Difference between revisions of "Marshaluke"

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 +
==Comments==
 +
You've done a great job overall well done!  However, your answers could have been elaborated more thoroughly. If you have any queries or want more detailed feedback on your computational lab, please contact Prof. Hunt.
 +
 
==NH<sub>3</sub> Molecule==
 
==NH<sub>3</sub> Molecule==
 
===Calculation Data===
 
===Calculation Data===
Line 37: Line 40:
 
logfile: [[Media:LAM_OPT_NH3_POP.LOG]]
 
logfile: [[Media:LAM_OPT_NH3_POP.LOG]]
 
<jmol><jmolApplet>
 
<jmol><jmolApplet>
−
   <title>Optimised NH<sub>3</sub> Molecule</title>
+
   <title>Optimised NH3 Molecule</title>
 
   <color>#67CCFF</color>
 
   <color>#67CCFF</color>
 
   <size>249</size>
 
   <size>249</size>
Line 58: Line 61:
 
|Mode||1||2||3||4||5||6
 
|Mode||1||2||3||4||5||6
 
|-
 
|-
−
|Wavenumber(cm<sup>-1</sup>)|| 1089.37|| 1693.93|| 1693.93|| 3461.38|| 3589.93|| 3589.93
+
|Wavenumber(cm<sup>-1</sup>)|| 1089|| 1694|| 1694|| 3461|| 3590|| 3590
 
|-
 
|-
 
|Symmetry|| A<sub>1</sub>|| E|| E|| A<sub>1</sub>|| E|| E
 
|Symmetry|| A<sub>1</sub>|| E|| E|| A<sub>1</sub>|| E|| E
Line 70: Line 73:
  
 
====Questions and Answers====
 
====Questions and Answers====
 +
1. how many modes do you expect from the 3N-6 rule?
 +
 +
3N-6 where N=the number of atoms, N=4 so 12-6=6, therefore we expect 6 modes which we have
 +
 +
2. how many bands (peaks) do you see in the computed spectrum of gaseous ammonia?
 +
 +
only TWO vibrational bands in the spectrum! We calculate ALL the vibrations, unlike experiments where you can only "see" some of the bands due to specific vibrations.
 +
 +
3. which modes are degenerate (ie have the same energy)?
 +
 +
the E modes at 1694 and 3590 cm-1 each have 2 components which are degenerate, ie have the same energy
 +
 +
4. which modes have essentially no intensity?
  
 +
the A1 3461 cm-1 and E 3590 cm-1 modes have essentially no intensity. Modes must include a dipole moment change to be "allowed" in an IR spectrum, both of these vibrations must have no dipole moment change
 +
 +
5. why are there fewer modes in the spectrum than you would predict from the 3N-6 rule?
 +
 +
some vibrations have an essentially zero intensity, and two of the modes are degenerate and so only appear as a single peak
 +
 +
6. which modes are "bending" vibrations and which are "bond stretch" vibrations?
 +
 +
stretches => high energy these are modes 4,5,6, bends => low energy these are modes 1,2,3
 +
 +
7. one mode is known as the "umbrella" mode, which one is this?
 +
 +
mode 1 is the umbrella mode, for obvious reasons!
 +
 +
8. why is the umbrella mode so intense?
 +
 +
this mode is very intense because there is a large dipole moment change
  
 
===Charges===
 
===Charges===
Line 94: Line 127:
 
|}
 
|}
  
−
==Project Molecule==
+
==Project Molecule: N<sub>2</sub>F<sub>2</sub>==
 
===Calculation Data===
 
===Calculation Data===
 
{| class="wikitable"
 
{| class="wikitable"
−
|Log file name|| LAM_N2F2_OPT_POP.LOG
+
|Log file name|| LAM_N2F2_OPT_POP_fine.LOG
 
|-
 
|-
 
|Molecule|| N<sub>2</sub>F<sub>2</sub>
 
|Molecule|| N<sub>2</sub>F<sub>2</sub>
Line 107: Line 140:
 
|Final Energy|| -309.012413
 
|Final Energy|| -309.012413
 
|-
 
|-
−
|RMS Gradient|| 0.000004
+
|RMS Gradient|| 0.000003
 
|-
 
|-
 
|Point Group|| C2v
 
|Point Group|| C2v
Line 115: Line 148:
 
<pre>  
 
<pre>  
 
         Item          Value        Threshold  Converged?
 
