 RMS     Displacement     0.001143     0.001200     YES

Low frequencies

 Low frequencies ---   -5.1413   -2.9822   -0.0040   -0.0023    0.0006    2.8476
 Low frequencies ---   36.2291   64.4325   80.8238

Rounded to accurate significant figures:

 Low frequencies ---   -5   -3    0   0    0    3
 Low frequencies ---   36   64   81

HMim-Cl (b)

Item Table

         Item               Value     Threshold  Converged?
 Maximum Force            0.000030     0.000450     YES
 RMS     Force            0.000008     0.000300     YES
 Maximum Displacement     0.001181     0.001800     YES
 RMS     Displacement     0.000318     0.001200     YES

Low frequencies

 Low frequencies ---   -4.5351   -2.2938   -0.0010    0.0014    0.0015    1.1916
 Low frequencies ---   45.5744  162.0373  198.8263

Rounded to accurate significant figures:

 Low frequencies ---   -5   -2    0    0    0    1
 Low frequencies ---   46  162  199

HMim-Cl (c)

Item Table

         Item               Value     Threshold  Converged?
 Maximum Force            0.000013     0.000450     YES
 RMS     Force            0.000004     0.000300     YES
 Maximum Displacement     0.000848     0.001800     YES
 RMS     Displacement     0.000168     0.001200     YES

Low frequencies

 Low frequencies ---   -3.9219   -3.0567   -0.0023    0.0025    0.0030    2.3020
 Low frequencies ---   52.1725  102.5709  107.1144

Rounded to accurate significant figures:

 Low frequencies ---   -4   -3    0    0    0    2
 Low frequencies ---   52  103  107

HMim⁺ (a/b)

Item Table

         Item               Value     Threshold  Converged?
 Maximum Force            0.000019     0.000450     YES
 RMS     Force            0.000005     0.000300     YES
 Maximum Displacement     0.000246     0.001800     YES
 RMS     Displacement     0.000068     0.001200     YES

Low frequencies

 Low frequencies ---   -0.0006   -0.0004    0.0004    1.4614    3.5947    4.3281
 Low frequencies ---   80.9935  248.1855  352.9294

Rounded to accurate significant figures:

 Low frequencies ---    0    0    0    1    4    4
 Low frequencies ---   81  248  353

HMim⁺ (c)

Item Table

         Item               Value     Threshold  Converged?
 Maximum Force            0.000003     0.000450     YES
 RMS     Force            0.000001     0.000300     YES
 Maximum Displacement     0.000077     0.001800     YES
 RMS     Displacement     0.000022     0.001200     YES

Low frequencies

 Low frequencies ---   -0.0010   -0.0003    0.0005    1.0236    2.4241    4.0797
 Low frequencies ---   71.8861   73.8214  193.3113

Rounded to accurate significant figures:

 Low frequencies ---    0    0    0    1    2    4
 Low frequencies ---   72   74  193

Cl^-

Item Table

         Item               Value     Threshold  Converged?
 Maximum Force            0.000000     0.000450     YES
 RMS     Force            0.000000     0.000300     YES
 Maximum Displacement     0.000000     0.001800     YES
 RMS     Displacement     0.000000     0.001200     YES

Low frequencies

 Low frequencies ---   -0.0066   -0.0066   -0.0066

Rounded to accurate significant figures:

 Low frequencies ---   0   0   0

H-Cl bond distances

Ion pair	HMim-Cl (a)	HMim-Cl (b)	HMim-Cl (c)
r(H-Cl) (Â)	1.720	2.277 (Methyl C-H-Cl) 2.134 (Alkene C-H-Cl)	2.417 (Methyl C-H-Cl) 2.030 (Alkene C-H-Cl)

• The H-Cl bond of HMim-Cl (a) is a similar length to that of Me₃NH-Cl (1.720Â vs 1.728Â respectively), while the H-Cl bonds in HMim-Cl (b), (c) are significantly longer than the Me₃NH-Cl H-Cl bond (2.0-2.4Â vs 1.728Â). This also concides with the nature of the H involved in the bonding, as HMim-Cl (b), (c) both use a C-H bond while interacting with the Cl, whereas HMim-Cl (a) and Me₃NH-Cl use an N-H bond while interacting with the Cl. This may be due to the difference in electronegativity of N and C (3.04 vs 2.55 on the Pauling scale) compared to Cl (3.16 on the Pauling scale). Since N is more electronegative, it polarises the N-H bond more effectively, causing a stronger H-bond to the Cl which results in a shorter H-Cl bond length compared to C.
• The bonds found in these complexes show lengths somewhat shorter than the combined van de Waals radii of H and Cl (1.10Â + 1.75Â = 2.85Â). This is characteristic of H-bonding. The fact that species (a), (c) have a delocalised positive charge involved in the H-bonding will have some effect on this, however the distance based comparisons still can be applied. It is noticeable that the more ionic N-H-Cl bonding is considerably shorter than the combined van der Waals radii (r(H-Cl) = ~60% of r(H) + r(Cl)), but this still falls in the expected range. Carbon-based H-bonding is normally quite weak, but HMim-Cl (c) is able to form decent H-bonds due to the cationic charge creating better bond polarisation.

Association energies

Molecule/ion	HMim-Cl (a)	HMim-Cl (b)	HMim-Cl (c)	HMim+ (a/b)	HMim+ (c)	Cl-
Energy (au)	-722.687898	-722.666201	-761.779525	-264.455119	-303.559223	-458.057087
Association energy (au)	-0.175692	-0.153995	-0.163215
Association energy (kJ/mol)	-461	-404	-429
Dissociation energy (kJ/mol)	461	404	429

• The relative energy of isomers (a), (b) is 57kJ/mol. This suggests that isomer (a) is the more stable configuration of this ion pair, which can be rationalised by considering the nature of the H-bonding in each structure. (a) features a N-H-Cl hydrogen bonding scheme, with a delocalised positive charge on the nitrogen. (b) interacts with the Cl via two instances of C-H-Cl bonding. While H-bonding through carbon is generally weaker than through nitrogen, especially with cationic character, the difference in association energies suggests that the effect of two H-bonding sites in (b) counteracts this effect to a degree.
• (c) has an intermediate dissociation energy compared to (a) and (b), meaning it bonds to the chloride more stably than (b), but less stably than (a). This suggests that a positive charge on carbon has a stronger effect on the strength of the hydrogen bonding than that of bonding through two sites at once, but not as strong as using an N-H bond.

Rigid scan

A rigid scan of (a) was performed, measuring the energy of the ion pair as the N-H bond distance was varied from 0.8Â to 2.1Â in 0.1Â increments, with the N-Cl distance set at 3.2Â.
Note: the optimised structure for HMim-Cl (a) had a bond angle θ(N-H-Cl) of 172.88°, this was manually adjusted to 180° via translation of the Cl atom for the scan. (checked with Prof. Hunt)

The following potential energy surface was generated:

This surface can then be plotted alongside the analogous scan for Me₃NH-Cl:

• The scans show some similarities, such as a sharp increase in energy at both extremes of the scan due to electrostatic repulsion between the H and the N/Cl at each extreme. Additionally, both show a minimum energy at r(N-H) = 1.1-1.2Â, representing the ideal H-bonding distances for each compound.
• Differences are primarily found as the hydrogen approaches the Cl. In Me₃NH-Cl the energy reaches a "plateau", but continues to increase until it reaches the electrostatic repulsion distance. In HMim-Cl, the intermediate distances show a secondary local minimum, showing a local equilibrium bond distance at r(N-H) ≈ 1.7Â. The formation of H-Cl is a source of stability in the scans of both ion pairs, but the local minimum in the HMim-Cl scan suggests that the delocalisation of the lone pair on N in HMim in a Cl-H⋯N bonding scheme is more stable than that in Me₃N. A possible reason for this is that imidazole is aromatic, allowing for many stabilisation effects. Meanwhile, Me₃N can only reconcile this instability via alkyl induction.

lab marking

You have a good working wiki. It would be good if you report values of wavenumber in your answers. Overall a very good attempt. If you have any specific questions, do email Prof. Hunt

NH₃

Calculation Data

Optimisation of NH₃ was performed using the following parameters:

Log file	AH_opf_pop.log
Molecule	NH3
Method	RB3LYP
Basis set	6-31G(d,p)
Final energy	-56.55777 au
RMS gradient	0.000000
Point group	C3V

Log file

Media:AH_NH3_OPF_POP.LOG

Convergence data

The following data was collected from the log file, confirming convergence.

Item table

         Item               Value     Threshold  Converged?
 Maximum Force            0.000000     0.000015     YES
 RMS     Force            0.000000     0.000010     YES
 Maximum Displacement     0.000003     0.000060     YES
 RMS     Displacement     0.000001     0.000040     YES

Low frequencies

 Low frequencies ---   -5.6864   -3.6131   -3.6124    0.0017    0.0048    0.0162
 Low frequencies --- 1089.3674 1693.9284 1693.9284

Optimised molecule

Molecule parameters

• r(N-H): 1.02Â
  
• θ(H-N-H): 106°

Molecular structure

NH₃ top-down view

NH₃ 3D view

Vibrational analysis and IR spectrum

Mode	1	2	3	4	5	6
Wavenumber (cm-1)	1089	1694	1694	3461	3590	3590
Symmetry	A1	E	E	A1	E	E
Intensity	145	14	14	1	0	0

Charge distribution

Atom	N	H
Charge (e)	-1.13	+0.38

cis-N₂F₂ (Project molecule)

Calculation Data

Optimisation of N₂F₂ was performed using the following parameters:

Log file	AH_N2F2_OPTF_POP.LOG
Molecule	N2F2
Method	RB3LYP
Basis set	6-31G(d,p)
Final energy	-309.01241 au
RMS gradient	0.000000
Point group	C2V

Log file

Media:AH_N2F2_OPTF_POP.LOG

Convergence data

The following data was collected from the log file, confirming convergence.

Item table

         Item               Value     Threshold  Converged?
 Maximum Force            0.000001     0.000015     YES
 RMS     Force            0.000000     0.000010     YES
 Maximum Displacement     0.000001     0.000060     YES
 RMS     Displacement     0.000001     0.000040     YES

Low frequencies

 Low frequencies ---    0.0014    0.0022    0.0022    3.2225    4.3532    5.1001
 Low frequencies ---  347.8772  561.2472  771.6105

Optimised molecule

Molecule parameters

• r(N-F): 1.39Â
• r(N=N): 1.22Â
• θ(F-N=N): 114°
• θ(F-N=N-F): 0°

Molecular structure

N₂F₂ 2D view

N₂F₂ 3D view

Vibrational analysis and IR spectrum

Data

Mode	1	2	3	4	5	6
Wavenumber (cm-1)	348	561	772	949	987	1637
Symmetry	A1	A2	B2	A1	B2	A1
Intensity	1	0	75	75	81	21

• The 3N-6 rule gives us an expected 6 vibrations (3 × 4 - 6 = 6).
• There are only 4 peaks on the IR spectrum because two of the vibrational modes have a negligible change in dipole moment, so they are not visible via IR spectroscopy.
• Vibrational mode 3 represents the asymmetric N-F stretching vibration.
• The highest energy mode is the N=N stretching vibration.

Charge distribution

cis-N₂F₂ has a charge separation driven by the high electronegativity of the fluorine atoms.

Atom	N	F
Charge (e)	+0.22	-0.22

Molecular orbital analysis

• MOs 1-4 correspond to the core orbitals of the atoms.

Molecular Orbital 9

The 9th molecular orbital of cis-N₂F₂ can be represented as the in-phase addition of the p_z orbitals on the N and F atoms.