ChemWiki - User contributions [en]

Rep:Mod:feihemodule3

2008-12-17T14:14:02Z

Fh106: /* Module 3 */

=Module 3 (Experiment 3)=

Rep:Mod:feihemodule3

2008-12-17T13:47:30Z

Fh106: /* Module 3 */

=Module 3=

Rep:Mod:feihemodule2

2008-12-17T13:43:09Z

Fh106: /* '''Mini Project''' */

='''Module 2'''=

=='''Introduction'''==

The aim of this module 2 is familiar with the Gussview programme and uses the programme to optimise the molecules.

Now look at the following simple molecule BH3.

===Create a molecule of BH3===

Use the Gussview programme to create the BH3 molecule. And we can the following picture of the molecule.

[[Image:FeiBh3.jpg]]

Picture of BH3 molecule.

And we can use label and symbol the molecule to get the following picture.

[[Image:FeiLabelledBH3.JPG]]

Labelled and symbol picture of BH3.

Then we set the all the three B-H bonds to 1.5 angstrom and get the following sturcure of BH3.

[[Image:FeiBh3fixedbondlength.JPG]]

Fixed bond distance picture of BH3

So the molecule is set up.

===Optimising a molecule of BH3===

Use the BLYP method and 3-21G basic set to optimise the molecule of BH3. And then we can the following optimised structure of the molecule.

[[Image:FeiOptimisedBH3.JPG]]

Optimised structure of BH3 molecule

Then we can determine the optimised B-H bond distance and H-B-H bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:FeiBH3bonddistance.JPG]]</td>
<td align="center">[[Image:FeiBH3bondangle.JPG]]</td>
</tr>
<tr>
<td align="center">Bond distance is 1.19435</td>
<td align="center">Bond angle is 120.000</td>
</tr>
</table>

And we can get a summary table to show some information about the molecule.

[[Image:FeiResulttable.JPG]]

Summary of the optimised molecule

From the above summary, we can see that the file of file is .log, calculation type is FOPT, calculation method is RB3LYP, basic set is 3-21G, final energy is -26.46226438 au, dipole moment is 0.000 debye, point group is D3H and the duration of calculation is 19.0 seconds.

We can get a “real” text based .log file as well.

[[Image:FeiRealresulttable.JPG]]

===Understanding optimisation part a===

Open the finished optimised file of the above molecule and tick “read intermediate geometries”. Then an energy and gradient against optimisation graph is obtained.

[[Image:FeiOptimisationgraph.JPG]]

There are 2 graphs in the above picture, the 1st one is energy against each step of optimisation and the 2nd one is the gradient of energy against each step of optimisation.

The green button in the molecule window is click and the animation of optimisation steps is obtained and we can see that the final structure has the least energy and smallest gradient of energy. So the stable structure is with the minimum energy and it is the final structure in the animation.

[[Image:FeiAnimation.JPG]]

=='''Exercise 1'''==

===Find information about BCl3===

Following the method introduced in the introduction section, repeat the calculation for molecule BCl3.

Firstly, create the molecule of BCl3. And measure its B-Cl bond distance and Cl-B-Cl bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:FeiBCL3bonddistance.JPG]]</td>
<td align="center">[[Image:BCL3bondangle.JPG]]</td>
</tr>
<tr>
<td align="center">Bond distance: 1.87000</td>
<td align="center">Bond angle is 120.000</td>
</tr>
</table>

Secondly, restrict the symmetry of BCl3 to D3h and set the tolerance from the default to “very tight (0.0001)” and obtain the following picture.

[[Image:FeiRestrictedBCL3.JPG]]

Restricted BCl3 molecule

Thirdly, do the calculation to optimise the BCl3 molecule and obtain the optimised structure of BCl3.

[[Image:FeiOptimisedBCL3.JPG]]

Optimised BCl3 molecule

And we then obtain the optimised B-Cl bond distance and optimised Cl-B-Cl bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:FeiOptimisedbonddistance.JPG]]</td>
<td align="center">[[Image:Optimisedbondangle.JPG]]</td>
</tr>
<tr>
<td align="center">Bond distance: 1.86592</td>
<td align="center">Bond angle is 120.000</td>
</tr>
</table>

Finally, we then get the summary of the optimised molecule.

[[Image:FeiSummary2.JPG]]

From the above summary table, we can know that the file type is .log, calculation type is FORT, calculation method is RB3LYP, basic set is LANL2MB, final energy is -69.43928112 AU, dipole moment is 0.000 debye, point group is D3h and the duration of calculation is 12.0 seconds.

===Independent work===

I chose H2O as my own molecule. Firstly, set up the molecule of H2O. And we can get the O-H bond distance and H-O-H bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:H2Obonddistance.JPG]]</td>
<td align="center">[[Image:H2Obondangle.JPG]]</td>
</tr>
<tr>
<td align="center">Bond distance: 0.96000</td>
<td align="center">Bond angle is 109.500</td>
</tr>
</table>

Since O atom and H atom is above second row, we do not need to use pseudo-potential.
Therefore, we use the same method as above in above section but we set the basis set to 3-21G and obtain the following optimised H2O molecule with its summary table.

[[Image:FeiH2Osummary.JPG]]

From the above summary table, we can see that the calculation method is RB3LYP, basis set is 3-21G, final energy is -75.97396515 AU, dipole moment is 2.2381 Debye, point group is C2v and duration of calculation is 17.0 seconds.

We now can get the optimised bond distance and bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:Optimisedbonddistance.jpg]]</td>
<td align="center">[[Image:Optimisedbondangle.jpg]]</td>
</tr>
<tr>
<td align="center">Optimised bond distance: 0.99683</td>
<td align="center">Optimised bond angle: 103.991</td>
</tr>
</table>

Now I set the basis set to higher level in order to increase the accuracy. Use the first optimised output file to do another optimisation using higher level basis set. And use the second optimised output file to do another optimisation using even higher basis set.

<table width="663" border="1">
<tr>
<th width="176" scope="col"> </th>
<th scope="col">First trial</th>
<th scope="col">Second trail</th>
<th scope="col">Third trail</th>
</tr>
<tr>
<th scope="row">Bond distance/AU</th>
<td width="143" valign="top">0.99683 </td>
<td width="149" valign="top">0.96526</td>
<td width="167" valign="top">0.96203</td>
</tr>
<tr>
<th scope="row">Bond angle/degree</th>
<td width="143" valign="top">103.991</td>
<td width="149" valign="top">103.696</td>
<td width="167" valign="top">105.057</td>
</tr>
<tr>
<th scope="row">Calculation method</th>
<td width="143" valign="top">RB3LYP</td>
<td width="149" valign="top">RB3LYP</td>
<td width="167" valign="top">RB3LYP</td>
</tr>
<tr>
<th scope="row">Basis set</th>
<td width="143" valign="top">3-21G</td>
<td width="149" valign="top">6-31G(d.p)</td>
<td width="167" valign="top">6-311+G(d,p)</td>
</tr>
<tr>
<th scope="row">Final energy/J</th>
<td width="143" valign="top">-75.97396515</td>
<td width="149" valign="top">-76.41973659</td>
<td width="167" valign="top">-76.45846294</td>
</tr>
<tr>
<th scope="row">Dipole moment/debye</th>
<td width="143" valign="top">2.2381</td>
<td width="149" valign="top">2.0436</td>
<td width="167" valign="top">2.1610</td>
</tr>
<tr>
<th scope="row">Point group</th>
<td width="143" valign="top">C2v</td>
<td width="149" valign="top">C2v</td>
<td width="167" valign="top">C2v</td>
</tr>
<tr>
<th scope="row">Duration of calculation/s</th>
<td width="143" valign="top">17.0</td>
<td width="149" valign="top">17.0</td>
<td width="167" valign="top">18.0</td>
</tr>
</table>

===Vibrational analysis and confirming minima===

In this section, we are going to use vibrational analysis to confirm the minimum structure.
Firstly, open the optimised BH3 file and do the vibrational analysis to confirm its minimum structure. So we get the following structure with its summary.

[[Image:FeiBH3frequncy.jpg]]

From the above summary table, we can see that the energy is -26.46226438 whereas the energy of the optimised one is -26.46226438. So they have got the same value.

===Animating the vibrations===

Open the vibrations result.

[[Image:FeiVibrations.jpg]]

Show display vectors of each vibration.

[[Image:FeiVibration2.jpg]]

The following table is to a summary of motions, frequency, intensities and symmetry.

<table width="716" border="1">
<tr>
<td width="24" valign="top">No.</td>
<td width="473" valign="top">Form of vibration</td>
<td width="59" valign="top">frequency</td>
<td width="65" valign="top">intensity</td>
<td width="61" valign="top">Symmetry 
D3h point group</td>
</tr>
<tr>
<td valign="top">1 </td>
<td valign="top">all the H atoms move in and out together in the same direction, the B atom moves in the opposite direction of that of H atom</td>
<td valign="top">1145.71</td>
<td valign="top">92.6991</td>
<td valign="top">A"2</td>
</tr>
<tr>
<td valign="top">2</td>
<td valign="top">2 bottomed H atoms moves towards and away from each other whereas B atom and top H atom is quite stationary</td>
<td valign="top">1204.66</td>
<td valign="top">12.3789</td>
<td valign="top">E'</td>
</tr>
<tr>
<td valign="top">3</td>
<td valign="top">Each of the bottomed H atom moves away and towards to the top H atom whereas B atom is quite stationary</td>
<td valign="top">1204.66</td>
<td valign="top">12.3814</td>
<td valign="top">E'</td>
</tr>
<tr>
<td valign="top">4</td>
<td valign="top">All H atoms move in and out together in a concerted motion whereas B atom is unmoved</td>
<td valign="top">2591.65</td>
<td valign="top">0.0</td>
<td valign="top">A'1</td>
</tr>
<tr>
<td valign="top">5</td>
<td valign="top">2 bottomed H atoms move towards or away from B atom simultaneously 
Top H atom and B atom is quite stationary</td>
<td valign="top">2731.31</td>
<td valign="top">103.837</td>
<td valign="top">E"</td>
</tr>
<tr>
<td valign="top">6</td>
<td valign="top">Bottomed H atoms move in and out whereas the top H atom moves in different order as the bottomed H atoms. The B atom is quite stationary</td>
<td valign="top">2731.31</td>
<td valign="top">103.83</td>
<td valign="top">E"</td>
</tr>
</table>

The following graph is IR spectrum.

[[Image:FeiIR.jpg]]

From the IR spectrum, we can see that there are only 3 peaks. But there are 6 vibrations. In theory, we should get 6 peaks. This is due to peaks of no.2 and no.3 vibrations are combined together as having the nearly the same frequency, this is the same for peaks of no.5 and no.6 vibrations. And for no. 4 vibration, it is totally symmetric and this means there is not dipole moment and hence there will show no peak. So there will be 3 peaks in total shown in the spectrum.

===Molecular orbitals of BH3===

Create .chk file of the optimised BH3 molecule and open it to run another optimisation. Then I open the MOs from the “edit” section.

[[Image:FeiMOs.JPG]]

Then click the “update” button but there is nothing happened and the MOs is not obtained.
While doing the updating, the surface did appear around the molecule.

=='''Exercise 2'''==

Isomers of Mo(CO)4L2

=='''Exercise 3'''==

===Ammonia===

Firstly, generate a molecule of NH3 by using GussianView programme and start to optimise it by using B3LYP method with 6-31G basis set. And then we can get an optimised NH3 molecule with its summary table.

[[Image:FeiNH3summary.jpg]]

From the summary table, we can see that the symmetry is C3v.

Now generate another NH3 molecule and make one of its bond lengths to 1.01 Å. The symmetry is ignored here in the general section of the optimisation section. Then we can a optimised molecule with its summary table.

[[Image:FeiNH3summary2.JPG]]

From the summary table, we can see that the symmetry of this molecule is C1.

Download the file from the website and run the optimisation, hence get the following summary table.

[[Image:FeiNH3summary3.JPG]]

From the summary table, we can see that the symmetry of this molecule is D3h.

From the above 3 molecules, we can see that the symmetry does not make any difference to the final obtained structure, but the symmetry did give a difference to the duration of the calculation. The lone pairs of the N atom imply the symmetry to do a calculation. During an optimisation, a molecule can break symmetry. The D3h molecule has got the lowest energy geometry. The energy difference between C3v and D3h is 3.4401*10^-4 AU (i.e. 0.9032 kJ/mol), the difference between C1 and D3h is -3.457*10^-4 AU (i.e. 0.9077 kJ/mol). The energy difference between these structures is quite significant, the C1 and C3v structures are mirror-image to each other, and therefore they have got similar energies whereas the D3h one has the lowest energy due to its stable structure.

===Method===

In this section, we are going to use the same method with higher basis set level to improve the accuracy of the optimisation. Firstly, NH3 molecule is generated and is run with 6-311+G(d,p) basis set. But there is no “include all electrons” box in the method section of the optimisation.

[[Image:FeiNh3summary1.JPG]]

Using the given file and run the optimisation to obtain the following information.

[[Image:FeiNh3summary2.JPG]]

In this section, the durations of calculation are 29.0 seconds and 78 seconds respectively. However, the durations of the calculation with lower basis set are 30.0 second and 76 seconds which are shorter than those of calculation with higher basis set. The barrier height to inversion is 6.3223*10^-3 AU (i.e. 16.60 kJ/mol) which is much higher than the barrier in the lower basis set level. And this figure is reasonable so we can see that high level of basis set increase the accuracy of the optimisation. The experimental determined barrier is 24.3 which is higher than theoretical 16.6 value.

===The inversion mechanism===

Download the given file and open it to obtain the following picture.

[[Image:FeiNh3.JPG]]

Then we can get the “SCAN” which is showing the chemical reaction over time.

[[Image:FeiEnergyv.s.eigenvalue.JPG]]

From the above curves, we can see that eigen value 12 has got the lowest energy value and this is the most stable state.

===Vibrational analysis===

Get the frequency analysis for D3h optimised molecule.

[[Image:FeiD3h.JPG]]

Get the frequency analysis for C3v optimised molecule as well.

[[Image:FeiC3v.JPG]]

From the 2 vibrational frequencies of the C3v and D3h structures, we can see that there are 5 positive frequencies in D3h structure whereas 6 positives ones in C3v structure. C3v structure is a ground state structure and D3h is a transition state structure. This means C3v will have all positive frequencies whereas D3h will have only one negative frequency. From the above 2 graphs, we can see that only D3h has got one negative frequency which is -768.258 cm^-1. The vibration 4 with the lowest intensity value in the C3v and D3h structures will follow the inversion reaction. The calculated frequencies for C3v structure are higher than the experimental frequencies.

=='''Mini Project'''==

In this section, I am going to compare 2 isomers and thery are trans or cis isomer of Pt(Cl)4(NH3)2.
The following are their structures by using GaussianView. Since Pt and Cl atoms are below row 2, I am going to use LanL2MB basis set to optimise them.

The following picture is the optimised cis-isomer with its summary table.

[[Image:Cisoptimisation.JPG]]

From the above information from the summary table, we can see that using the medium level of basis set will curse a lot of time to run the calculation.

Now I need to optimise the trans-isomer by using the above method with the same basis set, otherwise I couldnot compare their final energies.

Rep:Mod:feihemodule2

2008-12-17T13:40:49Z

Fh106: /* '''Mini Project''' */

='''Module 2'''=

=='''Introduction'''==

The aim of this module 2 is familiar with the Gussview programme and uses the programme to optimise the molecules.

Now look at the following simple molecule BH3.

===Create a molecule of BH3===

Use the Gussview programme to create the BH3 molecule. And we can the following picture of the molecule.

[[Image:FeiBh3.jpg]]

Picture of BH3 molecule.

And we can use label and symbol the molecule to get the following picture.

[[Image:FeiLabelledBH3.JPG]]

Labelled and symbol picture of BH3.

Then we set the all the three B-H bonds to 1.5 angstrom and get the following sturcure of BH3.

[[Image:FeiBh3fixedbondlength.JPG]]

Fixed bond distance picture of BH3

So the molecule is set up.

===Optimising a molecule of BH3===

Use the BLYP method and 3-21G basic set to optimise the molecule of BH3. And then we can the following optimised structure of the molecule.

[[Image:FeiOptimisedBH3.JPG]]

Optimised structure of BH3 molecule

Then we can determine the optimised B-H bond distance and H-B-H bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:FeiBH3bonddistance.JPG]]</td>
<td align="center">[[Image:FeiBH3bondangle.JPG]]</td>
</tr>
<tr>
<td align="center">Bond distance is 1.19435</td>
<td align="center">Bond angle is 120.000</td>
</tr>
</table>

And we can get a summary table to show some information about the molecule.

[[Image:FeiResulttable.JPG]]

Summary of the optimised molecule

From the above summary, we can see that the file of file is .log, calculation type is FOPT, calculation method is RB3LYP, basic set is 3-21G, final energy is -26.46226438 au, dipole moment is 0.000 debye, point group is D3H and the duration of calculation is 19.0 seconds.

We can get a “real” text based .log file as well.

[[Image:FeiRealresulttable.JPG]]

===Understanding optimisation part a===

Open the finished optimised file of the above molecule and tick “read intermediate geometries”. Then an energy and gradient against optimisation graph is obtained.

[[Image:FeiOptimisationgraph.JPG]]

There are 2 graphs in the above picture, the 1st one is energy against each step of optimisation and the 2nd one is the gradient of energy against each step of optimisation.

The green button in the molecule window is click and the animation of optimisation steps is obtained and we can see that the final structure has the least energy and smallest gradient of energy. So the stable structure is with the minimum energy and it is the final structure in the animation.

[[Image:FeiAnimation.JPG]]

=='''Exercise 1'''==

===Find information about BCl3===

Following the method introduced in the introduction section, repeat the calculation for molecule BCl3.

Firstly, create the molecule of BCl3. And measure its B-Cl bond distance and Cl-B-Cl bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:FeiBCL3bonddistance.JPG]]</td>
<td align="center">[[Image:BCL3bondangle.JPG]]</td>
</tr>
<tr>
<td align="center">Bond distance: 1.87000</td>
<td align="center">Bond angle is 120.000</td>
</tr>
</table>

Secondly, restrict the symmetry of BCl3 to D3h and set the tolerance from the default to “very tight (0.0001)” and obtain the following picture.

[[Image:FeiRestrictedBCL3.JPG]]

Restricted BCl3 molecule

Thirdly, do the calculation to optimise the BCl3 molecule and obtain the optimised structure of BCl3.

[[Image:FeiOptimisedBCL3.JPG]]

Optimised BCl3 molecule

And we then obtain the optimised B-Cl bond distance and optimised Cl-B-Cl bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:FeiOptimisedbonddistance.JPG]]</td>
<td align="center">[[Image:Optimisedbondangle.JPG]]</td>
</tr>
<tr>
<td align="center">Bond distance: 1.86592</td>
<td align="center">Bond angle is 120.000</td>
</tr>
</table>

Finally, we then get the summary of the optimised molecule.

[[Image:FeiSummary2.JPG]]

From the above summary table, we can know that the file type is .log, calculation type is FORT, calculation method is RB3LYP, basic set is LANL2MB, final energy is -69.43928112 AU, dipole moment is 0.000 debye, point group is D3h and the duration of calculation is 12.0 seconds.

===Independent work===

I chose H2O as my own molecule. Firstly, set up the molecule of H2O. And we can get the O-H bond distance and H-O-H bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:H2Obonddistance.JPG]]</td>
<td align="center">[[Image:H2Obondangle.JPG]]</td>
</tr>
<tr>
<td align="center">Bond distance: 0.96000</td>
<td align="center">Bond angle is 109.500</td>
</tr>
</table>

Since O atom and H atom is above second row, we do not need to use pseudo-potential.
Therefore, we use the same method as above in above section but we set the basis set to 3-21G and obtain the following optimised H2O molecule with its summary table.

[[Image:FeiH2Osummary.JPG]]

From the above summary table, we can see that the calculation method is RB3LYP, basis set is 3-21G, final energy is -75.97396515 AU, dipole moment is 2.2381 Debye, point group is C2v and duration of calculation is 17.0 seconds.

We now can get the optimised bond distance and bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:Optimisedbonddistance.jpg]]</td>
<td align="center">[[Image:Optimisedbondangle.jpg]]</td>
</tr>
<tr>
<td align="center">Optimised bond distance: 0.99683</td>
<td align="center">Optimised bond angle: 103.991</td>
</tr>
</table>

Now I set the basis set to higher level in order to increase the accuracy. Use the first optimised output file to do another optimisation using higher level basis set. And use the second optimised output file to do another optimisation using even higher basis set.

<table width="663" border="1">
<tr>
<th width="176" scope="col"> </th>
<th scope="col">First trial</th>
<th scope="col">Second trail</th>
<th scope="col">Third trail</th>
</tr>
<tr>
<th scope="row">Bond distance/AU</th>
<td width="143" valign="top">0.99683 </td>
<td width="149" valign="top">0.96526</td>
<td width="167" valign="top">0.96203</td>
</tr>
<tr>
<th scope="row">Bond angle/degree</th>
<td width="143" valign="top">103.991</td>
<td width="149" valign="top">103.696</td>
<td width="167" valign="top">105.057</td>
</tr>
<tr>
<th scope="row">Calculation method</th>
<td width="143" valign="top">RB3LYP</td>
<td width="149" valign="top">RB3LYP</td>
<td width="167" valign="top">RB3LYP</td>
</tr>
<tr>
<th scope="row">Basis set</th>
<td width="143" valign="top">3-21G</td>
<td width="149" valign="top">6-31G(d.p)</td>
<td width="167" valign="top">6-311+G(d,p)</td>
</tr>
<tr>
<th scope="row">Final energy/J</th>
<td width="143" valign="top">-75.97396515</td>
<td width="149" valign="top">-76.41973659</td>
<td width="167" valign="top">-76.45846294</td>
</tr>
<tr>
<th scope="row">Dipole moment/debye</th>
<td width="143" valign="top">2.2381</td>
<td width="149" valign="top">2.0436</td>
<td width="167" valign="top">2.1610</td>
</tr>
<tr>
<th scope="row">Point group</th>
<td width="143" valign="top">C2v</td>
<td width="149" valign="top">C2v</td>
<td width="167" valign="top">C2v</td>
</tr>
<tr>
<th scope="row">Duration of calculation/s</th>
<td width="143" valign="top">17.0</td>
<td width="149" valign="top">17.0</td>
<td width="167" valign="top">18.0</td>
</tr>
</table>

===Vibrational analysis and confirming minima===

In this section, we are going to use vibrational analysis to confirm the minimum structure.
Firstly, open the optimised BH3 file and do the vibrational analysis to confirm its minimum structure. So we get the following structure with its summary.

[[Image:FeiBH3frequncy.jpg]]

From the above summary table, we can see that the energy is -26.46226438 whereas the energy of the optimised one is -26.46226438. So they have got the same value.

===Animating the vibrations===

Open the vibrations result.

[[Image:FeiVibrations.jpg]]

Show display vectors of each vibration.

[[Image:FeiVibration2.jpg]]

The following table is to a summary of motions, frequency, intensities and symmetry.

<table width="716" border="1">
<tr>
<td width="24" valign="top">No.</td>
<td width="473" valign="top">Form of vibration</td>
<td width="59" valign="top">frequency</td>
<td width="65" valign="top">intensity</td>
<td width="61" valign="top">Symmetry 
D3h point group</td>
</tr>
<tr>
<td valign="top">1 </td>
<td valign="top">all the H atoms move in and out together in the same direction, the B atom moves in the opposite direction of that of H atom</td>
<td valign="top">1145.71</td>
<td valign="top">92.6991</td>
<td valign="top">A"2</td>
</tr>
<tr>
<td valign="top">2</td>
<td valign="top">2 bottomed H atoms moves towards and away from each other whereas B atom and top H atom is quite stationary</td>
<td valign="top">1204.66</td>
<td valign="top">12.3789</td>
<td valign="top">E'</td>
</tr>
<tr>
<td valign="top">3</td>
<td valign="top">Each of the bottomed H atom moves away and towards to the top H atom whereas B atom is quite stationary</td>
<td valign="top">1204.66</td>
<td valign="top">12.3814</td>
<td valign="top">E'</td>
</tr>
<tr>
<td valign="top">4</td>
<td valign="top">All H atoms move in and out together in a concerted motion whereas B atom is unmoved</td>
<td valign="top">2591.65</td>
<td valign="top">0.0</td>
<td valign="top">A'1</td>
</tr>
<tr>
<td valign="top">5</td>
<td valign="top">2 bottomed H atoms move towards or away from B atom simultaneously 
Top H atom and B atom is quite stationary</td>
<td valign="top">2731.31</td>
<td valign="top">103.837</td>
<td valign="top">E"</td>
</tr>
<tr>
<td valign="top">6</td>
<td valign="top">Bottomed H atoms move in and out whereas the top H atom moves in different order as the bottomed H atoms. The B atom is quite stationary</td>
<td valign="top">2731.31</td>
<td valign="top">103.83</td>
<td valign="top">E"</td>
</tr>
</table>

The following graph is IR spectrum.

[[Image:FeiIR.jpg]]

From the IR spectrum, we can see that there are only 3 peaks. But there are 6 vibrations. In theory, we should get 6 peaks. This is due to peaks of no.2 and no.3 vibrations are combined together as having the nearly the same frequency, this is the same for peaks of no.5 and no.6 vibrations. And for no. 4 vibration, it is totally symmetric and this means there is not dipole moment and hence there will show no peak. So there will be 3 peaks in total shown in the spectrum.

===Molecular orbitals of BH3===

Create .chk file of the optimised BH3 molecule and open it to run another optimisation. Then I open the MOs from the “edit” section.

[[Image:FeiMOs.JPG]]

Then click the “update” button but there is nothing happened and the MOs is not obtained.
While doing the updating, the surface did appear around the molecule.

=='''Exercise 2'''==

Isomers of Mo(CO)4L2

=='''Exercise 3'''==

===Ammonia===

Firstly, generate a molecule of NH3 by using GussianView programme and start to optimise it by using B3LYP method with 6-31G basis set. And then we can get an optimised NH3 molecule with its summary table.

[[Image:FeiNH3summary.jpg]]

From the summary table, we can see that the symmetry is C3v.

Now generate another NH3 molecule and make one of its bond lengths to 1.01 Å. The symmetry is ignored here in the general section of the optimisation section. Then we can a optimised molecule with its summary table.

[[Image:FeiNH3summary2.JPG]]

From the summary table, we can see that the symmetry of this molecule is C1.

Download the file from the website and run the optimisation, hence get the following summary table.

[[Image:FeiNH3summary3.JPG]]

From the summary table, we can see that the symmetry of this molecule is D3h.

From the above 3 molecules, we can see that the symmetry does not make any difference to the final obtained structure, but the symmetry did give a difference to the duration of the calculation. The lone pairs of the N atom imply the symmetry to do a calculation. During an optimisation, a molecule can break symmetry. The D3h molecule has got the lowest energy geometry. The energy difference between C3v and D3h is 3.4401*10^-4 AU (i.e. 0.9032 kJ/mol), the difference between C1 and D3h is -3.457*10^-4 AU (i.e. 0.9077 kJ/mol). The energy difference between these structures is quite significant, the C1 and C3v structures are mirror-image to each other, and therefore they have got similar energies whereas the D3h one has the lowest energy due to its stable structure.

===Method===

In this section, we are going to use the same method with higher basis set level to improve the accuracy of the optimisation. Firstly, NH3 molecule is generated and is run with 6-311+G(d,p) basis set. But there is no “include all electrons” box in the method section of the optimisation.

[[Image:FeiNh3summary1.JPG]]

Using the given file and run the optimisation to obtain the following information.

[[Image:FeiNh3summary2.JPG]]

In this section, the durations of calculation are 29.0 seconds and 78 seconds respectively. However, the durations of the calculation with lower basis set are 30.0 second and 76 seconds which are shorter than those of calculation with higher basis set. The barrier height to inversion is 6.3223*10^-3 AU (i.e. 16.60 kJ/mol) which is much higher than the barrier in the lower basis set level. And this figure is reasonable so we can see that high level of basis set increase the accuracy of the optimisation. The experimental determined barrier is 24.3 which is higher than theoretical 16.6 value.

===The inversion mechanism===

Download the given file and open it to obtain the following picture.

[[Image:FeiNh3.JPG]]

Then we can get the “SCAN” which is showing the chemical reaction over time.

[[Image:FeiEnergyv.s.eigenvalue.JPG]]

From the above curves, we can see that eigen value 12 has got the lowest energy value and this is the most stable state.

===Vibrational analysis===

Get the frequency analysis for D3h optimised molecule.

[[Image:FeiD3h.JPG]]

Get the frequency analysis for C3v optimised molecule as well.

[[Image:FeiC3v.JPG]]

From the 2 vibrational frequencies of the C3v and D3h structures, we can see that there are 5 positive frequencies in D3h structure whereas 6 positives ones in C3v structure. C3v structure is a ground state structure and D3h is a transition state structure. This means C3v will have all positive frequencies whereas D3h will have only one negative frequency. From the above 2 graphs, we can see that only D3h has got one negative frequency which is -768.258 cm^-1. The vibration 4 with the lowest intensity value in the C3v and D3h structures will follow the inversion reaction. The calculated frequencies for C3v structure are higher than the experimental frequencies.

=='''Mini Project'''==

In this section, I am going to compare 2 isomers and one of them is cis-isomer and the other is trans-isomer.
The following are their structures by using GaussianView. Since Pt and Cl atoms are below row 2, I am going to use LanL2MB basis set to optimise them.

The following picture is the optimised cis-isomer with its summary table.

[[Image:Cisoptimisation.JPG]]

From the above information from the summary table, we can see that using the medium level of basis set will curse a lot of time to run the calculation.

Now I need to optimise the trans-isomer by using the above method with the same basis set, otherwise I couldnot compare their final energies.

Rep:Mod:feihemodule2

2008-12-17T13:39:14Z

Fh106: /* '''Mini Project''' */

='''Module 2'''=

=='''Introduction'''==

The aim of this module 2 is familiar with the Gussview programme and uses the programme to optimise the molecules.

Now look at the following simple molecule BH3.

===Create a molecule of BH3===

Use the Gussview programme to create the BH3 molecule. And we can the following picture of the molecule.

[[Image:FeiBh3.jpg]]

Picture of BH3 molecule.

And we can use label and symbol the molecule to get the following picture.

[[Image:FeiLabelledBH3.JPG]]

Labelled and symbol picture of BH3.

Then we set the all the three B-H bonds to 1.5 angstrom and get the following sturcure of BH3.

[[Image:FeiBh3fixedbondlength.JPG]]

Fixed bond distance picture of BH3

So the molecule is set up.

===Optimising a molecule of BH3===

Use the BLYP method and 3-21G basic set to optimise the molecule of BH3. And then we can the following optimised structure of the molecule.

[[Image:FeiOptimisedBH3.JPG]]

Optimised structure of BH3 molecule

Then we can determine the optimised B-H bond distance and H-B-H bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:FeiBH3bonddistance.JPG]]</td>
<td align="center">[[Image:FeiBH3bondangle.JPG]]</td>
</tr>
<tr>
<td align="center">Bond distance is 1.19435</td>
<td align="center">Bond angle is 120.000</td>
</tr>
</table>

And we can get a summary table to show some information about the molecule.

[[Image:FeiResulttable.JPG]]

Summary of the optimised molecule

From the above summary, we can see that the file of file is .log, calculation type is FOPT, calculation method is RB3LYP, basic set is 3-21G, final energy is -26.46226438 au, dipole moment is 0.000 debye, point group is D3H and the duration of calculation is 19.0 seconds.

We can get a “real” text based .log file as well.

[[Image:FeiRealresulttable.JPG]]

===Understanding optimisation part a===

Open the finished optimised file of the above molecule and tick “read intermediate geometries”. Then an energy and gradient against optimisation graph is obtained.

[[Image:FeiOptimisationgraph.JPG]]

There are 2 graphs in the above picture, the 1st one is energy against each step of optimisation and the 2nd one is the gradient of energy against each step of optimisation.

The green button in the molecule window is click and the animation of optimisation steps is obtained and we can see that the final structure has the least energy and smallest gradient of energy. So the stable structure is with the minimum energy and it is the final structure in the animation.

[[Image:FeiAnimation.JPG]]

=='''Exercise 1'''==

===Find information about BCl3===

Following the method introduced in the introduction section, repeat the calculation for molecule BCl3.

Firstly, create the molecule of BCl3. And measure its B-Cl bond distance and Cl-B-Cl bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:FeiBCL3bonddistance.JPG]]</td>
<td align="center">[[Image:BCL3bondangle.JPG]]</td>
</tr>
<tr>
<td align="center">Bond distance: 1.87000</td>
<td align="center">Bond angle is 120.000</td>
</tr>
</table>

Secondly, restrict the symmetry of BCl3 to D3h and set the tolerance from the default to “very tight (0.0001)” and obtain the following picture.

[[Image:FeiRestrictedBCL3.JPG]]

Restricted BCl3 molecule

Thirdly, do the calculation to optimise the BCl3 molecule and obtain the optimised structure of BCl3.

[[Image:FeiOptimisedBCL3.JPG]]

Optimised BCl3 molecule

And we then obtain the optimised B-Cl bond distance and optimised Cl-B-Cl bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:FeiOptimisedbonddistance.JPG]]</td>
<td align="center">[[Image:Optimisedbondangle.JPG]]</td>
</tr>
<tr>
<td align="center">Bond distance: 1.86592</td>
<td align="center">Bond angle is 120.000</td>
</tr>
</table>

Finally, we then get the summary of the optimised molecule.

[[Image:FeiSummary2.JPG]]

From the above summary table, we can know that the file type is .log, calculation type is FORT, calculation method is RB3LYP, basic set is LANL2MB, final energy is -69.43928112 AU, dipole moment is 0.000 debye, point group is D3h and the duration of calculation is 12.0 seconds.

===Independent work===

I chose H2O as my own molecule. Firstly, set up the molecule of H2O. And we can get the O-H bond distance and H-O-H bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:H2Obonddistance.JPG]]</td>
<td align="center">[[Image:H2Obondangle.JPG]]</td>
</tr>
<tr>
<td align="center">Bond distance: 0.96000</td>
<td align="center">Bond angle is 109.500</td>
</tr>
</table>

Since O atom and H atom is above second row, we do not need to use pseudo-potential.
Therefore, we use the same method as above in above section but we set the basis set to 3-21G and obtain the following optimised H2O molecule with its summary table.

[[Image:FeiH2Osummary.JPG]]

From the above summary table, we can see that the calculation method is RB3LYP, basis set is 3-21G, final energy is -75.97396515 AU, dipole moment is 2.2381 Debye, point group is C2v and duration of calculation is 17.0 seconds.

We now can get the optimised bond distance and bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:Optimisedbonddistance.jpg]]</td>
<td align="center">[[Image:Optimisedbondangle.jpg]]</td>
</tr>
<tr>
<td align="center">Optimised bond distance: 0.99683</td>
<td align="center">Optimised bond angle: 103.991</td>
</tr>
</table>

Now I set the basis set to higher level in order to increase the accuracy. Use the first optimised output file to do another optimisation using higher level basis set. And use the second optimised output file to do another optimisation using even higher basis set.

<table width="663" border="1">
<tr>
<th width="176" scope="col"> </th>
<th scope="col">First trial</th>
<th scope="col">Second trail</th>
<th scope="col">Third trail</th>
</tr>
<tr>
<th scope="row">Bond distance/AU</th>
<td width="143" valign="top">0.99683 </td>
<td width="149" valign="top">0.96526</td>
<td width="167" valign="top">0.96203</td>
</tr>
<tr>
<th scope="row">Bond angle/degree</th>
<td width="143" valign="top">103.991</td>
<td width="149" valign="top">103.696</td>
<td width="167" valign="top">105.057</td>
</tr>
<tr>
<th scope="row">Calculation method</th>
<td width="143" valign="top">RB3LYP</td>
<td width="149" valign="top">RB3LYP</td>
<td width="167" valign="top">RB3LYP</td>
</tr>
<tr>
<th scope="row">Basis set</th>
<td width="143" valign="top">3-21G</td>
<td width="149" valign="top">6-31G(d.p)</td>
<td width="167" valign="top">6-311+G(d,p)</td>
</tr>
<tr>
<th scope="row">Final energy/J</th>
<td width="143" valign="top">-75.97396515</td>
<td width="149" valign="top">-76.41973659</td>
<td width="167" valign="top">-76.45846294</td>
</tr>
<tr>
<th scope="row">Dipole moment/debye</th>
<td width="143" valign="top">2.2381</td>
<td width="149" valign="top">2.0436</td>
<td width="167" valign="top">2.1610</td>
</tr>
<tr>
<th scope="row">Point group</th>
<td width="143" valign="top">C2v</td>
<td width="149" valign="top">C2v</td>
<td width="167" valign="top">C2v</td>
</tr>
<tr>
<th scope="row">Duration of calculation/s</th>
<td width="143" valign="top">17.0</td>
<td width="149" valign="top">17.0</td>
<td width="167" valign="top">18.0</td>
</tr>
</table>

===Vibrational analysis and confirming minima===

In this section, we are going to use vibrational analysis to confirm the minimum structure.
Firstly, open the optimised BH3 file and do the vibrational analysis to confirm its minimum structure. So we get the following structure with its summary.

[[Image:FeiBH3frequncy.jpg]]

From the above summary table, we can see that the energy is -26.46226438 whereas the energy of the optimised one is -26.46226438. So they have got the same value.

===Animating the vibrations===

Open the vibrations result.

[[Image:FeiVibrations.jpg]]

Show display vectors of each vibration.

[[Image:FeiVibration2.jpg]]

The following table is to a summary of motions, frequency, intensities and symmetry.

<table width="716" border="1">
<tr>
<td width="24" valign="top">No.</td>
<td width="473" valign="top">Form of vibration</td>
<td width="59" valign="top">frequency</td>
<td width="65" valign="top">intensity</td>
<td width="61" valign="top">Symmetry 
D3h point group</td>
</tr>
<tr>
<td valign="top">1 </td>
<td valign="top">all the H atoms move in and out together in the same direction, the B atom moves in the opposite direction of that of H atom</td>
<td valign="top">1145.71</td>
<td valign="top">92.6991</td>
<td valign="top">A"2</td>
</tr>
<tr>
<td valign="top">2</td>
<td valign="top">2 bottomed H atoms moves towards and away from each other whereas B atom and top H atom is quite stationary</td>
<td valign="top">1204.66</td>
<td valign="top">12.3789</td>
<td valign="top">E'</td>
</tr>
<tr>
<td valign="top">3</td>
<td valign="top">Each of the bottomed H atom moves away and towards to the top H atom whereas B atom is quite stationary</td>
<td valign="top">1204.66</td>
<td valign="top">12.3814</td>
<td valign="top">E'</td>
</tr>
<tr>
<td valign="top">4</td>
<td valign="top">All H atoms move in and out together in a concerted motion whereas B atom is unmoved</td>
<td valign="top">2591.65</td>
<td valign="top">0.0</td>
<td valign="top">A'1</td>
</tr>
<tr>
<td valign="top">5</td>
<td valign="top">2 bottomed H atoms move towards or away from B atom simultaneously 
Top H atom and B atom is quite stationary</td>
<td valign="top">2731.31</td>
<td valign="top">103.837</td>
<td valign="top">E"</td>
</tr>
<tr>
<td valign="top">6</td>
<td valign="top">Bottomed H atoms move in and out whereas the top H atom moves in different order as the bottomed H atoms. The B atom is quite stationary</td>
<td valign="top">2731.31</td>
<td valign="top">103.83</td>
<td valign="top">E"</td>
</tr>
</table>

The following graph is IR spectrum.

[[Image:FeiIR.jpg]]

From the IR spectrum, we can see that there are only 3 peaks. But there are 6 vibrations. In theory, we should get 6 peaks. This is due to peaks of no.2 and no.3 vibrations are combined together as having the nearly the same frequency, this is the same for peaks of no.5 and no.6 vibrations. And for no. 4 vibration, it is totally symmetric and this means there is not dipole moment and hence there will show no peak. So there will be 3 peaks in total shown in the spectrum.

===Molecular orbitals of BH3===

Create .chk file of the optimised BH3 molecule and open it to run another optimisation. Then I open the MOs from the “edit” section.

[[Image:FeiMOs.JPG]]

Then click the “update” button but there is nothing happened and the MOs is not obtained.
While doing the updating, the surface did appear around the molecule.

=='''Exercise 2'''==

Isomers of Mo(CO)4L2

=='''Exercise 3'''==

===Ammonia===

Firstly, generate a molecule of NH3 by using GussianView programme and start to optimise it by using B3LYP method with 6-31G basis set. And then we can get an optimised NH3 molecule with its summary table.

[[Image:FeiNH3summary.jpg]]

From the summary table, we can see that the symmetry is C3v.

Now generate another NH3 molecule and make one of its bond lengths to 1.01 Å. The symmetry is ignored here in the general section of the optimisation section. Then we can a optimised molecule with its summary table.

[[Image:FeiNH3summary2.JPG]]

From the summary table, we can see that the symmetry of this molecule is C1.

Download the file from the website and run the optimisation, hence get the following summary table.

[[Image:FeiNH3summary3.JPG]]

From the summary table, we can see that the symmetry of this molecule is D3h.

From the above 3 molecules, we can see that the symmetry does not make any difference to the final obtained structure, but the symmetry did give a difference to the duration of the calculation. The lone pairs of the N atom imply the symmetry to do a calculation. During an optimisation, a molecule can break symmetry. The D3h molecule has got the lowest energy geometry. The energy difference between C3v and D3h is 3.4401*10^-4 AU (i.e. 0.9032 kJ/mol), the difference between C1 and D3h is -3.457*10^-4 AU (i.e. 0.9077 kJ/mol). The energy difference between these structures is quite significant, the C1 and C3v structures are mirror-image to each other, and therefore they have got similar energies whereas the D3h one has the lowest energy due to its stable structure.

===Method===

In this section, we are going to use the same method with higher basis set level to improve the accuracy of the optimisation. Firstly, NH3 molecule is generated and is run with 6-311+G(d,p) basis set. But there is no “include all electrons” box in the method section of the optimisation.

[[Image:FeiNh3summary1.JPG]]

Using the given file and run the optimisation to obtain the following information.

[[Image:FeiNh3summary2.JPG]]

In this section, the durations of calculation are 29.0 seconds and 78 seconds respectively. However, the durations of the calculation with lower basis set are 30.0 second and 76 seconds which are shorter than those of calculation with higher basis set. The barrier height to inversion is 6.3223*10^-3 AU (i.e. 16.60 kJ/mol) which is much higher than the barrier in the lower basis set level. And this figure is reasonable so we can see that high level of basis set increase the accuracy of the optimisation. The experimental determined barrier is 24.3 which is higher than theoretical 16.6 value.

===The inversion mechanism===

Download the given file and open it to obtain the following picture.

[[Image:FeiNh3.JPG]]

Then we can get the “SCAN” which is showing the chemical reaction over time.

[[Image:FeiEnergyv.s.eigenvalue.JPG]]

From the above curves, we can see that eigen value 12 has got the lowest energy value and this is the most stable state.

===Vibrational analysis===

Get the frequency analysis for D3h optimised molecule.

[[Image:FeiD3h.JPG]]

Get the frequency analysis for C3v optimised molecule as well.

[[Image:FeiC3v.JPG]]

From the 2 vibrational frequencies of the C3v and D3h structures, we can see that there are 5 positive frequencies in D3h structure whereas 6 positives ones in C3v structure. C3v structure is a ground state structure and D3h is a transition state structure. This means C3v will have all positive frequencies whereas D3h will have only one negative frequency. From the above 2 graphs, we can see that only D3h has got one negative frequency which is -768.258 cm^-1. The vibration 4 with the lowest intensity value in the C3v and D3h structures will follow the inversion reaction. The calculated frequencies for C3v structure are higher than the experimental frequencies.

=='''Mini Project'''==

In this section, I am going to compare 2 isomers and one of them is cis-isomer and the other is trans-isomer.
The following are their structures by using GaussianView. Since Pt and Cl atoms are below row 2, I am going to use LanL2MB basis set to optimise them.

The following picture is the optimised cis-isomer with its summary table.

