Wolfeka

to do

• what does she mean by torsion angle
• redo some of the accuracies

Me₃NH Cl molecule

Calculation data

name of submitted log file	KATW_Me3NH-Clactual.log
molecule	Me3NH Cl
method	RB3LYP
basis set	6-31G(d,p)
final energy	-635.31113au
RMS gradient	4.0214e-05au/bohr
point group	C1

The above point group was not set to be C3v, which it should be, so the program assigned it C1.

Item table

Optimizing item table

         Item               Value     Threshold  Converged?
 Maximum Force            0.000126     0.000450     YES
 RMS     Force            0.000032     0.000300     YES
 Maximum Displacement     0.000835     0.001800     YES
 RMS     Displacement     0.000219     0.001200     YES

Frequency item table

         Item               Value     Threshold  Converged?
 Maximum Force            0.000126     0.000450     YES
 RMS     Force            0.000032     0.000300     YES
 Maximum Displacement     0.001285     0.001800     YES
 RMS     Displacement     0.000457     0.001200     YES

Optimised molecule image

3D Me3NH Cl molecule

Key bond distances and angles

• add another decimal point to each

r(N-C) bond distance	1.48Â
r(N-H) bond distance	0.80Â
r(N-Cl) bond distance	3.20Â
r(C-H) bond distance	1.09Â
θ(C-N-C) bond angle	112°
θ(C-N-H) bond angle	106°
θ(H-C-H) bond angle	110°

File history

Media:KATW ME3NH-CLACTUAL.LOG

NH₃BH₃ frequencies

 Low frequencies ---   -3.0077   -0.5001   -0.0059   -0.0053   -0.0047    6.2314
 Low frequencies ---   81.5384   81.6770  183.6441

NH₃BH₃ scan of total energy

Snapshot:

X-Axis: Scan Coordinate

Y-Axis: Total Energy (Hartree)

                 X                   Y
       0.8000000000     -635.2162861320
       0.9000000000     -635.2709452560
       1.0000000000     -635.2930688430
       1.1000000000     -635.2992906270
       1.2000000000     -635.2988745370
       1.3000000000     -635.2968157070
       1.4000000000     -635.2956086330
       1.5000000000     -635.2962523740
       1.6000000000     -635.2987711990
       1.7000000000     -635.3023546920
       1.8000000000     -635.3052254510
       1.9000000000     -635.3042681400
       2.0000000000     -635.2943300920
       2.1000000000     -635.2670421330

Scan of the potential energy surface original graph:

Relative energies

molecule	Energy (au)	Energy (kJ/mol)	3	4	5	6
NH3	-56.557769	-148492	1213	2583	2716	2716
BH3	-26.615324	-69879	E	A1	E	E
NH3BH3	-83.2246894	-218506	14	0	126	126

E(NH3BH3)=

BH₃ molecule

Calculation data

name of submitted log file	BH3_optimization_KATW.log
molecule	BH3
method	RB3LYP
basis set	6-31G(d,p)
final energy	-26.615324au
RMS gradient	2.114e-06au/bohr
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

3D BH molecule

Key bond distances and angles

r(B-H) bond distance	1.19Â
θ(H-B-H) bond angle	120°

File history

Media:BH3 OPTIMIZATION KATW.LOG

BH₃ IR spectrum

BH₃ frequencies

 Low frequencies ---  -11.6940  -11.6861   -6.5543   -0.0006    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

NH₃BH₃ molecule

Calculation data

name of submitted log file	KATW_NH3BH3_opt.log
molecule	NH3BH3
method	RB3LYP
basis set	6-31G(d,p)
final energy	-83.2246894au
RMS gradient	1.264e-06au/bohr
point group	C1

Item table

         Item               Value     Threshold  Converged?
 Maximum Force            0.000002     0.000015     YES
 RMS     Force            0.000001     0.000010     YES
 Maximum Displacement     0.000016     0.000060     YES
 RMS     Displacement     0.000007     0.000040     YES

Optimised molecule image

3D BH molecule

Key bond distances and angles

r(N-H) bond distance	1.02Â
r(B-H) bond distance	1.21Â
θ(H-N-H) bond angle	108°
θ(H-B-H) bond angle	114°
θ(H-B-N) bond angle	105°
θ(H-N-B) bond angle	111°

File history

Media:KATW NH3BH3 OPT.LOG

NH₃BH₃ frequencies

 Low frequencies ---   -2.7658   -2.2718   -0.0013   -0.0013   -0.0010    2.9530
 Low frequencies ---  263.4333  632.9750  638.4461

Lab1 Marking

It's good that you have a working wiki. However, data in your item table don't match the values in the log file, and you have missed to include the torsion angle. If you have any queries, please contact Prof. Hunt.

NH₃ molecule

Calculation data

name of submitted log file	KATW307_nh3opt1.log
molecule	NH3
method	RB3LYP
basis set	6-31G(d,p)
final energy	-56.557769au
RMS gradient	1.53e-07au/bohr
point group	C3v

Item table

         Item               Value     Threshold  Converged?
 Maximum Force            0.000002     0.000015     YES
 RMS     Force            0.000001     0.000010     YES
 Maximum Displacement     0.000010     0.000060     YES
 RMS     Displacement     0.000006     0.000040     YES

Optimised molecule image

3D NH molecule

Key bond distances and angles

r(N-H) bond distance	1.02Â
θ(H-N-H) bond angle	106°

File history

Media:KATW307 NH3OPT1.LOG

NH₃ IR spectrum

NH₃ frequencies

 Low frequencies ---   -5.6864   -3.6131   -3.6124    0.0022    0.0047    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

NH₃ charges

Atom	Charge (e)
N	-1.13
H3	0.38

N₂F₂ molecule

Calculation data

name of submitted log file	KATW307_n2f2opt1.log
molecule	N2F2
method	RB3LYP
basis set	6-31G(d,p)
final energy	-309.0124au
RMS gradient	1.218e-06au/bohr
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     0.000003     0.000060     YES
 RMS     Displacement     0.000001     0.000040     YES

Optimised molecule image

3D NH molecule

Key bond distances and angles

r(N-N) bond distance	1.22Â
r(N-F) bond distance	1.39Â
θ(N-N-F) bond angle	114°

File history

Media:KATW307 N2F2OPT1.log

N₂F₂ IR spectrum

N₂F₂ frequencies

 Low frequencies ---   -0.0011    0.0008    0.0019    3.4929    4.3715    5.1621
 Low frequencies ---  347.8732  561.2460  771.6039

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 units)	1	0	75	75	81	21

N₂F₂ charges

Atom	Charge (e)
N2	0.22
F2	-0.22

Questions and answers

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

The program running the optimization works under an assumption of what the length of the F and N atoms should be, and since the optimization put their bond length as longer than this assumed value, the program did not include a bond there. As the atoms get closer the program will include a bond between the atoms.

2. For your IR analysis how many vibrations are expected from the 3N-6 rule?

3N-6 where N is the number of atoms would give N=4 and 3(4)-6= 6 vibrational modes, this is consistent with the number of vibrational modes obtained in the optimization as well.

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

The A1 vibrational mode at 348 cm^-1 and the A2 vibrational mode at 561 cm^-1 both have an intensity of close to zero and were not detected by the IR

4. For your IR analysis which vibration is the asymmetric N-F stretch?

Vibrational mode 3

5. For your IR analysis what is the nature of the highest energy vibration?

Symmetrical N-N bond stretching, vibrational mode 6

6. Which MOs are core orbital MOs?

The 1-4 molecular orbitals which are only tied to their respective nuclei and not involved in bonding

7. Provide a picture of MO 9 and beside it the LCAO diagram