ChemWiki - User contributions [en]

MRD:sk4915

2017-05-04T13:46:16Z

Sk4915:

== Exercise 1: H + H2 system ==

''What value does the total gradient of the potential energy surface have at a minimum and at a transition structure? Briefly explain how minima and transition structures can be distinguished using the curvature of the potential energy surface.''

The gradient at both the minima and at transition structures is zero. The minima and transition structures can be distinguished as transition structures only occur at maxima.
[[File:Sk4915InternucleardistanceTime.png|thumb|This plot shows internuclear distance vs time. All distances remain constant indicating that the system is static, in this case at the transition state.]]

''Report your best estimate of the transition state position (rts) and explain your reasoning illustrating it with a “Internuclear Distances vs Time” screenshot for a relevant trajectory.''

Transition state position = 0.9077425 A. It can be seen that the internuclear distance doesn't appear to change when the system is started with r1 = r2 = 0.9077425 and with p1 = p2 = 0. Furthermore, a kinetic energy-time graph shows the small vibration about the bond equilibrium with a total kinetic energy of 1.8e-15 J.

''Comment on how the mep and the trajectory you just calculated differ.''

With the starting conditions as r1 = rts + 0.01, r2 = rts and p1 = p2 = 0, the same calculation to show the surface plot for the reaction was run with two different methods. When run in mep the trajectory follows the valley floor very closely and doesn't oscillate unlike the dynamics trajectory which does oscillate.
When the r1 and r1 are switched the reaction proceed in the opposite direction.

Table to show how initial momentum affects trajectories, making them reactive or unreactive, with initial positions r1 = 0.74 and r2 = 2.0:
{| class="wikitable"
|-
! p1
! p2
! Reactivity
! Trajectory
|-
| -1.25
| -2.5
| Reactive
|[[File:Sk4915surfaceplot1.png|thumb|The reaction proceeds through the lowest energy route with some small oscillations as a result of the atomic vibration.]]
|-
| -1.5
| -2.0
| Unreactive
|[[File:Sk4915surfaceplot2.png|thumb|The kinetic energy of the reactants is too high while r1 is too short for a reaction to occur so they bounce off each other.]]
|-
| -1.5
| -2.5
| Reactive
|[[File:Sk4915surfaceplot3.png|thumb|The reactants take the lowest energy route, with some vibration, to form the products.]]
|-
| -2.5
| -5.0
| Unreactive
|[[File:Sk4915surfaceplot4.png|thumb|The unbonded atom doesn't have enough energy to react however the collision does increase the vibration of the bonded atoms.]]
|-
| -2.5
| -5.2
| Reactive
|[[File:Sk4915surfaceplot5.png|thumb|The unbonded H has enough momentum to get close enough to the bonded pair and react. The high initial momentum causes the products vibrate more strongly.]]
|}

''State what are the main assumptions of Transition State Theory. Given the results you have obtained, how will Transition State Theory predictions for reaction rate values compare with experimental values?''

Transition state theory assumes that nuclei behave according to classical physics and ignores quantum effect such as tunneling which can have significant effects for reactions with low activation energies. This could mean that reaction rates predicted with transition state theory will be lower than experimental values as tunneling would increase the number of particles that cross the potential barrier. Further, transition state theory assumes that each step in the reaction is long lived enough to reach a Boltzmann distribution of energies. Experimentally this may not always be the case so some steps will have different energies than the theory predicts, changing the speed at which products are formed and also possibly changing which products are formed.

== Exercise 2: F - H - H system ==

''Classify the F + H2 and H + HF reactions according to their energetics (endothermic or exothermic). How does this relate to the bond strength of the chemical species involved?''

F + H2 is an exothermic reaction and H + HF is endothermic. This is because more energy is released when an F-H bond is formed than is needed to break an H-H indicating that the F-H bond is the much stronger bond type.

''Locate the approximate position of the transition state.''

For the reaction F + H2, according to the Hammond postulate the transition state will more closely resemble the reactants than the products as the reaction is exothermic. As a result it can be seen that the transition state occurs at approximately r1 = 0.80, r2 = 0.75.
Additionally, by looking at the potential energy surface it can be determined that the activation energy for the F + H2 reaction is 0.2 kcalmol-1 and 30.2 kcalmol-1 for FH + H reaction.

''In light of the fact that energy is conserved, discuss the mechanism of release of the reaction energy. How could this be confirmed experimentally?''

The reaction F + H2 is exothermic which means that some of the kinetic energy used to cause the reaction is stored in the newly formed F-H bond, which is much stronger than the previous H-H bond. To confirm experimentally that this is where the energy is going, the reverse endothermic reaction could be carried out where the amount energy that must be added is equal to the energy 'lost' during the exothermic reaction.

''Discuss how the distribution of energy between different modes (translation and vibration) affect the efficiency of the reaction, and how this is influenced by the position of the transition state.''

For reactions with early transition states the reaction efficiency will be greater when there is
initially more translational energy than vibrational energy as the reactants quite closely resemble the transition state and so can rearrange to form the transition state with little additional energy. Therefore, the close proximity of the reactants is more valued more highly and more collisions will occur when the translational energy is higher. The inverse is true for reactions with late transition states.

MRD:sk4915

2017-05-04T13:06:49Z

Sk4915:

File:Sk4915surfaceplot5.png

2017-05-04T12:30:06Z

Sk4915:

File:Sk4915surfaceplot4.png

2017-05-04T12:29:44Z

Sk4915:

File:Sk4915surfaceplot3.png

2017-05-04T12:29:31Z

Sk4915:

File:Sk4915surfaceplot2.png

2017-05-04T12:26:51Z

Sk4915:

File:Sk4915surfaceplot1.png

2017-05-04T12:22:19Z

Sk4915:

File:Sk4915KEtime.png

2017-05-04T12:21:30Z

Sk4915:

File:Sk4915InternucleardistanceTime.png

2017-05-04T12:12:00Z

Sk4915: This plot shows internuclear distance vs time. All distances remain constant indicating that the system is static, in this case at the transition state.

This plot shows internuclear distance vs time. All distances remain constant indicating that the system is static, in this case at the transition state.

MRD:sk4915

2017-05-04T11:45:13Z

Sk4915:

MRD:sk4915

2017-05-04T11:37:32Z

Sk4915:

MRD:sk4915

2017-05-02T20:07:59Z

Sk4915:

MRD:sk4915

2017-05-02T16:05:38Z

Sk4915:

''What value does the total gradient of the potential energy surface have at a minimum and at a transition structure? Briefly explain how minima and transition structures can be distinguished using the curvature of the potential energy surface.''

The gradient at both the minima and at transition structures is zero. The minima and transition structures can be distinguished as transition structures only occur at maxima.

''Report your best estimate of the transition state position (rts) and explain your reasoning illustrating it with a “Internuclear Distances vs Time” screenshot for a relevant trajectory.''

Transition state position = 0.9077425 A. It can be seen that the internuclear distance doesn't appear to change when the system is started with r1 = r2 = 0.9077425 and with p1 = p2 = 0. Furthermore, a kinetic energy-time graph shows the small vibration about the bond equilibrium with a total kinetic energy of 1.8e-15 J.

''Comment on how the mep and the trajectory you just calculated differ.''
With the starting conditions as r1 = rts + 0.01, r2 = rts and p1 = p2 = 0, the same calculation to show the surface plot for the reaction was run with two different methods. When run in mep the trajectory follows the valley floor very closely and doesn't oscillate unlike the dynamics trajectory which does oscillate.
When the r1 and r1 are switched the reaction proceed in the opposite direction.

