ChemWiki - User contributions [en]

Rep:Mod:SHMod3Phys

2010-11-12T12:08:00Z

Sh1308: /* Stuart Haylock - Computational Lab - Module 3 - Physical Computational Chemistry Experiments */

= Stuart Haylock - Computational Lab - Module 3 - Physical Computational Chemistry Experiments =

==Aim:==
The aim of this experiment is to characterise transition structures on potential energy surfaces for both the Cope rearrangement and the Diels Alder cycloaddition reactions. In these calculations, instead of using molecular orbital-based methods, I will be numerically solving the Schrödinger equation to locate transition structures.

==The Cope Rearrangement==

[[Image:stuCope_Rearrangement.gif|centre|Cope Rearrangement]]

In this section I will be finding the energy minima of the transition structures within the Cope rearrangement (above). The Cope rearrangement is a [3,3]-sigmatropic shift and has numerous computational studies<ref>Houk et al.,{{DOI|10.1021/ja00101a078}}</ref>.

The first optimisation of 1,5 hexadiene with an "anti" linkage was done with the HF/3.21G level.

<jmol> <jmolAppletButton> <uploadedFileContents>stuANTI_2.mol</uploadedFileContents> <text>Anti 1,5 Hexadiene</text> </jmolAppletButton> </jmol>

{| class="wikitable" border="1"
|+ Anti 1,5 Hexadiene Optimisation
|-
| File Name || Anti
|-
| File Type || .log
|-
| Calculation Type || FOPT
|-
| Calculation Method || RHF
|-
| Basis Set || 3-21G
|-
| Charge || 0
|-
| Spin || Singlet
|-
| E(RB3LYP) || -231.69253522 a.u.
|-
| RMS Gradient Norm || 0.00002849 a.u.
|-
| Dipole Moment || 0.0000 Debye
|}

The symmetry of this molecule is Ci.

The second optimisation of 1,5 hexadiene with an "gauche" linkage was done with the HF/3.21G level.

<jmol> <jmolAppletButton> <uploadedFileContents>StuGAUCHE_1.mol</uploadedFileContents> <text>Gauche 1,5 Hexadiene</text> </jmolAppletButton> </jmol>

{| class="wikitable" border="1"
|+ Gauche 1,5 Hexadiene Optimisation
|-
| File Name || Gauche
|-
| File Type || .log
|-
| Calculation Type || FOPT
|-
| Calculation Method || RHF
|-
| Basis Set || 3-21G
|-
| Charge || 0
|-
| Spin || Singlet
|-
| E(RB3LYP) || -231.68771616 a.u.
|-
| RMS Gradient Norm || 0.00000491 a.u.
|-
| Dipole Moment || 0.4556 Debye
|}

The symmetry of this gauche molecule is C2.

From this you can see that the anti conformation is the lowest in energy, although the gauche conformation is close in energy this may be due to secondary orbital interactions inducing a stabilisation effect ("gecko effect") and therefore lowering the energy of this conformation.

According to the conformation table in the instructions page<ref>https://www.ch.ic.ac.uk/wiki/index.php/Mod:phys3#Appendix_1</ref> the molecules I have sketched are the Gauche 1 conformer and the Anti 2 conformer, judging by the energy, symmetry groups and the general design of the molecule.

As my anti hexadiene molecule already has a Ci symmetry group I then reoptimised the structure with a B3LYP/6.31G level which the following summary output.

{| class="wikitable" border="1"
|+ Anti 1,5 Hexadiene Optimisation
|-
| File Name || DFT Anti
|-
| File Type || .log
|-
| Calculation Type || FOPT
|-
| Calculation Method || RB3LYP
|-
| Basis Set || 6-31G
|-
| Charge || 0
|-
| Spin || Singlet
|-
| E(RB3LYP) || -234.55970424 a.u.
|-
| RMS Gradient Norm || 0.00004654 a.u.
|-
| Dipole Moment || 0.0000 Debye
|}

Which still has a Ci point group. With the more accurate basis set and method you can see that the energy has decreased relatively substantially although there is almost no visible difference in the geometry of the molecule itself.

From the frequency analysis you can see there are no imaginary vibrations which means the molecule has optimised correctly.

{| class="wikitable" border="1"
|+ Thermochemistry of the Anti-2 Structure
! !! Values
|-
| Sum of electronic and zero-point energies|| 234.416244
|-
| Sum of electronic and thermal energies|| 234.408954
|-
| Sum of electronic and thermal enthalpies || 234.408010
|-
| Sum of electronic and thermal free energies || 234.447849
|}

When these values are compared with literature<ref>E. Ventura, S. Andrade do Monte, M. Dallos, H. Lischka, ''J. Phys. Chem. A'', '''2003''', 107 (8), pp1175-1180. {{DOI|10.1021/jp0259014}}</ref> you can see a very good agreement with the experimental data with respect to energetic stability showing that this computed structure is practically the same as a experimental molecule.

===Optimisation of the "Chair" and "Boat" transition structures===

By computing the force constants for a reaction and using a specific coordinates for the transition structure bonds you can optimise a transition structure, and you can also calculate the activation energies.

[[Image:stuTransition_Structures.gif|centre|Two Transition Structures]]

[[Image:stuCope_Rearrangement_Vibration.gif|Right]]The chair structure is the first that was sketched and optimised. The frequency calculation showed just one vibration which corresponded to the cope rearrangement. (right)

==References==
<references/>

File:StuCope Rearrangement Vibration.gif

2010-11-12T12:07:25Z

Sh1308:

Rep:Mod:SHMod3Phys

2010-11-12T12:07:10Z

Sh1308: /* Stuart Haylock - Computational Lab - Module 3 - Physical Computational Chemistry Experiments */

= Stuart Haylock - Computational Lab - Module 3 - Physical Computational Chemistry Experiments =

==Aim:==
The aim of this experiment is to characterise transition structures on potential energy surfaces for both the Cope rearrangement and the Diels Alder cycloaddition reactions. In these calculations, instead of using molecular orbital-based methods, I will be numerically solving the Schrödinger equation to locate transition structures.

==The Cope Rearrangement==

[[Image:stuCope_Rearrangement.gif|centre|Cope Rearrangement]]

In this section I will be finding the energy minima of the transition structures within the Cope rearrangement (above). The Cope rearrangement is a [3,3]-sigmatropic shift and has numerous computational studies<ref>Houk et al.,{{DOI|10.1021/ja00101a078}}</ref>.

The first optimisation of 1,5 hexadiene with an "anti" linkage was done with the HF/3.21G level.

<jmol> <jmolAppletButton> <uploadedFileContents>stuANTI_2.mol</uploadedFileContents> <text>Anti 1,5 Hexadiene</text> </jmolAppletButton> </jmol>

{| class="wikitable" border="1"
|+ Anti 1,5 Hexadiene Optimisation
|-
| File Name || Anti
|-
| File Type || .log
|-
| Calculation Type || FOPT
|-
| Calculation Method || RHF
|-
| Basis Set || 3-21G
|-
| Charge || 0
|-
| Spin || Singlet
|-
| E(RB3LYP) || -231.69253522 a.u.
|-
| RMS Gradient Norm || 0.00002849 a.u.
|-
| Dipole Moment || 0.0000 Debye
|}

The symmetry of this molecule is Ci.

The second optimisation of 1,5 hexadiene with an "gauche" linkage was done with the HF/3.21G level.

<jmol> <jmolAppletButton> <uploadedFileContents>StuGAUCHE_1.mol</uploadedFileContents> <text>Gauche 1,5 Hexadiene</text> </jmolAppletButton> </jmol>

{| class="wikitable" border="1"
|+ Gauche 1,5 Hexadiene Optimisation
|-
| File Name || Gauche
|-
| File Type || .log
|-
| Calculation Type || FOPT
|-
| Calculation Method || RHF
|-
| Basis Set || 3-21G
|-
| Charge || 0
|-
| Spin || Singlet
|-
| E(RB3LYP) || -231.68771616 a.u.
|-
| RMS Gradient Norm || 0.00000491 a.u.
|-
| Dipole Moment || 0.4556 Debye
|}

The symmetry of this gauche molecule is C2.

From this you can see that the anti conformation is the lowest in energy, although the gauche conformation is close in energy this may be due to secondary orbital interactions inducing a stabilisation effect ("gecko effect") and therefore lowering the energy of this conformation.

According to the conformation table in the instructions page<ref>https://www.ch.ic.ac.uk/wiki/index.php/Mod:phys3#Appendix_1</ref> the molecules I have sketched are the Gauche 1 conformer and the Anti 2 conformer, judging by the energy, symmetry groups and the general design of the molecule.

As my anti hexadiene molecule already has a Ci symmetry group I then reoptimised the structure with a B3LYP/6.31G level which the following summary output.

{| class="wikitable" border="1"
|+ Anti 1,5 Hexadiene Optimisation
|-
| File Name || DFT Anti
|-
| File Type || .log
|-
| Calculation Type || FOPT
|-
| Calculation Method || RB3LYP
|-
| Basis Set || 6-31G
|-
| Charge || 0
|-
| Spin || Singlet
|-
| E(RB3LYP) || -234.55970424 a.u.
|-
| RMS Gradient Norm || 0.00004654 a.u.
|-
| Dipole Moment || 0.0000 Debye
|}

Which still has a Ci point group. With the more accurate basis set and method you can see that the energy has decreased relatively substantially although there is almost no visible difference in the geometry of the molecule itself.

From the frequency analysis you can see there are no imaginary vibrations which means the molecule has optimised correctly.

{| class="wikitable" border="1"
|+ Thermochemistry of the Anti-2 Structure
! !! Values
|-
| Sum of electronic and zero-point energies|| 234.416244
|-
| Sum of electronic and thermal energies|| 234.408954
|-
| Sum of electronic and thermal enthalpies || 234.408010
|-
| Sum of electronic and thermal free energies || 234.447849
|}

When these values are compared with literature<ref>E. Ventura, S. Andrade do Monte, M. Dallos, H. Lischka, ''J. Phys. Chem. A'', '''2003''', 107 (8), pp1175-1180. {{DOI|10.1021/jp0259014}}</ref> you can see a very good agreement with the experimental data with respect to energetic stability showing that this computed structure is practically the same as a experimental molecule.

===Optimisation of the "Chair" and "Boat" transition structures===

By computing the force constants for a reaction and using a specific coordinates for the transition structure bonds you can optimise a transition structure, and you can also calculate the activation energies.

[[Image:stuTransition_Structures.gif|centre|Two Transition Structures]]

The chair structure is the first that was sketched and optimised. The frequency calculation showed just one vibration which corresponded to the cope rearrangement. (right)

==References==
<references/>

Rep:Mod:SHMod3Phys

2010-11-12T11:40:30Z

Sh1308: /* Stuart Haylock - Computational Lab - Module 3 - Physical Computational Chemistry Experiments */

= Stuart Haylock - Computational Lab - Module 3 - Physical Computational Chemistry Experiments =

==Aim:==
The aim of this experiment is to characterise transition structures on potential energy surfaces for both the Cope rearrangement and the Diels Alder cycloaddition reactions. In these calculations, instead of using molecular orbital-based methods, I will be numerically solving the Schrödinger equation to locate transition structures.

==The Cope Rearrangement==

[[Image:stuCope_Rearrangement.gif|centre|Cope Rearrangement]]

In this section I will be finding the energy minima of the transition structures within the Cope rearrangement (above). The Cope rearrangement is a [3,3]-sigmatropic shift and has numerous computational studies<ref>Houk et al.,{{DOI|10.1021/ja00101a078}}</ref>.

[[Image:stuTransition_Structures.gif|centre|Two Transition Structures]]

The first optimisation of 1,5 hexadiene with an "anti" linkage was done with the HF/3.21G level.

<jmol> <jmolAppletButton> <uploadedFileContents>stuANTI_2.mol</uploadedFileContents> <text>Anti 1,5 Hexadiene</text> </jmolAppletButton> </jmol>

{| class="wikitable" border="1"
|+ Anti 1,5 Hexadiene Optimisation
|-
| File Name || Anti
|-
| File Type || .log
|-
| Calculation Type || FOPT
|-
| Calculation Method || RHF
|-
| Basis Set || 3-21G
|-
| Charge || 0
|-
| Spin || Singlet
|-
| E(RB3LYP) || -231.69253522 a.u.
|-
| RMS Gradient Norm || 0.00002849 a.u.
|-
| Dipole Moment || 0.0000 Debye
|}

The symmetry of this molecule is Ci.

The second optimisation of 1,5 hexadiene with an "gauche" linkage was done with the HF/3.21G level.

<jmol> <jmolAppletButton> <uploadedFileContents>StuGAUCHE_1.mol</uploadedFileContents> <text>Gauche 1,5 Hexadiene</text> </jmolAppletButton> </jmol>

{| class="wikitable" border="1"
|+ Gauche 1,5 Hexadiene Optimisation
|-
| File Name || Gauche
|-
| File Type || .log
|-
| Calculation Type || FOPT
|-
| Calculation Method || RHF
|-
| Basis Set || 3-21G
|-
| Charge || 0
|-
| Spin || Singlet
|-
| E(RB3LYP) || -231.68771616 a.u.
|-
| RMS Gradient Norm || 0.00000491 a.u.
|-
| Dipole Moment || 0.4556 Debye
|}

The symmetry of this gauche molecule is C2.

From this you can see that the anti conformation is the lowest in energy, although the gauche conformation is close in energy this may be due to secondary orbital interactions inducing a stabilisation effect ("gecko effect") and therefore lowering the energy of this conformation.

According to the conformation table in the instructions page<ref>https://www.ch.ic.ac.uk/wiki/index.php/Mod:phys3#Appendix_1</ref> the molecules I have sketched are the Gauche 1 conformer and the Anti 2 conformer, judging by the energy, symmetry groups and the general design of the molecule.

As my anti hexadiene molecule already has a Ci symmetry group I then reoptimised the structure with a B3LYP/6.31G level which the following summary output.

{| class="wikitable" border="1"
|+ Anti 1,5 Hexadiene Optimisation
|-
| File Name || DFT Anti
|-
| File Type || .log
|-
| Calculation Type || FOPT
|-
| Calculation Method || RB3LYP
|-
| Basis Set || 6-31G
|-
| Charge || 0
|-
| Spin || Singlet
|-
| E(RB3LYP) || -234.55970424 a.u.
|-
| RMS Gradient Norm || 0.00004654 a.u.
|-
| Dipole Moment || 0.0000 Debye
|}

Which still has a Ci point group. With the more accurate basis set and method you can see that the energy has decreased relatively substantially although there is almost no visible difference in the geometry of the molecule itself.

From the frequency analysis you can see there are no imaginary vibrations which means the molecule has optimised correctly.

{| class="wikitable" border="1"
|+ Thermochemistry of the Anti-2 Structure
! !! Values
|-
| Sum of electronic and zero-point energies|| 234.416244
|-
| Sum of electronic and thermal energies|| 234.408954
|-
| Sum of electronic and thermal enthalpies || 234.408010
|-
| Sum of electronic and thermal free energies || 234.447849
|}

When these values are compared with experimental data<ref>E. Ventura, S. Andrade do Monte, M. Dallos, H. Lischka, ''J. Phys. Chem. A'', '''2003''', 107 (8), pp1175-1180. {{DOI|10.1021/jp0259014}}</ref> you can see a very close

==References==
<references/>

Rep:Mod:SHMod3Phys

Rep:Mod:SHMod3Phys

2010-11-12T10:23:27Z

Sh1308: New page: = Stuart Haylock - Computational Lab - Module 3 - Physical Computational Chemistry Experiments = ==Aim:== The aim of this experiment is to characterise transition structures on potential ...

Rep:Mod:SHMod2Inorg

2010-11-02T17:47:24Z

Sh1308: /* Siloxane */

= Stuart Haylock - Computational Lab - Module 2 - Inorganic Computational Chemistry Experiments =

==Aim:==
The aim of this experiment is to give an insight into the structure and bonding of inorganic complexes. Inorganic complexes are much more complicated then organic ones, however computational experimentation can prove to be a very useful method of showing why certain complexes form over others and can help with designing catalysts.

==Borane BH3 Optimisation==
The optimisation of a molecule involves trying different geometries to find the lowest energy one. The process is made of two parts.
# The position of the nuclei is plugged into the Schrödinger equation and is solved for the electrons and energy. ('''SCF''')
# Then the nuclei are moved and the SCF cycle repeated at each geometry, eventually giving the positions with the lowest energy. ('''OPT''')
Each Optimisation then has a method and basis set where the method determines the type of approximations made in solving the Schrödinger equation and the basis set determines how accurately it is calculated (and therefore how long the calculation will take in computational time).

For BH3 the method will be B3LYP and basis set will be 3-21G, these are very low accuracy sets but will provide fast results, also with small molecules the accuracy isn't too much of an issue as there aren't as many factors to take into account.

<jmol> <jmolAppletButton> <uploadedFileContents>StuBH3_OPT.mol</uploadedFileContents> <text>Optimised BH3</text> </jmolAppletButton> </jmol>

The bond distance for the optimised BH3 is 1.194Å.
The H-B-H bond angle is 120o.

This agrees well with literature values for the bond length of 1.20Å<ref>R. Konechny, D.J. Doren, ''J. Phys. Chem. B'', '''1997''', 101 (51), pp 10983–10985, {{DOI|10.1021/jp9726246}} </ref>. Also as the boron is sp2 hybridised we expect the bond angles to be 120o. This shows that while the method and basis set are inaccurate they still provide correlated results and are a very good approximation.

{| class="wikitable" border="1"
|+ BH3 Optimisation
|-
| File Name || BH3 OPT
|-
| File Type || .log
|-
| Calculation Type || FOPT
|-
| Calculation Method || RB3LYP
|-
| Basis Set || 3-21G
|-
| Charge || 0
|-
| Spin || Singlet
|-
| E(RB3LYP) || -26.46226447 a.u.
|-
| RMS Gradient Norm || 0.00000434 a.u.
|-
| Imaginary Freq ||
|-
| Dipole Moment || 0 Debye
|-
| Point Group || D3H
|-
| Cpu Time || 30.0 seconds
|}

To make sure the that optimisation process has succeeded the RMS end gradient of the total energy against the calculation step must be very close to zero. According to the summary data (above) the gradient was very close to zero indicating that the optimisation worked successfully as the energy has levelled out to to 0.

You can also see that the molecule has D3H symmetry which I know is true from my own symmetry calculations, further showing the optimisation process has worked.

[[Image:stuBH3_Opt_Graph.jpg|Optimisation Graphs]]
[[Image:stuBH3_Opt_Graph_2.jpg|Optimisation Graphs]]

These two graphs further show how the optimisation has worked. The both graphs show a decline followed by a levelling showing that as each new step passes the gradient tends to 0. This means that with each new step the molecule is getting closer to the optimised energy and geometry.

The Optimised file can be found here:
https://www.ch.imperial.ac.uk/wiki/images/f/fe/StuBH3_OPT.LOG

==Thallium Bromide TlBr3 Optimisation==

In order to understand optimisation fully you must understand how larger basis sets work and what happens with different molecules.

For a molecule of TlBr3 the same method is used however a different basis set is used, the LanL2DZ option is slightly more accurate for heavier elements (such as thallium) but is approximate enough for the calculation to take a reasonable amount of time. This molecule must also have its symmetry to be confined as D3H trigonal planar as later analysis requires this symmetry in the optimisation process.

<jmol> <jmolAppletButton> <uploadedFileContents>StuTlBr3_OPT.mol</uploadedFileContents> <text>Optimised TlBr3</text> </jmolAppletButton> </jmol>

The optimised bond distance is 2.65Å, and the optimised bond angle is 120o.

The literature value for the Tl-Br bond length is 2.52<ref>J. Blixt, J. Glaser, J. Mink, I. Persson, P. Persson, M. Sandstrom, ''J. Am. Chem. SOC.'', '''1995''',117, 5089-5104 {{DOI|10.1021/ja00123a011}}</ref> which is close but not completely accurate to the optimisation, this shows that as heavier elements are introduced computation can become less accurate at lower basis sets and methods. Also the bond angle of 120o is in concordance with constraining the symmetry to trigonal planar D3H.

{| class="wikitable" border="1"
|+ BH3 Optimisation
|-
| File Name || TLBR3 OPT INPUT
|-
| File Type || .log
|-
| Calculation Type || FOPT
|-
| Calculation Method || RB3LYP
|-
| Basis Set || LANL2DZ
|-
| Charge || 0
|-
| Spin || Singlet
|-
| E(RB3LYP) || -91.21812851 a.u.
|-
| RMS Gradient Norm || 0.00000090 a.u.
|-
| Imaginary Freq ||
|-
| Dipole Moment || 0 Debye
|-
| Point Group || D3H
|-
| Cpu Time || 43.0 seconds
|}

The summary shows that the final gradient is very close to 0 showing the optimisation has been successful.

According to the frequency analysis the vibrations of the centre of mass of the molecule were an order of magnitude lower then the lowest real mode of vibration which was at 46.567. The frequency analysis is used to show how accurate the molecule optimisation is, and in this case it is relatively accurate.

[[Image:stuTlBr3_Bond.jpg|thumb|Center|Bonds Missing! ]]

Occasionally the bonds will be missing from a molecule, this is as Gaussview has a limited range of bond lengths in its system and once a bond length goes beyond a specific level the visable bond disappears.

The bond however is still there as a bond is nothing more than the forces of attraction that hold a molecule together, these may be ionic, covalent, metallic or even intermolecular. Just because it is not visible on the system doesn't mean the atoms aren't being held together.

The Optimisation file can be found here:
https://www.ch.imperial.ac.uk/wiki/images/3/30/StuTLBR3_OPT_INPUT.LOG

==Borane BH3 Analysis==

===Molecular Orbitals===

A molecular orbital analysis was then carried out on the BH3 molecule<ref>{{DOI|10042/to-5438}}</ref>.

[[Image:StuBH3_MO_Diagram.gif|BH3 Mo Diagram]]

{| class="wikitable" border="1"
|+ MO Visualisations
! !! A !! B !! C !! D
|-
| MO's || [[Image:stuBH3_A.jpg|thumb|MO A]]|| [[Image:stuBH3_B.jpg|thumb|MO B]] || [[Image:stuBH3_C.jpg|thumb|MO C]] || [[Image:stuBH3_D.jpg|thumb|MO D]]
|-
| Relative Energy || -6.73049 || -0.51765 || -0.35681 || -0.35681
|}

{| class="wikitable" border="1"
! E !! F !! G !! H
|-
|| [[Image:stuBH3_E.jpg|thumb|MO E]] || [[Image:stuBH3_F.jpg|thumb|MO F]] || [[Image:stuBH3_G.jpg|thumb|MO G]] || [[Image:StuBH3_H.jpg|thumb|MO H]]
|-
| -0.07458 || 0.19192 || 0.18859 || 0.18860
|}

According to these energies there is only one difference between the calculated MO's and the real ones, and that is that the calculated F molecular orbital is higher then the calculated G & H molecular orbitals, whereas my diagram shows it the other way round.
This can be explained in two ways.
# That my MO diagram is wrong and the F orbital is actually higher then G & H.
# Or (more likely) that the calculations isn't very accurate at the current basis set and method. The F,G & H orbitals are very close in relative energy and so a more accurate basis set may reveal that the F orbital is actually lower then the G & H.

===Natural Bond Orbital (NBO)===

[[Image:stuBH3_NBO.jpg|thumb|center|NBO Analysis]]

This diagram shows the atomic charges of each of the nuclei. The log file from MO analysis shows alot more NBO analysis data.

===Vibrational Analysis===

{| class="wikitable" border="1"
|+ Vibrations of BH3
! Vibrations !! Relative Frequency !! Intensity !! Symmetry Group
|-
| [[Image:stuBH3_Vibration_1.jpg|thumb|Symmetric Bending of all Hydrogens]]|| 1145.74 || 92.71 || A2 ''
|-
| [[Image:stuBH3_Vibration_2.jpg|thumb|Asymmetric bending of 2 hydrogens]] || 1204.64 || 12.38 || E'
|-
| [[Image:stuBH3_Vibration_3.jpg|thumb|Symmetric bending of 2 hydrogens and asymmetric bend of 1]] || 1204.78 || 12.37 || E'
|-
| [[Image:stuBH3_Vibration_4.jpg|thumb|Symmetric stretching of all hydrogens]] || 2592.85 || 0.00 || A1 '
|-
| [[Image:stuBH3_Vibration_5.jpg|thumb|Asymmetric stretching of 2 hydrogens]] || 2731.32 || 103.85 || E'
|-
| [[Image:stuBH3_Vibration_6.jpg|thumb|Symmetric stretch of 2 hydrogens and antisymmetric stretch of 1]] || 2731.43 || 103.82 || E'
|}

According to the frequency analysis the vibrations of the centre of mass of the molecule were more than an order of magnitude lower then the lowest real mode of vibration which was at 1145.675. The frequency analysis is used to show how accurate the molecule optimisation is, and in this case it is very accurate.

[[Image:stuBH3_IR.jpg|IR Spectrum of BH3]]

This IR shows only 3 peaks, this is explained as one of the vibrations has an intensity of 0 and so wouldn't appear, also vibration 5 & 6; and vibration 2 & 3 are at similar energies and therefore would overlap together.

==Cis/Trans Isomers of Mo(CO)4(PPh3)2 Optimisation & Analysis==

In this section I will be computing the spectral characteristics of two isomers of a molecule, showing which isomer is more stable etc.

For this optimisation I will be using the same method but for the basis set the LanL2MB is first used to clean the molecule up as its a less accurate basis set. Then the LanL2DZ is used to optimise the molecule further after ensuring the right conformations of the phosphorus groups.

<jmol> <jmolApplet> <uploadedFileContents>StuCis_Optimal.mol</uploadedFileContents> <text>Optimised Cis Isomer</text> </jmolApplet> </jmol>
Optimised Cis Isomer of Mo(CO)4(PPh3)2<ref>{{DOI|10042/to-5481}}</ref>

{| class="wikitable" border="1"
|+ Cis Optimisation
|-
| File Name || Cis Optimal
|-
| File Type || .log
|-
| Calculation Type || FOPT
|-
| Calculation Method || RB3LYP
|-
| Basis Set || LanL2DZ
|-
| Charge || 0
|-
| Spin || Singlet
|-
| E(RB3LYP) || -623.57707177 a.u.
|-
| RMS Gradient Norm || 0.00004393 a.u.
|-
| Imaginary Freq ||
|-
| Dipole Moment || 1.3074 Debye
|-
| Point Group || C1
|-
| Cpu Time || 38 mins 28.6 seconds
|}

<jmol> <jmolApplet> <uploadedFileContents>StuTrans_Optimal.mol</uploadedFileContents> <text>Optimised Trans Isomer</text> </jmolApplet> </jmol>
Optimised Trans Isomer of Mo(CO)4(PPh3)2<ref>{{DOI|10042/to-5480}}</ref>

{| class="wikitable" border="1"
|+ Trans Optimisation
|-
| File Name || Trans Optimal
|-
| File Type || .log
|-
| Calculation Type || FOPT
|-
| Calculation Method || RB3LYP
|-
| Basis Set || LanL2DZ
|-
| Charge || 0
|-
| Spin || Singlet
|-
| E(RB3LYP) || -623.57592150 a.u.
|-
| RMS Gradient Norm || 0.00003324 a.u.
|-
| Imaginary Freq ||
|-
| Dipole Moment || 0.0111 Debye
|-
| Point Group || C1
|-
| Cpu Time || 1 hour 2 mins 19.4 seconds
|}

Both Optimisations show a gradient of near to zero and so both optimisations have proceeded to completetion.

The frequency analysis was also carried out on both the cis isomer<ref>{{DOI|10042/to-5484}}</ref> and the trans isomer<ref>{{DOI|10042/to-5485}}</ref>. The analysis of these vibrations is shown in the section below.

==Cis/Trans Isomers of Mo(CO)4(PPh3)2 Discussion==

{| class="wikitable" border="1"
|+ CO Vibrations
! Cis Isomer !! Trans Isomer
|-
| [[Image:stuCis_Vibration_1.jpg|thumb|Frequency 1945.41]]|| [[Image:stuTrans_Vibrations_1.jpg|thumb|Frequency 1950.22]]
|-
| [[Image:stuCis_Vibration_2.jpg|thumb|Frequncy 1948.90]]|| [[Image:stuTrans_Vibrations_2.jpg|thumb|Frequency 1950.96]]
|-
| [[Image:stuCis_Vibration_3.jpg|thumb|Frequency 1958.52]]
|-
| [[Image:stuCis_Vibration_4.jpg|thumb|Frequency 2023.51]]
|}

[[Image:stuCis_IR.jpg|thumb|Centre|Cis IR (CO Stretch Region]]

[[Image:stuTrans_IR.jpg|thumb|Centre|Trans IR (CO Stretch Region]]

As shown by the trans isomer vibration there are two degenerate CO stretches. Each is the anti of the other in terms of stretches and the marginal difference in frequency is due to calculatory error due to lesser basis sets. The cis isomer is a bit different and has 4 separate vibrations.

The free CO frequency for vibration is approximately 2150cm-1 but the exact frequency of vibration depends upon the back bonding from the metal and its ligands<ref>''Advanced Inorganic Chemistry'' F.A. Cotton & G. Wilkinson(5th Edn.) pp. 58 - 62 .</ref>. A larger amount of back bonding from the metal will result in a lower wavenumber stretching frequency. As the trans isomer is symmetrical the carbonyls all experience the same amount of back bonding giving rise to only one CO vibrational peak in the IR. However the cis isomer is no longer symmetrical and so each CO experiences a differing amount of back bonding. Another effect that may be affecting the CO ligand stretching in the cis complex is the "cis effect"<ref>L. Cattalini, A. Orio, M.L. Tobe, ''Inorg. Chem.'', '''1967''', 6 (1), pp 75–78, {{DOI| 10.1021/ic50047a016}}</ref>. The cis effect is similar to the trans effect in that the substituents surrounding ligands can have their bonds altered in some way by cis ligands, this may also help to explain why there are 4 CO vibrational frequencies.

Judging by the very small difference in energy between the two molecules (-623.57592150 for trans and -623.57707177 for cis) and that the vibrations are also very similar in energy I would say that neither molecule is particularly more stable. However if the Cl's were to be changed with more bulky groups the cis isomer would be at a higher energy due to steric clashes between the bulky groups. Unfortunatly I did not have time to investigate this effect further.

==Mini-Project - Heteroatom Silanes & Organic Silanes==

In this mini project I will be investigating how changing the middle atom in a silane chain affects the stability and other features. Then I will be investigating the siloxane further to try to explain why siloxanes have massive stability.
(In this experiment I will be replacing the hydrogens with chlorines in order to simplify the experiment as hydrogens can be hard to compute for)

The log files for each optimisation can be found here:
https://www.ch.imperial.ac.uk/wiki/images/7/71/StuSI-SI-SIINPUT.LOG
https://www.ch.imperial.ac.uk/wiki/images/7/71/StuSI-C-SIINPUT.LOG
https://www.ch.imperial.ac.uk/wiki/images/7/71/StuSI-N-SIINPUT.LOG
https://www.ch.imperial.ac.uk/wiki/images/7/71/StuSI-O-SIINPUT.LOG

{| class="wikitable" border="1"
|+ Silanes
! !! Si-Si-Si !! Si-C-Si !! Si-N-Si !! Si-O-Si
|-
| ||
<jmol><jmolApplet><title>Si-Si-Si</title><color>white</color> <size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script> <uploadedFileContents>stuSI-SI-SI.mol</uploadedFileContents> </jmolApplet></jmol>
||
<jmol><jmolApplet><title>Si-Si-Si</title><color>white</color> <size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script> <uploadedFileContents>stuSI-C-SI.mol</uploadedFileContents> </jmolApplet></jmol>
||
<jmol><jmolApplet><title>Si-Si-Si</title><color>white</color> <size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script> <uploadedFileContents>stuSI-N-SI.mol</uploadedFileContents> </jmolApplet></jmol>
||
<jmol><jmolApplet><title>Si-Si-Si</title><color>white</color> <size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script> <uploadedFileContents>stuSI-O-SI.mol</uploadedFileContents> </jmolApplet></jmol>
|-
| Basis Set || LanL2DZ || LanL2DZ || LanL2DZ || LanL2DZ
|-
| Charge || 0 || 0 || 0 || 0
|-
| Spin || Singlet || Singlet || Singlet || Singlet
|-
| E(RB3LYP)(a.u.) || -131.46846391 || -165.59412689 || -167.30141714 || -172.92180704
|-
| RMS Gradient Norm (a.u.) || 0.00001966 || 0.00001185 || 0.00001383 || 0.00008043
|-
| Dipole Moment (Debye) || 0.0736 || 0.4318 || 0.5021 || 0.0159
|-
| Point Group || C1 || C1 || C1 || CS
|}

The frequency calculations can be found here:
https://www.ch.imperial.ac.uk/wiki/images/f/f1/STUARTHAYLOCK_SISISI_FREQ.LOG
https://www.ch.imperial.ac.uk/wiki/images/f/f1/STUARTHAYLOCK_SICSI_FREQ.LOG
https://www.ch.imperial.ac.uk/wiki/images/f/f1/STUARTHAYLOCK_SINSI_FREQ.LOG
https://www.ch.imperial.ac.uk/wiki/images/f/f1/STUARTHAYLOCK_SIOSI_FREQ.LOG

===Siloxane===

The MO's, NBO, Vibrations and Frequency Analysis of siloxane should help to show why it is the most stable of all the silanes.

Firstly my optimised structure for Si-O-Si shows a linear bond length of 1.64Å which compared with the literature value of 1.61Å<ref>L. Pauling, ''American Mineralogist'', Volume 65, pages 321-323, '''1980'''</ref> shows a very close correlation to calculations. Also a bond length of 1.64Å is approximately 0.2Å away from the single bond length which is why the molecule is shown with double bonds.

However, this doesn't explain why the structure is linear instead of bent as a normal oxygen molecule is. For this we must look at the MO's<ref>{{DOI|10042/to-5497}}</ref>.

{| class="wikitable" border="1"
|+ 6 HOMO's and 3 LUMO's
|-
| [[Image:stuMO_1.jpg|thumb|HOMO-5]]|| [[Image:stuMO_2.jpg|thumb|HOMO-4]] || [[Image:stuMO_3.jpg|thumb|HOMO-3]]
|-
| [[Image:stuMO_4.jpg|thumb|HOMO-2]] || [[Image:stuMO_5.jpg|thumb|HOMO-1]] || [[Image:stuMO_6.jpg|thumb|HOMO]]
|-
| [[Image:stuMO_7.jpg|thumb|LUMO]]|| [[Image:stuMO_8.jpg|thumb|LUMO+1]] || [[Image:stuMO_9.jpg|thumb|LUMO+2]]
|}

These MO's show mostly that the linear bond of Si-O-Si is explained by secondary orbital overlap between the oxygen atom and the chlorine groups on the silicon.

[[Image:stuNBO.jpg|thumb|Center|NBO]]

The NBO only shows what we previously knew that most of the charge is localised on the oxygen and chlorine.

[[Image:stuSi-O_Vibration.gif|Si-O Vibration]]

The only vibration that affects the Si-O bond is this vibration at 1176.05cm-1 which supports the idea that the molecule is symmetrical and completely linear. The previous literature reference for siloxanes also showed that the 180o siloxanes are possible.

==References==
<references/>

File:StuSi-O Vibration.gif

2010-11-02T17:43:42Z

Sh1308:

Rep:Mod:SHMod2Inorg

2010-11-02T17:41:12Z

2010-11-02T17:29:46Z

Sh1308: /* Mini-Project - Heteroatom Silanes & Organic Silanes */

= Stuart Haylock - Computational Lab - Module 2 - Inorganic Computational Chemistry Experiments =

==Aim:==
The aim of this experiment is to give an insight into the structure and bonding of inorganic complexes. Inorganic complexes are much more complicated then organic ones, however computational experimentation can prove to be a very useful method of showing why certain complexes form over others and can help with designing catalysts.

==Borane BH3 Optimisation==
The optimisation of a molecule involves trying different geometries to find the lowest energy one. The process is made of two parts.
# The position of the nuclei is plugged into the Schrödinger equation and is solved for the electrons and energy. ('''SCF''')
# Then the nuclei are moved and the SCF cycle repeated at each geometry, eventually giving the positions with the lowest energy. ('''OPT''')
Each Optimisation then has a method and basis set where the method determines the type of approximations made in solving the Schrödinger equation and the basis set determines how accurately it is calculated (and therefore how long the calculation will take in computational time).

For BH3 the method will be B3LYP and basis set will be 3-21G, these are very low accuracy sets but will provide fast results, also with small molecules the accuracy isn't too much of an issue as there aren't as many factors to take into account.

<jmol> <jmolAppletButton> <uploadedFileContents>StuBH3_OPT.mol</uploadedFileContents> <text>Optimised BH3</text> </jmolAppletButton> </jmol>

The bond distance for the optimised BH3 is 1.194Å.
The H-B-H bond angle is 120o.

This agrees well with literature values for the bond length of 1.20Å<ref>R. Konechny, D.J. Doren, ''J. Phys. Chem. B'', '''1997''', 101 (51), pp 10983–10985, {{DOI|10.1021/jp9726246}} </ref>. Also as the boron is sp2 hybridised we expect the bond angles to be 120o. This shows that while the method and basis set are inaccurate they still provide correlated results and are a very good approximation.

{| class="wikitable" border="1"
|+ BH3 Optimisation
|-
| File Name || BH3 OPT
|-
| File Type || .log
|-
| Calculation Type || FOPT
|-
| Calculation Method || RB3LYP
|-
| Basis Set || 3-21G
|-
| Charge || 0
|-
| Spin || Singlet
|-
| E(RB3LYP) || -26.46226447 a.u.
|-
| RMS Gradient Norm || 0.00000434 a.u.
|-
| Imaginary Freq ||
|-
| Dipole Moment || 0 Debye
|-
| Point Group || D3H
|-
| Cpu Time || 30.0 seconds
|}

To make sure the that optimisation process has succeeded the RMS end gradient of the total energy against the calculation step must be very close to zero. According to the summary data (above) the gradient was very close to zero indicating that the optimisation worked successfully as the energy has levelled out to to 0.

You can also see that the molecule has D3H symmetry which I know is true from my own symmetry calculations, further showing the optimisation process has worked.

[[Image:stuBH3_Opt_Graph.jpg|Optimisation Graphs]]
[[Image:stuBH3_Opt_Graph_2.jpg|Optimisation Graphs]]

These two graphs further show how the optimisation has worked. The both graphs show a decline followed by a levelling showing that as each new step passes the gradient tends to 0. This means that with each new step the molecule is getting closer to the optimised energy and geometry.

The Optimised file can be found here:
https://www.ch.imperial.ac.uk/wiki/images/f/fe/StuBH3_OPT.LOG

==Thallium Bromide TlBr3 Optimisation==

In order to understand optimisation fully you must understand how larger basis sets work and what happens with different molecules.

For a molecule of TlBr3 the same method is used however a different basis set is used, the LanL2DZ option is slightly more accurate for heavier elements (such as thallium) but is approximate enough for the calculation to take a reasonable amount of time. This molecule must also have its symmetry to be confined as D3H trigonal planar as later analysis requires this symmetry in the optimisation process.

<jmol> <jmolAppletButton> <uploadedFileContents>StuTlBr3_OPT.mol</uploadedFileContents> <text>Optimised TlBr3</text> </jmolAppletButton> </jmol>

The optimised bond distance is 2.65Å, and the optimised bond angle is 120o.

The literature value for the Tl-Br bond length is 2.52<ref>J. Blixt, J. Glaser, J. Mink, I. Persson, P. Persson, M. Sandstrom, ''J. Am. Chem. SOC.'', '''1995''',117, 5089-5104 {{DOI|10.1021/ja00123a011}}</ref> which is close but not completely accurate to the optimisation, this shows that as heavier elements are introduced computation can become less accurate at lower basis sets and methods. Also the bond angle of 120o is in concordance with constraining the symmetry to trigonal planar D3H.

{| class="wikitable" border="1"
|+ BH3 Optimisation
|-
| File Name || TLBR3 OPT INPUT
|-
| File Type || .log
|-
| Calculation Type || FOPT
|-
| Calculation Method || RB3LYP
|-
| Basis Set || LANL2DZ
|-
| Charge || 0
|-
| Spin || Singlet
|-
| E(RB3LYP) || -91.21812851 a.u.
|-
| RMS Gradient Norm || 0.00000090 a.u.
|-
| Imaginary Freq ||
|-
| Dipole Moment || 0 Debye
|-
| Point Group || D3H
|-
| Cpu Time || 43.0 seconds
|}

The summary shows that the final gradient is very close to 0 showing the optimisation has been successful.

According to the frequency analysis the vibrations of the centre of mass of the molecule were an order of magnitude lower then the lowest real mode of vibration which was at 46.567. The frequency analysis is used to show how accurate the molecule optimisation is, and in this case it is relatively accurate.

[[Image:stuTlBr3_Bond.jpg|thumb|Center|Bonds Missing! ]]

Occasionally the bonds will be missing from a molecule, this is as Gaussview has a limited range of bond lengths in its system and once a bond length goes beyond a specific level the visable bond disappears.

