== NH3 ==
To find the optimized structure for ammonia on Gaussian the following was used:
- The calculation method was B3LYP
- The basis set was 6-31G (D,P)
- The final energy was -56.55776873 au
- The RMS Gradient was 0.00000485 au
- The point group was C3
The bond length between N and H is 1.01798 angstroms
The bond angle for H - N - H is 105.741 degrees
<jmol><jmolApplet><script>frame 1.12</script>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ANISHA SRI NH3 OPTF POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
The link to my NH3 file is [[Media:ANISHA SRI NH3 OPTF POP.LOG|here]]
The display vibrations for NH3
[[File:Anisha sri display vibrations nh3.PNG]]

The expected number of vibrational modes should be 6 but due to degeneracy there are actually only 4 vibrational modes. Of these vibrational modes the bending modes are at 1089.54 s -1 and 1693.95 s -1 , whilst the bond stretching modes are at 3461.29 s s-1 and 3589.82 s -1 . The highly symmetric mode 3461.29 s-1 is at and the umbrella mode is at 1089.54 s -1. The number of bands expected in an experimental spectrum of gaseous ammonia is 1 as the bonds are all the same, however there are 2 bands in the spectrum as shown below. The reason for two peaks is because the vibrations at 2 frequencies(1089.54s-1 and 1693.95s-1)have intensities (145.3814, 13.5533) that are high enough to be seen on the spectrum

[[File:Anisha sri nh3ir.PNG]]

The charges expected for nitrogen was -1 and for hydrogen was +0.5 because nitrogen is more electronegative so would withdraw more electron density towards its nucleus. The values found on Gaussian was -1.125 for nitrogen and +0.375 for hydrogen.

===N2===
To find the optimized structure for nitrogen on Gaussian the following was used:
- The calculation method was B3LYP
- The basis set was 6-31G (D,P)
- The final energy was -109.52412868 au
- The RMS Gradient was 0.00000365 au
- The point group was D∞h
The bond length between N and N is 1.10550 angstroms
<jmol><jmolApplet><script>frame 1.12</script>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ANISHA SRI N2 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>
The link to my N2 file is [[Media:ANISHA SRI N2 OPT.LOG|here]]
A nitrogen molecule has one vibrational mode at a frequency of 2457.31 s-1

===H2===
To find the optimized structure for hydrogen on Gaussian the following was used:
- The calculation method was B3LYP
- The basis set was 6-31G (D,P)
- The final energy was -1.17853930 au
- The RMS Gradient was 0.00012170 au
- The point group was D∞h
The bond length between H and H is 0.74309 angstroms
<jmol><jmolApplet><script>frame 1.12</script>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ANISHA SRI H2 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>
The link to my H2 file is [[Media:ANISHA SRI H2 OPT.LOG|here]]
A hydrogen molecule has one vibrational mode at a frequency of 4461.48 s-1

===Reaction Energy===
- E(NH3)= -56.55776873 au
- 2*E(NH3)= -113.11553746 au
- E(N2)= -109.52412868 au
- E(H2)= -1.17853930 au
- 3*E(H2)= -3.5356179 au
- ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.05579096 au

The energy required to form ammonia gas from nitrogen gas and hydrogen gas in the Haber-Bosch reaction is -146.48 KJmol-1.

Nitrogen gas and hydrogen gas are not as stable as ammonia gas and so as it has the most exothermic energy and so is the most stable. Nitrogen gas, however, is around 10 times more stable than hydrogen gas, so is closer in stability to ammonia than hydrogen gas.