[[Image:Cisoptimisation.JPG]]
From the above information from the summary table, we can see that using the medium level of basis set will curse a lot of time to run the calculation.

Rep:Mod:feihemodule2

2008-12-17T13:35:57Z

Fh106: /* '''Mini Project''' */

='''Module 2'''=

=='''Introduction'''==

The aim of this module 2 is familiar with the Gussview programme and uses the programme to optimise the molecules.

Now look at the following simple molecule BH3.

===Create a molecule of BH3===

Use the Gussview programme to create the BH3 molecule. And we can the following picture of the molecule.

[[Image:FeiBh3.jpg]]

Picture of BH3 molecule.

And we can use label and symbol the molecule to get the following picture.

[[Image:FeiLabelledBH3.JPG]]

Labelled and symbol picture of BH3.

Then we set the all the three B-H bonds to 1.5 angstrom and get the following sturcure of BH3.

[[Image:FeiBh3fixedbondlength.JPG]]

Fixed bond distance picture of BH3

So the molecule is set up.

===Optimising a molecule of BH3===

Use the BLYP method and 3-21G basic set to optimise the molecule of BH3. And then we can the following optimised structure of the molecule.

[[Image:FeiOptimisedBH3.JPG]]

Optimised structure of BH3 molecule

Then we can determine the optimised B-H bond distance and H-B-H bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:FeiBH3bonddistance.JPG]]</td>
<td align="center">[[Image:FeiBH3bondangle.JPG]]</td>
</tr>
<tr>
<td align="center">Bond distance is 1.19435</td>
<td align="center">Bond angle is 120.000</td>
</tr>
</table>

And we can get a summary table to show some information about the molecule.

[[Image:FeiResulttable.JPG]]

Summary of the optimised molecule

From the above summary, we can see that the file of file is .log, calculation type is FOPT, calculation method is RB3LYP, basic set is 3-21G, final energy is -26.46226438 au, dipole moment is 0.000 debye, point group is D3H and the duration of calculation is 19.0 seconds.

We can get a “real” text based .log file as well.

[[Image:FeiRealresulttable.JPG]]

===Understanding optimisation part a===

Open the finished optimised file of the above molecule and tick “read intermediate geometries”. Then an energy and gradient against optimisation graph is obtained.

[[Image:FeiOptimisationgraph.JPG]]

There are 2 graphs in the above picture, the 1st one is energy against each step of optimisation and the 2nd one is the gradient of energy against each step of optimisation.

The green button in the molecule window is click and the animation of optimisation steps is obtained and we can see that the final structure has the least energy and smallest gradient of energy. So the stable structure is with the minimum energy and it is the final structure in the animation.

[[Image:FeiAnimation.JPG]]

=='''Exercise 1'''==

===Find information about BCl3===

Following the method introduced in the introduction section, repeat the calculation for molecule BCl3.

Firstly, create the molecule of BCl3. And measure its B-Cl bond distance and Cl-B-Cl bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:FeiBCL3bonddistance.JPG]]</td>
<td align="center">[[Image:BCL3bondangle.JPG]]</td>
</tr>
<tr>
<td align="center">Bond distance: 1.87000</td>
<td align="center">Bond angle is 120.000</td>
</tr>
</table>

Secondly, restrict the symmetry of BCl3 to D3h and set the tolerance from the default to “very tight (0.0001)” and obtain the following picture.

[[Image:FeiRestrictedBCL3.JPG]]

Restricted BCl3 molecule

Thirdly, do the calculation to optimise the BCl3 molecule and obtain the optimised structure of BCl3.

[[Image:FeiOptimisedBCL3.JPG]]

Optimised BCl3 molecule

And we then obtain the optimised B-Cl bond distance and optimised Cl-B-Cl bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:FeiOptimisedbonddistance.JPG]]</td>
<td align="center">[[Image:Optimisedbondangle.JPG]]</td>
</tr>
<tr>
<td align="center">Bond distance: 1.86592</td>
<td align="center">Bond angle is 120.000</td>
</tr>
</table>

Finally, we then get the summary of the optimised molecule.

[[Image:FeiSummary2.JPG]]

From the above summary table, we can know that the file type is .log, calculation type is FORT, calculation method is RB3LYP, basic set is LANL2MB, final energy is -69.43928112 AU, dipole moment is 0.000 debye, point group is D3h and the duration of calculation is 12.0 seconds.

===Independent work===

I chose H2O as my own molecule. Firstly, set up the molecule of H2O. And we can get the O-H bond distance and H-O-H bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:H2Obonddistance.JPG]]</td>
<td align="center">[[Image:H2Obondangle.JPG]]</td>
</tr>
<tr>
<td align="center">Bond distance: 0.96000</td>
<td align="center">Bond angle is 109.500</td>
</tr>
</table>

Since O atom and H atom is above second row, we do not need to use pseudo-potential.
Therefore, we use the same method as above in above section but we set the basis set to 3-21G and obtain the following optimised H2O molecule with its summary table.

[[Image:FeiH2Osummary.JPG]]

From the above summary table, we can see that the calculation method is RB3LYP, basis set is 3-21G, final energy is -75.97396515 AU, dipole moment is 2.2381 Debye, point group is C2v and duration of calculation is 17.0 seconds.

We now can get the optimised bond distance and bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:Optimisedbonddistance.jpg]]</td>
<td align="center">[[Image:Optimisedbondangle.jpg]]</td>
</tr>
<tr>
<td align="center">Optimised bond distance: 0.99683</td>
<td align="center">Optimised bond angle: 103.991</td>
</tr>
</table>

Now I set the basis set to higher level in order to increase the accuracy. Use the first optimised output file to do another optimisation using higher level basis set. And use the second optimised output file to do another optimisation using even higher basis set.

<table width="663" border="1">
<tr>
<th width="176" scope="col"> </th>
<th scope="col">First trial</th>
<th scope="col">Second trail</th>
<th scope="col">Third trail</th>
</tr>
<tr>
<th scope="row">Bond distance/AU</th>
<td width="143" valign="top">0.99683 </td>
<td width="149" valign="top">0.96526</td>
<td width="167" valign="top">0.96203</td>
</tr>
<tr>
<th scope="row">Bond angle/degree</th>
<td width="143" valign="top">103.991</td>
<td width="149" valign="top">103.696</td>
<td width="167" valign="top">105.057</td>
</tr>
<tr>
<th scope="row">Calculation method</th>
<td width="143" valign="top">RB3LYP</td>
<td width="149" valign="top">RB3LYP</td>
<td width="167" valign="top">RB3LYP</td>
</tr>
<tr>
<th scope="row">Basis set</th>
<td width="143" valign="top">3-21G</td>
<td width="149" valign="top">6-31G(d.p)</td>
<td width="167" valign="top">6-311+G(d,p)</td>
</tr>
<tr>
<th scope="row">Final energy/J</th>
<td width="143" valign="top">-75.97396515</td>
<td width="149" valign="top">-76.41973659</td>
<td width="167" valign="top">-76.45846294</td>
</tr>
<tr>
<th scope="row">Dipole moment/debye</th>
<td width="143" valign="top">2.2381</td>
<td width="149" valign="top">2.0436</td>
<td width="167" valign="top">2.1610</td>
</tr>
<tr>
<th scope="row">Point group</th>
<td width="143" valign="top">C2v</td>
<td width="149" valign="top">C2v</td>
<td width="167" valign="top">C2v</td>
</tr>
<tr>
<th scope="row">Duration of calculation/s</th>
<td width="143" valign="top">17.0</td>
<td width="149" valign="top">17.0</td>
<td width="167" valign="top">18.0</td>
</tr>
</table>

===Vibrational analysis and confirming minima===

In this section, we are going to use vibrational analysis to confirm the minimum structure.
Firstly, open the optimised BH3 file and do the vibrational analysis to confirm its minimum structure. So we get the following structure with its summary.

[[Image:FeiBH3frequncy.jpg]]

From the above summary table, we can see that the energy is -26.46226438 whereas the energy of the optimised one is -26.46226438. So they have got the same value.

===Animating the vibrations===

Open the vibrations result.

[[Image:FeiVibrations.jpg]]

Show display vectors of each vibration.

[[Image:FeiVibration2.jpg]]

The following table is to a summary of motions, frequency, intensities and symmetry.

<table width="716" border="1">
<tr>
<td width="24" valign="top">No.</td>
<td width="473" valign="top">Form of vibration</td>
<td width="59" valign="top">frequency</td>
<td width="65" valign="top">intensity</td>
<td width="61" valign="top">Symmetry 
D3h point group</td>
</tr>
<tr>
<td valign="top">1 </td>
<td valign="top">all the H atoms move in and out together in the same direction, the B atom moves in the opposite direction of that of H atom</td>
<td valign="top">1145.71</td>
<td valign="top">92.6991</td>
<td valign="top">A"2</td>
</tr>
<tr>
<td valign="top">2</td>
<td valign="top">2 bottomed H atoms moves towards and away from each other whereas B atom and top H atom is quite stationary</td>
<td valign="top">1204.66</td>
<td valign="top">12.3789</td>
<td valign="top">E'</td>
</tr>
<tr>
<td valign="top">3</td>
<td valign="top">Each of the bottomed H atom moves away and towards to the top H atom whereas B atom is quite stationary</td>
<td valign="top">1204.66</td>
<td valign="top">12.3814</td>
<td valign="top">E'</td>
</tr>
<tr>
<td valign="top">4</td>
<td valign="top">All H atoms move in and out together in a concerted motion whereas B atom is unmoved</td>
<td valign="top">2591.65</td>
<td valign="top">0.0</td>
<td valign="top">A'1</td>
</tr>
<tr>
<td valign="top">5</td>
<td valign="top">2 bottomed H atoms move towards or away from B atom simultaneously 
Top H atom and B atom is quite stationary</td>
<td valign="top">2731.31</td>
<td valign="top">103.837</td>
<td valign="top">E"</td>
</tr>
<tr>
<td valign="top">6</td>
<td valign="top">Bottomed H atoms move in and out whereas the top H atom moves in different order as the bottomed H atoms. The B atom is quite stationary</td>
<td valign="top">2731.31</td>
<td valign="top">103.83</td>
<td valign="top">E"</td>
</tr>
</table>

The following graph is IR spectrum.

[[Image:FeiIR.jpg]]

From the IR spectrum, we can see that there are only 3 peaks. But there are 6 vibrations. In theory, we should get 6 peaks. This is due to peaks of no.2 and no.3 vibrations are combined together as having the nearly the same frequency, this is the same for peaks of no.5 and no.6 vibrations. And for no. 4 vibration, it is totally symmetric and this means there is not dipole moment and hence there will show no peak. So there will be 3 peaks in total shown in the spectrum.

===Molecular orbitals of BH3===

Create .chk file of the optimised BH3 molecule and open it to run another optimisation. Then I open the MOs from the “edit” section.

[[Image:FeiMOs.JPG]]

Then click the “update” button but there is nothing happened and the MOs is not obtained.
While doing the updating, the surface did appear around the molecule.

=='''Exercise 2'''==

Isomers of Mo(CO)4L2

=='''Exercise 3'''==

===Ammonia===

Firstly, generate a molecule of NH3 by using GussianView programme and start to optimise it by using B3LYP method with 6-31G basis set. And then we can get an optimised NH3 molecule with its summary table.

[[Image:FeiNH3summary.jpg]]

From the summary table, we can see that the symmetry is C3v.

Now generate another NH3 molecule and make one of its bond lengths to 1.01 Å. The symmetry is ignored here in the general section of the optimisation section. Then we can a optimised molecule with its summary table.

[[Image:FeiNH3summary2.JPG]]

From the summary table, we can see that the symmetry of this molecule is C1.

Download the file from the website and run the optimisation, hence get the following summary table.

[[Image:FeiNH3summary3.JPG]]

From the summary table, we can see that the symmetry of this molecule is D3h.

From the above 3 molecules, we can see that the symmetry does not make any difference to the final obtained structure, but the symmetry did give a difference to the duration of the calculation. The lone pairs of the N atom imply the symmetry to do a calculation. During an optimisation, a molecule can break symmetry. The D3h molecule has got the lowest energy geometry. The energy difference between C3v and D3h is 3.4401*10^-4 AU (i.e. 0.9032 kJ/mol), the difference between C1 and D3h is -3.457*10^-4 AU (i.e. 0.9077 kJ/mol). The energy difference between these structures is quite significant, the C1 and C3v structures are mirror-image to each other, and therefore they have got similar energies whereas the D3h one has the lowest energy due to its stable structure.

===Method===

In this section, we are going to use the same method with higher basis set level to improve the accuracy of the optimisation. Firstly, NH3 molecule is generated and is run with 6-311+G(d,p) basis set. But there is no “include all electrons” box in the method section of the optimisation.

[[Image:FeiNh3summary1.JPG]]

Using the given file and run the optimisation to obtain the following information.

[[Image:FeiNh3summary2.JPG]]

In this section, the durations of calculation are 29.0 seconds and 78 seconds respectively. However, the durations of the calculation with lower basis set are 30.0 second and 76 seconds which are shorter than those of calculation with higher basis set. The barrier height to inversion is 6.3223*10^-3 AU (i.e. 16.60 kJ/mol) which is much higher than the barrier in the lower basis set level. And this figure is reasonable so we can see that high level of basis set increase the accuracy of the optimisation. The experimental determined barrier is 24.3 which is higher than theoretical 16.6 value.

===The inversion mechanism===

Download the given file and open it to obtain the following picture.

[[Image:FeiNh3.JPG]]

Then we can get the “SCAN” which is showing the chemical reaction over time.

[[Image:FeiEnergyv.s.eigenvalue.JPG]]

From the above curves, we can see that eigen value 12 has got the lowest energy value and this is the most stable state.

===Vibrational analysis===

Get the frequency analysis for D3h optimised molecule.

[[Image:FeiD3h.JPG]]

Get the frequency analysis for C3v optimised molecule as well.

[[Image:FeiC3v.JPG]]

From the 2 vibrational frequencies of the C3v and D3h structures, we can see that there are 5 positive frequencies in D3h structure whereas 6 positives ones in C3v structure. C3v structure is a ground state structure and D3h is a transition state structure. This means C3v will have all positive frequencies whereas D3h will have only one negative frequency. From the above 2 graphs, we can see that only D3h has got one negative frequency which is -768.258 cm^-1. The vibration 4 with the lowest intensity value in the C3v and D3h structures will follow the inversion reaction. The calculated frequencies for C3v structure are higher than the experimental frequencies.

=='''Mini Project'''==

In this section, I am going to compare 2 isomers and one of them is cis-isomer and the other is trans-isomer.
The following are their structures by using GaussianView. Since Pt and Cl atoms are below row 2, I am going to use LanL2MB basis set to optimise them.

The following picture is the optimised cis-isomer with its summary table.

[[Image:Cisoptimisation.JPG]]

File:Cisoptimisation.JPG

2008-12-17T13:35:13Z

Fh106:

File:Cisoptimisation.bmp

2008-12-17T13:34:38Z

Fh106:

Rep:Mod:feihemodule2

2008-12-17T13:33:48Z

Fh106: /* '''Mini Project''' */

='''Module 2'''=

=='''Introduction'''==

The aim of this module 2 is familiar with the Gussview programme and uses the programme to optimise the molecules.

Now look at the following simple molecule BH3.

===Create a molecule of BH3===

Use the Gussview programme to create the BH3 molecule. And we can the following picture of the molecule.

[[Image:FeiBh3.jpg]]

Picture of BH3 molecule.

And we can use label and symbol the molecule to get the following picture.

[[Image:FeiLabelledBH3.JPG]]

Labelled and symbol picture of BH3.

Then we set the all the three B-H bonds to 1.5 angstrom and get the following sturcure of BH3.

[[Image:FeiBh3fixedbondlength.JPG]]

Fixed bond distance picture of BH3

So the molecule is set up.

===Optimising a molecule of BH3===

Use the BLYP method and 3-21G basic set to optimise the molecule of BH3. And then we can the following optimised structure of the molecule.

[[Image:FeiOptimisedBH3.JPG]]

Optimised structure of BH3 molecule

Then we can determine the optimised B-H bond distance and H-B-H bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:FeiBH3bonddistance.JPG]]</td>
<td align="center">[[Image:FeiBH3bondangle.JPG]]</td>
</tr>
<tr>
<td align="center">Bond distance is 1.19435</td>
<td align="center">Bond angle is 120.000</td>
</tr>
</table>

And we can get a summary table to show some information about the molecule.

[[Image:FeiResulttable.JPG]]

Summary of the optimised molecule

From the above summary, we can see that the file of file is .log, calculation type is FOPT, calculation method is RB3LYP, basic set is 3-21G, final energy is -26.46226438 au, dipole moment is 0.000 debye, point group is D3H and the duration of calculation is 19.0 seconds.

We can get a “real” text based .log file as well.

[[Image:FeiRealresulttable.JPG]]

===Understanding optimisation part a===

Open the finished optimised file of the above molecule and tick “read intermediate geometries”. Then an energy and gradient against optimisation graph is obtained.

[[Image:FeiOptimisationgraph.JPG]]

There are 2 graphs in the above picture, the 1st one is energy against each step of optimisation and the 2nd one is the gradient of energy against each step of optimisation.

The green button in the molecule window is click and the animation of optimisation steps is obtained and we can see that the final structure has the least energy and smallest gradient of energy. So the stable structure is with the minimum energy and it is the final structure in the animation.

[[Image:FeiAnimation.JPG]]

=='''Exercise 1'''==

===Find information about BCl3===

Following the method introduced in the introduction section, repeat the calculation for molecule BCl3.

Firstly, create the molecule of BCl3. And measure its B-Cl bond distance and Cl-B-Cl bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:FeiBCL3bonddistance.JPG]]</td>
<td align="center">[[Image:BCL3bondangle.JPG]]</td>
</tr>
<tr>
<td align="center">Bond distance: 1.87000</td>
<td align="center">Bond angle is 120.000</td>
</tr>
</table>

Secondly, restrict the symmetry of BCl3 to D3h and set the tolerance from the default to “very tight (0.0001)” and obtain the following picture.

[[Image:FeiRestrictedBCL3.JPG]]

Restricted BCl3 molecule

Thirdly, do the calculation to optimise the BCl3 molecule and obtain the optimised structure of BCl3.

[[Image:FeiOptimisedBCL3.JPG]]

Optimised BCl3 molecule

And we then obtain the optimised B-Cl bond distance and optimised Cl-B-Cl bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:FeiOptimisedbonddistance.JPG]]</td>
<td align="center">[[Image:Optimisedbondangle.JPG]]</td>
</tr>
<tr>
<td align="center">Bond distance: 1.86592</td>
<td align="center">Bond angle is 120.000</td>
</tr>
</table>

Finally, we then get the summary of the optimised molecule.

[[Image:FeiSummary2.JPG]]

From the above summary table, we can know that the file type is .log, calculation type is FORT, calculation method is RB3LYP, basic set is LANL2MB, final energy is -69.43928112 AU, dipole moment is 0.000 debye, point group is D3h and the duration of calculation is 12.0 seconds.

===Independent work===

I chose H2O as my own molecule. Firstly, set up the molecule of H2O. And we can get the O-H bond distance and H-O-H bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:H2Obonddistance.JPG]]</td>
<td align="center">[[Image:H2Obondangle.JPG]]</td>
</tr>
<tr>
<td align="center">Bond distance: 0.96000</td>
<td align="center">Bond angle is 109.500</td>
</tr>
</table>

Since O atom and H atom is above second row, we do not need to use pseudo-potential.
Therefore, we use the same method as above in above section but we set the basis set to 3-21G and obtain the following optimised H2O molecule with its summary table.

[[Image:FeiH2Osummary.JPG]]

From the above summary table, we can see that the calculation method is RB3LYP, basis set is 3-21G, final energy is -75.97396515 AU, dipole moment is 2.2381 Debye, point group is C2v and duration of calculation is 17.0 seconds.

We now can get the optimised bond distance and bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:Optimisedbonddistance.jpg]]</td>
<td align="center">[[Image:Optimisedbondangle.jpg]]</td>
</tr>
<tr>
<td align="center">Optimised bond distance: 0.99683</td>
<td align="center">Optimised bond angle: 103.991</td>
</tr>
</table>

Now I set the basis set to higher level in order to increase the accuracy. Use the first optimised output file to do another optimisation using higher level basis set. And use the second optimised output file to do another optimisation using even higher basis set.

<table width="663" border="1">
<tr>
<th width="176" scope="col"> </th>
<th scope="col">First trial</th>
<th scope="col">Second trail</th>
<th scope="col">Third trail</th>
</tr>
<tr>
<th scope="row">Bond distance/AU</th>
<td width="143" valign="top">0.99683 </td>
<td width="149" valign="top">0.96526</td>
<td width="167" valign="top">0.96203</td>
</tr>
<tr>
<th scope="row">Bond angle/degree</th>
<td width="143" valign="top">103.991</td>
<td width="149" valign="top">103.696</td>
<td width="167" valign="top">105.057</td>
</tr>
<tr>
<th scope="row">Calculation method</th>
<td width="143" valign="top">RB3LYP</td>
<td width="149" valign="top">RB3LYP</td>
<td width="167" valign="top">RB3LYP</td>
</tr>
<tr>
<th scope="row">Basis set</th>
<td width="143" valign="top">3-21G</td>
<td width="149" valign="top">6-31G(d.p)</td>
<td width="167" valign="top">6-311+G(d,p)</td>
</tr>
<tr>
<th scope="row">Final energy/J</th>
<td width="143" valign="top">-75.97396515</td>
<td width="149" valign="top">-76.41973659</td>
<td width="167" valign="top">-76.45846294</td>
</tr>
<tr>
<th scope="row">Dipole moment/debye</th>
<td width="143" valign="top">2.2381</td>
<td width="149" valign="top">2.0436</td>
<td width="167" valign="top">2.1610</td>
</tr>
<tr>
<th scope="row">Point group</th>
<td width="143" valign="top">C2v</td>
<td width="149" valign="top">C2v</td>
<td width="167" valign="top">C2v</td>
</tr>
<tr>
<th scope="row">Duration of calculation/s</th>
<td width="143" valign="top">17.0</td>
<td width="149" valign="top">17.0</td>
<td width="167" valign="top">18.0</td>
</tr>
</table>

===Vibrational analysis and confirming minima===

In this section, we are going to use vibrational analysis to confirm the minimum structure.
Firstly, open the optimised BH3 file and do the vibrational analysis to confirm its minimum structure. So we get the following structure with its summary.

