Building molecules and polymers with Zoa v3.0

1. Building molecules and polymers with Zoa v3.0 J.P. Calbert

2. Create Template Build molecules or polymers • Creating templates • Building molecules • Building polymers 2D builder or Chemwindow or Existing structure

3. I. Creating templates : 2D builder • Rough/fast molecule drawing • Add missing Hydrogen • Export to the main view • Cleanup

4. Hydrogen adjust I. Creating templates : Import from Chemwindow New in Zoa v3.0

5. You have You want I. Creating templates : From existing structure • Delete all unwanted atoms EXCEPT the first attached carbon • Select it and set it as an Hydrogen atom

6. 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 …

7. I. Creating templates • 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 theatom numbers change during the creation of the template !!!) • That’s all, the new template is now in the list

8. II. Building molecules Creating simple molecules can be done like the fragments, for more complex there is the « 3D builder » • Principle: • From an initial molecule or fragment, select the atoms where you want to attach a template • Click « add » • 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)

9. O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O II. Building molecules : real exemple • Think and decompose • Create template • Build the molecule

10. O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O II. Building molecules : real exemple • Think and decompose • Create template • Build the molecule 3 templates are needed

11. II. Building molecules : real exemple • Think and decompose • Create template (w/ 2D builder or chemdraw) • Build the molecule t1 t2 t3 3 « end » atoms

12. O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O II. Building molecules : real exemple • Think and decompose • Create template • Build the molecule New benzeneselect the 6 hydrogen Add the phenyl template with a torsion of 40-45° Add twice the template t1

13. O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O II. Building molecules : real exemple • Think and decompose • Create template • Build the molecule Add template t2 Add template t3,« et voilà »

14. 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. (Maxwell-Boltzmann Distribution)

15. 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

16. III. Building polymers : different type of polymers Click 1 Click 2 Grafting Select atoms + build

17. III. Building polymers : Interface Random between two limits

18. From file (currently cerius2 (*.grf)) Potential torsion of thiophene, thanks to Patrick

19. III. Building polymers : angle from torsion potential Random number generator + Linear interpolation between two points T=50K Low probability T=273K High probability Low probability T=500K T=2000K

20. III. Building polymers : results Random 0 - 360 Maxwell-Boltzmann Distribution

21. Solution: create copolymer A-B with templates like this: Solution: create template like this: And at the end ask to recompute bonding III. Building polymers : tricks Problem: Need two torsion angle for one monomer Problem: Torsion between non-linked atoms

22. Questions ?