== PH5 ==
To find the optimized structure for PH5 on Gaussian the following was used:
- The calculation method was B3LYP
- The basis set was 6-31G (D,P)
- The final energy was -344.25491049 au
- The RMS Gradient was 0.00000456 au
- The point group was C3
The bond lengths between P and H are 1.48691 angstroms (2 H in the same plane) and 1.43320 angstroms (3 H in the same plane)
The bond angle between the 2 H atoms in the same plane is 180 degrees, the bond angle between the 3 H atoms in the same plane is 120 degrees and the bond angle between the H atoms in different planes is 89.999 degrees.
<jmol><jmolApplet><script>frame 1.12</script>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ANISHA SRI PH5 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>
The link to my PH5 file is [[Media:ANISHA SRI PH5 OPT.LOG|here]]

PH5 has 12 vibrational modes but due to degeneracy there are actually 8 vibrational modes at the following frequencies; 498.01s-1(bending mode), 1206.92s-1(bending mode), 1272.94s-1(bending mode), 1469.97s-1(bending mode), 1847.92s-1(stretching mode), 1940.95s-1(stretching mode), 2296.29s-1(stretching mode), and 2301.98s-1(stretching mode). On the infrared spectrum, only 5 peaks can be seen because the intensities are high and significant enough to be visible on the infrared spectrum.

[[File:Anisha sri ph5ir.PNG]]

The charge distribution for PH5 is as follows, phosphorous has a charge of +0.412, the 3 hydrogen atoms planar to each other have a charge of -0.015 and the 2 hydrogen atoms linear to each other have a a charge of -0.183. Phosphorous is a much larger atom than hydrogen so even though the nuclear charge is much higher, the surrounding electrons shield this charge, making phosphorous less electronegative than hydrogen hence the result in the charge distribution of PH5. Overall, however, the molecule is neutral.

Hydrogen has an electron configuration of 1s1. Phosphorous has an electron configuration of 1s2 2s2 2p6 3s2 3p3. The electrons involved in bonding are the electrons in the 3s and 3p orbitals of phosphorous and the electron found in each 1s orbital of the hydrogen atoms.

take a snapshot of 5 MOs that you find interesting include them in your wiki. Include a few sentences describing the character of your chosen MOs. For example, what AOs contribute to the MO? Is the MO bonding, anti bonding or a mixture. Is the MO deep in energy, in the HOMO/LUMO region or high in energy? Is the MO occupied or unoccupied? What effect will your MOs have on bonding?

Molecular Orbital 1-
This molecular orbital is an occupied sigma gerada bonding orbital made up of the 3s atomic orbital of phosphorous and a 1s atomic orbital from hydrogen.

[[File:Molecular Orbital 1.PNG]]

Molecular Orbital 2-
This molecular orbital is an occupied sigma gerada bonding orbital made up of the 3px atomic orbital of phosphorous and the atomic 1s orbitals of the 2 hydrogen atoms in the same plane as they are in the same phase as the 3px orbital phases.

[[File:Anisha sri Molecular Orbital 1.PNG]]

Molecular Orbital 3-
This molecular orbital is an occupied sigma gerada bonding orbital made up of the 3py atomic orbital of phosphorous and 1s atomic orbitals of the 3 hydrogen atoms in the same plane as the phases are the same as the 3py orbital which allows orbital mixing.

[[File:Anisha Sri MO3.PNG]]

Molecular Orbital 4-
This molecular orbital is an occupied sigma gerada bonding orbital made up of the 3pz atomic orbital of phosphorous and a 1s atomic orbitals of the 2 hydrogen atoms in the same plane as they are in the same phase as the 3pz orbital.

[[File:Anisha Sri MO4.PNG]]

Molecular Orbital 5-
This molecular orbital is one that is too deep in energy to be used in bonding as it depicts the 2p orbitals of the phosphorous atom. It is degenerate in energy as there are 3 full 2p orbitals that are all equal in energy and so all have the same orbital structure along each of the Cartesian axes (x,y,z).

[[File:Anisha Sri MO5.PNG]]

Molecular Orbital 6-
This molecular orbital is the highest occupying molecular orbital and uses atomic orbitals from the phosphorous and atomic orbitals from the hydrogen atoms, the 3 hydrogen atoms in the same plane mix with one phase of the phosphorous orbital and the 2 hydrogen atoms in the same plane mix with the other phase of the phosphorous orbital to form the molecular orbital that involves all the atoms in the molecule.

[[File:Anisha Sri MO6.PNG]]

== Log Book ==
=== NH3 ===
<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>

===N2===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000002 0.001800 YES
RMS Displacement 0.000003 0.001200 YES
</pre>

===H2===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000211 0.000450 YES
RMS Force 0.000211 0.000300 YES
Maximum Displacement 0.000278 0.001800 YES
RMS Displacement 0.000393 0.001200 YES
</pre>

===PH5===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000046 0.001800 YES
RMS Displacement 0.000019 0.001200 YES
</pre>

Molecular modelling01368873

2018-03-15T16:03:57Z

2018-03-15T14:58:34Z

As11117:

== NH3 ==
To find the optimized structure for ammonia on Gaussian the following was used:
- The calculation method was B3LYP
- The basis set was 6-31G (D,P)
- The final energy was -56.55776873 au
- The RMS Gradient was 0.00000485 au
- The point group was C3
The bond length between N and H is 1.01798 angstroms
The bond angle for H - N - H is 105.741 degrees
<jmol><jmolApplet><script>frame 1.12</script>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ANISHA SRI NH3 OPTF POP.LOG</uploadedFileContents>
</jmolApplet></jmol>
The link to my NH3 file is [[Media:ANISHA SRI NH3 OPTF POP.LOG|here]]
The display vibrations for NH3
[[File:Anisha sri display vibrations nh3.PNG]]

The expected number of vibrational modes should be 6 but due to degeneracy there are actually only 4 vibrational modes. Of these vibrational modes the bending modes are at 1089.54 s -1 and 1693.95 s -1 , whilst the bond stretching modes are at 3461.29 s s-1 and 3589.82 s -1 . The highly symmetric mode 3461.29 s-1 is at and the umbrella mode is at 1089.54 s -1. The number of bands expected in an experimental spectrum of gaseous ammonia is 1 as the bonds are all the same, however there are 2 bands in the spectrum as shown below. The reason for two peaks is because the vibrations at 2 frequencies(1089.54s-1 and 1693.95s-1)have intensities (145.3814, 13.5533) that are high enough to be seen on the spectrum

[[File:Anisha sri nh3ir.PNG]]

The charges expected for nitrogen was -1 and for hydrogen was +0.5 because nitrogen is more electronegative so would withdraw more electron density towards its nucleus. The values found on Gaussian was -1.125 for nitrogen and +0.375 for hydrogen.

===N2===
To find the optimized structure for nitrogen on Gaussian the following was used:
- The calculation method was B3LYP
- The basis set was 6-31G (D,P)
- The final energy was -109.52412868 au
- The RMS Gradient was 0.00000365 au
- The point group was D∞h
The bond length between N and N is 1.10550 angstroms
<jmol><jmolApplet><script>frame 1.12</script>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ANISHA SRI N2 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>
The link to my N2 file is [[Media:ANISHA SRI N2 OPT.LOG|here]]
A nitrogen molecule has one vibrational mode at a frequency of 2457.31 s-1

===H2===
To find the optimized structure for hydrogen on Gaussian the following was used:
- The calculation method was B3LYP
- The basis set was 6-31G (D,P)
- The final energy was -1.17853930 au
- The RMS Gradient was 0.00012170 au
- The point group was D∞h
The bond length between H and H is 0.74309 angstroms
<jmol><jmolApplet><script>frame 1.12</script>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ANISHA SRI H2 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>
The link to my H2 file is [[Media:ANISHA SRI H2 OPT.LOG|here]]
A hydrogen molecule has one vibrational mode at a frequency of 4461.48 s-1

===Reaction Energy===
- E(NH3)= -56.55776873 au
- 2*E(NH3)= -113.11553746 au
- E(N2)= -109.52412868 au
- E(H2)= -1.17853930 au
- 3*E(H2)= -3.5356179 au
- ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.05579096 au

The energy required to form ammonia gas from nitrogen gas and hydrogen gas in the Haber-Bosch reaction is -146.48 KJmol-1.

Nitrogen gas and hydrogen gas are not as stable as ammonia gas and so as it has the most exothermic energy and so is the most stable. Nitrogen gas, however, is around 10 times more stable than hydrogen gas, so is closer in stability to ammonia than hydrogen gas.

== PH5 ==
To find the optimized structure for PH5 on Gaussian the following was used:
- The calculation method was B3LYP
- The basis set was 6-31G (D,P)
- The final energy was -344.25491049 au
- The RMS Gradient was 0.00000456 au
- The point group was C3
The bond lengths between P and H are 1.48691 angstroms (2 H in the same plane) and 1.43320 angstroms (3 H in the same plane)
The bond angle between the 2 H atoms in the same plane is 180 degrees, the bond angle between the 3 H atoms in the same plane is 120 degrees and the bond angle between the H atoms in different planes is 89.999 degrees.
<jmol><jmolApplet><script>frame 1.12</script>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ANISHA SRI PH5 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>
The link to my PH5 file is [[Media:ANISHA SRI PH5 OPT.LOG|here]]

PH5 has 12 vibrational modes but due to degeneracy there are actually 8 vibrational modes at the following frequencies; 498.01s-1(bending mode), 1206.92s-1(bending mode), 1272.94s-1(bending mode), 1469.97s-1(bending mode), 1847.92s-1(stretching mode), 1940.95s-1(stretching mode), 2296.29s-1(stretching mode), and 2301.98s-1(stretching mode). On the infrared spectrum, only 5 peaks can be seen because the intensities are high and significant enough to be visible on the infrared spectrum.

[[File:Anisha sri ph5ir.PNG]]

The charge distribution for PH5 is as follows, phosphorous has a charge of +0.412, the 3 hydrogen atoms planar to each other have a charge of -0.015 and the 2 hydrogen atoms linear to each other have a a charge of -0.183. Phosphorous is a much larger atom than hydrogen so even though the nuclear charge is much higher, the surrounding electrons shield this charge, making phosphorous less electronegative than hydrogen hence the result in the charge distribution of PH5. Overall, however, the molecule is neutral.

Hydrogen has an electron configuration of 1s1. Phosphorous has an electron configuration of 1s2 2s2 2p6 3s2 3p3. The electrons involved in bonding are the electrons in the 3s and 3p orbitals of phosphorous and the electron found in each 1s orbital of the hydrogen atoms.

take a snapshot of 5 MOs that you find interesting include them in your wiki. Include a few sentences describing the character of your chosen MOs. For example, what AOs contribute to the MO? Is the MO bondng, antibonding or a mixture. Is the MO deep in energy, in the HOMO/LUMO region or high in energy? Is the MO occupied or unoccupied? What effect will your MOs have on bonding?

Molecular Orbital 1
This molecular orbital is an occupied sigma bonding orbital made up of an electron from the 3s atomic orbital of phosphorous and a 1s atomic orbital from hydrogen.
[[File:Molecular Orbital 1.PNG]]

== Log Book ==
=== NH3 ===
<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>

===N2===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000002 0.001800 YES
RMS Displacement 0.000003 0.001200 YES
</pre>

===H2===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000211 0.000450 YES
RMS Force 0.000211 0.000300 YES
Maximum Displacement 0.000278 0.001800 YES
RMS Displacement 0.000393 0.001200 YES
</pre>

===PH5===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000046 0.001800 YES
RMS Displacement 0.000019 0.001200 YES
</pre>

File:Molecular Orbital 1.PNG

2018-03-15T14:56:21Z

As11117:

Molecular modelling01368873