File:C2h6 mo list ppx2.jpg

2010-11-02T06:00:31Z

Ppx07:

File:Bh3nh3 mo list ppx2.jpg

2010-11-02T06:00:02Z

Ppx07:

Rep:Mod:thugaim

2010-11-02T05:57:58Z

Ppx07: /* Structure */

=Module 2=
 
==Part 1==
 
===BH3===
 
A molecule of BH3 was constructed in Gaussview 3.0 and optimized using DFT B3LYP with the following results:
<jmol> <jmolAppletButton> <uploadedFileContents>Bh3_opt_ppx2.mol</uploadedFileContents> <text>Load</text> </jmolAppletButton> </jmol>

B-H bond length = 1.19435Å

H-B-H bond angle = 120o

[[Image:Bh3_opt_summary_ppx2.jpg| ]]

===TlBr3===
 
TlBr3 was confined to point group D3h and then optimised using pseudo potential LanL2DZ. <jmol> <jmolAppletButton> <uploadedFileContents>TLBR3_OPT_ppx2.mol</uploadedFileContents> <text>Load</text> </jmolAppletButton> </jmol>
http://hdl.handle.net/10042/to-5432

Tl-Br bond distance = 2.65095Å

Br-Tl-Br bond angle = 120o

Summary:

[[Image:Tibr3_opt_summary_ppx2.jpg|| ]]

The lit. value for Tl-Br bond distance in TlBr3 is 2.521Å<ref>J. Glaser et al. ''On the structures of hydrated Thallium(III)ion and its bromide complexes in aqueous solution'' '''1982'''</ref> this value does not fall within the error of 0.01Å of the programme used for the calculation. This maybe caused by the need to use pseudo-potentials for such calculation as Tl has 81 electrons and Br has 35, needless to say, the method which we used (LanL2DZ) only has a 'medium' level of accuracy as better basis sets and pseudo potentials would require much longer calculations.

In some structures gaussview does not draw in the bonds where we expect, however this only means that gaussview does not recognise the distance between the bonding atoms when compared to its database of bond distances. A bond is simply the attraction caused by the electromagnetic force between opposing charges that allows the formation of chemical compounds.
 

===BH3===
 
Molecular orbitals of BH3 were calculated from the optimised structure. Digital Repository link http://hdl.handle.net/10042/to-5356

The NBO charges for boron was -0.053 and 0.018 for hydrogen.

[[Image:Bh3_ir_ppx2.jpg|frame|left|IR of BH3 ]]

{| class="wikitable" border="1"
|+ '''IR Summary'''
! Form Of Vibration !! Freqency !! Intensity !! Symmetry D3h Point Group
|-
| Wagging of all 3 H atoms || 1145.71 || 92.70 || A"2
|-
| Scissor or H atoms 2 and 3 || 1204.66 || 12.38||E'
|-
|Rocking of all 3 H atoms ||1204.66||12.38||E'
|-
|Symmetric stretch of all 3 H atoms || 2592.79||0||A'1
|-
|Asymmetric stretch of H atoms 2 and 3 || 2731.31 ||103.84||E'
|-
|Symmetric stretch of H atoms 2 and 3,
asymmetric stretch of H atom 1
|| 2731.31 || 103.83||E'
|}

There are not 6 peaks on the spectrum because the symmetric stretch of the 3 H atoms has an intensity of 0, this is because the symmetric stretch vibration does not change the overall dipole moment.

[[Image:Bh3_mo_comparison_ppx2.jpg |frame|left]]
 

From the comparison of LCAO and Real MOs, we can see the major difference between the 2 is that the LCAO approach has a heavier focus on atomic orbitals (hence the name) while the real MOs shows electron density in a molecular fashion, having said that the qualitative approach of LCAO has accurately predicted key features such as nodal planes in all real MOs. This proves the vital importance of qualitative MO theory as quick and accurate assumptions can be made without relying on computer software.

===Cis and Trans Isomers===

Both trans and cis-[MoCo4(PCl3)2)] were created by fragments using gaussview 3.0. Following the procedures outlined in the script, both molecules first went under optimisation by B3LYP with pseudo-potential LanL2MB (loose convergence).

<s>'''Cis isomer after initial optimisation: 30032

Trans isomer after initial optimisation: 30033'''</s>

To avoid optimisting to the wrong minima of energy, the molecules were modified thus the cis isomer has Cl from one PCl3 group pointing up parrallel to the axial bond and Cl from the other PCl3 group pointing down; while the trans conformer had both PCl3 groups eclipsed and that one Cl of each group was parallel to one Mo-C bond. Both conformers were subjected to optimisation using a much better basis set and pseudo-potential LanL2DZ, with increased electronic convergence.

<s>'''Cis isomer after final optimisation: 30034 <jmol> <jmolAppletButton> <uploadedFileContents>Moco4_cis_opted_ppx2.mol</uploadedFileContents> <text>Load</text> </jmolAppletButton> </jmol>

Trans isomer after initial optimisation: 30035'''</s> <jmol> <jmolAppletButton> <uploadedFileContents>Moco4_trans_opted_ppx2.mol</uploadedFileContents> <text>Load</text> </jmolAppletButton> </jmol>

In the optimised structures, the following Mo-C bond distances were obtained:

{| class="wikitable" border="1"
|+ '''C=O bond distance'''
! Type !! Bond Distance in Å (Cis) !! Bond Distance in Å (Trans)
|-
| Axial||2.05782||-
|-
| Equatorial||2.01156||2.06044
|}

Frequency analysis was only calculated using the optimised structures of the cis and trans conformers. However due to complications, calculations did not yield valid results, therefore a separate combined opt+freq calculation was used on the initially optimised conformers, whilst retaining the better basis set and pseudo potential and increased electronic convergence keywords. This is done so that the opt+freq analysis would be identical to the result of the freq-only analysis had the calculation gone ahead successfully.

<s>'''
Cis isomer after opt+freq: 30135

Trans isomer after opt+freq: 30136'''</s>

[[Image:Moco4_cis_ir_ppx2.jpg|Frequency Analysis of Cis conformer|left|frame]]
[[Image:Moco4_trans_ir_ppx2.jpg|Frequency Analysis of Trans conformer|left|frame]]

{| class="wikitable" border="1"
|+ '''Cis C=O Stretch'''
! Type !!Freqency!! Intensity
|-
| Equatorial Asymmetric|| 1945.34|| 764.095
|-
| Axial Asymmetric||1948.61|| 1487.15
|-
| Equatorial-Axial Asymmetric||1958.37||632.266
|-
|Equatorial-Axial Symmetric ||2023.27||598.17
|}

{| class="wikitable" border="1"
|+ '''Trans C=O Stretch'''
! Type!! Frequency!! Intensity
|-
| 1,3 Equatorial Asymmetric || 1950.11||1474.94
|-
| 2,4 Equatorial Asymmetric|| 1950.71||1466.8
|-
|1,2,3,4 Equatorial Asymmetric|| 1977.02||0.7215
|-
|1,2,3,4 Equatorial Symmetric|| 2030.8||3.9078
|}

30032, 30033, 30034, 30035, 30038, 30039, 30135, 30136. email to m.j.harvey@ic.ac.uk

==Part 2 Miniproject:==
 
===Introduction===
This miniproject will compare the difference in structural and electronic properties between ammonia borane and ethane. My interest in this field arose from my assigned research project 'Boron-nitrogen dehydrocoupling: a route to hydrogen storage materials'. A quick search on boron based hydrogen storage yielded a simple molecule, BH3NH3<ref>Karkamkar, A.; Aardahl, C.; Autrey, T. ''Material Matters'', '''2007''', 2.2, 62</ref> to be an efficient storage medium as it can bind significant amounts of hydrogen and release under mind conditions. Ammonia borane specifically releases 13% of hydrogen in 2 steps at 100oC according to the following scheme.<ref>http://www.sigmaaldrich.com/materials-science/alternative-energy-materials/boron-hydrogen-storage.html</ref> The interesting thing to note here is that, even though ammonia borane is isoelectric to ethene, and adopts a similar structure, their boiling points differ by 284oC! Perhaps by investigating their molecular orbitals and electron density, we can somehow rationalise this fact.

[[Image:Bh3nh3_release_scheme.jpg|left|frame]]
 

===Structure===
 
Structures of ammonia borane and ethane were minimised using B3YLP and 6-31G d,p on gaussian.

Ammonia Borane: 30486

[[Image:Bh3nh3_summary_ppx2.jpg|left|frame]]

{| class="wikitable" border="1"
|+''' Bond Lengths'''
! Bond!! Length (Å)!!Lit. (Å)<ref>J. Yang et al. ''APPLIED PHYSICS LETTERS 92'', 091916 '''2008'''</ref>
|-
| N-H || 1.02213||1.011
|-
| B-H || 1.21288||1.208
|-
|N-B||1.68447 || -
|}

{| class="wikitable" border="1"
|+ '''Bond Angles'''
!Bond!! Angle (o)!! Lit.(o)
|-
| H1-B-H2 || 113.11286||114.4
|-
| H4-N-H5 || 110.20458||105.8
|}

Ethane: 30487

[[Image:C2h6_summary_ppx2.jpg |left|frame]]

{| class="wikitable" border="1"
|+''' Bond Lengths'''
! Bond!! Length (Å)!!Lit. (Å)
|-
|C-H||1.07000||1.12
|-
|C-C || 1.54000||1.54
|}

{| class="wikitable" border="1"
|+ '''Bond Angles'''
!Bond!! Angle (o)!! Lit.(o)
|-
| H1-C-H2 || 109.47118||109
|}

=References=
 
<references />

Rep:Mod:thugaim

2010-11-02T05:57:37Z

Ppx07: /* Structure */

=Module 2=
 
==Part 1==
 
===BH3===
 
A molecule of BH3 was constructed in Gaussview 3.0 and optimized using DFT B3LYP with the following results:
<jmol> <jmolAppletButton> <uploadedFileContents>Bh3_opt_ppx2.mol</uploadedFileContents> <text>Load</text> </jmolAppletButton> </jmol>

B-H bond length = 1.19435Å

H-B-H bond angle = 120o

[[Image:Bh3_opt_summary_ppx2.jpg| ]]

===TlBr3===
 
TlBr3 was confined to point group D3h and then optimised using pseudo potential LanL2DZ. <jmol> <jmolAppletButton> <uploadedFileContents>TLBR3_OPT_ppx2.mol</uploadedFileContents> <text>Load</text> </jmolAppletButton> </jmol>
http://hdl.handle.net/10042/to-5432

Tl-Br bond distance = 2.65095Å

Br-Tl-Br bond angle = 120o

Summary:

[[Image:Tibr3_opt_summary_ppx2.jpg|| ]]

The lit. value for Tl-Br bond distance in TlBr3 is 2.521Å<ref>J. Glaser et al. ''On the structures of hydrated Thallium(III)ion and its bromide complexes in aqueous solution'' '''1982'''</ref> this value does not fall within the error of 0.01Å of the programme used for the calculation. This maybe caused by the need to use pseudo-potentials for such calculation as Tl has 81 electrons and Br has 35, needless to say, the method which we used (LanL2DZ) only has a 'medium' level of accuracy as better basis sets and pseudo potentials would require much longer calculations.

In some structures gaussview does not draw in the bonds where we expect, however this only means that gaussview does not recognise the distance between the bonding atoms when compared to its database of bond distances. A bond is simply the attraction caused by the electromagnetic force between opposing charges that allows the formation of chemical compounds.
 

===BH3===
 
Molecular orbitals of BH3 were calculated from the optimised structure. Digital Repository link http://hdl.handle.net/10042/to-5356

The NBO charges for boron was -0.053 and 0.018 for hydrogen.

[[Image:Bh3_ir_ppx2.jpg|frame|left|IR of BH3 ]]

{| class="wikitable" border="1"
|+ '''IR Summary'''
! Form Of Vibration !! Freqency !! Intensity !! Symmetry D3h Point Group
|-
| Wagging of all 3 H atoms || 1145.71 || 92.70 || A"2
|-
| Scissor or H atoms 2 and 3 || 1204.66 || 12.38||E'
|-
|Rocking of all 3 H atoms ||1204.66||12.38||E'
|-
|Symmetric stretch of all 3 H atoms || 2592.79||0||A'1
|-
|Asymmetric stretch of H atoms 2 and 3 || 2731.31 ||103.84||E'
|-
|Symmetric stretch of H atoms 2 and 3,
asymmetric stretch of H atom 1
|| 2731.31 || 103.83||E'
|}

There are not 6 peaks on the spectrum because the symmetric stretch of the 3 H atoms has an intensity of 0, this is because the symmetric stretch vibration does not change the overall dipole moment.

[[Image:Bh3_mo_comparison_ppx2.jpg |frame|left]]
 

From the comparison of LCAO and Real MOs, we can see the major difference between the 2 is that the LCAO approach has a heavier focus on atomic orbitals (hence the name) while the real MOs shows electron density in a molecular fashion, having said that the qualitative approach of LCAO has accurately predicted key features such as nodal planes in all real MOs. This proves the vital importance of qualitative MO theory as quick and accurate assumptions can be made without relying on computer software.

===Cis and Trans Isomers===

Both trans and cis-[MoCo4(PCl3)2)] were created by fragments using gaussview 3.0. Following the procedures outlined in the script, both molecules first went under optimisation by B3LYP with pseudo-potential LanL2MB (loose convergence).

<s>'''Cis isomer after initial optimisation: 30032

Trans isomer after initial optimisation: 30033'''</s>

To avoid optimisting to the wrong minima of energy, the molecules were modified thus the cis isomer has Cl from one PCl3 group pointing up parrallel to the axial bond and Cl from the other PCl3 group pointing down; while the trans conformer had both PCl3 groups eclipsed and that one Cl of each group was parallel to one Mo-C bond. Both conformers were subjected to optimisation using a much better basis set and pseudo-potential LanL2DZ, with increased electronic convergence.

<s>'''Cis isomer after final optimisation: 30034 <jmol> <jmolAppletButton> <uploadedFileContents>Moco4_cis_opted_ppx2.mol</uploadedFileContents> <text>Load</text> </jmolAppletButton> </jmol>

Trans isomer after initial optimisation: 30035'''</s> <jmol> <jmolAppletButton> <uploadedFileContents>Moco4_trans_opted_ppx2.mol</uploadedFileContents> <text>Load</text> </jmolAppletButton> </jmol>

In the optimised structures, the following Mo-C bond distances were obtained:

{| class="wikitable" border="1"
|+ '''C=O bond distance'''
! Type !! Bond Distance in Å (Cis) !! Bond Distance in Å (Trans)
|-
| Axial||2.05782||-
|-
| Equatorial||2.01156||2.06044
|}

Frequency analysis was only calculated using the optimised structures of the cis and trans conformers. However due to complications, calculations did not yield valid results, therefore a separate combined opt+freq calculation was used on the initially optimised conformers, whilst retaining the better basis set and pseudo potential and increased electronic convergence keywords. This is done so that the opt+freq analysis would be identical to the result of the freq-only analysis had the calculation gone ahead successfully.

<s>'''
Cis isomer after opt+freq: 30135

Trans isomer after opt+freq: 30136'''</s>

[[Image:Moco4_cis_ir_ppx2.jpg|Frequency Analysis of Cis conformer|left|frame]]
[[Image:Moco4_trans_ir_ppx2.jpg|Frequency Analysis of Trans conformer|left|frame]]

{| class="wikitable" border="1"
|+ '''Cis C=O Stretch'''
! Type !!Freqency!! Intensity
|-
| Equatorial Asymmetric|| 1945.34|| 764.095
|-
| Axial Asymmetric||1948.61|| 1487.15
|-
| Equatorial-Axial Asymmetric||1958.37||632.266
|-
|Equatorial-Axial Symmetric ||2023.27||598.17
|}

{| class="wikitable" border="1"
|+ '''Trans C=O Stretch'''
! Type!! Frequency!! Intensity
|-
| 1,3 Equatorial Asymmetric || 1950.11||1474.94
|-
| 2,4 Equatorial Asymmetric|| 1950.71||1466.8
|-
|1,2,3,4 Equatorial Asymmetric|| 1977.02||0.7215
|-
|1,2,3,4 Equatorial Symmetric|| 2030.8||3.9078
|}

30032, 30033, 30034, 30035, 30038, 30039, 30135, 30136. email to m.j.harvey@ic.ac.uk

==Part 2 Miniproject:==
 
===Introduction===
This miniproject will compare the difference in structural and electronic properties between ammonia borane and ethane. My interest in this field arose from my assigned research project 'Boron-nitrogen dehydrocoupling: a route to hydrogen storage materials'. A quick search on boron based hydrogen storage yielded a simple molecule, BH3NH3<ref>Karkamkar, A.; Aardahl, C.; Autrey, T. ''Material Matters'', '''2007''', 2.2, 62</ref> to be an efficient storage medium as it can bind significant amounts of hydrogen and release under mind conditions. Ammonia borane specifically releases 13% of hydrogen in 2 steps at 100oC according to the following scheme.<ref>http://www.sigmaaldrich.com/materials-science/alternative-energy-materials/boron-hydrogen-storage.html</ref> The interesting thing to note here is that, even though ammonia borane is isoelectric to ethene, and adopts a similar structure, their boiling points differ by 284oC! Perhaps by investigating their molecular orbitals and electron density, we can somehow rationalise this fact.

[[Image:Bh3nh3_release_scheme.jpg|left|frame]]
 

===Structure===
 
Structures of ammonia borane and ethane were minimised using B3YLP and 6-31G d,p on gaussian.

Ammonia Borane: 30486

[[Image:Bh3nh3_summary_ppx2.jpg|left|frame]]

{| class="wikitable" border="1"
|+''' Bond Lengths'''
! Bond!! Length (Å)!!Lit. (Å)<ref>J. Yang et al. ''APPLIED PHYSICS LETTERS 92'', 091916 '''2008'''</ref>
|-
| N-H || 1.02213||1.011
|-
| B-H || 1.21288||1.208
|-
|N-B||1.68447 || -
|}

{| class="wikitable" border="1"
|+ '''Bond Angles'''
!Bond!! Angle (o)!! Lit.(o)
|-
| H1-B-H2 || 113.11286||114.4
|-
| H4-N-H5 || 110.20458||105.8
|}

Ethane: 30487

[[Image:C2h6_summary_ppx2.jpg |left|frame]]

{| class="wikitable" border="1"
|+''' Bond Lengths'''
! Bond!! Length (Å)!!Lit. (Å)
|-
|C-H||1.07000||1.12
|-
|C-C || 1.54000||1.54
|}

{| class="wikitable" border="1"
|+ '''Bond Angles'''
!Bond!! Angle (o)!! Lit.(o)
|-
| H1-C-H2 || 109.47118||109
|}

=References=
 
<references />

Rep:Mod:thugaim

2010-11-02T05:52:33Z

Ppx07: /* Structure */

=Module 2=
 
==Part 1==
 
===BH3===
 
A molecule of BH3 was constructed in Gaussview 3.0 and optimized using DFT B3LYP with the following results:
<jmol> <jmolAppletButton> <uploadedFileContents>Bh3_opt_ppx2.mol</uploadedFileContents> <text>Load</text> </jmolAppletButton> </jmol>

B-H bond length = 1.19435Å

H-B-H bond angle = 120o

[[Image:Bh3_opt_summary_ppx2.jpg| ]]

===TlBr3===
 
TlBr3 was confined to point group D3h and then optimised using pseudo potential LanL2DZ. <jmol> <jmolAppletButton> <uploadedFileContents>TLBR3_OPT_ppx2.mol</uploadedFileContents> <text>Load</text> </jmolAppletButton> </jmol>
http://hdl.handle.net/10042/to-5432

Tl-Br bond distance = 2.65095Å

Br-Tl-Br bond angle = 120o

Summary:

[[Image:Tibr3_opt_summary_ppx2.jpg|| ]]

The lit. value for Tl-Br bond distance in TlBr3 is 2.521Å<ref>J. Glaser et al. ''On the structures of hydrated Thallium(III)ion and its bromide complexes in aqueous solution'' '''1982'''</ref> this value does not fall within the error of 0.01Å of the programme used for the calculation. This maybe caused by the need to use pseudo-potentials for such calculation as Tl has 81 electrons and Br has 35, needless to say, the method which we used (LanL2DZ) only has a 'medium' level of accuracy as better basis sets and pseudo potentials would require much longer calculations.

In some structures gaussview does not draw in the bonds where we expect, however this only means that gaussview does not recognise the distance between the bonding atoms when compared to its database of bond distances. A bond is simply the attraction caused by the electromagnetic force between opposing charges that allows the formation of chemical compounds.
 

===BH3===
 
Molecular orbitals of BH3 were calculated from the optimised structure. Digital Repository link http://hdl.handle.net/10042/to-5356

The NBO charges for boron was -0.053 and 0.018 for hydrogen.

[[Image:Bh3_ir_ppx2.jpg|frame|left|IR of BH3 ]]

{| class="wikitable" border="1"
|+ '''IR Summary'''
! Form Of Vibration !! Freqency !! Intensity !! Symmetry D3h Point Group
|-
| Wagging of all 3 H atoms || 1145.71 || 92.70 || A"2
|-
| Scissor or H atoms 2 and 3 || 1204.66 || 12.38||E'
|-
|Rocking of all 3 H atoms ||1204.66||12.38||E'
|-
|Symmetric stretch of all 3 H atoms || 2592.79||0||A'1
|-
|Asymmetric stretch of H atoms 2 and 3 || 2731.31 ||103.84||E'
|-
|Symmetric stretch of H atoms 2 and 3,
asymmetric stretch of H atom 1
|| 2731.31 || 103.83||E'
|}

There are not 6 peaks on the spectrum because the symmetric stretch of the 3 H atoms has an intensity of 0, this is because the symmetric stretch vibration does not change the overall dipole moment.

[[Image:Bh3_mo_comparison_ppx2.jpg |frame|left]]
 

From the comparison of LCAO and Real MOs, we can see the major difference between the 2 is that the LCAO approach has a heavier focus on atomic orbitals (hence the name) while the real MOs shows electron density in a molecular fashion, having said that the qualitative approach of LCAO has accurately predicted key features such as nodal planes in all real MOs. This proves the vital importance of qualitative MO theory as quick and accurate assumptions can be made without relying on computer software.

===Cis and Trans Isomers===

Both trans and cis-[MoCo4(PCl3)2)] were created by fragments using gaussview 3.0. Following the procedures outlined in the script, both molecules first went under optimisation by B3LYP with pseudo-potential LanL2MB (loose convergence).

<s>'''Cis isomer after initial optimisation: 30032

Trans isomer after initial optimisation: 30033'''</s>

To avoid optimisting to the wrong minima of energy, the molecules were modified thus the cis isomer has Cl from one PCl3 group pointing up parrallel to the axial bond and Cl from the other PCl3 group pointing down; while the trans conformer had both PCl3 groups eclipsed and that one Cl of each group was parallel to one Mo-C bond. Both conformers were subjected to optimisation using a much better basis set and pseudo-potential LanL2DZ, with increased electronic convergence.

<s>'''Cis isomer after final optimisation: 30034 <jmol> <jmolAppletButton> <uploadedFileContents>Moco4_cis_opted_ppx2.mol</uploadedFileContents> <text>Load</text> </jmolAppletButton> </jmol>

Trans isomer after initial optimisation: 30035'''</s> <jmol> <jmolAppletButton> <uploadedFileContents>Moco4_trans_opted_ppx2.mol</uploadedFileContents> <text>Load</text> </jmolAppletButton> </jmol>

In the optimised structures, the following Mo-C bond distances were obtained:

{| class="wikitable" border="1"
|+ '''C=O bond distance'''
! Type !! Bond Distance in Å (Cis) !! Bond Distance in Å (Trans)
|-
| Axial||2.05782||-
|-
| Equatorial||2.01156||2.06044
|}

Frequency analysis was only calculated using the optimised structures of the cis and trans conformers. However due to complications, calculations did not yield valid results, therefore a separate combined opt+freq calculation was used on the initially optimised conformers, whilst retaining the better basis set and pseudo potential and increased electronic convergence keywords. This is done so that the opt+freq analysis would be identical to the result of the freq-only analysis had the calculation gone ahead successfully.

<s>'''
Cis isomer after opt+freq: 30135

Trans isomer after opt+freq: 30136'''</s>

[[Image:Moco4_cis_ir_ppx2.jpg|Frequency Analysis of Cis conformer|left|frame]]
[[Image:Moco4_trans_ir_ppx2.jpg|Frequency Analysis of Trans conformer|left|frame]]

{| class="wikitable" border="1"
|+ '''Cis C=O Stretch'''
! Type !!Freqency!! Intensity
|-
| Equatorial Asymmetric|| 1945.34|| 764.095
|-
| Axial Asymmetric||1948.61|| 1487.15
|-
| Equatorial-Axial Asymmetric||1958.37||632.266
|-
|Equatorial-Axial Symmetric ||2023.27||598.17
|}

{| class="wikitable" border="1"
|+ '''Trans C=O Stretch'''
! Type!! Frequency!! Intensity
|-
| 1,3 Equatorial Asymmetric || 1950.11||1474.94
|-
| 2,4 Equatorial Asymmetric|| 1950.71||1466.8
|-
|1,2,3,4 Equatorial Asymmetric|| 1977.02||0.7215
|-
|1,2,3,4 Equatorial Symmetric|| 2030.8||3.9078
|}

30032, 30033, 30034, 30035, 30038, 30039, 30135, 30136. email to m.j.harvey@ic.ac.uk

==Part 2 Miniproject:==
 
===Introduction===
This miniproject will compare the difference in structural and electronic properties between ammonia borane and ethane. My interest in this field arose from my assigned research project 'Boron-nitrogen dehydrocoupling: a route to hydrogen storage materials'. A quick search on boron based hydrogen storage yielded a simple molecule, BH3NH3<ref>Karkamkar, A.; Aardahl, C.; Autrey, T. ''Material Matters'', '''2007''', 2.2, 62</ref> to be an efficient storage medium as it can bind significant amounts of hydrogen and release under mind conditions. Ammonia borane specifically releases 13% of hydrogen in 2 steps at 100oC according to the following scheme.<ref>http://www.sigmaaldrich.com/materials-science/alternative-energy-materials/boron-hydrogen-storage.html</ref> The interesting thing to note here is that, even though ammonia borane is isoelectric to ethene, and adopts a similar structure, their boiling points differ by 284oC! Perhaps by investigating their molecular orbitals and electron density, we can somehow rationalise this fact.

[[Image:Bh3nh3_release_scheme.jpg|left|frame]]
 

===Structure===
 
Structures of ammonia borane and ethane were minimised using B3YLP and 6-31G d,p on gaussian.

Ammonia Borane: 30486

[[Image:Bh3nh3_summary_ppx2.jpg|left|frame]]

{| class="wikitable" border="1"
|+''' Bond Lengths'''
! Bond!! Length (Å)!!Lit. (Å)<ref>J. Yang et al. ''APPLIED PHYSICS LETTERS 92'', 091916 '''2008'''</ref>
|-
| N-H || 1.02213||1.011
|-
| B-H || 1.21288||1.208
|-
|N-B||1.68447 || -
|}

{| class="wikitable" border="1"
|+ '''Bond Angles'''
!Bond!! Angle (o)!! Lit.(o)
|-
| H1-B-H2 || 113.11286||114.4
|-
| H4-N-H5 || 110.20458||105.8
|}

Ethane: 30487

[[Image:C2h6_summary_ppx2.jpg |left|frame]]

{| class="wikitable" border="1"
|+''' Bond Lengths'''
! Bond!! Length (Å)!!Lit. (Å)
|-
|C-H|| 1.02213||1.011
|-
|C-C || 1.21288||1.208
|}

{| class="wikitable" border="1"
|+ '''Bond Angles'''
!Bond!! Angle (o)!! Lit.(o)
|-
| H1-C-H2 || 113.11286||114.4
|}

=References=
 
<references />

File:C2h6 summary ppx2.jpg

2010-11-02T05:51:26Z

Ppx07:

Rep:Mod:thugaim

2010-11-02T05:49:19Z

Ppx07: /* Introduction */

=Module 2=
 
==Part 1==
 
===BH3===
 
A molecule of BH3 was constructed in Gaussview 3.0 and optimized using DFT B3LYP with the following results:
<jmol> <jmolAppletButton> <uploadedFileContents>Bh3_opt_ppx2.mol</uploadedFileContents> <text>Load</text> </jmolAppletButton> </jmol>

B-H bond length = 1.19435Å

H-B-H bond angle = 120o

[[Image:Bh3_opt_summary_ppx2.jpg| ]]

===TlBr3===
 
TlBr3 was confined to point group D3h and then optimised using pseudo potential LanL2DZ. <jmol> <jmolAppletButton> <uploadedFileContents>TLBR3_OPT_ppx2.mol</uploadedFileContents> <text>Load</text> </jmolAppletButton> </jmol>
http://hdl.handle.net/10042/to-5432

Tl-Br bond distance = 2.65095Å

Br-Tl-Br bond angle = 120o

Summary:

[[Image:Tibr3_opt_summary_ppx2.jpg|| ]]

The lit. value for Tl-Br bond distance in TlBr3 is 2.521Å<ref>J. Glaser et al. ''On the structures of hydrated Thallium(III)ion and its bromide complexes in aqueous solution'' '''1982'''</ref> this value does not fall within the error of 0.01Å of the programme used for the calculation. This maybe caused by the need to use pseudo-potentials for such calculation as Tl has 81 electrons and Br has 35, needless to say, the method which we used (LanL2DZ) only has a 'medium' level of accuracy as better basis sets and pseudo potentials would require much longer calculations.

In some structures gaussview does not draw in the bonds where we expect, however this only means that gaussview does not recognise the distance between the bonding atoms when compared to its database of bond distances. A bond is simply the attraction caused by the electromagnetic force between opposing charges that allows the formation of chemical compounds.
 

===BH3===
 
Molecular orbitals of BH3 were calculated from the optimised structure. Digital Repository link http://hdl.handle.net/10042/to-5356

The NBO charges for boron was -0.053 and 0.018 for hydrogen.

[[Image:Bh3_ir_ppx2.jpg|frame|left|IR of BH3 ]]

{| class="wikitable" border="1"
|+ '''IR Summary'''
! Form Of Vibration !! Freqency !! Intensity !! Symmetry D3h Point Group
|-
| Wagging of all 3 H atoms || 1145.71 || 92.70 || A"2
|-
| Scissor or H atoms 2 and 3 || 1204.66 || 12.38||E'
|-
|Rocking of all 3 H atoms ||1204.66||12.38||E'
|-
|Symmetric stretch of all 3 H atoms || 2592.79||0||A'1
|-
|Asymmetric stretch of H atoms 2 and 3 || 2731.31 ||103.84||E'
|-
|Symmetric stretch of H atoms 2 and 3,
asymmetric stretch of H atom 1
|| 2731.31 || 103.83||E'
|}

There are not 6 peaks on the spectrum because the symmetric stretch of the 3 H atoms has an intensity of 0, this is because the symmetric stretch vibration does not change the overall dipole moment.

[[Image:Bh3_mo_comparison_ppx2.jpg |frame|left]]
 

From the comparison of LCAO and Real MOs, we can see the major difference between the 2 is that the LCAO approach has a heavier focus on atomic orbitals (hence the name) while the real MOs shows electron density in a molecular fashion, having said that the qualitative approach of LCAO has accurately predicted key features such as nodal planes in all real MOs. This proves the vital importance of qualitative MO theory as quick and accurate assumptions can be made without relying on computer software.

===Cis and Trans Isomers===

Both trans and cis-[MoCo4(PCl3)2)] were created by fragments using gaussview 3.0. Following the procedures outlined in the script, both molecules first went under optimisation by B3LYP with pseudo-potential LanL2MB (loose convergence).

<s>'''Cis isomer after initial optimisation: 30032

Trans isomer after initial optimisation: 30033'''</s>

To avoid optimisting to the wrong minima of energy, the molecules were modified thus the cis isomer has Cl from one PCl3 group pointing up parrallel to the axial bond and Cl from the other PCl3 group pointing down; while the trans conformer had both PCl3 groups eclipsed and that one Cl of each group was parallel to one Mo-C bond. Both conformers were subjected to optimisation using a much better basis set and pseudo-potential LanL2DZ, with increased electronic convergence.

<s>'''Cis isomer after final optimisation: 30034 <jmol> <jmolAppletButton> <uploadedFileContents>Moco4_cis_opted_ppx2.mol</uploadedFileContents> <text>Load</text> </jmolAppletButton> </jmol>

Trans isomer after initial optimisation: 30035'''</s> <jmol> <jmolAppletButton> <uploadedFileContents>Moco4_trans_opted_ppx2.mol</uploadedFileContents> <text>Load</text> </jmolAppletButton> </jmol>

In the optimised structures, the following Mo-C bond distances were obtained:

{| class="wikitable" border="1"
|+ '''C=O bond distance'''
! Type !! Bond Distance in Å (Cis) !! Bond Distance in Å (Trans)
|-
| Axial||2.05782||-
|-
| Equatorial||2.01156||2.06044
|}

Frequency analysis was only calculated using the optimised structures of the cis and trans conformers. However due to complications, calculations did not yield valid results, therefore a separate combined opt+freq calculation was used on the initially optimised conformers, whilst retaining the better basis set and pseudo potential and increased electronic convergence keywords. This is done so that the opt+freq analysis would be identical to the result of the freq-only analysis had the calculation gone ahead successfully.

<s>'''
Cis isomer after opt+freq: 30135

Trans isomer after opt+freq: 30136'''</s>

[[Image:Moco4_cis_ir_ppx2.jpg|Frequency Analysis of Cis conformer|left|frame]]
[[Image:Moco4_trans_ir_ppx2.jpg|Frequency Analysis of Trans conformer|left|frame]]

{| class="wikitable" border="1"
|+ '''Cis C=O Stretch'''
! Type !!Freqency!! Intensity
|-
| Equatorial Asymmetric|| 1945.34|| 764.095
|-
| Axial Asymmetric||1948.61|| 1487.15
|-
| Equatorial-Axial Asymmetric||1958.37||632.266
|-
|Equatorial-Axial Symmetric ||2023.27||598.17
|}

{| class="wikitable" border="1"
|+ '''Trans C=O Stretch'''
! Type!! Frequency!! Intensity
|-
| 1,3 Equatorial Asymmetric || 1950.11||1474.94
|-
| 2,4 Equatorial Asymmetric|| 1950.71||1466.8
|-
|1,2,3,4 Equatorial Asymmetric|| 1977.02||0.7215
|-
|1,2,3,4 Equatorial Symmetric|| 2030.8||3.9078
|}

30032, 30033, 30034, 30035, 30038, 30039, 30135, 30136. email to m.j.harvey@ic.ac.uk

==Part 2 Miniproject:==
 
===Introduction===
This miniproject will compare the difference in structural and electronic properties between ammonia borane and ethane. My interest in this field arose from my assigned research project 'Boron-nitrogen dehydrocoupling: a route to hydrogen storage materials'. A quick search on boron based hydrogen storage yielded a simple molecule, BH3NH3<ref>Karkamkar, A.; Aardahl, C.; Autrey, T. ''Material Matters'', '''2007''', 2.2, 62</ref> to be an efficient storage medium as it can bind significant amounts of hydrogen and release under mind conditions. Ammonia borane specifically releases 13% of hydrogen in 2 steps at 100oC according to the following scheme.<ref>http://www.sigmaaldrich.com/materials-science/alternative-energy-materials/boron-hydrogen-storage.html</ref> The interesting thing to note here is that, even though ammonia borane is isoelectric to ethene, and adopts a similar structure, their boiling points differ by 284oC! Perhaps by investigating their molecular orbitals and electron density, we can somehow rationalise this fact.

[[Image:Bh3nh3_release_scheme.jpg|left|frame]]
 

===Structure===
 
Structures of ammonia borane and ethane were minimised using B3YLP and 6-31G d,p on gaussian.

Ammonia Borane: 30486

[[Image:Bh3nh3_summary_ppx2.jpg|left|frame]]

{| class="wikitable" border="1"
|+''' Bond Lengths'''
! Bond!! Length (Å)!!Lit. (Å)<ref>J. Yang et al. ''APPLIED PHYSICS LETTERS 92'', 091916 '''2008'''</ref>
|-
| N-H || 1.02213||1.011
|-
| B-H || 1.21288||1.208
|-
|N-B||1.68447 || -
|}

{| class="wikitable" border="1"
|+ '''Bond Angles'''
!Bond!! Angle (o)!! Lit.(o)
|-
| H1-B-H2 || 113.11286||114.4
|-
| H4-N-H5 || 110.20458||105.8
|}

Ethane: 30487

{| class="wikitable" border="1"
|+''' Bond Lengths'''
! Bond!! Length (Å)!!Lit. (Å)
|-
|C-H|| 1.02213||1.011
|-
|C-C || 1.21288||1.208
|}

{| class="wikitable" border="1"
|+ '''Bond Angles'''
!Bond!! Angle (o)!! Lit.(o)
|-
| H1-B-H2 || 113.11286||114.4
|-
| H4-N-H5 || 110.20458||105.8
|}

=References=
 
<references />

Rep:Mod:thugaim

2010-11-02T05:48:38Z

Ppx07: /* Structure */

=Module 2=
 
==Part 1==
 
===BH3===
 
A molecule of BH3 was constructed in Gaussview 3.0 and optimized using DFT B3LYP with the following results:
<jmol> <jmolAppletButton> <uploadedFileContents>Bh3_opt_ppx2.mol</uploadedFileContents> <text>Load</text> </jmolAppletButton> </jmol>

B-H bond length = 1.19435Å

H-B-H bond angle = 120o

[[Image:Bh3_opt_summary_ppx2.jpg| ]]

===TlBr3===
 
TlBr3 was confined to point group D3h and then optimised using pseudo potential LanL2DZ. <jmol> <jmolAppletButton> <uploadedFileContents>TLBR3_OPT_ppx2.mol</uploadedFileContents> <text>Load</text> </jmolAppletButton> </jmol>
http://hdl.handle.net/10042/to-5432

Tl-Br bond distance = 2.65095Å

Br-Tl-Br bond angle = 120o

Summary:

[[Image:Tibr3_opt_summary_ppx2.jpg|| ]]

The lit. value for Tl-Br bond distance in TlBr3 is 2.521Å<ref>J. Glaser et al. ''On the structures of hydrated Thallium(III)ion and its bromide complexes in aqueous solution'' '''1982'''</ref> this value does not fall within the error of 0.01Å of the programme used for the calculation. This maybe caused by the need to use pseudo-potentials for such calculation as Tl has 81 electrons and Br has 35, needless to say, the method which we used (LanL2DZ) only has a 'medium' level of accuracy as better basis sets and pseudo potentials would require much longer calculations.

In some structures gaussview does not draw in the bonds where we expect, however this only means that gaussview does not recognise the distance between the bonding atoms when compared to its database of bond distances. A bond is simply the attraction caused by the electromagnetic force between opposing charges that allows the formation of chemical compounds.
 

===BH3===
 
Molecular orbitals of BH3 were calculated from the optimised structure. Digital Repository link http://hdl.handle.net/10042/to-5356

The NBO charges for boron was -0.053 and 0.018 for hydrogen.

[[Image:Bh3_ir_ppx2.jpg|frame|left|IR of BH3 ]]

{| class="wikitable" border="1"
|+ '''IR Summary'''
! Form Of Vibration !! Freqency !! Intensity !! Symmetry D3h Point Group
|-
| Wagging of all 3 H atoms || 1145.71 || 92.70 || A"2
|-
| Scissor or H atoms 2 and 3 || 1204.66 || 12.38||E'
|-
|Rocking of all 3 H atoms ||1204.66||12.38||E'
|-
|Symmetric stretch of all 3 H atoms || 2592.79||0||A'1
|-
|Asymmetric stretch of H atoms 2 and 3 || 2731.31 ||103.84||E'
|-
|Symmetric stretch of H atoms 2 and 3,
asymmetric stretch of H atom 1
|| 2731.31 || 103.83||E'
|}

There are not 6 peaks on the spectrum because the symmetric stretch of the 3 H atoms has an intensity of 0, this is because the symmetric stretch vibration does not change the overall dipole moment.

[[Image:Bh3_mo_comparison_ppx2.jpg |frame|left]]
 

From the comparison of LCAO and Real MOs, we can see the major difference between the 2 is that the LCAO approach has a heavier focus on atomic orbitals (hence the name) while the real MOs shows electron density in a molecular fashion, having said that the qualitative approach of LCAO has accurately predicted key features such as nodal planes in all real MOs. This proves the vital importance of qualitative MO theory as quick and accurate assumptions can be made without relying on computer software.

===Cis and Trans Isomers===

Both trans and cis-[MoCo4(PCl3)2)] were created by fragments using gaussview 3.0. Following the procedures outlined in the script, both molecules first went under optimisation by B3LYP with pseudo-potential LanL2MB (loose convergence).

<s>'''Cis isomer after initial optimisation: 30032

Trans isomer after initial optimisation: 30033'''</s>

To avoid optimisting to the wrong minima of energy, the molecules were modified thus the cis isomer has Cl from one PCl3 group pointing up parrallel to the axial bond and Cl from the other PCl3 group pointing down; while the trans conformer had both PCl3 groups eclipsed and that one Cl of each group was parallel to one Mo-C bond. Both conformers were subjected to optimisation using a much better basis set and pseudo-potential LanL2DZ, with increased electronic convergence.

<s>'''Cis isomer after final optimisation: 30034 <jmol> <jmolAppletButton> <uploadedFileContents>Moco4_cis_opted_ppx2.mol</uploadedFileContents> <text>Load</text> </jmolAppletButton> </jmol>

Trans isomer after initial optimisation: 30035'''</s> <jmol> <jmolAppletButton> <uploadedFileContents>Moco4_trans_opted_ppx2.mol</uploadedFileContents> <text>Load</text> </jmolAppletButton> </jmol>

In the optimised structures, the following Mo-C bond distances were obtained:

{| class="wikitable" border="1"
|+ '''C=O bond distance'''
! Type !! Bond Distance in Å (Cis) !! Bond Distance in Å (Trans)
|-
| Axial||2.05782||-
|-
| Equatorial||2.01156||2.06044
|}

Frequency analysis was only calculated using the optimised structures of the cis and trans conformers. However due to complications, calculations did not yield valid results, therefore a separate combined opt+freq calculation was used on the initially optimised conformers, whilst retaining the better basis set and pseudo potential and increased electronic convergence keywords. This is done so that the opt+freq analysis would be identical to the result of the freq-only analysis had the calculation gone ahead successfully.

<s>'''
Cis isomer after opt+freq: 30135

Trans isomer after opt+freq: 30136'''</s>

[[Image:Moco4_cis_ir_ppx2.jpg|Frequency Analysis of Cis conformer|left|frame]]
[[Image:Moco4_trans_ir_ppx2.jpg|Frequency Analysis of Trans conformer|left|frame]]

{| class="wikitable" border="1"
|+ '''Cis C=O Stretch'''
! Type !!Freqency!! Intensity
|-
| Equatorial Asymmetric|| 1945.34|| 764.095
|-
| Axial Asymmetric||1948.61|| 1487.15
|-
| Equatorial-Axial Asymmetric||1958.37||632.266
|-
|Equatorial-Axial Symmetric ||2023.27||598.17
|}

{| class="wikitable" border="1"
|+ '''Trans C=O Stretch'''
! Type!! Frequency!! Intensity
|-
| 1,3 Equatorial Asymmetric || 1950.11||1474.94
|-
| 2,4 Equatorial Asymmetric|| 1950.71||1466.8
|-
|1,2,3,4 Equatorial Asymmetric|| 1977.02||0.7215
|-
|1,2,3,4 Equatorial Symmetric|| 2030.8||3.9078
|}

30032, 30033, 30034, 30035, 30038, 30039, 30135, 30136. email to m.j.harvey@ic.ac.uk

==Part 2 Miniproject:==
 
===Introduction===
This miniproject will compare the difference in structural and electronic properties between ammonia borane and ethane. My interest in this field arose from my assigned research project 'Boron-nitrogen dehydrocoupling: a route to hydrogen storage materials'. A quick search on boron based hydrogen storage yielded a simple molecule, BH3NH3<ref>Karkamkar, A.; Aardahl, C.; Autrey, T. Material Matters, 2007, 2.2, 62</ref> to be an efficient storage medium as it can bind significant amounts of hydrogen and release under mind conditions. Ammonia borane specifically releases 13% of hydrogen in 2 steps at 100oC according to the following scheme.<ref>http://www.sigmaaldrich.com/materials-science/alternative-energy-materials/boron-hydrogen-storage.html</ref> The interesting thing to note here is that, even though ammonia borane is isoelectric to ethene, and adopts a similar structure, their boiling points differ by 284oC! Perhaps by investigating their molecular orbitals and electron density, we can somehow rationalise this fact.

[[Image:Bh3nh3_release_scheme.jpg|left|frame]]
 

===Structure===
 
Structures of ammonia borane and ethane were minimised using B3YLP and 6-31G d,p on gaussian.

Ammonia Borane: 30486

[[Image:Bh3nh3_summary_ppx2.jpg|left|frame]]

{| class="wikitable" border="1"
|+''' Bond Lengths'''
! Bond!! Length (Å)!!Lit. (Å)<ref>J. Yang et al. ''APPLIED PHYSICS LETTERS 92'', 091916 '''2008'''</ref>
|-
| N-H || 1.02213||1.011
|-
| B-H || 1.21288||1.208
|-
|N-B||1.68447 || -
|}

{| class="wikitable" border="1"
|+ '''Bond Angles'''
!Bond!! Angle (o)!! Lit.(o)
|-
| H1-B-H2 || 113.11286||114.4
|-
| H4-N-H5 || 110.20458||105.8
|}

Ethane: 30487

{| class="wikitable" border="1"
|+''' Bond Lengths'''
! Bond!! Length (Å)!!Lit. (Å)
|-
|C-H|| 1.02213||1.011
|-
|C-C || 1.21288||1.208
|}

{| class="wikitable" border="1"
|+ '''Bond Angles'''
!Bond!! Angle (o)!! Lit.(o)
|-
| H1-B-H2 || 113.11286||114.4
|-
| H4-N-H5 || 110.20458||105.8
|}

=References=
 
<references />

Rep:Mod:thugaim

2010-11-02T05:44:56Z

Ppx07: /* Structure */

=Module 2=
 
==Part 1==
 
===BH3===
 
A molecule of BH3 was constructed in Gaussview 3.0 and optimized using DFT B3LYP with the following results:
<jmol> <jmolAppletButton> <uploadedFileContents>Bh3_opt_ppx2.mol</uploadedFileContents> <text>Load</text> </jmolAppletButton> </jmol>

B-H bond length = 1.19435Å

H-B-H bond angle = 120o

[[Image:Bh3_opt_summary_ppx2.jpg| ]]

===TlBr3===
 
TlBr3 was confined to point group D3h and then optimised using pseudo potential LanL2DZ. <jmol> <jmolAppletButton> <uploadedFileContents>TLBR3_OPT_ppx2.mol</uploadedFileContents> <text>Load</text> </jmolAppletButton> </jmol>
http://hdl.handle.net/10042/to-5432

Tl-Br bond distance = 2.65095Å

Br-Tl-Br bond angle = 120o

Summary:

[[Image:Tibr3_opt_summary_ppx2.jpg|| ]]

The lit. value for Tl-Br bond distance in TlBr3 is 2.521Å<ref>J. Glaser et al. ''On the structures of hydrated Thallium(III)ion and its bromide complexes in aqueous solution'' '''1982'''</ref> this value does not fall within the error of 0.01Å of the programme used for the calculation. This maybe caused by the need to use pseudo-potentials for such calculation as Tl has 81 electrons and Br has 35, needless to say, the method which we used (LanL2DZ) only has a 'medium' level of accuracy as better basis sets and pseudo potentials would require much longer calculations.

In some structures gaussview does not draw in the bonds where we expect, however this only means that gaussview does not recognise the distance between the bonding atoms when compared to its database of bond distances. A bond is simply the attraction caused by the electromagnetic force between opposing charges that allows the formation of chemical compounds.
 

===BH3===
 
Molecular orbitals of BH3 were calculated from the optimised structure. Digital Repository link http://hdl.handle.net/10042/to-5356

The NBO charges for boron was -0.053 and 0.018 for hydrogen.

[[Image:Bh3_ir_ppx2.jpg|frame|left|IR of BH3 ]]

{| class="wikitable" border="1"
|+ '''IR Summary'''
! Form Of Vibration !! Freqency !! Intensity !! Symmetry D3h Point Group
|-
| Wagging of all 3 H atoms || 1145.71 || 92.70 || A"2
|-
| Scissor or H atoms 2 and 3 || 1204.66 || 12.38||E'
|-
|Rocking of all 3 H atoms ||1204.66||12.38||E'
|-
|Symmetric stretch of all 3 H atoms || 2592.79||0||A'1
|-
|Asymmetric stretch of H atoms 2 and 3 || 2731.31 ||103.84||E'
|-
|Symmetric stretch of H atoms 2 and 3,
asymmetric stretch of H atom 1
|| 2731.31 || 103.83||E'
|}

There are not 6 peaks on the spectrum because the symmetric stretch of the 3 H atoms has an intensity of 0, this is because the symmetric stretch vibration does not change the overall dipole moment.

[[Image:Bh3_mo_comparison_ppx2.jpg |frame|left]]
 

From the comparison of LCAO and Real MOs, we can see the major difference between the 2 is that the LCAO approach has a heavier focus on atomic orbitals (hence the name) while the real MOs shows electron density in a molecular fashion, having said that the qualitative approach of LCAO has accurately predicted key features such as nodal planes in all real MOs. This proves the vital importance of qualitative MO theory as quick and accurate assumptions can be made without relying on computer software.

===Cis and Trans Isomers===

Both trans and cis-[MoCo4(PCl3)2)] were created by fragments using gaussview 3.0. Following the procedures outlined in the script, both molecules first went under optimisation by B3LYP with pseudo-potential LanL2MB (loose convergence).

<s>'''Cis isomer after initial optimisation: 30032

Trans isomer after initial optimisation: 30033'''</s>

To avoid optimisting to the wrong minima of energy, the molecules were modified thus the cis isomer has Cl from one PCl3 group pointing up parrallel to the axial bond and Cl from the other PCl3 group pointing down; while the trans conformer had both PCl3 groups eclipsed and that one Cl of each group was parallel to one Mo-C bond. Both conformers were subjected to optimisation using a much better basis set and pseudo-potential LanL2DZ, with increased electronic convergence.

<s>'''Cis isomer after final optimisation: 30034 <jmol> <jmolAppletButton> <uploadedFileContents>Moco4_cis_opted_ppx2.mol</uploadedFileContents> <text>Load</text> </jmolAppletButton> </jmol>

Trans isomer after initial optimisation: 30035'''</s> <jmol> <jmolAppletButton> <uploadedFileContents>Moco4_trans_opted_ppx2.mol</uploadedFileContents> <text>Load</text> </jmolAppletButton> </jmol>

In the optimised structures, the following Mo-C bond distances were obtained:

{| class="wikitable" border="1"
|+ '''C=O bond distance'''
! Type !! Bond Distance in Å (Cis) !! Bond Distance in Å (Trans)
|-
| Axial||2.05782||-
|-
| Equatorial||2.01156||2.06044
|}

Frequency analysis was only calculated using the optimised structures of the cis and trans conformers. However due to complications, calculations did not yield valid results, therefore a separate combined opt+freq calculation was used on the initially optimised conformers, whilst retaining the better basis set and pseudo potential and increased electronic convergence keywords. This is done so that the opt+freq analysis would be identical to the result of the freq-only analysis had the calculation gone ahead successfully.

<s>'''
Cis isomer after opt+freq: 30135

Trans isomer after opt+freq: 30136'''</s>

[[Image:Moco4_cis_ir_ppx2.jpg|Frequency Analysis of Cis conformer|left|frame]]
[[Image:Moco4_trans_ir_ppx2.jpg|Frequency Analysis of Trans conformer|left|frame]]

{| class="wikitable" border="1"
|+ '''Cis C=O Stretch'''
! Type !!Freqency!! Intensity
|-
| Equatorial Asymmetric|| 1945.34|| 764.095
|-
| Axial Asymmetric||1948.61|| 1487.15
|-
| Equatorial-Axial Asymmetric||1958.37||632.266
|-
|Equatorial-Axial Symmetric ||2023.27||598.17
|}

{| class="wikitable" border="1"
|+ '''Trans C=O Stretch'''
! Type!! Frequency!! Intensity
|-
| 1,3 Equatorial Asymmetric || 1950.11||1474.94
|-
| 2,4 Equatorial Asymmetric|| 1950.71||1466.8
|-
|1,2,3,4 Equatorial Asymmetric|| 1977.02||0.7215
|-
|1,2,3,4 Equatorial Symmetric|| 2030.8||3.9078
|}

30032, 30033, 30034, 30035, 30038, 30039, 30135, 30136. email to m.j.harvey@ic.ac.uk

==Part 2 Miniproject:==
 
===Introduction===
This miniproject will compare the difference in structural and electronic properties between ammonia borane and ethane. My interest in this field arose from my assigned research project 'Boron-nitrogen dehydrocoupling: a route to hydrogen storage materials'. A quick search on boron based hydrogen storage yielded a simple molecule, BH3NH3<ref>Karkamkar, A.; Aardahl, C.; Autrey, T. Material Matters, 2007, 2.2, 62</ref> to be an efficient storage medium as it can bind significant amounts of hydrogen and release under mind conditions. Ammonia borane specifically releases 13% of hydrogen in 2 steps at 100oC according to the following scheme.<ref>http://www.sigmaaldrich.com/materials-science/alternative-energy-materials/boron-hydrogen-storage.html</ref> The interesting thing to note here is that, even though ammonia borane is isoelectric to ethene, and adopts a similar structure, their boiling points differ by 284oC! Perhaps by investigating their molecular orbitals and electron density, we can somehow rationalise this fact.

[[Image:Bh3nh3_release_scheme.jpg|left|frame]]
 

===Structure===
 
Structures of ammonia borane and ethane were minimised using B3YLP and 6-31G d,p on gaussian.

Ammonia Borane: 30486

[[Image:Bh3nh3_summary_ppx2.jpg|left|frame]]

{| class="wikitable" border="1"
|+''' Bond Lengths'''
! Bond!! Length (Å)!!Lit. (Å)
|-
| N-H || 1.02213||1.011
|-
| B-H || 1.21288||1.208
|-
|N-B||1.68447 || -
|}

{| class="wikitable" border="1"
|+ '''Bond Angles'''
!Bond!! Angle (o)!! Lit.(o)
|-
| H1-B-H2 || 113.11286||114.4
|-
| H4-N-H5 || 110.20458||105.8
|}

Ethane:

=References=
 
<references />

Rep:Mod:thugaim

2010-11-02T05:44:43Z

Ppx07: /* Structure */

=Module 2=
 
==Part 1==
 
===BH3===
 
A molecule of BH3 was constructed in Gaussview 3.0 and optimized using DFT B3LYP with the following results:
<jmol> <jmolAppletButton> <uploadedFileContents>Bh3_opt_ppx2.mol</uploadedFileContents> <text>Load</text> </jmolAppletButton> </jmol>

B-H bond length = 1.19435Å

H-B-H bond angle = 120o

[[Image:Bh3_opt_summary_ppx2.jpg| ]]

===TlBr3===
 
TlBr3 was confined to point group D3h and then optimised using pseudo potential LanL2DZ. <jmol> <jmolAppletButton> <uploadedFileContents>TLBR3_OPT_ppx2.mol</uploadedFileContents> <text>Load</text> </jmolAppletButton> </jmol>
http://hdl.handle.net/10042/to-5432

Tl-Br bond distance = 2.65095Å

Br-Tl-Br bond angle = 120o

Summary:

[[Image:Tibr3_opt_summary_ppx2.jpg|| ]]

The lit. value for Tl-Br bond distance in TlBr3 is 2.521Å<ref>J. Glaser et al. ''On the structures of hydrated Thallium(III)ion and its bromide complexes in aqueous solution'' '''1982'''</ref> this value does not fall within the error of 0.01Å of the programme used for the calculation. This maybe caused by the need to use pseudo-potentials for such calculation as Tl has 81 electrons and Br has 35, needless to say, the method which we used (LanL2DZ) only has a 'medium' level of accuracy as better basis sets and pseudo potentials would require much longer calculations.

In some structures gaussview does not draw in the bonds where we expect, however this only means that gaussview does not recognise the distance between the bonding atoms when compared to its database of bond distances. A bond is simply the attraction caused by the electromagnetic force between opposing charges that allows the formation of chemical compounds.
 

===BH3===
 
Molecular orbitals of BH3 were calculated from the optimised structure. Digital Repository link http://hdl.handle.net/10042/to-5356

The NBO charges for boron was -0.053 and 0.018 for hydrogen.

[[Image:Bh3_ir_ppx2.jpg|frame|left|IR of BH3 ]]

{| class="wikitable" border="1"
|+ '''IR Summary'''
! Form Of Vibration !! Freqency !! Intensity !! Symmetry D3h Point Group
|-
| Wagging of all 3 H atoms || 1145.71 || 92.70 || A"2
|-
| Scissor or H atoms 2 and 3 || 1204.66 || 12.38||E'
|-
|Rocking of all 3 H atoms ||1204.66||12.38||E'
|-
|Symmetric stretch of all 3 H atoms || 2592.79||0||A'1
|-
|Asymmetric stretch of H atoms 2 and 3 || 2731.31 ||103.84||E'
|-
|Symmetric stretch of H atoms 2 and 3,
asymmetric stretch of H atom 1
|| 2731.31 || 103.83||E'
|}

There are not 6 peaks on the spectrum because the symmetric stretch of the 3 H atoms has an intensity of 0, this is because the symmetric stretch vibration does not change the overall dipole moment.

[[Image:Bh3_mo_comparison_ppx2.jpg |frame|left]]
 

From the comparison of LCAO and Real MOs, we can see the major difference between the 2 is that the LCAO approach has a heavier focus on atomic orbitals (hence the name) while the real MOs shows electron density in a molecular fashion, having said that the qualitative approach of LCAO has accurately predicted key features such as nodal planes in all real MOs. This proves the vital importance of qualitative MO theory as quick and accurate assumptions can be made without relying on computer software.

===Cis and Trans Isomers===

Both trans and cis-[MoCo4(PCl3)2)] were created by fragments using gaussview 3.0. Following the procedures outlined in the script, both molecules first went under optimisation by B3LYP with pseudo-potential LanL2MB (loose convergence).

<s>'''Cis isomer after initial optimisation: 30032

Trans isomer after initial optimisation: 30033'''</s>

To avoid optimisting to the wrong minima of energy, the molecules were modified thus the cis isomer has Cl from one PCl3 group pointing up parrallel to the axial bond and Cl from the other PCl3 group pointing down; while the trans conformer had both PCl3 groups eclipsed and that one Cl of each group was parallel to one Mo-C bond. Both conformers were subjected to optimisation using a much better basis set and pseudo-potential LanL2DZ, with increased electronic convergence.

<s>'''Cis isomer after final optimisation: 30034 <jmol> <jmolAppletButton> <uploadedFileContents>Moco4_cis_opted_ppx2.mol</uploadedFileContents> <text>Load</text> </jmolAppletButton> </jmol>

Trans isomer after initial optimisation: 30035'''</s> <jmol> <jmolAppletButton> <uploadedFileContents>Moco4_trans_opted_ppx2.mol</uploadedFileContents> <text>Load</text> </jmolAppletButton> </jmol>

In the optimised structures, the following Mo-C bond distances were obtained:

{| class="wikitable" border="1"
|+ '''C=O bond distance'''
! Type !! Bond Distance in Å (Cis) !! Bond Distance in Å (Trans)
|-
| Axial||2.05782||-
|-
| Equatorial||2.01156||2.06044
|}

Frequency analysis was only calculated using the optimised structures of the cis and trans conformers. However due to complications, calculations did not yield valid results, therefore a separate combined opt+freq calculation was used on the initially optimised conformers, whilst retaining the better basis set and pseudo potential and increased electronic convergence keywords. This is done so that the opt+freq analysis would be identical to the result of the freq-only analysis had the calculation gone ahead successfully.

<s>'''
Cis isomer after opt+freq: 30135

Trans isomer after opt+freq: 30136'''</s>

[[Image:Moco4_cis_ir_ppx2.jpg|Frequency Analysis of Cis conformer|left|frame]]
[[Image:Moco4_trans_ir_ppx2.jpg|Frequency Analysis of Trans conformer|left|frame]]

{| class="wikitable" border="1"
|+ '''Cis C=O Stretch'''
! Type !!Freqency!! Intensity
|-
| Equatorial Asymmetric|| 1945.34|| 764.095
|-
| Axial Asymmetric||1948.61|| 1487.15
|-
| Equatorial-Axial Asymmetric||1958.37||632.266
|-
|Equatorial-Axial Symmetric ||2023.27||598.17
|}

{| class="wikitable" border="1"
|+ '''Trans C=O Stretch'''
! Type!! Frequency!! Intensity
|-
| 1,3 Equatorial Asymmetric || 1950.11||1474.94
|-
| 2,4 Equatorial Asymmetric|| 1950.71||1466.8
|-
|1,2,3,4 Equatorial Asymmetric|| 1977.02||0.7215
|-
|1,2,3,4 Equatorial Symmetric|| 2030.8||3.9078
|}

30032, 30033, 30034, 30035, 30038, 30039, 30135, 30136. email to m.j.harvey@ic.ac.uk

==Part 2 Miniproject:==
 
===Introduction===
This miniproject will compare the difference in structural and electronic properties between ammonia borane and ethane. My interest in this field arose from my assigned research project 'Boron-nitrogen dehydrocoupling: a route to hydrogen storage materials'. A quick search on boron based hydrogen storage yielded a simple molecule, BH3NH3<ref>Karkamkar, A.; Aardahl, C.; Autrey, T. Material Matters, 2007, 2.2, 62</ref> to be an efficient storage medium as it can bind significant amounts of hydrogen and release under mind conditions. Ammonia borane specifically releases 13% of hydrogen in 2 steps at 100oC according to the following scheme.<ref>http://www.sigmaaldrich.com/materials-science/alternative-energy-materials/boron-hydrogen-storage.html</ref> The interesting thing to note here is that, even though ammonia borane is isoelectric to ethene, and adopts a similar structure, their boiling points differ by 284oC! Perhaps by investigating their molecular orbitals and electron density, we can somehow rationalise this fact.

[[Image:Bh3nh3_release_scheme.jpg|left|frame]]
 

===Structure===
 
Structures of ammonia borane and ethane were minimised using B3YLP and 6-31G d,p on gaussian.

Ammonia Borane: 30486

[[Image:Bh3nh3_summary_ppx2.jpg|center]]

{| class="wikitable" border="1"
|+''' Bond Lengths'''
! Bond!! Length (Å)!!Lit. (Å)
|-
| N-H || 1.02213||1.011
|-
| B-H || 1.21288||1.208
|-
|N-B||1.68447 || -
|}

{| class="wikitable" border="1"
|+ '''Bond Angles'''
!Bond!! Angle (o)!! Lit.(o)
|-
| H1-B-H2 || 113.11286||114.4
|-
| H4-N-H5 || 110.20458||105.8
|}

Ethane:

=References=
 
<references />

2010-11-02T02:00:44Z

Ppx07: /* Cis and Trans Isomers */

[[Image:nerie.jpg|thumb|200px|Nerie Anne Catingdig]]
=Module 2=
 
==Part 1==
 
===BH3===
 
A molecule of BH3 was constructed in Gaussview 3.0 and optimized using DFT B3LYP with the following results:
<jmol> <jmolAppletButton> <uploadedFileContents>Bh3_opt_ppx2.mol</uploadedFileContents> <text>Load</text> </jmolAppletButton> </jmol>

B-H bond length = 1.19435Å

H-B-H bond angle = 120o

[[Image:Bh3_opt_summary_ppx2.jpg| ]]

===TlBr3===
 
TlBr3 was confined to point group D3h and then optimised using pseudo potential LanL2DZ. <jmol> <jmolAppletButton> <uploadedFileContents>TLBR3_OPT_ppx2.mol</uploadedFileContents> <text>Load</text> </jmolAppletButton> </jmol>
http://hdl.handle.net/10042/to-5432

Tl-Br bond distance = 2.65095Å

Br-Tl-Br bond angle = 120o

Summary:

[[Image:Tibr3_opt_summary_ppx2.jpg|| ]]

The lit. value for Tl-Br bond distance in TlBr3 is 2.521Å<ref>J. Glaser et al. ''On the structures of hydrated Thallium(III)ion and its bromide complexes in aqueous solution'' '''1982'''</ref> this value does not fall within the error of 0.01Å of the programme used for the calculation. This maybe caused by the need to use pseudo-potentials for such calculation as Tl has 81 electrons and Br has 35, needless to say, the method which we used (LanL2DZ) only has a 'medium' level of accuracy as better basis sets and pseudo potentials would require much longer calculations.

In some structures gaussview does not draw in the bonds where we expect, however this only means that gaussview does not recognise the distance between the bonding atoms when compared to its database of bond distances. A bond is simply the attraction caused by the electromagnetic force between opposing charges that allows the formation of chemical compounds.
 

===BH3===
 
Molecular orbitals of BH3 were calculated from the optimised structure. Digital Repository link http://hdl.handle.net/10042/to-5356

The NBO charges for boron was -0.053 and 0.018 for hydrogen.

[[Image:Bh3_ir_ppx2.jpg|frame|left|IR of BH3 ]]

{| class="wikitable" border="1"
|+ '''IR Summary'''
! Form Of Vibration !! Freqency !! Intensity !! Symmetry D3h Point Group
|-
| Wagging of all 3 H atoms || 1145.71 || 92.70 || A"2
|-
| Scissor or H atoms 2 and 3 || 1204.66 || 12.38||E'
|-
|Rocking of all 3 H atoms ||1204.66||12.38||E'
|-
|Symmetric stretch of all 3 H atoms || 2592.79||0||A'1
|-
|Asymmetric stretch of H atoms 2 and 3 || 2731.31 ||103.84||E'
|-
|Symmetric stretch of H atoms 2 and 3,
asymmetric stretch of H atom 1
|| 2731.31 || 103.83||E'
|}

There are not 6 peaks on the spectrum because the symmetric stretch of the 3 H atoms has an intensity of 0, this is because the symmetric stretch vibration does not change the overall dipole moment.

[[Image:Bh3_mo_comparison_ppx2.jpg |frame|left]]
 

From the comparison of LCAO and Real MOs, we can see the major difference between the 2 is that the LCAO approach has a heavier focus on atomic orbitals (hence the name) while the real MOs shows electron density in a molecular fashion, having said that the qualitative approach of LCAO has accurately predicted key features such as nodal planes in all real MOs. This proves the vital importance of qualitative MO theory as quick and accurate assumptions can be made without relying on computer software.

==Cis and Trans Isomers==

Both trans and cis-[MoCo4(PCl3)2)] were created by fragments using gaussview 3.0. Following the procedures outlined in the script, both molecules first went under optimisation by B3LYP with pseudo-potential LanL2MB (loose convergence).

<s>'''Cis isomer after initial optimisation: 30032

Trans isomer after initial optimisation: 30033'''</s>

To avoid optimisting to the wrong minima of energy, the molecules were modified thus the cis isomer has Cl from one PCl3 group pointing up parrallel to the axial bond and Cl from the other PCl3 group pointing down; while the trans conformer had both PCl3 groups eclipsed and that one Cl of each group was parallel to one Mo-C bond. Both conformers were subjected to optimisation using a much better basis set and pseudo-potential LanL2DZ, with increased electronic convergence.

<s>'''Cis isomer after final optimisation: 30034 <jmol> <jmolAppletButton> <uploadedFileContents>Moco4_cis_opted_ppx2.mol</uploadedFileContents> <text>Load</text> </jmolAppletButton> </jmol>

Trans isomer after initial optimisation: 30035'''</s> <jmol> <jmolAppletButton> <uploadedFileContents>Moco4_trans_opted_ppx2.mol</uploadedFileContents> <text>Load</text> </jmolAppletButton> </jmol>

Frequency analysis was only calculated using the optimised structures of the cis and trans conformers. However due to complications, calculations did not yield valid results, therefore a separate combined opt+freq calculation was used on the initially optimised conformers, whilst retaining the better basis set and pseudo potential and increased electronic convergence keywords. This is done so that the opt+freq analysis would be identical to the result of the freq-only analysis had the calculation gone ahead successfully.

<s>'''
Cis isomer after opt+freq: 30135

Trans isomer after opt+freq: 30136'''</s>

[[Image:Moco4_cis_ir_ppx2.jpg|Frequency Analysis of Cis conformer|left|frame]]
[[Image:Moco4_trans_ir_ppx2.jpg|Frequency Analysis of Trans conformer|left|frame]]
 

=shit i gotta do:=

:write up on bh3 and tlbr3

:do shit with trans cis isomers
::publish initial +final opted shit on dspace
::publish ir shit on dspace
::write up on some other shit

:email bh3nh3 to trisha hunt ask for approval

==job ids that need publishing:==

30032, 30033, 30034, 30035, 30038, 30039, 30135, 30136. email to m.j.harvey@ic.ac.uk

=References=
 
<references />