Building molecules and polymers with Zoa v3.0 Building molecules and polymers with Zoa v3.0
J.P. Calbert
I.I. Creating templatesCreating templatesII.II. Building moleculesBuilding moleculesIII.III. Building polymersBuilding polymers
2D builder or Chemwindow or Existing structure2D builder or Chemwindow or Existing structure
Create TemplateCreate Template
Build molecules or polymersBuild molecules or polymers
I. Creating templates : 2D builderI. 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 ChemwindowI. Creating templates : Import from Chemwindow
Hydrogen adjust
New in Zoa v3.0
I. Creating templates : From existing structureI. Creating templates : From existing structure
You want
You have
1) Delete all unwanted atoms EXCEPT the first attached carbon2) Select it and set it as an Hydrogen atom
I. Creating templates : From existing structureI. Creating templates : From existing structure
3) Open the 3D builder4) Change the C-H bond length
Now that we know how to create a fragment …
I. Creating templatesI. Creating templates
1) Display atom numbers (from the render options tool)2) Open the 3D builder3) Enter the « begin atom » (where the template will be connected)4) Click “Create template”5) Give a file name6) 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 moleculesII. 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 exempleII. Building molecules : real exemple
OO
O
OO
O
OO
O
OO
O
OO
O
OO
O
O
O
O
O
O
O
O
O
O
O
O
OO
O
O
O
O
O
O
O
O
O
O
O
1) Think and decompose2) Create template3) Build the molecule
II. Building molecules : real exempleII. Building molecules : real exemple
OO
O
OO
O
OO
O
OO
O
OO
O
OO
O
O
O
O
O
O
O
O
O
O
O
O
OO
O
O
O
O
O
O
O
O
O
O
O
1) Think and decompose2) Create template3) Build the molecule
3 templates are needed3 templates are needed
II. Building molecules : real exempleII. Building molecules : real exemple
1) Think and decompose2) Create template (w/ 2D builder or chemdraw)3) Build the molecule
3 « end » atoms
t1 t2 t3
II. Building molecules : real exempleII. Building molecules : real exemple
1) Think and decompose2) Create template3) Build the molecule
New benzeneselect the 6 hydrogen Add the phenyl template
with a torsion of 40-45°
Add twice the template t1
OO
O
O O O
OO
O
OO
O
OOO
OO
OO
O
OO
O
O
O
O
OO
OOO
O
OO
O
OO
O
OO
OO
II. Building molecules : real exempleII. Building molecules : real exemple
1) Think and decompose2) Create template3) Build the molecule
Add template t2 Add template t3,« et voilà »
OO
O
O O O
OO
O
OO
O
OOO
OO
OO
O
OO
O
O
O
O
OO
OOO
O
OO
O
OO
O
OO
OO
III. Building polymersIII. 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. (Maxwell-Boltzmann Distribution)
Probability of monomer BProbability of monomer B
Number of iteration = number Number of iteration = number of monomers (for non-of monomers (for non-ramified monomers)ramified monomers)
Not yet availableNot yet available
Warning! Symetrical growth
III. Building polymers : different type of polymersIII. Building polymers : different type of polymers
Click 1Click 1 Click 2Click 2
Grafting
Select atoms + buildSelect atoms + build
III. Building polymers : different type of polymersIII. Building polymers : different type of polymers
Random between two limits
III. Building polymers : InterfaceIII. Building polymers : Interface
From file (currently cerius2 (*.grf))
jj kTE
kTETP
)/exp(
)/exp(),(
i
TiPF ),(
10 F
Potential torsion of thiophene, thanks to Patrick
10 F
Random number generator
+ Linear interpolation between two points+ Linear interpolation between two points
Low probability
Low probability
High probability
T=50K
T=273K
T=500K
T=2000K
III. Building polymers : angle from torsion potentialIII. Building polymers : angle from torsion potential
Random 0 - 360 Maxwell-Boltzmann Distribution
III. Building polymers : resultsIII. Building polymers : results
Problem: Torsion between non-linked atoms
Problem: Need two torsion angle for one monomer
HH H
H
H
H
Solution: create copolymer A-B with templates like this:
H H
Solution: create template like this:
And at the end ask to recompute bonding
III. Building polymers : tricksIII. Building polymers : tricks
Questions ?