View source for Rep:Mod:yg5515

=== NH3 ===

==== summary ====
{| class="wikitable"
|molecule name
|NH3
|-
|calculation method
|RB3LYP
|-
|Calculation type
|FREQ
|-
|Basis set
|6-31G(d,p)
|-
|E(RB3LYP)
|<nowiki>-56.55776863 a.u.</nowiki>
|-
|RMS Gradient Norm
|0.00000478 a.u.
|-
|point group
|C3V
|-
|'''bond length''' 
|1.01797
|-
|'''bond angle'''
|105.743
|}

====item table====
{| class="wikitable"
!item
!value
!threshold
!converged?
|-
|maximum force
|0.000004
|0.000450
|Yes
|-
|RMS force
|0.000004
|0.000300
|Yes
|-
|maximum displacement
|0.000071
|0.001800
|Yes
|-
|RMS displacement
|0.000034 
|0.001200
|Yes
|}
Predicted change in Energy=-5.828496D-10
 Optimization completed.
 	<jmol><jmolApplet>
  <title>NH3</title>
  <color>black</color>
  <size>200</size>
  <uploadedFileContents>Yihan Gao NH3 OPTF POP.GJF.LOG </uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:Yihan Gao NH3 OPTF POP.GJF.LOG|here]]

====frequency analysis====

[[File:Windowyg5515.png]]

Questions:
* 6 modes are expected from the rule, however, from the experimental observation, two pairs of the vibrations are degenerate. 
* modes 2 and 3, 5 and 6 are degenerate
* bending has lower energy than stretching. Modes1, 2,and 3 are bending which correspond to lower frequency. Modes 4,5, and 6 are stretching which have higher frequency. It can be confirmed by running the animation.
* Modes 1 and 4 are highly symmetric
* mode 1 is umbrella mode.
* 4 bands are observed. The two different modes which have frequencies 3461 and 3589 are low in intensity.
====charge analysis====
[[File:MH3 2 charge.jpg|300px]]


N:-1.125

H:0.375

The result is expected, because N is more electronegative than H, it draws electrons towards itself. So the energy of N should be more negative than H.

==N2==
====summary====
Name: N2

calculation type:FREQ

calculation method :RB3LYP

Basis set:6-31G(d.p)

E(RB3LYP):-109.52412868 a.u.

RMS gradient:0.00000060

point group : D<sub>infh</sub>

bond length :1.10550

bond angle :180

====item table====
 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=-3.400898D-13
 Optimization completed.
<jmol><jmolApplet>
  <title>N2</title>
  <color>black</color>
  <size>200</size>
  <uploadedFileContents>YG5515 N2.LOG</uploadedFileContents>
</jmolApplet></jmol>
The optimisation file is liked to [[Media:YG5515 N2.LOG|here]]
====frequency analysis====
[[File:window2.png]]


questions:
N2 shows one mode only.

==H2==
====summary====
Name: H2

calculation type:FREQ

calculation method :RB3LYP

Basis set:6-31G(d.p)

E(RB3LYP)-1.17853936 a.u.

RMS gradient:0.00000017

point group : D<sub>infh</sub>

bond length :0.60000

bond angle :180

====item table====
  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
 Optimization completed.
<jmol><jmolApplet>
  <title>H2</title>
  <color>black</color>
  <size>200</size>
  <uploadedFileContents>YG5515_H2_OPMITIZATION.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[Media:YG5515_H2_OPMITIZATION.LOG|here]]
    
====frequency analysis====
[[File:Window3.png]]


question:
only one mode is observed.

==Energy calculation==

•	E(NH3)= -56.55776863

•	2*E(NH3)= -113.11553726

•	E(N2)= -109.52412868

•	E(H2)= -1.17853936

•	3*E(H2)= -3.53561808

•	ΔE=2*E(NH3)-[E(N2)+3*E(H2)]=-0.0557907a.u.  / -146.48KJ/mol


The energy change is negative. This is an exothermic reaction and it is energetically favorable.

== My project molecule: H<sub>2</sub>O ==

====summary====

H2O optimization

File Name	yg5515 H2O

File Type	.log

Calculation Type	FREQ

Calculation Method	RB3LYP

Basis Set	6-31G(d,p)

Charge	0

Spin	Singlet

E(RB3LYP)	-76.41892999	 a.u.

RMS Gradient Norm	0.00684281	 a.u.

Imaginary Freq

Dipole Moment	1.9531	 Debye

Point Group	C<sub>2</sub>V

====item table====
Item               Value     Threshold  Converged?
 Maximum Force            0.000099     0.000450     YES
 RMS     Force            0.000081     0.000300     YES
 Maximum Displacement     0.000115     0.001800     YES
 RMS     Displacement     0.000120     0.001200     YES
 Predicted change in Energy=-1.939669D-08
 Optimization completed.

<jmol><jmolApplet>
  <title>H2O</title>
  <color>black</color>
  <size>200</size>
  <uploadedFileContents>YG5515_H2O.LOG</uploadedFileContents>
</jmolApplet></jmol>
The optimisation file is liked to [[Media:YG5515_H2O.LOG|here]]

====frequency analysis====
[[File:Frequency.png]]


Totally, there are three modes. The first mode is bending. The socond and the third are symmetric and unsymmetrical stretchings.

====charge distribution====

[[File:Window4.png|300px]]


O is more electronegative, it draws the electrons towards itself, so the charge of O is negative.

====MO analysis====
=====MO diagram=====
The electronic configuration of O is 1S<sup>2</sup> 2S<sup>2</sup> 2P<sup>4</sup>
H: 1S<sup>2


[[File:Google.png]](Fig.1)


[[File:google2.png]](Fig.2)



http://www1.lsbu.ac.uk/water/h2o_orbitals.html
https://en.wikipedia.org/wiki/Molecular_orbital_diagram

=====MO images=====
[[File:MO(1).png]]


This is the orbital which has the lowest energy. The two electrons are all from the 1S orbital of the O. Orbitals which have the same symmetry and are closer in energy are allowed to mix to generate new sets of molecular orbitals. Because the 1S electrons are too low in energy, they are not involved in the orbital mixing. The orbital is the 1a<sub>1</sub> in the Fig.1.

[[File:MO2.png]]

This occupied bonding orbital is 2a<sub>1</sub> in the figures. Mixing of the oxygen 2s AO and the hydrogen σ MO generate the MO orbital.


[[File:MO3.png]]

1b<sub>2</sub> is an occupied bonding MO and it is from mixing of the oxygen 2p<sub>y</sub> AO and the hydrogen σ* MO.

[[File:MO4.png]]

Mixing of the oxygen 2p<sub>z</sub> AO and the hydrogen σ MO generate the occupied bonding 3a<sub>1</sub> MO.

[[File:MO5.png]]

This is 1b<sub>1</sub> nonbonding MO from the oxygen 2p<sub>x</sub> AO (the p-orbital perpendicular to the molecular plane). Importantly, this is the HOMO.

It should be noted that MO mixing can occur. If two molecular orbitals have the correct symmetry and similar energy they can mix to produce two new molecular orbitals.  2a<sub>1</sub> and 3a<sub>1</sub> can mix.  2a<sub>1</sub> and 4a<sub>1</sub> can also mix.