Cover Page The handle

Cover Page

The handle http://hdl.handle.net/1887/66669 holds various files of this Leiden University

dissertation.

Author: Ruiter, J.M. de

Title: Explorations of water oxidation catalysis in explicit solvent

Issue Date: 2018-10-30

Explorations of

Water Oxidation Catalysis

in Explicit Solvent

Jessica M. de Ruiter

Explorations of Water Oxidation Catalysis

in Explicit Solvent

PROEFSCHRIFT

ter verkrijging van

de Graad van Doctor aan de Universiteit Leiden, op gezag van Rector Magnificus prof. mr. C. J. J. M. Stolker,

volgens besluit van het College voor Promoties te verdedigen op dinsdag 30 oktober 2018

klokke 13.45 uur

door

Jessica M. de Ruiter

geboren te Nelson, Nieuw-Zeeland in 1989

Promotiecommissie

Promoter: Prof. dr. Huub J. M. de Groot Co-promoter: Dr. Francesco Buda

Overige leden: Prof. dr. Marc. T. M. Koper Prof. dr. Hermen S. Overkleeft Prof. dr. Shirin Faraji

(University of Groningen, The Netherlands) Prof. dr. Leif Hammarström

(Uppsala University, Sweden)

Jessica M. de Ruiter

Explorations of Water Oxidation Catalysis in Explicit Solvent Ph.D. thesis, Leiden University

ISBN: 978-94-6332-412-0

Cover and bookmark designed by Nico de Ruiter This thesis was printed on 100% recycled paper.

This research was financed by Leiden University, and co-financed by the Dutch Ministry of Economic Affairs as part of the BioSolar Cells research project C1.9.

The use of supercomputer facilities was sponsored by NWO Exact and Natural Sciences, with financial support from the Netherlands Organization for Scientific Research (NWO).

i

Table of Contents

List of Abbreviations... v

General Introduction & Computational Tools ... 1

1.1. The search for sustainable energy solutions ... 3

1.2. Computational Tools ...7

1.2.1. Density Functional Theory ...7

1.2.2. Time Dependent Density Functional Theory ... 9

1.2.3. Car-Parrinello Molecular Dynamics ... 11

1.2.4. Calculating changes in Relative Free Energies ... 12

1.3. Main Results ... 13

1.4. References ... 14

The Fundamentals: A Combined Experimental & Theoretical Study 17 2.1. Introduction ... 19

2.2. Experimental Methods ... 20

2.2.1. Computational method and details ... 22

2.3. Results and Discussion ... 23

2.3.1. Characterisation of the catalytic intermediates of Ru-bpc ... 23

2.3.2. Derivative catalysts ... 30

2.4. Conclusions ... 35

2.5. References ... 36

2.A. Appendix ... 38

2.A.1. Calculated multiplicity proposed intermediates ... 38

2.A.2. Validation of the TDDFT methodology ... 39

2.A.3. Raman frequency calculations ... 40

2.A.4. Time-dependent UV-Vis absorption of Ce^IV ... 41

2.A.5. Calculated absorption spectra entire cycle Ru-bpy ... 41

2.A.6. Calculated spin density localisation proposed intermediates .... 42

2.A.7. Orbital comparison of [Ru^IV=O]²⁺ intermediates ... 43

2.A.8. UV-Vis absorption data for [Ru^II-OH2]²⁺ complexes ... 44

ii | Table of Contents

2.A.9. Elucidation [Ru^III-OH]²⁺ ... 44

2.A.10. Initial investigation of two proposed dimeric intermediates ... 49

Introducing a Closed System Approach ... 51

3.1. The call for the Closed System Approach – Mechanistic Considerations ... 53

3.2. Computational method and details ... 55

3.3. Results and Discussion ... 57

3.3.1. Static Thermodynamics of the Catalytic Cycles ... 57

3.3.2. Ab-Initio Constrained Molecular Dynamics of System 1 ... 60

3.3.3. Closed System Analysis of the [Cu^II(O)(O)] intermediate ... 61

3.3.4. Closed System Analysis of the [Cu^III(OH)(O)] intermediate ... 62

3.3.5. Implication of Ion Inclusion ... 67

3.4. Conclusions ... 67

3.5. References ... 68

3.A. Appendix ... 70

3.A.1. Geometrical Investigation ... 70

3.A.2. Example of convergence of <λ> ... 75

Energetic Effects of a Closed System Approach ... 77

4.1. The Call for the Closed System Approach – Energetics ... 79

4.2. Computational Method and Details ... 82

4.3. Results and Discussion ... 84

4.3.1. Energetic analysis of the PCET step [Ru^II-OH2]²⁺ → [Ru^III-OH]²⁺ . ... 85

4.3.2. Proton Diffusion [Ru^III-OH2]³⁺ → [Ru^III-OH]²⁺ ... 86

4.3.3. Energetic analysis of the PCET step [Ru^III-OH]²⁺ → [Ru^IV=O]²⁺ 87 4.3.4. Experimental Comparison and Evaluation ... 91

4.4. Conclusions ... 92

4.5. References ... 92

4.A. Appendix ... 93

4.A.1. CSA with an electron acceptor in a constrained environment .... 93

4.A.2. Consideration of the first reaction step proceeding via [Ru^II-OH]⁺ + H+solv + Mn³⁺ ... 94

4.A.3. Calculation standard deviation Δ𝐺_𝐻⁺ ... 96

Table of Contents | iii 4.A.4. Radial Distribution Functions Ru – O during proton diffusion . 96

4.A.5. <λ> for [Ru^III-OH]²⁺ including initial accelerated contraction .. 97

4.A.6. Gaussian fits of KS Energies for Δ𝐸𝑒⁻ ... 98

Increasing Deprotonation Rate: Tuning the Environment ... 99

5.1. Introduction ... 101

5.2. Computational Method and Details ... 102

5.3. Results and Discussion ... 104

5.3.1. Proton Transport... 104

5.3.2. O – O bond formation via nucleophilic attack on [Ru^IV=O]²⁺: proton transfer coupled with multiplicity interchange ... 107

5.4. Conclusions ... 112

5.5. References ... 112

Conclusions and Outlook ... 115

6.1. Conclusions ... 117

6.2. Outlook ... 118

6.3. References ... 119

Summary ... 121

Samenvatting ... 123

Curriculum Vitae ... Error! Bookmark not defined. Publications ... 125

v

List of Abbreviations

ADF Amsterdam Density Functional AIMD Ab Initio Molecular Dynamics

ALDA Adiabatic Local Density Approximation B3LYP Becke 3 parameter; Lee Yang Parr BJDAMP Becke Johnson DAMPing

BOA Born-Oppenheimer Approximation

CE Counter Electrode

CFF Consistent Force Field

CHARMM Chemistry at HARvard Macromolecular Mechanics COSMO Conductor Like Screening Model

CPMD Car-Parrinello Molecular Dynamics

CSA Closed System Approach

CV Cyclic Voltammetry

d(X→Y) Distance constraint/constrained distance between X and Y DCACP Dispersion-Corrected Atom-Centred Potential

DFT Density Functional Theory

EQCN Electrochemical Quartz Crystal Nanobalance

GC Glassy Carbon

GGA Generalised Gradient Approximation GTH Goedecker Teter Hutter

HF Hartree-Fock

KS Kohn-Sham

LanL2DZ Los Alamos National Laboratory 2 Double Zeta LMCT Ligand-to-Metal Charge Transfer

MD Molecular Dynamics

MLCT Metal-to-Ligand Charge Transfer

NHE Normal Hydrogen Electrode

OPBE OPTX Perdew Burke Ernzerhof

OPTX Handy’s OPTimised eXchange functional OLEMS Online Electrochemical Mass Spectrometry PBEc Perdew Burke Ernzerhof Correlation functional PCET Proton-Coupled Electron Transfer

PCM Polarisable Continuum Model PS II PhotoSystem II

QM/MM Quantum Mechanics/Molecular Mechanics

vi | List of Abbreviations

RHE Reversible Hydrogen Electrode SCE Saturated Calomel Electrode

SERS Surface Enhanced Raman Spectroscopy TDDFT Time Dependent Density Functional Theory TZP Triple Zeta Polarised

VMD Visual Molecular Dynamics visualisation program

WE Working Electrode

WOC Water Oxidation Catalyst