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[[VB_workshop_tutorials_program|<< Return to the program]]
+
[[VB_tutorial|<<< VB tutorials main page]]
 
 
 
 
<font color=red> '''How to modify this page''' : </font>
 
* first : '''<font color=blue>log in</font>''' (top right of this page) ;
 
* click on '''[<font color=blue>edit</font>]''' (far right) to edit a section of the page ;
 
* write your text directly in the wiki page, and click on the "Save page" button (bottom left) to save your modifications
 
Pictures : [[Insert a picture| how to insert a picture]] in your text
 
 
 
See also [http://en.wikipedia.org/wiki/Wikipedia:Cheatsheet this page] for an introduction to the basics of the wiki syntax
 
  
  
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{| class="collapsible collapsed wikitable"
 
{| class="collapsible collapsed wikitable"
 
|-
 
|-
!<big><big>'''To the tutors'''</big></big>
+
!<big>'''BLW within GAMESS (Version: MAR-25-2010 R2)'''</big>
|-
 
|'''[[Sason_remarks|Sason remarks and prospective 2 hours talk]]'''
 
 
 
Philippe's remark on the initially proposed tutorial. are included in '''bold'''.
 
 
 
'''Qualitative'''
 
* ?...
 
 
 
'''Computational'''
 
 
 
Proposal from Yirong
 
# benzene and formamide - focus is on the structural and energetic impact from conjugation, and how to correlate the results with experimental evidences;
 
# butadiene - focus is on the conjugation in the planar structure and the hyperconjugation in the staggered structure, and their impact on the rotational barrier;
 
# acid-base and H-bonding systems: BLW energy decomposition analyses.
 
# visualize the results. I have been using GaussView and ChemDraw, but other graphical software should be fine with me as well.
 
# Questions from any participant can be discussed and tested on site.
 
 
 
|}
 
 
 
 
 
{| class="collapsible collapsed wikitable"
 
|-
 
!<big><big>'''BLW within GAMESS (Version: MAR-25-2010 R2)'''</big></big>
 
 
|-
 
|-
 
|
 
|
[[BLW | BLW ]] is provided by [http://homepages.wmich.edu/~ymo/ Yirong Mo]  (Western Michigan University - USA). It allows to optimize local wave function.
+
[[BLW | BLW ]] is provided by [http://homepages.wmich.edu/~ymo/ Yirong Mo]  (Western Michigan University - USA). It allows to optimize local wave functions. DFT approaches allow to include a part of correlation into the structure.
Gradients are available for geometry optimization. DFT approaches allow to include a part of correlation into the structure.
+
Gradients are available for geometry optimization. Structures can interact with $BLWCI group.  
 
 
Structures can interact with $BLWCI group.  
 
  
 
During the workshop, a BLW computation of file.inp is obtained with the command "blwrun  file "
 
During the workshop, a BLW computation of file.inp is obtained with the command "blwrun  file "
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{| class="collapsible collapsed wikitable"
 
{| class="collapsible collapsed wikitable"
 
|-
 
|-
!<big><big>'''HuLiS : a Huckel-based code'''</big></big>
+
!<big>'''HuLiS : a Huckel-based code'''</big>
 
|-
 
|-
 
|
 
|
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|}
 
|}
  
 
{| class="collapsible collapsed wikitable"
 
|-
 
!<big><big><big>'''Paper Exercices'''</big></big></big>
 
|-
 
|
 
 
Here are two HuLiS  exercices : find the weights in formamide with HL-CI and use HLP to get coefficients for the allyl radical.
 
 
====Formamide with HL-CI====
 
[[File:Formamide.png|400px|thumb|right]]
 
Formamide can be written as a resonance between two Lewis strutures. We shall find the weights of this scheme using HL-CI.
 
 
In HL-CI we define an effective CI hamiltonian that concerns the interaction between  the (localized) Lewis structures <math> \Psi_{I}</math> and <math> \Psi_{II}</math>: <math> \Psi_{HL-CI}=c_{I}\Psi_{I}+c_{II}\Psi_{II}</math>. This CI must give the Huckel energy of the delocalized wave function. <math> E_{HL-CI}=E_{Huckel}</math>
 
 
Formamide's Huckel energy <math>E_{Huckel}= 4\alpha + 6.548\beta</math>
 
 
The (localized) Lewis structures '''I''' and '''II''' have an energy of
 
** <math>E_{I}= 2*(\alpha + 1.370\beta)+2*(\alpha+1.651\beta)= 4\alpha + 6.041\beta</math> 
 
** <math>E_{II}= 2*(\alpha + 1.808\beta)+2*(\alpha+0.970\beta)= 4\alpha + 5.556\beta</math> 
 
 
These values are used as  <math>H_{I-I}</math> and <math>H_{II-II}</math> for the CI matrix.
 
 
*1/ Write the expression of the CI secular determinant that has the energy ot the delocalized wave function, and show that the off-diagonal term is <math>H_{I-II}=0.71\beta</math>. (in HL-CI the off diagonal term is supposed <0).
 
 
*2/ Resolve the secular equations of the CI and find that
 
<math> \Psi_{HL-CI}=0.81\Psi_{I}+0.58\Psi_{II}</math>, hence the weights of the structures (I/II)=(66%/34%)
 
 
Note that in HL-CI <math><Psi_{I}|\Psi_{II}>=0</math>
 
 
====Allyl Radical with HLP====
 
[[File:Allyl_radical.png|250px|thumb|right]]
 
Allyl radical can be written as a resonance between two Lewis strutures: <math> \Psi_{HLP}=c_{I}\Psi_{I}+c_{II}\Psi_{II}</math>.
 
We shall find the coefficients of this CI via HLP. The Huckel orbitals are considered as :
 
 
** <math> \phi_1=0.5 p_1 + 0.7 p_2 + 0.5 p_3 </math>
 
** <math> \phi_2=0.7 p_1 + 0.0 p_2 - 0.7 p_3 </math>
 
** <math> \phi_3=0.5 p_1 - 0.7 p_2 + 0.5 p_3 </math>
 
In the following the Huckel wave function is expressed as a Salter determinant: <math> \Psi_{Huckel}=|\phi_{1}\bar{\phi_{1}}\phi_2|</math>
 
In the HLP scheme we search the coefficient of the structures I and II by projection of the Huckel wave function  onto the localized structures <math> \Psi_{I}=|\pi_{12}\bar{\pi_{12}}p_3|</math> and <math>\Psi_{II}=|p_1\pi_{23}\bar{\pi_{23}}|</math>. 
 
======Overlap between Lewis structures ======
 
Within Huckel approximation, (<math> <p_{i}|p_{j}>=\delta_{ij}</math>)
 
*1/ Find that <math> <\Psi_{I}|\Psi_{II}>=-0.25</math>.
 
*2/ Suppose that <math> <\Psi_{I}|\Psi_{Huckel}>=-0.73</math> and <math><\Psi_{II}|\Psi_{Huckel}>=+0.73</math>.
 
Find <math>c_I</math> and <math>c_{II}</math> by solving the equations that derive from
 
**<math><\Psi_I|\Psi_{Huckel}>=<\Psi_I|\Psi_{HLP}></math>
 
**<math><\Psi_{II}|\Psi_{Huckel}>=<\Psi_{II}|\Psi_{HLP}></math>
 
*3/ Compute the trust factor <math>\tau=<\Psi_{HLP}|\Psi_{huckel}></math>
 
 
*4/ Remark: HL-CI fails to give the correct signs because it supposes <math>H_{I-II}<0</math>.
 
This drawback can be shown using the energies of the occupied Huckel orbitals <math> \epsilon_1=\alpha+1.41\beta</math> and<math> \epsilon_2=\alpha</math>
 
 
|}
 
  
  
 
{| class="collapsible collapsed wikitable"
 
{| class="collapsible collapsed wikitable"
 
|-
 
|-
!<big><big><big>'''Computer Exercices'''</big></big></big>
+
!<big><big><big>'''Main exercises'''</big></big></big>
 
|-
 
|-
 
|  
 
|  
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|}
 
|}
  
The cc-pVTZ basis set will be used in the following, unless a different choice is specified.  
+
The 6-31G(d) basis set will be used in the following.  
  
 
1/ Vertical Resonance Energy - at the  geometry of benzene.
 
1/ Vertical Resonance Energy - at the  geometry of benzene.
With the BLW program, and using the provided optimized geometry of benzene molecule, define one 1,3,5-cyclohexadiene Lewis structure, and optimize it's orbitals. 4 blocks need to be defined 3 blocks for 3 pi bond, one for all the sigma electrons.
 
: by compairison to benzene energy, calculate the Vertical Resonance Energy (VRE), using the cc-pvTZ basis set.
 
: recompute the VRE using the aug-cc-pVTZ basis set, and then the aug-cc-pVQZ basis set. Comment on the differences : which basis set(s) is suitable for VB computations ?
 
  
 +
With the BLW program, and using the provided optimized geometry of benzene molecule, define one 1,3,5-cyclohexadiene Lewis structure, and optimize it's orbitals. 4 blocks need to be defined : 3 blocks for 3 pi bond, and 1 for all the sigma electrons.
 +
Using benzene energy, calculate the Vertical Resonance Energy (VRE).
 +
 +
 +
2/ Adiabatic Resonance Energy (ARE)- relax the Lewis structure geometry
  
2/ Adiabatic Resonance Energy - relax the Lewis structure geometry
 
 
With the BLW program, relax the Lewis' structure geometry.
 
With the BLW program, relax the Lewis' structure geometry.
 
: Compare the C-C bond distances to benzene's. Ensure that it is consistent with the Lewis structure.
 
: Compare the C-C bond distances to benzene's. Ensure that it is consistent with the Lewis structure.
Ligne 162 : Ligne 76 :
  
 
3/ With HuLiS, evaluate the space spanned by Lewis structures compared to that of delocalized wave functions.
 
3/ With HuLiS, evaluate the space spanned by Lewis structures compared to that of delocalized wave functions.
 +
 
: Draw the benzene with the Huckel tools (blue, left) and create two Kekules structures with the Lewis tools. Double bonds are obtained by clicking a single bond - A second click returns to the Single bond.
 
: Draw the benzene with the Huckel tools (blue, left) and create two Kekules structures with the Lewis tools. Double bonds are obtained by clicking a single bond - A second click returns to the Single bond.
 
::Note the low value of the trust factor <math>{\tau}</math>.
 
::Note the low value of the trust factor <math>{\tau}</math>.
Ligne 170 : Ligne 85 :
 
::Note the value of <math>{\tau}</math>, and the weight of all Lewis structures needed ([Results]).
 
::Note the value of <math>{\tau}</math>, and the weight of all Lewis structures needed ([Results]).
  
[[VBFile 4-1 | all input files are there]]
+
[[VBFile 4-1 | FILES FOR BENZENE]]
  
 
== Exercice 2 (allyl) ==
 
== Exercice 2 (allyl) ==
Ligne 176 : Ligne 91 :
  
 
*1/ With the BLW code calculate the relative energies of the three Lewis structures of the allyl cation at the HF level. By comparison with the energy of the allyl cation, determine the VRE and the ARE. Compare the C-C bond distances.
 
*1/ With the BLW code calculate the relative energies of the three Lewis structures of the allyl cation at the HF level. By comparison with the energy of the allyl cation, determine the VRE and the ARE. Compare the C-C bond distances.
 +
 +
{| class="collapsible collapsed wikitable"
 +
|-
 +
!'''Hints'''
 +
|-
 +
|
 +
* Starting from the delocalized geometry, the first iteration of the optimization of the localized structure will give the VRE.
 +
|}
  
 
*2/ Repeat the first question at the B3LYP level.
 
*2/ Repeat the first question at the B3LYP level.
  
 
*3/ Repeat questions 1 and 2 for the allyl radical.
 
*3/ Repeat questions 1 and 2 for the allyl radical.
 
*4/ With XMVB, for the allyl cation put in resonance  structures '''I''' and '''II''', then add  structure '''III'''. What is the gain in energy due to the inclusion of this third structure?
 
  
 
[[VBFile 4-2 | FILES FOR THE ALLYLS]]
 
[[VBFile 4-2 | FILES FOR THE ALLYLS]]
  
== Exercice 3 (Butadiene deconjugation without hyperconjugation) ==
+
== Exercise 3 (BH3... NH3) electronics  at the B3LYP 6-31G(d) level ==
[[File:Rotated_butadiene.png|right|150px|alt=butadiene - Lewis alt text | planar butadiene ]]
 
[[File:planar_butadiene.png|right|150px|alt=butadiene - Lewis alt text | planar butadiene ]]
 
Examine the conjugation in planar butadiene and the hyperconjugation in perpendicular butadiene, and explain the rotational barrier.
 
 
 
Note that often people rotate one participating group to disable the conjugation and use the barrier to measure the conjugation energy. What is the inconvenience of this approach?
 
 
 
BLW shall be used
 
* to compute the deconjugated planar form, and compare to the conjugated form at the same geometry.
 
* to inhibit at will the hyperconjugaison in the perpendicular form, hence to mesure its stabilizing  contribution to the rotation barrier.
 
 
 
[[VBFile 4-3 | FILES ARE HERE]]
 
 
 
== Exercice 4 (BH3... NH3) electronics  at the B3LYP 6-31G(d) level ==
 
  
 
BLW energy decomposition analysis can be used to shed light into the nature of intermolecular interactions. Example of NH3∙∙∙BH3. Visualize the polarization and electron transfer effects using the electron density difference (EDD) maps.
 
BLW energy decomposition analysis can be used to shed light into the nature of intermolecular interactions. Example of NH3∙∙∙BH3. Visualize the polarization and electron transfer effects using the electron density difference (EDD) maps.
Ligne 284 : Ligne 192 :
 
  don't forget to name the cube file.   
 
  don't forget to name the cube file.   
 
  '''test.cube_BLW'''  
 
  '''test.cube_BLW'''  
  see also [[VBFile_4-4#gaussiancube.com | gaussiancube file]]
+
  see also [[VBFile_4-3#gaussiancube.com | gaussiancube file]]
 +
 
 +
|}
 +
 
 +
[[VBFile 4-3 | FILES FOR THE NH3 ... BH3]]
  
 
|}
 
|}
  
[[VBFile 4-4 | all input files are there]]
+
 
 +
{| class="collapsible collapsed wikitable"
 +
|-
 +
!<big><big><big>'''Optional exercises - homework'''</big></big></big>
 +
|-
 +
|
 +
 
 +
== Exercise 4 (Butadiene deconjugation without hyperconjugation) ==
 +
[[File:Rotated_butadiene.png|right|150px|alt=butadiene - Lewis alt text | planar butadiene ]]
 +
[[File:planar_butadiene.png|right|200px|alt=butadiene - Lewis alt text | planar butadiene ]]
 +
Examine the conjugation in planar butadiene and the hyperconjugation in perpendicular butadiene, and explain the rotational barrier.
 +
 
 +
Note that often people rotate one participating group to disable the conjugation and use the barrier to measure the conjugation energy. What is the inconvenience of this approach?
 +
 
 +
 +
* Compute the conjugated planar form with a standard B3LYP/6-31G(d) calculation
 +
* Using BLW, localize the pi electrons on C1=C2 and on C3=C4 double bonds. (view the geometrie to verify that the pi system is along the X axis.
 +
* Compare the energies to calculate the conjugaison energy.
 +
 
 +
{| class="collapsible collapsed wikitable"
 +
|-
 +
!'''Planar geometry'''
 +
|-
 +
|
 +
<html><pre>
 +
C    6.0  0.0000000000  0.6097325637  1.7490045499
 +
C    6.0  0.0000000000  0.6038280097  0.4085967284
 +
C    6.0  0.0000000000  -0.6038307169  -0.4085950903
 +
C    6.0  0.0000000000  -0.6097309803  -1.7490029472
 +
H    1.0  0.0000000000  1.5343833559  2.3190652626
 +
H    1.0  0.0000000000  -0.3149186339  2.3230080652
 +
H    1.0  0.0000000000  1.5514513284  -0.1322302753
 +
H    1.0  0.0000000000  -1.5514569088  0.1322266423
 +
H    1.0  0.0000000000  -1.5343794820  -2.3190677945
 +
H    1.0  0.0000000000  0.3149214640  -2.3230051413
 +
</pre></html>
 +
|}
 +
* Use the perpendicular form given below to compute the "deconjugated" system. The comparairison with the planar standard calculation gives an estimate of the conjugaison, which is contaminated by some hyperconjugaison.
 +
* To inhibit hyperconjugaison in the perpendicular form, localize the electrons on the C1=C2 and on C3=C4 double bond. (note that the C3=C4 vinyl group has rotated along the XZ plane; hence its pi system is along the Y axis.
 +
 
 +
{| class="collapsible collapsed wikitable"
 +
|-
 +
!'''Twisted (perpendicular) geometry'''
 +
|-
 +
|
 +
 
 +
<html><pre>
 +
C    6.0  0.000000  -1.086858    2.236154
 +
C    6.0  0.000000    0.000000    1.489418
 +
C    6.0  0.000000    0.000000    0.000000
 +
C    6.0  -1.086858    0.000000  -0.746736
 +
H    1.0  0.967527    0.000000  -0.478451
 +
H    1.0  0.000000    0.967527    1.967869
 +
H    1.0  -2.072275    0.000000  -0.314213
 +
H    1.0  -1.029400    0.000000  -1.820913
 +
H    1.0  0.000000  -2.072275    1.803631
 +
H    1.0  0.000000  -1.029400    3.310331
 +
$END
 +
 
 +
</pre></html>
 +
[[File:Rotated_butadiene.png|right|250px|alt=butadiene - Lewis alt text | planar butadiene The C3=C4 has rotated along the XZ plane; hence its pi system is along the Y axis.]]
 +
 
 +
|}
 +
[[VBFile 4-4 | FILES FOR THE BUTADIENE DECONJUGAISON ]]
 +
 
 +
== Exercise 5 : formamide and allyl radical with HuLiS ==
 +
 
 +
Here are two HuLiS  exercices : find the weights in formamide with HL-CI and use HLP to get coefficients for the allyl radical.
 +
 
 +
====Formamide with HL-CI====
 +
[[File:Formamide.png|400px|thumb|right]]
 +
Formamide can be written as a resonance between two Lewis strutures. We shall find the weights of this scheme using HL-CI.
 +
 
 +
In HL-CI we define an effective CI hamiltonian that concerns the interaction between  the (localized) Lewis structures <math> \Psi_{I}</math> and <math> \Psi_{II}</math>: <math> \Psi_{HL-CI}=c_{I}\Psi_{I}+c_{II}\Psi_{II}</math>. This CI must give the Huckel energy of the delocalized wave function. <math> E_{HL-CI}=E_{Huckel}</math>
 +
 
 +
*1/ Write the expression of the CI secular determinant that has the energy ot the delocalized wave function, and show that the off-diagonal term is <math>H_{I-II}=0.71\beta</math>. (in HL-CI the off diagonal term is supposed <0).
 +
 
 +
*2/ Resolve the secular equations of the CI and find that
 +
<math> \Psi_{HL-CI}=0.81\Psi_{I}+0.58\Psi_{II}</math>, hence the weights of the structures (I/II)=(66%/34%)
 +
 
 +
Note that in HL-CI <math><\Psi_{I}|\Psi_{II}>=0</math>
 +
{| class="collapsible collapsed wikitable"
 +
|-
 +
!'''help'''
 +
|-
 +
|
 +
Formamide's Huckel energy <math>E_{Huckel}= 4\alpha + 6.548\beta</math>
 +
 
 +
The (localized) Lewis structures '''I''' and '''II''' have an energy of
 +
** <math>E_{I}= 2*(\alpha + 1.370\beta)+2*(\alpha+1.651\beta)= 4\alpha + 6.041\beta</math> 
 +
** <math>E_{II}= 2*(\alpha + 1.808\beta)+2*(\alpha+0.970\beta)= 4\alpha + 5.556\beta</math> 
 +
 
 +
These values are used as  <math>H_{I-I}</math> and <math>H_{II-II}</math> for the CI matrix.
 +
|}
 +
 
 +
====Allyl Radical with HLP====
 +
[[File:Allyl_radical.png|250px|thumb|right]]
 +
Allyl radical can be written as a resonance between two Lewis strutures: <math> \Psi_{HLP}=c_{I}\Psi_{I}+c_{II}\Psi_{II}</math>.
 +
We shall find the coefficients of this CI via HLP. The Huckel orbitals are considered as :
 +
 
 +
** <math> \phi_1=0.5 p_1 + 0.7 p_2 + 0.5 p_3 </math>
 +
** <math> \phi_2=0.7 p_1 + 0.0 p_2 - 0.7 p_3 </math>
 +
** <math> \phi_3=0.5 p_1 - 0.7 p_2 + 0.5 p_3 </math>
 +
In the following the Huckel wave function is expressed as a Salter determinant: <math> \Psi_{Huckel}=|\phi_{1}\bar{\phi_{1}}\phi_2|</math>
 +
In the HLP scheme we search the coefficient of the structures I and II by projection of the Huckel wave function  onto the localized structures <math> \Psi_{I}=|\pi_{12}\bar{\pi_{12}}p_3|</math> and <math>\Psi_{II}=|p_1\pi_{23}\bar{\pi_{23}}|</math>. 
 +
======Overlap between Lewis structures ======
 +
Within Huckel approximation, (<math> <p_{i}|p_{j}>=\delta_{ij}</math>)
 +
*1/ Find that <math> <\Psi_{I}|\Psi_{II}>=-0.25</math>.
 +
*2/ Suppose that <math> <\Psi_{I}|\Psi_{Huckel}>=-0.73</math> and <math><\Psi_{II}|\Psi_{Huckel}>=+0.73</math>.
 +
Find <math>c_I</math> and <math>c_{II}</math> by solving the equations that derive from
 +
**<math><\Psi_I|\Psi_{Huckel}>=<\Psi_I|\Psi_{HLP}></math>
 +
**<math><\Psi_{II}|\Psi_{Huckel}>=<\Psi_{II}|\Psi_{HLP}></math>
 +
*3/ Compute the trust factor <math>\tau=<\Psi_{HLP}|\Psi_{huckel}></math>
 +
 
 +
*4/ Remark: HL-CI fails to give the correct signs because it supposes <math>H_{I-II}<0</math>.
 +
This drawback can be shown using the energies of the occupied Huckel orbitals <math> \epsilon_1=\alpha+1.41\beta</math> and<math> \epsilon_2=\alpha</math>
  
 
|}
 
|}

Dernière version du 14 février 2013 à 08:27

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BLW method & HuLiS program