Leeryan

Lab1 Marking

It's good that you have a working wiki. However, you have reported wrong bond distance and IR intensities, and have missed to include the torsion angle. Don't forget to consider the accuracy to which you report your data the next time. If you have any queries, please contact Prof. Hunt.

BH₃ Molecule

Calculation Data

Name of submitted log file	BH3_OPTIMISATION_RL.LOG
Molecule	BH3
Method	RB3LYP
Basis Set	6-31(d,p)
Final Energy	-26.615324
RMS Gradient	0.000002
Point Group	D3H

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

Optimised Molecule Image

Jmol Rotatable Molecule

logfile: Media:BH3_OPTIMISATION_RL.LOG

Optimised NH Molecule

Important Geometric Parameters

Optimised bond distance and angle for NH₃
r(N-H)= 1.192Â
θ(H-N-H)= 119.9°

Vibrational Modes

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

Mode	1	2	3	4	5	6
Wavenumber (cm-1)	1163	1213	1213	2583	2716	2716
Symmetry	A2"	E'	E'	A1'	E'	E'
Intensity	93	14	14	0	126	126

IR Spectrum

NH₃BH₃ Molecule

Calculation Data

Name of submitted log file	NH3BH3_OPTIMISATION_RL.LOG
Molecule	NH3BH3
Method	RB3LYP
Basis Set	6-31(d,p)
Final Energy	-83.224689
RMS Gradient	0.000001
Point Group	C1

In the literature, the point group for the molecule is C3v, but the output has a C1 point group. This could be because...

Item Table

         Item               Value     Threshold  Converged?
 Maximum Force            0.000001     0.000015     YES
 RMS     Force            0.000001     0.000010     YES
 Maximum Displacement     0.000043     0.000060     YES
 RMS     Displacement     0.000019     0.000040     YES

Optimised Molecule Image

Jmol Rotatable Molecule

logfile: Media:NH3BH3_OPTIMISATION_RL.LOG

Optimised NH Molecule

Important Geometric Parameters

Optimised bond distance and angle for NH₃
r(N-H)= 1.018Â
r(B-H)= 1.210Â
r(N-B)= 1.668Â
θ(H-N-H)= 107.9°
θ(H-B-H)= 113.9°
θ(H-N-B)= 111.0°
θ(H-B-N)= 104.6°

Vibrational Modes

 Low frequencies ---   -5.0462   -2.8839   -0.0009   -0.0008   -0.0006    0.6098
 Low frequencies ---  263.3824  632.9842  638.4292

Mode	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18
Wavenumber (cm-1)	263	633	638	638	1069	1069	1196	1204	1204	1329	1676	1676	2472	2532	2532	3464	3581	3581
Symmetry	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A
Intensity	0	14	4	4	41	41	109	3	3	114	28	28	67	231	231	3	28	28

IR Spectrum

Association Energy

E(NH₃)= -56.557769 a.u.
E(BH₃)= -26.615324 a.u.
E(NH₃BH₃)= -83.224689 a.u.

ΔE= -83.224689 - (-56.557769 - 26.615324) = -0.051595 a.u or -130.33150 kJ/mol

Me₃NH-Cl

Calculation Data

Name of submitted log file	ME3NHCL_OPTIMISATION_RL.LOG
Molecule	Trimethylamine Chloride
Method	RB3LYP
Basis Set	3-21G(d, p)
Final Energy	-632.162083
RMS Gradient	0.000079
Point Group	C1

Item Table and Low Frequencies

         Item               Value     Threshold  Converged?
 Maximum Force            0.000357     0.000450     YES
 RMS     Force            0.000054     0.000300     YES
 Maximum Displacement     0.003416     0.001800     NO 
 RMS     Displacement     0.000902     0.001200     YES

 Low frequencies ---   -3.4097   -0.0033   -0.0024   -0.0014    4.6007    7.7513
 Low frequencies ---   55.8433   56.0482  188.9635

The maximum displacement has not converged to the applied threshold, and its value is approximately twice that of the threshold. However, all the low frequencies reported are between the limits of ±10, so the molecule is very near to fully optimized, and this optimization result is able to be used for a scan.

Structural Information

r(H-Cl)= 1.739Â
r(N-H)= 1.165Â

Optimized structure:

PES Analysis

Log file:File:ME3NHCL OPTIMISATION RL SCAN3A.LOG

The PES scan simulates an increasing bond distance r(N-H), stepping 14 times from 0.8Â to 2.1Â. The minimum energy corresponds to the ion pair of Me₃NH⁺ and Cl^- at a distance of 1.1 to 1.2Â. As r(N-H) increases from the minimum, the total energy also increases, showing that the neutral pair of Me₃NH and HCl is a much less stable state than the ion pair.

1-methyl-imidazolium chloride (Structure A)

Calculation Table

Name of submitted log file	HMIMCL_STRUCTUREA_OPTIMISATION_RL.LOG
Molecule	1-methyl-imidazolium chloride
Method	RB3LYP
Basis Set	3-21G
Final Energy	-722.687898
RMS Gradient	0.000018
Point Group	C1

Log file:File:HMIMCL STRUCTUREA OPTIMISATION RL.LOG

Item Table & Low Frequencies

         Item               Value     Threshold  Converged?
 Maximum Force            0.000046     0.000450     YES
 RMS     Force            0.000010     0.000300     YES
 Maximum Displacement     0.009564     0.001800     NO 
 RMS     Displacement     0.001631     0.001200     NO 

 Low frequencies ---   -5.2982   -2.6328   -0.0039   -0.0029    0.0029    2.7560
 Low frequencies ---   36.0122   64.3158   80.7655

The displacement values have not converged; the RMS displacement is very close to the threshold, and the maximum displacement is approximately 5 times larger. Given that the low frequencies were all in acceptable range, it was opted to use this optimisation for the PES scan.

Structural Information

Bond distances:
r(H-Cl)= 1.720Â
r(H-N)= 1.178Â

Optimized Molecule:

PES Analysis

Log file:[[File:HMIMCL_STRUCTUREA_RL_SCAN4.LOG]

1-methyl-imidazolium chloride (Structure B)

Calculation Table

Name of submitted log file	HMIMCL_STRUCTUREB_OPTIMISATION_RL.LOG
Molecule	1-methyl-imidazolium chloride
Method	RB3LYP
Basis Set	3-21G
Final Energy	-722.666200
RMS Gradient	0.000021
Point Group	C1

Log file:File:HMIMCL STRUCTUREB OPTIMISATION RL.LOG

Item Table & Low Frequencies

         Item               Value     Threshold  Converged?
 Maximum Force            0.000037     0.000450     YES
 RMS     Force            0.000010     0.000300     YES
 Maximum Displacement     0.001264     0.001800     YES
 RMS     Displacement     0.000201     0.001200     YES

 Low frequencies ---   -5.5466   -3.0692    0.0013    0.0026    0.0038    2.1695
 Low frequencies ---   45.2073  162.2239  198.8914

Structural Information

Bond distances:
r(Cl-H1(methyl)) = 2.276
r(Cl-H2) = 2.134

rC(H-Cl) = 2.030 rC(H-Cl(close methyl)) = 2.417 rC(H-Cl(far methyl)) = 4.131

1-methyl-imidazolium chloride (Structure C)

Calculation Table

Name of submitted log file	HMIMCL_STRUCTUREC_OPTIMISATION_RL.LOG
Molecule	1-methyl-imidazolium chloride
Method	RB3LYP
Basis Set	3-21G
Final Energy	-722.666200
RMS Gradient	0.000021
Point Group	C1

Log file:File:HMIMCL STRUCTUREC OPTIMISATION RL.LOG

Item Table & Low Frequencies

         Item               Value     Threshold  Converged?
 Maximum Force            0.000066     0.000450     YES
 RMS     Force            0.000014     0.000300     YES
 Maximum Displacement     0.006632     0.001800     NO 
 RMS     Displacement     0.001600     0.001200     NO 

 Low frequencies ---   -3.0686   -2.1693   -0.0010    0.0006    0.0029    3.3295
 Low frequencies ---   52.4049  102.2473  107.1324

The displacement values have not converged; the RMS displacement is very close to the threshold, and the maximum displacement is approximately 4 times larger. Given that the low frequencies were all in acceptable range, it was opted to use this optimisation for further analysis.

Structural Information

Bond distances:
rC(H-Cl) = 2.030
rC(H-Cl(close methyl)) = 2.417
rC(H-Cl(far methyl)) = 4.131

NH₃ Molecule

Calculation Data

Name of submitted log file	RL_nh3_optf_pop.log
Molecule	NH3
Method	RB3LYP
Basis Set	6-31G(d, p)
Final Energy	-56.557769
RMS Gradient	0.000000
Point Group	C1

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

Optimised Molecule Image

Jmol Rotatable Molecule

logfile: Media:RL_nh3_optf_pop.log

Optimised NH Molecule

Important Geometric Parameters

Optimised bond distance and angle for NH₃
r(N-H)= 1.2Â
θ(H-N-H)= 106°

Vibrational Modes

 Low frequencies ---   -5.6864   -3.6131   -3.6124   -0.0012    0.0045    0.0163
 Low frequencies --- 1089.3674 1693.9284 1693.9284

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

IR Spectrum

Atomic Charges

Atom	Charge (e)
N	-1.125
H1	0.375
H2	0.375
H3	0.375

Project Molecule: cis-N₂F₂

Calculation Data

Name of submitted log file	leeryan_n2f2_optf.log
Molecule	N2F2
Method	RB3LYP
Basis Set	6-31G(d, p)
Final Energy	-309.012413
RMS Gradient	0.000000
Point Group	C2v

logfile: Media:LEERYAN_N2F2_OPTF.LOG

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

The item table shows that value(s) have converged and the optimisation was successful.

Optimised Molecule Image

Jmol Rotatable Molecule

Optimised NF Molecule

Important Geometric Parameters

Optimised bond distance and angle for N₂F₂
r(N-N)= 1.2Â
r(N-F)= 1.4Â
θ(N-N-F)= 114°

Vibrational Modes

 Low frequencies ---    0.0008    0.0016    0.0019    3.2233    4.3533    5.0998
 Low frequencies ---  347.8772  561.2472  771.6105

All low frequencies in the first row are less than 20, which indicates that the optimisation was successful.

Mode	1	2	3	4	5	6
Wavenumber (cm-1)	348	561	772	949	987	1637
Symmetry	A1	A2	B2	A1	B2	A1
Intensity	0	15	75	75	81	21

IR Spectrum

Atomic Charges

Atom	Charge (e)
N1	0.215
N2	0.215
F1	-0.215
F2	-0.215

Questions about N₂F₂

1. Why does the visualisation from the .log file not show N-F bonds?

This is likely an 'error' imposed from the Gaussian program, as the distance between of 1.4Â is a reasonable bond length. During optimisation, whether the bond actually exists is not necessarily considered, so longer bonds within the molecule might not be visualized correctly when viewing the .log file.

2. How many vibrations are expected from the 3N - 6 rule?

There are four atoms (2 N and 2 F), so: (3 × 4) - 6 = 12 - 6 = 6. There are six vibrations expected.

3. Why are only 4 peaks visible in the IR spectrum?

cis-N₂F₂ is highly symmetrical, so some specific vibrational modes do not have an overall dipole moment. The vibrational modes calculated at 348 cm<sup)-1 and 561 cm^-1 have low intensity on an IR because of their low overall dipole moment.

4. Which vibration is the asymmetric N-F stretch?

The vibration at 949 cm^-1 is the asymmetric N-F stretch.

5. What is the nature of the highest energy vibration?

The highest energy vibration at 1637 cm^-1 is the N=N stretch.

6. Which molecular orbitals are core MOs?

The core molecular orbitals are MOs 1, 2, 3 and 4.

7. Provide a picture of MO9 and draw an LCAO diagram.

Molecular orbital 9:

LCAO diagram: