KusabsOliv

Lab1 Marking

It's good that you have a working wiki. However, you have optimised N2F2 with a wrong symmetry, have reported wrong charges, and have missed to include the low frequencies, torsion angle, and NN distance. 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.

Lab2 Marking

It's good that you have a working wiki. The formula you used for NH3BH3 association energy is correct however your final answer is incorrect. Don't forget to consider the accuracy to which you report your data the next time. Your charges on ions in the project molecule and the subsequent calculations and discussions are incorrect. Overall, good job! If you have any queries, please contact Prof. Hunt.

BH₃ Molecule

Optimized Molecule Image

calculation data

logfile	KUSABSOLIV_BH3_OPTF_POP.LOG
molecule	BH3
method	RB3LYP
basis set	6-31G(d,p)
final energy	-26.615324
RMS gradient	0.000002
point group	D3h

Low frequencies

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

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

Jmol rotatable molecule

logfile:Media:KUSABSOLIV_BH3_OPTF_POP.LOG

optimised BHmolecule

Important geometric parameters

optimized bond distance and angle for BH₃
r(B-H)=1.192Â
θ(H-B-H)=130.0°

Vibrational data

mode	1	2	2	4	5	6
wavenumber(cm-1)	1163	1213.14	1213.14	2582.58	2715.72	2715.72
symmetry	A2"	E'	E'	A1'	E'	E'
intensity	93	14	14	0	126	126

IR Spectrum

NH₃BH₃ Molecule

Optimized Molecule Image

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calculation data

molecule	NH3BH3
method	RB3LYP
basis set	6-31G(d,p)
final energy	-83.224689
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

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

Jmol rotatable molecule

logfile:Media:OK_NH3BH3_OPTF_POP.LOG

optimised NHmolecule

Important geometric parameters

optimized bond distance and angle for NH₃BH₃
r(N-H)=1.018Â
r(B-H)=1.210Â
r=(B-N)=1.668Â
θ(H-N-H)=108°
θ(H-B-H)=114°
θ(H-N-B)=105°
θ(H-B-N)=112°

Vibrational data

mode	1	2	2	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

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-0.05168 Hartrees
= -135.68584 kJ/mol
= 135.68584 kJ/mol (5 d.p)

Me₃NH-Cl Molecule

Optimised Molecule

Calculation data

logfile	OK_ME3NHCL_OPTF_POP.log
molecule	Me3NH-Cl
method	RB3LYP
basis set	3-21G
final energy	-632.16208
RMS gradient	5e-06
point group	C1

Item Table

Item Value Threshold Converged?

Maximum Force            0.000008     0.000450     YES
RMS     Force            0.000003     0.000300     YES
Maximum Displacement     0.000932     0.001800     YES
RMS     Displacement     0.000257     0.001200     YES

Low Frequencies

Low frequencies	-14	-2	-0	0	0	3
Low frequencies	56	56	90

Jmol Rotatable Image

logfile:Media:OK_ME3NHCL_OPTF_POP.LOG

optimised MeNHClmolecule

Important Geometric Parameters

r(N-H)= 1.164Â
r(H-Cl)= 1.738 Â
r(N-Cl)= 2.902 Â

Me₃HNCl Rigid Scan

Rigid Scan Raw Data Plot

log file: Media: OK_ME3NHCL_OPTF_HOPEFULLYSCAN_RIGID.LOG

PES Raw Data Table

Scan Coordinate Â	Total Energy (Hartrees)	Relative Total Energy (kJmol-1)
0.8	-632.066252	229.9
0.9	-632.122420	82.4
1.000	-632.146069	20.3
1.100	-632.153508	0.8
1.200	-632.153801	0.0
1.300	-632.151576	5.8
1.400	-632.149019	12.6
1.500	-632.147018	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	-632.093223	159.0

Me₃NHCl Scan Formal Graph

Plot of Total Relative Energy (kJ/mol) vs. Scan Coordinate (Â)

The scan coordinate, which corresponds to the N-H bond length, starts at 0.8 Â and increasing in 0.1 Âincrements to 2.1 Â. When the N-Cl bond distance is set to 3.2 Â,the scan data plot shows that a minima occurs at 1.2Â. This displays an ion-pair Me₃NH⁺ --- Cl^-, and the minima proves that this is the most stable state. The graph captures the gradual shift of the proton between as the proton is pushed over to the Cl, where it forms a neutral pair Me₃N---HCl. The energy goes up, with no stable minima formed, rather a 'shelf' appears in the PES. The ion-pair, forms a doubly ionic H-bond between the Me₃NH⁺ and Cl^-, the neutral pair forms a normal bond between Me₃N and HCl.

