Herramientas computacionales para la modelización y simulación de polímeros

en Materials Studio 7.0

Javier Ramos Biophysics of Macromolecular Systems group

(BIOPHYM)

Departamento de Física Macromolecular

Instituto de Estructura de la Materia – CSIC

j.ramos@iem.cfmac.csic.es

Webinar, 27 de Noviembre 2014

Anteriores webinars

Como conseguir los videos y las presentaciones de anteriores webminars:

Linkedin: Grupo de Química Computacional

http://www.linkedin.com/groups/Química-computacional-7487634

http://www.addlink.es/eventos-materials-studio

Introducción a Materials Studio en la Investigación Química y de Ciencias de los Materiales.

Mecánica y Dinámica Molecular con Forcite en Materials Studio

Herramientas mecano-cuánticas basadas en DFT para el estudio de moléculas y materiales en Materials Studio 7.0

Materials Studio tools for polymers

Building and characterizing a polymer crystal

Building a repeat unit (monomer)

Building a polymer chain

Forcite & Compass Force Field (Atomistic simulations)

Amorphous builder

Example: Solubility parameter of PPDO and PVph from atomistic

simulations

Blends Module

Example: Binary mixtures of PVDF and POSS

DPD Simulations of polymer systems

Example: Phase behavior of a loaded amphiphilic copolymer

Synthia module

Example: Properties of an acrylamide random copolymer

Índice

Materials Studio Tools for Polymers

Synthia

Blends

Mesocite

Mesodyn

DPD

Mesoscale and

coarse-grained tools

Equilibria

Amorphous Builder

Conformers

Forcite & Discover Atomistic tools

Compass Force Field

Statistical tools (QSPR). Bicerano

Crystal Builder

Materials Studio Tools for Polymers

Synthia

Blends

Mesocite

Mesodyn

DPD

Mesoscale and

coarse-grained tools

Equilibria

Amorphous Builder

Conformers

Forcite & Discover Atomistic tools

Compass Force Field

Statistical tools (QSPR). Bicerano

Crystal Builder

Building and characterizing a polymer crystal

Poly(1-butene)

Dorset DL et al. “Direct determination of polymer crystal structures by electron crystallography – Isotactic Poly(1-butene),

Form(III)”, Acta Cryst. 1994, B50, 201-208

Kaszonyiova M. et al, “Polymorphism of isotactic poly(butene-1)”, J. Macrom. Sci. Part B: Physics 2005, 44:377-396

File import: cr0447.cif

Building and characterizing a polymer crystal

Poly(1-butene)

Dorset DL et al. “Direct determination of polymer crystal structures by electron crystallography – Isotactic Poly(1-butene),

Form(III)”, Acta Cryst. 1994, B50, 201-208

Kaszonyiova M. et al, “Polymorphism of isotactic poly(butene-1)”, J. Macrom. Sci. Part B: Physics 2005, 44:377-396

Building and characterizing a polymer crystal

Poly(1-butene)

Dorset DL et al. “Direct determination of polymer crystal structures by electron crystallography – Isotactic Poly(1-butene),

Form(III)”, Acta Cryst. 1994, B50, 201-208

Kaszonyiova M. et al, “Polymorphism of isotactic poly(butene-1)”, J. Macrom. Sci. Part B: Physics 2005, 44:377-396

Building and characterizing a polymer crystal

Poly(1-butene)

Dorset DL et al. “Direct determination of polymer crystal structures by electron crystallography – Isotactic Poly(1-butene),

Form(III)”, Acta Cryst. 1994, B50, 201-208

Kaszonyiova M. et al, “Polymorphism of isotactic poly(butene-1)”, J. Macrom. Sci. Part B: Physics 2005, 44:377-396

Reflex: Powder diffraction

Building and characterizing a polymer crystal

Reflex is the module that allows you to simulate and analyze X-ray, electron and neutron diffraction data.

Pattern processing: Data processing on experimental power diffraction data.

Powder diffraction: Powder diffraction simulation of a polymer crystal.

Powder Indexing: Search all possible space groups given an experimental powder diffraction pattern and a unit cell.

Powder Refinement: Both Pawley and Rietveld refinement of a crystal structure against experimental data.

Powder QPA: Determination of relative amounts of different phases in a mixture.

Powder Cristallinity: Determination of the degree of crystallinity of a sample from X-ray powder diffraction pattern.

Powder Solve: Simulated annealing to determine the positions, orientations and conformations of molecules within a crystal lattice which minimize the difference between simulated and experimental X-ray or neutron powder diffraction patterns.

Building Repeat Unit

Materials Studio includes an extensive library of common monomer units, but it can also be used with custom repeat units

Building Repeat Unit

Materials Studio includes an extensive library of common monomer units, but it can also be used with custom repeat units

Building Repeat Unit

Materials Studio includes an extensive library of common monomer units, but it can also be used with custom repeat units

Building a repeat unit

3,3’,4,4’-BPDA-ODA

3,3’,4,4’-BisPhenyleneDiamine-Oxydianiline

Building Repeat Unit

Materials Studio includes an extensive library of common monomer units, but it can also be used with custom repeat units

Building a repeat unit

3,3’,4,4’-BPDA-ODA

3,3’,4,4’-BisPhenyleneDiamine-Oxydianiline

Building a polymer chain

Building a polymer chain

Monomer 1

Monomer 2

Monomer 3

Forcite & Compass Force Field (Atomistic simulations)

Rigby, et al. “Computer Simulations of Poly(ethylene oxide): Forcefield, PVT Diagram and Cyclization Behavior,” Polymer International, 1997, 44, 311-330.

Sun, H.,“COMPASS: An Ab Initio Forcefield Optimized for Condensed-Phase Application-Overview with Details on Alkane and Benzene Compounds,” J. Phys. Chem., 1998,

B102, 7338-7364.

Sun, H., Ren, P., and Fried, J. R.,“The COMPASS Forcefield: Parameterization and Validation for Phosphazenes,” Comput. Theor. Polymer Sci., 1998, 8, 229-246.

Forcite & Compass Force Field (Atomistic simulations)

Rigby, et al. “Computer Simulations of Poly(ethylene oxide): Forcefield, PVT Diagram and Cyclization Behavior,” Polymer International, 1997, 44, 311-330.

Sun, H.,“COMPASS: An Ab Initio Forcefield Optimized for Condensed-Phase Application-Overview with Details on Alkane and Benzene Compounds,” J. Phys. Chem., 1998,

B102, 7338-7364.

Sun, H., Ren, P., and Fried, J. R.,“The COMPASS Forcefield: Parameterization and Validation for Phosphazenes,” Comput. Theor. Polymer Sci., 1998, 8, 229-246.

Forcite & Compass Force Field (Atomistic simulations)

Rigby, et al. “Computer Simulations of Poly(ethylene oxide): Forcefield, PVT Diagram and Cyclization Behavior,” Polymer International, 1997, 44, 311-330.

Sun, H.,“COMPASS: An Ab Initio Forcefield Optimized for Condensed-Phase Application-Overview with Details on Alkane and Benzene Compounds,” J. Phys. Chem., 1998,

B102, 7338-7364.

Sun, H., Ren, P., and Fried, J. R.,“The COMPASS Forcefield: Parameterization and Validation for Phosphazenes,” Comput. Theor. Polymer Sci., 1998, 8, 229-246.

COMPASS: Condensed-phase Optimized Molecular Potentials for Atomistic Simulation Studies

Alkanes, alkanes, alkynes,

aromatics, cycloalkanes,

Ethers, acetals, alcohols, phenols,

amines, ammonia, aldehyde,

ketones, acids, esters, carbonates,

amides, carbamate,

siloxanes, silanes, halides,

phosphazenes , nitro groups,

nitriles, isocyanides,

sulfides, thiols, amineoxides, cyanamides,

nitrates, sulfates, solfonates, metals, …

Amorphous builder

This module allows one to build in a Monte Carlo fashion a 3D-periodic structure of molecular liquids and amorphous polymeric systems.

Theodorou D.N and Sutter UW “Detailed molecular structure of a vinyl polymer glass”, Macromolecules, 1985 18 (7), 1467-1478

Ramos J, Peristeras LD, Theodorou D.N . “Monte Carlo simulation of short chain branched polyolefins in the molten state” Macromolecules, 2007, 40 (26), 9640-9650

Amorphous builder

This module allows one to build in a Monte Carlo fashion a 3D-periodic structure of molecular liquids and amorphous polymeric systems.

Torsions are determined by the selected force field (continuous rather than discrete RIS). If not torsion angles are available the molecule will be treated as a rigid body

Boltzmann distribution of the torsional potential

Theodorou D.N and Sutter UW “Detailed molecular structure of a vinyl polymer glass”, Macromolecules, 1985 18 (7), 1467-1478

Ramos J, Peristeras LD, Theodorou D.N . “Monte Carlo simulation of short chain branched polyolefins in the molten state” Macromolecules, 2007, 40 (26), 9640-9650

Amorphous builder

This module allows one to build in a Monte Carlo fashion a 3D-periodic structure of molecular liquids and amorphous polymeric systems.

Torsions are determined by the selected force field (continuous rather than discrete RIS). If not torsion angles are available the molecule will be treated as a rigid body

Boltzmann distribution of the torsional potential

Structure by growing polymers into a box in a stepwise manner using “look ahead”.

Growth chain

New Segment

Growth chain

New Segment

Theodorou D.N and Sutter UW “Detailed molecular structure of a vinyl polymer glass”, Macromolecules, 1985 18 (7), 1467-1478

Ramos J, Peristeras LD, Theodorou D.N . “Monte Carlo simulation of short chain branched polyolefins in the molten state” Macromolecules, 2007, 40 (26), 9640-9650

Amorphous builder

This module allows one to build in a Monte Carlo fashion a 3D-periodic structure of molecular liquids and amorphous polymeric systems.

Torsions are determined by the selected force field (continuous rather than discrete RIS). If not torsion angles are available the molecule will be treated as a rigid body

Boltzmann distribution of the torsional potential

Structure by growing polymers into a box in a stepwise manner using “look ahead”.

Growth chain

New Segment

Growth chain

New Segment

Close contacts are reject (overlap criterion). If the molecules contain rings -> Check for ring smearing

Theodorou D.N and Sutter UW “Detailed molecular structure of a vinyl polymer glass”, Macromolecules, 1985 18 (7), 1467-1478

Ramos J, Peristeras LD, Theodorou D.N . “Monte Carlo simulation of short chain branched polyolefins in the molten state” Macromolecules, 2007, 40 (26), 9640-9650

Amorphous builder

poly(p-dioxanone)

(PPDO)

poly(etherester)

Tail

Head

Build a polymer with 10 repeat units.

Amorphous builder

poly(p-dioxanone)

(PPDO)

poly(etherester)

Tail

Head

Build a polymer with 10 repeat units.

Amorphous builder

poly(p-dioxanone)

(PPDO)

poly(etherester)

Tail

Head

Build a polymer with 10 repeat units.

Amorphous builder => Equilibration

Amorphous builder => Equilibration

Amorphous builder => Equilibration

Before Minimization 442.4 kcal/mol

After Minimization 332.5 kcal/mol

1. Equilibration protocol

a) Geometry Optimization

b) NVT-MD, 750K, 30 ps

c) NVT-MD, 600K, 20 ps

d) NVT-MD, 450K, 20 ps

e) NVT-MD, 303 K, 100 ps

f) NPT-MD, 303K ,100 ps

2. Production protocol

a) NPT-MD, 303K, 1000 ps or

b) NVT-MD, 303K, 1000 ps.

Amorphous builder => Equilibration (Example)

Example: Solubility parameter of PPDO and PVph from atomistic simulations

NVT 200ps, 298K

COMPASS

PPDO PVph

Martínez de Arenaza I et al . “Competing Specific Interactions Investigated by Molecular Dynamics: Analysis of

Poly(p‐dioxanone)/Poly(vinylphenol) Blends”, J. Phys. Chem. B 2013, 117, 719−724

Example: Solubility parameter of PPDO and PVph from atomistic simulations

NVT 200ps, 298K

COMPASS

PPDO PVph

Martínez de Arenaza I et al . “Competing Specific Interactions Investigated by Molecular Dynamics: Analysis of

Poly(p‐dioxanone)/Poly(vinylphenol) Blends”, J. Phys. Chem. B 2013, 117, 719−724

Example: Solubility parameter of PPDO and PVph from atomistic simulations

NVT 200ps, 298K

COMPASS

PPDO PVph

δexp = 27.4 (J/cm3)0.5 (ε = 9%) δexp = 24.5 (J/cm3)0.5 (ε = 12%)

Martínez de Arenaza I et al . “Competing Specific Interactions Investigated by Molecular Dynamics: Analysis of

Poly(p‐dioxanone)/Poly(vinylphenol) Blends”, J. Phys. Chem. B 2013, 117, 719−724

Example: Solubility parameter of PPDO and PVph from atomistic simulations

NVT 200ps, 298K

COMPASS

PPDO PVph

δexp = 27.4 (J/cm3)0.5 (ε = 9%) δexp = 24.5 (J/cm3)0.5 (ε = 12%)

Martínez de Arenaza I et al . “Competing Specific Interactions Investigated by Molecular Dynamics: Analysis of

Poly(p‐dioxanone)/Poly(vinylphenol) Blends”, J. Phys. Chem. B 2013, 117, 719−724

Blends Module

Miscibility of polymers => Extended Flory-Huggins model

Molecular segments are no longer required to be on a regular lattice (off-lattice) Explicit temperature dependence of χ(T) is taken into account.

Fan, C. F.; Olafson, B. D.; Blanco, M.; Hsu, S. L.”Application of Molecular Simulation To Derive

Phase Diagrams of Binary Mixtures.” Macromolecules, 25, 3667 (1992).

Blends Module

Miscibility of polymers => Extended Flory-Huggins model

Molecular segments are no longer required to be on a regular lattice (off-lattice) Explicit temperature dependence of χ(T) is taken into account.

Fan, C. F.; Olafson, B. D.; Blanco, M.; Hsu, S. L.”Application of Molecular Simulation To Derive

Phase Diagrams of Binary Mixtures.” Macromolecules, 25, 3667 (1992).

Blends Module

Miscibility of polymers => Extended Flory-Huggins model

Molecular segments are no longer required to be on a regular lattice (off-lattice) Explicit temperature dependence of χ(T) is taken into account.

Fan, C. F.; Olafson, B. D.; Blanco, M.; Hsu, S. L.”Application of Molecular Simulation To Derive

Phase Diagrams of Binary Mixtures.” Macromolecules, 25, 3667 (1992).

Blends Module

Miscibility of polymers => Extended Flory-Huggins model

Molecular segments are no longer required to be on a regular lattice (off-lattice) Explicit temperature dependence of χ(T) is taken into account.

Fan, C. F.; Olafson, B. D.; Blanco, M.; Hsu, S. L.”Application of Molecular Simulation To Derive

Phase Diagrams of Binary Mixtures.” Macromolecules, 25, 3667 (1992).

Blends Module

Miscibility of polymers => Extended Flory-Huggins model

Molecular segments are no longer required to be on a regular lattice (off-lattice) Explicit temperature dependence of χ(T) is taken into account.

Advantages : Quick evaluation of the miscibility of two components Disadvantages: Isolated molecular segment interactions = Bulk polymer interaction ?????

Fan, C. F.; Olafson, B. D.; Blanco, M.; Hsu, S. L.”Application of Molecular Simulation To Derive

Phase Diagrams of Binary Mixtures.” Macromolecules, 25, 3667 (1992).

Blends Module

Setting up Blends Module calculations in Materials Studio

Blends Module

Setting up Blends Module calculations in Materials Studio

Blends Module

Setting up Blends Module calculations in Materials Studio

Example: Binary mixtures of PVDF and POSS

Zeng et al. «Molecular simulations of the miscibility in binary mixtures of PVDF and POSS compounds», Modelling Simul. Mater. Sci. Eng., 2009, 17, 075002

Zeng et al. «Nanoindentation, Nanoscratch, and Nanotensile Testing of PVDF-POSS Nanocomposites», J. POL. SCI.: PART B: POL. PHYS. 2012, 50, 1597–161

Example: Binary mixtures of PVDF and POSS

poly(vinylidene difluoride) (PVDF)

Zeng et al. «Molecular simulations of the miscibility in binary mixtures of PVDF and POSS compounds», Modelling Simul. Mater. Sci. Eng., 2009, 17, 075002

Zeng et al. «Nanoindentation, Nanoscratch, and Nanotensile Testing of PVDF-POSS Nanocomposites», J. POL. SCI.: PART B: POL. PHYS. 2012, 50, 1597–161

(trifluoropropyl)8Si8O12

(FP-POSS)

Example: Binary mixtures of PVDF and POSS

poly(vinylidene difluoride) (PVDF)

(ethyl)8Si8O12

(E-POSS)

Zeng et al. «Molecular simulations of the miscibility in binary mixtures of PVDF and POSS compounds», Modelling Simul. Mater. Sci. Eng., 2009, 17, 075002

Zeng et al. «Nanoindentation, Nanoscratch, and Nanotensile Testing of PVDF-POSS Nanocomposites», J. POL. SCI.: PART B: POL. PHYS. 2012, 50, 1597–161

(trifluoropropyl)8Si8O12

(FP-POSS)

Example: Binary mixtures of PVDF and POSS

poly(vinylidene difluoride) (PVDF)

(ethyl)8Si8O12

(E-POSS)

Zeng et al. «Molecular simulations of the miscibility in binary mixtures of PVDF and POSS compounds», Modelling Simul. Mater. Sci. Eng., 2009, 17, 075002

Zeng et al. «Nanoindentation, Nanoscratch, and Nanotensile Testing of PVDF-POSS Nanocomposites», J. POL. SCI.: PART B: POL. PHYS. 2012, 50, 1597–161

(trifluoropropyl)8Si8O12

(FP-POSS)

Example: Binary mixtures of PVDF and POSS

poly(vinylidene difluoride) (PVDF)

(ethyl)8Si8O12

(E-POSS)

Zeng et al. «Molecular simulations of the miscibility in binary mixtures of PVDF and POSS compounds», Modelling Simul. Mater. Sci. Eng., 2009, 17, 075002

Zeng et al. «Nanoindentation, Nanoscratch, and Nanotensile Testing of PVDF-POSS Nanocomposites», J. POL. SCI.: PART B: POL. PHYS. 2012, 50, 1597–161

(trifluoropropyl)8Si8O12

(FP-POSS)

Example: Binary mixtures of PVDF and POSS

poly(vinylidene difluoride) (PVDF)

(ethyl)8Si8O12

(E-POSS)

Zeng et al. «Molecular simulations of the miscibility in binary mixtures of PVDF and POSS compounds», Modelling Simul. Mater. Sci. Eng., 2009, 17, 075002

Zeng et al. «Nanoindentation, Nanoscratch, and Nanotensile Testing of PVDF-POSS Nanocomposites», J. POL. SCI.: PART B: POL. PHYS. 2012, 50, 1597–161

(trifluoropropyl)8Si8O12

(FP-POSS)

Example: Binary mixtures of PVDF and POSS

poly(vinylidene difluoride) (PVDF)

(ethyl)8Si8O12

(E-POSS)

Zeng et al. «Molecular simulations of the miscibility in binary mixtures of PVDF and POSS compounds», Modelling Simul. Mater. Sci. Eng., 2009, 17, 075002

Zeng et al. «Nanoindentation, Nanoscratch, and Nanotensile Testing of PVDF-POSS Nanocomposites», J. POL. SCI.: PART B: POL. PHYS. 2012, 50, 1597–161

Dissipative Particle Dynamics (DPD) Simulations of polymer systems

Dissipative Particle Dynamics (DPD) Simulations of polymer systems

A bead (CG particle) is defined as a set of atoms

Dissipative Particle Dynamics (DPD) Simulations of polymer systems

Three forces are considered

Conservative force (soft repulsion)

Dissipative force Random force

A bead (CG particle) is defined as a set of atoms

Dissipative Particle Dynamics (DPD) Simulations of polymer systems

Three forces are considered

Conservative force (soft repulsion)

Dissipative force Random force

Groot and Warren made a link between the repulsive parameter and the Flory–Huggins parameters.

A bead (CG particle) is defined as a set of atoms

Dissipative Particle Dynamics (DPD) Simulations of polymer systems

Three forces are considered

Conservative force (soft repulsion)

Dissipative force Random force

Groot and Warren made a link between the repulsive parameter and the Flory–Huggins parameters.

A bead (CG particle) is defined as a set of atoms

A harmonic spring keeps the chain connectivity

DPD Simulations of polymer systems

Hydrophobic Hydrophilic

DPD Simulations of polymer systems

Setting up DPD Module calculations in Materials

Studio

DPD Simulations of polymer systems

Setting up DPD Module calculations in Materials

Studio

DPD Simulations of polymer systems

Setting up DPD Module calculations in Materials

Studio

DPD Simulations of polymer systems

Setting up DPD Module calculations in Materials

Studio

DPD Simulations of polymer systems

Setting up DPD Module calculations in Materials

Studio

Example: Phase behavior of a loaded amphiphilic copolymer

Water : 90.2%

DMF : 4.7%

Paclitaxel : 1.9%

EO11- LLA9 : 3.2%

Water : 52.2%

DMF : 2.8%

Paclitaxel : 17.6%

EO11- LLA9 : 27.4%

Synthia

• By using empirical correlation methods, large numbers of polymers, or copolymers of varying composition, can be rapidly screened for desired properties.

• QSPR methods are fast, provide large numbers of properties, and are the easiest modeling tool to use

• Synthia is based on work conducted by Dr. Bicerano of The Dow Chemical Company, where the methodology has been extensively tested in practical work

Synthia

• By using empirical correlation methods, large numbers of polymers, or copolymers of varying composition, can be rapidly screened for desired properties.

• QSPR methods are fast, provide large numbers of properties, and are the easiest modeling tool to use

• Synthia is based on work conducted by Dr. Bicerano of The Dow Chemical Company, where the methodology has been extensively tested in practical work

Synthia

Synthia

Synthia

Example: Properties of an acrylamide random copolymer

Random copolymer

Example: Properties of an acrylamide random copolymer

N-benzyl

N-methyl

N-benzyl

N-methyl

Random copolymer