Transcript Building molecules and polymers with Zoa

Building molecules and polymers with Zoa v3.0
J.P. Calbert
I. Creating templates
II. Building molecules
III. Building polymers
2D builder or Chemwindow or Existing structure
Create Template
Build molecules or polymers
I. Creating templates : 2D builder
1)
Rough/fast molecule drawing
2)
Add missing Hydrogen
3)
Export to the main view
4)
Cleanup
I. Creating templates : Import from Chemwindow
Hydrogen adjust
I. Creating templates : From existing structure
You have
You want
1) Delete all unwanted atoms EXCEPT the first attached carbon
2) Select it and set it as an Hydrogen atom
I. Creating templates : From existing structure
3) Open the 3D builder
4) Change the C-H bond length
Now that we know how to create a fragment …
I. Creating templates
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Display atom numbers (from the render options tool)
Open the 3D builder
Enter the « begin atom » (where the template will be connected)
Click “Create template”
Give a file name
Give the “End” atom (!!! Check the end atom when Zoa asks, because the
atom numbers change during the creation of the template !!!)
7) That’s all, the new template is now in the list
II. Building molecules
Creating simple molecules can be done like the fragments,
for more complex there is the « 3D builder »
Principle:
1) From an initial molecule or fragment, select the atoms where you
want to attach a template
2) Click « add »
3) The « end » atoms are automatically selected, so the process can
continue
If several atoms are selected, the template is attached to all selected atoms
A template can have more than one “end” atom
(need to manually edit the template file)
II. Building molecules : real exemple
1) Think and decompose
2) Create template
3) Build the molecule
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II. Building molecules : real exemple
1) Think and decompose
2) Create template
3) Build the molecule
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3 templates are needed
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II. Building molecules : real exemple
1) Think and decompose
2) Create template (w/ 2D builder or chemdraw)
3) Build the molecule
t1
t2
3 « end » atoms
t3
II. Building molecules : real exemple
1) Think and decompose
2) Create template
3) Build the molecule
New benzene
select the
6 hydrogen
Add the phenyl template
with a torsion of 40-45°
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Add twice the template t1
II. Building molecules : real exemple
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Add template t2
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1) Think and decompose
2) Create template
3) Build the molecule
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Add template t3,
« et voilà »
III. Building polymers
• Create different type of polymer
(homopolymer, copolymer A-B and
random copolymer).
• Generate chain with random torsion
and bond angles.
• Use torsion and bond angle potential
as input for the generation. (MaxwellBoltzmann Distribution)
III. Building polymers : different type of polymers
Probability of monomer B
Number of iteration = number
of monomers (for non-ramified
monomers)
Not yet available
Warning! Symetrical growth
III. Building polymers : different type of polymers
Click 1
Click 2
Grafting
Select atoms + build
III. Building polymers : Interface
Random between two limits
From file (currently cerius2 (*.grf))
P( , T ) 
exp(  E / kT )
 exp(  E j / kT )
j
F   P(i, T )
i 
0  F  1
Potential torsion of thiophene, thanks to Patrick
III. Building polymers : angle from torsion potential
Random number generator
0  F  1
+ Linear interpolation between two points
T=50K
Low probability
T=273K
High probability
Low probability
T=500K
T=2000K
III. Building polymers : results
Random 0 - 360
Maxwell-Boltzmann Distribution
III. Building polymers : tricks
Problem: Need two torsion angle for one monomer
Solution: create copolymer A-B with templates like this:
H
H
H
H
H
H
Problem: Torsion between non-linked atoms
Solution: create template like this:
H
H
And at the end ask to recompute bonding
Questions ?