ChemWiki - User contributions [en]

User:Ck1510

2014-08-18T10:52:37Z

Ck1510: /* Chris and Imperial College Union */

=Intro=

Welcome to Christopher Kaye's wiki page.

[[File:Christopherkaye.png|200px|thumb|left|Christopher Kaye on a rare day off from chemistry]]

=About Chris=

Christopher Kaye was born in Bristol in 1991, just within the sound of the Avonmouth chemical spill warning siren. He completed his A-levels in chemistry, biology, physics and mathematics at North Bristol Post 16 Centre. He is currently studying towards a MSci & ARCS degree in Chemistry at Imperial College London.

The preliminary title of his final year master's project is "''Tandem catalysis to produce substituted amino-alcohols and derivatives''", supervised by Dr. Mimi (King Kuok) Hii.

When not studying chemistry, Christopher enjoys eating Chinese cuisine in Chinatown and drinking real ales in London's many fine boozers. He also takes a keen interest in World politics, and often stays up for the results of elections.

Christopher spends most of his free time during the day in the Chemistry Café in the South Kensington Campus drinking cappuccino. In the evenings, he will often be found at Eastside Bar or perhaps on the odd occasion, Oriental Canteen.

==Chris and Felix==
Chris is a regular contributor to Felix and writes powerful and passionate debate articles such as [http://felixonline.co.uk/comment/3051/democracy-and-the-law/ Democracy and the Law] and [http://felixonline.co.uk/comment/3679/deportation-woes/ Deportation Woes]

[[File:271012_0062.jpg|thumb|200px|Christopher on another fun day out.]]

==Chris and Imperial College Union==

Chris is the Deputy President (Welfare) at Imperial College Union for 2014-15.

=Chris' Work=

[[Mod:mod2scientiadecusettutamen|Module 2 project]]

[[Mod:mod3 christopherkaye|Module 3 project]]

User:Ck1510

2013-06-18T13:02:05Z

Ck1510:

=Intro=

Welcome to Christopher Kaye's wiki page. Chris will be completing two modules towards his computational labs project of 2013.

[[File:Christopherkaye.png|200px|thumb|left|Christopher Kaye on a rare day off from chemistry]]

=About Chris=

Christopher Kaye was born in Bristol in 1991, just within the sound of the Avonmouth chemical spill warning siren. He completed his A-levels in chemistry, biology, physics and mathematics at North Bristol Post 16 Centre. He is currently studying towards a MSci & ARCS degree in Chemistry at Imperial College London.

When not studying chemistry, Chris enjoys eating Chinese cuisine in Chinatown and drinking real ales in London's many fine boozers. He also takes a keen interest in World politics, and often stays up for the results of elections.

==Chris and Felix==
Chris is a regular contributor to Felix and writes powerful and passionate debate articles such as [http://felixonline.co.uk/comment/3051/democracy-and-the-law/ Democracy and the Law] and [http://felixonline.co.uk/comment/3679/deportation-woes/ Deportation Woes]

==Chris and Imperial College Union==

Chris is Campaigns Officer for the academic year 2013-14. You can read his manifesto [https://vote.union.ic.ac.uk/manifestos.php?pid=663 here]

=Chris' work=

[[Mod:mod2scientiadecusettutamen|Module 2 project]]

[[Mod:mod3 christopherkaye|Module 3 project]]

User:Ck1510

2013-06-18T12:59:25Z

Ck1510: /* Chris and Felix */

=Intro=

Welcome to Christopher Kaye's wiki page. Chris will be completing two modules towards his computational labs project of 2013.

[[File:Christopherkaye.png|200px|thumb|left|Christopher Kaye on a rare day off from chemistry]]

=About Chris=

Christopher Kaye was born in Bristol in 1991, just within the sound of the Avonmouth chemical spill warning siren. He completed his A-levels in chemistry, biology, physics and mathematics at North Bristol Post 16 Centre. He is currently studying towards a MSci & ARCS degree in Chemistry at Imperial College London.

When not studying chemistry, Chris enjoys eating Chinese cuisine in Chinatown and drinking real ales in London's many fine boozers. He also takes a keen interest in World politics, and often stays up for the results of elections.

==Chris and Felix==
Chris is a regular contributor to Felix and writes powerful and passionate debate articles such as [http://felixonline.co.uk/comment/3051/democracy-and-the-law/ Democracy and the Law] and [http://felixonline.co.uk/comment/3679/deportation-woes/ Deportation Woes]

=Chris' work=

[[Mod:mod2scientiadecusettutamen|Module 2 project]]

[[Mod:mod3 christopherkaye|Module 3 project]]

Rep:Mod:mod3 christopherkaye

2013-03-16T17:00:07Z

Ck1510: /* Activation energies */

=Christopher Kaye, ck1510, Module 3 Computational=

Extension granted by Dr Hunt to 16th March.

=Introduction=

This module uses Gaussian software to model transition states of reactions. A transition state is the maximum saddle point on a potential energy surface. These states are not observable spectroscopically as they are so short-lived, assumed to be on a similar order of magnitude to bond vibrations - approximately 10-18 s. <ref>Biochemistry by Reginald H. Garrett, Charles M. Grisham</ref>

Investigating transitions states is helpful in understanding kinetics and mechanisms of reactions. Gaussian modelling allows geometries and energies of transition states to be predicted.

In this module, two reactions' transition states are being investigated: the Cope Rearrangement, and Diels-Alder.

=Cope Rearrangement=

[[File:Cope rearrangement for 15hexadiene.png|200px]]

The Cope rearrangement is a pericyclic reaction, specifically a [3+3] sigmatropic rearrangement. Like all pericyclic reactions, it is concerted in nature and passes through a transition state and no intermediates. In the case of 1,5-hexadiene, the transition state goes through a chair-like or a boat-like transition state <ref> Futher Perspectives in Organic Chemistry by CIBA Foundation Symposium</ref>
Gaussian was used to identify low energy conformers and then to attempt to find boat and chair transition states.

==Optimisation of conformers==

Using Hartree-Fock method and 3-21G basis set in each case, various conformers were chosen and optimised. The gauche3 conformer was found to be the lowest energy conformer due to the 'gauche effect' of London forces and favourable orbital interactions. Where sterics become more important, it is expected that antiperiplanar would become the most stable conformer. <ref>Carbohydrate Chemistry and Biochemistry: Structure and Mechanism by M. L. Sinnott</ref>
===Optimisation of antiperiplanar1 1,5-hexadiene===

{{DOI|10042/24051}} Link to D-space optimisation output

[[File:Results summary anti ckaye.png|200px|thumb|center|Results summary of optimisation of anti-peri-planar 1,5-hexadiene]]

[[File:Anti1 ckaye.png]]
Using 'Symmetrize'(sic) the molecule was found to have C2 symmetry.

===Optimisation of gauche4 1,5-hexadiene===

By changing the conformation manually to a gauche linkage, and optimising as above, the following results summary was produced.

[[File:Results summary gauche4 ckaye.png|thumb|center|Results summary of optimisation of gauche 1,5-hexadiene]]

[[File:Gauche 4 picture ckaye.png]]

Link to .log file [[File:GAUCHE4 OPT CKAYE.LOG]]

===Optimisation of gauche6 1,5-hexadiene===

[[File:Results summary gauche6 ckaye.png]]

[[File:Gauche 6 picture ckaye.png]]

Link to .log file [[File:OPT GAUCHE6 CKAYE.LOG]]

===Optimisation of gauche3 1,5-hexadiene===

[[file:Results summary gauche3.png]]

[[file:gauche_3_picture_ckaye.png]]

Link to .log file[[File:FOR GAUCHE 3 INPUT CKAYE.LOG]]

===Optimisation of gauche1 1,5-hexadiene===

[[File:Results summary gauche1 ckaye.png]]

[[File:Gauche 1 picture ckaye.png]]

Link to .log file [[File:GAUCHE 1 CKAYE.LOG]]

===Optimisation of anti2 1,5-hexadiene===

[[File:Results summary anti2 ckaye.png]]

[[File:Anti 2 picture ckaye.png]]

Link to .log file [[File:ANTI 2 OPTIMISATION CKAYE.LOG]]

===Higher optimisation of anti2 1,5-hexadiene===

[[File:Anti 2 higher optimisation ckaye picture.png]]

Link to .log file [[File:ANTI 2 HIGHER OPTIMISATION CKAYE.LOG]]

=='Comparison' of two optimisations of anti2 1,5-hexadiene==

It is a '''major''' ''faux pas'' to directly compare optimisations using different basis sets. Both optimisations were carried out using Hartree-Fock method. The higher basis set yielded a much lower final energy, by approximately 3 atomic units. The bond lengths however are nearly identical, as can be seen below.

[[File:Bond lengths comparison ckaye.gif]]

==Frequency analysis of anti2==

From the frequency analysis of the higher optimised structure of anti2 1,5-hexadiene, the output file confirmed that there were no negative frequencies, which ensures that the molecule is at an energy minimum.

<pre> Low frequencies --- -18.8360 -11.7255 -0.0010 -0.0004 0.0004 1.7210
Low frequencies --- 72.7084 80.1375 120.0085</pre>

==Predicted infrared spectrum of anti2==

[[File:App2 ir spectrum ckaye.png]]

In the output file it can be seen that there are many vibrational modes. However, many have intensities of 0 because they do not involve a change in dipole moment, which is required for an interaction with electromagnetic field. Hence they do not appear on an IR spectrum.

==Optimisation of chair transition state structure==

An allylic H2CCHCH2 fragment was optimised using HF/3-21G basis set. This was later used to form the chair transition state below.

By fixing the bond forming/breaking distances of the terminal carbon atoms to approximately 2.2 Å and performing an opt+freq using the same basis set as before, but with TS(berny) selected and opt=noeigen, to allow imaginary frequencies. An imaginary frequency was observed at 818 cm-1, relating to the transition state. The displacement vectors of the vibration can be seen below

[[File:Transitionstateimaginaryvibration ckaye.png|center|thumb|imaginary vibration (still image, displacement vectors) of the transition state]]

==Intrinsic Reaction Co-ordinate (IRC) analysis of chair transition state from frozen co-ordinate==

[[File:Chair gradient stuffs ckaye.png|400px|center|thumb]]

With 'forward only' steps. As the gradient approaches zero, the energy is being minimised as gaussian translates the molecule to minimise the energy.

==Optimisation of boat transition state structure==

By using the same allylic H2CCHCH2 fragment that was optimised using HF/3-21G basis set for the chair TS.

Using the same method as for the chair transition state.

Yielded an imaginary frequency at 840 cm-1 corresponding to the transition state

[[File:Boat transition state cope vibration ckaye.png]]

==Activation energies==

The data obtained from the transition states and the optimised anti2 molecule can be used to calculate the activation energy for each of the chair and the boat structures. The results are in kj mol-1 converted from Hartree atomic units

=Diels-Alder=

[[File:Da ckaye scheme.png|300px|thumb|center|Reaction scheme of Diels-Alder cycloaddition]]

==Introduction==

A Diels-Alder reaction is a [4+2] cycloaddition between a conjugated diene and a dienophile, forming a 6-membered ring. The driving force of the reaction is likely to be enthalpic in nature due to the formation of (stronger) sigma bonds at the 'expense' of (weaker) pi bonds. The enthalpic contribution usually overrides any entropic disfavourability<ref>Biotechnology: Bridging Research and Applications edited by Daphne Kamely, Ananda M. Chakrabarty, Steven E. Kornguth</ref> (from the inherent ordering of two molecules into one).

Here, the diene is butadiene and the dienophile is ethylene.

Molecular orbital analysis is important because the symmetry of the reactant MOs is vital to establishing if the reaction occurs or not. If the reactants differ in symmetry then the required orbital overlap does not occur and so the reaction does not. (Woodward Hoffman rules)

==Optimisation==

Using semi-empirical AM1 basis set, a molecule of ''cis''-butadiene was optimised.

[[File:OPTIMISATION BUTADIENE CKAYE.LOG]] Link to .log file of optimisation of butadiene

[[File:Butadiene summary ckaye.png|200px|center|thumb|summary of output of optimisation]]

==MO of ''cis''-butadiene==

The molecular orbitals were obtained, with HOMO and LUMO of particular interest.

[[File:Lumo butadiene ckaye.png|200px|thumb|center|LUMO of butadiene]]
[[File:Homo butadiene ckaye.png|200px|thumb|center|HOMO of butadiene]]

As can be seen above, the LUMO is symmetric with respect to a plane down the middle of the molecule. The HOMO however is antisymmetric since it does not have a plane of symmetry.

The relative energies of the MOs of ''cis''-butadiene can be seen below.

[[File:Energylist butadiene ckaye.png|200px|thumb|center|List of MOs]]

==Formation of TS==

A guess structure of the TS was obtained using 2.20 Å fixed distance.

[[File:TS OPT CKAYE.LOG]] Link to .log file of TS optimisation

[[File:Ts picture ckaye.png|200px|center|thumb|TS picture]]

An imaginary frequency was found at 956 cm-1

Low frequencies --- -956.2090 -0.0435 -0.0282 -0.0032 1.6785 3.3690
Low frequencies --- 4.2132 147.3980 246.6385

Terminal carbon-carbon distances = 2.12 Å

==Regioselectivity of Diels Alder reaction==

==Using maleic anhydride to explore endo vs exo TS==

===Endo===

[[File:OPTIMISATION CYCLOHEXAMAL ENDO CKAYE 2.LOG]] Link to .log file

[[File:Ts results .png|200px|center|thumb|Summary of optimisation]]

[[File:Ts endo homo ckaye.png|200px|center|thumb|TS of endo]]

===Exo===

[[File:OPTIMISATION CYCLOHEXAMAL EXO TS CKAYE.LOG]] Link to .log file

[[File:Partial bond length ckaye exo ts.png|200px|center|thumb|TS with TS bond distance]]

==Conclusion==

Had all the calculations been done in time, transition state bond lengths could have been compared to know bond lengths to indicate the extent of bond formation / bonding interactions.

Reactions of the pi and pi* orbitals of ethylene and the HOMO of ''cis''-butadiene. The formation of C-C sigma bonds create an asymmetric MO. The HOMO of the TS is found to be asymmetric, allowing the reaction to occur.

=References=

<references/>

Rep:Mod:mod3 christopherkaye

2013-03-16T16:58:44Z

Ck1510: /* Activation energies */

=Christopher Kaye, ck1510, Module 3 Computational=

Extension granted by Dr Hunt to 16th March.

=Introduction=

This module uses Gaussian software to model transition states of reactions. A transition state is the maximum saddle point on a potential energy surface. These states are not observable spectroscopically as they are so short-lived, assumed to be on a similar order of magnitude to bond vibrations - approximately 10-18 s. <ref>Biochemistry by Reginald H. Garrett, Charles M. Grisham</ref>

Investigating transitions states is helpful in understanding kinetics and mechanisms of reactions. Gaussian modelling allows geometries and energies of transition states to be predicted.

In this module, two reactions' transition states are being investigated: the Cope Rearrangement, and Diels-Alder.

=Cope Rearrangement=

[[File:Cope rearrangement for 15hexadiene.png|200px]]

The Cope rearrangement is a pericyclic reaction, specifically a [3+3] sigmatropic rearrangement. Like all pericyclic reactions, it is concerted in nature and passes through a transition state and no intermediates. In the case of 1,5-hexadiene, the transition state goes through a chair-like or a boat-like transition state <ref> Futher Perspectives in Organic Chemistry by CIBA Foundation Symposium</ref>
Gaussian was used to identify low energy conformers and then to attempt to find boat and chair transition states.

==Optimisation of conformers==

Using Hartree-Fock method and 3-21G basis set in each case, various conformers were chosen and optimised. The gauche3 conformer was found to be the lowest energy conformer due to the 'gauche effect' of London forces and favourable orbital interactions. Where sterics become more important, it is expected that antiperiplanar would become the most stable conformer. <ref>Carbohydrate Chemistry and Biochemistry: Structure and Mechanism by M. L. Sinnott</ref>
===Optimisation of antiperiplanar1 1,5-hexadiene===

{{DOI|10042/24051}} Link to D-space optimisation output

[[File:Results summary anti ckaye.png|200px|thumb|center|Results summary of optimisation of anti-peri-planar 1,5-hexadiene]]

[[File:Anti1 ckaye.png]]
Using 'Symmetrize'(sic) the molecule was found to have C2 symmetry.

===Optimisation of gauche4 1,5-hexadiene===

By changing the conformation manually to a gauche linkage, and optimising as above, the following results summary was produced.

[[File:Results summary gauche4 ckaye.png|thumb|center|Results summary of optimisation of gauche 1,5-hexadiene]]

[[File:Gauche 4 picture ckaye.png]]

Link to .log file [[File:GAUCHE4 OPT CKAYE.LOG]]

===Optimisation of gauche6 1,5-hexadiene===

[[File:Results summary gauche6 ckaye.png]]

[[File:Gauche 6 picture ckaye.png]]

Link to .log file [[File:OPT GAUCHE6 CKAYE.LOG]]

===Optimisation of gauche3 1,5-hexadiene===

[[file:Results summary gauche3.png]]

[[file:gauche_3_picture_ckaye.png]]

Link to .log file[[File:FOR GAUCHE 3 INPUT CKAYE.LOG]]

===Optimisation of gauche1 1,5-hexadiene===

[[File:Results summary gauche1 ckaye.png]]

[[File:Gauche 1 picture ckaye.png]]

Link to .log file [[File:GAUCHE 1 CKAYE.LOG]]

===Optimisation of anti2 1,5-hexadiene===

[[File:Results summary anti2 ckaye.png]]

[[File:Anti 2 picture ckaye.png]]

Link to .log file [[File:ANTI 2 OPTIMISATION CKAYE.LOG]]

===Higher optimisation of anti2 1,5-hexadiene===

[[File:Anti 2 higher optimisation ckaye picture.png]]

Link to .log file [[File:ANTI 2 HIGHER OPTIMISATION CKAYE.LOG]]

=='Comparison' of two optimisations of anti2 1,5-hexadiene==

It is a '''major''' ''faux pas'' to directly compare optimisations using different basis sets. Both optimisations were carried out using Hartree-Fock method. The higher basis set yielded a much lower final energy, by approximately 3 atomic units. The bond lengths however are nearly identical, as can be seen below.

[[File:Bond lengths comparison ckaye.gif]]

==Frequency analysis of anti2==

From the frequency analysis of the higher optimised structure of anti2 1,5-hexadiene, the output file confirmed that there were no negative frequencies, which ensures that the molecule is at an energy minimum.

<pre> Low frequencies --- -18.8360 -11.7255 -0.0010 -0.0004 0.0004 1.7210
Low frequencies --- 72.7084 80.1375 120.0085</pre>

==Predicted infrared spectrum of anti2==

[[File:App2 ir spectrum ckaye.png]]

In the output file it can be seen that there are many vibrational modes. However, many have intensities of 0 because they do not involve a change in dipole moment, which is required for an interaction with electromagnetic field. Hence they do not appear on an IR spectrum.

==Optimisation of chair transition state structure==

An allylic H2CCHCH2 fragment was optimised using HF/3-21G basis set. This was later used to form the chair transition state below.

By fixing the bond forming/breaking distances of the terminal carbon atoms to approximately 2.2 Å and performing an opt+freq using the same basis set as before, but with TS(berny) selected and opt=noeigen, to allow imaginary frequencies. An imaginary frequency was observed at 818 cm-1, relating to the transition state. The displacement vectors of the vibration can be seen below

[[File:Transitionstateimaginaryvibration ckaye.png|center|thumb|imaginary vibration (still image, displacement vectors) of the transition state]]

==Intrinsic Reaction Co-ordinate (IRC) analysis of chair transition state from frozen co-ordinate==

[[File:Chair gradient stuffs ckaye.png|400px|center|thumb]]

With 'forward only' steps. As the gradient approaches zero, the energy is being minimised as gaussian translates the molecule to minimise the energy.

==Optimisation of boat transition state structure==

By using the same allylic H2CCHCH2 fragment that was optimised using HF/3-21G basis set for the chair TS.

Using the same method as for the chair transition state.

Yielded an imaginary frequency at 840 cm-1 corresponding to the transition state

[[File:Boat transition state cope vibration ckaye.png]]

==Activation energies==

The data obtained from the transition states and the optimised anti2 molecule can be used to calculate the activation energy for each of the chair and the boat structures. The results are in kj mol-1 converted from Hartree atomic units

Chair 144
Boat 180

=Diels-Alder=

[[File:Da ckaye scheme.png|300px|thumb|center|Reaction scheme of Diels-Alder cycloaddition]]

==Introduction==

A Diels-Alder reaction is a [4+2] cycloaddition between a conjugated diene and a dienophile, forming a 6-membered ring. The driving force of the reaction is likely to be enthalpic in nature due to the formation of (stronger) sigma bonds at the 'expense' of (weaker) pi bonds. The enthalpic contribution usually overrides any entropic disfavourability<ref>Biotechnology: Bridging Research and Applications edited by Daphne Kamely, Ananda M. Chakrabarty, Steven E. Kornguth</ref> (from the inherent ordering of two molecules into one).

Here, the diene is butadiene and the dienophile is ethylene.

Molecular orbital analysis is important because the symmetry of the reactant MOs is vital to establishing if the reaction occurs or not. If the reactants differ in symmetry then the required orbital overlap does not occur and so the reaction does not. (Woodward Hoffman rules)

==Optimisation==

Using semi-empirical AM1 basis set, a molecule of ''cis''-butadiene was optimised.

[[File:OPTIMISATION BUTADIENE CKAYE.LOG]] Link to .log file of optimisation of butadiene

[[File:Butadiene summary ckaye.png|200px|center|thumb|summary of output of optimisation]]

==MO of ''cis''-butadiene==

The molecular orbitals were obtained, with HOMO and LUMO of particular interest.

[[File:Lumo butadiene ckaye.png|200px|thumb|center|LUMO of butadiene]]
[[File:Homo butadiene ckaye.png|200px|thumb|center|HOMO of butadiene]]

As can be seen above, the LUMO is symmetric with respect to a plane down the middle of the molecule. The HOMO however is antisymmetric since it does not have a plane of symmetry.

The relative energies of the MOs of ''cis''-butadiene can be seen below.

[[File:Energylist butadiene ckaye.png|200px|thumb|center|List of MOs]]

==Formation of TS==

A guess structure of the TS was obtained using 2.20 Å fixed distance.

[[File:TS OPT CKAYE.LOG]] Link to .log file of TS optimisation

[[File:Ts picture ckaye.png|200px|center|thumb|TS picture]]

An imaginary frequency was found at 956 cm-1

Low frequencies --- -956.2090 -0.0435 -0.0282 -0.0032 1.6785 3.3690
Low frequencies --- 4.2132 147.3980 246.6385

Terminal carbon-carbon distances = 2.12 Å

==Regioselectivity of Diels Alder reaction==

==Using maleic anhydride to explore endo vs exo TS==

===Endo===

[[File:OPTIMISATION CYCLOHEXAMAL ENDO CKAYE 2.LOG]] Link to .log file

[[File:Ts results .png|200px|center|thumb|Summary of optimisation]]

[[File:Ts endo homo ckaye.png|200px|center|thumb|TS of endo]]

===Exo===

[[File:OPTIMISATION CYCLOHEXAMAL EXO TS CKAYE.LOG]] Link to .log file

[[File:Partial bond length ckaye exo ts.png|200px|center|thumb|TS with TS bond distance]]

==Conclusion==

Had all the calculations been done in time, transition state bond lengths could have been compared to know bond lengths to indicate the extent of bond formation / bonding interactions.

Reactions of the pi and pi* orbitals of ethylene and the HOMO of ''cis''-butadiene. The formation of C-C sigma bonds create an asymmetric MO. The HOMO of the TS is found to be asymmetric, allowing the reaction to occur.

=References=

<references/>

Rep:Mod:mod3 christopherkaye

2013-03-16T16:56:54Z

Ck1510:

=Christopher Kaye, ck1510, Module 3 Computational=

Extension granted by Dr Hunt to 16th March.

=Introduction=

This module uses Gaussian software to model transition states of reactions. A transition state is the maximum saddle point on a potential energy surface. These states are not observable spectroscopically as they are so short-lived, assumed to be on a similar order of magnitude to bond vibrations - approximately 10-18 s. <ref>Biochemistry by Reginald H. Garrett, Charles M. Grisham</ref>

Investigating transitions states is helpful in understanding kinetics and mechanisms of reactions. Gaussian modelling allows geometries and energies of transition states to be predicted.

In this module, two reactions' transition states are being investigated: the Cope Rearrangement, and Diels-Alder.

=Cope Rearrangement=

[[File:Cope rearrangement for 15hexadiene.png|200px]]

The Cope rearrangement is a pericyclic reaction, specifically a [3+3] sigmatropic rearrangement. Like all pericyclic reactions, it is concerted in nature and passes through a transition state and no intermediates. In the case of 1,5-hexadiene, the transition state goes through a chair-like or a boat-like transition state <ref> Futher Perspectives in Organic Chemistry by CIBA Foundation Symposium</ref>
Gaussian was used to identify low energy conformers and then to attempt to find boat and chair transition states.

==Optimisation of conformers==

Using Hartree-Fock method and 3-21G basis set in each case, various conformers were chosen and optimised. The gauche3 conformer was found to be the lowest energy conformer due to the 'gauche effect' of London forces and favourable orbital interactions. Where sterics become more important, it is expected that antiperiplanar would become the most stable conformer. <ref>Carbohydrate Chemistry and Biochemistry: Structure and Mechanism by M. L. Sinnott</ref>
===Optimisation of antiperiplanar1 1,5-hexadiene===

{{DOI|10042/24051}} Link to D-space optimisation output

[[File:Results summary anti ckaye.png|200px|thumb|center|Results summary of optimisation of anti-peri-planar 1,5-hexadiene]]

[[File:Anti1 ckaye.png]]
Using 'Symmetrize'(sic) the molecule was found to have C2 symmetry.

===Optimisation of gauche4 1,5-hexadiene===

By changing the conformation manually to a gauche linkage, and optimising as above, the following results summary was produced.

[[File:Results summary gauche4 ckaye.png|thumb|center|Results summary of optimisation of gauche 1,5-hexadiene]]

[[File:Gauche 4 picture ckaye.png]]

Link to .log file [[File:GAUCHE4 OPT CKAYE.LOG]]

===Optimisation of gauche6 1,5-hexadiene===

[[File:Results summary gauche6 ckaye.png]]

[[File:Gauche 6 picture ckaye.png]]

Link to .log file [[File:OPT GAUCHE6 CKAYE.LOG]]

===Optimisation of gauche3 1,5-hexadiene===

[[file:Results summary gauche3.png]]

[[file:gauche_3_picture_ckaye.png]]

Link to .log file[[File:FOR GAUCHE 3 INPUT CKAYE.LOG]]

===Optimisation of gauche1 1,5-hexadiene===

[[File:Results summary gauche1 ckaye.png]]

[[File:Gauche 1 picture ckaye.png]]

Link to .log file [[File:GAUCHE 1 CKAYE.LOG]]

===Optimisation of anti2 1,5-hexadiene===

[[File:Results summary anti2 ckaye.png]]

[[File:Anti 2 picture ckaye.png]]

Link to .log file [[File:ANTI 2 OPTIMISATION CKAYE.LOG]]

===Higher optimisation of anti2 1,5-hexadiene===

[[File:Anti 2 higher optimisation ckaye picture.png]]

Link to .log file [[File:ANTI 2 HIGHER OPTIMISATION CKAYE.LOG]]

=='Comparison' of two optimisations of anti2 1,5-hexadiene==

It is a '''major''' ''faux pas'' to directly compare optimisations using different basis sets. Both optimisations were carried out using Hartree-Fock method. The higher basis set yielded a much lower final energy, by approximately 3 atomic units. The bond lengths however are nearly identical, as can be seen below.

[[File:Bond lengths comparison ckaye.gif]]

==Frequency analysis of anti2==

From the frequency analysis of the higher optimised structure of anti2 1,5-hexadiene, the output file confirmed that there were no negative frequencies, which ensures that the molecule is at an energy minimum.

<pre> Low frequencies --- -18.8360 -11.7255 -0.0010 -0.0004 0.0004 1.7210
Low frequencies --- 72.7084 80.1375 120.0085</pre>

==Predicted infrared spectrum of anti2==

[[File:App2 ir spectrum ckaye.png]]

In the output file it can be seen that there are many vibrational modes. However, many have intensities of 0 because they do not involve a change in dipole moment, which is required for an interaction with electromagnetic field. Hence they do not appear on an IR spectrum.

==Optimisation of chair transition state structure==

An allylic H2CCHCH2 fragment was optimised using HF/3-21G basis set. This was later used to form the chair transition state below.

By fixing the bond forming/breaking distances of the terminal carbon atoms to approximately 2.2 Å and performing an opt+freq using the same basis set as before, but with TS(berny) selected and opt=noeigen, to allow imaginary frequencies. An imaginary frequency was observed at 818 cm-1, relating to the transition state. The displacement vectors of the vibration can be seen below

[[File:Transitionstateimaginaryvibration ckaye.png|center|thumb|imaginary vibration (still image, displacement vectors) of the transition state]]

==Intrinsic Reaction Co-ordinate (IRC) analysis of chair transition state from frozen co-ordinate==

[[File:Chair gradient stuffs ckaye.png|400px|center|thumb]]

With 'forward only' steps. As the gradient approaches zero, the energy is being minimised as gaussian translates the molecule to minimise the energy.

==Optimisation of boat transition state structure==

By using the same allylic H2CCHCH2 fragment that was optimised using HF/3-21G basis set for the chair TS.

Using the same method as for the chair transition state.

Yielded an imaginary frequency at 840 cm-1 corresponding to the transition state

[[File:Boat transition state cope vibration ckaye.png]]

==Activation energies==

The data obtained from the transiition states and the optimised anti2 molecule can be used to calculate the activation energy for each of the chair and the boat structures. The results are in Hartrees

=Diels-Alder=

[[File:Da ckaye scheme.png|300px|thumb|center|Reaction scheme of Diels-Alder cycloaddition]]

==Introduction==

A Diels-Alder reaction is a [4+2] cycloaddition between a conjugated diene and a dienophile, forming a 6-membered ring. The driving force of the reaction is likely to be enthalpic in nature due to the formation of (stronger) sigma bonds at the 'expense' of (weaker) pi bonds. The enthalpic contribution usually overrides any entropic disfavourability<ref>Biotechnology: Bridging Research and Applications edited by Daphne Kamely, Ananda M. Chakrabarty, Steven E. Kornguth</ref> (from the inherent ordering of two molecules into one).

Here, the diene is butadiene and the dienophile is ethylene.

Molecular orbital analysis is important because the symmetry of the reactant MOs is vital to establishing if the reaction occurs or not. If the reactants differ in symmetry then the required orbital overlap does not occur and so the reaction does not. (Woodward Hoffman rules)

==Optimisation==

Using semi-empirical AM1 basis set, a molecule of ''cis''-butadiene was optimised.

[[File:OPTIMISATION BUTADIENE CKAYE.LOG]] Link to .log file of optimisation of butadiene

[[File:Butadiene summary ckaye.png|200px|center|thumb|summary of output of optimisation]]

==MO of ''cis''-butadiene==

The molecular orbitals were obtained, with HOMO and LUMO of particular interest.

[[File:Lumo butadiene ckaye.png|200px|thumb|center|LUMO of butadiene]]
[[File:Homo butadiene ckaye.png|200px|thumb|center|HOMO of butadiene]]

As can be seen above, the LUMO is symmetric with respect to a plane down the middle of the molecule. The HOMO however is antisymmetric since it does not have a plane of symmetry.

The relative energies of the MOs of ''cis''-butadiene can be seen below.

[[File:Energylist butadiene ckaye.png|200px|thumb|center|List of MOs]]

==Formation of TS==

A guess structure of the TS was obtained using 2.20 Å fixed distance.

[[File:TS OPT CKAYE.LOG]] Link to .log file of TS optimisation

[[File:Ts picture ckaye.png|200px|center|thumb|TS picture]]

An imaginary frequency was found at 956 cm-1

Low frequencies --- -956.2090 -0.0435 -0.0282 -0.0032 1.6785 3.3690
Low frequencies --- 4.2132 147.3980 246.6385

Terminal carbon-carbon distances = 2.12 Å

==Regioselectivity of Diels Alder reaction==

==Using maleic anhydride to explore endo vs exo TS==

===Endo===

[[File:OPTIMISATION CYCLOHEXAMAL ENDO CKAYE 2.LOG]] Link to .log file

[[File:Ts results .png|200px|center|thumb|Summary of optimisation]]

[[File:Ts endo homo ckaye.png|200px|center|thumb|TS of endo]]

===Exo===

[[File:OPTIMISATION CYCLOHEXAMAL EXO TS CKAYE.LOG]] Link to .log file

[[File:Partial bond length ckaye exo ts.png|200px|center|thumb|TS with TS bond distance]]

==Conclusion==

Had all the calculations been done in time, transition state bond lengths could have been compared to know bond lengths to indicate the extent of bond formation / bonding interactions.

Reactions of the pi and pi* orbitals of ethylene and the HOMO of ''cis''-butadiene. The formation of C-C sigma bonds create an asymmetric MO. The HOMO of the TS is found to be asymmetric, allowing the reaction to occur.

=References=

<references/>

Rep:Mod:mod3 christopherkaye

2013-03-16T16:45:29Z

Ck1510:

=Christopher Kaye, ck1510, Module 3 Computational=

Extension granted by Dr Hunt to 16th March.

=Introduction=

This module uses Gaussian software to model transition states of reactions. A transition state is the maximum saddle point on a potential energy surface. These states are not observable spectroscopically as they are so short-lived, assumed to be on a similar order of magnitude to bond vibrations - approximately 10-18 s. <ref>Biochemistry by Reginald H. Garrett, Charles M. Grisham</ref>

Investigating transitions states is helpful in understanding kinetics and mechanisms of reactions. Gaussian modelling allows geometries and energies of transition states to be predicted.

In this module, two reactions' transition states are being investigated: the Cope Rearrangement, and Diels-Alder.

=Cope Rearrangement=

[[File:Cope rearrangement for 15hexadiene.png|200px]]

The Cope rearrangement is a pericyclic reaction, specifically a [3+3] sigmatropic rearrangement. Like all pericyclic reactions, it is concerted in nature and passes through a transition state and no intermediates. In the case of 1,5-hexadiene, the transition state goes through a chair-like or a boat-like transition state <ref> Futher Perspectives in Organic Chemistry by CIBA Foundation Symposium</ref>
Gaussian was used to identify low energy conformers and then to attempt to find boat and chair transition states.

==Optimisation of conformers==

Using Hartree-Fock method and 3-21G basis set in each case, various conformers were chosen and optimised. The gauche3 conformer was found to be the lowest energy conformer due to the 'gauche effect' of London forces and favourable orbital interactions. Where sterics become more important, it is expected that antiperiplanar would become the most stable conformer. <ref>Carbohydrate Chemistry and Biochemistry: Structure and Mechanism by M. L. Sinnott</ref>
===Optimisation of antiperiplanar1 1,5-hexadiene===

{{DOI|10042/24051}} Link to D-space optimisation output

[[File:Results summary anti ckaye.png|200px|thumb|center|Results summary of optimisation of anti-peri-planar 1,5-hexadiene]]

[[File:Anti1 ckaye.png]]
Using 'Symmetrize'(sic) the molecule was found to have C2 symmetry.

===Optimisation of gauche4 1,5-hexadiene===

By changing the conformation manually to a gauche linkage, and optimising as above, the following results summary was produced.

[[File:Results summary gauche4 ckaye.png|thumb|center|Results summary of optimisation of gauche 1,5-hexadiene]]

[[File:Gauche 4 picture ckaye.png]]

Link to .log file [[File:GAUCHE4 OPT CKAYE.LOG]]

===Optimisation of gauche6 1,5-hexadiene===

[[File:Results summary gauche6 ckaye.png]]

[[File:Gauche 6 picture ckaye.png]]

Link to .log file [[File:OPT GAUCHE6 CKAYE.LOG]]

===Optimisation of gauche3 1,5-hexadiene===

[[file:Results summary gauche3.png]]

[[file:gauche_3_picture_ckaye.png]]

Link to .log file[[File:FOR GAUCHE 3 INPUT CKAYE.LOG]]

===Optimisation of gauche1 1,5-hexadiene===

[[File:Results summary gauche1 ckaye.png]]

[[File:Gauche 1 picture ckaye.png]]

Link to .log file [[File:GAUCHE 1 CKAYE.LOG]]

===Optimisation of anti2 1,5-hexadiene===

[[File:Results summary anti2 ckaye.png]]

[[File:Anti 2 picture ckaye.png]]

Link to .log file [[File:ANTI 2 OPTIMISATION CKAYE.LOG]]

===Higher optimisation of anti2 1,5-hexadiene===

[[File:Anti 2 higher optimisation ckaye picture.png]]

Link to .log file [[File:ANTI 2 HIGHER OPTIMISATION CKAYE.LOG]]

==='Comparison' of two optimisations of anti2 1,5-hexadiene===

It is a '''major''' ''faux pas'' to directly compare optimisations using different basis sets. Both optimisations were carried out using Hartree-Fock method. The higher basis set yielded a much lower final energy, by approximately 3 atomic units. The bond lengths however are nearly identical, as can be seen below.

[[File:Bond lengths comparison ckaye.gif]]

===Frequency analysis of anti2===

From the frequency analysis of the higher optimised structure of anti2 1,5-hexadiene, the output file confirmed that there were no negative frequencies, which ensures that the molecule is at an energy minimum.

<pre> Low frequencies --- -18.8360 -11.7255 -0.0010 -0.0004 0.0004 1.7210
Low frequencies --- 72.7084 80.1375 120.0085</pre>

===Predicted infrared spectrum of anti2===

[[File:App2 ir spectrum ckaye.png]]

In the output file it can be seen that there are many vibrational modes. However, many have intensities of 0 because they do not involve a change in dipole moment, which is required for an interaction with electromagnetic field. Hence they do not appear on an IR spectrum.

===Optimisation of chair transition state structure===

An allylic H2CCHCH2 fragment was optimised using HF/3-21G basis set. This was later used to form the chair transition state below.

By fixing the bond forming/breaking distances of the terminal carbon atoms to approximately 2.2 Å and performing an opt+freq using the same basis set as before, but with TS(berny) selected and opt=noeigen, to allow imaginary frequencies. An imaginary frequency was observed at 818 cm-1, relating to the transition state. The displacement vectors of the vibration can be seen below

[[File:Transitionstateimaginaryvibration ckaye.png|center|thumb|imaginary vibration (still image, displacement vectors) of the transition state]]

===Intrinsic Reaction Co-ordinate (IRC) analysis of chair transition state from frozen co-ordinate===

[[File:Chair gradient stuffs ckaye.png|400px|center|thumb]]

With 'forward only' steps. As the gradient approaches zero, the energy is being minimised as gaussian translates the molecule to minimise the energy.

===Optimisation of boat transition state structure===

By using the same allylic H2CCHCH2 fragment that was optimised using HF/3-21G basis set for the chair TS.

Using the same method as for the chair transition state.

Yielded an imaginary frequency at 840 cm-1 corresponding to the transition state

[[File:Boat transition state cope vibration ckaye.png]]

==Conclusion==

=Diels-Alder=

[[File:Da ckaye scheme.png|300px|thumb|center|Reaction scheme of Diels-Alder cycloaddition]]

==Introduction==

A Diels-Alder reaction is a [4+2] cycloaddition between a conjugated diene and a dienophile, forming a 6-membered ring. The driving force of the reaction is likely to be enthalpic in nature due to the formation of (stronger) sigma bonds at the 'expense' of (weaker) pi bonds. The enthalpic contribution usually overrides any entropic disfavourability<ref>Biotechnology: Bridging Research and Applications edited by Daphne Kamely, Ananda M. Chakrabarty, Steven E. Kornguth</ref> (from the inherent ordering of two molecules into one).

Here, the diene is butadiene and the dienophile is ethylene.

Molecular orbital analysis is important because the symmetry of the reactant MOs is vital to establishing if the reaction occurs or not. If the reactants differ in symmetry then the required orbital overlap does not occur and so the reaction does not. (Woodward Hoffman rules)

==Optimisation==

Using semi-empirical AM1 basis set, a molecule of ''cis''-butadiene was optimised.

[[File:OPTIMISATION BUTADIENE CKAYE.LOG]] Link to .log file of optimisation of butadiene

[[File:Butadiene summary ckaye.png|200px|center|thumb|summary of output of optimisation]]

==MO of ''cis''-butadiene==

The molecular orbitals were obtained, with HOMO and LUMO of particular interest.

[[File:Lumo butadiene ckaye.png|200px|thumb|center|LUMO of butadiene]]
[[File:Homo butadiene ckaye.png|200px|thumb|center|HOMO of butadiene]]

As can be seen above, the LUMO is symmetric with respect to a plane down the middle of the molecule. The HOMO however is antisymmetric since it does not have a plane of symmetry.

The relative energies of the MOs of ''cis''-butadiene can be seen below.

[[File:Energylist butadiene ckaye.png|200px|thumb|center|List of MOs]]

==Formation of TS==

A guess structure of the TS was obtained using 2.20 Å fixed distance.

[[File:TS OPT CKAYE.LOG]] Link to .log file of TS optimisation

[[File:Ts picture ckaye.png|200px|center|thumb|TS picture]]

An imaginary frequency was found at 956 cm-1

Low frequencies --- -956.2090 -0.0435 -0.0282 -0.0032 1.6785 3.3690
Low frequencies --- 4.2132 147.3980 246.6385

Terminal carbon-carbon distances = 2.12 Å

==Regioselectivity of Diels Alder reaction==

==Using maleic anhydride to explore endo vs exo TS==

===Endo===

[[File:OPTIMISATION CYCLOHEXAMAL ENDO CKAYE 2.LOG]] Link to .log file

[[File:Ts results .png|200px|center|thumb|Summary of optimisation]]

[[File:Ts endo homo ckaye.png|200px|center|thumb|TS of endo]]

===Exo===

[[File:OPTIMISATION CYCLOHEXAMAL EXO TS CKAYE.LOG]] Link to .log file

[[File:Partial bond length ckaye exo ts.png|200px|center|thumb|TS with TS bond distance]]

=References=

<references/>

Rep:Mod:mod3 christopherkaye

2013-03-16T16:42:39Z

Ck1510: /* Endo */

=Christopher Kaye, ck1510, Module 3 Computational=

Extension granted by Dr Hunt to 16th March.

=Introduction=

This module uses Gaussian software to model transition states of reactions. A transition state is the maximum saddle point on a potential energy surface. These states are not observable spectroscopically as they are so short-lived, assumed to be on a similar order of magnitude to bond vibrations - approximately 10-18 s. <ref>Biochemistry by Reginald H. Garrett, Charles M. Grisham</ref>

Investigating transitions states is helpful in understanding kinetics and mechanisms of reactions. Gaussian modelling allows geometries and energies of transition states to be predicted.

In this module, two reactions' transition states are being investigated: the Cope Rearrangement, and Diels-Alder.

=Cope Rearrangement=

[[File:Cope rearrangement for 15hexadiene.png|200px]]

The Cope rearrangement is a pericyclic reaction, specifically a [3+3] sigmatropic rearrangement. Like all pericyclic reactions, it is concerted in nature and passes through a transition state and no intermediates. In the case of 1,5-hexadiene, the transition state goes through a chair-like or a boat-like transition state <ref> Futher Perspectives in Organic Chemistry by CIBA Foundation Symposium</ref>
Gaussian was used to identify low energy conformers and then to attempt to find boat and chair transition states.

=Optimisation of conformers=

Using Hartree-Fock method and 3-21G basis set in each case, various conformers were chosen and optimised. The gauche3 conformer was found to be the lowest energy conformer due to the 'gauche effect' of London forces and favourable orbital interactions. Where sterics become more important, it is expected that antiperiplanar would become the most stable conformer. <ref>Carbohydrate Chemistry and Biochemistry: Structure and Mechanism by M. L. Sinnott</ref>
==Optimisation of antiperiplanar1 1,5-hexadiene==

{{DOI|10042/24051}} Link to D-space optimisation output

[[File:Results summary anti ckaye.png|200px|thumb|center|Results summary of optimisation of anti-peri-planar 1,5-hexadiene]]

[[File:Anti1 ckaye.png]]
Using 'Symmetrize'(sic) the molecule was found to have C2 symmetry.

==Optimisation of gauche4 1,5-hexadiene==

By changing the conformation manually to a gauche linkage, and optimising as above, the following results summary was produced.

[[File:Results summary gauche4 ckaye.png|thumb|center|Results summary of optimisation of gauche 1,5-hexadiene]]

[[File:Gauche 4 picture ckaye.png]]

Link to .log file [[File:GAUCHE4 OPT CKAYE.LOG]]

==Optimisation of gauche6 1,5-hexadiene==

[[File:Results summary gauche6 ckaye.png]]

[[File:Gauche 6 picture ckaye.png]]

Link to .log file [[File:OPT GAUCHE6 CKAYE.LOG]]

==Optimisation of gauche3 1,5-hexadiene==

[[file:Results summary gauche3.png]]

[[file:gauche_3_picture_ckaye.png]]

Link to .log file[[File:FOR GAUCHE 3 INPUT CKAYE.LOG]]

==Optimisation of gauche1 1,5-hexadiene==

[[File:Results summary gauche1 ckaye.png]]

[[File:Gauche 1 picture ckaye.png]]

Link to .log file [[File:GAUCHE 1 CKAYE.LOG]]

==Optimisation of anti2 1,5-hexadiene==

[[File:Results summary anti2 ckaye.png]]

[[File:Anti 2 picture ckaye.png]]

Link to .log file [[File:ANTI 2 OPTIMISATION CKAYE.LOG]]

==Higher optimisation of anti2 1,5-hexadiene==

[[File:Anti 2 higher optimisation ckaye picture.png]]

Link to .log file [[File:ANTI 2 HIGHER OPTIMISATION CKAYE.LOG]]

=='Comparison' of two optimisations of anti2 1,5-hexadiene==

It is a '''major''' ''faux pas'' to directly compare optimisations using different basis sets. Both optimisations were carried out using Hartree-Fock method. The higher basis set yielded a much lower final energy, by approximately 3 atomic units. The bond lengths however are nearly identical, as can be seen below.

[[File:Bond lengths comparison ckaye.gif]]

==Frequency analysis of anti2==

From the frequency analysis of the higher optimised structure of anti2 1,5-hexadiene, the output file confirmed that there were no negative frequencies, which ensures that the molecule is at an energy minimum.

<pre> Low frequencies --- -18.8360 -11.7255 -0.0010 -0.0004 0.0004 1.7210
Low frequencies --- 72.7084 80.1375 120.0085</pre>

==Predicted infrared spectrum of anti2==

[[File:App2 ir spectrum ckaye.png]]

In the output file it can be seen that there are many vibrational modes. However, many have intensities of 0 because they do not involve a change in dipole moment, which is required for an interaction with electromagnetic field. Hence they do not appear on an IR spectrum.

==Optimisation of chair transition state structure==

An allylic H2CCHCH2 fragment was optimised using HF/3-21G basis set. This was later used to form the chair transition state below.

By fixing the bond forming/breaking distances of the terminal carbon atoms to approximately 2.2 Å and performing an opt+freq using the same basis set as before, but with TS(berny) selected and opt=noeigen, to allow imaginary frequencies. An imaginary frequency was observed at 818 cm-1, relating to the transition state. The displacement vectors of the vibration can be seen below

[[File:Transitionstateimaginaryvibration ckaye.png|center|thumb|imaginary vibration (still image, displacement vectors) of the transition state]]

==Intrinsic Reaction Co-ordinate (IRC) analysis of chair transition state from frozen co-ordinate==

[[File:Chair gradient stuffs ckaye.png|400px|center|thumb]]

With 'forward only' steps. As the gradient approaches zero, the energy is being minimised as gaussian translates the molecule to minimise the energy.

==Optimisation of boat transition state structure==

By using the same allylic H2CCHCH2 fragment that was optimised using HF/3-21G basis set for the chair TS.

Using the same method as for the chair transition state.

Yielded an imaginary frequency at 840 cm-1 corresponding to the transition state

[[File:Boat transition state cope vibration ckaye.png]]

=Diels-Alder=

[[File:Da ckaye scheme.png|300px|thumb|center|Reaction scheme of Diels-Alder cycloaddition]]

==Introduction==

A Diels-Alder reaction is a [4+2] cycloaddition between a conjugated diene and a dienophile, forming a 6-membered ring. The driving force of the reaction is likely to be enthalpic in nature due to the formation of (stronger) sigma bonds at the 'expense' of (weaker) pi bonds. The enthalpic contribution usually overrides any entropic disfavourability<ref>Biotechnology: Bridging Research and Applications edited by Daphne Kamely, Ananda M. Chakrabarty, Steven E. Kornguth</ref> (from the inherent ordering of two molecules into one).

Here, the diene is butadiene and the dienophile is ethylene.

Molecular orbital analysis is important because the symmetry of the reactant MOs is vital to establishing if the reaction occurs or not. If the reactants differ in symmetry then the required orbital overlap does not occur and so the reaction does not. (Woodward Hoffman rules)

==Optimisation==

Using semi-empirical AM1 basis set, a molecule of ''cis''-butadiene was optimised.

[[File:OPTIMISATION BUTADIENE CKAYE.LOG]] Link to .log file of optimisation of butadiene

[[File:Butadiene summary ckaye.png|200px|center|thumb|summary of output of optimisation]]

==MO of ''cis''-butadiene==

The molecular orbitals were obtained, with HOMO and LUMO of particular interest.

[[File:Lumo butadiene ckaye.png|200px|thumb|center|LUMO of butadiene]]
[[File:Homo butadiene ckaye.png|200px|thumb|center|HOMO of butadiene]]

As can be seen above, the LUMO is symmetric with respect to a plane down the middle of the molecule. The HOMO however is antisymmetric since it does not have a plane of symmetry.

The relative energies of the MOs of ''cis''-butadiene can be seen below.

[[File:Energylist butadiene ckaye.png|200px|thumb|center|List of MOs]]

==Formation of TS==

A guess structure of the TS was obtained using 2.20 Å fixed distance.

[[File:TS OPT CKAYE.LOG]] Link to .log file of TS optimisation

[[File:Ts picture ckaye.png|200px|center|thumb|TS picture]]

An imaginary frequency was found at 956 cm-1

Low frequencies --- -956.2090 -0.0435 -0.0282 -0.0032 1.6785 3.3690
Low frequencies --- 4.2132 147.3980 246.6385

Terminal carbon-carbon distances = 2.12 Å

==Regioselectivity of Diels Alder reaction==

==Using maleic anhydride to explore endo vs exo TS==

===Endo===

[[File:OPTIMISATION CYCLOHEXAMAL ENDO CKAYE 2.LOG]] Link to .log file

[[File:Ts results .png|200px|center|thumb|Summary of optimisation]]

[[File:Ts endo homo ckaye.png|200px|center|thumb|TS of endo]]

===Exo===

[[File:OPTIMISATION CYCLOHEXAMAL EXO TS CKAYE.LOG]] Link to .log file

[[File:Partial bond length ckaye exo ts.png|200px|center|thumb|TS with TS bond distance]]

=References=

<references/>

File:Ts results .png

2013-03-16T16:41:40Z

Ck1510:

Rep:Mod:mod3 christopherkaye

2013-03-16T16:39:04Z

Ck1510: /* MO of TS */

=Christopher Kaye, ck1510, Module 3 Computational=

Extension granted by Dr Hunt to 16th March.

=Introduction=

This module uses Gaussian software to model transition states of reactions. A transition state is the maximum saddle point on a potential energy surface. These states are not observable spectroscopically as they are so short-lived, assumed to be on a similar order of magnitude to bond vibrations - approximately 10-18 s. <ref>Biochemistry by Reginald H. Garrett, Charles M. Grisham</ref>

Investigating transitions states is helpful in understanding kinetics and mechanisms of reactions. Gaussian modelling allows geometries and energies of transition states to be predicted.

In this module, two reactions' transition states are being investigated: the Cope Rearrangement, and Diels-Alder.

=Cope Rearrangement=

[[File:Cope rearrangement for 15hexadiene.png|200px]]

The Cope rearrangement is a pericyclic reaction, specifically a [3+3] sigmatropic rearrangement. Like all pericyclic reactions, it is concerted in nature and passes through a transition state and no intermediates. In the case of 1,5-hexadiene, the transition state goes through a chair-like or a boat-like transition state <ref> Futher Perspectives in Organic Chemistry by CIBA Foundation Symposium</ref>
Gaussian was used to identify low energy conformers and then to attempt to find boat and chair transition states.

=Optimisation of conformers=

Using Hartree-Fock method and 3-21G basis set in each case, various conformers were chosen and optimised. The gauche3 conformer was found to be the lowest energy conformer due to the 'gauche effect' of London forces and favourable orbital interactions. Where sterics become more important, it is expected that antiperiplanar would become the most stable conformer. <ref>Carbohydrate Chemistry and Biochemistry: Structure and Mechanism by M. L. Sinnott</ref>
==Optimisation of antiperiplanar1 1,5-hexadiene==

{{DOI|10042/24051}} Link to D-space optimisation output

[[File:Results summary anti ckaye.png|200px|thumb|center|Results summary of optimisation of anti-peri-planar 1,5-hexadiene]]

[[File:Anti1 ckaye.png]]
Using 'Symmetrize'(sic) the molecule was found to have C2 symmetry.

==Optimisation of gauche4 1,5-hexadiene==

By changing the conformation manually to a gauche linkage, and optimising as above, the following results summary was produced.

[[File:Results summary gauche4 ckaye.png|thumb|center|Results summary of optimisation of gauche 1,5-hexadiene]]

[[File:Gauche 4 picture ckaye.png]]

Link to .log file [[File:GAUCHE4 OPT CKAYE.LOG]]

==Optimisation of gauche6 1,5-hexadiene==

[[File:Results summary gauche6 ckaye.png]]

[[File:Gauche 6 picture ckaye.png]]

Link to .log file [[File:OPT GAUCHE6 CKAYE.LOG]]

==Optimisation of gauche3 1,5-hexadiene==

[[file:Results summary gauche3.png]]

[[file:gauche_3_picture_ckaye.png]]

Link to .log file[[File:FOR GAUCHE 3 INPUT CKAYE.LOG]]

==Optimisation of gauche1 1,5-hexadiene==

[[File:Results summary gauche1 ckaye.png]]

[[File:Gauche 1 picture ckaye.png]]

Link to .log file [[File:GAUCHE 1 CKAYE.LOG]]

==Optimisation of anti2 1,5-hexadiene==

[[File:Results summary anti2 ckaye.png]]

[[File:Anti 2 picture ckaye.png]]

Link to .log file [[File:ANTI 2 OPTIMISATION CKAYE.LOG]]

==Higher optimisation of anti2 1,5-hexadiene==

[[File:Anti 2 higher optimisation ckaye picture.png]]

Link to .log file [[File:ANTI 2 HIGHER OPTIMISATION CKAYE.LOG]]

=='Comparison' of two optimisations of anti2 1,5-hexadiene==

It is a '''major''' ''faux pas'' to directly compare optimisations using different basis sets. Both optimisations were carried out using Hartree-Fock method. The higher basis set yielded a much lower final energy, by approximately 3 atomic units. The bond lengths however are nearly identical, as can be seen below.

[[File:Bond lengths comparison ckaye.gif]]

==Frequency analysis of anti2==

From the frequency analysis of the higher optimised structure of anti2 1,5-hexadiene, the output file confirmed that there were no negative frequencies, which ensures that the molecule is at an energy minimum.

<pre> Low frequencies --- -18.8360 -11.7255 -0.0010 -0.0004 0.0004 1.7210
Low frequencies --- 72.7084 80.1375 120.0085</pre>

==Predicted infrared spectrum of anti2==

[[File:App2 ir spectrum ckaye.png]]

In the output file it can be seen that there are many vibrational modes. However, many have intensities of 0 because they do not involve a change in dipole moment, which is required for an interaction with electromagnetic field. Hence they do not appear on an IR spectrum.

==Optimisation of chair transition state structure==

An allylic H2CCHCH2 fragment was optimised using HF/3-21G basis set. This was later used to form the chair transition state below.

By fixing the bond forming/breaking distances of the terminal carbon atoms to approximately 2.2 Å and performing an opt+freq using the same basis set as before, but with TS(berny) selected and opt=noeigen, to allow imaginary frequencies. An imaginary frequency was observed at 818 cm-1, relating to the transition state. The displacement vectors of the vibration can be seen below

[[File:Transitionstateimaginaryvibration ckaye.png|center|thumb|imaginary vibration (still image, displacement vectors) of the transition state]]

==Intrinsic Reaction Co-ordinate (IRC) analysis of chair transition state from frozen co-ordinate==

[[File:Chair gradient stuffs ckaye.png|400px|center|thumb]]

With 'forward only' steps. As the gradient approaches zero, the energy is being minimised as gaussian translates the molecule to minimise the energy.

==Optimisation of boat transition state structure==

By using the same allylic H2CCHCH2 fragment that was optimised using HF/3-21G basis set for the chair TS.

Using the same method as for the chair transition state.

Yielded an imaginary frequency at 840 cm-1 corresponding to the transition state

[[File:Boat transition state cope vibration ckaye.png]]

=Diels-Alder=

[[File:Da ckaye scheme.png|300px|thumb|center|Reaction scheme of Diels-Alder cycloaddition]]

==Introduction==

A Diels-Alder reaction is a [4+2] cycloaddition between a conjugated diene and a dienophile, forming a 6-membered ring. The driving force of the reaction is likely to be enthalpic in nature due to the formation of (stronger) sigma bonds at the 'expense' of (weaker) pi bonds. The enthalpic contribution usually overrides any entropic disfavourability<ref>Biotechnology: Bridging Research and Applications edited by Daphne Kamely, Ananda M. Chakrabarty, Steven E. Kornguth</ref> (from the inherent ordering of two molecules into one).

Here, the diene is butadiene and the dienophile is ethylene.

Molecular orbital analysis is important because the symmetry of the reactant MOs is vital to establishing if the reaction occurs or not. If the reactants differ in symmetry then the required orbital overlap does not occur and so the reaction does not. (Woodward Hoffman rules)

==Optimisation==

Using semi-empirical AM1 basis set, a molecule of ''cis''-butadiene was optimised.

[[File:OPTIMISATION BUTADIENE CKAYE.LOG]] Link to .log file of optimisation of butadiene

[[File:Butadiene summary ckaye.png|200px|center|thumb|summary of output of optimisation]]

==MO of ''cis''-butadiene==

The molecular orbitals were obtained, with HOMO and LUMO of particular interest.

[[File:Lumo butadiene ckaye.png|200px|thumb|center|LUMO of butadiene]]
[[File:Homo butadiene ckaye.png|200px|thumb|center|HOMO of butadiene]]

As can be seen above, the LUMO is symmetric with respect to a plane down the middle of the molecule. The HOMO however is antisymmetric since it does not have a plane of symmetry.

The relative energies of the MOs of ''cis''-butadiene can be seen below.

[[File:Energylist butadiene ckaye.png|200px|thumb|center|List of MOs]]

==Formation of TS==

A guess structure of the TS was obtained using 2.20 Å fixed distance.

[[File:TS OPT CKAYE.LOG]] Link to .log file of TS optimisation

[[File:Ts picture ckaye.png|200px|center|thumb|TS picture]]

An imaginary frequency was found at 956 cm-1

Low frequencies --- -956.2090 -0.0435 -0.0282 -0.0032 1.6785 3.3690
Low frequencies --- 4.2132 147.3980 246.6385

Terminal carbon-carbon distances = 2.12 Å

==Regioselectivity of Diels Alder reaction==

==Using maleic anhydride to explore endo vs exo TS==

===Endo===

[[File:OPTIMISATION CYCLOHEXAMAL ENDO CKAYE 2.LOG]] Link to .log file

[[File:Ts endo homo ckaye.png|200px|center|thumb|TS of endo]]

===Exo===

[[File:OPTIMISATION CYCLOHEXAMAL EXO TS CKAYE.LOG]] Link to .log file

[[File:Partial bond length ckaye exo ts.png|200px|center|thumb|TS with TS bond distance]]

=References=

<references/>

Rep:Mod:mod3 christopherkaye

2013-03-16T16:37:28Z

Ck1510: /* Introduction */

=Christopher Kaye, ck1510, Module 3 Computational=

Extension granted by Dr Hunt to 16th March.

=Introduction=

This module uses Gaussian software to model transition states of reactions. A transition state is the maximum saddle point on a potential energy surface. These states are not observable spectroscopically as they are so short-lived, assumed to be on a similar order of magnitude to bond vibrations - approximately 10-18 s. <ref>Biochemistry by Reginald H. Garrett, Charles M. Grisham</ref>

Investigating transitions states is helpful in understanding kinetics and mechanisms of reactions. Gaussian modelling allows geometries and energies of transition states to be predicted.

In this module, two reactions' transition states are being investigated: the Cope Rearrangement, and Diels-Alder.

=Cope Rearrangement=

[[File:Cope rearrangement for 15hexadiene.png|200px]]

The Cope rearrangement is a pericyclic reaction, specifically a [3+3] sigmatropic rearrangement. Like all pericyclic reactions, it is concerted in nature and passes through a transition state and no intermediates. In the case of 1,5-hexadiene, the transition state goes through a chair-like or a boat-like transition state <ref> Futher Perspectives in Organic Chemistry by CIBA Foundation Symposium</ref>
Gaussian was used to identify low energy conformers and then to attempt to find boat and chair transition states.

=Optimisation of conformers=

Using Hartree-Fock method and 3-21G basis set in each case, various conformers were chosen and optimised. The gauche3 conformer was found to be the lowest energy conformer due to the 'gauche effect' of London forces and favourable orbital interactions. Where sterics become more important, it is expected that antiperiplanar would become the most stable conformer. <ref>Carbohydrate Chemistry and Biochemistry: Structure and Mechanism by M. L. Sinnott</ref>
==Optimisation of antiperiplanar1 1,5-hexadiene==

{{DOI|10042/24051}} Link to D-space optimisation output

[[File:Results summary anti ckaye.png|200px|thumb|center|Results summary of optimisation of anti-peri-planar 1,5-hexadiene]]

[[File:Anti1 ckaye.png]]
Using 'Symmetrize'(sic) the molecule was found to have C2 symmetry.

==Optimisation of gauche4 1,5-hexadiene==

By changing the conformation manually to a gauche linkage, and optimising as above, the following results summary was produced.

[[File:Results summary gauche4 ckaye.png|thumb|center|Results summary of optimisation of gauche 1,5-hexadiene]]

[[File:Gauche 4 picture ckaye.png]]

Link to .log file [[File:GAUCHE4 OPT CKAYE.LOG]]

==Optimisation of gauche6 1,5-hexadiene==

[[File:Results summary gauche6 ckaye.png]]

[[File:Gauche 6 picture ckaye.png]]

Link to .log file [[File:OPT GAUCHE6 CKAYE.LOG]]

==Optimisation of gauche3 1,5-hexadiene==

[[file:Results summary gauche3.png]]

[[file:gauche_3_picture_ckaye.png]]

Link to .log file[[File:FOR GAUCHE 3 INPUT CKAYE.LOG]]

==Optimisation of gauche1 1,5-hexadiene==

[[File:Results summary gauche1 ckaye.png]]

[[File:Gauche 1 picture ckaye.png]]

Link to .log file [[File:GAUCHE 1 CKAYE.LOG]]

==Optimisation of anti2 1,5-hexadiene==

[[File:Results summary anti2 ckaye.png]]

[[File:Anti 2 picture ckaye.png]]

Link to .log file [[File:ANTI 2 OPTIMISATION CKAYE.LOG]]

==Higher optimisation of anti2 1,5-hexadiene==

[[File:Anti 2 higher optimisation ckaye picture.png]]

Link to .log file [[File:ANTI 2 HIGHER OPTIMISATION CKAYE.LOG]]

=='Comparison' of two optimisations of anti2 1,5-hexadiene==

It is a '''major''' ''faux pas'' to directly compare optimisations using different basis sets. Both optimisations were carried out using Hartree-Fock method. The higher basis set yielded a much lower final energy, by approximately 3 atomic units. The bond lengths however are nearly identical, as can be seen below.

[[File:Bond lengths comparison ckaye.gif]]

==Frequency analysis of anti2==

From the frequency analysis of the higher optimised structure of anti2 1,5-hexadiene, the output file confirmed that there were no negative frequencies, which ensures that the molecule is at an energy minimum.

<pre> Low frequencies --- -18.8360 -11.7255 -0.0010 -0.0004 0.0004 1.7210
Low frequencies --- 72.7084 80.1375 120.0085</pre>

==Predicted infrared spectrum of anti2==

[[File:App2 ir spectrum ckaye.png]]

In the output file it can be seen that there are many vibrational modes. However, many have intensities of 0 because they do not involve a change in dipole moment, which is required for an interaction with electromagnetic field. Hence they do not appear on an IR spectrum.

==Optimisation of chair transition state structure==

An allylic H2CCHCH2 fragment was optimised using HF/3-21G basis set. This was later used to form the chair transition state below.

By fixing the bond forming/breaking distances of the terminal carbon atoms to approximately 2.2 Å and performing an opt+freq using the same basis set as before, but with TS(berny) selected and opt=noeigen, to allow imaginary frequencies. An imaginary frequency was observed at 818 cm-1, relating to the transition state. The displacement vectors of the vibration can be seen below

[[File:Transitionstateimaginaryvibration ckaye.png|center|thumb|imaginary vibration (still image, displacement vectors) of the transition state]]

==Intrinsic Reaction Co-ordinate (IRC) analysis of chair transition state from frozen co-ordinate==

[[File:Chair gradient stuffs ckaye.png|400px|center|thumb]]

With 'forward only' steps. As the gradient approaches zero, the energy is being minimised as gaussian translates the molecule to minimise the energy.

==Optimisation of boat transition state structure==

By using the same allylic H2CCHCH2 fragment that was optimised using HF/3-21G basis set for the chair TS.

Using the same method as for the chair transition state.

Yielded an imaginary frequency at 840 cm-1 corresponding to the transition state

[[File:Boat transition state cope vibration ckaye.png]]

=Diels-Alder=

[[File:Da ckaye scheme.png|300px|thumb|center|Reaction scheme of Diels-Alder cycloaddition]]

==Introduction==

A Diels-Alder reaction is a [4+2] cycloaddition between a conjugated diene and a dienophile, forming a 6-membered ring. The driving force of the reaction is likely to be enthalpic in nature due to the formation of (stronger) sigma bonds at the 'expense' of (weaker) pi bonds. The enthalpic contribution usually overrides any entropic disfavourability<ref>Biotechnology: Bridging Research and Applications edited by Daphne Kamely, Ananda M. Chakrabarty, Steven E. Kornguth</ref> (from the inherent ordering of two molecules into one).

Here, the diene is butadiene and the dienophile is ethylene.

Molecular orbital analysis is important because the symmetry of the reactant MOs is vital to establishing if the reaction occurs or not. If the reactants differ in symmetry then the required orbital overlap does not occur and so the reaction does not. (Woodward Hoffman rules)

==Optimisation==

Using semi-empirical AM1 basis set, a molecule of ''cis''-butadiene was optimised.

[[File:OPTIMISATION BUTADIENE CKAYE.LOG]] Link to .log file of optimisation of butadiene

[[File:Butadiene summary ckaye.png|200px|center|thumb|summary of output of optimisation]]

==MO of ''cis''-butadiene==

The molecular orbitals were obtained, with HOMO and LUMO of particular interest.

[[File:Lumo butadiene ckaye.png|200px|thumb|center|LUMO of butadiene]]
[[File:Homo butadiene ckaye.png|200px|thumb|center|HOMO of butadiene]]

As can be seen above, the LUMO is symmetric with respect to a plane down the middle of the molecule. The HOMO however is antisymmetric since it does not have a plane of symmetry.

The relative energies of the MOs of ''cis''-butadiene can be seen below.

[[File:Energylist butadiene ckaye.png|200px|thumb|center|List of MOs]]

==Formation of TS==

A guess structure of the TS was obtained using 2.20 Å fixed distance.

[[File:TS OPT CKAYE.LOG]] Link to .log file of TS optimisation

[[File:Ts picture ckaye.png|200px|center|thumb|TS picture]]

An imaginary frequency was found at 956 cm-1

Low frequencies --- -956.2090 -0.0435 -0.0282 -0.0032 1.6785 3.3690
Low frequencies --- 4.2132 147.3980 246.6385

Terminal carbon-carbon distances = 2.12 Å

==MO of TS==

[[File:Ts homo ckaye.png|200px|thumb|center|HOMO of TS]]

[[File:Ts lumo ckaye.png|200px|thumb|center|LUMO of TS]]

==Regioselectivity of Diels Alder reaction==

==Using maleic anhydride to explore endo vs exo TS==

===Endo===

[[File:OPTIMISATION CYCLOHEXAMAL ENDO CKAYE 2.LOG]] Link to .log file

[[File:Ts endo homo ckaye.png|200px|center|thumb|TS of endo]]

===Exo===

[[File:OPTIMISATION CYCLOHEXAMAL EXO TS CKAYE.LOG]] Link to .log file

[[File:Partial bond length ckaye exo ts.png|200px|center|thumb|TS with TS bond distance]]

=References=

<references/>

Rep:Mod:mod3 christopherkaye

2013-03-16T16:35:44Z

Ck1510: /* Intrinsic Reaction Co-ordinate (IRC) analysis of chair transition state from frozen co-ordinate */

=Christopher Kaye, ck1510, Module 3 Computational=

Extension granted by Dr Hunt to 16th March.

=Introduction=

This module uses Gaussian software to model transition states of reactions. A transition state is the maximum saddle point on a potential energy surface. These states are not observable spectroscopically as they are so short-lived, assumed to be on a similar order of magnitude to bond vibrations - approximately 10-18 s. <ref>Biochemistry by Reginald H. Garrett, Charles M. Grisham</ref>

Investigating transitions states is helpful in understanding kinetics and mechanisms of reactions. Gaussian modelling allows geometries and energies of transition states to be predicted.

In this module, two reactions' transition states are being investigated: the Cope Rearrangement, and Diels-Alder.

=Cope Rearrangement=

[[File:Cope rearrangement for 15hexadiene.png|200px]]

The Cope rearrangement is a pericyclic reaction, specifically a [3+3] sigmatropic rearrangement. Like all pericyclic reactions, it is concerted in nature and passes through a transition state and no intermediates. In the case of 1,5-hexadiene, the transition state goes through a chair-like or a boat-like transition state <ref> Futher Perspectives in Organic Chemistry by CIBA Foundation Symposium</ref>
Gaussian was used to identify low energy conformers and then to attempt to find boat and chair transition states.

=Optimisation of conformers=

Using Hartree-Fock method and 3-21G basis set in each case, various conformers were chosen and optimised. The gauche3 conformer was found to be the lowest energy conformer due to the 'gauche effect' of London forces and favourable orbital interactions. Where sterics become more important, it is expected that antiperiplanar would become the most stable conformer. <ref>Carbohydrate Chemistry and Biochemistry: Structure and Mechanism by M. L. Sinnott</ref>
==Optimisation of antiperiplanar1 1,5-hexadiene==

{{DOI|10042/24051}} Link to D-space optimisation output

[[File:Results summary anti ckaye.png|200px|thumb|center|Results summary of optimisation of anti-peri-planar 1,5-hexadiene]]

[[File:Anti1 ckaye.png]]
Using 'Symmetrize'(sic) the molecule was found to have C2 symmetry.

==Optimisation of gauche4 1,5-hexadiene==

By changing the conformation manually to a gauche linkage, and optimising as above, the following results summary was produced.

[[File:Results summary gauche4 ckaye.png|thumb|center|Results summary of optimisation of gauche 1,5-hexadiene]]

[[File:Gauche 4 picture ckaye.png]]

Link to .log file [[File:GAUCHE4 OPT CKAYE.LOG]]

==Optimisation of gauche6 1,5-hexadiene==

[[File:Results summary gauche6 ckaye.png]]

[[File:Gauche 6 picture ckaye.png]]

Link to .log file [[File:OPT GAUCHE6 CKAYE.LOG]]

==Optimisation of gauche3 1,5-hexadiene==

[[file:Results summary gauche3.png]]

[[file:gauche_3_picture_ckaye.png]]

Link to .log file[[File:FOR GAUCHE 3 INPUT CKAYE.LOG]]

==Optimisation of gauche1 1,5-hexadiene==

[[File:Results summary gauche1 ckaye.png]]

[[File:Gauche 1 picture ckaye.png]]

Link to .log file [[File:GAUCHE 1 CKAYE.LOG]]

==Optimisation of anti2 1,5-hexadiene==

[[File:Results summary anti2 ckaye.png]]

[[File:Anti 2 picture ckaye.png]]

Link to .log file [[File:ANTI 2 OPTIMISATION CKAYE.LOG]]

==Higher optimisation of anti2 1,5-hexadiene==

[[File:Anti 2 higher optimisation ckaye picture.png]]

Link to .log file [[File:ANTI 2 HIGHER OPTIMISATION CKAYE.LOG]]

=='Comparison' of two optimisations of anti2 1,5-hexadiene==

It is a '''major''' ''faux pas'' to directly compare optimisations using different basis sets. Both optimisations were carried out using Hartree-Fock method. The higher basis set yielded a much lower final energy, by approximately 3 atomic units. The bond lengths however are nearly identical, as can be seen below.

[[File:Bond lengths comparison ckaye.gif]]

==Frequency analysis of anti2==

From the frequency analysis of the higher optimised structure of anti2 1,5-hexadiene, the output file confirmed that there were no negative frequencies, which ensures that the molecule is at an energy minimum.

<pre> Low frequencies --- -18.8360 -11.7255 -0.0010 -0.0004 0.0004 1.7210
Low frequencies --- 72.7084 80.1375 120.0085</pre>

==Predicted infrared spectrum of anti2==

[[File:App2 ir spectrum ckaye.png]]

In the output file it can be seen that there are many vibrational modes. However, many have intensities of 0 because they do not involve a change in dipole moment, which is required for an interaction with electromagnetic field. Hence they do not appear on an IR spectrum.

==Optimisation of chair transition state structure==

An allylic H2CCHCH2 fragment was optimised using HF/3-21G basis set. This was later used to form the chair transition state below.

By fixing the bond forming/breaking distances of the terminal carbon atoms to approximately 2.2 Å and performing an opt+freq using the same basis set as before, but with TS(berny) selected and opt=noeigen, to allow imaginary frequencies. An imaginary frequency was observed at 818 cm-1, relating to the transition state. The displacement vectors of the vibration can be seen below

[[File:Transitionstateimaginaryvibration ckaye.png|center|thumb|imaginary vibration (still image, displacement vectors) of the transition state]]

==Intrinsic Reaction Co-ordinate (IRC) analysis of chair transition state from frozen co-ordinate==

[[File:Chair gradient stuffs ckaye.png|400px|center|thumb]]

With 'forward only' steps. As the gradient approaches zero, the energy is being minimised as gaussian translates the molecule to minimise the energy.

==Optimisation of boat transition state structure==

By using the same allylic H2CCHCH2 fragment that was optimised using HF/3-21G basis set for the chair TS.

Using the same method as for the chair transition state.

Yielded an imaginary frequency at 840 cm-1 corresponding to the transition state

[[File:Boat transition state cope vibration ckaye.png]]

=Diels-Alder=

[[File:Da ckaye scheme.png|300px|thumb|center|Reaction scheme of Diels-Alder cycloaddition]]

==Introduction==

A Diels-Alder reaction is a [4+2] cycloaddition between a conjugated diene and a dienophile, forming a 6-membered ring. The driving force of the reaction is likely to be enthalpic in nature due to the formation of (stronger) sigma bonds at the 'expense' of (weaker) pi bonds. The enthalpic contribution usually overrides any entropic disfavourability<ref>Biotechnology: Bridging Research and Applications edited by Daphne Kamely, Ananda M. Chakrabarty, Steven E. Kornguth</ref> (from the inherent ordering of two molecules into one).

Here, the diene is butadiene and the dienophile is ethylene.

Molecular orbital analysis is important because the symmetry of the reactant MOs is vital to establishing if the reaction occurs or not. If the reactants differ in symmetry then the required orbital overlap does not occur and so the reaction does not.

==Optimisation==

Using semi-empirical AM1 basis set, a molecule of ''cis''-butadiene was optimised.

[[File:OPTIMISATION BUTADIENE CKAYE.LOG]] Link to .log file of optimisation of butadiene

[[File:Butadiene summary ckaye.png|200px|center|thumb|summary of output of optimisation]]

==MO of ''cis''-butadiene==

The molecular orbitals were obtained, with HOMO and LUMO of particular interest.

[[File:Lumo butadiene ckaye.png|200px|thumb|center|LUMO of butadiene]]
[[File:Homo butadiene ckaye.png|200px|thumb|center|HOMO of butadiene]]

As can be seen above, the LUMO is symmetric with respect to a plane down the middle of the molecule. The HOMO however is antisymmetric since it does not have a plane of symmetry.

The relative energies of the MOs of ''cis''-butadiene can be seen below.

[[File:Energylist butadiene ckaye.png|200px|thumb|center|List of MOs]]

==Formation of TS==

A guess structure of the TS was obtained using 2.20 Å fixed distance.

[[File:TS OPT CKAYE.LOG]] Link to .log file of TS optimisation

[[File:Ts picture ckaye.png|200px|center|thumb|TS picture]]

An imaginary frequency was found at 956 cm-1

Low frequencies --- -956.2090 -0.0435 -0.0282 -0.0032 1.6785 3.3690
Low frequencies --- 4.2132 147.3980 246.6385

Terminal carbon-carbon distances = 2.12 Å

==MO of TS==

[[File:Ts homo ckaye.png|200px|thumb|center|HOMO of TS]]

[[File:Ts lumo ckaye.png|200px|thumb|center|LUMO of TS]]

==Regioselectivity of Diels Alder reaction==

==Using maleic anhydride to explore endo vs exo TS==

===Endo===

[[File:OPTIMISATION CYCLOHEXAMAL ENDO CKAYE 2.LOG]] Link to .log file

[[File:Ts endo homo ckaye.png|200px|center|thumb|TS of endo]]

===Exo===

[[File:OPTIMISATION CYCLOHEXAMAL EXO TS CKAYE.LOG]] Link to .log file

[[File:Partial bond length ckaye exo ts.png|200px|center|thumb|TS with TS bond distance]]

=References=

<references/>

Rep:Mod:mod3 christopherkaye

2013-03-16T16:35:29Z

Ck1510: /* Intrinsic Reaction Co-ordinate (IRC) analysis of chair transition state from frozen co-ordinate */

=Christopher Kaye, ck1510, Module 3 Computational=

Extension granted by Dr Hunt to 16th March.

=Introduction=

This module uses Gaussian software to model transition states of reactions. A transition state is the maximum saddle point on a potential energy surface. These states are not observable spectroscopically as they are so short-lived, assumed to be on a similar order of magnitude to bond vibrations - approximately 10-18 s. <ref>Biochemistry by Reginald H. Garrett, Charles M. Grisham</ref>

Investigating transitions states is helpful in understanding kinetics and mechanisms of reactions. Gaussian modelling allows geometries and energies of transition states to be predicted.

In this module, two reactions' transition states are being investigated: the Cope Rearrangement, and Diels-Alder.

=Cope Rearrangement=

[[File:Cope rearrangement for 15hexadiene.png|200px]]

The Cope rearrangement is a pericyclic reaction, specifically a [3+3] sigmatropic rearrangement. Like all pericyclic reactions, it is concerted in nature and passes through a transition state and no intermediates. In the case of 1,5-hexadiene, the transition state goes through a chair-like or a boat-like transition state <ref> Futher Perspectives in Organic Chemistry by CIBA Foundation Symposium</ref>
Gaussian was used to identify low energy conformers and then to attempt to find boat and chair transition states.

=Optimisation of conformers=

Using Hartree-Fock method and 3-21G basis set in each case, various conformers were chosen and optimised. The gauche3 conformer was found to be the lowest energy conformer due to the 'gauche effect' of London forces and favourable orbital interactions. Where sterics become more important, it is expected that antiperiplanar would become the most stable conformer. <ref>Carbohydrate Chemistry and Biochemistry: Structure and Mechanism by M. L. Sinnott</ref>
==Optimisation of antiperiplanar1 1,5-hexadiene==

{{DOI|10042/24051}} Link to D-space optimisation output

[[File:Results summary anti ckaye.png|200px|thumb|center|Results summary of optimisation of anti-peri-planar 1,5-hexadiene]]

[[File:Anti1 ckaye.png]]
Using 'Symmetrize'(sic) the molecule was found to have C2 symmetry.

==Optimisation of gauche4 1,5-hexadiene==

By changing the conformation manually to a gauche linkage, and optimising as above, the following results summary was produced.

[[File:Results summary gauche4 ckaye.png|thumb|center|Results summary of optimisation of gauche 1,5-hexadiene]]

[[File:Gauche 4 picture ckaye.png]]

Link to .log file [[File:GAUCHE4 OPT CKAYE.LOG]]

==Optimisation of gauche6 1,5-hexadiene==

[[File:Results summary gauche6 ckaye.png]]

[[File:Gauche 6 picture ckaye.png]]

Link to .log file [[File:OPT GAUCHE6 CKAYE.LOG]]

==Optimisation of gauche3 1,5-hexadiene==

[[file:Results summary gauche3.png]]

[[file:gauche_3_picture_ckaye.png]]

Link to .log file[[File:FOR GAUCHE 3 INPUT CKAYE.LOG]]

==Optimisation of gauche1 1,5-hexadiene==

[[File:Results summary gauche1 ckaye.png]]

[[File:Gauche 1 picture ckaye.png]]

Link to .log file [[File:GAUCHE 1 CKAYE.LOG]]

==Optimisation of anti2 1,5-hexadiene==

[[File:Results summary anti2 ckaye.png]]

[[File:Anti 2 picture ckaye.png]]

Link to .log file [[File:ANTI 2 OPTIMISATION CKAYE.LOG]]

==Higher optimisation of anti2 1,5-hexadiene==

[[File:Anti 2 higher optimisation ckaye picture.png]]

Link to .log file [[File:ANTI 2 HIGHER OPTIMISATION CKAYE.LOG]]

=='Comparison' of two optimisations of anti2 1,5-hexadiene==

It is a '''major''' ''faux pas'' to directly compare optimisations using different basis sets. Both optimisations were carried out using Hartree-Fock method. The higher basis set yielded a much lower final energy, by approximately 3 atomic units. The bond lengths however are nearly identical, as can be seen below.

[[File:Bond lengths comparison ckaye.gif]]

==Frequency analysis of anti2==

From the frequency analysis of the higher optimised structure of anti2 1,5-hexadiene, the output file confirmed that there were no negative frequencies, which ensures that the molecule is at an energy minimum.

<pre> Low frequencies --- -18.8360 -11.7255 -0.0010 -0.0004 0.0004 1.7210
Low frequencies --- 72.7084 80.1375 120.0085</pre>

==Predicted infrared spectrum of anti2==

[[File:App2 ir spectrum ckaye.png]]

In the output file it can be seen that there are many vibrational modes. However, many have intensities of 0 because they do not involve a change in dipole moment, which is required for an interaction with electromagnetic field. Hence they do not appear on an IR spectrum.

==Optimisation of chair transition state structure==

An allylic H2CCHCH2 fragment was optimised using HF/3-21G basis set. This was later used to form the chair transition state below.

By fixing the bond forming/breaking distances of the terminal carbon atoms to approximately 2.2 Å and performing an opt+freq using the same basis set as before, but with TS(berny) selected and opt=noeigen, to allow imaginary frequencies. An imaginary frequency was observed at 818 cm-1, relating to the transition state. The displacement vectors of the vibration can be seen below

[[File:Transitionstateimaginaryvibration ckaye.png|center|thumb|imaginary vibration (still image, displacement vectors) of the transition state]]

==Intrinsic Reaction Co-ordinate (IRC) analysis of chair transition state from frozen co-ordinate==

[[File:Chair gradient stuffs ckaye.png|200px|center|thumb]]

With 'forward only' steps. As the gradient approaches zero, the energy is being minimised as gaussian translates the molecule to minimise the energy.

==Optimisation of boat transition state structure==

By using the same allylic H2CCHCH2 fragment that was optimised using HF/3-21G basis set for the chair TS.

Using the same method as for the chair transition state.

Yielded an imaginary frequency at 840 cm-1 corresponding to the transition state

[[File:Boat transition state cope vibration ckaye.png]]

=Diels-Alder=

[[File:Da ckaye scheme.png|300px|thumb|center|Reaction scheme of Diels-Alder cycloaddition]]

==Introduction==

A Diels-Alder reaction is a [4+2] cycloaddition between a conjugated diene and a dienophile, forming a 6-membered ring. The driving force of the reaction is likely to be enthalpic in nature due to the formation of (stronger) sigma bonds at the 'expense' of (weaker) pi bonds. The enthalpic contribution usually overrides any entropic disfavourability<ref>Biotechnology: Bridging Research and Applications edited by Daphne Kamely, Ananda M. Chakrabarty, Steven E. Kornguth</ref> (from the inherent ordering of two molecules into one).

Here, the diene is butadiene and the dienophile is ethylene.

Molecular orbital analysis is important because the symmetry of the reactant MOs is vital to establishing if the reaction occurs or not. If the reactants differ in symmetry then the required orbital overlap does not occur and so the reaction does not.

==Optimisation==

Using semi-empirical AM1 basis set, a molecule of ''cis''-butadiene was optimised.

[[File:OPTIMISATION BUTADIENE CKAYE.LOG]] Link to .log file of optimisation of butadiene

[[File:Butadiene summary ckaye.png|200px|center|thumb|summary of output of optimisation]]

==MO of ''cis''-butadiene==

The molecular orbitals were obtained, with HOMO and LUMO of particular interest.

[[File:Lumo butadiene ckaye.png|200px|thumb|center|LUMO of butadiene]]
[[File:Homo butadiene ckaye.png|200px|thumb|center|HOMO of butadiene]]

As can be seen above, the LUMO is symmetric with respect to a plane down the middle of the molecule. The HOMO however is antisymmetric since it does not have a plane of symmetry.

The relative energies of the MOs of ''cis''-butadiene can be seen below.

[[File:Energylist butadiene ckaye.png|200px|thumb|center|List of MOs]]

==Formation of TS==

A guess structure of the TS was obtained using 2.20 Å fixed distance.

[[File:TS OPT CKAYE.LOG]] Link to .log file of TS optimisation

[[File:Ts picture ckaye.png|200px|center|thumb|TS picture]]

An imaginary frequency was found at 956 cm-1

Low frequencies --- -956.2090 -0.0435 -0.0282 -0.0032 1.6785 3.3690
Low frequencies --- 4.2132 147.3980 246.6385

Terminal carbon-carbon distances = 2.12 Å

==MO of TS==

[[File:Ts homo ckaye.png|200px|thumb|center|HOMO of TS]]

[[File:Ts lumo ckaye.png|200px|thumb|center|LUMO of TS]]

==Regioselectivity of Diels Alder reaction==

==Using maleic anhydride to explore endo vs exo TS==

===Endo===

[[File:OPTIMISATION CYCLOHEXAMAL ENDO CKAYE 2.LOG]] Link to .log file

[[File:Ts endo homo ckaye.png|200px|center|thumb|TS of endo]]

===Exo===

[[File:OPTIMISATION CYCLOHEXAMAL EXO TS CKAYE.LOG]] Link to .log file

[[File:Partial bond length ckaye exo ts.png|200px|center|thumb|TS with TS bond distance]]

=References=

<references/>

Rep:Mod:mod3 christopherkaye

2013-03-16T16:34:36Z

Ck1510: /* IRC analysis of chair transition state */

=Christopher Kaye, ck1510, Module 3 Computational=

Extension granted by Dr Hunt to 16th March.

=Introduction=

This module uses Gaussian software to model transition states of reactions. A transition state is the maximum saddle point on a potential energy surface. These states are not observable spectroscopically as they are so short-lived, assumed to be on a similar order of magnitude to bond vibrations - approximately 10-18 s. <ref>Biochemistry by Reginald H. Garrett, Charles M. Grisham</ref>

Investigating transitions states is helpful in understanding kinetics and mechanisms of reactions. Gaussian modelling allows geometries and energies of transition states to be predicted.

In this module, two reactions' transition states are being investigated: the Cope Rearrangement, and Diels-Alder.

=Cope Rearrangement=

[[File:Cope rearrangement for 15hexadiene.png|200px]]

The Cope rearrangement is a pericyclic reaction, specifically a [3+3] sigmatropic rearrangement. Like all pericyclic reactions, it is concerted in nature and passes through a transition state and no intermediates. In the case of 1,5-hexadiene, the transition state goes through a chair-like or a boat-like transition state <ref> Futher Perspectives in Organic Chemistry by CIBA Foundation Symposium</ref>
Gaussian was used to identify low energy conformers and then to attempt to find boat and chair transition states.

=Optimisation of conformers=

Using Hartree-Fock method and 3-21G basis set in each case, various conformers were chosen and optimised. The gauche3 conformer was found to be the lowest energy conformer due to the 'gauche effect' of London forces and favourable orbital interactions. Where sterics become more important, it is expected that antiperiplanar would become the most stable conformer. <ref>Carbohydrate Chemistry and Biochemistry: Structure and Mechanism by M. L. Sinnott</ref>
==Optimisation of antiperiplanar1 1,5-hexadiene==

{{DOI|10042/24051}} Link to D-space optimisation output

[[File:Results summary anti ckaye.png|200px|thumb|center|Results summary of optimisation of anti-peri-planar 1,5-hexadiene]]

[[File:Anti1 ckaye.png]]
Using 'Symmetrize'(sic) the molecule was found to have C2 symmetry.

==Optimisation of gauche4 1,5-hexadiene==

By changing the conformation manually to a gauche linkage, and optimising as above, the following results summary was produced.

[[File:Results summary gauche4 ckaye.png|thumb|center|Results summary of optimisation of gauche 1,5-hexadiene]]

[[File:Gauche 4 picture ckaye.png]]

Link to .log file [[File:GAUCHE4 OPT CKAYE.LOG]]

==Optimisation of gauche6 1,5-hexadiene==

[[File:Results summary gauche6 ckaye.png]]

[[File:Gauche 6 picture ckaye.png]]

Link to .log file [[File:OPT GAUCHE6 CKAYE.LOG]]

==Optimisation of gauche3 1,5-hexadiene==

[[file:Results summary gauche3.png]]

[[file:gauche_3_picture_ckaye.png]]

Link to .log file[[File:FOR GAUCHE 3 INPUT CKAYE.LOG]]

==Optimisation of gauche1 1,5-hexadiene==

[[File:Results summary gauche1 ckaye.png]]

[[File:Gauche 1 picture ckaye.png]]

Link to .log file [[File:GAUCHE 1 CKAYE.LOG]]

==Optimisation of anti2 1,5-hexadiene==

[[File:Results summary anti2 ckaye.png]]

[[File:Anti 2 picture ckaye.png]]

Link to .log file [[File:ANTI 2 OPTIMISATION CKAYE.LOG]]

==Higher optimisation of anti2 1,5-hexadiene==

[[File:Anti 2 higher optimisation ckaye picture.png]]

Link to .log file [[File:ANTI 2 HIGHER OPTIMISATION CKAYE.LOG]]

=='Comparison' of two optimisations of anti2 1,5-hexadiene==

It is a '''major''' ''faux pas'' to directly compare optimisations using different basis sets. Both optimisations were carried out using Hartree-Fock method. The higher basis set yielded a much lower final energy, by approximately 3 atomic units. The bond lengths however are nearly identical, as can be seen below.

[[File:Bond lengths comparison ckaye.gif]]

==Frequency analysis of anti2==

From the frequency analysis of the higher optimised structure of anti2 1,5-hexadiene, the output file confirmed that there were no negative frequencies, which ensures that the molecule is at an energy minimum.

<pre> Low frequencies --- -18.8360 -11.7255 -0.0010 -0.0004 0.0004 1.7210
Low frequencies --- 72.7084 80.1375 120.0085</pre>

==Predicted infrared spectrum of anti2==

[[File:App2 ir spectrum ckaye.png]]

In the output file it can be seen that there are many vibrational modes. However, many have intensities of 0 because they do not involve a change in dipole moment, which is required for an interaction with electromagnetic field. Hence they do not appear on an IR spectrum.

==Optimisation of chair transition state structure==

An allylic H2CCHCH2 fragment was optimised using HF/3-21G basis set. This was later used to form the chair transition state below.

By fixing the bond forming/breaking distances of the terminal carbon atoms to approximately 2.2 Å and performing an opt+freq using the same basis set as before, but with TS(berny) selected and opt=noeigen, to allow imaginary frequencies. An imaginary frequency was observed at 818 cm-1, relating to the transition state. The displacement vectors of the vibration can be seen below

[[File:Transitionstateimaginaryvibration ckaye.png|center|thumb|imaginary vibration (still image, displacement vectors) of the transition state]]

==Intrinsic Reaction Co-ordinate (IRC) analysis of chair transition state from frozen co-ordinate==

[[File:Chair gradient stuffs ckaye.png|200px|center|thumb]]

With 'forward only' steps. As the gradient approaches zero

==Optimisation of boat transition state structure==

By using the same allylic H2CCHCH2 fragment that was optimised using HF/3-21G basis set for the chair TS.

Using the same method as for the chair transition state.

Yielded an imaginary frequency at 840 cm-1 corresponding to the transition state

[[File:Boat transition state cope vibration ckaye.png]]

=Diels-Alder=

[[File:Da ckaye scheme.png|300px|thumb|center|Reaction scheme of Diels-Alder cycloaddition]]

==Introduction==

A Diels-Alder reaction is a [4+2] cycloaddition between a conjugated diene and a dienophile, forming a 6-membered ring. The driving force of the reaction is likely to be enthalpic in nature due to the formation of (stronger) sigma bonds at the 'expense' of (weaker) pi bonds. The enthalpic contribution usually overrides any entropic disfavourability<ref>Biotechnology: Bridging Research and Applications edited by Daphne Kamely, Ananda M. Chakrabarty, Steven E. Kornguth</ref> (from the inherent ordering of two molecules into one).

Here, the diene is butadiene and the dienophile is ethylene.

Molecular orbital analysis is important because the symmetry of the reactant MOs is vital to establishing if the reaction occurs or not. If the reactants differ in symmetry then the required orbital overlap does not occur and so the reaction does not.

==Optimisation==

Using semi-empirical AM1 basis set, a molecule of ''cis''-butadiene was optimised.

[[File:OPTIMISATION BUTADIENE CKAYE.LOG]] Link to .log file of optimisation of butadiene

[[File:Butadiene summary ckaye.png|200px|center|thumb|summary of output of optimisation]]

==MO of ''cis''-butadiene==

The molecular orbitals were obtained, with HOMO and LUMO of particular interest.

[[File:Lumo butadiene ckaye.png|200px|thumb|center|LUMO of butadiene]]
[[File:Homo butadiene ckaye.png|200px|thumb|center|HOMO of butadiene]]

As can be seen above, the LUMO is symmetric with respect to a plane down the middle of the molecule. The HOMO however is antisymmetric since it does not have a plane of symmetry.

The relative energies of the MOs of ''cis''-butadiene can be seen below.

[[File:Energylist butadiene ckaye.png|200px|thumb|center|List of MOs]]

==Formation of TS==

A guess structure of the TS was obtained using 2.20 Å fixed distance.

[[File:TS OPT CKAYE.LOG]] Link to .log file of TS optimisation

[[File:Ts picture ckaye.png|200px|center|thumb|TS picture]]

An imaginary frequency was found at 956 cm-1

Low frequencies --- -956.2090 -0.0435 -0.0282 -0.0032 1.6785 3.3690
Low frequencies --- 4.2132 147.3980 246.6385

Terminal carbon-carbon distances = 2.12 Å

==MO of TS==

[[File:Ts homo ckaye.png|200px|thumb|center|HOMO of TS]]

[[File:Ts lumo ckaye.png|200px|thumb|center|LUMO of TS]]

==Regioselectivity of Diels Alder reaction==

==Using maleic anhydride to explore endo vs exo TS==

===Endo===

[[File:OPTIMISATION CYCLOHEXAMAL ENDO CKAYE 2.LOG]] Link to .log file

[[File:Ts endo homo ckaye.png|200px|center|thumb|TS of endo]]

===Exo===

[[File:OPTIMISATION CYCLOHEXAMAL EXO TS CKAYE.LOG]] Link to .log file

[[File:Partial bond length ckaye exo ts.png|200px|center|thumb|TS with TS bond distance]]

=References=

<references/>

Rep:Mod:mod3 christopherkaye

2013-03-16T16:30:19Z

Ck1510: /* Optimisation of chair transition state structure */

=Christopher Kaye, ck1510, Module 3 Computational=

Extension granted by Dr Hunt to 16th March.

=Introduction=

This module uses Gaussian software to model transition states of reactions. A transition state is the maximum saddle point on a potential energy surface. These states are not observable spectroscopically as they are so short-lived, assumed to be on a similar order of magnitude to bond vibrations - approximately 10-18 s. <ref>Biochemistry by Reginald H. Garrett, Charles M. Grisham</ref>

Investigating transitions states is helpful in understanding kinetics and mechanisms of reactions. Gaussian modelling allows geometries and energies of transition states to be predicted.

In this module, two reactions' transition states are being investigated: the Cope Rearrangement, and Diels-Alder.

=Cope Rearrangement=

[[File:Cope rearrangement for 15hexadiene.png|200px]]

The Cope rearrangement is a pericyclic reaction, specifically a [3+3] sigmatropic rearrangement. Like all pericyclic reactions, it is concerted in nature and passes through a transition state and no intermediates. In the case of 1,5-hexadiene, the transition state goes through a chair-like or a boat-like transition state <ref> Futher Perspectives in Organic Chemistry by CIBA Foundation Symposium</ref>
Gaussian was used to identify low energy conformers and then to attempt to find boat and chair transition states.

=Optimisation of conformers=

Using Hartree-Fock method and 3-21G basis set in each case, various conformers were chosen and optimised. The gauche3 conformer was found to be the lowest energy conformer due to the 'gauche effect' of London forces and favourable orbital interactions. Where sterics become more important, it is expected that antiperiplanar would become the most stable conformer. <ref>Carbohydrate Chemistry and Biochemistry: Structure and Mechanism by M. L. Sinnott</ref>
==Optimisation of antiperiplanar1 1,5-hexadiene==

{{DOI|10042/24051}} Link to D-space optimisation output

[[File:Results summary anti ckaye.png|200px|thumb|center|Results summary of optimisation of anti-peri-planar 1,5-hexadiene]]

[[File:Anti1 ckaye.png]]
Using 'Symmetrize'(sic) the molecule was found to have C2 symmetry.

==Optimisation of gauche4 1,5-hexadiene==

By changing the conformation manually to a gauche linkage, and optimising as above, the following results summary was produced.

[[File:Results summary gauche4 ckaye.png|thumb|center|Results summary of optimisation of gauche 1,5-hexadiene]]

[[File:Gauche 4 picture ckaye.png]]

Link to .log file [[File:GAUCHE4 OPT CKAYE.LOG]]

==Optimisation of gauche6 1,5-hexadiene==

[[File:Results summary gauche6 ckaye.png]]

[[File:Gauche 6 picture ckaye.png]]

Link to .log file [[File:OPT GAUCHE6 CKAYE.LOG]]

==Optimisation of gauche3 1,5-hexadiene==

[[file:Results summary gauche3.png]]

[[file:gauche_3_picture_ckaye.png]]

Link to .log file[[File:FOR GAUCHE 3 INPUT CKAYE.LOG]]

==Optimisation of gauche1 1,5-hexadiene==

[[File:Results summary gauche1 ckaye.png]]

[[File:Gauche 1 picture ckaye.png]]

Link to .log file [[File:GAUCHE 1 CKAYE.LOG]]

==Optimisation of anti2 1,5-hexadiene==

[[File:Results summary anti2 ckaye.png]]

[[File:Anti 2 picture ckaye.png]]

Link to .log file [[File:ANTI 2 OPTIMISATION CKAYE.LOG]]

==Higher optimisation of anti2 1,5-hexadiene==

[[File:Anti 2 higher optimisation ckaye picture.png]]

Link to .log file [[File:ANTI 2 HIGHER OPTIMISATION CKAYE.LOG]]

=='Comparison' of two optimisations of anti2 1,5-hexadiene==

It is a '''major''' ''faux pas'' to directly compare optimisations using different basis sets. Both optimisations were carried out using Hartree-Fock method. The higher basis set yielded a much lower final energy, by approximately 3 atomic units. The bond lengths however are nearly identical, as can be seen below.

[[File:Bond lengths comparison ckaye.gif]]

==Frequency analysis of anti2==

From the frequency analysis of the higher optimised structure of anti2 1,5-hexadiene, the output file confirmed that there were no negative frequencies, which ensures that the molecule is at an energy minimum.

<pre> Low frequencies --- -18.8360 -11.7255 -0.0010 -0.0004 0.0004 1.7210
Low frequencies --- 72.7084 80.1375 120.0085</pre>

==Predicted infrared spectrum of anti2==

[[File:App2 ir spectrum ckaye.png]]

In the output file it can be seen that there are many vibrational modes. However, many have intensities of 0 because they do not involve a change in dipole moment, which is required for an interaction with electromagnetic field. Hence they do not appear on an IR spectrum.

==Optimisation of chair transition state structure==

An allylic H2CCHCH2 fragment was optimised using HF/3-21G basis set. This was later used to form the chair transition state below.

By fixing the bond forming/breaking distances of the terminal carbon atoms to approximately 2.2 Å and performing an opt+freq using the same basis set as before, but with TS(berny) selected and opt=noeigen, to allow imaginary frequencies. An imaginary frequency was observed at 818 cm-1, relating to the transition state. The displacement vectors of the vibration can be seen below

[[File:Transitionstateimaginaryvibration ckaye.png|center|thumb|imaginary vibration (still image, displacement vectors) of the transition state]]

==IRC analysis of chair transition state==

[[File:Chair gradient stuffs ckaye.png|200px|center|thumb]]

==Optimisation of boat transition state structure==

By using the same allylic H2CCHCH2 fragment that was optimised using HF/3-21G basis set for the chair TS.

Using the same method as for the chair transition state.

Yielded an imaginary frequency at 840 cm-1 corresponding to the transition state

[[File:Boat transition state cope vibration ckaye.png]]

=Diels-Alder=

[[File:Da ckaye scheme.png|300px|thumb|center|Reaction scheme of Diels-Alder cycloaddition]]

==Introduction==

A Diels-Alder reaction is a [4+2] cycloaddition between a conjugated diene and a dienophile, forming a 6-membered ring. The driving force of the reaction is likely to be enthalpic in nature due to the formation of (stronger) sigma bonds at the 'expense' of (weaker) pi bonds. The enthalpic contribution usually overrides any entropic disfavourability<ref>Biotechnology: Bridging Research and Applications edited by Daphne Kamely, Ananda M. Chakrabarty, Steven E. Kornguth</ref> (from the inherent ordering of two molecules into one).

Here, the diene is butadiene and the dienophile is ethylene.

Molecular orbital analysis is important because the symmetry of the reactant MOs is vital to establishing if the reaction occurs or not. If the reactants differ in symmetry then the required orbital overlap does not occur and so the reaction does not.

==Optimisation==

Using semi-empirical AM1 basis set, a molecule of ''cis''-butadiene was optimised.

[[File:OPTIMISATION BUTADIENE CKAYE.LOG]] Link to .log file of optimisation of butadiene

[[File:Butadiene summary ckaye.png|200px|center|thumb|summary of output of optimisation]]

==MO of ''cis''-butadiene==

The molecular orbitals were obtained, with HOMO and LUMO of particular interest.

[[File:Lumo butadiene ckaye.png|200px|thumb|center|LUMO of butadiene]]
[[File:Homo butadiene ckaye.png|200px|thumb|center|HOMO of butadiene]]

As can be seen above, the LUMO is symmetric with respect to a plane down the middle of the molecule. The HOMO however is antisymmetric since it does not have a plane of symmetry.

The relative energies of the MOs of ''cis''-butadiene can be seen below.

[[File:Energylist butadiene ckaye.png|200px|thumb|center|List of MOs]]

==Formation of TS==

A guess structure of the TS was obtained using 2.20 Å fixed distance.

[[File:TS OPT CKAYE.LOG]] Link to .log file of TS optimisation

[[File:Ts picture ckaye.png|200px|center|thumb|TS picture]]

An imaginary frequency was found at 956 cm-1

Low frequencies --- -956.2090 -0.0435 -0.0282 -0.0032 1.6785 3.3690
Low frequencies --- 4.2132 147.3980 246.6385

Terminal carbon-carbon distances = 2.12 Å

==MO of TS==

[[File:Ts homo ckaye.png|200px|thumb|center|HOMO of TS]]

[[File:Ts lumo ckaye.png|200px|thumb|center|LUMO of TS]]

==Regioselectivity of Diels Alder reaction==

==Using maleic anhydride to explore endo vs exo TS==

===Endo===

[[File:OPTIMISATION CYCLOHEXAMAL ENDO CKAYE 2.LOG]] Link to .log file

[[File:Ts endo homo ckaye.png|200px|center|thumb|TS of endo]]

===Exo===

[[File:OPTIMISATION CYCLOHEXAMAL EXO TS CKAYE.LOG]] Link to .log file

[[File:Partial bond length ckaye exo ts.png|200px|center|thumb|TS with TS bond distance]]

=References=

<references/>

File:Chair gradient stuffs ckaye.png

2013-03-16T16:29:19Z

Ck1510:

Rep:Mod:mod3 christopherkaye

2013-03-16T16:26:02Z

Ck1510: /* Formation of TS */

=Christopher Kaye, ck1510, Module 3 Computational=

Extension granted by Dr Hunt to 16th March.

=Introduction=

This module uses Gaussian software to model transition states of reactions. A transition state is the maximum saddle point on a potential energy surface. These states are not observable spectroscopically as they are so short-lived, assumed to be on a similar order of magnitude to bond vibrations - approximately 10-18 s. <ref>Biochemistry by Reginald H. Garrett, Charles M. Grisham</ref>

Investigating transitions states is helpful in understanding kinetics and mechanisms of reactions. Gaussian modelling allows geometries and energies of transition states to be predicted.

In this module, two reactions' transition states are being investigated: the Cope Rearrangement, and Diels-Alder.

=Cope Rearrangement=

[[File:Cope rearrangement for 15hexadiene.png|200px]]

The Cope rearrangement is a pericyclic reaction, specifically a [3+3] sigmatropic rearrangement. Like all pericyclic reactions, it is concerted in nature and passes through a transition state and no intermediates. In the case of 1,5-hexadiene, the transition state goes through a chair-like or a boat-like transition state <ref> Futher Perspectives in Organic Chemistry by CIBA Foundation Symposium</ref>
Gaussian was used to identify low energy conformers and then to attempt to find boat and chair transition states.

=Optimisation of conformers=

Using Hartree-Fock method and 3-21G basis set in each case, various conformers were chosen and optimised. The gauche3 conformer was found to be the lowest energy conformer due to the 'gauche effect' of London forces and favourable orbital interactions. Where sterics become more important, it is expected that antiperiplanar would become the most stable conformer. <ref>Carbohydrate Chemistry and Biochemistry: Structure and Mechanism by M. L. Sinnott</ref>
==Optimisation of antiperiplanar1 1,5-hexadiene==

{{DOI|10042/24051}} Link to D-space optimisation output

[[File:Results summary anti ckaye.png|200px|thumb|center|Results summary of optimisation of anti-peri-planar 1,5-hexadiene]]

[[File:Anti1 ckaye.png]]
Using 'Symmetrize'(sic) the molecule was found to have C2 symmetry.

==Optimisation of gauche4 1,5-hexadiene==

By changing the conformation manually to a gauche linkage, and optimising as above, the following results summary was produced.

[[File:Results summary gauche4 ckaye.png|thumb|center|Results summary of optimisation of gauche 1,5-hexadiene]]

[[File:Gauche 4 picture ckaye.png]]

Link to .log file [[File:GAUCHE4 OPT CKAYE.LOG]]

==Optimisation of gauche6 1,5-hexadiene==

[[File:Results summary gauche6 ckaye.png]]

[[File:Gauche 6 picture ckaye.png]]

Link to .log file [[File:OPT GAUCHE6 CKAYE.LOG]]

==Optimisation of gauche3 1,5-hexadiene==

[[file:Results summary gauche3.png]]

[[file:gauche_3_picture_ckaye.png]]

Link to .log file[[File:FOR GAUCHE 3 INPUT CKAYE.LOG]]

==Optimisation of gauche1 1,5-hexadiene==

[[File:Results summary gauche1 ckaye.png]]

[[File:Gauche 1 picture ckaye.png]]

Link to .log file [[File:GAUCHE 1 CKAYE.LOG]]

==Optimisation of anti2 1,5-hexadiene==

[[File:Results summary anti2 ckaye.png]]

[[File:Anti 2 picture ckaye.png]]

Link to .log file [[File:ANTI 2 OPTIMISATION CKAYE.LOG]]

==Higher optimisation of anti2 1,5-hexadiene==

[[File:Anti 2 higher optimisation ckaye picture.png]]

Link to .log file [[File:ANTI 2 HIGHER OPTIMISATION CKAYE.LOG]]

=='Comparison' of two optimisations of anti2 1,5-hexadiene==

It is a '''major''' ''faux pas'' to directly compare optimisations using different basis sets. Both optimisations were carried out using Hartree-Fock method. The higher basis set yielded a much lower final energy, by approximately 3 atomic units. The bond lengths however are nearly identical, as can be seen below.

[[File:Bond lengths comparison ckaye.gif]]

==Frequency analysis of anti2==

From the frequency analysis of the higher optimised structure of anti2 1,5-hexadiene, the output file confirmed that there were no negative frequencies, which ensures that the molecule is at an energy minimum.

<pre> Low frequencies --- -18.8360 -11.7255 -0.0010 -0.0004 0.0004 1.7210
Low frequencies --- 72.7084 80.1375 120.0085</pre>

==Predicted infrared spectrum of anti2==

[[File:App2 ir spectrum ckaye.png]]

In the output file it can be seen that there are many vibrational modes. However, many have intensities of 0 because they do not involve a change in dipole moment, which is required for an interaction with electromagnetic field. Hence they do not appear on an IR spectrum.

==Optimisation of chair transition state structure==

An allylic H2CCHCH2 fragment was optimised using HF/3-21G basis set. This was later used to form the chair transition state below.

By fixing the bond forming/breaking distances of the terminal carbon atoms to approximately 2.2 Å and performing an opt+freq using the same basis set as before, but with TS(berny) selected and opt=noeigen, to allow imaginary frequencies. An imaginary frequency was observed at 818 cm-1, relating to the transition state. The displacement vectors of the vibration can be seen below

[[File:Transitionstateimaginaryvibration ckaye.png|center|thumb|imaginary vibration (still image, displacement vectors) of the transition state]]

==Optimisation of boat transition state structure==

By using the same allylic H2CCHCH2 fragment that was optimised using HF/3-21G basis set for the chair TS.

Using the same method as for the chair transition state.

Yielded an imaginary frequency at 840 cm-1 corresponding to the transition state

[[File:Boat transition state cope vibration ckaye.png]]

=Diels-Alder=

[[File:Da ckaye scheme.png|300px|thumb|center|Reaction scheme of Diels-Alder cycloaddition]]

==Introduction==

A Diels-Alder reaction is a [4+2] cycloaddition between a conjugated diene and a dienophile, forming a 6-membered ring. The driving force of the reaction is likely to be enthalpic in nature due to the formation of (stronger) sigma bonds at the 'expense' of (weaker) pi bonds. The enthalpic contribution usually overrides any entropic disfavourability<ref>Biotechnology: Bridging Research and Applications edited by Daphne Kamely, Ananda M. Chakrabarty, Steven E. Kornguth</ref> (from the inherent ordering of two molecules into one).

Here, the diene is butadiene and the dienophile is ethylene.

Molecular orbital analysis is important because the symmetry of the reactant MOs is vital to establishing if the reaction occurs or not. If the reactants differ in symmetry then the required orbital overlap does not occur and so the reaction does not.

==Optimisation==

Using semi-empirical AM1 basis set, a molecule of ''cis''-butadiene was optimised.

[[File:OPTIMISATION BUTADIENE CKAYE.LOG]] Link to .log file of optimisation of butadiene

[[File:Butadiene summary ckaye.png|200px|center|thumb|summary of output of optimisation]]

==MO of ''cis''-butadiene==

The molecular orbitals were obtained, with HOMO and LUMO of particular interest.

[[File:Lumo butadiene ckaye.png|200px|thumb|center|LUMO of butadiene]]
[[File:Homo butadiene ckaye.png|200px|thumb|center|HOMO of butadiene]]

As can be seen above, the LUMO is symmetric with respect to a plane down the middle of the molecule. The HOMO however is antisymmetric since it does not have a plane of symmetry.

The relative energies of the MOs of ''cis''-butadiene can be seen below.

[[File:Energylist butadiene ckaye.png|200px|thumb|center|List of MOs]]

==Formation of TS==

A guess structure of the TS was obtained using 2.20 Å fixed distance.

[[File:TS OPT CKAYE.LOG]] Link to .log file of TS optimisation

[[File:Ts picture ckaye.png|200px|center|thumb|TS picture]]

An imaginary frequency was found at 956 cm-1

Low frequencies --- -956.2090 -0.0435 -0.0282 -0.0032 1.6785 3.3690
Low frequencies --- 4.2132 147.3980 246.6385

Terminal carbon-carbon distances = 2.12 Å

==MO of TS==

[[File:Ts homo ckaye.png|200px|thumb|center|HOMO of TS]]

[[File:Ts lumo ckaye.png|200px|thumb|center|LUMO of TS]]

==Regioselectivity of Diels Alder reaction==

==Using maleic anhydride to explore endo vs exo TS==

===Endo===

[[File:OPTIMISATION CYCLOHEXAMAL ENDO CKAYE 2.LOG]] Link to .log file

[[File:Ts endo homo ckaye.png|200px|center|thumb|TS of endo]]

===Exo===

[[File:OPTIMISATION CYCLOHEXAMAL EXO TS CKAYE.LOG]] Link to .log file

[[File:Partial bond length ckaye exo ts.png|200px|center|thumb|TS with TS bond distance]]

=References=

<references/>

Rep:Mod:mod3 christopherkaye

2013-03-16T16:20:44Z

Ck1510: /* Formation of TS */

=Christopher Kaye, ck1510, Module 3 Computational=

Extension granted by Dr Hunt to 16th March.

=Introduction=

This module uses Gaussian software to model transition states of reactions. A transition state is the maximum saddle point on a potential energy surface. These states are not observable spectroscopically as they are so short-lived, assumed to be on a similar order of magnitude to bond vibrations - approximately 10-18 s. <ref>Biochemistry by Reginald H. Garrett, Charles M. Grisham</ref>

Investigating transitions states is helpful in understanding kinetics and mechanisms of reactions. Gaussian modelling allows geometries and energies of transition states to be predicted.

In this module, two reactions' transition states are being investigated: the Cope Rearrangement, and Diels-Alder.

=Cope Rearrangement=

[[File:Cope rearrangement for 15hexadiene.png|200px]]

The Cope rearrangement is a pericyclic reaction, specifically a [3+3] sigmatropic rearrangement. Like all pericyclic reactions, it is concerted in nature and passes through a transition state and no intermediates. In the case of 1,5-hexadiene, the transition state goes through a chair-like or a boat-like transition state <ref> Futher Perspectives in Organic Chemistry by CIBA Foundation Symposium</ref>
Gaussian was used to identify low energy conformers and then to attempt to find boat and chair transition states.

=Optimisation of conformers=

Using Hartree-Fock method and 3-21G basis set in each case, various conformers were chosen and optimised. The gauche3 conformer was found to be the lowest energy conformer due to the 'gauche effect' of London forces and favourable orbital interactions. Where sterics become more important, it is expected that antiperiplanar would become the most stable conformer. <ref>Carbohydrate Chemistry and Biochemistry: Structure and Mechanism by M. L. Sinnott</ref>
==Optimisation of antiperiplanar1 1,5-hexadiene==

{{DOI|10042/24051}} Link to D-space optimisation output

[[File:Results summary anti ckaye.png|200px|thumb|center|Results summary of optimisation of anti-peri-planar 1,5-hexadiene]]

[[File:Anti1 ckaye.png]]
Using 'Symmetrize'(sic) the molecule was found to have C2 symmetry.

==Optimisation of gauche4 1,5-hexadiene==

By changing the conformation manually to a gauche linkage, and optimising as above, the following results summary was produced.

[[File:Results summary gauche4 ckaye.png|thumb|center|Results summary of optimisation of gauche 1,5-hexadiene]]

[[File:Gauche 4 picture ckaye.png]]

Link to .log file [[File:GAUCHE4 OPT CKAYE.LOG]]

==Optimisation of gauche6 1,5-hexadiene==

[[File:Results summary gauche6 ckaye.png]]

[[File:Gauche 6 picture ckaye.png]]

Link to .log file [[File:OPT GAUCHE6 CKAYE.LOG]]

==Optimisation of gauche3 1,5-hexadiene==

[[file:Results summary gauche3.png]]

[[file:gauche_3_picture_ckaye.png]]

Link to .log file[[File:FOR GAUCHE 3 INPUT CKAYE.LOG]]

==Optimisation of gauche1 1,5-hexadiene==

[[File:Results summary gauche1 ckaye.png]]

[[File:Gauche 1 picture ckaye.png]]

Link to .log file [[File:GAUCHE 1 CKAYE.LOG]]

==Optimisation of anti2 1,5-hexadiene==

[[File:Results summary anti2 ckaye.png]]

[[File:Anti 2 picture ckaye.png]]

Link to .log file [[File:ANTI 2 OPTIMISATION CKAYE.LOG]]

==Higher optimisation of anti2 1,5-hexadiene==

[[File:Anti 2 higher optimisation ckaye picture.png]]

Link to .log file [[File:ANTI 2 HIGHER OPTIMISATION CKAYE.LOG]]

=='Comparison' of two optimisations of anti2 1,5-hexadiene==

It is a '''major''' ''faux pas'' to directly compare optimisations using different basis sets. Both optimisations were carried out using Hartree-Fock method. The higher basis set yielded a much lower final energy, by approximately 3 atomic units. The bond lengths however are nearly identical, as can be seen below.

[[File:Bond lengths comparison ckaye.gif]]

==Frequency analysis of anti2==

From the frequency analysis of the higher optimised structure of anti2 1,5-hexadiene, the output file confirmed that there were no negative frequencies, which ensures that the molecule is at an energy minimum.

<pre> Low frequencies --- -18.8360 -11.7255 -0.0010 -0.0004 0.0004 1.7210
Low frequencies --- 72.7084 80.1375 120.0085</pre>

==Predicted infrared spectrum of anti2==

[[File:App2 ir spectrum ckaye.png]]

In the output file it can be seen that there are many vibrational modes. However, many have intensities of 0 because they do not involve a change in dipole moment, which is required for an interaction with electromagnetic field. Hence they do not appear on an IR spectrum.

==Optimisation of chair transition state structure==

An allylic H2CCHCH2 fragment was optimised using HF/3-21G basis set. This was later used to form the chair transition state below.

By fixing the bond forming/breaking distances of the terminal carbon atoms to approximately 2.2 Å and performing an opt+freq using the same basis set as before, but with TS(berny) selected and opt=noeigen, to allow imaginary frequencies. An imaginary frequency was observed at 818 cm-1, relating to the transition state. The displacement vectors of the vibration can be seen below

[[File:Transitionstateimaginaryvibration ckaye.png|center|thumb|imaginary vibration (still image, displacement vectors) of the transition state]]

==Optimisation of boat transition state structure==

By using the same allylic H2CCHCH2 fragment that was optimised using HF/3-21G basis set for the chair TS.

Using the same method as for the chair transition state.

Yielded an imaginary frequency at 840 cm-1 corresponding to the transition state

[[File:Boat transition state cope vibration ckaye.png]]

=Diels-Alder=

[[File:Da ckaye scheme.png|300px|thumb|center|Reaction scheme of Diels-Alder cycloaddition]]

==Introduction==

A Diels-Alder reaction is a [4+2] cycloaddition between a conjugated diene and a dienophile, forming a 6-membered ring. The driving force of the reaction is likely to be enthalpic in nature due to the formation of (stronger) sigma bonds at the 'expense' of (weaker) pi bonds. The enthalpic contribution usually overrides any entropic disfavourability<ref>Biotechnology: Bridging Research and Applications edited by Daphne Kamely, Ananda M. Chakrabarty, Steven E. Kornguth</ref> (from the inherent ordering of two molecules into one).

Here, the diene is butadiene and the dienophile is ethylene.

Molecular orbital analysis is important because the symmetry of the reactant MOs is vital to establishing if the reaction occurs or not. If the reactants differ in symmetry then the required orbital overlap does not occur and so the reaction does not.

==Optimisation==

Using semi-empirical AM1 basis set, a molecule of ''cis''-butadiene was optimised.

[[File:OPTIMISATION BUTADIENE CKAYE.LOG]] Link to .log file of optimisation of butadiene

[[File:Butadiene summary ckaye.png|200px|center|thumb|summary of output of optimisation]]

==MO of ''cis''-butadiene==

The molecular orbitals were obtained, with HOMO and LUMO of particular interest.

[[File:Lumo butadiene ckaye.png|200px|thumb|center|LUMO of butadiene]]
[[File:Homo butadiene ckaye.png|200px|thumb|center|HOMO of butadiene]]

As can be seen above, the LUMO is symmetric with respect to a plane down the middle of the molecule. The HOMO however is antisymmetric since it does not have a plane of symmetry.

The relative energies of the MOs of ''cis''-butadiene can be seen below.

[[File:Energylist butadiene ckaye.png|200px|thumb|center|List of MOs]]

==Formation of TS==

A guess structure of the TS was obtained using 2.20 Å fixed distance.

[[File:TS OPT CKAYE.LOG]] Link to .log file of TS optimisation

[[File:Ts picture ckaye.png|200px|center|thumb|TS picture]]

An imaginary frequency was found at 956 cm-1

Low frequencies --- -956.2090 -0.0435 -0.0282 -0.0032 1.6785 3.3690
Low frequencies --- 4.2132 147.3980 246.6385

==MO of TS==

[[File:Ts homo ckaye.png|200px|thumb|center|HOMO of TS]]

[[File:Ts lumo ckaye.png|200px|thumb|center|LUMO of TS]]

==Regioselectivity of Diels Alder reaction==

==Using maleic anhydride to explore endo vs exo TS==

===Endo===

[[File:OPTIMISATION CYCLOHEXAMAL ENDO CKAYE 2.LOG]] Link to .log file

[[File:Ts endo homo ckaye.png|200px|center|thumb|TS of endo]]

===Exo===

[[File:OPTIMISATION CYCLOHEXAMAL EXO TS CKAYE.LOG]] Link to .log file

[[File:Partial bond length ckaye exo ts.png|200px|center|thumb|TS with TS bond distance]]

=References=

<references/>

Rep:Mod:mod3 christopherkaye

2013-03-16T16:20:18Z

Ck1510: /* Formation of TS */

=Christopher Kaye, ck1510, Module 3 Computational=

Extension granted by Dr Hunt to 16th March.

=Introduction=

This module uses Gaussian software to model transition states of reactions. A transition state is the maximum saddle point on a potential energy surface. These states are not observable spectroscopically as they are so short-lived, assumed to be on a similar order of magnitude to bond vibrations - approximately 10-18 s. <ref>Biochemistry by Reginald H. Garrett, Charles M. Grisham</ref>

Investigating transitions states is helpful in understanding kinetics and mechanisms of reactions. Gaussian modelling allows geometries and energies of transition states to be predicted.

In this module, two reactions' transition states are being investigated: the Cope Rearrangement, and Diels-Alder.

=Cope Rearrangement=

[[File:Cope rearrangement for 15hexadiene.png|200px]]

The Cope rearrangement is a pericyclic reaction, specifically a [3+3] sigmatropic rearrangement. Like all pericyclic reactions, it is concerted in nature and passes through a transition state and no intermediates. In the case of 1,5-hexadiene, the transition state goes through a chair-like or a boat-like transition state <ref> Futher Perspectives in Organic Chemistry by CIBA Foundation Symposium</ref>
Gaussian was used to identify low energy conformers and then to attempt to find boat and chair transition states.

=Optimisation of conformers=

Using Hartree-Fock method and 3-21G basis set in each case, various conformers were chosen and optimised. The gauche3 conformer was found to be the lowest energy conformer due to the 'gauche effect' of London forces and favourable orbital interactions. Where sterics become more important, it is expected that antiperiplanar would become the most stable conformer. <ref>Carbohydrate Chemistry and Biochemistry: Structure and Mechanism by M. L. Sinnott</ref>
==Optimisation of antiperiplanar1 1,5-hexadiene==

{{DOI|10042/24051}} Link to D-space optimisation output

[[File:Results summary anti ckaye.png|200px|thumb|center|Results summary of optimisation of anti-peri-planar 1,5-hexadiene]]

[[File:Anti1 ckaye.png]]
Using 'Symmetrize'(sic) the molecule was found to have C2 symmetry.

==Optimisation of gauche4 1,5-hexadiene==

By changing the conformation manually to a gauche linkage, and optimising as above, the following results summary was produced.

[[File:Results summary gauche4 ckaye.png|thumb|center|Results summary of optimisation of gauche 1,5-hexadiene]]

[[File:Gauche 4 picture ckaye.png]]

Link to .log file [[File:GAUCHE4 OPT CKAYE.LOG]]

==Optimisation of gauche6 1,5-hexadiene==

[[File:Results summary gauche6 ckaye.png]]

[[File:Gauche 6 picture ckaye.png]]

Link to .log file [[File:OPT GAUCHE6 CKAYE.LOG]]

==Optimisation of gauche3 1,5-hexadiene==

[[file:Results summary gauche3.png]]

[[file:gauche_3_picture_ckaye.png]]

Link to .log file[[File:FOR GAUCHE 3 INPUT CKAYE.LOG]]

==Optimisation of gauche1 1,5-hexadiene==

[[File:Results summary gauche1 ckaye.png]]

[[File:Gauche 1 picture ckaye.png]]

Link to .log file [[File:GAUCHE 1 CKAYE.LOG]]

==Optimisation of anti2 1,5-hexadiene==

[[File:Results summary anti2 ckaye.png]]

[[File:Anti 2 picture ckaye.png]]

Link to .log file [[File:ANTI 2 OPTIMISATION CKAYE.LOG]]

==Higher optimisation of anti2 1,5-hexadiene==

[[File:Anti 2 higher optimisation ckaye picture.png]]

Link to .log file [[File:ANTI 2 HIGHER OPTIMISATION CKAYE.LOG]]

=='Comparison' of two optimisations of anti2 1,5-hexadiene==

It is a '''major''' ''faux pas'' to directly compare optimisations using different basis sets. Both optimisations were carried out using Hartree-Fock method. The higher basis set yielded a much lower final energy, by approximately 3 atomic units. The bond lengths however are nearly identical, as can be seen below.

[[File:Bond lengths comparison ckaye.gif]]

==Frequency analysis of anti2==

From the frequency analysis of the higher optimised structure of anti2 1,5-hexadiene, the output file confirmed that there were no negative frequencies, which ensures that the molecule is at an energy minimum.

<pre> Low frequencies --- -18.8360 -11.7255 -0.0010 -0.0004 0.0004 1.7210
Low frequencies --- 72.7084 80.1375 120.0085</pre>

==Predicted infrared spectrum of anti2==

[[File:App2 ir spectrum ckaye.png]]

In the output file it can be seen that there are many vibrational modes. However, many have intensities of 0 because they do not involve a change in dipole moment, which is required for an interaction with electromagnetic field. Hence they do not appear on an IR spectrum.

==Optimisation of chair transition state structure==

An allylic H2CCHCH2 fragment was optimised using HF/3-21G basis set. This was later used to form the chair transition state below.

By fixing the bond forming/breaking distances of the terminal carbon atoms to approximately 2.2 Å and performing an opt+freq using the same basis set as before, but with TS(berny) selected and opt=noeigen, to allow imaginary frequencies. An imaginary frequency was observed at 818 cm-1, relating to the transition state. The displacement vectors of the vibration can be seen below

[[File:Transitionstateimaginaryvibration ckaye.png|center|thumb|imaginary vibration (still image, displacement vectors) of the transition state]]

==Optimisation of boat transition state structure==

By using the same allylic H2CCHCH2 fragment that was optimised using HF/3-21G basis set for the chair TS.

Using the same method as for the chair transition state.

Yielded an imaginary frequency at 840 cm-1 corresponding to the transition state

[[File:Boat transition state cope vibration ckaye.png]]

=Diels-Alder=

[[File:Da ckaye scheme.png|300px|thumb|center|Reaction scheme of Diels-Alder cycloaddition]]

==Introduction==

A Diels-Alder reaction is a [4+2] cycloaddition between a conjugated diene and a dienophile, forming a 6-membered ring. The driving force of the reaction is likely to be enthalpic in nature due to the formation of (stronger) sigma bonds at the 'expense' of (weaker) pi bonds. The enthalpic contribution usually overrides any entropic disfavourability<ref>Biotechnology: Bridging Research and Applications edited by Daphne Kamely, Ananda M. Chakrabarty, Steven E. Kornguth</ref> (from the inherent ordering of two molecules into one).

Here, the diene is butadiene and the dienophile is ethylene.

Molecular orbital analysis is important because the symmetry of the reactant MOs is vital to establishing if the reaction occurs or not. If the reactants differ in symmetry then the required orbital overlap does not occur and so the reaction does not.

==Optimisation==

Using semi-empirical AM1 basis set, a molecule of ''cis''-butadiene was optimised.

[[File:OPTIMISATION BUTADIENE CKAYE.LOG]] Link to .log file of optimisation of butadiene

[[File:Butadiene summary ckaye.png|200px|center|thumb|summary of output of optimisation]]

==MO of ''cis''-butadiene==

The molecular orbitals were obtained, with HOMO and LUMO of particular interest.

[[File:Lumo butadiene ckaye.png|200px|thumb|center|LUMO of butadiene]]
[[File:Homo butadiene ckaye.png|200px|thumb|center|HOMO of butadiene]]

As can be seen above, the LUMO is symmetric with respect to a plane down the middle of the molecule. The HOMO however is antisymmetric since it does not have a plane of symmetry.

The relative energies of the MOs of ''cis''-butadiene can be seen below.

[[File:Energylist butadiene ckaye.png|200px|thumb|center|List of MOs]]

==Formation of TS==

A guess structure of the TS was obtained using 2.20 Å fixed distance.

[[File:TS OPT CKAYE.LOG]] Link to .log file of TS optimisation

[[File:Ts picture ckaye.png|200px|center|thumb|TS picture]]

An imaginary frequency was found at 956 cm-1

==MO of TS==

[[File:Ts homo ckaye.png|200px|thumb|center|HOMO of TS]]

[[File:Ts lumo ckaye.png|200px|thumb|center|LUMO of TS]]

==Regioselectivity of Diels Alder reaction==

==Using maleic anhydride to explore endo vs exo TS==

===Endo===

[[File:OPTIMISATION CYCLOHEXAMAL ENDO CKAYE 2.LOG]] Link to .log file

[[File:Ts endo homo ckaye.png|200px|center|thumb|TS of endo]]

===Exo===

[[File:OPTIMISATION CYCLOHEXAMAL EXO TS CKAYE.LOG]] Link to .log file

[[File:Partial bond length ckaye exo ts.png|200px|center|thumb|TS with TS bond distance]]

=References=

<references/>

Rep:Mod:mod3 christopherkaye

2013-03-16T16:19:38Z

Ck1510: /* Formation of TS */

=Christopher Kaye, ck1510, Module 3 Computational=

Extension granted by Dr Hunt to 16th March.

=Introduction=

This module uses Gaussian software to model transition states of reactions. A transition state is the maximum saddle point on a potential energy surface. These states are not observable spectroscopically as they are so short-lived, assumed to be on a similar order of magnitude to bond vibrations - approximately 10-18 s. <ref>Biochemistry by Reginald H. Garrett, Charles M. Grisham</ref>

Investigating transitions states is helpful in understanding kinetics and mechanisms of reactions. Gaussian modelling allows geometries and energies of transition states to be predicted.

In this module, two reactions' transition states are being investigated: the Cope Rearrangement, and Diels-Alder.

=Cope Rearrangement=

[[File:Cope rearrangement for 15hexadiene.png|200px]]

The Cope rearrangement is a pericyclic reaction, specifically a [3+3] sigmatropic rearrangement. Like all pericyclic reactions, it is concerted in nature and passes through a transition state and no intermediates. In the case of 1,5-hexadiene, the transition state goes through a chair-like or a boat-like transition state <ref> Futher Perspectives in Organic Chemistry by CIBA Foundation Symposium</ref>
Gaussian was used to identify low energy conformers and then to attempt to find boat and chair transition states.

=Optimisation of conformers=

Using Hartree-Fock method and 3-21G basis set in each case, various conformers were chosen and optimised. The gauche3 conformer was found to be the lowest energy conformer due to the 'gauche effect' of London forces and favourable orbital interactions. Where sterics become more important, it is expected that antiperiplanar would become the most stable conformer. <ref>Carbohydrate Chemistry and Biochemistry: Structure and Mechanism by M. L. Sinnott</ref>
==Optimisation of antiperiplanar1 1,5-hexadiene==

{{DOI|10042/24051}} Link to D-space optimisation output

[[File:Results summary anti ckaye.png|200px|thumb|center|Results summary of optimisation of anti-peri-planar 1,5-hexadiene]]

[[File:Anti1 ckaye.png]]
Using 'Symmetrize'(sic) the molecule was found to have C2 symmetry.

==Optimisation of gauche4 1,5-hexadiene==

By changing the conformation manually to a gauche linkage, and optimising as above, the following results summary was produced.

[[File:Results summary gauche4 ckaye.png|thumb|center|Results summary of optimisation of gauche 1,5-hexadiene]]

[[File:Gauche 4 picture ckaye.png]]

Link to .log file [[File:GAUCHE4 OPT CKAYE.LOG]]

==Optimisation of gauche6 1,5-hexadiene==

[[File:Results summary gauche6 ckaye.png]]

[[File:Gauche 6 picture ckaye.png]]

Link to .log file [[File:OPT GAUCHE6 CKAYE.LOG]]

==Optimisation of gauche3 1,5-hexadiene==

[[file:Results summary gauche3.png]]

[[file:gauche_3_picture_ckaye.png]]

Link to .log file[[File:FOR GAUCHE 3 INPUT CKAYE.LOG]]

==Optimisation of gauche1 1,5-hexadiene==

[[File:Results summary gauche1 ckaye.png]]

[[File:Gauche 1 picture ckaye.png]]

Link to .log file [[File:GAUCHE 1 CKAYE.LOG]]

==Optimisation of anti2 1,5-hexadiene==

[[File:Results summary anti2 ckaye.png]]

[[File:Anti 2 picture ckaye.png]]

Link to .log file [[File:ANTI 2 OPTIMISATION CKAYE.LOG]]

==Higher optimisation of anti2 1,5-hexadiene==

[[File:Anti 2 higher optimisation ckaye picture.png]]

Link to .log file [[File:ANTI 2 HIGHER OPTIMISATION CKAYE.LOG]]

=='Comparison' of two optimisations of anti2 1,5-hexadiene==

It is a '''major''' ''faux pas'' to directly compare optimisations using different basis sets. Both optimisations were carried out using Hartree-Fock method. The higher basis set yielded a much lower final energy, by approximately 3 atomic units. The bond lengths however are nearly identical, as can be seen below.

[[File:Bond lengths comparison ckaye.gif]]

==Frequency analysis of anti2==

From the frequency analysis of the higher optimised structure of anti2 1,5-hexadiene, the output file confirmed that there were no negative frequencies, which ensures that the molecule is at an energy minimum.

<pre> Low frequencies --- -18.8360 -11.7255 -0.0010 -0.0004 0.0004 1.7210
Low frequencies --- 72.7084 80.1375 120.0085</pre>

==Predicted infrared spectrum of anti2==

[[File:App2 ir spectrum ckaye.png]]

In the output file it can be seen that there are many vibrational modes. However, many have intensities of 0 because they do not involve a change in dipole moment, which is required for an interaction with electromagnetic field. Hence they do not appear on an IR spectrum.

==Optimisation of chair transition state structure==

An allylic H2CCHCH2 fragment was optimised using HF/3-21G basis set. This was later used to form the chair transition state below.

By fixing the bond forming/breaking distances of the terminal carbon atoms to approximately 2.2 Å and performing an opt+freq using the same basis set as before, but with TS(berny) selected and opt=noeigen, to allow imaginary frequencies. An imaginary frequency was observed at 818 cm-1, relating to the transition state. The displacement vectors of the vibration can be seen below

[[File:Transitionstateimaginaryvibration ckaye.png|center|thumb|imaginary vibration (still image, displacement vectors) of the transition state]]

==Optimisation of boat transition state structure==

By using the same allylic H2CCHCH2 fragment that was optimised using HF/3-21G basis set for the chair TS.

Using the same method as for the chair transition state.

Yielded an imaginary frequency at 840 cm-1 corresponding to the transition state

[[File:Boat transition state cope vibration ckaye.png]]

=Diels-Alder=

[[File:Da ckaye scheme.png|300px|thumb|center|Reaction scheme of Diels-Alder cycloaddition]]

==Introduction==

A Diels-Alder reaction is a [4+2] cycloaddition between a conjugated diene and a dienophile, forming a 6-membered ring. The driving force of the reaction is likely to be enthalpic in nature due to the formation of (stronger) sigma bonds at the 'expense' of (weaker) pi bonds. The enthalpic contribution usually overrides any entropic disfavourability<ref>Biotechnology: Bridging Research and Applications edited by Daphne Kamely, Ananda M. Chakrabarty, Steven E. Kornguth</ref> (from the inherent ordering of two molecules into one).

Here, the diene is butadiene and the dienophile is ethylene.

Molecular orbital analysis is important because the symmetry of the reactant MOs is vital to establishing if the reaction occurs or not. If the reactants differ in symmetry then the required orbital overlap does not occur and so the reaction does not.

==Optimisation==

Using semi-empirical AM1 basis set, a molecule of ''cis''-butadiene was optimised.

[[File:OPTIMISATION BUTADIENE CKAYE.LOG]] Link to .log file of optimisation of butadiene

[[File:Butadiene summary ckaye.png|200px|center|thumb|summary of output of optimisation]]

==MO of ''cis''-butadiene==

The molecular orbitals were obtained, with HOMO and LUMO of particular interest.

[[File:Lumo butadiene ckaye.png|200px|thumb|center|LUMO of butadiene]]
[[File:Homo butadiene ckaye.png|200px|thumb|center|HOMO of butadiene]]

As can be seen above, the LUMO is symmetric with respect to a plane down the middle of the molecule. The HOMO however is antisymmetric since it does not have a plane of symmetry.

The relative energies of the MOs of ''cis''-butadiene can be seen below.

[[File:Energylist butadiene ckaye.png|200px|thumb|center|List of MOs]]

==Formation of TS==

A guess structure of the TS was obtained using 2.20 Å fixed distance.

[[File:TS OPT CKAYE.LOG]] Link to .log file of TS optimisation

[[File:Ts picture ckaye.png|200px|center|thumb|TS picture]]

==MO of TS==

[[File:Ts homo ckaye.png|200px|thumb|center|HOMO of TS]]

[[File:Ts lumo ckaye.png|200px|thumb|center|LUMO of TS]]

==Regioselectivity of Diels Alder reaction==

==Using maleic anhydride to explore endo vs exo TS==

===Endo===

[[File:OPTIMISATION CYCLOHEXAMAL ENDO CKAYE 2.LOG]] Link to .log file

[[File:Ts endo homo ckaye.png|200px|center|thumb|TS of endo]]

===Exo===

[[File:OPTIMISATION CYCLOHEXAMAL EXO TS CKAYE.LOG]] Link to .log file

[[File:Partial bond length ckaye exo ts.png|200px|center|thumb|TS with TS bond distance]]

=References=

<references/>

Rep:Mod:mod3 christopherkaye

2013-03-16T16:18:02Z

Ck1510: /* MO of cis-butadiene */

=Christopher Kaye, ck1510, Module 3 Computational=

Extension granted by Dr Hunt to 16th March.

=Introduction=

This module uses Gaussian software to model transition states of reactions. A transition state is the maximum saddle point on a potential energy surface. These states are not observable spectroscopically as they are so short-lived, assumed to be on a similar order of magnitude to bond vibrations - approximately 10-18 s. <ref>Biochemistry by Reginald H. Garrett, Charles M. Grisham</ref>

Investigating transitions states is helpful in understanding kinetics and mechanisms of reactions. Gaussian modelling allows geometries and energies of transition states to be predicted.

In this module, two reactions' transition states are being investigated: the Cope Rearrangement, and Diels-Alder.

=Cope Rearrangement=

[[File:Cope rearrangement for 15hexadiene.png|200px]]

The Cope rearrangement is a pericyclic reaction, specifically a [3+3] sigmatropic rearrangement. Like all pericyclic reactions, it is concerted in nature and passes through a transition state and no intermediates. In the case of 1,5-hexadiene, the transition state goes through a chair-like or a boat-like transition state <ref> Futher Perspectives in Organic Chemistry by CIBA Foundation Symposium</ref>
Gaussian was used to identify low energy conformers and then to attempt to find boat and chair transition states.

=Optimisation of conformers=

Using Hartree-Fock method and 3-21G basis set in each case, various conformers were chosen and optimised. The gauche3 conformer was found to be the lowest energy conformer due to the 'gauche effect' of London forces and favourable orbital interactions. Where sterics become more important, it is expected that antiperiplanar would become the most stable conformer. <ref>Carbohydrate Chemistry and Biochemistry: Structure and Mechanism by M. L. Sinnott</ref>
==Optimisation of antiperiplanar1 1,5-hexadiene==

{{DOI|10042/24051}} Link to D-space optimisation output

[[File:Results summary anti ckaye.png|200px|thumb|center|Results summary of optimisation of anti-peri-planar 1,5-hexadiene]]

[[File:Anti1 ckaye.png]]
Using 'Symmetrize'(sic) the molecule was found to have C2 symmetry.

==Optimisation of gauche4 1,5-hexadiene==

By changing the conformation manually to a gauche linkage, and optimising as above, the following results summary was produced.

[[File:Results summary gauche4 ckaye.png|thumb|center|Results summary of optimisation of gauche 1,5-hexadiene]]

[[File:Gauche 4 picture ckaye.png]]

Link to .log file [[File:GAUCHE4 OPT CKAYE.LOG]]

==Optimisation of gauche6 1,5-hexadiene==

[[File:Results summary gauche6 ckaye.png]]

[[File:Gauche 6 picture ckaye.png]]

Link to .log file [[File:OPT GAUCHE6 CKAYE.LOG]]

==Optimisation of gauche3 1,5-hexadiene==

[[file:Results summary gauche3.png]]

[[file:gauche_3_picture_ckaye.png]]

Link to .log file[[File:FOR GAUCHE 3 INPUT CKAYE.LOG]]

==Optimisation of gauche1 1,5-hexadiene==

[[File:Results summary gauche1 ckaye.png]]

[[File:Gauche 1 picture ckaye.png]]

Link to .log file [[File:GAUCHE 1 CKAYE.LOG]]

==Optimisation of anti2 1,5-hexadiene==

[[File:Results summary anti2 ckaye.png]]

[[File:Anti 2 picture ckaye.png]]

Link to .log file [[File:ANTI 2 OPTIMISATION CKAYE.LOG]]

==Higher optimisation of anti2 1,5-hexadiene==

[[File:Anti 2 higher optimisation ckaye picture.png]]

Link to .log file [[File:ANTI 2 HIGHER OPTIMISATION CKAYE.LOG]]

=='Comparison' of two optimisations of anti2 1,5-hexadiene==

It is a '''major''' ''faux pas'' to directly compare optimisations using different basis sets. Both optimisations were carried out using Hartree-Fock method. The higher basis set yielded a much lower final energy, by approximately 3 atomic units. The bond lengths however are nearly identical, as can be seen below.

[[File:Bond lengths comparison ckaye.gif]]

==Frequency analysis of anti2==

From the frequency analysis of the higher optimised structure of anti2 1,5-hexadiene, the output file confirmed that there were no negative frequencies, which ensures that the molecule is at an energy minimum.

<pre> Low frequencies --- -18.8360 -11.7255 -0.0010 -0.0004 0.0004 1.7210
Low frequencies --- 72.7084 80.1375 120.0085</pre>

==Predicted infrared spectrum of anti2==

[[File:App2 ir spectrum ckaye.png]]

In the output file it can be seen that there are many vibrational modes. However, many have intensities of 0 because they do not involve a change in dipole moment, which is required for an interaction with electromagnetic field. Hence they do not appear on an IR spectrum.

==Optimisation of chair transition state structure==

An allylic H2CCHCH2 fragment was optimised using HF/3-21G basis set. This was later used to form the chair transition state below.

By fixing the bond forming/breaking distances of the terminal carbon atoms to approximately 2.2 Å and performing an opt+freq using the same basis set as before, but with TS(berny) selected and opt=noeigen, to allow imaginary frequencies. An imaginary frequency was observed at 818 cm-1, relating to the transition state. The displacement vectors of the vibration can be seen below

[[File:Transitionstateimaginaryvibration ckaye.png|center|thumb|imaginary vibration (still image, displacement vectors) of the transition state]]

==Optimisation of boat transition state structure==

By using the same allylic H2CCHCH2 fragment that was optimised using HF/3-21G basis set for the chair TS.

Using the same method as for the chair transition state.

Yielded an imaginary frequency at 840 cm-1 corresponding to the transition state

[[File:Boat transition state cope vibration ckaye.png]]

=Diels-Alder=

[[File:Da ckaye scheme.png|300px|thumb|center|Reaction scheme of Diels-Alder cycloaddition]]

==Introduction==

A Diels-Alder reaction is a [4+2] cycloaddition between a conjugated diene and a dienophile, forming a 6-membered ring. The driving force of the reaction is likely to be enthalpic in nature due to the formation of (stronger) sigma bonds at the 'expense' of (weaker) pi bonds. The enthalpic contribution usually overrides any entropic disfavourability<ref>Biotechnology: Bridging Research and Applications edited by Daphne Kamely, Ananda M. Chakrabarty, Steven E. Kornguth</ref> (from the inherent ordering of two molecules into one).

Here, the diene is butadiene and the dienophile is ethylene.

Molecular orbital analysis is important because the symmetry of the reactant MOs is vital to establishing if the reaction occurs or not. If the reactants differ in symmetry then the required orbital overlap does not occur and so the reaction does not.

==Optimisation==

Using semi-empirical AM1 basis set, a molecule of ''cis''-butadiene was optimised.

[[File:OPTIMISATION BUTADIENE CKAYE.LOG]] Link to .log file of optimisation of butadiene

[[File:Butadiene summary ckaye.png|200px|center|thumb|summary of output of optimisation]]

==MO of ''cis''-butadiene==

The molecular orbitals were obtained, with HOMO and LUMO of particular interest.

[[File:Lumo butadiene ckaye.png|200px|thumb|center|LUMO of butadiene]]
[[File:Homo butadiene ckaye.png|200px|thumb|center|HOMO of butadiene]]

As can be seen above, the LUMO is symmetric with respect to a plane down the middle of the molecule. The HOMO however is antisymmetric since it does not have a plane of symmetry.

The relative energies of the MOs of ''cis''-butadiene can be seen below.

[[File:Energylist butadiene ckaye.png|200px|thumb|center|List of MOs]]

==Formation of TS==

[[File:TS OPT CKAYE.LOG]] Link to .log file of TS optimisation

[[File:Ts picture ckaye.png|200px|center|thumb|TS picture]]

==MO of TS==

[[File:Ts homo ckaye.png|200px|thumb|center|HOMO of TS]]

[[File:Ts lumo ckaye.png|200px|thumb|center|LUMO of TS]]

==Regioselectivity of Diels Alder reaction==

==Using maleic anhydride to explore endo vs exo TS==

===Endo===

[[File:OPTIMISATION CYCLOHEXAMAL ENDO CKAYE 2.LOG]] Link to .log file

[[File:Ts endo homo ckaye.png|200px|center|thumb|TS of endo]]

===Exo===

[[File:OPTIMISATION CYCLOHEXAMAL EXO TS CKAYE.LOG]] Link to .log file

[[File:Partial bond length ckaye exo ts.png|200px|center|thumb|TS with TS bond distance]]

=References=

<references/>

Rep:Mod:mod3 christopherkaye

2013-03-16T16:17:25Z

Ck1510: /* Optimisation */

=Christopher Kaye, ck1510, Module 3 Computational=

Extension granted by Dr Hunt to 16th March.

=Introduction=

This module uses Gaussian software to model transition states of reactions. A transition state is the maximum saddle point on a potential energy surface. These states are not observable spectroscopically as they are so short-lived, assumed to be on a similar order of magnitude to bond vibrations - approximately 10-18 s. <ref>Biochemistry by Reginald H. Garrett, Charles M. Grisham</ref>

Investigating transitions states is helpful in understanding kinetics and mechanisms of reactions. Gaussian modelling allows geometries and energies of transition states to be predicted.

In this module, two reactions' transition states are being investigated: the Cope Rearrangement, and Diels-Alder.

=Cope Rearrangement=

[[File:Cope rearrangement for 15hexadiene.png|200px]]

The Cope rearrangement is a pericyclic reaction, specifically a [3+3] sigmatropic rearrangement. Like all pericyclic reactions, it is concerted in nature and passes through a transition state and no intermediates. In the case of 1,5-hexadiene, the transition state goes through a chair-like or a boat-like transition state <ref> Futher Perspectives in Organic Chemistry by CIBA Foundation Symposium</ref>
Gaussian was used to identify low energy conformers and then to attempt to find boat and chair transition states.

=Optimisation of conformers=

Using Hartree-Fock method and 3-21G basis set in each case, various conformers were chosen and optimised. The gauche3 conformer was found to be the lowest energy conformer due to the 'gauche effect' of London forces and favourable orbital interactions. Where sterics become more important, it is expected that antiperiplanar would become the most stable conformer. <ref>Carbohydrate Chemistry and Biochemistry: Structure and Mechanism by M. L. Sinnott</ref>
==Optimisation of antiperiplanar1 1,5-hexadiene==

{{DOI|10042/24051}} Link to D-space optimisation output

[[File:Results summary anti ckaye.png|200px|thumb|center|Results summary of optimisation of anti-peri-planar 1,5-hexadiene]]

[[File:Anti1 ckaye.png]]
Using 'Symmetrize'(sic) the molecule was found to have C2 symmetry.

==Optimisation of gauche4 1,5-hexadiene==

By changing the conformation manually to a gauche linkage, and optimising as above, the following results summary was produced.

[[File:Results summary gauche4 ckaye.png|thumb|center|Results summary of optimisation of gauche 1,5-hexadiene]]

[[File:Gauche 4 picture ckaye.png]]

Link to .log file [[File:GAUCHE4 OPT CKAYE.LOG]]

==Optimisation of gauche6 1,5-hexadiene==

[[File:Results summary gauche6 ckaye.png]]

[[File:Gauche 6 picture ckaye.png]]

Link to .log file [[File:OPT GAUCHE6 CKAYE.LOG]]

==Optimisation of gauche3 1,5-hexadiene==

[[file:Results summary gauche3.png]]

[[file:gauche_3_picture_ckaye.png]]

Link to .log file[[File:FOR GAUCHE 3 INPUT CKAYE.LOG]]

==Optimisation of gauche1 1,5-hexadiene==

[[File:Results summary gauche1 ckaye.png]]

[[File:Gauche 1 picture ckaye.png]]

Link to .log file [[File:GAUCHE 1 CKAYE.LOG]]

==Optimisation of anti2 1,5-hexadiene==

[[File:Results summary anti2 ckaye.png]]

[[File:Anti 2 picture ckaye.png]]

Link to .log file [[File:ANTI 2 OPTIMISATION CKAYE.LOG]]

==Higher optimisation of anti2 1,5-hexadiene==

[[File:Anti 2 higher optimisation ckaye picture.png]]

Link to .log file [[File:ANTI 2 HIGHER OPTIMISATION CKAYE.LOG]]

=='Comparison' of two optimisations of anti2 1,5-hexadiene==

It is a '''major''' ''faux pas'' to directly compare optimisations using different basis sets. Both optimisations were carried out using Hartree-Fock method. The higher basis set yielded a much lower final energy, by approximately 3 atomic units. The bond lengths however are nearly identical, as can be seen below.

[[File:Bond lengths comparison ckaye.gif]]

==Frequency analysis of anti2==

From the frequency analysis of the higher optimised structure of anti2 1,5-hexadiene, the output file confirmed that there were no negative frequencies, which ensures that the molecule is at an energy minimum.

<pre> Low frequencies --- -18.8360 -11.7255 -0.0010 -0.0004 0.0004 1.7210
Low frequencies --- 72.7084 80.1375 120.0085</pre>

==Predicted infrared spectrum of anti2==

[[File:App2 ir spectrum ckaye.png]]

In the output file it can be seen that there are many vibrational modes. However, many have intensities of 0 because they do not involve a change in dipole moment, which is required for an interaction with electromagnetic field. Hence they do not appear on an IR spectrum.

==Optimisation of chair transition state structure==

An allylic H2CCHCH2 fragment was optimised using HF/3-21G basis set. This was later used to form the chair transition state below.

By fixing the bond forming/breaking distances of the terminal carbon atoms to approximately 2.2 Å and performing an opt+freq using the same basis set as before, but with TS(berny) selected and opt=noeigen, to allow imaginary frequencies. An imaginary frequency was observed at 818 cm-1, relating to the transition state. The displacement vectors of the vibration can be seen below

[[File:Transitionstateimaginaryvibration ckaye.png|center|thumb|imaginary vibration (still image, displacement vectors) of the transition state]]

==Optimisation of boat transition state structure==

By using the same allylic H2CCHCH2 fragment that was optimised using HF/3-21G basis set for the chair TS.

Using the same method as for the chair transition state.

Yielded an imaginary frequency at 840 cm-1 corresponding to the transition state

[[File:Boat transition state cope vibration ckaye.png]]

=Diels-Alder=

[[File:Da ckaye scheme.png|300px|thumb|center|Reaction scheme of Diels-Alder cycloaddition]]

==Introduction==

A Diels-Alder reaction is a [4+2] cycloaddition between a conjugated diene and a dienophile, forming a 6-membered ring. The driving force of the reaction is likely to be enthalpic in nature due to the formation of (stronger) sigma bonds at the 'expense' of (weaker) pi bonds. The enthalpic contribution usually overrides any entropic disfavourability<ref>Biotechnology: Bridging Research and Applications edited by Daphne Kamely, Ananda M. Chakrabarty, Steven E. Kornguth</ref> (from the inherent ordering of two molecules into one).

Here, the diene is butadiene and the dienophile is ethylene.

Molecular orbital analysis is important because the symmetry of the reactant MOs is vital to establishing if the reaction occurs or not. If the reactants differ in symmetry then the required orbital overlap does not occur and so the reaction does not.

==Optimisation==

Using semi-empirical AM1 basis set, a molecule of ''cis''-butadiene was optimised.

[[File:OPTIMISATION BUTADIENE CKAYE.LOG]] Link to .log file of optimisation of butadiene

[[File:Butadiene summary ckaye.png|200px|center|thumb|summary of output of optimisation]]

==MO of ''cis''-butadiene==

[[File:Lumo butadiene ckaye.png|200px|thumb|center|LUMO of butadiene]]
[[File:Homo butadiene ckaye.png|200px|thumb|center|HOMO of butadiene]]

As can be seen above, the LUMO is symmetric with respect to a plane down the middle of the molecule. The HOMO however is antisymmetric since it does not have a plane of symmetry.

The relative energies of the MOs of ''cis''-butadiene can be seen below.

[[File:Energylist butadiene ckaye.png|200px|thumb|center|List of MOs]]

==Formation of TS==

[[File:TS OPT CKAYE.LOG]] Link to .log file of TS optimisation

[[File:Ts picture ckaye.png|200px|center|thumb|TS picture]]

==MO of TS==

[[File:Ts homo ckaye.png|200px|thumb|center|HOMO of TS]]

[[File:Ts lumo ckaye.png|200px|thumb|center|LUMO of TS]]

==Regioselectivity of Diels Alder reaction==

==Using maleic anhydride to explore endo vs exo TS==

===Endo===

[[File:OPTIMISATION CYCLOHEXAMAL ENDO CKAYE 2.LOG]] Link to .log file

[[File:Ts endo homo ckaye.png|200px|center|thumb|TS of endo]]

===Exo===

[[File:OPTIMISATION CYCLOHEXAMAL EXO TS CKAYE.LOG]] Link to .log file

[[File:Partial bond length ckaye exo ts.png|200px|center|thumb|TS with TS bond distance]]

=References=

<references/>

Rep:Mod:mod3 christopherkaye

2013-03-16T16:17:01Z

Ck1510: /* Optimisation */

=Christopher Kaye, ck1510, Module 3 Computational=

Extension granted by Dr Hunt to 16th March.

=Introduction=

This module uses Gaussian software to model transition states of reactions. A transition state is the maximum saddle point on a potential energy surface. These states are not observable spectroscopically as they are so short-lived, assumed to be on a similar order of magnitude to bond vibrations - approximately 10-18 s. <ref>Biochemistry by Reginald H. Garrett, Charles M. Grisham</ref>

Investigating transitions states is helpful in understanding kinetics and mechanisms of reactions. Gaussian modelling allows geometries and energies of transition states to be predicted.

In this module, two reactions' transition states are being investigated: the Cope Rearrangement, and Diels-Alder.

=Cope Rearrangement=

[[File:Cope rearrangement for 15hexadiene.png|200px]]

The Cope rearrangement is a pericyclic reaction, specifically a [3+3] sigmatropic rearrangement. Like all pericyclic reactions, it is concerted in nature and passes through a transition state and no intermediates. In the case of 1,5-hexadiene, the transition state goes through a chair-like or a boat-like transition state <ref> Futher Perspectives in Organic Chemistry by CIBA Foundation Symposium</ref>
Gaussian was used to identify low energy conformers and then to attempt to find boat and chair transition states.

=Optimisation of conformers=

Using Hartree-Fock method and 3-21G basis set in each case, various conformers were chosen and optimised. The gauche3 conformer was found to be the lowest energy conformer due to the 'gauche effect' of London forces and favourable orbital interactions. Where sterics become more important, it is expected that antiperiplanar would become the most stable conformer. <ref>Carbohydrate Chemistry and Biochemistry: Structure and Mechanism by M. L. Sinnott</ref>
==Optimisation of antiperiplanar1 1,5-hexadiene==

{{DOI|10042/24051}} Link to D-space optimisation output

[[File:Results summary anti ckaye.png|200px|thumb|center|Results summary of optimisation of anti-peri-planar 1,5-hexadiene]]

[[File:Anti1 ckaye.png]]
Using 'Symmetrize'(sic) the molecule was found to have C2 symmetry.

==Optimisation of gauche4 1,5-hexadiene==

By changing the conformation manually to a gauche linkage, and optimising as above, the following results summary was produced.

[[File:Results summary gauche4 ckaye.png|thumb|center|Results summary of optimisation of gauche 1,5-hexadiene]]

[[File:Gauche 4 picture ckaye.png]]

Link to .log file [[File:GAUCHE4 OPT CKAYE.LOG]]

==Optimisation of gauche6 1,5-hexadiene==

[[File:Results summary gauche6 ckaye.png]]

[[File:Gauche 6 picture ckaye.png]]

Link to .log file [[File:OPT GAUCHE6 CKAYE.LOG]]

==Optimisation of gauche3 1,5-hexadiene==

[[file:Results summary gauche3.png]]

[[file:gauche_3_picture_ckaye.png]]

Link to .log file[[File:FOR GAUCHE 3 INPUT CKAYE.LOG]]

==Optimisation of gauche1 1,5-hexadiene==

[[File:Results summary gauche1 ckaye.png]]

[[File:Gauche 1 picture ckaye.png]]

Link to .log file [[File:GAUCHE 1 CKAYE.LOG]]

==Optimisation of anti2 1,5-hexadiene==

[[File:Results summary anti2 ckaye.png]]

[[File:Anti 2 picture ckaye.png]]

Link to .log file [[File:ANTI 2 OPTIMISATION CKAYE.LOG]]

==Higher optimisation of anti2 1,5-hexadiene==

[[File:Anti 2 higher optimisation ckaye picture.png]]

Link to .log file [[File:ANTI 2 HIGHER OPTIMISATION CKAYE.LOG]]

=='Comparison' of two optimisations of anti2 1,5-hexadiene==

It is a '''major''' ''faux pas'' to directly compare optimisations using different basis sets. Both optimisations were carried out using Hartree-Fock method. The higher basis set yielded a much lower final energy, by approximately 3 atomic units. The bond lengths however are nearly identical, as can be seen below.

[[File:Bond lengths comparison ckaye.gif]]

==Frequency analysis of anti2==

From the frequency analysis of the higher optimised structure of anti2 1,5-hexadiene, the output file confirmed that there were no negative frequencies, which ensures that the molecule is at an energy minimum.

<pre> Low frequencies --- -18.8360 -11.7255 -0.0010 -0.0004 0.0004 1.7210
Low frequencies --- 72.7084 80.1375 120.0085</pre>

==Predicted infrared spectrum of anti2==

[[File:App2 ir spectrum ckaye.png]]

In the output file it can be seen that there are many vibrational modes. However, many have intensities of 0 because they do not involve a change in dipole moment, which is required for an interaction with electromagnetic field. Hence they do not appear on an IR spectrum.

==Optimisation of chair transition state structure==

An allylic H2CCHCH2 fragment was optimised using HF/3-21G basis set. This was later used to form the chair transition state below.

By fixing the bond forming/breaking distances of the terminal carbon atoms to approximately 2.2 Å and performing an opt+freq using the same basis set as before, but with TS(berny) selected and opt=noeigen, to allow imaginary frequencies. An imaginary frequency was observed at 818 cm-1, relating to the transition state. The displacement vectors of the vibration can be seen below

[[File:Transitionstateimaginaryvibration ckaye.png|center|thumb|imaginary vibration (still image, displacement vectors) of the transition state]]

==Optimisation of boat transition state structure==

By using the same allylic H2CCHCH2 fragment that was optimised using HF/3-21G basis set for the chair TS.

Using the same method as for the chair transition state.

Yielded an imaginary frequency at 840 cm-1 corresponding to the transition state

[[File:Boat transition state cope vibration ckaye.png]]

=Diels-Alder=

[[File:Da ckaye scheme.png|300px|thumb|center|Reaction scheme of Diels-Alder cycloaddition]]

==Introduction==

A Diels-Alder reaction is a [4+2] cycloaddition between a conjugated diene and a dienophile, forming a 6-membered ring. The driving force of the reaction is likely to be enthalpic in nature due to the formation of (stronger) sigma bonds at the 'expense' of (weaker) pi bonds. The enthalpic contribution usually overrides any entropic disfavourability<ref>Biotechnology: Bridging Research and Applications edited by Daphne Kamely, Ananda M. Chakrabarty, Steven E. Kornguth</ref> (from the inherent ordering of two molecules into one).

Here, the diene is butadiene and the dienophile is ethylene.

Molecular orbital analysis is important because the symmetry of the reactant MOs is vital to establishing if the reaction occurs or not. If the reactants differ in symmetry then the required orbital overlap does not occur and so the reaction does not.

==Optimisation==

Using HF/3-21G as before, a molecule of ''cis''-butadiene was optimised.

[[File:OPTIMISATION BUTADIENE CKAYE.LOG]] Link to .log file of optimisation of butadiene

[[File:Butadiene summary ckaye.png|200px|center|thumb|summary of output of optimisation]]

==MO of ''cis''-butadiene==

[[File:Lumo butadiene ckaye.png|200px|thumb|center|LUMO of butadiene]]
[[File:Homo butadiene ckaye.png|200px|thumb|center|HOMO of butadiene]]

As can be seen above, the LUMO is symmetric with respect to a plane down the middle of the molecule. The HOMO however is antisymmetric since it does not have a plane of symmetry.

The relative energies of the MOs of ''cis''-butadiene can be seen below.

[[File:Energylist butadiene ckaye.png|200px|thumb|center|List of MOs]]

==Formation of TS==

[[File:TS OPT CKAYE.LOG]] Link to .log file of TS optimisation

[[File:Ts picture ckaye.png|200px|center|thumb|TS picture]]

==MO of TS==

[[File:Ts homo ckaye.png|200px|thumb|center|HOMO of TS]]

[[File:Ts lumo ckaye.png|200px|thumb|center|LUMO of TS]]

==Regioselectivity of Diels Alder reaction==

==Using maleic anhydride to explore endo vs exo TS==

===Endo===

[[File:OPTIMISATION CYCLOHEXAMAL ENDO CKAYE 2.LOG]] Link to .log file

[[File:Ts endo homo ckaye.png|200px|center|thumb|TS of endo]]

===Exo===

[[File:OPTIMISATION CYCLOHEXAMAL EXO TS CKAYE.LOG]] Link to .log file

[[File:Partial bond length ckaye exo ts.png|200px|center|thumb|TS with TS bond distance]]

=References=

<references/>

Rep:Mod:mod3 christopherkaye

2013-03-16T15:40:45Z

Ck1510: /* Exo */

=Christopher Kaye, ck1510, Module 3 Computational=

Extension granted by Dr Hunt to 16th March.

=Introduction=

This module uses Gaussian software to model transition states of reactions. A transition state is the maximum saddle point on a potential energy surface. These states are not observable spectroscopically as they are so short-lived, assumed to be on a similar order of magnitude to bond vibrations - approximately 10-18 s. <ref>Biochemistry by Reginald H. Garrett, Charles M. Grisham</ref>

Investigating transitions states is helpful in understanding kinetics and mechanisms of reactions. Gaussian modelling allows geometries and energies of transition states to be predicted.

In this module, two reactions' transition states are being investigated: the Cope Rearrangement, and Diels-Alder.

=Cope Rearrangement=

[[File:Cope rearrangement for 15hexadiene.png|200px]]

The Cope rearrangement is a pericyclic reaction, specifically a [3+3] sigmatropic rearrangement. Like all pericyclic reactions, it is concerted in nature and passes through a transition state and no intermediates. In the case of 1,5-hexadiene, the transition state goes through a chair-like or a boat-like transition state <ref> Futher Perspectives in Organic Chemistry by CIBA Foundation Symposium</ref>
Gaussian was used to identify low energy conformers and then to attempt to find boat and chair transition states.

=Optimisation of conformers=

Using Hartree-Fock method and 3-21G basis set in each case, various conformers were chosen and optimised. The gauche3 conformer was found to be the lowest energy conformer due to the 'gauche effect' of London forces and favourable orbital interactions. Where sterics become more important, it is expected that antiperiplanar would become the most stable conformer. <ref>Carbohydrate Chemistry and Biochemistry: Structure and Mechanism by M. L. Sinnott</ref>
==Optimisation of antiperiplanar1 1,5-hexadiene==

{{DOI|10042/24051}} Link to D-space optimisation output

[[File:Results summary anti ckaye.png|200px|thumb|center|Results summary of optimisation of anti-peri-planar 1,5-hexadiene]]

[[File:Anti1 ckaye.png]]
Using 'Symmetrize'(sic) the molecule was found to have C2 symmetry.

==Optimisation of gauche4 1,5-hexadiene==

By changing the conformation manually to a gauche linkage, and optimising as above, the following results summary was produced.

[[File:Results summary gauche4 ckaye.png|thumb|center|Results summary of optimisation of gauche 1,5-hexadiene]]

[[File:Gauche 4 picture ckaye.png]]

Link to .log file [[File:GAUCHE4 OPT CKAYE.LOG]]

==Optimisation of gauche6 1,5-hexadiene==

[[File:Results summary gauche6 ckaye.png]]

[[File:Gauche 6 picture ckaye.png]]

Link to .log file [[File:OPT GAUCHE6 CKAYE.LOG]]

==Optimisation of gauche3 1,5-hexadiene==

[[file:Results summary gauche3.png]]

[[file:gauche_3_picture_ckaye.png]]

Link to .log file[[File:FOR GAUCHE 3 INPUT CKAYE.LOG]]

==Optimisation of gauche1 1,5-hexadiene==

[[File:Results summary gauche1 ckaye.png]]

[[File:Gauche 1 picture ckaye.png]]

Link to .log file [[File:GAUCHE 1 CKAYE.LOG]]

==Optimisation of anti2 1,5-hexadiene==

[[File:Results summary anti2 ckaye.png]]

[[File:Anti 2 picture ckaye.png]]

Link to .log file [[File:ANTI 2 OPTIMISATION CKAYE.LOG]]

==Higher optimisation of anti2 1,5-hexadiene==

[[File:Anti 2 higher optimisation ckaye picture.png]]

Link to .log file [[File:ANTI 2 HIGHER OPTIMISATION CKAYE.LOG]]

=='Comparison' of two optimisations of anti2 1,5-hexadiene==

It is a '''major''' ''faux pas'' to directly compare optimisations using different basis sets. Both optimisations were carried out using Hartree-Fock method. The higher basis set yielded a much lower final energy, by approximately 3 atomic units. The bond lengths however are nearly identical, as can be seen below.

[[File:Bond lengths comparison ckaye.gif]]

==Frequency analysis of anti2==

From the frequency analysis of the higher optimised structure of anti2 1,5-hexadiene, the output file confirmed that there were no negative frequencies, which ensures that the molecule is at an energy minimum.

<pre> Low frequencies --- -18.8360 -11.7255 -0.0010 -0.0004 0.0004 1.7210
Low frequencies --- 72.7084 80.1375 120.0085</pre>

==Predicted infrared spectrum of anti2==

[[File:App2 ir spectrum ckaye.png]]

In the output file it can be seen that there are many vibrational modes. However, many have intensities of 0 because they do not involve a change in dipole moment, which is required for an interaction with electromagnetic field. Hence they do not appear on an IR spectrum.

==Optimisation of chair transition state structure==

An allylic H2CCHCH2 fragment was optimised using HF/3-21G basis set. This was later used to form the chair transition state below.

By fixing the bond forming/breaking distances of the terminal carbon atoms to approximately 2.2 Å and performing an opt+freq using the same basis set as before, but with TS(berny) selected and opt=noeigen, to allow imaginary frequencies. An imaginary frequency was observed at 818 cm-1, relating to the transition state. The displacement vectors of the vibration can be seen below

[[File:Transitionstateimaginaryvibration ckaye.png|center|thumb|imaginary vibration (still image, displacement vectors) of the transition state]]

==Optimisation of boat transition state structure==

By using the same allylic H2CCHCH2 fragment that was optimised using HF/3-21G basis set for the chair TS.

Using the same method as for the chair transition state.

Yielded an imaginary frequency at 840 cm-1 corresponding to the transition state

[[File:Boat transition state cope vibration ckaye.png]]

=Diels-Alder=

[[File:Da ckaye scheme.png|300px|thumb|center|Reaction scheme of Diels-Alder cycloaddition]]

==Introduction==

A Diels-Alder reaction is a [4+2] cycloaddition between a conjugated diene and a dienophile, forming a 6-membered ring. The driving force of the reaction is likely to be enthalpic in nature due to the formation of (stronger) sigma bonds at the 'expense' of (weaker) pi bonds. The enthalpic contribution usually overrides any entropic disfavourability<ref>Biotechnology: Bridging Research and Applications edited by Daphne Kamely, Ananda M. Chakrabarty, Steven E. Kornguth</ref> (from the inherent ordering of two molecules into one).

Here, the diene is butadiene and the dienophile is ethylene.

Molecular orbital analysis is important because the symmetry of the reactant MOs is vital to establishing if the reaction occurs or not. If the reactants differ in symmetry then the required orbital overlap does not occur and so the reaction does not.

==Optimisation==

[[File:OPTIMISATION BUTADIENE CKAYE.LOG]] Link to .log file of optimisation of butadiene]]

[[File:Butadiene summary ckaye.png|200px|center|thumb|summary of output of optimisation]]

==MO of ''cis''-butadiene==

[[File:Lumo butadiene ckaye.png|200px|thumb|center|LUMO of butadiene]]
[[File:Homo butadiene ckaye.png|200px|thumb|center|HOMO of butadiene]]

As can be seen above, the LUMO is symmetric with respect to a plane down the middle of the molecule. The HOMO however is antisymmetric since it does not have a plane of symmetry.

The relative energies of the MOs of ''cis''-butadiene can be seen below.

[[File:Energylist butadiene ckaye.png|200px|thumb|center|List of MOs]]

==Formation of TS==

[[File:TS OPT CKAYE.LOG]] Link to .log file of TS optimisation

[[File:Ts picture ckaye.png|200px|center|thumb|TS picture]]

==MO of TS==

[[File:Ts homo ckaye.png|200px|thumb|center|HOMO of TS]]

[[File:Ts lumo ckaye.png|200px|thumb|center|LUMO of TS]]

==Regioselectivity of Diels Alder reaction==

==Using maleic anhydride to explore endo vs exo TS==

===Endo===

[[File:OPTIMISATION CYCLOHEXAMAL ENDO CKAYE 2.LOG]] Link to .log file

[[File:Ts endo homo ckaye.png|200px|center|thumb|TS of endo]]

===Exo===

[[File:OPTIMISATION CYCLOHEXAMAL EXO TS CKAYE.LOG]] Link to .log file

[[File:Partial bond length ckaye exo ts.png|200px|center|thumb|TS with TS bond distance]]

=References=

<references/>

Rep:Mod:mod3 christopherkaye

2013-03-16T15:40:06Z

Ck1510: /* Using maleic anhydride to explore endo vs exo TS */

=Christopher Kaye, ck1510, Module 3 Computational=

Extension granted by Dr Hunt to 16th March.

=Introduction=

This module uses Gaussian software to model transition states of reactions. A transition state is the maximum saddle point on a potential energy surface. These states are not observable spectroscopically as they are so short-lived, assumed to be on a similar order of magnitude to bond vibrations - approximately 10-18 s. <ref>Biochemistry by Reginald H. Garrett, Charles M. Grisham</ref>

Investigating transitions states is helpful in understanding kinetics and mechanisms of reactions. Gaussian modelling allows geometries and energies of transition states to be predicted.

In this module, two reactions' transition states are being investigated: the Cope Rearrangement, and Diels-Alder.

=Cope Rearrangement=

[[File:Cope rearrangement for 15hexadiene.png|200px]]

The Cope rearrangement is a pericyclic reaction, specifically a [3+3] sigmatropic rearrangement. Like all pericyclic reactions, it is concerted in nature and passes through a transition state and no intermediates. In the case of 1,5-hexadiene, the transition state goes through a chair-like or a boat-like transition state <ref> Futher Perspectives in Organic Chemistry by CIBA Foundation Symposium</ref>
Gaussian was used to identify low energy conformers and then to attempt to find boat and chair transition states.

=Optimisation of conformers=

Using Hartree-Fock method and 3-21G basis set in each case, various conformers were chosen and optimised. The gauche3 conformer was found to be the lowest energy conformer due to the 'gauche effect' of London forces and favourable orbital interactions. Where sterics become more important, it is expected that antiperiplanar would become the most stable conformer. <ref>Carbohydrate Chemistry and Biochemistry: Structure and Mechanism by M. L. Sinnott</ref>
==Optimisation of antiperiplanar1 1,5-hexadiene==

{{DOI|10042/24051}} Link to D-space optimisation output

[[File:Results summary anti ckaye.png|200px|thumb|center|Results summary of optimisation of anti-peri-planar 1,5-hexadiene]]

[[File:Anti1 ckaye.png]]
Using 'Symmetrize'(sic) the molecule was found to have C2 symmetry.

==Optimisation of gauche4 1,5-hexadiene==

By changing the conformation manually to a gauche linkage, and optimising as above, the following results summary was produced.

[[File:Results summary gauche4 ckaye.png|thumb|center|Results summary of optimisation of gauche 1,5-hexadiene]]

[[File:Gauche 4 picture ckaye.png]]

Link to .log file [[File:GAUCHE4 OPT CKAYE.LOG]]

==Optimisation of gauche6 1,5-hexadiene==

[[File:Results summary gauche6 ckaye.png]]

[[File:Gauche 6 picture ckaye.png]]

Link to .log file [[File:OPT GAUCHE6 CKAYE.LOG]]

==Optimisation of gauche3 1,5-hexadiene==

[[file:Results summary gauche3.png]]

[[file:gauche_3_picture_ckaye.png]]

Link to .log file[[File:FOR GAUCHE 3 INPUT CKAYE.LOG]]

==Optimisation of gauche1 1,5-hexadiene==

[[File:Results summary gauche1 ckaye.png]]

[[File:Gauche 1 picture ckaye.png]]

Link to .log file [[File:GAUCHE 1 CKAYE.LOG]]

==Optimisation of anti2 1,5-hexadiene==

[[File:Results summary anti2 ckaye.png]]

[[File:Anti 2 picture ckaye.png]]

Link to .log file [[File:ANTI 2 OPTIMISATION CKAYE.LOG]]

==Higher optimisation of anti2 1,5-hexadiene==

[[File:Anti 2 higher optimisation ckaye picture.png]]

Link to .log file [[File:ANTI 2 HIGHER OPTIMISATION CKAYE.LOG]]

=='Comparison' of two optimisations of anti2 1,5-hexadiene==

It is a '''major''' ''faux pas'' to directly compare optimisations using different basis sets. Both optimisations were carried out using Hartree-Fock method. The higher basis set yielded a much lower final energy, by approximately 3 atomic units. The bond lengths however are nearly identical, as can be seen below.

[[File:Bond lengths comparison ckaye.gif]]

==Frequency analysis of anti2==

From the frequency analysis of the higher optimised structure of anti2 1,5-hexadiene, the output file confirmed that there were no negative frequencies, which ensures that the molecule is at an energy minimum.

<pre> Low frequencies --- -18.8360 -11.7255 -0.0010 -0.0004 0.0004 1.7210
Low frequencies --- 72.7084 80.1375 120.0085</pre>

==Predicted infrared spectrum of anti2==

[[File:App2 ir spectrum ckaye.png]]

In the output file it can be seen that there are many vibrational modes. However, many have intensities of 0 because they do not involve a change in dipole moment, which is required for an interaction with electromagnetic field. Hence they do not appear on an IR spectrum.

==Optimisation of chair transition state structure==

An allylic H2CCHCH2 fragment was optimised using HF/3-21G basis set. This was later used to form the chair transition state below.

By fixing the bond forming/breaking distances of the terminal carbon atoms to approximately 2.2 Å and performing an opt+freq using the same basis set as before, but with TS(berny) selected and opt=noeigen, to allow imaginary frequencies. An imaginary frequency was observed at 818 cm-1, relating to the transition state. The displacement vectors of the vibration can be seen below

[[File:Transitionstateimaginaryvibration ckaye.png|center|thumb|imaginary vibration (still image, displacement vectors) of the transition state]]

==Optimisation of boat transition state structure==

By using the same allylic H2CCHCH2 fragment that was optimised using HF/3-21G basis set for the chair TS.

Using the same method as for the chair transition state.

Yielded an imaginary frequency at 840 cm-1 corresponding to the transition state

[[File:Boat transition state cope vibration ckaye.png]]

=Diels-Alder=

[[File:Da ckaye scheme.png|300px|thumb|center|Reaction scheme of Diels-Alder cycloaddition]]

==Introduction==

A Diels-Alder reaction is a [4+2] cycloaddition between a conjugated diene and a dienophile, forming a 6-membered ring. The driving force of the reaction is likely to be enthalpic in nature due to the formation of (stronger) sigma bonds at the 'expense' of (weaker) pi bonds. The enthalpic contribution usually overrides any entropic disfavourability<ref>Biotechnology: Bridging Research and Applications edited by Daphne Kamely, Ananda M. Chakrabarty, Steven E. Kornguth</ref> (from the inherent ordering of two molecules into one).

Here, the diene is butadiene and the dienophile is ethylene.

Molecular orbital analysis is important because the symmetry of the reactant MOs is vital to establishing if the reaction occurs or not. If the reactants differ in symmetry then the required orbital overlap does not occur and so the reaction does not.

==Optimisation==

[[File:OPTIMISATION BUTADIENE CKAYE.LOG]] Link to .log file of optimisation of butadiene]]

[[File:Butadiene summary ckaye.png|200px|center|thumb|summary of output of optimisation]]

==MO of ''cis''-butadiene==

[[File:Lumo butadiene ckaye.png|200px|thumb|center|LUMO of butadiene]]
[[File:Homo butadiene ckaye.png|200px|thumb|center|HOMO of butadiene]]

As can be seen above, the LUMO is symmetric with respect to a plane down the middle of the molecule. The HOMO however is antisymmetric since it does not have a plane of symmetry.

The relative energies of the MOs of ''cis''-butadiene can be seen below.

[[File:Energylist butadiene ckaye.png|200px|thumb|center|List of MOs]]

==Formation of TS==

[[File:TS OPT CKAYE.LOG]] Link to .log file of TS optimisation

[[File:Ts picture ckaye.png|200px|center|thumb|TS picture]]

==MO of TS==

[[File:Ts homo ckaye.png|200px|thumb|center|HOMO of TS]]

[[File:Ts lumo ckaye.png|200px|thumb|center|LUMO of TS]]

==Regioselectivity of Diels Alder reaction==

==Using maleic anhydride to explore endo vs exo TS==

===Endo===

[[File:OPTIMISATION CYCLOHEXAMAL ENDO CKAYE 2.LOG]] Link to .log file

[[File:Ts endo homo ckaye.png|200px|center|thumb|TS of endo]]

===Exo===

[[File:Partial bond length ckaye exo ts.png|200px|center|thumb|TS with TS bond distance]]

=References=

<references/>

Rep:Mod:mod3 christopherkaye

2013-03-16T15:39:05Z

Ck1510: /* Regioselectivity of Diels Alder reaction */

=Christopher Kaye, ck1510, Module 3 Computational=

Extension granted by Dr Hunt to 16th March.

=Introduction=

This module uses Gaussian software to model transition states of reactions. A transition state is the maximum saddle point on a potential energy surface. These states are not observable spectroscopically as they are so short-lived, assumed to be on a similar order of magnitude to bond vibrations - approximately 10-18 s. <ref>Biochemistry by Reginald H. Garrett, Charles M. Grisham</ref>

Investigating transitions states is helpful in understanding kinetics and mechanisms of reactions. Gaussian modelling allows geometries and energies of transition states to be predicted.

In this module, two reactions' transition states are being investigated: the Cope Rearrangement, and Diels-Alder.

=Cope Rearrangement=

[[File:Cope rearrangement for 15hexadiene.png|200px]]

The Cope rearrangement is a pericyclic reaction, specifically a [3+3] sigmatropic rearrangement. Like all pericyclic reactions, it is concerted in nature and passes through a transition state and no intermediates. In the case of 1,5-hexadiene, the transition state goes through a chair-like or a boat-like transition state <ref> Futher Perspectives in Organic Chemistry by CIBA Foundation Symposium</ref>
Gaussian was used to identify low energy conformers and then to attempt to find boat and chair transition states.

=Optimisation of conformers=

Using Hartree-Fock method and 3-21G basis set in each case, various conformers were chosen and optimised. The gauche3 conformer was found to be the lowest energy conformer due to the 'gauche effect' of London forces and favourable orbital interactions. Where sterics become more important, it is expected that antiperiplanar would become the most stable conformer. <ref>Carbohydrate Chemistry and Biochemistry: Structure and Mechanism by M. L. Sinnott</ref>
==Optimisation of antiperiplanar1 1,5-hexadiene==

{{DOI|10042/24051}} Link to D-space optimisation output

[[File:Results summary anti ckaye.png|200px|thumb|center|Results summary of optimisation of anti-peri-planar 1,5-hexadiene]]

[[File:Anti1 ckaye.png]]
Using 'Symmetrize'(sic) the molecule was found to have C2 symmetry.

==Optimisation of gauche4 1,5-hexadiene==

By changing the conformation manually to a gauche linkage, and optimising as above, the following results summary was produced.

[[File:Results summary gauche4 ckaye.png|thumb|center|Results summary of optimisation of gauche 1,5-hexadiene]]

[[File:Gauche 4 picture ckaye.png]]

Link to .log file [[File:GAUCHE4 OPT CKAYE.LOG]]

==Optimisation of gauche6 1,5-hexadiene==

[[File:Results summary gauche6 ckaye.png]]

[[File:Gauche 6 picture ckaye.png]]

Link to .log file [[File:OPT GAUCHE6 CKAYE.LOG]]

==Optimisation of gauche3 1,5-hexadiene==

[[file:Results summary gauche3.png]]

[[file:gauche_3_picture_ckaye.png]]

Link to .log file[[File:FOR GAUCHE 3 INPUT CKAYE.LOG]]

==Optimisation of gauche1 1,5-hexadiene==

[[File:Results summary gauche1 ckaye.png]]

[[File:Gauche 1 picture ckaye.png]]

Link to .log file [[File:GAUCHE 1 CKAYE.LOG]]

==Optimisation of anti2 1,5-hexadiene==

[[File:Results summary anti2 ckaye.png]]

[[File:Anti 2 picture ckaye.png]]

Link to .log file [[File:ANTI 2 OPTIMISATION CKAYE.LOG]]

==Higher optimisation of anti2 1,5-hexadiene==

[[File:Anti 2 higher optimisation ckaye picture.png]]

Link to .log file [[File:ANTI 2 HIGHER OPTIMISATION CKAYE.LOG]]

=='Comparison' of two optimisations of anti2 1,5-hexadiene==

It is a '''major''' ''faux pas'' to directly compare optimisations using different basis sets. Both optimisations were carried out using Hartree-Fock method. The higher basis set yielded a much lower final energy, by approximately 3 atomic units. The bond lengths however are nearly identical, as can be seen below.

[[File:Bond lengths comparison ckaye.gif]]

==Frequency analysis of anti2==

From the frequency analysis of the higher optimised structure of anti2 1,5-hexadiene, the output file confirmed that there were no negative frequencies, which ensures that the molecule is at an energy minimum.

<pre> Low frequencies --- -18.8360 -11.7255 -0.0010 -0.0004 0.0004 1.7210
Low frequencies --- 72.7084 80.1375 120.0085</pre>

==Predicted infrared spectrum of anti2==

[[File:App2 ir spectrum ckaye.png]]

In the output file it can be seen that there are many vibrational modes. However, many have intensities of 0 because they do not involve a change in dipole moment, which is required for an interaction with electromagnetic field. Hence they do not appear on an IR spectrum.

==Optimisation of chair transition state structure==

An allylic H2CCHCH2 fragment was optimised using HF/3-21G basis set. This was later used to form the chair transition state below.

By fixing the bond forming/breaking distances of the terminal carbon atoms to approximately 2.2 Å and performing an opt+freq using the same basis set as before, but with TS(berny) selected and opt=noeigen, to allow imaginary frequencies. An imaginary frequency was observed at 818 cm-1, relating to the transition state. The displacement vectors of the vibration can be seen below

[[File:Transitionstateimaginaryvibration ckaye.png|center|thumb|imaginary vibration (still image, displacement vectors) of the transition state]]

==Optimisation of boat transition state structure==

By using the same allylic H2CCHCH2 fragment that was optimised using HF/3-21G basis set for the chair TS.

Using the same method as for the chair transition state.

Yielded an imaginary frequency at 840 cm-1 corresponding to the transition state

[[File:Boat transition state cope vibration ckaye.png]]

=Diels-Alder=

[[File:Da ckaye scheme.png|300px|thumb|center|Reaction scheme of Diels-Alder cycloaddition]]

==Introduction==

A Diels-Alder reaction is a [4+2] cycloaddition between a conjugated diene and a dienophile, forming a 6-membered ring. The driving force of the reaction is likely to be enthalpic in nature due to the formation of (stronger) sigma bonds at the 'expense' of (weaker) pi bonds. The enthalpic contribution usually overrides any entropic disfavourability<ref>Biotechnology: Bridging Research and Applications edited by Daphne Kamely, Ananda M. Chakrabarty, Steven E. Kornguth</ref> (from the inherent ordering of two molecules into one).

Here, the diene is butadiene and the dienophile is ethylene.

Molecular orbital analysis is important because the symmetry of the reactant MOs is vital to establishing if the reaction occurs or not. If the reactants differ in symmetry then the required orbital overlap does not occur and so the reaction does not.

==Optimisation==

[[File:OPTIMISATION BUTADIENE CKAYE.LOG]] Link to .log file of optimisation of butadiene]]

[[File:Butadiene summary ckaye.png|200px|center|thumb|summary of output of optimisation]]

==MO of ''cis''-butadiene==

[[File:Lumo butadiene ckaye.png|200px|thumb|center|LUMO of butadiene]]
[[File:Homo butadiene ckaye.png|200px|thumb|center|HOMO of butadiene]]

As can be seen above, the LUMO is symmetric with respect to a plane down the middle of the molecule. The HOMO however is antisymmetric since it does not have a plane of symmetry.

The relative energies of the MOs of ''cis''-butadiene can be seen below.

[[File:Energylist butadiene ckaye.png|200px|thumb|center|List of MOs]]

==Formation of TS==

[[File:TS OPT CKAYE.LOG]] Link to .log file of TS optimisation

[[File:Ts picture ckaye.png|200px|center|thumb|TS picture]]

==MO of TS==

[[File:Ts homo ckaye.png|200px|thumb|center|HOMO of TS]]

[[File:Ts lumo ckaye.png|200px|thumb|center|LUMO of TS]]

==Regioselectivity of Diels Alder reaction==

==Using maleic anhydride to explore endo vs exo TS==

[[File:OPTIMISATION CYCLOHEXAMAL ENDO CKAYE 2.LOG]] Link to .log file

[[File:Partial bond length ckaye exo ts.png|200px|center|thumb|TS with TS bond distance]]

=References=

<references/>

Rep:Mod:mod3 christopherkaye

2013-03-16T15:38:39Z

Ck1510: /* Regioselectivity of Diels Alder reaction */

=Christopher Kaye, ck1510, Module 3 Computational=

Extension granted by Dr Hunt to 16th March.

=Introduction=

This module uses Gaussian software to model transition states of reactions. A transition state is the maximum saddle point on a potential energy surface. These states are not observable spectroscopically as they are so short-lived, assumed to be on a similar order of magnitude to bond vibrations - approximately 10-18 s. <ref>Biochemistry by Reginald H. Garrett, Charles M. Grisham</ref>

Investigating transitions states is helpful in understanding kinetics and mechanisms of reactions. Gaussian modelling allows geometries and energies of transition states to be predicted.

In this module, two reactions' transition states are being investigated: the Cope Rearrangement, and Diels-Alder.

=Cope Rearrangement=

[[File:Cope rearrangement for 15hexadiene.png|200px]]

The Cope rearrangement is a pericyclic reaction, specifically a [3+3] sigmatropic rearrangement. Like all pericyclic reactions, it is concerted in nature and passes through a transition state and no intermediates. In the case of 1,5-hexadiene, the transition state goes through a chair-like or a boat-like transition state <ref> Futher Perspectives in Organic Chemistry by CIBA Foundation Symposium</ref>
Gaussian was used to identify low energy conformers and then to attempt to find boat and chair transition states.

=Optimisation of conformers=

Using Hartree-Fock method and 3-21G basis set in each case, various conformers were chosen and optimised. The gauche3 conformer was found to be the lowest energy conformer due to the 'gauche effect' of London forces and favourable orbital interactions. Where sterics become more important, it is expected that antiperiplanar would become the most stable conformer. <ref>Carbohydrate Chemistry and Biochemistry: Structure and Mechanism by M. L. Sinnott</ref>
==Optimisation of antiperiplanar1 1,5-hexadiene==

{{DOI|10042/24051}} Link to D-space optimisation output

[[File:Results summary anti ckaye.png|200px|thumb|center|Results summary of optimisation of anti-peri-planar 1,5-hexadiene]]

[[File:Anti1 ckaye.png]]
Using 'Symmetrize'(sic) the molecule was found to have C2 symmetry.

==Optimisation of gauche4 1,5-hexadiene==

By changing the conformation manually to a gauche linkage, and optimising as above, the following results summary was produced.

[[File:Results summary gauche4 ckaye.png|thumb|center|Results summary of optimisation of gauche 1,5-hexadiene]]

[[File:Gauche 4 picture ckaye.png]]

Link to .log file [[File:GAUCHE4 OPT CKAYE.LOG]]

==Optimisation of gauche6 1,5-hexadiene==

[[File:Results summary gauche6 ckaye.png]]

[[File:Gauche 6 picture ckaye.png]]

Link to .log file [[File:OPT GAUCHE6 CKAYE.LOG]]

==Optimisation of gauche3 1,5-hexadiene==

[[file:Results summary gauche3.png]]

[[file:gauche_3_picture_ckaye.png]]

Link to .log file[[File:FOR GAUCHE 3 INPUT CKAYE.LOG]]

==Optimisation of gauche1 1,5-hexadiene==

[[File:Results summary gauche1 ckaye.png]]

[[File:Gauche 1 picture ckaye.png]]

Link to .log file [[File:GAUCHE 1 CKAYE.LOG]]

==Optimisation of anti2 1,5-hexadiene==

[[File:Results summary anti2 ckaye.png]]

[[File:Anti 2 picture ckaye.png]]

Link to .log file [[File:ANTI 2 OPTIMISATION CKAYE.LOG]]

==Higher optimisation of anti2 1,5-hexadiene==

[[File:Anti 2 higher optimisation ckaye picture.png]]

Link to .log file [[File:ANTI 2 HIGHER OPTIMISATION CKAYE.LOG]]

=='Comparison' of two optimisations of anti2 1,5-hexadiene==

It is a '''major''' ''faux pas'' to directly compare optimisations using different basis sets. Both optimisations were carried out using Hartree-Fock method. The higher basis set yielded a much lower final energy, by approximately 3 atomic units. The bond lengths however are nearly identical, as can be seen below.

[[File:Bond lengths comparison ckaye.gif]]

==Frequency analysis of anti2==

From the frequency analysis of the higher optimised structure of anti2 1,5-hexadiene, the output file confirmed that there were no negative frequencies, which ensures that the molecule is at an energy minimum.

<pre> Low frequencies --- -18.8360 -11.7255 -0.0010 -0.0004 0.0004 1.7210
Low frequencies --- 72.7084 80.1375 120.0085</pre>

==Predicted infrared spectrum of anti2==

[[File:App2 ir spectrum ckaye.png]]

In the output file it can be seen that there are many vibrational modes. However, many have intensities of 0 because they do not involve a change in dipole moment, which is required for an interaction with electromagnetic field. Hence they do not appear on an IR spectrum.

==Optimisation of chair transition state structure==

An allylic H2CCHCH2 fragment was optimised using HF/3-21G basis set. This was later used to form the chair transition state below.

By fixing the bond forming/breaking distances of the terminal carbon atoms to approximately 2.2 Å and performing an opt+freq using the same basis set as before, but with TS(berny) selected and opt=noeigen, to allow imaginary frequencies. An imaginary frequency was observed at 818 cm-1, relating to the transition state. The displacement vectors of the vibration can be seen below

[[File:Transitionstateimaginaryvibration ckaye.png|center|thumb|imaginary vibration (still image, displacement vectors) of the transition state]]

==Optimisation of boat transition state structure==

By using the same allylic H2CCHCH2 fragment that was optimised using HF/3-21G basis set for the chair TS.

Using the same method as for the chair transition state.

Yielded an imaginary frequency at 840 cm-1 corresponding to the transition state

[[File:Boat transition state cope vibration ckaye.png]]

=Diels-Alder=

[[File:Da ckaye scheme.png|300px|thumb|center|Reaction scheme of Diels-Alder cycloaddition]]

==Introduction==

A Diels-Alder reaction is a [4+2] cycloaddition between a conjugated diene and a dienophile, forming a 6-membered ring. The driving force of the reaction is likely to be enthalpic in nature due to the formation of (stronger) sigma bonds at the 'expense' of (weaker) pi bonds. The enthalpic contribution usually overrides any entropic disfavourability<ref>Biotechnology: Bridging Research and Applications edited by Daphne Kamely, Ananda M. Chakrabarty, Steven E. Kornguth</ref> (from the inherent ordering of two molecules into one).

Here, the diene is butadiene and the dienophile is ethylene.

Molecular orbital analysis is important because the symmetry of the reactant MOs is vital to establishing if the reaction occurs or not. If the reactants differ in symmetry then the required orbital overlap does not occur and so the reaction does not.

==Optimisation==

[[File:OPTIMISATION BUTADIENE CKAYE.LOG]] Link to .log file of optimisation of butadiene]]

[[File:Butadiene summary ckaye.png|200px|center|thumb|summary of output of optimisation]]

==MO of ''cis''-butadiene==

[[File:Lumo butadiene ckaye.png|200px|thumb|center|LUMO of butadiene]]
[[File:Homo butadiene ckaye.png|200px|thumb|center|HOMO of butadiene]]

As can be seen above, the LUMO is symmetric with respect to a plane down the middle of the molecule. The HOMO however is antisymmetric since it does not have a plane of symmetry.

The relative energies of the MOs of ''cis''-butadiene can be seen below.

[[File:Energylist butadiene ckaye.png|200px|thumb|center|List of MOs]]

==Formation of TS==

[[File:TS OPT CKAYE.LOG]] Link to .log file of TS optimisation

[[File:Ts picture ckaye.png|200px|center|thumb|TS picture]]

==MO of TS==

[[File:Ts homo ckaye.png|200px|thumb|center|HOMO of TS]]

[[File:Ts lumo ckaye.png|200px|thumb|center|LUMO of TS]]

==Regioselectivity of Diels Alder reaction==

[[File:OPTIMISATION CYCLOHEXAMAL ENDO CKAYE 2.LOG]] Link to .log file

[[File:Partial bond length ckaye exo ts.png|200px|center|thumb|TS with TS bond distance]]

=References=

<references/>

Rep:Mod:mod3 christopherkaye

2013-03-16T15:38:24Z

Ck1510: /* Regioselectivity of Diels Alder reaction */

=Christopher Kaye, ck1510, Module 3 Computational=

Extension granted by Dr Hunt to 16th March.

=Introduction=

This module uses Gaussian software to model transition states of reactions. A transition state is the maximum saddle point on a potential energy surface. These states are not observable spectroscopically as they are so short-lived, assumed to be on a similar order of magnitude to bond vibrations - approximately 10-18 s. <ref>Biochemistry by Reginald H. Garrett, Charles M. Grisham</ref>

Investigating transitions states is helpful in understanding kinetics and mechanisms of reactions. Gaussian modelling allows geometries and energies of transition states to be predicted.

In this module, two reactions' transition states are being investigated: the Cope Rearrangement, and Diels-Alder.

=Cope Rearrangement=

[[File:Cope rearrangement for 15hexadiene.png|200px]]

The Cope rearrangement is a pericyclic reaction, specifically a [3+3] sigmatropic rearrangement. Like all pericyclic reactions, it is concerted in nature and passes through a transition state and no intermediates. In the case of 1,5-hexadiene, the transition state goes through a chair-like or a boat-like transition state <ref> Futher Perspectives in Organic Chemistry by CIBA Foundation Symposium</ref>
Gaussian was used to identify low energy conformers and then to attempt to find boat and chair transition states.

=Optimisation of conformers=

Using Hartree-Fock method and 3-21G basis set in each case, various conformers were chosen and optimised. The gauche3 conformer was found to be the lowest energy conformer due to the 'gauche effect' of London forces and favourable orbital interactions. Where sterics become more important, it is expected that antiperiplanar would become the most stable conformer. <ref>Carbohydrate Chemistry and Biochemistry: Structure and Mechanism by M. L. Sinnott</ref>
==Optimisation of antiperiplanar1 1,5-hexadiene==

{{DOI|10042/24051}} Link to D-space optimisation output

[[File:Results summary anti ckaye.png|200px|thumb|center|Results summary of optimisation of anti-peri-planar 1,5-hexadiene]]

[[File:Anti1 ckaye.png]]
Using 'Symmetrize'(sic) the molecule was found to have C2 symmetry.

==Optimisation of gauche4 1,5-hexadiene==

By changing the conformation manually to a gauche linkage, and optimising as above, the following results summary was produced.

[[File:Results summary gauche4 ckaye.png|thumb|center|Results summary of optimisation of gauche 1,5-hexadiene]]

[[File:Gauche 4 picture ckaye.png]]

Link to .log file [[File:GAUCHE4 OPT CKAYE.LOG]]

==Optimisation of gauche6 1,5-hexadiene==

[[File:Results summary gauche6 ckaye.png]]

[[File:Gauche 6 picture ckaye.png]]

Link to .log file [[File:OPT GAUCHE6 CKAYE.LOG]]

==Optimisation of gauche3 1,5-hexadiene==

[[file:Results summary gauche3.png]]

[[file:gauche_3_picture_ckaye.png]]

Link to .log file[[File:FOR GAUCHE 3 INPUT CKAYE.LOG]]

==Optimisation of gauche1 1,5-hexadiene==

[[File:Results summary gauche1 ckaye.png]]

[[File:Gauche 1 picture ckaye.png]]

Link to .log file [[File:GAUCHE 1 CKAYE.LOG]]

==Optimisation of anti2 1,5-hexadiene==

[[File:Results summary anti2 ckaye.png]]

[[File:Anti 2 picture ckaye.png]]

Link to .log file [[File:ANTI 2 OPTIMISATION CKAYE.LOG]]

==Higher optimisation of anti2 1,5-hexadiene==

[[File:Anti 2 higher optimisation ckaye picture.png]]

Link to .log file [[File:ANTI 2 HIGHER OPTIMISATION CKAYE.LOG]]

=='Comparison' of two optimisations of anti2 1,5-hexadiene==

It is a '''major''' ''faux pas'' to directly compare optimisations using different basis sets. Both optimisations were carried out using Hartree-Fock method. The higher basis set yielded a much lower final energy, by approximately 3 atomic units. The bond lengths however are nearly identical, as can be seen below.

[[File:Bond lengths comparison ckaye.gif]]

==Frequency analysis of anti2==

From the frequency analysis of the higher optimised structure of anti2 1,5-hexadiene, the output file confirmed that there were no negative frequencies, which ensures that the molecule is at an energy minimum.

<pre> Low frequencies --- -18.8360 -11.7255 -0.0010 -0.0004 0.0004 1.7210
Low frequencies --- 72.7084 80.1375 120.0085</pre>

==Predicted infrared spectrum of anti2==

[[File:App2 ir spectrum ckaye.png]]

In the output file it can be seen that there are many vibrational modes. However, many have intensities of 0 because they do not involve a change in dipole moment, which is required for an interaction with electromagnetic field. Hence they do not appear on an IR spectrum.

==Optimisation of chair transition state structure==

An allylic H2CCHCH2 fragment was optimised using HF/3-21G basis set. This was later used to form the chair transition state below.

By fixing the bond forming/breaking distances of the terminal carbon atoms to approximately 2.2 Å and performing an opt+freq using the same basis set as before, but with TS(berny) selected and opt=noeigen, to allow imaginary frequencies. An imaginary frequency was observed at 818 cm-1, relating to the transition state. The displacement vectors of the vibration can be seen below

[[File:Transitionstateimaginaryvibration ckaye.png|center|thumb|imaginary vibration (still image, displacement vectors) of the transition state]]

==Optimisation of boat transition state structure==

By using the same allylic H2CCHCH2 fragment that was optimised using HF/3-21G basis set for the chair TS.

Using the same method as for the chair transition state.

Yielded an imaginary frequency at 840 cm-1 corresponding to the transition state

[[File:Boat transition state cope vibration ckaye.png]]

=Diels-Alder=

[[File:Da ckaye scheme.png|300px|thumb|center|Reaction scheme of Diels-Alder cycloaddition]]

==Introduction==

A Diels-Alder reaction is a [4+2] cycloaddition between a conjugated diene and a dienophile, forming a 6-membered ring. The driving force of the reaction is likely to be enthalpic in nature due to the formation of (stronger) sigma bonds at the 'expense' of (weaker) pi bonds. The enthalpic contribution usually overrides any entropic disfavourability<ref>Biotechnology: Bridging Research and Applications edited by Daphne Kamely, Ananda M. Chakrabarty, Steven E. Kornguth</ref> (from the inherent ordering of two molecules into one).

Here, the diene is butadiene and the dienophile is ethylene.

Molecular orbital analysis is important because the symmetry of the reactant MOs is vital to establishing if the reaction occurs or not. If the reactants differ in symmetry then the required orbital overlap does not occur and so the reaction does not.

==Optimisation==

[[File:OPTIMISATION BUTADIENE CKAYE.LOG]] Link to .log file of optimisation of butadiene]]

[[File:Butadiene summary ckaye.png|200px|center|thumb|summary of output of optimisation]]

==MO of ''cis''-butadiene==

[[File:Lumo butadiene ckaye.png|200px|thumb|center|LUMO of butadiene]]
[[File:Homo butadiene ckaye.png|200px|thumb|center|HOMO of butadiene]]

As can be seen above, the LUMO is symmetric with respect to a plane down the middle of the molecule. The HOMO however is antisymmetric since it does not have a plane of symmetry.

The relative energies of the MOs of ''cis''-butadiene can be seen below.

[[File:Energylist butadiene ckaye.png|200px|thumb|center|List of MOs]]

==Formation of TS==

[[File:TS OPT CKAYE.LOG]] Link to .log file of TS optimisation

[[File:Ts picture ckaye.png|200px|center|thumb|TS picture]]

==MO of TS==

[[File:Ts homo ckaye.png|200px|thumb|center|HOMO of TS]]

[[File:Ts lumo ckaye.png|200px|thumb|center|LUMO of TS]]

==Regioselectivity of Diels Alder reaction==

[[File:OPTIMISATION CYCLOHEXAMAL ENDO CKAYE 2.LOG]] Link to .log file

[[File:Partial bond length ckaye exo ts.png|200px|center|thumb|TS]]

=References=

<references/>

Rep:Mod:mod3 christopherkaye

2013-03-16T15:37:48Z

Ck1510: /* Regioselectivity of Diels Alder reaction */

=Christopher Kaye, ck1510, Module 3 Computational=

Extension granted by Dr Hunt to 16th March.

=Introduction=

This module uses Gaussian software to model transition states of reactions. A transition state is the maximum saddle point on a potential energy surface. These states are not observable spectroscopically as they are so short-lived, assumed to be on a similar order of magnitude to bond vibrations - approximately 10-18 s. <ref>Biochemistry by Reginald H. Garrett, Charles M. Grisham</ref>

Investigating transitions states is helpful in understanding kinetics and mechanisms of reactions. Gaussian modelling allows geometries and energies of transition states to be predicted.

In this module, two reactions' transition states are being investigated: the Cope Rearrangement, and Diels-Alder.

=Cope Rearrangement=

[[File:Cope rearrangement for 15hexadiene.png|200px]]

The Cope rearrangement is a pericyclic reaction, specifically a [3+3] sigmatropic rearrangement. Like all pericyclic reactions, it is concerted in nature and passes through a transition state and no intermediates. In the case of 1,5-hexadiene, the transition state goes through a chair-like or a boat-like transition state <ref> Futher Perspectives in Organic Chemistry by CIBA Foundation Symposium</ref>
Gaussian was used to identify low energy conformers and then to attempt to find boat and chair transition states.

=Optimisation of conformers=

Using Hartree-Fock method and 3-21G basis set in each case, various conformers were chosen and optimised. The gauche3 conformer was found to be the lowest energy conformer due to the 'gauche effect' of London forces and favourable orbital interactions. Where sterics become more important, it is expected that antiperiplanar would become the most stable conformer. <ref>Carbohydrate Chemistry and Biochemistry: Structure and Mechanism by M. L. Sinnott</ref>
==Optimisation of antiperiplanar1 1,5-hexadiene==

{{DOI|10042/24051}} Link to D-space optimisation output

[[File:Results summary anti ckaye.png|200px|thumb|center|Results summary of optimisation of anti-peri-planar 1,5-hexadiene]]

[[File:Anti1 ckaye.png]]
Using 'Symmetrize'(sic) the molecule was found to have C2 symmetry.

==Optimisation of gauche4 1,5-hexadiene==

By changing the conformation manually to a gauche linkage, and optimising as above, the following results summary was produced.

[[File:Results summary gauche4 ckaye.png|thumb|center|Results summary of optimisation of gauche 1,5-hexadiene]]

[[File:Gauche 4 picture ckaye.png]]

Link to .log file [[File:GAUCHE4 OPT CKAYE.LOG]]

==Optimisation of gauche6 1,5-hexadiene==

[[File:Results summary gauche6 ckaye.png]]

[[File:Gauche 6 picture ckaye.png]]

Link to .log file [[File:OPT GAUCHE6 CKAYE.LOG]]

==Optimisation of gauche3 1,5-hexadiene==

[[file:Results summary gauche3.png]]

[[file:gauche_3_picture_ckaye.png]]

Link to .log file[[File:FOR GAUCHE 3 INPUT CKAYE.LOG]]

==Optimisation of gauche1 1,5-hexadiene==

[[File:Results summary gauche1 ckaye.png]]

[[File:Gauche 1 picture ckaye.png]]

Link to .log file [[File:GAUCHE 1 CKAYE.LOG]]

==Optimisation of anti2 1,5-hexadiene==

[[File:Results summary anti2 ckaye.png]]

[[File:Anti 2 picture ckaye.png]]

Link to .log file [[File:ANTI 2 OPTIMISATION CKAYE.LOG]]

==Higher optimisation of anti2 1,5-hexadiene==

[[File:Anti 2 higher optimisation ckaye picture.png]]

Link to .log file [[File:ANTI 2 HIGHER OPTIMISATION CKAYE.LOG]]

=='Comparison' of two optimisations of anti2 1,5-hexadiene==

It is a '''major''' ''faux pas'' to directly compare optimisations using different basis sets. Both optimisations were carried out using Hartree-Fock method. The higher basis set yielded a much lower final energy, by approximately 3 atomic units. The bond lengths however are nearly identical, as can be seen below.

[[File:Bond lengths comparison ckaye.gif]]

==Frequency analysis of anti2==

From the frequency analysis of the higher optimised structure of anti2 1,5-hexadiene, the output file confirmed that there were no negative frequencies, which ensures that the molecule is at an energy minimum.

<pre> Low frequencies --- -18.8360 -11.7255 -0.0010 -0.0004 0.0004 1.7210
Low frequencies --- 72.7084 80.1375 120.0085</pre>

==Predicted infrared spectrum of anti2==

[[File:App2 ir spectrum ckaye.png]]

In the output file it can be seen that there are many vibrational modes. However, many have intensities of 0 because they do not involve a change in dipole moment, which is required for an interaction with electromagnetic field. Hence they do not appear on an IR spectrum.

==Optimisation of chair transition state structure==

An allylic H2CCHCH2 fragment was optimised using HF/3-21G basis set. This was later used to form the chair transition state below.

By fixing the bond forming/breaking distances of the terminal carbon atoms to approximately 2.2 Å and performing an opt+freq using the same basis set as before, but with TS(berny) selected and opt=noeigen, to allow imaginary frequencies. An imaginary frequency was observed at 818 cm-1, relating to the transition state. The displacement vectors of the vibration can be seen below

[[File:Transitionstateimaginaryvibration ckaye.png|center|thumb|imaginary vibration (still image, displacement vectors) of the transition state]]

==Optimisation of boat transition state structure==

By using the same allylic H2CCHCH2 fragment that was optimised using HF/3-21G basis set for the chair TS.

Using the same method as for the chair transition state.

Yielded an imaginary frequency at 840 cm-1 corresponding to the transition state

[[File:Boat transition state cope vibration ckaye.png]]

=Diels-Alder=

[[File:Da ckaye scheme.png|300px|thumb|center|Reaction scheme of Diels-Alder cycloaddition]]

==Introduction==

A Diels-Alder reaction is a [4+2] cycloaddition between a conjugated diene and a dienophile, forming a 6-membered ring. The driving force of the reaction is likely to be enthalpic in nature due to the formation of (stronger) sigma bonds at the 'expense' of (weaker) pi bonds. The enthalpic contribution usually overrides any entropic disfavourability<ref>Biotechnology: Bridging Research and Applications edited by Daphne Kamely, Ananda M. Chakrabarty, Steven E. Kornguth</ref> (from the inherent ordering of two molecules into one).

Here, the diene is butadiene and the dienophile is ethylene.

Molecular orbital analysis is important because the symmetry of the reactant MOs is vital to establishing if the reaction occurs or not. If the reactants differ in symmetry then the required orbital overlap does not occur and so the reaction does not.

==Optimisation==

[[File:OPTIMISATION BUTADIENE CKAYE.LOG]] Link to .log file of optimisation of butadiene]]

[[File:Butadiene summary ckaye.png|200px|center|thumb|summary of output of optimisation]]

==MO of ''cis''-butadiene==

[[File:Lumo butadiene ckaye.png|200px|thumb|center|LUMO of butadiene]]
[[File:Homo butadiene ckaye.png|200px|thumb|center|HOMO of butadiene]]

As can be seen above, the LUMO is symmetric with respect to a plane down the middle of the molecule. The HOMO however is antisymmetric since it does not have a plane of symmetry.

The relative energies of the MOs of ''cis''-butadiene can be seen below.

[[File:Energylist butadiene ckaye.png|200px|thumb|center|List of MOs]]

==Formation of TS==

[[File:TS OPT CKAYE.LOG]] Link to .log file of TS optimisation

[[File:Ts picture ckaye.png|200px|center|thumb|TS picture]]

==MO of TS==

[[File:Ts homo ckaye.png|200px|thumb|center|HOMO of TS]]

[[File:Ts lumo ckaye.png|200px|thumb|center|LUMO of TS]]

==Regioselectivity of Diels Alder reaction==

[[File:OPTIMISATION CYCLOHEXAMAL ENDO CKAYE 2.LOG]] Link to .log file

=References=

<references/>

Rep:Mod:mod3 christopherkaye

2013-03-16T15:36:46Z

Ck1510: /* Formation of TS */

=Christopher Kaye, ck1510, Module 3 Computational=

Extension granted by Dr Hunt to 16th March.

=Introduction=

This module uses Gaussian software to model transition states of reactions. A transition state is the maximum saddle point on a potential energy surface. These states are not observable spectroscopically as they are so short-lived, assumed to be on a similar order of magnitude to bond vibrations - approximately 10-18 s. <ref>Biochemistry by Reginald H. Garrett, Charles M. Grisham</ref>

Investigating transitions states is helpful in understanding kinetics and mechanisms of reactions. Gaussian modelling allows geometries and energies of transition states to be predicted.

In this module, two reactions' transition states are being investigated: the Cope Rearrangement, and Diels-Alder.

=Cope Rearrangement=

[[File:Cope rearrangement for 15hexadiene.png|200px]]

The Cope rearrangement is a pericyclic reaction, specifically a [3+3] sigmatropic rearrangement. Like all pericyclic reactions, it is concerted in nature and passes through a transition state and no intermediates. In the case of 1,5-hexadiene, the transition state goes through a chair-like or a boat-like transition state <ref> Futher Perspectives in Organic Chemistry by CIBA Foundation Symposium</ref>
Gaussian was used to identify low energy conformers and then to attempt to find boat and chair transition states.

=Optimisation of conformers=

Using Hartree-Fock method and 3-21G basis set in each case, various conformers were chosen and optimised. The gauche3 conformer was found to be the lowest energy conformer due to the 'gauche effect' of London forces and favourable orbital interactions. Where sterics become more important, it is expected that antiperiplanar would become the most stable conformer. <ref>Carbohydrate Chemistry and Biochemistry: Structure and Mechanism by M. L. Sinnott</ref>
==Optimisation of antiperiplanar1 1,5-hexadiene==

{{DOI|10042/24051}} Link to D-space optimisation output

[[File:Results summary anti ckaye.png|200px|thumb|center|Results summary of optimisation of anti-peri-planar 1,5-hexadiene]]

[[File:Anti1 ckaye.png]]
Using 'Symmetrize'(sic) the molecule was found to have C2 symmetry.

==Optimisation of gauche4 1,5-hexadiene==

By changing the conformation manually to a gauche linkage, and optimising as above, the following results summary was produced.

[[File:Results summary gauche4 ckaye.png|thumb|center|Results summary of optimisation of gauche 1,5-hexadiene]]

[[File:Gauche 4 picture ckaye.png]]

Link to .log file [[File:GAUCHE4 OPT CKAYE.LOG]]

==Optimisation of gauche6 1,5-hexadiene==

[[File:Results summary gauche6 ckaye.png]]

[[File:Gauche 6 picture ckaye.png]]

Link to .log file [[File:OPT GAUCHE6 CKAYE.LOG]]

==Optimisation of gauche3 1,5-hexadiene==

[[file:Results summary gauche3.png]]

[[file:gauche_3_picture_ckaye.png]]

Link to .log file[[File:FOR GAUCHE 3 INPUT CKAYE.LOG]]

==Optimisation of gauche1 1,5-hexadiene==

[[File:Results summary gauche1 ckaye.png]]

[[File:Gauche 1 picture ckaye.png]]

Link to .log file [[File:GAUCHE 1 CKAYE.LOG]]

==Optimisation of anti2 1,5-hexadiene==

[[File:Results summary anti2 ckaye.png]]

[[File:Anti 2 picture ckaye.png]]

Link to .log file [[File:ANTI 2 OPTIMISATION CKAYE.LOG]]

==Higher optimisation of anti2 1,5-hexadiene==

[[File:Anti 2 higher optimisation ckaye picture.png]]

Link to .log file [[File:ANTI 2 HIGHER OPTIMISATION CKAYE.LOG]]

=='Comparison' of two optimisations of anti2 1,5-hexadiene==

It is a '''major''' ''faux pas'' to directly compare optimisations using different basis sets. Both optimisations were carried out using Hartree-Fock method. The higher basis set yielded a much lower final energy, by approximately 3 atomic units. The bond lengths however are nearly identical, as can be seen below.

[[File:Bond lengths comparison ckaye.gif]]

==Frequency analysis of anti2==

From the frequency analysis of the higher optimised structure of anti2 1,5-hexadiene, the output file confirmed that there were no negative frequencies, which ensures that the molecule is at an energy minimum.

<pre> Low frequencies --- -18.8360 -11.7255 -0.0010 -0.0004 0.0004 1.7210
Low frequencies --- 72.7084 80.1375 120.0085</pre>

==Predicted infrared spectrum of anti2==

[[File:App2 ir spectrum ckaye.png]]

In the output file it can be seen that there are many vibrational modes. However, many have intensities of 0 because they do not involve a change in dipole moment, which is required for an interaction with electromagnetic field. Hence they do not appear on an IR spectrum.

==Optimisation of chair transition state structure==

An allylic H2CCHCH2 fragment was optimised using HF/3-21G basis set. This was later used to form the chair transition state below.

By fixing the bond forming/breaking distances of the terminal carbon atoms to approximately 2.2 Å and performing an opt+freq using the same basis set as before, but with TS(berny) selected and opt=noeigen, to allow imaginary frequencies. An imaginary frequency was observed at 818 cm-1, relating to the transition state. The displacement vectors of the vibration can be seen below

[[File:Transitionstateimaginaryvibration ckaye.png|center|thumb|imaginary vibration (still image, displacement vectors) of the transition state]]

==Optimisation of boat transition state structure==

By using the same allylic H2CCHCH2 fragment that was optimised using HF/3-21G basis set for the chair TS.

Using the same method as for the chair transition state.

Yielded an imaginary frequency at 840 cm-1 corresponding to the transition state

[[File:Boat transition state cope vibration ckaye.png]]

=Diels-Alder=

[[File:Da ckaye scheme.png|300px|thumb|center|Reaction scheme of Diels-Alder cycloaddition]]

==Introduction==

A Diels-Alder reaction is a [4+2] cycloaddition between a conjugated diene and a dienophile, forming a 6-membered ring. The driving force of the reaction is likely to be enthalpic in nature due to the formation of (stronger) sigma bonds at the 'expense' of (weaker) pi bonds. The enthalpic contribution usually overrides any entropic disfavourability<ref>Biotechnology: Bridging Research and Applications edited by Daphne Kamely, Ananda M. Chakrabarty, Steven E. Kornguth</ref> (from the inherent ordering of two molecules into one).

Here, the diene is butadiene and the dienophile is ethylene.

Molecular orbital analysis is important because the symmetry of the reactant MOs is vital to establishing if the reaction occurs or not. If the reactants differ in symmetry then the required orbital overlap does not occur and so the reaction does not.

==Optimisation==

[[File:OPTIMISATION BUTADIENE CKAYE.LOG]] Link to .log file of optimisation of butadiene]]

[[File:Butadiene summary ckaye.png|200px|center|thumb|summary of output of optimisation]]

==MO of ''cis''-butadiene==

[[File:Lumo butadiene ckaye.png|200px|thumb|center|LUMO of butadiene]]
[[File:Homo butadiene ckaye.png|200px|thumb|center|HOMO of butadiene]]

As can be seen above, the LUMO is symmetric with respect to a plane down the middle of the molecule. The HOMO however is antisymmetric since it does not have a plane of symmetry.

The relative energies of the MOs of ''cis''-butadiene can be seen below.

[[File:Energylist butadiene ckaye.png|200px|thumb|center|List of MOs]]

==Formation of TS==

[[File:TS OPT CKAYE.LOG]] Link to .log file of TS optimisation

[[File:Ts picture ckaye.png|200px|center|thumb|TS picture]]

==MO of TS==

[[File:Ts homo ckaye.png|200px|thumb|center|HOMO of TS]]

[[File:Ts lumo ckaye.png|200px|thumb|center|LUMO of TS]]

==Regioselectivity of Diels Alder reaction==

=References=

<references/>

Rep:Mod:mod3 christopherkaye

2013-03-16T15:36:20Z

Ck1510: /* Formation of TS */

=Christopher Kaye, ck1510, Module 3 Computational=

Extension granted by Dr Hunt to 16th March.

=Introduction=

This module uses Gaussian software to model transition states of reactions. A transition state is the maximum saddle point on a potential energy surface. These states are not observable spectroscopically as they are so short-lived, assumed to be on a similar order of magnitude to bond vibrations - approximately 10-18 s. <ref>Biochemistry by Reginald H. Garrett, Charles M. Grisham</ref>

Investigating transitions states is helpful in understanding kinetics and mechanisms of reactions. Gaussian modelling allows geometries and energies of transition states to be predicted.

In this module, two reactions' transition states are being investigated: the Cope Rearrangement, and Diels-Alder.

=Cope Rearrangement=

[[File:Cope rearrangement for 15hexadiene.png|200px]]

The Cope rearrangement is a pericyclic reaction, specifically a [3+3] sigmatropic rearrangement. Like all pericyclic reactions, it is concerted in nature and passes through a transition state and no intermediates. In the case of 1,5-hexadiene, the transition state goes through a chair-like or a boat-like transition state <ref> Futher Perspectives in Organic Chemistry by CIBA Foundation Symposium</ref>
Gaussian was used to identify low energy conformers and then to attempt to find boat and chair transition states.

=Optimisation of conformers=

Using Hartree-Fock method and 3-21G basis set in each case, various conformers were chosen and optimised. The gauche3 conformer was found to be the lowest energy conformer due to the 'gauche effect' of London forces and favourable orbital interactions. Where sterics become more important, it is expected that antiperiplanar would become the most stable conformer. <ref>Carbohydrate Chemistry and Biochemistry: Structure and Mechanism by M. L. Sinnott</ref>
==Optimisation of antiperiplanar1 1,5-hexadiene==

{{DOI|10042/24051}} Link to D-space optimisation output

[[File:Results summary anti ckaye.png|200px|thumb|center|Results summary of optimisation of anti-peri-planar 1,5-hexadiene]]

[[File:Anti1 ckaye.png]]
Using 'Symmetrize'(sic) the molecule was found to have C2 symmetry.

==Optimisation of gauche4 1,5-hexadiene==

By changing the conformation manually to a gauche linkage, and optimising as above, the following results summary was produced.

[[File:Results summary gauche4 ckaye.png|thumb|center|Results summary of optimisation of gauche 1,5-hexadiene]]

[[File:Gauche 4 picture ckaye.png]]

Link to .log file [[File:GAUCHE4 OPT CKAYE.LOG]]

==Optimisation of gauche6 1,5-hexadiene==

[[File:Results summary gauche6 ckaye.png]]

[[File:Gauche 6 picture ckaye.png]]

Link to .log file [[File:OPT GAUCHE6 CKAYE.LOG]]

==Optimisation of gauche3 1,5-hexadiene==

[[file:Results summary gauche3.png]]

[[file:gauche_3_picture_ckaye.png]]

Link to .log file[[File:FOR GAUCHE 3 INPUT CKAYE.LOG]]

==Optimisation of gauche1 1,5-hexadiene==

[[File:Results summary gauche1 ckaye.png]]

[[File:Gauche 1 picture ckaye.png]]

Link to .log file [[File:GAUCHE 1 CKAYE.LOG]]

==Optimisation of anti2 1,5-hexadiene==

[[File:Results summary anti2 ckaye.png]]

[[File:Anti 2 picture ckaye.png]]

Link to .log file [[File:ANTI 2 OPTIMISATION CKAYE.LOG]]

==Higher optimisation of anti2 1,5-hexadiene==

[[File:Anti 2 higher optimisation ckaye picture.png]]

Link to .log file [[File:ANTI 2 HIGHER OPTIMISATION CKAYE.LOG]]

=='Comparison' of two optimisations of anti2 1,5-hexadiene==

It is a '''major''' ''faux pas'' to directly compare optimisations using different basis sets. Both optimisations were carried out using Hartree-Fock method. The higher basis set yielded a much lower final energy, by approximately 3 atomic units. The bond lengths however are nearly identical, as can be seen below.

[[File:Bond lengths comparison ckaye.gif]]

==Frequency analysis of anti2==

From the frequency analysis of the higher optimised structure of anti2 1,5-hexadiene, the output file confirmed that there were no negative frequencies, which ensures that the molecule is at an energy minimum.

<pre> Low frequencies --- -18.8360 -11.7255 -0.0010 -0.0004 0.0004 1.7210
Low frequencies --- 72.7084 80.1375 120.0085</pre>

==Predicted infrared spectrum of anti2==

[[File:App2 ir spectrum ckaye.png]]

In the output file it can be seen that there are many vibrational modes. However, many have intensities of 0 because they do not involve a change in dipole moment, which is required for an interaction with electromagnetic field. Hence they do not appear on an IR spectrum.

==Optimisation of chair transition state structure==

An allylic H2CCHCH2 fragment was optimised using HF/3-21G basis set. This was later used to form the chair transition state below.

By fixing the bond forming/breaking distances of the terminal carbon atoms to approximately 2.2 Å and performing an opt+freq using the same basis set as before, but with TS(berny) selected and opt=noeigen, to allow imaginary frequencies. An imaginary frequency was observed at 818 cm-1, relating to the transition state. The displacement vectors of the vibration can be seen below

[[File:Transitionstateimaginaryvibration ckaye.png|center|thumb|imaginary vibration (still image, displacement vectors) of the transition state]]

==Optimisation of boat transition state structure==

By using the same allylic H2CCHCH2 fragment that was optimised using HF/3-21G basis set for the chair TS.

Using the same method as for the chair transition state.

Yielded an imaginary frequency at 840 cm-1 corresponding to the transition state

[[File:Boat transition state cope vibration ckaye.png]]

=Diels-Alder=

[[File:Da ckaye scheme.png|300px|thumb|center|Reaction scheme of Diels-Alder cycloaddition]]

==Introduction==

A Diels-Alder reaction is a [4+2] cycloaddition between a conjugated diene and a dienophile, forming a 6-membered ring. The driving force of the reaction is likely to be enthalpic in nature due to the formation of (stronger) sigma bonds at the 'expense' of (weaker) pi bonds. The enthalpic contribution usually overrides any entropic disfavourability<ref>Biotechnology: Bridging Research and Applications edited by Daphne Kamely, Ananda M. Chakrabarty, Steven E. Kornguth</ref> (from the inherent ordering of two molecules into one).

Here, the diene is butadiene and the dienophile is ethylene.

Molecular orbital analysis is important because the symmetry of the reactant MOs is vital to establishing if the reaction occurs or not. If the reactants differ in symmetry then the required orbital overlap does not occur and so the reaction does not.

==Optimisation==

[[File:OPTIMISATION BUTADIENE CKAYE.LOG]] Link to .log file of optimisation of butadiene]]

[[File:Butadiene summary ckaye.png|200px|center|thumb|summary of output of optimisation]]

==MO of ''cis''-butadiene==

[[File:Lumo butadiene ckaye.png|200px|thumb|center|LUMO of butadiene]]
[[File:Homo butadiene ckaye.png|200px|thumb|center|HOMO of butadiene]]

As can be seen above, the LUMO is symmetric with respect to a plane down the middle of the molecule. The HOMO however is antisymmetric since it does not have a plane of symmetry.

The relative energies of the MOs of ''cis''-butadiene can be seen below.

[[File:Energylist butadiene ckaye.png|200px|thumb|center|List of MOs]]

==Formation of TS==

[[File:TS OPT CKAYE.LOG]] Link to .log file of TS optimisation

==MO of TS==

[[File:Ts homo ckaye.png|200px|thumb|center|HOMO of TS]]

[[File:Ts lumo ckaye.png|200px|thumb|center|LUMO of TS]]

==Regioselectivity of Diels Alder reaction==

=References=

<references/>

Rep:Mod:mod3 christopherkaye

2013-03-16T15:35:39Z

Ck1510: /* MO of cis-butadiene */

=Christopher Kaye, ck1510, Module 3 Computational=

Extension granted by Dr Hunt to 16th March.

=Introduction=

This module uses Gaussian software to model transition states of reactions. A transition state is the maximum saddle point on a potential energy surface. These states are not observable spectroscopically as they are so short-lived, assumed to be on a similar order of magnitude to bond vibrations - approximately 10-18 s. <ref>Biochemistry by Reginald H. Garrett, Charles M. Grisham</ref>

Investigating transitions states is helpful in understanding kinetics and mechanisms of reactions. Gaussian modelling allows geometries and energies of transition states to be predicted.

In this module, two reactions' transition states are being investigated: the Cope Rearrangement, and Diels-Alder.

=Cope Rearrangement=

[[File:Cope rearrangement for 15hexadiene.png|200px]]

The Cope rearrangement is a pericyclic reaction, specifically a [3+3] sigmatropic rearrangement. Like all pericyclic reactions, it is concerted in nature and passes through a transition state and no intermediates. In the case of 1,5-hexadiene, the transition state goes through a chair-like or a boat-like transition state <ref> Futher Perspectives in Organic Chemistry by CIBA Foundation Symposium</ref>
Gaussian was used to identify low energy conformers and then to attempt to find boat and chair transition states.

=Optimisation of conformers=

Using Hartree-Fock method and 3-21G basis set in each case, various conformers were chosen and optimised. The gauche3 conformer was found to be the lowest energy conformer due to the 'gauche effect' of London forces and favourable orbital interactions. Where sterics become more important, it is expected that antiperiplanar would become the most stable conformer. <ref>Carbohydrate Chemistry and Biochemistry: Structure and Mechanism by M. L. Sinnott</ref>
==Optimisation of antiperiplanar1 1,5-hexadiene==

{{DOI|10042/24051}} Link to D-space optimisation output

[[File:Results summary anti ckaye.png|200px|thumb|center|Results summary of optimisation of anti-peri-planar 1,5-hexadiene]]

[[File:Anti1 ckaye.png]]
Using 'Symmetrize'(sic) the molecule was found to have C2 symmetry.

==Optimisation of gauche4 1,5-hexadiene==

By changing the conformation manually to a gauche linkage, and optimising as above, the following results summary was produced.

[[File:Results summary gauche4 ckaye.png|thumb|center|Results summary of optimisation of gauche 1,5-hexadiene]]

[[File:Gauche 4 picture ckaye.png]]

Link to .log file [[File:GAUCHE4 OPT CKAYE.LOG]]

==Optimisation of gauche6 1,5-hexadiene==

[[File:Results summary gauche6 ckaye.png]]

[[File:Gauche 6 picture ckaye.png]]

Link to .log file [[File:OPT GAUCHE6 CKAYE.LOG]]

==Optimisation of gauche3 1,5-hexadiene==

[[file:Results summary gauche3.png]]

[[file:gauche_3_picture_ckaye.png]]

Link to .log file[[File:FOR GAUCHE 3 INPUT CKAYE.LOG]]

==Optimisation of gauche1 1,5-hexadiene==

[[File:Results summary gauche1 ckaye.png]]

[[File:Gauche 1 picture ckaye.png]]

Link to .log file [[File:GAUCHE 1 CKAYE.LOG]]

==Optimisation of anti2 1,5-hexadiene==

[[File:Results summary anti2 ckaye.png]]

[[File:Anti 2 picture ckaye.png]]

Link to .log file [[File:ANTI 2 OPTIMISATION CKAYE.LOG]]

==Higher optimisation of anti2 1,5-hexadiene==

[[File:Anti 2 higher optimisation ckaye picture.png]]

Link to .log file [[File:ANTI 2 HIGHER OPTIMISATION CKAYE.LOG]]

=='Comparison' of two optimisations of anti2 1,5-hexadiene==

It is a '''major''' ''faux pas'' to directly compare optimisations using different basis sets. Both optimisations were carried out using Hartree-Fock method. The higher basis set yielded a much lower final energy, by approximately 3 atomic units. The bond lengths however are nearly identical, as can be seen below.

[[File:Bond lengths comparison ckaye.gif]]

==Frequency analysis of anti2==

From the frequency analysis of the higher optimised structure of anti2 1,5-hexadiene, the output file confirmed that there were no negative frequencies, which ensures that the molecule is at an energy minimum.

<pre> Low frequencies --- -18.8360 -11.7255 -0.0010 -0.0004 0.0004 1.7210
Low frequencies --- 72.7084 80.1375 120.0085</pre>

==Predicted infrared spectrum of anti2==

[[File:App2 ir spectrum ckaye.png]]

In the output file it can be seen that there are many vibrational modes. However, many have intensities of 0 because they do not involve a change in dipole moment, which is required for an interaction with electromagnetic field. Hence they do not appear on an IR spectrum.

==Optimisation of chair transition state structure==

An allylic H2CCHCH2 fragment was optimised using HF/3-21G basis set. This was later used to form the chair transition state below.

By fixing the bond forming/breaking distances of the terminal carbon atoms to approximately 2.2 Å and performing an opt+freq using the same basis set as before, but with TS(berny) selected and opt=noeigen, to allow imaginary frequencies. An imaginary frequency was observed at 818 cm-1, relating to the transition state. The displacement vectors of the vibration can be seen below

[[File:Transitionstateimaginaryvibration ckaye.png|center|thumb|imaginary vibration (still image, displacement vectors) of the transition state]]

==Optimisation of boat transition state structure==

By using the same allylic H2CCHCH2 fragment that was optimised using HF/3-21G basis set for the chair TS.

Using the same method as for the chair transition state.

Yielded an imaginary frequency at 840 cm-1 corresponding to the transition state

[[File:Boat transition state cope vibration ckaye.png]]

=Diels-Alder=

[[File:Da ckaye scheme.png|300px|thumb|center|Reaction scheme of Diels-Alder cycloaddition]]

==Introduction==

A Diels-Alder reaction is a [4+2] cycloaddition between a conjugated diene and a dienophile, forming a 6-membered ring. The driving force of the reaction is likely to be enthalpic in nature due to the formation of (stronger) sigma bonds at the 'expense' of (weaker) pi bonds. The enthalpic contribution usually overrides any entropic disfavourability<ref>Biotechnology: Bridging Research and Applications edited by Daphne Kamely, Ananda M. Chakrabarty, Steven E. Kornguth</ref> (from the inherent ordering of two molecules into one).

Here, the diene is butadiene and the dienophile is ethylene.

Molecular orbital analysis is important because the symmetry of the reactant MOs is vital to establishing if the reaction occurs or not. If the reactants differ in symmetry then the required orbital overlap does not occur and so the reaction does not.

==Optimisation==

[[File:OPTIMISATION BUTADIENE CKAYE.LOG]] Link to .log file of optimisation of butadiene]]

[[File:Butadiene summary ckaye.png|200px|center|thumb|summary of output of optimisation]]

==MO of ''cis''-butadiene==

[[File:Lumo butadiene ckaye.png|200px|thumb|center|LUMO of butadiene]]
[[File:Homo butadiene ckaye.png|200px|thumb|center|HOMO of butadiene]]

As can be seen above, the LUMO is symmetric with respect to a plane down the middle of the molecule. The HOMO however is antisymmetric since it does not have a plane of symmetry.

The relative energies of the MOs of ''cis''-butadiene can be seen below.

[[File:Energylist butadiene ckaye.png|200px|thumb|center|List of MOs]]

==Formation of TS==

==MO of TS==

[[File:Ts homo ckaye.png|200px|thumb|center|HOMO of TS]]

[[File:Ts lumo ckaye.png|200px|thumb|center|LUMO of TS]]

==Regioselectivity of Diels Alder reaction==

=References=

<references/>

Rep:Mod:mod3 christopherkaye

2013-03-16T15:34:29Z

Ck1510: /* MO of cis-butadiene */

=Christopher Kaye, ck1510, Module 3 Computational=

Extension granted by Dr Hunt to 16th March.

=Introduction=

This module uses Gaussian software to model transition states of reactions. A transition state is the maximum saddle point on a potential energy surface. These states are not observable spectroscopically as they are so short-lived, assumed to be on a similar order of magnitude to bond vibrations - approximately 10-18 s. <ref>Biochemistry by Reginald H. Garrett, Charles M. Grisham</ref>

Investigating transitions states is helpful in understanding kinetics and mechanisms of reactions. Gaussian modelling allows geometries and energies of transition states to be predicted.

In this module, two reactions' transition states are being investigated: the Cope Rearrangement, and Diels-Alder.

=Cope Rearrangement=

[[File:Cope rearrangement for 15hexadiene.png|200px]]

The Cope rearrangement is a pericyclic reaction, specifically a [3+3] sigmatropic rearrangement. Like all pericyclic reactions, it is concerted in nature and passes through a transition state and no intermediates. In the case of 1,5-hexadiene, the transition state goes through a chair-like or a boat-like transition state <ref> Futher Perspectives in Organic Chemistry by CIBA Foundation Symposium</ref>
Gaussian was used to identify low energy conformers and then to attempt to find boat and chair transition states.

=Optimisation of conformers=

Using Hartree-Fock method and 3-21G basis set in each case, various conformers were chosen and optimised. The gauche3 conformer was found to be the lowest energy conformer due to the 'gauche effect' of London forces and favourable orbital interactions. Where sterics become more important, it is expected that antiperiplanar would become the most stable conformer. <ref>Carbohydrate Chemistry and Biochemistry: Structure and Mechanism by M. L. Sinnott</ref>
==Optimisation of antiperiplanar1 1,5-hexadiene==

{{DOI|10042/24051}} Link to D-space optimisation output

[[File:Results summary anti ckaye.png|200px|thumb|center|Results summary of optimisation of anti-peri-planar 1,5-hexadiene]]

[[File:Anti1 ckaye.png]]
Using 'Symmetrize'(sic) the molecule was found to have C2 symmetry.

==Optimisation of gauche4 1,5-hexadiene==

By changing the conformation manually to a gauche linkage, and optimising as above, the following results summary was produced.

[[File:Results summary gauche4 ckaye.png|thumb|center|Results summary of optimisation of gauche 1,5-hexadiene]]

[[File:Gauche 4 picture ckaye.png]]

Link to .log file [[File:GAUCHE4 OPT CKAYE.LOG]]

==Optimisation of gauche6 1,5-hexadiene==

[[File:Results summary gauche6 ckaye.png]]

[[File:Gauche 6 picture ckaye.png]]

Link to .log file [[File:OPT GAUCHE6 CKAYE.LOG]]

==Optimisation of gauche3 1,5-hexadiene==

[[file:Results summary gauche3.png]]

[[file:gauche_3_picture_ckaye.png]]

Link to .log file[[File:FOR GAUCHE 3 INPUT CKAYE.LOG]]

==Optimisation of gauche1 1,5-hexadiene==

[[File:Results summary gauche1 ckaye.png]]

[[File:Gauche 1 picture ckaye.png]]

Link to .log file [[File:GAUCHE 1 CKAYE.LOG]]

==Optimisation of anti2 1,5-hexadiene==

[[File:Results summary anti2 ckaye.png]]

[[File:Anti 2 picture ckaye.png]]

Link to .log file [[File:ANTI 2 OPTIMISATION CKAYE.LOG]]

==Higher optimisation of anti2 1,5-hexadiene==

[[File:Anti 2 higher optimisation ckaye picture.png]]

Link to .log file [[File:ANTI 2 HIGHER OPTIMISATION CKAYE.LOG]]

=='Comparison' of two optimisations of anti2 1,5-hexadiene==

It is a '''major''' ''faux pas'' to directly compare optimisations using different basis sets. Both optimisations were carried out using Hartree-Fock method. The higher basis set yielded a much lower final energy, by approximately 3 atomic units. The bond lengths however are nearly identical, as can be seen below.

[[File:Bond lengths comparison ckaye.gif]]

==Frequency analysis of anti2==

From the frequency analysis of the higher optimised structure of anti2 1,5-hexadiene, the output file confirmed that there were no negative frequencies, which ensures that the molecule is at an energy minimum.

<pre> Low frequencies --- -18.8360 -11.7255 -0.0010 -0.0004 0.0004 1.7210
Low frequencies --- 72.7084 80.1375 120.0085</pre>

==Predicted infrared spectrum of anti2==

[[File:App2 ir spectrum ckaye.png]]

In the output file it can be seen that there are many vibrational modes. However, many have intensities of 0 because they do not involve a change in dipole moment, which is required for an interaction with electromagnetic field. Hence they do not appear on an IR spectrum.

==Optimisation of chair transition state structure==

An allylic H2CCHCH2 fragment was optimised using HF/3-21G basis set. This was later used to form the chair transition state below.

By fixing the bond forming/breaking distances of the terminal carbon atoms to approximately 2.2 Å and performing an opt+freq using the same basis set as before, but with TS(berny) selected and opt=noeigen, to allow imaginary frequencies. An imaginary frequency was observed at 818 cm-1, relating to the transition state. The displacement vectors of the vibration can be seen below

[[File:Transitionstateimaginaryvibration ckaye.png|center|thumb|imaginary vibration (still image, displacement vectors) of the transition state]]

==Optimisation of boat transition state structure==

By using the same allylic H2CCHCH2 fragment that was optimised using HF/3-21G basis set for the chair TS.

Using the same method as for the chair transition state.

Yielded an imaginary frequency at 840 cm-1 corresponding to the transition state

[[File:Boat transition state cope vibration ckaye.png]]

=Diels-Alder=

[[File:Da ckaye scheme.png|300px|thumb|center|Reaction scheme of Diels-Alder cycloaddition]]

==Introduction==

A Diels-Alder reaction is a [4+2] cycloaddition between a conjugated diene and a dienophile, forming a 6-membered ring. The driving force of the reaction is likely to be enthalpic in nature due to the formation of (stronger) sigma bonds at the 'expense' of (weaker) pi bonds. The enthalpic contribution usually overrides any entropic disfavourability<ref>Biotechnology: Bridging Research and Applications edited by Daphne Kamely, Ananda M. Chakrabarty, Steven E. Kornguth</ref> (from the inherent ordering of two molecules into one).

Here, the diene is butadiene and the dienophile is ethylene.

Molecular orbital analysis is important because the symmetry of the reactant MOs is vital to establishing if the reaction occurs or not. If the reactants differ in symmetry then the required orbital overlap does not occur and so the reaction does not.

==Optimisation==

[[File:OPTIMISATION BUTADIENE CKAYE.LOG]] Link to .log file of optimisation of butadiene]]

[[File:Butadiene summary ckaye.png|200px|center|thumb|summary of output of optimisation]]

==MO of ''cis''-butadiene==

[[File:Lumo butadiene ckaye.png|200px|thumb|center|LUMO of butadiene]]
[[File:Homo butadiene ckaye.png|200px|thumb|center|HOMO of butadiene]]

As can be seen above, the LUMO is symmetric with respect to a plane down the middle of the molecule. The HOMO however is antisymmetric since it does not have a plane of symmetry.

==Formation of TS==

==MO of TS==

[[File:Ts homo ckaye.png|200px|thumb|center|HOMO of TS]]

[[File:Ts lumo ckaye.png|200px|thumb|center|LUMO of TS]]

==Regioselectivity of Diels Alder reaction==

=References=

<references/>

Rep:Mod:mod3 christopherkaye

2013-03-16T15:34:03Z

Ck1510: /* MO */

=Christopher Kaye, ck1510, Module 3 Computational=

Extension granted by Dr Hunt to 16th March.

=Introduction=

This module uses Gaussian software to model transition states of reactions. A transition state is the maximum saddle point on a potential energy surface. These states are not observable spectroscopically as they are so short-lived, assumed to be on a similar order of magnitude to bond vibrations - approximately 10-18 s. <ref>Biochemistry by Reginald H. Garrett, Charles M. Grisham</ref>

Investigating transitions states is helpful in understanding kinetics and mechanisms of reactions. Gaussian modelling allows geometries and energies of transition states to be predicted.

In this module, two reactions' transition states are being investigated: the Cope Rearrangement, and Diels-Alder.

=Cope Rearrangement=

[[File:Cope rearrangement for 15hexadiene.png|200px]]

The Cope rearrangement is a pericyclic reaction, specifically a [3+3] sigmatropic rearrangement. Like all pericyclic reactions, it is concerted in nature and passes through a transition state and no intermediates. In the case of 1,5-hexadiene, the transition state goes through a chair-like or a boat-like transition state <ref> Futher Perspectives in Organic Chemistry by CIBA Foundation Symposium</ref>
Gaussian was used to identify low energy conformers and then to attempt to find boat and chair transition states.

=Optimisation of conformers=

Using Hartree-Fock method and 3-21G basis set in each case, various conformers were chosen and optimised. The gauche3 conformer was found to be the lowest energy conformer due to the 'gauche effect' of London forces and favourable orbital interactions. Where sterics become more important, it is expected that antiperiplanar would become the most stable conformer. <ref>Carbohydrate Chemistry and Biochemistry: Structure and Mechanism by M. L. Sinnott</ref>
==Optimisation of antiperiplanar1 1,5-hexadiene==

{{DOI|10042/24051}} Link to D-space optimisation output

[[File:Results summary anti ckaye.png|200px|thumb|center|Results summary of optimisation of anti-peri-planar 1,5-hexadiene]]

[[File:Anti1 ckaye.png]]
Using 'Symmetrize'(sic) the molecule was found to have C2 symmetry.

==Optimisation of gauche4 1,5-hexadiene==

By changing the conformation manually to a gauche linkage, and optimising as above, the following results summary was produced.

[[File:Results summary gauche4 ckaye.png|thumb|center|Results summary of optimisation of gauche 1,5-hexadiene]]

[[File:Gauche 4 picture ckaye.png]]

Link to .log file [[File:GAUCHE4 OPT CKAYE.LOG]]

==Optimisation of gauche6 1,5-hexadiene==

[[File:Results summary gauche6 ckaye.png]]

[[File:Gauche 6 picture ckaye.png]]

Link to .log file [[File:OPT GAUCHE6 CKAYE.LOG]]

==Optimisation of gauche3 1,5-hexadiene==

[[file:Results summary gauche3.png]]

[[file:gauche_3_picture_ckaye.png]]

Link to .log file[[File:FOR GAUCHE 3 INPUT CKAYE.LOG]]

==Optimisation of gauche1 1,5-hexadiene==

[[File:Results summary gauche1 ckaye.png]]

[[File:Gauche 1 picture ckaye.png]]

Link to .log file [[File:GAUCHE 1 CKAYE.LOG]]

==Optimisation of anti2 1,5-hexadiene==

[[File:Results summary anti2 ckaye.png]]

[[File:Anti 2 picture ckaye.png]]

Link to .log file [[File:ANTI 2 OPTIMISATION CKAYE.LOG]]

==Higher optimisation of anti2 1,5-hexadiene==

[[File:Anti 2 higher optimisation ckaye picture.png]]

Link to .log file [[File:ANTI 2 HIGHER OPTIMISATION CKAYE.LOG]]

=='Comparison' of two optimisations of anti2 1,5-hexadiene==

It is a '''major''' ''faux pas'' to directly compare optimisations using different basis sets. Both optimisations were carried out using Hartree-Fock method. The higher basis set yielded a much lower final energy, by approximately 3 atomic units. The bond lengths however are nearly identical, as can be seen below.

[[File:Bond lengths comparison ckaye.gif]]

==Frequency analysis of anti2==

From the frequency analysis of the higher optimised structure of anti2 1,5-hexadiene, the output file confirmed that there were no negative frequencies, which ensures that the molecule is at an energy minimum.

<pre> Low frequencies --- -18.8360 -11.7255 -0.0010 -0.0004 0.0004 1.7210
Low frequencies --- 72.7084 80.1375 120.0085</pre>

==Predicted infrared spectrum of anti2==

[[File:App2 ir spectrum ckaye.png]]

In the output file it can be seen that there are many vibrational modes. However, many have intensities of 0 because they do not involve a change in dipole moment, which is required for an interaction with electromagnetic field. Hence they do not appear on an IR spectrum.

==Optimisation of chair transition state structure==

An allylic H2CCHCH2 fragment was optimised using HF/3-21G basis set. This was later used to form the chair transition state below.

By fixing the bond forming/breaking distances of the terminal carbon atoms to approximately 2.2 Å and performing an opt+freq using the same basis set as before, but with TS(berny) selected and opt=noeigen, to allow imaginary frequencies. An imaginary frequency was observed at 818 cm-1, relating to the transition state. The displacement vectors of the vibration can be seen below

[[File:Transitionstateimaginaryvibration ckaye.png|center|thumb|imaginary vibration (still image, displacement vectors) of the transition state]]

==Optimisation of boat transition state structure==

By using the same allylic H2CCHCH2 fragment that was optimised using HF/3-21G basis set for the chair TS.

Using the same method as for the chair transition state.

Yielded an imaginary frequency at 840 cm-1 corresponding to the transition state

[[File:Boat transition state cope vibration ckaye.png]]

=Diels-Alder=

[[File:Da ckaye scheme.png|300px|thumb|center|Reaction scheme of Diels-Alder cycloaddition]]

==Introduction==

A Diels-Alder reaction is a [4+2] cycloaddition between a conjugated diene and a dienophile, forming a 6-membered ring. The driving force of the reaction is likely to be enthalpic in nature due to the formation of (stronger) sigma bonds at the 'expense' of (weaker) pi bonds. The enthalpic contribution usually overrides any entropic disfavourability<ref>Biotechnology: Bridging Research and Applications edited by Daphne Kamely, Ananda M. Chakrabarty, Steven E. Kornguth</ref> (from the inherent ordering of two molecules into one).

Here, the diene is butadiene and the dienophile is ethylene.

Molecular orbital analysis is important because the symmetry of the reactant MOs is vital to establishing if the reaction occurs or not. If the reactants differ in symmetry then the required orbital overlap does not occur and so the reaction does not.

==Optimisation==

[[File:OPTIMISATION BUTADIENE CKAYE.LOG]] Link to .log file of optimisation of butadiene]]

[[File:Butadiene summary ckaye.png|200px|center|thumb|summary of output of optimisation]]

==MO of ''cis''-butadiene==

[[File:Lumo butadiene ckaye.png|200px|thumb|center|LUMO of butadiene]]
[[File:Homo butadiene ckaye.png|200px|thumb|center|HOMO of butadiene]]

As can be seen above, the LUMO is symmetric with respect to a plane down the middle of the molecule. The HOMO however is antisymmetric since it does not have a plane of symmetry.

==MO of TS==

[[File:Ts homo ckaye.png|200px|thumb|center|HOMO of TS]]

[[File:Ts lumo ckaye.png|200px|thumb|center|LUMO of TS]]

==Regioselectivity of Diels Alder reaction==

=References=

<references/>

Rep:Mod:mod3 christopherkaye

2013-03-16T15:33:14Z

Ck1510: /* Introduction */

=Christopher Kaye, ck1510, Module 3 Computational=

Extension granted by Dr Hunt to 16th March.

=Introduction=

This module uses Gaussian software to model transition states of reactions. A transition state is the maximum saddle point on a potential energy surface. These states are not observable spectroscopically as they are so short-lived, assumed to be on a similar order of magnitude to bond vibrations - approximately 10-18 s. <ref>Biochemistry by Reginald H. Garrett, Charles M. Grisham</ref>

Investigating transitions states is helpful in understanding kinetics and mechanisms of reactions. Gaussian modelling allows geometries and energies of transition states to be predicted.

In this module, two reactions' transition states are being investigated: the Cope Rearrangement, and Diels-Alder.

=Cope Rearrangement=

[[File:Cope rearrangement for 15hexadiene.png|200px]]

The Cope rearrangement is a pericyclic reaction, specifically a [3+3] sigmatropic rearrangement. Like all pericyclic reactions, it is concerted in nature and passes through a transition state and no intermediates. In the case of 1,5-hexadiene, the transition state goes through a chair-like or a boat-like transition state <ref> Futher Perspectives in Organic Chemistry by CIBA Foundation Symposium</ref>
Gaussian was used to identify low energy conformers and then to attempt to find boat and chair transition states.

=Optimisation of conformers=

Using Hartree-Fock method and 3-21G basis set in each case, various conformers were chosen and optimised. The gauche3 conformer was found to be the lowest energy conformer due to the 'gauche effect' of London forces and favourable orbital interactions. Where sterics become more important, it is expected that antiperiplanar would become the most stable conformer. <ref>Carbohydrate Chemistry and Biochemistry: Structure and Mechanism by M. L. Sinnott</ref>
==Optimisation of antiperiplanar1 1,5-hexadiene==

{{DOI|10042/24051}} Link to D-space optimisation output

[[File:Results summary anti ckaye.png|200px|thumb|center|Results summary of optimisation of anti-peri-planar 1,5-hexadiene]]

[[File:Anti1 ckaye.png]]
Using 'Symmetrize'(sic) the molecule was found to have C2 symmetry.

==Optimisation of gauche4 1,5-hexadiene==

By changing the conformation manually to a gauche linkage, and optimising as above, the following results summary was produced.

[[File:Results summary gauche4 ckaye.png|thumb|center|Results summary of optimisation of gauche 1,5-hexadiene]]

[[File:Gauche 4 picture ckaye.png]]

Link to .log file [[File:GAUCHE4 OPT CKAYE.LOG]]

==Optimisation of gauche6 1,5-hexadiene==

[[File:Results summary gauche6 ckaye.png]]

[[File:Gauche 6 picture ckaye.png]]

Link to .log file [[File:OPT GAUCHE6 CKAYE.LOG]]

==Optimisation of gauche3 1,5-hexadiene==

[[file:Results summary gauche3.png]]

[[file:gauche_3_picture_ckaye.png]]

Link to .log file[[File:FOR GAUCHE 3 INPUT CKAYE.LOG]]

==Optimisation of gauche1 1,5-hexadiene==

[[File:Results summary gauche1 ckaye.png]]

[[File:Gauche 1 picture ckaye.png]]

Link to .log file [[File:GAUCHE 1 CKAYE.LOG]]

==Optimisation of anti2 1,5-hexadiene==

[[File:Results summary anti2 ckaye.png]]

[[File:Anti 2 picture ckaye.png]]

Link to .log file [[File:ANTI 2 OPTIMISATION CKAYE.LOG]]

==Higher optimisation of anti2 1,5-hexadiene==

[[File:Anti 2 higher optimisation ckaye picture.png]]

Link to .log file [[File:ANTI 2 HIGHER OPTIMISATION CKAYE.LOG]]

=='Comparison' of two optimisations of anti2 1,5-hexadiene==

It is a '''major''' ''faux pas'' to directly compare optimisations using different basis sets. Both optimisations were carried out using Hartree-Fock method. The higher basis set yielded a much lower final energy, by approximately 3 atomic units. The bond lengths however are nearly identical, as can be seen below.

[[File:Bond lengths comparison ckaye.gif]]

==Frequency analysis of anti2==

From the frequency analysis of the higher optimised structure of anti2 1,5-hexadiene, the output file confirmed that there were no negative frequencies, which ensures that the molecule is at an energy minimum.

<pre> Low frequencies --- -18.8360 -11.7255 -0.0010 -0.0004 0.0004 1.7210
Low frequencies --- 72.7084 80.1375 120.0085</pre>

==Predicted infrared spectrum of anti2==

[[File:App2 ir spectrum ckaye.png]]

In the output file it can be seen that there are many vibrational modes. However, many have intensities of 0 because they do not involve a change in dipole moment, which is required for an interaction with electromagnetic field. Hence they do not appear on an IR spectrum.

==Optimisation of chair transition state structure==

An allylic H2CCHCH2 fragment was optimised using HF/3-21G basis set. This was later used to form the chair transition state below.

By fixing the bond forming/breaking distances of the terminal carbon atoms to approximately 2.2 Å and performing an opt+freq using the same basis set as before, but with TS(berny) selected and opt=noeigen, to allow imaginary frequencies. An imaginary frequency was observed at 818 cm-1, relating to the transition state. The displacement vectors of the vibration can be seen below

[[File:Transitionstateimaginaryvibration ckaye.png|center|thumb|imaginary vibration (still image, displacement vectors) of the transition state]]

==Optimisation of boat transition state structure==

By using the same allylic H2CCHCH2 fragment that was optimised using HF/3-21G basis set for the chair TS.

Using the same method as for the chair transition state.

Yielded an imaginary frequency at 840 cm-1 corresponding to the transition state

[[File:Boat transition state cope vibration ckaye.png]]

=Diels-Alder=

[[File:Da ckaye scheme.png|300px|thumb|center|Reaction scheme of Diels-Alder cycloaddition]]

==Introduction==

A Diels-Alder reaction is a [4+2] cycloaddition between a conjugated diene and a dienophile, forming a 6-membered ring. The driving force of the reaction is likely to be enthalpic in nature due to the formation of (stronger) sigma bonds at the 'expense' of (weaker) pi bonds. The enthalpic contribution usually overrides any entropic disfavourability<ref>Biotechnology: Bridging Research and Applications edited by Daphne Kamely, Ananda M. Chakrabarty, Steven E. Kornguth</ref> (from the inherent ordering of two molecules into one).

Here, the diene is butadiene and the dienophile is ethylene.

Molecular orbital analysis is important because the symmetry of the reactant MOs is vital to establishing if the reaction occurs or not. If the reactants differ in symmetry then the required orbital overlap does not occur and so the reaction does not.

==Optimisation==

[[File:OPTIMISATION BUTADIENE CKAYE.LOG]] Link to .log file of optimisation of butadiene]]

[[File:Butadiene summary ckaye.png|200px|center|thumb|summary of output of optimisation]]

==MO==

[[File:Lumo butadiene ckaye.png|200px|thumb|center|LUMO of butadiene]]
[[File:Homo butadiene ckaye.png|200px|thumb|center|HOMO of butadiene]]

As can be seen above, the LUMO is symmetric with respect to a plane down the middle of the molecule. The HOMO however is antisymmetric since it does not have a plane of symmetry.

==MO of TS==

[[File:Ts homo ckaye.png|200px|thumb|center|HOMO of TS]]

[[File:Ts lumo ckaye.png|200px|thumb|center|LUMO of TS]]

==Regioselectivity of Diels Alder reaction==

=References=

<references/>

Rep:Mod:mod3 christopherkaye

2013-03-16T15:29:28Z

Ck1510: /* Introduction */

=Christopher Kaye, ck1510, Module 3 Computational=

Extension granted by Dr Hunt to 16th March.

=Introduction=

This module uses Gaussian software to model transition states of reactions. A transition state is the maximum saddle point on a potential energy surface. These states are not observable spectroscopically as they are so short-lived, assumed to be on a similar order of magnitude to bond vibrations - approximately 10-18 s. <ref>Biochemistry by Reginald H. Garrett, Charles M. Grisham</ref>

Investigating transitions states is helpful in understanding kinetics and mechanisms of reactions. Gaussian modelling allows geometries and energies of transition states to be predicted.

In this module, two reactions' transition states are being investigated: the Cope Rearrangement, and Diels-Alder.

=Cope Rearrangement=

[[File:Cope rearrangement for 15hexadiene.png|200px]]

The Cope rearrangement is a pericyclic reaction, specifically a [3+3] sigmatropic rearrangement. Like all pericyclic reactions, it is concerted in nature and passes through a transition state and no intermediates. In the case of 1,5-hexadiene, the transition state goes through a chair-like or a boat-like transition state <ref> Futher Perspectives in Organic Chemistry by CIBA Foundation Symposium</ref>
Gaussian was used to identify low energy conformers and then to attempt to find boat and chair transition states.

=Optimisation of conformers=

Using Hartree-Fock method and 3-21G basis set in each case, various conformers were chosen and optimised. The gauche3 conformer was found to be the lowest energy conformer due to the 'gauche effect' of London forces and favourable orbital interactions. Where sterics become more important, it is expected that antiperiplanar would become the most stable conformer. <ref>Carbohydrate Chemistry and Biochemistry: Structure and Mechanism by M. L. Sinnott</ref>
==Optimisation of antiperiplanar1 1,5-hexadiene==

{{DOI|10042/24051}} Link to D-space optimisation output

[[File:Results summary anti ckaye.png|200px|thumb|center|Results summary of optimisation of anti-peri-planar 1,5-hexadiene]]

[[File:Anti1 ckaye.png]]
Using 'Symmetrize'(sic) the molecule was found to have C2 symmetry.

==Optimisation of gauche4 1,5-hexadiene==

By changing the conformation manually to a gauche linkage, and optimising as above, the following results summary was produced.

[[File:Results summary gauche4 ckaye.png|thumb|center|Results summary of optimisation of gauche 1,5-hexadiene]]

[[File:Gauche 4 picture ckaye.png]]

Link to .log file [[File:GAUCHE4 OPT CKAYE.LOG]]

==Optimisation of gauche6 1,5-hexadiene==

[[File:Results summary gauche6 ckaye.png]]

[[File:Gauche 6 picture ckaye.png]]

Link to .log file [[File:OPT GAUCHE6 CKAYE.LOG]]

==Optimisation of gauche3 1,5-hexadiene==

[[file:Results summary gauche3.png]]

[[file:gauche_3_picture_ckaye.png]]

Link to .log file[[File:FOR GAUCHE 3 INPUT CKAYE.LOG]]

==Optimisation of gauche1 1,5-hexadiene==

[[File:Results summary gauche1 ckaye.png]]

[[File:Gauche 1 picture ckaye.png]]

Link to .log file [[File:GAUCHE 1 CKAYE.LOG]]

==Optimisation of anti2 1,5-hexadiene==

[[File:Results summary anti2 ckaye.png]]

[[File:Anti 2 picture ckaye.png]]

Link to .log file [[File:ANTI 2 OPTIMISATION CKAYE.LOG]]

==Higher optimisation of anti2 1,5-hexadiene==

[[File:Anti 2 higher optimisation ckaye picture.png]]

Link to .log file [[File:ANTI 2 HIGHER OPTIMISATION CKAYE.LOG]]

=='Comparison' of two optimisations of anti2 1,5-hexadiene==

It is a '''major''' ''faux pas'' to directly compare optimisations using different basis sets. Both optimisations were carried out using Hartree-Fock method. The higher basis set yielded a much lower final energy, by approximately 3 atomic units. The bond lengths however are nearly identical, as can be seen below.

[[File:Bond lengths comparison ckaye.gif]]

==Frequency analysis of anti2==

From the frequency analysis of the higher optimised structure of anti2 1,5-hexadiene, the output file confirmed that there were no negative frequencies, which ensures that the molecule is at an energy minimum.

<pre> Low frequencies --- -18.8360 -11.7255 -0.0010 -0.0004 0.0004 1.7210
Low frequencies --- 72.7084 80.1375 120.0085</pre>

==Predicted infrared spectrum of anti2==

[[File:App2 ir spectrum ckaye.png]]

In the output file it can be seen that there are many vibrational modes. However, many have intensities of 0 because they do not involve a change in dipole moment, which is required for an interaction with electromagnetic field. Hence they do not appear on an IR spectrum.

==Optimisation of chair transition state structure==

An allylic H2CCHCH2 fragment was optimised using HF/3-21G basis set. This was later used to form the chair transition state below.

By fixing the bond forming/breaking distances of the terminal carbon atoms to approximately 2.2 Å and performing an opt+freq using the same basis set as before, but with TS(berny) selected and opt=noeigen, to allow imaginary frequencies. An imaginary frequency was observed at 818 cm-1, relating to the transition state. The displacement vectors of the vibration can be seen below

[[File:Transitionstateimaginaryvibration ckaye.png|center|thumb|imaginary vibration (still image, displacement vectors) of the transition state]]

==Optimisation of boat transition state structure==

By using the same allylic H2CCHCH2 fragment that was optimised using HF/3-21G basis set for the chair TS.

Using the same method as for the chair transition state.

Yielded an imaginary frequency at 840 cm-1 corresponding to the transition state

[[File:Boat transition state cope vibration ckaye.png]]

=Diels-Alder=

[[File:Da ckaye scheme.png|300px|thumb|center|Reaction scheme of Diels-Alder cycloaddition]]

==Introduction==

A Diels-Alder reaction is a [4+2] cycloaddition between a conjugated diene and a dienophile, forming a 6-membered ring. The driving force of the reaction is likely to be enthalpic in nature due to the formation of (stronger) sigma bonds at the 'expense' of (weaker) pi bonds. The enthalpic contribution usually overrides any entropic disfavourability<ref>Biotechnology: Bridging Research and Applications edited by Daphne Kamely, Ananda M. Chakrabarty, Steven E. Kornguth</ref> (from the inherent ordering of two molecules into one).

Here, the diene is butadiene and the dienophile is ethylene.

==Optimisation==

[[File:OPTIMISATION BUTADIENE CKAYE.LOG]] Link to .log file of optimisation of butadiene]]

[[File:Butadiene summary ckaye.png|200px|center|thumb|summary of output of optimisation]]

==MO==

[[File:Lumo butadiene ckaye.png|200px|thumb|center|LUMO of butadiene]]
[[File:Homo butadiene ckaye.png|200px|thumb|center|HOMO of butadiene]]

As can be seen above, the LUMO is symmetric with respect to a plane down the middle of the molecule. The HOMO however is antisymmetric since it does not have a plane of symmetry.

==MO of TS==

[[File:Ts homo ckaye.png|200px|thumb|center|HOMO of TS]]

[[File:Ts lumo ckaye.png|200px|thumb|center|LUMO of TS]]

==Regioselectivity of Diels Alder reaction==

=References=

<references/>

Rep:Mod:mod3 christopherkaye

2013-03-16T15:28:02Z

Ck1510: /* Introduction */

=Christopher Kaye, ck1510, Module 3 Computational=

Extension granted by Dr Hunt to 16th March.

=Introduction=

This module uses Gaussian software to model transition states of reactions. A transition state is the maximum saddle point on a potential energy surface. These states are not observable spectroscopically as they are so short-lived, assumed to be on a similar order of magnitude to bond vibrations - approximately 10-18 s. <ref>Biochemistry by Reginald H. Garrett, Charles M. Grisham</ref>

Investigating transitions states is helpful in understanding kinetics and mechanisms of reactions. Gaussian modelling allows geometries and energies of transition states to be predicted.

In this module, two reactions' transition states are being investigated: the Cope Rearrangement, and Diels-Alder.

=Cope Rearrangement=

[[File:Cope rearrangement for 15hexadiene.png|200px]]

The Cope rearrangement is a pericyclic reaction, specifically a [3+3] sigmatropic rearrangement. Like all pericyclic reactions, it is concerted in nature and passes through a transition state and no intermediates. In the case of 1,5-hexadiene, the transition state goes through a chair-like or a boat-like transition state <ref> Futher Perspectives in Organic Chemistry by CIBA Foundation Symposium</ref>
Gaussian was used to identify low energy conformers and then to attempt to find boat and chair transition states.

=Optimisation of conformers=

Using Hartree-Fock method and 3-21G basis set in each case, various conformers were chosen and optimised. The gauche3 conformer was found to be the lowest energy conformer due to the 'gauche effect' of London forces and favourable orbital interactions. Where sterics become more important, it is expected that antiperiplanar would become the most stable conformer. <ref>Carbohydrate Chemistry and Biochemistry: Structure and Mechanism by M. L. Sinnott</ref>
==Optimisation of antiperiplanar1 1,5-hexadiene==

{{DOI|10042/24051}} Link to D-space optimisation output

[[File:Results summary anti ckaye.png|200px|thumb|center|Results summary of optimisation of anti-peri-planar 1,5-hexadiene]]

[[File:Anti1 ckaye.png]]
Using 'Symmetrize'(sic) the molecule was found to have C2 symmetry.

==Optimisation of gauche4 1,5-hexadiene==

By changing the conformation manually to a gauche linkage, and optimising as above, the following results summary was produced.

[[File:Results summary gauche4 ckaye.png|thumb|center|Results summary of optimisation of gauche 1,5-hexadiene]]

[[File:Gauche 4 picture ckaye.png]]

Link to .log file [[File:GAUCHE4 OPT CKAYE.LOG]]

==Optimisation of gauche6 1,5-hexadiene==

[[File:Results summary gauche6 ckaye.png]]

[[File:Gauche 6 picture ckaye.png]]

Link to .log file [[File:OPT GAUCHE6 CKAYE.LOG]]

==Optimisation of gauche3 1,5-hexadiene==

[[file:Results summary gauche3.png]]

[[file:gauche_3_picture_ckaye.png]]

Link to .log file[[File:FOR GAUCHE 3 INPUT CKAYE.LOG]]

==Optimisation of gauche1 1,5-hexadiene==

[[File:Results summary gauche1 ckaye.png]]

[[File:Gauche 1 picture ckaye.png]]

Link to .log file [[File:GAUCHE 1 CKAYE.LOG]]

==Optimisation of anti2 1,5-hexadiene==

[[File:Results summary anti2 ckaye.png]]

[[File:Anti 2 picture ckaye.png]]

Link to .log file [[File:ANTI 2 OPTIMISATION CKAYE.LOG]]

==Higher optimisation of anti2 1,5-hexadiene==

[[File:Anti 2 higher optimisation ckaye picture.png]]

Link to .log file [[File:ANTI 2 HIGHER OPTIMISATION CKAYE.LOG]]

=='Comparison' of two optimisations of anti2 1,5-hexadiene==

It is a '''major''' ''faux pas'' to directly compare optimisations using different basis sets. Both optimisations were carried out using Hartree-Fock method. The higher basis set yielded a much lower final energy, by approximately 3 atomic units. The bond lengths however are nearly identical, as can be seen below.

[[File:Bond lengths comparison ckaye.gif]]

==Frequency analysis of anti2==

From the frequency analysis of the higher optimised structure of anti2 1,5-hexadiene, the output file confirmed that there were no negative frequencies, which ensures that the molecule is at an energy minimum.

<pre> Low frequencies --- -18.8360 -11.7255 -0.0010 -0.0004 0.0004 1.7210
Low frequencies --- 72.7084 80.1375 120.0085</pre>

==Predicted infrared spectrum of anti2==

[[File:App2 ir spectrum ckaye.png]]

In the output file it can be seen that there are many vibrational modes. However, many have intensities of 0 because they do not involve a change in dipole moment, which is required for an interaction with electromagnetic field. Hence they do not appear on an IR spectrum.

==Optimisation of chair transition state structure==

An allylic H2CCHCH2 fragment was optimised using HF/3-21G basis set. This was later used to form the chair transition state below.

By fixing the bond forming/breaking distances of the terminal carbon atoms to approximately 2.2 Å and performing an opt+freq using the same basis set as before, but with TS(berny) selected and opt=noeigen, to allow imaginary frequencies. An imaginary frequency was observed at 818 cm-1, relating to the transition state. The displacement vectors of the vibration can be seen below

[[File:Transitionstateimaginaryvibration ckaye.png|center|thumb|imaginary vibration (still image, displacement vectors) of the transition state]]

==Optimisation of boat transition state structure==

By using the same allylic H2CCHCH2 fragment that was optimised using HF/3-21G basis set for the chair TS.

Using the same method as for the chair transition state.

Yielded an imaginary frequency at 840 cm-1 corresponding to the transition state

[[File:Boat transition state cope vibration ckaye.png]]

=Diels-Alder=

[[File:Da ckaye scheme.png|300px|thumb|center|Reaction scheme of Diels-Alder cycloaddition]]

==Introduction==

A Diels-Alder reaction is a [4+2] cycloaddition between a conjugated diene and a dienophile, forming a 6-membered ring. The driving force of the reaction is likely to be enthalpic in nature due to the formation of (stronger) sigma bonds at the 'expense' of (weaker) pi bonds. The enthalpic contribution usually overrides any entropic disfavourability<ref>Biotechnology: Bridging Research and Applications edited by Daphne Kamely, Ananda M. Chakrabarty, Steven E. Kornguth</ref> (from the inherent ordering of two molecules into one).

Here, the diene is butadiene and the dienophile is ethylene.

==MO==

[[File:Lumo butadiene ckaye.png|200px|thumb|center|LUMO of butadiene]]
[[File:Homo butadiene ckaye.png|200px|thumb|center|HOMO of butadiene]]

As can be seen above, the LUMO is symmetric with respect to a plane down the middle of the molecule. The HOMO however is antisymmetric since it does not have a plane of symmetry.

==MO of TS==

[[File:Ts homo ckaye.png|200px|thumb|center|HOMO of TS]]

[[File:Ts lumo ckaye.png|200px|thumb|center|LUMO of TS]]

==Regioselectivity of Diels Alder reaction==

=References=

<references/>

Rep:Mod:mod3 christopherkaye

2013-03-16T15:27:21Z

Ck1510: /* MO */

=Christopher Kaye, ck1510, Module 3 Computational=

Extension granted by Dr Hunt to 16th March.

=Introduction=

This module uses Gaussian software to model transition states of reactions. A transition state is the maximum saddle point on a potential energy surface. These states are not observable spectroscopically as they are so short-lived, assumed to be on a similar order of magnitude to bond vibrations - approximately 10-18 s. <ref>Biochemistry by Reginald H. Garrett, Charles M. Grisham</ref>

Investigating transitions states is helpful in understanding kinetics and mechanisms of reactions. Gaussian modelling allows geometries and energies of transition states to be predicted.

In this module, two reactions' transition states are being investigated: the Cope Rearrangement, and Diels-Alder.

=Cope Rearrangement=

[[File:Cope rearrangement for 15hexadiene.png|200px]]

The Cope rearrangement is a pericyclic reaction, specifically a [3+3] sigmatropic rearrangement. Like all pericyclic reactions, it is concerted in nature and passes through a transition state and no intermediates. In the case of 1,5-hexadiene, the transition state goes through a chair-like or a boat-like transition state <ref> Futher Perspectives in Organic Chemistry by CIBA Foundation Symposium</ref>
Gaussian was used to identify low energy conformers and then to attempt to find boat and chair transition states.

=Optimisation of conformers=

Using Hartree-Fock method and 3-21G basis set in each case, various conformers were chosen and optimised. The gauche3 conformer was found to be the lowest energy conformer due to the 'gauche effect' of London forces and favourable orbital interactions. Where sterics become more important, it is expected that antiperiplanar would become the most stable conformer. <ref>Carbohydrate Chemistry and Biochemistry: Structure and Mechanism by M. L. Sinnott</ref>
==Optimisation of antiperiplanar1 1,5-hexadiene==

{{DOI|10042/24051}} Link to D-space optimisation output

[[File:Results summary anti ckaye.png|200px|thumb|center|Results summary of optimisation of anti-peri-planar 1,5-hexadiene]]

[[File:Anti1 ckaye.png]]
Using 'Symmetrize'(sic) the molecule was found to have C2 symmetry.

==Optimisation of gauche4 1,5-hexadiene==

By changing the conformation manually to a gauche linkage, and optimising as above, the following results summary was produced.

[[File:Results summary gauche4 ckaye.png|thumb|center|Results summary of optimisation of gauche 1,5-hexadiene]]

[[File:Gauche 4 picture ckaye.png]]

Link to .log file [[File:GAUCHE4 OPT CKAYE.LOG]]

==Optimisation of gauche6 1,5-hexadiene==

[[File:Results summary gauche6 ckaye.png]]

[[File:Gauche 6 picture ckaye.png]]

Link to .log file [[File:OPT GAUCHE6 CKAYE.LOG]]

==Optimisation of gauche3 1,5-hexadiene==

[[file:Results summary gauche3.png]]

[[file:gauche_3_picture_ckaye.png]]

Link to .log file[[File:FOR GAUCHE 3 INPUT CKAYE.LOG]]

==Optimisation of gauche1 1,5-hexadiene==

[[File:Results summary gauche1 ckaye.png]]

[[File:Gauche 1 picture ckaye.png]]

Link to .log file [[File:GAUCHE 1 CKAYE.LOG]]

==Optimisation of anti2 1,5-hexadiene==

[[File:Results summary anti2 ckaye.png]]

[[File:Anti 2 picture ckaye.png]]

Link to .log file [[File:ANTI 2 OPTIMISATION CKAYE.LOG]]

==Higher optimisation of anti2 1,5-hexadiene==

[[File:Anti 2 higher optimisation ckaye picture.png]]

Link to .log file [[File:ANTI 2 HIGHER OPTIMISATION CKAYE.LOG]]

=='Comparison' of two optimisations of anti2 1,5-hexadiene==

It is a '''major''' ''faux pas'' to directly compare optimisations using different basis sets. Both optimisations were carried out using Hartree-Fock method. The higher basis set yielded a much lower final energy, by approximately 3 atomic units. The bond lengths however are nearly identical, as can be seen below.

[[File:Bond lengths comparison ckaye.gif]]

==Frequency analysis of anti2==

From the frequency analysis of the higher optimised structure of anti2 1,5-hexadiene, the output file confirmed that there were no negative frequencies, which ensures that the molecule is at an energy minimum.

<pre> Low frequencies --- -18.8360 -11.7255 -0.0010 -0.0004 0.0004 1.7210
Low frequencies --- 72.7084 80.1375 120.0085</pre>

==Predicted infrared spectrum of anti2==

[[File:App2 ir spectrum ckaye.png]]

In the output file it can be seen that there are many vibrational modes. However, many have intensities of 0 because they do not involve a change in dipole moment, which is required for an interaction with electromagnetic field. Hence they do not appear on an IR spectrum.

==Optimisation of chair transition state structure==

An allylic H2CCHCH2 fragment was optimised using HF/3-21G basis set. This was later used to form the chair transition state below.

By fixing the bond forming/breaking distances of the terminal carbon atoms to approximately 2.2 Å and performing an opt+freq using the same basis set as before, but with TS(berny) selected and opt=noeigen, to allow imaginary frequencies. An imaginary frequency was observed at 818 cm-1, relating to the transition state. The displacement vectors of the vibration can be seen below

[[File:Transitionstateimaginaryvibration ckaye.png|center|thumb|imaginary vibration (still image, displacement vectors) of the transition state]]

==Optimisation of boat transition state structure==

By using the same allylic H2CCHCH2 fragment that was optimised using HF/3-21G basis set for the chair TS.

Using the same method as for the chair transition state.

Yielded an imaginary frequency at 840 cm-1 corresponding to the transition state

[[File:Boat transition state cope vibration ckaye.png]]

=Diels-Alder=

[[File:Da ckaye scheme.png|300px|thumb|center|Reaction scheme of Diels-Alder cycloaddition]]

==Introduction==

A Diels-Alder reaction is a [4+2] cycloaddition between a conjugated diene and a dienophile, forming a 6-membered ring. The driving force of the reaction is likely to be enthalpic in nature due to the formation of (stronger) sigma bonds at the 'expense' of (weaker) pi bonds. The enthalpic contribution usually overrides any entropic disfavourability<ref>Biotechnology: Bridging Research and Applications edited by Daphne Kamely, Ananda M. Chakrabarty, Steven E. Kornguth</ref> (from the inherent ordering of two molecules into one).

==MO==

[[File:Lumo butadiene ckaye.png|200px|thumb|center|LUMO of butadiene]]
[[File:Homo butadiene ckaye.png|200px|thumb|center|HOMO of butadiene]]

As can be seen above, the LUMO is symmetric with respect to a plane down the middle of the molecule. The HOMO however is antisymmetric since it does not have a plane of symmetry.

==MO of TS==

[[File:Ts homo ckaye.png|200px|thumb|center|HOMO of TS]]

[[File:Ts lumo ckaye.png|200px|thumb|center|LUMO of TS]]

==Regioselectivity of Diels Alder reaction==

=References=

<references/>

Rep:Mod:mod3 christopherkaye

2013-03-16T15:27:04Z

Ck1510: /* MO */

=Christopher Kaye, ck1510, Module 3 Computational=

Extension granted by Dr Hunt to 16th March.

=Introduction=

This module uses Gaussian software to model transition states of reactions. A transition state is the maximum saddle point on a potential energy surface. These states are not observable spectroscopically as they are so short-lived, assumed to be on a similar order of magnitude to bond vibrations - approximately 10-18 s. <ref>Biochemistry by Reginald H. Garrett, Charles M. Grisham</ref>

Investigating transitions states is helpful in understanding kinetics and mechanisms of reactions. Gaussian modelling allows geometries and energies of transition states to be predicted.

In this module, two reactions' transition states are being investigated: the Cope Rearrangement, and Diels-Alder.

=Cope Rearrangement=

[[File:Cope rearrangement for 15hexadiene.png|200px]]

The Cope rearrangement is a pericyclic reaction, specifically a [3+3] sigmatropic rearrangement. Like all pericyclic reactions, it is concerted in nature and passes through a transition state and no intermediates. In the case of 1,5-hexadiene, the transition state goes through a chair-like or a boat-like transition state <ref> Futher Perspectives in Organic Chemistry by CIBA Foundation Symposium</ref>
Gaussian was used to identify low energy conformers and then to attempt to find boat and chair transition states.

=Optimisation of conformers=

Using Hartree-Fock method and 3-21G basis set in each case, various conformers were chosen and optimised. The gauche3 conformer was found to be the lowest energy conformer due to the 'gauche effect' of London forces and favourable orbital interactions. Where sterics become more important, it is expected that antiperiplanar would become the most stable conformer. <ref>Carbohydrate Chemistry and Biochemistry: Structure and Mechanism by M. L. Sinnott</ref>
==Optimisation of antiperiplanar1 1,5-hexadiene==

{{DOI|10042/24051}} Link to D-space optimisation output

[[File:Results summary anti ckaye.png|200px|thumb|center|Results summary of optimisation of anti-peri-planar 1,5-hexadiene]]

[[File:Anti1 ckaye.png]]
Using 'Symmetrize'(sic) the molecule was found to have C2 symmetry.

==Optimisation of gauche4 1,5-hexadiene==

By changing the conformation manually to a gauche linkage, and optimising as above, the following results summary was produced.

[[File:Results summary gauche4 ckaye.png|thumb|center|Results summary of optimisation of gauche 1,5-hexadiene]]

[[File:Gauche 4 picture ckaye.png]]

Link to .log file [[File:GAUCHE4 OPT CKAYE.LOG]]

==Optimisation of gauche6 1,5-hexadiene==

[[File:Results summary gauche6 ckaye.png]]

[[File:Gauche 6 picture ckaye.png]]

Link to .log file [[File:OPT GAUCHE6 CKAYE.LOG]]

==Optimisation of gauche3 1,5-hexadiene==

[[file:Results summary gauche3.png]]

[[file:gauche_3_picture_ckaye.png]]

Link to .log file[[File:FOR GAUCHE 3 INPUT CKAYE.LOG]]

==Optimisation of gauche1 1,5-hexadiene==

[[File:Results summary gauche1 ckaye.png]]

[[File:Gauche 1 picture ckaye.png]]

Link to .log file [[File:GAUCHE 1 CKAYE.LOG]]

==Optimisation of anti2 1,5-hexadiene==

[[File:Results summary anti2 ckaye.png]]

[[File:Anti 2 picture ckaye.png]]

Link to .log file [[File:ANTI 2 OPTIMISATION CKAYE.LOG]]

==Higher optimisation of anti2 1,5-hexadiene==

[[File:Anti 2 higher optimisation ckaye picture.png]]

Link to .log file [[File:ANTI 2 HIGHER OPTIMISATION CKAYE.LOG]]

=='Comparison' of two optimisations of anti2 1,5-hexadiene==

It is a '''major''' ''faux pas'' to directly compare optimisations using different basis sets. Both optimisations were carried out using Hartree-Fock method. The higher basis set yielded a much lower final energy, by approximately 3 atomic units. The bond lengths however are nearly identical, as can be seen below.

[[File:Bond lengths comparison ckaye.gif]]

==Frequency analysis of anti2==

From the frequency analysis of the higher optimised structure of anti2 1,5-hexadiene, the output file confirmed that there were no negative frequencies, which ensures that the molecule is at an energy minimum.

<pre> Low frequencies --- -18.8360 -11.7255 -0.0010 -0.0004 0.0004 1.7210
Low frequencies --- 72.7084 80.1375 120.0085</pre>

==Predicted infrared spectrum of anti2==

[[File:App2 ir spectrum ckaye.png]]

In the output file it can be seen that there are many vibrational modes. However, many have intensities of 0 because they do not involve a change in dipole moment, which is required for an interaction with electromagnetic field. Hence they do not appear on an IR spectrum.

==Optimisation of chair transition state structure==

An allylic H2CCHCH2 fragment was optimised using HF/3-21G basis set. This was later used to form the chair transition state below.

By fixing the bond forming/breaking distances of the terminal carbon atoms to approximately 2.2 Å and performing an opt+freq using the same basis set as before, but with TS(berny) selected and opt=noeigen, to allow imaginary frequencies. An imaginary frequency was observed at 818 cm-1, relating to the transition state. The displacement vectors of the vibration can be seen below

[[File:Transitionstateimaginaryvibration ckaye.png|center|thumb|imaginary vibration (still image, displacement vectors) of the transition state]]

==Optimisation of boat transition state structure==

By using the same allylic H2CCHCH2 fragment that was optimised using HF/3-21G basis set for the chair TS.

Using the same method as for the chair transition state.

Yielded an imaginary frequency at 840 cm-1 corresponding to the transition state

[[File:Boat transition state cope vibration ckaye.png]]

=Diels-Alder=

[[File:Da ckaye scheme.png|300px|thumb|center|Reaction scheme of Diels-Alder cycloaddition]]

==Introduction==

A Diels-Alder reaction is a [4+2] cycloaddition between a conjugated diene and a dienophile, forming a 6-membered ring. The driving force of the reaction is likely to be enthalpic in nature due to the formation of (stronger) sigma bonds at the 'expense' of (weaker) pi bonds. The enthalpic contribution usually overrides any entropic disfavourability<ref>Biotechnology: Bridging Research and Applications edited by Daphne Kamely, Ananda M. Chakrabarty, Steven E. Kornguth</ref> (from the inherent ordering of two molecules into one).

==MO==

[[File:Lumo butadiene ckaye.png|200px|center|LUMO of butadiene]]
[[File:Homo butadiene ckaye.png|200px|center|HOMO of butadiene]]

As can be seen above, the LUMO is symmetric with respect to a plane down the middle of the molecule. The HOMO however is antisymmetric since it does not have a plane of symmetry.

==MO of TS==

[[File:Ts homo ckaye.png|200px|thumb|center|HOMO of TS]]

[[File:Ts lumo ckaye.png|200px|thumb|center|LUMO of TS]]

==Regioselectivity of Diels Alder reaction==

=References=

<references/>

Rep:Mod:mod3 christopherkaye

2013-03-16T15:26:15Z

Ck1510: /* MO */

=Christopher Kaye, ck1510, Module 3 Computational=

Extension granted by Dr Hunt to 16th March.

=Introduction=

This module uses Gaussian software to model transition states of reactions. A transition state is the maximum saddle point on a potential energy surface. These states are not observable spectroscopically as they are so short-lived, assumed to be on a similar order of magnitude to bond vibrations - approximately 10-18 s. <ref>Biochemistry by Reginald H. Garrett, Charles M. Grisham</ref>

Investigating transitions states is helpful in understanding kinetics and mechanisms of reactions. Gaussian modelling allows geometries and energies of transition states to be predicted.

In this module, two reactions' transition states are being investigated: the Cope Rearrangement, and Diels-Alder.

=Cope Rearrangement=

[[File:Cope rearrangement for 15hexadiene.png|200px]]

The Cope rearrangement is a pericyclic reaction, specifically a [3+3] sigmatropic rearrangement. Like all pericyclic reactions, it is concerted in nature and passes through a transition state and no intermediates. In the case of 1,5-hexadiene, the transition state goes through a chair-like or a boat-like transition state <ref> Futher Perspectives in Organic Chemistry by CIBA Foundation Symposium</ref>
Gaussian was used to identify low energy conformers and then to attempt to find boat and chair transition states.

=Optimisation of conformers=

Using Hartree-Fock method and 3-21G basis set in each case, various conformers were chosen and optimised. The gauche3 conformer was found to be the lowest energy conformer due to the 'gauche effect' of London forces and favourable orbital interactions. Where sterics become more important, it is expected that antiperiplanar would become the most stable conformer. <ref>Carbohydrate Chemistry and Biochemistry: Structure and Mechanism by M. L. Sinnott</ref>
==Optimisation of antiperiplanar1 1,5-hexadiene==

{{DOI|10042/24051}} Link to D-space optimisation output

[[File:Results summary anti ckaye.png|200px|thumb|center|Results summary of optimisation of anti-peri-planar 1,5-hexadiene]]

[[File:Anti1 ckaye.png]]
Using 'Symmetrize'(sic) the molecule was found to have C2 symmetry.

==Optimisation of gauche4 1,5-hexadiene==

By changing the conformation manually to a gauche linkage, and optimising as above, the following results summary was produced.

[[File:Results summary gauche4 ckaye.png|thumb|center|Results summary of optimisation of gauche 1,5-hexadiene]]

[[File:Gauche 4 picture ckaye.png]]

Link to .log file [[File:GAUCHE4 OPT CKAYE.LOG]]

==Optimisation of gauche6 1,5-hexadiene==

[[File:Results summary gauche6 ckaye.png]]

[[File:Gauche 6 picture ckaye.png]]

Link to .log file [[File:OPT GAUCHE6 CKAYE.LOG]]

==Optimisation of gauche3 1,5-hexadiene==

[[file:Results summary gauche3.png]]

[[file:gauche_3_picture_ckaye.png]]

Link to .log file[[File:FOR GAUCHE 3 INPUT CKAYE.LOG]]

==Optimisation of gauche1 1,5-hexadiene==

[[File:Results summary gauche1 ckaye.png]]

[[File:Gauche 1 picture ckaye.png]]

Link to .log file [[File:GAUCHE 1 CKAYE.LOG]]

==Optimisation of anti2 1,5-hexadiene==

[[File:Results summary anti2 ckaye.png]]

[[File:Anti 2 picture ckaye.png]]

Link to .log file [[File:ANTI 2 OPTIMISATION CKAYE.LOG]]

==Higher optimisation of anti2 1,5-hexadiene==

[[File:Anti 2 higher optimisation ckaye picture.png]]

Link to .log file [[File:ANTI 2 HIGHER OPTIMISATION CKAYE.LOG]]

=='Comparison' of two optimisations of anti2 1,5-hexadiene==

It is a '''major''' ''faux pas'' to directly compare optimisations using different basis sets. Both optimisations were carried out using Hartree-Fock method. The higher basis set yielded a much lower final energy, by approximately 3 atomic units. The bond lengths however are nearly identical, as can be seen below.

[[File:Bond lengths comparison ckaye.gif]]

==Frequency analysis of anti2==

From the frequency analysis of the higher optimised structure of anti2 1,5-hexadiene, the output file confirmed that there were no negative frequencies, which ensures that the molecule is at an energy minimum.

<pre> Low frequencies --- -18.8360 -11.7255 -0.0010 -0.0004 0.0004 1.7210
Low frequencies --- 72.7084 80.1375 120.0085</pre>

==Predicted infrared spectrum of anti2==

[[File:App2 ir spectrum ckaye.png]]

In the output file it can be seen that there are many vibrational modes. However, many have intensities of 0 because they do not involve a change in dipole moment, which is required for an interaction with electromagnetic field. Hence they do not appear on an IR spectrum.

==Optimisation of chair transition state structure==

An allylic H2CCHCH2 fragment was optimised using HF/3-21G basis set. This was later used to form the chair transition state below.

By fixing the bond forming/breaking distances of the terminal carbon atoms to approximately 2.2 Å and performing an opt+freq using the same basis set as before, but with TS(berny) selected and opt=noeigen, to allow imaginary frequencies. An imaginary frequency was observed at 818 cm-1, relating to the transition state. The displacement vectors of the vibration can be seen below

[[File:Transitionstateimaginaryvibration ckaye.png|center|thumb|imaginary vibration (still image, displacement vectors) of the transition state]]

==Optimisation of boat transition state structure==

By using the same allylic H2CCHCH2 fragment that was optimised using HF/3-21G basis set for the chair TS.

Using the same method as for the chair transition state.

Yielded an imaginary frequency at 840 cm-1 corresponding to the transition state

[[File:Boat transition state cope vibration ckaye.png]]

=Diels-Alder=

[[File:Da ckaye scheme.png|300px|thumb|center|Reaction scheme of Diels-Alder cycloaddition]]

==Introduction==

A Diels-Alder reaction is a [4+2] cycloaddition between a conjugated diene and a dienophile, forming a 6-membered ring. The driving force of the reaction is likely to be enthalpic in nature due to the formation of (stronger) sigma bonds at the 'expense' of (weaker) pi bonds. The enthalpic contribution usually overrides any entropic disfavourability<ref>Biotechnology: Bridging Research and Applications edited by Daphne Kamely, Ananda M. Chakrabarty, Steven E. Kornguth</ref> (from the inherent ordering of two molecules into one).

==MO==

[[File:Homo butadiene ckaye.png|200px|center|HOMO of butadiene]]

As can be seen above, the LUMO is antisymmetric with respect to a plane down the middle of the molecule. The HOMO however is symmetric since it does have a plane of symmetry.

==MO of TS==

[[File:Ts homo ckaye.png|200px|thumb|center|HOMO of TS]]

[[File:Ts lumo ckaye.png|200px|thumb|center|LUMO of TS]]

==Regioselectivity of Diels Alder reaction==

=References=

<references/>

Rep:Mod:mod3 christopherkaye

2013-03-16T15:25:00Z

Ck1510: /* Introduction */

=Christopher Kaye, ck1510, Module 3 Computational=

Extension granted by Dr Hunt to 16th March.

=Introduction=

This module uses Gaussian software to model transition states of reactions. A transition state is the maximum saddle point on a potential energy surface. These states are not observable spectroscopically as they are so short-lived, assumed to be on a similar order of magnitude to bond vibrations - approximately 10-18 s. <ref>Biochemistry by Reginald H. Garrett, Charles M. Grisham</ref>

Investigating transitions states is helpful in understanding kinetics and mechanisms of reactions. Gaussian modelling allows geometries and energies of transition states to be predicted.

In this module, two reactions' transition states are being investigated: the Cope Rearrangement, and Diels-Alder.

=Cope Rearrangement=

[[File:Cope rearrangement for 15hexadiene.png|200px]]

The Cope rearrangement is a pericyclic reaction, specifically a [3+3] sigmatropic rearrangement. Like all pericyclic reactions, it is concerted in nature and passes through a transition state and no intermediates. In the case of 1,5-hexadiene, the transition state goes through a chair-like or a boat-like transition state <ref> Futher Perspectives in Organic Chemistry by CIBA Foundation Symposium</ref>
Gaussian was used to identify low energy conformers and then to attempt to find boat and chair transition states.

=Optimisation of conformers=

Using Hartree-Fock method and 3-21G basis set in each case, various conformers were chosen and optimised. The gauche3 conformer was found to be the lowest energy conformer due to the 'gauche effect' of London forces and favourable orbital interactions. Where sterics become more important, it is expected that antiperiplanar would become the most stable conformer. <ref>Carbohydrate Chemistry and Biochemistry: Structure and Mechanism by M. L. Sinnott</ref>
==Optimisation of antiperiplanar1 1,5-hexadiene==

{{DOI|10042/24051}} Link to D-space optimisation output

[[File:Results summary anti ckaye.png|200px|thumb|center|Results summary of optimisation of anti-peri-planar 1,5-hexadiene]]

[[File:Anti1 ckaye.png]]
Using 'Symmetrize'(sic) the molecule was found to have C2 symmetry.

==Optimisation of gauche4 1,5-hexadiene==

By changing the conformation manually to a gauche linkage, and optimising as above, the following results summary was produced.

[[File:Results summary gauche4 ckaye.png|thumb|center|Results summary of optimisation of gauche 1,5-hexadiene]]

[[File:Gauche 4 picture ckaye.png]]

Link to .log file [[File:GAUCHE4 OPT CKAYE.LOG]]

==Optimisation of gauche6 1,5-hexadiene==

[[File:Results summary gauche6 ckaye.png]]

[[File:Gauche 6 picture ckaye.png]]

Link to .log file [[File:OPT GAUCHE6 CKAYE.LOG]]

==Optimisation of gauche3 1,5-hexadiene==

[[file:Results summary gauche3.png]]

[[file:gauche_3_picture_ckaye.png]]

Link to .log file[[File:FOR GAUCHE 3 INPUT CKAYE.LOG]]

==Optimisation of gauche1 1,5-hexadiene==

[[File:Results summary gauche1 ckaye.png]]

[[File:Gauche 1 picture ckaye.png]]

Link to .log file [[File:GAUCHE 1 CKAYE.LOG]]

==Optimisation of anti2 1,5-hexadiene==

[[File:Results summary anti2 ckaye.png]]

[[File:Anti 2 picture ckaye.png]]

Link to .log file [[File:ANTI 2 OPTIMISATION CKAYE.LOG]]

==Higher optimisation of anti2 1,5-hexadiene==

[[File:Anti 2 higher optimisation ckaye picture.png]]

Link to .log file [[File:ANTI 2 HIGHER OPTIMISATION CKAYE.LOG]]

=='Comparison' of two optimisations of anti2 1,5-hexadiene==

It is a '''major''' ''faux pas'' to directly compare optimisations using different basis sets. Both optimisations were carried out using Hartree-Fock method. The higher basis set yielded a much lower final energy, by approximately 3 atomic units. The bond lengths however are nearly identical, as can be seen below.

[[File:Bond lengths comparison ckaye.gif]]

==Frequency analysis of anti2==

From the frequency analysis of the higher optimised structure of anti2 1,5-hexadiene, the output file confirmed that there were no negative frequencies, which ensures that the molecule is at an energy minimum.

<pre> Low frequencies --- -18.8360 -11.7255 -0.0010 -0.0004 0.0004 1.7210
Low frequencies --- 72.7084 80.1375 120.0085</pre>

==Predicted infrared spectrum of anti2==

[[File:App2 ir spectrum ckaye.png]]

In the output file it can be seen that there are many vibrational modes. However, many have intensities of 0 because they do not involve a change in dipole moment, which is required for an interaction with electromagnetic field. Hence they do not appear on an IR spectrum.

==Optimisation of chair transition state structure==

An allylic H2CCHCH2 fragment was optimised using HF/3-21G basis set. This was later used to form the chair transition state below.

By fixing the bond forming/breaking distances of the terminal carbon atoms to approximately 2.2 Å and performing an opt+freq using the same basis set as before, but with TS(berny) selected and opt=noeigen, to allow imaginary frequencies. An imaginary frequency was observed at 818 cm-1, relating to the transition state. The displacement vectors of the vibration can be seen below

[[File:Transitionstateimaginaryvibration ckaye.png|center|thumb|imaginary vibration (still image, displacement vectors) of the transition state]]

==Optimisation of boat transition state structure==

By using the same allylic H2CCHCH2 fragment that was optimised using HF/3-21G basis set for the chair TS.

Using the same method as for the chair transition state.

Yielded an imaginary frequency at 840 cm-1 corresponding to the transition state

[[File:Boat transition state cope vibration ckaye.png]]

=Diels-Alder=

[[File:Da ckaye scheme.png|300px|thumb|center|Reaction scheme of Diels-Alder cycloaddition]]

==Introduction==

A Diels-Alder reaction is a [4+2] cycloaddition between a conjugated diene and a dienophile, forming a 6-membered ring. The driving force of the reaction is likely to be enthalpic in nature due to the formation of (stronger) sigma bonds at the 'expense' of (weaker) pi bonds. The enthalpic contribution usually overrides any entropic disfavourability<ref>Biotechnology: Bridging Research and Applications edited by Daphne Kamely, Ananda M. Chakrabarty, Steven E. Kornguth</ref> (from the inherent ordering of two molecules into one).

==MO==

The LUMO is antisymmetric with respect to a plane down the middle of the molecule. The HOMO however is symmetric since it does have a plane of symmetry.

==MO of TS==

[[File:Ts homo ckaye.png|200px|thumb|center|HOMO of TS]]

[[File:Ts lumo ckaye.png|200px|thumb|center|LUMO of TS]]

==Regioselectivity of Diels Alder reaction==

=References=

<references/>

Rep:Mod:mod3 christopherkaye

2013-03-16T15:23:20Z

Ck1510: /* MO of TS */

Rep:Mod:mod3 christopherkaye

2013-03-16T15:22:57Z

Ck1510: /* Predicted infrared spectrum of app2 */

Rep:Mod:mod3 christopherkaye

2013-03-16T15:21:47Z

Ck1510: /* MO of TS */

Rep:Mod:mod3 christopherkaye

2013-03-16T15:20:18Z

Ck1510: /* Diels-Alder */

File:Da ckaye scheme.png

2013-03-16T15:16:20Z

Ck1510:

Rep:Mod:mod3 christopherkaye

2013-03-16T15:12:13Z

Ck1510: /* Diels-Alder */

Rep:Mod:mod3 christopherkaye

2013-03-16T15:11:12Z

Ck1510:

Rep:Mod:mod3 christopherkaye

2013-03-16T15:03:56Z

Ck1510: /* Optimisation of boat transition state structure */

Rep:Mod:mod3 christopherkaye

2013-03-16T14:43:55Z

Ck1510: /* Optimisation of chair transition state structure */