Table to show how initial momentum affects trajectories, making them reactive or unreactive, with initial positions r1 = 0.74 and r2 = 2.0:
{| class="wikitable"
|-
! p1
! p2
! Reactivity
! Trajectory
|-
| -1.25
| -2.5
| Reactive
|
|-
| -1.5
| -2.0
| Unreactive
|
|-
| -1.5
| -2.5
|
|
|-
| -2.5
| -5.0
|
|
|-
| -2.5
| -5.2
|
|
|}

MRD:sk4915

2017-05-02T15:45:03Z

Sk4915: Created page with "''What value does the total gradient of the potential energy surface have at a minimum and at a transition structure? Briefly explain how minima and transition structures can..."

''What value does the total gradient of the potential energy surface have at a minimum and at a transition structure? Briefly explain how minima and transition structures can be distinguished using the curvature of the potential energy surface.''

The gradient at both the minima and at transition structures is zero. The minima and transition structures can be distinguished as transition structures only occur at maxima.

''Report your best estimate of the transition state position (rts) and explain your reasoning illustrating it with a “Internuclear Distances vs Time” screenshot for a relevant trajectory.''

Transition state position = 0.9077425 A. It can be seen that the internuclear distance doesn't appear to change when the system is started with r1 = r2 = 0.9077425 and with p1 = p2 = 0. Furthermore, a kinetic energy-time graph shows the small vibration about the bond equilibrium with a total kinetic energy of 1.8e-15 J.

''Comment on how the mep and the trajectory you just calculated differ.''
With the starting conditions as r1 = rts + 0.01, r2 = rts and p1 = p2 = 0, the same calculation to show the surface plot for the reaction was run with two different methods. When run in mep the trajectory follows the valley floor very closely and doesn't oscillate unlike the dynamics trajectory which does oscillate.
When the r1 and r1 are switched the reaction proceed in the opposite direction.

Table to show how initial momentum affects trajectories, making them reactive or unreactive:
{| class="wikitable"
|-
! p1
! p2
! Reactivity
! Surface Plot
|-
| -1.25
| -2.5
|
|
|-
| -1.5
| -2.0
|
|
|-
| -1.5
| -2.5
|
|
|-
| -2.5
| -5.0
|
|
|-
| -2.5
| -5.2
|
|
|}

Rep:Mod:AMZ1470

2016-02-26T12:51:53Z

Sk4915:

==NH3 Molecule==

===Key Information===

N-H bond length = 1.01798 A

H-N-H bond angle = 105.74115 degrees

Calculation Method: RB3LYP

Basis Set: 6-31G(d,p)

Final Energy: -56.55776873 au

RMS Gradient: 0.00000485 au

Point Group: C3V

<pre>

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
Predicted change in Energy=-5.986259D-10
</pre>

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>sk4915 NH3 optf pop.log</uploadedFileContents>
</jmolApplet></jmol>

Link to optimized file: [[File:Sk4915_NH3_optf_pop.log| optimized file]]

===Vibration===

[[File:NH3 vibration.png|300px|thumb|Vibrational modes in an NH3 molecule.]]

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

6

'''Which modes are degenerate (i.e have the same energy)?'''

Modes 2 & 3 are degenerate. Modes 5 & 6 also are degenerate.

'''Which modes are "bending" vibrations and which are "bond stretch" vibrations?'''

Modes 1, 2 & 3 are bending vibrations and modes 4, 5 & 6 are bond stretch vibrations.

'''Which mode is highly symmetric?'''

Mode 4.

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

Mode 1.

'''How many bands would you expect to see in an experimental spectrum of gaseous ammonia?'''

Two bands.

===Charge Distribution===

Charge on the N-atom: -1.125

Charge on the H-atoms: 0.375

These charges match expectations as Nitrogen is the most electronegative atom in this molecule and so more strongly attracts the bonding electrons, pulling the electrons further away from the Hydrogen atoms. Therefore, there is a slight negative charge on the Nitrogen and slight positive charges on the Hydrogen atoms.

==H2 Molecule==

===Key Information===

H-H bond length = 0.74279 A

Calculation Method: RB3LYP

Basis Set: 6-31G(d,p)

Final Energy: -1.17853936 au

RMS Gradient: 0.00000017 au

Point Group: D*H

<pre>

Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000001 0.001200 YES
Predicted change in Energy=-1.164080D-13
</pre>

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SK4915_H2.LOG</uploadedFileContents>
</jmolApplet></jmol>

Link to optimized file: [[File:SK4915_H2.LOG| optimized file]]

===Vibration===

[[File:H2 vibration.png|300px]]

Vibrational modes in an H2 molecule.

===Charge Distribution===

Charge on the H-atoms: 0.00 C

Both atoms in this molecule are identical so there is no dipole.

==N2 Molecule==

===Key Information===

N-N bond length = 1.09200 A

Calculation Method: RB3LYP

Basis Set: 6-31G(d,p)

Final Energy: -109.52359111 au

RMS Gradient: 0.02473091 au

Point Group: D*H

<pre>

Item Value Threshold Converged?
Maximum Force 0.000001 0.000450 YES
RMS Force 0.000001 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000000 0.001200 YES
Predicted change in Energy=-3.400935D-13
</pre>

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SK4915_N2.LOG</uploadedFileContents>
</jmolApplet></jmol>

Link to optimized file: [[File:SK4915_N2.LOG| optimized file]]

===Vibration===

[[File:N2 vibration.png|300px]]

Vibrational modes in an N2 molecule.

===Charge Distribution===

Charge on the N-atom: 0.00 C

Both atoms in this molecule are identical so there is no dipole.

==Energy Calculations==

'''Reaction:'''

'''N2 + 3H2 -> 2NH3'''

E(NH3) = -56.55776873 au

2*E(NH3) = -113.1155375 au

E(N2) = -109.52359111 au

E(H2) = -1.17853936 au

3*E(H2) = -3.53561808 au

ΔE = 2*E(NH3) - [E(N2) + E(H2)] = -0.05632827 au

''' = -147.890 kJmol-1'''

The Ammonia product is more stable than the gaseous reactants.

==CH4 Molecule==

===Key Information===

C-H bond length = 1.07000 A

H-C-H bond angle = 109.47122 degrees

Calculation Method: RB3LYP

Basis Set: 6-31G(d,p)

Final Energy: -40.52401404 au

RMS Gradient: 0.00003263 au

Point Group: TD

<pre>

Item Value Threshold Converged?
Maximum Force 0.000063 0.000450 YES
RMS Force 0.000034 0.000300 YES
Maximum Displacement 0.000179 0.001800 YES
RMS Displacement 0.000095 0.001200 YES
Predicted change in Energy=-2.256038D-08
</pre>

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SK4915_CH4.LOG</uploadedFileContents>
</jmolApplet></jmol>

Link to optimized file: [[File:SK4915_CH4.LOG| optimized file]]

===Vibration===

[[File:CH4 vibration.png|300px|thumb|Vibrational modes in an CH4 molecule.]]

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

9

'''Which modes are degenerate (i.e have the same energy)?'''

Modes 1, 2 & 3, modes 4 & 5 and modes 7, 8 & 9 are degenerate.

'''Which modes are "bending" vibrations and which are "bond stretch" vibrations?'''

Modes 1, 2, 3, 4 & 5 are bending vibrations and modes 6, 7, 8 & 9 are bond stretch vibrations.

'''Which mode is highly symmetric?'''

Mode 6.

===Charge Distribution===

Charge on the C-atom: -0.930

Charge on the H-atoms: 0.233

These charges match expectations as Carbon is the most electronegative atom in this molecule and so more strongly attracts the bonding electrons, pulling the electrons further away from the Hydrogen atoms. Therefore, there is a slight negative charge on the Carbon and slight positive charges on the Hydrogen atoms.

===Molecular Orbitals===

[[File:CH4 1s orbital.png|300px|thumb|right|The 1s molecular orbital in a methane molecule.]]