[[Image:FeiBH3frequncy.jpg]]

From the above summary table, we can see that the energy is -26.46226438 whereas the energy of the optimised one is -26.46226438. So they have got the same value.

===Animating the vibrations===

Open the vibrations result.

[[Image:FeiVibrations.jpg]]

Show display vectors of each vibration.

[[Image:FeiVibration2.jpg]]

The following table is to a summary of motions, frequency, intensities and symmetry.

<table width="716" border="1">
<tr>
<td width="24" valign="top">No.</td>
<td width="473" valign="top">Form of vibration</td>
<td width="59" valign="top">frequency</td>
<td width="65" valign="top">intensity</td>
<td width="61" valign="top">Symmetry 
D3h point group</td>
</tr>
<tr>
<td valign="top">1 </td>
<td valign="top">all the H atoms move in and out together in the same direction, the B atom moves in the opposite direction of that of H atom</td>
<td valign="top">1145.71</td>
<td valign="top">92.6991</td>
<td valign="top">A"2</td>
</tr>
<tr>
<td valign="top">2</td>
<td valign="top">2 bottomed H atoms moves towards and away from each other whereas B atom and top H atom is quite stationary</td>
<td valign="top">1204.66</td>
<td valign="top">12.3789</td>
<td valign="top">E'</td>
</tr>
<tr>
<td valign="top">3</td>
<td valign="top">Each of the bottomed H atom moves away and towards to the top H atom whereas B atom is quite stationary</td>
<td valign="top">1204.66</td>
<td valign="top">12.3814</td>
<td valign="top">E'</td>
</tr>
<tr>
<td valign="top">4</td>
<td valign="top">All H atoms move in and out together in a concerted motion whereas B atom is unmoved</td>
<td valign="top">2591.65</td>
<td valign="top">0.0</td>
<td valign="top">A'1</td>
</tr>
<tr>
<td valign="top">5</td>
<td valign="top">2 bottomed H atoms move towards or away from B atom simultaneously 
Top H atom and B atom is quite stationary</td>
<td valign="top">2731.31</td>
<td valign="top">103.837</td>
<td valign="top">E"</td>
</tr>
<tr>
<td valign="top">6</td>
<td valign="top">Bottomed H atoms move in and out whereas the top H atom moves in different order as the bottomed H atoms. The B atom is quite stationary</td>
<td valign="top">2731.31</td>
<td valign="top">103.83</td>
<td valign="top">E"</td>
</tr>
</table>

The following graph is IR spectrum.

[[Image:FeiIR.jpg]]

From the IR spectrum, we can see that there are only 3 peaks. But there are 6 vibrations. In theory, we should get 6 peaks. This is due to peaks of no.2 and no.3 vibrations are combined together as having the nearly the same frequency, this is the same for peaks of no.5 and no.6 vibrations. And for no. 4 vibration, it is totally symmetric and this means there is not dipole moment and hence there will show no peak. So there will be 3 peaks in total shown in the spectrum.

===Molecular orbitals of BH3===

Create .chk file of the optimised BH3 molecule and open it to run another optimisation. Then I open the MOs from the “edit” section.

[[Image:FeiMOs.JPG]]

Then click the “update” button but there is nothing happened and the MOs is not obtained.
While doing the updating, the surface did appear around the molecule.

=='''Exercise 2'''==

Isomers of Mo(CO)4L2

=='''Exercise 3'''==

===Ammonia===

Firstly, generate a molecule of NH3 by using GussianView programme and start to optimise it by using B3LYP method with 6-31G basis set. And then we can get an optimised NH3 molecule with its summary table.

[[Image:FeiNH3summary.jpg]]

From the summary table, we can see that the symmetry is C3v.

Now generate another NH3 molecule and make one of its bond lengths to 1.01 Å. The symmetry is ignored here in the general section of the optimisation section. Then we can a optimised molecule with its summary table.

[[Image:FeiNH3summary2.JPG]]

From the summary table, we can see that the symmetry of this molecule is C1.

Download the file from the website and run the optimisation, hence get the following summary table.

[[Image:FeiNH3summary3.JPG]]

From the summary table, we can see that the symmetry of this molecule is D3h.

From the above 3 molecules, we can see that the symmetry does not make any difference to the final obtained structure, but the symmetry did give a difference to the duration of the calculation. The lone pairs of the N atom imply the symmetry to do a calculation. During an optimisation, a molecule can break symmetry. The D3h molecule has got the lowest energy geometry. The energy difference between C3v and D3h is 3.4401*10^-4 AU (i.e. 0.9032 kJ/mol), the difference between C1 and D3h is -3.457*10^-4 AU (i.e. 0.9077 kJ/mol). The energy difference between these structures is quite significant, the C1 and C3v structures are mirror-image to each other, and therefore they have got similar energies whereas the D3h one has the lowest energy due to its stable structure.

===Method===

In this section, we are going to use the same method with higher basis set level to improve the accuracy of the optimisation. Firstly, NH3 molecule is generated and is run with 6-311+G(d,p) basis set. But there is no “include all electrons” box in the method section of the optimisation.

[[Image:FeiNh3summary1.JPG]]

Using the given file and run the optimisation to obtain the following information.

[[Image:FeiNh3summary2.JPG]]

In this section, the durations of calculation are 29.0 seconds and 78 seconds respectively. However, the durations of the calculation with lower basis set are 30.0 second and 76 seconds which are shorter than those of calculation with higher basis set. The barrier height to inversion is 6.3223*10^-3 AU (i.e. 16.60 kJ/mol) which is much higher than the barrier in the lower basis set level. And this figure is reasonable so we can see that high level of basis set increase the accuracy of the optimisation. The experimental determined barrier is 24.3 which is higher than theoretical 16.6 value.

===The inversion mechanism===

Download the given file and open it to obtain the following picture.

[[Image:FeiNh3.JPG]]

Then we can get the “SCAN” which is showing the chemical reaction over time.

[[Image:FeiEnergyv.s.eigenvalue.JPG]]

From the above curves, we can see that eigen value 12 has got the lowest energy value and this is the most stable state.

===Vibrational analysis===

Get the frequency analysis for D3h optimised molecule.

[[Image:FeiD3h.JPG]]

Get the frequency analysis for C3v optimised molecule as well.

[[Image:FeiC3v.JPG]]

From the 2 vibrational frequencies of the C3v and D3h structures, we can see that there are 5 positive frequencies in D3h structure whereas 6 positives ones in C3v structure. C3v structure is a ground state structure and D3h is a transition state structure. This means C3v will have all positive frequencies whereas D3h will have only one negative frequency. From the above 2 graphs, we can see that only D3h has got one negative frequency which is -768.258 cm^-1. The vibration 4 with the lowest intensity value in the C3v and D3h structures will follow the inversion reaction. The calculated frequencies for C3v structure are higher than the experimental frequencies.

=='''Mini Project'''==

In this section, I am going to compare 2 isomers and one of them is cis-isomer and the other is trans-isomer.
The following are their structures by using GaussianView. Since Pt and Cl atoms are below row 2, I am going to use LanL2MB basis set to optimise them.

The following picture is the optimised cis-isomer with its summary table.

Rep:Mod:feihemodule3

2008-12-17T13:18:18Z

Fh106: /* Module 3 */

=Module 3=

In this section, I am going to compare 2 isomers and one of them is cis-isomer and the other is trans-isomer.
The following are their structures by using GuassianView.

Rep:Mod:feihemodule3

2008-12-17T13:03:08Z

Fh106: New page: =Module 3=

=Module 3=

Rep:Mod:feihemodule2

2008-12-17T12:52:59Z

Fh106: /* '''Exercise 2''' */

Rep:Mod:feihemodule2

2008-12-17T12:47:17Z

Fh106: /* Animating the vibrations */

='''Module 2'''=

=='''Introduction'''==

The aim of this module 2 is familiar with the Gussview programme and uses the programme to optimise the molecules.

Now look at the following simple molecule BH3.

===Create a molecule of BH3===

Use the Gussview programme to create the BH3 molecule. And we can the following picture of the molecule.

[[Image:FeiBh3.jpg]]

Picture of BH3 molecule.

And we can use label and symbol the molecule to get the following picture.

[[Image:FeiLabelledBH3.JPG]]

Labelled and symbol picture of BH3.

Then we set the all the three B-H bonds to 1.5 angstrom and get the following sturcure of BH3.

[[Image:FeiBh3fixedbondlength.JPG]]

Fixed bond distance picture of BH3

So the molecule is set up.

===Optimising a molecule of BH3===

Use the BLYP method and 3-21G basic set to optimise the molecule of BH3. And then we can the following optimised structure of the molecule.

[[Image:FeiOptimisedBH3.JPG]]

Optimised structure of BH3 molecule

Then we can determine the optimised B-H bond distance and H-B-H bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:FeiBH3bonddistance.JPG]]</td>
<td align="center">[[Image:FeiBH3bondangle.JPG]]</td>
</tr>
<tr>
<td align="center">Bond distance is 1.19435</td>
<td align="center">Bond angle is 120.000</td>
</tr>
</table>

And we can get a summary table to show some information about the molecule.

[[Image:FeiResulttable.JPG]]

Summary of the optimised molecule

From the above summary, we can see that the file of file is .log, calculation type is FOPT, calculation method is RB3LYP, basic set is 3-21G, final energy is -26.46226438 au, dipole moment is 0.000 debye, point group is D3H and the duration of calculation is 19.0 seconds.

We can get a “real” text based .log file as well.

[[Image:FeiRealresulttable.JPG]]

===Understanding optimisation part a===

Open the finished optimised file of the above molecule and tick “read intermediate geometries”. Then an energy and gradient against optimisation graph is obtained.

[[Image:FeiOptimisationgraph.JPG]]

There are 2 graphs in the above picture, the 1st one is energy against each step of optimisation and the 2nd one is the gradient of energy against each step of optimisation.

The green button in the molecule window is click and the animation of optimisation steps is obtained and we can see that the final structure has the least energy and smallest gradient of energy. So the stable structure is with the minimum energy and it is the final structure in the animation.

[[Image:FeiAnimation.JPG]]

=='''Exercise 1'''==

===Find information about BCl3===

Following the method introduced in the introduction section, repeat the calculation for molecule BCl3.

Firstly, create the molecule of BCl3. And measure its B-Cl bond distance and Cl-B-Cl bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:FeiBCL3bonddistance.JPG]]</td>
<td align="center">[[Image:BCL3bondangle.JPG]]</td>
</tr>
<tr>
<td align="center">Bond distance: 1.87000</td>
<td align="center">Bond angle is 120.000</td>
</tr>
</table>

Secondly, restrict the symmetry of BCl3 to D3h and set the tolerance from the default to “very tight (0.0001)” and obtain the following picture.

[[Image:FeiRestrictedBCL3.JPG]]

Restricted BCl3 molecule

Thirdly, do the calculation to optimise the BCl3 molecule and obtain the optimised structure of BCl3.

[[Image:FeiOptimisedBCL3.JPG]]

Optimised BCl3 molecule

And we then obtain the optimised B-Cl bond distance and optimised Cl-B-Cl bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:FeiOptimisedbonddistance.JPG]]</td>
<td align="center">[[Image:Optimisedbondangle.JPG]]</td>
</tr>
<tr>
<td align="center">Bond distance: 1.86592</td>
<td align="center">Bond angle is 120.000</td>
</tr>
</table>

Finally, we then get the summary of the optimised molecule.

[[Image:FeiSummary2.JPG]]

From the above summary table, we can know that the file type is .log, calculation type is FORT, calculation method is RB3LYP, basic set is LANL2MB, final energy is -69.43928112 AU, dipole moment is 0.000 debye, point group is D3h and the duration of calculation is 12.0 seconds.

===Independent work===

I chose H2O as my own molecule. Firstly, set up the molecule of H2O. And we can get the O-H bond distance and H-O-H bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:H2Obonddistance.JPG]]</td>
<td align="center">[[Image:H2Obondangle.JPG]]</td>
</tr>
<tr>
<td align="center">Bond distance: 0.96000</td>
<td align="center">Bond angle is 109.500</td>
</tr>
</table>

Since O atom and H atom is above second row, we do not need to use pseudo-potential.
Therefore, we use the same method as above in above section but we set the basis set to 3-21G and obtain the following optimised H2O molecule with its summary table.

[[Image:FeiH2Osummary.JPG]]

From the above summary table, we can see that the calculation method is RB3LYP, basis set is 3-21G, final energy is -75.97396515 AU, dipole moment is 2.2381 Debye, point group is C2v and duration of calculation is 17.0 seconds.

We now can get the optimised bond distance and bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:Optimisedbonddistance.jpg]]</td>
<td align="center">[[Image:Optimisedbondangle.jpg]]</td>
</tr>
<tr>
<td align="center">Optimised bond distance: 0.99683</td>
<td align="center">Optimised bond angle: 103.991</td>
</tr>
</table>

Now I set the basis set to higher level in order to increase the accuracy. Use the first optimised output file to do another optimisation using higher level basis set. And use the second optimised output file to do another optimisation using even higher basis set.

<table width="663" border="1">
<tr>
<th width="176" scope="col"> </th>
<th scope="col">First trial</th>
<th scope="col">Second trail</th>
<th scope="col">Third trail</th>
</tr>
<tr>
<th scope="row">Bond distance/AU</th>
<td width="143" valign="top">0.99683 </td>
<td width="149" valign="top">0.96526</td>
<td width="167" valign="top">0.96203</td>
</tr>
<tr>
<th scope="row">Bond angle/degree</th>
<td width="143" valign="top">103.991</td>
<td width="149" valign="top">103.696</td>
<td width="167" valign="top">105.057</td>
</tr>
<tr>
<th scope="row">Calculation method</th>
<td width="143" valign="top">RB3LYP</td>
<td width="149" valign="top">RB3LYP</td>
<td width="167" valign="top">RB3LYP</td>
</tr>
<tr>
<th scope="row">Basis set</th>
<td width="143" valign="top">3-21G</td>
<td width="149" valign="top">6-31G(d.p)</td>
<td width="167" valign="top">6-311+G(d,p)</td>
</tr>
<tr>
<th scope="row">Final energy/J</th>
<td width="143" valign="top">-75.97396515</td>
<td width="149" valign="top">-76.41973659</td>
<td width="167" valign="top">-76.45846294</td>
</tr>
<tr>
<th scope="row">Dipole moment/debye</th>
<td width="143" valign="top">2.2381</td>
<td width="149" valign="top">2.0436</td>
<td width="167" valign="top">2.1610</td>
</tr>
<tr>
<th scope="row">Point group</th>
<td width="143" valign="top">C2v</td>
<td width="149" valign="top">C2v</td>
<td width="167" valign="top">C2v</td>
</tr>
<tr>
<th scope="row">Duration of calculation/s</th>
<td width="143" valign="top">17.0</td>
<td width="149" valign="top">17.0</td>
<td width="167" valign="top">18.0</td>
</tr>
</table>

===Vibrational analysis and confirming minima===

In this section, we are going to use vibrational analysis to confirm the minimum structure.
Firstly, open the optimised BH3 file and do the vibrational analysis to confirm its minimum structure. So we get the following structure with its summary.

[[Image:FeiBH3frequncy.jpg]]

From the above summary table, we can see that the energy is -26.46226438 whereas the energy of the optimised one is -26.46226438. So they have got the same value.

===Animating the vibrations===

Open the vibrations result.

[[Image:FeiVibrations.jpg]]

Show display vectors of each vibration.

[[Image:FeiVibration2.jpg]]

The following table is to a summary of motions, frequency, intensities and symmetry.

<table width="716" border="1">
<tr>
<td width="24" valign="top">No.</td>
<td width="473" valign="top">Form of vibration</td>
<td width="59" valign="top">frequency</td>
<td width="65" valign="top">intensity</td>
<td width="61" valign="top">Symmetry 
D3h point group</td>
</tr>
<tr>
<td valign="top">1 </td>
<td valign="top">all the H atoms move in and out together in the same direction, the B atom moves in the opposite direction of that of H atom</td>
<td valign="top">1145.71</td>
<td valign="top">92.6991</td>
<td valign="top">A"2</td>
</tr>
<tr>
<td valign="top">2</td>
<td valign="top">2 bottomed H atoms moves towards and away from each other whereas B atom and top H atom is quite stationary</td>
<td valign="top">1204.66</td>
<td valign="top">12.3789</td>
<td valign="top">E'</td>
</tr>
<tr>
<td valign="top">3</td>
<td valign="top">Each of the bottomed H atom moves away and towards to the top H atom whereas B atom is quite stationary</td>
<td valign="top">1204.66</td>
<td valign="top">12.3814</td>
<td valign="top">E'</td>
</tr>
<tr>
<td valign="top">4</td>
<td valign="top">All H atoms move in and out together in a concerted motion whereas B atom is unmoved</td>
<td valign="top">2591.65</td>
<td valign="top">0.0</td>
<td valign="top">A'1</td>
</tr>
<tr>
<td valign="top">5</td>
<td valign="top">2 bottomed H atoms move towards or away from B atom simultaneously 
Top H atom and B atom is quite stationary</td>
<td valign="top">2731.31</td>
<td valign="top">103.837</td>
<td valign="top">E"</td>
</tr>
<tr>
<td valign="top">6</td>
<td valign="top">Bottomed H atoms move in and out whereas the top H atom moves in different order as the bottomed H atoms. The B atom is quite stationary</td>
<td valign="top">2731.31</td>
<td valign="top">103.83</td>
<td valign="top">E"</td>
</tr>
</table>

The following graph is IR spectrum.

[[Image:FeiIR.jpg]]

From the IR spectrum, we can see that there are only 3 peaks. But there are 6 vibrations. In theory, we should get 6 peaks. This is due to peaks of no.2 and no.3 vibrations are combined together as having the nearly the same frequency, this is the same for peaks of no.5 and no.6 vibrations. And for no. 4 vibration, it is totally symmetric and this means there is not dipole moment and hence there will show no peak. So there will be 3 peaks in total shown in the spectrum.

===Molecular orbitals of BH3===

Create .chk file of the optimised BH3 molecule and open it to run another optimisation. Then I open the MOs from the “edit” section.

[[Image:FeiMOs.JPG]]

Then click the “update” button but there is nothing happened and the MOs is not obtained.
While doing the updating, the surface did appear around the molecule.

=='''Exercise 2'''==

=='''Exercise 3'''==

===Ammonia===

Firstly, generate a molecule of NH3 by using GussianView programme and start to optimise it by using B3LYP method with 6-31G basis set. And then we can get an optimised NH3 molecule with its summary table.

[[Image:FeiNH3summary.jpg]]

From the summary table, we can see that the symmetry is C3v.

Now generate another NH3 molecule and make one of its bond lengths to 1.01 Å. The symmetry is ignored here in the general section of the optimisation section. Then we can a optimised molecule with its summary table.

[[Image:FeiNH3summary2.JPG]]

From the summary table, we can see that the symmetry of this molecule is C1.

Download the file from the website and run the optimisation, hence get the following summary table.

[[Image:FeiNH3summary3.JPG]]

From the summary table, we can see that the symmetry of this molecule is D3h.

From the above 3 molecules, we can see that the symmetry does not make any difference to the final obtained structure, but the symmetry did give a difference to the duration of the calculation. The lone pairs of the N atom imply the symmetry to do a calculation. During an optimisation, a molecule can break symmetry. The D3h molecule has got the lowest energy geometry. The energy difference between C3v and D3h is 3.4401*10^-4 AU (i.e. 0.9032 kJ/mol), the difference between C1 and D3h is -3.457*10^-4 AU (i.e. 0.9077 kJ/mol). The energy difference between these structures is quite significant, the C1 and C3v structures are mirror-image to each other, and therefore they have got similar energies whereas the D3h one has the lowest energy due to its stable structure.

===Method===

In this section, we are going to use the same method with higher basis set level to improve the accuracy of the optimisation. Firstly, NH3 molecule is generated and is run with 6-311+G(d,p) basis set. But there is no “include all electrons” box in the method section of the optimisation.

[[Image:FeiNh3summary1.JPG]]

Using the given file and run the optimisation to obtain the following information.

[[Image:FeiNh3summary2.JPG]]

In this section, the durations of calculation are 29.0 seconds and 78 seconds respectively. However, the durations of the calculation with lower basis set are 30.0 second and 76 seconds which are shorter than those of calculation with higher basis set. The barrier height to inversion is 6.3223*10^-3 AU (i.e. 16.60 kJ/mol) which is much higher than the barrier in the lower basis set level. And this figure is reasonable so we can see that high level of basis set increase the accuracy of the optimisation. The experimental determined barrier is 24.3 which is higher than theoretical 16.6 value.

===The inversion mechanism===

Download the given file and open it to obtain the following picture.

[[Image:FeiNh3.JPG]]

Then we can get the “SCAN” which is showing the chemical reaction over time.

[[Image:FeiEnergyv.s.eigenvalue.JPG]]

From the above curves, we can see that eigen value 12 has got the lowest energy value and this is the most stable state.

===Vibrational analysis===

Get the frequency analysis for D3h optimised molecule.

[[Image:FeiD3h.JPG]]

Get the frequency analysis for C3v optimised molecule as well.

[[Image:FeiC3v.JPG]]

From the 2 vibrational frequencies of the C3v and D3h structures, we can see that there are 5 positive frequencies in D3h structure whereas 6 positives ones in C3v structure. C3v structure is a ground state structure and D3h is a transition state structure. This means C3v will have all positive frequencies whereas D3h will have only one negative frequency. From the above 2 graphs, we can see that only D3h has got one negative frequency which is -768.258 cm^-1. The vibration 4 with the lowest intensity value in the C3v and D3h structures will follow the inversion reaction. The calculated frequencies for C3v structure are higher than the experimental frequencies.

=='''Mini Project'''==

Rep:Mod:feihemodule2

2008-12-16T14:46:52Z

Fh106:

='''Module 2'''=

=='''Introduction'''==

The aim of this module 2 is familiar with the Gussview programme and uses the programme to optimise the molecules.

Now look at the following simple molecule BH3.

===Create a molecule of BH3===

Use the Gussview programme to create the BH3 molecule. And we can the following picture of the molecule.

[[Image:FeiBh3.jpg]]

Picture of BH3 molecule.

And we can use label and symbol the molecule to get the following picture.

[[Image:FeiLabelledBH3.JPG]]

Labelled and symbol picture of BH3.

Then we set the all the three B-H bonds to 1.5 angstrom and get the following sturcure of BH3.

[[Image:FeiBh3fixedbondlength.JPG]]

Fixed bond distance picture of BH3

So the molecule is set up.

===Optimising a molecule of BH3===

Use the BLYP method and 3-21G basic set to optimise the molecule of BH3. And then we can the following optimised structure of the molecule.

[[Image:FeiOptimisedBH3.JPG]]

Optimised structure of BH3 molecule

Then we can determine the optimised B-H bond distance and H-B-H bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:FeiBH3bonddistance.JPG]]</td>
<td align="center">[[Image:FeiBH3bondangle.JPG]]</td>
</tr>
<tr>
<td align="center">Bond distance is 1.19435</td>
<td align="center">Bond angle is 120.000</td>
</tr>
</table>

And we can get a summary table to show some information about the molecule.

[[Image:FeiResulttable.JPG]]

Summary of the optimised molecule

From the above summary, we can see that the file of file is .log, calculation type is FOPT, calculation method is RB3LYP, basic set is 3-21G, final energy is -26.46226438 au, dipole moment is 0.000 debye, point group is D3H and the duration of calculation is 19.0 seconds.

We can get a “real” text based .log file as well.

[[Image:FeiRealresulttable.JPG]]

===Understanding optimisation part a===

Open the finished optimised file of the above molecule and tick “read intermediate geometries”. Then an energy and gradient against optimisation graph is obtained.

[[Image:FeiOptimisationgraph.JPG]]

There are 2 graphs in the above picture, the 1st one is energy against each step of optimisation and the 2nd one is the gradient of energy against each step of optimisation.

The green button in the molecule window is click and the animation of optimisation steps is obtained and we can see that the final structure has the least energy and smallest gradient of energy. So the stable structure is with the minimum energy and it is the final structure in the animation.

[[Image:FeiAnimation.JPG]]

=='''Exercise 1'''==

===Find information about BCl3===

Following the method introduced in the introduction section, repeat the calculation for molecule BCl3.

Firstly, create the molecule of BCl3. And measure its B-Cl bond distance and Cl-B-Cl bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:FeiBCL3bonddistance.JPG]]</td>
<td align="center">[[Image:BCL3bondangle.JPG]]</td>
</tr>
<tr>
<td align="center">Bond distance: 1.87000</td>
<td align="center">Bond angle is 120.000</td>
</tr>
</table>

Secondly, restrict the symmetry of BCl3 to D3h and set the tolerance from the default to “very tight (0.0001)” and obtain the following picture.

[[Image:FeiRestrictedBCL3.JPG]]

Restricted BCl3 molecule

Thirdly, do the calculation to optimise the BCl3 molecule and obtain the optimised structure of BCl3.

[[Image:FeiOptimisedBCL3.JPG]]

Optimised BCl3 molecule

And we then obtain the optimised B-Cl bond distance and optimised Cl-B-Cl bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:FeiOptimisedbonddistance.JPG]]</td>
<td align="center">[[Image:Optimisedbondangle.JPG]]</td>
</tr>
<tr>
<td align="center">Bond distance: 1.86592</td>
<td align="center">Bond angle is 120.000</td>
</tr>
</table>

Finally, we then get the summary of the optimised molecule.

[[Image:FeiSummary2.JPG]]

From the above summary table, we can know that the file type is .log, calculation type is FORT, calculation method is RB3LYP, basic set is LANL2MB, final energy is -69.43928112 AU, dipole moment is 0.000 debye, point group is D3h and the duration of calculation is 12.0 seconds.

===Independent work===

I chose H2O as my own molecule. Firstly, set up the molecule of H2O. And we can get the O-H bond distance and H-O-H bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:H2Obonddistance.JPG]]</td>
<td align="center">[[Image:H2Obondangle.JPG]]</td>
</tr>
<tr>
<td align="center">Bond distance: 0.96000</td>
<td align="center">Bond angle is 109.500</td>
</tr>
</table>

Since O atom and H atom is above second row, we do not need to use pseudo-potential.
Therefore, we use the same method as above in above section but we set the basis set to 3-21G and obtain the following optimised H2O molecule with its summary table.

[[Image:FeiH2Osummary.JPG]]

From the above summary table, we can see that the calculation method is RB3LYP, basis set is 3-21G, final energy is -75.97396515 AU, dipole moment is 2.2381 Debye, point group is C2v and duration of calculation is 17.0 seconds.

We now can get the optimised bond distance and bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:Optimisedbonddistance.jpg]]</td>
<td align="center">[[Image:Optimisedbondangle.jpg]]</td>
</tr>
<tr>
<td align="center">Optimised bond distance: 0.99683</td>
<td align="center">Optimised bond angle: 103.991</td>
</tr>
</table>

Now I set the basis set to higher level in order to increase the accuracy. Use the first optimised output file to do another optimisation using higher level basis set. And use the second optimised output file to do another optimisation using even higher basis set.

<table width="663" border="1">
<tr>
<th width="176" scope="col"> </th>
<th scope="col">First trial</th>
<th scope="col">Second trail</th>
<th scope="col">Third trail</th>
</tr>
<tr>
<th scope="row">Bond distance/AU</th>
<td width="143" valign="top">0.99683 </td>
<td width="149" valign="top">0.96526</td>
<td width="167" valign="top">0.96203</td>
</tr>
<tr>
<th scope="row">Bond angle/degree</th>
<td width="143" valign="top">103.991</td>
<td width="149" valign="top">103.696</td>
<td width="167" valign="top">105.057</td>
</tr>
<tr>
<th scope="row">Calculation method</th>
<td width="143" valign="top">RB3LYP</td>
<td width="149" valign="top">RB3LYP</td>
<td width="167" valign="top">RB3LYP</td>
</tr>
<tr>
<th scope="row">Basis set</th>
<td width="143" valign="top">3-21G</td>
<td width="149" valign="top">6-31G(d.p)</td>
<td width="167" valign="top">6-311+G(d,p)</td>
</tr>
<tr>
<th scope="row">Final energy/J</th>
<td width="143" valign="top">-75.97396515</td>
<td width="149" valign="top">-76.41973659</td>
<td width="167" valign="top">-76.45846294</td>
</tr>
<tr>
<th scope="row">Dipole moment/debye</th>
<td width="143" valign="top">2.2381</td>
<td width="149" valign="top">2.0436</td>
<td width="167" valign="top">2.1610</td>
</tr>
<tr>
<th scope="row">Point group</th>
<td width="143" valign="top">C2v</td>
<td width="149" valign="top">C2v</td>
<td width="167" valign="top">C2v</td>
</tr>
<tr>
<th scope="row">Duration of calculation/s</th>
<td width="143" valign="top">17.0</td>
<td width="149" valign="top">17.0</td>
<td width="167" valign="top">18.0</td>
</tr>
</table>

===Vibrational analysis and confirming minima===

In this section, we are going to use vibrational analysis to confirm the minimum structure.
Firstly, open the optimised BH3 file and do the vibrational analysis to confirm its minimum structure. So we get the following structure with its summary.

[[Image:FeiBH3frequncy.jpg]]

From the above summary table, we can see that the energy is -26.46226438 whereas the energy of the optimised one is -26.46226438. So they have got the same value.

===Animating the vibrations===

Open the vibrations result.

[[Image:FeiVibrations.jpg]]

Show display vectors of each vibration.

[[Image:FeiVibration2.jpg]]

The following table is to a summary of motions, frequency, intensities and symmetry.

<table width="716" border="1">
<tr>
<td width="24" valign="top">No.</td>
<td width="473" valign="top">Form of vibration</td>
<td width="59" valign="top">frequency</td>
<td width="65" valign="top">intensity</td>
<td width="61" valign="top">Symmetry 
D3h point group</td>
</tr>
<tr>
<td valign="top">1 </td>
<td valign="top">all the H atoms move in and out together in the same direction, the B atom moves in the opposite direction of that of H atom</td>
<td valign="top">1145.71</td>
<td valign="top">92.6991</td>
<td valign="top"> </td>
</tr>
<tr>
<td valign="top">2</td>
<td valign="top">2 bottomed H atoms moves towards and away from each other whereas B atom and top H atom is quite stationary</td>
<td valign="top">1204.66</td>
<td valign="top">12.3789</td>
<td valign="top"> </td>
</tr>
<tr>
<td valign="top">3</td>
<td valign="top">Each of the bottomed H atom moves away and towards to the top H atom whereas B atom is quite stationary</td>
<td valign="top">1204.66</td>
<td valign="top">12.3814</td>
<td valign="top"> </td>
</tr>
<tr>
<td valign="top">4</td>
<td valign="top">All H atoms move in and out together in a concerted motion whereas B atom is unmoved</td>
<td valign="top">2591.65</td>
<td valign="top">0.0</td>
<td valign="top">A'1</td>
</tr>
<tr>
<td valign="top">5</td>
<td valign="top">2 bottomed H atoms move towards or away from B atom simultaneously 
Top H atom and B atom is quite stationary</td>
<td valign="top">2731.31</td>
<td valign="top">103.837</td>
<td valign="top"> </td>
</tr>
<tr>
<td valign="top">6</td>
<td valign="top">Bottomed H atoms move in and out whereas the top H atom moves in different order as the bottomed H atoms. The B atom is quite stationary</td>
<td valign="top">2731.31</td>
<td valign="top">103.83</td>
<td valign="top"> </td>
</tr>
</table>

The following graph is IR spectrum.

[[Image:FeiIR.jpg]]

From the IR spectrum, we can see that there are only 3 peaks. But there are 6 vibrations. In theory, we should get 6 peaks. This is due to peaks of no.2 and no.3 vibrations are combined together as having the nearly the same frequency, this is the same for peaks of no.5 and no.6 vibrations. And for no. 4 vibration, it is totally symmetric and this means there is not dipole moment and hence there will show no peak. So there will be 3 peaks in total shown in the spectrum.

===Molecular orbitals of BH3===

Create .chk file of the optimised BH3 molecule and open it to run another optimisation. Then I open the MOs from the “edit” section.

[[Image:FeiMOs.JPG]]

Then click the “update” button but there is nothing happened and the MOs is not obtained.
While doing the updating, the surface did appear around the molecule.

=='''Exercise 2'''==

=='''Exercise 3'''==

===Ammonia===

Firstly, generate a molecule of NH3 by using GussianView programme and start to optimise it by using B3LYP method with 6-31G basis set. And then we can get an optimised NH3 molecule with its summary table.

[[Image:FeiNH3summary.jpg]]

From the summary table, we can see that the symmetry is C3v.

Now generate another NH3 molecule and make one of its bond lengths to 1.01 Å. The symmetry is ignored here in the general section of the optimisation section. Then we can a optimised molecule with its summary table.

[[Image:FeiNH3summary2.JPG]]

From the summary table, we can see that the symmetry of this molecule is C1.

Download the file from the website and run the optimisation, hence get the following summary table.

[[Image:FeiNH3summary3.JPG]]

From the summary table, we can see that the symmetry of this molecule is D3h.

From the above 3 molecules, we can see that the symmetry does not make any difference to the final obtained structure, but the symmetry did give a difference to the duration of the calculation. The lone pairs of the N atom imply the symmetry to do a calculation. During an optimisation, a molecule can break symmetry. The D3h molecule has got the lowest energy geometry. The energy difference between C3v and D3h is 3.4401*10^-4 AU (i.e. 0.9032 kJ/mol), the difference between C1 and D3h is -3.457*10^-4 AU (i.e. 0.9077 kJ/mol). The energy difference between these structures is quite significant, the C1 and C3v structures are mirror-image to each other, and therefore they have got similar energies whereas the D3h one has the lowest energy due to its stable structure.

===Method===

In this section, we are going to use the same method with higher basis set level to improve the accuracy of the optimisation. Firstly, NH3 molecule is generated and is run with 6-311+G(d,p) basis set. But there is no “include all electrons” box in the method section of the optimisation.

[[Image:FeiNh3summary1.JPG]]

Using the given file and run the optimisation to obtain the following information.

[[Image:FeiNh3summary2.JPG]]

In this section, the durations of calculation are 29.0 seconds and 78 seconds respectively. However, the durations of the calculation with lower basis set are 30.0 second and 76 seconds which are shorter than those of calculation with higher basis set. The barrier height to inversion is 6.3223*10^-3 AU (i.e. 16.60 kJ/mol) which is much higher than the barrier in the lower basis set level. And this figure is reasonable so we can see that high level of basis set increase the accuracy of the optimisation. The experimental determined barrier is 24.3 which is higher than theoretical 16.6 value.

===The inversion mechanism===

Download the given file and open it to obtain the following picture.

[[Image:FeiNh3.JPG]]

Then we can get the “SCAN” which is showing the chemical reaction over time.

[[Image:FeiEnergyv.s.eigenvalue.JPG]]

From the above curves, we can see that eigen value 12 has got the lowest energy value and this is the most stable state.

===Vibrational analysis===

Get the frequency analysis for D3h optimised molecule.

[[Image:FeiD3h.JPG]]

Get the frequency analysis for C3v optimised molecule as well.

[[Image:FeiC3v.JPG]]

From the 2 vibrational frequencies of the C3v and D3h structures, we can see that there are 5 positive frequencies in D3h structure whereas 6 positives ones in C3v structure. C3v structure is a ground state structure and D3h is a transition state structure. This means C3v will have all positive frequencies whereas D3h will have only one negative frequency. From the above 2 graphs, we can see that only D3h has got one negative frequency which is -768.258 cm^-1. The vibration 4 with the lowest intensity value in the C3v and D3h structures will follow the inversion reaction. The calculated frequencies for C3v structure are higher than the experimental frequencies.

=='''Mini Project'''==

Rep:Mod:feihemodule2

2008-12-16T14:44:36Z

Fh106:

='''Module 2'''=

==='''Introduction'''===

The aim of this module 2 is familiar with the Gussview programme and uses the programme to optimise the molecules.

Now look at the following simple molecule BH3.

==Create a molecule of BH3==

Use the Gussview programme to create the BH3 molecule. And we can the following picture of the molecule.

[[Image:FeiBh3.jpg]]

Picture of BH3 molecule.

And we can use label and symbol the molecule to get the following picture.

[[Image:FeiLabelledBH3.JPG]]

Labelled and symbol picture of BH3.

Then we set the all the three B-H bonds to 1.5 angstrom and get the following sturcure of BH3.

[[Image:FeiBh3fixedbondlength.JPG]]

Fixed bond distance picture of BH3

So the molecule is set up.

==Optimising a molecule of BH3==

Use the BLYP method and 3-21G basic set to optimise the molecule of BH3. And then we can the following optimised structure of the molecule.

[[Image:FeiOptimisedBH3.JPG]]

Optimised structure of BH3 molecule

Then we can determine the optimised B-H bond distance and H-B-H bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:FeiBH3bonddistance.JPG]]</td>
<td align="center">[[Image:FeiBH3bondangle.JPG]]</td>
</tr>
<tr>
<td align="center">Bond distance is 1.19435</td>
<td align="center">Bond angle is 120.000</td>
</tr>
</table>

And we can get a summary table to show some information about the molecule.

[[Image:FeiResulttable.JPG]]

Summary of the optimised molecule

From the above summary, we can see that the file of file is .log, calculation type is FOPT, calculation method is RB3LYP, basic set is 3-21G, final energy is -26.46226438 au, dipole moment is 0.000 debye, point group is D3H and the duration of calculation is 19.0 seconds.

We can get a “real” text based .log file as well.

[[Image:FeiRealresulttable.JPG]]

==Understanding optimisation part a==

Open the finished optimised file of the above molecule and tick “read intermediate geometries”. Then an energy and gradient against optimisation graph is obtained.

[[Image:FeiOptimisationgraph.JPG]]

There are 2 graphs in the above picture, the 1st one is energy against each step of optimisation and the 2nd one is the gradient of energy against each step of optimisation.

The green button in the molecule window is click and the animation of optimisation steps is obtained and we can see that the final structure has the least energy and smallest gradient of energy. So the stable structure is with the minimum energy and it is the final structure in the animation.

[[Image:FeiAnimation.JPG]]

==='''Exercise 1'''===

==Find information about BCl3==

Following the method introduced in the introduction section, repeat the calculation for molecule BCl3.

Firstly, create the molecule of BCl3. And measure its B-Cl bond distance and Cl-B-Cl bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:FeiBCL3bonddistance.JPG]]</td>
<td align="center">[[Image:BCL3bondangle.JPG]]</td>
</tr>
<tr>
<td align="center">Bond distance: 1.87000</td>
<td align="center">Bond angle is 120.000</td>
</tr>
</table>

Secondly, restrict the symmetry of BCl3 to D3h and set the tolerance from the default to “very tight (0.0001)” and obtain the following picture.

[[Image:FeiRestrictedBCL3.JPG]]

Restricted BCl3 molecule

Thirdly, do the calculation to optimise the BCl3 molecule and obtain the optimised structure of BCl3.

[[Image:FeiOptimisedBCL3.JPG]]

Optimised BCl3 molecule

And we then obtain the optimised B-Cl bond distance and optimised Cl-B-Cl bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:FeiOptimisedbonddistance.JPG]]</td>
<td align="center">[[Image:Optimisedbondangle.JPG]]</td>
</tr>
<tr>
<td align="center">Bond distance: 1.86592</td>
<td align="center">Bond angle is 120.000</td>
</tr>
</table>

Finally, we then get the summary of the optimised molecule.

[[Image:FeiSummary2.JPG]]

From the above summary table, we can know that the file type is .log, calculation type is FORT, calculation method is RB3LYP, basic set is LANL2MB, final energy is -69.43928112 AU, dipole moment is 0.000 debye, point group is D3h and the duration of calculation is 12.0 seconds.

==Independent work==

I chose H2O as my own molecule. Firstly, set up the molecule of H2O. And we can get the O-H bond distance and H-O-H bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:H2Obonddistance.JPG]]</td>
<td align="center">[[Image:H2Obondangle.JPG]]</td>
</tr>
<tr>
<td align="center">Bond distance: 0.96000</td>
<td align="center">Bond angle is 109.500</td>
</tr>
</table>

Since O atom and H atom is above second row, we do not need to use pseudo-potential.
Therefore, we use the same method as above in above section but we set the basis set to 3-21G and obtain the following optimised H2O molecule with its summary table.

[[Image:FeiH2Osummary.JPG]]

From the above summary table, we can see that the calculation method is RB3LYP, basis set is 3-21G, final energy is -75.97396515 AU, dipole moment is 2.2381 Debye, point group is C2v and duration of calculation is 17.0 seconds.

We now can get the optimised bond distance and bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:Optimisedbonddistance.jpg]]</td>
<td align="center">[[Image:Optimisedbondangle.jpg]]</td>
</tr>
<tr>
<td align="center">Optimised bond distance: 0.99683</td>
<td align="center">Optimised bond angle: 103.991</td>
</tr>
</table>

Now I set the basis set to higher level in order to increase the accuracy. Use the first optimised output file to do another optimisation using higher level basis set. And use the second optimised output file to do another optimisation using even higher basis set.

<table width="663" border="1">
<tr>
<th width="176" scope="col"> </th>
<th scope="col">First trial</th>
<th scope="col">Second trail</th>
<th scope="col">Third trail</th>
</tr>
<tr>
<th scope="row">Bond distance/AU</th>
<td width="143" valign="top">0.99683 </td>
<td width="149" valign="top">0.96526</td>
<td width="167" valign="top">0.96203</td>
</tr>
<tr>
<th scope="row">Bond angle/degree</th>
<td width="143" valign="top">103.991</td>
<td width="149" valign="top">103.696</td>
<td width="167" valign="top">105.057</td>
</tr>
<tr>
<th scope="row">Calculation method</th>
<td width="143" valign="top">RB3LYP</td>
<td width="149" valign="top">RB3LYP</td>
<td width="167" valign="top">RB3LYP</td>
</tr>
<tr>
<th scope="row">Basis set</th>
<td width="143" valign="top">3-21G</td>
<td width="149" valign="top">6-31G(d.p)</td>
<td width="167" valign="top">6-311+G(d,p)</td>
</tr>
<tr>
<th scope="row">Final energy/J</th>
<td width="143" valign="top">-75.97396515</td>
<td width="149" valign="top">-76.41973659</td>
<td width="167" valign="top">-76.45846294</td>
</tr>
<tr>
<th scope="row">Dipole moment/debye</th>
<td width="143" valign="top">2.2381</td>
<td width="149" valign="top">2.0436</td>
<td width="167" valign="top">2.1610</td>
</tr>
<tr>
<th scope="row">Point group</th>
<td width="143" valign="top">C2v</td>
<td width="149" valign="top">C2v</td>
<td width="167" valign="top">C2v</td>
</tr>
<tr>
<th scope="row">Duration of calculation/s</th>
<td width="143" valign="top">17.0</td>
<td width="149" valign="top">17.0</td>
<td width="167" valign="top">18.0</td>
</tr>
</table>

==Vibrational analysis and confirming minima==

In this section, we are going to use vibrational analysis to confirm the minimum structure.
Firstly, open the optimised BH3 file and do the vibrational analysis to confirm its minimum structure. So we get the following structure with its summary.

[[Image:FeiBH3frequncy.jpg]]

From the above summary table, we can see that the energy is -26.46226438 whereas the energy of the optimised one is -26.46226438. So they have got the same value.

==Animating the vibrations==

Open the vibrations result.

[[Image:FeiVibrations.jpg]]

Show display vectors of each vibration.

[[Image:FeiVibration2.jpg]]

The following table is to a summary of motions, frequency, intensities and symmetry.

