ChemWiki - User contributions [en]

User:Htw16

2017-02-22T18:24:43Z

Htw14: Created page with "1 1.1"

1
1.1

User:Htw14

2016-12-15T15:52:47Z

Htw14: /* Symmetry requirement */

'''Computational Lab Year 3: Transition States and Reactivity'''
== Introduction ==

The exercise sets out to understand transition states of reactions, an aspect often difficult to study by experimental means. Through obtaining minimas and transition structures(TS) from energy-optimising computations, as well as further elucidating reaction pathways and trajectory approaches, the study ultimately aims to determine reactivity using energy profiles generated from computed data of studied molecules.

The topic of interest in this wiki concerns the Diels-Alder reaction, a reaction highly powerful in the construction of cyclic compounds within organic synthesis. It is important to understand beforehand that the reactions offers high levels of predictability through stereoselectivity, which would be beneficial in predicting transition structures prior to any computational studies.

Originated from the strict rules of orbital symmetry conservation, such reactions are performed in concerted fashion, meaning that configurations of both reactants will be fully retained in the product, and thus are stererospecific. (For example, a cis alkene will always yield a syn product).

The two terms that would be referred to frequently in this wiki are 'Exo' and 'Endo'. These refer to yet another type of stereoselectivty in Diels-Alder reactions, which governs the position adopted by dienophile substituents relative to the diene system. Such selectivity is attributed to secondary orbital interactions, which will be discussed further in below sections.

Through combining mechanistic and stereoelectronic knowledge of the reaction with computation techniques (such as energy determination and MO visualisations), we would be able to correctly determine the specific diastereomers from reactions.This grants us the ability of disastreoselection control of mutiple stereogenic centered products, which is a powerful skill in organic synthesis.

In the following exercises, three different instances of the reaction are studied.

== Exercise 1: Butadiene with Ethene ==

===Molecular Orbitals===

==== MO Diagram ====
As shown below, the diagram illustrates what a standard MO diagram for a general Diels Alder reaction would have. Though butadiene and ethene are used to provide frontier orbitals as reactants here, according to substituents of different reactants, the relative energies of reactants and product orbitals in specific reactions may differ.
[[Image:Hubert.png|499x499px|center|thumb|Butadiene-Ethene Diels Alder Reaction]]

==== Symmetry requirement ====
For a successful reaction, symmetries of the HOMO and the LUMO must match, while violations to this will lead a forbidden reaction. These orbitals generated from wavefunctions can be either symmetric or anti-symmetric. As shown in the MO diagram, as frontier orbitals Ψ<sub>2</sub> of butadiene and Ψ<sub>2</sub> of ethene are both symmetric,a MO-forming interaction is allowed. An interaction of Ψ<sub>3</sub> instead of Ψ<sub>2</sub> however, would be forbidden as only A-to-A and S-to-S interactions are allowed. The expression of the overlapping intergral shown below illustrates this concept mathematically:

[[File:Hubert_equ.png|center|150px]]

When S=0, this implies a zero overlap, which is typical when anti-symmetric and symmetric orbitals attmept to interact. On the other hand, any allowed overlap would have an S value in between close to 1, and these will be found in SS and AA overlaps.

==== Quantitative MO Visualisations ====
All MOs shown below correlates to the above MO diagram. It can be seen that the varying degree of delocalisation and shapes of the HOMOs and LUMOs correspond well with the phases of orbitals shown in the MO diagram.

{| class="wikitable"
|-
|
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<title>MO1 from TS</title>
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<title>Ψ2 LUMO from Ethene FOs</title>
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<uploadedFileContents>BUTADIENE_PM6_MO_VER.LOG</uploadedFileContents>
<title>Ψ2 HOMO from Butadiene FOs</title>
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<title>Ψ3 LUMO from Butadiene FOs</title>
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|}

=== Reaction Analysis ===

==== Bond Formation and Lengths ====
As shown in the diagram below, relationships between atoms can be divided into three categories, two of which being covalent interactions (sp3 and sp2) whilst the other a non-bonding interaction. These distances can be defined as the covalent and Van der Waal radius respectively. Typically, the distances (in Angstroms Å) between two carbon atoms of these relationships are as follows: Van de Waal (VdW): '''1.680 Å'''<ref name=":0">Pauling, Linus and L. O. Brockway. "Carbon—Carbon Bond Distances. The Electron Diffraction Investigation Of Ethane, Propane, Isobutane, Neopentane, Cyclopropane, Cyclopentane, Cyclohexane, Allene, Ethylene, Isobutene, Tetramethylethylene, Mesitylene, And Hexamethylbenzene. Revised Values Of Covalent Radii". ''Journal of the American Chemical Society'' 59.7 (1937): 1223-1236. Web.</ref>; Covalent sp3: '''1.537 Å'''<ref name=":0" />; Covalent sp2 : '''1.347 Å'''<ref name=":0" />

[[File:Trythis.png|center|330x330px]] <br style="clear:left">
{|border="1" cellpadding="5" cellspacing="0" align="center"
!Bonds
!Reactant
!Type
!TS
!Process
!Product
!Type
|-
|1,2
|1.33539
|sp<sup>2</sup>
|1.37978
|Lengthen
|1.50090
|sp<sup>3</sup>
|-
|2,3
|1.46834
|sp<sup>3</sup>
|1.41107
|Shorten
|1.33784
|sp<sup>2</sup>
|-
|3,4
|1.33539
|sp<sup>2</sup>
|1.37978
|Lengthen
|1.50090
|sp<sup>3</sup>
|-
|4,5
|3.41334
|2VdW
|2.11461
|Shorten
|1.54040
|sp<sup>3</sup>
|-
|5,6
|1.32736
|sp<sup>2</sup>
|1.38177
|Lengthen
|1.54091
|sp<sup>3</sup>
|-
|6,1
|3.41425
|2VdW
|2.11469
|Shorten
|1.54041
|sp<sup>3</sup>
|}

Firstly, it should be noted that the sum two Van de Waal radius of neigbouring atoms measures the internuclear distance of two non-interacting atoms prior to bond formation, hence it should be longer than those of bonding (i.e. sp2 and sp3). From the table, we can see that a smooth transition from non-bonding to sp3(shortening), sp3 to sp2 (shortening) and sp2 to sp3 (lengthening), thus turning the butadiene and alkene in to a cyclohexene in the process. As the alternating lengthening and shortening process of the bonds is yet another feature of the concerted process in the Diels Alder, the computated transiton state structure supports mechanism.

==== Vibrational Modes ====

{| class="wikitable"
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The vibrational mode corresponding to the transition state agrees with the concerted nature of the Diels-Alder reaction, during which two sp3 bonds are formed synchronously. The resultant single imgainary frequency proves that a maximum has been reached in only one dimension on the potential energy surface, which verifies the existence of a transition structure. Next to it shows the lowest positive frequency mode,where the two reactants rotates in opposite directions of a 2D plane. In comparison, the illustration on the right is non-reactive and minute in energy, which matches well with a typical rotational mode.

== Exercise 2: Benzoquinone with Cyclopentadiene ==

=== Molecular Orbitals ===
The orbitals below illustrates the four key resultant molecular orbitals (MO1-MO4) from the MO diagram shown in Exercise 1, where in this case are derived from the four frontier orbitals of cyclopentadiene (the diene equivalent) and the two from Benzoquinone (the alkene equivalent). Both the Exo and Endo reactions computated in this exercise are cases of normal electron demand, the most common electronic interaction in Diels-Alder reactions, where the dienophile is electron poor while the diene being electron rich. On the other hand, inverse demand suggests the opposite, thus allowing that the alkene HOMO to be at a close energy level to interact strongly the the diene LUMO. If this is the case MO1 (referring to the MO Diagram above) will be the HOMO of the transition state as opposed to MO2. By examining phases from both HOMOs of the Exo and Endo approaches, this is evident that the reaction is not a case inverse demand, as both corresponded to the phase pattern that a MO2 equivalent would possess. We can therefore conclude that the reaction is in '''normal electron demand'''.

==== Exo Approach Key MOs ====
{| class="wikitable"
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==== Endo Approach Key MOs ====
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<title>MO4</title>
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=== Reaction Analysis ===

==== Energetics and Pathway ====

Through analysing resultant thermodynamic data extracted from optimised structures of the reactants, products and transition states, a highly useful comparison could be made between the two reactant approaches. This will ultimately allow us to predict the reaction outcome expected in reality, thus showing the importance of computational techniques in chemistry. Such data is shown below:

{|border="1" cellpadding="5" cellspacing="0" align="center"
!Energy(kJ/mol)
!Exo
!Endo
|-
|Reactant
|<nowiki>-1510772.498</nowiki>
|<nowiki>-1510762.046</nowiki>
|-
|Product
|<nowiki>-1510782.951</nowiki>
|<nowiki>-1510783.751</nowiki>
|-
|TS
|<nowiki>-1510663.669</nowiki>
|<nowiki>-1510670.285</nowiki>
|-
|E<sub>a</sub>
|108.8296005
|91.761225
|-
|ΔE
|<nowiki>-10.4521155</nowiki>
|<nowiki>-21.7050085</nowiki>
|}

While the activation energy (Ea) gives information about the minimum energy input required to drive the reaction forwards, the total energy difference (ΔE) allows the judgement of the energy of stabilisation achievable for each reaction. From the table we see that less Ea is required initially, as well as a larger extent of stabilisation if the reaction were in the endo approach (reasons for this discussed in the below section). Therefore, we can conclude that the '''Endo''' adduct is both the '''Kinetic''' and '''Thermodynamic''' product.

[[File:cool1.png|right|295x295px|thumb|Endo Orbital Overlap]]

<br />

==== Orbital Stereoelectronics ====

The endo reaction undergoes with dienophile benzoquinone sitting on top of the cyclopentadiene (Cp), which grants an additional opportunity for a favourable orbital interaction. As seen on the right, the p orbitals at the 2,3 position of Cp is within proximate distance to interact with the rear C=C π* orbitals of the dienophile, alongside the bond-forming front C=C π* orbitals. From the white arrows indicated, the Cp HOMO is also in correct phase to overlap with the second double bond of the Benzoquinone. This is known as a '''secondary orbital interaction''', a stabilising interaction which does not involve bond formation.

Therefore, by having a second double bond within the same molecule in the dienephile, as opposed to a simpler alkene (eg. ethene), the additional interaction available plays the role in attracting the diene to adapt the Endo position while approaching. This '''lowers the activation energy''' of the Endo pathway, therefore transition structures are more favoured to be endo despite the associated sterics hinderance thermodynamically. This shows diels-alder reactions are often '''kinetically driven'''.

<br />
<br />
<br />

== Exercise 3: Xylylene with Sulphur Dioxide ==

=== Reactant Approach via IRC ===
{| class="wikitable"
!Diels Alder Endo
!Diels Alder Exo
!Cheletropic
|-
|[[File:Endo_irc_animation_for_wiki.gif]]
|[[File:Exo_irc_animation_for_wiki.gif]]
|[[File:Chele_irc_animation_for_wiki.gif]]
|}

=== Reaction Analysis ===

==== Energetics and Profile ====
The reaction of concern in the exercise introduces a possibility of a third reaction alongside the two approaches from the Hetero Diels Alder, known as the Cheletropic reaction. Again, computationally-calculated data of Gibbs free energy will be useful here to judge and compare the different reaction paths available, the reaction profile below should also provide a much clearer representation of how the three reactions compare:

{| border="1" cellpadding="5" cellspacing="0" align="center"
!Energy(kJ/mol)
!Exo
!Endo
!Cheletropic
|-
|Reactant
|177.69384
|178.3790955
|186.3606155
|-
|Product
|56.3301025
|56.983852
|<nowiki>-0.005251</nowiki>
|-
|TS
|241.745538
|237.7626545
|260.08203
|-
|E<sub>a</sub>
|64.051698
|59.383559
|73.7214145
|-
|ΔE
|<nowiki>-121.3637375</nowiki>
|<nowiki>-121.3952435</nowiki>
|<nowiki>-186.3658665</nowiki>
|}

[[File:Reactionhub.png|800px|center]]
With the lowest energy activation energy amongst all, the '''Endo''' pathway can be concluded to be the '''Kinetic product'''. In terms of the overall energy change, although very similar, endo also appears as the more thermodynamically favourable between the two Diels-Alder reactions. Though given the small margin of difference, such a statement should be treated with discretion. It is however very clear that the '''Cheletropic''' pathway is the '''Thermodynamic product''' overall over Endo and Exo. This margin of difference that Cheletropic reactions show owes to the relatively stable five-membered adduct, as opposed to a six-membered one.

Having identified the KE and TD products, reactions conditions as well as solvents can be altered in order to obtain a desired product specifically.

==== Reactant Transformation ====
Through studying the reaction visualisations from above, we can see that as the reactive butadiene fragment in xylene cyclizes, a conjugated system can been seen to establish at the rear ring. As the major driving force for all three reactions,which are all 2π electrons away from satisfying the Huckel rule of 4n+2 delocalised electrons, the aromatisation of xylyene provides sufficient aromatic stabilisation energy to the reactants to interact.

==== Pathway Alternative ====
A second Diels-Alder reaction possibility comes at the rear diene, as part of the 1,3 cyclohexadiene system. Compared to the Exo and Endo diels-alder reaction computed above, the clear inability to aromatise in this alternative pathway, where a bridged ring system will give rise to a sizable thermodynamic penalty for both orientation approaches.Though the bridged system does not incur significant additional thermodynamic instability (because bonds formed and broken are identical to its aromatisable alternative, and that both S=O bonds in the products are pointing towards empty space), it does suffer from the following kinetic implication: The o-xylylene group, being originally a fully planar structure with a coplanar eight π-orbital system, is forced to distort from its conformation, as carbons at the 1,4 positions are essentially 'pushed' upwards, in order to accommodate the approaching sulpur dioxide. As this effect is present for both Exo and Endo approaches, Kinetic unavailability will also be realized across this alternative position for cyclisation. In conclusion, the thermodynamic stability for a reaction at the this diene would be high thermodynamically and kinetically disfavored over the the acyclic diene (whose reaction is illustrated and discussed in the above sections). Thus, the latter will be the the overwhelming major product.

== Conclusion ==
Throughout the exercises, recognising relationships of different calculations with the potential energy surface has been important in understanding what each step had meant. By grasping specific PES positions through calculations, useful information can be extracted for the different structures of concern (such as reactants,products and transition states). This has allowed energetic comparisons, molecular orbital interactions and reaction visualisation to be obtained and understood.

The most common calculation used was the minimisation, which is often used to obtain the lowest energy conformation of a molecule. From the PES surface, this is the global minimum as opposed to other local minimums, therefore approximating calculations were often ran beforehand to ensure the reliability of the obtained minimum values. Therefore, a standard protocol would be to perform a semi-empirical calculation (the rough approximation), before moving on to the B3LYP (the accurate calculation, a basis set based method involving both HF and DFT functions).

As transition states would also have zero gradients, second derivatives are required to differentiate between the two. Frequency calculations act as the key method of such verification, where a single imaginative force constant (the second derivative) would prove the achievement of a TS. This point should have all but one dimension amongst the 3N-6 dimensions minimised, leaving a maximum just a single dimension.

Given all the computation methods utilized throughout the task, it can be argued that the DFT-based B3LYP method is the most attractive: As although the quantum mechanical method DFT are able to produce relatively reliable approximations, this is in expense of poor results in terms of exchange correlations.The ab intito HF on the other hand, is highly effective in analytically solving exchange correlations, but as the method ruses electron positions, this requires higher degrees of freedom in the process of solving and thus suffers from longer computation times. Thus, putting both factors of accuracy and time penalty into perspective, as B3LYP which is able to solve exchange correlations accurately by using the same analytical approach as the HF , benefits from strengths of both methods mentioned above. Moreover, its accuracy is considered to have made up for its expensiveness in terms of time.

All in all, the applications used for this exercise has demonstrated just a small part of the capabilities in computation chemistry. Higher levels of accuracies (via basis sets) and calculations method (other Ab Initito implementations) has yet to be explored. Complex biological molecules modelling, reaction dynamics, excited electronic states just some other key examples where computations are of high utility to chemists.

== References ==

User:Htw14

2016-12-15T15:48:10Z

Htw14: /* Symmetry requirement */

'''Computational Lab Year 3: Transition States and Reactivity'''
== Introduction ==

The exercise sets out to understand transition states of reactions, an aspect often difficult to study by experimental means. Through obtaining minimas and transition structures(TS) from energy-optimising computations, as well as further elucidating reaction pathways and trajectory approaches, the study ultimately aims to determine reactivity using energy profiles generated from computed data of studied molecules.

The topic of interest in this wiki concerns the Diels-Alder reaction, a reaction highly powerful in the construction of cyclic compounds within organic synthesis. It is important to understand beforehand that the reactions offers high levels of predictability through stereoselectivity, which would be beneficial in predicting transition structures prior to any computational studies.

Originated from the strict rules of orbital symmetry conservation, such reactions are performed in concerted fashion, meaning that configurations of both reactants will be fully retained in the product, and thus are stererospecific. (For example, a cis alkene will always yield a syn product).

The two terms that would be referred to frequently in this wiki are 'Exo' and 'Endo'. These refer to yet another type of stereoselectivty in Diels-Alder reactions, which governs the position adopted by dienophile substituents relative to the diene system. Such selectivity is attributed to secondary orbital interactions, which will be discussed further in below sections.

Through combining mechanistic and stereoelectronic knowledge of the reaction with computation techniques (such as energy determination and MO visualisations), we would be able to correctly determine the specific diastereomers from reactions.This grants us the ability of disastreoselection control of mutiple stereogenic centered products, which is a powerful skill in organic synthesis.

In the following exercises, three different instances of the reaction are studied.

== Exercise 1: Butadiene with Ethene ==

===Molecular Orbitals===

==== MO Diagram ====
As shown below, the diagram illustrates what a standard MO diagram for a general Diels Alder reaction would have. Though butadiene and ethene are used to provide frontier orbitals as reactants here, according to substituents of different reactants, the relative energies of reactants and product orbitals in specific reactions may differ.
[[Image:Hubert.png|499x499px|center|thumb|Butadiene-Ethene Diels Alder Reaction]]

==== Symmetry requirement ====
For a successful reaction, symmetries of the HOMO and the LUMO must match, while violations to this will lead a forbidden reaction. These orbitals generated from wavefunctions can be either symmetric or anti-symmetric. As shown in the MO diagram, as frontier orbitals Ψ<sub>2</sub> of butadiene and Ψ<sub>2</sub> of ethene are both symmetric,a MO-forming interaction is allowed. An interaction of Ψ<sub>3</sub> instead of Ψ<sub>2</sub> however, would be forbidden as only A-to-A and S-to-S interactions are allowed. The expression of the overlapping intergral shown below illustrates this concept mathematically:

[[File:Hubert_equ.png|center|150px]]

When S=0, this implies a zero overlap, while any allowed overlap would have an S value in between 0 and 1.

==== Quantitative MO Visualisations ====
All MOs shown below correlates to the above MO diagram. It can be seen that the varying degree of delocalisation and shapes of the HOMOs and LUMOs correspond well with the phases of orbitals shown in the MO diagram.

{| class="wikitable"
|-
|
<jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 14; mo 16; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>DA_STEP_2_PM6_OPT_MO_VER.LOG</uploadedFileContents>
<title>MO1 from TS</title>
</jmolApplet>
</jmol>
|
<jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 14; mo 17; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>DA_STEP_2_PM6_OPT_MO_VER.LOG</uploadedFileContents>
<title>MO2 HOMO from TS</title>
</jmolApplet>
</jmol>
|
<jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 14; mo 18; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>DA_STEP_2_PM6_OPT_MO_VER.LOG</uploadedFileContents>
<title>MO3 LUMO from TSs</title>
</jmolApplet>
</jmol>
|
<jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 14; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
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<title>MO4 from TS</title>
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|-
|
<jmol>
<jmolApplet>
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=== Reaction Analysis ===

==== Bond Formation and Lengths ====
As shown in the diagram below, relationships between atoms can be divided into three categories, two of which being covalent interactions (sp3 and sp2) whilst the other a non-bonding interaction. These distances can be defined as the covalent and Van der Waal radius respectively. Typically, the distances (in Angstroms Å) between two carbon atoms of these relationships are as follows: Van de Waal (VdW): '''1.680 Å'''<ref name=":0">Pauling, Linus and L. O. Brockway. "Carbon—Carbon Bond Distances. The Electron Diffraction Investigation Of Ethane, Propane, Isobutane, Neopentane, Cyclopropane, Cyclopentane, Cyclohexane, Allene, Ethylene, Isobutene, Tetramethylethylene, Mesitylene, And Hexamethylbenzene. Revised Values Of Covalent Radii". ''Journal of the American Chemical Society'' 59.7 (1937): 1223-1236. Web.</ref>; Covalent sp3: '''1.537 Å'''<ref name=":0" />; Covalent sp2 : '''1.347 Å'''<ref name=":0" />

[[File:Trythis.png|center|330x330px]] <br style="clear:left">
{|border="1" cellpadding="5" cellspacing="0" align="center"
!Bonds
!Reactant
!Type
!TS
!Process
!Product
!Type
|-
|1,2
|1.33539
|sp<sup>2</sup>
|1.37978
|Lengthen
|1.50090
|sp<sup>3</sup>
|-
|2,3
|1.46834
|sp<sup>3</sup>
|1.41107
|Shorten
|1.33784
|sp<sup>2</sup>
|-
|3,4
|1.33539
|sp<sup>2</sup>
|1.37978
|Lengthen
|1.50090
|sp<sup>3</sup>
|-
|4,5
|3.41334
|2VdW
|2.11461
|Shorten
|1.54040
|sp<sup>3</sup>
|-
|5,6
|1.32736
|sp<sup>2</sup>
|1.38177
|Lengthen
|1.54091
|sp<sup>3</sup>
|-
|6,1
|3.41425
|2VdW
|2.11469
|Shorten
|1.54041
|sp<sup>3</sup>
|}

Firstly, it should be noted that the sum two Van de Waal radius of neigbouring atoms measures the internuclear distance of two non-interacting atoms prior to bond formation, hence it should be longer than those of bonding (i.e. sp2 and sp3). From the table, we can see that a smooth transition from non-bonding to sp3(shortening), sp3 to sp2 (shortening) and sp2 to sp3 (lengthening), thus turning the butadiene and alkene in to a cyclohexene in the process. As the alternating lengthening and shortening process of the bonds is yet another feature of the concerted process in the Diels Alder, the computated transiton state structure supports mechanism.

==== Vibrational Modes ====

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The vibrational mode corresponding to the transition state agrees with the concerted nature of the Diels-Alder reaction, during which two sp3 bonds are formed synchronously. The resultant single imgainary frequency proves that a maximum has been reached in only one dimension on the potential energy surface, which verifies the existence of a transition structure. Next to it shows the lowest positive frequency mode,where the two reactants rotates in opposite directions of a 2D plane. In comparison, the illustration on the right is non-reactive and minute in energy, which matches well with a typical rotational mode.

== Exercise 2: Benzoquinone with Cyclopentadiene ==

=== Molecular Orbitals ===
The orbitals below illustrates the four key resultant molecular orbitals (MO1-MO4) from the MO diagram shown in Exercise 1, where in this case are derived from the four frontier orbitals of cyclopentadiene (the diene equivalent) and the two from Benzoquinone (the alkene equivalent). Both the Exo and Endo reactions computated in this exercise are cases of normal electron demand, the most common electronic interaction in Diels-Alder reactions, where the dienophile is electron poor while the diene being electron rich. On the other hand, inverse demand suggests the opposite, thus allowing that the alkene HOMO to be at a close energy level to interact strongly the the diene LUMO. If this is the case MO1 (referring to the MO Diagram above) will be the HOMO of the transition state as opposed to MO2. By examining phases from both HOMOs of the Exo and Endo approaches, this is evident that the reaction is not a case inverse demand, as both corresponded to the phase pattern that a MO2 equivalent would possess. We can therefore conclude that the reaction is in '''normal electron demand'''.

==== Exo Approach Key MOs ====
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==== Endo Approach Key MOs ====
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=== Reaction Analysis ===

==== Energetics and Pathway ====

Through analysing resultant thermodynamic data extracted from optimised structures of the reactants, products and transition states, a highly useful comparison could be made between the two reactant approaches. This will ultimately allow us to predict the reaction outcome expected in reality, thus showing the importance of computational techniques in chemistry. Such data is shown below:

{|border="1" cellpadding="5" cellspacing="0" align="center"
!Energy(kJ/mol)
!Exo
!Endo
|-
|Reactant
|<nowiki>-1510772.498</nowiki>
|<nowiki>-1510762.046</nowiki>
|-
|Product
|<nowiki>-1510782.951</nowiki>
|<nowiki>-1510783.751</nowiki>
|-
|TS
|<nowiki>-1510663.669</nowiki>
|<nowiki>-1510670.285</nowiki>
|-
|E<sub>a</sub>
|108.8296005
|91.761225
|-
|ΔE
|<nowiki>-10.4521155</nowiki>
|<nowiki>-21.7050085</nowiki>
|}

While the activation energy (Ea) gives information about the minimum energy input required to drive the reaction forwards, the total energy difference (ΔE) allows the judgement of the energy of stabilisation achievable for each reaction. From the table we see that less Ea is required initially, as well as a larger extent of stabilisation if the reaction were in the endo approach (reasons for this discussed in the below section). Therefore, we can conclude that the '''Endo''' adduct is both the '''Kinetic''' and '''Thermodynamic''' product.

[[File:cool1.png|right|295x295px|thumb|Endo Orbital Overlap]]

<br />

==== Orbital Stereoelectronics ====

The endo reaction undergoes with dienophile benzoquinone sitting on top of the cyclopentadiene (Cp), which grants an additional opportunity for a favourable orbital interaction. As seen on the right, the p orbitals at the 2,3 position of Cp is within proximate distance to interact with the rear C=C π* orbitals of the dienophile, alongside the bond-forming front C=C π* orbitals. From the white arrows indicated, the Cp HOMO is also in correct phase to overlap with the second double bond of the Benzoquinone. This is known as a '''secondary orbital interaction''', a stabilising interaction which does not involve bond formation.

Therefore, by having a second double bond within the same molecule in the dienephile, as opposed to a simpler alkene (eg. ethene), the additional interaction available plays the role in attracting the diene to adapt the Endo position while approaching. This '''lowers the activation energy''' of the Endo pathway, therefore transition structures are more favoured to be endo despite the associated sterics hinderance thermodynamically. This shows diels-alder reactions are often '''kinetically driven'''.

<br />
<br />
<br />

== Exercise 3: Xylylene with Sulphur Dioxide ==

=== Reactant Approach via IRC ===
{| class="wikitable"
!Diels Alder Endo
!Diels Alder Exo
!Cheletropic
|-
|[[File:Endo_irc_animation_for_wiki.gif]]
|[[File:Exo_irc_animation_for_wiki.gif]]
|[[File:Chele_irc_animation_for_wiki.gif]]
|}

=== Reaction Analysis ===

==== Energetics and Profile ====
The reaction of concern in the exercise introduces a possibility of a third reaction alongside the two approaches from the Hetero Diels Alder, known as the Cheletropic reaction. Again, computationally-calculated data of Gibbs free energy will be useful here to judge and compare the different reaction paths available, the reaction profile below should also provide a much clearer representation of how the three reactions compare:

{| border="1" cellpadding="5" cellspacing="0" align="center"
!Energy(kJ/mol)
!Exo
!Endo
!Cheletropic
|-
|Reactant
|177.69384
|178.3790955
|186.3606155
|-
|Product
|56.3301025
|56.983852
|<nowiki>-0.005251</nowiki>
|-
|TS
|241.745538
|237.7626545
|260.08203
|-
|E<sub>a</sub>
|64.051698
|59.383559
|73.7214145
|-
|ΔE
|<nowiki>-121.3637375</nowiki>
|<nowiki>-121.3952435</nowiki>
|<nowiki>-186.3658665</nowiki>
|}

[[File:Reactionhub.png|800px|center]]
With the lowest energy activation energy amongst all, the '''Endo''' pathway can be concluded to be the '''Kinetic product'''. In terms of the overall energy change, although very similar, endo also appears as the more thermodynamically favourable between the two Diels-Alder reactions. Though given the small margin of difference, such a statement should be treated with discretion. It is however very clear that the '''Cheletropic''' pathway is the '''Thermodynamic product''' overall over Endo and Exo. This margin of difference that Cheletropic reactions show owes to the relatively stable five-membered adduct, as opposed to a six-membered one.

Having identified the KE and TD products, reactions conditions as well as solvents can be altered in order to obtain a desired product specifically.

==== Reactant Transformation ====
Through studying the reaction visualisations from above, we can see that as the reactive butadiene fragment in xylene cyclizes, a conjugated system can been seen to establish at the rear ring. As the major driving force for all three reactions,which are all 2π electrons away from satisfying the Huckel rule of 4n+2 delocalised electrons, the aromatisation of xylyene provides sufficient aromatic stabilisation energy to the reactants to interact.

==== Pathway Alternative ====
A second Diels-Alder reaction possibility comes at the rear diene, as part of the 1,3 cyclohexadiene system. Compared to the Exo and Endo diels-alder reaction computed above, the clear inability to aromatise in this alternative pathway, where a bridged ring system will give rise to a sizable thermodynamic penalty for both orientation approaches.Though the bridged system does not incur significant additional thermodynamic instability (because bonds formed and broken are identical to its aromatisable alternative, and that both S=O bonds in the products are pointing towards empty space), it does suffer from the following kinetic implication: The o-xylylene group, being originally a fully planar structure with a coplanar eight π-orbital system, is forced to distort from its conformation, as carbons at the 1,4 positions are essentially 'pushed' upwards, in order to accommodate the approaching sulpur dioxide. As this effect is present for both Exo and Endo approaches, Kinetic unavailability will also be realized across this alternative position for cyclisation. In conclusion, the thermodynamic stability for a reaction at the this diene would be high thermodynamically and kinetically disfavored over the the acyclic diene (whose reaction is illustrated and discussed in the above sections). Thus, the latter will be the the overwhelming major product.

== Conclusion ==
Throughout the exercises, recognising relationships of different calculations with the potential energy surface has been important in understanding what each step had meant. By grasping specific PES positions through calculations, useful information can be extracted for the different structures of concern (such as reactants,products and transition states). This has allowed energetic comparisons, molecular orbital interactions and reaction visualisation to be obtained and understood.

The most common calculation used was the minimisation, which is often used to obtain the lowest energy conformation of a molecule. From the PES surface, this is the global minimum as opposed to other local minimums, therefore approximating calculations were often ran beforehand to ensure the reliability of the obtained minimum values. Therefore, a standard protocol would be to perform a semi-empirical calculation (the rough approximation), before moving on to the B3LYP (the accurate calculation, a basis set based method involving both HF and DFT functions).

As transition states would also have zero gradients, second derivatives are required to differentiate between the two. Frequency calculations act as the key method of such verification, where a single imaginative force constant (the second derivative) would prove the achievement of a TS. This point should have all but one dimension amongst the 3N-6 dimensions minimised, leaving a maximum just a single dimension.

Given all the computation methods utilized throughout the task, it can be argued that the DFT-based B3LYP method is the most attractive: As although the quantum mechanical method DFT are able to produce relatively reliable approximations, this is in expense of poor results in terms of exchange correlations.The ab intito HF on the other hand, is highly effective in analytically solving exchange correlations, but as the method ruses electron positions, this requires higher degrees of freedom in the process of solving and thus suffers from longer computation times. Thus, putting both factors of accuracy and time penalty into perspective, as B3LYP which is able to solve exchange correlations accurately by using the same analytical approach as the HF , benefits from strengths of both methods mentioned above. Moreover, its accuracy is considered to have made up for its expensiveness in terms of time.

All in all, the applications used for this exercise has demonstrated just a small part of the capabilities in computation chemistry. Higher levels of accuracies (via basis sets) and calculations method (other Ab Initito implementations) has yet to be explored. Complex biological molecules modelling, reaction dynamics, excited electronic states just some other key examples where computations are of high utility to chemists.

== References ==

User:Htw14

2016-12-15T15:44:58Z

Htw14: /* Pathway Alternative */

'''Computational Lab Year 3: Transition States and Reactivity'''
== Introduction ==

The exercise sets out to understand transition states of reactions, an aspect often difficult to study by experimental means. Through obtaining minimas and transition structures(TS) from energy-optimising computations, as well as further elucidating reaction pathways and trajectory approaches, the study ultimately aims to determine reactivity using energy profiles generated from computed data of studied molecules.

The topic of interest in this wiki concerns the Diels-Alder reaction, a reaction highly powerful in the construction of cyclic compounds within organic synthesis. It is important to understand beforehand that the reactions offers high levels of predictability through stereoselectivity, which would be beneficial in predicting transition structures prior to any computational studies.

Originated from the strict rules of orbital symmetry conservation, such reactions are performed in concerted fashion, meaning that configurations of both reactants will be fully retained in the product, and thus are stererospecific. (For example, a cis alkene will always yield a syn product).

The two terms that would be referred to frequently in this wiki are 'Exo' and 'Endo'. These refer to yet another type of stereoselectivty in Diels-Alder reactions, which governs the position adopted by dienophile substituents relative to the diene system. Such selectivity is attributed to secondary orbital interactions, which will be discussed further in below sections.

Through combining mechanistic and stereoelectronic knowledge of the reaction with computation techniques (such as energy determination and MO visualisations), we would be able to correctly determine the specific diastereomers from reactions.This grants us the ability of disastreoselection control of mutiple stereogenic centered products, which is a powerful skill in organic synthesis.

In the following exercises, three different instances of the reaction are studied.

== Exercise 1: Butadiene with Ethene ==

===Molecular Orbitals===

==== MO Diagram ====
As shown below, the diagram illustrates what a standard MO diagram for a general Diels Alder reaction would have. Though butadiene and ethene are used to provide frontier orbitals as reactants here, according to substituents of different reactants, the relative energies of reactants and product orbitals in specific reactions may differ.
[[Image:Hubert.png|499x499px|center|thumb|Butadiene-Ethene Diels Alder Reaction]]

==== Symmetry requirement ====
For a successful reaction, symmetries of the HOMO and the LUMO must match, while violations to this will lead a forbidden reaction. These orbitals generated from wavefunctions can be either symmetric or anti-symmetric and are distinguished by transformations under an inversion operation. If symmetric with respect to inversion, such an orbital is assigned the label of gerade(g), and vice versa for anti-symmetric cases, which are ungerade(u). As shown in the MO diagram, frontier orbitals Ψ<sub>2</sub> of butadiene and Ψ<sub>2</sub> of ethene are both symmetric (gerade) and thus an interaction is allowed. An interaction of Ψ<sub>3</sub>(u) instead of Ψ<sub>2</sub>(g)<sub> </sub>however, would be forbidden as only g-g u-u interactions are allowed. The expression of the overlapping intergral shown below illustrates this concept mathematically:

[[File:Hubert_equ.png|center|150px]]

When S=0, this implies a zero overlap, while any allowed overlap would have an S value in between 0 and 1.

==== Quantitative MO Visualisations ====
All MOs shown below correlates to the above MO diagram. It can be seen that the varying degree of delocalisation and shapes of the HOMOs and LUMOs correspond well with the phases of orbitals shown in the MO diagram.

{| class="wikitable"
|-
|
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=== Reaction Analysis ===

==== Bond Formation and Lengths ====
As shown in the diagram below, relationships between atoms can be divided into three categories, two of which being covalent interactions (sp3 and sp2) whilst the other a non-bonding interaction. These distances can be defined as the covalent and Van der Waal radius respectively. Typically, the distances (in Angstroms Å) between two carbon atoms of these relationships are as follows: Van de Waal (VdW): '''1.680 Å'''<ref name=":0">Pauling, Linus and L. O. Brockway. "Carbon—Carbon Bond Distances. The Electron Diffraction Investigation Of Ethane, Propane, Isobutane, Neopentane, Cyclopropane, Cyclopentane, Cyclohexane, Allene, Ethylene, Isobutene, Tetramethylethylene, Mesitylene, And Hexamethylbenzene. Revised Values Of Covalent Radii". ''Journal of the American Chemical Society'' 59.7 (1937): 1223-1236. Web.</ref>; Covalent sp3: '''1.537 Å'''<ref name=":0" />; Covalent sp2 : '''1.347 Å'''<ref name=":0" />

[[File:Trythis.png|center|330x330px]] <br style="clear:left">
{|border="1" cellpadding="5" cellspacing="0" align="center"
!Bonds
!Reactant
!Type
!TS
!Process
!Product
!Type
|-
|1,2
|1.33539
|sp<sup>2</sup>
|1.37978
|Lengthen
|1.50090
|sp<sup>3</sup>
|-
|2,3
|1.46834
|sp<sup>3</sup>
|1.41107
|Shorten
|1.33784
|sp<sup>2</sup>
|-
|3,4
|1.33539
|sp<sup>2</sup>
|1.37978
|Lengthen
|1.50090
|sp<sup>3</sup>
|-
|4,5
|3.41334
|2VdW
|2.11461
|Shorten
|1.54040
|sp<sup>3</sup>
|-
|5,6
|1.32736
|sp<sup>2</sup>
|1.38177
|Lengthen
|1.54091
|sp<sup>3</sup>
|-
|6,1
|3.41425
|2VdW
|2.11469
|Shorten
|1.54041
|sp<sup>3</sup>
|}

Firstly, it should be noted that the sum two Van de Waal radius of neigbouring atoms measures the internuclear distance of two non-interacting atoms prior to bond formation, hence it should be longer than those of bonding (i.e. sp2 and sp3). From the table, we can see that a smooth transition from non-bonding to sp3(shortening), sp3 to sp2 (shortening) and sp2 to sp3 (lengthening), thus turning the butadiene and alkene in to a cyclohexene in the process. As the alternating lengthening and shortening process of the bonds is yet another feature of the concerted process in the Diels Alder, the computated transiton state structure supports mechanism.

==== Vibrational Modes ====

{| class="wikitable"
|
<jmol>
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The vibrational mode corresponding to the transition state agrees with the concerted nature of the Diels-Alder reaction, during which two sp3 bonds are formed synchronously. The resultant single imgainary frequency proves that a maximum has been reached in only one dimension on the potential energy surface, which verifies the existence of a transition structure. Next to it shows the lowest positive frequency mode,where the two reactants rotates in opposite directions of a 2D plane. In comparison, the illustration on the right is non-reactive and minute in energy, which matches well with a typical rotational mode.

== Exercise 2: Benzoquinone with Cyclopentadiene ==

=== Molecular Orbitals ===
The orbitals below illustrates the four key resultant molecular orbitals (MO1-MO4) from the MO diagram shown in Exercise 1, where in this case are derived from the four frontier orbitals of cyclopentadiene (the diene equivalent) and the two from Benzoquinone (the alkene equivalent). Both the Exo and Endo reactions computated in this exercise are cases of normal electron demand, the most common electronic interaction in Diels-Alder reactions, where the dienophile is electron poor while the diene being electron rich. On the other hand, inverse demand suggests the opposite, thus allowing that the alkene HOMO to be at a close energy level to interact strongly the the diene LUMO. If this is the case MO1 (referring to the MO Diagram above) will be the HOMO of the transition state as opposed to MO2. By examining phases from both HOMOs of the Exo and Endo approaches, this is evident that the reaction is not a case inverse demand, as both corresponded to the phase pattern that a MO2 equivalent would possess. We can therefore conclude that the reaction is in '''normal electron demand'''.

==== Exo Approach Key MOs ====
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==== Endo Approach Key MOs ====
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=== Reaction Analysis ===

==== Energetics and Pathway ====

Through analysing resultant thermodynamic data extracted from optimised structures of the reactants, products and transition states, a highly useful comparison could be made between the two reactant approaches. This will ultimately allow us to predict the reaction outcome expected in reality, thus showing the importance of computational techniques in chemistry. Such data is shown below:

{|border="1" cellpadding="5" cellspacing="0" align="center"
!Energy(kJ/mol)
!Exo
!Endo
|-
|Reactant
|<nowiki>-1510772.498</nowiki>
|<nowiki>-1510762.046</nowiki>
|-
|Product
|<nowiki>-1510782.951</nowiki>
|<nowiki>-1510783.751</nowiki>
|-
|TS
|<nowiki>-1510663.669</nowiki>
|<nowiki>-1510670.285</nowiki>
|-
|E<sub>a</sub>
|108.8296005
|91.761225
|-
|ΔE
|<nowiki>-10.4521155</nowiki>
|<nowiki>-21.7050085</nowiki>
|}

While the activation energy (Ea) gives information about the minimum energy input required to drive the reaction forwards, the total energy difference (ΔE) allows the judgement of the energy of stabilisation achievable for each reaction. From the table we see that less Ea is required initially, as well as a larger extent of stabilisation if the reaction were in the endo approach (reasons for this discussed in the below section). Therefore, we can conclude that the '''Endo''' adduct is both the '''Kinetic''' and '''Thermodynamic''' product.

[[File:cool1.png|right|295x295px|thumb|Endo Orbital Overlap]]

<br />

==== Orbital Stereoelectronics ====

The endo reaction undergoes with dienophile benzoquinone sitting on top of the cyclopentadiene (Cp), which grants an additional opportunity for a favourable orbital interaction. As seen on the right, the p orbitals at the 2,3 position of Cp is within proximate distance to interact with the rear C=C π* orbitals of the dienophile, alongside the bond-forming front C=C π* orbitals. From the white arrows indicated, the Cp HOMO is also in correct phase to overlap with the second double bond of the Benzoquinone. This is known as a '''secondary orbital interaction''', a stabilising interaction which does not involve bond formation.

Therefore, by having a second double bond within the same molecule in the dienephile, as opposed to a simpler alkene (eg. ethene), the additional interaction available plays the role in attracting the diene to adapt the Endo position while approaching. This '''lowers the activation energy''' of the Endo pathway, therefore transition structures are more favoured to be endo despite the associated sterics hinderance thermodynamically. This shows diels-alder reactions are often '''kinetically driven'''.

<br />
<br />
<br />

== Exercise 3: Xylylene with Sulphur Dioxide ==

=== Reactant Approach via IRC ===
{| class="wikitable"
!Diels Alder Endo
!Diels Alder Exo
!Cheletropic
|-
|[[File:Endo_irc_animation_for_wiki.gif]]
|[[File:Exo_irc_animation_for_wiki.gif]]
|[[File:Chele_irc_animation_for_wiki.gif]]
|}

=== Reaction Analysis ===

==== Energetics and Profile ====
The reaction of concern in the exercise introduces a possibility of a third reaction alongside the two approaches from the Hetero Diels Alder, known as the Cheletropic reaction. Again, computationally-calculated data of Gibbs free energy will be useful here to judge and compare the different reaction paths available, the reaction profile below should also provide a much clearer representation of how the three reactions compare:

{| border="1" cellpadding="5" cellspacing="0" align="center"
!Energy(kJ/mol)
!Exo
!Endo
!Cheletropic
|-
|Reactant
|177.69384
|178.3790955
|186.3606155
|-
|Product
|56.3301025
|56.983852
|<nowiki>-0.005251</nowiki>
|-
|TS
|241.745538
|237.7626545
|260.08203
|-
|E<sub>a</sub>
|64.051698
|59.383559
|73.7214145
|-
|ΔE
|<nowiki>-121.3637375</nowiki>
|<nowiki>-121.3952435</nowiki>
|<nowiki>-186.3658665</nowiki>
|}

[[File:Reactionhub.png|800px|center]]
With the lowest energy activation energy amongst all, the '''Endo''' pathway can be concluded to be the '''Kinetic product'''. In terms of the overall energy change, although very similar, endo also appears as the more thermodynamically favourable between the two Diels-Alder reactions. Though given the small margin of difference, such a statement should be treated with discretion. It is however very clear that the '''Cheletropic''' pathway is the '''Thermodynamic product''' overall over Endo and Exo. This margin of difference that Cheletropic reactions show owes to the relatively stable five-membered adduct, as opposed to a six-membered one.

Having identified the KE and TD products, reactions conditions as well as solvents can be altered in order to obtain a desired product specifically.

==== Reactant Transformation ====
Through studying the reaction visualisations from above, we can see that as the reactive butadiene fragment in xylene cyclizes, a conjugated system can been seen to establish at the rear ring. As the major driving force for all three reactions,which are all 2π electrons away from satisfying the Huckel rule of 4n+2 delocalised electrons, the aromatisation of xylyene provides sufficient aromatic stabilisation energy to the reactants to interact.

==== Pathway Alternative ====
A second Diels-Alder reaction possibility comes at the rear diene, as part of the 1,3 cyclohexadiene system. Compared to the Exo and Endo diels-alder reaction computed above, the clear inability to aromatise in this alternative pathway, where a bridged ring system will give rise to a sizable thermodynamic penalty for both orientation approaches.Though the bridged system does not incur significant additional thermodynamic instability (because bonds formed and broken are identical to its aromatisable alternative, and that both S=O bonds in the products are pointing towards empty space), it does suffer from the following kinetic implication: The o-xylylene group, being originally a fully planar structure with a coplanar eight π-orbital system, is forced to distort from its conformation, as carbons at the 1,4 positions are essentially 'pushed' upwards, in order to accommodate the approaching sulpur dioxide. As this effect is present for both Exo and Endo approaches, Kinetic unavailability will also be realized across this alternative position for cyclisation. In conclusion, the thermodynamic stability for a reaction at the this diene would be high thermodynamically and kinetically disfavored over the the acyclic diene (whose reaction is illustrated and discussed in the above sections). Thus, the latter will be the the overwhelming major product.

== Conclusion ==
Throughout the exercises, recognising relationships of different calculations with the potential energy surface has been important in understanding what each step had meant. By grasping specific PES positions through calculations, useful information can be extracted for the different structures of concern (such as reactants,products and transition states). This has allowed energetic comparisons, molecular orbital interactions and reaction visualisation to be obtained and understood.

The most common calculation used was the minimisation, which is often used to obtain the lowest energy conformation of a molecule. From the PES surface, this is the global minimum as opposed to other local minimums, therefore approximating calculations were often ran beforehand to ensure the reliability of the obtained minimum values. Therefore, a standard protocol would be to perform a semi-empirical calculation (the rough approximation), before moving on to the B3LYP (the accurate calculation, a basis set based method involving both HF and DFT functions).

As transition states would also have zero gradients, second derivatives are required to differentiate between the two. Frequency calculations act as the key method of such verification, where a single imaginative force constant (the second derivative) would prove the achievement of a TS. This point should have all but one dimension amongst the 3N-6 dimensions minimised, leaving a maximum just a single dimension.

Given all the computation methods utilized throughout the task, it can be argued that the DFT-based B3LYP method is the most attractive: As although the quantum mechanical method DFT are able to produce relatively reliable approximations, this is in expense of poor results in terms of exchange correlations.The ab intito HF on the other hand, is highly effective in analytically solving exchange correlations, but as the method ruses electron positions, this requires higher degrees of freedom in the process of solving and thus suffers from longer computation times. Thus, putting both factors of accuracy and time penalty into perspective, as B3LYP which is able to solve exchange correlations accurately by using the same analytical approach as the HF , benefits from strengths of both methods mentioned above. Moreover, its accuracy is considered to have made up for its expensiveness in terms of time.

All in all, the applications used for this exercise has demonstrated just a small part of the capabilities in computation chemistry. Higher levels of accuracies (via basis sets) and calculations method (other Ab Initito implementations) has yet to be explored. Complex biological molecules modelling, reaction dynamics, excited electronic states just some other key examples where computations are of high utility to chemists.

== References ==

User:Htw14

2016-12-15T15:34:12Z

Htw14: /* Energetics and Profile */

'''Computational Lab Year 3: Transition States and Reactivity'''
== Introduction ==

The exercise sets out to understand transition states of reactions, an aspect often difficult to study by experimental means. Through obtaining minimas and transition structures(TS) from energy-optimising computations, as well as further elucidating reaction pathways and trajectory approaches, the study ultimately aims to determine reactivity using energy profiles generated from computed data of studied molecules.

The topic of interest in this wiki concerns the Diels-Alder reaction, a reaction highly powerful in the construction of cyclic compounds within organic synthesis. It is important to understand beforehand that the reactions offers high levels of predictability through stereoselectivity, which would be beneficial in predicting transition structures prior to any computational studies.

Originated from the strict rules of orbital symmetry conservation, such reactions are performed in concerted fashion, meaning that configurations of both reactants will be fully retained in the product, and thus are stererospecific. (For example, a cis alkene will always yield a syn product).

The two terms that would be referred to frequently in this wiki are 'Exo' and 'Endo'. These refer to yet another type of stereoselectivty in Diels-Alder reactions, which governs the position adopted by dienophile substituents relative to the diene system. Such selectivity is attributed to secondary orbital interactions, which will be discussed further in below sections.

Through combining mechanistic and stereoelectronic knowledge of the reaction with computation techniques (such as energy determination and MO visualisations), we would be able to correctly determine the specific diastereomers from reactions.This grants us the ability of disastreoselection control of mutiple stereogenic centered products, which is a powerful skill in organic synthesis.

In the following exercises, three different instances of the reaction are studied.

== Exercise 1: Butadiene with Ethene ==

===Molecular Orbitals===

==== MO Diagram ====
As shown below, the diagram illustrates what a standard MO diagram for a general Diels Alder reaction would have. Though butadiene and ethene are used to provide frontier orbitals as reactants here, according to substituents of different reactants, the relative energies of reactants and product orbitals in specific reactions may differ.
[[Image:Hubert.png|499x499px|center|thumb|Butadiene-Ethene Diels Alder Reaction]]

==== Symmetry requirement ====
For a successful reaction, symmetries of the HOMO and the LUMO must match, while violations to this will lead a forbidden reaction. These orbitals generated from wavefunctions can be either symmetric or anti-symmetric and are distinguished by transformations under an inversion operation. If symmetric with respect to inversion, such an orbital is assigned the label of gerade(g), and vice versa for anti-symmetric cases, which are ungerade(u). As shown in the MO diagram, frontier orbitals Ψ<sub>2</sub> of butadiene and Ψ<sub>2</sub> of ethene are both symmetric (gerade) and thus an interaction is allowed. An interaction of Ψ<sub>3</sub>(u) instead of Ψ<sub>2</sub>(g)<sub> </sub>however, would be forbidden as only g-g u-u interactions are allowed. The expression of the overlapping intergral shown below illustrates this concept mathematically:

[[File:Hubert_equ.png|center|150px]]

When S=0, this implies a zero overlap, while any allowed overlap would have an S value in between 0 and 1.

==== Quantitative MO Visualisations ====
All MOs shown below correlates to the above MO diagram. It can be seen that the varying degree of delocalisation and shapes of the HOMOs and LUMOs correspond well with the phases of orbitals shown in the MO diagram.

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=== Reaction Analysis ===

==== Bond Formation and Lengths ====
As shown in the diagram below, relationships between atoms can be divided into three categories, two of which being covalent interactions (sp3 and sp2) whilst the other a non-bonding interaction. These distances can be defined as the covalent and Van der Waal radius respectively. Typically, the distances (in Angstroms Å) between two carbon atoms of these relationships are as follows: Van de Waal (VdW): '''1.680 Å'''<ref name=":0">Pauling, Linus and L. O. Brockway. "Carbon—Carbon Bond Distances. The Electron Diffraction Investigation Of Ethane, Propane, Isobutane, Neopentane, Cyclopropane, Cyclopentane, Cyclohexane, Allene, Ethylene, Isobutene, Tetramethylethylene, Mesitylene, And Hexamethylbenzene. Revised Values Of Covalent Radii". ''Journal of the American Chemical Society'' 59.7 (1937): 1223-1236. Web.</ref>; Covalent sp3: '''1.537 Å'''<ref name=":0" />; Covalent sp2 : '''1.347 Å'''<ref name=":0" />

[[File:Trythis.png|center|330x330px]] <br style="clear:left">
{|border="1" cellpadding="5" cellspacing="0" align="center"
!Bonds
!Reactant
!Type
!TS
!Process
!Product
!Type
|-
|1,2
|1.33539
|sp<sup>2</sup>
|1.37978
|Lengthen
|1.50090
|sp<sup>3</sup>
|-
|2,3
|1.46834
|sp<sup>3</sup>
|1.41107
|Shorten
|1.33784
|sp<sup>2</sup>
|-
|3,4
|1.33539
|sp<sup>2</sup>
|1.37978
|Lengthen
|1.50090
|sp<sup>3</sup>
|-
|4,5
|3.41334
|2VdW
|2.11461
|Shorten
|1.54040
|sp<sup>3</sup>
|-
|5,6
|1.32736
|sp<sup>2</sup>
|1.38177
|Lengthen
|1.54091
|sp<sup>3</sup>
|-
|6,1
|3.41425
|2VdW
|2.11469
|Shorten
|1.54041
|sp<sup>3</sup>
|}

Firstly, it should be noted that the sum two Van de Waal radius of neigbouring atoms measures the internuclear distance of two non-interacting atoms prior to bond formation, hence it should be longer than those of bonding (i.e. sp2 and sp3). From the table, we can see that a smooth transition from non-bonding to sp3(shortening), sp3 to sp2 (shortening) and sp2 to sp3 (lengthening), thus turning the butadiene and alkene in to a cyclohexene in the process. As the alternating lengthening and shortening process of the bonds is yet another feature of the concerted process in the Diels Alder, the computated transiton state structure supports mechanism.

==== Vibrational Modes ====

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The vibrational mode corresponding to the transition state agrees with the concerted nature of the Diels-Alder reaction, during which two sp3 bonds are formed synchronously. The resultant single imgainary frequency proves that a maximum has been reached in only one dimension on the potential energy surface, which verifies the existence of a transition structure. Next to it shows the lowest positive frequency mode,where the two reactants rotates in opposite directions of a 2D plane. In comparison, the illustration on the right is non-reactive and minute in energy, which matches well with a typical rotational mode.

== Exercise 2: Benzoquinone with Cyclopentadiene ==

=== Molecular Orbitals ===
The orbitals below illustrates the four key resultant molecular orbitals (MO1-MO4) from the MO diagram shown in Exercise 1, where in this case are derived from the four frontier orbitals of cyclopentadiene (the diene equivalent) and the two from Benzoquinone (the alkene equivalent). Both the Exo and Endo reactions computated in this exercise are cases of normal electron demand, the most common electronic interaction in Diels-Alder reactions, where the dienophile is electron poor while the diene being electron rich. On the other hand, inverse demand suggests the opposite, thus allowing that the alkene HOMO to be at a close energy level to interact strongly the the diene LUMO. If this is the case MO1 (referring to the MO Diagram above) will be the HOMO of the transition state as opposed to MO2. By examining phases from both HOMOs of the Exo and Endo approaches, this is evident that the reaction is not a case inverse demand, as both corresponded to the phase pattern that a MO2 equivalent would possess. We can therefore conclude that the reaction is in '''normal electron demand'''.

==== Exo Approach Key MOs ====
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==== Endo Approach Key MOs ====
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|
<jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 14; mo 47; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>ENDO_TS_DFT_POP=FULL_GFPRINT.LOG</uploadedFileContents>
<title>MO3 (LUMO)</title>
</jmolApplet>
</jmol>
|
<jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 14; mo 48; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>ENDO_TS_DFT_POP=FULL_GFPRINT.LOG</uploadedFileContents>
<title>MO4</title>
</jmolApplet>
</jmol>
|}

=== Reaction Analysis ===

==== Energetics and Pathway ====

Through analysing resultant thermodynamic data extracted from optimised structures of the reactants, products and transition states, a highly useful comparison could be made between the two reactant approaches. This will ultimately allow us to predict the reaction outcome expected in reality, thus showing the importance of computational techniques in chemistry. Such data is shown below:

{|border="1" cellpadding="5" cellspacing="0" align="center"
!Energy(kJ/mol)
!Exo
!Endo
|-
|Reactant
|<nowiki>-1510772.498</nowiki>
|<nowiki>-1510762.046</nowiki>
|-
|Product
|<nowiki>-1510782.951</nowiki>
|<nowiki>-1510783.751</nowiki>
|-
|TS
|<nowiki>-1510663.669</nowiki>
|<nowiki>-1510670.285</nowiki>
|-
|E<sub>a</sub>
|108.8296005
|91.761225
|-
|ΔE
|<nowiki>-10.4521155</nowiki>
|<nowiki>-21.7050085</nowiki>
|}

While the activation energy (Ea) gives information about the minimum energy input required to drive the reaction forwards, the total energy difference (ΔE) allows the judgement of the energy of stabilisation achievable for each reaction. From the table we see that less Ea is required initially, as well as a larger extent of stabilisation if the reaction were in the endo approach (reasons for this discussed in the below section). Therefore, we can conclude that the '''Endo''' adduct is both the '''Kinetic''' and '''Thermodynamic''' product.

[[File:cool1.png|right|295x295px|thumb|Endo Orbital Overlap]]

<br />

==== Orbital Stereoelectronics ====

The endo reaction undergoes with dienophile benzoquinone sitting on top of the cyclopentadiene (Cp), which grants an additional opportunity for a favourable orbital interaction. As seen on the right, the p orbitals at the 2,3 position of Cp is within proximate distance to interact with the rear C=C π* orbitals of the dienophile, alongside the bond-forming front C=C π* orbitals. From the white arrows indicated, the Cp HOMO is also in correct phase to overlap with the second double bond of the Benzoquinone. This is known as a '''secondary orbital interaction''', a stabilising interaction which does not involve bond formation.

Therefore, by having a second double bond within the same molecule in the dienephile, as opposed to a simpler alkene (eg. ethene), the additional interaction available plays the role in attracting the diene to adapt the Endo position while approaching. This '''lowers the activation energy''' of the Endo pathway, therefore transition structures are more favoured to be endo despite the associated sterics hinderance thermodynamically. This shows diels-alder reactions are often '''kinetically driven'''.

<br />
<br />
<br />

== Exercise 3: Xylylene with Sulphur Dioxide ==

=== Reactant Approach via IRC ===
{| class="wikitable"
!Diels Alder Endo
!Diels Alder Exo
!Cheletropic
|-
|[[File:Endo_irc_animation_for_wiki.gif]]
|[[File:Exo_irc_animation_for_wiki.gif]]
|[[File:Chele_irc_animation_for_wiki.gif]]
|}

=== Reaction Analysis ===

==== Energetics and Profile ====
The reaction of concern in the exercise introduces a possibility of a third reaction alongside the two approaches from the Hetero Diels Alder, known as the Cheletropic reaction. Again, computationally-calculated data of Gibbs free energy will be useful here to judge and compare the different reaction paths available, the reaction profile below should also provide a much clearer representation of how the three reactions compare:

{| border="1" cellpadding="5" cellspacing="0" align="center"
!Energy(kJ/mol)
!Exo
!Endo
!Cheletropic
|-
|Reactant
|177.69384
|178.3790955
|186.3606155
|-
|Product
|56.3301025
|56.983852
|<nowiki>-0.005251</nowiki>
|-
|TS
|241.745538
|237.7626545
|260.08203
|-
|E<sub>a</sub>
|64.051698
|59.383559
|73.7214145
|-
|ΔE
|<nowiki>-121.3637375</nowiki>
|<nowiki>-121.3952435</nowiki>
|<nowiki>-186.3658665</nowiki>
|}

[[File:Reactionhub.png|800px|center]]
With the lowest energy activation energy amongst all, the '''Endo''' pathway can be concluded to be the '''Kinetic product'''. In terms of the overall energy change, although very similar, endo also appears as the more thermodynamically favourable between the two Diels-Alder reactions. Though given the small margin of difference, such a statement should be treated with discretion. It is however very clear that the '''Cheletropic''' pathway is the '''Thermodynamic product''' overall over Endo and Exo. This margin of difference that Cheletropic reactions show owes to the relatively stable five-membered adduct, as opposed to a six-membered one.

Having identified the KE and TD products, reactions conditions as well as solvents can be altered in order to obtain a desired product specifically.

==== Reactant Transformation ====
Through studying the reaction visualisations from above, we can see that as the reactive butadiene fragment in xylene cyclizes, a conjugated system can been seen to establish at the rear ring. As the major driving force for all three reactions,which are all 2π electrons away from satisfying the Huckel rule of 4n+2 delocalised electrons, the aromatisation of xylyene provides sufficient aromatic stabilisation energy to the reactants to interact.

==== Pathway Alternative ====
A second Diels-Alder reaction possibility comes at the rear diene, as part of the 1,3 cyclohexadiene system. Compared to the Exo and Endo diels-alder reaction computed above, the clear inability to aromatise in this alternative pathway, where a bridged ring system will give rise to a sizable thermodymanic penalty for both orientation approaches.Though the bridged system does not incur significant additional themodynamic instability (because bonds formed and broken are identical to its aromatisable alternative, and that both S=O bonds in the products are pointing towards empty space), it does suffer from the following kinetic implication: The o-xylylene group, being originally a fully planar structure with a coplanar eight π-orbital system, is forced to distort from its conformation, as carbons at the 1,4 positions are essentially 'pushed' upwards, in order to accommodate the approaching sulpur dioxide. As this effect is present for both Exo and Endo apporaches, Kinetic unfavourability will also be realized across this alternative position for cyclisation.

== Conclusion ==
Throughout the exercises, recognising relationships of different calculations with the potential energy surface has been important in understanding what each step had meant. By grasping specific PES positions through calculations, useful information can be extracted for the different structures of concern (such as reactants,products and transition states). This has allowed energetic comparisons, molecular orbital interactions and reaction visualisation to be obtained and understood.

The most common calculation used was the minimisation, which is often used to obtain the lowest energy conformation of a molecule. From the PES surface, this is the global minimum as opposed to other local minimums, therefore approximating calculations were often ran beforehand to ensure the reliability of the obtained minimum values. Therefore, a standard protocol would be to perform a semi-empirical calculation (the rough approximation), before moving on to the B3LYP (the accurate calculation, a basis set based method involving both HF and DFT functions).

As transition states would also have zero gradients, second derivatives are required to differentiate between the two. Frequency calculations act as the key method of such verification, where a single imaginative force constant (the second derivative) would prove the achievement of a TS. This point should have all but one dimension amongst the 3N-6 dimensions minimised, leaving a maximum just a single dimension.

Given all the computation methods utilized throughout the task, it can be argued that the DFT-based B3LYP method is the most attractive: As although the quantum mechanical method DFT are able to produce relatively reliable approximations, this is in expense of poor results in terms of exchange correlations.The ab intito HF on the other hand, is highly effective in analytically solving exchange correlations, but as the method ruses electron positions, this requires higher degrees of freedom in the process of solving and thus suffers from longer computation times. Thus, putting both factors of accuracy and time penalty into perspective, as B3LYP which is able to solve exchange correlations accurately by using the same analytical approach as the HF , benefits from strengths of both methods mentioned above. Moreover, its accuracy is considered to have made up for its expensiveness in terms of time.

All in all, the applications used for this exercise has demonstrated just a small part of the capabilities in computation chemistry. Higher levels of accuracies (via basis sets) and calculations method (other Ab Initito implementations) has yet to be explored. Complex biological molecules modelling, reaction dynamics, excited electronic states just some other key examples where computations are of high utility to chemists.

== References ==

File:Reactionhub.png

2016-12-15T15:32:51Z

Htw14:

File:Reactionnn.png

2016-12-15T15:31:12Z

Htw14: Htw14 uploaded a new version of File:Reactionnn.png

File:Reactionnn.png

2016-12-15T15:31:02Z

Htw14: Htw14 uploaded a new version of File:Reactionnn.png

File:Reactionnn.png

2016-12-15T15:30:31Z

Htw14: Htw14 uploaded a new version of File:Reactionnn.png

User:Htw14

2016-12-15T15:07:16Z

Htw14: /* Endo Approach Key MOs */

'''Computational Lab Year 3: Transition States and Reactivity'''
== Introduction ==

The exercise sets out to understand transition states of reactions, an aspect often difficult to study by experimental means. Through obtaining minimas and transition structures(TS) from energy-optimising computations, as well as further elucidating reaction pathways and trajectory approaches, the study ultimately aims to determine reactivity using energy profiles generated from computed data of studied molecules.

The topic of interest in this wiki concerns the Diels-Alder reaction, a reaction highly powerful in the construction of cyclic compounds within organic synthesis. It is important to understand beforehand that the reactions offers high levels of predictability through stereoselectivity, which would be beneficial in predicting transition structures prior to any computational studies.

Originated from the strict rules of orbital symmetry conservation, such reactions are performed in concerted fashion, meaning that configurations of both reactants will be fully retained in the product, and thus are stererospecific. (For example, a cis alkene will always yield a syn product).

The two terms that would be referred to frequently in this wiki are 'Exo' and 'Endo'. These refer to yet another type of stereoselectivty in Diels-Alder reactions, which governs the position adopted by dienophile substituents relative to the diene system. Such selectivity is attributed to secondary orbital interactions, which will be discussed further in below sections.

Through combining mechanistic and stereoelectronic knowledge of the reaction with computation techniques (such as energy determination and MO visualisations), we would be able to correctly determine the specific diastereomers from reactions.This grants us the ability of disastreoselection control of mutiple stereogenic centered products, which is a powerful skill in organic synthesis.

In the following exercises, three different instances of the reaction are studied.

== Exercise 1: Butadiene with Ethene ==

===Molecular Orbitals===

==== MO Diagram ====
As shown below, the diagram illustrates what a standard MO diagram for a general Diels Alder reaction would have. Though butadiene and ethene are used to provide frontier orbitals as reactants here, according to substituents of different reactants, the relative energies of reactants and product orbitals in specific reactions may differ.
[[Image:Hubert.png|499x499px|center|thumb|Butadiene-Ethene Diels Alder Reaction]]

==== Symmetry requirement ====
For a successful reaction, symmetries of the HOMO and the LUMO must match, while violations to this will lead a forbidden reaction. These orbitals generated from wavefunctions can be either symmetric or anti-symmetric and are distinguished by transformations under an inversion operation. If symmetric with respect to inversion, such an orbital is assigned the label of gerade(g), and vice versa for anti-symmetric cases, which are ungerade(u). As shown in the MO diagram, frontier orbitals Ψ<sub>2</sub> of butadiene and Ψ<sub>2</sub> of ethene are both symmetric (gerade) and thus an interaction is allowed. An interaction of Ψ<sub>3</sub>(u) instead of Ψ<sub>2</sub>(g)<sub> </sub>however, would be forbidden as only g-g u-u interactions are allowed. The expression of the overlapping intergral shown below illustrates this concept mathematically:

[[File:Hubert_equ.png|center|150px]]

When S=0, this implies a zero overlap, while any allowed overlap would have an S value in between 0 and 1.

==== Quantitative MO Visualisations ====
All MOs shown below correlates to the above MO diagram. It can be seen that the varying degree of delocalisation and shapes of the HOMOs and LUMOs correspond well with the phases of orbitals shown in the MO diagram.

{| class="wikitable"
|-
|
<jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 14; mo 16; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>DA_STEP_2_PM6_OPT_MO_VER.LOG</uploadedFileContents>
<title>MO1 from TS</title>
</jmolApplet>
</jmol>
|
<jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 14; mo 17; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>DA_STEP_2_PM6_OPT_MO_VER.LOG</uploadedFileContents>
<title>MO2 HOMO from TS</title>
</jmolApplet>
</jmol>
|
<jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 14; mo 18; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>DA_STEP_2_PM6_OPT_MO_VER.LOG</uploadedFileContents>
<title>MO3 LUMO from TSs</title>
</jmolApplet>
</jmol>
|
<jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 14; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>DA_STEP_2_PM6_OPT_MO_VER.LOG</uploadedFileContents>
<title>MO4 from TS</title>
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</jmol>
|-
|
<jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 12; mo 6; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>REFINED_ALKENE_PM6.LOG</uploadedFileContents>
<title>Ψ1 HOMO from Ethene FOs</title>
</jmolApplet>
</jmol>
|
<jmol>
<jmolApplet>
<color>white</color>
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<script>frame 12; mo 7; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>REFINED_ALKENE_PM6.LOG</uploadedFileContents>
<title>Ψ2 LUMO from Ethene FOs</title>
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<jmol>
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<uploadedFileContents>BUTADIENE_PM6_MO_VER.LOG</uploadedFileContents>
<title>Ψ2 HOMO from Butadiene FOs</title>
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<jmol>
<jmolApplet>
<color>white</color>
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<uploadedFileContents>BUTADIENE_PM6_MO_VER.LOG</uploadedFileContents>
<title>Ψ3 LUMO from Butadiene FOs</title>
</jmolApplet>
</jmol>
|}

=== Reaction Analysis ===

==== Bond Formation and Lengths ====
As shown in the diagram below, relationships between atoms can be divided into three categories, two of which being covalent interactions (sp3 and sp2) whilst the other a non-bonding interaction. These distances can be defined as the covalent and Van der Waal radius respectively. Typically, the distances (in Angstroms Å) between two carbon atoms of these relationships are as follows: Van de Waal (VdW): '''1.680 Å'''<ref name=":0">Pauling, Linus and L. O. Brockway. "Carbon—Carbon Bond Distances. The Electron Diffraction Investigation Of Ethane, Propane, Isobutane, Neopentane, Cyclopropane, Cyclopentane, Cyclohexane, Allene, Ethylene, Isobutene, Tetramethylethylene, Mesitylene, And Hexamethylbenzene. Revised Values Of Covalent Radii". ''Journal of the American Chemical Society'' 59.7 (1937): 1223-1236. Web.</ref>; Covalent sp3: '''1.537 Å'''<ref name=":0" />; Covalent sp2 : '''1.347 Å'''<ref name=":0" />

[[File:Trythis.png|center|330x330px]] <br style="clear:left">
{|border="1" cellpadding="5" cellspacing="0" align="center"
!Bonds
!Reactant
!Type
!TS
!Process
!Product
!Type
|-
|1,2
|1.33539
|sp<sup>2</sup>
|1.37978
|Lengthen
|1.50090
|sp<sup>3</sup>
|-
|2,3
|1.46834
|sp<sup>3</sup>
|1.41107
|Shorten
|1.33784
|sp<sup>2</sup>
|-
|3,4
|1.33539
|sp<sup>2</sup>
|1.37978
|Lengthen
|1.50090
|sp<sup>3</sup>
|-
|4,5
|3.41334
|2VdW
|2.11461
|Shorten
|1.54040
|sp<sup>3</sup>
|-
|5,6
|1.32736
|sp<sup>2</sup>
|1.38177
|Lengthen
|1.54091
|sp<sup>3</sup>
|-
|6,1
|3.41425
|2VdW
|2.11469
|Shorten
|1.54041
|sp<sup>3</sup>
|}

Firstly, it should be noted that the sum two Van de Waal radius of neigbouring atoms measures the internuclear distance of two non-interacting atoms prior to bond formation, hence it should be longer than those of bonding (i.e. sp2 and sp3). From the table, we can see that a smooth transition from non-bonding to sp3(shortening), sp3 to sp2 (shortening) and sp2 to sp3 (lengthening), thus turning the butadiene and alkene in to a cyclohexene in the process. As the alternating lengthening and shortening process of the bonds is yet another feature of the concerted process in the Diels Alder, the computated transiton state structure supports mechanism.

==== Vibrational Modes ====

{| class="wikitable"
|
<jmol>
<jmolApplet>
<title>TS reactive vibrational mode</title><color>white</color><size>300</size>
<script>frame 15;vectors 4;vectors scale 5.0;color vectors red;vibration 10;
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<jmol>
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The vibrational mode corresponding to the transition state agrees with the concerted nature of the Diels-Alder reaction, during which two sp3 bonds are formed synchronously. The resultant single imgainary frequency proves that a maximum has been reached in only one dimension on the potential energy surface, which verifies the existence of a transition structure. Next to it shows the lowest positive frequency mode,where the two reactants rotates in opposite directions of a 2D plane. In comparison, the illustration on the right is non-reactive and minute in energy, which matches well with a typical rotational mode.

== Exercise 2: Benzoquinone with Cyclopentadiene ==

=== Molecular Orbitals ===
The orbitals below illustrates the four key resultant molecular orbitals (MO1-MO4) from the MO diagram shown in Exercise 1, where in this case are derived from the four frontier orbitals of cyclopentadiene (the diene equivalent) and the two from Benzoquinone (the alkene equivalent). Both the Exo and Endo reactions computated in this exercise are cases of normal electron demand, the most common electronic interaction in Diels-Alder reactions, where the dienophile is electron poor while the diene being electron rich. On the other hand, inverse demand suggests the opposite, thus allowing that the alkene HOMO to be at a close energy level to interact strongly the the diene LUMO. If this is the case MO1 (referring to the MO Diagram above) will be the HOMO of the transition state as opposed to MO2. By examining phases from both HOMOs of the Exo and Endo approaches, this is evident that the reaction is not a case inverse demand, as both corresponded to the phase pattern that a MO2 equivalent would possess. We can therefore conclude that the reaction is in '''normal electron demand'''.

==== Exo Approach Key MOs ====
{| class="wikitable"
|-
|
<jmol>
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<title>MO4</title>
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==== Endo Approach Key MOs ====
{| class="wikitable"
|-
|<jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
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<uploadedFileContents>ENDO_TS_DFT_POP=FULL_GFPRINT.LOG</uploadedFileContents>
<title>MO2 (HOMO)</title>
</jmolApplet>
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|
<jmol>
<jmolApplet>
<color>white</color>
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<uploadedFileContents>ENDO_TS_DFT_POP=FULL_GFPRINT.LOG</uploadedFileContents>
<title>MO3 (LUMO)</title>
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|
<jmol>
<jmolApplet>
<color>white</color>
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<uploadedFileContents>ENDO_TS_DFT_POP=FULL_GFPRINT.LOG</uploadedFileContents>
<title>MO4</title>
</jmolApplet>
</jmol>
|}

=== Reaction Analysis ===

==== Energetics and Pathway ====

Through analysing resultant thermodynamic data extracted from optimised structures of the reactants, products and transition states, a highly useful comparison could be made between the two reactant approaches. This will ultimately allow us to predict the reaction outcome expected in reality, thus showing the importance of computational techniques in chemistry. Such data is shown below:

{|border="1" cellpadding="5" cellspacing="0" align="center"
!Energy(kJ/mol)
!Exo
!Endo
|-
|Reactant
|<nowiki>-1510772.498</nowiki>
|<nowiki>-1510762.046</nowiki>
|-
|Product
|<nowiki>-1510782.951</nowiki>
|<nowiki>-1510783.751</nowiki>
|-
|TS
|<nowiki>-1510663.669</nowiki>
|<nowiki>-1510670.285</nowiki>
|-
|E<sub>a</sub>
|108.8296005
|91.761225
|-
|ΔE
|<nowiki>-10.4521155</nowiki>
|<nowiki>-21.7050085</nowiki>
|}

While the activation energy (Ea) gives information about the minimum energy input required to drive the reaction forwards, the total energy difference (ΔE) allows the judgement of the energy of stabilisation achievable for each reaction. From the table we see that less Ea is required initially, as well as a larger extent of stabilisation if the reaction were in the endo approach (reasons for this discussed in the below section). Therefore, we can conclude that the '''Endo''' adduct is both the '''Kinetic''' and '''Thermodynamic''' product.

[[File:cool1.png|right|295x295px|thumb|Endo Orbital Overlap]]

<br />

==== Orbital Stereoelectronics ====

The endo reaction undergoes with dienophile benzoquinone sitting on top of the cyclopentadiene (Cp), which grants an additional opportunity for a favourable orbital interaction. As seen on the right, the p orbitals at the 2,3 position of Cp is within proximate distance to interact with the rear C=C π* orbitals of the dienophile, alongside the bond-forming front C=C π* orbitals. From the white arrows indicated, the Cp HOMO is also in correct phase to overlap with the second double bond of the Benzoquinone. This is known as a '''secondary orbital interaction''', a stabilising interaction which does not involve bond formation.

Therefore, by having a second double bond within the same molecule in the dienephile, as opposed to a simpler alkene (eg. ethene), the additional interaction available plays the role in attracting the diene to adapt the Endo position while approaching. This '''lowers the activation energy''' of the Endo pathway, therefore transition structures are more favoured to be endo despite the associated sterics hinderance thermodynamically. This shows diels-alder reactions are often '''kinetically driven'''.

<br />
<br />
<br />

== Exercise 3: Xylylene with Sulphur Dioxide ==

=== Reactant Approach via IRC ===
{| class="wikitable"
!Diels Alder Endo
!Diels Alder Exo
!Cheletropic
|-
|[[File:Endo_irc_animation_for_wiki.gif]]
|[[File:Exo_irc_animation_for_wiki.gif]]
|[[File:Chele_irc_animation_for_wiki.gif]]
|}

=== Reaction Analysis ===

==== Energetics and Profile ====
The reaction of concern in the exercise introduces a possibility of a third reaction alongside the two approaches from the Hetero Diels Alder, known as the Cheletropic reaction. Again, computationally-calculated data of Gibbs free energy will be useful here to judge and compare the different reaction paths available, the reaction profile below should also provide a much clearer representation of how the three reactions compare:

{| border="1" cellpadding="5" cellspacing="0" align="center"
!Energy(kJ/mol)
!Exo
!Endo
!Cheletropic
|-
|Reactant
|177.69384
|178.3790955
|186.3606155
|-
|Product
|56.3301025
|56.983852
|<nowiki>-0.005251</nowiki>
|-
|TS
|241.745538
|237.7626545
|260.08203
|-
|E<sub>a</sub>
|64.051698
|59.383559
|73.7214145
|-
|ΔE
|<nowiki>-121.3637375</nowiki>
|<nowiki>-121.3952435</nowiki>
|<nowiki>-186.3658665</nowiki>
|}

[[File:reactionnn.png|800px|center]]
With the lowest energy activation energy amongst all, the '''Endo''' pathway can be concluded to be the '''Kinetic product'''. In terms of the overall energy change, although very similar, endo also appears as the more thermodynamically favourable between the two Diels-Alder reactions. Though given the small margin of difference, such a statement should be treated with discretion. It is however very clear that the '''Cheletropic''' pathway is the '''Thermodynamic product''' overall over Endo and Exo. This margin of difference that Cheletropic reactions show owes to the relatively stable five-membered adduct, as opposed to a six-membered one.

Having identified the KE and TD products, reactions conditions as well as solvents can be altered in order to obtain a desired product specifically.

==== Reactant Transformation ====
Through studying the reaction visualisations from above, we can see that as the reactive butadiene fragment in xylene cyclizes, a conjugated system can been seen to establish at the rear ring. As the major driving force for all three reactions,which are all 2π electrons away from satisfying the Huckel rule of 4n+2 delocalised electrons, the aromatisation of xylyene provides sufficient aromatic stabilisation energy to the reactants to interact.

==== Pathway Alternative ====
A second Diels-Alder reaction possibility comes at the rear diene, as part of the 1,3 cyclohexadiene system. Compared to the Exo and Endo diels-alder reaction computed above, the clear inability to aromatise in this alternative pathway, where a bridged ring system will give rise to a sizable thermodymanic penalty for both orientation approaches.Though the bridged system does not incur significant additional themodynamic instability (because bonds formed and broken are identical to its aromatisable alternative, and that both S=O bonds in the products are pointing towards empty space), it does suffer from the following kinetic implication: The o-xylylene group, being originally a fully planar structure with a coplanar eight π-orbital system, is forced to distort from its conformation, as carbons at the 1,4 positions are essentially 'pushed' upwards, in order to accommodate the approaching sulpur dioxide. As this effect is present for both Exo and Endo apporaches, Kinetic unfavourability will also be realized across this alternative position for cyclisation.

== Conclusion ==
Throughout the exercises, recognising relationships of different calculations with the potential energy surface has been important in understanding what each step had meant. By grasping specific PES positions through calculations, useful information can be extracted for the different structures of concern (such as reactants,products and transition states). This has allowed energetic comparisons, molecular orbital interactions and reaction visualisation to be obtained and understood.

The most common calculation used was the minimisation, which is often used to obtain the lowest energy conformation of a molecule. From the PES surface, this is the global minimum as opposed to other local minimums, therefore approximating calculations were often ran beforehand to ensure the reliability of the obtained minimum values. Therefore, a standard protocol would be to perform a semi-empirical calculation (the rough approximation), before moving on to the B3LYP (the accurate calculation, a basis set based method involving both HF and DFT functions).

As transition states would also have zero gradients, second derivatives are required to differentiate between the two. Frequency calculations act as the key method of such verification, where a single imaginative force constant (the second derivative) would prove the achievement of a TS. This point should have all but one dimension amongst the 3N-6 dimensions minimised, leaving a maximum just a single dimension.

Given all the computation methods utilized throughout the task, it can be argued that the DFT-based B3LYP method is the most attractive: As although the quantum mechanical method DFT are able to produce relatively reliable approximations, this is in expense of poor results in terms of exchange correlations.The ab intito HF on the other hand, is highly effective in analytically solving exchange correlations, but as the method ruses electron positions, this requires higher degrees of freedom in the process of solving and thus suffers from longer computation times. Thus, putting both factors of accuracy and time penalty into perspective, as B3LYP which is able to solve exchange correlations accurately by using the same analytical approach as the HF , benefits from strengths of both methods mentioned above. Moreover, its accuracy is considered to have made up for its expensiveness in terms of time.

All in all, the applications used for this exercise has demonstrated just a small part of the capabilities in computation chemistry. Higher levels of accuracies (via basis sets) and calculations method (other Ab Initito implementations) has yet to be explored. Complex biological molecules modelling, reaction dynamics, excited electronic states just some other key examples where computations are of high utility to chemists.

== References ==

User:Htw14

2016-12-15T15:06:48Z

Htw14: /* Exo Approach Key MOs */

'''Computational Lab Year 3: Transition States and Reactivity'''
== Introduction ==

The exercise sets out to understand transition states of reactions, an aspect often difficult to study by experimental means. Through obtaining minimas and transition structures(TS) from energy-optimising computations, as well as further elucidating reaction pathways and trajectory approaches, the study ultimately aims to determine reactivity using energy profiles generated from computed data of studied molecules.

The topic of interest in this wiki concerns the Diels-Alder reaction, a reaction highly powerful in the construction of cyclic compounds within organic synthesis. It is important to understand beforehand that the reactions offers high levels of predictability through stereoselectivity, which would be beneficial in predicting transition structures prior to any computational studies.

Originated from the strict rules of orbital symmetry conservation, such reactions are performed in concerted fashion, meaning that configurations of both reactants will be fully retained in the product, and thus are stererospecific. (For example, a cis alkene will always yield a syn product).

The two terms that would be referred to frequently in this wiki are 'Exo' and 'Endo'. These refer to yet another type of stereoselectivty in Diels-Alder reactions, which governs the position adopted by dienophile substituents relative to the diene system. Such selectivity is attributed to secondary orbital interactions, which will be discussed further in below sections.

Through combining mechanistic and stereoelectronic knowledge of the reaction with computation techniques (such as energy determination and MO visualisations), we would be able to correctly determine the specific diastereomers from reactions.This grants us the ability of disastreoselection control of mutiple stereogenic centered products, which is a powerful skill in organic synthesis.

In the following exercises, three different instances of the reaction are studied.

== Exercise 1: Butadiene with Ethene ==

===Molecular Orbitals===

==== MO Diagram ====
As shown below, the diagram illustrates what a standard MO diagram for a general Diels Alder reaction would have. Though butadiene and ethene are used to provide frontier orbitals as reactants here, according to substituents of different reactants, the relative energies of reactants and product orbitals in specific reactions may differ.
[[Image:Hubert.png|499x499px|center|thumb|Butadiene-Ethene Diels Alder Reaction]]

==== Symmetry requirement ====
For a successful reaction, symmetries of the HOMO and the LUMO must match, while violations to this will lead a forbidden reaction. These orbitals generated from wavefunctions can be either symmetric or anti-symmetric and are distinguished by transformations under an inversion operation. If symmetric with respect to inversion, such an orbital is assigned the label of gerade(g), and vice versa for anti-symmetric cases, which are ungerade(u). As shown in the MO diagram, frontier orbitals Ψ<sub>2</sub> of butadiene and Ψ<sub>2</sub> of ethene are both symmetric (gerade) and thus an interaction is allowed. An interaction of Ψ<sub>3</sub>(u) instead of Ψ<sub>2</sub>(g)<sub> </sub>however, would be forbidden as only g-g u-u interactions are allowed. The expression of the overlapping intergral shown below illustrates this concept mathematically:

[[File:Hubert_equ.png|center|150px]]

When S=0, this implies a zero overlap, while any allowed overlap would have an S value in between 0 and 1.

==== Quantitative MO Visualisations ====
All MOs shown below correlates to the above MO diagram. It can be seen that the varying degree of delocalisation and shapes of the HOMOs and LUMOs correspond well with the phases of orbitals shown in the MO diagram.

{| class="wikitable"
|-
|
<jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 14; mo 16; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>DA_STEP_2_PM6_OPT_MO_VER.LOG</uploadedFileContents>
<title>MO1 from TS</title>
</jmolApplet>
</jmol>
|
<jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 14; mo 17; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>DA_STEP_2_PM6_OPT_MO_VER.LOG</uploadedFileContents>
<title>MO2 HOMO from TS</title>
</jmolApplet>
</jmol>
|
<jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 14; mo 18; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>DA_STEP_2_PM6_OPT_MO_VER.LOG</uploadedFileContents>
<title>MO3 LUMO from TSs</title>
</jmolApplet>
</jmol>
|
<jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 14; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>DA_STEP_2_PM6_OPT_MO_VER.LOG</uploadedFileContents>
<title>MO4 from TS</title>
</jmolApplet>
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<jmol>
<jmolApplet>
<color>white</color>
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<script>frame 12; mo 6; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>REFINED_ALKENE_PM6.LOG</uploadedFileContents>
<title>Ψ1 HOMO from Ethene FOs</title>
</jmolApplet>
</jmol>
|
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<script>frame 12; mo 7; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>REFINED_ALKENE_PM6.LOG</uploadedFileContents>
<title>Ψ2 LUMO from Ethene FOs</title>
</jmolApplet>
</jmol>
|
<jmol>
<jmolApplet>
<color>white</color>
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<script>frame 24; mo 11; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>BUTADIENE_PM6_MO_VER.LOG</uploadedFileContents>
<title>Ψ2 HOMO from Butadiene FOs</title>
</jmolApplet>
</jmol>
|
<jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 24; mo 12; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>BUTADIENE_PM6_MO_VER.LOG</uploadedFileContents>
<title>Ψ3 LUMO from Butadiene FOs</title>
</jmolApplet>
</jmol>
|}

=== Reaction Analysis ===

==== Bond Formation and Lengths ====
As shown in the diagram below, relationships between atoms can be divided into three categories, two of which being covalent interactions (sp3 and sp2) whilst the other a non-bonding interaction. These distances can be defined as the covalent and Van der Waal radius respectively. Typically, the distances (in Angstroms Å) between two carbon atoms of these relationships are as follows: Van de Waal (VdW): '''1.680 Å'''<ref name=":0">Pauling, Linus and L. O. Brockway. "Carbon—Carbon Bond Distances. The Electron Diffraction Investigation Of Ethane, Propane, Isobutane, Neopentane, Cyclopropane, Cyclopentane, Cyclohexane, Allene, Ethylene, Isobutene, Tetramethylethylene, Mesitylene, And Hexamethylbenzene. Revised Values Of Covalent Radii". ''Journal of the American Chemical Society'' 59.7 (1937): 1223-1236. Web.</ref>; Covalent sp3: '''1.537 Å'''<ref name=":0" />; Covalent sp2 : '''1.347 Å'''<ref name=":0" />

[[File:Trythis.png|center|330x330px]] <br style="clear:left">
{|border="1" cellpadding="5" cellspacing="0" align="center"
!Bonds
!Reactant
!Type
!TS
!Process
!Product
!Type
|-
|1,2
|1.33539
|sp<sup>2</sup>
|1.37978
|Lengthen
|1.50090
|sp<sup>3</sup>
|-
|2,3
|1.46834
|sp<sup>3</sup>
|1.41107
|Shorten
|1.33784
|sp<sup>2</sup>
|-
|3,4
|1.33539
|sp<sup>2</sup>
|1.37978
|Lengthen
|1.50090
|sp<sup>3</sup>
|-
|4,5
|3.41334
|2VdW
|2.11461
|Shorten
|1.54040
|sp<sup>3</sup>
|-
|5,6
|1.32736
|sp<sup>2</sup>
|1.38177
|Lengthen
|1.54091
|sp<sup>3</sup>
|-
|6,1
|3.41425
|2VdW
|2.11469
|Shorten
|1.54041
|sp<sup>3</sup>
|}

Firstly, it should be noted that the sum two Van de Waal radius of neigbouring atoms measures the internuclear distance of two non-interacting atoms prior to bond formation, hence it should be longer than those of bonding (i.e. sp2 and sp3). From the table, we can see that a smooth transition from non-bonding to sp3(shortening), sp3 to sp2 (shortening) and sp2 to sp3 (lengthening), thus turning the butadiene and alkene in to a cyclohexene in the process. As the alternating lengthening and shortening process of the bonds is yet another feature of the concerted process in the Diels Alder, the computated transiton state structure supports mechanism.

==== Vibrational Modes ====

{| class="wikitable"
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<jmol>
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<title>TS reactive vibrational mode</title><color>white</color><size>300</size>
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The vibrational mode corresponding to the transition state agrees with the concerted nature of the Diels-Alder reaction, during which two sp3 bonds are formed synchronously. The resultant single imgainary frequency proves that a maximum has been reached in only one dimension on the potential energy surface, which verifies the existence of a transition structure. Next to it shows the lowest positive frequency mode,where the two reactants rotates in opposite directions of a 2D plane. In comparison, the illustration on the right is non-reactive and minute in energy, which matches well with a typical rotational mode.

== Exercise 2: Benzoquinone with Cyclopentadiene ==

=== Molecular Orbitals ===
The orbitals below illustrates the four key resultant molecular orbitals (MO1-MO4) from the MO diagram shown in Exercise 1, where in this case are derived from the four frontier orbitals of cyclopentadiene (the diene equivalent) and the two from Benzoquinone (the alkene equivalent). Both the Exo and Endo reactions computated in this exercise are cases of normal electron demand, the most common electronic interaction in Diels-Alder reactions, where the dienophile is electron poor while the diene being electron rich. On the other hand, inverse demand suggests the opposite, thus allowing that the alkene HOMO to be at a close energy level to interact strongly the the diene LUMO. If this is the case MO1 (referring to the MO Diagram above) will be the HOMO of the transition state as opposed to MO2. By examining phases from both HOMOs of the Exo and Endo approaches, this is evident that the reaction is not a case inverse demand, as both corresponded to the phase pattern that a MO2 equivalent would possess. We can therefore conclude that the reaction is in '''normal electron demand'''.

==== Exo Approach Key MOs ====
{| class="wikitable"
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==== Endo Approach Key MOs ====
{| class="wikitable"
|-
|<jmol>
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<title>MO4</title>
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=== Reaction Analysis ===

==== Energetics and Pathway ====

Through analysing resultant thermodynamic data extracted from optimised structures of the reactants, products and transition states, a highly useful comparison could be made between the two reactant approaches. This will ultimately allow us to predict the reaction outcome expected in reality, thus showing the importance of computational techniques in chemistry. Such data is shown below:

{|border="1" cellpadding="5" cellspacing="0" align="center"
!Energy(kJ/mol)
!Exo
!Endo
|-
|Reactant
|<nowiki>-1510772.498</nowiki>
|<nowiki>-1510762.046</nowiki>
|-
|Product
|<nowiki>-1510782.951</nowiki>
|<nowiki>-1510783.751</nowiki>
|-
|TS
|<nowiki>-1510663.669</nowiki>
|<nowiki>-1510670.285</nowiki>
|-
|E<sub>a</sub>
|108.8296005
|91.761225
|-
|ΔE
|<nowiki>-10.4521155</nowiki>
|<nowiki>-21.7050085</nowiki>
|}

While the activation energy (Ea) gives information about the minimum energy input required to drive the reaction forwards, the total energy difference (ΔE) allows the judgement of the energy of stabilisation achievable for each reaction. From the table we see that less Ea is required initially, as well as a larger extent of stabilisation if the reaction were in the endo approach (reasons for this discussed in the below section). Therefore, we can conclude that the '''Endo''' adduct is both the '''Kinetic''' and '''Thermodynamic''' product.

[[File:cool1.png|right|295x295px|thumb|Endo Orbital Overlap]]

<br />

==== Orbital Stereoelectronics ====

The endo reaction undergoes with dienophile benzoquinone sitting on top of the cyclopentadiene (Cp), which grants an additional opportunity for a favourable orbital interaction. As seen on the right, the p orbitals at the 2,3 position of Cp is within proximate distance to interact with the rear C=C π* orbitals of the dienophile, alongside the bond-forming front C=C π* orbitals. From the white arrows indicated, the Cp HOMO is also in correct phase to overlap with the second double bond of the Benzoquinone. This is known as a '''secondary orbital interaction''', a stabilising interaction which does not involve bond formation.

Therefore, by having a second double bond within the same molecule in the dienephile, as opposed to a simpler alkene (eg. ethene), the additional interaction available plays the role in attracting the diene to adapt the Endo position while approaching. This '''lowers the activation energy''' of the Endo pathway, therefore transition structures are more favoured to be endo despite the associated sterics hinderance thermodynamically. This shows diels-alder reactions are often '''kinetically driven'''.

<br />
<br />
<br />

== Exercise 3: Xylylene with Sulphur Dioxide ==

=== Reactant Approach via IRC ===
{| class="wikitable"
!Diels Alder Endo
!Diels Alder Exo
!Cheletropic
|-
|[[File:Endo_irc_animation_for_wiki.gif]]
|[[File:Exo_irc_animation_for_wiki.gif]]
|[[File:Chele_irc_animation_for_wiki.gif]]
|}

=== Reaction Analysis ===

==== Energetics and Profile ====
The reaction of concern in the exercise introduces a possibility of a third reaction alongside the two approaches from the Hetero Diels Alder, known as the Cheletropic reaction. Again, computationally-calculated data of Gibbs free energy will be useful here to judge and compare the different reaction paths available, the reaction profile below should also provide a much clearer representation of how the three reactions compare:

{| border="1" cellpadding="5" cellspacing="0" align="center"
!Energy(kJ/mol)
!Exo
!Endo
!Cheletropic
|-
|Reactant
|177.69384
|178.3790955
|186.3606155
|-
|Product
|56.3301025
|56.983852
|<nowiki>-0.005251</nowiki>
|-
|TS
|241.745538
|237.7626545
|260.08203
|-
|E<sub>a</sub>
|64.051698
|59.383559
|73.7214145
|-
|ΔE
|<nowiki>-121.3637375</nowiki>
|<nowiki>-121.3952435</nowiki>
|<nowiki>-186.3658665</nowiki>
|}

[[File:reactionnn.png|800px|center]]
With the lowest energy activation energy amongst all, the '''Endo''' pathway can be concluded to be the '''Kinetic product'''. In terms of the overall energy change, although very similar, endo also appears as the more thermodynamically favourable between the two Diels-Alder reactions. Though given the small margin of difference, such a statement should be treated with discretion. It is however very clear that the '''Cheletropic''' pathway is the '''Thermodynamic product''' overall over Endo and Exo. This margin of difference that Cheletropic reactions show owes to the relatively stable five-membered adduct, as opposed to a six-membered one.

Having identified the KE and TD products, reactions conditions as well as solvents can be altered in order to obtain a desired product specifically.

==== Reactant Transformation ====
Through studying the reaction visualisations from above, we can see that as the reactive butadiene fragment in xylene cyclizes, a conjugated system can been seen to establish at the rear ring. As the major driving force for all three reactions,which are all 2π electrons away from satisfying the Huckel rule of 4n+2 delocalised electrons, the aromatisation of xylyene provides sufficient aromatic stabilisation energy to the reactants to interact.

==== Pathway Alternative ====
A second Diels-Alder reaction possibility comes at the rear diene, as part of the 1,3 cyclohexadiene system. Compared to the Exo and Endo diels-alder reaction computed above, the clear inability to aromatise in this alternative pathway, where a bridged ring system will give rise to a sizable thermodymanic penalty for both orientation approaches.Though the bridged system does not incur significant additional themodynamic instability (because bonds formed and broken are identical to its aromatisable alternative, and that both S=O bonds in the products are pointing towards empty space), it does suffer from the following kinetic implication: The o-xylylene group, being originally a fully planar structure with a coplanar eight π-orbital system, is forced to distort from its conformation, as carbons at the 1,4 positions are essentially 'pushed' upwards, in order to accommodate the approaching sulpur dioxide. As this effect is present for both Exo and Endo apporaches, Kinetic unfavourability will also be realized across this alternative position for cyclisation.

== Conclusion ==
Throughout the exercises, recognising relationships of different calculations with the potential energy surface has been important in understanding what each step had meant. By grasping specific PES positions through calculations, useful information can be extracted for the different structures of concern (such as reactants,products and transition states). This has allowed energetic comparisons, molecular orbital interactions and reaction visualisation to be obtained and understood.

The most common calculation used was the minimisation, which is often used to obtain the lowest energy conformation of a molecule. From the PES surface, this is the global minimum as opposed to other local minimums, therefore approximating calculations were often ran beforehand to ensure the reliability of the obtained minimum values. Therefore, a standard protocol would be to perform a semi-empirical calculation (the rough approximation), before moving on to the B3LYP (the accurate calculation, a basis set based method involving both HF and DFT functions).

As transition states would also have zero gradients, second derivatives are required to differentiate between the two. Frequency calculations act as the key method of such verification, where a single imaginative force constant (the second derivative) would prove the achievement of a TS. This point should have all but one dimension amongst the 3N-6 dimensions minimised, leaving a maximum just a single dimension.

Given all the computation methods utilized throughout the task, it can be argued that the DFT-based B3LYP method is the most attractive: As although the quantum mechanical method DFT are able to produce relatively reliable approximations, this is in expense of poor results in terms of exchange correlations.The ab intito HF on the other hand, is highly effective in analytically solving exchange correlations, but as the method ruses electron positions, this requires higher degrees of freedom in the process of solving and thus suffers from longer computation times. Thus, putting both factors of accuracy and time penalty into perspective, as B3LYP which is able to solve exchange correlations accurately by using the same analytical approach as the HF , benefits from strengths of both methods mentioned above. Moreover, its accuracy is considered to have made up for its expensiveness in terms of time.

All in all, the applications used for this exercise has demonstrated just a small part of the capabilities in computation chemistry. Higher levels of accuracies (via basis sets) and calculations method (other Ab Initito implementations) has yet to be explored. Complex biological molecules modelling, reaction dynamics, excited electronic states just some other key examples where computations are of high utility to chemists.

== References ==

File:Hubert.png

2016-12-15T15:05:55Z

Htw14: Htw14 uploaded a new version of File:Hubert.png

User:Htw14

2016-12-15T14:59:30Z

Htw14: /* Quantitative MO Visualisations */

'''Computational Lab Year 3: Transition States and Reactivity'''
== Introduction ==

The exercise sets out to understand transition states of reactions, an aspect often difficult to study by experimental means. Through obtaining minimas and transition structures(TS) from energy-optimising computations, as well as further elucidating reaction pathways and trajectory approaches, the study ultimately aims to determine reactivity using energy profiles generated from computed data of studied molecules.

The topic of interest in this wiki concerns the Diels-Alder reaction, a reaction highly powerful in the construction of cyclic compounds within organic synthesis. It is important to understand beforehand that the reactions offers high levels of predictability through stereoselectivity, which would be beneficial in predicting transition structures prior to any computational studies.

Originated from the strict rules of orbital symmetry conservation, such reactions are performed in concerted fashion, meaning that configurations of both reactants will be fully retained in the product, and thus are stererospecific. (For example, a cis alkene will always yield a syn product).

The two terms that would be referred to frequently in this wiki are 'Exo' and 'Endo'. These refer to yet another type of stereoselectivty in Diels-Alder reactions, which governs the position adopted by dienophile substituents relative to the diene system. Such selectivity is attributed to secondary orbital interactions, which will be discussed further in below sections.

Through combining mechanistic and stereoelectronic knowledge of the reaction with computation techniques (such as energy determination and MO visualisations), we would be able to correctly determine the specific diastereomers from reactions.This grants us the ability of disastreoselection control of mutiple stereogenic centered products, which is a powerful skill in organic synthesis.

In the following exercises, three different instances of the reaction are studied.

== Exercise 1: Butadiene with Ethene ==

===Molecular Orbitals===

==== MO Diagram ====
As shown below, the diagram illustrates what a standard MO diagram for a general Diels Alder reaction would have. Though butadiene and ethene are used to provide frontier orbitals as reactants here, according to substituents of different reactants, the relative energies of reactants and product orbitals in specific reactions may differ.
[[Image:Hubert.png|499x499px|center|thumb|Butadiene-Ethene Diels Alder Reaction]]

==== Symmetry requirement ====
For a successful reaction, symmetries of the HOMO and the LUMO must match, while violations to this will lead a forbidden reaction. These orbitals generated from wavefunctions can be either symmetric or anti-symmetric and are distinguished by transformations under an inversion operation. If symmetric with respect to inversion, such an orbital is assigned the label of gerade(g), and vice versa for anti-symmetric cases, which are ungerade(u). As shown in the MO diagram, frontier orbitals Ψ<sub>2</sub> of butadiene and Ψ<sub>2</sub> of ethene are both symmetric (gerade) and thus an interaction is allowed. An interaction of Ψ<sub>3</sub>(u) instead of Ψ<sub>2</sub>(g)<sub> </sub>however, would be forbidden as only g-g u-u interactions are allowed. The expression of the overlapping intergral shown below illustrates this concept mathematically:

[[File:Hubert_equ.png|center|150px]]

When S=0, this implies a zero overlap, while any allowed overlap would have an S value in between 0 and 1.

==== Quantitative MO Visualisations ====
All MOs shown below correlates to the above MO diagram. It can be seen that the varying degree of delocalisation and shapes of the HOMOs and LUMOs correspond well with the phases of orbitals shown in the MO diagram.

{| class="wikitable"
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=== Reaction Analysis ===

==== Bond Formation and Lengths ====
As shown in the diagram below, relationships between atoms can be divided into three categories, two of which being covalent interactions (sp3 and sp2) whilst the other a non-bonding interaction. These distances can be defined as the covalent and Van der Waal radius respectively. Typically, the distances (in Angstroms Å) between two carbon atoms of these relationships are as follows: Van de Waal (VdW): '''1.680 Å'''<ref name=":0">Pauling, Linus and L. O. Brockway. "Carbon—Carbon Bond Distances. The Electron Diffraction Investigation Of Ethane, Propane, Isobutane, Neopentane, Cyclopropane, Cyclopentane, Cyclohexane, Allene, Ethylene, Isobutene, Tetramethylethylene, Mesitylene, And Hexamethylbenzene. Revised Values Of Covalent Radii". ''Journal of the American Chemical Society'' 59.7 (1937): 1223-1236. Web.</ref>; Covalent sp3: '''1.537 Å'''<ref name=":0" />; Covalent sp2 : '''1.347 Å'''<ref name=":0" />

[[File:Trythis.png|center|330x330px]] <br style="clear:left">
{|border="1" cellpadding="5" cellspacing="0" align="center"
!Bonds
!Reactant
!Type
!TS
!Process
!Product
!Type
|-
|1,2
|1.33539
|sp<sup>2</sup>
|1.37978
|Lengthen
|1.50090
|sp<sup>3</sup>
|-
|2,3
|1.46834
|sp<sup>3</sup>
|1.41107
|Shorten
|1.33784
|sp<sup>2</sup>
|-
|3,4
|1.33539
|sp<sup>2</sup>
|1.37978
|Lengthen
|1.50090
|sp<sup>3</sup>
|-
|4,5
|3.41334
|2VdW
|2.11461
|Shorten
|1.54040
|sp<sup>3</sup>
|-
|5,6
|1.32736
|sp<sup>2</sup>
|1.38177
|Lengthen
|1.54091
|sp<sup>3</sup>
|-
|6,1
|3.41425
|2VdW
|2.11469
|Shorten
|1.54041
|sp<sup>3</sup>
|}

Firstly, it should be noted that the sum two Van de Waal radius of neigbouring atoms measures the internuclear distance of two non-interacting atoms prior to bond formation, hence it should be longer than those of bonding (i.e. sp2 and sp3). From the table, we can see that a smooth transition from non-bonding to sp3(shortening), sp3 to sp2 (shortening) and sp2 to sp3 (lengthening), thus turning the butadiene and alkene in to a cyclohexene in the process. As the alternating lengthening and shortening process of the bonds is yet another feature of the concerted process in the Diels Alder, the computated transiton state structure supports mechanism.

==== Vibrational Modes ====

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The vibrational mode corresponding to the transition state agrees with the concerted nature of the Diels-Alder reaction, during which two sp3 bonds are formed synchronously. The resultant single imgainary frequency proves that a maximum has been reached in only one dimension on the potential energy surface, which verifies the existence of a transition structure. Next to it shows the lowest positive frequency mode,where the two reactants rotates in opposite directions of a 2D plane. In comparison, the illustration on the right is non-reactive and minute in energy, which matches well with a typical rotational mode.

== Exercise 2: Benzoquinone with Cyclopentadiene ==

=== Molecular Orbitals ===
The orbitals below illustrates the four key resultant molecular orbitals (MO1-MO4) from the MO diagram shown in Exercise 1, where in this case are derived from the four frontier orbitals of cyclopentadiene (the diene equivalent) and the two from Benzoquinone (the alkene equivalent). Both the Exo and Endo reactions computated in this exercise are cases of normal electron demand, the most common electronic interaction in Diels-Alder reactions, where the dienophile is electron poor while the diene being electron rich. On the other hand, inverse demand suggests the opposite, thus allowing that the alkene HOMO to be at a close energy level to interact strongly the the diene LUMO. If this is the case MO1 (referring to the MO Diagram above) will be the HOMO of the transition state as opposed to MO2. By examining phases from both HOMOs of the Exo and Endo approaches, this is evident that the reaction is not a case inverse demand, as both corresponded to the phase pattern that a MO2 equivalent would possess. We can therefore conclude that the reaction is in '''normal electron demand'''.

==== Exo Approach Key MOs ====
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==== Endo Approach Key MOs ====
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=== Reaction Analysis ===

==== Energetics and Pathway ====

Through analysing resultant thermodynamic data extracted from optimised structures of the reactants, products and transition states, a highly useful comparison could be made between the two reactant approaches. This will ultimately allow us to predict the reaction outcome expected in reality, thus showing the importance of computational techniques in chemistry. Such data is shown below:

{|border="1" cellpadding="5" cellspacing="0" align="center"
!Energy(kJ/mol)
!Exo
!Endo
|-
|Reactant
|<nowiki>-1510772.498</nowiki>
|<nowiki>-1510762.046</nowiki>
|-
|Product
|<nowiki>-1510782.951</nowiki>
|<nowiki>-1510783.751</nowiki>
|-
|TS
|<nowiki>-1510663.669</nowiki>
|<nowiki>-1510670.285</nowiki>
|-
|E<sub>a</sub>
|108.8296005
|91.761225
|-
|ΔE
|<nowiki>-10.4521155</nowiki>
|<nowiki>-21.7050085</nowiki>
|}

While the activation energy (Ea) gives information about the minimum energy input required to drive the reaction forwards, the total energy difference (ΔE) allows the judgement of the energy of stabilisation achievable for each reaction. From the table we see that less Ea is required initially, as well as a larger extent of stabilisation if the reaction were in the endo approach (reasons for this discussed in the below section). Therefore, we can conclude that the '''Endo''' adduct is both the '''Kinetic''' and '''Thermodynamic''' product.

[[File:cool1.png|right|295x295px|thumb|Endo Orbital Overlap]]

<br />

==== Orbital Stereoelectronics ====

The endo reaction undergoes with dienophile benzoquinone sitting on top of the cyclopentadiene (Cp), which grants an additional opportunity for a favourable orbital interaction. As seen on the right, the p orbitals at the 2,3 position of Cp is within proximate distance to interact with the rear C=C π* orbitals of the dienophile, alongside the bond-forming front C=C π* orbitals. From the white arrows indicated, the Cp HOMO is also in correct phase to overlap with the second double bond of the Benzoquinone. This is known as a '''secondary orbital interaction''', a stabilising interaction which does not involve bond formation.

Therefore, by having a second double bond within the same molecule in the dienephile, as opposed to a simpler alkene (eg. ethene), the additional interaction available plays the role in attracting the diene to adapt the Endo position while approaching. This '''lowers the activation energy''' of the Endo pathway, therefore transition structures are more favoured to be endo despite the associated sterics hinderance thermodynamically. This shows diels-alder reactions are often '''kinetically driven'''.

<br />
<br />
<br />

== Exercise 3: Xylylene with Sulphur Dioxide ==

=== Reactant Approach via IRC ===
{| class="wikitable"
!Diels Alder Endo
!Diels Alder Exo
!Cheletropic
|-
|[[File:Endo_irc_animation_for_wiki.gif]]
|[[File:Exo_irc_animation_for_wiki.gif]]
|[[File:Chele_irc_animation_for_wiki.gif]]
|}

=== Reaction Analysis ===

==== Energetics and Profile ====
The reaction of concern in the exercise introduces a possibility of a third reaction alongside the two approaches from the Hetero Diels Alder, known as the Cheletropic reaction. Again, computationally-calculated data of Gibbs free energy will be useful here to judge and compare the different reaction paths available, the reaction profile below should also provide a much clearer representation of how the three reactions compare:

{| border="1" cellpadding="5" cellspacing="0" align="center"
!Energy(kJ/mol)
!Exo
!Endo
!Cheletropic
|-
|Reactant
|177.69384
|178.3790955
|186.3606155
|-
|Product
|56.3301025
|56.983852
|<nowiki>-0.005251</nowiki>
|-
|TS
|241.745538
|237.7626545
|260.08203
|-
|E<sub>a</sub>
|64.051698
|59.383559
|73.7214145
|-
|ΔE
|<nowiki>-121.3637375</nowiki>
|<nowiki>-121.3952435</nowiki>
|<nowiki>-186.3658665</nowiki>
|}

[[File:reactionnn.png|800px|center]]
With the lowest energy activation energy amongst all, the '''Endo''' pathway can be concluded to be the '''Kinetic product'''. In terms of the overall energy change, although very similar, endo also appears as the more thermodynamically favourable between the two Diels-Alder reactions. Though given the small margin of difference, such a statement should be treated with discretion. It is however very clear that the '''Cheletropic''' pathway is the '''Thermodynamic product''' overall over Endo and Exo. This margin of difference that Cheletropic reactions show owes to the relatively stable five-membered adduct, as opposed to a six-membered one.

Having identified the KE and TD products, reactions conditions as well as solvents can be altered in order to obtain a desired product specifically.

==== Reactant Transformation ====
Through studying the reaction visualisations from above, we can see that as the reactive butadiene fragment in xylene cyclizes, a conjugated system can been seen to establish at the rear ring. As the major driving force for all three reactions,which are all 2π electrons away from satisfying the Huckel rule of 4n+2 delocalised electrons, the aromatisation of xylyene provides sufficient aromatic stabilisation energy to the reactants to interact.

==== Pathway Alternative ====
A second Diels-Alder reaction possibility comes at the rear diene, as part of the 1,3 cyclohexadiene system. Compared to the Exo and Endo diels-alder reaction computed above, the clear inability to aromatise in this alternative pathway, where a bridged ring system will give rise to a sizable thermodymanic penalty for both orientation approaches.Though the bridged system does not incur significant additional themodynamic instability (because bonds formed and broken are identical to its aromatisable alternative, and that both S=O bonds in the products are pointing towards empty space), it does suffer from the following kinetic implication: The o-xylylene group, being originally a fully planar structure with a coplanar eight π-orbital system, is forced to distort from its conformation, as carbons at the 1,4 positions are essentially 'pushed' upwards, in order to accommodate the approaching sulpur dioxide. As this effect is present for both Exo and Endo apporaches, Kinetic unfavourability will also be realized across this alternative position for cyclisation.

== Conclusion ==
Throughout the exercises, recognising relationships of different calculations with the potential energy surface has been important in understanding what each step had meant. By grasping specific PES positions through calculations, useful information can be extracted for the different structures of concern (such as reactants,products and transition states). This has allowed energetic comparisons, molecular orbital interactions and reaction visualisation to be obtained and understood.

The most common calculation used was the minimisation, which is often used to obtain the lowest energy conformation of a molecule. From the PES surface, this is the global minimum as opposed to other local minimums, therefore approximating calculations were often ran beforehand to ensure the reliability of the obtained minimum values. Therefore, a standard protocol would be to perform a semi-empirical calculation (the rough approximation), before moving on to the B3LYP (the accurate calculation, a basis set based method involving both HF and DFT functions).

As transition states would also have zero gradients, second derivatives are required to differentiate between the two. Frequency calculations act as the key method of such verification, where a single imaginative force constant (the second derivative) would prove the achievement of a TS. This point should have all but one dimension amongst the 3N-6 dimensions minimised, leaving a maximum just a single dimension.

Given all the computation methods utilized throughout the task, it can be argued that the DFT-based B3LYP method is the most attractive: As although the quantum mechanical method DFT are able to produce relatively reliable approximations, this is in expense of poor results in terms of exchange correlations.The ab intito HF on the other hand, is highly effective in analytically solving exchange correlations, but as the method ruses electron positions, this requires higher degrees of freedom in the process of solving and thus suffers from longer computation times. Thus, putting both factors of accuracy and time penalty into perspective, as B3LYP which is able to solve exchange correlations accurately by using the same analytical approach as the HF , benefits from strengths of both methods mentioned above. Moreover, its accuracy is considered to have made up for its expensiveness in terms of time.

All in all, the applications used for this exercise has demonstrated just a small part of the capabilities in computation chemistry. Higher levels of accuracies (via basis sets) and calculations method (other Ab Initito implementations) has yet to be explored. Complex biological molecules modelling, reaction dynamics, excited electronic states just some other key examples where computations are of high utility to chemists.

== References ==

User:Htw14

2016-12-15T14:46:39Z

Htw14: /* Quantitative MO Visualisations */

'''Computational Lab Year 3: Transition States and Reactivity'''
== Introduction ==

The exercise sets out to understand transition states of reactions, an aspect often difficult to study by experimental means. Through obtaining minimas and transition structures(TS) from energy-optimising computations, as well as further elucidating reaction pathways and trajectory approaches, the study ultimately aims to determine reactivity using energy profiles generated from computed data of studied molecules.

The topic of interest in this wiki concerns the Diels-Alder reaction, a reaction highly powerful in the construction of cyclic compounds within organic synthesis. It is important to understand beforehand that the reactions offers high levels of predictability through stereoselectivity, which would be beneficial in predicting transition structures prior to any computational studies.

Originated from the strict rules of orbital symmetry conservation, such reactions are performed in concerted fashion, meaning that configurations of both reactants will be fully retained in the product, and thus are stererospecific. (For example, a cis alkene will always yield a syn product).

The two terms that would be referred to frequently in this wiki are 'Exo' and 'Endo'. These refer to yet another type of stereoselectivty in Diels-Alder reactions, which governs the position adopted by dienophile substituents relative to the diene system. Such selectivity is attributed to secondary orbital interactions, which will be discussed further in below sections.

Through combining mechanistic and stereoelectronic knowledge of the reaction with computation techniques (such as energy determination and MO visualisations), we would be able to correctly determine the specific diastereomers from reactions.This grants us the ability of disastreoselection control of mutiple stereogenic centered products, which is a powerful skill in organic synthesis.

In the following exercises, three different instances of the reaction are studied.

== Exercise 1: Butadiene with Ethene ==

===Molecular Orbitals===

==== MO Diagram ====
As shown below, the diagram illustrates what a standard MO diagram for a general Diels Alder reaction would have. Though butadiene and ethene are used to provide frontier orbitals as reactants here, according to substituents of different reactants, the relative energies of reactants and product orbitals in specific reactions may differ.
[[Image:Hubert.png|499x499px|center|thumb|Butadiene-Ethene Diels Alder Reaction]]

==== Symmetry requirement ====
For a successful reaction, symmetries of the HOMO and the LUMO must match, while violations to this will lead a forbidden reaction. These orbitals generated from wavefunctions can be either symmetric or anti-symmetric and are distinguished by transformations under an inversion operation. If symmetric with respect to inversion, such an orbital is assigned the label of gerade(g), and vice versa for anti-symmetric cases, which are ungerade(u). As shown in the MO diagram, frontier orbitals Ψ<sub>2</sub> of butadiene and Ψ<sub>2</sub> of ethene are both symmetric (gerade) and thus an interaction is allowed. An interaction of Ψ<sub>3</sub>(u) instead of Ψ<sub>2</sub>(g)<sub> </sub>however, would be forbidden as only g-g u-u interactions are allowed. The expression of the overlapping intergral shown below illustrates this concept mathematically:

[[File:Hubert_equ.png|center|150px]]

When S=0, this implies a zero overlap, while any allowed overlap would have an S value in between 0 and 1.

==== Quantitative MO Visualisations ====
All MOs shown below correlates to the above MO diagram. It can be seen that the varying degree of delocalisation and shapes of the HOMOs and LUMOs correspond well with the phases of orbitals shown in the MO diagram.

{| class="wikitable"
|-
|
<jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 14; mo 16; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
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<title>MO1 from TS</title>
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</jmol>
|
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<title>MO2 HOMO from TS</title>
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=== Reaction Analysis ===

==== Bond Formation and Lengths ====
As shown in the diagram below, relationships between atoms can be divided into three categories, two of which being covalent interactions (sp3 and sp2) whilst the other a non-bonding interaction. These distances can be defined as the covalent and Van der Waal radius respectively. Typically, the distances (in Angstroms Å) between two carbon atoms of these relationships are as follows: Van de Waal (VdW): '''1.680 Å'''<ref name=":0">Pauling, Linus and L. O. Brockway. "Carbon—Carbon Bond Distances. The Electron Diffraction Investigation Of Ethane, Propane, Isobutane, Neopentane, Cyclopropane, Cyclopentane, Cyclohexane, Allene, Ethylene, Isobutene, Tetramethylethylene, Mesitylene, And Hexamethylbenzene. Revised Values Of Covalent Radii". ''Journal of the American Chemical Society'' 59.7 (1937): 1223-1236. Web.</ref>; Covalent sp3: '''1.537 Å'''<ref name=":0" />; Covalent sp2 : '''1.347 Å'''<ref name=":0" />

[[File:Trythis.png|center|330x330px]] <br style="clear:left">
{|border="1" cellpadding="5" cellspacing="0" align="center"
!Bonds
!Reactant
!Type
!TS
!Process
!Product
!Type
|-
|1,2
|1.33539
|sp<sup>2</sup>
|1.37978
|Lengthen
|1.50090
|sp<sup>3</sup>
|-
|2,3
|1.46834
|sp<sup>3</sup>
|1.41107
|Shorten
|1.33784
|sp<sup>2</sup>
|-
|3,4
|1.33539
|sp<sup>2</sup>
|1.37978
|Lengthen
|1.50090
|sp<sup>3</sup>
|-
|4,5
|3.41334
|2VdW
|2.11461
|Shorten
|1.54040
|sp<sup>3</sup>
|-
|5,6
|1.32736
|sp<sup>2</sup>
|1.38177
|Lengthen
|1.54091
|sp<sup>3</sup>
|-
|6,1
|3.41425
|2VdW
|2.11469
|Shorten
|1.54041
|sp<sup>3</sup>
|}

Firstly, it should be noted that the sum two Van de Waal radius of neigbouring atoms measures the internuclear distance of two non-interacting atoms prior to bond formation, hence it should be longer than those of bonding (i.e. sp2 and sp3). From the table, we can see that a smooth transition from non-bonding to sp3(shortening), sp3 to sp2 (shortening) and sp2 to sp3 (lengthening), thus turning the butadiene and alkene in to a cyclohexene in the process. As the alternating lengthening and shortening process of the bonds is yet another feature of the concerted process in the Diels Alder, the computated transiton state structure supports mechanism.

==== Vibrational Modes ====

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The vibrational mode corresponding to the transition state agrees with the concerted nature of the Diels-Alder reaction, during which two sp3 bonds are formed synchronously. The resultant single imgainary frequency proves that a maximum has been reached in only one dimension on the potential energy surface, which verifies the existence of a transition structure. Next to it shows the lowest positive frequency mode,where the two reactants rotates in opposite directions of a 2D plane. In comparison, the illustration on the right is non-reactive and minute in energy, which matches well with a typical rotational mode.

== Exercise 2: Benzoquinone with Cyclopentadiene ==

=== Molecular Orbitals ===
The orbitals below illustrates the four key resultant molecular orbitals (MO1-MO4) from the MO diagram shown in Exercise 1, where in this case are derived from the four frontier orbitals of cyclopentadiene (the diene equivalent) and the two from Benzoquinone (the alkene equivalent). Both the Exo and Endo reactions computated in this exercise are cases of normal electron demand, the most common electronic interaction in Diels-Alder reactions, where the dienophile is electron poor while the diene being electron rich. On the other hand, inverse demand suggests the opposite, thus allowing that the alkene HOMO to be at a close energy level to interact strongly the the diene LUMO. If this is the case MO1 (referring to the MO Diagram above) will be the HOMO of the transition state as opposed to MO2. By examining phases from both HOMOs of the Exo and Endo approaches, this is evident that the reaction is not a case inverse demand, as both corresponded to the phase pattern that a MO2 equivalent would possess. We can therefore conclude that the reaction is in '''normal electron demand'''.

==== Exo Approach Key MOs ====
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==== Endo Approach Key MOs ====
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=== Reaction Analysis ===

==== Energetics and Pathway ====

Through analysing resultant thermodynamic data extracted from optimised structures of the reactants, products and transition states, a highly useful comparison could be made between the two reactant approaches. This will ultimately allow us to predict the reaction outcome expected in reality, thus showing the importance of computational techniques in chemistry. Such data is shown below:

{|border="1" cellpadding="5" cellspacing="0" align="center"
!Energy(kJ/mol)
!Exo
!Endo
|-
|Reactant
|<nowiki>-1510772.498</nowiki>
|<nowiki>-1510762.046</nowiki>
|-
|Product
|<nowiki>-1510782.951</nowiki>
|<nowiki>-1510783.751</nowiki>
|-
|TS
|<nowiki>-1510663.669</nowiki>
|<nowiki>-1510670.285</nowiki>
|-
|E<sub>a</sub>
|108.8296005
|91.761225
|-
|ΔE
|<nowiki>-10.4521155</nowiki>
|<nowiki>-21.7050085</nowiki>
|}

While the activation energy (Ea) gives information about the minimum energy input required to drive the reaction forwards, the total energy difference (ΔE) allows the judgement of the energy of stabilisation achievable for each reaction. From the table we see that less Ea is required initially, as well as a larger extent of stabilisation if the reaction were in the endo approach (reasons for this discussed in the below section). Therefore, we can conclude that the '''Endo''' adduct is both the '''Kinetic''' and '''Thermodynamic''' product.

[[File:cool1.png|right|295x295px|thumb|Endo Orbital Overlap]]

<br />

==== Orbital Stereoelectronics ====

The endo reaction undergoes with dienophile benzoquinone sitting on top of the cyclopentadiene (Cp), which grants an additional opportunity for a favourable orbital interaction. As seen on the right, the p orbitals at the 2,3 position of Cp is within proximate distance to interact with the rear C=C π* orbitals of the dienophile, alongside the bond-forming front C=C π* orbitals. From the white arrows indicated, the Cp HOMO is also in correct phase to overlap with the second double bond of the Benzoquinone. This is known as a '''secondary orbital interaction''', a stabilising interaction which does not involve bond formation.

Therefore, by having a second double bond within the same molecule in the dienephile, as opposed to a simpler alkene (eg. ethene), the additional interaction available plays the role in attracting the diene to adapt the Endo position while approaching. This '''lowers the activation energy''' of the Endo pathway, therefore transition structures are more favoured to be endo despite the associated sterics hinderance thermodynamically. This shows diels-alder reactions are often '''kinetically driven'''.

<br />
<br />
<br />

== Exercise 3: Xylylene with Sulphur Dioxide ==

=== Reactant Approach via IRC ===
{| class="wikitable"
!Diels Alder Endo
!Diels Alder Exo
!Cheletropic
|-
|[[File:Endo_irc_animation_for_wiki.gif]]
|[[File:Exo_irc_animation_for_wiki.gif]]
|[[File:Chele_irc_animation_for_wiki.gif]]
|}

=== Reaction Analysis ===

==== Energetics and Profile ====
The reaction of concern in the exercise introduces a possibility of a third reaction alongside the two approaches from the Hetero Diels Alder, known as the Cheletropic reaction. Again, computationally-calculated data of Gibbs free energy will be useful here to judge and compare the different reaction paths available, the reaction profile below should also provide a much clearer representation of how the three reactions compare:

{| border="1" cellpadding="5" cellspacing="0" align="center"
!Energy(kJ/mol)
!Exo
!Endo
!Cheletropic
|-
|Reactant
|177.69384
|178.3790955
|186.3606155
|-
|Product
|56.3301025
|56.983852
|<nowiki>-0.005251</nowiki>
|-
|TS
|241.745538
|237.7626545
|260.08203
|-
|E<sub>a</sub>
|64.051698
|59.383559
|73.7214145
|-
|ΔE
|<nowiki>-121.3637375</nowiki>
|<nowiki>-121.3952435</nowiki>
|<nowiki>-186.3658665</nowiki>
|}

[[File:reactionnn.png|800px|center]]
With the lowest energy activation energy amongst all, the '''Endo''' pathway can be concluded to be the '''Kinetic product'''. In terms of the overall energy change, although very similar, endo also appears as the more thermodynamically favourable between the two Diels-Alder reactions. Though given the small margin of difference, such a statement should be treated with discretion. It is however very clear that the '''Cheletropic''' pathway is the '''Thermodynamic product''' overall over Endo and Exo. This margin of difference that Cheletropic reactions show owes to the relatively stable five-membered adduct, as opposed to a six-membered one.

Having identified the KE and TD products, reactions conditions as well as solvents can be altered in order to obtain a desired product specifically.

==== Reactant Transformation ====
Through studying the reaction visualisations from above, we can see that as the reactive butadiene fragment in xylene cyclizes, a conjugated system can been seen to establish at the rear ring. As the major driving force for all three reactions,which are all 2π electrons away from satisfying the Huckel rule of 4n+2 delocalised electrons, the aromatisation of xylyene provides sufficient aromatic stabilisation energy to the reactants to interact.

==== Pathway Alternative ====
A second Diels-Alder reaction possibility comes at the rear diene, as part of the 1,3 cyclohexadiene system. Compared to the Exo and Endo diels-alder reaction computed above, the clear inability to aromatise in this alternative pathway, where a bridged ring system will give rise to a sizable thermodymanic penalty for both orientation approaches.Though the bridged system does not incur significant additional themodynamic instability (because bonds formed and broken are identical to its aromatisable alternative, and that both S=O bonds in the products are pointing towards empty space), it does suffer from the following kinetic implication: The o-xylylene group, being originally a fully planar structure with a coplanar eight π-orbital system, is forced to distort from its conformation, as carbons at the 1,4 positions are essentially 'pushed' upwards, in order to accommodate the approaching sulpur dioxide. As this effect is present for both Exo and Endo apporaches, Kinetic unfavourability will also be realized across this alternative position for cyclisation.

== Conclusion ==
Throughout the exercises, recognising relationships of different calculations with the potential energy surface has been important in understanding what each step had meant. By grasping specific PES positions through calculations, useful information can be extracted for the different structures of concern (such as reactants,products and transition states). This has allowed energetic comparisons, molecular orbital interactions and reaction visualisation to be obtained and understood.

The most common calculation used was the minimisation, which is often used to obtain the lowest energy conformation of a molecule. From the PES surface, this is the global minimum as opposed to other local minimums, therefore approximating calculations were often ran beforehand to ensure the reliability of the obtained minimum values. Therefore, a standard protocol would be to perform a semi-empirical calculation (the rough approximation), before moving on to the B3LYP (the accurate calculation, a basis set based method involving both HF and DFT functions).

As transition states would also have zero gradients, second derivatives are required to differentiate between the two. Frequency calculations act as the key method of such verification, where a single imaginative force constant (the second derivative) would prove the achievement of a TS. This point should have all but one dimension amongst the 3N-6 dimensions minimised, leaving a maximum just a single dimension.

Given all the computation methods utilized throughout the task, it can be argued that the DFT-based B3LYP method is the most attractive: As although the quantum mechanical method DFT are able to produce relatively reliable approximations, this is in expense of poor results in terms of exchange correlations.The ab intito HF on the other hand, is highly effective in analytically solving exchange correlations, but as the method ruses electron positions, this requires higher degrees of freedom in the process of solving and thus suffers from longer computation times. Thus, putting both factors of accuracy and time penalty into perspective, as B3LYP which is able to solve exchange correlations accurately by using the same analytical approach as the HF , benefits from strengths of both methods mentioned above. Moreover, its accuracy is considered to have made up for its expensiveness in terms of time.

All in all, the applications used for this exercise has demonstrated just a small part of the capabilities in computation chemistry. Higher levels of accuracies (via basis sets) and calculations method (other Ab Initito implementations) has yet to be explored. Complex biological molecules modelling, reaction dynamics, excited electronic states just some other key examples where computations are of high utility to chemists.

== References ==

User:Htw14

2016-12-01T16:12:32Z

Htw14: /* Endo Approach Key MOs */

'''Computational Lab Year 3: Transition States and Reactivity'''
== Introduction ==

The exercise sets out to understand transition states of reactions, an aspect often difficult to study by experimental means. Through obtaining minimas and transition structures(TS) from energy-optimising computations, as well as further elucidating reaction pathways and trajectory approaches, the study ultimately aims to determine reactivity using energy profiles generated from computed data of studied molecules.

The topic of interest in this wiki concerns the Diels-Alder reaction, a reaction highly powerful in the construction of cyclic compounds within organic synthesis. It is important to understand beforehand that the reactions offers high levels of predictability through stereoselectivity, which would be beneficial in predicting transition structures prior to any computational studies.

Originated from the strict rules of orbital symmetry conservation, such reactions are performed in concerted fashion, meaning that configurations of both reactants will be fully retained in the product, and thus are stererospecific. (For example, a cis alkene will always yield a syn product).

The two terms that would be referred to frequently in this wiki are 'Exo' and 'Endo'. These refer to yet another type of stereoselectivty in Diels-Alder reactions, which governs the position adopted by dienophile substituents relative to the diene system. Such selectivity is attributed to secondary orbital interactions, which will be discussed further in below sections.

Through combining mechanistic and stereoelectronic knowledge of the reaction with computation techniques (such as energy determination and MO visualisations), we would be able to correctly determine the specific diastereomers from reactions.This grants us the ability of disastreoselection control of mutiple stereogenic centered products, which is a powerful skill in organic synthesis.

In the following exercises, three different instances of the reaction are studied.

== Exercise 1: Butadiene with Ethene ==

===Molecular Orbitals===

==== MO Diagram ====
As shown below, the diagram illustrates what a standard MO diagram for a general Diels Alder reaction would have. Though butadiene and ethene are used to provide frontier orbitals as reactants here, according to substituents of different reactants, the relative energies of reactants and product orbitals in specific reactions may differ.
[[Image:Hubert.png|499x499px|center|thumb|Butadiene-Ethene Diels Alder Reaction]]

==== Symmetry requirement ====
For a successful reaction, symmetries of the HOMO and the LUMO must match, while violations to this will lead a forbidden reaction. These orbitals generated from wavefunctions can be either symmetric or anti-symmetric and are distinguished by transformations under an inversion operation. If symmetric with respect to inversion, such an orbital is assigned the label of gerade(g), and vice versa for anti-symmetric cases, which are ungerade(u). As shown in the MO diagram, frontier orbitals Ψ<sub>2</sub> of butadiene and Ψ<sub>2</sub> of ethene are both symmetric (gerade) and thus an interaction is allowed. An interaction of Ψ<sub>3</sub>(u) instead of Ψ<sub>2</sub>(g)<sub> </sub>however, would be forbidden as only g-g u-u interactions are allowed. The expression of the overlapping intergral shown below illustrates this concept mathematically:

[[File:Hubert_equ.png|center|150px]]

When S=0, this implies a zero overlap, while any allowed overlap would have an S value in between 0 and 1.

==== Quantitative MO Visualisations ====
All MOs shown below correlates to the above MO diagram. It can be seen that the varying degree of delocalisation and shapes of the HOMOs and LUMOs correspond well with the phases of orbitals shown in the MO diagram.

{| class="wikitable"
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=== Reaction Analysis ===

==== Bond Formation and Lengths ====
As shown in the diagram below, relationships between atoms can be divided into three categories, two of which being covalent interactions (sp3 and sp2) whilst the other a non-bonding interaction. These distances can be defined as the covalent and Van der Waal radius respectively. Typically, the distances (in Angstroms Å) between two carbon atoms of these relationships are as follows: Van de Waal (VdW): '''1.680 Å'''<ref name=":0">Pauling, Linus and L. O. Brockway. "Carbon—Carbon Bond Distances. The Electron Diffraction Investigation Of Ethane, Propane, Isobutane, Neopentane, Cyclopropane, Cyclopentane, Cyclohexane, Allene, Ethylene, Isobutene, Tetramethylethylene, Mesitylene, And Hexamethylbenzene. Revised Values Of Covalent Radii". ''Journal of the American Chemical Society'' 59.7 (1937): 1223-1236. Web.</ref>; Covalent sp3: '''1.537 Å'''<ref name=":0" />; Covalent sp2 : '''1.347 Å'''<ref name=":0" />

[[File:Trythis.png|center|330x330px]] <br style="clear:left">
{|border="1" cellpadding="5" cellspacing="0" align="center"
!Bonds
!Reactant
!Type
!TS
!Process
!Product
!Type
|-
|1,2
|1.33539
|sp<sup>2</sup>
|1.37978
|Lengthen
|1.50090
|sp<sup>3</sup>
|-
|2,3
|1.46834
|sp<sup>3</sup>
|1.41107
|Shorten
|1.33784
|sp<sup>2</sup>
|-
|3,4
|1.33539
|sp<sup>2</sup>
|1.37978
|Lengthen
|1.50090
|sp<sup>3</sup>
|-
|4,5
|3.41334
|2VdW
|2.11461
|Shorten
|1.54040
|sp<sup>3</sup>
|-
|5,6
|1.32736
|sp<sup>2</sup>
|1.38177
|Lengthen
|1.54091
|sp<sup>3</sup>
|-
|6,1
|3.41425
|2VdW
|2.11469
|Shorten
|1.54041
|sp<sup>3</sup>
|}

Firstly, it should be noted that the sum two Van de Waal radius of neigbouring atoms measures the internuclear distance of two non-interacting atoms prior to bond formation, hence it should be longer than those of bonding (i.e. sp2 and sp3). From the table, we can see that a smooth transition from non-bonding to sp3(shortening), sp3 to sp2 (shortening) and sp2 to sp3 (lengthening), thus turning the butadiene and alkene in to a cyclohexene in the process. As the alternating lengthening and shortening process of the bonds is yet another feature of the concerted process in the Diels Alder, the computated transiton state structure supports mechanism.

==== Vibrational Modes ====

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The vibrational mode corresponding to the transition state agrees with the concerted nature of the Diels-Alder reaction, during which two sp3 bonds are formed synchronously. The resultant single imgainary frequency proves that a maximum has been reached in only one dimension on the potential energy surface, which verifies the existence of a transition structure. Next to it shows the lowest positive frequency mode,where the two reactants rotates in opposite directions of a 2D plane. In comparison, the illustration on the right is non-reactive and minute in energy, which matches well with a typical rotational mode.

== Exercise 2: Benzoquinone with Cyclopentadiene ==

=== Molecular Orbitals ===
The orbitals below illustrates the four key resultant molecular orbitals (MO1-MO4) from the MO diagram shown in Exercise 1, where in this case are derived from the four frontier orbitals of cyclopentadiene (the diene equivalent) and the two from Benzoquinone (the alkene equivalent). Both the Exo and Endo reactions computated in this exercise are cases of normal electron demand, the most common electronic interaction in Diels-Alder reactions, where the dienophile is electron poor while the diene being electron rich. On the other hand, inverse demand suggests the opposite, thus allowing that the alkene HOMO to be at a close energy level to interact strongly the the diene LUMO. If this is the case MO1 (referring to the MO Diagram above) will be the HOMO of the transition state as opposed to MO2. By examining phases from both HOMOs of the Exo and Endo approaches, this is evident that the reaction is not a case inverse demand, as both corresponded to the phase pattern that a MO2 equivalent would possess. We can therefore conclude that the reaction is in '''normal electron demand'''.

==== Exo Approach Key MOs ====
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==== Endo Approach Key MOs ====
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<title>MO4</title>
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=== Reaction Analysis ===

==== Energetics and Pathway ====

Through analysing resultant thermodynamic data extracted from optimised structures of the reactants, products and transition states, a highly useful comparison could be made between the two reactant approaches. This will ultimately allow us to predict the reaction outcome expected in reality, thus showing the importance of computational techniques in chemistry. Such data is shown below:

{|border="1" cellpadding="5" cellspacing="0" align="center"
!Energy(kJ/mol)
!Exo
!Endo
|-
|Reactant
|<nowiki>-1510772.498</nowiki>
|<nowiki>-1510762.046</nowiki>
|-
|Product
|<nowiki>-1510782.951</nowiki>
|<nowiki>-1510783.751</nowiki>
|-
|TS
|<nowiki>-1510663.669</nowiki>
|<nowiki>-1510670.285</nowiki>
|-
|E<sub>a</sub>
|108.8296005
|91.761225
|-
|ΔE
|<nowiki>-10.4521155</nowiki>
|<nowiki>-21.7050085</nowiki>
|}

While the activation energy (Ea) gives information about the minimum energy input required to drive the reaction forwards, the total energy difference (ΔE) allows the judgement of the energy of stabilisation achievable for each reaction. From the table we see that less Ea is required initially, as well as a larger extent of stabilisation if the reaction were in the endo approach (reasons for this discussed in the below section). Therefore, we can conclude that the '''Endo''' adduct is both the '''Kinetic''' and '''Thermodynamic''' product.

[[File:cool1.png|right|295x295px|thumb|Endo Orbital Overlap]]

<br />

==== Orbital Stereoelectronics ====

The endo reaction undergoes with dienophile benzoquinone sitting on top of the cyclopentadiene (Cp), which grants an additional opportunity for a favourable orbital interaction. As seen on the right, the p orbitals at the 2,3 position of Cp is within proximate distance to interact with the rear C=C π* orbitals of the dienophile, alongside the bond-forming front C=C π* orbitals. From the white arrows indicated, the Cp HOMO is also in correct phase to overlap with the second double bond of the Benzoquinone. This is known as a '''secondary orbital interaction''', a stabilising interaction which does not involve bond formation.

Therefore, by having a second double bond within the same molecule in the dienephile, as opposed to a simpler alkene (eg. ethene), the additional interaction available plays the role in attracting the diene to adapt the Endo position while approaching. This '''lowers the activation energy''' of the Endo pathway, therefore transition structures are more favoured to be endo despite the associated sterics hinderance thermodynamically. This shows diels-alder reactions are often '''kinetically driven'''.

<br />
<br />
<br />

== Exercise 3: Xylylene with Sulphur Dioxide ==

=== Reactant Approach via IRC ===
{| class="wikitable"
!Diels Alder Endo
!Diels Alder Exo
!Cheletropic
|-
|[[File:Endo_irc_animation_for_wiki.gif]]
|[[File:Exo_irc_animation_for_wiki.gif]]
|[[File:Chele_irc_animation_for_wiki.gif]]
|}

=== Reaction Analysis ===

==== Energetics and Profile ====
The reaction of concern in the exercise introduces a possibility of a third reaction alongside the two approaches from the Hetero Diels Alder, known as the Cheletropic reaction. Again, computationally-calculated data of Gibbs free energy will be useful here to judge and compare the different reaction paths available, the reaction profile below should also provide a much clearer representation of how the three reactions compare:

{| border="1" cellpadding="5" cellspacing="0" align="center"
!Energy(kJ/mol)
!Exo
!Endo
!Cheletropic
|-
|Reactant
|177.69384
|178.3790955
|186.3606155
|-
|Product
|56.3301025
|56.983852
|<nowiki>-0.005251</nowiki>
|-
|TS
|241.745538
|237.7626545
|260.08203
|-
|E<sub>a</sub>
|64.051698
|59.383559
|73.7214145
|-
|ΔE
|<nowiki>-121.3637375</nowiki>
|<nowiki>-121.3952435</nowiki>
|<nowiki>-186.3658665</nowiki>
|}

[[File:reactionnn.png|800px|center]]
With the lowest energy activation energy amongst all, the '''Endo''' pathway can be concluded to be the '''Kinetic product'''. In terms of the overall energy change, although very similar, endo also appears as the more thermodynamically favourable between the two Diels-Alder reactions. Though given the small margin of difference, such a statement should be treated with discretion. It is however very clear that the '''Cheletropic''' pathway is the '''Thermodynamic product''' overall over Endo and Exo. This margin of difference that Cheletropic reactions show owes to the relatively stable five-membered adduct, as opposed to a six-membered one.

Having identified the KE and TD products, reactions conditions as well as solvents can be altered in order to obtain a desired product specifically.

==== Reactant Transformation ====
Through studying the reaction visualisations from above, we can see that as the reactive butadiene fragment in xylene cyclizes, a conjugated system can been seen to establish at the rear ring. As the major driving force for all three reactions,which are all 2π electrons away from satisfying the Huckel rule of 4n+2 delocalised electrons, the aromatisation of xylyene provides sufficient aromatic stabilisation energy to the reactants to interact.

==== Pathway Alternative ====
A second Diels-Alder reaction possibility comes at the rear diene, as part of the 1,3 cyclohexadiene system. Compared to the Exo and Endo diels-alder reaction computed above, the clear inability to aromatise in this alternative pathway, where a bridged ring system will give rise to a sizable thermodymanic penalty for both orientation approaches.Though the bridged system does not incur significant additional themodynamic instability (because bonds formed and broken are identical to its aromatisable alternative, and that both S=O bonds in the products are pointing towards empty space), it does suffer from the following kinetic implication: The o-xylylene group, being originally a fully planar structure with a coplanar eight π-orbital system, is forced to distort from its conformation, as carbons at the 1,4 positions are essentially 'pushed' upwards, in order to accommodate the approaching sulpur dioxide. As this effect is present for both Exo and Endo apporaches, Kinetic unfavourability will also be realized across this alternative position for cyclisation.

== Conclusion ==
Throughout the exercises, recognising relationships of different calculations with the potential energy surface has been important in understanding what each step had meant. By grasping specific PES positions through calculations, useful information can be extracted for the different structures of concern (such as reactants,products and transition states). This has allowed energetic comparisons, molecular orbital interactions and reaction visualisation to be obtained and understood.

The most common calculation used was the minimisation, which is often used to obtain the lowest energy conformation of a molecule. From the PES surface, this is the global minimum as opposed to other local minimums, therefore approximating calculations were often ran beforehand to ensure the reliability of the obtained minimum values. Therefore, a standard protocol would be to perform a semi-empirical calculation (the rough approximation), before moving on to the B3LYP (the accurate calculation, a basis set based method involving both HF and DFT functions).

As transition states would also have zero gradients, second derivatives are required to differentiate between the two. Frequency calculations act as the key method of such verification, where a single imaginative force constant (the second derivative) would prove the achievement of a TS. This point should have all but one dimension amongst the 3N-6 dimensions minimised, leaving a maximum just a single dimension.

Given all the computation methods utilized throughout the task, it can be argued that the DFT-based B3LYP method is the most attractive: As although the quantum mechanical method DFT are able to produce relatively reliable approximations, this is in expense of poor results in terms of exchange correlations.The ab intito HF on the other hand, is highly effective in analytically solving exchange correlations, but as the method ruses electron positions, this requires higher degrees of freedom in the process of solving and thus suffers from longer computation times. Thus, putting both factors of accuracy and time penalty into perspective, as B3LYP which is able to solve exchange correlations accurately by using the same analytical approach as the HF , benefits from strengths of both methods mentioned above. Moreover, its accuracy is considered to have made up for its expensiveness in terms of time.

All in all, the applications used for this exercise has demonstrated just a small part of the capabilities in computation chemistry. Higher levels of accuracies (via basis sets) and calculations method (other Ab Initito implementations) has yet to be explored. Complex biological molecules modelling, reaction dynamics, excited electronic states just some other key examples where computations are of high utility to chemists.

== References ==

User:Htw14

2016-12-01T16:12:13Z

Htw14: /* Exo Approach Key MOs */

'''Computational Lab Year 3: Transition States and Reactivity'''
== Introduction ==

The exercise sets out to understand transition states of reactions, an aspect often difficult to study by experimental means. Through obtaining minimas and transition structures(TS) from energy-optimising computations, as well as further elucidating reaction pathways and trajectory approaches, the study ultimately aims to determine reactivity using energy profiles generated from computed data of studied molecules.

The topic of interest in this wiki concerns the Diels-Alder reaction, a reaction highly powerful in the construction of cyclic compounds within organic synthesis. It is important to understand beforehand that the reactions offers high levels of predictability through stereoselectivity, which would be beneficial in predicting transition structures prior to any computational studies.

Originated from the strict rules of orbital symmetry conservation, such reactions are performed in concerted fashion, meaning that configurations of both reactants will be fully retained in the product, and thus are stererospecific. (For example, a cis alkene will always yield a syn product).

The two terms that would be referred to frequently in this wiki are 'Exo' and 'Endo'. These refer to yet another type of stereoselectivty in Diels-Alder reactions, which governs the position adopted by dienophile substituents relative to the diene system. Such selectivity is attributed to secondary orbital interactions, which will be discussed further in below sections.

Through combining mechanistic and stereoelectronic knowledge of the reaction with computation techniques (such as energy determination and MO visualisations), we would be able to correctly determine the specific diastereomers from reactions.This grants us the ability of disastreoselection control of mutiple stereogenic centered products, which is a powerful skill in organic synthesis.

In the following exercises, three different instances of the reaction are studied.

== Exercise 1: Butadiene with Ethene ==

===Molecular Orbitals===

==== MO Diagram ====
As shown below, the diagram illustrates what a standard MO diagram for a general Diels Alder reaction would have. Though butadiene and ethene are used to provide frontier orbitals as reactants here, according to substituents of different reactants, the relative energies of reactants and product orbitals in specific reactions may differ.
[[Image:Hubert.png|499x499px|center|thumb|Butadiene-Ethene Diels Alder Reaction]]

==== Symmetry requirement ====
For a successful reaction, symmetries of the HOMO and the LUMO must match, while violations to this will lead a forbidden reaction. These orbitals generated from wavefunctions can be either symmetric or anti-symmetric and are distinguished by transformations under an inversion operation. If symmetric with respect to inversion, such an orbital is assigned the label of gerade(g), and vice versa for anti-symmetric cases, which are ungerade(u). As shown in the MO diagram, frontier orbitals Ψ<sub>2</sub> of butadiene and Ψ<sub>2</sub> of ethene are both symmetric (gerade) and thus an interaction is allowed. An interaction of Ψ<sub>3</sub>(u) instead of Ψ<sub>2</sub>(g)<sub> </sub>however, would be forbidden as only g-g u-u interactions are allowed. The expression of the overlapping intergral shown below illustrates this concept mathematically:

[[File:Hubert_equ.png|center|150px]]

When S=0, this implies a zero overlap, while any allowed overlap would have an S value in between 0 and 1.

==== Quantitative MO Visualisations ====
All MOs shown below correlates to the above MO diagram. It can be seen that the varying degree of delocalisation and shapes of the HOMOs and LUMOs correspond well with the phases of orbitals shown in the MO diagram.

{| class="wikitable"
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=== Reaction Analysis ===

==== Bond Formation and Lengths ====
As shown in the diagram below, relationships between atoms can be divided into three categories, two of which being covalent interactions (sp3 and sp2) whilst the other a non-bonding interaction. These distances can be defined as the covalent and Van der Waal radius respectively. Typically, the distances (in Angstroms Å) between two carbon atoms of these relationships are as follows: Van de Waal (VdW): '''1.680 Å'''<ref name=":0">Pauling, Linus and L. O. Brockway. "Carbon—Carbon Bond Distances. The Electron Diffraction Investigation Of Ethane, Propane, Isobutane, Neopentane, Cyclopropane, Cyclopentane, Cyclohexane, Allene, Ethylene, Isobutene, Tetramethylethylene, Mesitylene, And Hexamethylbenzene. Revised Values Of Covalent Radii". ''Journal of the American Chemical Society'' 59.7 (1937): 1223-1236. Web.</ref>; Covalent sp3: '''1.537 Å'''<ref name=":0" />; Covalent sp2 : '''1.347 Å'''<ref name=":0" />

[[File:Trythis.png|center|330x330px]] <br style="clear:left">
{|border="1" cellpadding="5" cellspacing="0" align="center"
!Bonds
!Reactant
!Type
!TS
!Process
!Product
!Type
|-
|1,2
|1.33539
|sp<sup>2</sup>
|1.37978
|Lengthen
|1.50090
|sp<sup>3</sup>
|-
|2,3
|1.46834
|sp<sup>3</sup>
|1.41107
|Shorten
|1.33784
|sp<sup>2</sup>
|-
|3,4
|1.33539
|sp<sup>2</sup>
|1.37978
|Lengthen
|1.50090
|sp<sup>3</sup>
|-
|4,5
|3.41334
|2VdW
|2.11461
|Shorten
|1.54040
|sp<sup>3</sup>
|-
|5,6
|1.32736
|sp<sup>2</sup>
|1.38177
|Lengthen
|1.54091
|sp<sup>3</sup>
|-
|6,1
|3.41425
|2VdW
|2.11469
|Shorten
|1.54041
|sp<sup>3</sup>
|}

Firstly, it should be noted that the sum two Van de Waal radius of neigbouring atoms measures the internuclear distance of two non-interacting atoms prior to bond formation, hence it should be longer than those of bonding (i.e. sp2 and sp3). From the table, we can see that a smooth transition from non-bonding to sp3(shortening), sp3 to sp2 (shortening) and sp2 to sp3 (lengthening), thus turning the butadiene and alkene in to a cyclohexene in the process. As the alternating lengthening and shortening process of the bonds is yet another feature of the concerted process in the Diels Alder, the computated transiton state structure supports mechanism.

==== Vibrational Modes ====

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The vibrational mode corresponding to the transition state agrees with the concerted nature of the Diels-Alder reaction, during which two sp3 bonds are formed synchronously. The resultant single imgainary frequency proves that a maximum has been reached in only one dimension on the potential energy surface, which verifies the existence of a transition structure. Next to it shows the lowest positive frequency mode,where the two reactants rotates in opposite directions of a 2D plane. In comparison, the illustration on the right is non-reactive and minute in energy, which matches well with a typical rotational mode.

== Exercise 2: Benzoquinone with Cyclopentadiene ==

=== Molecular Orbitals ===
The orbitals below illustrates the four key resultant molecular orbitals (MO1-MO4) from the MO diagram shown in Exercise 1, where in this case are derived from the four frontier orbitals of cyclopentadiene (the diene equivalent) and the two from Benzoquinone (the alkene equivalent). Both the Exo and Endo reactions computated in this exercise are cases of normal electron demand, the most common electronic interaction in Diels-Alder reactions, where the dienophile is electron poor while the diene being electron rich. On the other hand, inverse demand suggests the opposite, thus allowing that the alkene HOMO to be at a close energy level to interact strongly the the diene LUMO. If this is the case MO1 (referring to the MO Diagram above) will be the HOMO of the transition state as opposed to MO2. By examining phases from both HOMOs of the Exo and Endo approaches, this is evident that the reaction is not a case inverse demand, as both corresponded to the phase pattern that a MO2 equivalent would possess. We can therefore conclude that the reaction is in '''normal electron demand'''.

==== Exo Approach Key MOs ====
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==== Endo Approach Key MOs ====
insert 4 here

=== Reaction Analysis ===

==== Energetics and Pathway ====

Through analysing resultant thermodynamic data extracted from optimised structures of the reactants, products and transition states, a highly useful comparison could be made between the two reactant approaches. This will ultimately allow us to predict the reaction outcome expected in reality, thus showing the importance of computational techniques in chemistry. Such data is shown below:

{|border="1" cellpadding="5" cellspacing="0" align="center"
!Energy(kJ/mol)
!Exo
!Endo
|-
|Reactant
|<nowiki>-1510772.498</nowiki>
|<nowiki>-1510762.046</nowiki>
|-
|Product
|<nowiki>-1510782.951</nowiki>
|<nowiki>-1510783.751</nowiki>
|-
|TS
|<nowiki>-1510663.669</nowiki>
|<nowiki>-1510670.285</nowiki>
|-
|E<sub>a</sub>
|108.8296005
|91.761225
|-
|ΔE
|<nowiki>-10.4521155</nowiki>
|<nowiki>-21.7050085</nowiki>
|}

While the activation energy (Ea) gives information about the minimum energy input required to drive the reaction forwards, the total energy difference (ΔE) allows the judgement of the energy of stabilisation achievable for each reaction. From the table we see that less Ea is required initially, as well as a larger extent of stabilisation if the reaction were in the endo approach (reasons for this discussed in the below section). Therefore, we can conclude that the '''Endo''' adduct is both the '''Kinetic''' and '''Thermodynamic''' product.

[[File:cool1.png|right|295x295px|thumb|Endo Orbital Overlap]]

<br />

==== Orbital Stereoelectronics ====

The endo reaction undergoes with dienophile benzoquinone sitting on top of the cyclopentadiene (Cp), which grants an additional opportunity for a favourable orbital interaction. As seen on the right, the p orbitals at the 2,3 position of Cp is within proximate distance to interact with the rear C=C π* orbitals of the dienophile, alongside the bond-forming front C=C π* orbitals. From the white arrows indicated, the Cp HOMO is also in correct phase to overlap with the second double bond of the Benzoquinone. This is known as a '''secondary orbital interaction''', a stabilising interaction which does not involve bond formation.

Therefore, by having a second double bond within the same molecule in the dienephile, as opposed to a simpler alkene (eg. ethene), the additional interaction available plays the role in attracting the diene to adapt the Endo position while approaching. This '''lowers the activation energy''' of the Endo pathway, therefore transition structures are more favoured to be endo despite the associated sterics hinderance thermodynamically. This shows diels-alder reactions are often '''kinetically driven'''.

<br />
<br />
<br />

== Exercise 3: Xylylene with Sulphur Dioxide ==

=== Reactant Approach via IRC ===
{| class="wikitable"
!Diels Alder Endo
!Diels Alder Exo
!Cheletropic
|-
|[[File:Endo_irc_animation_for_wiki.gif]]
|[[File:Exo_irc_animation_for_wiki.gif]]
|[[File:Chele_irc_animation_for_wiki.gif]]
|}

=== Reaction Analysis ===

==== Energetics and Profile ====
The reaction of concern in the exercise introduces a possibility of a third reaction alongside the two approaches from the Hetero Diels Alder, known as the Cheletropic reaction. Again, computationally-calculated data of Gibbs free energy will be useful here to judge and compare the different reaction paths available, the reaction profile below should also provide a much clearer representation of how the three reactions compare:

{| border="1" cellpadding="5" cellspacing="0" align="center"
!Energy(kJ/mol)
!Exo
!Endo
!Cheletropic
|-
|Reactant
|177.69384
|178.3790955
|186.3606155
|-
|Product
|56.3301025
|56.983852
|<nowiki>-0.005251</nowiki>
|-
|TS
|241.745538
|237.7626545
|260.08203
|-
|E<sub>a</sub>
|64.051698
|59.383559
|73.7214145
|-
|ΔE
|<nowiki>-121.3637375</nowiki>
|<nowiki>-121.3952435</nowiki>
|<nowiki>-186.3658665</nowiki>
|}

[[File:reactionnn.png|800px|center]]
With the lowest energy activation energy amongst all, the '''Endo''' pathway can be concluded to be the '''Kinetic product'''. In terms of the overall energy change, although very similar, endo also appears as the more thermodynamically favourable between the two Diels-Alder reactions. Though given the small margin of difference, such a statement should be treated with discretion. It is however very clear that the '''Cheletropic''' pathway is the '''Thermodynamic product''' overall over Endo and Exo. This margin of difference that Cheletropic reactions show owes to the relatively stable five-membered adduct, as opposed to a six-membered one.

Having identified the KE and TD products, reactions conditions as well as solvents can be altered in order to obtain a desired product specifically.

==== Reactant Transformation ====
Through studying the reaction visualisations from above, we can see that as the reactive butadiene fragment in xylene cyclizes, a conjugated system can been seen to establish at the rear ring. As the major driving force for all three reactions,which are all 2π electrons away from satisfying the Huckel rule of 4n+2 delocalised electrons, the aromatisation of xylyene provides sufficient aromatic stabilisation energy to the reactants to interact.

==== Pathway Alternative ====
A second Diels-Alder reaction possibility comes at the rear diene, as part of the 1,3 cyclohexadiene system. Compared to the Exo and Endo diels-alder reaction computed above, the clear inability to aromatise in this alternative pathway, where a bridged ring system will give rise to a sizable thermodymanic penalty for both orientation approaches.Though the bridged system does not incur significant additional themodynamic instability (because bonds formed and broken are identical to its aromatisable alternative, and that both S=O bonds in the products are pointing towards empty space), it does suffer from the following kinetic implication: The o-xylylene group, being originally a fully planar structure with a coplanar eight π-orbital system, is forced to distort from its conformation, as carbons at the 1,4 positions are essentially 'pushed' upwards, in order to accommodate the approaching sulpur dioxide. As this effect is present for both Exo and Endo apporaches, Kinetic unfavourability will also be realized across this alternative position for cyclisation.

== Conclusion ==
Throughout the exercises, recognising relationships of different calculations with the potential energy surface has been important in understanding what each step had meant. By grasping specific PES positions through calculations, useful information can be extracted for the different structures of concern (such as reactants,products and transition states). This has allowed energetic comparisons, molecular orbital interactions and reaction visualisation to be obtained and understood.

The most common calculation used was the minimisation, which is often used to obtain the lowest energy conformation of a molecule. From the PES surface, this is the global minimum as opposed to other local minimums, therefore approximating calculations were often ran beforehand to ensure the reliability of the obtained minimum values. Therefore, a standard protocol would be to perform a semi-empirical calculation (the rough approximation), before moving on to the B3LYP (the accurate calculation, a basis set based method involving both HF and DFT functions).

As transition states would also have zero gradients, second derivatives are required to differentiate between the two. Frequency calculations act as the key method of such verification, where a single imaginative force constant (the second derivative) would prove the achievement of a TS. This point should have all but one dimension amongst the 3N-6 dimensions minimised, leaving a maximum just a single dimension.

Given all the computation methods utilized throughout the task, it can be argued that the DFT-based B3LYP method is the most attractive: As although the quantum mechanical method DFT are able to produce relatively reliable approximations, this is in expense of poor results in terms of exchange correlations.The ab intito HF on the other hand, is highly effective in analytically solving exchange correlations, but as the method ruses electron positions, this requires higher degrees of freedom in the process of solving and thus suffers from longer computation times. Thus, putting both factors of accuracy and time penalty into perspective, as B3LYP which is able to solve exchange correlations accurately by using the same analytical approach as the HF , benefits from strengths of both methods mentioned above. Moreover, its accuracy is considered to have made up for its expensiveness in terms of time.

All in all, the applications used for this exercise has demonstrated just a small part of the capabilities in computation chemistry. Higher levels of accuracies (via basis sets) and calculations method (other Ab Initito implementations) has yet to be explored. Complex biological molecules modelling, reaction dynamics, excited electronic states just some other key examples where computations are of high utility to chemists.

== References ==

User:Htw14

2016-12-01T16:11:36Z

Htw14: /* Vibrational Modes */

'''Computational Lab Year 3: Transition States and Reactivity'''
== Introduction ==

The exercise sets out to understand transition states of reactions, an aspect often difficult to study by experimental means. Through obtaining minimas and transition structures(TS) from energy-optimising computations, as well as further elucidating reaction pathways and trajectory approaches, the study ultimately aims to determine reactivity using energy profiles generated from computed data of studied molecules.

The topic of interest in this wiki concerns the Diels-Alder reaction, a reaction highly powerful in the construction of cyclic compounds within organic synthesis. It is important to understand beforehand that the reactions offers high levels of predictability through stereoselectivity, which would be beneficial in predicting transition structures prior to any computational studies.

Originated from the strict rules of orbital symmetry conservation, such reactions are performed in concerted fashion, meaning that configurations of both reactants will be fully retained in the product, and thus are stererospecific. (For example, a cis alkene will always yield a syn product).

The two terms that would be referred to frequently in this wiki are 'Exo' and 'Endo'. These refer to yet another type of stereoselectivty in Diels-Alder reactions, which governs the position adopted by dienophile substituents relative to the diene system. Such selectivity is attributed to secondary orbital interactions, which will be discussed further in below sections.

Through combining mechanistic and stereoelectronic knowledge of the reaction with computation techniques (such as energy determination and MO visualisations), we would be able to correctly determine the specific diastereomers from reactions.This grants us the ability of disastreoselection control of mutiple stereogenic centered products, which is a powerful skill in organic synthesis.

In the following exercises, three different instances of the reaction are studied.

== Exercise 1: Butadiene with Ethene ==

===Molecular Orbitals===

==== MO Diagram ====
As shown below, the diagram illustrates what a standard MO diagram for a general Diels Alder reaction would have. Though butadiene and ethene are used to provide frontier orbitals as reactants here, according to substituents of different reactants, the relative energies of reactants and product orbitals in specific reactions may differ.
[[Image:Hubert.png|499x499px|center|thumb|Butadiene-Ethene Diels Alder Reaction]]

==== Symmetry requirement ====
For a successful reaction, symmetries of the HOMO and the LUMO must match, while violations to this will lead a forbidden reaction. These orbitals generated from wavefunctions can be either symmetric or anti-symmetric and are distinguished by transformations under an inversion operation. If symmetric with respect to inversion, such an orbital is assigned the label of gerade(g), and vice versa for anti-symmetric cases, which are ungerade(u). As shown in the MO diagram, frontier orbitals Ψ<sub>2</sub> of butadiene and Ψ<sub>2</sub> of ethene are both symmetric (gerade) and thus an interaction is allowed. An interaction of Ψ<sub>3</sub>(u) instead of Ψ<sub>2</sub>(g)<sub> </sub>however, would be forbidden as only g-g u-u interactions are allowed. The expression of the overlapping intergral shown below illustrates this concept mathematically:

[[File:Hubert_equ.png|center|150px]]

When S=0, this implies a zero overlap, while any allowed overlap would have an S value in between 0 and 1.

==== Quantitative MO Visualisations ====
All MOs shown below correlates to the above MO diagram. It can be seen that the varying degree of delocalisation and shapes of the HOMOs and LUMOs correspond well with the phases of orbitals shown in the MO diagram.

{| class="wikitable"
|-
|
<jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 2; mo 16; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>DA_STEP_2_PM6_OPT_MO_VER.LOG</uploadedFileContents>
<title>MO1 from TS</title>
</jmolApplet>
</jmol>
|
<jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 2; mo 17; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>DA_STEP_2_PM6_OPT_MO_VER.LOG</uploadedFileContents>
<title>MO2 HOMO from TS</title>
</jmolApplet>
</jmol>
|
<jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 2; mo 18; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>DA_STEP_2_PM6_OPT_MO_VER.LOG</uploadedFileContents>
<title>MO3 LUMO from TSs</title>
</jmolApplet>
</jmol>
|
<jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 2; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>DA_STEP_2_PM6_OPT_MO_VER.LOG</uploadedFileContents>
<title>MO4 from TS</title>
</jmolApplet>
</jmol>
|-
|
<jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 2; mo 6; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>REFINED_ALKENE_PM6.LOG</uploadedFileContents>
<title>Ψ1 HOMO from Ethene FOs</title>
</jmolApplet>
</jmol>
|
<jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 2; mo 7; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>REFINED_ALKENE_PM6.LOG</uploadedFileContents>
<title>Ψ2 LUMO from Ethene FOs</title>
</jmolApplet>
</jmol>
|
<jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 2; mo 11; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>BUTADIENE_PM6_MO_VER.LOG</uploadedFileContents>
<title>Ψ2 HOMO from Butadiene FOs</title>
</jmolApplet>
</jmol>
|
<jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 2; mo 12; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>BUTADIENE_PM6_MO_VER.LOG</uploadedFileContents>
<title>Ψ3 LUMO from Butadiene FOs</title>
</jmolApplet>
</jmol>
|}

=== Reaction Analysis ===

==== Bond Formation and Lengths ====
As shown in the diagram below, relationships between atoms can be divided into three categories, two of which being covalent interactions (sp3 and sp2) whilst the other a non-bonding interaction. These distances can be defined as the covalent and Van der Waal radius respectively. Typically, the distances (in Angstroms Å) between two carbon atoms of these relationships are as follows: Van de Waal (VdW): '''1.680 Å'''<ref name=":0">Pauling, Linus and L. O. Brockway. "Carbon—Carbon Bond Distances. The Electron Diffraction Investigation Of Ethane, Propane, Isobutane, Neopentane, Cyclopropane, Cyclopentane, Cyclohexane, Allene, Ethylene, Isobutene, Tetramethylethylene, Mesitylene, And Hexamethylbenzene. Revised Values Of Covalent Radii". ''Journal of the American Chemical Society'' 59.7 (1937): 1223-1236. Web.</ref>; Covalent sp3: '''1.537 Å'''<ref name=":0" />; Covalent sp2 : '''1.347 Å'''<ref name=":0" />

[[File:Trythis.png|center|330x330px]] <br style="clear:left">
{|border="1" cellpadding="5" cellspacing="0" align="center"
!Bonds
!Reactant
!Type
!TS
!Process
!Product
!Type
|-
|1,2
|1.33539
|sp<sup>2</sup>
|1.37978
|Lengthen
|1.50090
|sp<sup>3</sup>
|-
|2,3
|1.46834
|sp<sup>3</sup>
|1.41107
|Shorten
|1.33784
|sp<sup>2</sup>
|-
|3,4
|1.33539
|sp<sup>2</sup>
|1.37978
|Lengthen
|1.50090
|sp<sup>3</sup>
|-
|4,5
|3.41334
|2VdW
|2.11461
|Shorten
|1.54040
|sp<sup>3</sup>
|-
|5,6
|1.32736
|sp<sup>2</sup>
|1.38177
|Lengthen
|1.54091
|sp<sup>3</sup>
|-
|6,1
|3.41425
|2VdW
|2.11469
|Shorten
|1.54041
|sp<sup>3</sup>
|}

Firstly, it should be noted that the sum two Van de Waal radius of neigbouring atoms measures the internuclear distance of two non-interacting atoms prior to bond formation, hence it should be longer than those of bonding (i.e. sp2 and sp3). From the table, we can see that a smooth transition from non-bonding to sp3(shortening), sp3 to sp2 (shortening) and sp2 to sp3 (lengthening), thus turning the butadiene and alkene in to a cyclohexene in the process. As the alternating lengthening and shortening process of the bonds is yet another feature of the concerted process in the Diels Alder, the computated transiton state structure supports mechanism.

==== Vibrational Modes ====

{| class="wikitable"
|
<jmol>
<jmolApplet>
<title>TS reactive vibrational mode</title><color>white</color><size>300</size>
<script>frame 15;vectors 4;vectors scale 5.0;color vectors red;vibration 10;
</script>
<uploadedFileContents>DA_STEP_2_PM6_OPT_sucess.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|
<jmol>
<jmolApplet>
<title>Lowest Frequency mode: Non-reactive twist</title><color>white</color><size>300</size>
<script>frame 16;vectors 4;vectors scale 5.0;color vectors red;vibration 10;
</script>
<uploadedFileContents>DA_STEP_2_PM6_OPT_sucess.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

The vibrational mode corresponding to the transition state agrees with the concerted nature of the Diels-Alder reaction, during which two sp3 bonds are formed synchronously. The resultant single imgainary frequency proves that a maximum has been reached in only one dimension on the potential energy surface, which verifies the existence of a transition structure. Next to it shows the lowest positive frequency mode,where the two reactants rotates in opposite directions of a 2D plane. In comparison, the illustration on the right is non-reactive and minute in energy, which matches well with a typical rotational mode.

== Exercise 2: Benzoquinone with Cyclopentadiene ==

=== Molecular Orbitals ===
The orbitals below illustrates the four key resultant molecular orbitals (MO1-MO4) from the MO diagram shown in Exercise 1, where in this case are derived from the four frontier orbitals of cyclopentadiene (the diene equivalent) and the two from Benzoquinone (the alkene equivalent). Both the Exo and Endo reactions computated in this exercise are cases of normal electron demand, the most common electronic interaction in Diels-Alder reactions, where the dienophile is electron poor while the diene being electron rich. On the other hand, inverse demand suggests the opposite, thus allowing that the alkene HOMO to be at a close energy level to interact strongly the the diene LUMO. If this is the case MO1 (referring to the MO Diagram above) will be the HOMO of the transition state as opposed to MO2. By examining phases from both HOMOs of the Exo and Endo approaches, this is evident that the reaction is not a case inverse demand, as both corresponded to the phase pattern that a MO2 equivalent would possess. We can therefore conclude that the reaction is in '''normal electron demand'''.

==== Exo Approach Key MOs ====
insert 4 here

==== Endo Approach Key MOs ====
insert 4 here

=== Reaction Analysis ===

==== Energetics and Pathway ====

Through analysing resultant thermodynamic data extracted from optimised structures of the reactants, products and transition states, a highly useful comparison could be made between the two reactant approaches. This will ultimately allow us to predict the reaction outcome expected in reality, thus showing the importance of computational techniques in chemistry. Such data is shown below:

{|border="1" cellpadding="5" cellspacing="0" align="center"
!Energy(kJ/mol)
!Exo
!Endo
|-
|Reactant
|<nowiki>-1510772.498</nowiki>
|<nowiki>-1510762.046</nowiki>
|-
|Product
|<nowiki>-1510782.951</nowiki>
|<nowiki>-1510783.751</nowiki>
|-
|TS
|<nowiki>-1510663.669</nowiki>
|<nowiki>-1510670.285</nowiki>
|-
|E<sub>a</sub>
|108.8296005
|91.761225
|-
|ΔE
|<nowiki>-10.4521155</nowiki>
|<nowiki>-21.7050085</nowiki>
|}

While the activation energy (Ea) gives information about the minimum energy input required to drive the reaction forwards, the total energy difference (ΔE) allows the judgement of the energy of stabilisation achievable for each reaction. From the table we see that less Ea is required initially, as well as a larger extent of stabilisation if the reaction were in the endo approach (reasons for this discussed in the below section). Therefore, we can conclude that the '''Endo''' adduct is both the '''Kinetic''' and '''Thermodynamic''' product.

[[File:cool1.png|right|295x295px|thumb|Endo Orbital Overlap]]

<br />

==== Orbital Stereoelectronics ====

The endo reaction undergoes with dienophile benzoquinone sitting on top of the cyclopentadiene (Cp), which grants an additional opportunity for a favourable orbital interaction. As seen on the right, the p orbitals at the 2,3 position of Cp is within proximate distance to interact with the rear C=C π* orbitals of the dienophile, alongside the bond-forming front C=C π* orbitals. From the white arrows indicated, the Cp HOMO is also in correct phase to overlap with the second double bond of the Benzoquinone. This is known as a '''secondary orbital interaction''', a stabilising interaction which does not involve bond formation.

Therefore, by having a second double bond within the same molecule in the dienephile, as opposed to a simpler alkene (eg. ethene), the additional interaction available plays the role in attracting the diene to adapt the Endo position while approaching. This '''lowers the activation energy''' of the Endo pathway, therefore transition structures are more favoured to be endo despite the associated sterics hinderance thermodynamically. This shows diels-alder reactions are often '''kinetically driven'''.

<br />
<br />
<br />

== Exercise 3: Xylylene with Sulphur Dioxide ==

=== Reactant Approach via IRC ===
{| class="wikitable"
!Diels Alder Endo
!Diels Alder Exo
!Cheletropic
|-
|[[File:Endo_irc_animation_for_wiki.gif]]
|[[File:Exo_irc_animation_for_wiki.gif]]
|[[File:Chele_irc_animation_for_wiki.gif]]
|}

=== Reaction Analysis ===

==== Energetics and Profile ====
The reaction of concern in the exercise introduces a possibility of a third reaction alongside the two approaches from the Hetero Diels Alder, known as the Cheletropic reaction. Again, computationally-calculated data of Gibbs free energy will be useful here to judge and compare the different reaction paths available, the reaction profile below should also provide a much clearer representation of how the three reactions compare:

{| border="1" cellpadding="5" cellspacing="0" align="center"
!Energy(kJ/mol)
!Exo
!Endo
!Cheletropic
|-
|Reactant
|177.69384
|178.3790955
|186.3606155
|-
|Product
|56.3301025
|56.983852
|<nowiki>-0.005251</nowiki>
|-
|TS
|241.745538
|237.7626545
|260.08203
|-
|E<sub>a</sub>
|64.051698
|59.383559
|73.7214145
|-
|ΔE
|<nowiki>-121.3637375</nowiki>
|<nowiki>-121.3952435</nowiki>
|<nowiki>-186.3658665</nowiki>
|}

[[File:reactionnn.png|800px|center]]
With the lowest energy activation energy amongst all, the '''Endo''' pathway can be concluded to be the '''Kinetic product'''. In terms of the overall energy change, although very similar, endo also appears as the more thermodynamically favourable between the two Diels-Alder reactions. Though given the small margin of difference, such a statement should be treated with discretion. It is however very clear that the '''Cheletropic''' pathway is the '''Thermodynamic product''' overall over Endo and Exo. This margin of difference that Cheletropic reactions show owes to the relatively stable five-membered adduct, as opposed to a six-membered one.

Having identified the KE and TD products, reactions conditions as well as solvents can be altered in order to obtain a desired product specifically.

==== Reactant Transformation ====
Through studying the reaction visualisations from above, we can see that as the reactive butadiene fragment in xylene cyclizes, a conjugated system can been seen to establish at the rear ring. As the major driving force for all three reactions,which are all 2π electrons away from satisfying the Huckel rule of 4n+2 delocalised electrons, the aromatisation of xylyene provides sufficient aromatic stabilisation energy to the reactants to interact.

==== Pathway Alternative ====
A second Diels-Alder reaction possibility comes at the rear diene, as part of the 1,3 cyclohexadiene system. Compared to the Exo and Endo diels-alder reaction computed above, the clear inability to aromatise in this alternative pathway, where a bridged ring system will give rise to a sizable thermodymanic penalty for both orientation approaches.Though the bridged system does not incur significant additional themodynamic instability (because bonds formed and broken are identical to its aromatisable alternative, and that both S=O bonds in the products are pointing towards empty space), it does suffer from the following kinetic implication: The o-xylylene group, being originally a fully planar structure with a coplanar eight π-orbital system, is forced to distort from its conformation, as carbons at the 1,4 positions are essentially 'pushed' upwards, in order to accommodate the approaching sulpur dioxide. As this effect is present for both Exo and Endo apporaches, Kinetic unfavourability will also be realized across this alternative position for cyclisation.

== Conclusion ==
Throughout the exercises, recognising relationships of different calculations with the potential energy surface has been important in understanding what each step had meant. By grasping specific PES positions through calculations, useful information can be extracted for the different structures of concern (such as reactants,products and transition states). This has allowed energetic comparisons, molecular orbital interactions and reaction visualisation to be obtained and understood.

The most common calculation used was the minimisation, which is often used to obtain the lowest energy conformation of a molecule. From the PES surface, this is the global minimum as opposed to other local minimums, therefore approximating calculations were often ran beforehand to ensure the reliability of the obtained minimum values. Therefore, a standard protocol would be to perform a semi-empirical calculation (the rough approximation), before moving on to the B3LYP (the accurate calculation, a basis set based method involving both HF and DFT functions).

As transition states would also have zero gradients, second derivatives are required to differentiate between the two. Frequency calculations act as the key method of such verification, where a single imaginative force constant (the second derivative) would prove the achievement of a TS. This point should have all but one dimension amongst the 3N-6 dimensions minimised, leaving a maximum just a single dimension.

Given all the computation methods utilized throughout the task, it can be argued that the DFT-based B3LYP method is the most attractive: As although the quantum mechanical method DFT are able to produce relatively reliable approximations, this is in expense of poor results in terms of exchange correlations.The ab intito HF on the other hand, is highly effective in analytically solving exchange correlations, but as the method ruses electron positions, this requires higher degrees of freedom in the process of solving and thus suffers from longer computation times. Thus, putting both factors of accuracy and time penalty into perspective, as B3LYP which is able to solve exchange correlations accurately by using the same analytical approach as the HF , benefits from strengths of both methods mentioned above. Moreover, its accuracy is considered to have made up for its expensiveness in terms of time.

All in all, the applications used for this exercise has demonstrated just a small part of the capabilities in computation chemistry. Higher levels of accuracies (via basis sets) and calculations method (other Ab Initito implementations) has yet to be explored. Complex biological molecules modelling, reaction dynamics, excited electronic states just some other key examples where computations are of high utility to chemists.

== References ==

User:Htw14

2016-12-01T16:10:49Z

Htw14: /* Quantitative MO Visualisations */

'''Computational Lab Year 3: Transition States and Reactivity'''
== Introduction ==

The exercise sets out to understand transition states of reactions, an aspect often difficult to study by experimental means. Through obtaining minimas and transition structures(TS) from energy-optimising computations, as well as further elucidating reaction pathways and trajectory approaches, the study ultimately aims to determine reactivity using energy profiles generated from computed data of studied molecules.

The topic of interest in this wiki concerns the Diels-Alder reaction, a reaction highly powerful in the construction of cyclic compounds within organic synthesis. It is important to understand beforehand that the reactions offers high levels of predictability through stereoselectivity, which would be beneficial in predicting transition structures prior to any computational studies.

Originated from the strict rules of orbital symmetry conservation, such reactions are performed in concerted fashion, meaning that configurations of both reactants will be fully retained in the product, and thus are stererospecific. (For example, a cis alkene will always yield a syn product).

The two terms that would be referred to frequently in this wiki are 'Exo' and 'Endo'. These refer to yet another type of stereoselectivty in Diels-Alder reactions, which governs the position adopted by dienophile substituents relative to the diene system. Such selectivity is attributed to secondary orbital interactions, which will be discussed further in below sections.

Through combining mechanistic and stereoelectronic knowledge of the reaction with computation techniques (such as energy determination and MO visualisations), we would be able to correctly determine the specific diastereomers from reactions.This grants us the ability of disastreoselection control of mutiple stereogenic centered products, which is a powerful skill in organic synthesis.

In the following exercises, three different instances of the reaction are studied.

== Exercise 1: Butadiene with Ethene ==

===Molecular Orbitals===

==== MO Diagram ====
As shown below, the diagram illustrates what a standard MO diagram for a general Diels Alder reaction would have. Though butadiene and ethene are used to provide frontier orbitals as reactants here, according to substituents of different reactants, the relative energies of reactants and product orbitals in specific reactions may differ.
[[Image:Hubert.png|499x499px|center|thumb|Butadiene-Ethene Diels Alder Reaction]]

==== Symmetry requirement ====
For a successful reaction, symmetries of the HOMO and the LUMO must match, while violations to this will lead a forbidden reaction. These orbitals generated from wavefunctions can be either symmetric or anti-symmetric and are distinguished by transformations under an inversion operation. If symmetric with respect to inversion, such an orbital is assigned the label of gerade(g), and vice versa for anti-symmetric cases, which are ungerade(u). As shown in the MO diagram, frontier orbitals Ψ<sub>2</sub> of butadiene and Ψ<sub>2</sub> of ethene are both symmetric (gerade) and thus an interaction is allowed. An interaction of Ψ<sub>3</sub>(u) instead of Ψ<sub>2</sub>(g)<sub> </sub>however, would be forbidden as only g-g u-u interactions are allowed. The expression of the overlapping intergral shown below illustrates this concept mathematically:

[[File:Hubert_equ.png|center|150px]]

When S=0, this implies a zero overlap, while any allowed overlap would have an S value in between 0 and 1.

==== Quantitative MO Visualisations ====
All MOs shown below correlates to the above MO diagram. It can be seen that the varying degree of delocalisation and shapes of the HOMOs and LUMOs correspond well with the phases of orbitals shown in the MO diagram.

{| class="wikitable"
|-
|
<jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 2; mo 16; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>DA_STEP_2_PM6_OPT_MO_VER.LOG</uploadedFileContents>
<title>MO1 from TS</title>
</jmolApplet>
</jmol>
|
<jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 2; mo 17; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>DA_STEP_2_PM6_OPT_MO_VER.LOG</uploadedFileContents>
<title>MO2 HOMO from TS</title>
</jmolApplet>
</jmol>
|
<jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 2; mo 18; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>DA_STEP_2_PM6_OPT_MO_VER.LOG</uploadedFileContents>
<title>MO3 LUMO from TSs</title>
</jmolApplet>
</jmol>
|
<jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 2; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>DA_STEP_2_PM6_OPT_MO_VER.LOG</uploadedFileContents>
<title>MO4 from TS</title>
</jmolApplet>
</jmol>
|-
|
<jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 2; mo 6; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>REFINED_ALKENE_PM6.LOG</uploadedFileContents>
<title>Ψ1 HOMO from Ethene FOs</title>
</jmolApplet>
</jmol>
|
<jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 2; mo 7; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>REFINED_ALKENE_PM6.LOG</uploadedFileContents>
<title>Ψ2 LUMO from Ethene FOs</title>
</jmolApplet>
</jmol>
|
<jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 2; mo 11; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>BUTADIENE_PM6_MO_VER.LOG</uploadedFileContents>
<title>Ψ2 HOMO from Butadiene FOs</title>
</jmolApplet>
</jmol>
|
<jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 2; mo 12; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>BUTADIENE_PM6_MO_VER.LOG</uploadedFileContents>
<title>Ψ3 LUMO from Butadiene FOs</title>
</jmolApplet>
</jmol>
|}

=== Reaction Analysis ===

==== Bond Formation and Lengths ====
As shown in the diagram below, relationships between atoms can be divided into three categories, two of which being covalent interactions (sp3 and sp2) whilst the other a non-bonding interaction. These distances can be defined as the covalent and Van der Waal radius respectively. Typically, the distances (in Angstroms Å) between two carbon atoms of these relationships are as follows: Van de Waal (VdW): '''1.680 Å'''<ref name=":0">Pauling, Linus and L. O. Brockway. "Carbon—Carbon Bond Distances. The Electron Diffraction Investigation Of Ethane, Propane, Isobutane, Neopentane, Cyclopropane, Cyclopentane, Cyclohexane, Allene, Ethylene, Isobutene, Tetramethylethylene, Mesitylene, And Hexamethylbenzene. Revised Values Of Covalent Radii". ''Journal of the American Chemical Society'' 59.7 (1937): 1223-1236. Web.</ref>; Covalent sp3: '''1.537 Å'''<ref name=":0" />; Covalent sp2 : '''1.347 Å'''<ref name=":0" />

[[File:Trythis.png|center|330x330px]] <br style="clear:left">
{|border="1" cellpadding="5" cellspacing="0" align="center"
!Bonds
!Reactant
!Type
!TS
!Process
!Product
!Type
|-
|1,2
|1.33539
|sp<sup>2</sup>
|1.37978
|Lengthen
|1.50090
|sp<sup>3</sup>
|-
|2,3
|1.46834
|sp<sup>3</sup>
|1.41107
|Shorten
|1.33784
|sp<sup>2</sup>
|-
|3,4
|1.33539
|sp<sup>2</sup>
|1.37978
|Lengthen
|1.50090
|sp<sup>3</sup>
|-
|4,5
|3.41334
|2VdW
|2.11461
|Shorten
|1.54040
|sp<sup>3</sup>
|-
|5,6
|1.32736
|sp<sup>2</sup>
|1.38177
|Lengthen
|1.54091
|sp<sup>3</sup>
|-
|6,1
|3.41425
|2VdW
|2.11469
|Shorten
|1.54041
|sp<sup>3</sup>
|}

Firstly, it should be noted that the sum two Van de Waal radius of neigbouring atoms measures the internuclear distance of two non-interacting atoms prior to bond formation, hence it should be longer than those of bonding (i.e. sp2 and sp3). From the table, we can see that a smooth transition from non-bonding to sp3(shortening), sp3 to sp2 (shortening) and sp2 to sp3 (lengthening), thus turning the butadiene and alkene in to a cyclohexene in the process. As the alternating lengthening and shortening process of the bonds is yet another feature of the concerted process in the Diels Alder, the computated transiton state structure supports mechanism.

==== Vibrational Modes ====

two jmols here

The vibrational mode corresponding to the transition state agrees with the concerted nature of the Diels-Alder reaction, during which two sp3 bonds are formed synchronously. The resultant single imgainary frequency proves that a maximum has been reached in only one dimension on the potential energy surface, which verifies the existence of a transition structure. Next to it shows the lowest positive frequency mode,where the two reactants rotates in opposite directions of a 2D plane. In comparison, the illustration on the right is non-reactive and minute in energy, which matches well with a typical rotational mode.

== Exercise 2: Benzoquinone with Cyclopentadiene ==

=== Molecular Orbitals ===
The orbitals below illustrates the four key resultant molecular orbitals (MO1-MO4) from the MO diagram shown in Exercise 1, where in this case are derived from the four frontier orbitals of cyclopentadiene (the diene equivalent) and the two from Benzoquinone (the alkene equivalent). Both the Exo and Endo reactions computated in this exercise are cases of normal electron demand, the most common electronic interaction in Diels-Alder reactions, where the dienophile is electron poor while the diene being electron rich. On the other hand, inverse demand suggests the opposite, thus allowing that the alkene HOMO to be at a close energy level to interact strongly the the diene LUMO. If this is the case MO1 (referring to the MO Diagram above) will be the HOMO of the transition state as opposed to MO2. By examining phases from both HOMOs of the Exo and Endo approaches, this is evident that the reaction is not a case inverse demand, as both corresponded to the phase pattern that a MO2 equivalent would possess. We can therefore conclude that the reaction is in '''normal electron demand'''.

==== Exo Approach Key MOs ====
insert 4 here

==== Endo Approach Key MOs ====
insert 4 here

=== Reaction Analysis ===

==== Energetics and Pathway ====

Through analysing resultant thermodynamic data extracted from optimised structures of the reactants, products and transition states, a highly useful comparison could be made between the two reactant approaches. This will ultimately allow us to predict the reaction outcome expected in reality, thus showing the importance of computational techniques in chemistry. Such data is shown below:

{|border="1" cellpadding="5" cellspacing="0" align="center"
!Energy(kJ/mol)
!Exo
!Endo
|-
|Reactant
|<nowiki>-1510772.498</nowiki>
|<nowiki>-1510762.046</nowiki>
|-
|Product
|<nowiki>-1510782.951</nowiki>
|<nowiki>-1510783.751</nowiki>
|-
|TS
|<nowiki>-1510663.669</nowiki>
|<nowiki>-1510670.285</nowiki>
|-
|E<sub>a</sub>
|108.8296005
|91.761225
|-
|ΔE
|<nowiki>-10.4521155</nowiki>
|<nowiki>-21.7050085</nowiki>
|}

While the activation energy (Ea) gives information about the minimum energy input required to drive the reaction forwards, the total energy difference (ΔE) allows the judgement of the energy of stabilisation achievable for each reaction. From the table we see that less Ea is required initially, as well as a larger extent of stabilisation if the reaction were in the endo approach (reasons for this discussed in the below section). Therefore, we can conclude that the '''Endo''' adduct is both the '''Kinetic''' and '''Thermodynamic''' product.

[[File:cool1.png|right|295x295px|thumb|Endo Orbital Overlap]]

<br />

==== Orbital Stereoelectronics ====

The endo reaction undergoes with dienophile benzoquinone sitting on top of the cyclopentadiene (Cp), which grants an additional opportunity for a favourable orbital interaction. As seen on the right, the p orbitals at the 2,3 position of Cp is within proximate distance to interact with the rear C=C π* orbitals of the dienophile, alongside the bond-forming front C=C π* orbitals. From the white arrows indicated, the Cp HOMO is also in correct phase to overlap with the second double bond of the Benzoquinone. This is known as a '''secondary orbital interaction''', a stabilising interaction which does not involve bond formation.

Therefore, by having a second double bond within the same molecule in the dienephile, as opposed to a simpler alkene (eg. ethene), the additional interaction available plays the role in attracting the diene to adapt the Endo position while approaching. This '''lowers the activation energy''' of the Endo pathway, therefore transition structures are more favoured to be endo despite the associated sterics hinderance thermodynamically. This shows diels-alder reactions are often '''kinetically driven'''.

<br />
<br />
<br />

== Exercise 3: Xylylene with Sulphur Dioxide ==

=== Reactant Approach via IRC ===
{| class="wikitable"
!Diels Alder Endo
!Diels Alder Exo
!Cheletropic
|-
|[[File:Endo_irc_animation_for_wiki.gif]]
|[[File:Exo_irc_animation_for_wiki.gif]]
|[[File:Chele_irc_animation_for_wiki.gif]]
|}

=== Reaction Analysis ===

==== Energetics and Profile ====
The reaction of concern in the exercise introduces a possibility of a third reaction alongside the two approaches from the Hetero Diels Alder, known as the Cheletropic reaction. Again, computationally-calculated data of Gibbs free energy will be useful here to judge and compare the different reaction paths available, the reaction profile below should also provide a much clearer representation of how the three reactions compare:

{| border="1" cellpadding="5" cellspacing="0" align="center"
!Energy(kJ/mol)
!Exo
!Endo
!Cheletropic
|-
|Reactant
|177.69384
|178.3790955
|186.3606155
|-
|Product
|56.3301025
|56.983852
|<nowiki>-0.005251</nowiki>
|-
|TS
|241.745538
|237.7626545
|260.08203
|-
|E<sub>a</sub>
|64.051698
|59.383559
|73.7214145
|-
|ΔE
|<nowiki>-121.3637375</nowiki>
|<nowiki>-121.3952435</nowiki>
|<nowiki>-186.3658665</nowiki>
|}

[[File:reactionnn.png|800px|center]]
With the lowest energy activation energy amongst all, the '''Endo''' pathway can be concluded to be the '''Kinetic product'''. In terms of the overall energy change, although very similar, endo also appears as the more thermodynamically favourable between the two Diels-Alder reactions. Though given the small margin of difference, such a statement should be treated with discretion. It is however very clear that the '''Cheletropic''' pathway is the '''Thermodynamic product''' overall over Endo and Exo. This margin of difference that Cheletropic reactions show owes to the relatively stable five-membered adduct, as opposed to a six-membered one.

Having identified the KE and TD products, reactions conditions as well as solvents can be altered in order to obtain a desired product specifically.

==== Reactant Transformation ====
Through studying the reaction visualisations from above, we can see that as the reactive butadiene fragment in xylene cyclizes, a conjugated system can been seen to establish at the rear ring. As the major driving force for all three reactions,which are all 2π electrons away from satisfying the Huckel rule of 4n+2 delocalised electrons, the aromatisation of xylyene provides sufficient aromatic stabilisation energy to the reactants to interact.

==== Pathway Alternative ====
A second Diels-Alder reaction possibility comes at the rear diene, as part of the 1,3 cyclohexadiene system. Compared to the Exo and Endo diels-alder reaction computed above, the clear inability to aromatise in this alternative pathway, where a bridged ring system will give rise to a sizable thermodymanic penalty for both orientation approaches.Though the bridged system does not incur significant additional themodynamic instability (because bonds formed and broken are identical to its aromatisable alternative, and that both S=O bonds in the products are pointing towards empty space), it does suffer from the following kinetic implication: The o-xylylene group, being originally a fully planar structure with a coplanar eight π-orbital system, is forced to distort from its conformation, as carbons at the 1,4 positions are essentially 'pushed' upwards, in order to accommodate the approaching sulpur dioxide. As this effect is present for both Exo and Endo apporaches, Kinetic unfavourability will also be realized across this alternative position for cyclisation.

== Conclusion ==
Throughout the exercises, recognising relationships of different calculations with the potential energy surface has been important in understanding what each step had meant. By grasping specific PES positions through calculations, useful information can be extracted for the different structures of concern (such as reactants,products and transition states). This has allowed energetic comparisons, molecular orbital interactions and reaction visualisation to be obtained and understood.

The most common calculation used was the minimisation, which is often used to obtain the lowest energy conformation of a molecule. From the PES surface, this is the global minimum as opposed to other local minimums, therefore approximating calculations were often ran beforehand to ensure the reliability of the obtained minimum values. Therefore, a standard protocol would be to perform a semi-empirical calculation (the rough approximation), before moving on to the B3LYP (the accurate calculation, a basis set based method involving both HF and DFT functions).

As transition states would also have zero gradients, second derivatives are required to differentiate between the two. Frequency calculations act as the key method of such verification, where a single imaginative force constant (the second derivative) would prove the achievement of a TS. This point should have all but one dimension amongst the 3N-6 dimensions minimised, leaving a maximum just a single dimension.

Given all the computation methods utilized throughout the task, it can be argued that the DFT-based B3LYP method is the most attractive: As although the quantum mechanical method DFT are able to produce relatively reliable approximations, this is in expense of poor results in terms of exchange correlations.The ab intito HF on the other hand, is highly effective in analytically solving exchange correlations, but as the method ruses electron positions, this requires higher degrees of freedom in the process of solving and thus suffers from longer computation times. Thus, putting both factors of accuracy and time penalty into perspective, as B3LYP which is able to solve exchange correlations accurately by using the same analytical approach as the HF , benefits from strengths of both methods mentioned above. Moreover, its accuracy is considered to have made up for its expensiveness in terms of time.

All in all, the applications used for this exercise has demonstrated just a small part of the capabilities in computation chemistry. Higher levels of accuracies (via basis sets) and calculations method (other Ab Initito implementations) has yet to be explored. Complex biological molecules modelling, reaction dynamics, excited electronic states just some other key examples where computations are of high utility to chemists.

== References ==

User:Htw14

2016-12-01T16:10:33Z

Htw14: /* Pathway Alternative */

'''Computational Lab Year 3: Transition States and Reactivity'''
== Introduction ==

The exercise sets out to understand transition states of reactions, an aspect often difficult to study by experimental means. Through obtaining minimas and transition structures(TS) from energy-optimising computations, as well as further elucidating reaction pathways and trajectory approaches, the study ultimately aims to determine reactivity using energy profiles generated from computed data of studied molecules.

The topic of interest in this wiki concerns the Diels-Alder reaction, a reaction highly powerful in the construction of cyclic compounds within organic synthesis. It is important to understand beforehand that the reactions offers high levels of predictability through stereoselectivity, which would be beneficial in predicting transition structures prior to any computational studies.

Originated from the strict rules of orbital symmetry conservation, such reactions are performed in concerted fashion, meaning that configurations of both reactants will be fully retained in the product, and thus are stererospecific. (For example, a cis alkene will always yield a syn product).

The two terms that would be referred to frequently in this wiki are 'Exo' and 'Endo'. These refer to yet another type of stereoselectivty in Diels-Alder reactions, which governs the position adopted by dienophile substituents relative to the diene system. Such selectivity is attributed to secondary orbital interactions, which will be discussed further in below sections.

Through combining mechanistic and stereoelectronic knowledge of the reaction with computation techniques (such as energy determination and MO visualisations), we would be able to correctly determine the specific diastereomers from reactions.This grants us the ability of disastreoselection control of mutiple stereogenic centered products, which is a powerful skill in organic synthesis.

In the following exercises, three different instances of the reaction are studied.

== Exercise 1: Butadiene with Ethene ==

===Molecular Orbitals===

==== MO Diagram ====
As shown below, the diagram illustrates what a standard MO diagram for a general Diels Alder reaction would have. Though butadiene and ethene are used to provide frontier orbitals as reactants here, according to substituents of different reactants, the relative energies of reactants and product orbitals in specific reactions may differ.
[[Image:Hubert.png|499x499px|center|thumb|Butadiene-Ethene Diels Alder Reaction]]

==== Symmetry requirement ====
For a successful reaction, symmetries of the HOMO and the LUMO must match, while violations to this will lead a forbidden reaction. These orbitals generated from wavefunctions can be either symmetric or anti-symmetric and are distinguished by transformations under an inversion operation. If symmetric with respect to inversion, such an orbital is assigned the label of gerade(g), and vice versa for anti-symmetric cases, which are ungerade(u). As shown in the MO diagram, frontier orbitals Ψ<sub>2</sub> of butadiene and Ψ<sub>2</sub> of ethene are both symmetric (gerade) and thus an interaction is allowed. An interaction of Ψ<sub>3</sub>(u) instead of Ψ<sub>2</sub>(g)<sub> </sub>however, would be forbidden as only g-g u-u interactions are allowed. The expression of the overlapping intergral shown below illustrates this concept mathematically:

[[File:Hubert_equ.png|center|150px]]

When S=0, this implies a zero overlap, while any allowed overlap would have an S value in between 0 and 1.

==== Quantitative MO Visualisations ====
All MOs shown below correlates to the above MO diagram. It can be seen that the varying degree of delocalisation and shapes of the HOMOs and LUMOs correspond well with the phases of orbitals shown in the MO diagram.

Jmols 4x2 here

=== Reaction Analysis ===

==== Bond Formation and Lengths ====
As shown in the diagram below, relationships between atoms can be divided into three categories, two of which being covalent interactions (sp3 and sp2) whilst the other a non-bonding interaction. These distances can be defined as the covalent and Van der Waal radius respectively. Typically, the distances (in Angstroms Å) between two carbon atoms of these relationships are as follows: Van de Waal (VdW): '''1.680 Å'''<ref name=":0">Pauling, Linus and L. O. Brockway. "Carbon—Carbon Bond Distances. The Electron Diffraction Investigation Of Ethane, Propane, Isobutane, Neopentane, Cyclopropane, Cyclopentane, Cyclohexane, Allene, Ethylene, Isobutene, Tetramethylethylene, Mesitylene, And Hexamethylbenzene. Revised Values Of Covalent Radii". ''Journal of the American Chemical Society'' 59.7 (1937): 1223-1236. Web.</ref>; Covalent sp3: '''1.537 Å'''<ref name=":0" />; Covalent sp2 : '''1.347 Å'''<ref name=":0" />

[[File:Trythis.png|center|330x330px]] <br style="clear:left">
{|border="1" cellpadding="5" cellspacing="0" align="center"
!Bonds
!Reactant
!Type
!TS
!Process
!Product
!Type
|-
|1,2
|1.33539
|sp<sup>2</sup>
|1.37978
|Lengthen
|1.50090
|sp<sup>3</sup>
|-
|2,3
|1.46834
|sp<sup>3</sup>
|1.41107
|Shorten
|1.33784
|sp<sup>2</sup>
|-
|3,4
|1.33539
|sp<sup>2</sup>
|1.37978
|Lengthen
|1.50090
|sp<sup>3</sup>
|-
|4,5
|3.41334
|2VdW
|2.11461
|Shorten
|1.54040
|sp<sup>3</sup>
|-
|5,6
|1.32736
|sp<sup>2</sup>
|1.38177
|Lengthen
|1.54091
|sp<sup>3</sup>
|-
|6,1
|3.41425
|2VdW
|2.11469
|Shorten
|1.54041
|sp<sup>3</sup>
|}

Firstly, it should be noted that the sum two Van de Waal radius of neigbouring atoms measures the internuclear distance of two non-interacting atoms prior to bond formation, hence it should be longer than those of bonding (i.e. sp2 and sp3). From the table, we can see that a smooth transition from non-bonding to sp3(shortening), sp3 to sp2 (shortening) and sp2 to sp3 (lengthening), thus turning the butadiene and alkene in to a cyclohexene in the process. As the alternating lengthening and shortening process of the bonds is yet another feature of the concerted process in the Diels Alder, the computated transiton state structure supports mechanism.

==== Vibrational Modes ====

two jmols here

The vibrational mode corresponding to the transition state agrees with the concerted nature of the Diels-Alder reaction, during which two sp3 bonds are formed synchronously. The resultant single imgainary frequency proves that a maximum has been reached in only one dimension on the potential energy surface, which verifies the existence of a transition structure. Next to it shows the lowest positive frequency mode,where the two reactants rotates in opposite directions of a 2D plane. In comparison, the illustration on the right is non-reactive and minute in energy, which matches well with a typical rotational mode.

== Exercise 2: Benzoquinone with Cyclopentadiene ==

=== Molecular Orbitals ===
The orbitals below illustrates the four key resultant molecular orbitals (MO1-MO4) from the MO diagram shown in Exercise 1, where in this case are derived from the four frontier orbitals of cyclopentadiene (the diene equivalent) and the two from Benzoquinone (the alkene equivalent). Both the Exo and Endo reactions computated in this exercise are cases of normal electron demand, the most common electronic interaction in Diels-Alder reactions, where the dienophile is electron poor while the diene being electron rich. On the other hand, inverse demand suggests the opposite, thus allowing that the alkene HOMO to be at a close energy level to interact strongly the the diene LUMO. If this is the case MO1 (referring to the MO Diagram above) will be the HOMO of the transition state as opposed to MO2. By examining phases from both HOMOs of the Exo and Endo approaches, this is evident that the reaction is not a case inverse demand, as both corresponded to the phase pattern that a MO2 equivalent would possess. We can therefore conclude that the reaction is in '''normal electron demand'''.

==== Exo Approach Key MOs ====
insert 4 here

==== Endo Approach Key MOs ====
insert 4 here

=== Reaction Analysis ===

==== Energetics and Pathway ====

Through analysing resultant thermodynamic data extracted from optimised structures of the reactants, products and transition states, a highly useful comparison could be made between the two reactant approaches. This will ultimately allow us to predict the reaction outcome expected in reality, thus showing the importance of computational techniques in chemistry. Such data is shown below:

{|border="1" cellpadding="5" cellspacing="0" align="center"
!Energy(kJ/mol)
!Exo
!Endo
|-
|Reactant
|<nowiki>-1510772.498</nowiki>
|<nowiki>-1510762.046</nowiki>
|-
|Product
|<nowiki>-1510782.951</nowiki>
|<nowiki>-1510783.751</nowiki>
|-
|TS
|<nowiki>-1510663.669</nowiki>
|<nowiki>-1510670.285</nowiki>
|-
|E<sub>a</sub>
|108.8296005
|91.761225
|-
|ΔE
|<nowiki>-10.4521155</nowiki>
|<nowiki>-21.7050085</nowiki>
|}

While the activation energy (Ea) gives information about the minimum energy input required to drive the reaction forwards, the total energy difference (ΔE) allows the judgement of the energy of stabilisation achievable for each reaction. From the table we see that less Ea is required initially, as well as a larger extent of stabilisation if the reaction were in the endo approach (reasons for this discussed in the below section). Therefore, we can conclude that the '''Endo''' adduct is both the '''Kinetic''' and '''Thermodynamic''' product.

[[File:cool1.png|right|295x295px|thumb|Endo Orbital Overlap]]

<br />

==== Orbital Stereoelectronics ====

The endo reaction undergoes with dienophile benzoquinone sitting on top of the cyclopentadiene (Cp), which grants an additional opportunity for a favourable orbital interaction. As seen on the right, the p orbitals at the 2,3 position of Cp is within proximate distance to interact with the rear C=C π* orbitals of the dienophile, alongside the bond-forming front C=C π* orbitals. From the white arrows indicated, the Cp HOMO is also in correct phase to overlap with the second double bond of the Benzoquinone. This is known as a '''secondary orbital interaction''', a stabilising interaction which does not involve bond formation.

Therefore, by having a second double bond within the same molecule in the dienephile, as opposed to a simpler alkene (eg. ethene), the additional interaction available plays the role in attracting the diene to adapt the Endo position while approaching. This '''lowers the activation energy''' of the Endo pathway, therefore transition structures are more favoured to be endo despite the associated sterics hinderance thermodynamically. This shows diels-alder reactions are often '''kinetically driven'''.

<br />
<br />
<br />

== Exercise 3: Xylylene with Sulphur Dioxide ==

=== Reactant Approach via IRC ===
{| class="wikitable"
!Diels Alder Endo
!Diels Alder Exo
!Cheletropic
|-
|[[File:Endo_irc_animation_for_wiki.gif]]
|[[File:Exo_irc_animation_for_wiki.gif]]
|[[File:Chele_irc_animation_for_wiki.gif]]
|}

=== Reaction Analysis ===

==== Energetics and Profile ====
The reaction of concern in the exercise introduces a possibility of a third reaction alongside the two approaches from the Hetero Diels Alder, known as the Cheletropic reaction. Again, computationally-calculated data of Gibbs free energy will be useful here to judge and compare the different reaction paths available, the reaction profile below should also provide a much clearer representation of how the three reactions compare:

{| border="1" cellpadding="5" cellspacing="0" align="center"
!Energy(kJ/mol)
!Exo
!Endo
!Cheletropic
|-
|Reactant
|177.69384
|178.3790955
|186.3606155
|-
|Product
|56.3301025
|56.983852
|<nowiki>-0.005251</nowiki>
|-
|TS
|241.745538
|237.7626545
|260.08203
|-
|E<sub>a</sub>
|64.051698
|59.383559
|73.7214145
|-
|ΔE
|<nowiki>-121.3637375</nowiki>
|<nowiki>-121.3952435</nowiki>
|<nowiki>-186.3658665</nowiki>
|}

[[File:reactionnn.png|800px|center]]
With the lowest energy activation energy amongst all, the '''Endo''' pathway can be concluded to be the '''Kinetic product'''. In terms of the overall energy change, although very similar, endo also appears as the more thermodynamically favourable between the two Diels-Alder reactions. Though given the small margin of difference, such a statement should be treated with discretion. It is however very clear that the '''Cheletropic''' pathway is the '''Thermodynamic product''' overall over Endo and Exo. This margin of difference that Cheletropic reactions show owes to the relatively stable five-membered adduct, as opposed to a six-membered one.

Having identified the KE and TD products, reactions conditions as well as solvents can be altered in order to obtain a desired product specifically.

==== Reactant Transformation ====
Through studying the reaction visualisations from above, we can see that as the reactive butadiene fragment in xylene cyclizes, a conjugated system can been seen to establish at the rear ring. As the major driving force for all three reactions,which are all 2π electrons away from satisfying the Huckel rule of 4n+2 delocalised electrons, the aromatisation of xylyene provides sufficient aromatic stabilisation energy to the reactants to interact.

==== Pathway Alternative ====
A second Diels-Alder reaction possibility comes at the rear diene, as part of the 1,3 cyclohexadiene system. Compared to the Exo and Endo diels-alder reaction computed above, the clear inability to aromatise in this alternative pathway, where a bridged ring system will give rise to a sizable thermodymanic penalty for both orientation approaches.Though the bridged system does not incur significant additional themodynamic instability (because bonds formed and broken are identical to its aromatisable alternative, and that both S=O bonds in the products are pointing towards empty space), it does suffer from the following kinetic implication: The o-xylylene group, being originally a fully planar structure with a coplanar eight π-orbital system, is forced to distort from its conformation, as carbons at the 1,4 positions are essentially 'pushed' upwards, in order to accommodate the approaching sulpur dioxide. As this effect is present for both Exo and Endo apporaches, Kinetic unfavourability will also be realized across this alternative position for cyclisation.

== Conclusion ==
Throughout the exercises, recognising relationships of different calculations with the potential energy surface has been important in understanding what each step had meant. By grasping specific PES positions through calculations, useful information can be extracted for the different structures of concern (such as reactants,products and transition states). This has allowed energetic comparisons, molecular orbital interactions and reaction visualisation to be obtained and understood.

The most common calculation used was the minimisation, which is often used to obtain the lowest energy conformation of a molecule. From the PES surface, this is the global minimum as opposed to other local minimums, therefore approximating calculations were often ran beforehand to ensure the reliability of the obtained minimum values. Therefore, a standard protocol would be to perform a semi-empirical calculation (the rough approximation), before moving on to the B3LYP (the accurate calculation, a basis set based method involving both HF and DFT functions).

As transition states would also have zero gradients, second derivatives are required to differentiate between the two. Frequency calculations act as the key method of such verification, where a single imaginative force constant (the second derivative) would prove the achievement of a TS. This point should have all but one dimension amongst the 3N-6 dimensions minimised, leaving a maximum just a single dimension.

Given all the computation methods utilized throughout the task, it can be argued that the DFT-based B3LYP method is the most attractive: As although the quantum mechanical method DFT are able to produce relatively reliable approximations, this is in expense of poor results in terms of exchange correlations.The ab intito HF on the other hand, is highly effective in analytically solving exchange correlations, but as the method ruses electron positions, this requires higher degrees of freedom in the process of solving and thus suffers from longer computation times. Thus, putting both factors of accuracy and time penalty into perspective, as B3LYP which is able to solve exchange correlations accurately by using the same analytical approach as the HF , benefits from strengths of both methods mentioned above. Moreover, its accuracy is considered to have made up for its expensiveness in terms of time.

All in all, the applications used for this exercise has demonstrated just a small part of the capabilities in computation chemistry. Higher levels of accuracies (via basis sets) and calculations method (other Ab Initito implementations) has yet to be explored. Complex biological molecules modelling, reaction dynamics, excited electronic states just some other key examples where computations are of high utility to chemists.

== References ==

User:Htw14

2016-12-01T15:01:01Z

Htw14: /* Pathway Alternative */

User:Htw14

2016-11-14T18:35:20Z

Htw14: /* Energetics and Pathway */

User:Htw14

2016-11-14T18:35:00Z

Htw14: /* Energetics and Pathway */

User:Htw14

2016-11-14T18:34:32Z

Htw14: /* Orbital Stereoelectronics */

User:Htw14

2016-11-14T18:34:03Z

Htw14: /* Orbital Stereoelectronics */

User:Htw14

2016-11-14T18:33:00Z

Htw14: /* Exo Approach Key MOs */

User:Htw14

2016-11-14T18:32:38Z

Htw14: /* Molecular Orbitals */

User:Htw15

2016-11-14T18:31:20Z

Htw14:

{| class="wikitable"
|-
|
<jmol>
<jmolApplet>
<color>white</color>
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<script>frame 2; mo 16; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
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<title>MO1 from TS</title>
</jmolApplet>
</jmol>
|
<jmol>
<jmolApplet>
<color>white</color>
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<script>frame 2; mo 17; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
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<title>MO2 HOMO from TS</title>
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<jmol>
<jmolApplet>
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<script>frame 2; mo 18; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
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<title>MO3 LUMO from TSs</title>
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</jmol>
|
<jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 2; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>DA_STEP_2_PM6_OPT_MO_VER.LOG</uploadedFileContents>
<title>MO4 from TS</title>
</jmolApplet>
</jmol>
|-
|
<jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 2; mo 6; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>REFINED_ALKENE_PM6.LOG</uploadedFileContents>
<title>Ψ1 HOMO from Ethene FOs</title>
</jmolApplet>
</jmol>
|
<jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 2; mo 7; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>REFINED_ALKENE_PM6.LOG</uploadedFileContents>
<title>Ψ2 LUMO from Ethene FOs</title>
</jmolApplet>
</jmol>
|
<jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 2; mo 11; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>BUTADIENE_PM6_MO_VER.LOG</uploadedFileContents>
<title>Ψ2 HOMO from Butadiene FOs</title>
</jmolApplet>
</jmol>
|
<jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 2; mo 12; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>BUTADIENE_PM6_MO_VER.LOG</uploadedFileContents>
<title>Ψ3 LUMO from Butadiene FOs</title>
</jmolApplet>
</jmol>
|}

Next part

{| class="wikitable"
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<jmol>
<jmolApplet>
<title>TS reactive vibrational mode</title><color>white</color><size>300</size>
<script>frame 15;vectors 4;vectors scale 5.0;color vectors red;vibration 10;
</script>
<uploadedFileContents>DA_STEP_2_PM6_OPT_sucess.LOG</uploadedFileContents>
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<jmol>
<jmolApplet>
<title>Lowest Frequency mode: Non-reactive twist</title><color>white</color><size>300</size>
<script>frame 16;vectors 4;vectors scale 5.0;color vectors red;vibration 10;
</script>
<uploadedFileContents>DA_STEP_2_PM6_OPT_sucess.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|}

<jmol>
<jmolApplet>
<title>Pentahelicene</title><color>yellow</color><size>400</size>
<script>zoom 80; cpk on;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;</script>
<uploadedFileContents>Pentahelicene.mol</uploadedFileContents>
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<menuHeight>-1</menuHeight>
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<script>console</script>
<text>open a console window</text>
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<jmol><jmolAppletButton><title>Show CIYSIM.cif in popup window</title><color>cyan</color>
<uploadedFileContents>CIYSIM.cif</uploadedFileContents></jmolAppletButton>
</jmol>
next

Endo Approach Key MOs

{| class="wikitable"
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<jmol>
<jmolApplet>
<color>white</color>
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<script>frame 2; mo 45; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
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<title>MO1</title>
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<jmol>
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<jmol>
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<uploadedFileContents>EXO_TS_DFT_POP=FULL_GFPRINT.LOG</uploadedFileContents>
<title>MO4</title>
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</jmol>
|}

Endo Approach Key MOs

{| class="wikitable"
|-
|<jmol>
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<jmol>
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<title>MO2 (HOMO)</title>
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<jmol>
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<jmol>
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<title>MO4</title>
</jmolApplet>
</jmol>
|}

User:Htw15

2016-11-14T18:27:17Z

Htw14:

{| class="wikitable"
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<jmol>
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<title>MO1 from TS</title>
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</jmol>
|
<jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 2; mo 17; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>DA_STEP_2_PM6_OPT_MO_VER.LOG</uploadedFileContents>
<title>MO2 HOMO from TS</title>
</jmolApplet>
</jmol>
|
<jmol>
<jmolApplet>
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<script>frame 2; mo 18; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>DA_STEP_2_PM6_OPT_MO_VER.LOG</uploadedFileContents>
<title>MO3 LUMO from TSs</title>
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</jmol>
|
<jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 2; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>DA_STEP_2_PM6_OPT_MO_VER.LOG</uploadedFileContents>
<title>MO4 from TS</title>
</jmolApplet>
</jmol>
|-
|
<jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 2; mo 6; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>REFINED_ALKENE_PM6.LOG</uploadedFileContents>
<title>Ψ1 HOMO from Ethene FOs</title>
</jmolApplet>
</jmol>
|
<jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 2; mo 7; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>REFINED_ALKENE_PM6.LOG</uploadedFileContents>
<title>Ψ2 LUMO from Ethene FOs</title>
</jmolApplet>
</jmol>
|
<jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 2; mo 11; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>BUTADIENE_PM6_MO_VER.LOG</uploadedFileContents>
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</jmol>
|
<jmol>
<jmolApplet>
<color>white</color>
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<script>frame 2; mo 12; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>BUTADIENE_PM6_MO_VER.LOG</uploadedFileContents>
<title>Ψ3 LUMO from Butadiene FOs</title>
</jmolApplet>
</jmol>
|}

Next part

{| class="wikitable"
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<jmol>
<jmolApplet>
<title>TS reactive vibrational mode</title><color>white</color><size>300</size>
<script>frame 15;vectors 4;vectors scale 5.0;color vectors red;vibration 10;
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<jmol>
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<script>frame 16;vectors 4;vectors scale 5.0;color vectors red;vibration 10;
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|}

<jmol>
<jmolApplet>
<title>Pentahelicene</title><color>yellow</color><size>400</size>
<script>zoom 80; cpk on;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;</script>
<uploadedFileContents>Pentahelicene.mol</uploadedFileContents>
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<jmolMenu>
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<item><text>Stop spinning</text><script>spin off</script></item>
<menuHeight>-1</menuHeight>
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<jmolButton>
<script>console</script>
<text>open a console window</text>
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</jmol>
<jmol><jmolAppletButton><title>Show CIYSIM.cif in popup window</title><color>cyan</color>
<uploadedFileContents>CIYSIM.cif</uploadedFileContents></jmolAppletButton>
</jmol>
next
{| class="wikitable"
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<jmolApplet>
<color>white</color>
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<uploadedFileContents>EXO_TS_DFT_POP=FULL_GFPRINT.LOG</uploadedFileContents>
<title>MO1 from TS</title>
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</jmol>
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<jmol>
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<color>white</color>
<size>250</size>
<script>frame 2; mo 46; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>EXO_TS_DFT_POP=FULL_GFPRINT.LOG</uploadedFileContents>
<title>MO1 from TS</title>
</jmolApplet>
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<jmol>
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<color>white</color>
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<script>frame 2; mo 47; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
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<title>MO1 from TS</title>
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<jmol>
<jmolApplet>
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<script>frame 2; mo 48; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>EXO_TS_DFT_POP=FULL_GFPRINT.LOG</uploadedFileContents>
<title>MO1 from TS</title>
</jmolApplet>
</jmol>
|}
{| class="wikitable"
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|<jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 2; mo 45; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>ENDO_TS_DFT_POP=FULL_GFPRINT.LOG</uploadedFileContents>
<title>MO1 from TS</title>
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</jmol>
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<jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 2; mo 46; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>ENDO_TS_DFT_POP=FULL_GFPRINT.LOG</uploadedFileContents>
<title>MO1 from TS</title>
</jmolApplet>
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<jmol>
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<color>white</color>
<size>250</size>
<script>frame 2; mo 47; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>ENDO_TS_DFT_POP=FULL_GFPRINT.LOG</uploadedFileContents>
<title>MO1 from TS</title>
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<color>white</color>
<size>250</size>
<script>frame 2; mo 48; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
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<title>MO1 from TS</title>
</jmolApplet>
</jmol>
|}

User:Htw14

2016-11-14T13:05:58Z

Htw14: /* Endo Approach Key MOs */

User:Htw14

2016-11-14T13:05:46Z

Htw14: /* Endo Approach Key MOs */

User:Htw15

2016-11-14T13:03:29Z

Htw14:

{| class="wikitable"
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<jmolApplet>
<color>white</color>
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<title>MO1 from TS</title>
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</jmol>
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<jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 2; mo 17; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
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<title>MO2 HOMO from TS</title>
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</jmol>
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<jmol>
<jmolApplet>
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<size>250</size>
<script>frame 2; mo 18; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
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<jmol>
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<color>white</color>
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<script>frame 2; mo 19; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
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<title>MO4 from TS</title>
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<color>white</color>
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<script>frame 2; mo 6; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
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<script>frame 2; mo 7; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>REFINED_ALKENE_PM6.LOG</uploadedFileContents>
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<jmol>
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<color>white</color>
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<script>frame 2; mo 11; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
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<jmol>
<jmolApplet>
<color>white</color>
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<script>frame 2; mo 12; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>BUTADIENE_PM6_MO_VER.LOG</uploadedFileContents>
<title>Ψ3 LUMO from Butadiene FOs</title>
</jmolApplet>
</jmol>
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{| class="wikitable"
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<script>frame 15;vectors 4;vectors scale 5.0;color vectors red;vibration 10;
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</jmol>
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<jmol>
<jmolApplet>
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<script>frame 16;vectors 4;vectors scale 5.0;color vectors red;vibration 10;
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<uploadedFileContents>DA_STEP_2_PM6_OPT_sucess.LOG</uploadedFileContents>
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</jmol>
|}

<jmol>
<jmolApplet>
<title>Pentahelicene</title><color>yellow</color><size>400</size>
<script>zoom 80; cpk on;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;</script>
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File:ENDO TS DFT POP=FULL GFPRINT.LOG

2016-11-14T13:00:12Z

Htw14:

User:Htw15

2016-11-14T12:59:05Z

Htw14:

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User:Htw14

2016-11-14T12:56:36Z

Htw14: /* Exercise 2: Benzoquinone with Cyclopentadiene */

'''Computational Lab Year 3: Transition States and Reactivity'''
== Introduction ==

The exercise sets out to understand transition states of reactions, an aspect often difficult to study by experimental means. Through obtaining minimas and transition structures(TS) from energy-optimising computations, as well as further elucidating reaction pathways and trajectory approaches, the study ultimately aims to determine reactivity using energy profiles generated from computed data of studied molecules.

The topic of interest in this wiki concerns the Diels-Alder reaction, a reaction highly powerful in the construction of cyclic compounds within organic synthesis. It is important to understand beforehand that the reactions offers high levels of predictability through stereoselectivity, which would be beneficial in predicting transition structures prior to any computational studies.

Originated from the strict rules of orbital symmetry conservation, such reactions are performed in concerted fashion, meaning that configurations of both reactants will be fully retained in the product, and thus are stererospecific. (For example, a cis alkene will always yield a syn product).

The two terms that would be referred to frequently in this wiki are 'Exo' and 'Endo'. These refer to yet another type of stereoselectivty in Diels-Alder reactions, which governs the position adopted by dienophile substituents relative to the diene system. Such selectivity is attributed to secondary orbital interactions, which will be discussed further in below sections.

Through combining mechanistic and stereoelectronic knowledge of the reaction with computation techniques (such as energy determination and MO visualisations), we would be able to correctly determine the specific diastereomers from reactions.This grants us the ability of disastreoselection control of mutiple stereogenic centered products, which is a powerful skill in organic synthesis.

In the following exercises, three different instances of the reaction are studied.

== Exercise 1: Butadiene with Ethene ==

===Molecular Orbitals===

==== MO Diagram ====
As shown below, the diagram illustrates what a standard MO diagram for a general Diels Alder reaction would have. Though butadiene and ethene are used to provide frontier orbitals as reactants here, according to substituents of different reactants, the relative energies of reactants and product orbitals in specific reactions may differ.
[[Image:Hubert.png|499x499px|center|thumb|Butadiene-Ethene Diels Alder Reaction]]

==== Symmetry requirement ====
For a successful reaction, symmetries of the HOMO and the LUMO must match, while violations to this will lead a forbidden reaction. These orbitals generated from wavefunctions can be either symmetric or anti-symmetric and are distinguished by transformations under an inversion operation. If symmetric with respect to inversion, such an orbital is assigned the label of gerade(g), and vice versa for anti-symmetric cases, which are ungerade(u). As shown in the MO diagram, frontier orbitals Ψ<sub>2</sub> of butadiene and Ψ<sub>2</sub> of ethene are both symmetric (gerade) and thus an interaction is allowed. An interaction of Ψ<sub>3</sub>(u) instead of Ψ<sub>2</sub>(g)<sub> </sub>however, would be forbidden as only g-g u-u interactions are allowed. The expression of the overlapping intergral shown below illustrates this concept mathematically:

[[File:Hubert_equ.png|center|150px]]

When S=0, this implies a zero overlap, while any allowed overlap would have an S value in between 0 and 1.

==== Quantitative MO Visualisations ====
All MOs shown below correlates to the above MO diagram. It can be seen that the varying degree of delocalisation and shapes of the HOMOs and LUMOs correspond well with the phases of orbitals shown in the MO diagram.

Jmols 4x2 here

=== Reaction Analysis ===

==== Bond Formation and Lengths ====
As shown in the diagram below, relationships between atoms can be divided into three categories, two of which being covalent interactions (sp3 and sp2) whilst the other a non-bonding interaction. These distances can be defined as the covalent and Van der Waal radius respectively. Typically, the distances (in Angstroms Å) between two carbon atoms of these relationships are as follows: Van de Waal (VdW): '''1.680 Å'''<ref name=":0">Pauling, Linus and L. O. Brockway. "Carbon—Carbon Bond Distances. The Electron Diffraction Investigation Of Ethane, Propane, Isobutane, Neopentane, Cyclopropane, Cyclopentane, Cyclohexane, Allene, Ethylene, Isobutene, Tetramethylethylene, Mesitylene, And Hexamethylbenzene. Revised Values Of Covalent Radii". ''Journal of the American Chemical Society'' 59.7 (1937): 1223-1236. Web.</ref>; Covalent sp3: '''1.537 Å'''<ref name=":0" />; Covalent sp2 : '''1.347 Å'''<ref name=":0" />

[[File:Trythis.png|center|330x330px]] <br style="clear:left">
{|border="1" cellpadding="5" cellspacing="0" align="center"
!Bonds
!Reactant
!Type
!TS
!Process
!Product
!Type
|-
|1,2
|1.33539
|sp<sup>2</sup>
|1.37978
|Lengthen
|1.50090
|sp<sup>3</sup>
|-
|2,3
|1.46834
|sp<sup>3</sup>
|1.41107
|Shorten
|1.33784
|sp<sup>2</sup>
|-
|3,4
|1.33539
|sp<sup>2</sup>
|1.37978
|Lengthen
|1.50090
|sp<sup>3</sup>
|-
|4,5
|3.41334
|2VdW
|2.11461
|Shorten
|1.54040
|sp<sup>3</sup>
|-
|5,6
|1.32736
|sp<sup>2</sup>
|1.38177
|Lengthen
|1.54091
|sp<sup>3</sup>
|-
|6,1
|3.41425
|2VdW
|2.11469
|Shorten
|1.54041
|sp<sup>3</sup>
|}

Firstly, it should be noted that the sum two Van de Waal radius of neigbouring atoms measures the internuclear distance of two non-interacting atoms prior to bond formation, hence it should be longer than those of bonding (i.e. sp2 and sp3). From the table, we can see that a smooth transition from non-bonding to sp3(shortening), sp3 to sp2 (shortening) and sp2 to sp3 (lengthening), thus turning the butadiene and alkene in to a cyclohexene in the process. As the alternating lengthening and shortening process of the bonds is yet another feature of the concerted process in the Diels Alder, the computated transiton state structure supports mechanism.

==== Vibrational Modes ====

two jmols here

The vibrational mode corresponding to the transition state agrees with the concerted nature of the Diels-Alder reaction, during whichtwo sp3 bonds are formed synchronously. The resultant single imgainary frequency proves that a maximum has been reached in only one dimension on the potential energy surface, which verifies the existence of a transition structure. Next to it shows the lowest positive frequency mode,where the two reactants rotates in opposite directions of a 2D plane. In comparison, the illustration on the right is non-reactive and minute in energy, which matches well with a typical rotational mode.

== Exercise 2: Benzoquinone with Cyclopentadiene ==

=== Molecular Orbitals ===
The orbitals below illustrates the four key resultant molecular orbitals (MO1-MO4) from the MO diagram shown in Exercise 1, where in this case are derived from the four frontier orbitals of cyclopentadiene (the diene equivalent) and the two from Benzoquinone (the alkene equivalent). Both the Exo and Endo reactions computated in this exercise are cases of normal electron demand, the most common electronic interaction in Diels-Alder reactions, where the dienophile is electron poor while the diene being electron rich. On the other hand, inverse demand suggests the opposite, thus allowing that the alkene HOMO to be at a close energy level to interact strongly the the diene LUMO. If this is the case MO1 (referring to the MO Diagram above) will be the HOMO of the transition state as opposed to MO2. By examining phases from both HOMOs of the Exo and Endo approaches, this is evident that the reaction is not a case inverse demand, as both corresponded to the phase pattern that a MO2 equivalent would possess. We can therefore conclude that the reaction is in '''normal electron demand'''.

==== Endo Approach Key MOs ====
{| class="wikitable"
!MO1
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!MO3 (LUMO)
!MO4
|-
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|[[File:cool.png|300px]]
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|[[File:cool.png|300px]]
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==== Exo Approach Key MOs ====
{| class="wikitable"
!MO1
!MO2 (HOMO)
!MO3 (LUMO)
!MO4
|-
|[[File:cool.png|300px]]
|[[File:cool.png|300px]]
|[[File:cool.png|300px]]
|[[File:cool.png|300px]]
|}

=== Reaction Analysis ===

==== Energetics and Pathway ====

Through analysing resultant thermodynamic data extracted from optimised structures of the reactants, products and transition states, a highly useful comparison could be made between the two reactant approaches. This will ultimately allow us to predict the reaction outcome expected in reality, thus showing the importance of computational techniques in chemistry. Such data is shown below:

{|border="1" cellpadding="5" cellspacing="0" align="center"
!Energy(kJ/mol)
!Exo
!Endo
|-
|Reactant
|<nowiki>-1510772.498</nowiki>
|<nowiki>-1510762.046</nowiki>
|-
|Product
|<nowiki>-1510782.951</nowiki>
|<nowiki>-1510783.751</nowiki>
|-
|TS
|<nowiki>-1510663.669</nowiki>
|<nowiki>-1510670.285</nowiki>
|-
|E<sub>a</sub>
|108.8296005
|91.761225
|-
|ΔE
|<nowiki>-10.4521155</nowiki>
|<nowiki>-21.7050085</nowiki>
|}

While the activation energy (Ea) gives information about the minimum energy input required to drive the reaction forwards, the total energy difference (ΔE) allows the judgement of the energy of stabilisation achievable for each reaction. From the table we see that less Ea is required initially, as well as a larger extent of stabilisation if the reaction were in the endo approach (reasons for this discussed in the below section). Therefore, we can conclude that the '''Endo''' adduct is both the '''Kinetic''' and '''Thermodynamic''' product.

[[File:cool1.png|right|295x295px|thumb|Endo Orbital Overlap]]

==== Orbital Stereoelectronics ====

The endo reaction undergoes with dienophile benzoquinone sitting on top of the cyclopentadiene (Cp), which grants an additional opportunity for a favourable orbital interaction. As seen on the right, the p orbitals at the 2,3 position of Cp is within proximate distance to interact with the rear C=C π* orbitals of the dienophile, alongside the bond-forming front C=C π* orbitals. From the white arrows indicated, the Cp HOMO is also in correct phase to overlap with the second double bond of the Benzoquinone. This is known as a '''secondary orbital interaction''', a stabilising interaction which does not involve bond formation.

Therefore, by having a second double bond within the same molecule in the dienephile, as opposed to a simpler alkene (eg. ethene), the additional interaction available plays the role in attracting the diene to adapt the Endo position while approaching. This '''lowers the activation energy''' of the Endo pathway, therefore transition structures are more favoured to be endo despite the associated sterics hinderance thermodynamically. This shows diels-alder reactions are often '''kinetically driven'''.

<br />
<br />

== Exercise 3: Xylylene with Sulphur Dioxide ==

=== Reactant Approach via IRC ===
{| class="wikitable"
!Diels Alder Endo
!Diels Alder Exo
!Cheletropic
|-
|[[File:Endo_irc_animation_for_wiki.gif]]
|[[File:Exo_irc_animation_for_wiki.gif]]
|[[File:Chele_irc_animation_for_wiki.gif]]
|}

=== Reaction Analysis ===

==== Energetics and Profile ====
The reaction of concern in the exercise introduces a possibility of a third reaction alongside the two approaches from the Hetero Diels Alder, known as the Cheletropic reaction. Again, computationally-calculated data of Gibbs free energy will be useful here to judge and compare the different reaction paths available, the reaction profile below should also provide a much clearer representation of how the three reactions compare:

{| border="1" cellpadding="5" cellspacing="0" align="center"
!Energy(kJ/mol)
!Exo
!Endo
!Cheletropic
|-
|Reactant
|177.69384
|178.3790955
|186.3606155
|-
|Product
|56.3301025
|56.983852
|<nowiki>-0.005251</nowiki>
|-
|TS
|241.745538
|237.7626545
|260.08203
|-
|E<sub>a</sub>
|64.051698
|59.383559
|73.7214145
|-
|ΔE
|<nowiki>-121.3637375</nowiki>
|<nowiki>-121.3952435</nowiki>
|<nowiki>-186.3658665</nowiki>
|}

[[File:reactionnn.png|800px|center]]
With the lowest energy activation energy amongst all, the '''Endo''' pathway can be concluded to be the '''Kinetic product'''. In terms of the overall energy change, although very similar, endo also appears as the more thermodynamically favourable between the two Diels-Alder reactions. Though given the small margin of difference, such a statement should be treated with discretion. It is however very clear that the '''Cheletropic''' pathway is the '''Thermodynamic product''' overall over Endo and Exo. This margin of difference that Cheletropic reactions show owes to the relatively stable five-membered adduct, as opposed to a six-membered one.

Having identified the KE and TD products, reactions conditions as well as solvents can be altered in order to obtain a desired product specifically.

==== Reactant Transformation ====
Through studying the reaction visualisations from above, we can see that as the reactive butadiene fragment in xylene cyclizes, a conjugated system can been seen to establish at the rear ring. As the major driving force for all three reactions,which are all 2π electrons away from satisfying the Huckel rule of 4n+2 delocalised electrons, the aromatisation of xylyene provides sufficient aromatic stabilisation energy to the reactants to interact.

==== Pathway Alternative ====
find out from PGs

== Conclusion ==
Throughout the exercises, recognising relationships of different calculations with the potential energy surface has been important in understanding what each step had meant. By grasping specific PES positions through calculations, useful information can be extracted for the different structures of concern (such as reactants,products and transition states). This has allowed energetic comparisons, molecular orbital interactions and reaction visualisation to be obtained and understood.

The most common calculation used was the minimisation, which is often used to obtain the lowest energy conformation of a molecule. From the PES surface, this is the global minimum as opposed to other local minimums, therefore approximating calculations were often ran beforehand to ensure the reliability of the obtained minimum values. Therefore, a standard protocol would be to perform a semi-empirical calculation (the rough approximation), before moving on to the B3LYP (the accurate calculation, a basis set based method involving both HF and DFT functions).

As transition states would also have zero gradients, second derivatives are required to differentiate between the two. Frequency calculations act as the key method of such verification, where a single imaginative force constant (the second derivative) would prove the achievement of a TS. This point should have all but one dimension amongst the 3N-6 dimensions minimised, leaving a maximum just a single dimension.

All in all, the applications used for this exercise has demonstrated just a small part of the capabilities in computation chemistry. Higher levels of accuracies (via basis sets) and calculations method (other Ab Initito implementations) has yet to be explored. Complex biological molecules modelling, reaction dynamics, excited electronic states just some other key examples where computations are of high utility to chemists.

== References ==

User:Htw14

2016-11-14T12:55:09Z

Htw14: /* Endo Approach Key MOs */

'''Computational Lab Year 3: Transition States and Reactivity'''
== Introduction ==

The exercise sets out to understand transition states of reactions, an aspect often difficult to study by experimental means. Through obtaining minimas and transition structures(TS) from energy-optimising computations, as well as further elucidating reaction pathways and trajectory approaches, the study ultimately aims to determine reactivity using energy profiles generated from computed data of studied molecules.

The topic of interest in this wiki concerns the Diels-Alder reaction, a reaction highly powerful in the construction of cyclic compounds within organic synthesis. It is important to understand beforehand that the reactions offers high levels of predictability through stereoselectivity, which would be beneficial in predicting transition structures prior to any computational studies.

Originated from the strict rules of orbital symmetry conservation, such reactions are performed in concerted fashion, meaning that configurations of both reactants will be fully retained in the product, and thus are stererospecific. (For example, a cis alkene will always yield a syn product).

The two terms that would be referred to frequently in this wiki are 'Exo' and 'Endo'. These refer to yet another type of stereoselectivty in Diels-Alder reactions, which governs the position adopted by dienophile substituents relative to the diene system. Such selectivity is attributed to secondary orbital interactions, which will be discussed further in below sections.

Through combining mechanistic and stereoelectronic knowledge of the reaction with computation techniques (such as energy determination and MO visualisations), we would be able to correctly determine the specific diastereomers from reactions.This grants us the ability of disastreoselection control of mutiple stereogenic centered products, which is a powerful skill in organic synthesis.

In the following exercises, three different instances of the reaction are studied.

== Exercise 1: Butadiene with Ethene ==

===Molecular Orbitals===

==== MO Diagram ====
As shown below, the diagram illustrates what a standard MO diagram for a general Diels Alder reaction would have. Though butadiene and ethene are used to provide frontier orbitals as reactants here, according to substituents of different reactants, the relative energies of reactants and product orbitals in specific reactions may differ.
[[Image:Hubert.png|499x499px|center|thumb|Butadiene-Ethene Diels Alder Reaction]]

==== Symmetry requirement ====
For a successful reaction, symmetries of the HOMO and the LUMO must match, while violations to this will lead a forbidden reaction. These orbitals generated from wavefunctions can be either symmetric or anti-symmetric and are distinguished by transformations under an inversion operation. If symmetric with respect to inversion, such an orbital is assigned the label of gerade(g), and vice versa for anti-symmetric cases, which are ungerade(u). As shown in the MO diagram, frontier orbitals Ψ<sub>2</sub> of butadiene and Ψ<sub>2</sub> of ethene are both symmetric (gerade) and thus an interaction is allowed. An interaction of Ψ<sub>3</sub>(u) instead of Ψ<sub>2</sub>(g)<sub> </sub>however, would be forbidden as only g-g u-u interactions are allowed. The expression of the overlapping intergral shown below illustrates this concept mathematically:

[[File:Hubert_equ.png|center|150px]]

When S=0, this implies a zero overlap, while any allowed overlap would have an S value in between 0 and 1.

==== Quantitative MO Visualisations ====
All MOs shown below correlates to the above MO diagram. It can be seen that the varying degree of delocalisation and shapes of the HOMOs and LUMOs correspond well with the phases of orbitals shown in the MO diagram.

Jmols 4x2 here

=== Reaction Analysis ===

==== Bond Formation and Lengths ====
As shown in the diagram below, relationships between atoms can be divided into three categories, two of which being covalent interactions (sp3 and sp2) whilst the other a non-bonding interaction. These distances can be defined as the covalent and Van der Waal radius respectively. Typically, the distances (in Angstroms Å) between two carbon atoms of these relationships are as follows: Van de Waal (VdW): '''1.680 Å'''<ref name=":0">Pauling, Linus and L. O. Brockway. "Carbon—Carbon Bond Distances. The Electron Diffraction Investigation Of Ethane, Propane, Isobutane, Neopentane, Cyclopropane, Cyclopentane, Cyclohexane, Allene, Ethylene, Isobutene, Tetramethylethylene, Mesitylene, And Hexamethylbenzene. Revised Values Of Covalent Radii". ''Journal of the American Chemical Society'' 59.7 (1937): 1223-1236. Web.</ref>; Covalent sp3: '''1.537 Å'''<ref name=":0" />; Covalent sp2 : '''1.347 Å'''<ref name=":0" />

[[File:Trythis.png|center|330x330px]] <br style="clear:left">
{|border="1" cellpadding="5" cellspacing="0" align="center"
!Bonds
!Reactant
!Type
!TS
!Process
!Product
!Type
|-
|1,2
|1.33539
|sp<sup>2</sup>
|1.37978
|Lengthen
|1.50090
|sp<sup>3</sup>
|-
|2,3
|1.46834
|sp<sup>3</sup>
|1.41107
|Shorten
|1.33784
|sp<sup>2</sup>
|-
|3,4
|1.33539
|sp<sup>2</sup>
|1.37978
|Lengthen
|1.50090
|sp<sup>3</sup>
|-
|4,5
|3.41334
|2VdW
|2.11461
|Shorten
|1.54040
|sp<sup>3</sup>
|-
|5,6
|1.32736
|sp<sup>2</sup>
|1.38177
|Lengthen
|1.54091
|sp<sup>3</sup>
|-
|6,1
|3.41425
|2VdW
|2.11469
|Shorten
|1.54041
|sp<sup>3</sup>
|}

Firstly, it should be noted that the sum two Van de Waal radius of neigbouring atoms measures the internuclear distance of two non-interacting atoms prior to bond formation, hence it should be longer than those of bonding (i.e. sp2 and sp3). From the table, we can see that a smooth transition from non-bonding to sp3(shortening), sp3 to sp2 (shortening) and sp2 to sp3 (lengthening), thus turning the butadiene and alkene in to a cyclohexene in the process. As the alternating lengthening and shortening process of the bonds is yet another feature of the concerted process in the Diels Alder, the computated transiton state structure supports mechanism.

==== Vibrational Modes ====

two jmols here

The vibrational mode corresponding to the transition state agrees with the concerted nature of the Diels-Alder reaction, during whichtwo sp3 bonds are formed synchronously. The resultant single imgainary frequency proves that a maximum has been reached in only one dimension on the potential energy surface, which verifies the existence of a transition structure. Next to it shows the lowest positive frequency mode,where the two reactants rotates in opposite directions of a 2D plane. In comparison, the illustration on the right is non-reactive and minute in energy, which matches well with a typical rotational mode.

== Exercise 2: Benzoquinone with Cyclopentadiene ==

=== Molecular Orbitals ===
The orbitals below illustrates the four key resultant molecular orbitals (MO1-MO4) from the MO diagram shown in Exercise 1, where in this case are derived from the four frontier orbitals of cyclopentadiene (the diene equivalent) and the two from Benzoquinone (the alkene equivalent). Both the Exo and Endo reactions computated in this exercise are cases of normal electron demand, the most common electronic interaction in Diels-Alder reactions, where the dienophile is electron poor while the diene being electron rich. On the other hand, inverse demand suggests the opposite, thus allowing that the alkene HOMO to be at a close energy level to interact strongly the the diene LUMO. If this is the case MO1 (referring to the MO Diagram above) will be the HOMO of the transition state as opposed to MO2. By examining phases from both HOMOs of the Exo and Endo approaches, this is evident that the reaction is not a case inverse demand, as both corresponded to the phase pattern that a MO2 equivalent would possess. We can therefore conclude that the reaction is in '''normal electron demand'''.

==== Endo Approach Key MOs ====
{| class="wikitable"
!MO1
!MO2 (HOMO)
!MO3 (LUMO)
!MO4
|-
|<jmol>
<jmolApplet>
<color>white</color>
<size>250</size>
<script>frame 2; mo 45; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>EXO_TS_DFT_POP=FULL_GFPRINT.LOG.LOG</uploadedFileContents>
</jmolApplet>
</jmol>
|[[File:cool.png|300px]]
|[[File:cool.png|300px]]
|[[File:cool.png|300px]]
|}
<jmol>
<jmolApplet>
<color>white</color>
<size>500</size>
<script>frame 2; mo 45; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>EXO_TS_DFT_POP=FULL_GFPRINT.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

==== Exo Approach Key MOs ====
{| class="wikitable"
!MO1
!MO2 (HOMO)
!MO3 (LUMO)
!MO4
|-
|[[File:cool.png|300px]]
|[[File:cool.png|300px]]
|[[File:cool.png|300px]]
|[[File:cool.png|300px]]
|}

=== Reaction Analysis ===

==== Energetics and Pathway ====

Through analysing resultant thermodynamic data extracted from optimised structures of the reactants, products and transition states, a highly useful comparison could be made between the two reactant approaches. This will ultimately allow us to predict the reaction outcome expected in reality, thus showing the importance of computational techniques in chemistry. Such data is shown below:

{|border="1" cellpadding="5" cellspacing="0" align="center"
!Energy(kJ/mol)
!Exo
!Endo
|-
|Reactant
|<nowiki>-1510772.498</nowiki>
|<nowiki>-1510762.046</nowiki>
|-
|Product
|<nowiki>-1510782.951</nowiki>
|<nowiki>-1510783.751</nowiki>
|-
|TS
|<nowiki>-1510663.669</nowiki>
|<nowiki>-1510670.285</nowiki>
|-
|E<sub>a</sub>
|108.8296005
|91.761225
|-
|ΔE
|<nowiki>-10.4521155</nowiki>
|<nowiki>-21.7050085</nowiki>
|}

While the activation energy (Ea) gives information about the minimum energy input required to drive the reaction forwards, the total energy difference (ΔE) allows the judgement of the energy of stabilisation achievable for each reaction. From the table we see that less Ea is required initially, as well as a larger extent of stabilisation if the reaction were in the endo approach (reasons for this discussed in the below section). Therefore, we can conclude that the '''Endo''' adduct is both the '''Kinetic''' and '''Thermodynamic''' product.

[[File:cool1.png|right|295x295px|thumb|Endo Orbital Overlap]]

==== Orbital Stereoelectronics ====

The endo reaction undergoes with dienophile benzoquinone sitting on top of the cyclopentadiene (Cp), which grants an additional opportunity for a favourable orbital interaction. As seen on the right, the p orbitals at the 2,3 position of Cp is within proximate distance to interact with the rear C=C π* orbitals of the dienophile, alongside the bond-forming front C=C π* orbitals. From the white arrows indicated, the Cp HOMO is also in correct phase to overlap with the second double bond of the Benzoquinone. This is known as a '''secondary orbital interaction''', a stabilising interaction which does not involve bond formation.

Therefore, by having a second double bond within the same molecule in the dienephile, as opposed to a simpler alkene (eg. ethene), the additional interaction available plays the role in attracting the diene to adapt the Endo position while approaching. This '''lowers the activation energy''' of the Endo pathway, therefore transition structures are more favoured to be endo despite the associated sterics hinderance thermodynamically. This shows diels-alder reactions are often '''kinetically driven'''.

<br />
<br />

== Exercise 3: Xylylene with Sulphur Dioxide ==

=== Reactant Approach via IRC ===
{| class="wikitable"
!Diels Alder Endo
!Diels Alder Exo
!Cheletropic
|-
|[[File:Endo_irc_animation_for_wiki.gif]]
|[[File:Exo_irc_animation_for_wiki.gif]]
|[[File:Chele_irc_animation_for_wiki.gif]]
|}

=== Reaction Analysis ===

==== Energetics and Profile ====
The reaction of concern in the exercise introduces a possibility of a third reaction alongside the two approaches from the Hetero Diels Alder, known as the Cheletropic reaction. Again, computationally-calculated data of Gibbs free energy will be useful here to judge and compare the different reaction paths available, the reaction profile below should also provide a much clearer representation of how the three reactions compare:

{| border="1" cellpadding="5" cellspacing="0" align="center"
!Energy(kJ/mol)
!Exo
!Endo
!Cheletropic
|-
|Reactant
|177.69384
|178.3790955
|186.3606155
|-
|Product
|56.3301025
|56.983852
|<nowiki>-0.005251</nowiki>
|-
|TS
|241.745538
|237.7626545
|260.08203
|-
|E<sub>a</sub>
|64.051698
|59.383559
|73.7214145
|-
|ΔE
|<nowiki>-121.3637375</nowiki>
|<nowiki>-121.3952435</nowiki>
|<nowiki>-186.3658665</nowiki>
|}

[[File:reactionnn.png|800px|center]]
With the lowest energy activation energy amongst all, the '''Endo''' pathway can be concluded to be the '''Kinetic product'''. In terms of the overall energy change, although very similar, endo also appears as the more thermodynamically favourable between the two Diels-Alder reactions. Though given the small margin of difference, such a statement should be treated with discretion. It is however very clear that the '''Cheletropic''' pathway is the '''Thermodynamic product''' overall over Endo and Exo. This margin of difference that Cheletropic reactions show owes to the relatively stable five-membered adduct, as opposed to a six-membered one.

Having identified the KE and TD products, reactions conditions as well as solvents can be altered in order to obtain a desired product specifically.

==== Reactant Transformation ====
Through studying the reaction visualisations from above, we can see that as the reactive butadiene fragment in xylene cyclizes, a conjugated system can been seen to establish at the rear ring. As the major driving force for all three reactions,which are all 2π electrons away from satisfying the Huckel rule of 4n+2 delocalised electrons, the aromatisation of xylyene provides sufficient aromatic stabilisation energy to the reactants to interact.

==== Pathway Alternative ====
find out from PGs

== Conclusion ==
Throughout the exercises, recognising relationships of different calculations with the potential energy surface has been important in understanding what each step had meant. By grasping specific PES positions through calculations, useful information can be extracted for the different structures of concern (such as reactants,products and transition states). This has allowed energetic comparisons, molecular orbital interactions and reaction visualisation to be obtained and understood.

The most common calculation used was the minimisation, which is often used to obtain the lowest energy conformation of a molecule. From the PES surface, this is the global minimum as opposed to other local minimums, therefore approximating calculations were often ran beforehand to ensure the reliability of the obtained minimum values. Therefore, a standard protocol would be to perform a semi-empirical calculation (the rough approximation), before moving on to the B3LYP (the accurate calculation, a basis set based method involving both HF and DFT functions).

As transition states would also have zero gradients, second derivatives are required to differentiate between the two. Frequency calculations act as the key method of such verification, where a single imaginative force constant (the second derivative) would prove the achievement of a TS. This point should have all but one dimension amongst the 3N-6 dimensions minimised, leaving a maximum just a single dimension.

All in all, the applications used for this exercise has demonstrated just a small part of the capabilities in computation chemistry. Higher levels of accuracies (via basis sets) and calculations method (other Ab Initito implementations) has yet to be explored. Complex biological molecules modelling, reaction dynamics, excited electronic states just some other key examples where computations are of high utility to chemists.

== References ==

Mod:Cheatsheet

2016-11-14T12:52:49Z

Htw14: /* MOs with Jmol */

==Text Formatting==

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Description:
! style="background: #0D4F8B; color: white;" | Input:
! style="background: #0D4F8B; color: white;" | Result:
! style="background: #0D4F8B; color: white;" | Where it can be used:
! style="background: #0D4F8B; color: white;" | Notes:
|-
| Bold
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| '''Bold'''
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<nowiki>| <pre>Preformatted Text</pre></nowiki><br>
<nowiki>|}</nowiki>
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|-
| Ignore Formatting
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|-
| Headers
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<nowiki>===Level 3===</nowiki><br>
<nowiki>====Level 4====</nowiki><br>
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|

==Level 2==
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| Start of line
| Do not use Level 1, as this is reserved for titles. <br>
All section headers are placed into the contents box and ordered once there are enough sections.
|-
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<nowiki>** Bullet within a bullet</nowiki>
|
* Bullet point
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## Point 1.1
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|
No indent
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| Start of line
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|}

===Forced Line Break <nowiki><br></nowiki>===

Sometimes a line break is needed to separate paragraphs or text in tables. Placing <nowiki><br></nowiki> between two<br> words creates a new line at that point.

[[File:Benzene.png|right|x200px]]

If there's an image aligned to the right and you need to clear it, it's often best to use <nowiki><br style="clear:right"></nowiki> instead of dozens of <nowiki><br></nowiki>'s.

<br style="clear:right">

Now the image isn't getting in the way of unrelated text.

==Table Formatting==

Placing {| at the start of a line creates a table, provided it is closed with |} on a new line at the end of a table. The type of table and general settings are placed after {|. Typically, class="wikitable" is used. Wiki tables have default settings - titles (!) are centred and bold, cell sizes adjust automatically and have default colours.

To create a basic, 3x3 table, copy and paste this code:

{| width=20%
|<pre>{| class="wikitable"
! Column 1, Row 1
! Column 2, Row 1
! Column 3, Row 1
|-
| Column 1, Row 2
| Column 2, Row 2
| Column 3, Row 2
|-
| Column 1, Row 3
| Column 2, Row 3
| Column 3, Row 3
|} </pre>
|}

The result will be:

{| class="wikitable"
! Column 1, Row 1
! Column 2, Row 1
! Column 3, Row 1
|-
| Column 1, Row 2
| Column 2, Row 2
| Column 3, Row 2
|-
| Column 1, Row 3
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|}

Each <nowiki>"!"</nowiki> and <nowiki>"|"</nowiki> represents a new column, the equivalent of moving right in a table, and each <nowiki>"|-"</nowiki> represents a new line, the equivalent of moving down and to the very left. The end tag <nowiki>"|}"</nowiki> defines the end of the table and should be used only once per table. To create a new row, copy from the last separator <nowiki>( |- )</nowiki> to the last text before the table's end tag <nowiki>( |} )</nowiki> and paste on a new line after before the end tag. For the above example this would be:

{| width=20%
|<pre>|-
| Column 1, Row 3
| Column 2, Row 3
| Column 3, Row 3</pre>
|}

To create a new column, add a new <nowiki>"!"</nowiki> for the title row and <nowiki>"|"</nowiki> for every other row.

===Table Styles===

Colour can be added to a table if you feel like breaking away from grey and white. Copy the following code into each cell you want to style:

{| width=20%
|<pre> style="background: #0D4F8B; color: white;" |</pre>
|}

Paste it just after the <nowiki>"!"</nowiki> or <nowiki>"|"</nowiki> for each cell so

{| width=20%
|<pre>{| class="wikitable"
! Column 1, Row 1
! Column 2, Row 1
! Column 3, Row 1
|-
| Column 1, Row 2
| Column 2, Row 2
| Column 3, Row 2
|-
| Column 1, Row 3
| Column 2, Row 3
| Column 3, Row 3
|}</pre>
|}

becomes

{| width=20%
|<pre>{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Column 1, Row 1
! style="background: #0D4F8B; color: white;" | Column 2, Row 1
! style="background: #0D4F8B; color: white;" | Column 3, Row 1
|-
| Column 1, Row 2
| Column 2, Row 2
| Column 3, Row 2
|-
| Column 1, Row 3
| Column 2, Row 3
| Column 3, Row 3
|}</pre>
|}

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Column 1, Row 1
! style="background: #0D4F8B; color: white;" | Column 2, Row 1
! style="background: #0D4F8B; color: white;" | Column 3, Row 1
|-
| Column 1, Row 2
| Column 2, Row 2
| Column 3, Row 2
|-
| Column 1, Row 3
| Column 2, Row 3
| Column 3, Row 3
|}

The #0D4F8B is a web colour, in this case producing a blue colour. [http://www.color-hex.com/ www.color-hex.com] is a good website for converting known colours into hexadecimal web colours.

As is shown in the Text Formatting section, all basic text formats can be used in tables when required, but two other useful controls are alignment and spans:

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Alignment:
! style="background: #0D4F8B; color: white;" | Input:
! style="background: #0D4F8B; color: white;" | Result:
! style="background: #0D4F8B; color: #0D4F8B;" | :::.
|-
| Left
| <nowiki>style="text-align: left;" | Left</nowiki>
| style="text-align: left;" | Left
|
|-
| Centre
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| style="text-align: center;" | Centre
|
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| style="text-align: right;" | Right
|
|-
| Span 2 columns
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| colspan="2" | Span 2 columns
|-
| Span 2 rows
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| rowspan="2" | Span 2 rows
|
|-
|
|
|
|}

New "styles" are added after a semi colon, and must end in a semi colon before the end quotation mark. For example:

: | style="text-align: left; color: red; background: white;" |

Otherwise, functions are added side by side before the "|" and separated with a space. For example:

: | rowspan="2" style="color: red;" |

Room should be made to accommodate col- and rowspans. It should also be noted that rowspans expand the table downwards and colspans expand to the right.

==Images==

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'''{{fontcolor1|red|white|Note that .tiff files are not compatible in the wiki - save images as .jpg or preferably .png files}}'''

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Modifiers are separated by vertical lines "|". These modifiers include image position, size, name, caption and frame.

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Type:
! style="background: #0D4F8B; color: white;" | Modifier:
! style="background: #0D4F8B; color: white;" | Result:
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|-
| rowspan="2" style="background: #B7C3D0;" | Size:
| x200px
| Scales image to a height of 200 pixels
|
|-
| 200px
| Scales image to a width of 200 pixels
|
|-
| rowspan="2" style="background: #B7C3D0;" | Frame:
| frame
| Places a frame around the image
|
|-
| none
| Removes a frame from an image
|
|-
| rowspan="3" style="background: #B7C3D0;" | Position:
| left
| Places the image left of the page/cell
|
|-
| center
| Places the image to the centre of the page/cell
|
|-
| right
| Places the image to the right of the page/cell
|
|-
| style="background: #B7C3D0;" | Text:
| ''Anything''
| Places text in a caption under the image. Can include links and references
| Must be placed on the very right of the modifiers
|}

==Jmol Applets==

One of the biggest advantages of writing up in a wiki is the ability to embed HTML objects such as Jmol applets. This chapter provides the basics to inserting and manipulating Jmol applets.

<jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 15; vibration 2;rotate x -20; </script>
<uploadedFileContents>AnthMalTS631tam10.log</uploadedFileContents>
</jmolApplet>
</jmol>

Have a look at the source code for the above Jmol object. Every object must be surrounded by the html tags <nowiki><jmol><jmolApplet></nowiki> and <nowiki></jmol></jmolApplet></nowiki>. This will initialise a Jmol object. The table below shows a few HTML tags you can place inside this object:

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Opening Tag:
! style="background: #0D4F8B; color: white;" | Closing Tag:
! style="background: #0D4F8B; color: white;" | Purpose:
! style="background: #0D4F8B; color: white;" | Essential:
|-
| <nowiki><uploadedFileContents></nowiki>
| <nowiki></uploadedFileContents></nowiki>
| span="col" style="width: 500px" | Put your filename in here. Can be single geometry file (eg .xyz, .mol) or a collection of geometries (eg .log).
| Yes
|-
| <nowiki><color></nowiki>
| <nowiki></color></nowiki>
| The background colour. Single word, such as "white" or "black".
| No
|-
| <nowiki><size></nowiki>
| <nowiki></size></nowiki>
| The size of the object, in pixels, eg "400".
| No
|-
| <nowiki><script></nowiki>
| <nowiki></script></nowiki>
| Allows JSmol script to be interpreted and applied. See below for the essentials, or [http://chemapps.stolaf.edu/jmol/docs/ here] for the full list of JSmol script.
| No
|}

===Script in Jmol===

Within the script tags (<nowiki><script></script></nowiki>), commands can be inserted. The commands are interpreted by the Jmol Applet and are essential, for example, for displaying vibrations. Each command must be separated by a semicolon, eg.

<pre>frame 12; vibration 2;</pre>

A few examples are given below.

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Script:
! style="background: #0D4F8B; color: white;" | Example:
! style="background: #0D4F8B; color: white;" | Purpose:
! style="background: #0D4F8B; color: white;" | Notes:
|-
| span="col" style="width: 300px;" | frame MODEL
| span="col" style="width: 200px;" | frame 10
| span="col" style="width: 400px;" | Selects model 10 from a collection of models and displays it.
| span="col" style="width: 400px;" | To see which model you need, run the Jmol without any script. Right click, select "Model" and find it within the collection. The model number will now be displayed when you right click again.
|-
| vibration PERIOD
| vibration 1
| Displays the vibration of the ''current'' model with a period specified in seconds.
|
|-
| rotate AXIS DEGREES
| rotate x 90
| Rotate about the specified axis.
| To find out which axis you need to rotate about, right click on the Jmol and select "Style" and check "Axes".
|-
| rotate spin AXIS RATE
| rotate spin y 45
| Spins about AXIS, RATE degrees per second.
| Use sparingly.
|-
| select atomno=ATOM_1_NUMBER, atomno=ATOM_2_NUMBER
| select atomno=8, atomno=15
| rowspan="2" | Selects atoms ATOM_1_NUMBER and ATOM_2_NUMBER.
| rowspan="2" | Once atoms are selected, bonds can be modified, or the atoms can be coloured.
|-
| select atomno=[ATOM_1_NUMBER ATOM_2_NUMBER]
| select atomno=[8 15]
|-
| connect BONDTYPE
| connect single<br>connect partial<br>connect none
| Displays the bondtype between selected atoms.
| Useful to highlight bonds, or delete incorrectly displayed bonds using "connect none".
|-
| measure ATOM_1_NUMBER ATOM_2_NUMBER
| measure 8 25
| Measures the distance between atoms ATOM_1_NUMBER and ATOM_2_NUMBER
|
|-
| measure ATOM_1_NUMBER ATOM_2_NUMBER ATOM_3_NUMBER
| measure 8 25 10
| Measures the angle between atoms ATOM_1_NUMBER, ATOM_2_NUMBER and ATOM_3_NUMBER
|
|-
| draw pointgroup
|
| Adds symmetry planes and axes for symmetric or nearly symmetric molecules.
|
|-
| label display
|
| Displays all selected atoms. By default this is all atoms, but use in conjunction with "select" to control which atoms are labelled.
|
|-
| color label COLOUR
| color label red
| Changes the colour of the selected label
| This can be used directly after "label display" ie "label display; color label red"
|}

You can test script before saving the page by right clicking on a Jmol object and selecting "Console". Try out some of the script on the Jmol above by typing in the script in the console and hitting enter.

===MOs with Jmol===

MOs can be displayed using Jmol. This section covers a procedure to achieve this.

<jmol>
<jmolApplet>
<color>white</color>
<size>500</size>
<script>frame 2; mo 47; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>EXO_TS_DFT_POP=FULL_GFPRINT.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

When you submit your job, add the keywords:

<pre>pop=full gfprint</pre>

'''Note:''' If this doesn't work, open the input file (.gjf or .com) and manually add this to the keyword line (where "opt", "freq" etc go).

This will save the MOs to the .log file. Upload the file to the wiki and create the Jmol using this file. Once the Jmol is loaded, right click on it and find the converged structure:

{| class="wikitable"
|[[File:Cheatsheet_MO_Model_Selection.png|400px]]
|-
|'''''Selecting the correct frame'''''
|}

The converged structure will be at the bottom of the list of energies (Note that for a TS calculation such as the above, it is not necessarily the lowest energy). The number on the left, after "1." corresponds to the frame (here it is 16). Use script to load this frame. To get Jmol to render an effect like above, use the following script:

<pre>mo MO_NUMBER; mo nodots nomesh fill translucent; mo titleformat ""</pre>

where MO_NUMBER is the integer representing the MO you wish to display. You can us a combination of dots/nodots, mesh/nomesh, fill/nofill, translucent/opaque to get the desired effect. The threshold density to display the surface (isovalue) can be controlled with:

<pre>mo cutoff ISOVALUE</pre>

where ISOVALUE is the threshold - typically 0.02 in GaussView.

Notice that all the MOs are available when right clicking on the Jmol and choosing "Surfaces/Molecular Orbitals". You can use this to find MO_NUMBER.

'''Note:''' If your molecular orbitals aren't displaying, check that you have selected the correct frame with "frame FRAME_NUMBER".

===Advanced Jmol Example===

If you are experienced with programming you may want to try some of the advanced features of Jmol. The example below includes setting variables, the IF statement, buttons and a dropdown menu. See [http://wiki.jmol.org/index.php/MediaWiki/ExtensionV3 the Jmol Extensions Page] for information about controls, and the [http://chemapps.stolaf.edu/jmol/docs/#if Jmol Interactive Scripting Page] for information about the IF statement.

'''Imaginary and lowest positive vibration of the TS of Anthracene and Maleic Anhydride'''
<jmol> //Group all the HTML within "jmol"
<jmolApplet> //Initialise the applet
<uploadedFileContents>AnthMalTS631tam10.log</uploadedFileContents>
<script>vibrating=0; spinning=0; frame 15; rotate x -20; frank off</script> //Set the variables (vibrating and spinning) as the applet initialises. Also switched off the frank (JSmol that normally appears on the bottom right)
<name>AnthMal</name> //The name of the applet must be set. This is the name that the controls refer to (the target)
</jmolApplet>
<jmolbutton> //Adding a jmol button, which executes code on the target
<script>if(vibrating==0) vibrating=1; vibration 2; else; vibrating=0; vibration off; endif</script> //Using IF functions to make a toggle. If it's not vibrating, set vibration period to 2 and change "vibrating" variable to 1, else switch off vibration and change "vibrating" to 0
<text>Vibration</text>
<target>AnthMal</target>
</jmolbutton>
<jmolbutton>
<script>measure 8 25; measure 7 26</script>
<text>C-C Distances</text>
<target>AnthMal</target>
</jmolbutton>
<jmolbutton>
<script>if(spinning==0) spinning=1; spin; else; spinning=0; spin off; endif</script>
<text>Spin</text>
<target>AnthMal</target>
</jmolbutton>
<jmolmenu> //The dropdown menu. Each item has to be declared individually and can execute script
<item>
<script>frame 15; if(vibrating==0) vibration off; else; vibration 2; endif</script> //Adding vibration code as a safety net. It might not be necessary but it ensures the applet behaves properly
<text>i469/cm</text>
<target>AnthMal</target>
</item>
<item>
<script>frame 16; if(vibrating==0) vibration off; else; vibration 2; endif</script>
<text>54/cm</text>
<target>AnthMal</target>
</item>
</jmolmenu>
</jmol>

Comments are given in the code for the above Jmol in the source code.

Mod:Cheatsheet

2016-11-14T12:51:42Z

Htw14: /* MOs with Jmol */

==Text Formatting==

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Description:
! style="background: #0D4F8B; color: white;" | Input:
! style="background: #0D4F8B; color: white;" | Result:
! style="background: #0D4F8B; color: white;" | Where it can be used:
! style="background: #0D4F8B; color: white;" | Notes:
|-
| Bold
| <nowiki>'''Bold'''</nowiki>
| '''Bold'''
| Anywhere
|
|-
| Italics
| <nowiki>''Italics''</nowiki>
| ''Italics''
| Anywhere
|
|-
| Bold and Italics
| <nowiki>'''''Bold and Italics'''''</nowiki>
| '''''Bold and Italics'''''
| Anywhere
|
|-
| Superscript
| <nowiki>Text<sup>Superscript</sup></nowiki>
| Text<sup>Superscript</sup>
| Anywhere
|
|-
| Subscript
| <nowiki>Text<sub>Subscript</sub></nowiki>
| Text<sub>Subscript</sub>
| Anywhere
|
|-
| rowspan="2" | Preformatted Text
| <nowiki><pre>Preformatted Text</pre></nowiki>
| <pre>Preformatted Text</pre>
| Anywhere
| No formatting can be used within a "pre" box, and it is useful for pasting information that would otherwise be interpreted as formatting.
|-
| <nowiki>{| width=20%</nowiki><br>
<nowiki>| <pre>Preformatted Text</pre></nowiki><br>
<nowiki>|}</nowiki>
|
{| width=20%
| <pre>Preformatted Text</pre>
|}
| Start of a line
| A good trick to use to stop pre boxes from running over the edge of a page is to create a new unformatted table with defined maximum width.
|-
| Ignore Formatting
| <nowiki><nowiki><pre>''Ignore Formatting''</pre></nowiki></nowiki>
| <nowiki><pre>''Ignore Formatting''</pre></nowiki>
| Anywhere
|
|-
| Font Colour
| <nowiki>{{fontcolor1|white|red|White on Red}}</nowiki>
| {{fontcolor1|white|red|White on Red}}
| Anywhere
|
|-
| Internal Links
| <nowiki>[[Main_Page|Chem wiki]]</nowiki>
| [[Main_Page|Chem wiki]]
| Anywhere
| Link name given after <nowiki>"|"</nowiki>
|-
| External Links
| <nowiki>[http://www.imperial.ac.uk/ Imperial Main Page]</nowiki>
| [http://www.imperial.ac.uk/ Imperial Main Page]
| Anywhere
| Link name given after a space " "
|-
| Headers
| <nowiki>==Level 2==</nowiki><br>
<nowiki>===Level 3===</nowiki><br>
<nowiki>====Level 4====</nowiki><br>
<nowiki>=====Level 5=====</nowiki>
|

==Level 2==
===Level 3===
====Level 4 ====
=====Level 5=====
| Start of line
| Do not use Level 1, as this is reserved for titles. <br>
All section headers are placed into the contents box and ordered once there are enough sections.
|-
| Bulleted List
| <nowiki>* Bullet point</nowiki><br>
<nowiki>** Bullet within a bullet</nowiki>
|
* Bullet point
** Bullet within a bullet
| Start of line
|
|-
| Numbered List
| <nowiki># Point 1</nowiki><br>
<nowiki>## Point 1.1</nowiki>
<nowiki># Point 2</nowiki>
|
# Point 1
## Point 1.1
# Point 2
| Start of line
|
|-
| Indent
| No indent <br>
<nowiki>:First indent</nowiki><br>
<nowiki>::Second indent</nowiki><br>
<nowiki>:::Third indent</nowiki>
|
No indent
:First indent
::Second indent
:::Third indent
| Start of line
|
|}

===Forced Line Break <nowiki><br></nowiki>===

Sometimes a line break is needed to separate paragraphs or text in tables. Placing <nowiki><br></nowiki> between two<br> words creates a new line at that point.

[[File:Benzene.png|right|x200px]]

If there's an image aligned to the right and you need to clear it, it's often best to use <nowiki><br style="clear:right"></nowiki> instead of dozens of <nowiki><br></nowiki>'s.

<br style="clear:right">

Now the image isn't getting in the way of unrelated text.

==Table Formatting==

Placing {| at the start of a line creates a table, provided it is closed with |} on a new line at the end of a table. The type of table and general settings are placed after {|. Typically, class="wikitable" is used. Wiki tables have default settings - titles (!) are centred and bold, cell sizes adjust automatically and have default colours.

To create a basic, 3x3 table, copy and paste this code:

{| width=20%
|<pre>{| class="wikitable"
! Column 1, Row 1
! Column 2, Row 1
! Column 3, Row 1
|-
| Column 1, Row 2
| Column 2, Row 2
| Column 3, Row 2
|-
| Column 1, Row 3
| Column 2, Row 3
| Column 3, Row 3
|} </pre>
|}

The result will be:

{| class="wikitable"
! Column 1, Row 1
! Column 2, Row 1
! Column 3, Row 1
|-
| Column 1, Row 2
| Column 2, Row 2
| Column 3, Row 2
|-
| Column 1, Row 3
| Column 2, Row 3
| Column 3, Row 3
|}

Each <nowiki>"!"</nowiki> and <nowiki>"|"</nowiki> represents a new column, the equivalent of moving right in a table, and each <nowiki>"|-"</nowiki> represents a new line, the equivalent of moving down and to the very left. The end tag <nowiki>"|}"</nowiki> defines the end of the table and should be used only once per table. To create a new row, copy from the last separator <nowiki>( |- )</nowiki> to the last text before the table's end tag <nowiki>( |} )</nowiki> and paste on a new line after before the end tag. For the above example this would be:

{| width=20%
|<pre>|-
| Column 1, Row 3
| Column 2, Row 3
| Column 3, Row 3</pre>
|}

To create a new column, add a new <nowiki>"!"</nowiki> for the title row and <nowiki>"|"</nowiki> for every other row.

===Table Styles===

Colour can be added to a table if you feel like breaking away from grey and white. Copy the following code into each cell you want to style:

{| width=20%
|<pre> style="background: #0D4F8B; color: white;" |</pre>
|}

Paste it just after the <nowiki>"!"</nowiki> or <nowiki>"|"</nowiki> for each cell so

{| width=20%
|<pre>{| class="wikitable"
! Column 1, Row 1
! Column 2, Row 1
! Column 3, Row 1
|-
| Column 1, Row 2
| Column 2, Row 2
| Column 3, Row 2
|-
| Column 1, Row 3
| Column 2, Row 3
| Column 3, Row 3
|}</pre>
|}

becomes

{| width=20%
|<pre>{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Column 1, Row 1
! style="background: #0D4F8B; color: white;" | Column 2, Row 1
! style="background: #0D4F8B; color: white;" | Column 3, Row 1
|-
| Column 1, Row 2
| Column 2, Row 2
| Column 3, Row 2
|-
| Column 1, Row 3
| Column 2, Row 3
| Column 3, Row 3
|}</pre>
|}

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Column 1, Row 1
! style="background: #0D4F8B; color: white;" | Column 2, Row 1
! style="background: #0D4F8B; color: white;" | Column 3, Row 1
|-
| Column 1, Row 2
| Column 2, Row 2
| Column 3, Row 2
|-
| Column 1, Row 3
| Column 2, Row 3
| Column 3, Row 3
|}

The #0D4F8B is a web colour, in this case producing a blue colour. [http://www.color-hex.com/ www.color-hex.com] is a good website for converting known colours into hexadecimal web colours.

As is shown in the Text Formatting section, all basic text formats can be used in tables when required, but two other useful controls are alignment and spans:

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Alignment:
! style="background: #0D4F8B; color: white;" | Input:
! style="background: #0D4F8B; color: white;" | Result:
! style="background: #0D4F8B; color: #0D4F8B;" | :::.
|-
| Left
| <nowiki>style="text-align: left;" | Left</nowiki>
| style="text-align: left;" | Left
|
|-
| Centre
| <nowiki>style="text-align: center;" | Centre</nowiki>
| style="text-align: center;" | Centre
|
|-
| Right
| <nowiki>style="text-align: right;" | Right</nowiki>
| style="text-align: right;" | Right
|
|-
| Span 2 columns
| <nowiki>colspan="2" | Span 2 columns</nowiki>
| colspan="2" | Span 2 columns
|-
| Span 2 rows
| <nowiki>rowspan="2" | Span 2 rows</nowiki>
| rowspan="2" | Span 2 rows
|
|-
|
|
|
|}

New "styles" are added after a semi colon, and must end in a semi colon before the end quotation mark. For example:

: | style="text-align: left; color: red; background: white;" |

Otherwise, functions are added side by side before the "|" and separated with a space. For example:

: | rowspan="2" style="color: red;" |

Room should be made to accommodate col- and rowspans. It should also be noted that rowspans expand the table downwards and colspans expand to the right.

==Images==

Images are uploaded via the [[Special:Upload|Upload File]] link in the toolbox. Multiple images can be uploaded via [[Special:MultiUpload|this link]]. All uploaded files are placed in the same location on the server, and so it is important to give each file a '''unique name''', otherwise it may be replaced. This is easily done by writing your username before each file name.

'''{{fontcolor1|red|white|Note that .tiff files are not compatible in the wiki - save images as .jpg or preferably .png files}}'''

An image file's name, once uploaded, looks like this:

File:''name''.''filetype''

Images are embedded onto the page using a pair of double square brackets, <nowiki>"[["</nowiki> and <nowiki>"]]"</nowiki>. The result looks like this:

<nowiki>[[</nowiki>File:''name''.''filetype''|''modifier 1''|''modifier 2''<nowiki>]]</nowiki>

Modifiers are separated by vertical lines "|". These modifiers include image position, size, name, caption and frame.

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Type:
! style="background: #0D4F8B; color: white;" | Modifier:
! style="background: #0D4F8B; color: white;" | Result:
! style="background: #0D4F8B; color: white;" | Notes:
|-
| rowspan="2" style="background: #B7C3D0;" | Size:
| x200px
| Scales image to a height of 200 pixels
|
|-
| 200px
| Scales image to a width of 200 pixels
|
|-
| rowspan="2" style="background: #B7C3D0;" | Frame:
| frame
| Places a frame around the image
|
|-
| none
| Removes a frame from an image
|
|-
| rowspan="3" style="background: #B7C3D0;" | Position:
| left
| Places the image left of the page/cell
|
|-
| center
| Places the image to the centre of the page/cell
|
|-
| right
| Places the image to the right of the page/cell
|
|-
| style="background: #B7C3D0;" | Text:
| ''Anything''
| Places text in a caption under the image. Can include links and references
| Must be placed on the very right of the modifiers
|}

==Jmol Applets==

One of the biggest advantages of writing up in a wiki is the ability to embed HTML objects such as Jmol applets. This chapter provides the basics to inserting and manipulating Jmol applets.

<jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 15; vibration 2;rotate x -20; </script>
<uploadedFileContents>AnthMalTS631tam10.log</uploadedFileContents>
</jmolApplet>
</jmol>

Have a look at the source code for the above Jmol object. Every object must be surrounded by the html tags <nowiki><jmol><jmolApplet></nowiki> and <nowiki></jmol></jmolApplet></nowiki>. This will initialise a Jmol object. The table below shows a few HTML tags you can place inside this object:

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Opening Tag:
! style="background: #0D4F8B; color: white;" | Closing Tag:
! style="background: #0D4F8B; color: white;" | Purpose:
! style="background: #0D4F8B; color: white;" | Essential:
|-
| <nowiki><uploadedFileContents></nowiki>
| <nowiki></uploadedFileContents></nowiki>
| span="col" style="width: 500px" | Put your filename in here. Can be single geometry file (eg .xyz, .mol) or a collection of geometries (eg .log).
| Yes
|-
| <nowiki><color></nowiki>
| <nowiki></color></nowiki>
| The background colour. Single word, such as "white" or "black".
| No
|-
| <nowiki><size></nowiki>
| <nowiki></size></nowiki>
| The size of the object, in pixels, eg "400".
| No
|-
| <nowiki><script></nowiki>
| <nowiki></script></nowiki>
| Allows JSmol script to be interpreted and applied. See below for the essentials, or [http://chemapps.stolaf.edu/jmol/docs/ here] for the full list of JSmol script.
| No
|}

===Script in Jmol===

Within the script tags (<nowiki><script></script></nowiki>), commands can be inserted. The commands are interpreted by the Jmol Applet and are essential, for example, for displaying vibrations. Each command must be separated by a semicolon, eg.

<pre>frame 12; vibration 2;</pre>

A few examples are given below.

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Script:
! style="background: #0D4F8B; color: white;" | Example:
! style="background: #0D4F8B; color: white;" | Purpose:
! style="background: #0D4F8B; color: white;" | Notes:
|-
| span="col" style="width: 300px;" | frame MODEL
| span="col" style="width: 200px;" | frame 10
| span="col" style="width: 400px;" | Selects model 10 from a collection of models and displays it.
| span="col" style="width: 400px;" | To see which model you need, run the Jmol without any script. Right click, select "Model" and find it within the collection. The model number will now be displayed when you right click again.
|-
| vibration PERIOD
| vibration 1
| Displays the vibration of the ''current'' model with a period specified in seconds.
|
|-
| rotate AXIS DEGREES
| rotate x 90
| Rotate about the specified axis.
| To find out which axis you need to rotate about, right click on the Jmol and select "Style" and check "Axes".
|-
| rotate spin AXIS RATE
| rotate spin y 45
| Spins about AXIS, RATE degrees per second.
| Use sparingly.
|-
| select atomno=ATOM_1_NUMBER, atomno=ATOM_2_NUMBER
| select atomno=8, atomno=15
| rowspan="2" | Selects atoms ATOM_1_NUMBER and ATOM_2_NUMBER.
| rowspan="2" | Once atoms are selected, bonds can be modified, or the atoms can be coloured.
|-
| select atomno=[ATOM_1_NUMBER ATOM_2_NUMBER]
| select atomno=[8 15]
|-
| connect BONDTYPE
| connect single<br>connect partial<br>connect none
| Displays the bondtype between selected atoms.
| Useful to highlight bonds, or delete incorrectly displayed bonds using "connect none".
|-
| measure ATOM_1_NUMBER ATOM_2_NUMBER
| measure 8 25
| Measures the distance between atoms ATOM_1_NUMBER and ATOM_2_NUMBER
|
|-
| measure ATOM_1_NUMBER ATOM_2_NUMBER ATOM_3_NUMBER
| measure 8 25 10
| Measures the angle between atoms ATOM_1_NUMBER, ATOM_2_NUMBER and ATOM_3_NUMBER
|
|-
| draw pointgroup
|
| Adds symmetry planes and axes for symmetric or nearly symmetric molecules.
|
|-
| label display
|
| Displays all selected atoms. By default this is all atoms, but use in conjunction with "select" to control which atoms are labelled.
|
|-
| color label COLOUR
| color label red
| Changes the colour of the selected label
| This can be used directly after "label display" ie "label display; color label red"
|}

You can test script before saving the page by right clicking on a Jmol object and selecting "Console". Try out some of the script on the Jmol above by typing in the script in the console and hitting enter.

===MOs with Jmol===

MOs can be displayed using Jmol. This section covers a procedure to achieve this.

<jmol>
<jmolApplet>
<color>white</color>
<size>500</size>
<script>frame 2; mo 46; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>EXO_TS_DFT_POP=FULL_GFPRINT.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

When you submit your job, add the keywords:

<pre>pop=full gfprint</pre>

'''Note:''' If this doesn't work, open the input file (.gjf or .com) and manually add this to the keyword line (where "opt", "freq" etc go).

This will save the MOs to the .log file. Upload the file to the wiki and create the Jmol using this file. Once the Jmol is loaded, right click on it and find the converged structure:

{| class="wikitable"
|[[File:Cheatsheet_MO_Model_Selection.png|400px]]
|-
|'''''Selecting the correct frame'''''
|}

The converged structure will be at the bottom of the list of energies (Note that for a TS calculation such as the above, it is not necessarily the lowest energy). The number on the left, after "1." corresponds to the frame (here it is 16). Use script to load this frame. To get Jmol to render an effect like above, use the following script:

<pre>mo MO_NUMBER; mo nodots nomesh fill translucent; mo titleformat ""</pre>

where MO_NUMBER is the integer representing the MO you wish to display. You can us a combination of dots/nodots, mesh/nomesh, fill/nofill, translucent/opaque to get the desired effect. The threshold density to display the surface (isovalue) can be controlled with:

<pre>mo cutoff ISOVALUE</pre>

where ISOVALUE is the threshold - typically 0.02 in GaussView.

Notice that all the MOs are available when right clicking on the Jmol and choosing "Surfaces/Molecular Orbitals". You can use this to find MO_NUMBER.

'''Note:''' If your molecular orbitals aren't displaying, check that you have selected the correct frame with "frame FRAME_NUMBER".

===Advanced Jmol Example===

If you are experienced with programming you may want to try some of the advanced features of Jmol. The example below includes setting variables, the IF statement, buttons and a dropdown menu. See [http://wiki.jmol.org/index.php/MediaWiki/ExtensionV3 the Jmol Extensions Page] for information about controls, and the [http://chemapps.stolaf.edu/jmol/docs/#if Jmol Interactive Scripting Page] for information about the IF statement.

'''Imaginary and lowest positive vibration of the TS of Anthracene and Maleic Anhydride'''
<jmol> //Group all the HTML within "jmol"
<jmolApplet> //Initialise the applet
<uploadedFileContents>AnthMalTS631tam10.log</uploadedFileContents>
<script>vibrating=0; spinning=0; frame 15; rotate x -20; frank off</script> //Set the variables (vibrating and spinning) as the applet initialises. Also switched off the frank (JSmol that normally appears on the bottom right)
<name>AnthMal</name> //The name of the applet must be set. This is the name that the controls refer to (the target)
</jmolApplet>
<jmolbutton> //Adding a jmol button, which executes code on the target
<script>if(vibrating==0) vibrating=1; vibration 2; else; vibrating=0; vibration off; endif</script> //Using IF functions to make a toggle. If it's not vibrating, set vibration period to 2 and change "vibrating" variable to 1, else switch off vibration and change "vibrating" to 0
<text>Vibration</text>
<target>AnthMal</target>
</jmolbutton>
<jmolbutton>
<script>measure 8 25; measure 7 26</script>
<text>C-C Distances</text>
<target>AnthMal</target>
</jmolbutton>
<jmolbutton>
<script>if(spinning==0) spinning=1; spin; else; spinning=0; spin off; endif</script>
<text>Spin</text>
<target>AnthMal</target>
</jmolbutton>
<jmolmenu> //The dropdown menu. Each item has to be declared individually and can execute script
<item>
<script>frame 15; if(vibrating==0) vibration off; else; vibration 2; endif</script> //Adding vibration code as a safety net. It might not be necessary but it ensures the applet behaves properly
<text>i469/cm</text>
<target>AnthMal</target>
</item>
<item>
<script>frame 16; if(vibrating==0) vibration off; else; vibration 2; endif</script>
<text>54/cm</text>
<target>AnthMal</target>
</item>
</jmolmenu>
</jmol>

Comments are given in the code for the above Jmol in the source code.

Mod:Cheatsheet

2016-11-14T12:50:55Z

Htw14: /* MOs with Jmol */

==Text Formatting==

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Description:
! style="background: #0D4F8B; color: white;" | Input:
! style="background: #0D4F8B; color: white;" | Result:
! style="background: #0D4F8B; color: white;" | Where it can be used:
! style="background: #0D4F8B; color: white;" | Notes:
|-
| Bold
| <nowiki>'''Bold'''</nowiki>
| '''Bold'''
| Anywhere
|
|-
| Italics
| <nowiki>''Italics''</nowiki>
| ''Italics''
| Anywhere
|
|-
| Bold and Italics
| <nowiki>'''''Bold and Italics'''''</nowiki>
| '''''Bold and Italics'''''
| Anywhere
|
|-
| Superscript
| <nowiki>Text<sup>Superscript</sup></nowiki>
| Text<sup>Superscript</sup>
| Anywhere
|
|-
| Subscript
| <nowiki>Text<sub>Subscript</sub></nowiki>
| Text<sub>Subscript</sub>
| Anywhere
|
|-
| rowspan="2" | Preformatted Text
| <nowiki><pre>Preformatted Text</pre></nowiki>
| <pre>Preformatted Text</pre>
| Anywhere
| No formatting can be used within a "pre" box, and it is useful for pasting information that would otherwise be interpreted as formatting.
|-
| <nowiki>{| width=20%</nowiki><br>
<nowiki>| <pre>Preformatted Text</pre></nowiki><br>
<nowiki>|}</nowiki>
|
{| width=20%
| <pre>Preformatted Text</pre>
|}
| Start of a line
| A good trick to use to stop pre boxes from running over the edge of a page is to create a new unformatted table with defined maximum width.
|-
| Ignore Formatting
| <nowiki><nowiki><pre>''Ignore Formatting''</pre></nowiki></nowiki>
| <nowiki><pre>''Ignore Formatting''</pre></nowiki>
| Anywhere
|
|-
| Font Colour
| <nowiki>{{fontcolor1|white|red|White on Red}}</nowiki>
| {{fontcolor1|white|red|White on Red}}
| Anywhere
|
|-
| Internal Links
| <nowiki>[[Main_Page|Chem wiki]]</nowiki>
| [[Main_Page|Chem wiki]]
| Anywhere
| Link name given after <nowiki>"|"</nowiki>
|-
| External Links
| <nowiki>[http://www.imperial.ac.uk/ Imperial Main Page]</nowiki>
| [http://www.imperial.ac.uk/ Imperial Main Page]
| Anywhere
| Link name given after a space " "
|-
| Headers
| <nowiki>==Level 2==</nowiki><br>
<nowiki>===Level 3===</nowiki><br>
<nowiki>====Level 4====</nowiki><br>
<nowiki>=====Level 5=====</nowiki>
|

==Level 2==
===Level 3===
====Level 4 ====
=====Level 5=====
| Start of line
| Do not use Level 1, as this is reserved for titles. <br>
All section headers are placed into the contents box and ordered once there are enough sections.
|-
| Bulleted List
| <nowiki>* Bullet point</nowiki><br>
<nowiki>** Bullet within a bullet</nowiki>
|
* Bullet point
** Bullet within a bullet
| Start of line
|
|-
| Numbered List
| <nowiki># Point 1</nowiki><br>
<nowiki>## Point 1.1</nowiki>
<nowiki># Point 2</nowiki>
|
# Point 1
## Point 1.1
# Point 2
| Start of line
|
|-
| Indent
| No indent <br>
<nowiki>:First indent</nowiki><br>
<nowiki>::Second indent</nowiki><br>
<nowiki>:::Third indent</nowiki>
|
No indent
:First indent
::Second indent
:::Third indent
| Start of line
|
|}

===Forced Line Break <nowiki><br></nowiki>===

Sometimes a line break is needed to separate paragraphs or text in tables. Placing <nowiki><br></nowiki> between two<br> words creates a new line at that point.

[[File:Benzene.png|right|x200px]]

If there's an image aligned to the right and you need to clear it, it's often best to use <nowiki><br style="clear:right"></nowiki> instead of dozens of <nowiki><br></nowiki>'s.

<br style="clear:right">

Now the image isn't getting in the way of unrelated text.

==Table Formatting==

Placing {| at the start of a line creates a table, provided it is closed with |} on a new line at the end of a table. The type of table and general settings are placed after {|. Typically, class="wikitable" is used. Wiki tables have default settings - titles (!) are centred and bold, cell sizes adjust automatically and have default colours.

To create a basic, 3x3 table, copy and paste this code:

{| width=20%
|<pre>{| class="wikitable"
! Column 1, Row 1
! Column 2, Row 1
! Column 3, Row 1
|-
| Column 1, Row 2
| Column 2, Row 2
| Column 3, Row 2
|-
| Column 1, Row 3
| Column 2, Row 3
| Column 3, Row 3
|} </pre>
|}

The result will be:

{| class="wikitable"
! Column 1, Row 1
! Column 2, Row 1
! Column 3, Row 1
|-
| Column 1, Row 2
| Column 2, Row 2
| Column 3, Row 2
|-
| Column 1, Row 3
| Column 2, Row 3
| Column 3, Row 3
|}

Each <nowiki>"!"</nowiki> and <nowiki>"|"</nowiki> represents a new column, the equivalent of moving right in a table, and each <nowiki>"|-"</nowiki> represents a new line, the equivalent of moving down and to the very left. The end tag <nowiki>"|}"</nowiki> defines the end of the table and should be used only once per table. To create a new row, copy from the last separator <nowiki>( |- )</nowiki> to the last text before the table's end tag <nowiki>( |} )</nowiki> and paste on a new line after before the end tag. For the above example this would be:

{| width=20%
|<pre>|-
| Column 1, Row 3
| Column 2, Row 3
| Column 3, Row 3</pre>
|}

To create a new column, add a new <nowiki>"!"</nowiki> for the title row and <nowiki>"|"</nowiki> for every other row.

===Table Styles===

Colour can be added to a table if you feel like breaking away from grey and white. Copy the following code into each cell you want to style:

{| width=20%
|<pre> style="background: #0D4F8B; color: white;" |</pre>
|}

Paste it just after the <nowiki>"!"</nowiki> or <nowiki>"|"</nowiki> for each cell so

{| width=20%
|<pre>{| class="wikitable"
! Column 1, Row 1
! Column 2, Row 1
! Column 3, Row 1
|-
| Column 1, Row 2
| Column 2, Row 2
| Column 3, Row 2
|-
| Column 1, Row 3
| Column 2, Row 3
| Column 3, Row 3
|}</pre>
|}

becomes

{| width=20%
|<pre>{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Column 1, Row 1
! style="background: #0D4F8B; color: white;" | Column 2, Row 1
! style="background: #0D4F8B; color: white;" | Column 3, Row 1
|-
| Column 1, Row 2
| Column 2, Row 2
| Column 3, Row 2
|-
| Column 1, Row 3
| Column 2, Row 3
| Column 3, Row 3
|}</pre>
|}

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Column 1, Row 1
! style="background: #0D4F8B; color: white;" | Column 2, Row 1
! style="background: #0D4F8B; color: white;" | Column 3, Row 1
|-
| Column 1, Row 2
| Column 2, Row 2
| Column 3, Row 2
|-
| Column 1, Row 3
| Column 2, Row 3
| Column 3, Row 3
|}

The #0D4F8B is a web colour, in this case producing a blue colour. [http://www.color-hex.com/ www.color-hex.com] is a good website for converting known colours into hexadecimal web colours.

As is shown in the Text Formatting section, all basic text formats can be used in tables when required, but two other useful controls are alignment and spans:

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Alignment:
! style="background: #0D4F8B; color: white;" | Input:
! style="background: #0D4F8B; color: white;" | Result:
! style="background: #0D4F8B; color: #0D4F8B;" | :::.
|-
| Left
| <nowiki>style="text-align: left;" | Left</nowiki>
| style="text-align: left;" | Left
|
|-
| Centre
| <nowiki>style="text-align: center;" | Centre</nowiki>
| style="text-align: center;" | Centre
|
|-
| Right
| <nowiki>style="text-align: right;" | Right</nowiki>
| style="text-align: right;" | Right
|
|-
| Span 2 columns
| <nowiki>colspan="2" | Span 2 columns</nowiki>
| colspan="2" | Span 2 columns
|-
| Span 2 rows
| <nowiki>rowspan="2" | Span 2 rows</nowiki>
| rowspan="2" | Span 2 rows
|
|-
|
|
|
|}

New "styles" are added after a semi colon, and must end in a semi colon before the end quotation mark. For example:

: | style="text-align: left; color: red; background: white;" |

Otherwise, functions are added side by side before the "|" and separated with a space. For example:

: | rowspan="2" style="color: red;" |

Room should be made to accommodate col- and rowspans. It should also be noted that rowspans expand the table downwards and colspans expand to the right.

==Images==

Images are uploaded via the [[Special:Upload|Upload File]] link in the toolbox. Multiple images can be uploaded via [[Special:MultiUpload|this link]]. All uploaded files are placed in the same location on the server, and so it is important to give each file a '''unique name''', otherwise it may be replaced. This is easily done by writing your username before each file name.

'''{{fontcolor1|red|white|Note that .tiff files are not compatible in the wiki - save images as .jpg or preferably .png files}}'''

An image file's name, once uploaded, looks like this:

File:''name''.''filetype''

Images are embedded onto the page using a pair of double square brackets, <nowiki>"[["</nowiki> and <nowiki>"]]"</nowiki>. The result looks like this:

<nowiki>[[</nowiki>File:''name''.''filetype''|''modifier 1''|''modifier 2''<nowiki>]]</nowiki>

Modifiers are separated by vertical lines "|". These modifiers include image position, size, name, caption and frame.

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Type:
! style="background: #0D4F8B; color: white;" | Modifier:
! style="background: #0D4F8B; color: white;" | Result:
! style="background: #0D4F8B; color: white;" | Notes:
|-
| rowspan="2" style="background: #B7C3D0;" | Size:
| x200px
| Scales image to a height of 200 pixels
|
|-
| 200px
| Scales image to a width of 200 pixels
|
|-
| rowspan="2" style="background: #B7C3D0;" | Frame:
| frame
| Places a frame around the image
|
|-
| none
| Removes a frame from an image
|
|-
| rowspan="3" style="background: #B7C3D0;" | Position:
| left
| Places the image left of the page/cell
|
|-
| center
| Places the image to the centre of the page/cell
|
|-
| right
| Places the image to the right of the page/cell
|
|-
| style="background: #B7C3D0;" | Text:
| ''Anything''
| Places text in a caption under the image. Can include links and references
| Must be placed on the very right of the modifiers
|}

==Jmol Applets==

One of the biggest advantages of writing up in a wiki is the ability to embed HTML objects such as Jmol applets. This chapter provides the basics to inserting and manipulating Jmol applets.

<jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 15; vibration 2;rotate x -20; </script>
<uploadedFileContents>AnthMalTS631tam10.log</uploadedFileContents>
</jmolApplet>
</jmol>

Have a look at the source code for the above Jmol object. Every object must be surrounded by the html tags <nowiki><jmol><jmolApplet></nowiki> and <nowiki></jmol></jmolApplet></nowiki>. This will initialise a Jmol object. The table below shows a few HTML tags you can place inside this object:

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Opening Tag:
! style="background: #0D4F8B; color: white;" | Closing Tag:
! style="background: #0D4F8B; color: white;" | Purpose:
! style="background: #0D4F8B; color: white;" | Essential:
|-
| <nowiki><uploadedFileContents></nowiki>
| <nowiki></uploadedFileContents></nowiki>
| span="col" style="width: 500px" | Put your filename in here. Can be single geometry file (eg .xyz, .mol) or a collection of geometries (eg .log).
| Yes
|-
| <nowiki><color></nowiki>
| <nowiki></color></nowiki>
| The background colour. Single word, such as "white" or "black".
| No
|-
| <nowiki><size></nowiki>
| <nowiki></size></nowiki>
| The size of the object, in pixels, eg "400".
| No
|-
| <nowiki><script></nowiki>
| <nowiki></script></nowiki>
| Allows JSmol script to be interpreted and applied. See below for the essentials, or [http://chemapps.stolaf.edu/jmol/docs/ here] for the full list of JSmol script.
| No
|}

===Script in Jmol===

Within the script tags (<nowiki><script></script></nowiki>), commands can be inserted. The commands are interpreted by the Jmol Applet and are essential, for example, for displaying vibrations. Each command must be separated by a semicolon, eg.

<pre>frame 12; vibration 2;</pre>

A few examples are given below.

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Script:
! style="background: #0D4F8B; color: white;" | Example:
! style="background: #0D4F8B; color: white;" | Purpose:
! style="background: #0D4F8B; color: white;" | Notes:
|-
| span="col" style="width: 300px;" | frame MODEL
| span="col" style="width: 200px;" | frame 10
| span="col" style="width: 400px;" | Selects model 10 from a collection of models and displays it.
| span="col" style="width: 400px;" | To see which model you need, run the Jmol without any script. Right click, select "Model" and find it within the collection. The model number will now be displayed when you right click again.
|-
| vibration PERIOD
| vibration 1
| Displays the vibration of the ''current'' model with a period specified in seconds.
|
|-
| rotate AXIS DEGREES
| rotate x 90
| Rotate about the specified axis.
| To find out which axis you need to rotate about, right click on the Jmol and select "Style" and check "Axes".
|-
| rotate spin AXIS RATE
| rotate spin y 45
| Spins about AXIS, RATE degrees per second.
| Use sparingly.
|-
| select atomno=ATOM_1_NUMBER, atomno=ATOM_2_NUMBER
| select atomno=8, atomno=15
| rowspan="2" | Selects atoms ATOM_1_NUMBER and ATOM_2_NUMBER.
| rowspan="2" | Once atoms are selected, bonds can be modified, or the atoms can be coloured.
|-
| select atomno=[ATOM_1_NUMBER ATOM_2_NUMBER]
| select atomno=[8 15]
|-
| connect BONDTYPE
| connect single<br>connect partial<br>connect none
| Displays the bondtype between selected atoms.
| Useful to highlight bonds, or delete incorrectly displayed bonds using "connect none".
|-
| measure ATOM_1_NUMBER ATOM_2_NUMBER
| measure 8 25
| Measures the distance between atoms ATOM_1_NUMBER and ATOM_2_NUMBER
|
|-
| measure ATOM_1_NUMBER ATOM_2_NUMBER ATOM_3_NUMBER
| measure 8 25 10
| Measures the angle between atoms ATOM_1_NUMBER, ATOM_2_NUMBER and ATOM_3_NUMBER
|
|-
| draw pointgroup
|
| Adds symmetry planes and axes for symmetric or nearly symmetric molecules.
|
|-
| label display
|
| Displays all selected atoms. By default this is all atoms, but use in conjunction with "select" to control which atoms are labelled.
|
|-
| color label COLOUR
| color label red
| Changes the colour of the selected label
| This can be used directly after "label display" ie "label display; color label red"
|}

You can test script before saving the page by right clicking on a Jmol object and selecting "Console". Try out some of the script on the Jmol above by typing in the script in the console and hitting enter.

===MOs with Jmol===

MOs can be displayed using Jmol. This section covers a procedure to achieve this.

<jmol>
<jmolApplet>
<color>white</color>
<size>500</size>
<script>frame 2; mo 45; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>EXO_TS_DFT_POP=FULL_GFPRINT.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

When you submit your job, add the keywords:

<pre>pop=full gfprint</pre>

'''Note:''' If this doesn't work, open the input file (.gjf or .com) and manually add this to the keyword line (where "opt", "freq" etc go).

This will save the MOs to the .log file. Upload the file to the wiki and create the Jmol using this file. Once the Jmol is loaded, right click on it and find the converged structure:

{| class="wikitable"
|[[File:Cheatsheet_MO_Model_Selection.png|400px]]
|-
|'''''Selecting the correct frame'''''
|}

The converged structure will be at the bottom of the list of energies (Note that for a TS calculation such as the above, it is not necessarily the lowest energy). The number on the left, after "1." corresponds to the frame (here it is 16). Use script to load this frame. To get Jmol to render an effect like above, use the following script:

<pre>mo MO_NUMBER; mo nodots nomesh fill translucent; mo titleformat ""</pre>

where MO_NUMBER is the integer representing the MO you wish to display. You can us a combination of dots/nodots, mesh/nomesh, fill/nofill, translucent/opaque to get the desired effect. The threshold density to display the surface (isovalue) can be controlled with:

<pre>mo cutoff ISOVALUE</pre>

where ISOVALUE is the threshold - typically 0.02 in GaussView.

Notice that all the MOs are available when right clicking on the Jmol and choosing "Surfaces/Molecular Orbitals". You can use this to find MO_NUMBER.

'''Note:''' If your molecular orbitals aren't displaying, check that you have selected the correct frame with "frame FRAME_NUMBER".

===Advanced Jmol Example===

If you are experienced with programming you may want to try some of the advanced features of Jmol. The example below includes setting variables, the IF statement, buttons and a dropdown menu. See [http://wiki.jmol.org/index.php/MediaWiki/ExtensionV3 the Jmol Extensions Page] for information about controls, and the [http://chemapps.stolaf.edu/jmol/docs/#if Jmol Interactive Scripting Page] for information about the IF statement.

'''Imaginary and lowest positive vibration of the TS of Anthracene and Maleic Anhydride'''
<jmol> //Group all the HTML within "jmol"
<jmolApplet> //Initialise the applet
<uploadedFileContents>AnthMalTS631tam10.log</uploadedFileContents>
<script>vibrating=0; spinning=0; frame 15; rotate x -20; frank off</script> //Set the variables (vibrating and spinning) as the applet initialises. Also switched off the frank (JSmol that normally appears on the bottom right)
<name>AnthMal</name> //The name of the applet must be set. This is the name that the controls refer to (the target)
</jmolApplet>
<jmolbutton> //Adding a jmol button, which executes code on the target
<script>if(vibrating==0) vibrating=1; vibration 2; else; vibrating=0; vibration off; endif</script> //Using IF functions to make a toggle. If it's not vibrating, set vibration period to 2 and change "vibrating" variable to 1, else switch off vibration and change "vibrating" to 0
<text>Vibration</text>
<target>AnthMal</target>
</jmolbutton>
<jmolbutton>
<script>measure 8 25; measure 7 26</script>
<text>C-C Distances</text>
<target>AnthMal</target>
</jmolbutton>
<jmolbutton>
<script>if(spinning==0) spinning=1; spin; else; spinning=0; spin off; endif</script>
<text>Spin</text>
<target>AnthMal</target>
</jmolbutton>
<jmolmenu> //The dropdown menu. Each item has to be declared individually and can execute script
<item>
<script>frame 15; if(vibrating==0) vibration off; else; vibration 2; endif</script> //Adding vibration code as a safety net. It might not be necessary but it ensures the applet behaves properly
<text>i469/cm</text>
<target>AnthMal</target>
</item>
<item>
<script>frame 16; if(vibrating==0) vibration off; else; vibration 2; endif</script>
<text>54/cm</text>
<target>AnthMal</target>
</item>
</jmolmenu>
</jmol>

Comments are given in the code for the above Jmol in the source code.

Mod:Cheatsheet

2016-11-14T12:48:34Z

Htw14: /* MOs with Jmol */

==Text Formatting==

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Description:
! style="background: #0D4F8B; color: white;" | Input:
! style="background: #0D4F8B; color: white;" | Result:
! style="background: #0D4F8B; color: white;" | Where it can be used:
! style="background: #0D4F8B; color: white;" | Notes:
|-
| Bold
| <nowiki>'''Bold'''</nowiki>
| '''Bold'''
| Anywhere
|
|-
| Italics
| <nowiki>''Italics''</nowiki>
| ''Italics''
| Anywhere
|
|-
| Bold and Italics
| <nowiki>'''''Bold and Italics'''''</nowiki>
| '''''Bold and Italics'''''
| Anywhere
|
|-
| Superscript
| <nowiki>Text<sup>Superscript</sup></nowiki>
| Text<sup>Superscript</sup>
| Anywhere
|
|-
| Subscript
| <nowiki>Text<sub>Subscript</sub></nowiki>
| Text<sub>Subscript</sub>
| Anywhere
|
|-
| rowspan="2" | Preformatted Text
| <nowiki><pre>Preformatted Text</pre></nowiki>
| <pre>Preformatted Text</pre>
| Anywhere
| No formatting can be used within a "pre" box, and it is useful for pasting information that would otherwise be interpreted as formatting.
|-
| <nowiki>{| width=20%</nowiki><br>
<nowiki>| <pre>Preformatted Text</pre></nowiki><br>
<nowiki>|}</nowiki>
|
{| width=20%
| <pre>Preformatted Text</pre>
|}
| Start of a line
| A good trick to use to stop pre boxes from running over the edge of a page is to create a new unformatted table with defined maximum width.
|-
| Ignore Formatting
| <nowiki><nowiki><pre>''Ignore Formatting''</pre></nowiki></nowiki>
| <nowiki><pre>''Ignore Formatting''</pre></nowiki>
| Anywhere
|
|-
| Font Colour
| <nowiki>{{fontcolor1|white|red|White on Red}}</nowiki>
| {{fontcolor1|white|red|White on Red}}
| Anywhere
|
|-
| Internal Links
| <nowiki>[[Main_Page|Chem wiki]]</nowiki>
| [[Main_Page|Chem wiki]]
| Anywhere
| Link name given after <nowiki>"|"</nowiki>
|-
| External Links
| <nowiki>[http://www.imperial.ac.uk/ Imperial Main Page]</nowiki>
| [http://www.imperial.ac.uk/ Imperial Main Page]
| Anywhere
| Link name given after a space " "
|-
| Headers
| <nowiki>==Level 2==</nowiki><br>
<nowiki>===Level 3===</nowiki><br>
<nowiki>====Level 4====</nowiki><br>
<nowiki>=====Level 5=====</nowiki>
|

==Level 2==
===Level 3===
====Level 4 ====
=====Level 5=====
| Start of line
| Do not use Level 1, as this is reserved for titles. <br>
All section headers are placed into the contents box and ordered once there are enough sections.
|-
| Bulleted List
| <nowiki>* Bullet point</nowiki><br>
<nowiki>** Bullet within a bullet</nowiki>
|
* Bullet point
** Bullet within a bullet
| Start of line
|
|-
| Numbered List
| <nowiki># Point 1</nowiki><br>
<nowiki>## Point 1.1</nowiki>
<nowiki># Point 2</nowiki>
|
# Point 1
## Point 1.1
# Point 2
| Start of line
|
|-
| Indent
| No indent <br>
<nowiki>:First indent</nowiki><br>
<nowiki>::Second indent</nowiki><br>
<nowiki>:::Third indent</nowiki>
|
No indent
:First indent
::Second indent
:::Third indent
| Start of line
|
|}

===Forced Line Break <nowiki><br></nowiki>===

Sometimes a line break is needed to separate paragraphs or text in tables. Placing <nowiki><br></nowiki> between two<br> words creates a new line at that point.

[[File:Benzene.png|right|x200px]]

If there's an image aligned to the right and you need to clear it, it's often best to use <nowiki><br style="clear:right"></nowiki> instead of dozens of <nowiki><br></nowiki>'s.

<br style="clear:right">

Now the image isn't getting in the way of unrelated text.

==Table Formatting==

Placing {| at the start of a line creates a table, provided it is closed with |} on a new line at the end of a table. The type of table and general settings are placed after {|. Typically, class="wikitable" is used. Wiki tables have default settings - titles (!) are centred and bold, cell sizes adjust automatically and have default colours.

To create a basic, 3x3 table, copy and paste this code:

{| width=20%
|<pre>{| class="wikitable"
! Column 1, Row 1
! Column 2, Row 1
! Column 3, Row 1
|-
| Column 1, Row 2
| Column 2, Row 2
| Column 3, Row 2
|-
| Column 1, Row 3
| Column 2, Row 3
| Column 3, Row 3
|} </pre>
|}

The result will be:

{| class="wikitable"
! Column 1, Row 1
! Column 2, Row 1
! Column 3, Row 1
|-
| Column 1, Row 2
| Column 2, Row 2
| Column 3, Row 2
|-
| Column 1, Row 3
| Column 2, Row 3
| Column 3, Row 3
|}

Each <nowiki>"!"</nowiki> and <nowiki>"|"</nowiki> represents a new column, the equivalent of moving right in a table, and each <nowiki>"|-"</nowiki> represents a new line, the equivalent of moving down and to the very left. The end tag <nowiki>"|}"</nowiki> defines the end of the table and should be used only once per table. To create a new row, copy from the last separator <nowiki>( |- )</nowiki> to the last text before the table's end tag <nowiki>( |} )</nowiki> and paste on a new line after before the end tag. For the above example this would be:

{| width=20%
|<pre>|-
| Column 1, Row 3
| Column 2, Row 3
| Column 3, Row 3</pre>
|}

To create a new column, add a new <nowiki>"!"</nowiki> for the title row and <nowiki>"|"</nowiki> for every other row.

===Table Styles===

Colour can be added to a table if you feel like breaking away from grey and white. Copy the following code into each cell you want to style:

{| width=20%
|<pre> style="background: #0D4F8B; color: white;" |</pre>
|}

Paste it just after the <nowiki>"!"</nowiki> or <nowiki>"|"</nowiki> for each cell so

{| width=20%
|<pre>{| class="wikitable"
! Column 1, Row 1
! Column 2, Row 1
! Column 3, Row 1
|-
| Column 1, Row 2
| Column 2, Row 2
| Column 3, Row 2
|-
| Column 1, Row 3
| Column 2, Row 3
| Column 3, Row 3
|}</pre>
|}

becomes

{| width=20%
|<pre>{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Column 1, Row 1
! style="background: #0D4F8B; color: white;" | Column 2, Row 1
! style="background: #0D4F8B; color: white;" | Column 3, Row 1
|-
| Column 1, Row 2
| Column 2, Row 2
| Column 3, Row 2
|-
| Column 1, Row 3
| Column 2, Row 3
| Column 3, Row 3
|}</pre>
|}

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Column 1, Row 1
! style="background: #0D4F8B; color: white;" | Column 2, Row 1
! style="background: #0D4F8B; color: white;" | Column 3, Row 1
|-
| Column 1, Row 2
| Column 2, Row 2
| Column 3, Row 2
|-
| Column 1, Row 3
| Column 2, Row 3
| Column 3, Row 3
|}

The #0D4F8B is a web colour, in this case producing a blue colour. [http://www.color-hex.com/ www.color-hex.com] is a good website for converting known colours into hexadecimal web colours.

As is shown in the Text Formatting section, all basic text formats can be used in tables when required, but two other useful controls are alignment and spans:

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Alignment:
! style="background: #0D4F8B; color: white;" | Input:
! style="background: #0D4F8B; color: white;" | Result:
! style="background: #0D4F8B; color: #0D4F8B;" | :::.
|-
| Left
| <nowiki>style="text-align: left;" | Left</nowiki>
| style="text-align: left;" | Left
|
|-
| Centre
| <nowiki>style="text-align: center;" | Centre</nowiki>
| style="text-align: center;" | Centre
|
|-
| Right
| <nowiki>style="text-align: right;" | Right</nowiki>
| style="text-align: right;" | Right
|
|-
| Span 2 columns
| <nowiki>colspan="2" | Span 2 columns</nowiki>
| colspan="2" | Span 2 columns
|-
| Span 2 rows
| <nowiki>rowspan="2" | Span 2 rows</nowiki>
| rowspan="2" | Span 2 rows
|
|-
|
|
|
|}

New "styles" are added after a semi colon, and must end in a semi colon before the end quotation mark. For example:

: | style="text-align: left; color: red; background: white;" |

Otherwise, functions are added side by side before the "|" and separated with a space. For example:

: | rowspan="2" style="color: red;" |

Room should be made to accommodate col- and rowspans. It should also be noted that rowspans expand the table downwards and colspans expand to the right.

==Images==

Images are uploaded via the [[Special:Upload|Upload File]] link in the toolbox. Multiple images can be uploaded via [[Special:MultiUpload|this link]]. All uploaded files are placed in the same location on the server, and so it is important to give each file a '''unique name''', otherwise it may be replaced. This is easily done by writing your username before each file name.

'''{{fontcolor1|red|white|Note that .tiff files are not compatible in the wiki - save images as .jpg or preferably .png files}}'''

An image file's name, once uploaded, looks like this:

File:''name''.''filetype''

Images are embedded onto the page using a pair of double square brackets, <nowiki>"[["</nowiki> and <nowiki>"]]"</nowiki>. The result looks like this:

<nowiki>[[</nowiki>File:''name''.''filetype''|''modifier 1''|''modifier 2''<nowiki>]]</nowiki>

Modifiers are separated by vertical lines "|". These modifiers include image position, size, name, caption and frame.

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Type:
! style="background: #0D4F8B; color: white;" | Modifier:
! style="background: #0D4F8B; color: white;" | Result:
! style="background: #0D4F8B; color: white;" | Notes:
|-
| rowspan="2" style="background: #B7C3D0;" | Size:
| x200px
| Scales image to a height of 200 pixels
|
|-
| 200px
| Scales image to a width of 200 pixels
|
|-
| rowspan="2" style="background: #B7C3D0;" | Frame:
| frame
| Places a frame around the image
|
|-
| none
| Removes a frame from an image
|
|-
| rowspan="3" style="background: #B7C3D0;" | Position:
| left
| Places the image left of the page/cell
|
|-
| center
| Places the image to the centre of the page/cell
|
|-
| right
| Places the image to the right of the page/cell
|
|-
| style="background: #B7C3D0;" | Text:
| ''Anything''
| Places text in a caption under the image. Can include links and references
| Must be placed on the very right of the modifiers
|}

==Jmol Applets==

One of the biggest advantages of writing up in a wiki is the ability to embed HTML objects such as Jmol applets. This chapter provides the basics to inserting and manipulating Jmol applets.

<jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 15; vibration 2;rotate x -20; </script>
<uploadedFileContents>AnthMalTS631tam10.log</uploadedFileContents>
</jmolApplet>
</jmol>

Have a look at the source code for the above Jmol object. Every object must be surrounded by the html tags <nowiki><jmol><jmolApplet></nowiki> and <nowiki></jmol></jmolApplet></nowiki>. This will initialise a Jmol object. The table below shows a few HTML tags you can place inside this object:

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Opening Tag:
! style="background: #0D4F8B; color: white;" | Closing Tag:
! style="background: #0D4F8B; color: white;" | Purpose:
! style="background: #0D4F8B; color: white;" | Essential:
|-
| <nowiki><uploadedFileContents></nowiki>
| <nowiki></uploadedFileContents></nowiki>
| span="col" style="width: 500px" | Put your filename in here. Can be single geometry file (eg .xyz, .mol) or a collection of geometries (eg .log).
| Yes
|-
| <nowiki><color></nowiki>
| <nowiki></color></nowiki>
| The background colour. Single word, such as "white" or "black".
| No
|-
| <nowiki><size></nowiki>
| <nowiki></size></nowiki>
| The size of the object, in pixels, eg "400".
| No
|-
| <nowiki><script></nowiki>
| <nowiki></script></nowiki>
| Allows JSmol script to be interpreted and applied. See below for the essentials, or [http://chemapps.stolaf.edu/jmol/docs/ here] for the full list of JSmol script.
| No
|}

===Script in Jmol===

Within the script tags (<nowiki><script></script></nowiki>), commands can be inserted. The commands are interpreted by the Jmol Applet and are essential, for example, for displaying vibrations. Each command must be separated by a semicolon, eg.

<pre>frame 12; vibration 2;</pre>

A few examples are given below.

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Script:
! style="background: #0D4F8B; color: white;" | Example:
! style="background: #0D4F8B; color: white;" | Purpose:
! style="background: #0D4F8B; color: white;" | Notes:
|-
| span="col" style="width: 300px;" | frame MODEL
| span="col" style="width: 200px;" | frame 10
| span="col" style="width: 400px;" | Selects model 10 from a collection of models and displays it.
| span="col" style="width: 400px;" | To see which model you need, run the Jmol without any script. Right click, select "Model" and find it within the collection. The model number will now be displayed when you right click again.
|-
| vibration PERIOD
| vibration 1
| Displays the vibration of the ''current'' model with a period specified in seconds.
|
|-
| rotate AXIS DEGREES
| rotate x 90
| Rotate about the specified axis.
| To find out which axis you need to rotate about, right click on the Jmol and select "Style" and check "Axes".
|-
| rotate spin AXIS RATE
| rotate spin y 45
| Spins about AXIS, RATE degrees per second.
| Use sparingly.
|-
| select atomno=ATOM_1_NUMBER, atomno=ATOM_2_NUMBER
| select atomno=8, atomno=15
| rowspan="2" | Selects atoms ATOM_1_NUMBER and ATOM_2_NUMBER.
| rowspan="2" | Once atoms are selected, bonds can be modified, or the atoms can be coloured.
|-
| select atomno=[ATOM_1_NUMBER ATOM_2_NUMBER]
| select atomno=[8 15]
|-
| connect BONDTYPE
| connect single<br>connect partial<br>connect none
| Displays the bondtype between selected atoms.
| Useful to highlight bonds, or delete incorrectly displayed bonds using "connect none".
|-
| measure ATOM_1_NUMBER ATOM_2_NUMBER
| measure 8 25
| Measures the distance between atoms ATOM_1_NUMBER and ATOM_2_NUMBER
|
|-
| measure ATOM_1_NUMBER ATOM_2_NUMBER ATOM_3_NUMBER
| measure 8 25 10
| Measures the angle between atoms ATOM_1_NUMBER, ATOM_2_NUMBER and ATOM_3_NUMBER
|
|-
| draw pointgroup
|
| Adds symmetry planes and axes for symmetric or nearly symmetric molecules.
|
|-
| label display
|
| Displays all selected atoms. By default this is all atoms, but use in conjunction with "select" to control which atoms are labelled.
|
|-
| color label COLOUR
| color label red
| Changes the colour of the selected label
| This can be used directly after "label display" ie "label display; color label red"
|}

You can test script before saving the page by right clicking on a Jmol object and selecting "Console". Try out some of the script on the Jmol above by typing in the script in the console and hitting enter.

===MOs with Jmol===

MOs can be displayed using Jmol. This section covers a procedure to achieve this.

<jmol>
<jmolApplet>
<color>white</color>
<size>500</size>
<script>frame 2; mo ; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>EXO_TS_DFT_POP=FULL_GFPRINT.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

When you submit your job, add the keywords:

<pre>pop=full gfprint</pre>

'''Note:''' If this doesn't work, open the input file (.gjf or .com) and manually add this to the keyword line (where "opt", "freq" etc go).

This will save the MOs to the .log file. Upload the file to the wiki and create the Jmol using this file. Once the Jmol is loaded, right click on it and find the converged structure:

{| class="wikitable"
|[[File:Cheatsheet_MO_Model_Selection.png|400px]]
|-
|'''''Selecting the correct frame'''''
|}

The converged structure will be at the bottom of the list of energies (Note that for a TS calculation such as the above, it is not necessarily the lowest energy). The number on the left, after "1." corresponds to the frame (here it is 16). Use script to load this frame. To get Jmol to render an effect like above, use the following script:

<pre>mo MO_NUMBER; mo nodots nomesh fill translucent; mo titleformat ""</pre>

where MO_NUMBER is the integer representing the MO you wish to display. You can us a combination of dots/nodots, mesh/nomesh, fill/nofill, translucent/opaque to get the desired effect. The threshold density to display the surface (isovalue) can be controlled with:

<pre>mo cutoff ISOVALUE</pre>

where ISOVALUE is the threshold - typically 0.02 in GaussView.

Notice that all the MOs are available when right clicking on the Jmol and choosing "Surfaces/Molecular Orbitals". You can use this to find MO_NUMBER.

'''Note:''' If your molecular orbitals aren't displaying, check that you have selected the correct frame with "frame FRAME_NUMBER".

===Advanced Jmol Example===

If you are experienced with programming you may want to try some of the advanced features of Jmol. The example below includes setting variables, the IF statement, buttons and a dropdown menu. See [http://wiki.jmol.org/index.php/MediaWiki/ExtensionV3 the Jmol Extensions Page] for information about controls, and the [http://chemapps.stolaf.edu/jmol/docs/#if Jmol Interactive Scripting Page] for information about the IF statement.

'''Imaginary and lowest positive vibration of the TS of Anthracene and Maleic Anhydride'''
<jmol> //Group all the HTML within "jmol"
<jmolApplet> //Initialise the applet
<uploadedFileContents>AnthMalTS631tam10.log</uploadedFileContents>
<script>vibrating=0; spinning=0; frame 15; rotate x -20; frank off</script> //Set the variables (vibrating and spinning) as the applet initialises. Also switched off the frank (JSmol that normally appears on the bottom right)
<name>AnthMal</name> //The name of the applet must be set. This is the name that the controls refer to (the target)
</jmolApplet>
<jmolbutton> //Adding a jmol button, which executes code on the target
<script>if(vibrating==0) vibrating=1; vibration 2; else; vibrating=0; vibration off; endif</script> //Using IF functions to make a toggle. If it's not vibrating, set vibration period to 2 and change "vibrating" variable to 1, else switch off vibration and change "vibrating" to 0
<text>Vibration</text>
<target>AnthMal</target>
</jmolbutton>
<jmolbutton>
<script>measure 8 25; measure 7 26</script>
<text>C-C Distances</text>
<target>AnthMal</target>
</jmolbutton>
<jmolbutton>
<script>if(spinning==0) spinning=1; spin; else; spinning=0; spin off; endif</script>
<text>Spin</text>
<target>AnthMal</target>
</jmolbutton>
<jmolmenu> //The dropdown menu. Each item has to be declared individually and can execute script
<item>
<script>frame 15; if(vibrating==0) vibration off; else; vibration 2; endif</script> //Adding vibration code as a safety net. It might not be necessary but it ensures the applet behaves properly
<text>i469/cm</text>
<target>AnthMal</target>
</item>
<item>
<script>frame 16; if(vibrating==0) vibration off; else; vibration 2; endif</script>
<text>54/cm</text>
<target>AnthMal</target>
</item>
</jmolmenu>
</jmol>

Comments are given in the code for the above Jmol in the source code.

Mod:Cheatsheet

2016-11-14T12:47:52Z

Htw14: /* MOs with Jmol */

==Text Formatting==

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Description:
! style="background: #0D4F8B; color: white;" | Input:
! style="background: #0D4F8B; color: white;" | Result:
! style="background: #0D4F8B; color: white;" | Where it can be used:
! style="background: #0D4F8B; color: white;" | Notes:
|-
| Bold
| <nowiki>'''Bold'''</nowiki>
| '''Bold'''
| Anywhere
|
|-
| Italics
| <nowiki>''Italics''</nowiki>
| ''Italics''
| Anywhere
|
|-
| Bold and Italics
| <nowiki>'''''Bold and Italics'''''</nowiki>
| '''''Bold and Italics'''''
| Anywhere
|
|-
| Superscript
| <nowiki>Text<sup>Superscript</sup></nowiki>
| Text<sup>Superscript</sup>
| Anywhere
|
|-
| Subscript
| <nowiki>Text<sub>Subscript</sub></nowiki>
| Text<sub>Subscript</sub>
| Anywhere
|
|-
| rowspan="2" | Preformatted Text
| <nowiki><pre>Preformatted Text</pre></nowiki>
| <pre>Preformatted Text</pre>
| Anywhere
| No formatting can be used within a "pre" box, and it is useful for pasting information that would otherwise be interpreted as formatting.
|-
| <nowiki>{| width=20%</nowiki><br>
<nowiki>| <pre>Preformatted Text</pre></nowiki><br>
<nowiki>|}</nowiki>
|
{| width=20%
| <pre>Preformatted Text</pre>
|}
| Start of a line
| A good trick to use to stop pre boxes from running over the edge of a page is to create a new unformatted table with defined maximum width.
|-
| Ignore Formatting
| <nowiki><nowiki><pre>''Ignore Formatting''</pre></nowiki></nowiki>
| <nowiki><pre>''Ignore Formatting''</pre></nowiki>
| Anywhere
|
|-
| Font Colour
| <nowiki>{{fontcolor1|white|red|White on Red}}</nowiki>
| {{fontcolor1|white|red|White on Red}}
| Anywhere
|
|-
| Internal Links
| <nowiki>[[Main_Page|Chem wiki]]</nowiki>
| [[Main_Page|Chem wiki]]
| Anywhere
| Link name given after <nowiki>"|"</nowiki>
|-
| External Links
| <nowiki>[http://www.imperial.ac.uk/ Imperial Main Page]</nowiki>
| [http://www.imperial.ac.uk/ Imperial Main Page]
| Anywhere
| Link name given after a space " "
|-
| Headers
| <nowiki>==Level 2==</nowiki><br>
<nowiki>===Level 3===</nowiki><br>
<nowiki>====Level 4====</nowiki><br>
<nowiki>=====Level 5=====</nowiki>
|

==Level 2==
===Level 3===
====Level 4 ====
=====Level 5=====
| Start of line
| Do not use Level 1, as this is reserved for titles. <br>
All section headers are placed into the contents box and ordered once there are enough sections.
|-
| Bulleted List
| <nowiki>* Bullet point</nowiki><br>
<nowiki>** Bullet within a bullet</nowiki>
|
* Bullet point
** Bullet within a bullet
| Start of line
|
|-
| Numbered List
| <nowiki># Point 1</nowiki><br>
<nowiki>## Point 1.1</nowiki>
<nowiki># Point 2</nowiki>
|
# Point 1
## Point 1.1
# Point 2
| Start of line
|
|-
| Indent
| No indent <br>
<nowiki>:First indent</nowiki><br>
<nowiki>::Second indent</nowiki><br>
<nowiki>:::Third indent</nowiki>
|
No indent
:First indent
::Second indent
:::Third indent
| Start of line
|
|}

===Forced Line Break <nowiki><br></nowiki>===

Sometimes a line break is needed to separate paragraphs or text in tables. Placing <nowiki><br></nowiki> between two<br> words creates a new line at that point.

[[File:Benzene.png|right|x200px]]

If there's an image aligned to the right and you need to clear it, it's often best to use <nowiki><br style="clear:right"></nowiki> instead of dozens of <nowiki><br></nowiki>'s.

<br style="clear:right">

Now the image isn't getting in the way of unrelated text.

==Table Formatting==

Placing {| at the start of a line creates a table, provided it is closed with |} on a new line at the end of a table. The type of table and general settings are placed after {|. Typically, class="wikitable" is used. Wiki tables have default settings - titles (!) are centred and bold, cell sizes adjust automatically and have default colours.

To create a basic, 3x3 table, copy and paste this code:

{| width=20%
|<pre>{| class="wikitable"
! Column 1, Row 1
! Column 2, Row 1
! Column 3, Row 1
|-
| Column 1, Row 2
| Column 2, Row 2
| Column 3, Row 2
|-
| Column 1, Row 3
| Column 2, Row 3
| Column 3, Row 3
|} </pre>
|}

The result will be:

{| class="wikitable"
! Column 1, Row 1
! Column 2, Row 1
! Column 3, Row 1
|-
| Column 1, Row 2
| Column 2, Row 2
| Column 3, Row 2
|-
| Column 1, Row 3
| Column 2, Row 3
| Column 3, Row 3
|}

Each <nowiki>"!"</nowiki> and <nowiki>"|"</nowiki> represents a new column, the equivalent of moving right in a table, and each <nowiki>"|-"</nowiki> represents a new line, the equivalent of moving down and to the very left. The end tag <nowiki>"|}"</nowiki> defines the end of the table and should be used only once per table. To create a new row, copy from the last separator <nowiki>( |- )</nowiki> to the last text before the table's end tag <nowiki>( |} )</nowiki> and paste on a new line after before the end tag. For the above example this would be:

{| width=20%
|<pre>|-
| Column 1, Row 3
| Column 2, Row 3
| Column 3, Row 3</pre>
|}

To create a new column, add a new <nowiki>"!"</nowiki> for the title row and <nowiki>"|"</nowiki> for every other row.

===Table Styles===

Colour can be added to a table if you feel like breaking away from grey and white. Copy the following code into each cell you want to style:

{| width=20%
|<pre> style="background: #0D4F8B; color: white;" |</pre>
|}

Paste it just after the <nowiki>"!"</nowiki> or <nowiki>"|"</nowiki> for each cell so

{| width=20%
|<pre>{| class="wikitable"
! Column 1, Row 1
! Column 2, Row 1
! Column 3, Row 1
|-
| Column 1, Row 2
| Column 2, Row 2
| Column 3, Row 2
|-
| Column 1, Row 3
| Column 2, Row 3
| Column 3, Row 3
|}</pre>
|}

becomes

{| width=20%
|<pre>{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Column 1, Row 1
! style="background: #0D4F8B; color: white;" | Column 2, Row 1
! style="background: #0D4F8B; color: white;" | Column 3, Row 1
|-
| Column 1, Row 2
| Column 2, Row 2
| Column 3, Row 2
|-
| Column 1, Row 3
| Column 2, Row 3
| Column 3, Row 3
|}</pre>
|}

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Column 1, Row 1
! style="background: #0D4F8B; color: white;" | Column 2, Row 1
! style="background: #0D4F8B; color: white;" | Column 3, Row 1
|-
| Column 1, Row 2
| Column 2, Row 2
| Column 3, Row 2
|-
| Column 1, Row 3
| Column 2, Row 3
| Column 3, Row 3
|}

The #0D4F8B is a web colour, in this case producing a blue colour. [http://www.color-hex.com/ www.color-hex.com] is a good website for converting known colours into hexadecimal web colours.

As is shown in the Text Formatting section, all basic text formats can be used in tables when required, but two other useful controls are alignment and spans:

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Alignment:
! style="background: #0D4F8B; color: white;" | Input:
! style="background: #0D4F8B; color: white;" | Result:
! style="background: #0D4F8B; color: #0D4F8B;" | :::.
|-
| Left
| <nowiki>style="text-align: left;" | Left</nowiki>
| style="text-align: left;" | Left
|
|-
| Centre
| <nowiki>style="text-align: center;" | Centre</nowiki>
| style="text-align: center;" | Centre
|
|-
| Right
| <nowiki>style="text-align: right;" | Right</nowiki>
| style="text-align: right;" | Right
|
|-
| Span 2 columns
| <nowiki>colspan="2" | Span 2 columns</nowiki>
| colspan="2" | Span 2 columns
|-
| Span 2 rows
| <nowiki>rowspan="2" | Span 2 rows</nowiki>
| rowspan="2" | Span 2 rows
|
|-
|
|
|
|}

New "styles" are added after a semi colon, and must end in a semi colon before the end quotation mark. For example:

: | style="text-align: left; color: red; background: white;" |

Otherwise, functions are added side by side before the "|" and separated with a space. For example:

: | rowspan="2" style="color: red;" |

Room should be made to accommodate col- and rowspans. It should also be noted that rowspans expand the table downwards and colspans expand to the right.

==Images==

Images are uploaded via the [[Special:Upload|Upload File]] link in the toolbox. Multiple images can be uploaded via [[Special:MultiUpload|this link]]. All uploaded files are placed in the same location on the server, and so it is important to give each file a '''unique name''', otherwise it may be replaced. This is easily done by writing your username before each file name.

'''{{fontcolor1|red|white|Note that .tiff files are not compatible in the wiki - save images as .jpg or preferably .png files}}'''

An image file's name, once uploaded, looks like this:

File:''name''.''filetype''

Images are embedded onto the page using a pair of double square brackets, <nowiki>"[["</nowiki> and <nowiki>"]]"</nowiki>. The result looks like this:

<nowiki>[[</nowiki>File:''name''.''filetype''|''modifier 1''|''modifier 2''<nowiki>]]</nowiki>

Modifiers are separated by vertical lines "|". These modifiers include image position, size, name, caption and frame.

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Type:
! style="background: #0D4F8B; color: white;" | Modifier:
! style="background: #0D4F8B; color: white;" | Result:
! style="background: #0D4F8B; color: white;" | Notes:
|-
| rowspan="2" style="background: #B7C3D0;" | Size:
| x200px
| Scales image to a height of 200 pixels
|
|-
| 200px
| Scales image to a width of 200 pixels
|
|-
| rowspan="2" style="background: #B7C3D0;" | Frame:
| frame
| Places a frame around the image
|
|-
| none
| Removes a frame from an image
|
|-
| rowspan="3" style="background: #B7C3D0;" | Position:
| left
| Places the image left of the page/cell
|
|-
| center
| Places the image to the centre of the page/cell
|
|-
| right
| Places the image to the right of the page/cell
|
|-
| style="background: #B7C3D0;" | Text:
| ''Anything''
| Places text in a caption under the image. Can include links and references
| Must be placed on the very right of the modifiers
|}

==Jmol Applets==

One of the biggest advantages of writing up in a wiki is the ability to embed HTML objects such as Jmol applets. This chapter provides the basics to inserting and manipulating Jmol applets.

<jmol>
<jmolApplet>
<color>white</color>
<size>300</size>
<script>frame 15; vibration 2;rotate x -20; </script>
<uploadedFileContents>AnthMalTS631tam10.log</uploadedFileContents>
</jmolApplet>
</jmol>

Have a look at the source code for the above Jmol object. Every object must be surrounded by the html tags <nowiki><jmol><jmolApplet></nowiki> and <nowiki></jmol></jmolApplet></nowiki>. This will initialise a Jmol object. The table below shows a few HTML tags you can place inside this object:

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Opening Tag:
! style="background: #0D4F8B; color: white;" | Closing Tag:
! style="background: #0D4F8B; color: white;" | Purpose:
! style="background: #0D4F8B; color: white;" | Essential:
|-
| <nowiki><uploadedFileContents></nowiki>
| <nowiki></uploadedFileContents></nowiki>
| span="col" style="width: 500px" | Put your filename in here. Can be single geometry file (eg .xyz, .mol) or a collection of geometries (eg .log).
| Yes
|-
| <nowiki><color></nowiki>
| <nowiki></color></nowiki>
| The background colour. Single word, such as "white" or "black".
| No
|-
| <nowiki><size></nowiki>
| <nowiki></size></nowiki>
| The size of the object, in pixels, eg "400".
| No
|-
| <nowiki><script></nowiki>
| <nowiki></script></nowiki>
| Allows JSmol script to be interpreted and applied. See below for the essentials, or [http://chemapps.stolaf.edu/jmol/docs/ here] for the full list of JSmol script.
| No
|}

===Script in Jmol===

Within the script tags (<nowiki><script></script></nowiki>), commands can be inserted. The commands are interpreted by the Jmol Applet and are essential, for example, for displaying vibrations. Each command must be separated by a semicolon, eg.

<pre>frame 12; vibration 2;</pre>

A few examples are given below.

{| class="wikitable"
! style="background: #0D4F8B; color: white;" | Script:
! style="background: #0D4F8B; color: white;" | Example:
! style="background: #0D4F8B; color: white;" | Purpose:
! style="background: #0D4F8B; color: white;" | Notes:
|-
| span="col" style="width: 300px;" | frame MODEL
| span="col" style="width: 200px;" | frame 10
| span="col" style="width: 400px;" | Selects model 10 from a collection of models and displays it.
| span="col" style="width: 400px;" | To see which model you need, run the Jmol without any script. Right click, select "Model" and find it within the collection. The model number will now be displayed when you right click again.
|-
| vibration PERIOD
| vibration 1
| Displays the vibration of the ''current'' model with a period specified in seconds.
|
|-
| rotate AXIS DEGREES
| rotate x 90
| Rotate about the specified axis.
| To find out which axis you need to rotate about, right click on the Jmol and select "Style" and check "Axes".
|-
| rotate spin AXIS RATE
| rotate spin y 45
| Spins about AXIS, RATE degrees per second.
| Use sparingly.
|-
| select atomno=ATOM_1_NUMBER, atomno=ATOM_2_NUMBER
| select atomno=8, atomno=15
| rowspan="2" | Selects atoms ATOM_1_NUMBER and ATOM_2_NUMBER.
| rowspan="2" | Once atoms are selected, bonds can be modified, or the atoms can be coloured.
|-
| select atomno=[ATOM_1_NUMBER ATOM_2_NUMBER]
| select atomno=[8 15]
|-
| connect BONDTYPE
| connect single<br>connect partial<br>connect none
| Displays the bondtype between selected atoms.
| Useful to highlight bonds, or delete incorrectly displayed bonds using "connect none".
|-
| measure ATOM_1_NUMBER ATOM_2_NUMBER
| measure 8 25
| Measures the distance between atoms ATOM_1_NUMBER and ATOM_2_NUMBER
|
|-
| measure ATOM_1_NUMBER ATOM_2_NUMBER ATOM_3_NUMBER
| measure 8 25 10
| Measures the angle between atoms ATOM_1_NUMBER, ATOM_2_NUMBER and ATOM_3_NUMBER
|
|-
| draw pointgroup
|
| Adds symmetry planes and axes for symmetric or nearly symmetric molecules.
|
|-
| label display
|
| Displays all selected atoms. By default this is all atoms, but use in conjunction with "select" to control which atoms are labelled.
|
|-
| color label COLOUR
| color label red
| Changes the colour of the selected label
| This can be used directly after "label display" ie "label display; color label red"
|}

You can test script before saving the page by right clicking on a Jmol object and selecting "Console". Try out some of the script on the Jmol above by typing in the script in the console and hitting enter.

===MOs with Jmol===

MOs can be displayed using Jmol. This section covers a procedure to achieve this.

<jmol>
<jmolApplet>
<color>white</color>
<size>500</size>
<script>frame 2; mo 17; mo nodots nomesh fill translucent; mo titleformat ""; set antialiasdisplay on</script>
<uploadedFileContents>EXO_TS_DFT_POP=FULL_GFPRINT.LOG</uploadedFileContents>
</jmolApplet>
</jmol>

When you submit your job, add the keywords:

<pre>pop=full gfprint</pre>

'''Note:''' If this doesn't work, open the input file (.gjf or .com) and manually add this to the keyword line (where "opt", "freq" etc go).

This will save the MOs to the .log file. Upload the file to the wiki and create the Jmol using this file. Once the Jmol is loaded, right click on it and find the converged structure:

{| class="wikitable"
|[[File:Cheatsheet_MO_Model_Selection.png|400px]]
|-
|'''''Selecting the correct frame'''''
|}

The converged structure will be at the bottom of the list of energies (Note that for a TS calculation such as the above, it is not necessarily the lowest energy). The number on the left, after "1." corresponds to the frame (here it is 16). Use script to load this frame. To get Jmol to render an effect like above, use the following script:

<pre>mo MO_NUMBER; mo nodots nomesh fill translucent; mo titleformat ""</pre>

where MO_NUMBER is the integer representing the MO you wish to display. You can us a combination of dots/nodots, mesh/nomesh, fill/nofill, translucent/opaque to get the desired effect. The threshold density to display the surface (isovalue) can be controlled with:

<pre>mo cutoff ISOVALUE</pre>

where ISOVALUE is the threshold - typically 0.02 in GaussView.

Notice that all the MOs are available when right clicking on the Jmol and choosing "Surfaces/Molecular Orbitals". You can use this to find MO_NUMBER.

'''Note:''' If your molecular orbitals aren't displaying, check that you have selected the correct frame with "frame FRAME_NUMBER".

===Advanced Jmol Example===

If you are experienced with programming you may want to try some of the advanced features of Jmol. The example below includes setting variables, the IF statement, buttons and a dropdown menu. See [http://wiki.jmol.org/index.php/MediaWiki/ExtensionV3 the Jmol Extensions Page] for information about controls, and the [http://chemapps.stolaf.edu/jmol/docs/#if Jmol Interactive Scripting Page] for information about the IF statement.

'''Imaginary and lowest positive vibration of the TS of Anthracene and Maleic Anhydride'''
<jmol> //Group all the HTML within "jmol"
<jmolApplet> //Initialise the applet
<uploadedFileContents>AnthMalTS631tam10.log</uploadedFileContents>
<script>vibrating=0; spinning=0; frame 15; rotate x -20; frank off</script> //Set the variables (vibrating and spinning) as the applet initialises. Also switched off the frank (JSmol that normally appears on the bottom right)
<name>AnthMal</name> //The name of the applet must be set. This is the name that the controls refer to (the target)
</jmolApplet>
<jmolbutton> //Adding a jmol button, which executes code on the target
<script>if(vibrating==0) vibrating=1; vibration 2; else; vibrating=0; vibration off; endif</script> //Using IF functions to make a toggle. If it's not vibrating, set vibration period to 2 and change "vibrating" variable to 1, else switch off vibration and change "vibrating" to 0
<text>Vibration</text>
<target>AnthMal</target>
</jmolbutton>
<jmolbutton>
<script>measure 8 25; measure 7 26</script>
<text>C-C Distances</text>
<target>AnthMal</target>
</jmolbutton>
<jmolbutton>
<script>if(spinning==0) spinning=1; spin; else; spinning=0; spin off; endif</script>
<text>Spin</text>
<target>AnthMal</target>
</jmolbutton>
<jmolmenu> //The dropdown menu. Each item has to be declared individually and can execute script
<item>
<script>frame 15; if(vibrating==0) vibration off; else; vibration 2; endif</script> //Adding vibration code as a safety net. It might not be necessary but it ensures the applet behaves properly
<text>i469/cm</text>
<target>AnthMal</target>
</item>
<item>
<script>frame 16; if(vibrating==0) vibration off; else; vibration 2; endif</script>
<text>54/cm</text>
<target>AnthMal</target>
</item>
</jmolmenu>
</jmol>

Comments are given in the code for the above Jmol in the source code.

User:Htw14

2016-11-14T12:46:44Z

Htw14: /* Endo Approach Key MOs */

User:Htw14

2016-11-14T12:45:42Z

Htw14: /* Endo Approach Key MOs */

File:EXO TS DFT POP=FULL GFPRINT.LOG

2016-11-14T12:44:30Z

Htw14:

User:Htw14

2016-11-13T12:11:26Z

Htw14: /* Conclusion */

User:Htw14

2016-11-13T12:09:05Z

Htw14: /* Conclusion */

User:Htw14

2016-11-12T23:26:56Z

Htw14: /* Reactant Transformation */

User:Htw14

2016-11-12T22:58:36Z

Htw14: /* Energetics and Profile */

User:Htw14

2016-11-12T22:54:32Z

Htw14: /* Energetics and Profile */

User:Htw14

2016-11-12T22:54:12Z

Htw14: /* Energetics and Profile */

User:Htw14

2016-11-12T22:53:27Z

Htw14: /* Reaction Analysis */