The highest occupied molecular orbital in methane is the 2p orbital and the HOMO-LUMO gap in methane is 0.50655 au.

[[File:CH4 2p orbital.png|300px|thumb|right|The 2p molecular orbital in a methane molecule, one of three degenerate orbitals.]]

[[File:CH4 2s orbital.png|300px|thumb|left|The 2s molecular orbital in a methane molecule.]]

[[File:CH4 3p orbital.png|300px|thumb|right|The 3p molecular orbital in a methane molecule, one of three degenerate orbitals. This orbital is unoccupied.]]

[[File:CH4 3s orbital.png|300px|thumb|left|The 3s molecular orbital in a methane molecule. This orbital is unoccupied.]]

Rep:Mod:AMZ1470

2016-02-26T12:36:08Z

Sk4915:

==NH3 Molecule==

===Key Information===

N-H bond length = 1.01798 A

H-N-H bond angle = 105.74115 degrees

Calculation Method: RB3LYP

Basis Set: 6-31G(d,p)

Final Energy: -56.55776873 au

RMS Gradient: 0.00000485 au

Point Group: C3V

<pre>

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
Predicted change in Energy=-5.986259D-10
</pre>

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>sk4915 NH3 optf pop.log</uploadedFileContents>
</jmolApplet></jmol>

Link to optimized file: [[File:Sk4915_NH3_optf_pop.log| optimized file]]

===Vibration===

[[File:NH3 vibration.png|300px|thumb|Vibrational modes in an NH3 molecule.]]

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

6

'''Which modes are degenerate (i.e have the same energy)?'''

Modes 2 & 3 are degenerate. Modes 5 & 6 also are degenerate.

'''Which modes are "bending" vibrations and which are "bond stretch" vibrations?'''

Modes 1, 2 & 3 are bending vibrations and modes 4, 5 & 6 are bond stretch vibrations.

'''Which mode is highly symmetric?'''

Mode 4.

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

Mode 1.

'''How many bands would you expect to see in an experimental spectrum of gaseous ammonia?'''

Two bands.

===Charge Distribution===

Charge on the N-atom: -1.125

Charge on the H-atoms: 0.375

These charges match expectations as Nitrogen is the most electronegative atom in this molecule and so more strongly attracts the bonding electrons, pulling the electrons further away from the Hydrogen atoms. Therefore, there is a slight negative charge on the Nitrogen and slight positive charges on the Hydrogen atoms.

==H2 Molecule==

===Key Information===

H-H bond length = 0.74279 A

Calculation Method: RB3LYP

Basis Set: 6-31G(d,p)

Final Energy: -1.17853936 au

RMS Gradient: 0.00000017 au

Point Group: D*H

<pre>

Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000001 0.001200 YES
Predicted change in Energy=-1.164080D-13
</pre>

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SK4915_H2.LOG</uploadedFileContents>
</jmolApplet></jmol>

Link to optimized file: [[File:SK4915_H2.LOG| optimized file]]

===Vibration===

[[File:H2 vibration.png|300px]]

Vibrational modes in an H2 molecule.

===Charge Distribution===

Charge on the H-atoms: 0.00 C

Both atoms in this molecule are identical so there is no dipole.

==N2 Molecule==

===Key Information===

N-N bond length = 1.09200 A

Calculation Method: RB3LYP

Basis Set: 6-31G(d,p)

Final Energy: -109.52359111 au

RMS Gradient: 0.02473091 au

Point Group: D*H

<pre>

Item Value Threshold Converged?
Maximum Force 0.000001 0.000450 YES
RMS Force 0.000001 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000000 0.001200 YES
Predicted change in Energy=-3.400935D-13
</pre>

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SK4915_N2.LOG</uploadedFileContents>
</jmolApplet></jmol>

Link to optimized file: [[File:SK4915_N2.LOG| optimized file]]

===Vibration===

[[File:N2 vibration.png|300px]]

Vibrational modes in an N2 molecule.

===Charge Distribution===

Charge on the N-atom: 0.00 C

Both atoms in this molecule are identical so there is no dipole.

==Energy Calculations==

'''Reaction:'''

'''N2 + 3H2 -> 2NH3'''

E(NH3) = -56.55776873 au

2*E(NH3) = -113.1155375 au

E(N2) = -109.52359111 au

E(H2) = -1.17853936 au

3*E(H2) = -3.53561808 au

ΔE = 2*E(NH3) - [E(N2) + E(H2)] = -0.05632827 au

''' = -147.890 kJmol-1'''

The Ammonia product is more stable than the gaseous reactants.

==CH4 Molecule==

===Key Information===

C-H bond length = 1.07000 A

H-C-H bond angle = 109.47122 degrees

Calculation Method: RB3LYP

Basis Set: 6-31G(d,p)

Final Energy: -40.52401404 au

RMS Gradient: 0.00003263 au

Point Group: TD

<pre>

Item Value Threshold Converged?
Maximum Force 0.000063 0.000450 YES
RMS Force 0.000034 0.000300 YES
Maximum Displacement 0.000179 0.001800 YES
RMS Displacement 0.000095 0.001200 YES
Predicted change in Energy=-2.256038D-08
</pre>

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SK4915_CH4.LOG</uploadedFileContents>
</jmolApplet></jmol>

Link to optimized file: [[File:SK4915_CH4.LOG| optimized file]]

===Vibration===

[[File:CH4 vibration.png|300px|thumb|Vibrational modes in an CH4 molecule.]]

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

9

'''Which modes are degenerate (i.e have the same energy)?'''

Modes 1, 2 & 3, modes 4 & 5 and modes 7, 8 & 9 are degenerate.

'''Which modes are "bending" vibrations and which are "bond stretch" vibrations?'''

Modes 1, 2, 3, 4 & 5 are bending vibrations and modes 6, 7, 8 & 9 are bond stretch vibrations.

'''Which mode is highly symmetric?'''

Mode 6.

===Charge Distribution===

Charge on the C-atom: -0.930

Charge on the H-atoms: 0.233

These charges match expectations as Carbon is the most electronegative atom in this molecule and so more strongly attracts the bonding electrons, pulling the electrons further away from the Hydrogen atoms. Therefore, there is a slight negative charge on the Carbon and slight positive charges on the Hydrogen atoms.

===Molecular Orbitals===

[[File:CH4 1s orbital.png|300px|thumb|right|The 1s molecular orbital in a methane molecule.]]

txt

[[File:CH4 2p orbital.png|300px|thumb|right|The 2p molecular orbital in a methane molecule.]]

[[File:CH4 2s orbital.png|300px|thumb|left|The 2s molecular orbital in a methane molecule.]]

[[File:CH4 3p orbital.png|300px|thumb|right|The 3p molecular orbital in a methane molecule.]]

[[File:CH4 3s orbital.png|300px|thumb|left|The 3s molecular orbital in a methane molecule.]]

File:CH4 3s orbital.png

2016-02-26T12:27:24Z

Sk4915:

File:CH4 3p orbital.png

2016-02-26T12:27:11Z

Sk4915:

File:CH4 2s orbital.png

2016-02-26T12:26:53Z

Sk4915:

File:CH4 2p orbital.png

2016-02-26T12:26:39Z

Sk4915:

File:CH4 1s orbital.png

2016-02-26T12:26:22Z

Sk4915:

Rep:Mod:AMZ1470

2016-02-26T12:11:57Z

Sk4915:

Rep:Mod:AMZ1470

2016-02-26T12:09:18Z

Sk4915:

==NH3 Molecule==

===Key Information===

N-H bond length = 1.01798 A

H-N-H bond angle = 105.74115 degrees

Calculation Method: RB3LYP

Basis Set: 6-31G(d,p)

Final Energy: -56.55776873 au

RMS Gradient: 0.00000485 au

Point Group: C3V

<pre>

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000072 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
Predicted change in Energy=-5.986259D-10
</pre>

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>sk4915 NH3 optf pop.log</uploadedFileContents>
</jmolApplet></jmol>

Link to optimized file: [[File:Sk4915_NH3_optf_pop.log| optimized file]]

===Vibration===

[[File:NH3 vibration.png|300px|thumb|Vibrational modes in an NH3 molecule.]]

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

6

'''Which modes are degenerate (i.e have the same energy)?'''

Modes 2 & 3 are degenerate. Modes 5 & 6 also are degenerate.

'''Which modes are "bending" vibrations and which are "bond stretch" vibrations?'''

Modes 1, 2 & 3 are bending vibrations and modes 4, 5 & 6 are bond stretch vibrations.

'''Which mode is highly symmetric?'''

Mode 4.

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

Mode 1.

'''How many bands would you expect to see in an experimental spectrum of gaseous ammonia?'''

Two bands.

===Charge Distribution===

Charge on the N-atom: -1.125

Charge on the H-atoms: 0.375

These charges match expectations as Nitrogen is the most electronegative atom in this molecule and so more strongly attracts the bonding electrons, pulling the electrons further away from the Hydrogen atoms. Therefore, there is a slight negative charge on the Nitrogen and slight positive charges on the Hydrogen atoms.

==H2 Molecule==

===Key Information===

H-H bond length = 0.74279 A

Calculation Method: RB3LYP

Basis Set: 6-31G(d,p)

Final Energy: -1.17853936 au

RMS Gradient: 0.00000017 au

Point Group: D*H

<pre>

Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000001 0.001200 YES
Predicted change in Energy=-1.164080D-13
</pre>

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SK4915_H2.LOG</uploadedFileContents>
</jmolApplet></jmol>

Link to optimized file: [[File:SK4915_H2.LOG| optimized file]]

===Vibration===

[[File:H2 vibration.png|300px]]

Vibrational modes in an H2 molecule.

===Charge Distribution===

Charge on the H-atoms: 0.00 C

Both atoms in this molecule are identical so there is no dipole.

==N2 Molecule==

===Key Information===

N-N bond length = 1.09200 A

Calculation Method: RB3LYP

Basis Set: 6-31G(d,p)

Final Energy: -109.52359111 au

RMS Gradient: 0.02473091 au

Point Group: D*H

<pre>

Item Value Threshold Converged?
Maximum Force 0.000001 0.000450 YES
RMS Force 0.000001 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000000 0.001200 YES
Predicted change in Energy=-3.400935D-13
</pre>

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SK4915_N2.LOG</uploadedFileContents>
</jmolApplet></jmol>

Link to optimized file: [[File:SK4915_N2.LOG| optimized file]]

===Vibration===

[[File:N2 vibration.png|300px]]

Vibrational modes in an N2 molecule.

===Charge Distribution===

Charge on the N-atom: 0.00 C

Both atoms in this molecule are identical so there is no dipole.

==Energy Calculations==

'''Reaction:'''

'''N2 + 3H2 -> 2NH3'''

E(NH3) = -56.55776873 au

2*E(NH3) = -113.1155375 au

E(N2) = -109.52359111 au

E(H2) = -1.17853936 au

3*E(H2) = -3.53561808 au

ΔE = 2*E(NH3) - [E(N2) + E(H2)] = -0.05632827 au

''' = -147.890 kJmol-1'''

The Ammonia product is more stable than the gaseous reactants.

==CH4 Molecule==

===Key Information===

C-H bond length = 1.07000 A

H-C-H bond angle = 109.47122 degrees

Calculation Method: RB3LYP

Basis Set: 6-31G(d,p)

Final Energy: -40.52401404 au

RMS Gradient: 0.00003263 au

Point Group: TD

<pre>

Item Value Threshold Converged?
Maximum Force 0.000063 0.000450 YES
RMS Force 0.000034 0.000300 YES
Maximum Displacement 0.000179 0.001800 YES
RMS Displacement 0.000095 0.001200 YES
Predicted change in Energy=-2.256038D-08
</pre>

<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>sk4915 CH4.log</uploadedFileContents>
</jmolApplet></jmol>

Link to optimized file: [[File:Sk4915_CH4.log| optimized file]]

===Vibration===

[[File:CH4 vibration.png|300px|thumb|Vibrational modes in an CH4 molecule.]]

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

9

'''Which modes are degenerate (i.e have the same energy)?'''

Modes 1, 2 & 3, modes 4 & 5 and modes 7, 8 & 9 are degenerate.

'''Which modes are "bending" vibrations and which are "bond stretch" vibrations?'''

Modes 1, 2, 3, 4 & 5 are bending vibrations and modes 6, 7, 8 & 9 are bond stretch vibrations.

'''Which mode is highly symmetric?'''

Mode 6.

===Charge Distribution===

Charge on the C-atom: -0.930

Charge on the H-atoms: 0.233

These charges match expectations as Carbon is the most electronegative atom in this molecule and so more strongly attracts the bonding electrons, pulling the electrons further away from the Hydrogen atoms. Therefore, there is a slight negative charge on the Carbon and slight positive charges on the Hydrogen atoms.

===Molecular Orbitals===

File:CH4 vibration.png

2016-02-26T12:04:37Z

Sk4915:

File:SK4915 CH4.LOG

2016-02-26T12:01:02Z

Sk4915:

Rep:Mod:AMZ1470

2016-02-25T14:56:59Z

Sk4915:

Rep:Mod:AMZ1470

2016-02-25T14:49:50Z

Sk4915:

Rep:Mod:AMZ1470

2016-02-25T14:42:09Z

Sk4915:

File:N2 vibration.png

2016-02-25T14:39:03Z

Sk4915:

File:SK4915 N2.LOG

2016-02-25T14:37:44Z

Sk4915:

Rep:Mod:AMZ1470

2016-02-25T14:26:56Z

Sk4915:

File:H2 vibration.png

2016-02-25T14:25:44Z

Sk4915:

Rep:Mod:AMZ1470

2016-02-25T14:17:28Z

Sk4915:

File:SK4915 H2.LOG

2016-02-25T14:07:18Z

Sk4915:

Rep:Mod:AMZ1470

2016-02-25T13:37:46Z

Sk4915:

File:NH3 vibration.png

2016-02-25T13:29:54Z

Sk4915:

Rep:Mod:AMZ1470

2016-02-25T13:28:39Z

Sk4915:

Rep:Mod:AMZ1470

2016-02-25T13:01:33Z

Sk4915:

File:Sk4915 NH3 optf pop.log

2016-02-25T13:00:02Z

Sk4915:

Rep:Mod:AMZ1470

2016-02-25T12:50:48Z

Sk4915:

Rep:Mod:AMZ1470

2016-02-25T12:41:01Z

Sk4915:

===NH3 Molecule===

N-H bond length = 1.01798 A

H-N-H bond angle = 105.74115 degrees

Calculation Method: RB3LYP

Basis Set: 6-31G(d,p)

Final Energy: -56.55776873 au

RMS Gradient: 0.00000485 au

Point Group: C3V

Rep:Mod:AMZ1470

2016-02-24T14:36:48Z

Sk4915: Created page with "'''NH3 Molecule''' N-H bond length = 1.01798 A H-N-H bond angle = 105.74115 degrees Calculation Method: RB3LYP Basis Set: 6-31G(d,p) Final Energy: -56.55776873..."

'''NH3 Molecule'''

N-H bond length = 1.01798 A

H-N-H bond angle = 105.74115 degrees

Calculation Method: RB3LYP

Basis Set: 6-31G(d,p)

Final Energy: -56.55776873 au

RMS Gradient: 0.00000485 au

Point Group: C3V