Ionic Liquid pair Analysis - 1-methyl Imidazolium chloride (HMim-Cl)

Optimised molecule

Calculation data

name of submitted log file	KUSABS_IMIDA_A_OPTF.LOG
molecule	HMim-Cl a)
method	RB3LYP
basis set	3-21G
RMS gradient	3.88e-07
final energy	-722.6879
point group	C1

Item Table

Item               Value     Threshold  Converged?
Maximum Force            0.000008     0.000450     YES
RMS     Force            0.000003     0.000300     YES
Maximum Displacement     0.000932     0.001800     YES
RMS     Displacement     0.000257     0.001200     YES

Low Frequencies

Low frequencies	-14	-2	0	0	0	3
Low frequencies	56	56	190

logfile:Media:OK_ME3NHCL_OPTF_POP.LOG

Important Geometric Parameters

(9-7)r(N-H) =1.178 Â
(9-14)r(N-Cl) = 2.891 Â
(7-14)r(H-Cl) = 1.719 Â
(1-4)r(C-H) = 1.075Â

HMim-Cl Molecule a) Scan

HMim-Cl Scan Plot

PES Raw Data Table

Scan Coordinate Â	Total Energy (Hartrees)	Relative Total Energy (kJmol-1)
0.800	-722.595818	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	-722.6753547	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

Hmim-Cl Formal Graph

Plot of Total Relative Energy (kJ/mol) vs. Scan Coordinate (Â)

Optimised Molecule

Calculation Data

name of submitted log file	KUSABS_IMIDA_B_OPTF.LOG
molecule	HMim-Cl (b)
method	RB3LYP
basis set	3-21G
Final energy	-722.666
RMS gradient	2.0678e-05
Point group	C1

Item Table

Maximum Force            0.000053     0.000450     YES
RMS     Force            0.000013     0.000300     YES
Maximum Displacement     0.000652     0.001800     YES
RMS     Displacement     0.000171     0.001200     YES

Low Frequencies

Low frequencies	-6	-3	-2	0	0	0
Low frequencies	45	162	199

logfile:Media:KUSABS_IMIDA_B_OPTF.LOG

Important Geometric Parameters

(5-14) r(H-Cl)=2.134 Â
(13-14)r(H-Cl)=2.277 Â
(8-14) r(N-Cl)=3.650 Â
(8-2) r(N-C)= 1.403 Â

Optimised Molecule

Calculation data

Logfile	KUSABS_IMIDA_C_OPTF2.LOG
Name of Molecule	HMim-Cl c)
Method	RB3LYP
Basis Set	3-21G
Final Energy	-761.77953
RMS Gradient	5.903e-06
Point Group	C1

Item Table

Maximum Force            0.000014     0.000450     YES
RMS     Force            0.000004     0.000300     YES
Maximum Displacement     0.001169     0.001800     YES
RMS     Displacement     0.000303     0.001200     YES

Low Frequencies

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

Important Geometeric Parameters

(4-17) r(H-Cl) = 2.030 Â
(8-17) r(N-Cl) = 3.666Â

logfile:Media:KUSABS_IMIDA_C_OPTF2.LOG

Ionic (H-Cl) bond comparison

Ionic pair molecule	H-Cl Bond	Additional H-Cl bond
HMim-Cl (a)	1.719 Â
HMim-Cl (b)	2.277 Â	2.13401 Â
HMim-Cl (c)	2.030 Â
Me3 NH-CL	1.738 Â

How do the H-bonds of Me₃ NH and HMim compare? How do the H-bonds of the N-H and C-H compare?
The H-Cl bond in Me₃NH (1.74Â) and HMim-Cl molecule (a) (1.72Â) are both relatively strong bonds, and exhibit very close distances with a difference of only 0.02 Â. In both molecules, the hydrogen of interest is attached to a nitrogen, which gives a polar N-H bond that interacts strongly with the chloride. The other HMim-Cl molecules, (b) and (c), show longer H-Cl bond distances than those of molecule (a) and Me₃ NH-Cl, which correspond to weaker hydrogen bonding interactions in the molecules. HMim-Cl molecule (b) has a H-Cl bond length of 2.27688 Â from the cis-alkene proton to the chloride, as well as a H-Cl bond length of 2.13401 Â from the methyl protons to the chloride. Sharing the H-Cl between two bonds results in delocalised interactions and the longest H-Cl bond.

HMim-Cl (c) has a H-Cl bond length of 2.02997. In both the(b) and (c) molecules, the Cl interacts with C-H protons as opposed to N-H protons. As C-H bonds are less polar than N-H bonds, due to the greater electronegativity difference between N and H compared to C and H, the hydrogen will carry a smaller delta positive charge in C-H bonds and will form weaker hydrogen bonds with the chloride.

Are these distances representative of an H-bond?

Van Der Waal Radius Cl = 1.75 Â
Van Der Waal Radius H = 1.20 Â

The combined Van der Waals radius of a Cl-H bond is 2.95 Â (1.20+1.75). All the H-Cl bonds observed in these molecules are shorter than expected from Van der Waals contact, which indicates that there are attractive hydrogen-bonding interactions that are stronger than simple intramolecular bonding. The significantly shorter bonds in HMim-Cl (a) and Me₃ NH can be attributed to the ionic character in the H-bonds. Therefore, these distances are representative of an H-bond. The ionic nature of the ions will affect a distance-based assessment of H-bonding. This is because the positive and negative ions attract each other in ion pairs, and this can shorten the H-Cl bond lengths.

As a result, it is important not to rely solely on bond distance when assessing the strength of the H-bonding.

Cationic Analysis

Optimised Molecule HMim+ A + B

The cation cluster of molecules a and b are the same, thus, the same optimisation can be used.

Calculation Data

logfile	KUSABS_IMIDA_A_CATION_OPTF.LOG
molecule	HMim+ (a)+(b)
method	UB3LYP
basis set	3-21G
Final energy	-264.57554
RMS gradient	5.0014e-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     0.000641     0.001800     YES
RMS     Displacement     0.000190     0.001200     YES

Low frequencies

Low frequencies	-878	-407	-196	-76	-1	-1
Low frequencies	0	0	0

These low frequencies are significantly lower than expected, which can be explained by the fact that the cation was created by simply removing the chloride ion from the already optimised HMim-Cl (a), and this optimisation of an already optimised molecule has led to unusually low frequencies.

Jmol Rotatable image

logfile:Media:KUSABS_IMIDA_A_CATION_OPTF.LOG

optimised HMim+ cation molecule

Optimised HMim+ Cation Cluster (c)

Calculation Data

logfile	KUSABS_IMIDA_C_OPTF_CATION2.LOG
molecule	HMim+ (c)
method	UB3LYP
basis set	3-21G
final energy	-303.6874
RMS gradient	1.58e-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     0.000026     0.000060     YES
RMS     Displacement     0.000006     0.000040     YES

Low frequencies

Low frequencies	-4	0	0	0	3	4
Low frequencies	83	98	147

Jmol Rotatable Molecule

logfile: Media:KUSABS_IMIDA_C_OPTF_CATION2.LOG

optimised HMim+ cation cluster (c)

Chlorine Ion Optimisation

Optimised Molecule

calculation Data

Name of submitted logfile	KUSABS_CL_ION_OPTF.LOG
Molecule	Cl-
Method	UB3LYP
Basis set	3-21G
Final energy	-457.94573
RMS gradient	0.00000
Point group	OH

Item Table

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

Low frequencies

Low frequencies

0

0

0

Jmol Rotatable Molecule

logfile:Media:KUSABS_CL_ION_OPTF.LOG

optimised chlorine anion

Association Energy Table

HMim-Cl isomer	Total Energy (au)	Association Energy(au)	Association Energy (kJ mol-1
a)	-722.6879	-0.16663	-437
b)	-722.666	-0.14473	-380
c)	-761.77953	-0.1464	-384
HMim+ cation (a+b)	-264.57554
HMim+ cation c)	-303.6874
Chlorine anion	-457.94573

ΔE = E(Products) - [E(Reactants)]
= E(Ion pair) - [E(Cation) + E(Anion)]

Association energy of (b) relative to (a)
-379.98862 - (-437.4837065) = + 57.4985kJmol^-1(4 d.p)

Association energy of (c) relative to (a)
-384.3732 -(-437.4837065) = +53.1139kJmol^-1(4 d.p)

Association energy of (c) relative to (b)
-384.3732 -(-379.98862)= -4.3846kJmol^-1(4 d.p)

Rationalise why one conformer is less stable than the other.

The association energy of HMim-Cl (b) is 57 kJ mol ^-1 higher than that of HMim-Cl (a), indicating that the HMim-Cl (a) isomer is lower in energy and therefore more stable than (b). This is expected, as HMim-Cl(a) forms a stronger N-H-Cl bond and has a shorter H-Cl bond distance of 1.72 Â. The more negative association energies equate to a conformer requiring more energy for it to dissociate. This is attributed to the high polarisation of N-H, with the hydrogen carrying a partial positive charge that interacts with the chloride anion strongly. This makes (a) highly unfavourable to dissociate. In comparison, HMim (b) has weaker C-H-Cl interactions and a longer H-Cl distance of 2.27688 Â, with the additional H-Cl bond from the methyl protons of 2.13401 Â. The C-H bonds are less polar than the N-H bonds, and so there will be less electrostatic attraction to the chloride ion. With the lowest association energy, (a) is the most stable conformer and requires the most energy to dissociate.

Discuss the dissociation energy of (c) relative to (a) and (b). What does the comparison tell us about the H-bonding?

The association energy of HMim-Cl (c) is -384kJmol^-1, which is 53.11kJmol^-1 higher than the association energy of HMim-Cl (a) (-437kJmol^-1) but 4.38kJmol^-1 lower than that of HMim-Cl (b) (-380kJmol^-1), indicates that molecule (c) has intermediate stability and intermediate strength of H-bonding. As more negative association energies correspond to both larger dissociation energies and stronger stabilisation, this suggests that HMim-Cl (c) forms a stronger ion-pair interaction than HMim-Cl (b), but weaker than HMim-Cl (a). This comparison highlights how the C-H bonds in (b) are less polarised than the N-H bonds in both (a) and (c), which results in a lower association energy.

Chemical diagram of the two protonation states for HMim-Cl

Combined PES plot of Me₃NH-Cl and HMim-Cl

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

Both plots exhibit very similar curves. The plots of Me₃NH-Cl and HMim-Cl both show a clear minima of 1.1 Â (HMim-Cl)and 1.2Â(Me₃NH-Cl), which correspond to the lowest energy and thus the most stable N-H-Cl bond interaction. A difference seen here is that the energy values of HMim-Cl are slightly lower than those of Me₃NH-Cl, which suggests that HMim-Cl is more stabilised and is able to remain stabilised over the range of bond distances. There is a more gradual increase in energy at bond distances longer than 1.2Â for HMim-Cl, as the N-H interactions with the Cl ion are reduced and the H moves to form the H-Cl ion-pair, and the system moves towards dissociation. This further proves that the HMim-Cl molecule is lower in energy and more stable.

At distances shorter than 1.1Â, the nuclei are forced too close together, which causes strong repulsion. As a result, there is a drastic rise in energy, which is shown on the plots of both nuclei. Here, there is a larger energy for the Me₃NH-Cl compared to HMim-Cl. This higher energy supports the idea that Me₃NH-Cl is less stable than HMim-Cl, and is more affected by changes in bond distance. There is also a steeper increase in energy after 1.2Â, seen as the 'shelf' in the plot, when the H moves further from the molecule towards the Cl ion, which confirms less stability. These differences are likely due to the differences in their structures and how the positive charge is distributed. In HMim-Cl, the imidazolium ring helps delocalise the positive charge, which increases the N-H polar bond and stabilises the ion-pair more than Me₃NH-Cl. This results in HMim-Cl having a stronger and more stable interaction with the chloride ion than Me₃NH-Cl, which these PES plots confirm.

NH₃ Molecule

calculation data

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

Optimized Molecule Image

Jmol rotatable molecule

logfile:Media:KUSABSOLIV_NH3_OPTF_POP.LOG

optimised NHmolecule

Important geometric parameters

optimized bond distance and angle for NH₃
r(N-H)=1.018Â
θ(H-N-H)=106°

Vibrational data

mode	1	2	2	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

Charge Distribution Model

Atom	Charge
Nitrogen	-1.13
Hydrogen	0.375

N₂F₂ Molecule

calculation data

molecule	N2F2
method	RB3LYP
basis set	6-31G(d,p)
final energy	-309.01241
RMS gradient	3.685e-06
point group	C2v

Item Table

Item               Value     Threshold  Converged?
Maximum Force            0.000006     0.000015     YES
RMS     Force            0.000005     0.000010     YES
Maximum Displacement     0.000024     0.000060     YES
RMS     Displacement     0.000017     0.000040     YES

Low frequencies

Low frequencies	-0.0012	-0.0012	0.0013	2.4177	4.2047	4.8781
Low frequencies	347.8622	561.2409	771.6170

Optimised Model Image

Jmol Rotatable Molecule

logfile:Media:KUSABSOLIV_N2F2_OPTF_POP.LOG

optimised NFmolecule

Important geometric parameters

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

Vibrational data

mode	1	2	2	4	5	6
wavenumber(cm-1)	348	561	772	949	987	1637
symmetry	A	A	B	A	B	A
intensity	1	0	75	75	81	21

IR spectrum

Charge Distribution Model

Atom	Charge
Nitrogen	-0.22
Fluorine	0.22

the molecule from the log file does not have bonds between the F and N atoms, what is going on here?

IR analysis

As there are 4 atoms in N₂F₂, 6 vibrations are expected from the 3N-6 rule. This matches to the 6 vibrations seen. There are four strong IR peaks shown at 772, 949, 989 and 1637. However, the peak at 348 does not show up as it is likely too low to detected, and the peak at 561 (A2, out of plane bending) is likely IR inactive as it does not change the molecules dipole. The vibration at 772cm-1, mode 3, is the asymmetric N-F stretch. The highest energy vibration at 1637cm-1 is the N=N double bond stretch.

Molecular Orbital Analysis

In N₂F₂, the core molecular orbitals are 1,2,3 and 4

MO9 for N₂F₂