ChemWiki - User contributions [en]

Mod:Hunt Research Group/hpc connections

2018-07-20T15:04:51Z

Gn116:

''First version on 25th June 09 – Hieu Nguyen''

HPC system runs on Unix so if you are using Macintosh, Linux or any other Unix-based operating systems, simply open a terminal and use the ssh command line:

e.g. : ssh username@login.cx1.hpc.ic.ac.uk

If you are Windows users, you have to use a ssh client in order to connect to HPC. There are quite a few available online for free such as PuTTY, OpenSSH, MobaXterm ….
Winscp has been recommended to me: http://winscp.net/eng/docs/introduction

Another option is: http://www.cc.uoa.gr/fileadmin/cc.uoa.gr/uploads/files/software/SSHSecureShellClient-3.2.9.exe

An example for using PuTTY and MobaXterm will be demonstrated below:

=== PuTTY ===
- Go to : http://chiark.greenend.org.uk/~sgtatham/putty/download.html to download the latest version of the software. Choose to download the file putty.exe (make sure you allow authentication for your firewall/Anti-virus to run the file) to a destination on your PC.

- Run putty.exe. There will be a promt:

[[Image:Putty1.JPG]]

- In the Host Name (or IP address) box, type login.cx1.hpc.ic.ac.uk and press Open. It will open a terminal and a dialogue box:

[[Image:Putty2.JPG]]

- Click on Yes to continue.
- In the terminal window, key in your username in the space after ‘ login as ‘ and Enter. You will be required to type in your password in order to login in the next line:

[[Image:Putty3.JPG]]

- Press Enter after your password and you will be connected to HPC.

=== MobaXterm ===
- Go to :https://mobaxterm.mobatek.net/[https://mobaxterm.mobatek.net/] to download the latest version of the software. Choose 'Get MobaXterm Now' to download the program to a destination on your PC.

-Ensure that you select the 'Home Edition' version

-Once installed, open the program and select 'start local terminal' to begin a session

[[File:MobaXterm.png|693x693px]]

Mod:Hunt Research Group/hpc connections

2018-07-20T15:04:19Z

Gn116:

File:MobaXterm.png

2018-07-20T15:03:02Z

Gn116:

Mod:Hunt Research Group/hpc connections

2018-07-20T14:53:19Z

Gn116:

Mod:Hunt Research Group/hpc connections

2018-07-20T14:36:43Z

Gn116:

Mod:Hunt Research Group/hpc connections

2018-07-20T14:34:31Z

Gn116:

''First version on 25th June 09 – Hieu Nguyen''

HPC system runs on Unix so if you are using Macintosh, Linux or any other Unix-based operating systems, simply open a terminal and use the ssh command line:

e.g. : ssh username@login.cx1.hpc.ic.ac.uk

If you are Windows users, you have to use a ssh client in order to connect to HPC. There are quite a few available online for free such as PuTTY, OpenSSH,MobaXterm ….
Winscp has been recommended to me: http://winscp.net/eng/docs/introduction

Another option is: http://www.cc.uoa.gr/fileadmin/cc.uoa.gr/uploads/files/software/SSHSecureShellClient-3.2.9.exe

An example for using PuTTY will be demonstrated below:

- Go to : http://chiark.greenend.org.uk/~sgtatham/putty/download.html to download the latest version of the software. Choose to download the file putty.exe (make sure you allow authentication for your firewall/Anti-virus to run the file) to a destination on your PC.

- Run putty.exe. There will be a promt:

[[Image:Putty1.JPG]]

- In the Host Name (or IP address) box, type login.cx1.hpc.ic.ac.uk and press Open. It will open a terminal and a dialogue box:

[[Image:Putty2.JPG]]

- Click on Yes to continue.
- In the terminal window, key in your username in the space after ‘ login as ‘ and Enter. You will be required to type in your password in order to login in the next line:

[[Image:Putty3.JPG]]

- Press Enter after your password and you will be connected to HPC.

and some new stuff here

Rep:Mod:asdfgh1234

2018-03-13T17:05:46Z

Gn116:

== '''NH3 molecule''' ==

N-H bond distance = 1.01798

H-N-H bond angle = 37.129

'''Key information from optimised job'''

Molecule name = NH3

Calculation method = RB3LYP

Basis set = 6-31G(d,p)

Final energy E(RB3LYP) in atomic units = -56.55776873

Point group of molecule = C3V

'''Item table'''
<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
</pre>

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>blue</color>
<size>400</size>
<uploadedFileContents>gn116_NH3_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.01798.37.129</script>
</jmolApplet></jmol>

The optimisation file is linked to [[Media:gn116_NH3_OPTF_POP.LOG| here]]

'''Vibrations and charges'''

[[File:Gn116_nh3_vibrations_resized.JPG]]

-6 modes would be expected from the 3N-6 rule

-Modes 2 + 3 and 5 + 6 are degenerate (ie have the same energy)

-Vibration modes 1, 2 + 3 are bending. Whereas, 4, 5 + 6 are stretching

-Mode 4 is highly symmetric

-Mode 1 is known as the "umbrella" mode

-You would expect to see 6 bands in an experimental spectrum of gaseous ammonia

'''Charge distribution'''

We would expect hydrogen to be positive and, as a consequence, the nitrogen to be negative

H = 0.375

N = -1.125

== '''N2 Molecule'''==

N-N bond distance = 1.09200

'''Key information from optimised job'''

Molecule name = Nitrogen gas

Calculation method = RB3LYP

Basis set = 6-31G(d,p)

Final energy E(RB3LYP) in atomic units = -109.52359111

Point group of molecule = D*H

'''Item table'''
<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
</pre>

There was just one mode of vibration identified; frequency = 2457.33, infrared = 0

== '''H2 Molecule'''==

H-H bond distance = 0.60000

'''Key information from optimised job'''

Molecule name = Hydrogen gas

Calculation method = RB3LYP

Basis set = 6-31G(d,p)

Final energy E(RB3LYP) in atomic units = -1.15928020

Point group of molecule = D*H

'''Item table'''
<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
</pre>

There was just one mode of vibration identified; frequency = 4465.68, infrared = 0

== '''Reaction energies''' ==

N2 + 3H2 --> 2NH3

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.11410576 a.u

-0.11410576*2625.5 = -299.58 kJ/mol

== '''Choice of Small Molecule''' ==

Molecule = CH4

C-H Bond distance = 1.07000

Bond angle = 109.471

'''Key information from optimised job'''

Molecule name = Methane

Calculation method = RB3LYP

Basis set = 6-31G(d,p)

Final energy E(RB3LYP) in atomic units = -40.52275298

Point group of molecule = T

'''Item table'''
<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
</pre>

<jmol><jmolApplet>
<title>CH4 Molecule</title>
<color>blue</color>
<size>400</size>
<uploadedFileContents>GN116_CH4_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.07000.109.471</script>
</jmolApplet></jmol>

The optimisation file is linked to [[Media:GN116_CH4_OPTF_POP.LOG| here]]

'''Vibrations and charges'''

[[File:Gn116_CH4_vibrations.JPG]]

'''Molecular Orbitals'''

Worth revisiting this when I am with the group in Chemistry

[[File:CH4_1_-10.16707.JPG]]

This MO is deep in energy. No overlap, held tightly to nuclei and not involved in chemical bonding

[[File:CH4_2_-0.69041.JPG]]

Combination of valence orbitals bonding and antibonding. Strong overlap, likely to be involved in chemical bonding

[[File:3_-0.38831_ch4.JPG]]

Orbitals lie along the bond. Sit side by side, etc.

