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

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1) Think and decompose2) Create template3) Build the molecule

II. Building molecules : real exempleII. Building molecules : real exemple

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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

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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 »

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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 ?