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Building molecules and polymers with Zoa v3.0

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Building molecules and polymers with Zoa v3.0. J.P. Calbert. Create Template. Build molecules or polymers. Creating templates Building molecules Building polymers. 2D builder or Chemwindow or Existing structure. I. Creating templates : 2D builder. Rough/fast molecule drawing

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Presentation Transcript
slide2

Create Template

Build molecules or polymers

  • Creating templates
  • Building molecules
  • Building polymers

2D builder or Chemwindow or Existing structure

slide3

I. Creating templates : 2D builder

  • Rough/fast molecule drawing
  • Add missing Hydrogen
  • Export to the main view
  • Cleanup
slide4

Hydrogen adjust

I. Creating templates : Import from Chemwindow

New in Zoa v3.0

slide5

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
slide6

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 …

slide7

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
slide8

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)

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II. Building molecules : real exemple

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

  • Think and decompose
  • Create template
  • Build the molecule

3 templates are needed

slide11

II. Building molecules : real exemple

  • Think and decompose
  • Create template (w/ 2D builder or chemdraw)
  • Build the molecule

t1

t2

t3

3 « end » atoms

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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

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II. Building molecules : real exemple

  • Think and decompose
  • Create template
  • Build the molecule

Add template t2

Add template t3,« et voilà »

slide14

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)
slide15

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

slide16

III. Building polymers : different type of polymers

Click 1

Click 2

Grafting

Select atoms + build

slide17

III. Building polymers : Interface

Random between two limits

slide18

From file (currently cerius2 (*.grf))

Potential torsion of thiophene, thanks to Patrick

slide19

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

slide20

III. Building polymers : results

Random 0 - 360

Maxwell-Boltzmann Distribution

slide21

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

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