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Rep:Mod:Eb1613 Ex1

2016-12-02T11:19:05Z

Eb1613: /* MO analysis */

Page List

[[Mod:eb1613 files| The Calculations Log files can be found here]]

[[Mod:Emily1394| For main Introduction/conclusion page click here]]

[[Mod:Eb1613 Ex1| For Excerise 1 page click here]]

[[Mod:Eb1613 Ex2| For Excerise 2 page click here]]

[[Mod:Eb1613 Ex3| For Excerise 3 page click here]]

= Third Year Computational Lab Transition States - Emily Brown =

=== Exercise 1: Reaction of Butadiene with Ethene ===

[[File:ex1_scheme2.png]]

=== Bond Distances ===

{| class="wikitable" border="1"
|+ style="background: #38A5A5;"| Carbon-Carbon Bond Distances (Angstroms)
! style="background: #38A5A5;"| !! style="background: #38A5A5;"|C1-C2!! style="background: #38A5A5;"|C2-C3!! style="background: #38A5A5;"|C3-C4!! style="background: #38A5A5;"|C4-C5!! style="background: #38A5A5;"| C5-C6!! style="background: #38A5A5;"| C6-C1
|-
| style="background: #38A5A5;"| Butadiene||style="background: #EFECD9;"| 1.33530||style="background: #EFECD9;"| 1.46838 || style="background: #EFECD9;"|1.33525 ||style="background: #EFECD9;"| ||style="background: #EFECD9;"| ||style="background: #EFECD9;"|
|-
| style="background: #38A5A5;"|TS||style="background: #EFECD9;"| 1.37981 ||style="background: #EFECD9;"| 1.41112 ||style="background: #EFECD9;"| 1.37976 ||style="background: #EFECD9;"| 2.11496 || style="background: #EFECD9;"|1.38177 ||style="background: #EFECD9;"| 2.11452
|-
| style="background: #38A5A5;"|Product|| style="background: #EFECD9;"|1.50086 ||style="background: #EFECD9;"| 1.33698 || style="background: #EFECD9;"|1.50086 ||style="background: #EFECD9;"| 1.53717 ||style="background: #EFECD9;"| 1.53459 ||style="background: #EFECD9;"| 1.53717
|-
|}

Carbon-Carbon Sigma bonds are longer than double bonds. the bond length between C1-C2 and C3-C4 increase as they transform from double to single bonds in the reaction. The C2-C3 bond length shortens due to the reaction as a double bond forms here. The C5-C6 bond lengthens as it transforms from a single to a double bond. Due to the system being within a ring the carbon carbon single bonds are slightly shorter than the literature values which is for alkane chains. The bond distances of the forming bonds C1-C6 and C4-C5 decrease to values corresponding to those of single bonds. The Van der Waals radi for carbon is 1.70 angstroms. <ref name="vander" /> The length of bonds C1-C6 and C4-C5 at the transition state are less than twice the Van der Waals radius which indicates that a bond a forming.

Literature C-C bond distances <ref name="carbon" />

{| class="wikitable" border="1"
! colspan="2" style="background: #38A5A5;"| Carbon-Carbon Bond Distances (Angstroms)
|-
!style="background: #EFECD9;"|Sp3 C-C!! style="background: #EFECD9;"|Sp2 C-C
|-
| style="background: #EFECD9;"|1.57|| style="background: #EFECD9;"|1.33
|}

=== MO analysis ===

It can be seen from the MOs that there is a high symmetry requirement for the reaction the HOMO-1 (v2) orbital interaction lowers the energy of the electrons from the diene; the HOMO (π3) interactions stabilizes the electron pair coming from the dieneophile.

The overlap integral is zero for the interactions labelled π3 and π*5 and non-zero for interactions labelled π2 and π*4.

The MOs diagram highlights that the reaction is allowed as the orbitals of the same parity are interacting: u<->u g<->g.

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;" style="background: #38A5A5;" | MO diagram for the Diels Alder Reaction, self drawn. 
|-
|style="background: white;"| [[File:Mo_diagrma_draw_eb1613.png]]
|-
|}

Using a Frontier Orbital Approach to justify the diels alder reactivity in this reaction. This can be seen in the HOMO of the TS which shows the favorable overlap from combining the butadiene HOMO with the ethene LUMO.

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;" style="background: #38A5A5;"|Butadiene
|-
! style="background: #EFECD9;"|HOMO!!style="background: #EFECD9;"| LUMO
|-
| style="background: white;"| [[File:Eb1613_butadiene_LUMO.png]] || style="background: white;"|[[File:Eb1613_butadiene_HOMO.png]]
|-
|colspan="2" style="text-align: center;" style="background: #38A5A5;"| Ethene
|-
! style="background: #EFECD9;"|HOMO!!style="background: #EFECD9;"| LUMO
|-
|style="background: white;"| [[File:Eb1613_ethene_lumo.png]] || style="background: white;"|[[File:Eb1613_ethene_homo.png]]
|-
|colspan="2" style="text-align: center; style="background: #38A5A5;"|Transition State
|-
| colspan="2" style="text-align: center;" style="background: #EFECD9;"| LUMO + 1 = π*5
|-
| colspan="2" style="text-align: center; style="background: white;"| [[File:Lumo_minus_one_eb1613.png]]
|-
| colspan="2" style="text-align: center;" style="background: #EFECD9;"| LUMO = = π*4
|-
| colspan="2" style="text-align: center; style="background: white;"| [[File:Eb1613_TS_lumo.png]]
|-
| colspan="2" style="text-align: center;" style="background: #EFECD9;"| HOMO = = π3
|-
| colspan="2" style="text-align: center;" style="background: white;"| [[File:Eb1613_TS_homo.png]]
|-
| colspan="2" style="text-align: center;" style="background: #EFECD9;"| HOMO - 1 = = π2
|-
| colspan="2" style="text-align: center;" style="background: white;"| [[File:Homo_minus_one_eb1613.png]]
|}

The four MOs produced in the TS are π*5, π*4, π3 and π2. These are shown in the MO diagram above and were found were located using the guassian check point file.

=== Transition state analysis ===

The reactants were initially optimised to the PM6 semi-empirical level and then re-optimised to the DFT B3LYP/6-31G(d) level to save computational time. The reactants were aligned and then the atoms which form bonds were frozen using the opt=modredundant keywords in the calculation; this system was optimised to a minimum allowing parameters to reach a minimum whilst holding the reactants together at a distance of 2.2 angstroms. The resultant geometry from this calculation was used in a new calculation which optimised the structure to a TS (Berry) and allowed force constants to be calculated once. The transition state was located and confirmed by the presence of a single negative frequency which had an imaginary vibrational node which corresponded to the forming/breaking of bonds involved in the reactions transition state. This transition state geometry was then calculated using the higher DFT B3LYP/6-31G(d) calculation method. The transition state was further confirmed via the IRC calculated which allows force constants to be calculated always. The IRC requests that a reaction path be followed by integrating the intrinsic reaction coordinate. <ref name="IRC" /> It was found that using 10 steps in the IRC calculation was not nearly enough to look over the whole reaction coordinate and so 10000 steps was used for the repeated calculation. The visualisation of the transition state can be seen in the GIF files below along with the IRC calculation results. Furthermore the intrinsic reaction coordinate graph shows that there are no intermediates or other transition states involved in this reaction.

{| class="wikitable" border="1"
! style="background: #38A5A5;" |IRC movie captured || style="background: #38A5A5;" |IRC Graph
|-
| style="background: white;" | [[File:IRC_movie_eb1613.gif]] || style="background: white;" | [[File:IRC_exercise1_eb1613.png]]
|}

The Diels-Alder cyclic addition reaction occurs via a concerted transition state as shown below. The two new sigma bonds are formed at the same time therefore the reaction is synchronous. The animations below show how this compares to the first positive frequency, which is seen to be asynchronous rocking.

{| class="wikitable" border="1"
! style="background: #38A5A5;" | Negative Frequency = -948.76 cm-1
|-
|style="background: white;" | [[File:Test3_files_eb1613.gif]]
|-
! style="background: #38A5A5;" | First Positive Frequency = 145.08 cm-1
|-
| style="background: white;" | [[File:Eb1613_first_pos_vib_ex1.gif]]
|}

=== Optimization of Reactants, TS and Products ===

All structures have been optimised at the semi-empirical PM6 level and then further optimised to the DFT B3LYP/6-31G(d) level to save computational time. The lack of negative frequencies in the frequency calculation indicates that the structure is optimised to a true minimum, the presence of one negative frequency indicates that a transition state has been reached, more than one negative frequency means that a saddle point structure has been reached.

{| class="wikitable" border="1"
|+ Files
! style="background: #38A5A5;"|Butadiene !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with PM6 level</title> <color>white</color> <size>200</size> <uploadedFileContents>Eb1613_butadiene_PM6_opt_freq.log</uploadedFileContents> </jmolApplet></jmol> || [[File:But_eb1613_energy_new.png]]
|-
! style="background: #38A5A5;"|Ethene !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with PM6 level</title> <color>white</color> <size>200</size> <uploadedFileContents>Eb1613_ETHENE_PM6_OPT_FREQ.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Eb1613_ethene_energy.png]]
|-
! style="background: #38A5A5;"|Transition State !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Transition State</title> <color>white</color> <size>300</size> <uploadedFileContents>TS_FREEZE2_OPT.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Eb1613_TS_energy.png]]
|-
! style="background: #38A5A5;"|Product !! style="background: #38A5A5;"|Gaussian imagine of product
|-
| <jmol><jmolApplet> <title>Jmol of PM6 optimised product</title> <color>white</color> <size>300</size> <uploadedFileContents>Eb1613_PRODUCT_PM6_OPT_MANDISP1PT0_FREQ.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Product_ex1.png]]
|-
! colspan="2" style="text-align: center;" style="background: #38A5A5;"| Optimization Summary
|-
|colspan="2" style="text-align: center;"| [[File:Eb1613_product_summary.png]]
|}

=== References ===

<references>
<ref name="carbon">J.M. Berg, J. L. Tymoczko, L. Stryer, in Biochemistry., W.H. Freeman, New York, 5th edn., 2002, Appendix C: Standard Bond Lengths, https://www.ncbi.nlm.nih.gov/books/NBK21220/, (accessed 23rd November, 2016).</ref>
<ref name="vander">A. Bondi, J. Phys. Chem., 1964, 68 (3), 441-451.</ref>
<ref name="IRC">http://www.gaussian.com/g_tech/g_ur/k_irc.htm (accessed 23rd November, 2016)</ref>

</references>

Rep:Mod:Eb1613 Ex1

2016-12-02T11:18:48Z

Eb1613:

Page List

[[Mod:eb1613 files| The Calculations Log files can be found here]]

[[Mod:Emily1394| For main Introduction/conclusion page click here]]

[[Mod:Eb1613 Ex1| For Excerise 1 page click here]]

[[Mod:Eb1613 Ex2| For Excerise 2 page click here]]

[[Mod:Eb1613 Ex3| For Excerise 3 page click here]]

= Third Year Computational Lab Transition States - Emily Brown =

=== Exercise 1: Reaction of Butadiene with Ethene ===

[[File:ex1_scheme2.png]]

=== Bond Distances ===

{| class="wikitable" border="1"
|+ style="background: #38A5A5;"| Carbon-Carbon Bond Distances (Angstroms)
! style="background: #38A5A5;"| !! style="background: #38A5A5;"|C1-C2!! style="background: #38A5A5;"|C2-C3!! style="background: #38A5A5;"|C3-C4!! style="background: #38A5A5;"|C4-C5!! style="background: #38A5A5;"| C5-C6!! style="background: #38A5A5;"| C6-C1
|-
| style="background: #38A5A5;"| Butadiene||style="background: #EFECD9;"| 1.33530||style="background: #EFECD9;"| 1.46838 || style="background: #EFECD9;"|1.33525 ||style="background: #EFECD9;"| ||style="background: #EFECD9;"| ||style="background: #EFECD9;"|
|-
| style="background: #38A5A5;"|TS||style="background: #EFECD9;"| 1.37981 ||style="background: #EFECD9;"| 1.41112 ||style="background: #EFECD9;"| 1.37976 ||style="background: #EFECD9;"| 2.11496 || style="background: #EFECD9;"|1.38177 ||style="background: #EFECD9;"| 2.11452
|-
| style="background: #38A5A5;"|Product|| style="background: #EFECD9;"|1.50086 ||style="background: #EFECD9;"| 1.33698 || style="background: #EFECD9;"|1.50086 ||style="background: #EFECD9;"| 1.53717 ||style="background: #EFECD9;"| 1.53459 ||style="background: #EFECD9;"| 1.53717
|-
|}

Carbon-Carbon Sigma bonds are longer than double bonds. the bond length between C1-C2 and C3-C4 increase as they transform from double to single bonds in the reaction. The C2-C3 bond length shortens due to the reaction as a double bond forms here. The C5-C6 bond lengthens as it transforms from a single to a double bond. Due to the system being within a ring the carbon carbon single bonds are slightly shorter than the literature values which is for alkane chains. The bond distances of the forming bonds C1-C6 and C4-C5 decrease to values corresponding to those of single bonds. The Van der Waals radi for carbon is 1.70 angstroms. <ref name="vander" /> The length of bonds C1-C6 and C4-C5 at the transition state are less than twice the Van der Waals radius which indicates that a bond a forming.

Literature C-C bond distances <ref name="carbon" />

{| class="wikitable" border="1"
! colspan="2" style="background: #38A5A5;"| Carbon-Carbon Bond Distances (Angstroms)
|-
!style="background: #EFECD9;"|Sp3 C-C!! style="background: #EFECD9;"|Sp2 C-C
|-
| style="background: #EFECD9;"|1.57|| style="background: #EFECD9;"|1.33
|}

=== MO analysis ===

It can be seen from the MOs that there is a high symmetry requirement for the reaction the HOMO-1 (v2) orbital interaction lowers the energy of the electrons from the diene; the HOMO (π3) interactions stabilizes the electron pair coming from the dieneophile.

The overlap integral is zero for the interactions labelled π3 and π*5 and non-zero for interactions labelled π2 and π*4.

The MOs diagram highlights that the reaction is allowed as the orbitals of the same parity are interacting: u<->u g<->g.

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;" style="background: #38A5A5;" | MO diagram for the Diels Alder Reaction, self drawn with help from multiple book/web/course sources 
|-
|style="background: white;"| [[File:Mo_diagrma_draw_eb1613.png]]
|-
|}

Using a Frontier Orbital Approach to justify the diels alder reactivity in this reaction. This can be seen in the HOMO of the TS which shows the favorable overlap from combining the butadiene HOMO with the ethene LUMO.

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;" style="background: #38A5A5;"|Butadiene
|-
! style="background: #EFECD9;"|HOMO!!style="background: #EFECD9;"| LUMO
|-
| style="background: white;"| [[File:Eb1613_butadiene_LUMO.png]] || style="background: white;"|[[File:Eb1613_butadiene_HOMO.png]]
|-
|colspan="2" style="text-align: center;" style="background: #38A5A5;"| Ethene
|-
! style="background: #EFECD9;"|HOMO!!style="background: #EFECD9;"| LUMO
|-
|style="background: white;"| [[File:Eb1613_ethene_lumo.png]] || style="background: white;"|[[File:Eb1613_ethene_homo.png]]
|-
|colspan="2" style="text-align: center; style="background: #38A5A5;"|Transition State
|-
| colspan="2" style="text-align: center;" style="background: #EFECD9;"| LUMO + 1 = π*5
|-
| colspan="2" style="text-align: center; style="background: white;"| [[File:Lumo_minus_one_eb1613.png]]
|-
| colspan="2" style="text-align: center;" style="background: #EFECD9;"| LUMO = = π*4
|-
| colspan="2" style="text-align: center; style="background: white;"| [[File:Eb1613_TS_lumo.png]]
|-
| colspan="2" style="text-align: center;" style="background: #EFECD9;"| HOMO = = π3
|-
| colspan="2" style="text-align: center;" style="background: white;"| [[File:Eb1613_TS_homo.png]]
|-
| colspan="2" style="text-align: center;" style="background: #EFECD9;"| HOMO - 1 = = π2
|-
| colspan="2" style="text-align: center;" style="background: white;"| [[File:Homo_minus_one_eb1613.png]]
|}

The four MOs produced in the TS are π*5, π*4, π3 and π2. These are shown in the MO diagram above and were found were located using the guassian check point file.

=== Transition state analysis ===

The reactants were initially optimised to the PM6 semi-empirical level and then re-optimised to the DFT B3LYP/6-31G(d) level to save computational time. The reactants were aligned and then the atoms which form bonds were frozen using the opt=modredundant keywords in the calculation; this system was optimised to a minimum allowing parameters to reach a minimum whilst holding the reactants together at a distance of 2.2 angstroms. The resultant geometry from this calculation was used in a new calculation which optimised the structure to a TS (Berry) and allowed force constants to be calculated once. The transition state was located and confirmed by the presence of a single negative frequency which had an imaginary vibrational node which corresponded to the forming/breaking of bonds involved in the reactions transition state. This transition state geometry was then calculated using the higher DFT B3LYP/6-31G(d) calculation method. The transition state was further confirmed via the IRC calculated which allows force constants to be calculated always. The IRC requests that a reaction path be followed by integrating the intrinsic reaction coordinate. <ref name="IRC" /> It was found that using 10 steps in the IRC calculation was not nearly enough to look over the whole reaction coordinate and so 10000 steps was used for the repeated calculation. The visualisation of the transition state can be seen in the GIF files below along with the IRC calculation results. Furthermore the intrinsic reaction coordinate graph shows that there are no intermediates or other transition states involved in this reaction.

{| class="wikitable" border="1"
! style="background: #38A5A5;" |IRC movie captured || style="background: #38A5A5;" |IRC Graph
|-
| style="background: white;" | [[File:IRC_movie_eb1613.gif]] || style="background: white;" | [[File:IRC_exercise1_eb1613.png]]
|}

The Diels-Alder cyclic addition reaction occurs via a concerted transition state as shown below. The two new sigma bonds are formed at the same time therefore the reaction is synchronous. The animations below show how this compares to the first positive frequency, which is seen to be asynchronous rocking.

{| class="wikitable" border="1"
! style="background: #38A5A5;" | Negative Frequency = -948.76 cm-1
|-
|style="background: white;" | [[File:Test3_files_eb1613.gif]]
|-
! style="background: #38A5A5;" | First Positive Frequency = 145.08 cm-1
|-
| style="background: white;" | [[File:Eb1613_first_pos_vib_ex1.gif]]
|}

=== Optimization of Reactants, TS and Products ===

All structures have been optimised at the semi-empirical PM6 level and then further optimised to the DFT B3LYP/6-31G(d) level to save computational time. The lack of negative frequencies in the frequency calculation indicates that the structure is optimised to a true minimum, the presence of one negative frequency indicates that a transition state has been reached, more than one negative frequency means that a saddle point structure has been reached.

{| class="wikitable" border="1"
|+ Files
! style="background: #38A5A5;"|Butadiene !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with PM6 level</title> <color>white</color> <size>200</size> <uploadedFileContents>Eb1613_butadiene_PM6_opt_freq.log</uploadedFileContents> </jmolApplet></jmol> || [[File:But_eb1613_energy_new.png]]
|-
! style="background: #38A5A5;"|Ethene !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with PM6 level</title> <color>white</color> <size>200</size> <uploadedFileContents>Eb1613_ETHENE_PM6_OPT_FREQ.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Eb1613_ethene_energy.png]]
|-
! style="background: #38A5A5;"|Transition State !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Transition State</title> <color>white</color> <size>300</size> <uploadedFileContents>TS_FREEZE2_OPT.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Eb1613_TS_energy.png]]
|-
! style="background: #38A5A5;"|Product !! style="background: #38A5A5;"|Gaussian imagine of product
|-
| <jmol><jmolApplet> <title>Jmol of PM6 optimised product</title> <color>white</color> <size>300</size> <uploadedFileContents>Eb1613_PRODUCT_PM6_OPT_MANDISP1PT0_FREQ.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Product_ex1.png]]
|-
! colspan="2" style="text-align: center;" style="background: #38A5A5;"| Optimization Summary
|-
|colspan="2" style="text-align: center;"| [[File:Eb1613_product_summary.png]]
|}

=== References ===

<references>
<ref name="carbon">J.M. Berg, J. L. Tymoczko, L. Stryer, in Biochemistry., W.H. Freeman, New York, 5th edn., 2002, Appendix C: Standard Bond Lengths, https://www.ncbi.nlm.nih.gov/books/NBK21220/, (accessed 23rd November, 2016).</ref>
<ref name="vander">A. Bondi, J. Phys. Chem., 1964, 68 (3), 441-451.</ref>
<ref name="IRC">http://www.gaussian.com/g_tech/g_ur/k_irc.htm (accessed 23rd November, 2016)</ref>

</references>

Rep:Mod:Emily1394

2016-12-02T11:17:24Z

Eb1613: /* Reference */

Page List

[[Mod:eb1613 files| The Calculations Log files can be found here]]

[[Mod:Emily1394| For main Introduction/conclusion page click here]]

[[Mod:Eb1613 Ex1| For Excerise 1 page click here]]

[[Mod:Eb1613 Ex2| For Excerise 2 page click here]]

[[Mod:Eb1613 Ex3| For Excerise 3 page click here]]

= Third Year Computational Lab Transition States - Emily Brown =

Please note each page has its own references at the bottom of the page.

=== Introduction ===

==== Theory ====

'''Transition State:''' This is a maxima on the reaction coordinate graph. At the point the gradient/first derivative is zero and can be referred to as a turning point on the graph.

'''Potential Energy Surface:''' This has 3N-6 dimensions and if you travel in one dimension you can draw a reaction coordinate graph as shown below. <ref name="waterbottle" /> The PES is a function of energy vs every coordinate. <ref name="Hunt" />

[[File:Eb1613_PE_RC.png|thumb|center|Potential energy surface on left and corresponding reaction coordinate graph to right <ref name="waterbottle" /> ]]

Due to the transition state being a turning point on the reaction coordinate graph it can be found by setting the first derivative to zero as at a minima/maxima the gradient is zero. The potential energy surface allows you to travel in directions which may be away from the reaction coordinate you are trying to locate. The potential energy surface has 3N-6 dimensions.<ref name="Hunt" /> Programs like GuassView take advantage of the fact that all these dimensions are positive in curvature apart from one which is the minimum energy path. This results in an imaginary frequency which is the single negative frequency found in the frequency calculation of a transition state geometry. Energy minimas have zero negative frequencies in their frequency calculations and saddle points have multiple. <ref name="Hunt" />

Reactions can be controlled by a number of different factors some of these being sterics and secondary orbital effects. Reactions often compromise between multiple aspects for example a reaction may be sterically disfavored but that particular reaction path could result in good orbital overlap. Secondary oribtal interactions tend to favor the endo-adduct being formed in Diels-Alder reactions.

The reactants tend to form the products via the higher energy transition state which is shown as an energy maximum on the above graph, the energy required to overcome this barrier is known as the activation energy and can be seen in the arrhenius equation as the symbol Ea. The activation energy depends on many factors and programmes like gaussian can be used to estimate this energy and predict whether reactions are likely to occur. For example there are two cis dienes present in the reactant in exercise 3 but only one is involved int he dies alder reactions as the other is known to have a high transition state making it very kinetically unfavourable.

Diels Alder reactions are classified as [4+2] cycloadditions typically between a diene and a dieneophile. The reactions occur via a concerted mechanism with a cyclic transition state. The reaction involves the breaking of 2π bonds and the formation of 2 new σ bonds and a single new π bond. The breaking of the pi bonds is the enthalpic driving force in the reaction as breaking a carbon carbon double bond releases a lot of energy. Cycloaddition reactions have been categorised by Woodward Hoffman to state whether they are thermally or photochemically allowed. Diels-alder reactions can also be classified as normal electron demand or inverse electron demand. Normal electron demand is the case when the HOMO of the diene reacts with the LUMO of the dieneohile, where as inverse electron demand is when the LUMO of the diene reacts with the HOMO of the dieneophile. It has been shown that adding electron donating groups/ electron withdrawing groups to certain positions on the diene/dieneophile can facilitate the Diels-Alder reaction by effecting the energy levels of their HOMO/LUMO thus narrowing the energy gap between the interacting HOMO and LUMO thus facilitating a better orbital overlap.

Cheleotropic reactions is a class of pericyclic reactions which present themselves in exercise 3 which is the cyclic addition of SO2 to a diene. These reactions were exploded in the Woodward and Hoffman's famous publication. <ref name="woodsman" />

==== Computational ====
Initially structures will be optimized using method1 and then using method2. Doing the initial 'tidy up' allows computational time to be saved. Locating transition states has proved difficult for certain systems which results in different approaches being undertaken such as freezing certain bonds by using the '''opt=modredundant''' keywords thus locking atoms together to perform initial optimizations. Another approach is to start from the products or reactants and lengthen certain bonds in an attempt to locate the transition state. Structures were confirmed via frequency calculations: the lack of negative frequencies in the frequency calculation indicates that the structure is optimised to a true minimum, the presence of one negative frequency indicates that a transition state has been reached, more than one negative frequency means that a saddle point structure has been reached. <ref name="book book" />

It proved necessary at times to freeze bonds to locate a transition state however once found all structures were later re-optimised under no symmetry constraints. The '''int=ultrafine''' keywords are expressed in the DFT calculations as optimisation with many low level vibration modes will often proceed more reliably when a larger DFT integration grid is requested. <ref name="integral" />

'''Method 1:''' Opt+Freq, semi empirical, PM6.

'''Method 2:''' Opt+Freq, DFT B3LYP/631G(d).

Both the density function theory (DFT) and semi-empirical methods are able to describe quantum states as many electron systems; they both use the born-opinhiemer approximation where you first solve for the electronic degrees of freedom. <ref name="electrons" /> In DFT the many-electron wavefunction is completely bypassed in favor of the electron density, the variational principle is used to minimise the energy with respect to electron density. However a key problem with this method is that the energy functional is not know. <ref name="electrons" /> Semi-empirical Methods are a simplified versions of Hartree-Fock theory using empirical corrections in order to improve performance; these can be preformed prior to DFT calculations in order to save computational time. <ref name="mug mug" /> The PM6 part of the calculation specifics that the PM6 hamiltonian is to use in the semi-empirical calculation. <ref name="IwantTEA" />

'''Notes:''' When optimising to a transition state I used: TS (Berry), Force constants allowed to calculate once. When optimising to a minimum use: minimum and force constants are allowed to calculate never. Occasional calculations were run on the colleges HPC to save computational time as these servers use more processors than my local computer in college. The 09 version of gaussian suite was used when on windows college computers.

==== Exercises ====

Each exercise is contained on its own page which are linked to below and above the contents section of each page. Each page containing an exercise has Jmol files of all structures used in that exercise at the end of the page, they are accompanied by the 'results summary' section of their opt/freq calculation to confirm the existence of the correct number of negative frequencies and to allow the geometry of each structure to be viewed.

[[Mod:Eb1613 Ex1| Page for Excerise 1]]

[[Mod:Eb1613 Ex2| Page for Excerise 2]]

[[Mod:Eb1613 Ex3| Page for Excerise 3]]

=== Conclusion ===

The transition states were successfully located for multiple reaction following a similar procedure in each case. Orbital analysis was undertaken and HOMO+1, HOMO, LUMO and LUMO-1 levels were explored. The transition states were be further identified by looking into the IRC, thus allowing endo/exo transition states to be confidently labeled. The IRC also revealed information about the reaction coordinate such that no other intermediates existed and that no other transition states were encountered for our reactions.

This computational lab has also highlighed some key difference between the semi-empirical based basis sets and those of basis sets belonging to the density functional theory family. The lab has drawn attention to the importance of chosen the correct basis set and has given me the ability to use Gaussian programs to confidently locate transition states for reactions and highlighted some key methods to further understand the transition states found such as IRC.

=== References ===

<references>
<ref name="waterbottle">https://commons.wikimedia.org/wiki/File:Potential_Energy_Surface_and_Corresponding_Reaction_Coordinate_Diagram.png (accessed 23rd November)</ref>
<ref name="electrons">https://www.quora.com/What-is-the-difference-between-density-functional-theory-and-hartree-fock (accessed 25th November 2016)</ref>
<ref name="integral">http://www.gaussian.com/g_tech/g_ur/k_opt.htm (accessed 25th November 2016)</ref>
<ref name="IwantTEA ">http://www.gaussian.com/g_tech/g_ur/k_semiempirical.html (accessed 25th November 2016)</ref>
<ref name="mug mug ">http://www.cup.uni-muenchen.de/ch/compchem/energy/semi1.html (accessed 25th November 2016)</ref>
<ref name="Hunt "> Dr. Hunt's year 4 lecture course: "Computational Inorganic Chemistry" Lecture4, Handout3. http://www.huntresearchgroup.org.uk/teaching/teaching_comp_chem_year4/L4_PES.pdf (accessed 25th November 2016)</ref>
<ref name="book book "> Foresman, J. and Frisch, A. (1996). Exploring Chemistry With Electronic Structure Methods: A Guide to Using Gaussian. 2nd ed. Guassian, Chapter 1.</ref>
<ref name="woodsman">Woodward, R.B.; Hoffman, R. Angew. Chem. Int. Ed. Engl. 1969, 8, 781. DOI:10.1002/anie.196907811 </ref>
</references>

Rep:Mod:Emily1394

2016-12-02T11:15:19Z

Eb1613: /* Conclusion */

Page List

[[Mod:eb1613 files| The Calculations Log files can be found here]]

[[Mod:Emily1394| For main Introduction/conclusion page click here]]

[[Mod:Eb1613 Ex1| For Excerise 1 page click here]]

[[Mod:Eb1613 Ex2| For Excerise 2 page click here]]

[[Mod:Eb1613 Ex3| For Excerise 3 page click here]]

= Third Year Computational Lab Transition States - Emily Brown =

Please note each page has its own references at the bottom of the page.

=== Introduction ===

==== Theory ====

'''Transition State:''' This is a maxima on the reaction coordinate graph. At the point the gradient/first derivative is zero and can be referred to as a turning point on the graph.

'''Potential Energy Surface:''' This has 3N-6 dimensions and if you travel in one dimension you can draw a reaction coordinate graph as shown below. <ref name="waterbottle" /> The PES is a function of energy vs every coordinate. <ref name="Hunt" />

[[File:Eb1613_PE_RC.png|thumb|center|Potential energy surface on left and corresponding reaction coordinate graph to right <ref name="waterbottle" /> ]]

Due to the transition state being a turning point on the reaction coordinate graph it can be found by setting the first derivative to zero as at a minima/maxima the gradient is zero. The potential energy surface allows you to travel in directions which may be away from the reaction coordinate you are trying to locate. The potential energy surface has 3N-6 dimensions.<ref name="Hunt" /> Programs like GuassView take advantage of the fact that all these dimensions are positive in curvature apart from one which is the minimum energy path. This results in an imaginary frequency which is the single negative frequency found in the frequency calculation of a transition state geometry. Energy minimas have zero negative frequencies in their frequency calculations and saddle points have multiple. <ref name="Hunt" />

Reactions can be controlled by a number of different factors some of these being sterics and secondary orbital effects. Reactions often compromise between multiple aspects for example a reaction may be sterically disfavored but that particular reaction path could result in good orbital overlap. Secondary oribtal interactions tend to favor the endo-adduct being formed in Diels-Alder reactions.

The reactants tend to form the products via the higher energy transition state which is shown as an energy maximum on the above graph, the energy required to overcome this barrier is known as the activation energy and can be seen in the arrhenius equation as the symbol Ea. The activation energy depends on many factors and programmes like gaussian can be used to estimate this energy and predict whether reactions are likely to occur. For example there are two cis dienes present in the reactant in exercise 3 but only one is involved int he dies alder reactions as the other is known to have a high transition state making it very kinetically unfavourable.

Diels Alder reactions are classified as [4+2] cycloadditions typically between a diene and a dieneophile. The reactions occur via a concerted mechanism with a cyclic transition state. The reaction involves the breaking of 2π bonds and the formation of 2 new σ bonds and a single new π bond. The breaking of the pi bonds is the enthalpic driving force in the reaction as breaking a carbon carbon double bond releases a lot of energy. Cycloaddition reactions have been categorised by Woodward Hoffman to state whether they are thermally or photochemically allowed. Diels-alder reactions can also be classified as normal electron demand or inverse electron demand. Normal electron demand is the case when the HOMO of the diene reacts with the LUMO of the dieneohile, where as inverse electron demand is when the LUMO of the diene reacts with the HOMO of the dieneophile. It has been shown that adding electron donating groups/ electron withdrawing groups to certain positions on the diene/dieneophile can facilitate the Diels-Alder reaction by effecting the energy levels of their HOMO/LUMO thus narrowing the energy gap between the interacting HOMO and LUMO thus facilitating a better orbital overlap.

Cheleotropic reactions is a class of pericyclic reactions which present themselves in exercise 3 which is the cyclic addition of SO2 to a diene. These reactions were exploded in the Woodward and Hoffman's famous publication. <ref name="woodsman" />

==== Computational ====
Initially structures will be optimized using method1 and then using method2. Doing the initial 'tidy up' allows computational time to be saved. Locating transition states has proved difficult for certain systems which results in different approaches being undertaken such as freezing certain bonds by using the '''opt=modredundant''' keywords thus locking atoms together to perform initial optimizations. Another approach is to start from the products or reactants and lengthen certain bonds in an attempt to locate the transition state. Structures were confirmed via frequency calculations: the lack of negative frequencies in the frequency calculation indicates that the structure is optimised to a true minimum, the presence of one negative frequency indicates that a transition state has been reached, more than one negative frequency means that a saddle point structure has been reached. <ref name="book book" />

It proved necessary at times to freeze bonds to locate a transition state however once found all structures were later re-optimised under no symmetry constraints. The '''int=ultrafine''' keywords are expressed in the DFT calculations as optimisation with many low level vibration modes will often proceed more reliably when a larger DFT integration grid is requested. <ref name="integral" />

'''Method 1:''' Opt+Freq, semi empirical, PM6.

'''Method 2:''' Opt+Freq, DFT B3LYP/631G(d).

Both the density function theory (DFT) and semi-empirical methods are able to describe quantum states as many electron systems; they both use the born-opinhiemer approximation where you first solve for the electronic degrees of freedom. <ref name="electrons" /> In DFT the many-electron wavefunction is completely bypassed in favor of the electron density, the variational principle is used to minimise the energy with respect to electron density. However a key problem with this method is that the energy functional is not know. <ref name="electrons" /> Semi-empirical Methods are a simplified versions of Hartree-Fock theory using empirical corrections in order to improve performance; these can be preformed prior to DFT calculations in order to save computational time. <ref name="mug mug" /> The PM6 part of the calculation specifics that the PM6 hamiltonian is to use in the semi-empirical calculation. <ref name="IwantTEA" />

'''Notes:''' When optimising to a transition state I used: TS (Berry), Force constants allowed to calculate once. When optimising to a minimum use: minimum and force constants are allowed to calculate never. Occasional calculations were run on the colleges HPC to save computational time as these servers use more processors than my local computer in college. The 09 version of gaussian suite was used when on windows college computers.

==== Exercises ====

Each exercise is contained on its own page which are linked to below and above the contents section of each page. Each page containing an exercise has Jmol files of all structures used in that exercise at the end of the page, they are accompanied by the 'results summary' section of their opt/freq calculation to confirm the existence of the correct number of negative frequencies and to allow the geometry of each structure to be viewed.

[[Mod:Eb1613 Ex1| Page for Excerise 1]]

[[Mod:Eb1613 Ex2| Page for Excerise 2]]

[[Mod:Eb1613 Ex3| Page for Excerise 3]]

=== Conclusion ===

The transition states were successfully located for multiple reaction following a similar procedure in each case. Orbital analysis was undertaken and HOMO+1, HOMO, LUMO and LUMO-1 levels were explored. The transition states were be further identified by looking into the IRC, thus allowing endo/exo transition states to be confidently labeled. The IRC also revealed information about the reaction coordinate such that no other intermediates existed and that no other transition states were encountered for our reactions.

This computational lab has also highlighed some key difference between the semi-empirical based basis sets and those of basis sets belonging to the density functional theory family. The lab has drawn attention to the importance of chosen the correct basis set and has given me the ability to use Gaussian programs to confidently locate transition states for reactions and highlighted some key methods to further understand the transition states found such as IRC.

=== Reference ===

<references>
<ref name="waterbottle">https://commons.wikimedia.org/wiki/File:Potential_Energy_Surface_and_Corresponding_Reaction_Coordinate_Diagram.png (accessed 23rd November)</ref>
<ref name="electrons">https://www.quora.com/What-is-the-difference-between-density-functional-theory-and-hartree-fock (accessed 25th November 2016)</ref>
<ref name="integral">http://www.gaussian.com/g_tech/g_ur/k_opt.htm (accessed 25th November 2016)</ref>
<ref name="IwantTEA ">http://www.gaussian.com/g_tech/g_ur/k_semiempirical.html (accessed 25th November 2016)</ref>
<ref name="mug mug ">http://www.cup.uni-muenchen.de/ch/compchem/energy/semi1.html (accessed 25th November 2016)</ref>
<ref name="Hunt "> Dr. Hunt's year 4 lecture course: "Computational Inorganic Chemistry" Lecture4, Handout3. http://www.huntresearchgroup.org.uk/teaching/teaching_comp_chem_year4/L4_PES.pdf (accessed 25th November 2016)</ref>
<ref name="book book "> Foresman, J. and Frisch, A. (1996). Exploring Chemistry With Electronic Structure Methods: A Guide to Using Gaussian. 2nd ed. Guassian, Chapter 1.</ref>
<ref name="woodsman">Woodward, R.B.; Hoffman, R. Angew. Chem. Int. Ed. Engl. 1969, 8, 781. DOI:10.1002/anie.196907811 </ref>
</references>

Rep:Mod:Eb1613 Ex2

2016-12-02T11:14:24Z

Eb1613: /* MO analysis */

Page List

[[Mod:eb1613 files| The Calculations Log files can be found here]]

[[Mod:Emily1394| For main Introduction/conclusion page click here]]

[[Mod:Eb1613 Ex1| For Excerise 1 page click here]]

[[Mod:Eb1613 Ex2| For Excerise 2 page click here]]

[[Mod:Eb1613 Ex3| For Excerise 3 page click here]]

= Third Year Computational Lab Transition States - Emily Brown =

=== Exercise 2 ===

[[File:Ex2_scheme.png]]

Two different products are known to form in this Diels-Alder reaction, they are known as the endo and exo adducts.

=== Transition state 2 ===

These GIFs make it east to see where the Endo-TS has favorable secondary orbital interactions, towards the left hand side it can be seen that the oxygens p-oribtals could interact with those of the 6-carbon ring near it in a favorable manner.

{| class="wikitable" border="1"
! style="background: #38A5A5;"|Exo Transition State. Negative Frequency = -520.92 cm-1
|-
| style="background: white;"| [[File:Eb1613_exo_ts_movie.gif]]
|-
! style="background: #38A5A5;"|Endo Transition State. Negative Frequency = -528.82 cm-1
|-
| style="background: white;"| [[File:Eb1613_endo_ts_movie2.gif]]
|}

=== Thermochemistry anaylsis 2 ===

[[File:Exercise_reaction_coordin_eb1613.png]]

'''Electronic and Thermal free energies relative to reactants(KJ/mol) (2dp)'''

{| class="wikitable" border="1"
! style="background: #38A5A5;" | !! style="background: #38A5A5;" |Reactants !! style="background: #38A5A5;" |Transition state !! style="background: #38A5A5;"| Products
|-
| style="background: #38A5A5;" | Exo ||style="background: #EFECD9;" | 0 || style="background: #EFECD9;" |+159.81 ||style="background: #EFECD9;" | -67.41
|-
| style="background: #38A5A5;" | Endo || style="background: #EFECD9;" |0 || style="background: #EFECD9;" |+167.65|| style="background: #EFECD9;" |-63.77
|}

From the thermochemistry relative energy values it can be seen that the Exo product has an activation energy which is 7.84 KJ/mol lower than that of the Exo product. The Exo-Adduct is 3.64 KJ/mol more stable than the Endo-adduct making it the thermodynamicly favoured product as well as the kinetically favoured product as it has a lower energy TS.

=== MO analysis ===

This reaction and that the reaction in exercise 2 are both Diels-Alder reactions the MO diagram from exercise 1 is still valid to be used to understand/explain the MO interactions within this reaction.

{| class="wikitable" border="3"
|colspan="2" style="text-align: center;" style="background: #38A5A5;"| MO diagram for the Diels Alder Reaction in exercise 1 
|-
| style="background: white;"| [[File:Mo_diagrma_draw_eb1613.png]]
|-
|}

From looking at the molcular orbitals below one can identify which orbitals are interacting in the Transition states. For example: it can be seen that the Endo TS LUMO is formed by the overlap of the Cyclohexadiene LUMO-1 and the 1,3-Dioxole LUMO.

{| class="wikitable" border: 2px solid black;"
! colspan="4" style="text-align: centre;" style="background: #328B8B;"|MOs
|-
| colspan="2" style="text-align: center;" style="background: #38A5A5;"| '''Reactants'''
| colspan="2" style="text-align: center;" style="background: #38A5A5;"| '''Transition States'''
|-
!style="background: #3DCACA;"| '''1,3-Dioxole''' !!style="background: #3DCACA;"| '''Cyclohexadiene''' !!style="background: #3DCACA;"| '''Endo-TS''' !!style="background: #3DCACA;"| '''Exo-TS'''
|-
! style="background: #D9C02F;"| HOMO+1 !!style="background: #D9C02F;"| HOMO+1 !!style="background: #D9C02F;"| HOMO+1 !!style="background: #D9C02F;"| HOMO+1
|-
| style="background: white;"| [[File:Homo_plus_one_o_ring.png|256px]] || style="background: white;"|[[File:Homo_plus_1_c_ring.png|256px]] || style="background: white;"|[[File:Exo_homo+plus1.png|256px]] ||style="background: white;"| [[File:New_exo_homoplus1.png|256px]]
|-
! style="background: #D9C02F;"|HOMO !! style="background: #D9C02F;"|HOMO!!style="background: #D9C02F;"| HOMO !!style="background: #D9C02F;"| HOMO
|-
|style="background: white;"| [[File:Homo_o_ring.png|256px]] ||style="background: white;"| [[File:Homo__c_ring.png|256px]] ||style="background: white;"| [[File:Exo_homo121.png|256px]] || style="background: white;"|[[File:New_exo_homo_eb1613.png|256px]]
|-
! style="background: #D9C02F;"|LUMO !!style="background: #D9C02F;"| LUMO !!style="background: #D9C02F;"| LUMO !!style="background: #D9C02F;"| LUMO
|-
|style="background: white;"| [[File:Lumo_o_ring.png|256px]] ||style="background: white;"| [[File:Lumo__c_ring.png|256px]] ||style="background: white;"| [[File:Exo_lumo121.png|256px]] ||style="background: white;"| [[File:New_exo_lumo_eb1613.png|256px]]
|-
!style="background: #D9C02F;"| LUMO-1!! style="background: #D9C02F;"|LUMO-1 !!style="background: #D9C02F;"| LUMO-1 !! style="background: #D9C02F;"|LUMO-1
|-
|style="background: white;"| [[File:Lumo_minus1_o_ring.png|256px]] || style="background: white;"|[[File:Lumo_minus1__c_ring.png|256px]] ||style="background: white;"| [[File:Exo_lumo_minus121.png|256px]] || style="background: white;"|[[File:New_exo_lumominus1_eb1613.png|256px]]
|- <td class=”ms-rteTableEvenCol-default” style=”width: 50%; background-color: #ffffff;”></td>
|}

=== Structure Optimisation ===

All optimized to the B3LYP/6-31G(d) level but initially with the semi-empirical PM6 method. Everything but the transition states was confirmed to be a true minima by lack of negative frequencies in the frequency calculations as shown below. Finding a single negative frequency confirms the structures to in fact be the end and eco transition states desired.
{| class="wikitable" border="1"
|+ Reactants
! style="background: #38A5A5;"| Cyclohexadiene !!style="background: #38A5A5;"| Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>CARBON_RING_FREQ23.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Carbon_ring_summary.png]]
|-
!style="background: #38A5A5;"| 1,3-Dioxole !!style="background: #38A5A5;"| Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Oxygen_ring.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Oxygen_ring_sum_eb1613.png]]
|}

{| class="wikitable" border="1"
|+ Transition State
! style="background: #38A5A5;"|Exo-TS!! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Exo_ts_99999.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Exo_ex2_ts_table.png]]
|-
! style="background: #38A5A5;"|Endo-Ts !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with PM6 level</title> <color>white</color> <size>200</size> <uploadedFileContents>ENDO_TS_OPT_631GD.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Endo_ts_summary_eb1613.png]]
|}

{| class="wikitable" border="1"
|+ Products
! style="background: #38A5A5;"|Exo-Product!! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Product_exo_631Gd.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Exo_TS_eb1613333.png]]
|-
! style="background: #38A5A5;"|Endo-Product !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with PM6 level</title> <color>white</color> <size>200</size> <uploadedFileContents>Endo_product_freqqq.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Endo_product_summmmmm.png]]
|}

Rep:Mod:Eb1613 Ex2

2016-12-02T11:13:46Z

Eb1613: /* Exercise 2 */

Page List

[[Mod:eb1613 files| The Calculations Log files can be found here]]

[[Mod:Emily1394| For main Introduction/conclusion page click here]]

[[Mod:Eb1613 Ex1| For Excerise 1 page click here]]

[[Mod:Eb1613 Ex2| For Excerise 2 page click here]]

[[Mod:Eb1613 Ex3| For Excerise 3 page click here]]

= Third Year Computational Lab Transition States - Emily Brown =

=== Exercise 2 ===

[[File:Ex2_scheme.png]]

Two different products are known to form in this Diels-Alder reaction, they are known as the endo and exo adducts.

=== Transition state 2 ===

These GIFs make it east to see where the Endo-TS has favorable secondary orbital interactions, towards the left hand side it can be seen that the oxygens p-oribtals could interact with those of the 6-carbon ring near it in a favorable manner.

{| class="wikitable" border="1"
! style="background: #38A5A5;"|Exo Transition State. Negative Frequency = -520.92 cm-1
|-
| style="background: white;"| [[File:Eb1613_exo_ts_movie.gif]]
|-
! style="background: #38A5A5;"|Endo Transition State. Negative Frequency = -528.82 cm-1
|-
| style="background: white;"| [[File:Eb1613_endo_ts_movie2.gif]]
|}

=== Thermochemistry anaylsis 2 ===

[[File:Exercise_reaction_coordin_eb1613.png]]

'''Electronic and Thermal free energies relative to reactants(KJ/mol) (2dp)'''

{| class="wikitable" border="1"
! style="background: #38A5A5;" | !! style="background: #38A5A5;" |Reactants !! style="background: #38A5A5;" |Transition state !! style="background: #38A5A5;"| Products
|-
| style="background: #38A5A5;" | Exo ||style="background: #EFECD9;" | 0 || style="background: #EFECD9;" |+159.81 ||style="background: #EFECD9;" | -67.41
|-
| style="background: #38A5A5;" | Endo || style="background: #EFECD9;" |0 || style="background: #EFECD9;" |+167.65|| style="background: #EFECD9;" |-63.77
|}

From the thermochemistry relative energy values it can be seen that the Exo product has an activation energy which is 7.84 KJ/mol lower than that of the Exo product. The Exo-Adduct is 3.64 KJ/mol more stable than the Endo-adduct making it the thermodynamicly favoured product as well as the kinetically favoured product as it has a lower energy TS.

=== MO analysis ===

This reaction and that the reaction in exercise 2 are both Diels-Alder reactions the MO diagram from exercise 1 is still valid to be used to understand/explain the MO interactions within this reaction.

{| class="wikitable" border="3"
|colspan="2" style="text-align: center;" style="background: #38A5A5;"| MO diagram for the Diels Alder Reaction in exercise 1 
|-
| style="background: white;"| [[File:Mo_diagrma_draw_eb1613.png]]
|-
|}

Using your MO diagram for the Diels-Alder reaction, locate the occupied and unoccupied orbitals associated with the DA reaction for both TSs by symmetry. Find the relevant MOs and add them to your wiki (at an appropriate angle to show symmetry). Is this a normal or inverse demand DA reaction?

Look at the HOMO of the TSs. Are there any secondary orbital interactions or sterics that might affect the reaction barrier energy (Hint: in GaussView, set the isovalue to 0.01. In Jmol, change the mo cutoff to 0.01)? The Wikipedia page on Frontier Molecular Orbital Theory has some useful information on what these secondary orbital interactions are.

From looking at the molcular orbitals below one can identify which orbitals are interacting in the Transition states. For example: it can be seen that the Endo TS LUMO is formed by the overlap of the Cyclohexadiene LUMO-1 and the 1,3-Dioxole LUMO.

{| class="wikitable" border: 2px solid black;"
! colspan="4" style="text-align: centre;" style="background: #328B8B;"|MOs
|-
| colspan="2" style="text-align: center;" style="background: #38A5A5;"| '''Reactants'''
| colspan="2" style="text-align: center;" style="background: #38A5A5;"| '''Transition States'''
|-
!style="background: #3DCACA;"| '''1,3-Dioxole''' !!style="background: #3DCACA;"| '''Cyclohexadiene''' !!style="background: #3DCACA;"| '''Endo-TS''' !!style="background: #3DCACA;"| '''Exo-TS'''
|-
! style="background: #D9C02F;"| HOMO+1 !!style="background: #D9C02F;"| HOMO+1 !!style="background: #D9C02F;"| HOMO+1 !!style="background: #D9C02F;"| HOMO+1
|-
| style="background: white;"| [[File:Homo_plus_one_o_ring.png|256px]] || style="background: white;"|[[File:Homo_plus_1_c_ring.png|256px]] || style="background: white;"|[[File:Exo_homo+plus1.png|256px]] ||style="background: white;"| [[File:New_exo_homoplus1.png|256px]]
|-
! style="background: #D9C02F;"|HOMO !! style="background: #D9C02F;"|HOMO!!style="background: #D9C02F;"| HOMO !!style="background: #D9C02F;"| HOMO
|-
|style="background: white;"| [[File:Homo_o_ring.png|256px]] ||style="background: white;"| [[File:Homo__c_ring.png|256px]] ||style="background: white;"| [[File:Exo_homo121.png|256px]] || style="background: white;"|[[File:New_exo_homo_eb1613.png|256px]]
|-
! style="background: #D9C02F;"|LUMO !!style="background: #D9C02F;"| LUMO !!style="background: #D9C02F;"| LUMO !!style="background: #D9C02F;"| LUMO
|-
|style="background: white;"| [[File:Lumo_o_ring.png|256px]] ||style="background: white;"| [[File:Lumo__c_ring.png|256px]] ||style="background: white;"| [[File:Exo_lumo121.png|256px]] ||style="background: white;"| [[File:New_exo_lumo_eb1613.png|256px]]
|-
!style="background: #D9C02F;"| LUMO-1!! style="background: #D9C02F;"|LUMO-1 !!style="background: #D9C02F;"| LUMO-1 !! style="background: #D9C02F;"|LUMO-1
|-
|style="background: white;"| [[File:Lumo_minus1_o_ring.png|256px]] || style="background: white;"|[[File:Lumo_minus1__c_ring.png|256px]] ||style="background: white;"| [[File:Exo_lumo_minus121.png|256px]] || style="background: white;"|[[File:New_exo_lumominus1_eb1613.png|256px]]
|- <td class=”ms-rteTableEvenCol-default” style=”width: 50%; background-color: #ffffff;”></td>
|}

=== Structure Optimisation ===

All optimized to the B3LYP/6-31G(d) level but initially with the semi-empirical PM6 method. Everything but the transition states was confirmed to be a true minima by lack of negative frequencies in the frequency calculations as shown below. Finding a single negative frequency confirms the structures to in fact be the end and eco transition states desired.
{| class="wikitable" border="1"
|+ Reactants
! style="background: #38A5A5;"| Cyclohexadiene !!style="background: #38A5A5;"| Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>CARBON_RING_FREQ23.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Carbon_ring_summary.png]]
|-
!style="background: #38A5A5;"| 1,3-Dioxole !!style="background: #38A5A5;"| Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Oxygen_ring.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Oxygen_ring_sum_eb1613.png]]
|}

{| class="wikitable" border="1"
|+ Transition State
! style="background: #38A5A5;"|Exo-TS!! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Exo_ts_99999.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Exo_ex2_ts_table.png]]
|-
! style="background: #38A5A5;"|Endo-Ts !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with PM6 level</title> <color>white</color> <size>200</size> <uploadedFileContents>ENDO_TS_OPT_631GD.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Endo_ts_summary_eb1613.png]]
|}

{| class="wikitable" border="1"
|+ Products
! style="background: #38A5A5;"|Exo-Product!! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Product_exo_631Gd.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Exo_TS_eb1613333.png]]
|-
! style="background: #38A5A5;"|Endo-Product !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with PM6 level</title> <color>white</color> <size>200</size> <uploadedFileContents>Endo_product_freqqq.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Endo_product_summmmmm.png]]
|}

Rep:Mod:Eb1613 Ex2

2016-12-02T11:13:07Z

Eb1613: /* Transition state 2 */

Page List

[[Mod:eb1613 files| The Calculations Log files can be found here]]

[[Mod:Emily1394| For main Introduction/conclusion page click here]]

[[Mod:Eb1613 Ex1| For Excerise 1 page click here]]

[[Mod:Eb1613 Ex2| For Excerise 2 page click here]]

[[Mod:Eb1613 Ex3| For Excerise 3 page click here]]

= Third Year Computational Lab Transition States - Emily Brown =

=== Exercise 2 ===

[[File:Ex2_scheme.png]]

=== Transition state 2 ===

These GIFs make it east to see where the Endo-TS has favorable secondary orbital interactions, towards the left hand side it can be seen that the oxygens p-oribtals could interact with those of the 6-carbon ring near it in a favorable manner.

{| class="wikitable" border="1"
! style="background: #38A5A5;"|Exo Transition State. Negative Frequency = -520.92 cm-1
|-
| style="background: white;"| [[File:Eb1613_exo_ts_movie.gif]]
|-
! style="background: #38A5A5;"|Endo Transition State. Negative Frequency = -528.82 cm-1
|-
| style="background: white;"| [[File:Eb1613_endo_ts_movie2.gif]]
|}

=== Thermochemistry anaylsis 2 ===

[[File:Exercise_reaction_coordin_eb1613.png]]

'''Electronic and Thermal free energies relative to reactants(KJ/mol) (2dp)'''

{| class="wikitable" border="1"
! style="background: #38A5A5;" | !! style="background: #38A5A5;" |Reactants !! style="background: #38A5A5;" |Transition state !! style="background: #38A5A5;"| Products
|-
| style="background: #38A5A5;" | Exo ||style="background: #EFECD9;" | 0 || style="background: #EFECD9;" |+159.81 ||style="background: #EFECD9;" | -67.41
|-
| style="background: #38A5A5;" | Endo || style="background: #EFECD9;" |0 || style="background: #EFECD9;" |+167.65|| style="background: #EFECD9;" |-63.77
|}

From the thermochemistry relative energy values it can be seen that the Exo product has an activation energy which is 7.84 KJ/mol lower than that of the Exo product. The Exo-Adduct is 3.64 KJ/mol more stable than the Endo-adduct making it the thermodynamicly favoured product as well as the kinetically favoured product as it has a lower energy TS.

=== MO analysis ===

This reaction and that the reaction in exercise 2 are both Diels-Alder reactions the MO diagram from exercise 1 is still valid to be used to understand/explain the MO interactions within this reaction.

{| class="wikitable" border="3"
|colspan="2" style="text-align: center;" style="background: #38A5A5;"| MO diagram for the Diels Alder Reaction in exercise 1 
|-
| style="background: white;"| [[File:Mo_diagrma_draw_eb1613.png]]
|-
|}

Using your MO diagram for the Diels-Alder reaction, locate the occupied and unoccupied orbitals associated with the DA reaction for both TSs by symmetry. Find the relevant MOs and add them to your wiki (at an appropriate angle to show symmetry). Is this a normal or inverse demand DA reaction?

Look at the HOMO of the TSs. Are there any secondary orbital interactions or sterics that might affect the reaction barrier energy (Hint: in GaussView, set the isovalue to 0.01. In Jmol, change the mo cutoff to 0.01)? The Wikipedia page on Frontier Molecular Orbital Theory has some useful information on what these secondary orbital interactions are.

From looking at the molcular orbitals below one can identify which orbitals are interacting in the Transition states. For example: it can be seen that the Endo TS LUMO is formed by the overlap of the Cyclohexadiene LUMO-1 and the 1,3-Dioxole LUMO.

{| class="wikitable" border: 2px solid black;"
! colspan="4" style="text-align: centre;" style="background: #328B8B;"|MOs
|-
| colspan="2" style="text-align: center;" style="background: #38A5A5;"| '''Reactants'''
| colspan="2" style="text-align: center;" style="background: #38A5A5;"| '''Transition States'''
|-
!style="background: #3DCACA;"| '''1,3-Dioxole''' !!style="background: #3DCACA;"| '''Cyclohexadiene''' !!style="background: #3DCACA;"| '''Endo-TS''' !!style="background: #3DCACA;"| '''Exo-TS'''
|-
! style="background: #D9C02F;"| HOMO+1 !!style="background: #D9C02F;"| HOMO+1 !!style="background: #D9C02F;"| HOMO+1 !!style="background: #D9C02F;"| HOMO+1
|-
| style="background: white;"| [[File:Homo_plus_one_o_ring.png|256px]] || style="background: white;"|[[File:Homo_plus_1_c_ring.png|256px]] || style="background: white;"|[[File:Exo_homo+plus1.png|256px]] ||style="background: white;"| [[File:New_exo_homoplus1.png|256px]]
|-
! style="background: #D9C02F;"|HOMO !! style="background: #D9C02F;"|HOMO!!style="background: #D9C02F;"| HOMO !!style="background: #D9C02F;"| HOMO
|-
|style="background: white;"| [[File:Homo_o_ring.png|256px]] ||style="background: white;"| [[File:Homo__c_ring.png|256px]] ||style="background: white;"| [[File:Exo_homo121.png|256px]] || style="background: white;"|[[File:New_exo_homo_eb1613.png|256px]]
|-
! style="background: #D9C02F;"|LUMO !!style="background: #D9C02F;"| LUMO !!style="background: #D9C02F;"| LUMO !!style="background: #D9C02F;"| LUMO
|-
|style="background: white;"| [[File:Lumo_o_ring.png|256px]] ||style="background: white;"| [[File:Lumo__c_ring.png|256px]] ||style="background: white;"| [[File:Exo_lumo121.png|256px]] ||style="background: white;"| [[File:New_exo_lumo_eb1613.png|256px]]
|-
!style="background: #D9C02F;"| LUMO-1!! style="background: #D9C02F;"|LUMO-1 !!style="background: #D9C02F;"| LUMO-1 !! style="background: #D9C02F;"|LUMO-1
|-
|style="background: white;"| [[File:Lumo_minus1_o_ring.png|256px]] || style="background: white;"|[[File:Lumo_minus1__c_ring.png|256px]] ||style="background: white;"| [[File:Exo_lumo_minus121.png|256px]] || style="background: white;"|[[File:New_exo_lumominus1_eb1613.png|256px]]
|- <td class=”ms-rteTableEvenCol-default” style=”width: 50%; background-color: #ffffff;”></td>
|}

=== Structure Optimisation ===

All optimized to the B3LYP/6-31G(d) level but initially with the semi-empirical PM6 method. Everything but the transition states was confirmed to be a true minima by lack of negative frequencies in the frequency calculations as shown below. Finding a single negative frequency confirms the structures to in fact be the end and eco transition states desired.
{| class="wikitable" border="1"
|+ Reactants
! style="background: #38A5A5;"| Cyclohexadiene !!style="background: #38A5A5;"| Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>CARBON_RING_FREQ23.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Carbon_ring_summary.png]]
|-
!style="background: #38A5A5;"| 1,3-Dioxole !!style="background: #38A5A5;"| Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Oxygen_ring.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Oxygen_ring_sum_eb1613.png]]
|}

{| class="wikitable" border="1"
|+ Transition State
! style="background: #38A5A5;"|Exo-TS!! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Exo_ts_99999.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Exo_ex2_ts_table.png]]
|-
! style="background: #38A5A5;"|Endo-Ts !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with PM6 level</title> <color>white</color> <size>200</size> <uploadedFileContents>ENDO_TS_OPT_631GD.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Endo_ts_summary_eb1613.png]]
|}

{| class="wikitable" border="1"
|+ Products
! style="background: #38A5A5;"|Exo-Product!! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Product_exo_631Gd.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Exo_TS_eb1613333.png]]
|-
! style="background: #38A5A5;"|Endo-Product !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with PM6 level</title> <color>white</color> <size>200</size> <uploadedFileContents>Endo_product_freqqq.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Endo_product_summmmmm.png]]
|}

Rep:Mod:Eb1613 Ex3

2016-12-02T11:10:07Z

Eb1613: /* Transition states */

Page List

[[Mod:eb1613 files| The Calculations Log files can be found here]]

[[Mod:Emily1394| For main Introduction/conclusion page click here]]

[[Mod:Eb1613 Ex1| For Excerise 1 page click here]]

[[Mod:Eb1613 Ex2| For Excerise 2 page click here]]

[[Mod:Eb1613 Ex3| For Excerise 3 page click here]]

= Third Year Computational Lab Transition States - Emily Brown =

=== Exercise 3 ===

[[File:Exercise2_reaction_emily.png]]

Both cheletropic and Diels-Alder reactions are possible for the above reactants.

Initially the structures were optimized to the semi-empirical PM6 level and later the geometries were re-optimised to the DFT 6-31G(d)/b3LYP level of calculation. The reactants were aligned in different conformations and certain bonds were frozen to find the three transition states shown below. Every structure given has been optimized to the higher accuracy DFT 6-31G(d)/b3LYP level.

Unfortunately there was not enough time to investigate the other cis-butadiene fragment successfully.

==== Transition states ====

Below gif files are given to show the negative frequency vibration for the transition states which were located. The cheleotropic TS had the largest negative frequency values of the three.

{| class="wikitable" border="1"
! style="background: #38A5A5;" | Exo Transition State. Negative Frequency = -198.65 cm-1
|-
|style="background: white;" | [[File:Diels_alder_ts_1_movie.gif]]
|-
! style="background: #38A5A5;" | Endo Transition State. Negative Frequency = -200.42 cm-1
|-
|style="background: white;" | [[File:Diels_alder_ts_2_movie.gif]]
|-
! style="background: #38A5A5;" | Cheletropic Transition State. Negative Frequency = -221.18 cm-1
|-
|style="background: white;" | [[File:Chele_TS_movie_eb1613.gif]]
|}

==== Thermochemistry anaylsis ====

The energy profile was first plotted using excel and then using chemdraw to highlight the differences between the endo and exo paths. The endo-adduct has the lowest energy making it the thermodynamically preferred product. The cheleotropic transition state is of the highest energy and so is the least kinetically favored reaction path.

{| class="wikitable" border="1"
|-
| style="background: white;" | [[File:Energy profile ex3 eb1613.png]] || style="background: white;" | [[File:Reaction_path_ex3_eb1613.png]]
|}

Energy values given relative to the reactants in KJ/mol, from the values the Endo route appears to be the preferred route.

{| class="wikitable" border="1"
!style="background: #38A5A5;" | !!style="background: #38A5A5;" | Reactants !! style="background: #38A5A5;" | Transition state !! style="background: #38A5A5;" | Products
|-
| style="background: #38A5A5;" | Endo ||style="background: #EFECD9;" | 0 || style="background: #EFECD9;" |+46.17992 ||style="background: #EFECD9;" | -75.183818
|-
| style="background: #38A5A5;" | Exo ||style="background: #EFECD9;" | 0 ||style="background: #EFECD9;" | +46.23768|| style="background: #EFECD9;" |-73.886821
|-
| style="background: #38A5A5;" | Cheletropic||style="background: #EFECD9;" | 0 ||style="background: #EFECD9;" | +63.05663|| style="background: #EFECD9;" |-63.9650565
|}

Raw values with KJ/mol given to the nearest whole number

{| class="wikitable" border="1"
!style="background: #38A5A5;" | Structure!! style="background: #38A5A5;" | E( Hartrees) !! style="background: #38A5A5;" | E(KJ/mol)
|-
| style="background: #38A5A5;" | Diene ||style="background: #EFECD9;" | -309.504492|| style="background: #EFECD9;" |-812604
|-
| style="background: #38A5A5;" | Sulfur||style="background: #EFECD9;" | -548.604917|| style="background: #EFECD9;" |-1440362
|-
| style="background: #38A5A5;" | Sum of Reactants ||style="background: #EFECD9;" | -858.109409|| style="background: #EFECD9;" |-2252966
|-
| style="background: #38A5A5;" | Endo TS||style="background: #EFECD9;" | -858.09182|| style="background: #EFECD9;" |-2252920
|-
| style="background: #38A5A5;" | Endo Product||style="background: #EFECD9;" | -858.138045|| style="background: #EFECD9;" |-2253041
|-
| style="background: #38A5A5;" | Exo TS||style="background: #EFECD9;" | -858.091798|| style="background: #EFECD9;" |-2252920
|-
| style="background: #38A5A5;" | Exo Product||style="background: #EFECD9;" | -858.137551|| style="background: #EFECD9;" |-2253040
|-
| style="background: #38A5A5;" | Chele TS||style="background: #EFECD9;" | -858.085392|| style="background: #EFECD9;" |-2252903
|-
| style="background: #38A5A5;" | Chele Product||style="background: #EFECD9;" | -858.133772|| style="background: #EFECD9;" |-2253030
|}

Looking at the energy reaction barriers it can be seen that the Endo transition state is slightly below the cheletropic value making it the preferred reaction coordinate. however the value for the end transition state is only slightly below that for the cheletropic transition state and the calculation percentage errors/accuracies could effect this ordering.

==== IRC analysis ====

During the reaction the carbon-carbon bond lengths all become styled as 1.5 bond order suggesting an aromatic element to the ring. The IRC calculations proved very challenging throughout this lab and as such the ENDO TS IRC path is recorded in reverse and shows the detachment of the sulfur oxide molecule. Using the IRC plots it can be seen that the reaction proceed without any other intermediates or transition states as demonstrated by the smooth curve of the graph and lack of other turning points in the gradient.

{| class="wikitable" border="1"
! colspan="2" style="text-align: center;" style="background: #38A5A5;" |Cheletropic IRC path
|-
|style="background: white;" | [[File:Chele_IRC_movie.gif]] || style="background: white;" | [[File:Irc_chele_eb1613.png]]
|-
! colspan="2" style="text-align: center;" style="background: #38A5A5;" | Exo IRC path
|-
|style="background: white;" | [[File:Exo_IRC_movie_eb1613.gif]] || style="background: white;" | [[File:Exo_IRC.png]]
|-
!colspan="2" style="text-align: center;" style="background: #38A5A5;" | Endo IRC path
|-
|style="background: white;" | [[File:Endo_IRC_movie_eb1613.gif]] || style="background: white;" | [[File:IRC_path_ex3.png]]
|}

==== Structure files ====

{| class="wikitable" border="1"
|+ Structures
! style="background: #38A5A5;"|sulfur dioxde !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>SULFUR_FREQ_631GD.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Sulfur_eb1613_table.png]]
|-
! style="background: #38A5A5;"|Xylylene Diene !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Diene_mandisp1pt0.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Diene_mandisp1pt0_ex3_eb1613.png]]
|-
!style="background: #38A5A5;"| Diels-Alder Endo Transition state !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>DIELSALDER2_TS_FOUND_631GD_REOPT.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Diels_alder_ts_summary1_eb1613.png]]
|-
! style="background: #38A5A5;"|Diels-Alder Exo Transition state !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Opt_to_ts_631gd.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Da2_ts_ex3.png]]
|-
! style="background: #38A5A5;"|Cheletropic Transition state !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>CHELE_TS_TRY_631GD_FREQ.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Chele_ts_summary.png]]
|-
! style="background: #38A5A5;"|Diels-Alder Endo Product !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>DIELS_ALDER_631GD.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Diels_alder_product1ex3.png]]
|-
! style="background: #38A5A5;"|Diels-Alder Exo Product !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Diels_alder_2_631Gd.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Diels_alder2_product_ex3_eb1613.png]]
|-
! style="background: #38A5A5;"|Cheletropic Product !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Product_chele_mandisp1pt0.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Chele_product_eb1613.png ]]
|}

Rep:Mod:Eb1613 Ex3

2016-12-02T11:09:16Z

Eb1613: /* Thermochemistry anaylsis */

Page List

[[Mod:eb1613 files| The Calculations Log files can be found here]]

[[Mod:Emily1394| For main Introduction/conclusion page click here]]

[[Mod:Eb1613 Ex1| For Excerise 1 page click here]]

[[Mod:Eb1613 Ex2| For Excerise 2 page click here]]

[[Mod:Eb1613 Ex3| For Excerise 3 page click here]]

= Third Year Computational Lab Transition States - Emily Brown =

=== Exercise 3 ===

[[File:Exercise2_reaction_emily.png]]

Both cheletropic and Diels-Alder reactions are possible for the above reactants.

Initially the structures were optimized to the semi-empirical PM6 level and later the geometries were re-optimised to the DFT 6-31G(d)/b3LYP level of calculation. The reactants were aligned in different conformations and certain bonds were frozen to find the three transition states shown below. Every structure given has been optimized to the higher accuracy DFT 6-31G(d)/b3LYP level.

Unfortunately there was not enough time to investigate the other cis-butadiene fragment successfully.

==== Transition states ====

Below gif files are given to show the negative frequency vibration for the transition states which were located.

{| class="wikitable" border="1"
! style="background: #38A5A5;" | Exo Transition State. Negative Frequency = -198.65 cm-1
|-
|style="background: white;" | [[File:Diels_alder_ts_1_movie.gif]]
|-
! style="background: #38A5A5;" | Endo Transition State. Negative Frequency = -200.42 cm-1
|-
|style="background: white;" | [[File:Diels_alder_ts_2_movie.gif]]
|-
! style="background: #38A5A5;" | Cheletropic Transition State. Negative Frequency = -221.18 cm-1
|-
|style="background: white;" | [[File:Chele_TS_movie_eb1613.gif]]
|}

==== Thermochemistry anaylsis ====

The energy profile was first plotted using excel and then using chemdraw to highlight the differences between the endo and exo paths. The endo-adduct has the lowest energy making it the thermodynamically preferred product. The cheleotropic transition state is of the highest energy and so is the least kinetically favored reaction path.

{| class="wikitable" border="1"
|-
| style="background: white;" | [[File:Energy profile ex3 eb1613.png]] || style="background: white;" | [[File:Reaction_path_ex3_eb1613.png]]
|}

Energy values given relative to the reactants in KJ/mol, from the values the Endo route appears to be the preferred route.

{| class="wikitable" border="1"
!style="background: #38A5A5;" | !!style="background: #38A5A5;" | Reactants !! style="background: #38A5A5;" | Transition state !! style="background: #38A5A5;" | Products
|-
| style="background: #38A5A5;" | Endo ||style="background: #EFECD9;" | 0 || style="background: #EFECD9;" |+46.17992 ||style="background: #EFECD9;" | -75.183818
|-
| style="background: #38A5A5;" | Exo ||style="background: #EFECD9;" | 0 ||style="background: #EFECD9;" | +46.23768|| style="background: #EFECD9;" |-73.886821
|-
| style="background: #38A5A5;" | Cheletropic||style="background: #EFECD9;" | 0 ||style="background: #EFECD9;" | +63.05663|| style="background: #EFECD9;" |-63.9650565
|}

Raw values with KJ/mol given to the nearest whole number

{| class="wikitable" border="1"
!style="background: #38A5A5;" | Structure!! style="background: #38A5A5;" | E( Hartrees) !! style="background: #38A5A5;" | E(KJ/mol)
|-
| style="background: #38A5A5;" | Diene ||style="background: #EFECD9;" | -309.504492|| style="background: #EFECD9;" |-812604
|-
| style="background: #38A5A5;" | Sulfur||style="background: #EFECD9;" | -548.604917|| style="background: #EFECD9;" |-1440362
|-
| style="background: #38A5A5;" | Sum of Reactants ||style="background: #EFECD9;" | -858.109409|| style="background: #EFECD9;" |-2252966
|-
| style="background: #38A5A5;" | Endo TS||style="background: #EFECD9;" | -858.09182|| style="background: #EFECD9;" |-2252920
|-
| style="background: #38A5A5;" | Endo Product||style="background: #EFECD9;" | -858.138045|| style="background: #EFECD9;" |-2253041
|-
| style="background: #38A5A5;" | Exo TS||style="background: #EFECD9;" | -858.091798|| style="background: #EFECD9;" |-2252920
|-
| style="background: #38A5A5;" | Exo Product||style="background: #EFECD9;" | -858.137551|| style="background: #EFECD9;" |-2253040
|-
| style="background: #38A5A5;" | Chele TS||style="background: #EFECD9;" | -858.085392|| style="background: #EFECD9;" |-2252903
|-
| style="background: #38A5A5;" | Chele Product||style="background: #EFECD9;" | -858.133772|| style="background: #EFECD9;" |-2253030
|}

Looking at the energy reaction barriers it can be seen that the Endo transition state is slightly below the cheletropic value making it the preferred reaction coordinate. however the value for the end transition state is only slightly below that for the cheletropic transition state and the calculation percentage errors/accuracies could effect this ordering.

==== IRC analysis ====

During the reaction the carbon-carbon bond lengths all become styled as 1.5 bond order suggesting an aromatic element to the ring. The IRC calculations proved very challenging throughout this lab and as such the ENDO TS IRC path is recorded in reverse and shows the detachment of the sulfur oxide molecule. Using the IRC plots it can be seen that the reaction proceed without any other intermediates or transition states as demonstrated by the smooth curve of the graph and lack of other turning points in the gradient.

{| class="wikitable" border="1"
! colspan="2" style="text-align: center;" style="background: #38A5A5;" |Cheletropic IRC path
|-
|style="background: white;" | [[File:Chele_IRC_movie.gif]] || style="background: white;" | [[File:Irc_chele_eb1613.png]]
|-
! colspan="2" style="text-align: center;" style="background: #38A5A5;" | Exo IRC path
|-
|style="background: white;" | [[File:Exo_IRC_movie_eb1613.gif]] || style="background: white;" | [[File:Exo_IRC.png]]
|-
!colspan="2" style="text-align: center;" style="background: #38A5A5;" | Endo IRC path
|-
|style="background: white;" | [[File:Endo_IRC_movie_eb1613.gif]] || style="background: white;" | [[File:IRC_path_ex3.png]]
|}

==== Structure files ====

{| class="wikitable" border="1"
|+ Structures
! style="background: #38A5A5;"|sulfur dioxde !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>SULFUR_FREQ_631GD.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Sulfur_eb1613_table.png]]
|-
! style="background: #38A5A5;"|Xylylene Diene !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Diene_mandisp1pt0.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Diene_mandisp1pt0_ex3_eb1613.png]]
|-
!style="background: #38A5A5;"| Diels-Alder Endo Transition state !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>DIELSALDER2_TS_FOUND_631GD_REOPT.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Diels_alder_ts_summary1_eb1613.png]]
|-
! style="background: #38A5A5;"|Diels-Alder Exo Transition state !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Opt_to_ts_631gd.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Da2_ts_ex3.png]]
|-
! style="background: #38A5A5;"|Cheletropic Transition state !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>CHELE_TS_TRY_631GD_FREQ.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Chele_ts_summary.png]]
|-
! style="background: #38A5A5;"|Diels-Alder Endo Product !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>DIELS_ALDER_631GD.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Diels_alder_product1ex3.png]]
|-
! style="background: #38A5A5;"|Diels-Alder Exo Product !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Diels_alder_2_631Gd.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Diels_alder2_product_ex3_eb1613.png]]
|-
! style="background: #38A5A5;"|Cheletropic Product !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Product_chele_mandisp1pt0.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Chele_product_eb1613.png ]]
|}

Rep:Mod:Eb1613 Ex3

2016-12-02T11:08:20Z

Eb1613: /* Thermochemistry anaylsis */

Page List

[[Mod:eb1613 files| The Calculations Log files can be found here]]

[[Mod:Emily1394| For main Introduction/conclusion page click here]]

[[Mod:Eb1613 Ex1| For Excerise 1 page click here]]

[[Mod:Eb1613 Ex2| For Excerise 2 page click here]]

[[Mod:Eb1613 Ex3| For Excerise 3 page click here]]

= Third Year Computational Lab Transition States - Emily Brown =

=== Exercise 3 ===

[[File:Exercise2_reaction_emily.png]]

Both cheletropic and Diels-Alder reactions are possible for the above reactants.

Initially the structures were optimized to the semi-empirical PM6 level and later the geometries were re-optimised to the DFT 6-31G(d)/b3LYP level of calculation. The reactants were aligned in different conformations and certain bonds were frozen to find the three transition states shown below. Every structure given has been optimized to the higher accuracy DFT 6-31G(d)/b3LYP level.

Unfortunately there was not enough time to investigate the other cis-butadiene fragment successfully.

==== Transition states ====

Below gif files are given to show the negative frequency vibration for the transition states which were located.

{| class="wikitable" border="1"
! style="background: #38A5A5;" | Exo Transition State. Negative Frequency = -198.65 cm-1
|-
|style="background: white;" | [[File:Diels_alder_ts_1_movie.gif]]
|-
! style="background: #38A5A5;" | Endo Transition State. Negative Frequency = -200.42 cm-1
|-
|style="background: white;" | [[File:Diels_alder_ts_2_movie.gif]]
|-
! style="background: #38A5A5;" | Cheletropic Transition State. Negative Frequency = -221.18 cm-1
|-
|style="background: white;" | [[File:Chele_TS_movie_eb1613.gif]]
|}

==== Thermochemistry anaylsis ====

The energy profile was first plotted using excel and then using chemdraw to highlight the differences between the endo and exo paths. The endo-adduct has the lowest energy making it the thermodynamically preferred product.

{| class="wikitable" border="1"
|-
| style="background: white;" | [[File:Energy profile ex3 eb1613.png]] || style="background: white;" | [[File:Reaction_path_ex3_eb1613.png]]
|}

Energy values given relative to the reactants in KJ/mol, from the values the Endo route appears to be the preferred route.

{| class="wikitable" border="1"
!style="background: #38A5A5;" | !!style="background: #38A5A5;" | Reactants !! style="background: #38A5A5;" | Transition state !! style="background: #38A5A5;" | Products
|-
| style="background: #38A5A5;" | Endo ||style="background: #EFECD9;" | 0 || style="background: #EFECD9;" |+46.17992 ||style="background: #EFECD9;" | -75.183818
|-
| style="background: #38A5A5;" | Exo ||style="background: #EFECD9;" | 0 ||style="background: #EFECD9;" | +46.23768|| style="background: #EFECD9;" |-73.886821
|-
| style="background: #38A5A5;" | Cheletropic||style="background: #EFECD9;" | 0 ||style="background: #EFECD9;" | +63.05663|| style="background: #EFECD9;" |-63.9650565
|}

Raw values with KJ/mol given to the nearest whole number

{| class="wikitable" border="1"
!style="background: #38A5A5;" | Structure!! style="background: #38A5A5;" | E( Hartrees) !! style="background: #38A5A5;" | E(KJ/mol)
|-
| style="background: #38A5A5;" | Diene ||style="background: #EFECD9;" | -309.504492|| style="background: #EFECD9;" |-812604
|-
| style="background: #38A5A5;" | Sulfur||style="background: #EFECD9;" | -548.604917|| style="background: #EFECD9;" |-1440362
|-
| style="background: #38A5A5;" | Sum of Reactants ||style="background: #EFECD9;" | -858.109409|| style="background: #EFECD9;" |-2252966
|-
| style="background: #38A5A5;" | Endo TS||style="background: #EFECD9;" | -858.09182|| style="background: #EFECD9;" |-2252920
|-
| style="background: #38A5A5;" | Endo Product||style="background: #EFECD9;" | -858.138045|| style="background: #EFECD9;" |-2253041
|-
| style="background: #38A5A5;" | Exo TS||style="background: #EFECD9;" | -858.091798|| style="background: #EFECD9;" |-2252920
|-
| style="background: #38A5A5;" | Exo Product||style="background: #EFECD9;" | -858.137551|| style="background: #EFECD9;" |-2253040
|-
| style="background: #38A5A5;" | Chele TS||style="background: #EFECD9;" | -858.085392|| style="background: #EFECD9;" |-2252903
|-
| style="background: #38A5A5;" | Chele Product||style="background: #EFECD9;" | -858.133772|| style="background: #EFECD9;" |-2253030
|}

Looking at the energy reaction barriers it can be seen that the Endo transition state is slightly below the cheletropic value making it the preferred reaction coordinate. however the value for the end transition state is only slightly below that for the cheletropic transition state and the calculation percentage errors/accuracies could effect this ordering.

==== IRC analysis ====

During the reaction the carbon-carbon bond lengths all become styled as 1.5 bond order suggesting an aromatic element to the ring. The IRC calculations proved very challenging throughout this lab and as such the ENDO TS IRC path is recorded in reverse and shows the detachment of the sulfur oxide molecule. Using the IRC plots it can be seen that the reaction proceed without any other intermediates or transition states as demonstrated by the smooth curve of the graph and lack of other turning points in the gradient.

{| class="wikitable" border="1"
! colspan="2" style="text-align: center;" style="background: #38A5A5;" |Cheletropic IRC path
|-
|style="background: white;" | [[File:Chele_IRC_movie.gif]] || style="background: white;" | [[File:Irc_chele_eb1613.png]]
|-
! colspan="2" style="text-align: center;" style="background: #38A5A5;" | Exo IRC path
|-
|style="background: white;" | [[File:Exo_IRC_movie_eb1613.gif]] || style="background: white;" | [[File:Exo_IRC.png]]
|-
!colspan="2" style="text-align: center;" style="background: #38A5A5;" | Endo IRC path
|-
|style="background: white;" | [[File:Endo_IRC_movie_eb1613.gif]] || style="background: white;" | [[File:IRC_path_ex3.png]]
|}

==== Structure files ====

{| class="wikitable" border="1"
|+ Structures
! style="background: #38A5A5;"|sulfur dioxde !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>SULFUR_FREQ_631GD.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Sulfur_eb1613_table.png]]
|-
! style="background: #38A5A5;"|Xylylene Diene !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Diene_mandisp1pt0.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Diene_mandisp1pt0_ex3_eb1613.png]]
|-
!style="background: #38A5A5;"| Diels-Alder Endo Transition state !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>DIELSALDER2_TS_FOUND_631GD_REOPT.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Diels_alder_ts_summary1_eb1613.png]]
|-
! style="background: #38A5A5;"|Diels-Alder Exo Transition state !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Opt_to_ts_631gd.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Da2_ts_ex3.png]]
|-
! style="background: #38A5A5;"|Cheletropic Transition state !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>CHELE_TS_TRY_631GD_FREQ.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Chele_ts_summary.png]]
|-
! style="background: #38A5A5;"|Diels-Alder Endo Product !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>DIELS_ALDER_631GD.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Diels_alder_product1ex3.png]]
|-
! style="background: #38A5A5;"|Diels-Alder Exo Product !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Diels_alder_2_631Gd.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Diels_alder2_product_ex3_eb1613.png]]
|-
! style="background: #38A5A5;"|Cheletropic Product !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Product_chele_mandisp1pt0.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Chele_product_eb1613.png ]]
|}

File:Reaction path ex3 eb1613.png

2016-12-02T11:08:11Z

Eb1613:

Rep:Mod:Eb1613 Ex3

2016-12-02T11:06:38Z

Eb1613: /* Thermochemistry anaylsis */

Page List

[[Mod:eb1613 files| The Calculations Log files can be found here]]

[[Mod:Emily1394| For main Introduction/conclusion page click here]]

[[Mod:Eb1613 Ex1| For Excerise 1 page click here]]

[[Mod:Eb1613 Ex2| For Excerise 2 page click here]]

[[Mod:Eb1613 Ex3| For Excerise 3 page click here]]

= Third Year Computational Lab Transition States - Emily Brown =

=== Exercise 3 ===

[[File:Exercise2_reaction_emily.png]]

Both cheletropic and Diels-Alder reactions are possible for the above reactants.

Initially the structures were optimized to the semi-empirical PM6 level and later the geometries were re-optimised to the DFT 6-31G(d)/b3LYP level of calculation. The reactants were aligned in different conformations and certain bonds were frozen to find the three transition states shown below. Every structure given has been optimized to the higher accuracy DFT 6-31G(d)/b3LYP level.

Unfortunately there was not enough time to investigate the other cis-butadiene fragment successfully.

==== Transition states ====

Below gif files are given to show the negative frequency vibration for the transition states which were located.

{| class="wikitable" border="1"
! style="background: #38A5A5;" | Exo Transition State. Negative Frequency = -198.65 cm-1
|-
|style="background: white;" | [[File:Diels_alder_ts_1_movie.gif]]
|-
! style="background: #38A5A5;" | Endo Transition State. Negative Frequency = -200.42 cm-1
|-
|style="background: white;" | [[File:Diels_alder_ts_2_movie.gif]]
|-
! style="background: #38A5A5;" | Cheletropic Transition State. Negative Frequency = -221.18 cm-1
|-
|style="background: white;" | [[File:Chele_TS_movie_eb1613.gif]]
|}

==== Thermochemistry anaylsis ====

The energy profile was first plotted using excel and then using chemdraw to highlight the differences between the endo and exo paths. The endo-adduct has the lowest energy making it the thermodynamically preferred product.

{| class="wikitable" border="1"
|-
| style="background: white;" | [[File:Energy profile ex3 eb1613.png]] || style="background: white;" | [[File:Screen_Shot_2016-12-01_at_21.54.33.png]]
|}

Energy values given relative to the reactants in KJ/mol, from the values the Endo route appears to be the preferred route.

{| class="wikitable" border="1"
!style="background: #38A5A5;" | !!style="background: #38A5A5;" | Reactants !! style="background: #38A5A5;" | Transition state !! style="background: #38A5A5;" | Products
|-
| style="background: #38A5A5;" | Endo ||style="background: #EFECD9;" | 0 || style="background: #EFECD9;" |+46.17992 ||style="background: #EFECD9;" | -75.183818
|-
| style="background: #38A5A5;" | Exo ||style="background: #EFECD9;" | 0 ||style="background: #EFECD9;" | +46.23768|| style="background: #EFECD9;" |-73.886821
|-
| style="background: #38A5A5;" | Cheletropic||style="background: #EFECD9;" | 0 ||style="background: #EFECD9;" | +63.05663|| style="background: #EFECD9;" |-63.9650565
|}

Raw values with KJ/mol given to the nearest whole number

{| class="wikitable" border="1"
!style="background: #38A5A5;" | Structure!! style="background: #38A5A5;" | E( Hartrees) !! style="background: #38A5A5;" | E(KJ/mol)
|-
| style="background: #38A5A5;" | Diene ||style="background: #EFECD9;" | -309.504492|| style="background: #EFECD9;" |-812604
|-
| style="background: #38A5A5;" | Sulfur||style="background: #EFECD9;" | -548.604917|| style="background: #EFECD9;" |-1440362
|-
| style="background: #38A5A5;" | Sum of Reactants ||style="background: #EFECD9;" | -858.109409|| style="background: #EFECD9;" |-2252966
|-
| style="background: #38A5A5;" | Endo TS||style="background: #EFECD9;" | -858.09182|| style="background: #EFECD9;" |-2252920
|-
| style="background: #38A5A5;" | Endo Product||style="background: #EFECD9;" | -858.138045|| style="background: #EFECD9;" |-2253041
|-
| style="background: #38A5A5;" | Exo TS||style="background: #EFECD9;" | -858.091798|| style="background: #EFECD9;" |-2252920
|-
| style="background: #38A5A5;" | Exo Product||style="background: #EFECD9;" | -858.137551|| style="background: #EFECD9;" |-2253040
|-
| style="background: #38A5A5;" | Chele TS||style="background: #EFECD9;" | -858.085392|| style="background: #EFECD9;" |-2252903
|-
| style="background: #38A5A5;" | Chele Product||style="background: #EFECD9;" | -858.133772|| style="background: #EFECD9;" |-2253030
|}

Looking at the energy reaction barriers it can be seen that the Endo transition state is slightly below the cheletropic value making it the preferred reaction coordinate. however the value for the end transition state is only slightly below that for the cheletropic transition state and the calculation percentage errors/accuracies could effect this ordering.

==== IRC analysis ====

During the reaction the carbon-carbon bond lengths all become styled as 1.5 bond order suggesting an aromatic element to the ring. The IRC calculations proved very challenging throughout this lab and as such the ENDO TS IRC path is recorded in reverse and shows the detachment of the sulfur oxide molecule. Using the IRC plots it can be seen that the reaction proceed without any other intermediates or transition states as demonstrated by the smooth curve of the graph and lack of other turning points in the gradient.

{| class="wikitable" border="1"
! colspan="2" style="text-align: center;" style="background: #38A5A5;" |Cheletropic IRC path
|-
|style="background: white;" | [[File:Chele_IRC_movie.gif]] || style="background: white;" | [[File:Irc_chele_eb1613.png]]
|-
! colspan="2" style="text-align: center;" style="background: #38A5A5;" | Exo IRC path
|-
|style="background: white;" | [[File:Exo_IRC_movie_eb1613.gif]] || style="background: white;" | [[File:Exo_IRC.png]]
|-
!colspan="2" style="text-align: center;" style="background: #38A5A5;" | Endo IRC path
|-
|style="background: white;" | [[File:Endo_IRC_movie_eb1613.gif]] || style="background: white;" | [[File:IRC_path_ex3.png]]
|}

==== Structure files ====

{| class="wikitable" border="1"
|+ Structures
! style="background: #38A5A5;"|sulfur dioxde !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>SULFUR_FREQ_631GD.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Sulfur_eb1613_table.png]]
|-
! style="background: #38A5A5;"|Xylylene Diene !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Diene_mandisp1pt0.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Diene_mandisp1pt0_ex3_eb1613.png]]
|-
!style="background: #38A5A5;"| Diels-Alder Endo Transition state !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>DIELSALDER2_TS_FOUND_631GD_REOPT.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Diels_alder_ts_summary1_eb1613.png]]
|-
! style="background: #38A5A5;"|Diels-Alder Exo Transition state !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Opt_to_ts_631gd.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Da2_ts_ex3.png]]
|-
! style="background: #38A5A5;"|Cheletropic Transition state !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>CHELE_TS_TRY_631GD_FREQ.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Chele_ts_summary.png]]
|-
! style="background: #38A5A5;"|Diels-Alder Endo Product !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>DIELS_ALDER_631GD.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Diels_alder_product1ex3.png]]
|-
! style="background: #38A5A5;"|Diels-Alder Exo Product !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Diels_alder_2_631Gd.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Diels_alder2_product_ex3_eb1613.png]]
|-
! style="background: #38A5A5;"|Cheletropic Product !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Product_chele_mandisp1pt0.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Chele_product_eb1613.png ]]
|}

Rep:Mod:eb1613 files

2016-12-02T11:05:31Z

Eb1613: /* Log Files */

Rep:Mod:Eb1613 Ex2

2016-12-02T11:04:41Z

Eb1613: /* MO analysis */

Page List

[[Mod:eb1613 files| The Calculations Log files can be found here]]

[[Mod:Emily1394| For main Introduction/conclusion page click here]]

[[Mod:Eb1613 Ex1| For Excerise 1 page click here]]

[[Mod:Eb1613 Ex2| For Excerise 2 page click here]]

[[Mod:Eb1613 Ex3| For Excerise 3 page click here]]

= Third Year Computational Lab Transition States - Emily Brown =

=== Exercise 2 ===

[[File:Ex2_scheme.png]]

=== Transition state 2 ===

{| class="wikitable" border="1"
! style="background: #38A5A5;"|Exo Transition State. Negative Frequency = -520.92 cm-1
|-
| style="background: white;"| [[File:Eb1613_exo_ts_movie.gif]]
|-
! style="background: #38A5A5;"|Endo Transition State. Negative Frequency = -528.82 cm-1
|-
| style="background: white;"| [[File:Eb1613_endo_ts_movie2.gif]]
|}

=== Thermochemistry anaylsis 2 ===

[[File:Exercise_reaction_coordin_eb1613.png]]

'''Electronic and Thermal free energies relative to reactants(KJ/mol) (2dp)'''

{| class="wikitable" border="1"
! style="background: #38A5A5;" | !! style="background: #38A5A5;" |Reactants !! style="background: #38A5A5;" |Transition state !! style="background: #38A5A5;"| Products
|-
| style="background: #38A5A5;" | Exo ||style="background: #EFECD9;" | 0 || style="background: #EFECD9;" |+159.81 ||style="background: #EFECD9;" | -67.41
|-
| style="background: #38A5A5;" | Endo || style="background: #EFECD9;" |0 || style="background: #EFECD9;" |+167.65|| style="background: #EFECD9;" |-63.77
|}

From the thermochemistry relative energy values it can be seen that the Exo product has an activation energy which is 7.84 KJ/mol lower than that of the Exo product. The Exo-Adduct is 3.64 KJ/mol more stable than the Endo-adduct making it the thermodynamicly favoured product as well as the kinetically favoured product as it has a lower energy TS.

=== MO analysis ===

This reaction and that the reaction in exercise 2 are both Diels-Alder reactions the MO diagram from exercise 1 is still valid to be used to understand/explain the MO interactions within this reaction.

{| class="wikitable" border="3"
|colspan="2" style="text-align: center;" style="background: #38A5A5;"| MO diagram for the Diels Alder Reaction in exercise 1 
|-
| style="background: white;"| [[File:Mo_diagrma_draw_eb1613.png]]
|-
|}

Using your MO diagram for the Diels-Alder reaction, locate the occupied and unoccupied orbitals associated with the DA reaction for both TSs by symmetry. Find the relevant MOs and add them to your wiki (at an appropriate angle to show symmetry). Is this a normal or inverse demand DA reaction?

Look at the HOMO of the TSs. Are there any secondary orbital interactions or sterics that might affect the reaction barrier energy (Hint: in GaussView, set the isovalue to 0.01. In Jmol, change the mo cutoff to 0.01)? The Wikipedia page on Frontier Molecular Orbital Theory has some useful information on what these secondary orbital interactions are.

From looking at the molcular orbitals below one can identify which orbitals are interacting in the Transition states. For example: it can be seen that the Endo TS LUMO is formed by the overlap of the Cyclohexadiene LUMO-1 and the 1,3-Dioxole LUMO.

{| class="wikitable" border: 2px solid black;"
! colspan="4" style="text-align: centre;" style="background: #328B8B;"|MOs
|-
| colspan="2" style="text-align: center;" style="background: #38A5A5;"| '''Reactants'''
| colspan="2" style="text-align: center;" style="background: #38A5A5;"| '''Transition States'''
|-
!style="background: #3DCACA;"| '''1,3-Dioxole''' !!style="background: #3DCACA;"| '''Cyclohexadiene''' !!style="background: #3DCACA;"| '''Endo-TS''' !!style="background: #3DCACA;"| '''Exo-TS'''
|-
! style="background: #D9C02F;"| HOMO+1 !!style="background: #D9C02F;"| HOMO+1 !!style="background: #D9C02F;"| HOMO+1 !!style="background: #D9C02F;"| HOMO+1
|-
| style="background: white;"| [[File:Homo_plus_one_o_ring.png|256px]] || style="background: white;"|[[File:Homo_plus_1_c_ring.png|256px]] || style="background: white;"|[[File:Exo_homo+plus1.png|256px]] ||style="background: white;"| [[File:New_exo_homoplus1.png|256px]]
|-
! style="background: #D9C02F;"|HOMO !! style="background: #D9C02F;"|HOMO!!style="background: #D9C02F;"| HOMO !!style="background: #D9C02F;"| HOMO
|-
|style="background: white;"| [[File:Homo_o_ring.png|256px]] ||style="background: white;"| [[File:Homo__c_ring.png|256px]] ||style="background: white;"| [[File:Exo_homo121.png|256px]] || style="background: white;"|[[File:New_exo_homo_eb1613.png|256px]]
|-
! style="background: #D9C02F;"|LUMO !!style="background: #D9C02F;"| LUMO !!style="background: #D9C02F;"| LUMO !!style="background: #D9C02F;"| LUMO
|-
|style="background: white;"| [[File:Lumo_o_ring.png|256px]] ||style="background: white;"| [[File:Lumo__c_ring.png|256px]] ||style="background: white;"| [[File:Exo_lumo121.png|256px]] ||style="background: white;"| [[File:New_exo_lumo_eb1613.png|256px]]
|-
!style="background: #D9C02F;"| LUMO-1!! style="background: #D9C02F;"|LUMO-1 !!style="background: #D9C02F;"| LUMO-1 !! style="background: #D9C02F;"|LUMO-1
|-
|style="background: white;"| [[File:Lumo_minus1_o_ring.png|256px]] || style="background: white;"|[[File:Lumo_minus1__c_ring.png|256px]] ||style="background: white;"| [[File:Exo_lumo_minus121.png|256px]] || style="background: white;"|[[File:New_exo_lumominus1_eb1613.png|256px]]
|- <td class=”ms-rteTableEvenCol-default” style=”width: 50%; background-color: #ffffff;”></td>
|}

=== Structure Optimisation ===

All optimized to the B3LYP/6-31G(d) level but initially with the semi-empirical PM6 method. Everything but the transition states was confirmed to be a true minima by lack of negative frequencies in the frequency calculations as shown below. Finding a single negative frequency confirms the structures to in fact be the end and eco transition states desired.
{| class="wikitable" border="1"
|+ Reactants
! style="background: #38A5A5;"| Cyclohexadiene !!style="background: #38A5A5;"| Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>CARBON_RING_FREQ23.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Carbon_ring_summary.png]]
|-
!style="background: #38A5A5;"| 1,3-Dioxole !!style="background: #38A5A5;"| Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Oxygen_ring.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Oxygen_ring_sum_eb1613.png]]
|}

{| class="wikitable" border="1"
|+ Transition State
! style="background: #38A5A5;"|Exo-TS!! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Exo_ts_99999.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Exo_ex2_ts_table.png]]
|-
! style="background: #38A5A5;"|Endo-Ts !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with PM6 level</title> <color>white</color> <size>200</size> <uploadedFileContents>ENDO_TS_OPT_631GD.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Endo_ts_summary_eb1613.png]]
|}

{| class="wikitable" border="1"
|+ Products
! style="background: #38A5A5;"|Exo-Product!! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Product_exo_631Gd.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Exo_TS_eb1613333.png]]
|-
! style="background: #38A5A5;"|Endo-Product !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with PM6 level</title> <color>white</color> <size>200</size> <uploadedFileContents>Endo_product_freqqq.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Endo_product_summmmmm.png]]
|}

Rep:Mod:Eb1613 Ex1

2016-12-02T11:04:10Z

Eb1613: /* MO analysis */

Page List

[[Mod:eb1613 files| The Calculations Log files can be found here]]

[[Mod:Emily1394| For main Introduction/conclusion page click here]]

[[Mod:Eb1613 Ex1| For Excerise 1 page click here]]

[[Mod:Eb1613 Ex2| For Excerise 2 page click here]]

[[Mod:Eb1613 Ex3| For Excerise 3 page click here]]

= Third Year Computational Lab Transition States - Emily Brown =

=== Exercise 1: Reaction of Butadiene with Ethene ===

[[File:ex1_scheme2.png]]

=== Bond Distances ===

{| class="wikitable" border="1"
|+ style="background: #38A5A5;"| Carbon-Carbon Bond Distances (Angstroms)
! style="background: #38A5A5;"| !! style="background: #38A5A5;"|C1-C2!! style="background: #38A5A5;"|C2-C3!! style="background: #38A5A5;"|C3-C4!! style="background: #38A5A5;"|C4-C5!! style="background: #38A5A5;"| C5-C6!! style="background: #38A5A5;"| C6-C1
|-
| style="background: #38A5A5;"| Butadiene||style="background: #EFECD9;"| 1.33530||style="background: #EFECD9;"| 1.46838 || style="background: #EFECD9;"|1.33525 ||style="background: #EFECD9;"| ||style="background: #EFECD9;"| ||style="background: #EFECD9;"|
|-
| style="background: #38A5A5;"|TS||style="background: #EFECD9;"| 1.37981 ||style="background: #EFECD9;"| 1.41112 ||style="background: #EFECD9;"| 1.37976 ||style="background: #EFECD9;"| 2.11496 || style="background: #EFECD9;"|1.38177 ||style="background: #EFECD9;"| 2.11452
|-
| style="background: #38A5A5;"|Product|| style="background: #EFECD9;"|1.50086 ||style="background: #EFECD9;"| 1.33698 || style="background: #EFECD9;"|1.50086 ||style="background: #EFECD9;"| 1.53717 ||style="background: #EFECD9;"| 1.53459 ||style="background: #EFECD9;"| 1.53717
|-
|}

Carbon-Carbon Sigma bonds are longer than double bonds. the bond length between C1-C2 and C3-C4 increase as they transform from double to single bonds in the reaction. The C2-C3 bond length shortens due to the reaction as a double bond forms here. The C5-C6 bond lengthens as it transforms from a single to a double bond. Due to the system being within a ring the carbon carbon single bonds are slightly shorter than the literature values which is for alkane chains. The bond distances of the forming bonds C1-C6 and C4-C5 decrease to values corresponding to those of single bonds. The Van der Waals radi for carbon is 1.70 angstroms. <ref name="vander" /> The length of bonds C1-C6 and C4-C5 at the transition state are less than twice the Van der Waals radius which indicates that a bond a forming.

Literature C-C bond distances <ref name="carbon" />

{| class="wikitable" border="1"
! colspan="2" style="background: #38A5A5;"| Carbon-Carbon Bond Distances (Angstroms)
|-
!style="background: #EFECD9;"|Sp3 C-C!! style="background: #EFECD9;"|Sp2 C-C
|-
| style="background: #EFECD9;"|1.57|| style="background: #EFECD9;"|1.33
|}

=== MO analysis ===

It can be seen from the MOs that there is a high symmetry requirement for the reaction the HOMO-1 (v2) orbital interaction lowers the energy of the electrons from the diene; the HOMO (π3) interactions stabilizes the electron pair coming from the dieneophile.

The overlap integral is zero for the interactions labelled π3 and π*5 and non-zero for interactions labelled π2 and π*4.

The MOs diagram highlights that the reaction is allowed as the orbitals of the same parity are interacting: u<->u g<->g.

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;" style="background: #38A5A5;" | MO diagram for the Diels Alder Reaction 
|-
|style="background: white;"| [[File:Mo_diagrma_draw_eb1613.png]]
|-
|}

Using a Frontier Orbital Approach to justify the diels alder reactivity in this reaction. This can be seen in the HOMO of the TS which shows the favorable overlap from combining the butadiene HOMO with the ethene LUMO.

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;" style="background: #38A5A5;"|Butadiene
|-
! style="background: #EFECD9;"|HOMO!!style="background: #EFECD9;"| LUMO
|-
| style="background: white;"| [[File:Eb1613_butadiene_LUMO.png]] || style="background: white;"|[[File:Eb1613_butadiene_HOMO.png]]
|-
|colspan="2" style="text-align: center;" style="background: #38A5A5;"| Ethene
|-
! style="background: #EFECD9;"|HOMO!!style="background: #EFECD9;"| LUMO
|-
|style="background: white;"| [[File:Eb1613_ethene_lumo.png]] || style="background: white;"|[[File:Eb1613_ethene_homo.png]]
|-
|colspan="2" style="text-align: center; style="background: #38A5A5;"|Transition State
|-
| colspan="2" style="text-align: center;" style="background: #EFECD9;"| LUMO + 1 = π*5
|-
| colspan="2" style="text-align: center; style="background: white;"| [[File:Lumo_minus_one_eb1613.png]]
|-
| colspan="2" style="text-align: center;" style="background: #EFECD9;"| LUMO = = π*4
|-
| colspan="2" style="text-align: center; style="background: white;"| [[File:Eb1613_TS_lumo.png]]
|-
| colspan="2" style="text-align: center;" style="background: #EFECD9;"| HOMO = = π3
|-
| colspan="2" style="text-align: center;" style="background: white;"| [[File:Eb1613_TS_homo.png]]
|-
| colspan="2" style="text-align: center;" style="background: #EFECD9;"| HOMO - 1 = = π2
|-
| colspan="2" style="text-align: center;" style="background: white;"| [[File:Homo_minus_one_eb1613.png]]
|}

The four MOs produced in the TS are π*5, π*4, π3 and π2. These are shown in the MO diagram above and were found were located using the guassian check point file.

=== Transition state analysis ===

The reactants were initially optimised to the PM6 semi-empirical level and then re-optimised to the DFT B3LYP/6-31G(d) level to save computational time. The reactants were aligned and then the atoms which form bonds were frozen using the opt=modredundant keywords in the calculation; this system was optimised to a minimum allowing parameters to reach a minimum whilst holding the reactants together at a distance of 2.2 angstroms. The resultant geometry from this calculation was used in a new calculation which optimised the structure to a TS (Berry) and allowed force constants to be calculated once. The transition state was located and confirmed by the presence of a single negative frequency which had an imaginary vibrational node which corresponded to the forming/breaking of bonds involved in the reactions transition state. This transition state geometry was then calculated using the higher DFT B3LYP/6-31G(d) calculation method. The transition state was further confirmed via the IRC calculated which allows force constants to be calculated always. The IRC requests that a reaction path be followed by integrating the intrinsic reaction coordinate. <ref name="IRC" /> It was found that using 10 steps in the IRC calculation was not nearly enough to look over the whole reaction coordinate and so 10000 steps was used for the repeated calculation. The visualisation of the transition state can be seen in the GIF files below along with the IRC calculation results. Furthermore the intrinsic reaction coordinate graph shows that there are no intermediates or other transition states involved in this reaction.

{| class="wikitable" border="1"
! style="background: #38A5A5;" |IRC movie captured || style="background: #38A5A5;" |IRC Graph
|-
| style="background: white;" | [[File:IRC_movie_eb1613.gif]] || style="background: white;" | [[File:IRC_exercise1_eb1613.png]]
|}

The Diels-Alder cyclic addition reaction occurs via a concerted transition state as shown below. The two new sigma bonds are formed at the same time therefore the reaction is synchronous. The animations below show how this compares to the first positive frequency, which is seen to be asynchronous rocking.

{| class="wikitable" border="1"
! style="background: #38A5A5;" | Negative Frequency = -948.76 cm-1
|-
|style="background: white;" | [[File:Test3_files_eb1613.gif]]
|-
! style="background: #38A5A5;" | First Positive Frequency = 145.08 cm-1
|-
| style="background: white;" | [[File:Eb1613_first_pos_vib_ex1.gif]]
|}

=== Optimization of Reactants, TS and Products ===

All structures have been optimised at the semi-empirical PM6 level and then further optimised to the DFT B3LYP/6-31G(d) level to save computational time. The lack of negative frequencies in the frequency calculation indicates that the structure is optimised to a true minimum, the presence of one negative frequency indicates that a transition state has been reached, more than one negative frequency means that a saddle point structure has been reached.

{| class="wikitable" border="1"
|+ Files
! style="background: #38A5A5;"|Butadiene !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with PM6 level</title> <color>white</color> <size>200</size> <uploadedFileContents>Eb1613_butadiene_PM6_opt_freq.log</uploadedFileContents> </jmolApplet></jmol> || [[File:But_eb1613_energy_new.png]]
|-
! style="background: #38A5A5;"|Ethene !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with PM6 level</title> <color>white</color> <size>200</size> <uploadedFileContents>Eb1613_ETHENE_PM6_OPT_FREQ.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Eb1613_ethene_energy.png]]
|-
! style="background: #38A5A5;"|Transition State !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Transition State</title> <color>white</color> <size>300</size> <uploadedFileContents>TS_FREEZE2_OPT.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Eb1613_TS_energy.png]]
|-
! style="background: #38A5A5;"|Product !! style="background: #38A5A5;"|Gaussian imagine of product
|-
| <jmol><jmolApplet> <title>Jmol of PM6 optimised product</title> <color>white</color> <size>300</size> <uploadedFileContents>Eb1613_PRODUCT_PM6_OPT_MANDISP1PT0_FREQ.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Product_ex1.png]]
|-
! colspan="2" style="text-align: center;" style="background: #38A5A5;"| Optimization Summary
|-
|colspan="2" style="text-align: center;"| [[File:Eb1613_product_summary.png]]
|}

=== References ===

<references>
<ref name="carbon">J.M. Berg, J. L. Tymoczko, L. Stryer, in Biochemistry., W.H. Freeman, New York, 5th edn., 2002, Appendix C: Standard Bond Lengths, https://www.ncbi.nlm.nih.gov/books/NBK21220/, (accessed 23rd November, 2016).</ref>
<ref name="vander">A. Bondi, J. Phys. Chem., 1964, 68 (3), 441-451.</ref>
<ref name="IRC">http://www.gaussian.com/g_tech/g_ur/k_irc.htm (accessed 23rd November, 2016)</ref>

</references>

File:Mo diagrma draw eb1613.png

2016-12-02T11:04:01Z

Eb1613:

Rep:Mod:Eb1613 Ex1

2016-12-02T11:01:52Z

Eb1613: /* MO analysis */

Page List

[[Mod:eb1613 files| The Calculations Log files can be found here]]

[[Mod:Emily1394| For main Introduction/conclusion page click here]]

[[Mod:Eb1613 Ex1| For Excerise 1 page click here]]

[[Mod:Eb1613 Ex2| For Excerise 2 page click here]]

[[Mod:Eb1613 Ex3| For Excerise 3 page click here]]

= Third Year Computational Lab Transition States - Emily Brown =

=== Exercise 1: Reaction of Butadiene with Ethene ===

[[File:ex1_scheme2.png]]

=== Bond Distances ===

{| class="wikitable" border="1"
|+ style="background: #38A5A5;"| Carbon-Carbon Bond Distances (Angstroms)
! style="background: #38A5A5;"| !! style="background: #38A5A5;"|C1-C2!! style="background: #38A5A5;"|C2-C3!! style="background: #38A5A5;"|C3-C4!! style="background: #38A5A5;"|C4-C5!! style="background: #38A5A5;"| C5-C6!! style="background: #38A5A5;"| C6-C1
|-
| style="background: #38A5A5;"| Butadiene||style="background: #EFECD9;"| 1.33530||style="background: #EFECD9;"| 1.46838 || style="background: #EFECD9;"|1.33525 ||style="background: #EFECD9;"| ||style="background: #EFECD9;"| ||style="background: #EFECD9;"|
|-
| style="background: #38A5A5;"|TS||style="background: #EFECD9;"| 1.37981 ||style="background: #EFECD9;"| 1.41112 ||style="background: #EFECD9;"| 1.37976 ||style="background: #EFECD9;"| 2.11496 || style="background: #EFECD9;"|1.38177 ||style="background: #EFECD9;"| 2.11452
|-
| style="background: #38A5A5;"|Product|| style="background: #EFECD9;"|1.50086 ||style="background: #EFECD9;"| 1.33698 || style="background: #EFECD9;"|1.50086 ||style="background: #EFECD9;"| 1.53717 ||style="background: #EFECD9;"| 1.53459 ||style="background: #EFECD9;"| 1.53717
|-
|}

Carbon-Carbon Sigma bonds are longer than double bonds. the bond length between C1-C2 and C3-C4 increase as they transform from double to single bonds in the reaction. The C2-C3 bond length shortens due to the reaction as a double bond forms here. The C5-C6 bond lengthens as it transforms from a single to a double bond. Due to the system being within a ring the carbon carbon single bonds are slightly shorter than the literature values which is for alkane chains. The bond distances of the forming bonds C1-C6 and C4-C5 decrease to values corresponding to those of single bonds. The Van der Waals radi for carbon is 1.70 angstroms. <ref name="vander" /> The length of bonds C1-C6 and C4-C5 at the transition state are less than twice the Van der Waals radius which indicates that a bond a forming.

Literature C-C bond distances <ref name="carbon" />

{| class="wikitable" border="1"
! colspan="2" style="background: #38A5A5;"| Carbon-Carbon Bond Distances (Angstroms)
|-
!style="background: #EFECD9;"|Sp3 C-C!! style="background: #EFECD9;"|Sp2 C-C
|-
| style="background: #EFECD9;"|1.57|| style="background: #EFECD9;"|1.33
|}

=== MO analysis ===

It can be seen from the MOs that there is a high symmetry requirement for the reaction the HOMO-1 (v2) orbital interaction lowers the energy of the electrons from the diene; the HOMO (π3) interactions stabilizes the electron pair coming from the dieneophile.

The overlap integral is zero for the interactions labelled π3 and π*5 and non-zero for interactions labelled π2 and π*4.

The MOs diagram highlights that the reaction is allowed as the orbitals of the same parity are interacting: u<->u g<->g.

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;" style="background: #38A5A5;" | MO diagram for the Diels Alder Reaction 
|-
|style="background: white;"| [[File:IMG_7527_eb1613.JPG|width=50%!]]
|-
|}

Using a Frontier Orbital Approach to justify the diels alder reactivity in this reaction. This can be seen in the HOMO of the TS which shows the favorable overlap from combining the butadiene HOMO with the ethene LUMO.

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;" style="background: #38A5A5;"|Butadiene
|-
! style="background: #EFECD9;"|HOMO!!style="background: #EFECD9;"| LUMO
|-
| style="background: white;"| [[File:Eb1613_butadiene_LUMO.png]] || style="background: white;"|[[File:Eb1613_butadiene_HOMO.png]]
|-
|colspan="2" style="text-align: center;" style="background: #38A5A5;"| Ethene
|-
! style="background: #EFECD9;"|HOMO!!style="background: #EFECD9;"| LUMO
|-
|style="background: white;"| [[File:Eb1613_ethene_lumo.png]] || style="background: white;"|[[File:Eb1613_ethene_homo.png]]
|-
|colspan="2" style="text-align: center; style="background: #38A5A5;"|Transition State
|-
| colspan="2" style="text-align: center;" style="background: #EFECD9;"| LUMO + 1 = π*5
|-
| colspan="2" style="text-align: center; style="background: white;"| [[File:Lumo_minus_one_eb1613.png]]
|-
| colspan="2" style="text-align: center;" style="background: #EFECD9;"| LUMO = = π*4
|-
| colspan="2" style="text-align: center; style="background: white;"| [[File:Eb1613_TS_lumo.png]]
|-
| colspan="2" style="text-align: center;" style="background: #EFECD9;"| HOMO = = π3
|-
| colspan="2" style="text-align: center;" style="background: white;"| [[File:Eb1613_TS_homo.png]]
|-
| colspan="2" style="text-align: center;" style="background: #EFECD9;"| HOMO - 1 = = π2
|-
| colspan="2" style="text-align: center;" style="background: white;"| [[File:Homo_minus_one_eb1613.png]]
|}

The four MOs produced in the TS are π*5, π*4, π3 and π2. These are shown in the MO diagram above and were found were located using the guassian check point file.

=== Transition state analysis ===

The reactants were initially optimised to the PM6 semi-empirical level and then re-optimised to the DFT B3LYP/6-31G(d) level to save computational time. The reactants were aligned and then the atoms which form bonds were frozen using the opt=modredundant keywords in the calculation; this system was optimised to a minimum allowing parameters to reach a minimum whilst holding the reactants together at a distance of 2.2 angstroms. The resultant geometry from this calculation was used in a new calculation which optimised the structure to a TS (Berry) and allowed force constants to be calculated once. The transition state was located and confirmed by the presence of a single negative frequency which had an imaginary vibrational node which corresponded to the forming/breaking of bonds involved in the reactions transition state. This transition state geometry was then calculated using the higher DFT B3LYP/6-31G(d) calculation method. The transition state was further confirmed via the IRC calculated which allows force constants to be calculated always. The IRC requests that a reaction path be followed by integrating the intrinsic reaction coordinate. <ref name="IRC" /> It was found that using 10 steps in the IRC calculation was not nearly enough to look over the whole reaction coordinate and so 10000 steps was used for the repeated calculation. The visualisation of the transition state can be seen in the GIF files below along with the IRC calculation results. Furthermore the intrinsic reaction coordinate graph shows that there are no intermediates or other transition states involved in this reaction.

{| class="wikitable" border="1"
! style="background: #38A5A5;" |IRC movie captured || style="background: #38A5A5;" |IRC Graph
|-
| style="background: white;" | [[File:IRC_movie_eb1613.gif]] || style="background: white;" | [[File:IRC_exercise1_eb1613.png]]
|}

The Diels-Alder cyclic addition reaction occurs via a concerted transition state as shown below. The two new sigma bonds are formed at the same time therefore the reaction is synchronous. The animations below show how this compares to the first positive frequency, which is seen to be asynchronous rocking.

{| class="wikitable" border="1"
! style="background: #38A5A5;" | Negative Frequency = -948.76 cm-1
|-
|style="background: white;" | [[File:Test3_files_eb1613.gif]]
|-
! style="background: #38A5A5;" | First Positive Frequency = 145.08 cm-1
|-
| style="background: white;" | [[File:Eb1613_first_pos_vib_ex1.gif]]
|}

=== Optimization of Reactants, TS and Products ===

All structures have been optimised at the semi-empirical PM6 level and then further optimised to the DFT B3LYP/6-31G(d) level to save computational time. The lack of negative frequencies in the frequency calculation indicates that the structure is optimised to a true minimum, the presence of one negative frequency indicates that a transition state has been reached, more than one negative frequency means that a saddle point structure has been reached.

{| class="wikitable" border="1"
|+ Files
! style="background: #38A5A5;"|Butadiene !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with PM6 level</title> <color>white</color> <size>200</size> <uploadedFileContents>Eb1613_butadiene_PM6_opt_freq.log</uploadedFileContents> </jmolApplet></jmol> || [[File:But_eb1613_energy_new.png]]
|-
! style="background: #38A5A5;"|Ethene !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with PM6 level</title> <color>white</color> <size>200</size> <uploadedFileContents>Eb1613_ETHENE_PM6_OPT_FREQ.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Eb1613_ethene_energy.png]]
|-
! style="background: #38A5A5;"|Transition State !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Transition State</title> <color>white</color> <size>300</size> <uploadedFileContents>TS_FREEZE2_OPT.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Eb1613_TS_energy.png]]
|-
! style="background: #38A5A5;"|Product !! style="background: #38A5A5;"|Gaussian imagine of product
|-
| <jmol><jmolApplet> <title>Jmol of PM6 optimised product</title> <color>white</color> <size>300</size> <uploadedFileContents>Eb1613_PRODUCT_PM6_OPT_MANDISP1PT0_FREQ.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Product_ex1.png]]
|-
! colspan="2" style="text-align: center;" style="background: #38A5A5;"| Optimization Summary
|-
|colspan="2" style="text-align: center;"| [[File:Eb1613_product_summary.png]]
|}

=== References ===

<references>
<ref name="carbon">J.M. Berg, J. L. Tymoczko, L. Stryer, in Biochemistry., W.H. Freeman, New York, 5th edn., 2002, Appendix C: Standard Bond Lengths, https://www.ncbi.nlm.nih.gov/books/NBK21220/, (accessed 23rd November, 2016).</ref>
<ref name="vander">A. Bondi, J. Phys. Chem., 1964, 68 (3), 441-451.</ref>
<ref name="IRC">http://www.gaussian.com/g_tech/g_ur/k_irc.htm (accessed 23rd November, 2016)</ref>

</references>

Rep:Mod:Eb1613 Ex1

2016-12-02T10:59:20Z

Eb1613: /* MO analysis */

Page List

[[Mod:eb1613 files| The Calculations Log files can be found here]]

[[Mod:Emily1394| For main Introduction/conclusion page click here]]

[[Mod:Eb1613 Ex1| For Excerise 1 page click here]]

[[Mod:Eb1613 Ex2| For Excerise 2 page click here]]

[[Mod:Eb1613 Ex3| For Excerise 3 page click here]]

= Third Year Computational Lab Transition States - Emily Brown =

=== Exercise 1: Reaction of Butadiene with Ethene ===

[[File:ex1_scheme2.png]]

=== Bond Distances ===

{| class="wikitable" border="1"
|+ style="background: #38A5A5;"| Carbon-Carbon Bond Distances (Angstroms)
! style="background: #38A5A5;"| !! style="background: #38A5A5;"|C1-C2!! style="background: #38A5A5;"|C2-C3!! style="background: #38A5A5;"|C3-C4!! style="background: #38A5A5;"|C4-C5!! style="background: #38A5A5;"| C5-C6!! style="background: #38A5A5;"| C6-C1
|-
| style="background: #38A5A5;"| Butadiene||style="background: #EFECD9;"| 1.33530||style="background: #EFECD9;"| 1.46838 || style="background: #EFECD9;"|1.33525 ||style="background: #EFECD9;"| ||style="background: #EFECD9;"| ||style="background: #EFECD9;"|
|-
| style="background: #38A5A5;"|TS||style="background: #EFECD9;"| 1.37981 ||style="background: #EFECD9;"| 1.41112 ||style="background: #EFECD9;"| 1.37976 ||style="background: #EFECD9;"| 2.11496 || style="background: #EFECD9;"|1.38177 ||style="background: #EFECD9;"| 2.11452
|-
| style="background: #38A5A5;"|Product|| style="background: #EFECD9;"|1.50086 ||style="background: #EFECD9;"| 1.33698 || style="background: #EFECD9;"|1.50086 ||style="background: #EFECD9;"| 1.53717 ||style="background: #EFECD9;"| 1.53459 ||style="background: #EFECD9;"| 1.53717
|-
|}

Carbon-Carbon Sigma bonds are longer than double bonds. the bond length between C1-C2 and C3-C4 increase as they transform from double to single bonds in the reaction. The C2-C3 bond length shortens due to the reaction as a double bond forms here. The C5-C6 bond lengthens as it transforms from a single to a double bond. Due to the system being within a ring the carbon carbon single bonds are slightly shorter than the literature values which is for alkane chains. The bond distances of the forming bonds C1-C6 and C4-C5 decrease to values corresponding to those of single bonds. The Van der Waals radi for carbon is 1.70 angstroms. <ref name="vander" /> The length of bonds C1-C6 and C4-C5 at the transition state are less than twice the Van der Waals radius which indicates that a bond a forming.

Literature C-C bond distances <ref name="carbon" />

{| class="wikitable" border="1"
! colspan="2" style="background: #38A5A5;"| Carbon-Carbon Bond Distances (Angstroms)
|-
!style="background: #EFECD9;"|Sp3 C-C!! style="background: #EFECD9;"|Sp2 C-C
|-
| style="background: #EFECD9;"|1.57|| style="background: #EFECD9;"|1.33
|}

=== MO analysis ===

It can be seen from the MOs that there is a high symmetry requirement for the reaction the HOMO-1 (v2) orbital interaction lowers the energy of the electrons from the diene; the HOMO (π3) interactions stabilizes the electron pair coming from the dieneophile.

The overlap integral is zero for the interactions labelled π3 and π*5 and non-zero for interactions labelled π2 and π*4.

The MOs diagram highlights that the reaction is allowed as the orbitals of the same parity are interacting: u<->u g<->g.

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;" style="background: #38A5A5;" | MO diagram for the Diels Alder Reaction 
|-
|style="background: white;"| [[File:IMG_7527_eb1613.JPG]]
|-
|}

Using a Frontier Orbital Approach to justify the diels alder reactivity in this reaction. This can be seen in the HOMO of the TS which shows the favorable overlap from combining the butadiene HOMO with the ethene LUMO.

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;" style="background: #38A5A5;"|Butadiene
|-
! style="background: #EFECD9;"|HOMO!!style="background: #EFECD9;"| LUMO
|-
| style="background: white;"| [[File:Eb1613_butadiene_LUMO.png]] || style="background: white;"|[[File:Eb1613_butadiene_HOMO.png]]
|-
|colspan="2" style="text-align: center;" style="background: #38A5A5;"| Ethene
|-
! style="background: #EFECD9;"|HOMO!!style="background: #EFECD9;"| LUMO
|-
|style="background: white;"| [[File:Eb1613_ethene_lumo.png]] || style="background: white;"|[[File:Eb1613_ethene_homo.png]]
|-
|colspan="2" style="text-align: center; style="background: #38A5A5;"|Transition State
|-
| colspan="2" style="text-align: center;" style="background: #EFECD9;"| LUMO + 1 = π*5
|-
| colspan="2" style="text-align: center; style="background: white;"| [[File:Lumo_minus_one_eb1613.png]]
|-
| colspan="2" style="text-align: center;" style="background: #EFECD9;"| LUMO = = π*4
|-
| colspan="2" style="text-align: center; style="background: white;"| [[File:Eb1613_TS_lumo.png]]
|-
| colspan="2" style="text-align: center;" style="background: #EFECD9;"| HOMO = = π3
|-
| colspan="2" style="text-align: center;" style="background: white;"| [[File:Eb1613_TS_homo.png]]
|-
| colspan="2" style="text-align: center;" style="background: #EFECD9;"| HOMO - 1 = = π2
|-
| colspan="2" style="text-align: center;" style="background: white;"| [[File:Homo_minus_one_eb1613.png]]
|}

The four MOs produced in the TS are π*5, π*4, π3 and π2. These are shown in the MO diagram above and were found were located using the guassian check point file.

=== Transition state analysis ===

The reactants were initially optimised to the PM6 semi-empirical level and then re-optimised to the DFT B3LYP/6-31G(d) level to save computational time. The reactants were aligned and then the atoms which form bonds were frozen using the opt=modredundant keywords in the calculation; this system was optimised to a minimum allowing parameters to reach a minimum whilst holding the reactants together at a distance of 2.2 angstroms. The resultant geometry from this calculation was used in a new calculation which optimised the structure to a TS (Berry) and allowed force constants to be calculated once. The transition state was located and confirmed by the presence of a single negative frequency which had an imaginary vibrational node which corresponded to the forming/breaking of bonds involved in the reactions transition state. This transition state geometry was then calculated using the higher DFT B3LYP/6-31G(d) calculation method. The transition state was further confirmed via the IRC calculated which allows force constants to be calculated always. The IRC requests that a reaction path be followed by integrating the intrinsic reaction coordinate. <ref name="IRC" /> It was found that using 10 steps in the IRC calculation was not nearly enough to look over the whole reaction coordinate and so 10000 steps was used for the repeated calculation. The visualisation of the transition state can be seen in the GIF files below along with the IRC calculation results. Furthermore the intrinsic reaction coordinate graph shows that there are no intermediates or other transition states involved in this reaction.

{| class="wikitable" border="1"
! style="background: #38A5A5;" |IRC movie captured || style="background: #38A5A5;" |IRC Graph
|-
| style="background: white;" | [[File:IRC_movie_eb1613.gif]] || style="background: white;" | [[File:IRC_exercise1_eb1613.png]]
|}

The Diels-Alder cyclic addition reaction occurs via a concerted transition state as shown below. The two new sigma bonds are formed at the same time therefore the reaction is synchronous. The animations below show how this compares to the first positive frequency, which is seen to be asynchronous rocking.

{| class="wikitable" border="1"
! style="background: #38A5A5;" | Negative Frequency = -948.76 cm-1
|-
|style="background: white;" | [[File:Test3_files_eb1613.gif]]
|-
! style="background: #38A5A5;" | First Positive Frequency = 145.08 cm-1
|-
| style="background: white;" | [[File:Eb1613_first_pos_vib_ex1.gif]]
|}

=== Optimization of Reactants, TS and Products ===

All structures have been optimised at the semi-empirical PM6 level and then further optimised to the DFT B3LYP/6-31G(d) level to save computational time. The lack of negative frequencies in the frequency calculation indicates that the structure is optimised to a true minimum, the presence of one negative frequency indicates that a transition state has been reached, more than one negative frequency means that a saddle point structure has been reached.

{| class="wikitable" border="1"
|+ Files
! style="background: #38A5A5;"|Butadiene !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with PM6 level</title> <color>white</color> <size>200</size> <uploadedFileContents>Eb1613_butadiene_PM6_opt_freq.log</uploadedFileContents> </jmolApplet></jmol> || [[File:But_eb1613_energy_new.png]]
|-
! style="background: #38A5A5;"|Ethene !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with PM6 level</title> <color>white</color> <size>200</size> <uploadedFileContents>Eb1613_ETHENE_PM6_OPT_FREQ.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Eb1613_ethene_energy.png]]
|-
! style="background: #38A5A5;"|Transition State !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Transition State</title> <color>white</color> <size>300</size> <uploadedFileContents>TS_FREEZE2_OPT.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Eb1613_TS_energy.png]]
|-
! style="background: #38A5A5;"|Product !! style="background: #38A5A5;"|Gaussian imagine of product
|-
| <jmol><jmolApplet> <title>Jmol of PM6 optimised product</title> <color>white</color> <size>300</size> <uploadedFileContents>Eb1613_PRODUCT_PM6_OPT_MANDISP1PT0_FREQ.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Product_ex1.png]]
|-
! colspan="2" style="text-align: center;" style="background: #38A5A5;"| Optimization Summary
|-
|colspan="2" style="text-align: center;"| [[File:Eb1613_product_summary.png]]
|}

=== References ===

<references>
<ref name="carbon">J.M. Berg, J. L. Tymoczko, L. Stryer, in Biochemistry., W.H. Freeman, New York, 5th edn., 2002, Appendix C: Standard Bond Lengths, https://www.ncbi.nlm.nih.gov/books/NBK21220/, (accessed 23rd November, 2016).</ref>
<ref name="vander">A. Bondi, J. Phys. Chem., 1964, 68 (3), 441-451.</ref>
<ref name="IRC">http://www.gaussian.com/g_tech/g_ur/k_irc.htm (accessed 23rd November, 2016)</ref>

</references>

File:IMG 7527 eb1613.JPG

2016-12-02T10:59:03Z

Eb1613:

Rep:Mod:Emily1394

2016-12-02T10:33:20Z

Eb1613: /* Introduction */

Page List

[[Mod:eb1613 files| The Calculations Log files can be found here]]

[[Mod:Emily1394| For main Introduction/conclusion page click here]]

[[Mod:Eb1613 Ex1| For Excerise 1 page click here]]

[[Mod:Eb1613 Ex2| For Excerise 2 page click here]]

[[Mod:Eb1613 Ex3| For Excerise 3 page click here]]

= Third Year Computational Lab Transition States - Emily Brown =

Please note each page has its own references at the bottom of the page.

=== Introduction ===

==== Theory ====

'''Transition State:''' This is a maxima on the reaction coordinate graph. At the point the gradient/first derivative is zero and can be referred to as a turning point on the graph.

'''Potential Energy Surface:''' This has 3N-6 dimensions and if you travel in one dimension you can draw a reaction coordinate graph as shown below. <ref name="waterbottle" /> The PES is a function of energy vs every coordinate. <ref name="Hunt" />

[[File:Eb1613_PE_RC.png|thumb|center|Potential energy surface on left and corresponding reaction coordinate graph to right <ref name="waterbottle" /> ]]

Due to the transition state being a turning point on the reaction coordinate graph it can be found by setting the first derivative to zero as at a minima/maxima the gradient is zero. The potential energy surface allows you to travel in directions which may be away from the reaction coordinate you are trying to locate. The potential energy surface has 3N-6 dimensions.<ref name="Hunt" /> Programs like GuassView take advantage of the fact that all these dimensions are positive in curvature apart from one which is the minimum energy path. This results in an imaginary frequency which is the single negative frequency found in the frequency calculation of a transition state geometry. Energy minimas have zero negative frequencies in their frequency calculations and saddle points have multiple. <ref name="Hunt" />

Reactions can be controlled by a number of different factors some of these being sterics and secondary orbital effects. Reactions often compromise between multiple aspects for example a reaction may be sterically disfavored but that particular reaction path could result in good orbital overlap. Secondary oribtal interactions tend to favor the endo-adduct being formed in Diels-Alder reactions.

The reactants tend to form the products via the higher energy transition state which is shown as an energy maximum on the above graph, the energy required to overcome this barrier is known as the activation energy and can be seen in the arrhenius equation as the symbol Ea. The activation energy depends on many factors and programmes like gaussian can be used to estimate this energy and predict whether reactions are likely to occur. For example there are two cis dienes present in the reactant in exercise 3 but only one is involved int he dies alder reactions as the other is known to have a high transition state making it very kinetically unfavourable.

Diels Alder reactions are classified as [4+2] cycloadditions typically between a diene and a dieneophile. The reactions occur via a concerted mechanism with a cyclic transition state. The reaction involves the breaking of 2π bonds and the formation of 2 new σ bonds and a single new π bond. The breaking of the pi bonds is the enthalpic driving force in the reaction as breaking a carbon carbon double bond releases a lot of energy. Cycloaddition reactions have been categorised by Woodward Hoffman to state whether they are thermally or photochemically allowed. Diels-alder reactions can also be classified as normal electron demand or inverse electron demand. Normal electron demand is the case when the HOMO of the diene reacts with the LUMO of the dieneohile, where as inverse electron demand is when the LUMO of the diene reacts with the HOMO of the dieneophile. It has been shown that adding electron donating groups/ electron withdrawing groups to certain positions on the diene/dieneophile can facilitate the Diels-Alder reaction by effecting the energy levels of their HOMO/LUMO thus narrowing the energy gap between the interacting HOMO and LUMO thus facilitating a better orbital overlap.

Cheleotropic reactions is a class of pericyclic reactions which present themselves in exercise 3 which is the cyclic addition of SO2 to a diene. These reactions were exploded in the Woodward and Hoffman's famous publication. <ref name="woodsman" />

==== Computational ====
Initially structures will be optimized using method1 and then using method2. Doing the initial 'tidy up' allows computational time to be saved. Locating transition states has proved difficult for certain systems which results in different approaches being undertaken such as freezing certain bonds by using the '''opt=modredundant''' keywords thus locking atoms together to perform initial optimizations. Another approach is to start from the products or reactants and lengthen certain bonds in an attempt to locate the transition state. Structures were confirmed via frequency calculations: the lack of negative frequencies in the frequency calculation indicates that the structure is optimised to a true minimum, the presence of one negative frequency indicates that a transition state has been reached, more than one negative frequency means that a saddle point structure has been reached. <ref name="book book" />

It proved necessary at times to freeze bonds to locate a transition state however once found all structures were later re-optimised under no symmetry constraints. The '''int=ultrafine''' keywords are expressed in the DFT calculations as optimisation with many low level vibration modes will often proceed more reliably when a larger DFT integration grid is requested. <ref name="integral" />

'''Method 1:''' Opt+Freq, semi empirical, PM6.

'''Method 2:''' Opt+Freq, DFT B3LYP/631G(d).

Both the density function theory (DFT) and semi-empirical methods are able to describe quantum states as many electron systems; they both use the born-opinhiemer approximation where you first solve for the electronic degrees of freedom. <ref name="electrons" /> In DFT the many-electron wavefunction is completely bypassed in favor of the electron density, the variational principle is used to minimise the energy with respect to electron density. However a key problem with this method is that the energy functional is not know. <ref name="electrons" /> Semi-empirical Methods are a simplified versions of Hartree-Fock theory using empirical corrections in order to improve performance; these can be preformed prior to DFT calculations in order to save computational time. <ref name="mug mug" /> The PM6 part of the calculation specifics that the PM6 hamiltonian is to use in the semi-empirical calculation. <ref name="IwantTEA" />

'''Notes:''' When optimising to a transition state I used: TS (Berry), Force constants allowed to calculate once. When optimising to a minimum use: minimum and force constants are allowed to calculate never. Occasional calculations were run on the colleges HPC to save computational time as these servers use more processors than my local computer in college. The 09 version of gaussian suite was used when on windows college computers.

==== Exercises ====

Each exercise is contained on its own page which are linked to below and above the contents section of each page. Each page containing an exercise has Jmol files of all structures used in that exercise at the end of the page, they are accompanied by the 'results summary' section of their opt/freq calculation to confirm the existence of the correct number of negative frequencies and to allow the geometry of each structure to be viewed.

[[Mod:Eb1613 Ex1| Page for Excerise 1]]

[[Mod:Eb1613 Ex2| Page for Excerise 2]]

[[Mod:Eb1613 Ex3| Page for Excerise 3]]

=== Conclusion ===

The transition states were successfully located for multiple reaction following a similar procedure in each case. Orbital analysis was undertaken and HOMO+1, HOMO, LUMO and LUMO-1 levels were explored. The transition states were be further identified by looking into the IRC, thus allowing endo/exo transition states to be confidently labeled. The IRC also revealed information about the reaction coordinate such that no other intermediates existed and that no other transition states were encountered for our reactions.

This computational lab has also highlighed some key difference between the semi-empirical based basis sets and those of basis sets belonging to the density functional theory family. The lab has drawn attention to the importance of chosen the correct basis set and has given me the ability to use Gaussian programs to confidently locate transition states for reactions and highlighted some key methods to further understand the transition states found.

=== Reference ===

<references>
<ref name="waterbottle">https://commons.wikimedia.org/wiki/File:Potential_Energy_Surface_and_Corresponding_Reaction_Coordinate_Diagram.png (accessed 23rd November)</ref>
<ref name="electrons">https://www.quora.com/What-is-the-difference-between-density-functional-theory-and-hartree-fock (accessed 25th November 2016)</ref>
<ref name="integral">http://www.gaussian.com/g_tech/g_ur/k_opt.htm (accessed 25th November 2016)</ref>
<ref name="IwantTEA ">http://www.gaussian.com/g_tech/g_ur/k_semiempirical.html (accessed 25th November 2016)</ref>
<ref name="mug mug ">http://www.cup.uni-muenchen.de/ch/compchem/energy/semi1.html (accessed 25th November 2016)</ref>
<ref name="Hunt "> Dr. Hunt's year 4 lecture course: "Computational Inorganic Chemistry" Lecture4, Handout3. http://www.huntresearchgroup.org.uk/teaching/teaching_comp_chem_year4/L4_PES.pdf (accessed 25th November 2016)</ref>
<ref name="book book "> Foresman, J. and Frisch, A. (1996). Exploring Chemistry With Electronic Structure Methods: A Guide to Using Gaussian. 2nd ed. Guassian, Chapter 1.</ref>
<ref name="woodsman">Woodward, R.B.; Hoffman, R. Angew. Chem. Int. Ed. Engl. 1969, 8, 781. DOI:10.1002/anie.196907811 </ref>
</references>

Rep:Mod:Emily1394

2016-12-02T10:31:48Z

Eb1613: /* Introduction */

Page List

[[Mod:eb1613 files| The Calculations Log files can be found here]]

[[Mod:Emily1394| For main Introduction/conclusion page click here]]

[[Mod:Eb1613 Ex1| For Excerise 1 page click here]]

[[Mod:Eb1613 Ex2| For Excerise 2 page click here]]

[[Mod:Eb1613 Ex3| For Excerise 3 page click here]]

= Third Year Computational Lab Transition States - Emily Brown =

Please note each page has its own references at the bottom of the page.

=== Introduction ===

==== Theory ====

'''Transition State:''' This is a maxima on the reaction coordinate graph. At the point the gradient/first derivative is zero and can be referred to as a turning point on the graph.

'''Potential Energy Surface:''' This has 3N-6 dimensions and if you travel in one dimension you can draw a reaction coordinate graph as shown below. <ref name="waterbottle" /> The PES is a function of energy vs every coordinate. <ref name="Hunt" />

[[File:Eb1613_PE_RC.png|thumb|center|Potential energy surface on left and corresponding reaction coordinate graph to right <ref name="waterbottle" /> ]]

Due to the transition state being a turning point on the reaction coordinate graph it can be found by setting the first derivative to zero as at a minima/maxima the gradient is zero. The potential energy surface allows you to travel in directions which may be away from the reaction coordinate you are trying to locate. The potential energy surface has 3N-6 dimensions.<ref name="Hunt" /> Programs like GuassView take advantage of the fact that all these dimensions are positive in curvature apart from one which is the minimum energy path. This results in an imaginary frequency which is the single negative frequency found in the frequency calculation of a transition state geometry. Energy minimas have zero negative frequencies in their frequency calculations and saddle points have multiple. <ref name="Hunt" />

Reactions can be controlled by a number of different factors some of these being sterics and secondary orbital effects. Reactions often compromise between multiple aspects for example a reaction may be sterically disfavored but that particular reaction path could result in good orbital overlap. Secondary oribtal interactions tend to favor the endo-adduct being formed in Diels-Alder reactions.

The reactants tend to form the products via the higher energy transition state which is shown as an energy maximum on the above graph, the energy required to overcome this barrier is known as the activation energy and can be seen in the arrhenius equation as the symbol Ea. The activation energy depends on many factors and programmes like gaussian can be used to estimate this energy and predict whether reactions are likely to occur. For example there are two cis dienes present in the reactant in exercise 3 but only one is involved int he dies alder reactions as the other is known to have a high transition state making it very kinetically unfavourable.

Diels Alder reactions are classified as [4+2] cycloadditions typically between a diene and a dieneophile. The reactions occur via a concerted mechanism with a cyclic transition state. The reaction involves the breaking of 2π bonds and the formation of 2 new σ bonds and a single new π bond. The breaking of the pi bonds is the enthalpic driving force in the reaction as breaking a carbon carbon double bond releases a lot of energy. Cycloaddition reactions have been categorised by Woodward Hoffman to state whether they are thermally or photochemically allowed. Diels-alder reactions can also be classified as normal electron demand or inverse electron demand. Normal electron demand is the case when the HOMO of the diene reacts with the LUMO of the dieneohile, where as inverse electron demand is when the LUMO of the diene reacts with the HOMO of the dieneophile. It has been shown that adding electron donating groups/ electron withdrawing groups to certain positions on the diene/dieneophile can facilitate the Diels-Alder reaction by effecting the energy levels of their HOMO/LUMO thus narrowing the energy gap between the interacting HOMO and LUMO thus facilitating a better orbital overlap.

Cheleotropic reactions is a class of pericyclic reactions which present themselves in exercise 3 which is the cyclic addition of SO2 to a diene. These reactions were exploded by Woodward Hoffman. <ref name="woodsman" />

==== Computational ====
Initially structures will be optimized using method1 and then using method2. Doing the initial 'tidy up' allows computational time to be saved. Locating transition states has proved difficult for certain systems which results in different approaches being undertaken such as freezing certain bonds by using the '''opt=modredundant''' keywords thus locking atoms together to perform initial optimizations. Another approach is to start from the products or reactants and lengthen certain bonds in an attempt to locate the transition state. Structures were confirmed via frequency calculations: the lack of negative frequencies in the frequency calculation indicates that the structure is optimised to a true minimum, the presence of one negative frequency indicates that a transition state has been reached, more than one negative frequency means that a saddle point structure has been reached. <ref name="book book" />

It proved necessary at times to freeze bonds to locate a transition state however once found all structures were later re-optimised under no symmetry constraints. The '''int=ultrafine''' keywords are expressed in the DFT calculations as optimisation with many low level vibration modes will often proceed more reliably when a larger DFT integration grid is requested. <ref name="integral" />

'''Method 1:''' Opt+Freq, semi empirical, PM6.

'''Method 2:''' Opt+Freq, DFT B3LYP/631G(d).

Both the density function theory (DFT) and semi-empirical methods are able to describe quantum states as many electron systems; they both use the born-opinhiemer approximation where you first solve for the electronic degrees of freedom. <ref name="electrons" /> In DFT the many-electron wavefunction is completely bypassed in favor of the electron density, the variational principle is used to minimise the energy with respect to electron density. However a key problem with this method is that the energy functional is not know. <ref name="electrons" /> Semi-empirical Methods are a simplified versions of Hartree-Fock theory using empirical corrections in order to improve performance; these can be preformed prior to DFT calculations in order to save computational time. <ref name="mug mug" /> The PM6 part of the calculation specifics that the PM6 hamiltonian is to use in the semi-empirical calculation. <ref name="IwantTEA" />

'''Notes:''' When optimising to a transition state I used: TS (Berry), Force constants allowed to calculate once. When optimising to a minimum use: minimum and force constants are allowed to calculate never. Occasional calculations were run on the colleges HPC to save computational time as these servers use more processors than my local computer in college. The 09 version of gaussian suite was used when on windows college computers.

==== Exercises ====

Each exercise is contained on its own page which are linked to below and above the contents section of each page. Each page containing an exercise has Jmol files of all structures used in that exercise at the end of the page, they are accompanied by the 'results summary' section of their opt/freq calculation to confirm the existence of the correct number of negative frequencies and to allow the geometry of each structure to be viewed.

[[Mod:Eb1613 Ex1| Page for Excerise 1]]

[[Mod:Eb1613 Ex2| Page for Excerise 2]]

[[Mod:Eb1613 Ex3| Page for Excerise 3]]

=== Conclusion ===

The transition states were successfully located for multiple reaction following a similar procedure in each case. Orbital analysis was undertaken and HOMO+1, HOMO, LUMO and LUMO-1 levels were explored. The transition states were be further identified by looking into the IRC, thus allowing endo/exo transition states to be confidently labeled. The IRC also revealed information about the reaction coordinate such that no other intermediates existed and that no other transition states were encountered for our reactions.

This computational lab has also highlighed some key difference between the semi-empirical based basis sets and those of basis sets belonging to the density functional theory family. The lab has drawn attention to the importance of chosen the correct basis set and has given me the ability to use Gaussian programs to confidently locate transition states for reactions and highlighted some key methods to further understand the transition states found.

=== Reference ===

<references>
<ref name="waterbottle">https://commons.wikimedia.org/wiki/File:Potential_Energy_Surface_and_Corresponding_Reaction_Coordinate_Diagram.png (accessed 23rd November)</ref>
<ref name="electrons">https://www.quora.com/What-is-the-difference-between-density-functional-theory-and-hartree-fock (accessed 25th November 2016)</ref>
<ref name="integral">http://www.gaussian.com/g_tech/g_ur/k_opt.htm (accessed 25th November 2016)</ref>
<ref name="IwantTEA ">http://www.gaussian.com/g_tech/g_ur/k_semiempirical.html (accessed 25th November 2016)</ref>
<ref name="mug mug ">http://www.cup.uni-muenchen.de/ch/compchem/energy/semi1.html (accessed 25th November 2016)</ref>
<ref name="Hunt "> Dr. Hunt's year 4 lecture course: "Computational Inorganic Chemistry" Lecture4, Handout3. http://www.huntresearchgroup.org.uk/teaching/teaching_comp_chem_year4/L4_PES.pdf (accessed 25th November 2016)</ref>
<ref name="book book "> Foresman, J. and Frisch, A. (1996). Exploring Chemistry With Electronic Structure Methods: A Guide to Using Gaussian. 2nd ed. Guassian, Chapter 1.</ref>
<ref name="woodsman">Woodward, R.B.; Hoffman, R. Angew. Chem. Int. Ed. Engl. 1969, 8, 781. DOI:10.1002/anie.196907811 </ref>
</references>

Rep:Mod:Emily1394

2016-12-02T10:31:31Z

Eb1613:

Page List

[[Mod:eb1613 files| The Calculations Log files can be found here]]

[[Mod:Emily1394| For main Introduction/conclusion page click here]]

[[Mod:Eb1613 Ex1| For Excerise 1 page click here]]

[[Mod:Eb1613 Ex2| For Excerise 2 page click here]]

[[Mod:Eb1613 Ex3| For Excerise 3 page click here]]

= Third Year Computational Lab Transition States - Emily Brown =

Please note each page has its own references at the bottom of the page.

=== Introduction ===

==== Theory ====

'''Transition State:''' This is a maxima on the reaction coordinate graph. At the point the gradient/first derivative is zero and can be referred to as a turning point on the graph.

'''Potential Energy Surface:''' This has 3N-6 dimensions and if you travel in one dimension you can draw a reaction coordinate graph as shown below. <ref name="waterbottle" /> The PES is a function of energy vs every coordinate. <ref name="Hunt" />

[[File:Eb1613_PE_RC.png|thumb|center|Potential energy surface on left and corresponding reaction coordinate graph to right <ref name="waterbottle" /> ]]

Due to the transition state being a turning point on the reaction coordinate graph it can be found by setting the first derivative to zero as at a minima/maxima the gradient is zero. The potential energy surface allows you to travel in directions which may be away from the reaction coordinate you are trying to locate. The potential energy surface has 3N-6 dimensions.<ref name="Hunt" /> Programs like GuassView take advantage of the fact that all these dimensions are positive in curvature apart from one which is the minimum energy path. This results in an imaginary frequency which is the single negative frequency found in the frequency calculation of a transition state geometry. Energy minimas have zero negative frequencies in their frequency calculations and saddle points have multiple. <ref name="Hunt" />

Reactions can be controlled by a number of different factors some of these being sterics and secondary orbital effects. Reactions often compromise between multiple aspects for example a reaction may be sterically disfavored but that particular reaction path could result in good orbital overlap. Secondary oribtal interactions tend to favor the endo-adduct being formed in Diels-Alder reactions.

The reactants tend to form the products via the higher energy transition state which is shown as an energy maximum on the above graph, the energy required to overcome this barrier is known as the activation energy and can be seen in the arrhenius equation as the symbol Ea. The activation energy depends on many factors and programmes like gaussian can be used to estimate this energy and predict whether reactions are likely to occur. For example there are two cis dienes present in the reactant in exercise 3 but only one is involved int he dies alder reactions as the other is known to have a high transition state making it very kinetically unfavourable.

Diels Alder reactions are classified as [4+2] cycloadditions typically between a diene and a dieneophile. The reactions occur via a concerted mechanism with a cyclic transition state. The reaction involves the breaking of 2π bonds and the formation of 2 new σ bonds and a single new π bond. The breaking of the pi bonds is the enthalpic driving force in the reaction as breaking a carbon carbon double bond releases a lot of energy. Cycloaddition reactions have been categorised by Woodward Hoffman to state whether they are thermally or photochemically allowed. Diels-alder reactions can also be classified as normal electron demand or inverse electron demand. Normal electron demand is the case when the HOMO of the diene reacts with the LUMO of the dieneohile, where as inverse electron demand is when the LUMO of the diene reacts with the HOMO of the dieneophile. It has been shown that adding electron donating groups/ electron withdrawing groups to certain positions on the diene/dieneophile can facilitate the Diels-Alder reaction by effecting the energy levels of their HOMO/LUMO thus narrowing the energy gap between the interacting HOMO and LUMO thus facilitating a better orbital overlap.

Cheleotropic reactions is a class of pericyclic reactions which present themselves in exercise 3 which is the cyclic addition of SO2 to a diene. These reactions were exploded by Woodward Hoffman.

==== Computational ====
Initially structures will be optimized using method1 and then using method2. Doing the initial 'tidy up' allows computational time to be saved. Locating transition states has proved difficult for certain systems which results in different approaches being undertaken such as freezing certain bonds by using the '''opt=modredundant''' keywords thus locking atoms together to perform initial optimizations. Another approach is to start from the products or reactants and lengthen certain bonds in an attempt to locate the transition state. Structures were confirmed via frequency calculations: the lack of negative frequencies in the frequency calculation indicates that the structure is optimised to a true minimum, the presence of one negative frequency indicates that a transition state has been reached, more than one negative frequency means that a saddle point structure has been reached. <ref name="book book" />

It proved necessary at times to freeze bonds to locate a transition state however once found all structures were later re-optimised under no symmetry constraints. The '''int=ultrafine''' keywords are expressed in the DFT calculations as optimisation with many low level vibration modes will often proceed more reliably when a larger DFT integration grid is requested. <ref name="integral" />

'''Method 1:''' Opt+Freq, semi empirical, PM6.

'''Method 2:''' Opt+Freq, DFT B3LYP/631G(d).

Both the density function theory (DFT) and semi-empirical methods are able to describe quantum states as many electron systems; they both use the born-opinhiemer approximation where you first solve for the electronic degrees of freedom. <ref name="electrons" /> In DFT the many-electron wavefunction is completely bypassed in favor of the electron density, the variational principle is used to minimise the energy with respect to electron density. However a key problem with this method is that the energy functional is not know. <ref name="electrons" /> Semi-empirical Methods are a simplified versions of Hartree-Fock theory using empirical corrections in order to improve performance; these can be preformed prior to DFT calculations in order to save computational time. <ref name="mug mug" /> The PM6 part of the calculation specifics that the PM6 hamiltonian is to use in the semi-empirical calculation. <ref name="IwantTEA" />

'''Notes:''' When optimising to a transition state I used: TS (Berry), Force constants allowed to calculate once. When optimising to a minimum use: minimum and force constants are allowed to calculate never. Occasional calculations were run on the colleges HPC to save computational time as these servers use more processors than my local computer in college. The 09 version of gaussian suite was used when on windows college computers.

==== Exercises ====

Each exercise is contained on its own page which are linked to below and above the contents section of each page. Each page containing an exercise has Jmol files of all structures used in that exercise at the end of the page, they are accompanied by the 'results summary' section of their opt/freq calculation to confirm the existence of the correct number of negative frequencies and to allow the geometry of each structure to be viewed.

[[Mod:Eb1613 Ex1| Page for Excerise 1]]

[[Mod:Eb1613 Ex2| Page for Excerise 2]]

[[Mod:Eb1613 Ex3| Page for Excerise 3]]

=== Conclusion ===

The transition states were successfully located for multiple reaction following a similar procedure in each case. Orbital analysis was undertaken and HOMO+1, HOMO, LUMO and LUMO-1 levels were explored. The transition states were be further identified by looking into the IRC, thus allowing endo/exo transition states to be confidently labeled. The IRC also revealed information about the reaction coordinate such that no other intermediates existed and that no other transition states were encountered for our reactions.

This computational lab has also highlighed some key difference between the semi-empirical based basis sets and those of basis sets belonging to the density functional theory family. The lab has drawn attention to the importance of chosen the correct basis set and has given me the ability to use Gaussian programs to confidently locate transition states for reactions and highlighted some key methods to further understand the transition states found.

=== Reference ===

<references>
<ref name="waterbottle">https://commons.wikimedia.org/wiki/File:Potential_Energy_Surface_and_Corresponding_Reaction_Coordinate_Diagram.png (accessed 23rd November)</ref>
<ref name="electrons">https://www.quora.com/What-is-the-difference-between-density-functional-theory-and-hartree-fock (accessed 25th November 2016)</ref>
<ref name="integral">http://www.gaussian.com/g_tech/g_ur/k_opt.htm (accessed 25th November 2016)</ref>
<ref name="IwantTEA ">http://www.gaussian.com/g_tech/g_ur/k_semiempirical.html (accessed 25th November 2016)</ref>
<ref name="mug mug ">http://www.cup.uni-muenchen.de/ch/compchem/energy/semi1.html (accessed 25th November 2016)</ref>
<ref name="Hunt "> Dr. Hunt's year 4 lecture course: "Computational Inorganic Chemistry" Lecture4, Handout3. http://www.huntresearchgroup.org.uk/teaching/teaching_comp_chem_year4/L4_PES.pdf (accessed 25th November 2016)</ref>
<ref name="book book "> Foresman, J. and Frisch, A. (1996). Exploring Chemistry With Electronic Structure Methods: A Guide to Using Gaussian. 2nd ed. Guassian, Chapter 1.</ref>
<ref name="woodsman">Woodward, R.B.; Hoffman, R. Angew. Chem. Int. Ed. Engl. 1969, 8, 781. DOI:10.1002/anie.196907811 </ref>
</references>

Rep:Mod:Emily1394

2016-12-02T10:30:45Z

Eb1613:

Page List

[[Mod:eb1613 files| The Calculations Log files can be found here]]

[[Mod:Emily1394| For main Introduction/conclusion page click here]]

[[Mod:Eb1613 Ex1| For Excerise 1 page click here]]

[[Mod:Eb1613 Ex2| For Excerise 2 page click here]]

[[Mod:Eb1613 Ex3| For Excerise 3 page click here]]

= Third Year Computational Lab Transition States - Emily Brown =

Please note each page has its own references at the bottom of the page.

=== Introduction ===

==== Theory ====

'''Transition State:''' This is a maxima on the reaction coordinate graph. At the point the gradient/first derivative is zero and can be referred to as a turning point on the graph.

'''Potential Energy Surface:''' This has 3N-6 dimensions and if you travel in one dimension you can draw a reaction coordinate graph as shown below. <ref name="waterbottle" /> The PES is a function of energy vs every coordinate. <ref name="Hunt" />

[[File:Eb1613_PE_RC.png|thumb|center|Potential energy surface on left and corresponding reaction coordinate graph to right <ref name="waterbottle" /> ]]

Due to the transition state being a turning point on the reaction coordinate graph it can be found by setting the first derivative to zero as at a minima/maxima the gradient is zero. The potential energy surface allows you to travel in directions which may be away from the reaction coordinate you are trying to locate. The potential energy surface has 3N-6 dimensions.<ref name="Hunt" /> Programs like GuassView take advantage of the fact that all these dimensions are positive in curvature apart from one which is the minimum energy path. This results in an imaginary frequency which is the single negative frequency found in the frequency calculation of a transition state geometry. Energy minimas have zero negative frequencies in their frequency calculations and saddle points have multiple. <ref name="Hunt" />

Reactions can be controlled by a number of different factors some of these being sterics and secondary orbital effects. Reactions often compromise between multiple aspects for example a reaction may be sterically disfavored but that particular reaction path could result in good orbital overlap. Secondary oribtal interactions tend to favor the endo-adduct being formed in Diels-Alder reactions.

The reactants tend to form the products via the higher energy transition state which is shown as an energy maximum on the above graph, the energy required to overcome this barrier is known as the activation energy and can be seen in the arrhenius equation as the symbol Ea. The activation energy depends on many factors and programmes like gaussian can be used to estimate this energy and predict whether reactions are likely to occur. For example there are two cis dienes present in the reactant in exercise 3 but only one is involved int he dies alder reactions as the other is known to have a high transition state making it very kinetically unfavourable.

Diels Alder reactions are classified as [4+2] cycloadditions typically between a diene and a dieneophile. The reactions occur via a concerted mechanism with a cyclic transition state. The reaction involves the breaking of 2π bonds and the formation of 2 new σ bonds and a single new π bond. The breaking of the pi bonds is the enthalpic driving force in the reaction as breaking a carbon carbon double bond releases a lot of energy. Cycloaddition reactions have been categorised by Woodward Hoffman to state whether they are thermally or photochemically allowed. Diels-alder reactions can also be classified as normal electron demand or inverse electron demand. Normal electron demand is the case when the HOMO of the diene reacts with the LUMO of the dieneohile, where as inverse electron demand is when the LUMO of the diene reacts with the HOMO of the dieneophile. It has been shown that adding electron donating groups/ electron withdrawing groups to certain positions on the diene/dieneophile can facilitate the Diels-Alder reaction by effecting the energy levels of their HOMO/LUMO thus narrowing the energy gap between the interacting HOMO and LUMO thus facilitating a better orbital overlap.

Cheleotropic reactions is a class of pericyclic reactions which present themselves in exercise 3 which is the cyclic addition of SO2 to a diene. These reactions were exploded by Woodward Hoffman.

==== Computational ====
Initially structures will be optimized using method1 and then using method2. Doing the initial 'tidy up' allows computational time to be saved. Locating transition states has proved difficult for certain systems which results in different approaches being undertaken such as freezing certain bonds by using the '''opt=modredundant''' keywords thus locking atoms together to perform initial optimizations. Another approach is to start from the products or reactants and lengthen certain bonds in an attempt to locate the transition state. Structures were confirmed via frequency calculations: the lack of negative frequencies in the frequency calculation indicates that the structure is optimised to a true minimum, the presence of one negative frequency indicates that a transition state has been reached, more than one negative frequency means that a saddle point structure has been reached. <ref name="book book" />

It proved necessary at times to freeze bonds to locate a transition state however once found all structures were later re-optimised under no symmetry constraints. The '''int=ultrafine''' keywords are expressed in the DFT calculations as optimisation with many low level vibration modes will often proceed more reliably when a larger DFT integration grid is requested. <ref name="integral" />

'''Method 1:''' Opt+Freq, semi empirical, PM6.

'''Method 2:''' Opt+Freq, DFT B3LYP/631G(d).

Both the density function theory (DFT) and semi-empirical methods are able to describe quantum states as many electron systems; they both use the born-opinhiemer approximation where you first solve for the electronic degrees of freedom. <ref name="electrons" /> In DFT the many-electron wavefunction is completely bypassed in favor of the electron density, the variational principle is used to minimise the energy with respect to electron density. However a key problem with this method is that the energy functional is not know. <ref name="electrons" /> Semi-empirical Methods are a simplified versions of Hartree-Fock theory using empirical corrections in order to improve performance; these can be preformed prior to DFT calculations in order to save computational time. <ref name="mug mug" /> The PM6 part of the calculation specifics that the PM6 hamiltonian is to use in the semi-empirical calculation. <ref name="IwantTEA" />

'''Notes:''' When optimising to a transition state I used: TS (Berry), Force constants allowed to calculate once. When optimising to a minimum use: minimum and force constants are allowed to calculate never. Occasional calculations were run on the colleges HPC to save computational time as these servers use more processors than my local computer in college. The 09 version of gaussian suite was used when on windows college computers.

==== Exercises ====

Each exercise is contained on its own page which are linked to below and above the contents section of each page. Each page containing an exercise has Jmol files of all structures used in that exercise at the end of the page, they are accompanied by the 'results summary' section of their opt/freq calculation to confirm the existence of the correct number of negative frequencies and to allow the geometry of each structure to be viewed.

[[Mod:Eb1613 Ex1| Page for Excerise 1]]

[[Mod:Eb1613 Ex2| Page for Excerise 2]]

[[Mod:Eb1613 Ex3| Page for Excerise 3]]

=== Conclusion ===

The transition states were successfully located for multiple reaction following a similar procedure in each case. Orbital analysis was undertaken and HOMO+1, HOMO, LUMO and LUMO-1 levels were explored. The transition states were be further identified by looking into the IRC, thus allowing endo/exo transition states to be confidently labeled. The IRC also revealed information about the reaction coordinate such that no other intermediates existed and that no other transition states were encountered for our reactions.

This computational lab has also highlighed some key difference between the semi-empirical based basis sets and those of basis sets belonging to the density functional theory family. The lab has drawn attention to the importance of chosen the correct basis set and has given me the ability to use Gaussian programs to confidently locate transition states for reactions and highlighted some key methods to further understand the transition states found.

=== Reference ===

<references>
<ref name="waterbottle">https://commons.wikimedia.org/wiki/File:Potential_Energy_Surface_and_Corresponding_Reaction_Coordinate_Diagram.png (accessed 23rd November)</ref>
<ref name="electrons">https://www.quora.com/What-is-the-difference-between-density-functional-theory-and-hartree-fock (accessed 25th November 2016)</ref>
<ref name="integral">http://www.gaussian.com/g_tech/g_ur/k_opt.htm (accessed 25th November 2016)</ref>
<ref name="IwantTEA ">http://www.gaussian.com/g_tech/g_ur/k_semiempirical.html (accessed 25th November 2016)</ref>
<ref name="mug mug ">http://www.cup.uni-muenchen.de/ch/compchem/energy/semi1.html (accessed 25th November 2016)</ref>
<ref name="Hunt "> Dr. Hunt's year 4 lecture course: "Computational Inorganic Chemistry" Lecture4, Handout3. http://www.huntresearchgroup.org.uk/teaching/teaching_comp_chem_year4/L4_PES.pdf (accessed 25th November 2016)</ref>
<ref name="book book "> Foresman, J. and Frisch, A. (1996). Exploring Chemistry With Electronic Structure Methods: A Guide to Using Gaussian. 2nd ed. Guassian, Chapter 1.)</ref>
</references>

Rep:Mod:Emily1394

2016-12-02T10:28:03Z

Eb1613:

Page List

[[Mod:eb1613 files| The Calculations Log files can be found here]]

[[Mod:Emily1394| For main Introduction/conclusion page click here]]

[[Mod:Eb1613 Ex1| For Excerise 1 page click here]]

[[Mod:Eb1613 Ex2| For Excerise 2 page click here]]

[[Mod:Eb1613 Ex3| For Excerise 3 page click here]]

= Third Year Computational Lab Transition States - Emily Brown =

Please note each page has its own references at the bottom of the page.

=== Introduction ===

==== Theory ====

'''Transition State:''' This is a maxima on the reaction coordinate graph. At the point the gradient/first derivative is zero and can be referred to as a turning point on the graph.

'''Potential Energy Surface:''' This has 3N-6 dimensions and if you travel in one dimension you can draw a reaction coordinate graph as shown below. <ref name="waterbottle" /> The PES is a function of energy vs every coordinate. <ref name="Hunt" />

[[File:Eb1613_PE_RC.png|thumb|center|Potential energy surface on left and corresponding reaction coordinate graph to right <ref name="waterbottle" /> ]]

Due to the transition state being a turning point on the reaction coordinate graph it can be found by setting the first derivative to zero as at a minima/maxima the gradient is zero. The potential energy surface allows you to travel in directions which may be away from the reaction coordinate you are trying to locate. The potential energy surface has 3N-6 dimensions.<ref name="Hunt" /> Programs like GuassView take advantage of the fact that all these dimensions are positive in curvature apart from one which is the minimum energy path. This results in an imaginary frequency which is the single negative frequency found in the frequency calculation of a transition state geometry. Energy minimas have zero negative frequencies in their frequency calculations and saddle points have multiple. <ref name="Hunt" />

Reactions can be controlled by a number of different factors some of these being sterics and secondary orbital effects. Reactions often compromise between multiple aspects for example a reaction may be sterically disfavored but that particular reaction path could result in good orbital overlap. Secondary oribtal interactions tend to favor the endo-adduct being formed in Diels-Alder reactions.

The reactants tend to form the products via the higher energy transition state which is shown as an energy maximum on the above graph, the energy required to overcome this barrier is known as the activation energy and can be seen in the arrhenius equation as the symbol Ea. The activation energy depends on many factors and programmes like gaussian can be used to estimate this energy and predict whether reactions are likely to occur. For example there are two cis dienes present in the reactant in exercise 3 but only one is involved int he dies alder reactions as the other is known to have a high transition state making it very kinetically unfavourable.

Diels Alder reactions are classified as [4+2] cycloadditions typically between a diene and a dieneophile. The reactions occur via a concerted mechanism with a cyclic transition state. The reaction involves the breaking of 2π bonds and the formation of 2 new σ bonds and a single new π bond. The breaking of the pi bonds is the enthalpic driving force in the reaction as breaking a carbon carbon double bond releases a lot of energy. Cycloaddition reactions have been categorised by Woodward Hoffman to state whether they are thermally or photochemically allowed. Diels-alder reactions can also be classified as normal electron demand or inverse electron demand. Normal electron demand is the case when the HOMO of the diene reacts with the LUMO of the dieneohile, where as inverse electron demand is when the LUMO of the diene reacts with the HOMO of the dieneophile. It has been shown that adding electron donating groups/ electron withdrawing groups to certain positions on the diene/dieneophile can facilitate the Diels-Alder reaction by effecting the energy levels of their HOMO/LUMO thus narrowing the energy gap between the interacting HOMO and LUMO thus facilitating a better orbital overlap.

==== Computational ====
Initially structures will be optimized using method1 and then using method2. Doing the initial 'tidy up' allows computational time to be saved. Locating transition states has proved difficult for certain systems which results in different approaches being undertaken such as freezing certain bonds by using the '''opt=modredundant''' keywords thus locking atoms together to perform initial optimizations. Another approach is to start from the products or reactants and lengthen certain bonds in an attempt to locate the transition state. Structures were confirmed via frequency calculations: the lack of negative frequencies in the frequency calculation indicates that the structure is optimised to a true minimum, the presence of one negative frequency indicates that a transition state has been reached, more than one negative frequency means that a saddle point structure has been reached. <ref name="book book" />

It proved necessary at times to freeze bonds to locate a transition state however once found all structures were later re-optimised under no symmetry constraints. The '''int=ultrafine''' keywords are expressed in the DFT calculations as optimisation with many low level vibration modes will often proceed more reliably when a larger DFT integration grid is requested. <ref name="integral" />

'''Method 1:''' Opt+Freq, semi empirical, PM6.

'''Method 2:''' Opt+Freq, DFT B3LYP/631G(d).

Both the density function theory (DFT) and semi-empirical methods are able to describe quantum states as many electron systems; they both use the born-opinhiemer approximation where you first solve for the electronic degrees of freedom. <ref name="electrons" /> In DFT the many-electron wavefunction is completely bypassed in favor of the electron density, the variational principle is used to minimise the energy with respect to electron density. However a key problem with this method is that the energy functional is not know. <ref name="electrons" /> Semi-empirical Methods are a simplified versions of Hartree-Fock theory using empirical corrections in order to improve performance; these can be preformed prior to DFT calculations in order to save computational time. <ref name="mug mug" /> The PM6 part of the calculation specifics that the PM6 hamiltonian is to use in the semi-empirical calculation. <ref name="IwantTEA" />

'''Notes:''' When optimising to a transition state I used: TS (Berry), Force constants allowed to calculate once. When optimising to a minimum use: minimum and force constants are allowed to calculate never. Occasional calculations were run on the colleges HPC to save computational time as these servers use more processors than my local computer in college. The 09 version of gaussian suite was used when on windows college computers.

==== Exercises ====

Each exercise is contained on its own page which are linked to below and above the contents section of each page. Each page containing an exercise has Jmol files of all structures used in that exercise at the end of the page, they are accompanied by the 'results summary' section of their opt/freq calculation to confirm the existence of the correct number of negative frequencies and to allow the geometry of each structure to be viewed.

[[Mod:Eb1613 Ex1| Page for Excerise 1]]

[[Mod:Eb1613 Ex2| Page for Excerise 2]]

[[Mod:Eb1613 Ex3| Page for Excerise 3]]

=== Conclusion ===

The transition states were successfully located for multiple reaction following a similar procedure in each case. Orbital analysis was undertaken and HOMO+1, HOMO, LUMO and LUMO-1 levels were explored. The transition states were be further identified by looking into the IRC, thus allowing endo/exo transition states to be confidently labeled. The IRC also revealed information about the reaction coordinate such that no other intermediates existed and that no other transition states were encountered for our reactions.

This computational lab has also highlighed some key difference between the semi-empirical based basis sets and those of basis sets belonging to the density functional theory family. The lab has drawn attention to the importance of chosen the correct basis set and has given me the ability to use Gaussian programs to confidently locate transition states for reactions and highlighted some key methods to further understand the transition states found.

=== Reference ===

<references>
<ref name="waterbottle">https://commons.wikimedia.org/wiki/File:Potential_Energy_Surface_and_Corresponding_Reaction_Coordinate_Diagram.png (accessed 23rd November)</ref>
<ref name="electrons">https://www.quora.com/What-is-the-difference-between-density-functional-theory-and-hartree-fock (accessed 25th November 2016)</ref>
<ref name="integral">http://www.gaussian.com/g_tech/g_ur/k_opt.htm (accessed 25th November 2016)</ref>
<ref name="IwantTEA ">http://www.gaussian.com/g_tech/g_ur/k_semiempirical.html (accessed 25th November 2016)</ref>
<ref name="mug mug ">http://www.cup.uni-muenchen.de/ch/compchem/energy/semi1.html (accessed 25th November 2016)</ref>
<ref name="Hunt "> Dr. Hunt's year 4 lecture course: "Computational Inorganic Chemistry" Lecture4, Handout3. http://www.huntresearchgroup.org.uk/teaching/teaching_comp_chem_year4/L4_PES.pdf (accessed 25th November 2016)</ref>
<ref name="book book "> Foresman, J. and Frisch, A. (1996). Exploring Chemistry With Electronic Structure Methods: A Guide to Using Gaussian. 2nd ed. Guassian, Chapter 1.)</ref>
</references>

Rep:Mod:Emily1394

2016-12-01T22:56:32Z

Eb1613: /* Theory */

Page List

[[Mod:eb1613 files| The Calculations Log files can be found here]]

[[Mod:Emily1394| For main Introduction/conclusion page click here]]

[[Mod:Eb1613 Ex1| For Excerise 1 page click here]]

[[Mod:Eb1613 Ex2| For Excerise 2 page click here]]

[[Mod:Eb1613 Ex3| For Excerise 3 page click here]]

= Third Year Computational Lab Transition States - Emily Brown =

Please note each page has its own references at the bottom of the page.

=== Introduction ===

==== Theory ====

'''Transition State:''' This is a maxima on the reaction coordinate graph. At the point the gradient/first derivative is zero and can be referred to as a turning point on the graph.

'''Potential Energy Surface:''' This has 3N-6 dimensions and if you travel in one dimension you can draw a reaction coordinate graph as shown below. <ref name="waterbottle" /> The PES is a function of energy vs every coordinate. <ref name="Hunt" />

[[File:Eb1613_PE_RC.png|thumb|center|Potential energy surface on left and corresponding reaction coordinate graph to right <ref name="waterbottle" /> ]]

Due to the transition state being a turning point on the reaction coordinate graph it can be found by setting the first derivative to zero as at a minima/maxima the gradient is zero. The potential energy surface allows you to travel in directions which may be away from the reaction coordinate you are trying to locate. The potential energy surface has 3N-6 dimensions.<ref name="Hunt" /> Programs like GuassView take advantage of the fact that all these dimensions are positive in curvature apart from one which is the minimum energy path. This results in an imaginary frequency which is the single negative frequency found in the frequency calculation of a transition state geometry. Energy minimas have zero negative frequencies in their frequency calculations and saddle points have multiple. <ref name="Hunt" />

Reactions can be controlled by a number of different factors some of these being sterics and secondary orbital effects. Reactions often compromise between multiple aspects for example a reaction may be sterically disfavored but that particular reaction path could result in good orbital overlap.

The reactants tend to form the products via the higher energy transition state which is shown as an energy maximum on the above graph, the energy required to overcome this barrier is known as the activation energy and can be seen in the arrhenius equation as the symbol Ea. The activation energy depends on many factors and programmes like gaussian can be used to estimate this energy and predict whether reactions are likely to occur. For example there are two cis dienes present in the reactant in exercise 3 but only one is involved int he dies alder reactions as the other is known to have a high transition state making it very kinetically unfavourable.

Diels Alder reactions are classified as [4+2] cycloadditions typically between a diene and a dieneophile. The reactions occur via a concerted mechanism with a cyclic transition state. The reaction involves the breaking of 2 pi bonds and the formation of 2 new sigma bonds and a single pi new pi bond. The breaking of the pi bonds is the enthalpic driving force in the reaction as breaking a carbon carbon double bond releases a lot of energy. Cycloaddition reactions have been categorised by Woodward Hoffman to state whether they are thermally or photochemically allowed. Diels-alder reactions can also be classified as normal electron demand or inverse electron demand. Normal electron demand is the case when the HOMO of the diene reacts with the LUMO of the dieneohile, where as inverse electron demand is when the LUMO of the diene reacts with the HOMO of the dieneophile. it has been shown that adding electron donating groups/ electron withdrawing groups to certain positions on the diene/dieneophile can facilitate the Diels-Alder reaction by effecting the energy levels of their HOMO/LUMO thus narrowing the energy gap between the interacting HOMO and LUMO thus facilitating a better orbital overlap.

==== Computational ====
Initially structures will be optimized using method1 and then using method2. Doing the initial 'tidy up' allows computational time to be saved. Locating transition states has proved difficult for certain systems which results in different approaches being undertaken such as freezing certain bonds by using the opt=modredundant keywords thus locking atoms together to perform initial optimizations. Another approach is to start from the products or reactants and lengthen certain bonds in an attempt to locate the transition state. Structures were confirmed via frequency calculations: the lack of negative frequencies in the frequency calculation indicates that the structure is optimised to a true minimum, the presence of one negative frequency indicates that a transition state has been reached, more than one negative frequency means that a saddle point structure has been reached. <ref name="book book" />

It proved necessary at times to freeze bonds to locate a transition state however once found all structures were later re-optimised under no symmetry constraints. The int=ultrafine keywords are expressed in the DFT calculations as optimisation with many low level vibration modes will often proceed more reliably when a larger DFT integration grid is requested. <ref name="integral" />

'''Method 1:''' Opt+Freq, semi empirical, PM6.

'''Method 2:''' Opt+Freq, DFT B3LYP/631G(d).

Both the density function theory (DFT) and semi-empirical methods are able to describe quantum states as many electron systems; they both use the born-opinhiemer approximation where you first solve for the electronic degrees of freedom. <ref name="electrons" /> In DFT the many-electron wavefunction is completely bypassed in favor of the electron density, the variational principle is used to minimise the energy with respect to electron density. However a key problem with this method is that the energy functional is not know. <ref name="electrons" /> Semi-empirical Methods are a simplified versions of Hartree-Fock theory using empirical corrections in order to improve performance; these can be preformed prior to DFT calculations in order to save computational time. <ref name="mug mug" /> The PM6 part of the calculation specifics that the PM6 hamiltonian is to use in the semi-empirical calculation. <ref name="IwantTEA" />

'''Notes:''' When optimising to a transition state I used: TS (Berry), Force constants allowed to calculate once. When optimising to a minimum use: minimum and force constants are allowed to calculate never. Occasional calculations were run on the colleges HPC to save computational time as these servers use more processors than my local computer in college. The 09 version of gaussian suite was used when on windows college computers.

==== Exercises ====

Each exercise is contained on its own page which are linked to below and above the contents section of each page. Each page containing an exercise has Jmol files of all structures used in that exercise at the end of the page, they are accompanied by the 'results summary' section of their opt/freq calculation to confirm the existence of the correct number of negative frequencies and to allow the geometry of each structure to be viewed.

[[Mod:Eb1613 Ex1| Page for Excerise 1]]

[[Mod:Eb1613 Ex2| Page for Excerise 2]]

[[Mod:Eb1613 Ex3| Page for Excerise 3]]

=== Conclusion ===

The transition states were successfully located for multiple reaction following a similar procedure in each case. Orbital analysis was undertaken and HOMO+1, HOMO, LUMO and LUMO-1 levels were explored. The transition states were be further identified by looking into the IRC, thus allowing endo/exo transition states to be confidently labeled. The IRC also revealed information about the reaction coordinate such that no other intermediates existed and that no other transition states were encountered for our reactions.

This computational lab has also highlighed some key difference between the semi-empirical based basis sets and those of basis sets belonging to the density functional theory family. The lab has drawn attention to the importance of chosen the correct basis set and has given me the ability to use Gaussian programs to confidently locate transition states for reactions and highlighted some key methods to further understand the transition states found.

=== Reference ===

<references>
<ref name="waterbottle">https://commons.wikimedia.org/wiki/File:Potential_Energy_Surface_and_Corresponding_Reaction_Coordinate_Diagram.png (accessed 23rd November)</ref>
<ref name="electrons">https://www.quora.com/What-is-the-difference-between-density-functional-theory-and-hartree-fock (accessed 25th November 2016)</ref>
<ref name="integral">http://www.gaussian.com/g_tech/g_ur/k_opt.htm (accessed 25th November 2016)</ref>
<ref name="IwantTEA ">http://www.gaussian.com/g_tech/g_ur/k_semiempirical.html (accessed 25th November 2016)</ref>
<ref name="mug mug ">http://www.cup.uni-muenchen.de/ch/compchem/energy/semi1.html (accessed 25th November 2016)</ref>
<ref name="Hunt "> Dr. Hunt's year 4 lecture course: "Computational Inorganic Chemistry" Lecture4, Handout3. http://www.huntresearchgroup.org.uk/teaching/teaching_comp_chem_year4/L4_PES.pdf (accessed 25th November 2016)</ref>
<ref name="book book "> Foresman, J. and Frisch, A. (1996). Exploring Chemistry With Electronic Structure Methods: A Guide to Using Gaussian. 2nd ed. Guassian, Chapter 1.)</ref>
</references>

Rep:Mod:Emily1394

2016-12-01T22:55:34Z

Eb1613: /* Theory */

Page List

[[Mod:eb1613 files| The Calculations Log files can be found here]]

[[Mod:Emily1394| For main Introduction/conclusion page click here]]

[[Mod:Eb1613 Ex1| For Excerise 1 page click here]]

[[Mod:Eb1613 Ex2| For Excerise 2 page click here]]

[[Mod:Eb1613 Ex3| For Excerise 3 page click here]]

= Third Year Computational Lab Transition States - Emily Brown =

Please note each page has its own references at the bottom of the page.

=== Introduction ===

==== Theory ====

'''Transition State:''' This is a maxima on the reaction coordinate graph. At the point the gradient/first derivative is zero and can be referred to as a turning point on the graph.

'''Potential Energy Surface:''' This has 3N-6 dimensions and if you travel in one dimension you can draw a reaction coordinate graph as shown below. <ref name="waterbottle" /> The PES is a function of energy vs every coordinate. <ref name="Hunt" />

[[File:Eb1613_PE_RC.png|thumb|center|Potential energy surface on left and corresponding reaction coordinate graph to right <ref name="waterbottle" /> ]]

Due to the transition state being a turning point on the reaction coordinate graph it can be found by setting the first derivative to zero as at a minima/maxima the gradient is zero. The potential energy surface allows you to travel in directions which may be away from the reaction coordinate you are trying to locate. The potential energy surface has 3N-6 dimensions.<ref name="Hunt" /> Programs like GuassView take advantage of the fact that all these dimensions are positive in curvature apart from one which is the minimum energy path. This results in an imaginary frequency which is the single negative frequency found in the frequency calculation of a transition state geometry. Energy minimas have zero negative frequencies in their frequency calculations and saddle points have multiple. <ref name="Hunt" />

Reactions can be controlled by a number of different factors some of these being sterics and secondary orbital effects. Reactions often compromise between multiple aspects for example a reaction may be sterically disfavored but that particular reaction path could result in good orbital overlap.

The reactants tend to form the products via the higher energy transition state which is shown as an energy maximum on the above graph, the energy required to overcome this barrier is known as the activation energy and can be seen in the arrhenius equation as the symbol Ea. The activation energy depends on many factors and programmes like gaussian can be used to estimate this energy and predict whether reactions are likely to occur. For example there are two cis dienes present in the reactant in exercise 3 but only one is involved int he dies alder reactions as the other is known to have a high transition state making it very kinetically unfavourable.

Diels Alder reactions are classified as [4+2] cycloadditions typically between a diene and a dieneophile. The reactions occur via a concerted mechanism with a cyclic transition state. The reaction involves the breaking of 2 pi bonds and the formation of 2 new sigma bonds and a single pi new pi bond. The breaking of the pi bonds is the enthalpic driving force in the reaction as breaking a carbon carbon double bond releases a lot of energy. Cycloaddition reactions have been categorised by Woodward Hoffman to state whether they are thermally or photochemically allowed. Diels-alder reactions can also be classified as normal electron demand or inverse electron demand. Normal electron demand is the case when the HOMO of the diene reacts with the LUMO of the dieneohile, where as inverse electron demand is when the LUMO of the diene reacts with the HOMO of the dieneophile. it has been shown that adding electron donating groups/ electron withdrawing groups to certain positions on the diene/dieneophile can facility the diets alder reaction by effecting the energy levels of their HOMO/LUMO thus narrowing the energy gap between them facilitating a better orbital overlap.

==== Computational ====
Initially structures will be optimized using method1 and then using method2. Doing the initial 'tidy up' allows computational time to be saved. Locating transition states has proved difficult for certain systems which results in different approaches being undertaken such as freezing certain bonds by using the opt=modredundant keywords thus locking atoms together to perform initial optimizations. Another approach is to start from the products or reactants and lengthen certain bonds in an attempt to locate the transition state. Structures were confirmed via frequency calculations: the lack of negative frequencies in the frequency calculation indicates that the structure is optimised to a true minimum, the presence of one negative frequency indicates that a transition state has been reached, more than one negative frequency means that a saddle point structure has been reached. <ref name="book book" />

It proved necessary at times to freeze bonds to locate a transition state however once found all structures were later re-optimised under no symmetry constraints. The int=ultrafine keywords are expressed in the DFT calculations as optimisation with many low level vibration modes will often proceed more reliably when a larger DFT integration grid is requested. <ref name="integral" />

'''Method 1:''' Opt+Freq, semi empirical, PM6.

'''Method 2:''' Opt+Freq, DFT B3LYP/631G(d).

Both the density function theory (DFT) and semi-empirical methods are able to describe quantum states as many electron systems; they both use the born-opinhiemer approximation where you first solve for the electronic degrees of freedom. <ref name="electrons" /> In DFT the many-electron wavefunction is completely bypassed in favor of the electron density, the variational principle is used to minimise the energy with respect to electron density. However a key problem with this method is that the energy functional is not know. <ref name="electrons" /> Semi-empirical Methods are a simplified versions of Hartree-Fock theory using empirical corrections in order to improve performance; these can be preformed prior to DFT calculations in order to save computational time. <ref name="mug mug" /> The PM6 part of the calculation specifics that the PM6 hamiltonian is to use in the semi-empirical calculation. <ref name="IwantTEA" />

'''Notes:''' When optimising to a transition state I used: TS (Berry), Force constants allowed to calculate once. When optimising to a minimum use: minimum and force constants are allowed to calculate never. Occasional calculations were run on the colleges HPC to save computational time as these servers use more processors than my local computer in college. The 09 version of gaussian suite was used when on windows college computers.

==== Exercises ====

Each exercise is contained on its own page which are linked to below and above the contents section of each page. Each page containing an exercise has Jmol files of all structures used in that exercise at the end of the page, they are accompanied by the 'results summary' section of their opt/freq calculation to confirm the existence of the correct number of negative frequencies and to allow the geometry of each structure to be viewed.

[[Mod:Eb1613 Ex1| Page for Excerise 1]]

[[Mod:Eb1613 Ex2| Page for Excerise 2]]

[[Mod:Eb1613 Ex3| Page for Excerise 3]]

=== Conclusion ===

The transition states were successfully located for multiple reaction following a similar procedure in each case. Orbital analysis was undertaken and HOMO+1, HOMO, LUMO and LUMO-1 levels were explored. The transition states were be further identified by looking into the IRC, thus allowing endo/exo transition states to be confidently labeled. The IRC also revealed information about the reaction coordinate such that no other intermediates existed and that no other transition states were encountered for our reactions.

This computational lab has also highlighed some key difference between the semi-empirical based basis sets and those of basis sets belonging to the density functional theory family. The lab has drawn attention to the importance of chosen the correct basis set and has given me the ability to use Gaussian programs to confidently locate transition states for reactions and highlighted some key methods to further understand the transition states found.

=== Reference ===

<references>
<ref name="waterbottle">https://commons.wikimedia.org/wiki/File:Potential_Energy_Surface_and_Corresponding_Reaction_Coordinate_Diagram.png (accessed 23rd November)</ref>
<ref name="electrons">https://www.quora.com/What-is-the-difference-between-density-functional-theory-and-hartree-fock (accessed 25th November 2016)</ref>
<ref name="integral">http://www.gaussian.com/g_tech/g_ur/k_opt.htm (accessed 25th November 2016)</ref>
<ref name="IwantTEA ">http://www.gaussian.com/g_tech/g_ur/k_semiempirical.html (accessed 25th November 2016)</ref>
<ref name="mug mug ">http://www.cup.uni-muenchen.de/ch/compchem/energy/semi1.html (accessed 25th November 2016)</ref>
<ref name="Hunt "> Dr. Hunt's year 4 lecture course: "Computational Inorganic Chemistry" Lecture4, Handout3. http://www.huntresearchgroup.org.uk/teaching/teaching_comp_chem_year4/L4_PES.pdf (accessed 25th November 2016)</ref>
<ref name="book book "> Foresman, J. and Frisch, A. (1996). Exploring Chemistry With Electronic Structure Methods: A Guide to Using Gaussian. 2nd ed. Guassian, Chapter 1.)</ref>
</references>

Rep:Mod:Eb1613 Ex3

2016-12-01T22:40:30Z

Eb1613: /* Transition states */

Page List

[[Mod:eb1613 files| The Calculations Log files can be found here]]

[[Mod:Emily1394| For main Introduction/conclusion page click here]]

[[Mod:Eb1613 Ex1| For Excerise 1 page click here]]

[[Mod:Eb1613 Ex2| For Excerise 2 page click here]]

[[Mod:Eb1613 Ex3| For Excerise 3 page click here]]

= Third Year Computational Lab Transition States - Emily Brown =

=== Exercise 3 ===

[[File:Exercise2_reaction_emily.png]]

Both cheletropic and Diels-Alder reactions are possible for the above reactants.

Initially the structures were optimized to the semi-empirical PM6 level and later the geometries were re-optimised to the DFT 6-31G(d)/b3LYP level of calculation. The reactants were aligned in different conformations and certain bonds were frozen to find the three transition states shown below. Every structure given has been optimized to the higher accuracy DFT 6-31G(d)/b3LYP level.

Unfortunately there was not enough time to investigate the other cis-butadiene fragment successfully.

==== Transition states ====

Below gif files are given to show the negative frequency vibration for the transition states which were located.

{| class="wikitable" border="1"
! style="background: #38A5A5;" | Exo Transition State. Negative Frequency = -198.65 cm-1
|-
|style="background: white;" | [[File:Diels_alder_ts_1_movie.gif]]
|-
! style="background: #38A5A5;" | Endo Transition State. Negative Frequency = -200.42 cm-1
|-
|style="background: white;" | [[File:Diels_alder_ts_2_movie.gif]]
|-
! style="background: #38A5A5;" | Cheletropic Transition State. Negative Frequency = -221.18 cm-1
|-
|style="background: white;" | [[File:Chele_TS_movie_eb1613.gif]]
|}

==== Thermochemistry anaylsis ====

The energy profile was first plotted using excel and then using chemdraw to highlight the differences between the endo and exo paths.

{| class="wikitable" border="1"
|-
| style="background: white;" | [[File:Energy profile ex3 eb1613.png]] || style="background: white;" | [[File:Screen_Shot_2016-12-01_at_21.54.33.png]]
|}

Energy values given relative to the reactants in KJ/mol, from the values the Endo route appears to be the preferred route.

{| class="wikitable" border="1"
!style="background: #38A5A5;" | !!style="background: #38A5A5;" | Reactants !! style="background: #38A5A5;" | Transition state !! style="background: #38A5A5;" | Products
|-
| style="background: #38A5A5;" | Endo ||style="background: #EFECD9;" | 0 || style="background: #EFECD9;" |+46.17992 ||style="background: #EFECD9;" | -75.183818
|-
| style="background: #38A5A5;" | Exo ||style="background: #EFECD9;" | 0 ||style="background: #EFECD9;" | +46.23768|| style="background: #EFECD9;" |-73.886821
|-
| style="background: #38A5A5;" | Cheletropic||style="background: #EFECD9;" | 0 ||style="background: #EFECD9;" | +63.05663|| style="background: #EFECD9;" |-63.9650565
|}

Raw values with KJ/mol given to the nearest whole number

{| class="wikitable" border="1"
!style="background: #38A5A5;" | Structure!! style="background: #38A5A5;" | E( Hartrees) !! style="background: #38A5A5;" | E(KJ/mol)
|-
| style="background: #38A5A5;" | Diene ||style="background: #EFECD9;" | -309.504492|| style="background: #EFECD9;" |-812604
|-
| style="background: #38A5A5;" | Sulfur||style="background: #EFECD9;" | -548.604917|| style="background: #EFECD9;" |-1440362
|-
| style="background: #38A5A5;" | Sum of Reactants ||style="background: #EFECD9;" | -858.109409|| style="background: #EFECD9;" |-2252966
|-
| style="background: #38A5A5;" | Endo TS||style="background: #EFECD9;" | -858.09182|| style="background: #EFECD9;" |-2252920
|-
| style="background: #38A5A5;" | Endo Product||style="background: #EFECD9;" | -858.138045|| style="background: #EFECD9;" |-2253041
|-
| style="background: #38A5A5;" | Exo TS||style="background: #EFECD9;" | -858.091798|| style="background: #EFECD9;" |-2252920
|-
| style="background: #38A5A5;" | Exo Product||style="background: #EFECD9;" | -858.137551|| style="background: #EFECD9;" |-2253040
|-
| style="background: #38A5A5;" | Chele TS||style="background: #EFECD9;" | -858.085392|| style="background: #EFECD9;" |-2252903
|-
| style="background: #38A5A5;" | Chele Product||style="background: #EFECD9;" | -858.133772|| style="background: #EFECD9;" |-2253030
|}

Looking at the energy reaction barriers it can be seen that the Endo transition state is slightly below the cheletropic value making it the preferred reaction coordinate. however the value for the end transition state is only slightly below that for the cheletropic transition state and the calculation percentage errors/accuracies could effect this ordering.

==== IRC analysis ====

During the reaction the carbon-carbon bond lengths all become styled as 1.5 bond order suggesting an aromatic element to the ring. The IRC calculations proved very challenging throughout this lab and as such the ENDO TS IRC path is recorded in reverse and shows the detachment of the sulfur oxide molecule. Using the IRC plots it can be seen that the reaction proceed without any other intermediates or transition states as demonstrated by the smooth curve of the graph and lack of other turning points in the gradient.

{| class="wikitable" border="1"
! colspan="2" style="text-align: center;" style="background: #38A5A5;" |Cheletropic IRC path
|-
|style="background: white;" | [[File:Chele_IRC_movie.gif]] || style="background: white;" | [[File:Irc_chele_eb1613.png]]
|-
! colspan="2" style="text-align: center;" style="background: #38A5A5;" | Exo IRC path
|-
|style="background: white;" | [[File:Exo_IRC_movie_eb1613.gif]] || style="background: white;" | [[File:Exo_IRC.png]]
|-
!colspan="2" style="text-align: center;" style="background: #38A5A5;" | Endo IRC path
|-
|style="background: white;" | [[File:Endo_IRC_movie_eb1613.gif]] || style="background: white;" | [[File:IRC_path_ex3.png]]
|}

==== Structure files ====

{| class="wikitable" border="1"
|+ Structures
! style="background: #38A5A5;"|sulfur dioxde !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>SULFUR_FREQ_631GD.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Sulfur_eb1613_table.png]]
|-
! style="background: #38A5A5;"|Xylylene Diene !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Diene_mandisp1pt0.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Diene_mandisp1pt0_ex3_eb1613.png]]
|-
!style="background: #38A5A5;"| Diels-Alder Endo Transition state !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>DIELSALDER2_TS_FOUND_631GD_REOPT.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Diels_alder_ts_summary1_eb1613.png]]
|-
! style="background: #38A5A5;"|Diels-Alder Exo Transition state !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Opt_to_ts_631gd.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Da2_ts_ex3.png]]
|-
! style="background: #38A5A5;"|Cheletropic Transition state !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>CHELE_TS_TRY_631GD_FREQ.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Chele_ts_summary.png]]
|-
! style="background: #38A5A5;"|Diels-Alder Endo Product !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>DIELS_ALDER_631GD.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Diels_alder_product1ex3.png]]
|-
! style="background: #38A5A5;"|Diels-Alder Exo Product !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Diels_alder_2_631Gd.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Diels_alder2_product_ex3_eb1613.png]]
|-
! style="background: #38A5A5;"|Cheletropic Product !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Product_chele_mandisp1pt0.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Chele_product_eb1613.png ]]
|}

Rep:Mod:Eb1613 Ex3

2016-12-01T22:39:09Z

Eb1613: /* Exercise 3 */

Page List

[[Mod:eb1613 files| The Calculations Log files can be found here]]

[[Mod:Emily1394| For main Introduction/conclusion page click here]]

[[Mod:Eb1613 Ex1| For Excerise 1 page click here]]

[[Mod:Eb1613 Ex2| For Excerise 2 page click here]]

[[Mod:Eb1613 Ex3| For Excerise 3 page click here]]

= Third Year Computational Lab Transition States - Emily Brown =

=== Exercise 3 ===

[[File:Exercise2_reaction_emily.png]]

Both cheletropic and Diels-Alder reactions are possible for the above reactants.

Initially the structures were optimized to the semi-empirical PM6 level and later the geometries were re-optimised to the DFT 6-31G(d)/b3LYP level of calculation. The reactants were aligned in different conformations and certain bonds were frozen to find the three transition states shown below. Every structure given has been optimized to the higher accuracy DFT 6-31G(d)/b3LYP level.

Unfortunately there was not enough time to investigate the other cis-butadiene fragment successfully.

==== Transition states ====

{| class="wikitable" border="1"
! style="background: #38A5A5;" | Exo Transition State. Negative Frequency = -198.65 cm-1
|-
|style="background: white;" | [[File:Diels_alder_ts_1_movie.gif]]
|-
! style="background: #38A5A5;" | Endo Transition State. Negative Frequency = -200.42 cm-1
|-
|style="background: white;" | [[File:Diels_alder_ts_2_movie.gif]]
|-
! style="background: #38A5A5;" | Cheletropic Transition State. Negative Frequency = -221.18 cm-1
|-
|style="background: white;" | [[File:Chele_TS_movie_eb1613.gif]]
|}

==== Thermochemistry anaylsis ====

The energy profile was first plotted using excel and then using chemdraw to highlight the differences between the endo and exo paths.

{| class="wikitable" border="1"
|-
| style="background: white;" | [[File:Energy profile ex3 eb1613.png]] || style="background: white;" | [[File:Screen_Shot_2016-12-01_at_21.54.33.png]]
|}

Energy values given relative to the reactants in KJ/mol, from the values the Endo route appears to be the preferred route.

{| class="wikitable" border="1"
!style="background: #38A5A5;" | !!style="background: #38A5A5;" | Reactants !! style="background: #38A5A5;" | Transition state !! style="background: #38A5A5;" | Products
|-
| style="background: #38A5A5;" | Endo ||style="background: #EFECD9;" | 0 || style="background: #EFECD9;" |+46.17992 ||style="background: #EFECD9;" | -75.183818
|-
| style="background: #38A5A5;" | Exo ||style="background: #EFECD9;" | 0 ||style="background: #EFECD9;" | +46.23768|| style="background: #EFECD9;" |-73.886821
|-
| style="background: #38A5A5;" | Cheletropic||style="background: #EFECD9;" | 0 ||style="background: #EFECD9;" | +63.05663|| style="background: #EFECD9;" |-63.9650565
|}

Raw values with KJ/mol given to the nearest whole number

{| class="wikitable" border="1"
!style="background: #38A5A5;" | Structure!! style="background: #38A5A5;" | E( Hartrees) !! style="background: #38A5A5;" | E(KJ/mol)
|-
| style="background: #38A5A5;" | Diene ||style="background: #EFECD9;" | -309.504492|| style="background: #EFECD9;" |-812604
|-
| style="background: #38A5A5;" | Sulfur||style="background: #EFECD9;" | -548.604917|| style="background: #EFECD9;" |-1440362
|-
| style="background: #38A5A5;" | Sum of Reactants ||style="background: #EFECD9;" | -858.109409|| style="background: #EFECD9;" |-2252966
|-
| style="background: #38A5A5;" | Endo TS||style="background: #EFECD9;" | -858.09182|| style="background: #EFECD9;" |-2252920
|-
| style="background: #38A5A5;" | Endo Product||style="background: #EFECD9;" | -858.138045|| style="background: #EFECD9;" |-2253041
|-
| style="background: #38A5A5;" | Exo TS||style="background: #EFECD9;" | -858.091798|| style="background: #EFECD9;" |-2252920
|-
| style="background: #38A5A5;" | Exo Product||style="background: #EFECD9;" | -858.137551|| style="background: #EFECD9;" |-2253040
|-
| style="background: #38A5A5;" | Chele TS||style="background: #EFECD9;" | -858.085392|| style="background: #EFECD9;" |-2252903
|-
| style="background: #38A5A5;" | Chele Product||style="background: #EFECD9;" | -858.133772|| style="background: #EFECD9;" |-2253030
|}

Looking at the energy reaction barriers it can be seen that the Endo transition state is slightly below the cheletropic value making it the preferred reaction coordinate. however the value for the end transition state is only slightly below that for the cheletropic transition state and the calculation percentage errors/accuracies could effect this ordering.

==== IRC analysis ====

During the reaction the carbon-carbon bond lengths all become styled as 1.5 bond order suggesting an aromatic element to the ring. The IRC calculations proved very challenging throughout this lab and as such the ENDO TS IRC path is recorded in reverse and shows the detachment of the sulfur oxide molecule. Using the IRC plots it can be seen that the reaction proceed without any other intermediates or transition states as demonstrated by the smooth curve of the graph and lack of other turning points in the gradient.

{| class="wikitable" border="1"
! colspan="2" style="text-align: center;" style="background: #38A5A5;" |Cheletropic IRC path
|-
|style="background: white;" | [[File:Chele_IRC_movie.gif]] || style="background: white;" | [[File:Irc_chele_eb1613.png]]
|-
! colspan="2" style="text-align: center;" style="background: #38A5A5;" | Exo IRC path
|-
|style="background: white;" | [[File:Exo_IRC_movie_eb1613.gif]] || style="background: white;" | [[File:Exo_IRC.png]]
|-
!colspan="2" style="text-align: center;" style="background: #38A5A5;" | Endo IRC path
|-
|style="background: white;" | [[File:Endo_IRC_movie_eb1613.gif]] || style="background: white;" | [[File:IRC_path_ex3.png]]
|}

==== Structure files ====

{| class="wikitable" border="1"
|+ Structures
! style="background: #38A5A5;"|sulfur dioxde !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>SULFUR_FREQ_631GD.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Sulfur_eb1613_table.png]]
|-
! style="background: #38A5A5;"|Xylylene Diene !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Diene_mandisp1pt0.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Diene_mandisp1pt0_ex3_eb1613.png]]
|-
!style="background: #38A5A5;"| Diels-Alder Endo Transition state !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>DIELSALDER2_TS_FOUND_631GD_REOPT.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Diels_alder_ts_summary1_eb1613.png]]
|-
! style="background: #38A5A5;"|Diels-Alder Exo Transition state !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Opt_to_ts_631gd.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Da2_ts_ex3.png]]
|-
! style="background: #38A5A5;"|Cheletropic Transition state !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>CHELE_TS_TRY_631GD_FREQ.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Chele_ts_summary.png]]
|-
! style="background: #38A5A5;"|Diels-Alder Endo Product !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>DIELS_ALDER_631GD.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Diels_alder_product1ex3.png]]
|-
! style="background: #38A5A5;"|Diels-Alder Exo Product !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Diels_alder_2_631Gd.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Diels_alder2_product_ex3_eb1613.png]]
|-
! style="background: #38A5A5;"|Cheletropic Product !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Product_chele_mandisp1pt0.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Chele_product_eb1613.png ]]
|}

Rep:Mod:Emily1394

2016-12-01T22:36:26Z

Eb1613: /* Reference */

Page List

[[Mod:eb1613 files| The Calculations Log files can be found here]]

[[Mod:Emily1394| For main Introduction/conclusion page click here]]

[[Mod:Eb1613 Ex1| For Excerise 1 page click here]]

[[Mod:Eb1613 Ex2| For Excerise 2 page click here]]

[[Mod:Eb1613 Ex3| For Excerise 3 page click here]]

= Third Year Computational Lab Transition States - Emily Brown =

Please note each page has its own references at the bottom of the page.

=== Introduction ===

==== Theory ====

'''Transition State:''' This is a maxima on the reaction coordinate graph. At the point the gradient/first derivative is zero and can be referred to as a turning point on the graph.

'''Potential Energy Surface:''' This has 3N-6 dimensions and if you travel in one dimension you can draw a reaction coordinate graph as shown below. <ref name="waterbottle" /> The PES is a function of energy vs every coordinate. <ref name="Hunt" />

[[File:Eb1613_PE_RC.png|thumb|center|Potential energy surface on left and corresponding reaction coordinate graph to right <ref name="waterbottle" /> ]]

Due to the transition state being a turning point on the reaction coordinate graph it can be found by setting the first derivative to zero as at a minima/maxima the gradient is zero. The potential energy surface allows you to travel in directions which may be away from the reaction coordinate you are trying to locate. The potential energy surface has 3N-6 dimensions.<ref name="Hunt" /> Programs like GuassView take advantage of the fact that all these dimensions are positive in curvature apart from one which is the minimum energy path. This results in an imaginary frequency which is the single negative frequency found in the frequency calculation of a transition state geometry. Energy minimas have zero negative frequencies in their frequency calculations and saddle points have multiple. <ref name="Hunt" />

Reactions can be controlled by a number of different factors some of these being sterics and secondary orbital effects. Reactions often compromise between multiple aspects for example a reaction may be sterically disfavored but that particular reaction path could result in good orbital overlap.

The reactants tend to form the products via the higher energy transition state which is shown as an energy maximum on the above graph, the energy required to overcome this barrier is known as the activation energy and can be seen in the arrhenius equation as the symbol Ea. The activation energy depends on many factors and programmes like gaussian can be used to estimate this energy and predict whether reactions are likely to occur. For example there are two cis dienes present in the reactant in exercise 3 but only one is involved int he dies alder reactions as the other is known to have a high transition state making it very kinetically unfavourable.

==== Computational ====
Initially structures will be optimized using method1 and then using method2. Doing the initial 'tidy up' allows computational time to be saved. Locating transition states has proved difficult for certain systems which results in different approaches being undertaken such as freezing certain bonds by using the opt=modredundant keywords thus locking atoms together to perform initial optimizations. Another approach is to start from the products or reactants and lengthen certain bonds in an attempt to locate the transition state. Structures were confirmed via frequency calculations: the lack of negative frequencies in the frequency calculation indicates that the structure is optimised to a true minimum, the presence of one negative frequency indicates that a transition state has been reached, more than one negative frequency means that a saddle point structure has been reached. <ref name="book book" />

It proved necessary at times to freeze bonds to locate a transition state however once found all structures were later re-optimised under no symmetry constraints. The int=ultrafine keywords are expressed in the DFT calculations as optimisation with many low level vibration modes will often proceed more reliably when a larger DFT integration grid is requested. <ref name="integral" />

'''Method 1:''' Opt+Freq, semi empirical, PM6.

'''Method 2:''' Opt+Freq, DFT B3LYP/631G(d).

Both the density function theory (DFT) and semi-empirical methods are able to describe quantum states as many electron systems; they both use the born-opinhiemer approximation where you first solve for the electronic degrees of freedom. <ref name="electrons" /> In DFT the many-electron wavefunction is completely bypassed in favor of the electron density, the variational principle is used to minimise the energy with respect to electron density. However a key problem with this method is that the energy functional is not know. <ref name="electrons" /> Semi-empirical Methods are a simplified versions of Hartree-Fock theory using empirical corrections in order to improve performance; these can be preformed prior to DFT calculations in order to save computational time. <ref name="mug mug" /> The PM6 part of the calculation specifics that the PM6 hamiltonian is to use in the semi-empirical calculation. <ref name="IwantTEA" />

'''Notes:''' When optimising to a transition state I used: TS (Berry), Force constants allowed to calculate once. When optimising to a minimum use: minimum and force constants are allowed to calculate never. Occasional calculations were run on the colleges HPC to save computational time as these servers use more processors than my local computer in college. The 09 version of gaussian suite was used when on windows college computers.

==== Exercises ====

Each exercise is contained on its own page which are linked to below and above the contents section of each page. Each page containing an exercise has Jmol files of all structures used in that exercise at the end of the page, they are accompanied by the 'results summary' section of their opt/freq calculation to confirm the existence of the correct number of negative frequencies and to allow the geometry of each structure to be viewed.

[[Mod:Eb1613 Ex1| Page for Excerise 1]]

[[Mod:Eb1613 Ex2| Page for Excerise 2]]

[[Mod:Eb1613 Ex3| Page for Excerise 3]]

=== Conclusion ===

The transition states were successfully located for multiple reaction following a similar procedure in each case. Orbital analysis was undertaken and HOMO+1, HOMO, LUMO and LUMO-1 levels were explored. The transition states were be further identified by looking into the IRC, thus allowing endo/exo transition states to be confidently labeled. The IRC also revealed information about the reaction coordinate such that no other intermediates existed and that no other transition states were encountered for our reactions.

This computational lab has also highlighed some key difference between the semi-empirical based basis sets and those of basis sets belonging to the density functional theory family. The lab has drawn attention to the importance of chosen the correct basis set and has given me the ability to use Gaussian programs to confidently locate transition states for reactions and highlighted some key methods to further understand the transition states found.

=== Reference ===

<references>
<ref name="waterbottle">https://commons.wikimedia.org/wiki/File:Potential_Energy_Surface_and_Corresponding_Reaction_Coordinate_Diagram.png (accessed 23rd November)</ref>
<ref name="electrons">https://www.quora.com/What-is-the-difference-between-density-functional-theory-and-hartree-fock (accessed 25th November 2016)</ref>
<ref name="integral">http://www.gaussian.com/g_tech/g_ur/k_opt.htm (accessed 25th November 2016)</ref>
<ref name="IwantTEA ">http://www.gaussian.com/g_tech/g_ur/k_semiempirical.html (accessed 25th November 2016)</ref>
<ref name="mug mug ">http://www.cup.uni-muenchen.de/ch/compchem/energy/semi1.html (accessed 25th November 2016)</ref>
<ref name="Hunt "> Dr. Hunt's year 4 lecture course: "Computational Inorganic Chemistry" Lecture4, Handout3. http://www.huntresearchgroup.org.uk/teaching/teaching_comp_chem_year4/L4_PES.pdf (accessed 25th November 2016)</ref>
<ref name="book book "> Foresman, J. and Frisch, A. (1996). Exploring Chemistry With Electronic Structure Methods: A Guide to Using Gaussian. 2nd ed. Guassian, Chapter 1.)</ref>
</references>

Rep:Mod:Emily1394

2016-12-01T22:35:59Z

Eb1613: /* Computational */

Page List

[[Mod:eb1613 files| The Calculations Log files can be found here]]

[[Mod:Emily1394| For main Introduction/conclusion page click here]]

[[Mod:Eb1613 Ex1| For Excerise 1 page click here]]

[[Mod:Eb1613 Ex2| For Excerise 2 page click here]]

[[Mod:Eb1613 Ex3| For Excerise 3 page click here]]

= Third Year Computational Lab Transition States - Emily Brown =

Please note each page has its own references at the bottom of the page.

=== Introduction ===

==== Theory ====

'''Transition State:''' This is a maxima on the reaction coordinate graph. At the point the gradient/first derivative is zero and can be referred to as a turning point on the graph.

'''Potential Energy Surface:''' This has 3N-6 dimensions and if you travel in one dimension you can draw a reaction coordinate graph as shown below. <ref name="waterbottle" /> The PES is a function of energy vs every coordinate. <ref name="Hunt" />

[[File:Eb1613_PE_RC.png|thumb|center|Potential energy surface on left and corresponding reaction coordinate graph to right <ref name="waterbottle" /> ]]

Due to the transition state being a turning point on the reaction coordinate graph it can be found by setting the first derivative to zero as at a minima/maxima the gradient is zero. The potential energy surface allows you to travel in directions which may be away from the reaction coordinate you are trying to locate. The potential energy surface has 3N-6 dimensions.<ref name="Hunt" /> Programs like GuassView take advantage of the fact that all these dimensions are positive in curvature apart from one which is the minimum energy path. This results in an imaginary frequency which is the single negative frequency found in the frequency calculation of a transition state geometry. Energy minimas have zero negative frequencies in their frequency calculations and saddle points have multiple. <ref name="Hunt" />

Reactions can be controlled by a number of different factors some of these being sterics and secondary orbital effects. Reactions often compromise between multiple aspects for example a reaction may be sterically disfavored but that particular reaction path could result in good orbital overlap.

The reactants tend to form the products via the higher energy transition state which is shown as an energy maximum on the above graph, the energy required to overcome this barrier is known as the activation energy and can be seen in the arrhenius equation as the symbol Ea. The activation energy depends on many factors and programmes like gaussian can be used to estimate this energy and predict whether reactions are likely to occur. For example there are two cis dienes present in the reactant in exercise 3 but only one is involved int he dies alder reactions as the other is known to have a high transition state making it very kinetically unfavourable.

==== Computational ====
Initially structures will be optimized using method1 and then using method2. Doing the initial 'tidy up' allows computational time to be saved. Locating transition states has proved difficult for certain systems which results in different approaches being undertaken such as freezing certain bonds by using the opt=modredundant keywords thus locking atoms together to perform initial optimizations. Another approach is to start from the products or reactants and lengthen certain bonds in an attempt to locate the transition state. Structures were confirmed via frequency calculations: the lack of negative frequencies in the frequency calculation indicates that the structure is optimised to a true minimum, the presence of one negative frequency indicates that a transition state has been reached, more than one negative frequency means that a saddle point structure has been reached. <ref name="book book" />

It proved necessary at times to freeze bonds to locate a transition state however once found all structures were later re-optimised under no symmetry constraints. The int=ultrafine keywords are expressed in the DFT calculations as optimisation with many low level vibration modes will often proceed more reliably when a larger DFT integration grid is requested. <ref name="integral" />

'''Method 1:''' Opt+Freq, semi empirical, PM6.

'''Method 2:''' Opt+Freq, DFT B3LYP/631G(d).

Both the density function theory (DFT) and semi-empirical methods are able to describe quantum states as many electron systems; they both use the born-opinhiemer approximation where you first solve for the electronic degrees of freedom. <ref name="electrons" /> In DFT the many-electron wavefunction is completely bypassed in favor of the electron density, the variational principle is used to minimise the energy with respect to electron density. However a key problem with this method is that the energy functional is not know. <ref name="electrons" /> Semi-empirical Methods are a simplified versions of Hartree-Fock theory using empirical corrections in order to improve performance; these can be preformed prior to DFT calculations in order to save computational time. <ref name="mug mug" /> The PM6 part of the calculation specifics that the PM6 hamiltonian is to use in the semi-empirical calculation. <ref name="IwantTEA" />

'''Notes:''' When optimising to a transition state I used: TS (Berry), Force constants allowed to calculate once. When optimising to a minimum use: minimum and force constants are allowed to calculate never. Occasional calculations were run on the colleges HPC to save computational time as these servers use more processors than my local computer in college. The 09 version of gaussian suite was used when on windows college computers.

==== Exercises ====

Each exercise is contained on its own page which are linked to below and above the contents section of each page. Each page containing an exercise has Jmol files of all structures used in that exercise at the end of the page, they are accompanied by the 'results summary' section of their opt/freq calculation to confirm the existence of the correct number of negative frequencies and to allow the geometry of each structure to be viewed.

[[Mod:Eb1613 Ex1| Page for Excerise 1]]

[[Mod:Eb1613 Ex2| Page for Excerise 2]]

[[Mod:Eb1613 Ex3| Page for Excerise 3]]

=== Conclusion ===

The transition states were successfully located for multiple reaction following a similar procedure in each case. Orbital analysis was undertaken and HOMO+1, HOMO, LUMO and LUMO-1 levels were explored. The transition states were be further identified by looking into the IRC, thus allowing endo/exo transition states to be confidently labeled. The IRC also revealed information about the reaction coordinate such that no other intermediates existed and that no other transition states were encountered for our reactions.

This computational lab has also highlighed some key difference between the semi-empirical based basis sets and those of basis sets belonging to the density functional theory family. The lab has drawn attention to the importance of chosen the correct basis set and has given me the ability to use Gaussian programs to confidently locate transition states for reactions and highlighted some key methods to further understand the transition states found.

=== Reference ===

<references>
<ref name="waterbottle">https://commons.wikimedia.org/wiki/File:Potential_Energy_Surface_and_Corresponding_Reaction_Coordinate_Diagram.png (accessed 23rd November)</ref>
<ref name="electrons">https://www.quora.com/What-is-the-difference-between-density-functional-theory-and-hartree-fock (accessed 25th November 2016)</ref>
<ref name="integral">http://www.gaussian.com/g_tech/g_ur/k_opt.htm (accessed 25th November 2016)</ref>
<ref name="IwantTEA ">http://www.gaussian.com/g_tech/g_ur/k_semiempirical.html (accessed 25th November 2016)</ref>
<ref name="mug mug ">http://www.cup.uni-muenchen.de/ch/compchem/energy/semi1.html (accessed 25th November 2016)</ref>
<ref name="Hunt "> Dr. Hunt's year 4 lecture course: "Computational Inorganic Chemistry" Lecture4, Handout3. http://www.huntresearchgroup.org.uk/teaching/teaching_comp_chem_year4/L4_PES.pdf (accessed 25th November 2016)</ref>
<ref name="book book "> Foresman, J. and Frisch, A. (1996). Exploring Chemistry With Electronic Structure Methods: A Guide to Using Gaussian. 2nd ed. Guassian, p.Chapter 1.)</ref>
</references>

Rep:Mod:Emily1394

2016-12-01T22:35:40Z

Eb1613: /* Reference */

Page List

[[Mod:eb1613 files| The Calculations Log files can be found here]]

[[Mod:Emily1394| For main Introduction/conclusion page click here]]

[[Mod:Eb1613 Ex1| For Excerise 1 page click here]]

[[Mod:Eb1613 Ex2| For Excerise 2 page click here]]

[[Mod:Eb1613 Ex3| For Excerise 3 page click here]]

= Third Year Computational Lab Transition States - Emily Brown =

Please note each page has its own references at the bottom of the page.

=== Introduction ===

==== Theory ====

'''Transition State:''' This is a maxima on the reaction coordinate graph. At the point the gradient/first derivative is zero and can be referred to as a turning point on the graph.

'''Potential Energy Surface:''' This has 3N-6 dimensions and if you travel in one dimension you can draw a reaction coordinate graph as shown below. <ref name="waterbottle" /> The PES is a function of energy vs every coordinate. <ref name="Hunt" />

[[File:Eb1613_PE_RC.png|thumb|center|Potential energy surface on left and corresponding reaction coordinate graph to right <ref name="waterbottle" /> ]]

Due to the transition state being a turning point on the reaction coordinate graph it can be found by setting the first derivative to zero as at a minima/maxima the gradient is zero. The potential energy surface allows you to travel in directions which may be away from the reaction coordinate you are trying to locate. The potential energy surface has 3N-6 dimensions.<ref name="Hunt" /> Programs like GuassView take advantage of the fact that all these dimensions are positive in curvature apart from one which is the minimum energy path. This results in an imaginary frequency which is the single negative frequency found in the frequency calculation of a transition state geometry. Energy minimas have zero negative frequencies in their frequency calculations and saddle points have multiple. <ref name="Hunt" />

Reactions can be controlled by a number of different factors some of these being sterics and secondary orbital effects. Reactions often compromise between multiple aspects for example a reaction may be sterically disfavored but that particular reaction path could result in good orbital overlap.

The reactants tend to form the products via the higher energy transition state which is shown as an energy maximum on the above graph, the energy required to overcome this barrier is known as the activation energy and can be seen in the arrhenius equation as the symbol Ea. The activation energy depends on many factors and programmes like gaussian can be used to estimate this energy and predict whether reactions are likely to occur. For example there are two cis dienes present in the reactant in exercise 3 but only one is involved int he dies alder reactions as the other is known to have a high transition state making it very kinetically unfavourable.

==== Computational ====
Initially structures will be optimized using method1 and then using method2. Doing the initial 'tidy up' allows computational time to be saved. Locating transition states has proved difficult for certain systems which results in different approaches being undertaken such as freezing certain bonds by using the opt=modredundant keywords thus locking atoms together to perform initial optimizations. Another approach is to start from the products or reactants and lengthen certain bonds in an attempt to locate the transition state. Structures were confirmed via frequency calculations: the lack of negative frequencies in the frequency calculation indicates that the structure is optimised to a true minimum, the presence of one negative frequency indicates that a transition state has been reached, more than one negative frequency means that a saddle point structure has been reached.

It proved necessary at times to freeze bonds to locate a transition state however once found all structures were later re-optimised under no symmetry constraints. The int=ultrafine keywords are expressed in the DFT calculations as optimisation with many low level vibration modes will often proceed more reliably when a larger DFT integration grid is requested. <ref name="integral" />

'''Method 1:''' Opt+Freq, semi empirical, PM6.

'''Method 2:''' Opt+Freq, DFT B3LYP/631G(d).

Both the density function theory (DFT) and semi-empirical methods are able to describe quantum states as many electron systems; they both use the born-opinhiemer approximation where you first solve for the electronic degrees of freedom. <ref name="electrons" /> In DFT the many-electron wavefunction is completely bypassed in favor of the electron density, the variational principle is used to minimise the energy with respect to electron density. However a key problem with this method is that the energy functional is not know. <ref name="electrons" /> Semi-empirical Methods are a simplified versions of Hartree-Fock theory using empirical corrections in order to improve performance; these can be preformed prior to DFT calculations in order to save computational time. <ref name="mug mug" /> The PM6 part of the calculation specifics that the PM6 hamiltonian is to use in the semi-empirical calculation. <ref name="IwantTEA" />

'''Notes:''' When optimising to a transition state I used: TS (Berry), Force constants allowed to calculate once. When optimising to a minimum use: minimum and force constants are allowed to calculate never. Occasional calculations were run on the colleges HPC to save computational time as these servers use more processors than my local computer in college. The 09 version of gaussian suite was used when on windows college computers.

==== Exercises ====

Each exercise is contained on its own page which are linked to below and above the contents section of each page. Each page containing an exercise has Jmol files of all structures used in that exercise at the end of the page, they are accompanied by the 'results summary' section of their opt/freq calculation to confirm the existence of the correct number of negative frequencies and to allow the geometry of each structure to be viewed.

[[Mod:Eb1613 Ex1| Page for Excerise 1]]

[[Mod:Eb1613 Ex2| Page for Excerise 2]]

[[Mod:Eb1613 Ex3| Page for Excerise 3]]

=== Conclusion ===

The transition states were successfully located for multiple reaction following a similar procedure in each case. Orbital analysis was undertaken and HOMO+1, HOMO, LUMO and LUMO-1 levels were explored. The transition states were be further identified by looking into the IRC, thus allowing endo/exo transition states to be confidently labeled. The IRC also revealed information about the reaction coordinate such that no other intermediates existed and that no other transition states were encountered for our reactions.

This computational lab has also highlighed some key difference between the semi-empirical based basis sets and those of basis sets belonging to the density functional theory family. The lab has drawn attention to the importance of chosen the correct basis set and has given me the ability to use Gaussian programs to confidently locate transition states for reactions and highlighted some key methods to further understand the transition states found.

=== Reference ===

<references>
<ref name="waterbottle">https://commons.wikimedia.org/wiki/File:Potential_Energy_Surface_and_Corresponding_Reaction_Coordinate_Diagram.png (accessed 23rd November)</ref>
<ref name="electrons">https://www.quora.com/What-is-the-difference-between-density-functional-theory-and-hartree-fock (accessed 25th November 2016)</ref>
<ref name="integral">http://www.gaussian.com/g_tech/g_ur/k_opt.htm (accessed 25th November 2016)</ref>
<ref name="IwantTEA ">http://www.gaussian.com/g_tech/g_ur/k_semiempirical.html (accessed 25th November 2016)</ref>
<ref name="mug mug ">http://www.cup.uni-muenchen.de/ch/compchem/energy/semi1.html (accessed 25th November 2016)</ref>
<ref name="Hunt "> Dr. Hunt's year 4 lecture course: "Computational Inorganic Chemistry" Lecture4, Handout3. http://www.huntresearchgroup.org.uk/teaching/teaching_comp_chem_year4/L4_PES.pdf (accessed 25th November 2016)</ref>
<ref name="book book "> Foresman, J. and Frisch, A. (1996). Exploring Chemistry With Electronic Structure Methods: A Guide to Using Gaussian. 2nd ed. Guassian, p.Chapter 1.)</ref>
</references>

Rep:Mod:Emily1394

2016-12-01T22:27:35Z

Eb1613: /* Computational */

Page List

[[Mod:eb1613 files| The Calculations Log files can be found here]]

[[Mod:Emily1394| For main Introduction/conclusion page click here]]

[[Mod:Eb1613 Ex1| For Excerise 1 page click here]]

[[Mod:Eb1613 Ex2| For Excerise 2 page click here]]

[[Mod:Eb1613 Ex3| For Excerise 3 page click here]]

= Third Year Computational Lab Transition States - Emily Brown =

Please note each page has its own references at the bottom of the page.

=== Introduction ===

==== Theory ====

'''Transition State:''' This is a maxima on the reaction coordinate graph. At the point the gradient/first derivative is zero and can be referred to as a turning point on the graph.

'''Potential Energy Surface:''' This has 3N-6 dimensions and if you travel in one dimension you can draw a reaction coordinate graph as shown below. <ref name="waterbottle" /> The PES is a function of energy vs every coordinate. <ref name="Hunt" />

[[File:Eb1613_PE_RC.png|thumb|center|Potential energy surface on left and corresponding reaction coordinate graph to right <ref name="waterbottle" /> ]]

Due to the transition state being a turning point on the reaction coordinate graph it can be found by setting the first derivative to zero as at a minima/maxima the gradient is zero. The potential energy surface allows you to travel in directions which may be away from the reaction coordinate you are trying to locate. The potential energy surface has 3N-6 dimensions.<ref name="Hunt" /> Programs like GuassView take advantage of the fact that all these dimensions are positive in curvature apart from one which is the minimum energy path. This results in an imaginary frequency which is the single negative frequency found in the frequency calculation of a transition state geometry. Energy minimas have zero negative frequencies in their frequency calculations and saddle points have multiple. <ref name="Hunt" />

Reactions can be controlled by a number of different factors some of these being sterics and secondary orbital effects. Reactions often compromise between multiple aspects for example a reaction may be sterically disfavored but that particular reaction path could result in good orbital overlap.

The reactants tend to form the products via the higher energy transition state which is shown as an energy maximum on the above graph, the energy required to overcome this barrier is known as the activation energy and can be seen in the arrhenius equation as the symbol Ea. The activation energy depends on many factors and programmes like gaussian can be used to estimate this energy and predict whether reactions are likely to occur. For example there are two cis dienes present in the reactant in exercise 3 but only one is involved int he dies alder reactions as the other is known to have a high transition state making it very kinetically unfavourable.

==== Computational ====
Initially structures will be optimized using method1 and then using method2. Doing the initial 'tidy up' allows computational time to be saved. Locating transition states has proved difficult for certain systems which results in different approaches being undertaken such as freezing certain bonds by using the opt=modredundant keywords thus locking atoms together to perform initial optimizations. Another approach is to start from the products or reactants and lengthen certain bonds in an attempt to locate the transition state. Structures were confirmed via frequency calculations: the lack of negative frequencies in the frequency calculation indicates that the structure is optimised to a true minimum, the presence of one negative frequency indicates that a transition state has been reached, more than one negative frequency means that a saddle point structure has been reached.

It proved necessary at times to freeze bonds to locate a transition state however once found all structures were later re-optimised under no symmetry constraints. The int=ultrafine keywords are expressed in the DFT calculations as optimisation with many low level vibration modes will often proceed more reliably when a larger DFT integration grid is requested. <ref name="integral" />

'''Method 1:''' Opt+Freq, semi empirical, PM6.

'''Method 2:''' Opt+Freq, DFT B3LYP/631G(d).

Both the density function theory (DFT) and semi-empirical methods are able to describe quantum states as many electron systems; they both use the born-opinhiemer approximation where you first solve for the electronic degrees of freedom. <ref name="electrons" /> In DFT the many-electron wavefunction is completely bypassed in favor of the electron density, the variational principle is used to minimise the energy with respect to electron density. However a key problem with this method is that the energy functional is not know. <ref name="electrons" /> Semi-empirical Methods are a simplified versions of Hartree-Fock theory using empirical corrections in order to improve performance; these can be preformed prior to DFT calculations in order to save computational time. <ref name="mug mug" /> The PM6 part of the calculation specifics that the PM6 hamiltonian is to use in the semi-empirical calculation. <ref name="IwantTEA" />

'''Notes:''' When optimising to a transition state I used: TS (Berry), Force constants allowed to calculate once. When optimising to a minimum use: minimum and force constants are allowed to calculate never. Occasional calculations were run on the colleges HPC to save computational time as these servers use more processors than my local computer in college. The 09 version of gaussian suite was used when on windows college computers.

==== Exercises ====

Each exercise is contained on its own page which are linked to below and above the contents section of each page. Each page containing an exercise has Jmol files of all structures used in that exercise at the end of the page, they are accompanied by the 'results summary' section of their opt/freq calculation to confirm the existence of the correct number of negative frequencies and to allow the geometry of each structure to be viewed.

[[Mod:Eb1613 Ex1| Page for Excerise 1]]

[[Mod:Eb1613 Ex2| Page for Excerise 2]]

[[Mod:Eb1613 Ex3| Page for Excerise 3]]

=== Conclusion ===

The transition states were successfully located for multiple reaction following a similar procedure in each case. Orbital analysis was undertaken and HOMO+1, HOMO, LUMO and LUMO-1 levels were explored. The transition states were be further identified by looking into the IRC, thus allowing endo/exo transition states to be confidently labeled. The IRC also revealed information about the reaction coordinate such that no other intermediates existed and that no other transition states were encountered for our reactions.

This computational lab has also highlighed some key difference between the semi-empirical based basis sets and those of basis sets belonging to the density functional theory family. The lab has drawn attention to the importance of chosen the correct basis set and has given me the ability to use Gaussian programs to confidently locate transition states for reactions and highlighted some key methods to further understand the transition states found.

=== Reference ===

<references>
<ref name="waterbottle">https://commons.wikimedia.org/wiki/File:Potential_Energy_Surface_and_Corresponding_Reaction_Coordinate_Diagram.png (accessed 23rd November)</ref>
<ref name="electrons">https://www.quora.com/What-is-the-difference-between-density-functional-theory-and-hartree-fock (accessed 25th November 2016)</ref>
<ref name="integral">http://www.gaussian.com/g_tech/g_ur/k_opt.htm (accessed 25th November 2016)</ref>
<ref name="IwantTEA ">http://www.gaussian.com/g_tech/g_ur/k_semiempirical.html (accessed 25th November 2016)</ref>
<ref name="mug mug ">http://www.cup.uni-muenchen.de/ch/compchem/energy/semi1.html (accessed 25th November 2016)</ref>
<ref name="Hunt "> Dr. Hunt's year 4 lecture course: "Computational Inorganic Chemistry" Lecture4, Handout3. http://www.huntresearchgroup.org.uk/teaching/teaching_comp_chem_year4/L4_PES.pdf (accessed 25th November 2016)</ref>

</references>

Rep:Mod:Emily1394

2016-12-01T22:22:55Z

Eb1613: /* Third Year Computational Lab Transition States - Emily Brown */

Page List

[[Mod:eb1613 files| The Calculations Log files can be found here]]

[[Mod:Emily1394| For main Introduction/conclusion page click here]]

[[Mod:Eb1613 Ex1| For Excerise 1 page click here]]

[[Mod:Eb1613 Ex2| For Excerise 2 page click here]]

[[Mod:Eb1613 Ex3| For Excerise 3 page click here]]

= Third Year Computational Lab Transition States - Emily Brown =

Please note each page has its own references at the bottom of the page.

=== Introduction ===

==== Theory ====

'''Transition State:''' This is a maxima on the reaction coordinate graph. At the point the gradient/first derivative is zero and can be referred to as a turning point on the graph.

'''Potential Energy Surface:''' This has 3N-6 dimensions and if you travel in one dimension you can draw a reaction coordinate graph as shown below. <ref name="waterbottle" /> The PES is a function of energy vs every coordinate. <ref name="Hunt" />

[[File:Eb1613_PE_RC.png|thumb|center|Potential energy surface on left and corresponding reaction coordinate graph to right <ref name="waterbottle" /> ]]

Due to the transition state being a turning point on the reaction coordinate graph it can be found by setting the first derivative to zero as at a minima/maxima the gradient is zero. The potential energy surface allows you to travel in directions which may be away from the reaction coordinate you are trying to locate. The potential energy surface has 3N-6 dimensions.<ref name="Hunt" /> Programs like GuassView take advantage of the fact that all these dimensions are positive in curvature apart from one which is the minimum energy path. This results in an imaginary frequency which is the single negative frequency found in the frequency calculation of a transition state geometry. Energy minimas have zero negative frequencies in their frequency calculations and saddle points have multiple. <ref name="Hunt" />

Reactions can be controlled by a number of different factors some of these being sterics and secondary orbital effects. Reactions often compromise between multiple aspects for example a reaction may be sterically disfavored but that particular reaction path could result in good orbital overlap.

The reactants tend to form the products via the higher energy transition state which is shown as an energy maximum on the above graph, the energy required to overcome this barrier is known as the activation energy and can be seen in the arrhenius equation as the symbol Ea. The activation energy depends on many factors and programmes like gaussian can be used to estimate this energy and predict whether reactions are likely to occur. For example there are two cis dienes present in the reactant in exercise 3 but only one is involved int he dies alder reactions as the other is known to have a high transition state making it very kinetically unfavourable.

==== Computational ====
Initially structures will be optimized using method1 and then using method2. Doing the initial 'tidy up' allows computational time to be saved. Locating transition states has proved difficult for certain systems which results in different approaches being undertaken such as freezing certain bonds by using the opt=modredundant keywords thus locking atoms together to perform initial optimizations. Another approach is to start from the products or reactants and lengthen certain bonds in an attempt to locate the transition state.

It proved necessary at times to freeze bonds to locate a transition state however once found all structures were later re-optimised under no symmetry constraints. The int=ultrafine keywords are expressed in the DFT calculations as optimisation with many low level vibration modes will often proceed more reliably when a larger DFT integration grid is requested. <ref name="integral" />

'''Method 1:''' Opt+Freq, semi empirical, PM6.

'''Method 2:''' Opt+Freq, DFT B3LYP/631G(d).

Both the density function theory (DFT) and semi-empirical methods are able to describe quantum states as many electron systems; they both use the born-opinhiemer approximation where you first solve for the electronic degrees of freedom. <ref name="electrons" /> In DFT the many-electron wavefunction is completely bypassed in favor of the electron density, the variational principle is used to minimise the energy with respect to electron density. However a key problem with this method is that the energy functional is not know. <ref name="electrons" /> Semi-empirical Methods are a simplified versions of Hartree-Fock theory using empirical corrections in order to improve performance; these can be preformed prior to DFT calculations in order to save computational time. <ref name="mug mug" /> The PM6 part of the calculation specifics that the PM6 hamiltonian is to use in the semi-empirical calculation. <ref name="IwantTEA" />

'''Notes:''' When optimising to a transition state I used: TS (Berry), Force constants allowed to calculate once. When optimising to a minimum use: minimum and force constants are allowed to calculate never. Occasional calculations were run on the colleges HPC to save computational time as these servers use more processors than my local computer in college. The 09 version of gaussian suite was used when on windows college computers.

==== Exercises ====

Each exercise is contained on its own page which are linked to below and above the contents section of each page. Each page containing an exercise has Jmol files of all structures used in that exercise at the end of the page, they are accompanied by the 'results summary' section of their opt/freq calculation to confirm the existence of the correct number of negative frequencies and to allow the geometry of each structure to be viewed.

[[Mod:Eb1613 Ex1| Page for Excerise 1]]

[[Mod:Eb1613 Ex2| Page for Excerise 2]]

[[Mod:Eb1613 Ex3| Page for Excerise 3]]

=== Conclusion ===

The transition states were successfully located for multiple reaction following a similar procedure in each case. Orbital analysis was undertaken and HOMO+1, HOMO, LUMO and LUMO-1 levels were explored. The transition states were be further identified by looking into the IRC, thus allowing endo/exo transition states to be confidently labeled. The IRC also revealed information about the reaction coordinate such that no other intermediates existed and that no other transition states were encountered for our reactions.

This computational lab has also highlighed some key difference between the semi-empirical based basis sets and those of basis sets belonging to the density functional theory family. The lab has drawn attention to the importance of chosen the correct basis set and has given me the ability to use Gaussian programs to confidently locate transition states for reactions and highlighted some key methods to further understand the transition states found.

=== Reference ===

<references>
<ref name="waterbottle">https://commons.wikimedia.org/wiki/File:Potential_Energy_Surface_and_Corresponding_Reaction_Coordinate_Diagram.png (accessed 23rd November)</ref>
<ref name="electrons">https://www.quora.com/What-is-the-difference-between-density-functional-theory-and-hartree-fock (accessed 25th November 2016)</ref>
<ref name="integral">http://www.gaussian.com/g_tech/g_ur/k_opt.htm (accessed 25th November 2016)</ref>
<ref name="IwantTEA ">http://www.gaussian.com/g_tech/g_ur/k_semiempirical.html (accessed 25th November 2016)</ref>
<ref name="mug mug ">http://www.cup.uni-muenchen.de/ch/compchem/energy/semi1.html (accessed 25th November 2016)</ref>
<ref name="Hunt "> Dr. Hunt's year 4 lecture course: "Computational Inorganic Chemistry" Lecture4, Handout3. http://www.huntresearchgroup.org.uk/teaching/teaching_comp_chem_year4/L4_PES.pdf (accessed 25th November 2016)</ref>

</references>

Rep:Mod:Emily1394

2016-12-01T22:21:48Z

Eb1613: /* Reference */

Page List

[[Mod:eb1613 files| The Calculations Log files can be found here]]

[[Mod:Emily1394| For main Introduction/conclusion page click here]]

[[Mod:Eb1613 Ex1| For Excerise 1 page click here]]

[[Mod:Eb1613 Ex2| For Excerise 2 page click here]]

[[Mod:Eb1613 Ex3| For Excerise 3 page click here]]

= Third Year Computational Lab Transition States - Emily Brown =

=== Introduction ===

==== Theory ====

'''Transition State:''' This is a maxima on the reaction coordinate graph. At the point the gradient/first derivative is zero and can be referred to as a turning point on the graph.

'''Potential Energy Surface:''' This has 3N-6 dimensions and if you travel in one dimension you can draw a reaction coordinate graph as shown below. <ref name="waterbottle" /> The PES is a function of energy vs every coordinate. <ref name="Hunt" />

[[File:Eb1613_PE_RC.png|thumb|center|Potential energy surface on left and corresponding reaction coordinate graph to right <ref name="waterbottle" /> ]]

Due to the transition state being a turning point on the reaction coordinate graph it can be found by setting the first derivative to zero as at a minima/maxima the gradient is zero. The potential energy surface allows you to travel in directions which may be away from the reaction coordinate you are trying to locate. The potential energy surface has 3N-6 dimensions.<ref name="Hunt" /> Programs like GuassView take advantage of the fact that all these dimensions are positive in curvature apart from one which is the minimum energy path. This results in an imaginary frequency which is the single negative frequency found in the frequency calculation of a transition state geometry. Energy minimas have zero negative frequencies in their frequency calculations and saddle points have multiple. <ref name="Hunt" />

Reactions can be controlled by a number of different factors some of these being sterics and secondary orbital effects. Reactions often compromise between multiple aspects for example a reaction may be sterically disfavored but that particular reaction path could result in good orbital overlap.

The reactants tend to form the products via the higher energy transition state which is shown as an energy maximum on the above graph, the energy required to overcome this barrier is known as the activation energy and can be seen in the arrhenius equation as the symbol Ea. The activation energy depends on many factors and programmes like gaussian can be used to estimate this energy and predict whether reactions are likely to occur. For example there are two cis dienes present in the reactant in exercise 3 but only one is involved int he dies alder reactions as the other is known to have a high transition state making it very kinetically unfavourable.

==== Computational ====
Initially structures will be optimized using method1 and then using method2. Doing the initial 'tidy up' allows computational time to be saved. Locating transition states has proved difficult for certain systems which results in different approaches being undertaken such as freezing certain bonds by using the opt=modredundant keywords thus locking atoms together to perform initial optimizations. Another approach is to start from the products or reactants and lengthen certain bonds in an attempt to locate the transition state.

It proved necessary at times to freeze bonds to locate a transition state however once found all structures were later re-optimised under no symmetry constraints. The int=ultrafine keywords are expressed in the DFT calculations as optimisation with many low level vibration modes will often proceed more reliably when a larger DFT integration grid is requested. <ref name="integral" />

'''Method 1:''' Opt+Freq, semi empirical, PM6.

'''Method 2:''' Opt+Freq, DFT B3LYP/631G(d).

Both the density function theory (DFT) and semi-empirical methods are able to describe quantum states as many electron systems; they both use the born-opinhiemer approximation where you first solve for the electronic degrees of freedom. <ref name="electrons" /> In DFT the many-electron wavefunction is completely bypassed in favor of the electron density, the variational principle is used to minimise the energy with respect to electron density. However a key problem with this method is that the energy functional is not know. <ref name="electrons" /> Semi-empirical Methods are a simplified versions of Hartree-Fock theory using empirical corrections in order to improve performance; these can be preformed prior to DFT calculations in order to save computational time. <ref name="mug mug" /> The PM6 part of the calculation specifics that the PM6 hamiltonian is to use in the semi-empirical calculation. <ref name="IwantTEA" />

'''Notes:''' When optimising to a transition state I used: TS (Berry), Force constants allowed to calculate once. When optimising to a minimum use: minimum and force constants are allowed to calculate never. Occasional calculations were run on the colleges HPC to save computational time as these servers use more processors than my local computer in college. The 09 version of gaussian suite was used when on windows college computers.

==== Exercises ====

Each exercise is contained on its own page which are linked to below and above the contents section of each page. Each page containing an exercise has Jmol files of all structures used in that exercise at the end of the page, they are accompanied by the 'results summary' section of their opt/freq calculation to confirm the existence of the correct number of negative frequencies and to allow the geometry of each structure to be viewed.

[[Mod:Eb1613 Ex1| Page for Excerise 1]]

[[Mod:Eb1613 Ex2| Page for Excerise 2]]

[[Mod:Eb1613 Ex3| Page for Excerise 3]]

=== Conclusion ===

The transition states were successfully located for multiple reaction following a similar procedure in each case. Orbital analysis was undertaken and HOMO+1, HOMO, LUMO and LUMO-1 levels were explored. The transition states were be further identified by looking into the IRC, thus allowing endo/exo transition states to be confidently labeled. The IRC also revealed information about the reaction coordinate such that no other intermediates existed and that no other transition states were encountered for our reactions.

This computational lab has also highlighed some key difference between the semi-empirical based basis sets and those of basis sets belonging to the density functional theory family. The lab has drawn attention to the importance of chosen the correct basis set and has given me the ability to use Gaussian programs to confidently locate transition states for reactions and highlighted some key methods to further understand the transition states found.

=== Reference ===

<references>
<ref name="waterbottle">https://commons.wikimedia.org/wiki/File:Potential_Energy_Surface_and_Corresponding_Reaction_Coordinate_Diagram.png (accessed 23rd November)</ref>
<ref name="electrons">https://www.quora.com/What-is-the-difference-between-density-functional-theory-and-hartree-fock (accessed 25th November 2016)</ref>
<ref name="integral">http://www.gaussian.com/g_tech/g_ur/k_opt.htm (accessed 25th November 2016)</ref>
<ref name="IwantTEA ">http://www.gaussian.com/g_tech/g_ur/k_semiempirical.html (accessed 25th November 2016)</ref>
<ref name="mug mug ">http://www.cup.uni-muenchen.de/ch/compchem/energy/semi1.html (accessed 25th November 2016)</ref>
<ref name="Hunt "> Dr. Hunt's year 4 lecture course: "Computational Inorganic Chemistry" Lecture4, Handout3. http://www.huntresearchgroup.org.uk/teaching/teaching_comp_chem_year4/L4_PES.pdf (accessed 25th November 2016)</ref>

</references>

Rep:Mod:Emily1394

2016-12-01T22:21:19Z

Eb1613: /* Exercises */

Page List

[[Mod:eb1613 files| The Calculations Log files can be found here]]

[[Mod:Emily1394| For main Introduction/conclusion page click here]]

[[Mod:Eb1613 Ex1| For Excerise 1 page click here]]

[[Mod:Eb1613 Ex2| For Excerise 2 page click here]]

[[Mod:Eb1613 Ex3| For Excerise 3 page click here]]

= Third Year Computational Lab Transition States - Emily Brown =

=== Introduction ===

==== Theory ====

'''Transition State:''' This is a maxima on the reaction coordinate graph. At the point the gradient/first derivative is zero and can be referred to as a turning point on the graph.

'''Potential Energy Surface:''' This has 3N-6 dimensions and if you travel in one dimension you can draw a reaction coordinate graph as shown below. <ref name="waterbottle" /> The PES is a function of energy vs every coordinate. <ref name="Hunt" />

[[File:Eb1613_PE_RC.png|thumb|center|Potential energy surface on left and corresponding reaction coordinate graph to right <ref name="waterbottle" /> ]]

Due to the transition state being a turning point on the reaction coordinate graph it can be found by setting the first derivative to zero as at a minima/maxima the gradient is zero. The potential energy surface allows you to travel in directions which may be away from the reaction coordinate you are trying to locate. The potential energy surface has 3N-6 dimensions.<ref name="Hunt" /> Programs like GuassView take advantage of the fact that all these dimensions are positive in curvature apart from one which is the minimum energy path. This results in an imaginary frequency which is the single negative frequency found in the frequency calculation of a transition state geometry. Energy minimas have zero negative frequencies in their frequency calculations and saddle points have multiple. <ref name="Hunt" />

Reactions can be controlled by a number of different factors some of these being sterics and secondary orbital effects. Reactions often compromise between multiple aspects for example a reaction may be sterically disfavored but that particular reaction path could result in good orbital overlap.

The reactants tend to form the products via the higher energy transition state which is shown as an energy maximum on the above graph, the energy required to overcome this barrier is known as the activation energy and can be seen in the arrhenius equation as the symbol Ea. The activation energy depends on many factors and programmes like gaussian can be used to estimate this energy and predict whether reactions are likely to occur. For example there are two cis dienes present in the reactant in exercise 3 but only one is involved int he dies alder reactions as the other is known to have a high transition state making it very kinetically unfavourable.

==== Computational ====
Initially structures will be optimized using method1 and then using method2. Doing the initial 'tidy up' allows computational time to be saved. Locating transition states has proved difficult for certain systems which results in different approaches being undertaken such as freezing certain bonds by using the opt=modredundant keywords thus locking atoms together to perform initial optimizations. Another approach is to start from the products or reactants and lengthen certain bonds in an attempt to locate the transition state.

It proved necessary at times to freeze bonds to locate a transition state however once found all structures were later re-optimised under no symmetry constraints. The int=ultrafine keywords are expressed in the DFT calculations as optimisation with many low level vibration modes will often proceed more reliably when a larger DFT integration grid is requested. <ref name="integral" />

'''Method 1:''' Opt+Freq, semi empirical, PM6.

'''Method 2:''' Opt+Freq, DFT B3LYP/631G(d).

Both the density function theory (DFT) and semi-empirical methods are able to describe quantum states as many electron systems; they both use the born-opinhiemer approximation where you first solve for the electronic degrees of freedom. <ref name="electrons" /> In DFT the many-electron wavefunction is completely bypassed in favor of the electron density, the variational principle is used to minimise the energy with respect to electron density. However a key problem with this method is that the energy functional is not know. <ref name="electrons" /> Semi-empirical Methods are a simplified versions of Hartree-Fock theory using empirical corrections in order to improve performance; these can be preformed prior to DFT calculations in order to save computational time. <ref name="mug mug" /> The PM6 part of the calculation specifics that the PM6 hamiltonian is to use in the semi-empirical calculation. <ref name="IwantTEA" />

'''Notes:''' When optimising to a transition state I used: TS (Berry), Force constants allowed to calculate once. When optimising to a minimum use: minimum and force constants are allowed to calculate never. Occasional calculations were run on the colleges HPC to save computational time as these servers use more processors than my local computer in college. The 09 version of gaussian suite was used when on windows college computers.

==== Exercises ====

Each exercise is contained on its own page which are linked to below and above the contents section of each page. Each page containing an exercise has Jmol files of all structures used in that exercise at the end of the page, they are accompanied by the 'results summary' section of their opt/freq calculation to confirm the existence of the correct number of negative frequencies and to allow the geometry of each structure to be viewed.

[[Mod:Eb1613 Ex1| Page for Excerise 1]]

[[Mod:Eb1613 Ex2| Page for Excerise 2]]

[[Mod:Eb1613 Ex3| Page for Excerise 3]]

=== Conclusion ===

The transition states were successfully located for multiple reaction following a similar procedure in each case. Orbital analysis was undertaken and HOMO+1, HOMO, LUMO and LUMO-1 levels were explored. The transition states were be further identified by looking into the IRC, thus allowing endo/exo transition states to be confidently labeled. The IRC also revealed information about the reaction coordinate such that no other intermediates existed and that no other transition states were encountered for our reactions.

This computational lab has also highlighed some key difference between the semi-empirical based basis sets and those of basis sets belonging to the density functional theory family. The lab has drawn attention to the importance of chosen the correct basis set and has given me the ability to use Gaussian programs to confidently locate transition states for reactions and highlighted some key methods to further understand the transition states found.

=== Reference ===

<references>
<ref name="waterbottle">https://commons.wikimedia.org/wiki/File:Potential_Energy_Surface_and_Corresponding_Reaction_Coordinate_Diagram.png (accessed 23rd November)</ref>
<ref name="electrons">https://www.quora.com/What-is-the-difference-between-density-functional-theory-and-hartree-fock (accessed 25th November 2016)</ref>
<ref name="integral">http://www.gaussian.com/g_tech/g_ur/k_opt.htm (accessed 25th November 2016)</ref>
<ref name="IwantTEA ">http://www.gaussian.com/g_tech/g_ur/k_semiempirical.html (accessed 25th November 2016)</ref>
<ref name="mug mug ">http://www.cup.uni-muenchen.de/ch/compchem/energy/semi1.html (accessed 25th November 2016)</ref>
<ref name="Hunt "> Dr. Hunt's year 4 lecture course: "Computational Inorganic Chemistry" Lecture4, Handout3, Page3. http://www.huntresearchgroup.org.uk/teaching/teaching_comp_chem_year4/L4_PES.pdf (accessed 25th November 2016)</ref>

</references>

Rep:Mod:Emily1394

2016-12-01T22:19:13Z

Eb1613: /* Conclusion */

Page List

[[Mod:eb1613 files| The Calculations Log files can be found here]]

[[Mod:Emily1394| For main Introduction/conclusion page click here]]

[[Mod:Eb1613 Ex1| For Excerise 1 page click here]]

[[Mod:Eb1613 Ex2| For Excerise 2 page click here]]

[[Mod:Eb1613 Ex3| For Excerise 3 page click here]]

= Third Year Computational Lab Transition States - Emily Brown =

=== Introduction ===

==== Theory ====

'''Transition State:''' This is a maxima on the reaction coordinate graph. At the point the gradient/first derivative is zero and can be referred to as a turning point on the graph.

'''Potential Energy Surface:''' This has 3N-6 dimensions and if you travel in one dimension you can draw a reaction coordinate graph as shown below. <ref name="waterbottle" /> The PES is a function of energy vs every coordinate. <ref name="Hunt" />

[[File:Eb1613_PE_RC.png|thumb|center|Potential energy surface on left and corresponding reaction coordinate graph to right <ref name="waterbottle" /> ]]

Due to the transition state being a turning point on the reaction coordinate graph it can be found by setting the first derivative to zero as at a minima/maxima the gradient is zero. The potential energy surface allows you to travel in directions which may be away from the reaction coordinate you are trying to locate. The potential energy surface has 3N-6 dimensions.<ref name="Hunt" /> Programs like GuassView take advantage of the fact that all these dimensions are positive in curvature apart from one which is the minimum energy path. This results in an imaginary frequency which is the single negative frequency found in the frequency calculation of a transition state geometry. Energy minimas have zero negative frequencies in their frequency calculations and saddle points have multiple. <ref name="Hunt" />

Reactions can be controlled by a number of different factors some of these being sterics and secondary orbital effects. Reactions often compromise between multiple aspects for example a reaction may be sterically disfavored but that particular reaction path could result in good orbital overlap.

The reactants tend to form the products via the higher energy transition state which is shown as an energy maximum on the above graph, the energy required to overcome this barrier is known as the activation energy and can be seen in the arrhenius equation as the symbol Ea. The activation energy depends on many factors and programmes like gaussian can be used to estimate this energy and predict whether reactions are likely to occur. For example there are two cis dienes present in the reactant in exercise 3 but only one is involved int he dies alder reactions as the other is known to have a high transition state making it very kinetically unfavourable.

==== Computational ====
Initially structures will be optimized using method1 and then using method2. Doing the initial 'tidy up' allows computational time to be saved. Locating transition states has proved difficult for certain systems which results in different approaches being undertaken such as freezing certain bonds by using the opt=modredundant keywords thus locking atoms together to perform initial optimizations. Another approach is to start from the products or reactants and lengthen certain bonds in an attempt to locate the transition state.

It proved necessary at times to freeze bonds to locate a transition state however once found all structures were later re-optimised under no symmetry constraints. The int=ultrafine keywords are expressed in the DFT calculations as optimisation with many low level vibration modes will often proceed more reliably when a larger DFT integration grid is requested. <ref name="integral" />

'''Method 1:''' Opt+Freq, semi empirical, PM6.

'''Method 2:''' Opt+Freq, DFT B3LYP/631G(d).

Both the density function theory (DFT) and semi-empirical methods are able to describe quantum states as many electron systems; they both use the born-opinhiemer approximation where you first solve for the electronic degrees of freedom. <ref name="electrons" /> In DFT the many-electron wavefunction is completely bypassed in favor of the electron density, the variational principle is used to minimise the energy with respect to electron density. However a key problem with this method is that the energy functional is not know. <ref name="electrons" /> Semi-empirical Methods are a simplified versions of Hartree-Fock theory using empirical corrections in order to improve performance; these can be preformed prior to DFT calculations in order to save computational time. <ref name="mug mug" /> The PM6 part of the calculation specifics that the PM6 hamiltonian is to use in the semi-empirical calculation. <ref name="IwantTEA" />

'''Notes:''' When optimising to a transition state I used: TS (Berry), Force constants allowed to calculate once. When optimising to a minimum use: minimum and force constants are allowed to calculate never. Occasional calculations were run on the colleges HPC to save computational time as these servers use more processors than my local computer in college. The 09 version of gaussian suite was used when on windows college computers.

==== Exercises ====

Each exercise is contained on its own page which are linked to below and above the contents section of each page.

[[Mod:Eb1613 Ex1| Page for Excerise 1]]

[[Mod:Eb1613 Ex2| Page for Excerise 2]]

[[Mod:Eb1613 Ex3| Page for Excerise 3]]

=== Conclusion ===

The transition states were successfully located for multiple reaction following a similar procedure in each case. Orbital analysis was undertaken and HOMO+1, HOMO, LUMO and LUMO-1 levels were explored. The transition states were be further identified by looking into the IRC, thus allowing endo/exo transition states to be confidently labeled. The IRC also revealed information about the reaction coordinate such that no other intermediates existed and that no other transition states were encountered for our reactions.

This computational lab has also highlighed some key difference between the semi-empirical based basis sets and those of basis sets belonging to the density functional theory family. The lab has drawn attention to the importance of chosen the correct basis set and has given me the ability to use Gaussian programs to confidently locate transition states for reactions and highlighted some key methods to further understand the transition states found.

=== Reference ===

<references>
<ref name="waterbottle">https://commons.wikimedia.org/wiki/File:Potential_Energy_Surface_and_Corresponding_Reaction_Coordinate_Diagram.png (accessed 23rd November)</ref>
<ref name="electrons">https://www.quora.com/What-is-the-difference-between-density-functional-theory-and-hartree-fock (accessed 25th November 2016)</ref>
<ref name="integral">http://www.gaussian.com/g_tech/g_ur/k_opt.htm (accessed 25th November 2016)</ref>
<ref name="IwantTEA ">http://www.gaussian.com/g_tech/g_ur/k_semiempirical.html (accessed 25th November 2016)</ref>
<ref name="mug mug ">http://www.cup.uni-muenchen.de/ch/compchem/energy/semi1.html (accessed 25th November 2016)</ref>
<ref name="Hunt "> Dr. Hunt's year 4 lecture course: "Computational Inorganic Chemistry" Lecture4, Handout3, Page3. http://www.huntresearchgroup.org.uk/teaching/teaching_comp_chem_year4/L4_PES.pdf (accessed 25th November 2016)</ref>

</references>

Rep:Mod:Emily1394

2016-12-01T22:17:02Z

Eb1613: /* Exercises */

Rep:Mod:Emily1394

2016-12-01T22:16:33Z

Eb1613: /* Computational */

Rep:Mod:Emily1394

2016-12-01T22:13:37Z

Eb1613: /* Theory */

Rep:Mod:Eb1613 Ex3

2016-12-01T22:06:01Z

Eb1613:

Page List

[[Mod:eb1613 files| The Calculations Log files can be found here]]

[[Mod:Emily1394| For main Introduction/conclusion page click here]]

[[Mod:Eb1613 Ex1| For Excerise 1 page click here]]

[[Mod:Eb1613 Ex2| For Excerise 2 page click here]]

[[Mod:Eb1613 Ex3| For Excerise 3 page click here]]

= Third Year Computational Lab Transition States - Emily Brown =

=== Exercise 3 ===

[[File:Exercise2_reaction_emily.png]]

Both cheletropic and Diels-Alder reactions are possible for the above reactants.

Initially the structures were optimized to the semi-empirical PM6 level and later the geometries were re-optimised to the DFT 6-31G(d)/b3LYP level of calculation. The reactants were aligned in different conformations and certain bonds were frozen to find the three transition states shown below. Every structure given has been optimized to the higher accuracy DFT 6-31G(d)/b3LYP level.

Unfortunately there was not enough time to investigate the tendon cis-butadiene fragment successfully.

==== Transition states ====

{| class="wikitable" border="1"
! style="background: #38A5A5;" | Exo Transition State. Negative Frequency = -198.65 cm-1
|-
|style="background: white;" | [[File:Diels_alder_ts_1_movie.gif]]
|-
! style="background: #38A5A5;" | Endo Transition State. Negative Frequency = -200.42 cm-1
|-
|style="background: white;" | [[File:Diels_alder_ts_2_movie.gif]]
|-
! style="background: #38A5A5;" | Cheletropic Transition State. Negative Frequency = -221.18 cm-1
|-
|style="background: white;" | [[File:Chele_TS_movie_eb1613.gif]]
|}

==== Thermochemistry anaylsis ====

The energy profile was first plotted using excel and then using chemdraw to highlight the differences between the endo and exo paths.

{| class="wikitable" border="1"
|-
| style="background: white;" | [[File:Energy profile ex3 eb1613.png]] || style="background: white;" | [[File:Screen_Shot_2016-12-01_at_21.54.33.png]]
|}

Energy values given relative to the reactants in KJ/mol, from the values the Endo route appears to be the preferred route.

{| class="wikitable" border="1"
!style="background: #38A5A5;" | !!style="background: #38A5A5;" | Reactants !! style="background: #38A5A5;" | Transition state !! style="background: #38A5A5;" | Products
|-
| style="background: #38A5A5;" | Endo ||style="background: #EFECD9;" | 0 || style="background: #EFECD9;" |+46.17992 ||style="background: #EFECD9;" | -75.183818
|-
| style="background: #38A5A5;" | Exo ||style="background: #EFECD9;" | 0 ||style="background: #EFECD9;" | +46.23768|| style="background: #EFECD9;" |-73.886821
|-
| style="background: #38A5A5;" | Cheletropic||style="background: #EFECD9;" | 0 ||style="background: #EFECD9;" | +63.05663|| style="background: #EFECD9;" |-63.9650565
|}

Raw values with KJ/mol given to the nearest whole number

{| class="wikitable" border="1"
!style="background: #38A5A5;" | Structure!! style="background: #38A5A5;" | E( Hartrees) !! style="background: #38A5A5;" | E(KJ/mol)
|-
| style="background: #38A5A5;" | Diene ||style="background: #EFECD9;" | -309.504492|| style="background: #EFECD9;" |-812604
|-
| style="background: #38A5A5;" | Sulfur||style="background: #EFECD9;" | -548.604917|| style="background: #EFECD9;" |-1440362
|-
| style="background: #38A5A5;" | Sum of Reactants ||style="background: #EFECD9;" | -858.109409|| style="background: #EFECD9;" |-2252966
|-
| style="background: #38A5A5;" | Endo TS||style="background: #EFECD9;" | -858.09182|| style="background: #EFECD9;" |-2252920
|-
| style="background: #38A5A5;" | Endo Product||style="background: #EFECD9;" | -858.138045|| style="background: #EFECD9;" |-2253041
|-
| style="background: #38A5A5;" | Exo TS||style="background: #EFECD9;" | -858.091798|| style="background: #EFECD9;" |-2252920
|-
| style="background: #38A5A5;" | Exo Product||style="background: #EFECD9;" | -858.137551|| style="background: #EFECD9;" |-2253040
|-
| style="background: #38A5A5;" | Chele TS||style="background: #EFECD9;" | -858.085392|| style="background: #EFECD9;" |-2252903
|-
| style="background: #38A5A5;" | Chele Product||style="background: #EFECD9;" | -858.133772|| style="background: #EFECD9;" |-2253030
|}

Looking at the energy reaction barriers it can be seen that the Endo transition state is slightly below the cheletropic value making it the preferred reaction coordinate. however the value for the end transition state is only slightly below that for the cheletropic transition state and the calculation percentage errors/accuracies could effect this ordering.

==== IRC analysis ====

During the reaction the carbon-carbon bond lengths all become styled as 1.5 bond order suggesting an aromatic element to the ring. The IRC calculations proved very challenging throughout this lab and as such the ENDO TS IRC path is recorded in reverse and shows the detachment of the sulfur oxide molecule. Using the IRC plots it can be seen that the reaction proceed without any other intermediates or transition states as demonstrated by the smooth curve of the graph and lack of other turning points in the gradient.

{| class="wikitable" border="1"
! colspan="2" style="text-align: center;" style="background: #38A5A5;" |Cheletropic IRC path
|-
|style="background: white;" | [[File:Chele_IRC_movie.gif]] || style="background: white;" | [[File:Irc_chele_eb1613.png]]
|-
! colspan="2" style="text-align: center;" style="background: #38A5A5;" | Exo IRC path
|-
|style="background: white;" | [[File:Exo_IRC_movie_eb1613.gif]] || style="background: white;" | [[File:Exo_IRC.png]]
|-
!colspan="2" style="text-align: center;" style="background: #38A5A5;" | Endo IRC path
|-
|style="background: white;" | [[File:Endo_IRC_movie_eb1613.gif]] || style="background: white;" | [[File:IRC_path_ex3.png]]
|}

==== Structure files ====

{| class="wikitable" border="1"
|+ Structures
! style="background: #38A5A5;"|sulfur dioxde !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>SULFUR_FREQ_631GD.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Sulfur_eb1613_table.png]]
|-
! style="background: #38A5A5;"|Xylylene Diene !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Diene_mandisp1pt0.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Diene_mandisp1pt0_ex3_eb1613.png]]
|-
!style="background: #38A5A5;"| Diels-Alder Endo Transition state !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>DIELSALDER2_TS_FOUND_631GD_REOPT.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Diels_alder_ts_summary1_eb1613.png]]
|-
! style="background: #38A5A5;"|Diels-Alder Exo Transition state !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Opt_to_ts_631gd.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Da2_ts_ex3.png]]
|-
! style="background: #38A5A5;"|Cheletropic Transition state !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>CHELE_TS_TRY_631GD_FREQ.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Chele_ts_summary.png]]
|-
! style="background: #38A5A5;"|Diels-Alder Endo Product !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>DIELS_ALDER_631GD.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Diels_alder_product1ex3.png]]
|-
! style="background: #38A5A5;"|Diels-Alder Exo Product !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Diels_alder_2_631Gd.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Diels_alder2_product_ex3_eb1613.png]]
|-
! style="background: #38A5A5;"|Cheletropic Product !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Product_chele_mandisp1pt0.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Chele_product_eb1613.png ]]
|}

Rep:Mod:Eb1613 Ex2

2016-12-01T22:05:50Z

Eb1613:

Page List

[[Mod:eb1613 files| The Calculations Log files can be found here]]

[[Mod:Emily1394| For main Introduction/conclusion page click here]]

[[Mod:Eb1613 Ex1| For Excerise 1 page click here]]

[[Mod:Eb1613 Ex2| For Excerise 2 page click here]]

[[Mod:Eb1613 Ex3| For Excerise 3 page click here]]

= Third Year Computational Lab Transition States - Emily Brown =

=== Exercise 2 ===

[[File:Ex2_scheme.png]]

=== Transition state 2 ===

{| class="wikitable" border="1"
! style="background: #38A5A5;"|Exo Transition State. Negative Frequency = -520.92 cm-1
|-
| style="background: white;"| [[File:Eb1613_exo_ts_movie.gif]]
|-
! style="background: #38A5A5;"|Endo Transition State. Negative Frequency = -528.82 cm-1
|-
| style="background: white;"| [[File:Eb1613_endo_ts_movie2.gif]]
|}

=== Thermochemistry anaylsis 2 ===

[[File:Exercise_reaction_coordin_eb1613.png]]

'''Electronic and Thermal free energies relative to reactants(KJ/mol) (2dp)'''

{| class="wikitable" border="1"
! style="background: #38A5A5;" | !! style="background: #38A5A5;" |Reactants !! style="background: #38A5A5;" |Transition state !! style="background: #38A5A5;"| Products
|-
| style="background: #38A5A5;" | Exo ||style="background: #EFECD9;" | 0 || style="background: #EFECD9;" |+159.81 ||style="background: #EFECD9;" | -67.41
|-
| style="background: #38A5A5;" | Endo || style="background: #EFECD9;" |0 || style="background: #EFECD9;" |+167.65|| style="background: #EFECD9;" |-63.77
|}

From the thermochemistry relative energy values it can be seen that the Exo product has an activation energy which is 7.84 KJ/mol lower than that of the Exo product. The Exo-Adduct is 3.64 KJ/mol more stable than the Endo-adduct making it the thermodynamicly favoured product as well as the kinetically favoured product as it has a lower energy TS.

=== MO analysis ===

This reaction and that the reaction in exercise 2 are both Diels-Alder reactions the MO diagram from exercise 1 is still valid to be used to understand/explain the MO interactions within this reaction.

{| class="wikitable" border="3"
|colspan="2" style="text-align: center;" style="background: #38A5A5;"| MO diagram for the Diels Alder Reaction in exercise 1 
|-
| style="background: white;"| [[File:Eb1613_MO_diagram_ex1.png]]
|-
|}

Using your MO diagram for the Diels-Alder reaction, locate the occupied and unoccupied orbitals associated with the DA reaction for both TSs by symmetry. Find the relevant MOs and add them to your wiki (at an appropriate angle to show symmetry). Is this a normal or inverse demand DA reaction?

Look at the HOMO of the TSs. Are there any secondary orbital interactions or sterics that might affect the reaction barrier energy (Hint: in GaussView, set the isovalue to 0.01. In Jmol, change the mo cutoff to 0.01)? The Wikipedia page on Frontier Molecular Orbital Theory has some useful information on what these secondary orbital interactions are.

From looking at the molcular orbitals below one can identify which orbitals are interacting in the Transition states. For example: it can be seen that the Endo TS LUMO is formed by the overlap of the Cyclohexadiene LUMO-1 and the 1,3-Dioxole LUMO.

{| class="wikitable" border: 2px solid black;"
! colspan="4" style="text-align: centre;" style="background: #328B8B;"|MOs
|-
| colspan="2" style="text-align: center;" style="background: #38A5A5;"| '''Reactants'''
| colspan="2" style="text-align: center;" style="background: #38A5A5;"| '''Transition States'''
|-
!style="background: #3DCACA;"| '''1,3-Dioxole''' !!style="background: #3DCACA;"| '''Cyclohexadiene''' !!style="background: #3DCACA;"| '''Endo-TS''' !!style="background: #3DCACA;"| '''Exo-TS'''
|-
! style="background: #D9C02F;"| HOMO+1 !!style="background: #D9C02F;"| HOMO+1 !!style="background: #D9C02F;"| HOMO+1 !!style="background: #D9C02F;"| HOMO+1
|-
| style="background: white;"| [[File:Homo_plus_one_o_ring.png|256px]] || style="background: white;"|[[File:Homo_plus_1_c_ring.png|256px]] || style="background: white;"|[[File:Exo_homo+plus1.png|256px]] ||style="background: white;"| [[File:New_exo_homoplus1.png|256px]]
|-
! style="background: #D9C02F;"|HOMO !! style="background: #D9C02F;"|HOMO!!style="background: #D9C02F;"| HOMO !!style="background: #D9C02F;"| HOMO
|-
|style="background: white;"| [[File:Homo_o_ring.png|256px]] ||style="background: white;"| [[File:Homo__c_ring.png|256px]] ||style="background: white;"| [[File:Exo_homo121.png|256px]] || style="background: white;"|[[File:New_exo_homo_eb1613.png|256px]]
|-
! style="background: #D9C02F;"|LUMO !!style="background: #D9C02F;"| LUMO !!style="background: #D9C02F;"| LUMO !!style="background: #D9C02F;"| LUMO
|-
|style="background: white;"| [[File:Lumo_o_ring.png|256px]] ||style="background: white;"| [[File:Lumo__c_ring.png|256px]] ||style="background: white;"| [[File:Exo_lumo121.png|256px]] ||style="background: white;"| [[File:New_exo_lumo_eb1613.png|256px]]
|-
!style="background: #D9C02F;"| LUMO-1!! style="background: #D9C02F;"|LUMO-1 !!style="background: #D9C02F;"| LUMO-1 !! style="background: #D9C02F;"|LUMO-1
|-
|style="background: white;"| [[File:Lumo_minus1_o_ring.png|256px]] || style="background: white;"|[[File:Lumo_minus1__c_ring.png|256px]] ||style="background: white;"| [[File:Exo_lumo_minus121.png|256px]] || style="background: white;"|[[File:New_exo_lumominus1_eb1613.png|256px]]
|- <td class=”ms-rteTableEvenCol-default” style=”width: 50%; background-color: #ffffff;”></td>
|}

=== Structure Optimisation ===

All optimized to the B3LYP/6-31G(d) level but initially with the semi-empirical PM6 method. Everything but the transition states was confirmed to be a true minima by lack of negative frequencies in the frequency calculations as shown below. Finding a single negative frequency confirms the structures to in fact be the end and eco transition states desired.
{| class="wikitable" border="1"
|+ Reactants
! style="background: #38A5A5;"| Cyclohexadiene !!style="background: #38A5A5;"| Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>CARBON_RING_FREQ23.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Carbon_ring_summary.png]]
|-
!style="background: #38A5A5;"| 1,3-Dioxole !!style="background: #38A5A5;"| Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Oxygen_ring.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Oxygen_ring_sum_eb1613.png]]
|}

{| class="wikitable" border="1"
|+ Transition State
! style="background: #38A5A5;"|Exo-TS!! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Exo_ts_99999.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Exo_ex2_ts_table.png]]
|-
! style="background: #38A5A5;"|Endo-Ts !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with PM6 level</title> <color>white</color> <size>200</size> <uploadedFileContents>ENDO_TS_OPT_631GD.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Endo_ts_summary_eb1613.png]]
|}

{| class="wikitable" border="1"
|+ Products
! style="background: #38A5A5;"|Exo-Product!! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Product_exo_631Gd.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Exo_TS_eb1613333.png]]
|-
! style="background: #38A5A5;"|Endo-Product !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with PM6 level</title> <color>white</color> <size>200</size> <uploadedFileContents>Endo_product_freqqq.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Endo_product_summmmmm.png]]
|}

Rep:Mod:Eb1613 Ex1

2016-12-01T22:05:36Z

Eb1613:

Page List

[[Mod:eb1613 files| The Calculations Log files can be found here]]

[[Mod:Emily1394| For main Introduction/conclusion page click here]]

[[Mod:Eb1613 Ex1| For Excerise 1 page click here]]

[[Mod:Eb1613 Ex2| For Excerise 2 page click here]]

[[Mod:Eb1613 Ex3| For Excerise 3 page click here]]

= Third Year Computational Lab Transition States - Emily Brown =

=== Exercise 1: Reaction of Butadiene with Ethene ===

[[File:ex1_scheme2.png]]

=== Bond Distances ===

{| class="wikitable" border="1"
|+ style="background: #38A5A5;"| Carbon-Carbon Bond Distances (Angstroms)
! style="background: #38A5A5;"| !! style="background: #38A5A5;"|C1-C2!! style="background: #38A5A5;"|C2-C3!! style="background: #38A5A5;"|C3-C4!! style="background: #38A5A5;"|C4-C5!! style="background: #38A5A5;"| C5-C6!! style="background: #38A5A5;"| C6-C1
|-
| style="background: #38A5A5;"| Butadiene||style="background: #EFECD9;"| 1.33530||style="background: #EFECD9;"| 1.46838 || style="background: #EFECD9;"|1.33525 ||style="background: #EFECD9;"| ||style="background: #EFECD9;"| ||style="background: #EFECD9;"|
|-
| style="background: #38A5A5;"|TS||style="background: #EFECD9;"| 1.37981 ||style="background: #EFECD9;"| 1.41112 ||style="background: #EFECD9;"| 1.37976 ||style="background: #EFECD9;"| 2.11496 || style="background: #EFECD9;"|1.38177 ||style="background: #EFECD9;"| 2.11452
|-
| style="background: #38A5A5;"|Product|| style="background: #EFECD9;"|1.50086 ||style="background: #EFECD9;"| 1.33698 || style="background: #EFECD9;"|1.50086 ||style="background: #EFECD9;"| 1.53717 ||style="background: #EFECD9;"| 1.53459 ||style="background: #EFECD9;"| 1.53717
|-
|}

Carbon-Carbon Sigma bonds are longer than double bonds. the bond length between C1-C2 and C3-C4 increase as they transform from double to single bonds in the reaction. The C2-C3 bond length shortens due to the reaction as a double bond forms here. The C5-C6 bond lengthens as it transforms from a single to a double bond. Due to the system being within a ring the carbon carbon single bonds are slightly shorter than the literature values which is for alkane chains. The bond distances of the forming bonds C1-C6 and C4-C5 decrease to values corresponding to those of single bonds. The Van der Waals radi for carbon is 1.70 angstroms. <ref name="vander" /> The length of bonds C1-C6 and C4-C5 at the transition state are less than twice the Van der Waals radius which indicates that a bond a forming.

Literature C-C bond distances <ref name="carbon" />

{| class="wikitable" border="1"
! colspan="2" style="background: #38A5A5;"| Carbon-Carbon Bond Distances (Angstroms)
|-
!style="background: #EFECD9;"|Sp3 C-C!! style="background: #EFECD9;"|Sp2 C-C
|-
| style="background: #EFECD9;"|1.57|| style="background: #EFECD9;"|1.33
|}

=== MO analysis ===

It can be seen from the MOs that there is a high symmetry requirement for the reaction the HOMO-1 (v2) orbital interaction lowers the energy of the electrons from the diene; the HOMO (π3) interactions stabilizes the electron pair coming from the dieneophile.

The overlap integral is zero for the interactions labelled π3 and π*5 and non-zero for interactions labelled π2 and π*4.

The MOs diagram highlights that the reaction is allowed as the orbitals of the same parity are interacting: u<->u g<->g.

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;" style="background: #38A5A5;" | MO diagram for the Diels Alder Reaction 
|-
|style="background: white;"| [[File:Eb1613_MO_diagram_ex1.png]]
|-
|}

Using a Frontier Orbital Approach to justify the diels alder reactivity in this reaction. This can be seen in the HOMO of the TS which shows the favorable overlap from combining the butadiene HOMO with the ethene LUMO.

{| class="wikitable" border="1"
|colspan="2" style="text-align: center;" style="background: #38A5A5;"|Butadiene
|-
! style="background: #EFECD9;"|HOMO!!style="background: #EFECD9;"| LUMO
|-
| style="background: white;"| [[File:Eb1613_butadiene_LUMO.png]] || style="background: white;"|[[File:Eb1613_butadiene_HOMO.png]]
|-
|colspan="2" style="text-align: center;" style="background: #38A5A5;"| Ethene
|-
! style="background: #EFECD9;"|HOMO!!style="background: #EFECD9;"| LUMO
|-
|style="background: white;"| [[File:Eb1613_ethene_lumo.png]] || style="background: white;"|[[File:Eb1613_ethene_homo.png]]
|-
|colspan="2" style="text-align: center; style="background: #38A5A5;"|Transition State
|-
| colspan="2" style="text-align: center;" style="background: #EFECD9;"| LUMO + 1 = π*5
|-
| colspan="2" style="text-align: center; style="background: white;"| [[File:Lumo_minus_one_eb1613.png]]
|-
| colspan="2" style="text-align: center;" style="background: #EFECD9;"| LUMO = = π*4
|-
| colspan="2" style="text-align: center; style="background: white;"| [[File:Eb1613_TS_lumo.png]]
|-
| colspan="2" style="text-align: center;" style="background: #EFECD9;"| HOMO = = π3
|-
| colspan="2" style="text-align: center;" style="background: white;"| [[File:Eb1613_TS_homo.png]]
|-
| colspan="2" style="text-align: center;" style="background: #EFECD9;"| HOMO - 1 = = π2
|-
| colspan="2" style="text-align: center;" style="background: white;"| [[File:Homo_minus_one_eb1613.png]]
|}

The four MOs produced in the TS are π*5, π*4, π3 and π2. These are shown in the MO diagram above and were found were located using the guassian check point file.

=== Transition state analysis ===

The reactants were initially optimised to the PM6 semi-empirical level and then re-optimised to the DFT B3LYP/6-31G(d) level to save computational time. The reactants were aligned and then the atoms which form bonds were frozen using the opt=modredundant keywords in the calculation; this system was optimised to a minimum allowing parameters to reach a minimum whilst holding the reactants together at a distance of 2.2 angstroms. The resultant geometry from this calculation was used in a new calculation which optimised the structure to a TS (Berry) and allowed force constants to be calculated once. The transition state was located and confirmed by the presence of a single negative frequency which had an imaginary vibrational node which corresponded to the forming/breaking of bonds involved in the reactions transition state. This transition state geometry was then calculated using the higher DFT B3LYP/6-31G(d) calculation method. The transition state was further confirmed via the IRC calculated which allows force constants to be calculated always. The IRC requests that a reaction path be followed by integrating the intrinsic reaction coordinate. <ref name="IRC" /> It was found that using 10 steps in the IRC calculation was not nearly enough to look over the whole reaction coordinate and so 10000 steps was used for the repeated calculation. The visualisation of the transition state can be seen in the GIF files below along with the IRC calculation results. Furthermore the intrinsic reaction coordinate graph shows that there are no intermediates or other transition states involved in this reaction.

{| class="wikitable" border="1"
! style="background: #38A5A5;" |IRC movie captured || style="background: #38A5A5;" |IRC Graph
|-
| style="background: white;" | [[File:IRC_movie_eb1613.gif]] || style="background: white;" | [[File:IRC_exercise1_eb1613.png]]
|}

The Diels-Alder cyclic addition reaction occurs via a concerted transition state as shown below. The two new sigma bonds are formed at the same time therefore the reaction is synchronous. The animations below show how this compares to the first positive frequency, which is seen to be asynchronous rocking.

{| class="wikitable" border="1"
! style="background: #38A5A5;" | Negative Frequency = -948.76 cm-1
|-
|style="background: white;" | [[File:Test3_files_eb1613.gif]]
|-
! style="background: #38A5A5;" | First Positive Frequency = 145.08 cm-1
|-
| style="background: white;" | [[File:Eb1613_first_pos_vib_ex1.gif]]
|}

=== Optimization of Reactants, TS and Products ===

All structures have been optimised at the semi-empirical PM6 level and then further optimised to the DFT B3LYP/6-31G(d) level to save computational time. The lack of negative frequencies in the frequency calculation indicates that the structure is optimised to a true minimum, the presence of one negative frequency indicates that a transition state has been reached, more than one negative frequency means that a saddle point structure has been reached.

{| class="wikitable" border="1"
|+ Files
! style="background: #38A5A5;"|Butadiene !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with PM6 level</title> <color>white</color> <size>200</size> <uploadedFileContents>Eb1613_butadiene_PM6_opt_freq.log</uploadedFileContents> </jmolApplet></jmol> || [[File:But_eb1613_energy_new.png]]
|-
! style="background: #38A5A5;"|Ethene !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with PM6 level</title> <color>white</color> <size>200</size> <uploadedFileContents>Eb1613_ETHENE_PM6_OPT_FREQ.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Eb1613_ethene_energy.png]]
|-
! style="background: #38A5A5;"|Transition State !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Transition State</title> <color>white</color> <size>300</size> <uploadedFileContents>TS_FREEZE2_OPT.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Eb1613_TS_energy.png]]
|-
! style="background: #38A5A5;"|Product !! style="background: #38A5A5;"|Gaussian imagine of product
|-
| <jmol><jmolApplet> <title>Jmol of PM6 optimised product</title> <color>white</color> <size>300</size> <uploadedFileContents>Eb1613_PRODUCT_PM6_OPT_MANDISP1PT0_FREQ.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Product_ex1.png]]
|-
! colspan="2" style="text-align: center;" style="background: #38A5A5;"| Optimization Summary
|-
|colspan="2" style="text-align: center;"| [[File:Eb1613_product_summary.png]]
|}

=== References ===

<references>
<ref name="carbon">J.M. Berg, J. L. Tymoczko, L. Stryer, in Biochemistry., W.H. Freeman, New York, 5th edn., 2002, Appendix C: Standard Bond Lengths, https://www.ncbi.nlm.nih.gov/books/NBK21220/, (accessed 23rd November, 2016).</ref>
<ref name="vander">A. Bondi, J. Phys. Chem., 1964, 68 (3), 441-451.</ref>
<ref name="IRC">http://www.gaussian.com/g_tech/g_ur/k_irc.htm (accessed 23rd November, 2016)</ref>

</references>

Rep:Mod:eb1613 files

2016-12-01T22:05:22Z

Eb1613:

Rep:Mod:Emily1394

2016-12-01T22:04:56Z

Eb1613:

Rep:Mod:Eb1613 Ex3

2016-12-01T22:02:27Z

Eb1613: /* IRC analysis */

Page List

[[Mod:eb1613 files| The Calculations Log files can be found here]]

[[Mod:Emily1394| For Main Page click here]]

[[Mod:Eb1613 Ex1| Page for Excerise 1]]

[[Mod:Eb1613 Ex2| Page for Excerise 2]]

[[Mod:Eb1613 Ex3| Page for Excerise 3]]

= Third Year Computational Lab Transition States - Emily Brown =

=== Exercise 3 ===

[[File:Exercise2_reaction_emily.png]]

Both cheletropic and Diels-Alder reactions are possible for the above reactants.

Initially the structures were optimized to the semi-empirical PM6 level and later the geometries were re-optimised to the DFT 6-31G(d)/b3LYP level of calculation. The reactants were aligned in different conformations and certain bonds were frozen to find the three transition states shown below. Every structure given has been optimized to the higher accuracy DFT 6-31G(d)/b3LYP level.

Unfortunately there was not enough time to investigate the tendon cis-butadiene fragment successfully.

==== Transition states ====

{| class="wikitable" border="1"
! style="background: #38A5A5;" | Exo Transition State. Negative Frequency = -198.65 cm-1
|-
|style="background: white;" | [[File:Diels_alder_ts_1_movie.gif]]
|-
! style="background: #38A5A5;" | Endo Transition State. Negative Frequency = -200.42 cm-1
|-
|style="background: white;" | [[File:Diels_alder_ts_2_movie.gif]]
|-
! style="background: #38A5A5;" | Cheletropic Transition State. Negative Frequency = -221.18 cm-1
|-
|style="background: white;" | [[File:Chele_TS_movie_eb1613.gif]]
|}

==== Thermochemistry anaylsis ====

The energy profile was first plotted using excel and then using chemdraw to highlight the differences between the endo and exo paths.

{| class="wikitable" border="1"
|-
| style="background: white;" | [[File:Energy profile ex3 eb1613.png]] || style="background: white;" | [[File:Screen_Shot_2016-12-01_at_21.54.33.png]]
|}

Energy values given relative to the reactants in KJ/mol, from the values the Endo route appears to be the preferred route.

{| class="wikitable" border="1"
!style="background: #38A5A5;" | !!style="background: #38A5A5;" | Reactants !! style="background: #38A5A5;" | Transition state !! style="background: #38A5A5;" | Products
|-
| style="background: #38A5A5;" | Endo ||style="background: #EFECD9;" | 0 || style="background: #EFECD9;" |+46.17992 ||style="background: #EFECD9;" | -75.183818
|-
| style="background: #38A5A5;" | Exo ||style="background: #EFECD9;" | 0 ||style="background: #EFECD9;" | +46.23768|| style="background: #EFECD9;" |-73.886821
|-
| style="background: #38A5A5;" | Cheletropic||style="background: #EFECD9;" | 0 ||style="background: #EFECD9;" | +63.05663|| style="background: #EFECD9;" |-63.9650565
|}

Raw values with KJ/mol given to the nearest whole number

{| class="wikitable" border="1"
!style="background: #38A5A5;" | Structure!! style="background: #38A5A5;" | E( Hartrees) !! style="background: #38A5A5;" | E(KJ/mol)
|-
| style="background: #38A5A5;" | Diene ||style="background: #EFECD9;" | -309.504492|| style="background: #EFECD9;" |-812604
|-
| style="background: #38A5A5;" | Sulfur||style="background: #EFECD9;" | -548.604917|| style="background: #EFECD9;" |-1440362
|-
| style="background: #38A5A5;" | Sum of Reactants ||style="background: #EFECD9;" | -858.109409|| style="background: #EFECD9;" |-2252966
|-
| style="background: #38A5A5;" | Endo TS||style="background: #EFECD9;" | -858.09182|| style="background: #EFECD9;" |-2252920
|-
| style="background: #38A5A5;" | Endo Product||style="background: #EFECD9;" | -858.138045|| style="background: #EFECD9;" |-2253041
|-
| style="background: #38A5A5;" | Exo TS||style="background: #EFECD9;" | -858.091798|| style="background: #EFECD9;" |-2252920
|-
| style="background: #38A5A5;" | Exo Product||style="background: #EFECD9;" | -858.137551|| style="background: #EFECD9;" |-2253040
|-
| style="background: #38A5A5;" | Chele TS||style="background: #EFECD9;" | -858.085392|| style="background: #EFECD9;" |-2252903
|-
| style="background: #38A5A5;" | Chele Product||style="background: #EFECD9;" | -858.133772|| style="background: #EFECD9;" |-2253030
|}

Looking at the energy reaction barriers it can be seen that the Endo transition state is slightly below the cheletropic value making it the preferred reaction coordinate. however the value for the end transition state is only slightly below that for the cheletropic transition state and the calculation percentage errors/accuracies could effect this ordering.

==== IRC analysis ====

During the reaction the carbon-carbon bond lengths all become styled as 1.5 bond order suggesting an aromatic element to the ring. The IRC calculations proved very challenging throughout this lab and as such the ENDO TS IRC path is recorded in reverse and shows the detachment of the sulfur oxide molecule. Using the IRC plots it can be seen that the reaction proceed without any other intermediates or transition states as demonstrated by the smooth curve of the graph and lack of other turning points in the gradient.

{| class="wikitable" border="1"
! colspan="2" style="text-align: center;" style="background: #38A5A5;" |Cheletropic IRC path
|-
|style="background: white;" | [[File:Chele_IRC_movie.gif]] || style="background: white;" | [[File:Irc_chele_eb1613.png]]
|-
! colspan="2" style="text-align: center;" style="background: #38A5A5;" | Exo IRC path
|-
|style="background: white;" | [[File:Exo_IRC_movie_eb1613.gif]] || style="background: white;" | [[File:Exo_IRC.png]]
|-
!colspan="2" style="text-align: center;" style="background: #38A5A5;" | Endo IRC path
|-
|style="background: white;" | [[File:Endo_IRC_movie_eb1613.gif]] || style="background: white;" | [[File:IRC_path_ex3.png]]
|}

==== Structure files ====

{| class="wikitable" border="1"
|+ Structures
! style="background: #38A5A5;"|sulfur dioxde !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>SULFUR_FREQ_631GD.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Sulfur_eb1613_table.png]]
|-
! style="background: #38A5A5;"|Xylylene Diene !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Diene_mandisp1pt0.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Diene_mandisp1pt0_ex3_eb1613.png]]
|-
!style="background: #38A5A5;"| Diels-Alder Endo Transition state !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>DIELSALDER2_TS_FOUND_631GD_REOPT.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Diels_alder_ts_summary1_eb1613.png]]
|-
! style="background: #38A5A5;"|Diels-Alder Exo Transition state !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Opt_to_ts_631gd.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Da2_ts_ex3.png]]
|-
! style="background: #38A5A5;"|Cheletropic Transition state !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>CHELE_TS_TRY_631GD_FREQ.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Chele_ts_summary.png]]
|-
! style="background: #38A5A5;"|Diels-Alder Endo Product !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>DIELS_ALDER_631GD.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Diels_alder_product1ex3.png]]
|-
! style="background: #38A5A5;"|Diels-Alder Exo Product !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Diels_alder_2_631Gd.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Diels_alder2_product_ex3_eb1613.png]]
|-
! style="background: #38A5A5;"|Cheletropic Product !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Product_chele_mandisp1pt0.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Chele_product_eb1613.png ]]
|}

Rep:Mod:Eb1613 Ex3

2016-12-01T22:00:39Z

Eb1613: /* Exercise 3 */

Page List

[[Mod:eb1613 files| The Calculations Log files can be found here]]

[[Mod:Emily1394| For Main Page click here]]

[[Mod:Eb1613 Ex1| Page for Excerise 1]]

[[Mod:Eb1613 Ex2| Page for Excerise 2]]

[[Mod:Eb1613 Ex3| Page for Excerise 3]]

= Third Year Computational Lab Transition States - Emily Brown =

=== Exercise 3 ===

[[File:Exercise2_reaction_emily.png]]

Both cheletropic and Diels-Alder reactions are possible for the above reactants.

Initially the structures were optimized to the semi-empirical PM6 level and later the geometries were re-optimised to the DFT 6-31G(d)/b3LYP level of calculation. The reactants were aligned in different conformations and certain bonds were frozen to find the three transition states shown below. Every structure given has been optimized to the higher accuracy DFT 6-31G(d)/b3LYP level.

Unfortunately there was not enough time to investigate the tendon cis-butadiene fragment successfully.

==== Transition states ====

{| class="wikitable" border="1"
! style="background: #38A5A5;" | Exo Transition State. Negative Frequency = -198.65 cm-1
|-
|style="background: white;" | [[File:Diels_alder_ts_1_movie.gif]]
|-
! style="background: #38A5A5;" | Endo Transition State. Negative Frequency = -200.42 cm-1
|-
|style="background: white;" | [[File:Diels_alder_ts_2_movie.gif]]
|-
! style="background: #38A5A5;" | Cheletropic Transition State. Negative Frequency = -221.18 cm-1
|-
|style="background: white;" | [[File:Chele_TS_movie_eb1613.gif]]
|}

==== Thermochemistry anaylsis ====

The energy profile was first plotted using excel and then using chemdraw to highlight the differences between the endo and exo paths.

{| class="wikitable" border="1"
|-
| style="background: white;" | [[File:Energy profile ex3 eb1613.png]] || style="background: white;" | [[File:Screen_Shot_2016-12-01_at_21.54.33.png]]
|}

Energy values given relative to the reactants in KJ/mol, from the values the Endo route appears to be the preferred route.

{| class="wikitable" border="1"
!style="background: #38A5A5;" | !!style="background: #38A5A5;" | Reactants !! style="background: #38A5A5;" | Transition state !! style="background: #38A5A5;" | Products
|-
| style="background: #38A5A5;" | Endo ||style="background: #EFECD9;" | 0 || style="background: #EFECD9;" |+46.17992 ||style="background: #EFECD9;" | -75.183818
|-
| style="background: #38A5A5;" | Exo ||style="background: #EFECD9;" | 0 ||style="background: #EFECD9;" | +46.23768|| style="background: #EFECD9;" |-73.886821
|-
| style="background: #38A5A5;" | Cheletropic||style="background: #EFECD9;" | 0 ||style="background: #EFECD9;" | +63.05663|| style="background: #EFECD9;" |-63.9650565
|}

Raw values with KJ/mol given to the nearest whole number

{| class="wikitable" border="1"
!style="background: #38A5A5;" | Structure!! style="background: #38A5A5;" | E( Hartrees) !! style="background: #38A5A5;" | E(KJ/mol)
|-
| style="background: #38A5A5;" | Diene ||style="background: #EFECD9;" | -309.504492|| style="background: #EFECD9;" |-812604
|-
| style="background: #38A5A5;" | Sulfur||style="background: #EFECD9;" | -548.604917|| style="background: #EFECD9;" |-1440362
|-
| style="background: #38A5A5;" | Sum of Reactants ||style="background: #EFECD9;" | -858.109409|| style="background: #EFECD9;" |-2252966
|-
| style="background: #38A5A5;" | Endo TS||style="background: #EFECD9;" | -858.09182|| style="background: #EFECD9;" |-2252920
|-
| style="background: #38A5A5;" | Endo Product||style="background: #EFECD9;" | -858.138045|| style="background: #EFECD9;" |-2253041
|-
| style="background: #38A5A5;" | Exo TS||style="background: #EFECD9;" | -858.091798|| style="background: #EFECD9;" |-2252920
|-
| style="background: #38A5A5;" | Exo Product||style="background: #EFECD9;" | -858.137551|| style="background: #EFECD9;" |-2253040
|-
| style="background: #38A5A5;" | Chele TS||style="background: #EFECD9;" | -858.085392|| style="background: #EFECD9;" |-2252903
|-
| style="background: #38A5A5;" | Chele Product||style="background: #EFECD9;" | -858.133772|| style="background: #EFECD9;" |-2253030
|}

Looking at the energy reaction barriers it can be seen that the Endo transition state is slightly below the cheletropic value making it the preferred reaction coordinate. however the value for the end transition state is only slightly below that for the cheletropic transition state and the calculation percentage errors/accuracies could effect this ordering.

==== IRC analysis ====

Xylylene is highly unstable. Look at the IRCs for the reactions - what happens to the bonding of the 6-membered ring during the course of the reaction?

During the reaction the carbon-carbon bond lengths all become styled as 1.5 bond order suggesting an aromatic element to the ring. The IRC calculations proved very challenging throughout this lab and as such the ENDO TS IRC path is recorded in reverse and shows the detachment of the sulfur oxide molecule.

{| class="wikitable" border="1"
! colspan="2" style="text-align: center;" style="background: #38A5A5;" |Cheletropic IRC path
|-
|style="background: white;" | [[File:Chele_IRC_movie.gif]] || style="background: white;" | [[File:Irc_chele_eb1613.png]]
|-
! colspan="2" style="text-align: center;" style="background: #38A5A5;" | Exo IRC path
|-
|style="background: white;" | [[File:Exo_IRC_movie_eb1613.gif]] || style="background: white;" | [[File:Exo_IRC.png]]
|-
!colspan="2" style="text-align: center;" style="background: #38A5A5;" | Endo IRC path
|-
|style="background: white;" | [[File:Endo_IRC_movie_eb1613.gif]] || style="background: white;" | [[File:IRC_path_ex3.png]]
|}

==== Structure files ====

{| class="wikitable" border="1"
|+ Structures
! style="background: #38A5A5;"|sulfur dioxde !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>SULFUR_FREQ_631GD.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Sulfur_eb1613_table.png]]
|-
! style="background: #38A5A5;"|Xylylene Diene !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Diene_mandisp1pt0.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Diene_mandisp1pt0_ex3_eb1613.png]]
|-
!style="background: #38A5A5;"| Diels-Alder Endo Transition state !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>DIELSALDER2_TS_FOUND_631GD_REOPT.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Diels_alder_ts_summary1_eb1613.png]]
|-
! style="background: #38A5A5;"|Diels-Alder Exo Transition state !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Opt_to_ts_631gd.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Da2_ts_ex3.png]]
|-
! style="background: #38A5A5;"|Cheletropic Transition state !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>CHELE_TS_TRY_631GD_FREQ.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Chele_ts_summary.png]]
|-
! style="background: #38A5A5;"|Diels-Alder Endo Product !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>DIELS_ALDER_631GD.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Diels_alder_product1ex3.png]]
|-
! style="background: #38A5A5;"|Diels-Alder Exo Product !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Diels_alder_2_631Gd.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Diels_alder2_product_ex3_eb1613.png]]
|-
! style="background: #38A5A5;"|Cheletropic Product !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Product_chele_mandisp1pt0.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Chele_product_eb1613.png ]]
|}

Rep:Mod:Eb1613 Ex3

2016-12-01T21:58:29Z

Eb1613: /* Thermochemistry anaylsis */

Page List

[[Mod:eb1613 files| The Calculations Log files can be found here]]

[[Mod:Emily1394| For Main Page click here]]

[[Mod:Eb1613 Ex1| Page for Excerise 1]]

[[Mod:Eb1613 Ex2| Page for Excerise 2]]

[[Mod:Eb1613 Ex3| Page for Excerise 3]]

= Third Year Computational Lab Transition States - Emily Brown =

=== Exercise 3 ===

[[File:Exercise2_reaction_emily.png]]

Both cheletropic and Diels-Alder reactions are possible for the above reactants.

Initially the structures were optimized to the semi-empirical PM6 level and later the geometries were re-optimised to the DFT 6-31G(d)/b3LYP level of calculation. The reactants were aligned in different conformations and certain bonds were frozen to find the three transition states shown below. Every structure given has been optimized to the higher accuracy DFT 6-31G(d)/b3LYP level.

2) Visualise the reaction coordinate with an IRC calculation for each path. Include a .gif file in the wiki of these IRCs.

3) Calculate the activation and reaction energies (converting to kJ/mol) for each step as in Exercise 2 to determine which route is preferred.

4) Using Excel or Chemdraw, draw a reaction profile that contains relative heights of the energy levels of the reactants, TSs and products from the endo- and exo- Diels-Alder reactions and the cheletropic reaction. You can set the 0 energy level to the reactants at infinite separation.

Xylylene is highly unstable. Look at the IRCs for the reactions - what happens to the bonding of the 6-membered ring during the course of the reaction?

There is a second cis-butadiene fragment in o-xylylene that can undergo a Diels-Alder reaction. If you have time, prove that the endo and exo Diels-Alder reactions are very thermodynamically and kinetically unfavourable at this site.

==== Transition states ====

{| class="wikitable" border="1"
! style="background: #38A5A5;" | Exo Transition State. Negative Frequency = -198.65 cm-1
|-
|style="background: white;" | [[File:Diels_alder_ts_1_movie.gif]]
|-
! style="background: #38A5A5;" | Endo Transition State. Negative Frequency = -200.42 cm-1
|-
|style="background: white;" | [[File:Diels_alder_ts_2_movie.gif]]
|-
! style="background: #38A5A5;" | Cheletropic Transition State. Negative Frequency = -221.18 cm-1
|-
|style="background: white;" | [[File:Chele_TS_movie_eb1613.gif]]
|}

==== Thermochemistry anaylsis ====

The energy profile was first plotted using excel and then using chemdraw to highlight the differences between the endo and exo paths.

{| class="wikitable" border="1"
|-
| style="background: white;" | [[File:Energy profile ex3 eb1613.png]] || style="background: white;" | [[File:Screen_Shot_2016-12-01_at_21.54.33.png]]
|}

Energy values given relative to the reactants in KJ/mol, from the values the Endo route appears to be the preferred route.

{| class="wikitable" border="1"
!style="background: #38A5A5;" | !!style="background: #38A5A5;" | Reactants !! style="background: #38A5A5;" | Transition state !! style="background: #38A5A5;" | Products
|-
| style="background: #38A5A5;" | Endo ||style="background: #EFECD9;" | 0 || style="background: #EFECD9;" |+46.17992 ||style="background: #EFECD9;" | -75.183818
|-
| style="background: #38A5A5;" | Exo ||style="background: #EFECD9;" | 0 ||style="background: #EFECD9;" | +46.23768|| style="background: #EFECD9;" |-73.886821
|-
| style="background: #38A5A5;" | Cheletropic||style="background: #EFECD9;" | 0 ||style="background: #EFECD9;" | +63.05663|| style="background: #EFECD9;" |-63.9650565
|}

Raw values with KJ/mol given to the nearest whole number

{| class="wikitable" border="1"
!style="background: #38A5A5;" | Structure!! style="background: #38A5A5;" | E( Hartrees) !! style="background: #38A5A5;" | E(KJ/mol)
|-
| style="background: #38A5A5;" | Diene ||style="background: #EFECD9;" | -309.504492|| style="background: #EFECD9;" |-812604
|-
| style="background: #38A5A5;" | Sulfur||style="background: #EFECD9;" | -548.604917|| style="background: #EFECD9;" |-1440362
|-
| style="background: #38A5A5;" | Sum of Reactants ||style="background: #EFECD9;" | -858.109409|| style="background: #EFECD9;" |-2252966
|-
| style="background: #38A5A5;" | Endo TS||style="background: #EFECD9;" | -858.09182|| style="background: #EFECD9;" |-2252920
|-
| style="background: #38A5A5;" | Endo Product||style="background: #EFECD9;" | -858.138045|| style="background: #EFECD9;" |-2253041
|-
| style="background: #38A5A5;" | Exo TS||style="background: #EFECD9;" | -858.091798|| style="background: #EFECD9;" |-2252920
|-
| style="background: #38A5A5;" | Exo Product||style="background: #EFECD9;" | -858.137551|| style="background: #EFECD9;" |-2253040
|-
| style="background: #38A5A5;" | Chele TS||style="background: #EFECD9;" | -858.085392|| style="background: #EFECD9;" |-2252903
|-
| style="background: #38A5A5;" | Chele Product||style="background: #EFECD9;" | -858.133772|| style="background: #EFECD9;" |-2253030
|}

Looking at the energy reaction barriers it can be seen that the Endo transition state is slightly below the cheletropic value making it the preferred reaction coordinate. however the value for the end transition state is only slightly below that for the cheletropic transition state and the calculation percentage errors/accuracies could effect this ordering.

==== IRC analysis ====

Xylylene is highly unstable. Look at the IRCs for the reactions - what happens to the bonding of the 6-membered ring during the course of the reaction?

During the reaction the carbon-carbon bond lengths all become styled as 1.5 bond order suggesting an aromatic element to the ring. The IRC calculations proved very challenging throughout this lab and as such the ENDO TS IRC path is recorded in reverse and shows the detachment of the sulfur oxide molecule.

{| class="wikitable" border="1"
! colspan="2" style="text-align: center;" style="background: #38A5A5;" |Cheletropic IRC path
|-
|style="background: white;" | [[File:Chele_IRC_movie.gif]] || style="background: white;" | [[File:Irc_chele_eb1613.png]]
|-
! colspan="2" style="text-align: center;" style="background: #38A5A5;" | Exo IRC path
|-
|style="background: white;" | [[File:Exo_IRC_movie_eb1613.gif]] || style="background: white;" | [[File:Exo_IRC.png]]
|-
!colspan="2" style="text-align: center;" style="background: #38A5A5;" | Endo IRC path
|-
|style="background: white;" | [[File:Endo_IRC_movie_eb1613.gif]] || style="background: white;" | [[File:IRC_path_ex3.png]]
|}

==== Structure files ====

{| class="wikitable" border="1"
|+ Structures
! style="background: #38A5A5;"|sulfur dioxde !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>SULFUR_FREQ_631GD.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Sulfur_eb1613_table.png]]
|-
! style="background: #38A5A5;"|Xylylene Diene !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Diene_mandisp1pt0.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Diene_mandisp1pt0_ex3_eb1613.png]]
|-
!style="background: #38A5A5;"| Diels-Alder Endo Transition state !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>DIELSALDER2_TS_FOUND_631GD_REOPT.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Diels_alder_ts_summary1_eb1613.png]]
|-
! style="background: #38A5A5;"|Diels-Alder Exo Transition state !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Opt_to_ts_631gd.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Da2_ts_ex3.png]]
|-
! style="background: #38A5A5;"|Cheletropic Transition state !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>CHELE_TS_TRY_631GD_FREQ.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Chele_ts_summary.png]]
|-
! style="background: #38A5A5;"|Diels-Alder Endo Product !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>DIELS_ALDER_631GD.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Diels_alder_product1ex3.png]]
|-
! style="background: #38A5A5;"|Diels-Alder Exo Product !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Diels_alder_2_631Gd.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Diels_alder2_product_ex3_eb1613.png]]
|-
! style="background: #38A5A5;"|Cheletropic Product !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Product_chele_mandisp1pt0.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Chele_product_eb1613.png ]]
|}

Rep:Mod:Eb1613 Ex3

2016-12-01T21:56:58Z

Eb1613: /* Thermochemistry anaylsis */

Page List

[[Mod:eb1613 files| The Calculations Log files can be found here]]

[[Mod:Emily1394| For Main Page click here]]

[[Mod:Eb1613 Ex1| Page for Excerise 1]]

[[Mod:Eb1613 Ex2| Page for Excerise 2]]

[[Mod:Eb1613 Ex3| Page for Excerise 3]]

= Third Year Computational Lab Transition States - Emily Brown =

=== Exercise 3 ===

[[File:Exercise2_reaction_emily.png]]

Both cheletropic and Diels-Alder reactions are possible for the above reactants.

Initially the structures were optimized to the semi-empirical PM6 level and later the geometries were re-optimised to the DFT 6-31G(d)/b3LYP level of calculation. The reactants were aligned in different conformations and certain bonds were frozen to find the three transition states shown below. Every structure given has been optimized to the higher accuracy DFT 6-31G(d)/b3LYP level.

2) Visualise the reaction coordinate with an IRC calculation for each path. Include a .gif file in the wiki of these IRCs.

3) Calculate the activation and reaction energies (converting to kJ/mol) for each step as in Exercise 2 to determine which route is preferred.

4) Using Excel or Chemdraw, draw a reaction profile that contains relative heights of the energy levels of the reactants, TSs and products from the endo- and exo- Diels-Alder reactions and the cheletropic reaction. You can set the 0 energy level to the reactants at infinite separation.

Xylylene is highly unstable. Look at the IRCs for the reactions - what happens to the bonding of the 6-membered ring during the course of the reaction?

There is a second cis-butadiene fragment in o-xylylene that can undergo a Diels-Alder reaction. If you have time, prove that the endo and exo Diels-Alder reactions are very thermodynamically and kinetically unfavourable at this site.

==== Transition states ====

{| class="wikitable" border="1"
! style="background: #38A5A5;" | Exo Transition State. Negative Frequency = -198.65 cm-1
|-
|style="background: white;" | [[File:Diels_alder_ts_1_movie.gif]]
|-
! style="background: #38A5A5;" | Endo Transition State. Negative Frequency = -200.42 cm-1
|-
|style="background: white;" | [[File:Diels_alder_ts_2_movie.gif]]
|-
! style="background: #38A5A5;" | Cheletropic Transition State. Negative Frequency = -221.18 cm-1
|-
|style="background: white;" | [[File:Chele_TS_movie_eb1613.gif]]
|}

==== Thermochemistry anaylsis ====

The energy profile was first plotted using excel and then using chemdraw to highlight the differences between the endo and exo paths.

[[File:Energy profile ex3 eb1613.png]]

[[File:Screen_Shot_2016-12-01_at_21.54.33.png]]

Energy values given relative to the reactants in KJ/mol, from the values the Endo route appears to be the preferred route.

{| class="wikitable" border="1"
!style="background: #38A5A5;" | !!style="background: #38A5A5;" | Reactants !! style="background: #38A5A5;" | Transition state !! style="background: #38A5A5;" | Products
|-
| style="background: #38A5A5;" | Endo ||style="background: #EFECD9;" | 0 || style="background: #EFECD9;" |+46.17992 ||style="background: #EFECD9;" | -75.183818
|-
| style="background: #38A5A5;" | Exo ||style="background: #EFECD9;" | 0 ||style="background: #EFECD9;" | +46.23768|| style="background: #EFECD9;" |-73.886821
|-
| style="background: #38A5A5;" | Cheletropic||style="background: #EFECD9;" | 0 ||style="background: #EFECD9;" | +63.05663|| style="background: #EFECD9;" |-63.9650565
|}

Raw values with KJ/mol given to the nearest whole number

{| class="wikitable" border="1"
!style="background: #38A5A5;" | Structure!! style="background: #38A5A5;" | E( Hartrees) !! style="background: #38A5A5;" | E(KJ/mol)
|-
| style="background: #38A5A5;" | Diene ||style="background: #EFECD9;" | -309.504492|| style="background: #EFECD9;" |-812604
|-
| style="background: #38A5A5;" | Sulfur||style="background: #EFECD9;" | -548.604917|| style="background: #EFECD9;" |-1440362
|-
| style="background: #38A5A5;" | Sum of Reactants ||style="background: #EFECD9;" | -858.109409|| style="background: #EFECD9;" |-2252966
|-
| style="background: #38A5A5;" | Endo TS||style="background: #EFECD9;" | -858.09182|| style="background: #EFECD9;" |-2252920
|-
| style="background: #38A5A5;" | Endo Product||style="background: #EFECD9;" | -858.138045|| style="background: #EFECD9;" |-2253041
|-
| style="background: #38A5A5;" | Exo TS||style="background: #EFECD9;" | -858.091798|| style="background: #EFECD9;" |-2252920
|-
| style="background: #38A5A5;" | Exo Product||style="background: #EFECD9;" | -858.137551|| style="background: #EFECD9;" |-2253040
|-
| style="background: #38A5A5;" | Chele TS||style="background: #EFECD9;" | -858.085392|| style="background: #EFECD9;" |-2252903
|-
| style="background: #38A5A5;" | Chele Product||style="background: #EFECD9;" | -858.133772|| style="background: #EFECD9;" |-2253030
|}

Looking at the energy reaction barriers it can be seen that the Endo transition state is slightly below the cheletropic value making it the preferred reaction coordinate. however the value for the end transition state is only slightly below that for the cheletropic transition state and the calculation percentage errors/accuracies could effect this ordering.

==== IRC analysis ====

Xylylene is highly unstable. Look at the IRCs for the reactions - what happens to the bonding of the 6-membered ring during the course of the reaction?

During the reaction the carbon-carbon bond lengths all become styled as 1.5 bond order suggesting an aromatic element to the ring. The IRC calculations proved very challenging throughout this lab and as such the ENDO TS IRC path is recorded in reverse and shows the detachment of the sulfur oxide molecule.

{| class="wikitable" border="1"
! colspan="2" style="text-align: center;" style="background: #38A5A5;" |Cheletropic IRC path
|-
|style="background: white;" | [[File:Chele_IRC_movie.gif]] || style="background: white;" | [[File:Irc_chele_eb1613.png]]
|-
! colspan="2" style="text-align: center;" style="background: #38A5A5;" | Exo IRC path
|-
|style="background: white;" | [[File:Exo_IRC_movie_eb1613.gif]] || style="background: white;" | [[File:Exo_IRC.png]]
|-
!colspan="2" style="text-align: center;" style="background: #38A5A5;" | Endo IRC path
|-
|style="background: white;" | [[File:Endo_IRC_movie_eb1613.gif]] || style="background: white;" | [[File:IRC_path_ex3.png]]
|}

==== Structure files ====

{| class="wikitable" border="1"
|+ Structures
! style="background: #38A5A5;"|sulfur dioxde !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>SULFUR_FREQ_631GD.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Sulfur_eb1613_table.png]]
|-
! style="background: #38A5A5;"|Xylylene Diene !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Diene_mandisp1pt0.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Diene_mandisp1pt0_ex3_eb1613.png]]
|-
!style="background: #38A5A5;"| Diels-Alder Endo Transition state !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>DIELSALDER2_TS_FOUND_631GD_REOPT.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Diels_alder_ts_summary1_eb1613.png]]
|-
! style="background: #38A5A5;"|Diels-Alder Exo Transition state !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Opt_to_ts_631gd.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Da2_ts_ex3.png]]
|-
! style="background: #38A5A5;"|Cheletropic Transition state !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>CHELE_TS_TRY_631GD_FREQ.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Chele_ts_summary.png]]
|-
! style="background: #38A5A5;"|Diels-Alder Endo Product !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>DIELS_ALDER_631GD.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Diels_alder_product1ex3.png]]
|-
! style="background: #38A5A5;"|Diels-Alder Exo Product !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Diels_alder_2_631Gd.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Diels_alder2_product_ex3_eb1613.png]]
|-
! style="background: #38A5A5;"|Cheletropic Product !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Product_chele_mandisp1pt0.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Chele_product_eb1613.png ]]
|}

File:Screen Shot 2016-12-01 at 21.54.33.png

2016-12-01T21:55:50Z

Eb1613:

Rep:Mod:Eb1613 Ex3

2016-12-01T21:52:38Z

Eb1613: /* Thermochemistry anaylsis */

Page List

[[Mod:eb1613 files| The Calculations Log files can be found here]]

[[Mod:Emily1394| For Main Page click here]]

[[Mod:Eb1613 Ex1| Page for Excerise 1]]

[[Mod:Eb1613 Ex2| Page for Excerise 2]]

[[Mod:Eb1613 Ex3| Page for Excerise 3]]

= Third Year Computational Lab Transition States - Emily Brown =

=== Exercise 3 ===

[[File:Exercise2_reaction_emily.png]]

Both cheletropic and Diels-Alder reactions are possible for the above reactants.

Initially the structures were optimized to the semi-empirical PM6 level and later the geometries were re-optimised to the DFT 6-31G(d)/b3LYP level of calculation. The reactants were aligned in different conformations and certain bonds were frozen to find the three transition states shown below. Every structure given has been optimized to the higher accuracy DFT 6-31G(d)/b3LYP level.

2) Visualise the reaction coordinate with an IRC calculation for each path. Include a .gif file in the wiki of these IRCs.

3) Calculate the activation and reaction energies (converting to kJ/mol) for each step as in Exercise 2 to determine which route is preferred.

4) Using Excel or Chemdraw, draw a reaction profile that contains relative heights of the energy levels of the reactants, TSs and products from the endo- and exo- Diels-Alder reactions and the cheletropic reaction. You can set the 0 energy level to the reactants at infinite separation.

Xylylene is highly unstable. Look at the IRCs for the reactions - what happens to the bonding of the 6-membered ring during the course of the reaction?

There is a second cis-butadiene fragment in o-xylylene that can undergo a Diels-Alder reaction. If you have time, prove that the endo and exo Diels-Alder reactions are very thermodynamically and kinetically unfavourable at this site.

==== Transition states ====

{| class="wikitable" border="1"
! style="background: #38A5A5;" | Exo Transition State. Negative Frequency = -198.65 cm-1
|-
|style="background: white;" | [[File:Diels_alder_ts_1_movie.gif]]
|-
! style="background: #38A5A5;" | Endo Transition State. Negative Frequency = -200.42 cm-1
|-
|style="background: white;" | [[File:Diels_alder_ts_2_movie.gif]]
|-
! style="background: #38A5A5;" | Cheletropic Transition State. Negative Frequency = -221.18 cm-1
|-
|style="background: white;" | [[File:Chele_TS_movie_eb1613.gif]]
|}

==== Thermochemistry anaylsis ====

[[File:Energy profile ex3 eb1613.png]]

[[Media:Exercise3_path_eb1613.cdx]]

Energy values given relative to the reactants in KJ/mol, from the values the Endo route appears to be the preferred route.

{| class="wikitable" border="1"
!style="background: #38A5A5;" | !!style="background: #38A5A5;" | Reactants !! style="background: #38A5A5;" | Transition state !! style="background: #38A5A5;" | Products
|-
| style="background: #38A5A5;" | Endo ||style="background: #EFECD9;" | 0 || style="background: #EFECD9;" |+46.17992 ||style="background: #EFECD9;" | -75.183818
|-
| style="background: #38A5A5;" | Exo ||style="background: #EFECD9;" | 0 ||style="background: #EFECD9;" | +46.23768|| style="background: #EFECD9;" |-73.886821
|-
| style="background: #38A5A5;" | Cheletropic||style="background: #EFECD9;" | 0 ||style="background: #EFECD9;" | +63.05663|| style="background: #EFECD9;" |-63.9650565
|}

Raw values with KJ/mol given to the nearest whole number

{| class="wikitable" border="1"
!style="background: #38A5A5;" | Structure!! style="background: #38A5A5;" | E( Hartrees) !! style="background: #38A5A5;" | E(KJ/mol)
|-
| style="background: #38A5A5;" | Diene ||style="background: #EFECD9;" | -309.504492|| style="background: #EFECD9;" |-812604
|-
| style="background: #38A5A5;" | Sulfur||style="background: #EFECD9;" | -548.604917|| style="background: #EFECD9;" |-1440362
|-
| style="background: #38A5A5;" | Sum of Reactants ||style="background: #EFECD9;" | -858.109409|| style="background: #EFECD9;" |-2252966
|-
| style="background: #38A5A5;" | Endo TS||style="background: #EFECD9;" | -858.09182|| style="background: #EFECD9;" |-2252920
|-
| style="background: #38A5A5;" | Endo Product||style="background: #EFECD9;" | -858.138045|| style="background: #EFECD9;" |-2253041
|-
| style="background: #38A5A5;" | Exo TS||style="background: #EFECD9;" | -858.091798|| style="background: #EFECD9;" |-2252920
|-
| style="background: #38A5A5;" | Exo Product||style="background: #EFECD9;" | -858.137551|| style="background: #EFECD9;" |-2253040
|-
| style="background: #38A5A5;" | Chele TS||style="background: #EFECD9;" | -858.085392|| style="background: #EFECD9;" |-2252903
|-
| style="background: #38A5A5;" | Chele Product||style="background: #EFECD9;" | -858.133772|| style="background: #EFECD9;" |-2253030
|}

Looking at the energy reaction barriers it can be seen that the Endo transition state is slightly below the cheletropic value making it the preferred reaction coordinate. however the value for the end transition state is only slightly below that for the cheletropic transition state and the calculation percentage errors/accuracies could effect this ordering.

==== IRC analysis ====

Xylylene is highly unstable. Look at the IRCs for the reactions - what happens to the bonding of the 6-membered ring during the course of the reaction?

During the reaction the carbon-carbon bond lengths all become styled as 1.5 bond order suggesting an aromatic element to the ring. The IRC calculations proved very challenging throughout this lab and as such the ENDO TS IRC path is recorded in reverse and shows the detachment of the sulfur oxide molecule.

{| class="wikitable" border="1"
! colspan="2" style="text-align: center;" style="background: #38A5A5;" |Cheletropic IRC path
|-
|style="background: white;" | [[File:Chele_IRC_movie.gif]] || style="background: white;" | [[File:Irc_chele_eb1613.png]]
|-
! colspan="2" style="text-align: center;" style="background: #38A5A5;" | Exo IRC path
|-
|style="background: white;" | [[File:Exo_IRC_movie_eb1613.gif]] || style="background: white;" | [[File:Exo_IRC.png]]
|-
!colspan="2" style="text-align: center;" style="background: #38A5A5;" | Endo IRC path
|-
|style="background: white;" | [[File:Endo_IRC_movie_eb1613.gif]] || style="background: white;" | [[File:IRC_path_ex3.png]]
|}

==== Structure files ====

{| class="wikitable" border="1"
|+ Structures
! style="background: #38A5A5;"|sulfur dioxde !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>SULFUR_FREQ_631GD.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Sulfur_eb1613_table.png]]
|-
! style="background: #38A5A5;"|Xylylene Diene !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Diene_mandisp1pt0.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Diene_mandisp1pt0_ex3_eb1613.png]]
|-
!style="background: #38A5A5;"| Diels-Alder Endo Transition state !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>DIELSALDER2_TS_FOUND_631GD_REOPT.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Diels_alder_ts_summary1_eb1613.png]]
|-
! style="background: #38A5A5;"|Diels-Alder Exo Transition state !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Opt_to_ts_631gd.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Da2_ts_ex3.png]]
|-
! style="background: #38A5A5;"|Cheletropic Transition state !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>CHELE_TS_TRY_631GD_FREQ.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Chele_ts_summary.png]]
|-
! style="background: #38A5A5;"|Diels-Alder Endo Product !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>DIELS_ALDER_631GD.LOG</uploadedFileContents> </jmolApplet></jmol> || [[File:Diels_alder_product1ex3.png]]
|-
! style="background: #38A5A5;"|Diels-Alder Exo Product !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Diels_alder_2_631Gd.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Diels_alder2_product_ex3_eb1613.png]]
|-
! style="background: #38A5A5;"|Cheletropic Product !! style="background: #38A5A5;"|Optimization Summary
|-
| <jmol><jmolApplet> <title>Optimised with 6-31G(d) level</title> <color>white</color> <size>200</size> <uploadedFileContents>Product_chele_mandisp1pt0.log</uploadedFileContents> </jmolApplet></jmol> || [[File:Chele_product_eb1613.png ]]
|}