1. FROM ATOM TO POLYMER
creating and manipulating models of chemical compounds In BIOVIA Materials studio

2. What can be built in Materials Studio?
Single structures

3. What can be built in Materials Studio?
Homopolymers

4. What can be built in Materials Studio?
Block copolymers

5. What can be built in Materials Studio?
Dendrimers

6. What can be built in Materials Studio?
Nanotubes

7. What can be built in Materials Studio?
Multi-wall nanotubes

8. What can be built in Materials Studio?
Nanopores

9. What can be built in Materials Studio?
Crystals

10. Getting started with Materials Studio
Save it as polymer

11. Getting started with Materials Studio
Import structure and modifying
Sketching structure

12. Getting started with Materials Studio
Structures\repeat-units\imides\benzimid.msi

13. Getting started with Materials Studio

14. MS’s basic tools
Sketch atom
Sketch ring
Sketch fragment
Measure
Create centroid
Clean
Adjust hydrogen
Modify element
Modify bond
Modify hybridization
MS provides wide spectrum of constructing system tools.
There are two baisic panels:
3D Viever
Sketch
Selection
Rotation
Zoom
Translation
Reset view
Recenter
Fit to view
Display style

15. Getting started with Materials Studio
Click right button mouse on the background of 3D atomistic view

16. Getting started with Materials Studio
Select Ball and stick and set values Stick radius = 0,1 and Ball radius = 0,3

17. Getting started with Materials Studio
Import structure and modifying
Sketching structure

18. Getting started with Materials Studio
Select 3D Atomistic

19. Getting started with Materials Studio

20. Preparing the system A key elements of preparing simulations
Geometric parameters of the system
Coords.
Atom types
Masses
Charges
Velocities
Topologic parameters of the system
Bonds
Angles
Interactions between atoms and molecules
Forcefield

21. MS’s basic tools
Sketch atom
Sketch ring
Sketch fragment
Measure
Create centroid
Clean
Adjust hydrogen
Modify element
Modify bond
Modify hybridization
MS provides wide spectrum of constructing system tools.
There are two baisic panels:
3D Viever
Sketch
Selection
Rotation
Zoom
Translation
Reset view
Recenter
Fit to view
Display style

22. Water – H2O
File | New | 3D Atomistic Select Sketch atom, and change element to Oxygen form dropdown menu. Click somewhere on blackwindow. Change element to Hydrogen and add two atoms in the neighborhood Change Display style to Balls and Sticks.

23. Water – H2O
By clicking on one of the atoms and draging the line to another bond will be created.
Try to draw two bonds between oxygene and hydrogens.
Measure bonds lenghts and angles by Mesure.

24. Water – H2O Now we will clean H2O molecule. Click Clean .
Molceule is initially optimized and values of lenght and angle got closer to actual values.

25. Biphenyle – C6H12 Create new 3D Atomistic document.
Biphenyle is a molecule containing two phenyl rings.
They can be constructed in two ways:
Use Sketch fragment to draw two phenyl rings and conect them,
Use Sketch ring to draw phenyl rings.

26. Biphenyle – C6H12
To draw proper structure of phenyl rings hold ALT key using Sketch ring tool to set set partial double bonds between atoms of carbon
You can also select every bond in rings and change bond type by Modify bond type .

27. Biphenyle – C6H12 Now click Adjust hydrogenes .
Missing hydrogenes will appear.
At the end Clean your structure to obtain proper values of bonds lengts and angles.

28. Biphenyle – C6H12
Measure torsion angle between two phenyl rings using Measrure tool. (~180°)
Click Viev | Explorers | Properties explorer to turn on Properties explorer.
Highlight value of torsion angle an check the value in Angle box.
Click twice on Angle and change it to 44 (which is real value).

29. Vitamin A - C20H30O
Build your own molecule – add atoms, change bonds, optimize structure.

30. Vitamin A - C20H30O

31. Polymers Polymers Homopolymers Random copolymers Block copolymers
Dendrimers

32. How to create polymer? Step-by-Step:
1. Building or importing molecule.
2. Modifying molecule.
3. Setting options of monomer.
4. Setting options of polymer.
5. Multiplying monomers.

33. How to create polymer? Step-by-Step:
1. Building or importing molecule.
2. Modifying molecule.
3. Setting options of monomer.
4. Setting options of polymer.
5. Multiplying monomers.
Now let’s go through all the points with graphical tutorial.

34. How to create polymer? Step-by-Step:
1. Building or importing molecule.
2. Modifying molecule.
3. Setting options of monomer.
4. Setting options of polymer.
5. Multiplying monomers.
Now let’s go through all the points with graphical tutorial.

35. How to create polymer? Step-by-Step:
1. Building or importing molecule.
2. Modifying molecule.
3. Setting options of monomer.
4. Setting options of polymer.
5. Multiplying monomers.
Now let’s go through all the points with graphical tutorial.

36. How to create polymer? Step-by-Step:
1. Building or importing molecule.
2. Modifying molecule.
3. Setting options of monomer.
4. Setting options of polymer.
5. Multiplying monomers.
Now let’s go through all the points with graphical tutorial.

37. What do we want to get?

38. Building or importing molecules
Start new project and name it:
Poly-p-nitrostyrene

39. Building or importing molecules
Structures\repeat-units\vinyls\styrene.msi
Change Display Style to: Ball and stick (SR = 0,1, BR = 0,3)

40. Modifying molecule Choose Sketch fragment
Fragment Browser -> Functional Groups - >Nitro

41. Rename to: p-nitrostyrene
Modifying molecule
Rename to: p-nitrostyrene

42. Setting options of monomer

43. Setting options of monomer
Click hide

44. Setting options of monomer
Click Head Atom

45. Setting options of monomer
Click Tail Atom

46. Setting options of monomer
Click Chiral Center

47. Setting options of homopolymer

48. Why atactic?
Isotactic

49. Why atactic?
Syndiotactic

50. Why atactic?
Atactic

51. Setting options of homopolymer

52. Multiplying monomers
Click build!

53. Or you should get similar random structure of atactic homopolymer
Multiplying monomers
Or you should get similar random structure of atactic homopolymer