<table width="716" border="1">
<tr>
<td width="24" valign="top">No.</td>
<td width="473" valign="top">Form of vibration</td>
<td width="59" valign="top">frequency</td>
<td width="65" valign="top">intensity</td>
<td width="61" valign="top">Symmetry 
D3h point group</td>
</tr>
<tr>
<td valign="top">1 </td>
<td valign="top">all the H atoms move in and out together in the same direction, the B atom moves in the opposite direction of that of H atom</td>
<td valign="top">1145.71</td>
<td valign="top">92.6991</td>
<td valign="top"> </td>
</tr>
<tr>
<td valign="top">2</td>
<td valign="top">2 bottomed H atoms moves towards and away from each other whereas B atom and top H atom is quite stationary</td>
<td valign="top">1204.66</td>
<td valign="top">12.3789</td>
<td valign="top"> </td>
</tr>
<tr>
<td valign="top">3</td>
<td valign="top">Each of the bottomed H atom moves away and towards to the top H atom whereas B atom is quite stationary</td>
<td valign="top">1204.66</td>
<td valign="top">12.3814</td>
<td valign="top"> </td>
</tr>
<tr>
<td valign="top">4</td>
<td valign="top">All H atoms move in and out together in a concerted motion whereas B atom is unmoved</td>
<td valign="top">2591.65</td>
<td valign="top">0.0</td>
<td valign="top">A'1</td>
</tr>
<tr>
<td valign="top">5</td>
<td valign="top">2 bottomed H atoms move towards or away from B atom simultaneously 
Top H atom and B atom is quite stationary</td>
<td valign="top">2731.31</td>
<td valign="top">103.837</td>
<td valign="top"> </td>
</tr>
<tr>
<td valign="top">6</td>
<td valign="top">Bottomed H atoms move in and out whereas the top H atom moves in different order as the bottomed H atoms. The B atom is quite stationary</td>
<td valign="top">2731.31</td>
<td valign="top">103.83</td>
<td valign="top"> </td>
</tr>
</table>

The following graph is IR spectrum.

[[Image:FeiIR.jpg]]

From the IR spectrum, we can see that there are only 3 peaks. But there are 6 vibrations. In theory, we should get 6 peaks. This is due to peaks of no.2 and no.3 vibrations are combined together as having the nearly the same frequency, this is the same for peaks of no.5 and no.6 vibrations. And for no. 4 vibration, it is totally symmetric and this means there is not dipole moment and hence there will show no peak. So there will be 3 peaks in total shown in the spectrum.

==Molecular orbitals of BH3==

Create .chk file of the optimised BH3 molecule and open it to run another optimisation. Then I open the MOs from the “edit” section.

[[Image:FeiMOs.JPG]]

Then click the “update” button but there is nothing happened and the MOs is not obtained.
While doing the updating, the surface did appear around the molecule.

==='''Exercise 2'''===

==='''Exercise 3'''===

==Ammonia==

Firstly, generate a molecule of NH3 by using GussianView programme and start to optimise it by using B3LYP method with 6-31G basis set. And then we can get an optimised NH3 molecule with its summary table.

[[Image:FeiNH3summary.jpg]]

From the summary table, we can see that the symmetry is C3v.

Now generate another NH3 molecule and make one of its bond lengths to 1.01 Å. The symmetry is ignored here in the general section of the optimisation section. Then we can a optimised molecule with its summary table.

[[Image:FeiNH3summary2.JPG]]

From the summary table, we can see that the symmetry of this molecule is C1.

Download the file from the website and run the optimisation, hence get the following summary table.

[[Image:FeiNH3summary3.JPG]]

From the summary table, we can see that the symmetry of this molecule is D3h.

From the above 3 molecules, we can see that the symmetry does not make any difference to the final obtained structure, but the symmetry did give a difference to the duration of the calculation. The lone pairs of the N atom imply the symmetry to do a calculation. During an optimisation, a molecule can break symmetry. The D3h molecule has got the lowest energy geometry. The energy difference between C3v and D3h is 3.4401*10^-4 AU (i.e. 0.9032 kJ/mol), the difference between C1 and D3h is -3.457*10^-4 AU (i.e. 0.9077 kJ/mol). The energy difference between these structures is quite significant, the C1 and C3v structures are mirror-image to each other, and therefore they have got similar energies whereas the D3h one has the lowest energy due to its stable structure.

==Method==

In this section, we are going to use the same method with higher basis set level to improve the accuracy of the optimisation. Firstly, NH3 molecule is generated and is run with 6-311+G(d,p) basis set. But there is no “include all electrons” box in the method section of the optimisation.

[[Image:FeiNh3summary1.JPG]]

Using the given file and run the optimisation to obtain the following information.

[[Image:FeiNh3summary2.JPG]]

In this section, the durations of calculation are 29.0 seconds and 78 seconds respectively. However, the durations of the calculation with lower basis set are 30.0 second and 76 seconds which are shorter than those of calculation with higher basis set. The barrier height to inversion is 6.3223*10^-3 AU (i.e. 16.60 kJ/mol) which is much higher than the barrier in the lower basis set level. And this figure is reasonable so we can see that high level of basis set increase the accuracy of the optimisation. The experimental determined barrier is 24.3 which is higher than theoretical 16.6 value.

==The inversion mechanism==

Download the given file and open it to obtain the following picture.

[[Image:FeiNh3.JPG]]

Then we can get the “SCAN” which is showing the chemical reaction over time.

[[Image:FeiEnergyv.s.eigenvalue.JPG]]

From the above curves, we can see that eigen value 12 has got the lowest energy value and this is the most stable state.

==Vibrational analysis==

Get the frequency analysis for D3h optimised molecule.

[[Image:FeiD3h.JPG]]

Get the frequency analysis for C3v optimised molecule as well.

[[Image:FeiC3v.JPG]]

From the 2 vibrational frequencies of the C3v and D3h structures, we can see that there are 5 positive frequencies in D3h structure whereas 6 positives ones in C3v structure. C3v structure is a ground state structure and D3h is a transition state structure. This means C3v will have all positive frequencies whereas D3h will have only one negative frequency. From the above 2 graphs, we can see that only D3h has got one negative frequency which is -768.258 cm^-1. The vibration 4 with the lowest intensity value in the C3v and D3h structures will follow the inversion reaction. The calculated frequencies for C3v structure are higher than the experimental frequencies.

==='''Mini Project'''===

Rep:Mod:feihemodule2

2008-12-16T14:42:12Z

Fh106: /* Method */

='''Module 2'''=

==='''Introduction'''===

The aim of this module 2 is familiar with the Gussview programme and uses the programme to optimise the molecules.

Now look at the following simple molecule BH3.

==Create a molecule of BH3==

Use the Gussview programme to create the BH3 molecule. And we can the following picture of the molecule.

[[Image:FeiBh3.jpg]]

Picture of BH3 molecule.

And we can use label and symbol the molecule to get the following picture.

[[Image:FeiLabelledBH3.JPG]]

Labelled and symbol picture of BH3.

Then we set the all the three B-H bonds to 1.5 angstrom and get the following sturcure of BH3.

[[Image:FeiBh3fixedbondlength.JPG]]

Fixed bond distance picture of BH3

So the molecule is set up.

==Optimising a molecule of BH3==

Use the BLYP method and 3-21G basic set to optimise the molecule of BH3. And then we can the following optimised structure of the molecule.

[[Image:FeiOptimisedBH3.JPG]]

Optimised structure of BH3 molecule

Then we can determine the optimised B-H bond distance and H-B-H bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:FeiBH3bonddistance.JPG]]</td>
<td align="center">[[Image:FeiBH3bondangle.JPG]]</td>
</tr>
<tr>
<td align="center">Bond distance is 1.19435</td>
<td align="center">Bond angle is 120.000</td>
</tr>
</table>

And we can get a summary table to show some information about the molecule.

[[Image:FeiResulttable.JPG]]

Summary of the optimised molecule

From the above summary, we can see that the file of file is .log, calculation type is FOPT, calculation method is RB3LYP, basic set is 3-21G, final energy is -26.46226438 au, dipole moment is 0.000 debye, point group is D3H and the duration of calculation is 19.0 seconds.

We can get a “real” text based .log file as well.

[[Image:FeiRealresulttable.JPG]]

==Understanding optimisation part a==

Open the finished optimised file of the above molecule and tick “read intermediate geometries”. Then an energy and gradient against optimisation graph is obtained.

[[Image:FeiOptimisationgraph.JPG]]

There are 2 graphs in the above picture, the 1st one is energy against each step of optimisation and the 2nd one is the gradient of energy against each step of optimisation.

The green button in the molecule window is click and the animation of optimisation steps is obtained and we can see that the final structure has the least energy and smallest gradient of energy. So the stable structure is with the minimum energy and it is the final structure in the animation.

[[Image:FeiAnimation.JPG]]

==='''Exercuse 1'''===

==Find information about BCl3==

Following the method introduced in the introduction section, repeat the calculation for molecule BCl3.

Firstly, create the molecule of BCl3. And measure its B-Cl bond distance and Cl-B-Cl bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:FeiBCL3bonddistance.JPG]]</td>
<td align="center">[[Image:BCL3bondangle.JPG]]</td>
</tr>
<tr>
<td align="center">Bond distance: 1.87000</td>
<td align="center">Bond angle is 120.000</td>
</tr>
</table>

Secondly, restrict the symmetry of BCl3 to D3h and set the tolerance from the default to “very tight (0.0001)” and obtain the following picture.

[[Image:FeiRestrictedBCL3.JPG]]

Restricted BCl3 molecule

Thirdly, do the calculation to optimise the BCl3 molecule and obtain the optimised structure of BCl3.

[[Image:FeiOptimisedBCL3.JPG]]

Optimised BCl3 molecule

And we then obtain the optimised B-Cl bond distance and optimised Cl-B-Cl bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:FeiOptimisedbonddistance.JPG]]</td>
<td align="center">[[Image:Optimisedbondangle.JPG]]</td>
</tr>
<tr>
<td align="center">Bond distance: 1.86592</td>
<td align="center">Bond angle is 120.000</td>
</tr>
</table>

Finally, we then get the summary of the optimised molecule.

[[Image:FeiSummary2.JPG]]

From the above summary table, we can know that the file type is .log, calculation type is FORT, calculation method is RB3LYP, basic set is LANL2MB, final energy is -69.43928112 AU, dipole moment is 0.000 debye, point group is D3h and the duration of calculation is 12.0 seconds.

==Independent work==

I chose H2O as my own molecule. Firstly, set up the molecule of H2O. And we can get the O-H bond distance and H-O-H bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:H2Obonddistance.JPG]]</td>
<td align="center">[[Image:H2Obondangle.JPG]]</td>
</tr>
<tr>
<td align="center">Bond distance: 0.96000</td>
<td align="center">Bond angle is 109.500</td>
</tr>
</table>

Since O atom and H atom is above second row, we do not need to use pseudo-potential.
Therefore, we use the same method as above in above section but we set the basis set to 3-21G and obtain the following optimised H2O molecule with its summary table.

[[Image:FeiH2Osummary.JPG]]

From the above summary table, we can see that the calculation method is RB3LYP, basis set is 3-21G, final energy is -75.97396515 AU, dipole moment is 2.2381 Debye, point group is C2v and duration of calculation is 17.0 seconds.

We now can get the optimised bond distance and bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:Optimisedbonddistance.jpg]]</td>
<td align="center">[[Image:Optimisedbondangle.jpg]]</td>
</tr>
<tr>
<td align="center">Optimised bond distance: 0.99683</td>
<td align="center">Optimised bond angle: 103.991</td>
</tr>
</table>

Now I set the basis set to higher level in order to increase the accuracy. Use the first optimised output file to do another optimisation using higher level basis set. And use the second optimised output file to do another optimisation using even higher basis set.

<table width="663" border="1">
<tr>
<th width="176" scope="col"> </th>
<th scope="col">First trial</th>
<th scope="col">Second trail</th>
<th scope="col">Third trail</th>
</tr>
<tr>
<th scope="row">Bond distance/AU</th>
<td width="143" valign="top">0.99683 </td>
<td width="149" valign="top">0.96526</td>
<td width="167" valign="top">0.96203</td>
</tr>
<tr>
<th scope="row">Bond angle/degree</th>
<td width="143" valign="top">103.991</td>
<td width="149" valign="top">103.696</td>
<td width="167" valign="top">105.057</td>
</tr>
<tr>
<th scope="row">Calculation method</th>
<td width="143" valign="top">RB3LYP</td>
<td width="149" valign="top">RB3LYP</td>
<td width="167" valign="top">RB3LYP</td>
</tr>
<tr>
<th scope="row">Basis set</th>
<td width="143" valign="top">3-21G</td>
<td width="149" valign="top">6-31G(d.p)</td>
<td width="167" valign="top">6-311+G(d,p)</td>
</tr>
<tr>
<th scope="row">Final energy/J</th>
<td width="143" valign="top">-75.97396515</td>
<td width="149" valign="top">-76.41973659</td>
<td width="167" valign="top">-76.45846294</td>
</tr>
<tr>
<th scope="row">Dipole moment/debye</th>
<td width="143" valign="top">2.2381</td>
<td width="149" valign="top">2.0436</td>
<td width="167" valign="top">2.1610</td>
</tr>
<tr>
<th scope="row">Point group</th>
<td width="143" valign="top">C2v</td>
<td width="149" valign="top">C2v</td>
<td width="167" valign="top">C2v</td>
</tr>
<tr>
<th scope="row">Duration of calculation/s</th>
<td width="143" valign="top">17.0</td>
<td width="149" valign="top">17.0</td>
<td width="167" valign="top">18.0</td>
</tr>
</table>

==Vibrational analysis and confirming minima==

In this section, we are going to use vibrational analysis to confirm the minimum structure.
Firstly, open the optimised BH3 file and do the vibrational analysis to confirm its minimum structure. So we get the following structure with its summary.

[[Image:FeiBH3frequncy.jpg]]

From the above summary table, we can see that the energy is -26.46226438 whereas the energy of the optimised one is -26.46226438. So they have got the same value.

==Animating the vibrations==

Open the vibrations result.

[[Image:FeiVibrations.jpg]]

Show display vectors of each vibration.

[[Image:FeiVibration2.jpg]]

The following table is to a summary of motions, frequency, intensities and symmetry.

<table width="716" border="1">
<tr>
<td width="24" valign="top">No.</td>
<td width="473" valign="top">Form of vibration</td>
<td width="59" valign="top">frequency</td>
<td width="65" valign="top">intensity</td>
<td width="61" valign="top">Symmetry 
D3h point group</td>
</tr>
<tr>
<td valign="top">1 </td>
<td valign="top">all the H atoms move in and out together in the same direction, the B atom moves in the opposite direction of that of H atom</td>
<td valign="top">1145.71</td>
<td valign="top">92.6991</td>
<td valign="top"> </td>
</tr>
<tr>
<td valign="top">2</td>
<td valign="top">2 bottomed H atoms moves towards and away from each other whereas B atom and top H atom is quite stationary</td>
<td valign="top">1204.66</td>
<td valign="top">12.3789</td>
<td valign="top"> </td>
</tr>
<tr>
<td valign="top">3</td>
<td valign="top">Each of the bottomed H atom moves away and towards to the top H atom whereas B atom is quite stationary</td>
<td valign="top">1204.66</td>
<td valign="top">12.3814</td>
<td valign="top"> </td>
</tr>
<tr>
<td valign="top">4</td>
<td valign="top">All H atoms move in and out together in a concerted motion whereas B atom is unmoved</td>
<td valign="top">2591.65</td>
<td valign="top">0.0</td>
<td valign="top">A'1</td>
</tr>
<tr>
<td valign="top">5</td>
<td valign="top">2 bottomed H atoms move towards or away from B atom simultaneously 
Top H atom and B atom is quite stationary</td>
<td valign="top">2731.31</td>
<td valign="top">103.837</td>
<td valign="top"> </td>
</tr>
<tr>
<td valign="top">6</td>
<td valign="top">Bottomed H atoms move in and out whereas the top H atom moves in different order as the bottomed H atoms. The B atom is quite stationary</td>
<td valign="top">2731.31</td>
<td valign="top">103.83</td>
<td valign="top"> </td>
</tr>
</table>

The following graph is IR spectrum.

[[Image:FeiIR.jpg]]

From the IR spectrum, we can see that there are only 3 peaks. But there are 6 vibrations. In theory, we should get 6 peaks. This is due to peaks of no.2 and no.3 vibrations are combined together as having the nearly the same frequency, this is the same for peaks of no.5 and no.6 vibrations. And for no. 4 vibration, it is totally symmetric and this means there is not dipole moment and hence there will show no peak. So there will be 3 peaks in total shown in the spectrum.

==Molecular orbitals of BH3==

Create .chk file of the optimised BH3 molecule and open it to run another optimisation. Then I open the MOs from the “edit” section.

[[Image:FeiMOs.JPG]]

Then click the “update” button but there is nothing happened and the MOs is not obtained.
While doing the updating, the surface did appear around the molecule.

==='''Exercuse 2'''===

==='''Exercuse 3'''===

==Ammonia==

Firstly, generate a molecule of NH3 by using GussianView programme and start to optimise it by using B3LYP method with 6-31G basis set. And then we can get an optimised NH3 molecule with its summary table.

[[Image:FeiNH3summary.jpg]]

From the summary table, we can see that the symmetry is C3v.

Now generate another NH3 molecule and make one of its bond lengths to 1.01 Å. The symmetry is ignored here in the general section of the optimisation section. Then we can a optimised molecule with its summary table.

[[Image:FeiNH3summary2.JPG]]

From the summary table, we can see that the symmetry of this molecule is C1.

Download the file from the website and run the optimisation, hence get the following summary table.

[[Image:FeiNH3summary3.JPG]]

From the summary table, we can see that the symmetry of this molecule is D3h.

From the above 3 molecules, we can see that the symmetry does not make any difference to the final obtained structure, but the symmetry did give a difference to the duration of the calculation. The lone pairs of the N atom imply the symmetry to do a calculation. During an optimisation, a molecule can break symmetry. The D3h molecule has got the lowest energy geometry. The energy difference between C3v and D3h is 3.4401*10^-4 AU (i.e. 0.9032 kJ/mol), the difference between C1 and D3h is -3.457*10^-4 AU (i.e. 0.9077 kJ/mol). The energy difference between these structures is quite significant, the C1 and C3v structures are mirror-image to each other, and therefore they have got similar energies whereas the D3h one has the lowest energy due to its stable structure.

==Method==

In this section, we are going to use the same method with higher basis set level to improve the accuracy of the optimisation. Firstly, NH3 molecule is generated and is run with 6-311+G(d,p) basis set. But there is no “include all electrons” box in the method section of the optimisation.

[[Image:FeiNh3summary1.JPG]]

Using the given file and run the optimisation to obtain the following information.

[[Image:FeiNh3summary2.JPG]]

In this section, the durations of calculation are 29.0 seconds and 78 seconds respectively. However, the durations of the calculation with lower basis set are 30.0 second and 76 seconds which are shorter than those of calculation with higher basis set. The barrier height to inversion is 6.3223*10^-3 AU (i.e. 16.60 kJ/mol) which is much higher than the barrier in the lower basis set level. And this figure is reasonable so we can see that high level of basis set increase the accuracy of the optimisation. The experimental determined barrier is 24.3 which is higher than theoretical 16.6 value.

==The inversion mechanism==

Download the given file and open it to obtain the following picture.

[[Image:FeiNh3.JPG]]

Then we can get the “SCAN” which is showing the chemical reaction over time.

[[Image:FeiEnergyv.s.eigenvalue.JPG]]

From the above curves, we can see that eigen value 12 has got the lowest energy value and this is the most stable state.

==Vibrational analysis==

Get the frequency analysis for D3h optimised molecule.

[[Image:FeiD3h.JPG]]

Get the frequency analysis for C3v optimised molecule as well.

[[Image:FeiC3v.JPG]]

From the 2 vibrational frequencies of the C3v and D3h structures, we can see that there are 5 positive frequencies in D3h structure whereas 6 positives ones in C3v structure. C3v structure is a ground state structure and D3h is a transition state structure. This means C3v will have all positive frequencies whereas D3h will have only one negative frequency. From the above 2 graphs, we can see that only D3h has got one negative frequency which is -768.258 cm^-1. The vibration 4 with the lowest intensity value in the C3v and D3h structures will follow the inversion reaction. The calculated frequencies for C3v structure are higher than the experimental frequencies.

==='''Mini Project'''===

File:FeiC3v.JPG

2008-12-16T14:41:43Z

Fh106:

File:FeiD3h.JPG

2008-12-16T14:41:09Z

Fh106:

File:FeiEnergyv.s.eigenvalue.JPG

2008-12-16T14:38:48Z

Fh106:

File:FeiNh3.JPG

2008-12-16T14:38:08Z

Fh106:

File:FeiNh3summary2.JPG

2008-12-16T14:36:37Z

Fh106:

File:FeiNh3summary1.JPG

2008-12-16T14:36:03Z

Fh106: fei

fei

Rep:Mod:feihemodule2

2008-12-16T14:35:02Z

Fh106: /* '''Exercuse 3''' */

='''Module 2'''=

==='''Introduction'''===

The aim of this module 2 is familiar with the Gussview programme and uses the programme to optimise the molecules.

Now look at the following simple molecule BH3.

==Create a molecule of BH3==

Use the Gussview programme to create the BH3 molecule. And we can the following picture of the molecule.

[[Image:FeiBh3.jpg]]

Picture of BH3 molecule.

And we can use label and symbol the molecule to get the following picture.

[[Image:FeiLabelledBH3.JPG]]

Labelled and symbol picture of BH3.

Then we set the all the three B-H bonds to 1.5 angstrom and get the following sturcure of BH3.

[[Image:FeiBh3fixedbondlength.JPG]]

Fixed bond distance picture of BH3

So the molecule is set up.

==Optimising a molecule of BH3==

Use the BLYP method and 3-21G basic set to optimise the molecule of BH3. And then we can the following optimised structure of the molecule.

[[Image:FeiOptimisedBH3.JPG]]

Optimised structure of BH3 molecule

Then we can determine the optimised B-H bond distance and H-B-H bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:FeiBH3bonddistance.JPG]]</td>
<td align="center">[[Image:FeiBH3bondangle.JPG]]</td>
</tr>
<tr>
<td align="center">Bond distance is 1.19435</td>
<td align="center">Bond angle is 120.000</td>
</tr>
</table>

And we can get a summary table to show some information about the molecule.