'''Charge distribution'''

H = 0.233

C = -0.930

Rep:Mod:asdfgh1234

2018-03-13T17:02:48Z

Gn116:

Rep:Mod:asdfgh1234

2018-03-13T17:01:11Z

Gn116:

== '''NH3 molecule''' ==

N-H bond distance = 1.01798

H-N-H bond angle = 37.129

'''Key information from optimised job'''

Molecule name = NH3

Calculation method = RB3LYP

Basis set = 6-31G(d,p)

Final energy E(RB3LYP) in atomic units = -56.55776873

Point group of molecule = C3V

'''Item table'''
<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
</pre>

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>blue</color>
<size>400</size>
<uploadedFileContents>gn116_NH3_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.01798.37.129</script>
</jmolApplet></jmol>

The optimisation file is linked to [[Media:gn116_NH3_OPTF_POP.LOG| here]]

'''Vibrations and charges'''

[[File:Gn116_nh3_vibrations_resized.JPG]]

-6 modes would be expected from the 3N-6 rule

-Modes 2 + 3 and 5 + 6 are degenerate (ie have the same energy)

-Vibration modes 1, 2 + 3 are bending. Whereas, 4, 5 + 6 are stretching

-Mode 4 is highly symmetric

-Mode 1 is known as the "umbrella" mode

-You would expect to see 6 bands in an experimental spectrum of gaseous ammonia

'''Charge distribution'''

We would expect hydrogen to be positive and, as a consequence, the nitrogen to be negative

H = 0.375

N = -1.125

== '''N2 Molecule'''==

N-N bond distance = 1.09200

'''Key information from optimised job'''

Molecule name = Nitrogen gas

Calculation method = RB3LYP

Basis set = 6-31G(d,p)

Final energy E(RB3LYP) in atomic units = -109.52359111

Point group of molecule = D*H

'''Item table'''
<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
</pre>

There was just one mode of vibration identified; frequency = 2457.33, infrared = 0

== '''H2 Molecule'''==

H-H bond distance = 0.60000

'''Key information from optimised job'''

Molecule name = Hydrogen gas

Calculation method = RB3LYP

Basis set = 6-31G(d,p)

Final energy E(RB3LYP) in atomic units = -1.15928020

Point group of molecule = D*H

'''Item table'''
<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
</pre>

There was just one mode of vibration identified; frequency = 4465.68, infrared = 0

== '''Reaction energies''' ==

N2 + 3H2 --> 2NH3

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.11410576 a.u

-0.11410576*2625.5 = -299.58 kJ/mol

== '''Choice of Small Molecule''' ==

Molecule = CH4

C-H Bond distance = 1.07000

Bond angle = 109.471

'''Key information from optimised job'''

Molecule name = Methane

Calculation method = RB3LYP

Basis set = 6-31G(d,p)

Final energy E(RB3LYP) in atomic units = -40.52275298

Point group of molecule = T

'''Item table'''
<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
</pre>

<jmol><jmolApplet>
<title>CH4 Molecule</title>
<color>blue</color>
<size>400</size>
<uploadedFileContents>GN116_CH4_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.07000.109.471</script>
</jmolApplet></jmol>

The optimisation file is linked to [[Media:GN116_CH4_OPTF_POP.LOG| here]]

'''Vibrations and charges'''

[[File:Gn116_CH4_vibrations.JPG]]

'''Molecular Orbitals'''

Worth revisiting this when I am with the group in Chemistry

[[File:CH4_1_-10.16707.JPG]]
This MO is deep in energy. No overlap, held tightly to nuclei and not involved in chemical bonding

[[File:CH4_2_-0.69041.JPG]]

[[File:3_-0.38831_ch4.JPG]]

'''Charge distribution'''

H = 0.233

C = -0.930

Rep:Mod:asdfgh1234

2018-03-13T16:25:52Z

Gn116:

== '''NH3 molecule''' ==

N-H bond distance = 1.01798

H-N-H bond angle = 37.129

'''Key information from optimised job'''

Molecule name = NH3

Calculation method = RB3LYP

Basis set = 6-31G(d,p)

Final energy E(RB3LYP) in atomic units = -56.55776873

Point group of molecule = C3V

'''Item table'''
<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
</pre>

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>blue</color>
<size>400</size>
<uploadedFileContents>gn116_NH3_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.01798.37.129</script>
</jmolApplet></jmol>

The optimisation file is linked to [[Media:gn116_NH3_OPTF_POP.LOG| here]]

'''Vibrations and charges'''

[[File:Gn116_nh3_vibrations_resized.JPG]]

-6 modes would be expected from the 3N-6 rule

-Modes 2 + 3 and 5 + 6 are degenerate (ie have the same energy)

-Vibration modes 1, 2 + 3 are bending. Whereas, 4, 5 + 6 are stretching

-Mode 4 is highly symmetric

-Mode 1 is known as the "umbrella" mode

-You would expect to see 6 bands in an experimental spectrum of gaseous ammonia

'''Charge distribution'''

We would expect hydrogen to be positive and, as a consequence, the nitrogen to be negative

H = 0.375

N = -1.125

== '''N2 Molecule'''==

N-N bond distance = 1.09200

'''Key information from optimised job'''

Molecule name = Nitrogen gas

Calculation method = RB3LYP

Basis set = 6-31G(d,p)

Final energy E(RB3LYP) in atomic units = -109.52359111

Point group of molecule = D*H

'''Item table'''
<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
</pre>

There was just one mode of vibration identified; frequency = 2457.33, infrared = 0

== '''H2 Molecule'''==

H-H bond distance = 0.60000

'''Key information from optimised job'''

