The Influence of Light on a Three-Arm Azobenzene Star: A Computational Study

Autor:	Koch, Markus
Jazyk:	angličtina
Rok vydání:	2021
Předmět:	Azobenzene Photoisomerization Computersimulation Molecular Dynamics Light-Responsive Materials Azobenzol Photoisomerisation Computersimulation Molekulardynamik Lichtresponsive Materialien info:eu-repo/classification/ddc/540 ddc:540
Druh dokumentu:	Text<br />Doctoral Thesis
Popis:	Light is one of the most advantageous stimuli to manipulate functional materials because it can be applied contactless and with high precision. A common strategy to prepare light-responsive physical systems is the embedding of photoswitchable groups such as the dye molecule azobenzene (azo). Upon irradiation with UV light, azobenzene undergoes photoisomerization from the trans to the cis isomer, whereas blue light triggers the inverse conversion. The two isomers differ with respect to their shape, solubility, and light absorption. Up to now, comparatively little research has been focusing on compounds that unite several photoswitchable groups. Such so-called multiphotochromes are promising multi-state molecular systems that can be controlled by light. In this thesis, the object of study is a star-shaped multiphotochromic molecule denoted TrisAzo. It is composed of three azo groups, which are centrally linked by a light-inert BTA group. The molecule has four photoisomers, ranging from the all-trans to the all-cis isomer. Furthermore, TrisAzo is the elementary building block of light-responsive supramolecular aggregates in solution. Previous experimental works report severe morphological changes of the aggregates under UV–Vis light but the underlying molecular mechanisms are still debated. The objective of this thesis is to elucidate the effects of light on TrisAzo – first, concerning its molecular properties and second, regarding the structure and stability of its supramolecular aggregates. In the presented work, the photoisomers of an azobenzene star with a BTA core are studied for the first time via computational methods, particularly using density functional theory and fully atomistic molecular dynamics (MD) simulations. The solvational and optical properties of TrisAzo are quantified as a function of its isomerization state. The solubility of TrisAzo in polar solvents improves with an increasing fraction of the cis-azo arms due to a redistribution of electron density. The absorption spectra of the TrisAzo isomers are nearly linear superpositions of the individual azo arm spectra but with slight deviations. These deviations indicate weak electronic coupling effects between the connected azo groups. Supramolecular aggregates of TrisAzo molecules in water are modeled using fully atomistic MD simulations for extensive investigations on the molecular scale. In equilibrium conditions, it is verified that randomly distributed TrisAzo molecules self-assemble into column-shaped stacks. Simulations of pre-assembled TrisAzo stacks provide detailed insights into their intermolecular interactions. The binding energies are dominated by π-π interactions between conjugated parts of the stacked molecules, especially the azo groups, while hydrogen bonds between the BTA cores play a subordinate but stabilizing role. To implement the effects of light into the simulations, a stochastic model of the repeated photoisomerization of azobenzene is developed. This model reproduces the photoisomerization kinetics of TrisAzo in good agreement with theory and previous experimental results. Based on this approach, light of various intensities and wavelengths is applied on an equilibrated TrisAzo stack. In contrast to prior assumptions, the simulations indicate that a stacked TrisAzo aggregate irradiated by light does not break or disassemble into separate fragments. The stack instead develops defects in the form of molecular shifts and reorientations. As a result, the aggregate eventually loses its columnar shape. The mechanism and driving forces behind these structural changes are clarified based on the simulation results. Thus, this work provides a new interpretation of the experimentally observed morphological changes. The obtained insights on the molecular scale may facilitate the design of light-responsive gels and supramolecular polymers.:Abstract v Kurzfassung vii 1 Introduction 1 2 Properties of Azobenzene and Azobenzene-Containing Materials 5 2.1 Azobenzene 5 2.1.1 Isomers and Photoisomerization 6 2.1.2 The Photostationary State 10 2.2 Multiphotochromic Molecules Based on Azobenzene 10 2.2.1 Azobenzene Stars 11 2.2.2 The Benzene-1,3,5-Tricarboxamide Linker Unit 11 3 Computational Methods and Models 15 3.1 Density Functional Theory 15 3.1.1 Functional and Basis Set 16 3.1.2 Implicit Solvation Models 17 3.1.3 Time-Dependent Density Functional Theory 17 3.2 Molecular Dynamics Simulations 18 3.2.1 All-Atom MD Simulations 18 3.2.2 Force Fields 19 4 Simulation Techniques 23 4.1 Thermodynamic Integration 23 4.1.1 Implementation in Atomistic Simulations 24 4.2 Modeling Photoisomerization in MD Simulations 27 4.2.1 Implementation of the Rotation Pathway 28 4.3 Modeling Light-Irradiated Azo-Materials in MD Simulations 30 4.3.1 The Cyclic Photoisomerization Model 31 5 Photoisomers of an Azobenzene Star 35 5.1 Object of Study: The Molecule TrisAzo 35 5.1.1 Isomers and Conformers 35 5.2 Ground State Properties in the Gas Phase and in Solvents 36 5.2.1 Energies and Standard Enthalpies of Formation 37 5.2.2 Geometry and Shape Properties 38 5.2.3 Dipole Moments 42 5.2.4 Molecular Properties Upon Hydration in Explicit Water 44 5.3 Solubility 47 5.3.1 Influence of Solvent Polarity 48 5.3.2 Influence of Isomerization State 48 5.3.3 Hydration Free Energy 49 5.4 Absorption Spectra and Intramolecular Coupling 51 5.4.1 Influence of the Number of Azo Groups and Their Isomerization State 52 5.4.2 Effect of the Solvent Polarity 54 5.5 Summary 56 6 Equilibrium Properties of TrisAzo Clusters 59 6.1 Supramolecules of Azobenzene Stars in the Experiment 60 6.1.1 Light-Induced Morphological Transition 60 6.2 Self-Assembly Starting from a Random Distribution 62 6.2.1 Radial Distribution Function 63 6.2.2 Cluster Analysis 65 6.3 Intermolecular Energy of a TrisAzo Dimer 69 6.3.1 Total Intermolecular Energy 70 6.3.2 Energy Decomposition 71 6.4 Structural Properties of Columnar TrisAzo Clusters 75 6.4.1 Considered Cluster Arrangements (Cluster Types) 75 6.4.2 Inner Structure of the Clusters 79 6.4.3 Effect of Cluster Size 79 6.5 Intermolecular Energy of Columnar TrisAzo Clusters 82 6.5.1 Total Intermolecular Energy 82 6.5.2 Energy Decomposition 83 6.5.3 The Role of Hydrogen Bonding 88 6.5.4 Rationalizing the Structural Differences of the Considered Cluster Types 91 6.6 Summary 93 7 Columnar TrisAzo Clusters Under UV–Vis Light 97 7.1 TrisAzo Stacks in the Full Photoisomerization Model 97 7.1.1 Cluster Structure Before and After Irradiation 98 7.1.2 Intermolecular Energy 101 7.2 TrisAzo Stacks in the Cyclic Photosomerization Model 104 7.2.1 Photoisomerization Kinetics 104 7.2.2 Cluster Structure Under Irradiation 108 7.2.3 Intermolecular Energy of TrisAzo Stacks Under Irradiation 112 7.2.4 Mechanism of Defect Formation 116 7.2.5 Comparison with Simulations of Comparable Systems 118 7.3 Summary 118 8 Summary and Outlook 121 8.1 Summary 121 8.2 Outlook 123 A Functional Form of the Force Fields 125 A.1 DREIDING Force Field 125 A.2 Polymer Consistent Force Field (PCFF) 129 B Additional Details about Thermodynamic Integration 133 B.1 Derivation of the Formalism 133 B.2 Avoiding Singularities and Instabilities 134 C Details of the Computational Models 137 C.1 DFT and TD-DFT Calculations 137 C.1.1 DFT Calculations 137 C.1.2 TD-DFT Calculations 138 C.2 MD Simulations of TrisAzo Molecules in PCFF 138 C.2.1 Parametrization 139 C.2.2 Preparation of Initial Configurations 139 C.2.3 Simulation Settings 140 C.3 MD Simulations of TrisAzo Molecules in DREIDING 140 C.3.1 Parametrization 141 C.3.2 Preparation of Initial Configurations 141 C.3.3 Simulation Settings 141 C.4 Intermolecular Energy Calculations of TrisAzo Dimers in PCFF and DREIDING 142 C.5 Visualization of Molecular Structures 142 D Equilibrium Properties of TrisAzo Clusters: Additional Material 143 D.1 From Experiments to Simulations 143 D.2 Cluster Analysis for TrisAzo Self-Assembly: Additional Material 144 D.3 Intermolecular Energy of a TrisAzo Dimer: PCFF Results 145 D.3.1 Total Intermolecular Energy 145 D.3.2 Energy Decomposition 145 D.3.3 Estimated Total Intermolecular Energy of TrisAzo-H 148 D.4 Structural Properties of Columnar TrisAzo Clusters: Additional Material 149 D.5 Intermolecular Energy of Columnar TrisAzo Clusters: Additional Material 150 D.5.1 Defect Detection Algorithm 151 D.6 The Role of Hydrogen Bonds: Additional Material 152 E Columnar TrisAzo Clusters Under UV–Vis Light: Additional Material 155 E.1 TrisAzo Stacks in the Full Photoisomerization Model: Additional Material 155 E.2 TrisAzo Stacks in the Cyclic Photosomerization Model: Additional Material 156 F Code Availability 161 Bibliography 163 List of Publications 183 Copyright of Published Articles 187 Acknowledgements / Danksagung 189 List of Abbreviations 191 List of Symbols 193 List of Physical Constants and Unit Conversions 195 Eidesstattliche Erklärung 197 Licht ist einer der vorteilhaftesten Stimuli für die Manipulation responsiver Funktionsmaterialien, da es berührungslos und mit hoher Präzision angewendet werden kann. Ein weit verbreiteter Ansatz zur Herstellung lichtresponsiver physikalische Systeme ist der Einbau lichtschaltbarer Gruppen wie das Farbstoffmolekül Azobenzol (Azo). Unter UV-Licht vollzieht Azobenzol eine Photoisomerisation vom trans- zum cis-Isomer, während blaues Licht die umgekehrte Umwandlung auslöst. Die beiden Isomere unterscheiden sich vor allem durch ihre räumliche Gestalt, Löslichkeit und Lichtabsorption. Noch unzureichend erforscht sind Moleküle, die mehrere lichtschaltbare Gruppen in sich vereinen. Solche sogenannten Multiphotochrome sind vielversprechende molekulare Mehrzustandssysteme, die durch Licht geschaltet werden können. Untersuchungsobjekt dieser Arbeit ist ein sternförmiges multiphotochromes Molekül namens TrisAzo. Es besteht aus drei Azogruppen, die zentral über eine gegenüber Licht inerte BTA-Gruppe verknüpft sind. Dementsprechend existieren vier Photoisomere dieses Moleküls, vom all-trans- bis zum all-cis-Isomer. Des Weiteren ist TrisAzo der elementare Baustein lichtempfindlicher supramolekularer Aggregate in Lösung. Frühere experimentelle Arbeiten berichten starke morphologische Strukturänderungen der Aggregate unter Lichteinfluss, jedoch sind die zugrundeliegenden molekularen Mechanismen bisher ungeklärt. Ziel dieser Arbeit ist es, die Auswirkungen von Licht auf TrisAzo aufzuklären, erstens in Bezug auf dessen molekulare Eigenschaften und zweitens hinsichtlich der Struktur und Stabilität der supramolekularen Aggregate. In der vorgestellten Arbeit werden erstmals die Photoisomere eines Azosterns mit BTA-Kern auf Basis computerbasierter Methoden untersucht. Eingesetzt werden dabei Dichtefunktionaltheorie und atomistische Molekulardynamiksimulationen (MD). Insbesondere wird die Löslichkeit und das Lichtabsorptionsverhalten von TrisAzo in Abhängigkeit seines Isomerisationszustands analysiert. Die Löslichkeit von TrisAzo verbessert sich mit steigendem Anteil der cis-Azogruppen aufgrund einer damit einhergehenden Umverteilung der Elektronendichte. Die Absorptionsspektren der TrisAzo-Isomere sind in erster Näherung lineare Superpositionen der Einzelspektren jedes Molekülarms, jedoch mit geringen Abweichungen. Diese Abweichungen deuten auf schwache elektronische Kopplungseffekte zwischen den Azogruppen hin. Supramolekularen Aggregate von TrisAzo-Molekülen in Wasser werden für umfangreiche Untersuchungen auf molekularer Ebene in atomistischen MD-Simulationen modelliert. Im thermodynamischen Gleichgewicht bestätigt sich, dass sich zufällig verteilte TrisAzo-Moleküle in säulenförmig gestapelten Aggregaten zusammenfinden. Weitere Simulationen vorgestapelter TrisAzo-Aggregate liefern detaillierte Rückschlüsse auf deren intermolekulare Wechselwirkungen. Die Bindungsenergien werden von π-π-Wechselwirkungen zwischen den konjugierten Bereichen der aufeinanderliegenden Moleküle dominiert. Wasserstoffbrücken zwischen den BTA-Gruppen haben eine untergeordnete, aber stabilisierende Rolle. Um den Effekt von Licht in die Simulationen einzubauen, ist ein stochastisches Modell für die wiederholte Photoisomerisation der Azogruppen entwickelt worden. Dieses Modell reproduziert die Photoisomerisationskinetik von TrisAzo in guter Übereinstimmung mit Theorie und vorigen Experimenten. Basierend auf diesem Ansatz wird Licht verschiedener Intensitäten und Wellenlängen auf die gestapelten TrisAzo-Aggregate angewandt. Entgegen früherer Annahmen zerfallen die Aggregate daraufhin nicht in Einzelfragmente. Stattdessen entwickeln sie Defekte in Form von Molekülumordnungen sowie -reorientierungen und verlieren dadurch ihre säulenartige Form. Der Mechanismus und die Ursachen dieser Strukturänderungen werden anhand der Simulationen aufgeklärt. Damit liefert diese Arbeit eine neue Interpretation der experimentell beobachteten morphologischen Veränderungen. Die gewonnenen Erkenntnisse können die Entwicklung lichtresponsiver Gele und supramolekularer Polymere unterstützen.:Abstract v Kurzfassung vii 1 Introduction 1 2 Properties of Azobenzene and Azobenzene-Containing Materials 5 2.1 Azobenzene 5 2.1.1 Isomers and Photoisomerization 6 2.1.2 The Photostationary State 10 2.2 Multiphotochromic Molecules Based on Azobenzene 10 2.2.1 Azobenzene Stars 11 2.2.2 The Benzene-1,3,5-Tricarboxamide Linker Unit 11 3 Computational Methods and Models 15 3.1 Density Functional Theory 15 3.1.1 Functional and Basis Set 16 3.1.2 Implicit Solvation Models 17 3.1.3 Time-Dependent Density Functional Theory 17 3.2 Molecular Dynamics Simulations 18 3.2.1 All-Atom MD Simulations 18 3.2.2 Force Fields 19 4 Simulation Techniques 23 4.1 Thermodynamic Integration 23 4.1.1 Implementation in Atomistic Simulations 24 4.2 Modeling Photoisomerization in MD Simulations 27 4.2.1 Implementation of the Rotation Pathway 28 4.3 Modeling Light-Irradiated Azo-Materials in MD Simulations 30 4.3.1 The Cyclic Photoisomerization Model 31 5 Photoisomers of an Azobenzene Star 35 5.1 Object of Study: The Molecule TrisAzo 35 5.1.1 Isomers and Conformers 35 5.2 Ground State Properties in the Gas Phase and in Solvents 36 5.2.1 Energies and Standard Enthalpies of Formation 37 5.2.2 Geometry and Shape Properties 38 5.2.3 Dipole Moments 42 5.2.4 Molecular Properties Upon Hydration in Explicit Water 44 5.3 Solubility 47 5.3.1 Influence of Solvent Polarity 48 5.3.2 Influence of Isomerization State 48 5.3.3 Hydration Free Energy 49 5.4 Absorption Spectra and Intramolecular Coupling 51 5.4.1 Influence of the Number of Azo Groups and Their Isomerization State 52 5.4.2 Effect of the Solvent Polarity 54 5.5 Summary 56 6 Equilibrium Properties of TrisAzo Clusters 59 6.1 Supramolecules of Azobenzene Stars in the Experiment 60 6.1.1 Light-Induced Morphological Transition 60 6.2 Self-Assembly Starting from a Random Distribution 62 6.2.1 Radial Distribution Function 63 6.2.2 Cluster Analysis 65 6.3 Intermolecular Energy of a TrisAzo Dimer 69 6.3.1 Total Intermolecular Energy 70 6.3.2 Energy Decomposition 71 6.4 Structural Properties of Columnar TrisAzo Clusters 75 6.4.1 Considered Cluster Arrangements (Cluster Types) 75 6.4.2 Inner Structure of the Clusters 79 6.4.3 Effect of Cluster Size 79 6.5 Intermolecular Energy of Columnar TrisAzo Clusters 82 6.5.1 Total Intermolecular Energy 82 6.5.2 Energy Decomposition 83 6.5.3 The Role of Hydrogen Bonding 88 6.5.4 Rationalizing the Structural Differences of the Considered Cluster Types 91 6.6 Summary 93 7 Columnar TrisAzo Clusters Under UV–Vis Light 97 7.1 TrisAzo Stacks in the Full Photoisomerization Model 97 7.1.1 Cluster Structure Before and After Irradiation 98 7.1.2 Intermolecular Energy 101 7.2 TrisAzo Stacks in the Cyclic Photosomerization Model 104 7.2.1 Photoisomerization Kinetics 104 7.2.2 Cluster Structure Under Irradiation 108 7.2.3 Intermolecular Energy of TrisAzo Stacks Under Irradiation 112 7.2.4 Mechanism of Defect Formation 116 7.2.5 Comparison with Simulations of Comparable Systems 118 7.3 Summary 118 8 Summary and Outlook 121 8.1 Summary 121 8.2 Outlook 123 A Functional Form of the Force Fields 125 A.1 DREIDING Force Field 125 A.2 Polymer Consistent Force Field (PCFF) 129 B Additional Details about Thermodynamic Integration 133 B.1 Derivation of the Formalism 133 B.2 Avoiding Singularities and Instabilities 134 C Details of the Computational Models 137 C.1 DFT and TD-DFT Calculations 137 C.1.1 DFT Calculations 137 C.1.2 TD-DFT Calculations 138 C.2 MD Simulations of TrisAzo Molecules in PCFF 138 C.2.1 Parametrization 139 C.2.2 Preparation of Initial Configurations 139 C.2.3 Simulation Settings 140 C.3 MD Simulations of TrisAzo Molecules in DREIDING 140 C.3.1 Parametrization 141 C.3.2 Preparation of Initial Configurations 141 C.3.3 Simulation Settings 141 C.4 Intermolecular Energy Calculations of TrisAzo Dimers in PCFF and DREIDING 142 C.5 Visualization of Molecular Structures 142 D Equilibrium Properties of TrisAzo Clusters: Additional Material 143 D.1 From Experiments to Simulations 143 D.2 Cluster Analysis for TrisAzo Self-Assembly: Additional Material 144 D.3 Intermolecular Energy of a TrisAzo Dimer: PCFF Results 145 D.3.1 Total Intermolecular Energy 145 D.3.2 Energy Decomposition 145 D.3.3 Estimated Total Intermolecular Energy of TrisAzo-H 148 D.4 Structural Properties of Columnar TrisAzo Clusters: Additional Material 149 D.5 Intermolecular Energy of Columnar TrisAzo Clusters: Additional Material 150 D.5.1 Defect Detection Algorithm 151 D.6 The Role of Hydrogen Bonds: Additional Material 152 E Columnar TrisAzo Clusters Under UV–Vis Light: Additional Material 155 E.1 TrisAzo Stacks in the Full Photoisomerization Model: Additional Material 155 E.2 TrisAzo Stacks in the Cyclic Photosomerization Model: Additional Material 156 F Code Availability 161 Bibliography 163 List of Publications 183 Copyright of Published Articles 187 Acknowledgements / Danksagung 189 List of Abbreviations 191 List of Symbols 193 List of Physical Constants and Unit Conversions 195 Eidesstattliche Erklärung 197
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