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.

BH₃ Molecule

Optimized Molecule Image

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calculation data

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

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)=1.19232Â
θ(H-B-H)=130°

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	-5.0440	-2.8838	0.0010	0.0012	0.0014	0.6125
Low frequencies	263.3825	632.9842	638.4293

Jmol rotatable molecule

logfile:Media:OK_NH3BH3_OPTF_POP.LOG

optimised NHmolecule

Important geometric parameters

optimized bond distance and angle for NH₃BH₃br r(N-H)=1.01847Â
r(B-H)=1.20977Â
r=(B-N)=1.66770Â
θ(H-N-H)=108°
θ(H-B-H)=114°
θ(H-N-B)=105°
θ(H-B-N)=1118°

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

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	-13.6743	-1.8717	-0.0006	0.0026	0.0036	2.7014
Low frequencies	55.5069	56.3300	89.8235

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

PES Raw Data Table

Scan Coordinate Â	Total Energy (Hartrees)	Relative Total Energy (kJmol-1)
0.8	-632.0662517	229.8615
0.9	-632.1224204	82.39055
1.0	-632.1460690	20.30115
1.1	-632.1535075	0.771372
1.2	-632.1538013	0
1.3	-632.1515761	5.842263
1.4	-632.1490193	12.55514
1.5	-632.1470175	17.81087
1.6	-632.1457412	21.16179
1.7	-632.1447843	23.67413
1.8	-632.1429341	28.53183
1.9	-632.1375920	42.55752
2.0	-632.1238548	78.62454
2.1	-632.0932227	159.0491

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 1-methyl Imadizolium chloride (HMim-Cl)

Optimised molecule

Calculation data

name of submitted log file	KUSABS_IMIDA_A_OPTF.LOG
molecule	HMim-Cl b)
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	-13.6743	-1.8717	-0.0006	0.0026	0.0036	2.7014
Low frequencies	55.5609	56.3300	189.8235

logfile:Media:OK_ME3NHCL_OPTF_POP.LOG

Important Geometric Parameters

(9-7)r(N-H) =1.17767 Â
(9-14)r(N-Cl) = 2.89146 Â
(7-14)r(H-Cl) = 1.71933 Â
(1-4)r(C-H) = 1.07478 Â
(8-10)r(N-C) = 1.47703 Â
(2-5)r(C-H)=1.07442 Â
(2-8)r(C-N)=1.39999 Â

HMim-Cl Molecule a) Scan

HMim-Cl Scan Plot

PES Raw Data Table

Scan Coordinate Â	Total Energy (Hartrees)	Relative Total Energy (kJmol-1)
0.8000000000	-722.5958117770	219.390797
0.9000000000	-722.6503978670	76.07501772
1.0000000000	-722.6727650930	17.34986586
1.1000000000	-722.6793733070	0
1.2000000000	-722.6792906370	0.217050085
1.3000000000	-722.6772128790	5.672203714
1.4000000000	-722.6753243470	10.63054448
1.5000000000	-722.6744432030	12.94398805
1.6000000000	-722.6746286280	12.45715471
1.7000000000	-722.6753546570	10.55096558
1.8000000000	-722.6753493050	10.56501725
1.9000000000	-722.6721372910	18.99816001
2.0000000000	-722.6613012230	47.44825654
2.1000000000	-722.6354468750	115.3288472

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	1-methyl Imidazoliumm chloride 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	-5.7142	-3.2659	-1.6460	-0.0033	-0.0016	0.0018
Low frequencies	45.3690	162.0925	198.8365

logfile:Media:KUSABS_IMIDA_B_OPTF.LOG

Important Geometric Parameters

(5-14) r(H-Cl)=2.13401 Â
(13-14)r(H-Cl)=2.27688 Â
(8-14) r(N-Cl)=3.64967 Â
(8-2) r(N-C)= 1.40258 Â

Optimised Molecule

Calculation data

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	-3.6978	-2.9228	-0.0038	-0.0022	0.0022	2.6495
Low frequencies	52.1557	102.6185	107.1164

Important Geometeric Parameters

(4-17) r(H-Cl) = 2.02997 Â
(8-17) r(N-Cl) = 3.66575 Â

logfile:Media:KUSABS_IMIDA_C_OPTF2.LOG

Ionic Liquid Analysis

Ionic (H-Cl) bond comparisson

Ionic pair molecule	H-Cl Bond	Additional H-Cl bond
HMim-Cl (a)	1.71933 Â
HMim-Cl (b)	2.27688 Â	2.13401 Â
HMim-Cl (c)	2.02997
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 H-bonds compare?

Are these distances representative of a H-bond?

Van der Waals

Will the ionic nature of the ions effect a distance based assessment of H-bonding?

provide a table and comparison of the association energy for a-c

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

provide a chemical diagram of the two protonation states for HMim-Cl graph the MeNH-Cl and HMim-Cl scans on a single PES plot discuss your HMim-Cl PES plot, compare and contrast your results for the MeNH-Cl and HMim-Cl PES

Cationic Analysis

Optimised Molecule

Kusabs_imida_a_cation_optf.png

logfile:Media:KUSABS_IMIDA_A_CATION_OPTF.LOG

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