Molecule name = Hydrogen gas

Calculation method = RB3LYP

Basis set = 6-31G(d,p)

Final energy E(RB3LYP) in atomic units = -1.15928020

Point group of molecule = D*H

'''Item table'''
<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
</pre>

There was just one mode of vibration identified; frequency = 4465.68, infrared = 0

== '''Reaction energies''' ==

N2 + 3H2 --> 2NH3

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.11410576 a.u

-0.11410576*2625.5 = -299.58 kJ/mol

== '''Choice of Small Molecule''' ==

Molecule = CH4

C-H Bond distance = 1.07000

Bond angle = 109.471

'''Key information from optimised job'''

Molecule name = Methane

Calculation method = RB3LYP

Basis set = 6-31G(d,p)

Final energy E(RB3LYP) in atomic units = -40.52275298

Point group of molecule = T

'''Item table'''
<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
</pre>

<jmol><jmolApplet>
<title>CH4 Molecule</title>
<color>blue</color>
<size>400</size>
<uploadedFileContents>GN116_CH4_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.07000.109.471</script>
</jmolApplet></jmol>

The optimisation file is linked to [[Media:GN116_CH4_OPTF_POP.LOG| here]]

'''Vibrations and charges'''

[[File:Gn116_CH4_vibrations.JPG]]

'''Molecular Orbitals'''

[[File:CH4_1_-10.16707.JPG]]

[[File:CH4_2_-0.69041.JPG]]

[[File:3_-0.38831_ch4.JPG]]

'''Charge distribution'''

H = 0.233

C = -0.930

Rep:Mod:asdfgh1234

2018-03-13T16:19:42Z

Gn116:

== '''NH3 molecule''' ==

N-H bond distance = 1.01798

H-N-H bond angle = 37.129

'''Key information from optimised job'''

Molecule name = NH3

Calculation method = RB3LYP

Basis set = 6-31G(d,p)

Final energy E(RB3LYP) in atomic units = -56.55776873

Point group of molecule = C3V

'''Item table'''
<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
</pre>

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>blue</color>
<size>400</size>
<uploadedFileContents>gn116_NH3_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.01798.37.129</script>
</jmolApplet></jmol>

The optimisation file is linked to [[Media:gn116_NH3_OPTF_POP.LOG| here]]

'''Vibrations and charges'''

[[File:Gn116_nh3_vibrations_resized.JPG]]

-6 modes would be expected from the 3N-6 rule

-Modes 2 + 3 and 5 + 6 are degenerate (ie have the same energy)

-Vibration modes 1, 2 + 3 are bending. Whereas, 4, 5 + 6 are stretching

-Mode 4 is highly symmetric

-Mode 1 is known as the "umbrella" mode

-You would expect to see 6 bands in an experimental spectrum of gaseous ammonia

'''Charge distribution'''

We would expect hydrogen to be positive and, as a consequence, the nitrogen to be negative

H = 0.375

N = -1.125

== '''N2 Molecule'''==

N-N bond distance = 1.09200

'''Key information from optimised job'''

Molecule name = Nitrogen gas

Calculation method = RB3LYP

Basis set = 6-31G(d,p)

Final energy E(RB3LYP) in atomic units = -109.52359111

Point group of molecule = D*H

'''Item table'''
<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
</pre>

There was just one mode of vibration identified; frequency = 2457.33, infrared = 0

== '''H2 Molecule'''==

H-H bond distance = 0.60000

'''Key information from optimised job'''

Molecule name = Hydrogen gas

Calculation method = RB3LYP

Basis set = 6-31G(d,p)

Final energy E(RB3LYP) in atomic units = -1.15928020

Point group of molecule = D*H

'''Item table'''
<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
</pre>

There was just one mode of vibration identified; frequency = 4465.68, infrared = 0

== '''Reaction energies''' ==

N2 + 3H2 --> 2NH3

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.11410576 a.u

-0.11410576*2625.5 = -299.58 kJ/mol

== '''Choice of Small Molecule''' ==

Molecule = CH4

C-H Bond distance = 1.07000

Bond angle = 109.471

'''Key information from optimised job'''

Molecule name = Methane

Calculation method = RB3LYP

Basis set = 6-31G(d,p)

Final energy E(RB3LYP) in atomic units = -40.52275298

Point group of molecule = T

'''Item table'''
<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
</pre>

<jmol><jmolApplet>
<title>CH4 Molecule</title>
<color>blue</color>
<size>400</size>
<uploadedFileContents>GN116_CH4_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.07000.109.471</script>
</jmolApplet></jmol>

The optimisation file is linked to [[Media:GN116_CH4_OPTF_POP.LOG| here]]

'''Vibrations and charges'''

[[File:Gn116_CH4_vibrations.JPG]]

'''Molecular Orbits'''

[[File:CH4_1_-10.16707.JPG]]

[[File:CH4_2_-0.69041.JPG]]

[[File:3_-0.38831_ch4.JPG]]

'''Charge distribution'''

H = 0.233

C = -0.930

Rep:Mod:asdfgh1234

2018-03-13T16:19:14Z

Gn116:

== '''NH3 molecule''' ==

N-H bond distance = 1.01798

H-N-H bond angle = 37.129

'''Key information from optimised job'''

Molecule name = NH3

Calculation method = RB3LYP

Basis set = 6-31G(d,p)

Final energy E(RB3LYP) in atomic units = -56.55776873

Point group of molecule = C3V

'''Item table'''
<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
</pre>

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>blue</color>
<size>400</size>
<uploadedFileContents>gn116_NH3_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.01798.37.129</script>
</jmolApplet></jmol>

The optimisation file is linked to [[Media:gn116_NH3_OPTF_POP.LOG| here]]

'''Vibrations and charges'''

[[File:Gn116_nh3_vibrations_resized.JPG]]

-6 modes would be expected from the 3N-6 rule

-Modes 2 + 3 and 5 + 6 are degenerate (ie have the same energy)

-Vibration modes 1, 2 + 3 are bending. Whereas, 4, 5 + 6 are stretching

-Mode 4 is highly symmetric

-Mode 1 is known as the "umbrella" mode

-You would expect to see 6 bands in an experimental spectrum of gaseous ammonia

'''Charge distribution'''

We would expect hydrogen to be positive and, as a consequence, the nitrogen to be negative

H = 0.375

N = -1.125

== '''N2 Molecule'''==

N-N bond distance = 1.09200

'''Key information from optimised job'''

Molecule name = Nitrogen gas

Calculation method = RB3LYP

Basis set = 6-31G(d,p)

Final energy E(RB3LYP) in atomic units = -109.52359111

Point group of molecule = D*H

'''Item table'''
<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
</pre>

There was just one mode of vibration identified; frequency = 2457.33, infrared = 0

== '''H2 Molecule'''==

H-H bond distance = 0.60000

'''Key information from optimised job'''

Molecule name = Hydrogen gas

Calculation method = RB3LYP

Basis set = 6-31G(d,p)

Final energy E(RB3LYP) in atomic units = -1.15928020

Point group of molecule = D*H

'''Item table'''
<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
</pre>

There was just one mode of vibration identified; frequency = 4465.68, infrared = 0

== '''Reaction energies''' ==

N2 + 3H2 --> 2NH3

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.11410576 a.u

-0.11410576*2625.5 = -299.58 kJ/mol

== '''Choice of Small Molecule''' ==

Molecule = CH4

C-H Bond distance = 1.07000

Bond angle = 109.471

'''Key information from optimised job'''

Molecule name = Methane

Calculation method = RB3LYP

Basis set = 6-31G(d,p)

Final energy E(RB3LYP) in atomic units = -40.52275298

Point group of molecule = T

'''Item table'''
<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
</pre>

<jmol><jmolApplet>
<title>CH4 Molecule</title>
<color>blue</color>
<size>400</size>
<uploadedFileContents>GN116_CH4_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.07000.109.471</script>
</jmolApplet></jmol>

The optimisation file is linked to [[Media:GN116_CH4_OPTF_POP.LOG| here]]

'''Vibrations and charges'''
[[File:Gn116_CH4_vibrations.JPG]]

'''Molecular Orbits'''

[[File:CH4_1_-10.16707.JPG]]

[[File:CH4_2_-0.69041.JPG]]

[[File:3_-0.38831_ch4.JPG]]

'''Charge distribution'''

H = 0.233

C = -0.930

Rep:Mod:asdfgh1234

2018-03-13T16:14:47Z

Gn116:

File:3 -0.38831 ch4.JPG

2018-03-13T16:13:33Z

Gn116:

File:CH4 2 -0.69041.JPG

2018-03-13T16:13:16Z

Gn116:

File:CH4 1 -10.16707.JPG

2018-03-13T16:13:01Z

Gn116:

File:Gn116 CH4 vibrations.JPG

2018-03-13T16:12:24Z

Gn116:

Rep:Mod:asdfgh1234

2018-03-13T16:11:06Z

Gn116:

Rep:Mod:asdfgh1234

2018-03-13T16:10:28Z

Gn116:

Rep:Mod:asdfgh1234

2018-03-13T16:09:29Z

Gn116:

== '''NH3 molecule''' ==

N-H bond distance = 1.01798

H-N-H bond angle = 37.129

'''Key information from optimised job'''

Molecule name = NH3

Calculation method = RB3LYP

Basis set = 6-31G(d,p)

Final energy E(RB3LYP) in atomic units = -56.55776873

Point group of molecule = C3V

'''Item table'''
<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
</pre>

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>blue</color>
<size>400</size>
<uploadedFileContents>gn116_NH3_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.01798.37.129</script>
</jmolApplet></jmol>

The optimisation file is linked to [[Media:gn116_NH3_OPTF_POP.LOG| here]]

'''Vibrations and charges'''

[[File:Gn116_nh3_vibrations_resized.JPG]]

-6 modes would be expected from the 3N-6 rule

-Modes 2 + 3 and 5 + 6 are degenerate (ie have the same energy)

-Vibration modes 1, 2 + 3 are bending. Whereas, 4, 5 + 6 are stretching

-Mode 4 is highly symmetric

-Mode 1 is known as the "umbrella" mode

-You would expect to see 6 bands in an experimental spectrum of gaseous ammonia

'''Charge distribution'''

We would expect hydrogen to be positive and, as a consequence, the nitrogen to be negative

H = 0.375

N = -1.125

----

== '''N2 Molecule'''==

N-N bond distance = 1.09200

'''Key information from optimised job'''

Molecule name = Nitrogen gas

Calculation method = RB3LYP

Basis set = 6-31G(d,p)

Final energy E(RB3LYP) in atomic units = -109.52359111

Point group of molecule = D*H

'''Item table'''
<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
</pre>

There was just one mode of vibration identified; frequency = 2457.33, infrared = 0

----

== '''H2 Molecule'''==

H-H bond distance = 0.60000

'''Key information from optimised job'''

Molecule name = Hydrogen gas

Calculation method = RB3LYP

Basis set = 6-31G(d,p)

Final energy E(RB3LYP) in atomic units = -1.15928020

Point group of molecule = D*H

'''Item table'''
<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
</pre>

There was just one mode of vibration identified; frequency = 4465.68, infrared = 0

----

== '''Reaction energies''' ==

N2 + 3H2 --> 2NH3

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.11410576 a.u

-0.11410576*2625.5 = -299.58 kJ/mol

----

== '''Choice of Small Molecule''' ==

Molecule = CH4

C-H Bond distance = 1.07000

Bond angle = 109.471

'''Key information from optimised job'''

Molecule name = Methane

Calculation method = RB3LYP

Basis set = 6-31G(d,p)

Final energy E(RB3LYP) in atomic units = -40.52275298

Point group of molecule = T

'''Item table'''
<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
</pre>

<jmol><jmolApplet>
<title>CH4 Molecule</title>
<color>blue</color>
<size>400</size>
<uploadedFileContents>GN116_CH4_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.07000.109.471</script>
</jmolApplet></jmol>

The optimisation file is linked to [[Media:GN116_CH4_OPTF_POP.LOG| here]]

Rep:Mod:asdfgh1234

2018-03-13T16:04:18Z

Gn116:

== '''NH3 molecule''' ==

N-H bond distance = 1.01798

H-N-H bond angle = 37.129

'''Key information from optimised job'''

Molecule name = NH3

Calculation method = RB3LYP

Basis set = 6-31G(d,p)

Final energy E(RB3LYP) in atomic units = -56.55776873

Point group of molecule = C3V

'''Item table'''
<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
</pre>

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>blue</color>
<size>400</size>
<uploadedFileContents>gn116_NH3_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.01798.37.129</script>
</jmolApplet></jmol>

The optimisation file is linked to [[Media:gn116_NH3_OPTF_POP.LOG| here]]

'''Vibrations and charges'''

[[File:Gn116_nh3_vibrations_resized.JPG]]

-6 modes would be expected from the 3N-6 rule

-Modes 2 + 3 and 5 + 6 are degenerate (ie have the same energy)

-Vibration modes 1, 2 + 3 are bending. Whereas, 4, 5 + 6 are stretching

-Mode 4 is highly symmetric

-Mode 1 is known as the "umbrella" mode

-You would expect to see 6 bands in an experimental spectrum of gaseous ammonia

'''Charge distribution'''

We would expect hydrogen to be positive and, as a consequence, the nitrogen to be negative

H = 0.375

N = -1.125

----

'''N2 Molecule'''

N-N bond distance = 1.09200

'''Key information from optimised job'''

Molecule name = Nitrogen gas

Calculation method = RB3LYP

Basis set = 6-31G(d,p)

Final energy E(RB3LYP) in atomic units = -109.52359111

Point group of molecule = D*H

'''Item table'''
<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
</pre>

There was just one mode of vibration identified; frequency = 2457.33, infrared = 0

----

'''H2 Molecule'''

H-H bond distance = 0.60000

'''Key information from optimised job'''

Molecule name = Hydrogen gas

Calculation method = RB3LYP

Basis set = 6-31G(d,p)

Final energy E(RB3LYP) in atomic units = -1.15928020

Point group of molecule = D*H

'''Item table'''
<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
</pre>

There was just one mode of vibration identified; frequency = 2457.33, infrared = 0

----

'''Reaction energies'''

N2 + 3H2 --> 2NH3

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.11410576 a.u

-0.11410576*2625.5 = -299.58 kJ/mol

----

'''Choice of Small Molecule'''

Molecule = CH4

C-H Bond distance = 1.07000

Bond angle = 109.471

'''Key information from optimised job'''

Molecule name = Methane

Calculation method = RB3LYP

Basis set = 6-31G(d,p)

Final energy E(RB3LYP) in atomic units = -40.52275298

Point group of molecule = T

'''Item table'''
<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
</pre>

<jmol><jmolApplet>
<title>CH4 Molecule</title>
<color>blue</color>
<size>400</size>
<uploadedFileContents>GN116_CH4_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.07000.109.471</script>
</jmolApplet></jmol>

The optimisation file is linked to [[Media:GN116_CH4_OPTF_POP.LOG| here]]

Rep:Mod:asdfgh1234

2018-03-13T13:46:41Z

Gn116:

'''NH3 molecule'''

N-H bond distance = 1.01798

H-N-H bond angle = 37.129

'''Key information from optimised job'''

Molecule name = NH3

Calculation method = RB3LYP

Basis set = 6-31G(d,p)

Final energy E(RB3LYP) in atomic units = -56.55776873

Point group of molecule = C3V

'''Item table'''
<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
</pre>

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>blue</color>
<size>400</size>
<uploadedFileContents>gn116_NH3_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.01798.37.129</script>
</jmolApplet></jmol>

The optimisation file is linked to [[Media:gn116_NH3_OPTF_POP.LOG| here]]

'''Vibrations and charges'''

[[File:Gn116_nh3_vibrations_resized.JPG]]

-6 modes would be expected from the 3N-6 rule

-Modes 2 + 3 and 5 + 6 are degenerate (ie have the same energy)

-Vibration modes 1, 2 + 3 are bending. Whereas, 4, 5 + 6 are stretching

-Mode 4 is highly symmetric

-Mode 1 is known as the "umbrella" mode

-You would expect to see 6 bands in an experimental spectrum of gaseous ammonia

'''Charge distribution'''

We would expect hydrogen to be positive and, as a consequence, the nitrogen to be negative

H = 0.375

N = -1.125

----

'''N2 Molecule'''

N-N bond distance = 1.09200

'''Key information from optimised job'''

Molecule name = Nitrogen gas

Calculation method = RB3LYP

Basis set = 6-31G(d,p)

Final energy E(RB3LYP) in atomic units = -109.52359111

Point group of molecule = D*H

'''Item table'''
<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
</pre>

There was just one mode of vibration identified; frequency = 2457.33, infrared = 0

----

'''H2 Molecule'''

H-H bond distance = 0.60000

'''Key information from optimised job'''

Molecule name = Hydrogen gas

Calculation method = RB3LYP

Basis set = 6-31G(d,p)

Final energy E(RB3LYP) in atomic units = -1.15928020

Point group of molecule = D*H

'''Item table'''
<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
</pre>

There was just one mode of vibration identified; frequency = 2457.33, infrared = 0

----

'''Reaction energies'''

N2 + 3H2 --> 2NH3

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.11410576 a.u

-0.11410576*2625.5 = -299.58 kJ/mol

----

'''Choice of Small Molecule'''

Molecule = CH4

C-H Bond distance = 1.07000

Bond angle = 109.471

'''Key information from optimised job'''

Molecule name = Methane

Calculation method = RB3LYP

Basis set = 6-31G(d,p)

Final energy E(RB3LYP) in atomic units = -40.52275298

Point group of molecule = T

'''Item table'''
<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
</pre>

<jmol><jmolApplet>
<title>CH4 Molecule</title>
<color>blue</color>
<size>400</size>
<uploadedFileContents>GN116_CH4_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.07000.109.471</script>
</jmolApplet></jmol>

The optimisation file is linked to [[Media:GN116_CH4_OPTF_POP.LOG| here]]

Rep:Mod:asdfgh1234

2018-03-13T13:45:28Z

Gn116:

File:GN116 CH4 OPTF POP.LOG

2018-03-13T13:43:38Z

Gn116:

Rep:Mod:asdfgh1234

2018-03-13T13:42:57Z

Gn116:

Rep:Mod:asdfgh1234

2018-03-13T13:11:49Z

Gn116:

'''NH3 molecule'''

N-H bond distance = 1.01798

H-N-H bond angle = 37.129

'''Key information from optimised job'''

Molecule name = NH3

Calculation method = RB3LYP

Basis set = 6-31G(d,p)

Final energy E(RB3LYP) in atomic units = -56.55776873

Point group of molecule = C3V

'''Item table'''
<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
</pre>

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>blue</color>
<size>400</size>
<uploadedFileContents>gn116_NH3_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.01798.37.129</script>
</jmolApplet></jmol>

The optimisation file is linked to [[Media:gn116_NH3_OPTF_POP.LOG| here]]

'''Vibrations and charges'''

[[File:Gn116_nh3_vibrations_resized.JPG]]

-6 modes would be expected from the 3N-6 rule

-Modes 2 + 3 and 5 + 6 are degenerate (ie have the same energy)

-Vibration modes 1, 2 + 3 are bending. Whereas, 4, 5 + 6 are stretching

-Mode 4 is highly symmetric

-Mode 1 is known as the "umbrella" mode

-You would expect to see 6 bands in an experimental spectrum of gaseous ammonia

'''Charge distribution'''

We would expect hydrogen to be positive and, as a consequence, the nitrogen to be negative

H = 0.375

N = -1.125

----

'''N2 Molecule'''

N-N bond distance = 1.09200

'''Key information from optimised job'''

Molecule name = N2

Calculation method = RB3LYP

Basis set = 6-31G(d,p)

Final energy E(RB3LYP) in atomic units = -109.52359111

Point group of molecule = D*H

'''Item table'''
<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
</pre>

There was just one mode of vibration identified; frequency = 2457.33, infrared = 0

----

'''H2 Molecule'''

H-H bond distance = 0.60000

'''Key information from optimised job'''

Molecule name = H2

Calculation method = RB3LYP

Basis set = 6-31G(d,p)

Final energy E(RB3LYP) in atomic units = -1.15928020

Point group of molecule = D*H

'''Item table'''
<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
</pre>

There was just one mode of vibration identified; frequency = 2457.33, infrared = 0

----

'''Reaction energies'''

N2 + 3H2 --> 2NH3

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.11410576 a.u

-0.11410576*2625.5 = -299.58 kJ/mol

----

Rep:Mod:asdfgh1234

2018-03-13T12:37:03Z

Gn116:

'''NH3 molecule'''

N-H bond distance = 1.01798

H-N-H bond angle = 37.129

'''Key information from optimised job'''

Molecule name = NH3

Calculation method = RB3LYP

Basis set = 6-31G(d,p)

Final energy E(RB3LYP) in atomic units = -56.55776873

Point group of molecule = C3V

'''Item table'''
<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
</pre>

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>blue</color>
<size>400</size>
<uploadedFileContents>gn116_NH3_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.01798.37.129</script>
</jmolApplet></jmol>

The optimisation file is linked to [[Media:gn116_NH3_OPTF_POP.LOG| here]]

'''Vibrations and charges'''

[[File:Gn116_nh3_vibrations_resized.JPG]]

-6 modes would be expected from the 3N-6 rule

-Modes 2 + 3 and 5 + 6 are degenerate (ie have the same energy)

-Vibration modes 1, 2 + 3 are bending. Whereas, 4, 5 + 6 are stretching

-Mode 4 is highly symmetric

-Mode 1 is known as the "umbrella" mode

-You would expect to see 6 bands in an experimental spectrum of gaseous ammonia

'''Charge distribution'''

We would expect hydrogen to be positive and, as a consequence, the nitrogen to be negative

H = 0.375

N = -1.125

----

'''N2 Molecule'''

N-N bond distance = 1.09200

'''Key information from optimised job'''

Molecule name = N2

Calculation method = RB3LYP

Basis set = 6-31G(d,p)

Final energy E(RB3LYP) in atomic units = -109.52359111

Point group of molecule = D*H

'''Item table'''
<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
</pre>

There was just one mode of vibration identified; frequency = 2457.33, infrared = 0

----

'''H2 Molecule'''

H-H bond distance = 0.60000

'''Key information from optimised job'''

Molecule name = H2

Calculation method = RB3LYP

Basis set = 6-31G(d,p)

Final energy E(RB3LYP) in atomic units = -1.15928020

Point group of molecule = D*H

'''Item table'''
<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
</pre>

There was just one mode of vibration identified; frequency = 2457.33, infrared = 0

----

'''Reaction energies'''

N2 + 3H2 --> 2NH3

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.11410576 au

-0.11410576*2625.5 = -299.5846729

----

Rep:Mod:asdfgh1234

2018-03-13T12:35:05Z

Gn116:

'''NH3 molecule'''

N-H bond distance = 1.01798

H-N-H bond angle = 37.129

'''Key information from optimised job'''

Molecule name = NH3

Calculation method = RB3LYP

Basis set = 6-31G(d,p)

Final energy E(RB3LYP) in atomic units = -56.55776873

Point group of molecule = C3V

'''Item table'''
<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
</pre>

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>blue</color>
<size>400</size>
<uploadedFileContents>gn116_NH3_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.01798.37.129</script>
</jmolApplet></jmol>

The optimisation file is linked to [[Media:gn116_NH3_OPTF_POP.LOG| here]]

'''Vibrations and charges'''

[[File:Gn116_nh3_vibrations_resized.JPG]]

-6 modes would be expected from the 3N-6 rule

-Modes 2 + 3 and 5 + 6 are degenerate (ie have the same energy)

-Vibration modes 1, 2 + 3 are bending. Whereas, 4, 5 + 6 are stretching

-Mode 4 is highly symmetric

-Mode 1 is known as the "umbrella" mode

-You would expect to see 6 bands in an experimental spectrum of gaseous ammonia

'''Charge distribution'''

We would expect hydrogen to be positive and, as a consequence, the nitrogen to be negative

H = 0.375

N = -1.125

----

'''N2 Molecule'''

N-N bond distance = 1.09200

'''Key information from optimised job'''

Molecule name = N2

Calculation method = RB3LYP

Basis set = 6-31G(d,p)

Final energy E(RB3LYP) in atomic units = -109.52359111

Point group of molecule = D*H

''There was just one mode of vibration identified; frequency = 2457.33, infrared = 0''

'''Item table'''
<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
</pre>

----

'''H2 Molecule'''

H-H bond distance = 0.60000

'''Key information from optimised job'''

Molecule name = H2

Calculation method = RB3LYP

Basis set = 6-31G(d,p)

Final energy E(RB3LYP) in atomic units = -1.15928020

Point group of molecule = D*H

'''Item table'''
<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
</pre>

----

'''Reaction energies'''

N2 + 3H2 --> 2NH3

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.11410576 au

-0.11410576*2625.5 = -299.5846729

----

Rep:Mod:asdfgh1234

2018-03-13T12:15:21Z

Gn116:

'''NH3 molecule'''

N-H bond distance = 1.01798

H-N-H bond angle = 37.129

'''Key information from optimised job'''

Molecule name = NH3

Calculation method = RB3LYP

Basis set = 6-31G(d,p)

Final energy E(RB3LYP) in atomic units = -56.55776873

Point group of molecule = C3V

'''Item table'''
<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
</pre>

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>blue</color>
<size>400</size>
<uploadedFileContents>gn116_NH3_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.01798.37.129</script>
</jmolApplet></jmol>

The optimisation file is linked to [[Media:gn116_NH3_OPTF_POP.LOG| here]]

'''Vibrations and charges'''

[[File:Gn116_nh3_vibrations_resized.JPG]]

-6 modes would be expected from the 3N-6 rule

-Modes 2 + 3 and 5 + 6 are degenerate (ie have the same energy)

-Vibration modes 1, 2 + 3 are bending. Whereas, 4, 5 + 6 are stretching

-Mode 4 is highly symmetric

-Mode 1 is known as the "umbrella" mode

-You would expect to see 6 bands in an experimental spectrum of gaseous ammonia

'''Charge distribution'''

We would expect hydrogen to be positive and, as a consequence, the nitrogen to be negative

H = 0.375

N = -1.125

----

'''N2 Molecule'''

N-N bond distance = 1.09200

'''Key information from optimised job'''

Molecule name = N2

Calculation method = RB3LYP

Basis set = 6-31G(d,p)

Final energy E(RB3LYP) in atomic units = -109.52359111

Point group of molecule = D*H

'''Item table'''
<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
</pre>

----

'''H2 Molecule'''

H-H bond distance = 0.60000

'''Key information from optimised job'''

Molecule name = H2

Calculation method = RB3LYP

Basis set = 6-31G(d,p)

Final energy E(RB3LYP) in atomic units = -1.15928020

Point group of molecule = D*H

'''Item table'''
<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
</pre>

----

'''Reaction energies'''

N2 + 3H2 --> 2NH3

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.11410576 au

-0.11410576*2625.5 = -299.5846729

----

Rep:Mod:asdfgh1234

2018-03-13T11:50:26Z

Gn116:

'''NH3 molecule'''

N-H bond distance = 1.01798

H-N-H bond angle = 37.129

'''Key information from optimised job'''

Molecule name = NH3

Calculation method = RB3LYP

Basis set = 6-31G(d,p)

Final energy E(RB3LYP) in atomic units = -56.55776873

Point group of molecule = C3V

'''Item table'''
<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
</pre>

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>blue</color>
<size>400</size>
<uploadedFileContents>gn116_NH3_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.01798.37.129</script>
</jmolApplet></jmol>

The optimisation file is linked to [[Media:gn116_NH3_OPTF_POP.LOG| here]]

'''Vibrations and charges'''

[[File:Gn116_nh3_vibrations_resized.JPG]]

-6 modes would be expected from the 3N-6 rule

-Modes 2 + 3 and 5 + 6 are degenerate (ie have the same energy)

-Vibration modes 1, 2 + 3 are bending. Whereas, 4, 5 + 6 are stretching

-Mode 4 is highly symmetric

-Mode 1 is known as the "umbrella" mode

-You would expect to see 6 bands in an experimental spectrum of gaseous ammonia

'''Charge distribution'''

We would expect hydrogen to be positive and, as a consequence, the nitrogen to be negative

H = 0.375

N = -1.125

----

'''N2 Molecule'''

N-N bond distance = 1.09200

'''Key information from optimised job'''

Molecule name = N2

Calculation method = RB3LYP

Basis set = 6-31G(d,p)

Final energy E(RB3LYP) in atomic units = -109.52359111

Point group of molecule = D*H

'''Item table'''
<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
</pre>

----

'''H2 Molecule'''

H-H bond distance = 0.60000

'''Key information from optimised job'''

Molecule name = H2

Calculation method = RB3LYP

Basis set = 6-31G(d,p)

Final energy E(RB3LYP) in atomic units = -1.15928020

Point group of molecule = D*H

'''Item table'''
<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
</pre>

----

'''Reaction energies'''

N2 + 3H2 --> 2NH3

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.11410576 au

-0.11410576*2625.5 = -299.5846729

Rep:Mod:asdfgh1234

2018-03-13T11:40:24Z

Gn116:

Rep:Mod:asdfgh1234

2018-03-13T11:27:43Z

Gn116:

Rep:Mod:asdfgh1234

2018-03-13T11:10:56Z

Gn116:

Rep:Mod:asdfgh1234

2018-03-13T10:55:18Z

Gn116:

Rep:Mod:asdfgh1234

2018-03-13T10:51:32Z

Gn116:

Rep:Mod:asdfgh1234

2018-03-13T10:50:47Z

Gn116:

Rep:Mod:asdfgh1234

2018-03-13T10:50:03Z

Gn116:

'''NH3 molecule'''

----

N-H bond distance = 1.01798
H-N-H bond angle = 37.129

'''Key information from optimised job'''

Molecule name = NH3
Calculation method = RB3LYP
Basis set = 6-31G(d,p)
Final energy E(RB3LYP) in atomic units = -56.55776873
Point group of molecule = C3V

'''Item Table'''
<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
</pre>

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>blue</color>
<size>400</size>
<uploadedFileContents>gn116_NH3_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.01798.37.129</script>
</jmolApplet></jmol>

The optimisation file is linked to [[Media:gn116_NH3_OPTF_POP.LOG| here]]

'''Vibrations and charges'''

[[File:Gn116_nh3_vibrations_resized.JPG]]

-6 modes would be expected from the 3N-6 rule
-Modes 2 + 3 and 5 + 6 are degenerate (ie have the same energy)
-Vibration modes 1, 2 + 3 are bending. Whereas, 4, 5 + 6 are stretching
-Mode 4 is highly symmetric
-Mode 1 is known as the "umbrella" mode
-You would expect to see 6 bands in an experimental spectrum of gaseous ammonia

'''Charge distribution'''

We would expect hydrogen to be positive and, as a consequence, the nitrogen to be negative
H = 0.375
N = -1.125

Rep:Mod:asdfgh1234

2018-03-13T10:43:34Z

Gn116:

[['''NH3 molecule''']]

N-H bond distance = 1.01798 Å

H-N-H bond angle = 37.129

'''Key information from optimised job'''

Molecule name = NH3

Calculation method = RB3LYP

Basis set = 6-31G(d,p)

Final energy E(RB3LYP) in atomic units = -56.55776873

Point group of molecule = C3V

'''Item Table'''
<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
</pre>

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>blue</color>
<size>400</size>
<uploadedFileContents>gn116_NH3_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.01798.37.129</script>
</jmolApplet></jmol>

The optimisation file is linked to [[Media:gn116_NH3_OPTF_POP.LOG| here]]

'''Vibrations and charges'''

[[File:Gn116_nh3_vibrations_resized.JPG]]

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

Which modes are degenerate (ie have the same energy)? 2 and 3; 5 and 6

Which modes are "bending" vibrations and which are "bond stretch" vibrations? 1, 2 and 3 are bending vibrations. Whereas, 4, 5 and 6 are examples of bond stretching vibrations

Which mode is highly symmetric? Mode 4 is highly symmetric

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? 6

'''Charge distribution'''

N = 0.375
N = -1.125
Include in your wiki the charge of the atoms. when carrying out calculations it is always good to check your results against your expectations. write a sentence saying what charge positive or negative you would expect and why

Rep:Mod:asdfgh1234

2018-03-13T10:43:22Z

Gn116:

[['''NH3 molecule'''
]]

N-H bond distance = 1.01798 Å

H-N-H bond angle = 37.129

'''Key information from optimised job'''

Molecule name = NH3

Calculation method = RB3LYP

Basis set = 6-31G(d,p)

Final energy E(RB3LYP) in atomic units = -56.55776873

Point group of molecule = C3V

'''Item Table'''
<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
</pre>

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>blue</color>
<size>400</size>
<uploadedFileContents>gn116_NH3_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.01798.37.129</script>
</jmolApplet></jmol>

The optimisation file is linked to [[Media:gn116_NH3_OPTF_POP.LOG| here]]

'''Vibrations and charges'''

[[File:Gn116_nh3_vibrations_resized.JPG]]

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

Which modes are degenerate (ie have the same energy)? 2 and 3; 5 and 6

Which modes are "bending" vibrations and which are "bond stretch" vibrations? 1, 2 and 3 are bending vibrations. Whereas, 4, 5 and 6 are examples of bond stretching vibrations

Which mode is highly symmetric? Mode 4 is highly symmetric

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? 6

'''Charge distribution'''

N = 0.375
N = -1.125
Include in your wiki the charge of the atoms. when carrying out calculations it is always good to check your results against your expectations. write a sentence saying what charge positive or negative you would expect and why

Rep:Mod:asdfgh1234

2018-03-13T10:24:31Z

Gn116:

'''NH3 molecule'''

N-H bond distance = 1.01798 Å

H-N-H bond angle = 37.129

'''Key information from optimised job'''

Molecule name = NH3

Calculation method = RB3LYP

Basis set = 6-31G(d,p)

Final energy E(RB3LYP) in atomic units = -56.55776873

Point group of molecule = C3V

'''Item Table'''
<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
</pre>

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>blue</color>
<size>400</size>
<uploadedFileContents>gn116_NH3_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.01798.37.129</script>
</jmolApplet></jmol>

The optimisation file is linked to [[Media:gn116_NH3_OPTF_POP.LOG| here]]

'''Vibrations and charges'''

[[File:Gn116_nh3_vibrations_resized.JPG]]

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

Which modes are degenerate (ie have the same energy)? 2 and 3; 5 and 6

Which modes are "bending" vibrations and which are "bond stretch" vibrations? 1, 2 and 3 are bending vibrations. Whereas, 4, 5 and 6 are examples of bond stretching vibrations

Which mode is highly symmetric? Mode 4 is highly symmetric

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? 6

'''Charge distribution'''

N = 0.375
N = -1.125
Include in your wiki the charge of the atoms. when carrying out calculations it is always good to check your results against your expectations. write a sentence saying what charge positive or negative you would expect and why

Rep:Mod:asdfgh1234

2018-03-13T10:24:10Z

Gn116:

'''NH3 molecule'''

N-H bond distance = 1.01798 Å

H-N-H bond angle = 37.129

'''Key information from optimised job'''

Molecule name = NH3

Calculation method = RB3LYP

Basis set = 6-31G(d,p)

Final energy E(RB3LYP) in atomic units = -56.55776873

Point group of molecule = C3V

'''Item Table'''
<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
</pre>

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>blue</color>
<size>400</size>
<uploadedFileContents>gn116_NH3_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.01798.37.129</script>
</jmolApplet></jmol>

The optimisation file is linked to [[Media:gn116_NH3_OPTF_POP.LOG| here]]

'''Vibrations and charges'''

[[File:Gn116_nh3_vibrations_resized.JPG]]

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

Which modes are degenerate (ie have the same energy)? 2 and 3; 5 and 6

Which modes are "bending" vibrations and which are "bond stretch" vibrations? 1, 2 and 3 are bending vibrations. Whereas, 4, 5 and 6 are examples of bond stretching vibrations

Which mode is highly symmetric? Mode 4 is highly symmetric

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? 6

'''Charge distribution'''
N = 0.375
N = -1.125
Include in your wiki the charge of the atoms. when carrying out calculations it is always good to check your results against your expectations. write a sentence saying what charge positive or negative you would expect and why

Rep:Mod:asdfgh1234

2018-03-13T10:16:29Z

Gn116:

Rep:Mod:asdfgh1234

2018-03-13T10:06:12Z

Gn116:

'''NH3 molecule'''

N-H bond distance = 1.01798 Å

H-N-H bond angle = 37.129

'''Key information from optimised job'''

Molecule name = NH3

Calculation method = RB3LYP

Basis set = 6-31G(d,p)

Final energy E(RB3LYP) in atomic units = -56.55776873

Point group of molecule = C3V

'''Item Table'''
<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
</pre>

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>blue</color>
<size>400</size>
<uploadedFileContents>gn116_NH3_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.01798.37.129</script>
</jmolApplet></jmol>

The optimisation file is linked to [[Media:gn116_NH3_OPTF_POP.LOG| here]]

'''Vibrations and charges'''

[[File:Gn116_nh3_vibrations_resized.JPG]]

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

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

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

Which mode is highly symmetric?

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

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

Rep:Mod:asdfgh1234

2018-03-13T10:05:44Z

Gn116:

'''NH3 molecule'''

N-H bond distance = 1.01798 Å

H-N-H bond angle = 37.129

'''Key information from optimised job'''
Molecule name = NH3

Calculation method = RB3LYP

Basis set = 6-31G(d,p)

Final energy E(RB3LYP) in atomic units = -56.55776873

Point group of molecule = C3V

'''Item Table'''
<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
</pre>

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>blue</color>
<size>400</size>
<uploadedFileContents>gn116_NH3_OPTF_POP.LOG</uploadedFileContents>
<script>frame 1.01798.37.129</script>
</jmolApplet></jmol>

The optimisation file is linked to [[Media:gn116_NH3_OPTF_POP.LOG| here]]

'''Vibrations and Charges'''

[[File:Gn116_nh3_vibrations_resized.JPG]]

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

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

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

Which mode is highly symmetric?

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

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

Rep:Mod:asdfgh1234

2018-03-13T10:03:34Z

Gn116:

File:Gn116 nh3 vibrations resized.JPG

2018-03-13T10:02:55Z

Gn116:

Rep:Mod:asdfgh1234

2018-03-13T10:00:17Z

Gn116:

Rep:Mod:asdfgh1234

2018-03-13T09:59:30Z

Gn116:

File:Gn116 nh3 vibrations.jpg

2018-03-13T09:58:12Z

Gn116:

Rep:Mod:asdfgh1234

2018-03-13T09:34:20Z

Gn116: