DGIST Scholar: Numerical study of several self-assembly processes of polyelectrolytes: DNA as scaffold to assemble gold nanoparticles and assembly process in PEDOT:PSS by addition of ionic liquids

Title

Numerical study of several self-assembly processes of polyelectrolytes: DNA as scaffold to assemble gold nanoparticles and assembly process in PEDOT:PSS by addition of ionic liquids

Alternative Title

고분자전해질 자기조립 전산모사: DNA 상 금나노입자 조립 및 이온성액체에 의한 PEDOT:PSS 자기조립 조절

DGIST Authors

Izarra, Ambroise de ; Jang, YunHee ; Lansac, Yves

Advisor

장윤희

Co-Advisor(s)

Yves Lansac

Issued Date

2021

Awarded Date

2021/08

Citation

Ambroise de Izarra. (2021). Numerical study of several self-assembly processes of polyelectrolytes: DNA as scaffold to assemble gold nanoparticles and assembly process in PEDOT:PSS by addition of ionic liquids. doi: 10.22677/thesis.200000497173

Type

Thesis

Subject

Polyelectrolytes, Monte-Carlo simulation, Molecular dynamics

Description

Polyelectrolytes, Monte-Carlo simulation, Molecular dynamics

Abstract

Polyelectrolytes are polymers or macromolecules charged in solution which represents both a biological
and an industrial interest. Their assembly properties are largely controlled by long range electrostatic interac-
tions.
Despite a recent improvement in the understanding of the mechanisms involved, the predic-
tion/characterization of the assembly processes remain problematic. This is due to the fact that the formation
of complexes results from a delicate compromise between various interactions in addition to being sensitive to
many experimental parameters such as the preparation conditions, the nature of the polyelectrolytes, the tem-
perature and solvent effects...
It is the object of this thesis to better understand these assembly phenomena by an approach based on
molecular simulation. In particular, we will focus on two systems of interest for future technological applica-
tions.
A first project will consist in modeling by Monte Carlo simulations the assemblies of functionalized
gold nanoparticles in the presence of one or several DNAs. Then, it was reported that the properties of electri-
cal transport of a complex made up of a semi-conducting polymer, the poly (3,4-ethylene dioxythiophene)
(PEDOT) solubilized in water with its insulating counter-chain polystyrene sulfonate (PSS) have been im-
proved by adding ionic liquid. The objective of this project will consist in understanding the mechanism of
PEDOT:PSS conductivity enhancement by using the tools of molecular dynamics.

Table Of Contents

Abstract i
List of Figures viii
List of Tables xiv
Introduction 1

1 Nature and interactions of polyelectrolytes 5
1.1 Generalities on polyelectrolytes 6
1.1.1 Definition 6
1.1.2 Natural polyelectrolytes 7
1.1.2.1 Polysaccharides 7
1.1.2.2 Polypeptides and proteins 9
1.1.2.3 Polynucleotides 10
1.1.3 Artificial polyelectrolytes 10
1.1.3.1 Diblock copolymers 12
1.1.3.2 Hydrophobic modified polyelectrolytes 13
1.1.4 Conclusion 13
1.2 Some physical properties of polyelectrolytes 13
1.2.1 Polyelectrolytes in solution 14
1.2.1.1 Strength of polyelectrolytes 14
1.2.1.2 Dissociation of a ionomer in solution yields to polyelectrolyte 15
1.2.2 Electrostatic interactions in aqueous solution 18
1.2.2.1 Scale of electrostatic interactions in water 18
1.2.2.2 Modeling electrostatic interactions in solution 18
1.2.3 Physics of hydrophilic polyelectrolytes in solution 21
1.2.3.1 Conformation of a neutral chain in solution 21
1.2.3.2 Conformation of a weakly charged polyelectrolyte in solution 25
1.2.3.3 Model of a highly charged polyelectrolyte: Manning-Oosawa theory 28
1.2.4 Conclusion 32
1.3 Complexes of polyelectrolytes 33
1.3.1 Interactions driving polyelectrolyte complexation 33
1.3.2 Mechanism of complex formation 34
1.3.2.1 Thermodynamics for complex formation 34
1.3.2.2 Dynamic of complex formation 36
1.3.3 Possible structures of Polyelectrolytes 36
1.3.4 Conclusion 39

2 Studied polyelectrolyte systems 41
2.1 Project 1: Polyelectrolyte complexation between DNA and nanoparticles 43
2.1.1 Fundamental aspects of DNA compaction 43
2.1.1.1 The coil-globule transition 43
2.1.1.2 Compaction agents 44
2.1.1.3 Condensation of cationic agents on DNA 46
2.1.1.4 Mechanism of DNA compaction 47
2.1.1.5 DNA overcharging effect 49
2.1.1.6 Structures of compacted DNA : shape and stability 49
2.1.1.7 Factors that modified DNA compaction/decompaction 50
2.1.2 DNA compaction with functionalized gold nanoparticles 51
2.1.2.1 Synthesis of functionalized gold nanoparticles 51
2.1.2.2 Applications of ligand-stabilized gold nanoparticles 53
2.1.2.3 Self-assembly of ligand-stabilized gold nanoparticles on DNA templates 56
2.2 Project 2: Polyelectrolyte complexation between PEDOT:PSS and ionic liquids 61
2.2.1 Review about conducting polymers 61
2.2.1.1 Conjugation and π-bond 61
2.2.1.2 Semi-conducting polymers 62
2.2.1.3 Conduction of semi-conducting polymers 64
2.2.1.4 Conduction mechanism in semi-conducting polymers 66
2.2.2 The PEDOT semi-conducting polymer 67
2.2.2.1 Synthesis of PEDOT:PSS and PEDOT:Tos 67
2.2.2.2 Structure of PEDOT:PSS/PEDOT:Tos thin films 69
2.2.2.3 Applications of PEDOT:PSS 70
2.2.3 PEDOT:PSS conductivity enhancement by ionic liquids 72
2.2.3.1 Definition and general properties of ionic liquids 73
2.2.3.2 Controlling ordering in PEDOT:PSS solution with imidazoliumbased ionic liquid for PEDOT:PSS conductivity enhancement 74
2.3 Objectives of the thesis 80

3 Simulation Methods 83
3.1 Simulations at different scales 84
3.2 Molecular Monte Carlo Simulations 85
3.2.1 Motivations 85
3.2.2 Monte Carlo simulations in various ensemble 87
3.2.2.1 The canonical ensemble 87
3.2.2.2 Isobaric-isothermal ensemble 90
3.2.2.3 Grand Canonical ensemble 92
3.2.3 Implemented Trial Moves 94
3.2.3.1 Translational move 94
3.2.3.2 Rotational move 95
3.2.3.3 Collective move 96
3.2.4 Interactions in the simulation box 97
3.2.4.1 Periodic boundary conditions 98
3.2.4.2 Cell lists for pairwise hard core potential 100
3.2.4.3 Ewald summation method 101
3.2.5 The Widom insertion method 107
3.2.6 The Monte Carlo simulation package 110
3.3 Molecular dynamics simulations 111
3.3.1 General idea 112
3.3.2 Integration of equations of motion 113
3.3.3 Force Fields 115
3.3.3.1 Bonded interactions 115
3.3.3.2 Non-bonded interactions 117
3.3.4 Regulation of Pressure and Temperature 117
3.3.4.1 Thermostat 117
3.3.4.2 Barostat 120
3.3.5 Free energy calculation 122
3.3.6 Molecular dynamics simulation packages 126
3.3.7 How to perform a simulation with GROMACS? 127

4 Self-assembly of DNA mediated by cations or Nanoparticles 131
4.1 Choice of molecular model 133
4.1.1 Molecular model of DNA 133
4.1.2 Molecular model of cationic gold nanoparticles and multivalent counterions 135
4.2 Attraction and compaction of DNA molecules mediated by multivalent cations 139
4.2.1 Adsorption of salt on a DNA molecule in presence of counterions 139
4.2.1.1 Methods 140
4.2.1.2 Results 142
4.2.1.3 Conclusion 144
4.2.2 Effective force between a pair of DNA molecules 145
4.2.2.1 Methods 146
4.2.2.2 Results 148
4.2.2.3 Conclusion 150
4.2.3 Osmotic Pressure calculation in hexagonal DNA bundle 152
4.2.3.1 Notion of osmotic pressure 153
4.2.3.2 Methods 155
4.2.3.3 Influence of counterion charge on DNA lattice stability 156
4.2.3.4 Influence of counterion radius on DNA lattice stability 158
4.2.3.5 Conclusion 158
4.3 Self-Assembly of DNA mediated by nanoparticles 159
4.3.1 Aggregation of nanoparticles on a single fixed DNA 159
4.3.1.1 Methods 160
4.3.1.2 Adsorption of AuNPs on the DNA molecule 164
4.3.1.3 Density of AuNPs and ions in the vicinity of the DNA 166
4.3.1.4 DNA overcharging effect 170
4.3.1.5 Distribution of AuNP on the DNA 170
4.3.1.6 Conclusion 173
4.3.2 Effect of counterions on the adsorption of AuNP on DNA molecule: PMF calculations 174
4.3.2.1 Methods 174
4.3.2.2 Result 175
4.3.2.3 Conclusion 177
4.3.3 Redissolution of AuNPs from a single fixed DNA with excess of salt 178
4.3.3.1 Methods 178
4.3.3.2 Effect of the salt on the adsorption of AuNPs on DNA 179
4.3.3.3 Density of cations in the vicinity of the DNA 181
4.3.3.4 Conclusion 181
4.3.4 Effective force between a pair of DNA 182
4.3.4.1 Methods 182
4.3.4.2 Results 185
4.3.4.3 Conclusion 188
4.3.5 Osmotic pressure calculation in hexagonal and square DNA phases 189
4.3.5.1 Methods 189
4.3.5.2 Results 193
4.3.5.3 Conclusion 195

5 Self-assembly in PEDOT:PSS solution by addition of ionic liquids for conductivity enhancement 199
5.1 Choice of molecular model 200
5.1.1 Atomistic models for PEDOT:PSS 200
5.1.2 Atomistic models for ionic liquids 201
5.2 Morphology of aqueous solution of PEDOT:PSS 202
5.2.1 Methods 203
5.2.2 Morphology of aqueous PEDOT:PSS complexes - small systems case 205
5.2.3 Morphology of aqueous PEDOT:PSS complexes - larger systems case 207
5.2.4 Conclusion 209
5.3 Prediction of ion exchange between PEDOT:PSS/IL 209
5.3.1 Methods 211
5.3.2 Ion exchange free energy: PMF calculations 212
5.3.3 Solvation of IL anions in US simulations 218
5.3.4 Conclusion 221
5.4 Ionic exchange in mixed solutions: varying the IL anion 221
5.4.1 Methods 223
5.4.2 Morphology of mixed solution - small system cases 224
5.4.2.1 Morphology of tri-EDOT:PTS solutions 224
5.4.2.2 Morphology of tri-EDOT:16SS solution 229
5.4.2.3 Morphology of 6EDOT:16SS solution 233
5.4.3 Conclusion 235

Conclusion and future work 237

A Monte Carlo simulation package 243
A.1 Program to generate the coarse-grained system 244
A.1.1 Initialization_system.cpp 244
A.1.2 Initialization_system.h 260
A.1.3 Makefile 261
A.2 Program to generate system topology 262
A.2.1 Builiding_topology.cpp 262
A.2.2 Builiding_topology.h 270
A.2.3 Makefile 272
A.3 Program to perform a Monte Carlo simulation 272
A.3.1 Main.cpp 272
A.3.2 Move_MC.cpp 275
A.3.3 Move_MC.h 292
A.3.4 Potential_energy_calculation.cpp 296
A.3.5 Potential_energy_calculation.h 315
A.3.6 Cell_lists.cpp 322
A.3.7 Cell_lists.h 329
A.3.8 MersenneTwister.h 330
A.3.9 Makefile 333
A.4 Program to visualize a trajectory 333
A.4.1 Main.cpp 333
A.4.2 Visualization_trajectory.cpp 336
A.4.3 Visualization_trajectory.h 340
A.4.4 Read_trajectory.cpp 341
A.4.5 Read_trajectory.h 343
A.4.6 Makefile 344
A.5 Program to analyze a trajectory 345
A.5.1 Main.cpp 345
A.5.2 Analysis_trajectory.cpp 347
A.5.3 Analysis_trajectory.h 360
A.5.4 Makefile 362

B Some tests for the Monte Carlo simulation package 365
B.1 Test of the Ewald summation technique 365
B.1.1 Determination of Madelung constant for NaCl crystal 365
B.1.2 Electrostatic interactions in water 368
B.2 Properties of the Kratky-Porod model 369
B.3 Test of the grand canonical MC scheme 373

C Monte Carlo error analysis 375
C.1 Effective force between a pair of DNA with counterions 377
C.2 Osmotic pressure in a hexagonal bundle of DNA condensed with counterions 380
C.3 Effective force between a pair of DNA with AuNPs 382
C.4 Osmotic pressure in DNA lattices with AuNPs 388

D Force-field parameters for PEDOT:PSS and ionic 395
D.1 Force-field parameters for PEDOT:PSS 395
D.2 Force-field parameters for IL anions 400
D.3 Force-field parameters for IL cation 405

E Morphology of mixed solution of PEDOT:PSS - large system case 409
E.1 Definiton of the complementary domain analysis 409
E.2 Morphology of tri-EDOT:PTS solution 410
E.3 Morphology of tri-EDOT:16SS solution 416
E.4 Morphology of 6EDOT:16SS solution 422
E.5 Morphology of 6EDOT:PTS 428

F Supplemental material for the Umbrella Sampling calculation for tri-EDOT:X and EMIM:X ion pairs and ion exchange energy 433
F.1 Error on the PMF calculations for ion pairs and ion exchange energy 433
F.2 Umbrella sampling histograms 437
F.3 PEDOT:X and EMIM:X complexes snapshots 438
F.4 Comparison between our PMFs/binding constant to data literature 440

URI

http://dgist.dcollection.net/common/orgView/200000497173
http://hdl.handle.net/20.500.11750/16621

DOI

10.22677/thesis.200000497173

Degree

Doctor

Department

Energy Science & Engineering

Publisher

DGIST

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