[[Image:FeiResulttable.JPG]]

Summary of the optimised molecule

From the above summary, we can see that the file of file is .log, calculation type is FOPT, calculation method is RB3LYP, basic set is 3-21G, final energy is -26.46226438 au, dipole moment is 0.000 debye, point group is D3H and the duration of calculation is 19.0 seconds.

We can get a “real” text based .log file as well.

[[Image:FeiRealresulttable.JPG]]

==Understanding optimisation part a==

Open the finished optimised file of the above molecule and tick “read intermediate geometries”. Then an energy and gradient against optimisation graph is obtained.

[[Image:FeiOptimisationgraph.JPG]]

There are 2 graphs in the above picture, the 1st one is energy against each step of optimisation and the 2nd one is the gradient of energy against each step of optimisation.

The green button in the molecule window is click and the animation of optimisation steps is obtained and we can see that the final structure has the least energy and smallest gradient of energy. So the stable structure is with the minimum energy and it is the final structure in the animation.

[[Image:FeiAnimation.JPG]]

==='''Exercuse 1'''===

==Find information about BCl3==

Following the method introduced in the introduction section, repeat the calculation for molecule BCl3.

Firstly, create the molecule of BCl3. And measure its B-Cl bond distance and Cl-B-Cl bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:FeiBCL3bonddistance.JPG]]</td>
<td align="center">[[Image:BCL3bondangle.JPG]]</td>
</tr>
<tr>
<td align="center">Bond distance: 1.87000</td>
<td align="center">Bond angle is 120.000</td>
</tr>
</table>

Secondly, restrict the symmetry of BCl3 to D3h and set the tolerance from the default to “very tight (0.0001)” and obtain the following picture.

[[Image:FeiRestrictedBCL3.JPG]]

Restricted BCl3 molecule

Thirdly, do the calculation to optimise the BCl3 molecule and obtain the optimised structure of BCl3.

[[Image:FeiOptimisedBCL3.JPG]]

Optimised BCl3 molecule

And we then obtain the optimised B-Cl bond distance and optimised Cl-B-Cl bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:FeiOptimisedbonddistance.JPG]]</td>
<td align="center">[[Image:Optimisedbondangle.JPG]]</td>
</tr>
<tr>
<td align="center">Bond distance: 1.86592</td>
<td align="center">Bond angle is 120.000</td>
</tr>
</table>

Finally, we then get the summary of the optimised molecule.

[[Image:FeiSummary2.JPG]]

From the above summary table, we can know that the file type is .log, calculation type is FORT, calculation method is RB3LYP, basic set is LANL2MB, final energy is -69.43928112 AU, dipole moment is 0.000 debye, point group is D3h and the duration of calculation is 12.0 seconds.

==Independent work==

I chose H2O as my own molecule. Firstly, set up the molecule of H2O. And we can get the O-H bond distance and H-O-H bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:H2Obonddistance.JPG]]</td>
<td align="center">[[Image:H2Obondangle.JPG]]</td>
</tr>
<tr>
<td align="center">Bond distance: 0.96000</td>
<td align="center">Bond angle is 109.500</td>
</tr>
</table>

Since O atom and H atom is above second row, we do not need to use pseudo-potential.
Therefore, we use the same method as above in above section but we set the basis set to 3-21G and obtain the following optimised H2O molecule with its summary table.

[[Image:FeiH2Osummary.JPG]]

From the above summary table, we can see that the calculation method is RB3LYP, basis set is 3-21G, final energy is -75.97396515 AU, dipole moment is 2.2381 Debye, point group is C2v and duration of calculation is 17.0 seconds.

We now can get the optimised bond distance and bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:Optimisedbonddistance.jpg]]</td>
<td align="center">[[Image:Optimisedbondangle.jpg]]</td>
</tr>
<tr>
<td align="center">Optimised bond distance: 0.99683</td>
<td align="center">Optimised bond angle: 103.991</td>
</tr>
</table>

Now I set the basis set to higher level in order to increase the accuracy. Use the first optimised output file to do another optimisation using higher level basis set. And use the second optimised output file to do another optimisation using even higher basis set.

<table width="663" border="1">
<tr>
<th width="176" scope="col"> </th>
<th scope="col">First trial</th>
<th scope="col">Second trail</th>
<th scope="col">Third trail</th>
</tr>
<tr>
<th scope="row">Bond distance/AU</th>
<td width="143" valign="top">0.99683 </td>
<td width="149" valign="top">0.96526</td>
<td width="167" valign="top">0.96203</td>
</tr>
<tr>
<th scope="row">Bond angle/degree</th>
<td width="143" valign="top">103.991</td>
<td width="149" valign="top">103.696</td>
<td width="167" valign="top">105.057</td>
</tr>
<tr>
<th scope="row">Calculation method</th>
<td width="143" valign="top">RB3LYP</td>
<td width="149" valign="top">RB3LYP</td>
<td width="167" valign="top">RB3LYP</td>
</tr>
<tr>
<th scope="row">Basis set</th>
<td width="143" valign="top">3-21G</td>
<td width="149" valign="top">6-31G(d.p)</td>
<td width="167" valign="top">6-311+G(d,p)</td>
</tr>
<tr>
<th scope="row">Final energy/J</th>
<td width="143" valign="top">-75.97396515</td>
<td width="149" valign="top">-76.41973659</td>
<td width="167" valign="top">-76.45846294</td>
</tr>
<tr>
<th scope="row">Dipole moment/debye</th>
<td width="143" valign="top">2.2381</td>
<td width="149" valign="top">2.0436</td>
<td width="167" valign="top">2.1610</td>
</tr>
<tr>
<th scope="row">Point group</th>
<td width="143" valign="top">C2v</td>
<td width="149" valign="top">C2v</td>
<td width="167" valign="top">C2v</td>
</tr>
<tr>
<th scope="row">Duration of calculation/s</th>
<td width="143" valign="top">17.0</td>
<td width="149" valign="top">17.0</td>
<td width="167" valign="top">18.0</td>
</tr>
</table>

==Vibrational analysis and confirming minima==

In this section, we are going to use vibrational analysis to confirm the minimum structure.
Firstly, open the optimised BH3 file and do the vibrational analysis to confirm its minimum structure. So we get the following structure with its summary.

[[Image:FeiBH3frequncy.jpg]]

From the above summary table, we can see that the energy is -26.46226438 whereas the energy of the optimised one is -26.46226438. So they have got the same value.

==Animating the vibrations==

Open the vibrations result.

[[Image:FeiVibrations.jpg]]

Show display vectors of each vibration.

[[Image:FeiVibration2.jpg]]

The following table is to a summary of motions, frequency, intensities and symmetry.

<table width="716" border="1">
<tr>
<td width="24" valign="top">No.</td>
<td width="473" valign="top">Form of vibration</td>
<td width="59" valign="top">frequency</td>
<td width="65" valign="top">intensity</td>
<td width="61" valign="top">Symmetry 
D3h point group</td>
</tr>
<tr>
<td valign="top">1 </td>
<td valign="top">all the H atoms move in and out together in the same direction, the B atom moves in the opposite direction of that of H atom</td>
<td valign="top">1145.71</td>
<td valign="top">92.6991</td>
<td valign="top"> </td>
</tr>
<tr>
<td valign="top">2</td>
<td valign="top">2 bottomed H atoms moves towards and away from each other whereas B atom and top H atom is quite stationary</td>
<td valign="top">1204.66</td>
<td valign="top">12.3789</td>
<td valign="top"> </td>
</tr>
<tr>
<td valign="top">3</td>
<td valign="top">Each of the bottomed H atom moves away and towards to the top H atom whereas B atom is quite stationary</td>
<td valign="top">1204.66</td>
<td valign="top">12.3814</td>
<td valign="top"> </td>
</tr>
<tr>
<td valign="top">4</td>
<td valign="top">All H atoms move in and out together in a concerted motion whereas B atom is unmoved</td>
<td valign="top">2591.65</td>
<td valign="top">0.0</td>
<td valign="top">A'1</td>
</tr>
<tr>
<td valign="top">5</td>
<td valign="top">2 bottomed H atoms move towards or away from B atom simultaneously 
Top H atom and B atom is quite stationary</td>
<td valign="top">2731.31</td>
<td valign="top">103.837</td>
<td valign="top"> </td>
</tr>
<tr>
<td valign="top">6</td>
<td valign="top">Bottomed H atoms move in and out whereas the top H atom moves in different order as the bottomed H atoms. The B atom is quite stationary</td>
<td valign="top">2731.31</td>
<td valign="top">103.83</td>
<td valign="top"> </td>
</tr>
</table>

The following graph is IR spectrum.

[[Image:FeiIR.jpg]]

From the IR spectrum, we can see that there are only 3 peaks. But there are 6 vibrations. In theory, we should get 6 peaks. This is due to peaks of no.2 and no.3 vibrations are combined together as having the nearly the same frequency, this is the same for peaks of no.5 and no.6 vibrations. And for no. 4 vibration, it is totally symmetric and this means there is not dipole moment and hence there will show no peak. So there will be 3 peaks in total shown in the spectrum.

==Molecular orbitals of BH3==

Create .chk file of the optimised BH3 molecule and open it to run another optimisation. Then I open the MOs from the “edit” section.

[[Image:FeiMOs.JPG]]

Then click the “update” button but there is nothing happened and the MOs is not obtained.
While doing the updating, the surface did appear around the molecule.

==='''Exercuse 2'''===

==='''Exercuse 3'''===

==Ammonia==

Firstly, generate a molecule of NH3 by using GussianView programme and start to optimise it by using B3LYP method with 6-31G basis set. And then we can get an optimised NH3 molecule with its summary table.

[[Image:FeiNH3summary.jpg]]

From the summary table, we can see that the symmetry is C3v.

Now generate another NH3 molecule and make one of its bond lengths to 1.01 Å. The symmetry is ignored here in the general section of the optimisation section. Then we can a optimised molecule with its summary table.

[[Image:FeiNH3summary2.JPG]]

From the summary table, we can see that the symmetry of this molecule is C1.

Download the file from the website and run the optimisation, hence get the following summary table.

[[Image:FeiNH3summary3.JPG]]

From the summary table, we can see that the symmetry of this molecule is D3h.

From the above 3 molecules, we can see that the symmetry does not make any difference to the final obtained structure, but the symmetry did give a difference to the duration of the calculation. The lone pairs of the N atom imply the symmetry to do a calculation. During an optimisation, a molecule can break symmetry. The D3h molecule has got the lowest energy geometry. The energy difference between C3v and D3h is 3.4401*10^-4 AU (i.e. 0.9032 kJ/mol), the difference between C1 and D3h is -3.457*10^-4 AU (i.e. 0.9077 kJ/mol). The energy difference between these structures is quite significant, the C1 and C3v structures are mirror-image to each other, and therefore they have got similar energies whereas the D3h one has the lowest energy due to its stable structure.

==Method==

In this section, we are going to use the same method with higher basis set level to improve the accuracy of the optimisation. Firstly, NH3 molecule is generated and is run with 6-311+G(d,p) basis set. But there is no “include all electrons” box in the method section of the optimisation.

==='''Mini Project'''===

File:FeiNH3summary3.JPG

2008-12-16T14:33:01Z

Fh106:

File:FeiNH3summary2.JPG

2008-12-16T14:32:16Z

Fh106:

File:FeiNH3summary.jpg

2008-12-16T14:31:12Z

Fh106:

Rep:Mod:feihemodule2

2008-12-16T13:49:50Z

Fh106: /* '''Exercuse 3''' */

='''Module 2'''=

==='''Introduction'''===

The aim of this module 2 is familiar with the Gussview programme and uses the programme to optimise the molecules.

Now look at the following simple molecule BH3.

==Create a molecule of BH3==

Use the Gussview programme to create the BH3 molecule. And we can the following picture of the molecule.

[[Image:FeiBh3.jpg]]

Picture of BH3 molecule.

And we can use label and symbol the molecule to get the following picture.

[[Image:FeiLabelledBH3.JPG]]

Labelled and symbol picture of BH3.

Then we set the all the three B-H bonds to 1.5 angstrom and get the following sturcure of BH3.

[[Image:FeiBh3fixedbondlength.JPG]]

Fixed bond distance picture of BH3

So the molecule is set up.

==Optimising a molecule of BH3==

Use the BLYP method and 3-21G basic set to optimise the molecule of BH3. And then we can the following optimised structure of the molecule.

[[Image:FeiOptimisedBH3.JPG]]

Optimised structure of BH3 molecule

Then we can determine the optimised B-H bond distance and H-B-H bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:FeiBH3bonddistance.JPG]]</td>
<td align="center">[[Image:FeiBH3bondangle.JPG]]</td>
</tr>
<tr>
<td align="center">Bond distance is 1.19435</td>
<td align="center">Bond angle is 120.000</td>
</tr>
</table>

And we can get a summary table to show some information about the molecule.

[[Image:FeiResulttable.JPG]]

Summary of the optimised molecule

From the above summary, we can see that the file of file is .log, calculation type is FOPT, calculation method is RB3LYP, basic set is 3-21G, final energy is -26.46226438 au, dipole moment is 0.000 debye, point group is D3H and the duration of calculation is 19.0 seconds.

We can get a “real” text based .log file as well.

[[Image:FeiRealresulttable.JPG]]

==Understanding optimisation part a==

Open the finished optimised file of the above molecule and tick “read intermediate geometries”. Then an energy and gradient against optimisation graph is obtained.

[[Image:FeiOptimisationgraph.JPG]]

There are 2 graphs in the above picture, the 1st one is energy against each step of optimisation and the 2nd one is the gradient of energy against each step of optimisation.

The green button in the molecule window is click and the animation of optimisation steps is obtained and we can see that the final structure has the least energy and smallest gradient of energy. So the stable structure is with the minimum energy and it is the final structure in the animation.

[[Image:FeiAnimation.JPG]]

==='''Exercuse 1'''===

==Find information about BCl3==

Following the method introduced in the introduction section, repeat the calculation for molecule BCl3.

Firstly, create the molecule of BCl3. And measure its B-Cl bond distance and Cl-B-Cl bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:FeiBCL3bonddistance.JPG]]</td>
<td align="center">[[Image:BCL3bondangle.JPG]]</td>
</tr>
<tr>
<td align="center">Bond distance: 1.87000</td>
<td align="center">Bond angle is 120.000</td>
</tr>
</table>

Secondly, restrict the symmetry of BCl3 to D3h and set the tolerance from the default to “very tight (0.0001)” and obtain the following picture.

[[Image:FeiRestrictedBCL3.JPG]]

Restricted BCl3 molecule

Thirdly, do the calculation to optimise the BCl3 molecule and obtain the optimised structure of BCl3.

[[Image:FeiOptimisedBCL3.JPG]]

Optimised BCl3 molecule

And we then obtain the optimised B-Cl bond distance and optimised Cl-B-Cl bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:FeiOptimisedbonddistance.JPG]]</td>
<td align="center">[[Image:Optimisedbondangle.JPG]]</td>
</tr>
<tr>
<td align="center">Bond distance: 1.86592</td>
<td align="center">Bond angle is 120.000</td>
</tr>
</table>

Finally, we then get the summary of the optimised molecule.

[[Image:FeiSummary2.JPG]]

From the above summary table, we can know that the file type is .log, calculation type is FORT, calculation method is RB3LYP, basic set is LANL2MB, final energy is -69.43928112 AU, dipole moment is 0.000 debye, point group is D3h and the duration of calculation is 12.0 seconds.

==Independent work==

I chose H2O as my own molecule. Firstly, set up the molecule of H2O. And we can get the O-H bond distance and H-O-H bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:H2Obonddistance.JPG]]</td>
<td align="center">[[Image:H2Obondangle.JPG]]</td>
</tr>
<tr>
<td align="center">Bond distance: 0.96000</td>
<td align="center">Bond angle is 109.500</td>
</tr>
</table>

Since O atom and H atom is above second row, we do not need to use pseudo-potential.
Therefore, we use the same method as above in above section but we set the basis set to 3-21G and obtain the following optimised H2O molecule with its summary table.

[[Image:FeiH2Osummary.JPG]]

From the above summary table, we can see that the calculation method is RB3LYP, basis set is 3-21G, final energy is -75.97396515 AU, dipole moment is 2.2381 Debye, point group is C2v and duration of calculation is 17.0 seconds.

We now can get the optimised bond distance and bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:Optimisedbonddistance.jpg]]</td>
<td align="center">[[Image:Optimisedbondangle.jpg]]</td>
</tr>
<tr>
<td align="center">Optimised bond distance: 0.99683</td>
<td align="center">Optimised bond angle: 103.991</td>
</tr>
</table>

Now I set the basis set to higher level in order to increase the accuracy. Use the first optimised output file to do another optimisation using higher level basis set. And use the second optimised output file to do another optimisation using even higher basis set.

<table width="663" border="1">
<tr>
<th width="176" scope="col"> </th>
<th scope="col">First trial</th>
<th scope="col">Second trail</th>
<th scope="col">Third trail</th>
</tr>
<tr>
<th scope="row">Bond distance/AU</th>
<td width="143" valign="top">0.99683 </td>
<td width="149" valign="top">0.96526</td>
<td width="167" valign="top">0.96203</td>
</tr>
<tr>
<th scope="row">Bond angle/degree</th>
<td width="143" valign="top">103.991</td>
<td width="149" valign="top">103.696</td>
<td width="167" valign="top">105.057</td>
</tr>
<tr>
<th scope="row">Calculation method</th>
<td width="143" valign="top">RB3LYP</td>
<td width="149" valign="top">RB3LYP</td>
<td width="167" valign="top">RB3LYP</td>
</tr>
<tr>
<th scope="row">Basis set</th>
<td width="143" valign="top">3-21G</td>
<td width="149" valign="top">6-31G(d.p)</td>
<td width="167" valign="top">6-311+G(d,p)</td>
</tr>
<tr>
<th scope="row">Final energy/J</th>
<td width="143" valign="top">-75.97396515</td>
<td width="149" valign="top">-76.41973659</td>
<td width="167" valign="top">-76.45846294</td>
</tr>
<tr>
<th scope="row">Dipole moment/debye</th>
<td width="143" valign="top">2.2381</td>
<td width="149" valign="top">2.0436</td>
<td width="167" valign="top">2.1610</td>
</tr>
<tr>
<th scope="row">Point group</th>
<td width="143" valign="top">C2v</td>
<td width="149" valign="top">C2v</td>
<td width="167" valign="top">C2v</td>
</tr>
<tr>
<th scope="row">Duration of calculation/s</th>
<td width="143" valign="top">17.0</td>
<td width="149" valign="top">17.0</td>
<td width="167" valign="top">18.0</td>
</tr>
</table>

==Vibrational analysis and confirming minima==

In this section, we are going to use vibrational analysis to confirm the minimum structure.
Firstly, open the optimised BH3 file and do the vibrational analysis to confirm its minimum structure. So we get the following structure with its summary.

[[Image:FeiBH3frequncy.jpg]]

From the above summary table, we can see that the energy is -26.46226438 whereas the energy of the optimised one is -26.46226438. So they have got the same value.

==Animating the vibrations==

Open the vibrations result.

[[Image:FeiVibrations.jpg]]

Show display vectors of each vibration.

[[Image:FeiVibration2.jpg]]

The following table is to a summary of motions, frequency, intensities and symmetry.

<table width="716" border="1">
<tr>
<td width="24" valign="top">No.</td>
<td width="473" valign="top">Form of vibration</td>
<td width="59" valign="top">frequency</td>
<td width="65" valign="top">intensity</td>
<td width="61" valign="top">Symmetry 
D3h point group</td>
</tr>
<tr>
<td valign="top">1 </td>
<td valign="top">all the H atoms move in and out together in the same direction, the B atom moves in the opposite direction of that of H atom</td>
<td valign="top">1145.71</td>
<td valign="top">92.6991</td>
<td valign="top"> </td>
</tr>
<tr>
<td valign="top">2</td>
<td valign="top">2 bottomed H atoms moves towards and away from each other whereas B atom and top H atom is quite stationary</td>
<td valign="top">1204.66</td>
<td valign="top">12.3789</td>
<td valign="top"> </td>
</tr>
<tr>
<td valign="top">3</td>
<td valign="top">Each of the bottomed H atom moves away and towards to the top H atom whereas B atom is quite stationary</td>
<td valign="top">1204.66</td>
<td valign="top">12.3814</td>
<td valign="top"> </td>
</tr>
<tr>
<td valign="top">4</td>
<td valign="top">All H atoms move in and out together in a concerted motion whereas B atom is unmoved</td>
<td valign="top">2591.65</td>
<td valign="top">0.0</td>
<td valign="top">A'1</td>
</tr>
<tr>
<td valign="top">5</td>
<td valign="top">2 bottomed H atoms move towards or away from B atom simultaneously 
Top H atom and B atom is quite stationary</td>
<td valign="top">2731.31</td>
<td valign="top">103.837</td>
<td valign="top"> </td>
</tr>
<tr>
<td valign="top">6</td>
<td valign="top">Bottomed H atoms move in and out whereas the top H atom moves in different order as the bottomed H atoms. The B atom is quite stationary</td>
<td valign="top">2731.31</td>
<td valign="top">103.83</td>
<td valign="top"> </td>
</tr>
</table>

The following graph is IR spectrum.

[[Image:FeiIR.jpg]]

From the IR spectrum, we can see that there are only 3 peaks. But there are 6 vibrations. In theory, we should get 6 peaks. This is due to peaks of no.2 and no.3 vibrations are combined together as having the nearly the same frequency, this is the same for peaks of no.5 and no.6 vibrations. And for no. 4 vibration, it is totally symmetric and this means there is not dipole moment and hence there will show no peak. So there will be 3 peaks in total shown in the spectrum.

==Molecular orbitals of BH3==

Create .chk file of the optimised BH3 molecule and open it to run another optimisation. Then I open the MOs from the “edit” section.

[[Image:FeiMOs.JPG]]

Then click the “update” button but there is nothing happened and the MOs is not obtained.
While doing the updating, the surface did appear around the molecule.

==='''Exercuse 2'''===

==='''Exercuse 3'''===

'''Ammonia'''

Firstly, generate a molecule of NH3 by using GussianView programme and start to optimise it by using B3LYP method with 6-31G basis set. And then we can get a optimised NH3 molecule with its summary table.

==='''Mini Project'''===

Rep:Mod:feihemodule2

2008-12-16T12:39:41Z

Fh106: /* Animating the vibrations */

='''Module 2'''=

==='''Introduction'''===

The aim of this module 2 is familiar with the Gussview programme and uses the programme to optimise the molecules.

Now look at the following simple molecule BH3.

==Create a molecule of BH3==

Use the Gussview programme to create the BH3 molecule. And we can the following picture of the molecule.

[[Image:FeiBh3.jpg]]

Picture of BH3 molecule.

And we can use label and symbol the molecule to get the following picture.

[[Image:FeiLabelledBH3.JPG]]

Labelled and symbol picture of BH3.

Then we set the all the three B-H bonds to 1.5 angstrom and get the following sturcure of BH3.

[[Image:FeiBh3fixedbondlength.JPG]]

Fixed bond distance picture of BH3

So the molecule is set up.

==Optimising a molecule of BH3==

Use the BLYP method and 3-21G basic set to optimise the molecule of BH3. And then we can the following optimised structure of the molecule.

[[Image:FeiOptimisedBH3.JPG]]

Optimised structure of BH3 molecule

Then we can determine the optimised B-H bond distance and H-B-H bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:FeiBH3bonddistance.JPG]]</td>
<td align="center">[[Image:FeiBH3bondangle.JPG]]</td>
</tr>
<tr>
<td align="center">Bond distance is 1.19435</td>
<td align="center">Bond angle is 120.000</td>
</tr>
</table>

And we can get a summary table to show some information about the molecule.

[[Image:FeiResulttable.JPG]]

Summary of the optimised molecule

From the above summary, we can see that the file of file is .log, calculation type is FOPT, calculation method is RB3LYP, basic set is 3-21G, final energy is -26.46226438 au, dipole moment is 0.000 debye, point group is D3H and the duration of calculation is 19.0 seconds.

We can get a “real” text based .log file as well.

[[Image:FeiRealresulttable.JPG]]

==Understanding optimisation part a==

Open the finished optimised file of the above molecule and tick “read intermediate geometries”. Then an energy and gradient against optimisation graph is obtained.

[[Image:FeiOptimisationgraph.JPG]]

There are 2 graphs in the above picture, the 1st one is energy against each step of optimisation and the 2nd one is the gradient of energy against each step of optimisation.

The green button in the molecule window is click and the animation of optimisation steps is obtained and we can see that the final structure has the least energy and smallest gradient of energy. So the stable structure is with the minimum energy and it is the final structure in the animation.

[[Image:FeiAnimation.JPG]]

==='''Exercuse 1'''===

==Find information about BCl3==

Following the method introduced in the introduction section, repeat the calculation for molecule BCl3.

Firstly, create the molecule of BCl3. And measure its B-Cl bond distance and Cl-B-Cl bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:FeiBCL3bonddistance.JPG]]</td>
<td align="center">[[Image:BCL3bondangle.JPG]]</td>
</tr>
<tr>
<td align="center">Bond distance: 1.87000</td>
<td align="center">Bond angle is 120.000</td>
</tr>
</table>

Secondly, restrict the symmetry of BCl3 to D3h and set the tolerance from the default to “very tight (0.0001)” and obtain the following picture.

[[Image:FeiRestrictedBCL3.JPG]]

Restricted BCl3 molecule

Thirdly, do the calculation to optimise the BCl3 molecule and obtain the optimised structure of BCl3.

[[Image:FeiOptimisedBCL3.JPG]]

Optimised BCl3 molecule

And we then obtain the optimised B-Cl bond distance and optimised Cl-B-Cl bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:FeiOptimisedbonddistance.JPG]]</td>
<td align="center">[[Image:Optimisedbondangle.JPG]]</td>
</tr>
<tr>
<td align="center">Bond distance: 1.86592</td>
<td align="center">Bond angle is 120.000</td>
</tr>
</table>

Finally, we then get the summary of the optimised molecule.

[[Image:FeiSummary2.JPG]]

From the above summary table, we can know that the file type is .log, calculation type is FORT, calculation method is RB3LYP, basic set is LANL2MB, final energy is -69.43928112 AU, dipole moment is 0.000 debye, point group is D3h and the duration of calculation is 12.0 seconds.

==Independent work==

I chose H2O as my own molecule. Firstly, set up the molecule of H2O. And we can get the O-H bond distance and H-O-H bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:H2Obonddistance.JPG]]</td>
<td align="center">[[Image:H2Obondangle.JPG]]</td>
</tr>
<tr>
<td align="center">Bond distance: 0.96000</td>
<td align="center">Bond angle is 109.500</td>
</tr>
</table>

Since O atom and H atom is above second row, we do not need to use pseudo-potential.
Therefore, we use the same method as above in above section but we set the basis set to 3-21G and obtain the following optimised H2O molecule with its summary table.

[[Image:FeiH2Osummary.JPG]]

From the above summary table, we can see that the calculation method is RB3LYP, basis set is 3-21G, final energy is -75.97396515 AU, dipole moment is 2.2381 Debye, point group is C2v and duration of calculation is 17.0 seconds.

We now can get the optimised bond distance and bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:Optimisedbonddistance.jpg]]</td>
<td align="center">[[Image:Optimisedbondangle.jpg]]</td>
</tr>
<tr>
<td align="center">Optimised bond distance: 0.99683</td>
<td align="center">Optimised bond angle: 103.991</td>
</tr>
</table>

Now I set the basis set to higher level in order to increase the accuracy. Use the first optimised output file to do another optimisation using higher level basis set. And use the second optimised output file to do another optimisation using even higher basis set.

<table width="663" border="1">
<tr>
<th width="176" scope="col"> </th>
<th scope="col">First trial</th>
<th scope="col">Second trail</th>
<th scope="col">Third trail</th>
</tr>
<tr>
<th scope="row">Bond distance/AU</th>
<td width="143" valign="top">0.99683 </td>
<td width="149" valign="top">0.96526</td>
<td width="167" valign="top">0.96203</td>
</tr>
<tr>
<th scope="row">Bond angle/degree</th>
<td width="143" valign="top">103.991</td>
<td width="149" valign="top">103.696</td>
<td width="167" valign="top">105.057</td>
</tr>
<tr>
<th scope="row">Calculation method</th>
<td width="143" valign="top">RB3LYP</td>
<td width="149" valign="top">RB3LYP</td>
<td width="167" valign="top">RB3LYP</td>
</tr>
<tr>
<th scope="row">Basis set</th>
<td width="143" valign="top">3-21G</td>
<td width="149" valign="top">6-31G(d.p)</td>
<td width="167" valign="top">6-311+G(d,p)</td>
</tr>
<tr>
<th scope="row">Final energy/J</th>
<td width="143" valign="top">-75.97396515</td>
<td width="149" valign="top">-76.41973659</td>
<td width="167" valign="top">-76.45846294</td>
</tr>
<tr>
<th scope="row">Dipole moment/debye</th>
<td width="143" valign="top">2.2381</td>
<td width="149" valign="top">2.0436</td>
<td width="167" valign="top">2.1610</td>
</tr>
<tr>
<th scope="row">Point group</th>
<td width="143" valign="top">C2v</td>
<td width="149" valign="top">C2v</td>
<td width="167" valign="top">C2v</td>
</tr>
<tr>
<th scope="row">Duration of calculation/s</th>
<td width="143" valign="top">17.0</td>
<td width="149" valign="top">17.0</td>
<td width="167" valign="top">18.0</td>
</tr>
</table>

==Vibrational analysis and confirming minima==

In this section, we are going to use vibrational analysis to confirm the minimum structure.
Firstly, open the optimised BH3 file and do the vibrational analysis to confirm its minimum structure. So we get the following structure with its summary.

[[Image:FeiBH3frequncy.jpg]]

From the above summary table, we can see that the energy is -26.46226438 whereas the energy of the optimised one is -26.46226438. So they have got the same value.

==Animating the vibrations==

Open the vibrations result.

[[Image:FeiVibrations.jpg]]

Show display vectors of each vibration.

[[Image:FeiVibration2.jpg]]

The following table is to a summary of motions, frequency, intensities and symmetry.

<table width="716" border="1">
<tr>
<td width="24" valign="top">No.</td>
<td width="473" valign="top">Form of vibration</td>
<td width="59" valign="top">frequency</td>
<td width="65" valign="top">intensity</td>
<td width="61" valign="top">Symmetry 
D3h point group</td>
</tr>
<tr>
<td valign="top">1 </td>
<td valign="top">all the H atoms move in and out together in the same direction, the B atom moves in the opposite direction of that of H atom</td>
<td valign="top">1145.71</td>
<td valign="top">92.6991</td>
<td valign="top"> </td>
</tr>
<tr>
<td valign="top">2</td>
<td valign="top">2 bottomed H atoms moves towards and away from each other whereas B atom and top H atom is quite stationary</td>
<td valign="top">1204.66</td>
<td valign="top">12.3789</td>
<td valign="top"> </td>
</tr>
<tr>
<td valign="top">3</td>
<td valign="top">Each of the bottomed H atom moves away and towards to the top H atom whereas B atom is quite stationary</td>
<td valign="top">1204.66</td>
<td valign="top">12.3814</td>
<td valign="top"> </td>
</tr>
<tr>
<td valign="top">4</td>
<td valign="top">All H atoms move in and out together in a concerted motion whereas B atom is unmoved</td>
<td valign="top">2591.65</td>
<td valign="top">0.0</td>
<td valign="top">A'1</td>
</tr>
<tr>
<td valign="top">5</td>
<td valign="top">2 bottomed H atoms move towards or away from B atom simultaneously 
Top H atom and B atom is quite stationary</td>
<td valign="top">2731.31</td>
<td valign="top">103.837</td>
<td valign="top"> </td>
</tr>
<tr>
<td valign="top">6</td>
<td valign="top">Bottomed H atoms move in and out whereas the top H atom moves in different order as the bottomed H atoms. The B atom is quite stationary</td>
<td valign="top">2731.31</td>
<td valign="top">103.83</td>
<td valign="top"> </td>
</tr>
</table>

The following graph is IR spectrum.

[[Image:FeiIR.jpg]]

From the IR spectrum, we can see that there are only 3 peaks. But there are 6 vibrations. In theory, we should get 6 peaks. This is due to peaks of no.2 and no.3 vibrations are combined together as having the nearly the same frequency, this is the same for peaks of no.5 and no.6 vibrations. And for no. 4 vibration, it is totally symmetric and this means there is not dipole moment and hence there will show no peak. So there will be 3 peaks in total shown in the spectrum.

==Molecular orbitals of BH3==

Create .chk file of the optimised BH3 molecule and open it to run another optimisation. Then I open the MOs from the “edit” section.

[[Image:FeiMOs.JPG]]

Then click the “update” button but there is nothing happened and the MOs is not obtained.
While doing the updating, the surface did appear around the molecule.

==='''Exercuse 2'''===

==='''Exercuse 3'''===

==='''Mini Project'''===

Rep:Mod:feihemodule2

2008-12-16T12:15:31Z

Fh106: /* Find information about BCl3 */

='''Module 2'''=

==='''Introduction'''===

The aim of this module 2 is familiar with the Gussview programme and uses the programme to optimise the molecules.

Now look at the following simple molecule BH3.

==Create a molecule of BH3==

Use the Gussview programme to create the BH3 molecule. And we can the following picture of the molecule.

[[Image:FeiBh3.jpg]]

Picture of BH3 molecule.

And we can use label and symbol the molecule to get the following picture.

[[Image:FeiLabelledBH3.JPG]]

Labelled and symbol picture of BH3.

Then we set the all the three B-H bonds to 1.5 angstrom and get the following sturcure of BH3.

[[Image:FeiBh3fixedbondlength.JPG]]

Fixed bond distance picture of BH3

So the molecule is set up.

==Optimising a molecule of BH3==

Use the BLYP method and 3-21G basic set to optimise the molecule of BH3. And then we can the following optimised structure of the molecule.

[[Image:FeiOptimisedBH3.JPG]]

Optimised structure of BH3 molecule

Then we can determine the optimised B-H bond distance and H-B-H bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:FeiBH3bonddistance.JPG]]</td>
<td align="center">[[Image:FeiBH3bondangle.JPG]]</td>
</tr>
<tr>
<td align="center">Bond distance is 1.19435</td>
<td align="center">Bond angle is 120.000</td>
</tr>
</table>

And we can get a summary table to show some information about the molecule.

[[Image:FeiResulttable.JPG]]

Summary of the optimised molecule

From the above summary, we can see that the file of file is .log, calculation type is FOPT, calculation method is RB3LYP, basic set is 3-21G, final energy is -26.46226438 au, dipole moment is 0.000 debye, point group is D3H and the duration of calculation is 19.0 seconds.

We can get a “real” text based .log file as well.

[[Image:FeiRealresulttable.JPG]]

==Understanding optimisation part a==

Open the finished optimised file of the above molecule and tick “read intermediate geometries”. Then an energy and gradient against optimisation graph is obtained.

[[Image:FeiOptimisationgraph.JPG]]

There are 2 graphs in the above picture, the 1st one is energy against each step of optimisation and the 2nd one is the gradient of energy against each step of optimisation.

The green button in the molecule window is click and the animation of optimisation steps is obtained and we can see that the final structure has the least energy and smallest gradient of energy. So the stable structure is with the minimum energy and it is the final structure in the animation.

[[Image:FeiAnimation.JPG]]

==='''Exercuse 1'''===

==Find information about BCl3==

Following the method introduced in the introduction section, repeat the calculation for molecule BCl3.

Firstly, create the molecule of BCl3. And measure its B-Cl bond distance and Cl-B-Cl bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:FeiBCL3bonddistance.JPG]]</td>
<td align="center">[[Image:BCL3bondangle.JPG]]</td>
</tr>
<tr>
<td align="center">Bond distance: 1.87000</td>
<td align="center">Bond angle is 120.000</td>
</tr>
</table>

Secondly, restrict the symmetry of BCl3 to D3h and set the tolerance from the default to “very tight (0.0001)” and obtain the following picture.

[[Image:FeiRestrictedBCL3.JPG]]

Restricted BCl3 molecule

Thirdly, do the calculation to optimise the BCl3 molecule and obtain the optimised structure of BCl3.

[[Image:FeiOptimisedBCL3.JPG]]

Optimised BCl3 molecule

And we then obtain the optimised B-Cl bond distance and optimised Cl-B-Cl bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:FeiOptimisedbonddistance.JPG]]</td>
<td align="center">[[Image:Optimisedbondangle.JPG]]</td>
</tr>
<tr>
<td align="center">Bond distance: 1.86592</td>
<td align="center">Bond angle is 120.000</td>
</tr>
</table>

Finally, we then get the summary of the optimised molecule.

[[Image:FeiSummary2.JPG]]

From the above summary table, we can know that the file type is .log, calculation type is FORT, calculation method is RB3LYP, basic set is LANL2MB, final energy is -69.43928112 AU, dipole moment is 0.000 debye, point group is D3h and the duration of calculation is 12.0 seconds.

==Independent work==

I chose H2O as my own molecule. Firstly, set up the molecule of H2O. And we can get the O-H bond distance and H-O-H bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:H2Obonddistance.JPG]]</td>
<td align="center">[[Image:H2Obondangle.JPG]]</td>
</tr>
<tr>
<td align="center">Bond distance: 0.96000</td>
<td align="center">Bond angle is 109.500</td>
</tr>
</table>

Since O atom and H atom is above second row, we do not need to use pseudo-potential.
Therefore, we use the same method as above in above section but we set the basis set to 3-21G and obtain the following optimised H2O molecule with its summary table.

[[Image:FeiH2Osummary.JPG]]

From the above summary table, we can see that the calculation method is RB3LYP, basis set is 3-21G, final energy is -75.97396515 AU, dipole moment is 2.2381 Debye, point group is C2v and duration of calculation is 17.0 seconds.

We now can get the optimised bond distance and bond angle.

<table width="650" height="270" border="0">
<tr>
<td height="260", align="center">[[Image:Optimisedbonddistance.jpg]]</td>
<td align="center">[[Image:Optimisedbondangle.jpg]]</td>
</tr>
<tr>
<td align="center">Optimised bond distance: 0.99683</td>
<td align="center">Optimised bond angle: 103.991</td>
</tr>
</table>

Now I set the basis set to higher level in order to increase the accuracy. Use the first optimised output file to do another optimisation using higher level basis set. And use the second optimised output file to do another optimisation using even higher basis set.

<table width="663" border="1">
<tr>
<th width="176" scope="col"> </th>
<th scope="col">First trial</th>
<th scope="col">Second trail</th>
<th scope="col">Third trail</th>
</tr>
<tr>
<th scope="row">Bond distance/AU</th>
<td width="143" valign="top">0.99683 </td>
<td width="149" valign="top">0.96526</td>
<td width="167" valign="top">0.96203</td>
</tr>
<tr>
<th scope="row">Bond angle/degree</th>
<td width="143" valign="top">103.991</td>
<td width="149" valign="top">103.696</td>
<td width="167" valign="top">105.057</td>
</tr>
<tr>
<th scope="row">Calculation method</th>
<td width="143" valign="top">RB3LYP</td>
<td width="149" valign="top">RB3LYP</td>
<td width="167" valign="top">RB3LYP</td>
</tr>
<tr>
<th scope="row">Basis set</th>
<td width="143" valign="top">3-21G</td>
<td width="149" valign="top">6-31G(d.p)</td>
<td width="167" valign="top">6-311+G(d,p)</td>
</tr>
<tr>
<th scope="row">Final energy/J</th>
<td width="143" valign="top">-75.97396515</td>
<td width="149" valign="top">-76.41973659</td>
<td width="167" valign="top">-76.45846294</td>
</tr>
<tr>
<th scope="row">Dipole moment/debye</th>
<td width="143" valign="top">2.2381</td>
<td width="149" valign="top">2.0436</td>
<td width="167" valign="top">2.1610</td>
</tr>
<tr>
<th scope="row">Point group</th>
<td width="143" valign="top">C2v</td>
<td width="149" valign="top">C2v</td>
<td width="167" valign="top">C2v</td>
</tr>
<tr>
<th scope="row">Duration of calculation/s</th>
<td width="143" valign="top">17.0</td>
<td width="149" valign="top">17.0</td>
<td width="167" valign="top">18.0</td>
</tr>
</table>

==Vibrational analysis and confirming minima==

In this section, we are going to use vibrational analysis to confirm the minimum structure.
Firstly, open the optimised BH3 file and do the vibrational analysis to confirm its minimum structure. So we get the following structure with its summary.

[[Image:FeiBH3frequncy.jpg]]

From the above summary table, we can see that the energy is -26.46226438 whereas the energy of the optimised one is -26.46226438. So they have got the same value.

==Animating the vibrations==

Open the vibrations result.

[[Image:FeiVibrations.jpg]]

Show display vectors of each vibration.

[[Image:FeiVibration2.jpg]]

The following table is to a summary of motions, frequency, intensities and symmetry.

<table width="716" border="1">
<tr>
<td width="24" valign="top">No.</td>
<td width="473" valign="top">Form of vibration</td>
<td width="59" valign="top">frequency</td>
<td width="65" valign="top">intensity</td>
<td width="61" valign="top">Symmetry 
D3h point group</td>
</tr>
<tr>
<td valign="top">1 </td>
<td valign="top">all the H atoms move in and out together in the same direction, the B atom moves in the opposite direction of that of H atom</td>
<td valign="top">1145.71</td>
<td valign="top">92.6991</td>
<td valign="top"> </td>
</tr>
<tr>
<td valign="top">2</td>
<td valign="top">2 bottomed H atoms moves towards and away from each other whereas B atom and top H atom is quite stationary</td>
<td valign="top">1204.66</td>
<td valign="top">12.3789</td>
<td valign="top"> </td>
</tr>
<tr>
<td valign="top">3</td>
<td valign="top">Each of the bottomed H atom moves away and towards to the top H atom whereas B atom is quite stationary</td>
<td valign="top">1204.66</td>
<td valign="top">12.3814</td>
<td valign="top"> </td>
</tr>
<tr>
<td valign="top">4</td>
<td valign="top">All H atoms move in and out together in a concerted motion whereas B atom is unmoved</td>
<td valign="top">2591.65</td>
<td valign="top">0.0</td>
<td valign="top">A1</td>
</tr>
<tr>
<td valign="top">5</td>
<td valign="top">2 bottomed H atoms move towards or away from B atom simultaneously 
Top H atom and B atom is quite stationary</td>
<td valign="top">2731.31</td>
<td valign="top">103.837</td>
<td valign="top"> </td>
</tr>
<tr>
<td valign="top">6</td>
<td valign="top">Bottomed H atoms move in and out whereas the top H atom moves in different order as the bottomed H atoms. The B atom is quite stationary</td>
<td valign="top">2731.31</td>
<td valign="top">103.83</td>
<td valign="top"> </td>
</tr>
</table>

The following graph is IR spectrum.

[[Image:FeiIR.jpg]]

From the IR spectrum, we can see that there are only 3 peaks. But there are 6 vibrations. In theory, we should get 6 peaks. This is due to peaks of no.2 and no.3 vibrations are combined together as having the nearly the same frequency, this is the same for peaks of no.5 and no.6 vibrations. And for no. 4 vibration, it is totally symmetric and this means there is not dipole moment and hence there will show no peak. So there will be 3 peaks in total shown in the spectrum.

==Molecular orbitals of BH3==

Create .chk file of the optimised BH3 molecule and open it to run another optimisation. Then I open the MOs from the “edit” section.

[[Image:FeiMOs.JPG]]

Then click the “update” button but there is nothing happened and the MOs is not obtained.
While doing the updating, the surface did appear around the molecule.

==='''Exercuse 2'''===

==='''Exercuse 3'''===

==='''Mini Project'''===

File:FeiMOs.JPG

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File:FeiIR.jpg

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File:FeiVibration2.jpg

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File:H2Obonddistance.JPG

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File:FeiSummary2.JPG

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File:FeiOptimisedBCL3.JPG

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File:FeiRestrictedBCL3.JPG

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File:BCL3bondangle.JPG

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File:FeiBCL3bonddistance.JPG

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Rep:Mod:feihemodule2

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Fh106: /* '''Exercuse 1''' */

Rep:Mod:feihemodule2

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Fh106: /* '''Module 2''' */

File:FeiAnimation.JPG

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