Robertisla

Lab1 Marking

You did a great job especially with the formatting. However, you have tabulated wrong charges for N and F. If you have any queries, please contact Prof. Hunt.

BH₃ Molecule

Calculation data

name of submitted log file	IR_BH3_OPTF_POP.LOG
molecule	NH3
method	RB3LYP
basis set	6-31G(d,p)
final energy	-26.615112
RMS gradient	0.003053
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

Low frequencies data

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

Optimised molecule image

Jmol rotateable molecule

logfile: Media:IR BH3 OPTF POP.LOG

optimised BH molecule

Important geometric parameters

Optimised bond distance and angle for BH₃
r(B-H)=1.190Â
θ(H-B-H)=120.0°

Vibrational data

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

BH₃NH₃ Molecule

Calculation data

name of submitted log file	IR_NH3BH3_OPT.LOG
molecule	BH3NH3
method	RB3LYP
basis set	6-31G(d,p)
final energy	-83.22489
RMS gradient	0.000001
point group	C1

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

Low frequencies data

Low frequencies	-5	-3	0	0	0	1
Low frequencies	263	633	638

Optimised molecule image

Jmol rotateable molecule

logfile: Media:IR_NH3BH3_OPT.LOG

optimised BHNH molecule

Important geometric parameters

Optimised bond distances for BH₃ NH₃
r(B-H)=1.210Â
r(N-H)=1.018Â
r(N-B)=1.668Â

Optimised bond angles for BH₃ NH₃
θ(H-B-H)=114.0°
θ(H-N-H)=108.0°
θ(H-N-B)=111.0°
θ(H-B-N)=105.0°

Vibrational data

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 (arbitrary)	0	14	4	4	41	41	109	3	3	114	28	28	67	231	231	3	28	28

Total energies

E (NH₃) = -56.557769
E (BH₃) = -26.615112
E (BH₃NH₃) = -83.22489

Association Energy

ΔE= E(NH3BH3)-[E(NH3)+E(BH3)]
ΔE= -0.051989 Au
ΔE= -136.5 kJ/mol

Me₃NH-CL Molecule

Calculation data

name of submitted log file	IR_ME3NH-CL_OPT2.LOG
molecule	Me3NH-Cl
method	RB3LYP
basis set	6-31G(d,p)
final energy	-26.615112
RMS gradient	0.003053
point group	D3H

Item Table

         Item               Value     Threshold  Converged?
 Maximum Force            0.000019     0.000450     YES
 RMS     Force            0.000005     0.000300     YES
 Maximum Displacement     0.001834     0.001800     NO 
 RMS     Displacement     0.000343     0.001200     YES

Low frequencies data

Low frequencies	-14	-2	0	0	0	2
Low frequencies	56	56	190

Optimised molecule image

Jmol rotateable molecule

logfile: Media:IR_ME3NH-CL_OPT2.LOG

optimised MeNH-Cl molecule

Important geometric parameters

Optimised bond lengths for Me₃NH-Cl
r(N-H)= 1.164
r(H-Cl)= 1.738
r(N-Cl)= 2.902

Rigid Scan for Me₃NH-Cl

PES rigid scan raw data plot for Me₃NH-Cl

PES rigid scan raw data table for Me₃NH-Cl

Scan Coordinate Â	Total Energy (Hartrees)	Relative Total Energy kJ mol -1
0.800	-632.066250	229.9
0.900	-632.122419	82.4
1.000	-632.146048	20.4
1.100	-632.153507	0.8
1.200	-632.153801	0
1.300	-632.151576	5.8
1.400	-632.149019	12.6
1.500	-632.147017	17.8
1.600	-632.145741	21.2
1.700	-632.144784	23.7
1.800	-632.142934	28.5
1.900	-632.137592	42.6
2.000	-632.123855	78.6
2.100	-632.093222	159.1

HMim-CL PES Plot for Me₃NH-Cl

Plot of Total relative energy (kJ/mol) vs Scan coordinate (Â)

This graph shows that when the N-Cl distance is set at 3.2 Â a broad minima occurs, the most stable state is an ion-pair Me₃NH⁺ --- Cl^- and as the proton is pushed to the Cl forming a neutral pair Me₃N --- HCl the energy goes up, and no stable minima forms, rather there is a "shelf" in the PES. The ion-pair forms a doubly ionic H-bond between the Me₃NH⁺ and Cl^-, the neutral-pair forms a normal H-bond between the Me₃N and HCl.

