ChemWiki - User contributions [en]

Rep:Mod:TK2814

2016-10-21T04:11:12Z

Tk2814:

== Introduction ==
In this experiment, the transition structures of three Diels-Alder reactions and one Cheletropic reaction were modelled, calculated and compared by using Gaussview 5.0 via different optimization methods. The structures of the transition states and the activation energies were investigated to support the preferred pathways of the reactions.

== Reaction of Butadiene with Ethylene ==
The reaction between 1,3-butadiene with 4π electrons and ethylene with 2π electrons is described as a [4+2] cycloaddition reaction.
[[File:Reaction_of_Butadiene_with_Ethylene.png|500px|thumb|center|Reaction of Butadiene with Ethylene.]]

=== Optimization ===
1,3-butadiene and ethylene were constructed in the Gaussview 5.0 and optimized at PM6 level. The optimised reactants were joined together to construct the transition state, which was also optimized at PM6 level. The cyclohexene was construct and optimized at PM6 level as well.

=== Analysis ===
The MO diagram for the formation of the butadiene and ethlyene is shown below, where the HOMO of butadiene is ungerade, the LUMO of butadiene is gerade, the HOMO of ethlyene is gerade and the LUMO of ethlyene is ungerade.
[[File:Butadiene_Ethene_Cycloaddition123.png|500px|thumb|center]]The HOMOs and LUMOs of butadiene, ethlyene and TS were visualized.<gallery>
</gallery>
{| class="wikitable"
!
!1,3-butadiene
!ethylene
!transition state
|-
|HOMO
|<gallery>
Reactant1_HOMO.jpg
</gallery>
|<gallery>
Reactant2_HOMO.jpg
</gallery>
|<gallery>
TS_HOMO.jpg
</gallery>
|-
|LUMO
|<gallery>
Reactant1_LUMO.jpg
</gallery>
|<gallery>
Reactant2 LUMO.jpg
</gallery>
|<gallery>
TS_LUMO.jpg
</gallery>
|}
The HOMO of butadiene shows characteristic
of anti-bonding. The LUMO of ethylene is anti-bonded. The ungerade- ungerade
interaction results an anti-bonding orbital of the TS. The LUMO of butadiene
is a bonding orbital. The HOMO of ethylene also shows a strong bonding effect, the gerade- gerade interaction results a strong bonded orbital
in the TS.

In general, the length of C-C double bonds were shorter than that of single bonds. The length of C-C double bond decreased, the single bond increased during the reaction. The length C-C double bonds of reactant were 1.379A and the the length C-C single bond was 1.410A. The bond length remained the same at TS. The C-C double bond decreased to 1.33A and the single bonds increased to 1.49A and 1.53A for different bonds after the reaction.

[[File:TS_imaginary_freq.gif|500px|thumb|center|Vibration at imaginary frequency.]]

[[File:TS_lowest_+ve_freq.gif|500px|thumb|center|Vibration at lowest positive frequency.]]At the imaginary frequency, the transition state
is more like symmetricly stretching. The atoms that we expect to form bonds
between them are getting closer to each other, which is good for the reaction
to take place. Because of the symmetric stretch, the formation of the bonds is synchronous.
However, at the lowest positive frequency, the molecules are twisting, they
bend. The uneven movement of the atoms might cause the formation of the bonds asynchronous

== Reaction of Benzoquinone with Cyclopentadiene ==

=== Optimization ===
The Benzoquinone and
cyclopentadiene were constructed, optimized at PM6 level and refined at the B3LYP/6-31G (d) level. The optimised
molecules were joined and adjusted to the endo TS form and the exo TS form. The
bonds that would formed in the reaction were frozen. The two TS were optimised at
the B3LYP/6-31G (d) level,

=== Analysis ===
{| class="wikitable"
!
!Endo
!Exo
|-
|HOMO
|<gallery>
Endo_homo.jpg
</gallery>
|<gallery>
Exo_homo.jpg
</gallery>
|-
|LUMO
|<gallery>
Endo_lumo.jpg
</gallery>
|<gallery>
Exo_lumo.jpg
</gallery>
|}
From the MO above we can see this is an inverse demand DA reaction.

The secondary orbital interactions are the interactions between non-bonding orbitals. The exo-product is more thermodynamically stable. However, as we can see above, the are lots of anti-nonding charactors in the HOMO of endo-transition state, the activation energy is therefore lowered. The endo-product is more kinetically favorable and it is the major product.

== Diels-Alder vs Cheletropic ==

=== Optimization ===
The reactants, transition states and products for both the Diels-Alder and Cheletropic reactions were optimized at the PM6 level.

=== Analysis ===
[[File:TS_endo_IRC_movie.png|500px|thumb|center|Endo-TS total energy along IRC.]]
[[File:TS_endo_IRC_RMS.png|500px|thumb|center|Endo-TS RMS gradient.]]
[[File:TS_exo_IRC_movie.png|500px|thumb|center|Exo-TS total energy along IRC.]]
[[File:TS_exo_IRC_RMS.png|500px|thumb|center|Exo-TS RMS gradient.]]
{| class="wikitable"
!
!Sum of electronic and thermal Free Energies(Hartree/Particle)
|-
|
==== Xylylene ====
|0.178746
|-
|'''SO2'''
|<nowiki>-0.118614</nowiki>
|-
|'''Endo-TS'''
|0.031779
|-
|'''Exo-TS'''
|0.090559
|-
|'''Cheletropic'''
|0.054916
|}
Activation energy of Endo-product= -0.028353 Hartree/Particle

Activation energy of Exo-product= 0.030427 Hartree/Particle

Activation energy of Cheletropic product= -0.005216 Hartree/Particle

The Activation energy of Exo-product is highest and positive, indicates that the reaction will take place spontaneously.

[[File:Engery_profile_diagram.png|500px|thumb|center|Engery profile
.]]

== Conclusions ==
In conclusion the computational experiment has successfully simulated two of the pericyclic reactions by calculations of the cyclic transition state structures using TS(Berny) methods. Two different levels of theories were used: B3LYP/6-31G(d) and simi-empirical/PM6. One of the advantages of computational simulation is that it simulates an IR spectrum for the transition state of an reaction which would be impossible experimentally.

== Reference ==
# Fleming, Ian (1978). ''Frontier Orbitals and Organic Chemical Reactions''. London: Wiley. pp. 29–109. ISBN 0-471-01819-8
# Bondi, A. (1964). van der Waals Volumes and Radii. The Journal of Physical Chemistry, 68(3), pp.441-451.doi:http://pubs.acs.org/doi/abs/10.1021/j100785a00
# <nowiki>http://www.meta-synthesis.com/webbook/49_pericyclic/pericyclic.html</nowiki>

Rep:Mod:TK2814

2016-10-21T04:03:39Z

Tk2814:

File:Engery profile diagram.png

2016-10-21T04:02:32Z

Tk2814:

Rep:Mod:TK2814

2016-10-21T04:01:58Z

Tk2814:

Rep:Mod:TK2814

2016-10-21T03:31:49Z

Tk2814:

File:TS endo IRC RMS.png

2016-10-21T03:29:12Z

Tk2814:

File:TS exo IRC RMS.png

2016-10-21T03:27:56Z

Tk2814:

Rep:Mod:TK2814

2016-10-21T03:27:10Z

Tk2814:

== Introduction ==
In this experiment, the transition structures of three Diels-Alder reactions and one Cheletropic reaction were modelled, calculated and compared by using Gaussview 5.0 via different optimization methods. The structures of the transition states and the activation energies were investigated to support the preferred pathways of the reactions.

== Reaction of Butadiene with Ethylene ==
The reaction between 1,3-butadiene with 4π electrons and ethylene with 2π electrons is described as a [4+2] cycloaddition reaction.
[[File:Reaction_of_Butadiene_with_Ethylene.png|500px|thumb|center|Reaction of Butadiene with Ethylene.]]

=== Optimization ===
1,3-butadiene and ethylene were constructed in the Gaussview 5.0 and optimized at PM6 level. The optimised reactants were joined together to construct the transition state, which was also optimized at PM6 level. The cyclohexene was construct and optimized at PM6 level as well.

=== Analysis ===
The MO diagram for the formation of the butadiene and ethlyene is shown below, where the HOMO of butadiene is ungerade, the LUMO of butadiene is gerade, the HOMO of ethlyene is gerade and the LUMO of ethlyene is ungerade.
[[File:Butadiene_Ethene_Cycloaddition123.png|500px|thumb|center]]The HOMOs and LUMOs of butadiene, ethlyene and TS were visualized.<gallery>
</gallery>
{| class="wikitable"
!
!1,3-butadiene
!ethylene
!transition state
|-
|HOMO
|<gallery>
Reactant1_HOMO.jpg
</gallery>
|<gallery>
Reactant2_HOMO.jpg
</gallery>
|<gallery>
TS_HOMO.jpg
</gallery>
|-
|LUMO
|<gallery>
Reactant1_LUMO.jpg
</gallery>
|<gallery>
Reactant2 LUMO.jpg
</gallery>
|<gallery>
TS_LUMO.jpg
</gallery>
|}
The HOMO of butadiene shows characteristic
of anti-bonding. The LUMO of ethylene is anti-bonded. The ungerade- ungerade
interaction results an anti-bonding orbital of the TS. The LUMO of butadiene
is a bonding orbital. The HOMO of ethylene also shows a strong bonding effect, the gerade- gerade interaction results a strong bonded orbital
in the TS.

In general, the length of C-C double bonds were shorter than that of single bonds. The length of C-C double bond decreased, the single bond increased during the reaction. The length C-C double bonds of reactant were 1.379A and the the length C-C single bond was 1.410A. The bond length remained the same at TS. The C-C double bond decreased to 1.33A and the single bonds increased to 1.49A and 1.53A for different bonds after the reaction.

[[File:TS_imaginary_freq.gif|500px|thumb|center|Vibration at imaginary frequency.]]

[[File:TS_lowest_+ve_freq.gif|500px|thumb|center|Vibration at lowest positive frequency.]]At the imaginary frequency, the transition state
is more like symmetricly stretching. The atoms that we expect to form bonds
between them are getting closer to each other, which is good for the reaction
to take place. Because of the symmetric stretch, the formation of the bonds is synchronous.
However, at the lowest positive frequency, the molecules are twisting, they
bend. The uneven movement of the atoms might cause the formation of the bonds asynchronous

== Reaction of Benzoquinone with Cyclopentadiene ==

=== Optimization ===
The Benzoquinone and
cyclopentadiene were constructed, optimized at PM6 level and refined at the B3LYP/6-31G (d) level. The optimised
molecules were joined and adjusted to the endo TS form and the exo TS form. The
bonds that would formed in the reaction were frozen. The two TS were optimised at
the B3LYP/6-31G (d) level,

=== Analysis ===
{| class="wikitable"
!
!Endo
!Exo
|-
|HOMO
|<gallery>
Endo_homo.jpg
</gallery>
|<gallery>
Exo_homo.jpg
</gallery>
|-
|LUMO
|<gallery>
Endo_lumo.jpg
</gallery>
|<gallery>
Exo_lumo.jpg
</gallery>
|}
From the MO above we can see this is an inverse demand DA reaction.

The secondary orbital interactions are the interactions between non-bonding orbitals. The exo-product is more thermodynamically stable. However, as we can see above, the are lots of anti-nonding charactors in the HOMO of endo-transition state, the activation energy is therefore lowered. The endo-product is more kinetically favorable and it is the major product.

== Diels-Alder vs Cheletropic ==

=== Optimization ===
The reactants, transition states and products for both the Diels-Alder and Cheletropic reactions were optimized at the PM6 level.

=== Analysis ===
[[File:TS_endo_IRC_movie.png|500px|thumb|center|Vibration at imaginary frequency.]]
[[File:TS_endo_IRC_RMS.png|500px|thumb|center|Vibration at imaginary frequency.]]
[[File:TS_exo_IRC_movie.png|500px|thumb|center|Vibration at imaginary frequency.]]
[[File:TS_exo_IRC_RMS.png|500px|thumb|center|Vibration at imaginary frequency.]]

File:TS exo IRC movie.png

2016-10-21T03:26:39Z

Tk2814:

File:TS endo IRC movie.png

2016-10-21T03:24:41Z

Tk2814:

Rep:Mod:TK2814

2016-10-21T03:22:38Z

Tk2814: /* Optimization */

File:Exo lumo.jpg

2016-10-21T03:09:33Z

Tk2814: Tk2814 uploaded a new version of File:Exo lumo.jpg

File:Endo lumo.jpg

2016-10-21T03:09:07Z

Tk2814:

File:Exo homo.jpg

2016-10-21T03:08:36Z

Tk2814: Tk2814 uploaded a new version of File:Exo homo.jpg

File:Endo homo.jpg

2016-10-21T03:08:05Z

Tk2814:

Rep:Mod:TK2814

2016-10-21T02:53:52Z

Tk2814:

Rep:Mod:TK2814

2016-10-21T02:43:27Z

Tk2814:

File:TS lowest +ve freq.gif

2016-10-21T02:42:33Z

Tk2814:

Rep:Mod:TK2814

2016-10-21T02:40:27Z

Tk2814:

Rep:Mod:TK2814

2016-10-21T02:39:34Z

Tk2814: /* Analysis */

File:TS imaginary freq.gif

2016-10-21T02:38:49Z

Tk2814:

Rep:Mod:TK2814

2016-10-21T02:36:58Z

Tk2814:

Rep:Mod:TK2814

2016-10-21T02:25:46Z

Tk2814: /* Analysis */

Rep:Mod:TK2814

2016-10-21T02:13:04Z

Tk2814: /* Analysis */

Rep:Mod:TK2814

2016-10-21T02:09:44Z

Tk2814: /* Analysis */

Rep:Mod:TK2814

2016-10-21T02:05:02Z

Tk2814: /* Analysis */

Rep:Mod:TK2814

2016-10-21T02:03:48Z

Tk2814: /* Analysis */

Rep:Mod:TK2814

2016-10-21T02:01:59Z

Tk2814: /* Analysis */

File:Butadiene Ethene Cycloaddition123.png

2016-10-21T02:01:43Z

Tk2814:

Rep:Mod:TK2814

2016-10-21T01:55:38Z

Tk2814: /* Reaction of Butadiene with Ethylene */

File:TS LUMO.jpg

2016-10-21T01:55:15Z

Tk2814: Tk2814 uploaded a new version of File:TS LUMO.jpg

File:Reactant2 LUMO.jpg

2016-10-21T01:54:10Z

Tk2814:

File:Reactant1 LUMO.jpg

2016-10-21T01:53:30Z

Tk2814:

File:TS HOMO.jpg

2016-10-21T01:53:02Z

Tk2814: Tk2814 uploaded a new version of File:TS HOMO.jpg

File:Reactant2 HOMO.jpg

2016-10-21T01:52:09Z

Tk2814:

File:Reactant1 HOMO.jpg

2016-10-21T01:51:01Z

Tk2814:

Rep:Mod:TK2814

2016-10-21T01:32:42Z

Tk2814:

Rep:Mod:TK2814

2016-10-21T01:32:11Z

Tk2814: /* Reaction of Butadiene with Ethylene */

Rep:Mod:TK2814

2016-10-21T01:31:13Z

Tk2814: /* Reaction of Butadiene with Ethylene */

Rep:Mod:TK2814

2016-10-21T01:30:50Z

Tk2814: /* Reaction of Butadiene with Ethylene */

Rep:Mod:TK2814

2016-10-21T01:30:28Z

Tk2814: /* Reaction of Butadiene with Ethylene */

Rep:Mod:TK2814

2016-10-21T01:30:01Z

Tk2814: /* Reaction of Butadiene with Ethylene */

Rep:Mod:TK2814

2016-10-21T01:21:27Z

Tk2814: /* Reaction of Butadiene with Ethylene */

Rep:Mod:TK2814

2016-10-21T01:20:19Z

Tk2814: /* Reaction of Butadiene with Ethylene */

Rep:Mod:TK2814

2016-10-21T01:20:09Z

Tk2814: /* Reaction of Butadiene with Ethylene */

Rep:Mod:TK2814

2016-10-21T01:19:41Z

Tk2814: /* Reaction of Butadiene with Ethylene */

Rep:Mod:TK2814

2016-10-21T01:15:33Z

Tk2814: /* Reaction of Butadiene with Ethylene */

Rep:Mod:TK2814

2016-10-21T01:15:23Z

Tk2814: /* Reaction of Butadiene with Ethylene */

Rep:Mod:TK2814

2016-10-21T01:14:52Z

Tk2814: /* Reaction of Butadiene with Ethylene */

Rep:Mod:TK2814

2016-10-21T01:13:55Z

Tk2814: /* Reaction of Butadiene with Ethylene */