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

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

3. I. Creating templates : 2D builder 1)Rough/fast molecule drawing 2)Add missing Hydrogen 3)Export to the main view 4)Cleanup

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

5. I. Creating templates : From existing structure You want You have 1)Delete all unwanted atoms EXCEPT the first attached carbon 2)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 1)Display atom numbers (from the render options tool) 2)Open the 3D builder 3)Enter the « begin atom » (where the template will be connected) 4)Click “Create template” 5)Give a file name 6)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

8. 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)

9. II. Building molecules : real exemple 1)Think and decompose 2)Create template 3)Build the molecule

10. II. Building molecules : real exemple 1)Think and decompose 2)Create template 3)Build the molecule 3 templates are needed

11. II. Building molecules : real exemple 1)Think and decompose 2)Create template (w/ 2D builder or chemdraw) 3)Build the molecule 3 « end » atoms t1t2t3

12. 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° Add twice the template t1

13. II. Building molecules : real exemple 1)Think and decompose 2)Create template 3)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. 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

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

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

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

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

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

21. Problem: Torsion between non-linked atoms Problem: Need two torsion angle for one monomer 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

22. Questions ?