1-methyl-imidazolium chloride A

Calculation data

name of submitted log file	IR_IMIDA_A_OPT.LOG
molecule	1-methyl-imidazolium chloride A
method	RB3LYP
basis set	3-21G(d,p)
final energy	-722.687898
RMS gradient	1.96e-07
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     0.000004     0.000060     YES
 RMS     Displacement     0.000001     0.000040     YES

Low frequencies data

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

Optimised molecule image

logfile: Media:IR IMIDA A OPT.LOG

Important Geometric parameters

Optimised bond lengths

r(H-N)(3-5)= 1.1776 Â
r(H-Cl)(3-14)= 1.719 Â
r(N-Cl)(5-14)= 2.891 Â
r(C-H)(1-2)= 1.075 Â
r(C-H)(12-13)= 1.074 Â
r(N-C)(5-12)= 1.390 Â
r(C-N)(5-1)= 1.332 Â

Scan for 1-methyl-imidazolium chloride A

Raw data

Data Table

Scan Coordinate Â	Total Energy (Hartrees)	Relative Total Energy kJ mol -1
0.800	-722.595812	219.4
0.900	-722.650398	76.1
1.000	-722.672765	17.3
1.100	-722.679373	0
1.200	-722.679291	0.2
1.300	-722.677213	5.7
1.400	-722.675324	10.6
1.500	-722.674443	12.9
1.600	-722.674629	12.5
1.700	-722.675355	10.6
1.800	-722.675349	10.6
1.900	-722.672137	19.0
2.000	-722.661301	47.4
2.100	-722.635447	115.3

Formal Scan Graph for 1-methyl-imidazolium chloride A

1-methyl-imidazolium chloride B

Calculation data

name of submitted log file	IR_IMIDA_B_OPT.LOG
molecule	1-methyl-imidazolium chloride B
method	RB3LYP
basis set	3-21G(d,p)
final energy	-722.66620
RMS gradient	3.291e-06
point group	C1

Item Table

         Item               Value     Threshold  Converged?
 Maximum Force            0.000006     0.000450     YES
 RMS     Force            0.000002     0.000300     YES
 Maximum Displacement     0.000443     0.001800     YES
 RMS     Displacement     0.000078     0.001200     YES

Low frequencies data

Low frequencies	-5	-3	0	0	0	2
Low frequencies	45	162	199

Optimised molecule image and Jmol rotateable molecule

logfile: Media:IR IMIDA B OPT.LOG

Important Geometric parameters

Optimised bond lengths

r(H-N)(7-3)= 1.1044 Â
r(H-Cl)(7-14)= 2.134 Â
r(H-Cl)(13-14)= 2.277 Â
r(N-Cl)(8-14)= 3.650 Â
r(C-H)(3-7)= 1.1045 Â
r(C-H)(10-13)= 1.106 Â
r(N-C)(8-10)= 1.496 Â
r(C-N)(3-8)= 1.402 Â

1-methyl-imidazolium chloride C

Calculation data

name of submitted log file	IR_IMIDA_C_OPT.LOG
molecule	1-methyl-imidazolium chloride C
method	RB3LYP
basis set	3-21G(d,p)
final energy	-761.77953
RMS gradient	2.192e-06
point group	C1

Item Table

         Item               Value     Threshold  Converged?
 Maximum Force            0.000006     0.000450     YES
 RMS     Force            0.000002     0.000300     YES
 Maximum Displacement     0.000110     0.001800     YES
 RMS     Displacement     0.000036     0.001200     YES

Low frequencies data

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

Optimised molecule image

logfile: Media:IR IMIDA C OPT.LOG

Important Geometric parameters

Optimised bond lengths

r(H-C)(4-1)= 1.118 Â
r(H-Cl)(4-17)= 2.030 Â
r(H-Cl)(11-17)= 2.417 Â
r(N-Cl)(7-17)= 3.666 Â
r(C-H)(9-11)= 1.101 Â
r(N-C)(7-9)= 1.490 Â
r(C-N)(1-7)= 1.348 Â

Ionic liquid ion pair (1-methyl-imidazolium chloride (HMim-Cl) A, B, and C)

Optimised H--Cl bond lengths

Molecule Name	HMim-Cl A	HMim-Cl B	HMim-Cl C	Me3NH-Cl
Bond distance (Â)	1.719 Â	2.134 Â	2.030 Â	1.738
Additional H--Cl bond	N/A	2.277 Â	N/A	N/A

How do the H-bonds of the H--Cl of Me3NH and HMim compare and how do the H-bonds of the N-H and C-H H-bonds compare??
The H--Cl bonds of the Me₃NH-Cl molecule (1.738 Â) is very similar to the H--Cl of the HMim-Cl A (1.719 Â), whereas the H--Cl bonds of HMim-Cl B (2.134 Â, 2.277 Â) and HMim-Cl C (2.030 Â)are larger. This is because the hydrogen of the Me₃NH-Cl and HMim-Cl A is bonded to a nitrogen which leads to a more polar bond. The effects of this polarity cause stronger dipole dipole attraction leaving the hydrogen with a larger delta + which produces a greater attraction between the hydrogen and the negative chlorine. Additionally, the HMim-Cl B molecule shares the H--Cl bonding between two bonds therefore leading to a more delocalized interaction and the longest H--Cl bonds. This polarity also results in a Me₃NH-Cl
N-H bond length of 1.164 Â and a HMim-Cl A N-H bond length of 1.178 Â. Both these bonds end up being longer than the typical C-H bond because, although in general the N-H bond is more polar and leads to a stronger bond, the additional interaction with chlorine results in the sharing of the hydrogen lengthing the N-H. This is in comparison to the C-H bonds found for each HMim-Cl molecle which range between 1.070 - 1.100 Â. The N-H bond in the HMim-Cl B molecule is opposite from the site of the chlorine interaction therefore it has a shorter bond length of 1.014 Â as the hydrogen is not being shared between the chlorine atom and the nitorgen.

Are these distances representative of a H-bond and will the ionic nature of the ions effect a distance based assessment of H-bonding?
van der Waals radius for chlorine = 1.75 Â
van der Waals radius for hydrogen = 1.20 Â
Sum of van der Waals radius = 1.75 + 1.20 = 2.95 Â

Comparing the bonds we obtained to the standard sum of the van de Waals radii there is a noticeable difference in lengths, with the sum of van der Waals being between 0.673 Â to 1.231 Â longer than all of the Cl associated molecule. These results indicate that the ionic nature of these molecules does have an effect on the distance based assessment of H-bonding with the attractive interactions influencing the bond length.

Associated energies from 1-methyl-imidazolium chloride (HMim-Cl) A, B, and C

Optimised Ion and Jmol rotatable molecule for 1-methyl-imidazolium chloride ion A & B

Calculation data

name of submitted log file	IR_REATTEMPT_AB_ION.LOG
molecule	1-methyl-imidazolium chloride ion A & B
method	RB3LYP
basis set	3-21G
final energy	-264.58913
RMS gradient	1.0609e-05
point group	C1

Item Table

         Item               Value     Threshold  Converged?
 Maximum Force            0.000134     0.000450     YES
 RMS     Force            0.000028     0.000300     YES
 Maximum Displacement     0.000708     0.001800     YES
 RMS     Displacement     0.000190     0.001200     YES

Low frequencies data

Low frequencies	-5	-4	0	0	0	4
Low frequencies	91	155	336

Optimised Chlorine atom and Jmol rotatable molecule

Calculation data

name of submitted log file	IR_CHLORINE_ATOM_OPT.LOG
molecule	Chlorine atom
method	UB3LYP
basis set	3-21G
final energy	-457.94573
RMS gradient	0
point group	OH

Item Table

         Item               Value     Threshold  Converged?
 Maximum Force            0.000134     0.000450     YES
 RMS     Force            0.000028     0.000300     YES
 Maximum Displacement     0.000708     0.001800     YES
 RMS     Displacement     0.000190     0.001200     YES

Low frequencies data

Low frequencies

0

0

0

Optimised Ion and rotatable molecule for 1-methyl-imidazolium chloride ion C

logfile: Media:IR_IMIDA_C_OPT_ION.LOG

Calculation data

name of submitted log file	IR_IMIDA_C_OPT_ION.LOG
molecule	1-methyl-imidazolium chloride ion C
method	RB3LYP
basis set	3-21G
final energy	-303.68736
RMS gradient	2.4257e-05
point group	C1

Item Table

         Item               Value     Threshold  Converged?
 Maximum Force            0.000134     0.000450     YES
 RMS     Force            0.000028     0.000300     YES
 Maximum Displacement     0.000708     0.001800     YES
 RMS     Displacement     0.000190     0.001200     YES

Low frequencies data

Low frequencies	-870	-200	-191	-77	-53	0
Low frequencies	0	0	1

I theorize that the low frequencies have not meet the assumed range as the molecule that was optimized was the original optimized 1-methyl-imidazolium chloride (HMim-CL) C molecule that had it's chlorine atom removed and was optimized from there.

Table of Association energies

Molecule	(HMim-Cl) A	(HMim-Cl) B	(HMim-Cl) C	Chloride anion
E Ion (au)	-264.58913	-264.58913	-303.68736	-457.945733
E (HMim-Cl) (au)	-722.687898	-722.66620	-761.77953
Association energy ΔE (au)	-0.15301	-0.13130	-0.146437
Association energy (kJ/mol)	-401.7	-344.7	-384.5

Provide the relative energy of the two isomers (a) and (b)
ΔE = E_b - E_a = (-722.6662) - (-722.687898) = 0.021698 --> ΔE = 57.0 kJ/mol

This illustrates that the HMim-Cl B conformer is higher in energy than the HMim-Cl A conformer. This proves that the HMim-Cl A conformer has lower energy and is therefore a more stable conformer than B with greater polarity of bonds resulting in a stronger more favorable conformation.

Rationalise why one conformer is less stable than the other and discuss the dissociation energy of (c) relative to (a) and (b). What does the comparison tell us about the H-bonding?
The HMim-Cl A conformer is the most stable as it has the largest association energy indicating that the molecule has a stronger more stable bond and it is less favourable to dissociate in comparison to the other confomers.

The association energy of the HMim-Cl C conformer (-384.5 kJ/mol) lies in between the association energies of the HMim-Cl conformers A and B. The HMim-Cl B conformer has an association energy of -344.7 kJ/mol. Due to the lower association energy we can determine that the molecule is the least stable and the H-bonding is weaker. Conversely the HMim-Cl A conformer has a association energy of -401.7 kJ/mol this is larger than the HMim-Cl C conformer showing that although the H-bonding of this conformer is stronger than the HMim-Cl B conformer the H-bonding in the HMim-Cl A conformer is the strongest.

PES rigid scan graph comparing Me₃NH-Cl and (HMim)-Cl A

Discuss your HMim-Cl PES plot, compare and contrast your results for the Me₃NH-Cl and HMim-Cl PES.

The HMim-Cl A conformer has a minimum energy point at 1.1 Â while the Me₃NH-Cl has a minimum energy point at 1.2Â demonstrating that both molecules most stable conformation lay at a similar distance under rigid constraints.

As the proton moves from the HMim / Me₃N over to the chlorine the energy increases creating an shelf before the H bonds to the Cl forming the neutral-pair for both e.g. Me₃N and HCl / HMim and HCl, and the energy rises rapidly.

This scan shows us that for both molecules the most stable, low-energy conformation involves the charged ion-pairs with the ionic nature playing a role in creating a stronger stabilization of each molecule lowering the overall energy.

NH₃ Molecule

Calculation data

name of submitted log file	IRobertson_nh3_optf_pop.log
molecule	NH3
method	RB3LYP
basis set	6-31G(d,p)
final energy	-56.557769
RMS gradient	1.53e-07
point group	C3v

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 data

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

Optimised molecule image

Jmol rotateable molecule

logfile: Media:IROBERTSON_NH3_OPTF_POP.LOG

optimised NH molecule

Important geometric parameters

Optimised bond distance and angle for NH₃
r(N-H)=1.02Â
θ(H-N-H)=106°

Vibrational data

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

Optimised molecule image with charges

Atoms	N	H
Charge	-1.13	0.38

N₂F₂ Molecule

Calculation data

name of submitted log file	IJR_N2F2_C2V_OPTF.LOG
molecule	N2F2
method	RB3LYP
basis set	6-31G(d,p)
final energy	-309.01241
RMS gradient	3.17e-07
point group	C2V

Item Table

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

Optimised N₂F₂ molecule

Optimised N₂F₂ molecule image

Jmol rotatable molecule

logfile: Media:IJR_N2F2_C2V_OPTF.LOG

optimised NF molecule

Important geometric parameters

Optimised bond distance and angle for N₂F₂
r(N-F)=1.39Â
r(N-N)=1.22Â
θ(F-N-N)=114°
θ(F-N-N-F)=0°

Vibrational Data and analysis

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

Which vibration is the asymmetric N-F stretch?
Vibration 3 is asymmetric.

What is the nature of the highest energy vibration?
It is an N-N stretching vibration

N₂F₂ Spectrum

IR Analysis

How many vibrations are expected from the 3N-6 rule?
We would expect there to be 6 vibrations (3(4) - 6 = 6)

Why are there only 4 peaks in the IR spectrum?
The A1 347.88 cm-1 and the A2 561.25 cm-1 modes have essentially no intensity, as both of these modes must have no dipole change. Therefore only the remaining 4 modes can be observed in the IR spectrum as peaks.

Low frequencies data

Low frequencies	-0.0024	-0.0016	-0.0014	3.3364	4.3775	5.1348
Low frequencies	347.8779	561.2478	771.6088

Optimised molecule image with charges

Atoms	N	F
Charge	0.26	-0.26

Molecular Orbital analysis

N₂F₂ MO 9

Which MOs are core orbital MOs?
The core MOs are the first four MOs 1-4 with low lying energy.