ChemWiki - User contributions [en]

Rep:MOD:LYF1996

2016-10-20T18:47:43Z

Yl20414:

== '''Introduction''' ==
The transition state in potential energy surface would be a
stationary point which is the highest point on the reaction energy curve. It
means the just point of the reactant is forming their bonds or breaking their
bonds to form the product. However, a stationary point is not always the
transition state. It can still be the minimum energy point which means
physically stable point. That is the minimum point on the potential energy
surface. During a frequency calculation, the negative frequency is the
transition state which is called as an imaginary frequency. But, if only real frequencies exist, that is a minimum structure for the molecule.

== '''First part write up''' ==
In this part a Diels-Alder reaction (Butadiene with Ethylene)
is analysed about its MO diagram, bond length and bond formation at the
reactant, product and transition state.

First comes to the MO. The MO image of the reactant and transition
state are listed below. The shape of transition state can be found from the
four reactant MO graph if the whole MO is read from each partial MO. Transition
State 16 is formed from the HOMO of butadiene and LUMO of ethylene. Transition
State 17 is formed from the HOMO of ethylene and LUMO of butadiene. Transition
State 18 is formed from the HOMO of ethylene and LUMO of butadiene. Transition
State 19 is formed from the HOMO of butadiene and LUMO of ethylene. So, only
same symmetry can be used to form a MO. If the two reactant are at the same
symmetry, the overlap integral would be non-zero or it would be cancelled out
to give zero integral. This means a gerade-ungerade interaction gives zero
overlap integral, a gerade-gerade interaction gives a non-zero integral and an
ungerade-ungerade interaction gives a non-zero integral.
{| class="wikitable"
!<gallery>
E1r1.png
</gallery>HOMO of the ethylene
!<gallery>
E1r2.png
</gallery>LUMO of the ethylene
!<gallery>
Tshomo.png
</gallery>HOMO of transition state
!<gallery>
E1tslumo.png
</gallery>LUMO of transition state
|-
|<gallery>
E1r2homo.png
</gallery>HOMO of the butadiene
|<gallery>
E1r2lumo.png
</gallery>LUMO of butadiene
|<gallery>
Ts16.png
</gallery>Transition stae16
|<gallery>
Ts19.png
</gallery>Transition 19
|}
{| class="wikitable"
![[File:E1r1mo.PNG|thumb]]Energy level list for ethylene
![[File:E1r2mo.PNG|thumb]]Energy list for butadiene
![[File:Tsmo.PNG|thumb]]Energy list for transition state
|}

From the MO chart, it is easily compared and can be told
that this is a neutral Diels-Alder reaction.

Then comes to the bond length analysis. A labelled graph and
a table for the bond length for the C-C bond are shown below. The standard Sp2
and Sp3 C-C bond length are 1.47 Å and 1.54Å respectively. (1) And, the Van der
Waals radius of carbon atom is 1.7 Å, which means 3.4 Å for two atoms

.[[File:E1reaction.png|frameless|461x461px]]

[[File:Yifeiliaodetableandchart.PNG|thumb|718x718px|none]]
{| class="wikitable"
|It is shown that the bond length except between carbon 2 and
3 are increasing. If we compare the length values with the standard sp2 and sp3
c-c length, it is easily found that merely carbon-carbon bond between 2 and 3
are turning into a sp2 hybridised one while the other bond are changing from the sp2 like into sp3 like.

As for the Van der Waals radius comparison between two
carbon atoms and the carbon-carbon distance between atom 4 to 5 and 6 to 1, we
can found that the two bond length are both smaller than the Van der Waals
radius between two carbon atoms. This shows there is bond forming between the two
carbons or they should equal or larger than the Van der Waals radius.

Finally, the vibration that corresponds to the reaction path
at the transition state which is at the only negative frequency. The two end
carbon atoms of butadiene and the two atoms of the ethylene are vibrating in an opposite direction.
[[File:E1-frequency.gif|thumb|541x541px|none]]

{| class="wikitable"
|However, as for the smallest positive frequency, the two
compounds are shaking at two different direction (one into the screen, one out

of the screen).
|}
[[File:E1sf.gif|none|thumb|557x557px]]
{| class="wikitable"
|And from the IRC result, the bond forming is at the same
time between.
|}
[[File:E1irc.gif|none|thumb|553x553px]]

== S'''econd part write up''' ==
First, comes to the MO part. Both the transition state of
ENDO and EXO process are listed below.[[File:Lyfdmo.PNG|none|thumb|964x964px]][[File:Lyfd2mo.PNG|none|thumb|648x648px]]From the MO
diagram of the two reactants, the cyclopentadiene as diene role has higher
energy of both HOMO and LUMO then the Benzoquinone as an ene role. So, it tells
that the reaction is a normal electron demand reaction. [[File:Whatthef.png|none|thumb|469x469px]]Secondary orbital
interaction only takes place in ENDO Transition state but not in EXO transition
state. From the Endo transition state MO diagram, the two part side orbital turn
into a bit twist like. So, it could be concluded as a secondary interaction and
will act as a stabilization that lower barrier energy (2).

|}

== '''Third part write up''' ==

Both the Diels-Alder and Cheletropic IRC route are listed below.If they are considered from the product side to the reactant
side as the analysis done, the delocalised electron density from the six
membered ring is withdraw from the ring system during the reaction to form the
two outer double bond. This means inside the ring, six delocalised pi bonds are
changing into three discrete sp2 bonding. If they are considered as the reactants to products, the electrons from oxygen and sulfur atom is forming bond with the two outer carbon atoms and push electron( from double bond ) into the ring and formed a delocalised system.
[[File:ADIRC.gif|none|thumb|597x597px]]Diels-Alder route
[[File:C irc.gif|none|thumb|598x598px]]
Cheletropic route

The free energy data are list as table below
[[File:Tbofe31.PNG|none|thumb|515x515px]]
[[File:Tbofe33.PNG|none|thumb|394x394px]]
So, from the activation energy comparison and reaction energy comparison, it is known that Diels-Alder route is kinetically favored and cheletropic route is thermal dynamically favored.

As for the Cheletropic route, there is only exothermic reaction. The reaction profile is listed below.
[[File:Exoche.png|none|thumb]]
For the Diels-Alder route, both exo and endo type of route exist. They are listed below.
[[File:Exoche1.png|none|thumb]]
Exo of Diels-Alder route
[[File:Exoche12.png|none|thumb]]
Endo of Diels-Alder route

== '''Conclusion''' ==
From the analysis of three Diels-Alder reactions, method of
frequency calculation, optimization and IRC were used to carry out the data of
potential surface, MO diagram, free energy and reaction pathway. It is found
that the transition state is the highest energy point on the reaction energy
pathway with a negative frequency in the frequency calculation. And, the
potential energy surface, PES is a surface that combine many parameter that can
describe the energy profile. During the endo reaction, the extra secondary
orbital interaction (from MO) and steric are often found to stabilise the
product which makes the product thermodynamically favoured.

== '''Reference''' ==
1) Fox, Marye Anne; Whitesell, James K. (1995). Organische
Chemie: Grundlagen, Mechanismen, Bioorganische Anwendungen. Springer. ISBN
978-3-86025-249-9.

(2) Governing
organic reactions through secondary orbital interactions.
Semiempirical and density functional theory study of catalyzed
cycloaddition reactions between pyrrole and ether dienophiles

Branko S. Jursic Department of Chemistry,
University of New Orleans, New Orleans, Louisiana 70148, USA Received (in
Gainesville, FL) 18th May 1998, Accepted 7th December 1998

File:Whatthef.png

2016-10-20T18:46:53Z

Yl20414:

Rep:MOD:LYF1996

2016-10-20T17:58:10Z

Yl20414:

== '''Introduction''' ==
The transition state in potential energy surface would be a
stationary point which is the highest point on the reaction energy curve. It
means the just point of the reactant is forming their bonds or breaking their
bonds to form the product. However, a stationary point is not always the
transition state. It can still be the minimum energy point which means
physically stable point. That is the minimum point on the potential energy
surface. During a frequency calculation, the negative frequency is the
transition state which is called as an imaginary frequency. But, if only real frequencies exist, that is a minimum structure for the molecule.

== '''First part write up''' ==
In this part a Diels-Alder reaction (Butadiene with Ethylene)
is analysed about its MO diagram, bond length and bond formation at the
reactant, product and transition state.

First comes to the MO. The MO image of the reactant and transition
state are listed below. The shape of transition state can be found from the
four reactant MO graph if the whole MO is read from each partial MO. Transition
State 16 is formed from the HOMO of butadiene and LUMO of ethylene. Transition
State 17 is formed from the HOMO of ethylene and LUMO of butadiene. Transition
State 18 is formed from the HOMO of ethylene and LUMO of butadiene. Transition
State 19 is formed from the HOMO of butadiene and LUMO of ethylene. So, only
same symmetry can be used to form a MO. If the two reactant are at the same
symmetry, the overlap integral would be non-zero or it would be cancelled out
to give zero integral. This means a gerade-ungerade interaction gives zero
overlap integral, a gerade-gerade interaction gives a non-zero integral and an
ungerade-ungerade interaction gives a non-zero integral.
{| class="wikitable"
!<gallery>
E1r1.png
</gallery>HOMO of the ethylene
!<gallery>
E1r2.png
</gallery>LUMO of the ethylene
!<gallery>
Tshomo.png
</gallery>HOMO of transition state
!<gallery>
E1tslumo.png
</gallery>LUMO of transition state
|-
|<gallery>
E1r2homo.png
</gallery>HOMO of the butadiene
|<gallery>
E1r2lumo.png
</gallery>LUMO of butadiene
|<gallery>
Ts16.png
</gallery>Transition stae16
|<gallery>
Ts19.png
</gallery>Transition 19
|}
{| class="wikitable"
![[File:E1r1mo.PNG|thumb]]Energy level list for ethylene
![[File:E1r2mo.PNG|thumb]]Energy list for butadiene
![[File:Tsmo.PNG|thumb]]Energy list for transition state
|}

From the MO chart, it is easily compared and can be told
that this is a neutral Diels-Alder reaction.

Then comes to the bond length analysis. A labelled graph and
a table for the bond length for the C-C bond are shown below. The standard Sp2
and Sp3 C-C bond length are 1.47 Å and 1.54Å respectively. (1) And, the Van der
Waals radius of carbon atom is 1.7 Å, which means 3.4 Å for two atoms

.[[File:E1reaction.png|frameless|461x461px]]

[[File:Yifeiliaodetableandchart.PNG|thumb|718x718px|none]]
{| class="wikitable"
|It is shown that the bond length except between carbon 2 and
3 are increasing. If we compare the length values with the standard sp2 and sp3
c-c length, it is easily found that merely carbon-carbon bond between 2 and 3
are turning into a sp2 hybridised one while the other bond are changing from the sp2 like into sp3 like.

As for the Van der Waals radius comparison between two
carbon atoms and the carbon-carbon distance between atom 4 to 5 and 6 to 1, we
can found that the two bond length are both smaller than the Van der Waals
radius between two carbon atoms. This shows there is bond forming between the two
carbons or they should equal or larger than the Van der Waals radius.

Finally, the vibration that corresponds to the reaction path
at the transition state which is at the only negative frequency. The two end
carbon atoms of butadiene and the two atoms of the ethylene are vibrating in an opposite direction.
[[File:E1-frequency.gif|thumb|541x541px|none]]

{| class="wikitable"
|However, as for the smallest positive frequency, the two
compounds are shaking at two different direction (one into the screen, one out

of the screen).
|}
[[File:E1sf.gif|none|thumb|557x557px]]
{| class="wikitable"
|And from the IRC result, the bond forming is at the same
time between.
|}
[[File:E1irc.gif|none|thumb|553x553px]]

== S'''econd part write up''' ==
First, comes to the MO part. Both the transition state of
ENDO and EXO process are listed below.[[File:Lyfdmo.PNG|none|thumb|964x964px]][[File:Lyfd2mo.PNG|none|thumb|648x648px]]From the MO
diagram of the two reactants, the cyclopentadiene as diene role has higher
energy of both HOMO and LUMO then the Benzoquinone as an ene role. So, it tells
that the reaction is a normal electron demand reaction. [[File:Tableoneyfl.png|none|thumb|780x780px]][[File:Tb2e2.png|none|thumb|359x359px]]

Secondary orbital
interaction only takes place in ENDO Transition state but not in EXO transition
state. From the Endo transition state MO diagram, the two part side orbital turn
into a bit twist like. So, it could be concluded as a secondary interaction and
will act as a stabilization that lower barrier energy (2).

|}

== '''Third part write up''' ==

Both the Diels-Alder and Cheletropic IRC route are listed below.If they are considered from the product side to the reactant
side as the analysis done, the delocalised electron density from the six
membered ring is withdraw from the ring system during the reaction to form the
two outer double bond. This means inside the ring, six delocalised pi bonds are
changing into three discrete sp2 bonding. If they are considered as the reactants to products, the electrons from oxygen and sulfur atom is forming bond with the two outer carbon atoms and push electron( from double bond ) into the ring and formed a delocalised system.
[[File:ADIRC.gif|none|thumb|597x597px]]Diels-Alder route
[[File:C irc.gif|none|thumb|598x598px]]
Cheletropic route

The free energy data are list as table below
[[File:Tbofe31.PNG|none|thumb|515x515px]]
[[File:Tbofe33.PNG|none|thumb|394x394px]]
So, from the activation energy comparison and reaction energy comparison, it is known that Diels-Alder route is kinetically favored and cheletropic route is thermal dynamically favored.

As for the Cheletropic route, there is only exothermic reaction. The reaction profile is listed below.
[[File:Exoche.png|none|thumb]]
For the Diels-Alder route, both exo and endo type of route exist. They are listed below.
[[File:Exoche1.png|none|thumb]]
Exo of Diels-Alder route
[[File:Exoche12.png|none|thumb]]
Endo of Diels-Alder route

== '''Conclusion''' ==
From the analysis of three Diels-Alder reactions, method of
frequency calculation, optimization and IRC were used to carry out the data of
potential surface, MO diagram, free energy and reaction pathway. It is found
that the transition state is the highest energy point on the reaction energy
pathway with a negative frequency in the frequency calculation. And, the
potential energy surface, PES is a surface that combine many parameter that can
describe the energy profile. During the endo reaction, the extra secondary
orbital interaction (from MO) and steric are often found to stabilise the
product which makes the product thermodynamically favoured.

== '''Reference''' ==
1) Fox, Marye Anne; Whitesell, James K. (1995). Organische
Chemie: Grundlagen, Mechanismen, Bioorganische Anwendungen. Springer. ISBN
978-3-86025-249-9.

(2) Governing
organic reactions through secondary orbital interactions.
Semiempirical and density functional theory study of catalyzed
cycloaddition reactions between pyrrole and ether dienophiles

Branko S. Jursic Department of Chemistry,
University of New Orleans, New Orleans, Louisiana 70148, USA Received (in
Gainesville, FL) 18th May 1998, Accepted 7th December 1998

Rep:MOD:LYF1996

2016-10-20T17:49:29Z

Yl20414:

== '''Introduction''' ==
The transition state in potential energy surface would be a
stationary point which is the highest point on the reaction energy curve. It
means the just point of the reactant is forming their bonds or breaking their
bonds to form the product. However, a stationary point is not always the
transition state. It can still be the minimum energy point which means
physically stable point. That is the minimum point on the potential energy
surface. During a frequency calculation, the negative frequency is the
transition state which is called as an imaginary frequency. But, if only real frequencies exist, that is a minimum structure for the molecule.

== '''First part write up''' ==
In this part a Diels-Alder reaction (Butadiene with Ethylene)
is analysed about its MO diagram, bond length and bond formation at the
reactant, product and transition state.

First comes to the MO. The MO image of the reactant and transition
state are listed below. The shape of transition state can be found from the
four reactant MO graph if the whole MO is read from each partial MO. Transition
State 16 is formed from the HOMO of butadiene and LUMO of ethylene. Transition
State 17 is formed from the HOMO of ethylene and LUMO of butadiene. Transition
State 18 is formed from the HOMO of ethylene and LUMO of butadiene. Transition
State 19 is formed from the HOMO of butadiene and LUMO of ethylene. So, only
same symmetry can be used to form a MO. If the two reactant are at the same
symmetry, the overlap integral would be non-zero or it would be cancelled out
to give zero integral. This means a gerade-ungerade interaction gives zero
overlap integral, a gerade-gerade interaction gives a non-zero integral and an
ungerade-ungerade interaction gives a non-zero integral.
{| class="wikitable"
!<gallery>
E1r1.png
</gallery>HOMO of the ethylene
!<gallery>
E1r2.png
</gallery>LUMO of the ethylene
!<gallery>
Tshomo.png
</gallery>HOMO of transition state
!<gallery>
E1tslumo.png
</gallery>LUMO of transition state
|-
|<gallery>
E1r2homo.png
</gallery>HOMO of the butadiene
|<gallery>
E1r2lumo.png
</gallery>LUMO of butadiene
|<gallery>
Ts16.png
</gallery>Transition stae16
|<gallery>
Ts19.png
</gallery>Transition 19
|}
{| class="wikitable"
![[File:E1r1mo.PNG|thumb]]Energy level list for ethylene
![[File:E1r2mo.PNG|thumb]]Energy list for butadiene
![[File:Tsmo.PNG|thumb]]Energy list for transition state
|}

From the MO chart, it is easily compared and can be told
that this is a neutral Diels-Alder reaction.

Then comes to the bond length analysis. A labelled graph and
a table for the bond length for the C-C bond are shown below. The standard Sp2
and Sp3 C-C bond length are 1.47 Å and 1.54Å respectively. (1) And, the Van der
Waals radius of carbon atom is 1.7 Å, which means 3.4 Å for two atoms

.[[File:E1reaction.png|frameless|461x461px]]

[[File:Yifeiliaodetableandchart.PNG|thumb|718x718px|none]]
{| class="wikitable"
|It is shown that the bond length except between carbon 2 and
3 are increasing. If we compare the length values with the standard sp2 and sp3
c-c length, it is easily found that merely carbon-carbon bond between 2 and 3
are turning into a sp2 hybridised one while the other bond are changing from the sp2 like into sp3 like.

As for the Van der Waals radius comparison between two
carbon atoms and the carbon-carbon distance between atom 4 to 5 and 6 to 1, we
can found that the two bond length are both smaller than the Van der Waals
radius between two carbon atoms. This shows there is bond forming between the two
carbons or they should equal or larger than the Van der Waals radius.

Finally, the vibration that corresponds to the reaction path
at the transition state which is at the only negative frequency. The two end
carbon atoms of butadiene and the two atoms of the ethylene are vibrating in an opposite direction.
[[File:E1-frequency.gif|thumb|541x541px|none]]

{| class="wikitable"
|However, as for the smallest positive frequency, the two
compounds are shaking at two different direction (one into the screen, one out

of the screen).
|}
[[File:E1sf.gif|none|thumb|557x557px]]
{| class="wikitable"
|And from the IRC result, the bond forming is at the same
time between.
|}
[[File:E1irc.gif|none|thumb|553x553px]]

== S'''econd part write up''' ==
First, comes to the MO part. Both the transition state of
ENDO and EXO process are listed below.[[File:Lyfdmo.PNG|none|thumb|964x964px]][[File:Lyfd2mo.PNG|none|thumb|648x648px]]From the MO
diagram of the two reactants, the cyclopentadiene as diene role has higher
energy of both HOMO and LUMO then the Benzoquinone as an ene role. So, it tells
that the reaction is a normal electron demand reaction. [[File:Tableoneyfl.png|none|thumb|780x780px]][[File:Tb2e2.png|none|thumb|359x359px]]

Secondary orbital
interaction only takes place in ENDO Transition state but not in EXO transition
state. From the Endo transition state MO diagram, the two part side orbital turn
into a bit twist like. So, it could be concluded as a secondary interaction and
will act as a stabilization that lower barrier energy (2).

|}

== '''Third part write up''' ==

Both the Diels-Alder and Cheletropic IRC route are listed below.If they are considered from the product side to the reactant
side as the analysis done, the delocalised electron density from the six
membered ring is withdraw from the ring system during the reaction to form the
two outer double bond. This means inside the ring, six delocalised pi bonds are
changing into three discrete sp2 bonding. If they are considered as the reactants to products, the electrons from oxygen and sulfur atom is forming bond with the two outer carbon atoms and push electron( from double bond ) into the ring and formed a delocalised system.
[[File:ADIRC.gif|none|thumb|597x597px]]Diels-Alder route
[[File:C irc.gif|none|thumb|598x598px]]
Cheletropic route

The free energy data are list as table below
[[File:Tbofe31.PNG|none|thumb|515x515px]]
[[File:Tbofe33.PNG|none|thumb|394x394px]]
So, from the activation energy comparison and reaction energy comparison, it is known that Diels-Alder route is kinetically favored and cheletropic route is thermal dynamically favored.

As for the Cheletropic route, there is only exothermic reaction. The reaction profile is listed below.
[[File:Exoche.png|none|thumb]]
For the Diels-Alder route, both exo and endo type of route exist. They are listed below.
[[File:Exoche1.png|none|thumb]]
Exo of Diels-Alder route
[[File:Exoche12.png|none|thumb]]
Endo of Diels-Alder route

== '''Conclusion''' ==
From the analysis of three Diels-Alder reactions, method of
frequency calculation, optimization and IRC were used to carry out the data of
potential surface, MO diagram, free energy and reaction pathway. It is found
that the transition state is the highest energy point on the reaction energy
pathway with a negative frequency in the frequency calculation. And, the
potential energy surface, PES is a surface that combine many parameter that can
describe the energy profile. During the endo reaction, the extra secondary
orbital interaction (from MO) and steric are often found to stabilise the
product which makes the product thermodynamically favoured.

Rep:MOD:LYF1996

2016-10-20T17:24:14Z

Yl20414: /* Introduction */

== '''Introduction''' ==
The transition state in potential energy surface would be a
stationary point which is the highest point on the reaction energy curve. It
means the just point of the reactant is forming their bonds or breaking their
bonds to form the product. However, a stationary point is not always the
transition state. It can still be the minimum energy point which means
physically stable point. That is the minimum point on the potential energy
surface. During a frequency calculation, the negative frequency is the
transition state which is called as an imaginary frequency. But, if only real frequencies exist, that is a minimum structure for the molecule.

== '''First part write up''' ==
In this part a Diels-Alder reaction (Butadiene with Ethylene)
is analysed about its MO diagram, bond length and bond formation at the
reactant, product and transition state.

First comes to the MO. The MO image of the reactant and transition
state are listed below. The shape of transition state can be found from the
four reactant MO graph if the whole MO is read from each partial MO. Transition
State 16 is formed from the HOMO of butadiene and LUMO of ethylene. Transition
State 17 is formed from the HOMO of ethylene and LUMO of butadiene. Transition
State 18 is formed from the HOMO of ethylene and LUMO of butadiene. Transition
State 19 is formed from the HOMO of butadiene and LUMO of ethylene. So, only
same symmetry can be used to form a MO. If the two reactant are at the same
symmetry, the overlap integral would be non-zero or it would be cancelled out
to give zero integral. This means a gerade-ungerade interaction gives zero
overlap integral, a gerade-gerade interaction gives a non-zero integral and an
ungerade-ungerade interaction gives a non-zero integral.
{| class="wikitable"
!<gallery>
E1r1.png
</gallery>HOMO of the ethylene
!<gallery>
E1r2.png
</gallery>LUMO of the ethylene
!<gallery>
Tshomo.png
</gallery>HOMO of transition state
!<gallery>
E1tslumo.png
</gallery>LUMO of transition state
|-
|<gallery>
E1r2homo.png
</gallery>HOMO of the butadiene
|<gallery>
E1r2lumo.png
</gallery>LUMO of butadiene
|<gallery>
Ts16.png
</gallery>Transition stae16
|<gallery>
Ts19.png
</gallery>Transition 19
|}
{| class="wikitable"
![[File:E1r1mo.PNG|thumb]]Energy level list for ethylene
![[File:E1r2mo.PNG|thumb]]Energy list for butadiene
![[File:Tsmo.PNG|thumb]]Energy list for transition state
|}

From the MO chart, it is easily compared and can be told
that this is a neutral Diels-Alder reaction.

Then comes to the bond length analysis. A labelled graph and
a table for the bond length for the C-C bond are shown below. The standard Sp2
and Sp3 C-C bond length are 1.47 Å and 1.54Å respectively. (1) And, the Van der
Waals radius of carbon atom is 1.7 Å, which means 3.4 Å for two atoms

.[[File:E1reaction.png|frameless|461x461px]]

[[File:Yifeiliaodetableandchart.PNG|thumb|718x718px|none]]
{| class="wikitable"
|It is shown that the bond length except between carbon 2 and
3 are increasing. If we compare the length values with the standard sp2 and sp3
c-c length, it is easily found that merely carbon-carbon bond between 2 and 3
are turning into a sp2 hybridised one while the other bond are changing from the sp2 like into sp3 like.

As for the Van der Waals radius comparison between two
carbon atoms and the carbon-carbon distance between atom 4 to 5 and 6 to 1, we
can found that the two bond length are both smaller than the Van der Waals
radius between two carbon atoms. This shows there is bond forming between the two
carbons or they should equal or larger than the Van der Waals radius.

Finally, the vibration that corresponds to the reaction path
at the transition state which is at the only negative frequency. The two end
carbon atoms of butadiene and the two atoms of the ethylene are vibrating in an opposite direction.
[[File:E1-frequency.gif|thumb|541x541px|none]]

{| class="wikitable"
|However, as for the smallest positive frequency, the two
compounds are shaking at two different direction (one into the screen, one out

of the screen).
|}
[[File:E1sf.gif|none|thumb|557x557px]]
{| class="wikitable"
|And from the IRC result, the bond forming is at the same
time between.
|}
[[File:E1irc.gif|none|thumb|553x553px]]

== S'''econd part write up''' ==
First, comes to the MO part. Both the transition state of
ENDO and EXO process are listed below.[[File:Lyfdmo.PNG|none|thumb|964x964px]][[File:Lyfd2mo.PNG|none|thumb|648x648px]]From the MO
diagram of the two reactants, the cyclopentadiene as diene role has higher
energy of both HOMO and LUMO then the Benzoquinone as an ene role. So, it tells
that the reaction is a normal electron demand reaction. [[File:Tableoneyfl.png|none|thumb|780x780px]][[File:Tb2e2.png|none|thumb|359x359px]]

Secondary orbital
interaction only takes place in ENDO Transition state but not in EXO transition
state. From the Endo transition state MO diagram, the two part side orbital turn
into a bit twist like. So, it could be concluded as a secondary interaction and
will act as a stabilization that lower barrier energy (2).

|}

== '''Third part write up''' ==

Both the Diels-Alder and Cheletropic IRC route are listed below.If they are considered from the product side to the reactant
side as the analysis done, the delocalised electron density from the six
membered ring is withdraw from the ring system during the reaction to form the
two outer double bond. This means inside the ring, six delocalised pi bonds are
changing into three discrete sp2 bonding. If they are considered as the reactants to products, the electrons from oxygen and sulfur atom is forming bond with the two outer carbon atoms and push electron( from double bond ) into the ring and formed a delocalised system.
[[File:ADIRC.gif|none|thumb|597x597px]]Diels-Alder route
[[File:C irc.gif|none|thumb|598x598px]]
Cheletropic route

The free energy data are list as table below
[[File:Tbofe31.PNG|none|thumb|515x515px]]
[[File:Tbofe33.PNG|none|thumb|394x394px]]
So, from the activation energy comparison and reaction energy comparison, it is known that Diels-Alder route is kinetically favored and cheletropic route is thermal dynamically favored.

As for the Cheletropic route, there is only exothermic reaction. The reaction profile is listed below.
[[File:Exoche.png|none|thumb]]
For the Diels-Alder route, both exo and endo type of route exist. They are listed below.
[[File:Exoche1.png|none|thumb]]
Exo of Diels-Alder route
[[File:Exoche12.png|none|thumb]]
Endo of Diels-Alder route

== '''Conclusion''' ==

Rep:MOD:LYF1996

2016-10-20T15:10:08Z

Yl20414:

== '''Introduction''' ==
The transition state in potential energy surface would be a
stationary point which is the highest point on the reaction energy curve. It
means the just point of the reactant is forming their bonds or breaking their
bonds to form the product. However, a stationary point is not always the
transition state. It can still be the minimum energy point which means
physically stable point. That is the minimum point on the potential energy
surface. During a frequency calculation, the negative frequency is the
transition state which is called as an imaginary frequency. But, if only real frequencies exist, it is a minimum structure for the molecule.

== '''First part write up''' ==
In this part a Diels-Alder reaction (Butadiene with Ethylene)
is analysed about its MO diagram, bond length and bond formation at the
reactant, product and transition state.

First comes to the MO. The MO image of the reactant and transition
state are listed below. The shape of transition state can be found from the
four reactant MO graph if the whole MO is read from each partial MO. Transition
State 16 is formed from the HOMO of butadiene and LUMO of ethylene. Transition
State 17 is formed from the HOMO of ethylene and LUMO of butadiene. Transition
State 18 is formed from the HOMO of ethylene and LUMO of butadiene. Transition
State 19 is formed from the HOMO of butadiene and LUMO of ethylene. So, only
same symmetry can be used to form a MO. If the two reactant are at the same
symmetry, the overlap integral would be non-zero or it would be cancelled out
to give zero integral. This means a gerade-ungerade interaction gives zero
overlap integral, a gerade-gerade interaction gives a non-zero integral and an
ungerade-ungerade interaction gives a non-zero integral.
{| class="wikitable"
!<gallery>
E1r1.png
</gallery>HOMO of the ethylene
!<gallery>
E1r2.png
</gallery>LUMO of the ethylene
!<gallery>
Tshomo.png
</gallery>HOMO of transition state
!<gallery>
E1tslumo.png
</gallery>LUMO of transition state
|-
|<gallery>
E1r2homo.png
</gallery>HOMO of the butadiene
|<gallery>
E1r2lumo.png
</gallery>LUMO of butadiene
|<gallery>
Ts16.png
</gallery>Transition stae16
|<gallery>
Ts19.png
</gallery>Transition 19
|}
{| class="wikitable"
![[File:E1r1mo.PNG|thumb]]Energy level list for ethylene
![[File:E1r2mo.PNG|thumb]]Energy list for butadiene
![[File:Tsmo.PNG|thumb]]Energy list for transition state
|}

From the MO chart, it is easily compared and can be told
that this is a neutral Diels-Alder reaction.

Then comes to the bond length analysis. A labelled graph and
a table for the bond length for the C-C bond are shown below. The standard Sp2
and Sp3 C-C bond length are 1.47 Å and 1.54Å respectively. (1) And, the Van der
Waals radius of carbon atom is 1.7 Å, which means 3.4 Å for two atoms

.[[File:E1reaction.png|frameless|461x461px]]

[[File:Yifeiliaodetableandchart.PNG|thumb|718x718px|none]]
{| class="wikitable"
|It is shown that the bond length except between carbon 2 and
3 are increasing. If we compare the length values with the standard sp2 and sp3
c-c length, it is easily found that merely carbon-carbon bond between 2 and 3
are turning into a sp2 hybridised one while the other bond are changing from the sp2 like into sp3 like.

As for the Van der Waals radius comparison between two
carbon atoms and the carbon-carbon distance between atom 4 to 5 and 6 to 1, we
can found that the two bond length are both smaller than the Van der Waals
radius between two carbon atoms. This shows there is bond forming between the two
carbons or they should equal or larger than the Van der Waals radius.

Finally, the vibration that corresponds to the reaction path
at the transition state which is at the only negative frequency. The two end
carbon atoms of butadiene and the two atoms of the ethylene are vibrating in an opposite direction.
[[File:E1-frequency.gif|thumb|541x541px|none]]

{| class="wikitable"
|However, as for the smallest positive frequency, the two
compounds are shaking at two different direction (one into the screen, one out

of the screen).
|}
[[File:E1sf.gif|none|thumb|557x557px]]
{| class="wikitable"
|And from the IRC result, the bond forming is at the same
time between.
|}
[[File:E1irc.gif|none|thumb|553x553px]]

== S'''econd part write up''' ==
First, comes to the MO part. Both the transition state of
ENDO and EXO process are listed below.[[File:Lyfdmo.PNG|none|thumb|964x964px]][[File:Lyfd2mo.PNG|none|thumb|648x648px]]From the MO
diagram of the two reactants, the cyclopentadiene as diene role has higher
energy of both HOMO and LUMO then the Benzoquinone as an ene role. So, it tells
that the reaction is a normal electron demand reaction. [[File:Tableoneyfl.png|none|thumb|780x780px]][[File:Tb2e2.png|none|thumb|359x359px]]

Secondary orbital
interaction only takes place in ENDO Transition state but not in EXO transition
state. From the Endo transition state MO diagram, the two part side orbital turn
into a bit twist like. So, it could be concluded as a secondary interaction and
will act as a stabilization that lower barrier energy (2).

|}

== '''Third part write up''' ==

Both the Diels-Alder and Cheletropic IRC route are listed below.If they are considered from the product side to the reactant
side as the analysis done, the delocalised electron density from the six
membered ring is withdraw from the ring system during the reaction to form the
two outer double bond. This means inside the ring, six delocalised pi bonds are
changing into three discrete sp2 bonding. If they are considered as the reactants to products, the electrons from oxygen and sulfur atom is forming bond with the two outer carbon atoms and push electron( from double bond ) into the ring and formed a delocalised system.
[[File:ADIRC.gif|none|thumb|597x597px]]Diels-Alder route
[[File:C irc.gif|none|thumb|598x598px]]
Cheletropic route

The free energy data are list as table below
[[File:Tbofe31.PNG|none|thumb|515x515px]]
[[File:Tbofe33.PNG|none|thumb|394x394px]]
So, from the activation energy comparison and reaction energy comparison, it is known that Diels-Alder route is kinetically favored and cheletropic route is thermal dynamically favored.

As for the Cheletropic route, there is only exothermic reaction. The reaction profile is listed below.
[[File:Exoche.png|none|thumb]]
For the Diels-Alder route, both exo and endo type of route exist. They are listed below.
[[File:Exoche1.png|none|thumb]]
Exo of Diels-Alder route
[[File:Exoche12.png|none|thumb]]
Endo of Diels-Alder route

== '''Conclusion''' ==

File:Exoche12.png

2016-10-20T15:09:14Z

Yl20414:

File:Exoche1.png

2016-10-20T15:07:25Z

Yl20414:

File:Exoche1.cdx

2016-10-20T15:06:24Z

Yl20414:

File:Ts16.png

2016-10-20T13:03:47Z

Yl20414:

File:E1tslumo.png

2016-10-20T13:01:52Z

Yl20414: