FROM ATOM TO POLYMER. creating and manipulating models of chemical compounds In BIOVIA Materials studio
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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 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 Sketch atom Sketch ring Sketch fragment Measure Create centroid Clean Adjust hydrogen Modify element Modify bond Modify hybridization
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 Topologic parameters of the system Interactions between atoms and molecules Coords. Atom types Masses Charges Velocities Bonds Angles Forcefield
21 MS s basic tools 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 Sketch atom Sketch ring Sketch fragment Measure Create centroid Clean Adjust hydrogen Modify element Modify bond Modify hybridization
22 Water H 2 O 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 H 2 O 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 H 2 O Now we will clean H 2 O molecule. Click Clean. Molceule is initially optimized and values of lenght and angle got closer to actual values.
25 Biphenyle C 6 H 12 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 C 6 H 12 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 C 6 H 12 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 C 6 H 12 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 - C 20 H 30 O Build your own molecule add atoms, change bonds, optimize structure.
30 Vitamin A - C 20 H 30 O
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 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
53 Multiplying monomers Or you should get similar random structure of atactic homopolymer
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