         Item          Value        Threshold  Converged?
−
Maximum Force          0.000011     0.000015      YES
+
Maximum Force          0.000007     0.000015      YES
−
RMS    Force          0.000006     0.000010      YES
+
RMS    Force          0.000004     0.000010      YES
−
Maximum Displacement  0.000025     0.000060      YES
+
Maximum Displacement  0.000014     0.000060      YES
−
RMS    Displacement  0.000015     0.000040      YES
+
RMS    Displacement  0.000010     0.000040      YES
 
</pre>
 
</pre>
  
 
<pre>  
 
<pre>  
−
Low Frequencies-- -1.0715, -0.0014, -0.0011, -0.0009, 2.6488, 5.3711
+
Low Frequencies-- -0.0023, -0.0018, -0.0016, 3.7873, 4.1532, 5.0933
−
Low Frequencies-- 347.8610, 561.2419, 771.5834
+
Low Frequencies-- 347.8869, 561.2422, 771.6024
 
</pre>
 
</pre>
  
 
===Optimised Structure Image===
 
===Optimised Structure Image===
−
[[File:LAM_N2F2_OPT.png|150px]]
+
[[File:LAM_N2F2_OPT.png|300px]]
 +
 
 +
Why no bond between N and F?
 +
 
 +
Because Gaussview has a calculated distance for which a bond is formed, the calculated optimal distance between the fluorine and nitrogen is greater than the Gaussview specification removing the bond. The bond is still able to form just not within Gaussviews limits
  
 
===Jmol Rotateable Structure===
 
===Jmol Rotateable Structure===
−
logfile: [[Media:LAM_OPT_NH3_POP.LOG]]
+
logfile: [[Media:LAM N2F2 OPT POP fine.LOG]]
 
<jmol><jmolApplet>
 
<jmol><jmolApplet>
−
   <title>Optimised N<sub>2</sub>F<sub>2</sub> Molecule</title>
+
   <title>Optimised N2F2 Molecule</title>
−
   <color>#67CCFF</color>
+
   <color>#ADD8E6</color>
 
   <size>249</size>
 
   <size>249</size>
−
   <uploadedFileContents>LAM_OPT_NH3_POP.LOG</uploadedFileContents>
+
   <uploadedFileContents>LAM_N2F2_OPT_POP.LOG</uploadedFileContents>
 
</jmolApplet></jmol>
 
</jmolApplet></jmol>
  
Line 143: Line 180:
 
|Coord||Value
 
|Coord||Value
 
|-
 
|-
−
|r(N-H)||1.02&Aring;
+
|r(N=N)||1.22&Aring;
 +
|-
 +
|r(N-F)||1.39&Aring;
 +
|-
 +
|&theta;(F-N=N)||114&deg;
 
|-
 
|-
−
|&theta;||106&deg;
+
|&theta;(F-N=N-F)||0&deg;
 
|}
 
|}
  
Line 153: Line 194:
 
|Mode||1||2||3||4||5||6
 
|Mode||1||2||3||4||5||6
 
|-
 
|-
−
|Wavenumber(cm<sup>-1</sup>)|| 1089.37|| 1693.93|| 1693.93|| 3461.38|| 3589.93|| 3589.93
+
|Wavenumber(cm<sup>-1</sup>)|| 348|| 561|| 772|| 949|| 987|| 1637
 
|-
 
|-
−
|Symmetry|| A<sub>1</sub>|| E|| E|| A<sub>1</sub>|| E|| E
+
|Symmetry|| A<sub>1</sub>|| A<sub>2</sub>|| B<sub>2</sub>|| A<sub>1</sub>|| B<sub>2</sub>|| A<sub>1</sub>
 
|-
 
|-
−
|Intensity(arbitrary units)|| 145|| 14|| 14|| 1|| 0|| 0
+
|Intensity(arbitrary units)|| 1|| 0|| 75|| 75|| 81|| 21
 
|}
 
|}
  
 
Gaussian copy of IR spectra:
 
Gaussian copy of IR spectra:
  
−
[[File:LAM_OPT_NH3_POP_ir.png|400px]]
+
[[File:LAM_N2F2_OPT_POP_ir.png|400px]]
  
−
====Questions and Answers====
+
====Vibrations Questions and Answers====
−
1. how many modes do you expect from the 3N-6 rule?
+
1. How many vibrations are expected from the 3N-6 rule?
−
With N being the no. of atoms present, this being 4 in this case. Means that the modes of this molecule would be equal to (3x4)-6 = 6. Suggesting correctly that there are 6 modes
 
  
−
2. how many bands (peaks) do you see in the computed spectrum of gaseous ammonia?
+
Where N is the number of atoms it's (3x4)-6= 6. Which is accurate to the rest of the results
−
There are only two bands present as the other modes have little to no intensity
 
  
−
3. which modes are degenerate (ie have the same energy)?
+
2. Why are there only 4 peaks in the IR spectrum?
−
Modes 2 & 3, as well as 5 & 6 are degenerate.
 
  
−
4. which modes have essentially no intensity?
+
Because, two of the vibrations have very muted intensities making the peaks inseparable from the baseline.
−
Modes 4-6 have intensities lesser than 2 which renders them insignificant on the spectrum
 
  
−
5. why are there fewer modes in the spectrum than you would predict from the 3N-6 rule?
+
3. Which vibration is the asymmetric N-F stretch?
−
Because the degeneracy of some of them cause them to overlap and intensify as well as some of them
 
−
not being intense enough to visualise
 
  
−
6. which modes are "bending" vibrations and which are "bond stretch" vibrations?
+
Mode 3 with B2 symmetry is the asymmetric N-F stretching vibration.
−
1-3 are bending vibrations, while 4-6 are stretching vibrations as stretching is high energy and rare.
 
  
−
7. one mode is known as the "umbrella" mode, which one is this?
+
4. What is the nature of the highest energy vibration?
−
This is mode 1 as it's vibration looks similar to that of an umbrella caught in wind and at normal state.
 
  
−
8. why is the umbrella mode so intense?
+
It is stretching occurring between the two nitrogen atoms as they are the strongest bond as well as stretching being a high energy vibration results in this vibration being the highest in energy.
−
It causes a large dipole moment change
 
  
 
===Charges===
 
===Charges===
−
Image of NBO charges colour coded, red for negative, green for positive. Next to it is the scale and reference for the charge distribution. The scale is -1.125 to 1.125
+
Image of NBO charges colour coded, red for negative, green for positive. Next to it is the scale and reference for the charge distribution. The scale is -0.215 to 0.215
  
−
[[File:LAM_OPT_NH3_CHARGE.png|400px]]
+
[[File:N2F2_LAM_OPT_charge_NBO.png|400px]]
−
[[File:Colourrange.PNG|200px]]
+
[[File:N2F2_scale.PNG|200px]]
  
−
Table of NH<sub>3</sub> charges:
+
Table of N<sub>2</sub>F<sub>2</sub> charges:
 
{| class="wikitable"
 
{| class="wikitable"
 
|Atom||Charge
 
|Atom||Charge
 
|-
 
|-
−
|N||-1.13
+
|N||0.22
 
|-
 
|-
−
|H||0.38
+
|F||-0.22
 
|}
 
|}
  
 
===Molecular Orbitals===
 
===Molecular Orbitals===
 
{| class="wikitable"
 
{| class="wikitable"
−
|Real 2A1 Orbital||LCAO Orbital
+
|Real Ninth Orbital||LCAO Orbital
 
|-
 
|-
−
|[[File:LAM_OPT_NH3_POP_Orbitals.jpg|200px]]||[[File:LCAO.PNG|200px]]
+
|[[File:LAM_N2F2_OPT_MO9.png|200px]]||[[File:LCAO_N2F2_LAM.PNG|200px]]
 
|}
 
|}
 +
 +
====Orbital Questions and Answers====
 +
Which MO's are core orbital MO's?
 +
 +
Molecular orbitals 1-4 are core molecular orbitals as they don't merge with any other orbital, suggesting no bonding taking place which is characteristic of a core MO.

Latest revision as of 04:52, 11 May 2025

Comments

You've done a great job overall well done! However, your answers could have been elaborated more thoroughly. If you have any queries or want more detailed feedback on your computational lab, please contact Prof. Hunt.

NH3 Molecule

Calculation Data

Log file name LAM_OPT_NH3_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-- -5.6864, -3.6131, -3.6124, -0.0008, 0.0047, 0.0163
Low Frequencies-- 1089.3674, 1693.9284, 1693.9284

Optimised Structure Image

LAM NH3 OPTF.png

Jmol Rotateable Structure

logfile: Media:LAM_OPT_NH3_POP.LOG

Optimised NH3 Molecule

Important Geometric Parameters

Optimised bond angle and distance for NH3

Coord Value
r(N-H) 1.02Å
θ 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

Gaussian copy of IR spectra:

LAM OPT NH3 POP ir.png

Questions and Answers

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

3N-6 where N=the number of atoms, N=4 so 12-6=6, therefore we expect 6 modes which we have

2. how many bands (peaks) do you see in the computed spectrum of gaseous ammonia?

only TWO vibrational bands in the spectrum! We calculate ALL the vibrations, unlike experiments where you can only "see" some of the bands due to specific vibrations.

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

the E modes at 1694 and 3590 cm-1 each have 2 components which are degenerate, ie have the same energy

4. which modes have essentially no intensity?

the A1 3461 cm-1 and E 3590 cm-1 modes have essentially no intensity. Modes must include a dipole moment change to be "allowed" in an IR spectrum, both of these vibrations must have no dipole moment change

5. why are there fewer modes in the spectrum than you would predict from the 3N-6 rule?

some vibrations have an essentially zero intensity, and two of the modes are degenerate and so only appear as a single peak

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

stretches => high energy these are modes 4,5,6, bends => low energy these are modes 1,2,3

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

mode 1 is the umbrella mode, for obvious reasons!

8. why is the umbrella mode so intense?

this mode is very intense because there is a large dipole moment change

Charges

Image of NBO charges colour coded, red for negative, green for positive. Next to it is the scale and reference for the charge distribution. The scale is -1.125 to 1.125

LAM OPT NH3 CHARGE.png Colourrange.PNG

Table of NH3 charges:

Atom Charge
N -1.13
H 0.38

Molecular Orbitals

Real 2A1 Orbital LCAO Orbital
LAM OPT NH3 POP Orbitals.jpg LCAO.PNG

Project Molecule: N2F2

Calculation Data

Log file name LAM_N2F2_OPT_POP_fine.LOG
Molecule N2F2
Method RB3LYP
Basis Set 6-31G(d,p)
Final Energy -309.012413
RMS Gradient 0.000003
Point Group C2v

Item Table

 
        Item           Value        Threshold  Converged?
Maximum Force          0.000007     0.000015      YES
RMS     Force          0.000004     0.000010      YES
Maximum Displacement   0.000014     0.000060      YES
RMS     Displacement   0.000010     0.000040      YES

 
Low Frequencies-- -0.0023, -0.0018, -0.0016, 3.7873, 4.1532, 5.0933
Low Frequencies-- 347.8869, 561.2422, 771.6024

Optimised Structure Image

LAM N2F2 OPT.png

Why no bond between N and F?

Because Gaussview has a calculated distance for which a bond is formed, the calculated optimal distance between the fluorine and nitrogen is greater than the Gaussview specification removing the bond. The bond is still able to form just not within Gaussviews limits

Jmol Rotateable Structure

logfile: Media:LAM N2F2 OPT POP fine.LOG

Optimised N2F2 Molecule

Important Geometric Parameters

Optimised bond angle and distance for N2F2

Coord Value
r(N=N) 1.22Å
r(N-F) 1.39Å
θ(F-N=N) 114°
θ(F-N=N-F) 0°

Vibrations

Table of vibrations:

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

Gaussian copy of IR spectra:

LAM N2F2 OPT POP ir.png

Vibrations Questions and Answers

1. How many vibrations are expected from the 3N-6 rule?

Where N is the number of atoms it's (3x4)-6= 6. Which is accurate to the rest of the results

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

Because, two of the vibrations have very muted intensities making the peaks inseparable from the baseline.

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

Mode 3 with B2 symmetry is the asymmetric N-F stretching vibration.

4. What is the nature of the highest energy vibration?

It is stretching occurring between the two nitrogen atoms as they are the strongest bond as well as stretching being a high energy vibration results in this vibration being the highest in energy.

Charges

Image of NBO charges colour coded, red for negative, green for positive. Next to it is the scale and reference for the charge distribution. The scale is -0.215 to 0.215

N2F2 LAM OPT charge NBO.png N2F2 scale.PNG

Table of N2F2 charges:

Atom Charge
N 0.22
F -0.22

Molecular Orbitals

Real Ninth Orbital LCAO Orbital
LAM N2F2 OPT MO9.png LCAO N2F2 LAM.PNG

Orbital Questions and Answers

Which MO's are core orbital MO's?

Molecular orbitals 1-4 are core molecular orbitals as they don't merge with any other orbital, suggesting no bonding taking place which is characteristic of a core MO.

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