Lab:Shakeschel

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NH₃ Molecule

Calculation data

Name of submitted log file	Cshake_nh3_optf_pop.log
Molecule	NH3
Method	RB3LYP
Basis set	6-31G(d,p)
Final energy	-56.557769
RMS gradient	0.000000
Point group	C3v

Convergence

Confirm forces and displacements are converged

         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

Confirming a minimum, the CoM motion is near zero

 Low frequencies ---   -5.6864   -3.6131   -3.6124    0.0008    0.0045    0.0162
 Low frequencies --- 1089.3674 1693.9284 1693.9284

Optimised molecule image

Static image:

Jmol rotateable molecule

logfile: Media:CSHAKE_NH3_OPTF_POP.LOG

optimised NH molecule

Important geometric parameters

Optimised bond distance and angle for NH₃

Coord	Value
r(N-H)	1.02Â
θ(H-N-H)	106°

Vibrations

Table of vibrations:

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 units)	145	14	14	1	0	0

Copy of the computed spectrum from gaussview:

1. How many modes do you expect from the 3N-6 rule?

6 modes

2. How many bands do we see in the computed spectrum of gaseous ammonia?

2 bands

3. Which modes are degenerate (ie have the same energy)?

Modes 2 and 3 are degenerate, and Modes 5 and 6 are degenerate

4. Some modes have essentially no intensity, which ones?

Modes 4, 5 & 6

5. Why are there fewer modes than we expect from the 3N-6 rule?

Modes 4, 5, & 6 have too low of an intensity to be seen, and modes 2 and 3 are degenerate; they show up at the same wavenumber. Therefore, mode 2/3 is seen, as well as mode 1 is seen. Making for only two modes seen.

6. Which modes are "bending" vibrations and which are "bond stretch" vibrations?

Bending: 1, 2, 3. Bond stretching: 4, 5, 6

7. One mode is known as the "umbrella" mode, which one is this?

Mode 1

8. Why is the umbrella mode so intense?

It has the greatest change in dipole moment as the shape vibrates through the nitrogen atom moving in the opposite direction of the hydrogen atoms

Charges

Image of NBO charges colour coded red for negative and green for positive, the charge range is ±1.125e

Table of NH₃ charges:

Atom	Charge
N	-1.13
H	+0.38

Molecular Orbitals

The real 2a1 MO	The LCAO MO

Project Molecule Acetate

Calculation data

Name of submitted log file	CSHAKE_ACETATE_OPTF_POP.LOG
Molecule	acetate
Method	RB3LYP
Basis set	6-31G(d,p)
Final energy	-228.502197
RMS gradient	0.000003
Point group	Cs

Convergence

         Item               Value     Threshold  Converged?
 Maximum Force            0.000009     0.000015     YES
 RMS     Force            0.000002     0.000010     YES
 Maximum Displacement     0.000014     0.000060     YES
 RMS     Displacement     0.000007     0.000040     YES

 Low frequencies ---   -6.5511   -4.6849   -1.7453   -0.0015   -0.0012   -0.0009
 Low frequencies ---   28.7821  417.2751  601.5327

Jmol rotateable optimised molecule

logfile: Media:CSHAKE_ACETATE_OPTF_POP.LOG

optimised NH molecule

Vibrations

Table of vibrations:

mode	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15
wavenumber cm-1	29	417	602	612	863	985	1021	1318	1374	1481	1495	1756	2998	3061	3084
symmetry	A"	A'	A"	A'	A'	A'	A"	A'	A'	A'	A"	A'	A'	A"	A'
intensity (arbitrary units)	0	1	4	4	72	3	8	13	270	6	0	423	45	78	92

Copy of the computed spectrum from gaussview:

What is the nature of the lowest energy vibration?

Mode 1: CH₃ rotation

Which vibrations will not show up in an experimental spectrum (give the mode numbers)?

Modes: 1, 2, 3, 4, 6, 7, 8, 10, 11 as their intensities are too low

Which bond vibrations occur around 3000 cm-1?

2998 cm_-1: Mode 13, symmetric stretching of all C-H bonds

3061 cm_-1: Mode 14, asymmetric stretch of 2 C-H bonds

3083 cm_-1: Mode 15, asymmetric stretch all 3 C-H bonds (2 symmetric, 1 asymmetric)

What type of vibration is the intense peak at around 1700 cm-1?

Mode 12: asymmetric stretching C-O, symmetric bending C-C-H₃

What type of vibration is the intense peak at around 1400 cm-1?

Mode 9: symmetric stretch C-C, symmetric stretch C-O, symmetric bending C-H₃

Charges

Image of NBO charges colour coded red for negative and green for positive, the charge range is +-0.799e

Table of acetate charges:

Atom	Charge
C1	+0.78
C4	-0.79
O2	-0.80
O3	-0.79
H	+0.20

Why the charges on the two C atoms are so different?

C1 is bonded to two oxygen atoms that are more electronegative (pulling electron density away from carbon), making C1 a positive charge. C4 is bonded to three hydrogens for which carbon is more electronegative, therefore exhibits a negative charge.

Molecular Orbitals

Which MOs are core orbital MOs?

MOs 1, 2, 3 & 4

Provide a picture of MO 7

Which occupied orbitals have pseudo-pi symmetry? ie which orbitals change phase through the Cs plane of the molecule?

MOs 9, 13 & 14

Which atoms primarily contribute to the HOMO?

The oxygen atoms

Which orbital is depicted below? draw the LCAO diagram for this orbital

MO 11 - The real MO	The LCAO MO