The bond however is still there as a bond is nothing more than the forces of attraction that hold a molecule together, these may be ionic, covalent, metallic or even intermolecular. Just because it is not visible on the system doesn't mean the atoms aren't being held together.

The Optimisation file can be found here:
https://www.ch.imperial.ac.uk/wiki/images/3/30/StuTLBR3_OPT_INPUT.LOG

==Borane BH3 Analysis==

===Molecular Orbitals===

A molecular orbital analysis was then carried out on the BH3 molecule<ref>{{DOI|10042/to-5438}}</ref>.

[[Image:StuBH3_MO_Diagram.gif|BH3 Mo Diagram]]

{| class="wikitable" border="1"
|+ MO Visualisations
! !! A !! B !! C !! D
|-
| MO's || [[Image:stuBH3_A.jpg|thumb|MO A]]|| [[Image:stuBH3_B.jpg|thumb|MO B]] || [[Image:stuBH3_C.jpg|thumb|MO C]] || [[Image:stuBH3_D.jpg|thumb|MO D]]
|-
| Relative Energy || -6.73049 || -0.51765 || -0.35681 || -0.35681
|}

{| class="wikitable" border="1"
! E !! F !! G !! H
|-
|| [[Image:stuBH3_E.jpg|thumb|MO E]] || [[Image:stuBH3_F.jpg|thumb|MO F]] || [[Image:stuBH3_G.jpg|thumb|MO G]] || [[Image:StuBH3_H.jpg|thumb|MO H]]
|-
| -0.07458 || 0.19192 || 0.18859 || 0.18860
|}

According to these energies there is only one difference between the calculated MO's and the real ones, and that is that the calculated F molecular orbital is higher then the calculated G & H molecular orbitals, whereas my diagram shows it the other way round.
This can be explained in two ways.
# That my MO diagram is wrong and the F orbital is actually higher then G & H.
# Or (more likely) that the calculations isn't very accurate at the current basis set and method. The F,G & H orbitals are very close in relative energy and so a more accurate basis set may reveal that the F orbital is actually lower then the G & H.

===Natural Bond Orbital (NBO)===

[[Image:stuBH3_NBO.jpg|thumb|center|NBO Analysis]]

This diagram shows the atomic charges of each of the nuclei. The log file from MO analysis shows alot more NBO analysis data.

===Vibrational Analysis===

{| class="wikitable" border="1"
|+ Vibrations of BH3
! Vibrations !! Relative Frequency !! Intensity !! Symmetry Group
|-
| [[Image:stuBH3_Vibration_1.jpg|thumb|Symmetric Bending of all Hydrogens]]|| 1145.74 || 92.71 || A2 ''
|-
| [[Image:stuBH3_Vibration_2.jpg|thumb|Asymmetric bending of 2 hydrogens]] || 1204.64 || 12.38 || E'
|-
| [[Image:stuBH3_Vibration_3.jpg|thumb|Symmetric bending of 2 hydrogens and asymmetric bend of 1]] || 1204.78 || 12.37 || E'
|-
| [[Image:stuBH3_Vibration_4.jpg|thumb|Symmetric stretching of all hydrogens]] || 2592.85 || 0.00 || A1 '
|-
| [[Image:stuBH3_Vibration_5.jpg|thumb|Asymmetric stretching of 2 hydrogens]] || 2731.32 || 103.85 || E'
|-
| [[Image:stuBH3_Vibration_6.jpg|thumb|Symmetric stretch of 2 hydrogens and antisymmetric stretch of 1]] || 2731.43 || 103.82 || E'
|}

According to the frequency analysis the vibrations of the centre of mass of the molecule were more than an order of magnitude lower then the lowest real mode of vibration which was at 1145.675. The frequency analysis is used to show how accurate the molecule optimisation is, and in this case it is very accurate.

[[Image:stuBH3_IR.jpg|IR Spectrum of BH3]]

This IR shows only 3 peaks, this is explained as one of the vibrations has an intensity of 0 and so wouldn't appear, also vibration 5 & 6; and vibration 2 & 3 are at similar energies and therefore would overlap together.

==Cis/Trans Isomers of Mo(CO)4(PPh3)2 Optimisation & Analysis==

In this section I will be computing the spectral characteristics of two isomers of a molecule, showing which isomer is more stable etc.

For this optimisation I will be using the same method but for the basis set the LanL2MB is first used to clean the molecule up as its a less accurate basis set. Then the LanL2DZ is used to optimise the molecule further after ensuring the right conformations of the phosphorus groups.

<jmol> <jmolApplet> <uploadedFileContents>StuCis_Optimal.mol</uploadedFileContents> <text>Optimised Cis Isomer</text> </jmolApplet> </jmol>
Optimised Cis Isomer of Mo(CO)4(PPh3)2<ref>{{DOI|10042/to-5481}}</ref>

{| class="wikitable" border="1"
|+ Cis Optimisation
|-
| File Name || Cis Optimal
|-
| File Type || .log
|-
| Calculation Type || FOPT
|-
| Calculation Method || RB3LYP
|-
| Basis Set || LanL2DZ
|-
| Charge || 0
|-
| Spin || Singlet
|-
| E(RB3LYP) || -623.57707177 a.u.
|-
| RMS Gradient Norm || 0.00004393 a.u.
|-
| Imaginary Freq ||
|-
| Dipole Moment || 1.3074 Debye
|-
| Point Group || C1
|-
| Cpu Time || 38 mins 28.6 seconds
|}

<jmol> <jmolApplet> <uploadedFileContents>StuTrans_Optimal.mol</uploadedFileContents> <text>Optimised Trans Isomer</text> </jmolApplet> </jmol>
Optimised Trans Isomer of Mo(CO)4(PPh3)2<ref>{{DOI|10042/to-5480}}</ref>

{| class="wikitable" border="1"
|+ Trans Optimisation
|-
| File Name || Trans Optimal
|-
| File Type || .log
|-
| Calculation Type || FOPT
|-
| Calculation Method || RB3LYP
|-
| Basis Set || LanL2DZ
|-
| Charge || 0
|-
| Spin || Singlet
|-
| E(RB3LYP) || -623.57592150 a.u.
|-
| RMS Gradient Norm || 0.00003324 a.u.
|-
| Imaginary Freq ||
|-
| Dipole Moment || 0.0111 Debye
|-
| Point Group || C1
|-
| Cpu Time || 1 hour 2 mins 19.4 seconds
|}

Both Optimisations show a gradient of near to zero and so both optimisations have proceeded to completetion.

The frequency analysis was also carried out on both the cis isomer<ref>{{DOI|10042/to-5484}}</ref> and the trans isomer<ref>{{DOI|10042/to-5485}}</ref>. The analysis of these vibrations is shown in the section below.

==Cis/Trans Isomers of Mo(CO)4(PPh3)2 Discussion==

{| class="wikitable" border="1"
|+ CO Vibrations
! Cis Isomer !! Trans Isomer
|-
| [[Image:stuCis_Vibration_1.jpg|thumb|Frequency 1945.41]]|| [[Image:stuTrans_Vibrations_1.jpg|thumb|Frequency 1950.22]]
|-
| [[Image:stuCis_Vibration_2.jpg|thumb|Frequncy 1948.90]]|| [[Image:stuTrans_Vibrations_2.jpg|thumb|Frequency 1950.96]]
|-
| [[Image:stuCis_Vibration_3.jpg|thumb|Frequency 1958.52]]
|-
| [[Image:stuCis_Vibration_4.jpg|thumb|Frequency 2023.51]]
|}

[[Image:stuCis_IR.jpg|thumb|Centre|Cis IR (CO Stretch Region]]

[[Image:stuTrans_IR.jpg|thumb|Centre|Trans IR (CO Stretch Region]]

As shown by the trans isomer vibration there are two degenerate CO stretches. Each is the anti of the other in terms of stretches and the marginal difference in frequency is due to calculatory error due to lesser basis sets. The cis isomer is a bit different and has 4 separate vibrations.

The free CO frequency for vibration is approximately 2150cm-1 but the exact frequency of vibration depends upon the back bonding from the metal and its ligands<ref>''Advanced Inorganic Chemistry'' F.A. Cotton & G. Wilkinson(5th Edn.) pp. 58 - 62 .</ref>. A larger amount of back bonding from the metal will result in a lower wavenumber stretching frequency. As the trans isomer is symmetrical the carbonyls all experience the same amount of back bonding giving rise to only one CO vibrational peak in the IR. However the cis isomer is no longer symmetrical and so each CO experiences a differing amount of back bonding. Another effect that may be affecting the CO ligand stretching in the cis complex is the "cis effect"<ref>L. Cattalini, A. Orio, M.L. Tobe, ''Inorg. Chem.'', '''1967''', 6 (1), pp 75–78, {{DOI| 10.1021/ic50047a016}}</ref>. The cis effect is similar to the trans effect in that the substituents surrounding ligands can have their bonds altered in some way by cis ligands, this may also help to explain why there are 4 CO vibrational frequencies.

Judging by the very small difference in energy between the two molecules (-623.57592150 for trans and -623.57707177 for cis) and that the vibrations are also very similar in energy I would say that neither molecule is particularly more stable. However if the Cl's were to be changed with more bulky groups the cis isomer would be at a higher energy due to steric clashes between the bulky groups. Unfortunatly I did not have time to investigate this effect further.

==Mini-Project - Heteroatom Silanes & Organic Silanes==

In this mini project I will be investigating how changing the middle atom in a silane chain affects the stability and other features. Then I will be investigating the siloxane further to try to explain why siloxanes have massive stability.
(In this experiment I will be replacing the hydrogens with chlorines in order to simplify the experiment as hydrogens can be hard to compute for)

The log files for each optimisation can be found here:
https://www.ch.imperial.ac.uk/wiki/images/7/71/StuSI-SI-SIINPUT.LOG
https://www.ch.imperial.ac.uk/wiki/images/7/71/StuSI-C-SIINPUT.LOG
https://www.ch.imperial.ac.uk/wiki/images/7/71/StuSI-N-SIINPUT.LOG
https://www.ch.imperial.ac.uk/wiki/images/7/71/StuSI-O-SIINPUT.LOG

{| class="wikitable" border="1"
|+ Silanes
! !! Si-Si-Si !! Si-C-Si !! Si-N-Si !! Si-O-Si
|-
| ||
<jmol><jmolApplet><title>Si-Si-Si</title><color>white</color> <size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script> <uploadedFileContents>stuSI-SI-SI.mol</uploadedFileContents> </jmolApplet></jmol>
||
<jmol><jmolApplet><title>Si-Si-Si</title><color>white</color> <size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script> <uploadedFileContents>stuSI-C-SI.mol</uploadedFileContents> </jmolApplet></jmol>
||
<jmol><jmolApplet><title>Si-Si-Si</title><color>white</color> <size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script> <uploadedFileContents>stuSI-N-SI.mol</uploadedFileContents> </jmolApplet></jmol>
||
<jmol><jmolApplet><title>Si-Si-Si</title><color>white</color> <size>150</size><script>zoom 5;moveto 4 0 2 0 90 120;spin 2;</script> <uploadedFileContents>stuSI-O-SI.mol</uploadedFileContents> </jmolApplet></jmol>
|-
| Basis Set || LanL2DZ || LanL2DZ || LanL2DZ || LanL2DZ
|-
| Charge || 0 || 0 || 0 || 0
|-
| Spin || Singlet || Singlet || Singlet || Singlet
|-
| E(RB3LYP)(a.u.) || -131.46846391 || -165.59412689 || -167.30141714 || -172.92180704
|-
| RMS Gradient Norm (a.u.) || 0.00001966 || 0.00001185 || 0.00001383 || 0.00008043
|-
| Dipole Moment (Debye) || 0.0736 || 0.4318 || 0.5021 || 0.0159
|-
| Point Group || C1 || C1 || C1 || CS
|}

===Siloxane===

The MO's, NBO, Vibrations and Frequency Analysis of siloxane should help to show why it is the most stable of all the silanes.

Firstly my optimised structure for Si-O-Si shows a linear bond length of 1.64Å which compared with the literature value of 1.61Å<ref>L. Pauling, ''American Mineralogist'', Volume 65, pages 321-323, '''1980'''</ref> shows a very close correlation to calculations. Also a bond length of 1.64Å is approximately 0.2Å away from the single bond length which is why the molecule is shown with double bonds.

However, this doesn't explain why the structure is linear instead of bent as a normal oxygen molecule is. For this we must look at the MO's<ref>{{DOI|10042/to-5497}}</ref>.

{| class="wikitable" border="1"
|+ 6 HOMO's and 3 LUMO's
|-
| [[Image:stuMO_1.jpg|thumb|HOMO-5]]|| [[Image:stuMO_2.jpg|thumb|HOMO-4]] || [[Image:stuMO_3.jpg|thumb|HOMO-3]]
|-
| [[Image:stuMO_4.jpg|thumb|HOMO-2]] || [[Image:stuMO_5.jpg|thumb|HOMO-1]] || [[Image:stuMO_6.jpg|thumb|HOMO]]
|-
| [[Image:stuMO_7.jpg|thumb|LUMO]]|| [[Image:stuMO_8.jpg|thumb|LUMO+1]] || [[Image:stuMO_9.jpg|thumb|LUMO+2]]
|}

These MO's show mostly that the linear bond of Si-O-Si is explained by secondary orbital overlap between the oxygen atom and the chlorine groups on the silicon.

[[Image:stuNBO.jpg|thumb|Center|NBO]]

The NBO only shows what we previously knew that most of the charge is localised on the oxygen and chlorine.

==References==
<references/>

Rep:Mod:SHMod2Inorg

2010-11-02T17:28:36Z

File:StuNBO.jpg

2010-11-02T17:16:27Z

Sh1308:

Rep:Mod:SHMod2Inorg

2010-11-02T16:53:23Z

2010-11-02T16:49:36Z

Sh1308:

File:StuMO 3.jpg

2010-11-02T16:49:25Z

Sh1308: