Water splitting in natural and artificial photosynthetic systems

Sergey Koroidov

Department of Chemistry Umeå 2014

Responsible publisher under swedish law: the Dean of the Medical Faculty This work is protected by the Swedish Copyright Legislation (Act 1960:729) ISBN: 978-91-7459-800-1. Elektronisk version tillgänglig på http://umu.diva-portal.org/ Tryck/Printed by: Service Center KBC Umeå, Sweden 2014

This thesis is dedicated to the memory of my father

i

Table of Contents Abstract iii Abbreviations v List of Publications vii 1. Introduction 1

1.1. Solar energy 1 1.2. Oxygenic photosynthesis 2 1.2.1. Photosynthetic energy storage 2 1.2.2. Photosynthetic water oxidation 7 1.2.3. Structure of the Mn4CaO5 cluster. 12 1.2.4. Oxidation of the Mn4CaO5 cluster. 13 1.2.5. Substrate water binding to the WOC. 15 1.3. Hydrogen carbonate as a cofactor of the WOC 16 1.4. Water splitting in artificial photosynthetic systems. 17 1.4.1. Concept of artificial photosynthetic devices. 19 1.4.1.1. Semiconductor particles. 19 1.4.1.2. Electrolyzers. 20 1.4.1.3. The artificial leaf 20 1.4.1.4. Dye-sensitized solar cells 21 1.4.2. Molecular catalysts for artificial water splitting 21 1.4.3. Cobalt and manganese oxides as a catalysts for artificial water splitting 22 1.5. Relevance 24

2. Materials and Methods 26 2.1. Determination of the chlorophyll concentration 26 2.2. Membrane Inlet Mass Spectrometry 26 2.3. H2

18O – labeling 29 2.4. Joliot type electrode and flash induced oxygen evolution patterns 29 2.4.1. Data evaluation 30 2.5. Clark electrode measurements of oxygen evolution 31 2.6. X-ray spectroscopy 32 2.7. Illumination setup 32

3. Femto-second serial X-ray crystallography and spectroscopy: new tools for studying the Mn4CaO5 cluster in different oxidation states. 37

3.1. Optimization of parameters for the light-induced Si state turnover of PSII samples in a flow-illumination set-up. 40

ii

4. Role of hydrogen carbonate in PSII 47 5. Water splitting in artificial photosynthetic systems. 52

5.1. Manganese oxides 54 5.2. Cobalt oxides 55

6. Summary 57 Acknowledgements 59 References 60

iii

Abstract

Photosynthesis is the unique biological process that converts carbon dioxide into organic compounds, for example sugars, using the energy of sunlight. Thereby solar energy is converted into chemical energy. Nearly all life depends on this reaction, either directly, or indirectly as the ultimate source of their food. Oxygenic photosynthesis occurs in plants, algae and cyanobacteria. This process created the present level of oxygen in the atmosphere, which allowed the formation of higher life, since respiration allows extracting up to 15-times more energy from organic matter than anaerobic fermentation. Oxygenic photosynthesis uses as substrate for the ubiquitous water. The light-induced oxidation of water to molecular oxygen (O2), catalyzed by the Mn4CaO5 cluster associated with the photosystem II (PS II) complex, is thus one of the most important and wide spread chemical processes occurring in the biosphere. Understanding the mechanism of water-oxidation by the Mn4CaO5 cluster is one of today’s great challenges in science. It is believed that one can extract basic principles of catalyst design from the natural system that than can be applied to artificial systems. Such systems can be used in the future for the generation of fuel from sunlight.

In this thesis the light-induced production of molecular oxygen and carbon dioxide (CO2) by PSII was observed by membrane-inlet mass spectrometry. By analyzing this observation is shown that CO2 not only is the substrate in photosynthesis for the production of sugars, but that it also regulates the efficiency of the initial steps of the electron transport chain of oxygenic photosynthesis by acting, in form of HCO3-, as acceptor for protons produced during water-splitting. This finding concludes the 50-years old search for the function of CO2/HCO3

− in photosynthetic water oxidation.

For understanding the mechanism of water oxidation it is crucial to resolve the structures of all oxidation states, including transient once, of the Mn4CaO5 cluster. With this application in mind a new illumination setup was developed and characterized that allowed to bring the Mn4CaO5 cluster of PSII microcrystals into known oxidation states while they flow through a narrow capillary. The optimized illumination conditions were employed at the X-ray free electron laser at the Linac

iv

Coherent Light Source (LCLS) to obtain simultaneous x-ray diffraction (XRD) and x-ray emission spectroscopy (XES) at room temperature. This two methods probe the overall protein structure and the electronic structure of the Mn4CaO5 cluster, respectively. Data are presented from both the dark state (S1) and the first illuminated state (S2) of PS II. This approach opens new directions for studying structural changes during the catalytic cycle of the Mn4CaO5 cluster, and for resolving the mechanism of O-O bond formation.

In two other projects the mechanism of molecular oxygen formation by artificial water oxidation catalysts containing inexpensive and abundant elements were studied. Oxygen evolution catalyzed by calcium manganese and manganese only oxides was studied in 18O-enriched water. It was concluded that molecular oxygen is formed by entirely different pathways depending on what chemical oxidant was used. Only strong non-oxygen donating oxidants were found to support ‘true’ water-oxidation. For cobalt oxides a study was designed to understand the mechanistic details of how the O-O bond forms. The data demonstrate that O-O bond formation occurs by direct coupling between two terminal water-derived ligands. Moreover, by detailed theoretical modelling of the data the number of cobalt atoms per catalytic site was derived.

v

Abbreviations

ATP Adenosine triphosphate

Chl Chlorophyll

Ci Inorganic carbon (CO2, HCO3-, CO3

2-)

FIOP Flash-induced oxygen evolution pattern

MIMS Membrane-inlet mass spectrometry

NADPH Nicotinamide adenine dinucleotide phosphate

PSII Photosystem II

P680 Primary electron donor chlorophyll molecule in PSII

QA Primary plastoquinone electron acceptor in PSII

QB Secondary plastoquinone electron acceptor in PSII

RC Reaction center

Si states Oxidation states of the Mn4CaO5 cluster, where ‘i’ is the

number of stored oxidizing equivalents

WOC Water oxidizing complex

XES X-ray emission spectroscopy

XRD X-ray diffraction crystallography

YZ Redox active tyrosine 161 of the D1 protein of PSII

α Miss probability during flash-induced oxygen evolution

vi

β Double hit parameter during flash-induced oxygen

evolution

vii

List of Publications

I) Jan Kern, Roberto Alonso-Mori, Rosalie Tran, Johan Hattne, Richard J. Gildea, Nathaniel Echols, Carina Glöckner, Julia Hellmich, Hartawan Laksmono, Raymond G. Sierra, Benedikt Lassalle-Kaiser, Sergey Koroidov, Alyssa Lampe, Guangye Han, Sheraz Gul, Dörte DiFiore, Despina Milathianaki, Alan R. Fry, Alan Miahnahri, Donald W. Schafer, Marc Messerschmidt, M. Marvin Seibert, Jason E. Koglin, Dimosthenis Sokaras, Tsu-Chien Weng, Jonas Sellberg, Matthew J. Latimer, Ralf W. Grosse-Kunstleve, Petrus H. Zwart, William E. White, Pieter Glatzel, Paul D. Adams, Michael J. Bogan, Garth J. Williams, Sébastien Boutet, Johannes Messinger, Athina Zouni, Nicholas K. Sauter, Vittal K. Yachandra, Uwe Bergmann, Junko Yano. (2013) Simultaneous Femtosecond X-ray Spectroscopy and Diffraction of Photosystem II at Room Temperature. Science 340, 491-495

Reprinted with permission from Science 340, 491-495, 2013. Copyrights 2013 American Association for the Advancement of Science

II) Dmitriy Shevela, Birgit Nöring, Sergey Koroidov, Tatiana Shutova, Göran Samuelsson, Johannes Messinger (2013) Efficiency of photosynthetic water oxidation at ambient and depleted levels of inorganic carbon. Photosynth Research 117, 401-412

Reprinted with permission from Photosynthesis Research 340, 491-495, 2013. Copyrights 2013 Springer

III) Sergey Koroidov, Dmitriy Shevela, Tatiana Shutova, Göran Samuelsson, Johannes Messinger (2014) Mobile hydrogen carbonate acts as proton acceptor in photosynthetic water oxidation Submitted Manuscript

IV) Dmitriy Shevela, Sergey Koroidov, M. Mahdi Najafpour, Johannes Messinger, Philipp Kurz (2011) Calcium manganese oxides as oxygen evolution catalysts: O2 formation pathways indicated by 18O-labelling studies.  Chemistry - A European Journal 17, 5415-5423

viii

Reprinted with permission from Chemistry - A European Journal 17, 5415-5423 Copyright 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

V) Sergey Koroidov, Magnus Anderlund, Stenbjörn Styring, Anders Thapper, Johannes Messinger (2014) Mechanism of water oxidation by cobalt-oxides Manuscript

Author’s contribution:

Paper I: Conceived, setup and performed O2 evolution measurements

Paper II: Data analysis and interpretation. Helped with the revision of the manuscript.

Paper III: Design and conduction of experiments, data analysis and interpretation with contribution in writing of the manuscript.

Paper IV: Design and conduction of experiments, data analysis and interpretation. Helped with the revision of the manuscript.

Paper V: Design and conduction of experiments, data analysis and interpretation. Assisted in writing of the manuscript.

Publications not covered in the thesis

VI) Rolf Mitzner, Jens Rehanek, Jan Kern, Sheraz Gul, Johan Hattne, Taketo Taguchi, Roberto Alonso-Mori, Rosalie Tran, Christian Weniger, Henning Schröder, Wilson Quevedo, Hartawan Laksmono, Raymond G. Sierra, Guangye Han, Benedikt Lassalle-Kaiser, Sergey Koroidov, Katharina Kubicek, Simon Schreck, Kristjan Kunnus, Maria Brzhezinskaya, Alexander Firsov, Michael P. Minitti, Joshua J. Turner, Stefan Moeller, Nicholas K. Sauter, Michael J. Bogan, Dennis Nordlund, William F. Schlotter, Johannes Messinger, Andrew Borovik, Simone Techert, Frank M. F. de Groot, Alexander Föhlisch, Alexei Erko, Uwe Bergmann, Vittal K. Yachandra, Philippe Wernet, and Junko Yano (2013) L-Edge X-ray Absorption Spectroscopy of Dilute Systems Relevant to Metalloproteins Using an X-ray Free-Electron Laser. The Journal of Physical Chemistry Letters 4, (21):3641-3647.

ix

VII) Jan Kern, Rosalie Tran, Roberto Alonso-Mori, Sergey Koroidov, Nathaniel Echols, Johan Hattne, Julia Hellmich, Sheraz Gul, Hartawan Laksmono, Raymond G. Sierra, Richard J. Gildea, Guangye Han, Benedikt Lassalle-Kaiser, Ruchira Chatterjee, Mohamed Ibrahim, Aaron Brewster, Carina Glöckner, Alyssa Lampe, Dörte DiFiore, Despina Milathianaki, Alan R. Fry, M. Marvin Seibert, Jason E. Koglin, Dimosthenis Sokaras, Tsu-Chien Weng, Ralf W. Grosse-Kunstleve, Petrus H. Zwart, William E. White, Michael J. Bogan, Marc Messerschmidt, Pieter Glatzel, Garth J. Williams, Sébastien Boutet, Paul D. Adams, Athina Zouni, Johannes Messinger, Nicholas K. Sauter, Uwe Bergmann, Junko Yano, Vittal K. Yachandra (2013) Taking Snapshots of Photosynthetic Water Oxidation Using Femtosecond X-ray Diffraction and Spectroscopy Submitted Manuscript

VIII) Rosalie Tran, Jan Kern, Johan Hattne, Sergey Koroidov, Julia Hellmich, Roberto Alonso-Mori, Nicholas K. Sauter, Uwe Bergmann, Johannes Messinger, Athina Zouni, Junko Yano, Vittal K. Yachandra (2014) The Mn4Ca Photosynthetic Water-Oxidation Catalyst Studied by Simultaneous X-ray Spectroscopy and Crystallography Using an X-ray Free Electron Laser Submitted Manuscript

1

1. Introduction

1.1. Solar energy

World energy consumption is projected to increase from 13 TW in 2001 to 27 TW by 2050 and to 43 TW by 2100 (Hoffert et al., 1998; Barber, 2009). Currently, 85% of all energy comes from burning fossil fuel (U.S. Energy Information Administration, What is Energy: Energy Basics, 2011). These fossil fuels power our technologies and produce the wide range of products that support our life and heat our homes. The main problem in the current situation is not only limitation of fossil fuel, but also the consequences of combustion that leads to the accumulation of CO2 in the atmosphere. Notwithstanding the uncertainty about the precise effects of CO2 emissions, we can certainly look at the CO2 level from an historical perspective. For the last 800,000 years, for example, atmospheric CO2 concentration has been estimated to be between 210-300 ppm (Petit et al., 1999; Luthi et al., 2008). Over the past 100 years, however, the CO2 level has risen from 300 ppm to 395 ppm (Current Data for Atmospheric CO2), an increase that is most probably the result of man-made CO2 emission. If one imagines that all fossil fuel that exist is burnt then the level of carbon dioxide in our planet would reach to values equivalent to those prior to photosynthesis (Barber, 2009). Despite this fact, it is certain that fossil fuels will remain an important energy carrier for some time, but it is essential to stepwise reduce its usage and vital to develop technology that can derive energy form CO2-free or CO2-neutral sources.

One modern approach is to use renewable energy and from various renewable energy sources. By far the largest renewable energy resource is the sun. Solar energy is clean, abundant and economically very attractive energy source. The Earth is receiving solar energy at a rate of approximately 120000 TW (Hoffert et al., 2002; Blankenship et al., 2011) or 4.3 1020 J/hr (Lewis and Nocera, 2006). Sunlight provides thereby more energy in one hour than all of the energy consumed by the entire planet in one year. In order to satisfy the energy needs of humans until the end of the 21st century storage of only 0,03% from 120000 TW are needed. Nature has developed a way for utilization solar energy called photosynthesis.

2

Photosynthesis is the unique fundamental biological process that converts CO2 (about 380 Gtonnes of CO2 is fixed annually with release of 260 Gtonnes of O2 (Barber, 2004)) into organic compounds, for example sugars, using the energy of sunlight. Thus solar energy is converted into chemical forms of energy. Nearly all life depends on this reaction either directly as a source of energy, or indirectly as the ultimate source of their food. Oxygenic photosynthesis occurs only in plants, algae and cyanobacteria. Around 2.32 billion years ago, photosynthetic organisms started to be dominating and increased the O2 level of our atmosphere (Bekker et al., 2004). The development of oxygenic photosynthesis drastically changed the Earth by creating and presently by maintaining a level of about 20% Molecular oxygen in the atmosphere. This laid the basis for the formation of the protective ozone layer that absorbs a large part of the UV radiation from the sun. The increasing levels of atmospheric O2 allowed the development of an aerobic metabolism and more-advanced life forms (Olson and Blankenship, 2004).

1.2. Oxygenic photosynthesis

1.2.1. Photosynthetic energy storage

Solar energy supports life on Earth via photosynthesis, and this process evolved very early in the history of our planet. First organisms with ability to fix carbon appeared about 3.8 billion years ago (Schidlowski, 1988; Mojzsis et al., 1996). The earliest fossils of anoxygenic photosynthetic bacteria were found in 3.5 billion years old sediments (Schopf, 1993) that formed in the environment of low atmospheric oxygen (Awramik, 1992) and high level of reducing molecules, such as CH4, H2S, H2 and others. Later on, H2O started to be used by some photosynthetic organisms as the source of electrons and protons for CO2 reduction. This process released O2 as a by-product, and is hence called oxygenic photosynthesis. The organism that first performed this revolutionary process (cyanobacteria) were ancestors of the anoxygenic photosynthetic bacteria (Xiong et al., 2000). The O2 released was toxic for many organisms and only those organisms survived that devolved protective mechanism and/or the ability to use O2

for burning organic matter with mitochondria. Oxygenic photosynthesis performed by cyanobacteria algae and plants is the major process of solar energy conversion on the Earth today (Figure 1.1)

3

Figure 1.1. Global distribution of photosynthesis and production of organic matter showing values for land plants and ocean algal and cyanobacterial communities. Adapted from SeaWiFS Project, NASA/Goddard Space Flight Center and ORBIMAGE.

The basic equation of oxygenic photosynthesis can be written as:

energy2 2 6 12 6 26 6 6 Light

enzymeschlorophyll

CO H O C H O O (1.1.)

The photochemical reaction in photosynthesis is a redox reaction, with CO2 (removed from atmosphere) acting as an electron acceptor and H2O as electron donor. It results in the formation of glucose, which stores part of the solar energy in its chemical bonds, and in oxygen as a byproduct.

In higher plants photosynthesis occurs in organelles known as chloroplasts. Thylakoids, which span the inside of the chloroplasts, are the structural unit of the primary light-converting reactions in photosynthesis. The thylakoid membrane is a closed membrane system that separates the luminal (inner) space of thylakoids from the stromal (cytoplasmic) space of chloroplasts where CO2 fixation takes place. Figure 1.2 shows the protein complexes that participate in the light absorption, energy conversion and electron transfer reactions of oxygenic photosynthesis. These protein complexes, which are integral parts of the thylakoid membrane, are photosystem II (PSII) with light-harvesting

4

complex II (LHC-II), the Cyt b6f complex, photosystem I (PSI) with light-harvesting complex I (LHC-I), electron carriers ferredoxin (Fd) and ferredoxin-NADP-reductase (FNR) at a stromal, and plastocyanin (PC) at luminal sides, respectively, and the adenosine triphosphate (ATP) synthase.

The photosynthetic reactions are initiated by the absorption of light within the LHCs of PSII and PSI (Mullineaux, 1992; Nelson and Yocum, 2006; Collins et al., 2012), where it excites electrons into a higher molecular orbital. When the excitation energy generated in the antenna reaches the PSII or PSI reaction center (RC), respectively, this generates a charge separation, which is subsequently stabilized by further electron transfer events that increase the distance between the charged species and reduce their potential difference (Ben-Shem et al., 2003; Dau and Haumann, 2008; Renger, 2012)

PS II (Wydrzynski and Satoh, 2005; Govindjee et al., 2010) uses light in order to perform two chemical reaction: water oxidation and the reduction of plastoquinone (Messinger and Renger, 2008; Renger and Renger, 2008). In order to split water, four photochemical reactions are needed to take out four electrons and four protons from two water molecules. This leads to formation of one oxygen molecule. Protons form water are released into the lumen (donor side of PSII) and electrons are moved to the plastoquinone (QB) binding site. Fully reduced QB

2- picks up two protons from the stroma (acceptor side of PSII) side of the medium, yielding plastohydroquinone (PQH2) (Figure 1.2). PQH2 then leaves the PSII complex, and diffuses in the membrane to the Cyt b6f complex. The empty QB-pocket is filled by another plastoquinone (PQ) molecule from the PQ pool (for detail information look 1.2.2.).

42 2 22 2 4 2 4 h

stroma lumenH O PQ H O PQH H (1.2.)

5

Figure 1.2. Diagram of the main protein complexes that perform oxygenic photosynthesis in the thylakoid membrane of chloroplasts of higher plants. Adapted from Shevela (2008)

The cytochrome b6f complex is an electron transfer and proton translocating membrane enzyme acting as a redox link between PSII and PSI. (Berry et al., 2000; Hervás et al., 2003). Plastoquinol PQH2 binds to the Rieske iron-sulfur protein (FeS) where it is oxidized and deprotonated. Protons are released into lumen and one of the two electrons introduced into electron transport chain passes through Cyt f to the electron carrier plastocyanin (PC). The other one is transferred to cyt b6 and participates in the reduction of PQ molecules to regenerate PQH2. This process is known as Q cycle and increases the proton concentration difference between stroma and lumen (Bernat and Rögner, 2011; Cramer et al., 2011):

2 2 2 4 2 stroma ox lumen redPQH H PC PQ H PC (1.3.)

PSI is a large protein complex (Fromme, 1996; Amunts and Nelson, 2009) that reduces on the stromal side NADP+ to NADPH (nicotinamide adenine dinucleotide phosphate), and oxidizes PC on the luminal side. This transmembrane electron transfer is energetically driven by the light-induced excitation of the primary electron donor P700 (Lubitz, 2006). P700* transfers its excited electron to the chlorophyll molecule A0, which passes it on to the phylloquinone A1. From here it is transferred to Fd via three different four-iron four-sulfur [Fe4-S4] clusters known as Fx, Fa and Fb (Figure 1.3). The formed cation radical P700•+ it is reduced directly by the reduced form of the mobile

6

electron transfer protein plastocyanin, PCred. The overall reaction of PSI can therefore be written as:

hred ox ox redPC Fd PC Fd (1.4.)

The reduced Fd transfers its electron to ferredoxin-NADP-reductase (FNR), where the production of NADPH takes place (Vermaas, 2001).

2 2

2

FNRred storma

ox stroma

Fd H NADP

Fd NADPH H

(1.5.)

The overall process of linear electron transfer form water to NADP+ through PS II, Cyt b6f and PSI is presented in Z-scheme (Figure1.3).

There is, however another pathway where electron form reduced Fd is flowing back to Cyt b6f complex. This happens to increase an amount of protons for ATP synthesis.

The trans-membrane potential generated by the trans-membrane electron transfer reactions and via the accumulation of protons in the thylakoid lumen is used by the ATPase for the synthesis of ATP from ADP and Pi (adenosine triphosphate from adenosine diphosphate and inorganic phosphate). (McCarty et al., 2000; Junge and Nelson, 2005; Junge et al., 2009). In this process protons accumulated in the lumen pass through the ATPase and generate a rotary motion of the F0F1 unit that is required for ATP synthesis.

NADPH and ATP produced during photosynthesis provide the energy for the synthesis of sugars form CO2 and H2O which are taken form atmosphere and the roots, respectively. These processes of photosynthesis can be divided into the light-reactions and dark (light-independent) reactions:

3 22 8

42 2

2 2 3 3 4

2 3 3

lighth

H O NADP ADP HPO H

O NADPH ATP H O

(1.6.)

7

42 2

3 22 2 4

2 3 3

2 3 3

darkCO NADPH ATP H O

CH O H O NADP ADP HPO H

(1.7.)

The reaction pathways by which CO2 gets fixed during the light-independent reactions is known as the Calvin–Benson–Bassham cycle (Bassham et al., 1950).

Figure 1.3. Representation of the oxygenic photosynthesis Z-scheme on redox potential scale that trace electron transfer form water to NADPH. Adapted from Shevela (2008)

1.2.2. Photosynthetic water oxidation

PSII is the only natural pigment-protein complex known to oxidize water and release molecular oxygen. To drive this reaction it uses visible light (400-700nm) (Lubitz et al., 2008; Pace and Krausz, 2012; Cox and Messinger, 2013). However, recent measurements defined that 750 nm will drive PSII electron transfer rather efficiently (Thapper et al., 2009).

4 2 22 4 4 h

PSIIH O O H e (1.8.)

PS II is embedded into thylakoid membrane and has a total molecular mass of about 350 kDa. Crystal structures obtained from thermophilic cyanobacteria (Thermosynechococcus elongatus and Thermosynechococcus vulcanus) revealed the organization of PSII

8

(Zouni et al., 2001; Ferreira et al., 2004; Loll et al., 2005; Kawakami et al., 2009; Guskov et al., 2010; Umena et al., 2011). Based on the latest 1,9 Å resolution structure (Umena et al., 2011), each PS II core complex consists of 20 proteins, 35 Chl, 11 carotenoids, more than 20 lipids, 2 plastoquinons, two heme iron, one non-heme iron, 4 manganese atoms, 3 or 4 calcium atoms (one of which in Mn4CaO5 cluster), 3 chloride ions and one bicarbonate ion (Figure 1.4.). All cofactors that are involved in photosynthetic water oxidation and which are responsible for the electron transport within the reaction center are bound by the PSII core proteins D1 (PsbA) and D2 (PsbD) (Chua and Gillham, 1977; Debus, 1992, 2001; Nixon et al., 2005). The excitation energy generated by light absorption in the LHCII is transmitted to RC via the inner chlorophyll-binding proteins (CP43-PsbC and CP47-PsbB) (Bricker and Frankel, 2002; Eaton-Rye and Putnam-Evans, 2005).

In plants the extrinsic proteins PsbO (33kDa, also known as manganese-stabilizing protein), PsbQ (17kDa), and PsbP (23kDa) are located at lumen side and optimizing PSII activity, serve as enhancers of O2 evolution and protect Mn4CaO5 cluster form outer reductants and reactants in the surrounding aqueous phase (Seidler, 1996). The Mn4CaO5 cluster together with its functionally important protein environment and ligands forms a functional unit within PSII that is known as water oxidizing complex (WOC) or oxygen evolution complex (OEC) (Debus, 2005).

Absorption of the light by the inner or outer antenna of PSII leads to the formation of an exited chlorophyll (Chl) state, Chl*, that is transferred from the antenna to the primary electron donor in the RC, P680, which in turn is excited to P680*. P680 is named after its absorption maximum. The molecular equivalent is variously defined, either as the special pair PD1PD2, or to also include the monomeric ChlD1 and ChlD2 molecules (Figure 1.5 B).

* 1680 680 *antenna antennaChl P Chl P (1.9.)

9

Figure 1.4. Structure of PSII at a resolution of 1.9 Å. Reproduced from Umena (2011).

10

Figure 1.5. Simplified architecture of PSII. Red arrows represent excitation energy migration to P680, and black arrows show the path of the electrons trough the electron transfer chain. Adapted from Messinger and Shevela (2012).

After formation of the exited state P680* the primary electron acceptor pheophytin (Pheo) accepts within few picoseconds the excited electron from P680*. This charge separation leads to the formation of the

radical pair 1680 DP Pheo (Klevanik et al., 1977; Klimov et al., 1977):

1 *1 1680 680D DP Pheo P Pheo (1.10.)

11

P680•+ has an oxidation potential of about +1.2 – 1.3V, which is the highest known in nature (Jursinic and Govindjee, 1977; Klimov et al., 1979; Rappaport et al., 2002). Thus PSII needs a protection against oxidation and long-living triplet state 3P680* states that can be formed by charge recombination. The carotenoids and the Cyt b559 (proteins PsbE and PsbF) (Figure 1.5) are thought to be involved in this protection mechanism (Vass et al., 1992; Lubitz et al., 2008).

The primary charge separation is stabilized by electron transfer from Pheo•- to the primary plastoquinone molecule QA forming P680•+QA

•-. QA• is oxidized in a slower reaction by a second

plastoquinone molecule, QB, that after a second photo-chemical turnover becomes fully reduced to QB

2- and takes up two protons form the stroma, forming PQH2. PQH2 is displaced from its binding site by a plastoquinone molecule of dissolved in the thylakoid membrane, and is subsequently oxidized again by the Cyt b6f complex (Messinger et al., 2012). These ractions can be summarized as follows:

1

2

2 2

Fe 2 Fe

Fe Fe

D A A

A B A B

A B stroma A B

A B A B

Pheo Q Pheo Q

Q Fe Q Q Fe Q

Q Q H Q Q H

Q Q H PQ Q Q PQH

(1.11.)

The non-heme iron between QA and QB plays a structural role and also binds one hydrogen carbonate ion (HCO3

-), which was suggested to be involved in the protonation of QB

-/2- (McConnell et al., 2012; Shevela et al., 2012).

Tyrosine Z (D1-Tyr161, also termed YZ) (Ahlbrink et al., 1998; Debus, 2001; Ananyev et al., 2002) is a part of the WOC and directly involved in the light-induced electron transfer. It is an intermediate redox-active electron carrier between P680 and the Mn4CaO5 cluster that reduces P680•+ (Debus et al., 1988). Thus the Mn4CaO5 cluster at the donor side of PSII is oxidized by P680•+ through YZ, which can donate an electron much faster to P680•+ then the Mn4CaO5 cluster. His190 of D1 is proposed to be the base that accepts the proton released from YZ upon oxidation by P680•+. Proton may reversibly shift within a hydrogen bond towards His190 resulting in a [YZ–O•…..H+–N–His190] complex

12

( 0680 680Z ZP Y OH N His P Y O H N His )(Debus, 2005;

Meyer et al., 2007; Dau and Haumann, 2008).

Four successive oxidations lead to the release of one oxygen molecule. The quantum efficiency of the overall PSII chemistry described by equation 1.2 (plastoquinone reduction and water oxidation) may be as high as 90% under optimal light conditions (Dau and Zaharieva, 2009; Dau et al., 2012; Cox and Messinger, 2013) .

1.2.3. Structure of the Mn4CaO5 cluster.

The structure of the Mn4CaO5 cluster was recently resolved at a resolution of 1,9 Å by Shen and colleagues (Umena et al., 2011). This study identified five oxygen atoms that bridge the five metal atoms of the cluster. This is in good agreement with structures derived by Extended X-ray Absorption Fine Structure (EXAFS) spectroscopy and DFT calculations (Yano et al., 2006; Siegbahn, 2009). In Mn4CaO5 cluster one calcium, four oxygens and three manganese form an asymmetric structure of a ‘‘distorted chair’’. The fourth Mn is located outside of the cubane and is linked to Mn1 and Mn3 atoms of the cubane through two di-µ-oxo bridges involving the O5 and O4 atoms of the cluster (Figure 1.6.). The cubane-like structure was reported previously (Ferreira et al., 2004), but the oxo-bridges and the exact distances between atoms could be resolved.

Figure 1.6. Structure of the Mn4CaO5 cluster where numbers between atoms represent distances (in ångströms). Reproduced from Umena (2011).

13

The four closest water molecules to the Mn4CaO5 cluster are direct ligands of the cluster. W1 and W2 are attached to Mn4 and the other two (W3, W4) to Ca. Since no other water molecules ligate the Mn4CaO5 cluster, it has been suggested that some of these four waters can act as the substrate for water oxidation (Umena et al., 2011).

The unusually long distances between oxygen atom O5 and the metals atoms of the cluster have been interpreted to suggest that these bonds are weak and that O5 may be one of the oxygen substrates for di-oxygen formation. The W2 and W3 are within hydrogen bond distance with O5 and therefore may serve as the other substrate. On the other hand, W3 is close enough to YZ so that it is also an attractive candidate as a proton release group (Kargul and Barber, 2012) Thereby W3 rather O5 may be a hydroxide ion in the S1 state and based on this one can assume that the O-O bond formation may occur between W2 and W3 (Umena et al., 2011). In summary, the results of Shen and colleagues suggest that O-O bond formation occurs in two of these three species O5, W2, and W3.

However, the applied dose leads to a reduction of ~25% of the MnIII/IV ions to MnII (Yano et al., 2005; Umena et al., 2011), which also noticeably changes the atomic distances as compared to EXAFS (Yano et al., 2005; Grabolle et al., 2006; Glöckner et al., 2013). Thus, even at cryogenic temperatures SR-based XRD of the Mn4CaO5 structure in PS II is fundamentally limited by the radiation damage to the redox active metal site, making it difficult in obtaining structures of stable or transient reaction intermediates. A more detailed description is provided in Section 3.

1.2.4. Oxidation of the Mn4CaO5 cluster.

The splitting of two water molecules into molecular oxygen and four protons (see Equation 1.8) requires the accumulation of four oxidizing equivalents on the Mn4CaO5 cluster of the WOC. In 1969, Joliot and colleagues demonstrated that the flash-induced oxygen evolution of dark-adapted chloroplasts and cells of algae exhibits a periodicity of four (Joliot et al., 1969). Their finding can be sum up as follows: (i) almost no oxygen was seen in the first two flashes, (ii) maximum of oxygen release occurs after 3rd flash, (iii) four flashes are required for the detection of every next maximum of oxygen releases, (iv) the oscillation is damped and eventually all flashes generate same amount of O2. (Figure 1.7. A). On the basis of these observations, Kok and coworkers designed a model,

14

which is known as the Kok model (Figure 1.7. B). In this model the different oxidation states through which the WOC cycles during water oxidation are referred to Si states, where i represents the number of stored oxidizing equivalents (i=0,1,2,3 and 4) (Kok et al., 1970).

Figure 1.7. (A) FIOPs of dark adapted PSII samples, and (B) the extended Kok model. Adapted from Messinger and Renger (2008).

The state stable in the dark is the singly oxidized S1 state (MnIII

2MnIV2) (the other S states decay back to S1). That is why the first

maximum of oxygen evolution occurs after three flashes. The S0

(MnIII3MnIV) state converts into S1 in the dark due to electron transfer to

the oxidized form of tyrosine D (YDox) (Styring and Rutherford, 1987;

Vass and Styring, 1991; Messinger et al., 1993). YD is located on the D2 protein (D2-Tyr 160) of PSII in the symmetry related position to YZ. In contrast to YZ it does not participate in the fast electron transfer reactions. However, YD can be oxidized by P680•+ and it can act as reductant during the decay reactions of S2 to S1 or S3 to S2. (Vermaas et al., 1984; Vermaas et al., 1988; Messinger and Renger, 1993; Faller et al., 2001). The meta stable S2 (MnIIIMnIV

3) and S3 (MnIV4) states can also

decay to S1 if the electron created during light-induced charge separation is not quickly enough removed from acceptor site (QA and/or QB) (Diner, 1977; Robinson and Crofts, 1983; Rutherford and Inoue, 1984). The S4

state is an intermediate state that decays to S0 in a fast (1 ms) spontaneous reaction under the liberation of O2. Despite numerous attempts, the S4 state was not detected so far (Haumann et al., 2008; Shevela et al., 2011). However S3YZ

ox intermediate that is only stable in millisecond time range under certain conditions (O2 pressure and lowering pH under air) has been kinetically identified (Clausen and Junge, 2004, 2008)

15

The damping of flash-induced oxygen evolution patterns (FIOPs) was proposed to occur due to miss (α) and double hit (β) probabilities (Forbush et al., 1971). The miss probability represents the percentage of WOCs that have the same oxidation state before and after flash excitation (Si – flash – Si). The miss does not reflect a constant percentage of inhibited PSII centers, rather it is statistically distributed overall PSII centers within a flash train. The origin of the miss probability are the redox equilibria on the donor and acceptor side that lead to temporary blockage of stable charge separation in PSII (Renger and Hanssum, 1988; Shinkarev and Wraight, 1993). Moreover, the miss parameter can also originate from the kinetic mismatches of the rate of P680•+ reduction by YZ because it competes with charge recombination between P680•+ with a primary quinone electron acceptor, QA

- (Christen and Renger, 1999; Christen et al., 1999). Furthermore there is experimental data indicating that value of α is dependent on the redox state Si of the Mn4CaO5 cluster (Renger and Hanssum, 1988; Isgandarova et al., 2003; Han et al., 2012; Suzuki et al., 2012).

The double hit parameter reflects the percentage of PSII centers that have been exited twice during one flash (Si – flash – Si+2). This accounts for the small oxygen yield after the second flash. The double hit strongly depends on flash profile of the light source and can be avoided if laser flashes are used (Jursinic, 1981).

1.2.5. Substrate water binding to the WOC.

The first mass spectrometry measurements with good enough time resolution to detect the exchange rate of the substrate water molecules were done by Messinger and co-workers (Messinger et al., 1995). The authors have thoroughly examined the incorporation of oxygen atoms from bulk water into the dioxygen evolved by the WOC of PSII. Because of their experimental design, the rate of incorporation reflects the rate at which bulk water incorporates into the water-binding site of the WOC in a given S state.

The following points emerged from the MIMS studies (Messinger et al., 1995; Hillier et al., 1998; Hillier and Wydrzynski, 2000; Hendry and Wydrzynski, 2002, 2003; Cox and Messinger, 2013): (a) the two substrate water molecules bind to separate sites throughout the S state cycle; (b) The two sites are characterized by different exchange rates. The slow exchanging site exchanges ~ 20 times slower than the fast

16

exchanging site in the S3 state, ~ 60 times slower in the S2 state, and ~ 6000 times slower in the S1 state; (c) The two substrate waters are already bound to the WOC at the S2 state; (d) Ca2+ is involved in substrate water binding at the slow exchanging site; (e) The rate constants measured at 10 °C for the slow exchanging site range from 2× 10-2 s-1 in the S1 state to 10 s-1 in the S0 state, and those for the fast exchanging site range from 40 s-1 in the S3 state to ≥ 120 s-1 in the S1 and S2 states.

Information about water binding in the WOC has also been obtained by several different techniques: X-ray crystallography (XRD) (Umena et al., 2011), magnetic resonance (Rapatskiy et al., 2012), and FTIR spectroscopy (Debus, 2008; Noguchi, 2008).

1.3. Hydrogen carbonate as a cofactor of the WOC

Plants cannot perform photosynthesis without CO2. CO2 is fixed by Rubisco (ribulose-1.5-bisphosphate carboxylase/oxygenase) and further reduced into carbohydrates in the Calvin–Benson–Bassham cycle. Moreover, CO2 in the form of hydrogen carbonate (HCO3

-) (Figure 1.8) plays a direct role in the light reactions through a structural and regulatory role within PSII. Numerous data show that HCO3

- has effects both the acceptor and the donor side of PSII (McConnell et al., 2012; Shevela et al., 2012).

Figure 1.8 Conversions of inorganic carbon species (Ci). Adapted from (Shevela et al., 2012)

Based on the latest crystal structures HCO3- is a direct ligand of the

non-heme iron and forms hydrogen bonds to several amino asides of the D1 and D2 proteins (Figure 1.9). Its binding to acceptor side of PSII was already previously proven by electron paramagnetic resonance (EPR) and Fourier transform infrared spectroscopy (FTIR) (Diner et al., 1991; Petrouleas et al., 1994; Hienerwadel and Berthomieu, 1995). All these

17

data are in good agreement with the suggestion that HCO3- may stabiles

the QA-Fe-QB structure and allow efficient electron transport and protonation of QB

-/2-. Thus HCO3- becomes carbonate ion (CO3

2-) after protonation of QB

2- and may get a proton back form the stroma through D1-E244 (Müh et al., 2012). However future studies are needed for a better understanding of this protonation event.

On the donor side of PSII hydrogen carbonate has been suggested to play role in the assembly of Mn-cluster during phototactivation (Klimov et al., 1995; Baranov et al., 2000). Moreover, HCO3

- was proposed to play a role of base or proton transporter (Ananyev et al., 2005; Shutova et al., 2008).

A more detailed description of the role of HCO3- on the donor side

of PSII is provided in Section 4 and in the attached Papers II and III.

Figure 1.9. The ligand environment around Fe and HCO3- of the iron-

quinone center of PSII. The bonds between the non-heme iron and its ligands are shown as solid line, and the hydrogen bonds as dashed lines. Reproduced from Umena (2011).

1.4. Water splitting in artificial photosynthetic systems.

It is vital to develop technology which can derive energy from renewable resources. This idea was presented as far back as in 1912 by Giacomo Ciamician (Ciamician, 1912), when he stated:– “Solar radiation may be used for industrial purposes… Photochemistry will artificially

18

put solar energy to practical uses. To do this it would be sufficient to be able to imitate the assimilating processes of plants”.

Nowadays Ciamician’s idea for production of ‘solar fuel’ from inexpensive and abundant material such as water that could be split into oxygen and hydrogen is highly attractive. Often hydrogen is called fuel of the future since its combustion generates pure product as water. A promising way for the light driven water splitting in newly made device would be to mimic the molecular and supramolecular organization of the natural photosynthetic system, i.e. “artificial photosynthesis”. Today the concept of solar energy conversion as alternative to fossil fuels is an important field of research and artificial photosynthesis became as a highly promising scientific direction (Kirch et al., 1979; Lubitz et al., 2008; Dau et al., 2010; Nocera, 2012; Wiechen et al., 2012).

Figure 1.10 gives a basic overview of artificial photosynthesis. Artificial photosynthesis includes both oxidation and reduction reactions in which water molecule is directly involved (Equation 1.12). Similar to natural photosynthesis, the reaction starts with absorption of light by photoactive species (A and D), which reach their exited states (A* and D*). A* act a strong oxidant (by releasing an electron) in its excited state and D* yields a reduced state (by capturing an electron). Generated electron and electron holes can be transferred to water oxidizing catalyst (Catox) and to a catalyst forming hydrogen by proton reduction (Catred), respectively. Water oxidation and proton reduction reactions are linked by a relay molecule R that transfers a charge between the PSII-like and the PSI/hydrogenase-like units (Figure 1.10).

2 2

2

2 4 4

4 4 2

ox

red

Cat

Cat

H O O H e

H e H

(1.12.)

19

Figure 1.10. Scheme of artificial photosynthesis proposed by (Kirch et al., 1979). Adapted from Lubitz (2008).

Thus, artificial photosynthesis (AP) has the same principle of electron flow as natural photosynthesis: The reduction equivalents obtained by PSII during water oxidation are transferred through the redox carriers to PSI and are then used to produce “natural fuel” – NADPH.

1.4.1. Concept of artificial photosynthetic devices.

1.4.1.1. Semiconductor particles.

Light absorption results in the formation of energetic charge-separated states in both molecular donor-acceptor systems and semiconductor particles. Semiconductors are able to excite electrons into higher energy levels and overcome the band gap. Electron are exited from the valence band to the conduction band and created electron-hole pairs can be utilized for water splitting. The band gap of the catalyst supposed to be suitable for the absorption of sunlight and the accessible redox potentials must be suitable to the water-splitting reaction. Today there are two approaches for the light driving water splitting by semiconductor partials: (i) water splitting by single semiconductor partial (one step photo-excitation system), where catalyst partialy acts as Catox and Catred without need of electron retransfer (Maeda and Domen, 2010) and (ii) two different types of semiconductors (two step photo excitation system) for water splitting and proton reduction, respectively (Kudo, 2011).

Efficiency of 6.5% has been achieved with two step photo excitation system using WO3/Pt (Catox) and ZrO2/TaON (Catred) and IO3

-/I- as mediator to facilitate electron transfer (Maeda and Domen, 2010, 2011).

20

One step photo-excitation system have been realized by GaN/ZnO with Mn3O4 for O2 and Rh/Cr2O3 core/shell nano particles for H2 evolution (Maeda et al., 2010)

1.4.1.2. Electrolyzers.

In modern electrolyzers the electrocatalytic water-splitting is carried out by the catalysts, which are deposited on electrode surfaces. In alkaline water electrolyzers, dimensionally stable anodes are used, thin films of ruthenium or iridium oxide directly supported on metallic titanium (da Silva et al., 1997; Lassali et al., 1998). In case of polymer electrolyte membrane electrolyzers, porous carbon electrodes coated with platinum as a cathode and with noble metal oxides, like iridium or ruthenium as anodes, are the currently most widely used set-ups (Song et al., 2008; Millet et al., 2010; Zeng and Zhang, 2010).

Nowadays, commercially available electrolyzers typically have efficiencies of up to 80 % (Armaroli and Balzani, 2010; Dau et al., 2010). However, major drawbacks of current electrocatalytic water-splitting devices are the expensive metals (Ir and Ru) as well as to their complex constructions. Hydrogen production by water electrolysis is expensive today and only used to generate hydrogen of high purity (Armaroli and Balzani, 2010; Dau et al., 2010). In order to make electrolyzes more affordable and attractive for alternative energy production, one needs to find more cost-effective approaches. One way to optimize electrolyzers is to couple them to photovoltaic cells (PVs) (Pearce, 2002; Swanson, 2009). Here sunlight is converted in to electric energy by a photovoltaic cell to provide the required redox potential for water oxidation and proton reduction.

1.4.1.3. The artificial leaf

The artificial leaf is solar water-splitting cell including earth-abundant elements that operate in near-neutral pH conditions, both with and without connecting wires (Reece et al., 2011; Nocera, 2012). The cell is based on triple junction, amorphous silicon photovoltaic interfaced to Co catalyst (Catox as oxygen evolving catalyst), and NiMoZn catalyst (Catred as hydrogen evolving catalyst). Efficiency of water splitting reaction is 4.7% for a wired configuration and 2.5% for a wireless configuration.

21

1.4.1.4. Dye-sensitized solar cells

The light harvesting efficiency can be increased by immobilizing molecular dyes at the semiconductor’s surface. When the dye is absorbing light, it is transferred into its excited state. From the excited state, the dye injecting an electron into the conduction band of the semiconductor, generates a charge at the semiconductor-dye interface. In dye-sensitized solar cells, dye-sensitized semiconductor particles are immobilized at a conducting surface like indium doped tin oxide or fluorine doped tin oxide as anodes (O'Regan and Gratzel, 1991; Hagfeldt et al., 2010).

Today TiO2 (Lee et al., 2012), NiO (Li et al., 2012), Nb and W oxides (Abe et al., 2009) are used as semiconductors modified with organic molecules (Abe et al., 2009; Li et al., 2012) or Ru complexes as dyes (Lee et al., 2012). Here Ir (Catox) is used as water splinting catalyst (Lee et al., 2012) and Co (Catred) as a catalyst for hydrogen generation (Li et al., 2012).

Despite the progress made in development of artificial photosynthetic devises some problems remain. Major challenge is identification of effective materials that can act as Catox and Catred based on abundant elements which are stable for long period under working conditions.

1.4.2. Molecular catalysts for artificial water splitting

Today molecular catalysts for water splitting have resided substantial attention. This catalyst offers greate opportunity for structural design and tuning the WOC for optimal performance. However, relatively small amount of molecular water oxidation catalysts that operate with low overpotentials are known. Majority of them have been discovered in the last few years.

The first multinuclear ruthenium based water splitting catalyst (“ruthenium blue dimer”) was discovered in the early 1980s by Meyer and colleagues (Gersten et al., 1982; Gilbert et al., 1985; Concepcion et al., 2008). Later number of dinuclear ruthenium complexes showed to be more or less effective catalyst for water splitting (Wada et al., 2000; Wada et al., 2001; Deng et al., 2008; Geletii et al., 2008; Sartorel et al., 2008). This suggested that at least two metal centers are needed for

22

water oxidation. However, this suggestion was disproved and it is widely known now that water splitting is also possible with ruthenium mononuclear complexes (Zong and Thummel, 2005; Tseng et al., 2008; Concepcion et al., 2010; Duan et al., 2012).

In contrast to rapidly developing ruthenium water splitting catalyst, there are examples of catalyst containing other metal centers both for multinuclear or mononuclear systems. The water splitting ability of iridium catalysts was discovered by Bernhard and colleagues (McDaniel et al., 2007). Based on complex initially prepared in 1973 (Weakley et al., 1973), Hill and colleagues showed that compound that contains an active Co4 core and free of carbon-based organic ligands is catalytically active for water splitting (Yin et al., 2010).

Immobilization of molecular catalysts on the electrode surface and application of them in to artificial photosynthetic devises will not be discussed here, since molecular catalysts are beyond scope of this thesis. In this section and further, molecular catalysts are briefly discussed.

1.4.3. Cobalt and manganese oxides as a catalysts for artificial water splitting

Water oxidation to molecular oxygen is a four-electron four-proton reaction that requires an overall redox potential of 1.23. To be capable to drive this reaction by visible light one needs to avoid high energy species such HO• that would be formed by a one-electron oxidation of water. As such, transitions metals, or clusters thereof, that are able to support multi-electron reduction steps are most suitable as water oxidation catalysts. It is also highly important that the catalysts operate with low overpotentials.

A comparison of almost 20 different transition metals oxides by Harriman et.al. (Harriman et al., 1988) revealed that IrO2, Co3O4, RuO2, Mn2O3 function most efficiently as O2-evolving catalyst. Up to now situation has not changed very much and the most successful catalysts for water oxidation are made from the above mentioned oxides (Morris and Mallouk, 2002; Kanan and Nocera, 2008; Duan et al., 2009; Concepcion et al., 2010; Jiao and Frei, 2010; Najafpour et al., 2010; Duan et al., 2012). Oxides of noble metals are the most efficient water oxidation catalysts reported so far. However, these oxides are no promising catalytic components for artificial photosynthetic devices for

23

large scale solar fuel generation due to the low abundance and high costs of Ru and Ir

Mn and Co are favored by many chemists for synthesis of “PSII-like” artificial photosynthetic systems for water splitting since they are relatively abundant (especially Mn). Mn is found as free element in nature, for example at the ocean floor and the bottoms of many fresh-water lakes, as well as in many minerals (Post, 1999; Dismukes et al., 2001; Sauer and Yachandra, 2002). Moreover, Mn has the ability to attain a large number of different oxidation states. Both are likely reasons why it was chosen by nature as active center for water splitting (Armstrong, 2008). The structure of this center is in higher plants, algae, and in cyanobacteria. Artificial complexes that mimic the WOC, with multi-nuclear Mn connected through µ-oxo bridges were found to act as highly active water oxidation catalyst (Brimblecombe et al., 2008; Najafpour et al., 2010; Hocking et al., 2011; Wiechen et al., 2012). The metal centers of artificial Mn-complexes are cycling between MnIII and MnIV oxidation states during water oxidation process and that is why multi nuclear species, at least 4Mn, are required.

An interesting similarity was found between artificial Mn-complexes and Mn-cluster of the WOC: if calcium is added to synthetic Mn-catalyst, the oxygen evolving activity of Ca-Mn-catalyst increase more than ten times as compared to Mn-catalysts without calcium (Najafpour et al., 2010; Shevela et al., 2011; Tsui et al., 2013). Moreover study on Mn3X cluster containing Na+,Ca2+,Sr2+, Zn2+ or Y3+ showed that the reduction potential of Mn3X clearly depends on the charge of the redox–inactive metal ions (Tsui et al., 2013). The more highly charged Lewis acidic metal ions withdraw more electron density of the Mn3X cluster making it easier to reduce. The Mn3X cluster containing Ca2+ or Sr2+ ion exhibit the same reduction potential. Interestingly, that the WOC of PSII remains active without significant structural changes and still maintain enzymatic function only if Sr2+ ion replaced by Ca2+ (Hendry and Wydrzynski, 2003; Brudvig, 2008; Pushkar et al., 2008; Cox et al., 2011; Yachandra and Yano, 2011). Agapie and colleagues suggested that possible role of the calcium ion in the WOC is to modulate the redox potential of the cluster. This tuning of the cluster’s redox properties is essential for the transfer of four electrons that are needed for water splitting.

24

Cobalt oxide is known to be a good water oxidation catalyst for long time (Baxendale and Wells, 1957; Anbar and Pecht, 1967; Shafirovich et al., 1980; Elizarova et al., 1981). Co-based catalyst were studied by many research groups (Kanan and Nocera, 2008; Surendranath et al., 2010; Yin et al., 2010; Shevchenko et al., 2011; Li and Siegbahn, 2013). Known advantages are the efficiency at neutral pH, the stability under working conditions and abundance (though less abundant than Mn). Moreover, Co-oxide catalyst self-assemble upon the oxidation of Co2+ to Co3+ ion in aqueous solution and have a structure analog to that of the Mn4CaO5 cluster in PSII. X-ray absorption spectroscopy studies revealed that Co-catalyst structure consist of several Co(III)O6 octahedra units in incomplete and complete cubane blocks. (Risch et al., 2009; Kanan et al., 2010; Du et al., 2012). In the event of Ca-Co-catalyst no difference was observed in water oxidation activity(Risch et al., 2012).

In order to test artificial photosynthetic systems for their ability to act as water oxidation catalysts either electrochemistry or sacrificial oxidation agents (Parent et al., 2013) are used. In the latter case they must have a potential high enough to oxidize the catalysts that are used. However, oxidation agent such as Ce(IV) forms insoluble cerium oxide materials upon reduction to Ce(III) (Hayes et al., 2002). Formed cerium oxide can incorporate into the catalytically active metal (de Leitenburg et al., 1996).

In summary, both synthetic Co and Mn oxides are very promising candidates for large scale applications of artificial water oxidation chemistry, since they are abundant, inexpensive and non-toxic catalysts. One condition for this is, however, that their activity (turnover number and turnover frequency) can be improved. More detailed information about Co and Mn catalysts as their commonly used oxidation agents can be found in Section 5 and Papers IV and V.

1.5. Relevance

Knowledge of the basic principles of water oxidation and hydrogen conversion in nature is a presently a major goal for basic research, because it also promises to yield knowledge applicable for the energy needs of our society. This knowledge may allow us to use either use (modified) photosynthetic organisms – or the isolated enzymes – in biotechnological processes, or to design biomimetic (artificial) catalysts

25

for large-scale water splitting and hydrogen production. Such systems would combine the tasks of light-absorption, charge separation, water-splitting, proton transport and hydrogen formation all in one ‘device’. While biological systems can already be used, the artificial devices bear the promise to reach significantly higher efficiencies in the future.

26

2. Materials and Methods

2.1. Determination of the chlorophyll concentration

The Chl concentration of BBY fragments (Berthold et al., 1981) , PSII cores and PSII crystals (Kern et al., 2005) was determined after extraction in 80% (v/v) acetone, recording absorption at 646,6, 663,6, 664 and 750 nm on UV/VIS spectrophotometer. The formula used for estimation of Chl concentration (mg/ml) in BBY membrane fragment as follows (Porra et al., 1989).

646,6 750 663,6 750( ) 17,76( ) 7,34( )c Chl A A A A k (2.1.)

and in PS II cores and crystals, according to formula:

664 750( )( )

74000

A A kc Chl

(2.2.)

where k is dilution factor.

2.2. Membrane Inlet Mass Spectrometry

Mass spectrometry is a powerful technique that is used for experimental analysis of charged compounds from single atoms to mega-Dalton mass units. Mass spectrometry allows to study kinetics and dynamics in biological system with very high accuracy (Konermann et al., 2008). In this study a membrane inlet isotope ratio mass spectrometer (MIMS) was used (Thermo Scientific™ Delta XP and Delta V).

A huge impact for the development of isotope ratio MS instruments had the discovery of JJ. Thomson that Ne has two different isotopes, 20Ne and 22Ne (Thomson, 1910, 1912, 1913). Thereafter, it became obvious that isotope ratio MS is suitable for the analysis of many stable isotopes.

The MIMS set-up was developed by G. Hoch and B. Kok in the beginning of the 1960th (Hoch and Kok, 1963). They developed the idea to separate the liquid or gaseous medium in which the reaction of

27

interest takes place from the high vacuum of the MS by a semipermeable membrane, which allows only small gas molecules to pass through (pervaporate) into the MS. The high vacuum in the MS is needed in order to prevent collisions of the analyte molecules/ions with atmospheric molecules. Such collisions would change their trajectories and thus reduce both resolution and sensitivity of the MS. MS’s are able to detect charged molecules only. That is why neutral gases have to be ionized after entering into the MS. In both the Delata XP and the Delta V the ionization occurs by electron impact (Siuzdak et al., 1996). A heated filament plus a suitable electrical potential work as electron gun. The thus created high-energy electrons interact with the analyte gas molecules, M, creating positively charged analyte ions:

2M e M e (2.3.)

Reaction 2.3 shows that each ionized molecule has almost the same mass as before (without one electron), and that the mass to charge ratio represents the molecular mass of the analyte (M•+= m/z). After ionization and further acceleration the ions travel through a magnetic field, which separates them according to their occurs m/z ratio (Dempster, 1918). Mathematically this can be presented by the following formula:

2 2

2

B Rmz V (2.4.)

Where the ionized molecule with m/z will travel on a path of radius R when it reaches the magnetic field B after being accelerated by a potential V. The thus separated ions are detected by an instrument specific array of Faraday cups. Amount of a Faraday caps depend on a model of isotope ratio mass spectrometer. The detection principle of Faraday caps based on the impact of ions on a metal surface which leads to the release of electrons, which are collected directly. Then detector amplify the initial signal, before it is read out into a software.

28

Figure 2.1. displays a simplified scheme of a MIMS set up, and also describes different types of measurements, which were performed during this study.

Figure 2.1. Simplified scheme of a MIMS set up, in which the production of gaseous analyte is initiated by (A) illumination of degased photo-active samples (B) illumination of non-degassed samples that were subsequently injected into a degassed buffer and (C) the reaction of non-degased chemicals injected into the degased sample. The gaseous reaction products penetrate through the gas permeable membrane and reach the high vacuum section where they are ionized by electron impact (EI). The thus generated ions are separated by a magnetic field (MF) according to their mass-to-charge ratios and detected by Faraday cups. The resulting signals of the different isotopes are amplified and recorded online simultaneously.

29

2.3. H218O – labeling

H218O labeled water was used to understand possible pathways of

reactions that lead to the evolution of the isotopologues of O2 (16O2, 16O18O, 18O2) and CO2 (12C16O2, 12C16O18O, 12C18O2). The addition of H2

18O into the sample was done for MIMS measurements only. The lowest level of isotopic enrichment is given by Earth’s natural abundance (0.2 %). For a given 18O-enrichment b of water, the isotope composition of O2 or CO2 was calculated according to the binomial distribution function, which assumes the absence of isotope effects:

2 2 2

16 182 2

( ) 2

;

a b a ab b

a O b O

(2.4.)

or

2 232: 34: 36:2 :

44: 46: 48m a ab bz (2.5.)

Where 2 22 1a ab b is the total product.

Another way to follow changes in the level of enrichment (total fraction of 18O atoms in the product) as a function of reaction time is to apply the following formula (Mills and Urey, 1940; Silverman, 1982)

2

182 2

2 2

2( 2 )

ab b

a ab b

(2.6.)

The contribution of 17O to the total O2 and CO2 can be neglected due its very small natural abundance (10-5 %).

2.4. Joliot type electrode and flash induced oxygen evolution patterns

The FIOPs were obtained at defined temperature with a home-built Joliot type electrode (Joliot and Joliot, 1968; Joliot, 1972) that was modified by Messinger (Messinger, 1993). All measurements were done in the absence of electron acceptors. A scheme of the modified Joliot type electrode is shown on Figure 2.2.

30

Figure 2.2. Schematic cross-section of home-build Joliot type electrode. Adapted from (Shevela, 2008).

For each measurements 10 µl aliquot of the sample was transferred onto the surface of Pt-cathode in dim green light and then always kept there for 3 minutes in order to reach complete temperature adaptation and sedimentation. Before illumination of the sample with saturating flashes, which were provided by a xenon flash lamp, the polarization voltage of -750 mV was applied for 40 seconds. This time was necessary to achieve a constant signal background. The flash frequency was 2 Hz. Signals form the oxygen oscillation pattern were amplified and recorded with 3.6 points per ms sampling rate. The control of the flash sequence, and the recording of the data was done with a program (LabView software, National Instrument) developed by the author.

2.4.1. Data evaluation

The deconvolution of the oxygen oscillation pattern into the Si state populations was performed with Excel spreadsheet (Messinger et al., 1991) based on the method developed by (Delrieu, 1974; Lavorel, 1976)

1n nS K S (2.7.)

31

Where transition between states by light flashes are described by operation of a matrix K on a column vector S

0

1

2

3

0

0

0

0

nS

S

Sand K

S

S

(2.8.)

1ii n

S (2.9.)

where α, β and γ are the transition probabilities for the Si state transitions: α, misses (Si→Si); γ, single hit (Si→ Si+1); β, double hit (Si→ Si+2); with α+β+γ=1.

The oxygen yield produced by the nth flash Yn is thus related to components of a state vector

3 21 11( )n n n

Y S S

(2.10.)

2 31 1 and

n nS S

are the population of the redox states S2 and S3

before the nth flash.

2.5. Clark electrode measurements of oxygen evolution

In order to measure the oxygen evolving activity of either PS II samples or artificial compounds a Clack-type electrode (Qubit Systems and Rank Brothers Ltd.) was used (Clark et al., 1953). For this PSII samples were illuminated with saturating continues white light of a slide projector. The samples were measured at a concentration of 10-20 µg Chl ml-1 in a reaction chamber filled with designated buffers (final volume of 1 ml). The measurements were performed in the presence of 250 μM PPBQ (phenyl-p-benzoquinone) or 250 μM DCBQ (2.6-Dichloro-1.4-benzoqiuinone) and 5 mM FeCy (K3[Fe(CN)6]) as artificial electron acceptors. For measuring the oxygen evolution rate of artificial compounds the reaction was started by the addition of oxidizing agents such as CeIV ([(NH4)2[CeIV(NO3)6]]) or [RuIII(bipy)3]3+. To keep a constant temperature, the reaction mixture was thermostated to 20°C and stirred constantly during measurements with a magnetic stir bar.

32

The electrode was calibrated using air-saturated and nitrogen-saturated water at atmospheric pressure.

2.6. X-ray spectroscopy

X-ray measurements at Stanford Linear Accelerator Center (SALC) were conducted together with the members of YACHANDRA/YANO LAB (Lawrence National Lab, Berkeley, California, USA).

All conditions and parameters regarding illumination setup (such as light intensity, frequency, sample flow, S states population and so on) which were obtained by author and Johannes Messinger were applied at SLAC for the X-ray experiments (Figure 2.3.).

Figure 2.3. Setup of simultaneous x-ray spectroscopy and crystallography experiment at the Coherent X-ray Imaging instrument of Linac Coherent Light Source (left side). Scheme for the illumination setup used to advance PS II in the catalytic cycle and measure simultaneously the XRD and XES signal at LCLS (right side).

Whole setup of simultaneous x-ray spectroscopy and crystallography (Figure 2.3.) will not be discussed in material and method section, since the main task of the author was to develop new method for illumination of PSII crystals and suspensions.

2.7. Illumination setup

The samples employed were PSII core complexes that were isolated from Thermosynechococcus elongatus (T. elongatus) as described elsewhere (Kern et al., 2005). The rates of O2 evolution for

33

PSII cores typically were ~ 3500 µmol (O2)·mg (Chl)-1·h-1, and the number of Chl’s per reaction center was 29-34.

PSII crystals (2-25 µm) or PSII cores at Chl concentrations of 6-10 mg/ml were diluted with H2

18O (97.6 %) which contained 1.2 M sucrose or 27 % (w/v) glycerol and 5 mM CaCl2 to give a final 18O-enrichment of about 12-48 % and final salt concentration 5 mM CaCl2, 50 mM MES, 1.2 M Sucrose or 27 % glycerol. No electron acceptors were added. Samples were kept in darkness or very dim green light during all steps, except when illuminated with the laser. The 18O enriched samples were illuminated by a home build illumination setup (Figure 2.4.)

Figure 2.4.Top view of home-build illumination setup.

The setup is designed for the illumination of samples that flow inside of a silica capillary (inner diameter (ID) of 50-100 µm and outer diameter (OD) of 150 or 360 µm). For illumination ns-laser light pulses traveling through up to four optical fibers (400 µm core diameter) that were directly attached to the de-coated region of the capillary. The fiber tips were connected to the capillary in holder base (Figure 2.5.)

34

Figure 2.5. Picture illustrating the coupling of the fibers to the capillary in the holder base.

For the illumination the samples were pumped from their reservoir (gas-tight Hamilton syringe) at a constant rate through the capillary by a syringe pump. The illuminated samples were collected at the other end of the capillary with another gas-tight Hamilton syringe that was mounted onto another syringe pump that operated in the sample withdrawing mode. Both syringe pumps were synchronized to the same flow rate thus providing constant laminar flow through all length of the capillary. The flow rate was optimized so that at the given flash rate each sample region was illuminated only once with a flash.

The laser employed in this study was a Continuum Inlite II-20 (Nd:YAG laser, 532 nm, 7ns pulse width). To obtain stable output intensity of 3.5-7.0 µJ/fiber the laser was operated continuously at 20Hz. While the flash frequency was controlled via the Q-switch divider (20Hz or 10Hz). The illumination periods were set with the help of a fast shutter (SH05 operated with SC10 Controller; both Thorlabs).

The efficiency of the illumination of PSII was tested by recording the oxygen oscillation pattern. In contrast to the Joliot-type FIOP measurements, here each point needs to be collected separately (see below). For each point 13.5 µl of sample was pumped through the capillary and illuminated with the indicated number of capillaries. At the end of each illumination, the sample collected in the receiving syringe was injected into a degassed buffer of a MIMS cell. Since all experiments were performed in air-saturated buffers H2

18O enrichment (see above)

35

was employed to record the 34O2 signal, which has a comparatively small natural background. The traces obtained are displayed in Figure 2.6 A.

In order to calculate the flash pattern from these traces, the O2 signal obtained with ‘x’ fibers was subtracted from that obtained with ’x+1’ fibers. For the 1st flash, the background 34O2 signal of the non-illuminated sample was subtracted (Figure 2.6 B).

Figure 2.6. On-line MIMS measurements of light-induced O2 yield detected as mixed labelled 16O18O specie after illumination of photosystem II from T. elongatus with 0, 1, 2, 3 and 4 flashes at pH 6,5 and 20°C (panel A). Panel B displays the flash pattern derived from A by subtracting the signal of x fibers from that obtained with x+1 fibers.

Before the illuminations each fiber optic was tuned with an energy meter (OPHIR PE 10-C) so that the output energy of each individual fiber

36

did not vary more than ±5 % from a stable output intensity. A Newport LBP sensor was used for measuring beam profile of each fiber to be sure that the intensity in each point of fiber profile remains the same (Figure 2.7.). To monitor the flow rate of the samples inside the capillary a liquid flow sensor (Sensirion SLG64-0075) was used.

Figure 2.7. Profile of fiber optic.

37

3. Femto-second serial X-ray crystallography and spectroscopy: new tools for studying the Mn4CaO5 cluster in different oxidation states.

The water oxidation reaction in nature is accomplished by the WOC in PS II. This multi-subunit membrane protein found in green plants, algae, and cyanobacteria, uses light to catalyze the oxidation of water to oxygen. The WOC of PS II contains a heteronuclear Mn4CaO5 cluster that couples the four-electron oxidation of water with the one-electron photochemistry at the PS II reaction center, by acting as the locus of charge accumulation. Energy derived from the absorption of successive photons drives the WOC through the Kok cycle (Kok et al., 1970), a series of five intermediate Si-states, where i represents the number of oxidizing equivalents stored in the WOC. After the S4 state is reached, a spontaneous reaction occurs that releases O2 and returns to the WOC into the S0 state (Renger, 2011) (Figure 3.1.).

Figure 3.1. The Si state scheme for oxygen evolution. The proposed Mn oxidation states for each of the intermediate states are given (including

38

the proposed transient [S4] state). The structure of the S1 state proposed by Umena et.al. is displayed in the inset. Blue spheres, water molecules; magenta spheres, manganese ions; red spheres, μ-oxo bridges; yellow sphere, calcium

In the past years extensive studies of the dark stable S1 state using X-ray diffraction (XRD) have achieved enormous progress: the resolution was improved from 3.8 to 1.9 Å (Zouni et al., 2001; Kamiya and Shen, 2003; Ferreira et al., 2004; Loll et al., 2005; Guskov et al., 2009; Umena et al., 2011). In addition various techniques also have been used to elucidate the structure and mechanism of the WOC of PSII (Messinger et al., 1995; Haumann et al., 2005; Noguchi, 2008; Yano and Yachandra, 2008; Yeagle et al., 2008; Berthomieu and Hienerwadel, 2009; Cox et al., 2011). Between different method for obtaining detailed structures of PSII and the Mn4CaO5 cluster, XRD gives the most direct information about the overall arrangement of the atoms.

For XRD, however, the X-ray radiation damage (Yano et al., 2005) to the redox active Mn4CaO5 cluster has been an issue. The damage of the cluster leads to the reduction of Mn(III) and Mn(IV) present in the intact WOC to Mn(II) at an X-ray dose that is two to three orders of magnitude lower than the dose required to produce an observable decay in diffraction quality of PS II crystals (Yano et al., 2005; Grabolle et al., 2006). Such radiation damage occurs despite of the fact that the data collection is carried out at cryogenic temperature (100-150 K). The radiation damage and the cryogenic temperatures make it impossible to study transient reaction intermediates of PSII before and during O-O bond formation. Radiation damage does not only occur in PSII, but is a problem encountered also with many other redox active metallo-enzymes (Corbett et al., 2007; Meharenna et al., 2010; Antonyuk and Hough, 2011; Hersleth and Andersson, 2011; Daughtry et al., 2012; Sigfridsson et al., 2013).

The recent study by Umena et al. (2011), used a significantly lower X-ray dose than previous XRD studies. Nevertheless, this dose leads to the reduction of ~25% of the Mn to MnII. Despite of that the atomic structure of PS II could be resolved at 1.9 Å resolution. This structure revealed the positions of the four Mn and one Ca ions, and for the first time also the five oxo-bridges were visible (Umena et al., 2011). However, noticeable differences exist between the crystal structure and the EXAFS results (Yano et al., 2006; Yano et al., 2007; Pushkar et al., 2008; Yano

39

and Yachandra, 2008) in which the data were collected at much lower X-ray dose than in the XRD experiments by Shen and coworkers. Specifically it can be noticed that the Mn-ligand and Mn-Mn distances are significantly longer in the 1.9 Å crystal structure than those determined by EXAFS.

Recently a new crystallographic approach was developed: a femto second serial X-ray crystallography. In this new technique, suspension of microcrystals is injected into X-ray region. Femtosecond X-ray pulses, which are short enough pass the sample before significant electronic rearrangement and atomic displacement occur (diffraction before distraction) allow of collecting diffraction pattern form single randomly oriented crystal. Crystals have to be replaced after each exposure. Besides having the advantage that much smaller crystals can be studied than previously, this technique has two key advantages that make it very interesting for PSII research: (i) it is performed near room temperature, thus studies can be performed at transient states, and (ii) it over comes the problem of radiation damage. (Chapman et al., 2011; Hunter et al., 2011; Kirian et al., 2011; Lomb et al., 2011; Aquila et al., 2012; Barty et al., 2012; Boutet et al., 2012; Johansson et al., 2012; Koopmann et al., 2012).

The first X-ray Free-Electron Laser (XFEL) was realized at the Linac Coherent Light Source (LCLS) near Stanford, USA. The intense and ultra-short X-ray pulses (<70 fs) allow to collect diffraction data before the start of radiation damage (Neutze et al., 2000; Caleman et al., 2010). By combining serial X-ray crystallography with X-ray emission spectroscopy it was recently shown that the ‘probe-before destroy’ approach also works for the highly radiation sensitive Mn4CaO5 cluster in PS II (Alonso-Mori et al., 2012; Kern et al., 2012). This approach thereby provides the possibility to obtain molecular motions of the catalyst at work by recording snapshots at different time points in the catalytic cycle (Figure 3.1.). In such a study crystallography and spectroscopy can give complementary information: spectroscopy provides detailed information about changes in the Mn oxidation states, and crystallography probes the structural changes of the Mn4CaO5 cluster and the protein.

In order to study the Mn4CaO5 cluster at different oxidation states using this new combined approach it is essential to know the exact oxidation state of the cluster at each point of the measurements. The various oxidation states are set by in situ illumination of the crystals

40

while they travel to the interaction region with the X-ray pulse. Therefore, the setup that illuminates the samples and delivers them to the interaction region becomes a crucial part of the whole experiment.

3.1. Optimization of parameters for the light-induced Si

state turnover of PSII samples in a flow-illumination set-up.

To advance PS II samples into the different S states during the XFEL experiments a new illumination setup was developed that allowed illuminating the PSII samples while they are flowing through a capillary towards the interaction region with the fs-X-ray pulses. Since the XFEL experiments do not allow obtaining a fast feedback about the oxidation states that are reached by this new setup, an independent approach was required to obtain the best parameters for Si state turnover under these conditions. Parameters that need to be optimized include: laser light intensity, flow rate/flash frequency, optimal diameter and surface treatment of capillaries. Therefore, a copy of this setup was constructed in the Messinger lab at Umeå University. With this replica set up PSII crystal and core suspensions were illuminated inside a striped silica capillary with laser flashes that were delivered via fiber optics that were directly attached to the capillary. The turnover efficiency was determined from the quality of the oxygen oscillation pattern that were measured by MIMS. These measurements were done in the presence of H2

18O, since this allows to detect the oxygen production at m/z 34, which has a low natural background signal due to dissolved oxygen from the atmosphere (for more detailed information can be found in Section 2.7 and attached Paper I).

Before testing the PSII preparations in the new flow-illumination set up, the turnover of the samples was probed by illuminating them with Xe-flashes in presence and absence of added exogenous electron acceptors in a MIMS cell. The data presented in Figure 3.2 show that the PSII core preparations are able to perform one full Si state cycle in the absence of added electron acceptors. The data also show that these preparations have a normal miss parameter. Both findings are essential prerequisites for the subsequent flow-illumination studies. The O2 yield after the second flash was higher in presence of PPBQ due to reductant-induced oxidation of the non-heme iron (Petrouleas and Crofts, 2005).

41

Figure 3.2. Oxygen yield (m/z=34) measured by illumination of PSII core preparations of T. elongatus in a MIMS cell as a function of flash number. The PSII suspensions were measured with (black; 40µM PPBQ) and without (red) added electron acceptors. The traces are normalized to maximum yield in the first turn over cycle. A series of thirteen saturating Xe-flashes with intermittent dark times of 25 s was given at 20°C and pH 6.3. The H2

18O enrichment was 15 %, the chlorophyll concentration 0.1 mg Chl/ml.

It was the most critical to determine the effective width of the illumination regions (Figure 3.3). This can vary from the diameter of the optical fibers due to effective illumination area. This knowledge is important for determining the optimal combination of flow rate and illumination frequency. The optimal flow rate that is synchronized with flash frequency so that an almost uniform S state advancement of the whole sample is achieved. If the flow rate is too slow with regard to illumination frequency, double or even more illuminations will occur; if it is too fast, non-illuminated sections remain.

42

Figure 3.3. Schematic picture of PSII crystals that were illuminated inside a silica capillary with laser flashes.

While the flash frequency can be easily controlled, the flow sensor and the syringe pump speed represent the average flow rate only. Since sample is traveling through a capillary a laminar flow profile is generated. Under conditions of laminar flow, the nature of viscosity dictates a flow profile in which the velocity of the sample increases towards the center of the capillary, while it is zero at the walls. This is illustrated in Figure 3.4.

Figure 3.4. The flow profile of a fluid in a capillary shows that the fluid acts in layers that slides over one another. νm corresponds to a maximum velocity and ν is a velocity at the walls. Reproduced from (http://hyperphysics.phy-astr.gsu.edu/hbase/pfric.html#lam)

This non-uniform flow adds some complicity into the synchronization of the flow rate with illumination frequency. This shows that in a flow set up one needs to find the best compromise of all variables, and that one can never expect to see the same low misses and double hits as in a stationary sample (Figure 3.2).

Another important factor is the required light intensity for efficient turnover through the Si state cycle. To low intensities can lead to only partial turnover of the samples, while too high intensities increase the miss parameter via light scattering along the capillary, and may also inactivate the sample. The optimal light intensity can be found in two

43

ways: (i) by the quality of the O2 oscillation pattern (same as above; see Fig. 3.7), and (ii) by the total O2 produced per PSII complex and flash number. The first method should normally be sufficient, but a small uncertainty remains if there can be a certain part of the sample that never sees any light, and thus does not contribute to the oscillation pattern. To address this question approach (ii) needs to be employed, which requires the absolute calibration of the MIMS signals. This calibration was achieved by the injection of known volumes of air-saturated water into the MIMS cell. This value was used to determine the micromoles of O2 produced by PSII core complexes (PSII cc) by the illumination with 3 flashes. This number was then divided by the µmole PSII reaction center, which resulted, after accounting for diffusion losses of 34O2 out of the capillary (data not shown) in about 0.73 O2/RC. Since 3 consecutive flashes are required to produce one molecule of oxygen in a dark-adapted PSII reaction center, a maximum of one O2/RC can be expected under these conditions. The data in Figure 3.2 show that this is even true if they move slow and see more flashes. The above numbers of 73% oxygen yield directly translate into light saturation. For 100% light saturation we would expect a value of 73% (0.93), since even under stationary conditions an average ‘miss’ of 10% occurs due to charge equillibria within PSII. Thus, we conclude that light intensity of 7 µJ is high enough to be saturated the entire PSII cc sample (Figure 3.5).

44

Figure 3.5. Relative O2 yield per PSII as detected by MIMS as a function of flash number. Conditions were the following: for PS II solutions silicon capillary (ID = 75 µm, OD 160 µm), flow rate 0.5 µl/min and frequency 4 Hz, light intensity of each fiber was 7 µJ.

Figure 3.6 shows an example of an early flash pattern, in which the flash frequency was too fast as compared to the flow rate. Therefore the maximal O2 yield is reached only after the fourth flash.

45

Figure 3.6. MIMS measurements of light-induced O2 yield (m/z=34) after illumination of PS II microcrystals in a flow-illumination set up. Conditions were the following: silicon capillary (ID = 100 µm, OD 360 µm), flow rate 2.2 µl/min and frequency 10 Hz. Light intensity of each fiber was 7 µJ

After optimization of all parameters, the FIOPs for PSII crystals and cores displayed in Figure 3.7 were obtained. The result shows, despite a somewhat high O2 yield after the first flash, the typical O2 oscillation pattern with a maximum after the 3rd flash. They thus demonstrate that good enrichments of the PSII cc complexes in the various Si states can be reached with the new flow-illumination set up, and that the XFEL measurements with PSII samples are feasible.

46

Figure 3.7. MIMS measurements of light-induced O2 yield (m/z=34) after illumination of PS II solutions (black) and PS II microcrystals (red) in a flow-illumination set up. Conditions were the following: for PS II solutions silicon capillary (ID = 50 µm, OD 160 µm), flow rate 1.055 µl/min and frequency 20 Hz, for PS II microcrystals silicon capillary (ID = 100 µm, OD 360 µm), flow rate 2.0 µl/min and frequency 10 Hz. Light intensity of each fiber was 7 µJ

These illuminated conditions were used in the XFEL approach (discussed above) to collect the XES and XRD data of PSII presented in Paper I. The final goal of this project is to understand the water oxidation mechanism by probing the geometric structure, the oxidation state and electronic structure, and the changes in the Mn4CaO5 complex while it proceeds through the Si state cycle.

47

4. Role of hydrogen carbonate in PSII

CO2 is not only the most discussed greenhouse gas in the atmosphere of the Earth, but also a key metabolite in all living organisms that participate in the global biological processes such as photosynthesis. As a metabolite it exists in equilibrium with HCO3

–and carbonic acid (H2CO3) (Equations 4.1. and 4.2.). These three species are referred to collectively as inorganic carbon (Ci). Reversible conversion of Ci allows to transport CO2 and HCO3

- in all cells. HCO3– is poorly soluble in biological

lipid membranes compared to CO2, which can freely diffuse in and out of the cell. Therefore, the conversion of Ci according to reaction 4.1. facilitates the transport of HCO3

– and protons (H+) into the intracellular space, while reaction 4.2. helps trap carbon dioxide within the cell. Carbonic anhydrases (CA) catalyze the interconversion of the Ci species, and thus speed up reactions 4.1 and 4.2 up to 1000000 times (Henry, 1996; Krishnamurthy et al., 2008). In photosynthetic organisms (cyanobacteria, green algae and higher plants) CA is important for both carboxylation and decarboxylation reactions, ion transport and pH regulation (Moroney et al., 2001; Coleman, 2004).

13 2 3 2 2HCO H H CO CO H O (4.1.)

22 2 2 3 3CO H O H CO HCO H (4.2.)

The role of CO2 or HCO3- in photosynthesis was discovered by

Senebier who found in 1782 that the production of oxygen by plants depends on the presence of “fixed air” (CO2) (Bay, 1931). Today it is obvious that plants cannot perform the process of photosynthesis without CO2. CO2 is fixed by Rubisco and two photosystems facilitate to drive CO2 fixation by light reactions.

The possible roles of Ci in photosynthetic water-splitting have been a controversial issue ever since the first report by Otto Warburg and Günter Krippahl in 1958 on the ‘bicarbonate effects’ on electron flow in PSII. Warburg and Krippahl observed that CO2 is required for oxygen evolution reaction and their view was that HCO3

-, not water, is the source of oxygen produced by PSII (Warburg and Krippahl, 1958). This hypothesis has been disproven by time resolved 18O-labelling studies

48

(Hillier et al., 2006; Shevela et al., 2008). This was not easy, because the CA activity of PSII samples leads to a fast equilibration between the 18O-isotope label of water and CO2 (Figure 4.1)

Figure 4.1. MIMS measurements of a change in C18O2 concentration as a function of time after the 5 µl-injection and rapid mixing (<10 ms) of H2

18O (to final enrichment of 3.2%) into the 150 µl-MS cell at pH 6.3 and 10°C. The Chl concentration of spinach PSII samples was 0.0 mg ml–1

(only MNS buffer in the MS cell) (trace 1) and 0.3 mg ml–1 (trace 2). For better comparison the initial rise of the 18O-labeled CO2 content caused by the injection of H2

18O is not shown.

Since then studies by many research groups explored two sites for the ‘bicarbonate effects’ within PSII. The role and binding site for HCO3

– on the electron acceptor side of PSII is known (for review, see (Van Rensen, 2002; Guskov et al., 2010)). Here HCO3

– is known to bind to the non-heme iron (Fe2+ in Figure 4.1) and is thought to facilitate the reduction and protonation of the secondary plastoquinone electron acceptor (QB) (reviewed in (Govindjee and Van Rensen, 1993; Govindjee et al., 1997; Van Rensen et al., 1999; Van Rensen, 2002)). In contrast, the site of interaction of HCO3

– on the donor side is not obvious (Figure 4.2.).

49

Figure 4.2. Schematic presentation of PSII in high plants and green algae (only core proteins are shown) and two sites (donor and acceptor) where HCO3

- has effect. Arrows shows the pathway of electron flow through PSII. Reproduced from Shevela (2012)

The view that bicarbonate also has an effect on the donor side of PS II arose initially from a hypothesis made by Stemler (Stemler and Govindjee, 1973; Stemler et al., 1974). He suggested that the water-oxidizing side of PSII is a possible site for the HCO3 − effect. However, the first reliable evidence that HCO3

- has an effect on the donor side of PSII was derived by Klimov et al. (Klimov et al., 1995; Klimov et al., 1995). In the PS II structure from Thermosynechococcus elongatus obtained at a resolution of 3.5 Å by Ferreira et al. (Ferreira et al., 2004) HCO3

- has been tentatively included to bind as a ligand to the Mn4CaO5 cluster. However, based on X-ray crystallography (Guskov et al., 2010; Umena et al., 2011), FTIR spectroscopy (Aoyama et al., 2008), and mass spectrometry (Shevela et al., 2008; Ulas et al., 2008) data, HCO3

– does not bind tightly at or near the Mn4CaO5 cluster.

At the same time, the possibility for a weakly bound, rapidly exchanging HCO3

– in the vicinity of the cluster cannot be excluded (Van Rensen and Klimov, 2005). Thus, for instance, HCO3

– was recently proposed to act as a proton acceptor for the WOC (Ananyev et al., 2005), (Karlsson et al., 1995) (Figure 4.2.).

50

In this Ph.D. study the possible participation of HCO3– in the

proton removal from the water-oxidizing side of PSII is investigated in higher plant preparations. For this we used two different techniques: (i) isotope-ratio membrane-inlet mass spectrometry (MIMS) in combination with 18O-labelling (Beckmann et al., 2009; Shevela and Messinger, 2013), and (ii) Joliot-type electrode for measuring flash-induced oxygen evolution patterns (FIOPs) (Renger and Hanssum, 2009). These experiments were performed both at ambient and 20-times reduced levels of Ci. To achieve and maintain such low levels of Ci in both gas phase around the electrode and in the aqueous phase around the investigated sample, the FIOPs measurements were done inside of a glove-box filled with N2 and in Ci-depleted buffers (Figure 4.3.). Unlike to all previous reports, in the present FIOPs study we fully control the levels of the residual Ci upon CO2/HCO3

−-depletion procedure. Thus, the concentration of CO2 in gas phase above the sample was continuously monitored with an infrared CO2 analyzer, while the Ci levels in aqueous phase (sample medium) were detected by MIMS.

Figure 4.3. Picture of the experimental set-up that was used in this study for the measurements of FIOPs under various levels of HCO3

–/CO2. The Joliot electrode with the Xe-flash lamp used for the FIOPs measurements

51

as well as mini-centrifuge used for sample washings were places inside the glove box “Belle”.

From FIOPs important information about the turnover efficiency of PSII can be obtained. The increased magnitude of the α-values at Ci-low conditions can be either due to the changes of all redox equilibria and kinetics of the donor or the acceptor side of PSII (i.e., redox-potential differences between QB/QB

-/QB2-, P680/P680+•, YZ/YZ

ox and the Si states of the WOC) (Renger and Hanssum, 1988; Shinkarev and Wraight, 1993) or due to the slower reduction of P680+• by YZ in Ci-depleted samples (Christen et al., 1999). While the misses may reflect the properties of both the donor and the acceptor side of PSII, the double hits reflect the properties of only acceptor side and are related linearly to the rate of electron transfer from QA

–• to QB/QB–• (Messinger et al., 1993).

Comparison of misses with double hits would give information in interpretation of the “bicarbonate effect” and represent the origin of PSII side effect.

In case of MIMS measurements present proposals for the action of free or weakly bound HCO3

– in photosynthetic water-splitting should result in a light-induced release of CO2 concomitant with O2 evolution. If HCO3

- is a base for protons produced by photosynthetic water oxidation (Ananyev et al., 2005; Shutova et al., 2008), CO2 should be formed as a result of H2CO3 formation and its disproportionation into H2O and CO2:

3 2 3 2 2HCO H H CO CO H O (4.3.)

In Papers II and III it is shown that HCO3- is needed for efficient

turnover of the WOC. The data demonstrate that the lack of HCO3− leads

to a reduced oxygen evolution activity of PSII, and increase overall miss factor under HCO3

- depletion (Shevela et al., 2013). In Paper III it is shown that HCO3

− acts as mobile proton acceptor of PSII that leads to light induced CO2 evolution.

52

5. Water splitting in artificial photosynthetic systems.

Increased global attention to the effects of releasing carbon dioxide into the atmosphere by burning fossil fuels has led to investigations of alternative fuel sources. One of the most promising approaches is artificial photosynthesis. In this process, solar energy is collected and delivered to a water oxidizing catalyst that splits water into dioxygen, protons, and electrons. The extracted electrons can be used for the reduction of protons to form dihydrogen, or may be used to reduce either organic molecules or CO2 to products that can serve as fuels (Youngblood et al., 2009). The development of water oxidation catalysts from inexpensive and abundant elements would make artificial photosynthetic systems highly affordable and attractive for large scale applications of solar fuel devices.

For a better understanding of the water splitting reaction and the mechanism of O-O bond formation it is a common approach to use transition metal complexes and transition metal oxides (Kraatz and Metzler-Nolte, 2006) as models to mimic the WOC in PSII (Barber and Tran, 2013). However, is has been difficult to develop systems that imitate closely the complex arrangement of the Mn4CaO5 cluster. Therefore, a general strategy is the development of simplified structural models (Meyer, 2008; Cook and Borovik, 2013). In addition, such complexes are tested for their catalytic efficiency and theirby their potential to be used in artificial photosynthesis devices (Figure 5.1.)

53

Figure 5.1. Possible O-O bond formation mechanisms. Nucleophilic attack (red boxes), oxo/oxyl radical coupling (blue boxes). Reproduced from Cox (2013)

In order to split water with ‘naked’ synthetic catalysts, sacrificial oxidants are used that have a high-enough redox potential to oxidize the catalysts into the required oxidation states. Alternatively, the catalysts can be oxidized electrochemically or photoelectrochemically if attached for example to a semiconductor surface. The two most commonly used non-oxygen transferring, single-electron oxidation agents are CeIV and [Ru(bipy)3]3+. They can be used in experiments to screen for “real” water oxidation catalysts (equations 5.1., 5.2., 5.3.) (Xu et al., 2010; Shevela et al., 2011). CeIV and [Ru(bipy)3]3+ providing redox potentials of 1,7 V vs NHE (Hayes et al., 2002) and 1,3 V vs NHE (Harriman et al., 1981), respectively.

Catalyst2 24 2 4 4IV IIICe H O Ce O H (5.1.)

3 Catalyst3 2

2

3 2

4 ( ) 2

4 ( ) 4

Ru bpy H O

Ru bpy O H

(5.2.)

54

In case of photochemically generated [Ru(bipy)3]3+

2 2 *

3 3400 nm

2 * 32 23 2 8 3 4 4

2 * 3 23 4 3 4

2 *

3 3 5

3

3 3

( ) ( )

( ) ( )

( ) ( )

( ) ( )

( ) ( ) 5

h

III

II

Ru bpy Ru bpy

Ru bpy S O Ru bpy SO SO

Ru bpy SO Ru bpy SO

or

Ru bpy Co NH Cl

Ru bpy Co aq NH Cl

(5.3)

5.1. Manganese oxides

Dinuclear manganese compounds have been intensively used as a model systems in order to understand water splitting reaction and development of artificial catalysts (Yagi and Kaneko, 2001; Mukhopadhyay et al., 2004; Cady et al., 2008; Mullins and Pecoraro, 2008; Collomb and Deronzier, 2009; Wiechen et al., 2012). All of them have either a [Mn2(µ-O)] or a [Mn2(µ-O)2] core. The Mn-oxidation states vary, and different combination of MnII, MnIII and MnIV have been reported. It was shown that dinuclear Mn complexes in lower oxidation states can be oxidized in single electron steps that increase the oxidation state of one manganese center form MnIII to MnIV (Huang et al., 2002; Huang et al., 2004; Kurz et al., 2008; Berends et al., 2012).

However, no dinuclear manganese complexes showed water splitting activity in reaction with CeIV and [Ru(bipy)3]3+, but oxygen evolution was observed with H2O2 and HSO5

- (potassium peroxymonosulfate, also known as oxone). Our 18O labeling experiment in combination with MIMS provided information that neither H2O2 nor HSO5

- can act as oxidizing agents to drive ‘true’ water oxidation (see Paper IV). The isotope labelling observed rather provides evidence that the tested of Mn2-complexes can only catalyze oxygen formation with these oxidants via oxygen transfer reactions. This also calls in question an earlier study (Limburg et al., 1999) in which water oxidation by another dimeric manganese complexes was reported to occur after HSO5

-

addition.

55

Present experiments on PSII and artificial catalysts indicate water-oxidation chemistry involves a cycling between the oxidation states MnIII and MnIV. It is therefore important to increase manganese nuclearity of the compounds form dinuclear to tetranuclear complexes in order to improve their efficiency. This is needed because four electrons must be subtracted from water to allow O2 formation.

The groups of Kaneko (Ramaraj et al., 1987) and Yagi (Yagi and Narita, 2004; Yagi et al., 2007) reported that the attachment of dinuclear Mn complexes to the surface of the clay kaolin leads to the formation of active water-oxidation catalyst. Subsequent catalytic studies (Yagi et al., 2007) and EPR spectroscopy investigations (Li et al., 2009; Berends et al., 2011) showed that the catalytic units formed at the clay surface consist of more than two manganese ions, and that they have an oxidation state of III or higher. X-ray crystallography of the attached complexes demonstrated that Mn4-species are formed at the surface by dimerization of two Mn2-units via µ-oxido ligands. Similarly, a recent study found water oxidation for dimerized dinuclear manganese complexes, supporting again that four manganese ions are needed for efficient water oxidation at low overpotentials (Karlsson et al., 2011). Attachment of monomeric MnII to the surface of the same clay does not lead to catalytic activity (Berends et al., 2011).

It appears that a naturally occurring mineral discovered in Morocco in 1963, CaMn2O4 which is nowadays known as marokite, (Gaudefroy et al., 1963) is a very interesting model for the Mn4CaO5 cluster of PSII. It was concluded that the oxidation state of manganese is +III and that marokite can be successfully synthesizes in laboratory (Najafpour et al., 2010). The O2 formation pathways by CaMn2O4 and α-Mn2O3 have been investigated in this Ph.D. project. In Paper IV it is shown that entirely different pathways of dioxygen formation catalysis exist for reactions involving different oxidants

5.2. Cobalt oxides

Another promising candidate for large scale water splitting are Co-based water-oxidation catalysts. The potential of Co to support water oxidation is known for a long time (Noyes and Deahl, 1937; El Wakkad and Hickling, 1950; Baxendale and Wells, 1957; Anbar and Pecht, 1967; Shafirovich and Strelets, 1978). In 2008 the photo-electrochemically oxidation of water by cobalt oxide films was reinvestigated by Nocera and

56

co-workers (Kanan and Nocera, 2008). This study has attracted much interest due to ability of the Co-oxide catalyst to split water at neutral pH under ambient conditions. The catalysts also self-assembled from relatively low cost materials (Surendranath et al., 2009). Further studies showed: (i) water splitting occurs from the CoIV oxidation state (McAlpin et al., 2010; McAlpin et al., 2011) (ii) cobalt catalyst self-heal (Lutterman et al., 2009) (iii) does not require deionized water and even works in brine and river water (Esswein et al., 2011) suggesting that for example chloride ions do not inhibit oxygen evolution.

XAS measurements (Risch et al., 2009; Kanan et al., 2010) and theoretical calculation (Hu et al., 2012; Li and Siegbahn, 2013; Mattioli et al., 2013) revealed that the Co-catalyst structure forms by several CoIIIO6 octahedra units in incomplete and complete cubane blocks and that they have structural similarity to the Mn4CaO5-cluster in PSII.

Despite on all successful studies and constant progress there is still no agreement whether the O-O bond formation occurs at Co-oxides via nucleophilic attack or by direct coupling, and whether for example bridging oxygens are involved as substrate. Using time resolved 18O-labelling MIMS and by employing the previously introduced nanoparticular Co oxides (Co/M2P system) (Shevchenko et al., 2011) it is shown in Paper V that water oxidation on amorphous Co-oxides occurs via direct coupling of two pre-bound terminal water derived ligands.

57

6. Summary

The demonstration of light-induced CO2 formation by PSII and the dependence of CO2 evolution on the concentrations of Ci and added buffer in the medium demonstrate conclusively that HCO3

− acts as mobile proton acceptor of PSII and that HCO3

- is needed for efficient turnover of the WOC (see Papers II and III). The data demonstrate that the lack of HCO3

− leads to a reduced oxygen evolution activity of PSII, and that the light-induced Si state transitions of the Kok cycle occur with an increased overall miss factor under HCO3

- depletion (Shevela et al., 2013). Since strictly alternating electron and proton removals from the WOC appear to be an inherent and crucial part of the mechanism of water oxidation in PSII (Siegbahn, 2009; Klauss et al., 2012), it appears very likely that this function of HCO3

− developed early during evolution and can be found in all O2 evolving organisms (Dismukes et al., 2001). Paper III thus establishes the long sought mechanism for the CO2/HCO3

− dependence of O2 production by PSII. This finding adds a new component to the understanding of PSII and to the regulatory networks of photosynthesis in higher plants.

Illumination of PSII crystals and suspensions with the newly developed illumination setup revealed that the illuminated samples cycle through all S states with acceptable miss probability (Messinger and Renger, 2008). A clear maximum of O2 release after the 3rd flash was achieved by optimization of all parameters. This result enabled the collection of XES and XRD data of PSII at room temperature using the new approach of femto second serial X-ray crystallography combined with X-ray emission spectroscopy at the X-ray free-electron laser at LCLS. So far data were recoded from both the dark state (S1) and the first illuminated state (S2) (Kern et al., 2013). With the resolution obtained so far no indication of radiation damage could be found. Thus, using the developed illumination conditions further measurements will be performed that allow to characterize all other intermediates, including the kinetically unstable S3YZ

•, and possibly the S4 state, in which the O-O bond formation and the evolution of molecular oxygen occurs.

The presented 18O-labelling results on calcium manganese-oxides on oxygen formation show that such reactions can be grouped into three categories:

58

1. catalase-type reactions involving hydrogen peroxide, in which the bulk water is not involved in O2 formation, in agreement with (Haber and Weiss, 1934; Kremer and Stein, 1959)

2. oxygen-transfer reactions involving oxone, in which one oxygen atoms from the bulk water participates in the formation of dioxygen

3. water oxidation, in which both oxygen atoms of the O2 product carry the 18O label signature, and for which the use of non-oxygen-transferring oxidation agents is necessary.

Employing the previously introduced Co/M2P system (Shevchenko et al., 2011) in combination with the chemical oxidant ([Ru(bipy)3]3+) and time resolved 18O-labelling membrane-inlet mass spectrometry it is demonstrated in Paper V that the O-O bond formation in these amorphous Co-oxide catalysts occurs between two pre-bound, fast exchanging oxygen species, i.e. via direct coupling between two terminal water/hydroxide ligands. It is also shown that 2.35 Co form one catalytic site. Since it was previously demonstrated that in the resting state Co has an oxidation state of at least CoIII, (Kanan et al., 2010; McAlpin et al., 2010; Artero et al., 2011; Nocera, 2012) we conclude that the direct coupling mechanism involves at least one oxygen radical, in agreement with recent theoretical studies (Li and Siegbahn, 2013; Mattioli et al., 2013).

59

Acknowledgements

В первую очередь я хочу поблагодарить всех родных и близких, в особенности родителей - маму и папу, а также любимую жену Таню за их любовь, терпение, понимание и постоянную поддержку.

I also would like to express my special appreciation and thanks:

To my adviser Prof. Dr. Johannes Messinger, you have been a tremendous mentor for me. I would like to thank you for constant stimulation, useful discussion, patience and for allowing me to grow as a research scientist.

To my friend Dr. Dmitry Shevela, for inestimable help at the beginning of my Ph.D., grate discussions in different fields, bringing out laughter, no matter what and of course for preparation of the figures for my thesis.

To my lab-mats, for cozy atmosphere and enthusiasm in the laboratory

To all Members of Yachandra/Yano lab for nice environment and care during my stay in Berkeley, opportunity to be involved into amazing project and the fruitful collaboration.

To my friends for unforgettable time. I am lucky that I know all of you. Thank you All !!!

60

References

Abe R, Shinmei K, Hara K, Ohtani B (2009) Robust dye-sensitized overall water splitting system with two-step photoexcitation of coumarin dyes and metal oxide semiconductors. Chemical Communications: 3577-3579

Ahlbrink R, Haumann M, Cherepanov D, Bögershausen O, Mulkidjanian A, Junge W (1998) Function of tyrosine Z in water oxidation by photosystem II: electrostatical promoter instead of hydrogen abstractor. Biochemistry 37: 1131-1142

Alonso-Mori R, Kern J, Gildea RJ, Sokaras D, Weng T-C, Lassalle-Kaiser B, Tran R, Hattne J, Laksmono H, Hellmich J, Glöckner C, Echols N, Sierra RG, Schafer DW, Sellberg J, Kenney C, Herbst R, Pines J, Hart P, Herrmann S, Grosse-Kunstleve RW, Latimer MJ, Fry AR, Messerschmidt MM, Miahnahri A, Seibert MM, Zwart PH, White WE, Adams PD, Bogan MJ, Boutet S, Williams GJ, Zouni A, Messinger J, Glatzel P, Sauter NK, Yachandra VK, Yano J, Bergmann U (2012) Energy-dispersive X-ray emission spectroscopy using an X-ray free-electron laser in a shot-by-shot mode. Proceedings of the National Academy of Sciences 109: 19103-19107

Amunts A, Nelson N (2009) Plant photosystem I design in the light of evolution. Structure 17: 637-650

Ananyev G, Nguyen T, Putnam-Evans C, Dismukes GC (2005) Mutagenesis of CP43-arginine-357 to serine reveals new evidence for (bi)carbonate functioning in the water oxidizing complex of photosystem II. Photochemical & Photobiological Sciences 4: 991-998

Ananyev GA, Sakiyan I, Diner BA, Dismukes GC (2002) A functional role for tyrosine-D in assembly of the inorganic core of the water oxidase complex of photosystem II and the kinetics of water oxidation. Biochemistry 41: 974-980

61

Anbar M, Pecht I (1967) Oxidation of water by cobaltic aquo ions. Journal of the American Chemical Society 89: 2553-2556

Antonyuk SV, Hough MA (2011) Monitoring and validating active site redox states in protein crystals. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 1814: 778-784

Aoyama C, Suzuki H, Sugiura M, Noguchi T (2008) Flash-induced FTIR difference spectroscopy shows no evidence for the structural coupling of bicarbonate to the oxygen-evolving Mn cluster in photosystem II. Biochemistry 47: 2760-2765

Aquila A, Hunter MS, Doak RB, Kirian RA, Fromme P, White TA, Andreasson J, Arnlund D, Bajt Sa, Barends TRM, Barthelmess M, Bogan MJ, Bostedt C, Bottin H, Bozek JD, Caleman C, Coppola N, Davidsson J, DePonte DP, Elser V, Epp SW, Erk B, Fleckenstein H, Foucar L, Frank M, Fromme R, Graafsma H, Grotjohann I, Gumprecht L, Hajdu J, Hampton CY, Hartmann A, Hartmann R, Hau-Riege S, Hauser G, Hirsemann H, Holl P, Holton JM, Hömke A, Johansson L, Kimmel N, Kassemeyer S, Krasniqi F, Kühnel K-U, Liang M, Lomb L, Malmerberg E, Marchesini S, Martin AV, Maia FRNC, Messerschmidt M, Nass K, Reich C, Neutze R, Rolles D, Rudek B, Rudenko A, Schlichting I, Schmidt C, Schmidt KE, Schulz J, Seibert MM, Shoeman RL, Sierra R, Soltau H, Starodub D, Stellato F, Stern S, Strüder L, Timneanu N, Ullrich J, Wang X, Williams GJ, Weidenspointner G, Weierstall U, Wunderer C, Barty A, Spence JCH, Chapman HN (2012) Time-resolved protein nanocrystallography using an X-ray free-electron laser. Optics Express 20: 2706-2716

Armaroli N, Balzani V (2010) Front Matter. In Energy for a sustainable world. Wiley-VCH Verlag GmbH & Co. KGaA, pp I-XXI

Armstrong FA (2008) Why did Nature choose manganese to make oxygen? Philosophical Transactions of the Royal Society B: Biological Sciences 363: 1263-1270

62

Artero V, Chavarot-KM, Fontecave M (2011) Splitting water with cobalt. Angewandte Chemie International Edition 50: 7238-7266

Awramik S (1992) The oldest records of photosynthesis. Photosynthesis Research 33: 75-89

Baranov SV, Ananyev GM, Klimov VV, Dismukes GC (2000) Bicarbonate accelerates assembly of the inorganic core of the water-oxidizing complex in manganese depleted photosystem II: a proposed biogeochemical role for atmospheric carbon dioxide in oxygenic photosynthesis. Biochemistry 39: 6060 -6065

Barber J (2004) Water, water everywhere, and its remarkable chemistry. Biochimica et Biophysica Acta 1655: 123-132

Barber J (2009) Photosynthetic energy conversion: natural and artificial. Chemical Society Reviews 38: 185-196

Barber J, Tran PD (2013) From natural to artificial photosynthesis. Journal of The Royal Society Interface 10

Barty A, Caleman C, Aquila A, Timneanu N, Lomb L, White TA, Andreasson J, Arnlund D, Bajt S, Barends TRM, Barthelmess M, Bogan MJ, Bostedt C, Bozek JD, Coffee R, Coppola N, Davidsson J, DePonte DP, Doak RB, Ekeberg T, Elser V, Epp SW, Erk B, Fleckenstein H, Foucar L, Fromme P, Graafsma H, Gumprecht L, Hajdu J, Hampton CY, Hartmann R, Hartmann A, Hauser G, Hirsemann H, Holl P, Hunter MS, Johansson L, Kassemeyer S, Kimmel N, Kirian RA, Liang M, Maia FRNC, Malmerberg E, Marchesini S, Martin AV, Nass K, Neutze R, Reich C, Rolles D, Rudek B, Rudenko A, Scott H, Schlichting I, Schulz J, Seibert MM, Shoeman RL, Sierra RG, Soltau H, Spence JCH, Stellato F, Stern S, Struder L, Ullrich J, WangX, Weidenspointner G, Weierstall U, Wunderer CB, Chapman HN (2012) Self-terminating diffraction gates femtosecond X-ray nanocrystallography measurements. Nat Photon 6: 35-40

63

Bassham JA, Benson AA, Calvin M (1950) The path of carbon in photosynthesis: VIII. The role of malic acid. Journal of Biological Chemistry 185: 781-787

Baxendale JH, Wells CF (1957) The reactions of Co(III) with water and with hydrogen peroxide. Transactions of the Faraday Society 53: 800-812

Bay JC (1931) Jean Senebier. Plant Physiol. 6: 188-193

Beckmann K, Messinger J, Badger MR, Wydrzynski T, Hillier W (2009) On-line mass spectrometry: membrane inlet sampling. Photosynthesis Research 102: 511-522

Bekker A, Holland HD, Wang PL, Rumble D, Stein HJ, Hannah JL, Coetzee LL, Beukes NJ (2004) Dating the rise of atmospheric oxygen. Nature 427: 117-120

Ben-Shem A, Frolow F, Nelson N (2003) Crystal structure of plant photosystem I. Nature 426: 630-635

Berends H-M, Homburg T, Kunz I, Kurz P (2011) K10 montmorillonite supported manganese catalysts for the oxidation of water to dioxygen. Applied Clay Science 53: 174-180

Berends H-M, Manke A-M, Nather C, Tuczek F, Kurz P (2012) A manganese oxido complex bearing facially coordinating trispyridyl ligands - is coordination geometry crucial for water oxidation catalysis? Dalton Transactions 41: 6215-6224

Bernat G, Rögner M (2011) Center of the cyanobacteria electron transport network: The cytochrome b6f complex. In GA Peschek, C Obinger, G Renger, eds, Bioenergetic Processes of Cyanobacteria: From Evolutionary Singularity to Ecological Diversity. Springer, Dordrecht, pp 573-606

Berry EA, Guergova-Kuras M, Huang L-S, Crofts AR (2000) Structure and function of cytochrome bc complexes. Annual Review of Biochemistry 69: 1005-1075

64

Berthold DA, Babcock GT, Yocum CF (1981) A highly resolved, oxygen-evolving photosystem II preparation from spinach thylakoid membranes. FEBS Letters 134: 231-234

Berthomieu C, Hienerwadel R (2009) Fourier transform infrared (FTIR) spectroscopy. Photosynthesis Research 101: 157-170

Blankenship RE, Tiede DM, Barber J, Brudvig GW, Fleming G, Ghirardi M, Gunner MR, Junge W, Kramer DM, Melis A, Moore TA, Moser CC, Nocera DG, Nozik AJ, Ort DR, Parson WW, Prince RC, Sayre RT (2011) Comparing Photosynthetic and Photovoltaic Efficiencies and Recognizing the Potential for Improvement. Science 332: 805-809

Boutet S, Lomb L, Williams GJ, Barends TRM, Aquila A, Doak RB, Weierstall U, DePonte DP, Steinbrener J, Shoeman RL, Messerschmidt M, Barty A, White TA, Kassemeyer S, Kirian RA, Seibert MM, Montanez PA, Kenney C, Herbst R, Hart P, Pines J, Haller G, Gruner SM, Philipp HT, Tate MW, Hromalik M, Koerner LJ, van Bakel N, Morse J, Ghonsalves W, Arnlund D, Bogan MJ, Caleman C, Fromme R, Hampton CY, Hunter MS, Johansson LC, Katona G, Kupitz C, Liang M, Martin AV, Nass K, Redecke L, Stellato F, Timneanu N, Wang D, Zatsepin NA, Schafer D, Defever J, Neutze R, Fromme P, Spence JCH, Chapman HN, Schlichting I (2012) High-resolution protein structure determination by serial femtosecond crystallography. Science 337: 362-364

Bricker T, Frankel L (2002) The structure and function of CP47 and CP43 in Photosystem II. Photosynthesis Research 72: 131-146

Brimblecombe R, Swiegers GF, Dismukes GC, Spiccia L (2008) Sustained water oxidation photocatalysis by a bioinspired manganese cluster. Angewandte Chemie International Edition 47: 7335-7338

Brudvig GW (2008) Water oxidation chemistry of photosystem II. Philosophical Transactions of the Royal Society B: Biological Sciences 363: 1211-1219

65

Cady CW, Crabtree RH, Brudvig GW (2008) Functional models for the oxygen-evolving complex of photosystem II. Coordination Chemistry Reviews 252: 444-455

Caleman C, Huldt G, Maia FRNC, Ortiz C, Parak FG, Hajdu J, van der Spoel D, Chapman HN, Timneanu N (2010) On the feasibility of nanocrystal imaging using intense and ultrashort X-ray pulses. ACS Nano 5: 139-146

Chapman HN, Fromme P, Barty A, White TA, Kirian RA, Aquila A, Hunter MS, Schulz J, DePonte DP, Weierstall U, Doak RB, Maia FRNC, Martin AV, Schlichting I, Lomb L, Coppola N, Shoeman RL, Epp SW, Hartmann R, Rolles D, Rudenko A, Foucar L, Kimmel N, Weidenspointner G, Holl P, Liang M, Barthelmess M, Caleman C, Boutet S, Bogan MJ, Krzywinski J, Bostedt C, Bajt S, Gumprecht L, Rudek B, Erk B, Schmidt C, Homke A, Reich C, Pietschner D, Struder L, Hauser G, Gorke H, Ullrich J, Herrmann S, Schaller G, Schopper F, Soltau H, Kuhnel K-U, Messerschmidt M, Bozek JD, Hau-Riege SP, Frank M, Hampton CY, Sierra RG, Starodub D, Williams GJ, Hajdu J, Timneanu N, Seibert MM, Andreasson J, Rocker A, Jonsson O, Svenda M, Stern S, Nass K, Andritschke R, Schroter C-D, Krasniqi F, Bott M, Schmidt KE, Wang X, Grotjohann I, Holton JM, Barends TRM, Neutze R, Marchesini S, Fromme R, Schorb S, Rupp D, Adolph M, Gorkhover T, Andersson I, Hirsemann H, Potdevin G, Graafsma H, Nilsson B, Spence JCH (2011) Femtosecond X-ray protein nanocrystallography. Nature 470: 73-77

Christen G, Renger G (1999) The role of hydrogen bonds for the multiphasic P680+· reduction by YZ in photosystem II with intact oxygen evolution capacity. Analysis of kinetic H/D isotope exchange effects. Biochemistry 38: 2068-2077

Christen G, Seeliger A, Renger G (1999) P680+· reduction kinetics and redox transition probability of the water oxidizing complex as a function of pH and H/D isotope exchange in spinach thylakoids. Biochemistry 38: 6082-6092

66

Chua NH, Gillham NW (1977) The sites of synthesis of the principal thylakoid membrane polypeptides in Chlamydomonas reinhardtii. The Journal of Cell Biology 74: 441-452

Ciamician G (1912) The photochemistry of the future. Science 36: 385-394

Clark LC, Wolf R, Granger D, Taylor Z (1953) Continuous recording of blood oxygen tensions by polarography. Journal of Applied Physiology 6: 189-193

Clausen J, Junge W (2004) Detection of an intermediate of photosynthetic water oxidation. Nature 430: 480-483

Clausen J, Junge W (2008) The terminal reaction cascade of water oxidation: Proton and oxygen release. Biochimica et Biophysica Acta-Bioenergetics 1777: 1311-1318

Coleman JR (2004) Carbonic anhydrase and its role in photosynthesis. In RC Leegood, TD Sharkey, S von Caemmerer, eds, Photosynthesis: Physiology and Methabolism, Vol 9. Kluwer Academic Publishers, Dordrecht, pp 353-367

Collins AM, Wen J, Blankenship RE (2012) Photosynthetic light-harvesting complexes. In T Wydrzynski, W Hillier, eds, Molecular Solar Fuels. RSC Publishing, Cambridge, pp 85-106

Collomb M-N, Deronzier A (2009) Electro- and photoinduced formation and transformation of oxido-bridged multinuclear Mn complexes. European Journal of Inorganic Chemistry 2009: 2025-2046

Concepcion JJ, Jurss JW, Templeton JL, Meyer TJ (2008) Mediator-assisted water oxidation by the ruthenium “blue dimer” cis,cis-[(bpy)2(H2O)RuORu(OH2)(bpy)2]4+. Proceedings of the National Academy of Sciences 105: 17632-17635

Concepcion JJ, Tsai M-K, Muckerman JT, Meyer TJ (2010) Mechanism of water oxidation by single-site ruthenium complex catalysts. Journal of the American Chemical Society 132: 1545-1557

67

Cook SA, Borovik AS (2013) Inorganic chemistry: Deconstructing water oxidation. Nat Chem 5: 259-260

Corbett MC, Latimer MJ, Poulos TL, Sevrioukova IF, Hodgson KO, Hedman B (2007) Photoreduction of the active site of the metalloprotein putidaredoxin by synchrotron radiation. Acta Crystallographica Section D 63: 951-960

Cox N, Messinger J (2013) Reflections on substrate water and dioxygen formation. Biochimica et Biophysica Acta: in press

Cox N, Rapatskiy L, Su J-H, Pantazis DA, Sugiura M, Kulik L, Dorlet P, Rutherford AW, Neese F, Boussac A, Lubitz W, Messinger J (2011) Effect of Ca2+/Sr2+ substitution on the electronic structure of the oxygen-evolving complex of photosystem II: A combined multifrequency EPR, 55Mn-ENDOR, and DFT study of the S2 state. Journal of the American Chemical Society 133: 3635-3648

Cramer WA, Hasan SS, Yamashita E (2011) The Q cycle of cytochrome bc complexes: A structure perspective. Biochimica et Biophysica Acta - Bioenergetics 1807: 788-802

Current Data for Atmospheric CO2. In, http://co2now.org/

da Silva LA, Alves VA, da Silva MAP, Trasatti S, Boodts JFC (1997) Oxygen evolution in acid solution on IrO2 + TiO2 ceramic films. A study by impedance, voltammetry and SEM. Electrochimica Acta 42: 271-281

Dau H, Haumann M (2008) The manganese complex of photosystem II in its reaction cycle - Basic framework and possible realization at the atomic level. Coordination Chemistry Reviews 252: 273-295

Dau H, Limberg C, Reier T, Risch M, Roggan S, Strasser P (2010) The mechanism of water oxidation: from electrolysis via homogeneous to biological catalysis. ChemCatChem 2: 724-761

68

Dau H, Zaharieva I (2009) Principles, efficiency, and blueprint character of solar-energy conversion in photosynthetic water oxidation. Accounts of Chemical Research 42: 1861-1870

Dau H, Zaharieva I, Haumann M (2012) Recent developments in research on water oxidation by photosystem II. Current Opinion in Chemical Biology 16: 3-10

Daughtry KD, Xiao Y, Stoner-Ma D, Cho E, Orville AM, Liu P, Allen KN (2012) Quaternary ammonium oxidative demethylation: X-ray crystallographic, resonance raman, and UV–visible spectroscopic analysis of a rieske-type demethylase. Journal of the American Chemical Society 134: 2823-2834

de Leitenburg C, Trovarelli A, Llorca J, Cavani F, Bini G (1996) The effect of doping CeO2 with zirconium in the oxidation of isobutane. Applied Catalysis A: General 139: 161-173

Debus R (2005) The catalytic manganese cluster: protein ligation. In T Wydrzynski, K Satoh, eds, Photosystem II. The Light Driven Water:Plastiquinone Oxidoreductase, Vol 22. Springer, Dordrecht, pp 261-284

Debus RJ (1992) The manganese and calcium ions of photosynthetic oxygen evolution. Biochimica et Biophysica Acta 1102: 269-352

Debus RJ (2001) Amino acid residues that modulate the properties of tyrosine YZ and the manganese cluster in the water oxidizing complex of photosystem II. Biochimica et Biophysica Acta 1503: 164-186

Debus RJ (2008) Protein ligation of the photosynthetic oxygen-evolving center. Coordination Chemistry Reviews 252: 244-258

Debus RJ, Barry BA, Sithole I, Babcock GT, Mcintosh L (1988) Directed mutagenesis indicates that the donor to P680+ in photosystem II is tyrosine-161 of the D1 polypeptide. Biochemistry 27: 9071-9074

69

Delrieu MJ (1974) Simple explanation of the misses in the cooperation of charges in photosynthetic O2 evolution. Photochemistry and Photobiology 20: 441-454

Dempster AJ (1918) A new method of positive ray analysis. Physical Review 11: 316-325

Deng Z, Tseng H-W, Zong R, Wang D, Thummel R (2008) Preparation and study of a family of dinuclear Ru(II) complexes that catalyze the decomposition of water. Inorganic Chemistry 47: 1835-1848

Diner BA (1977) Dependence of deactivation reactions of photosystem II on redox state of plastoquinone pool A varied under anaerobic conditions. Equilibria on the acceptor side of photosystem II. Biochimica et Biophysica Acta 460: 247-258

Diner BA, Petrouleas V, Wendoloski JJ (1991) The iron-quinone electron-acceptor complex of photosystem II. Physiologia Plantarum 81: 423-436

Dismukes GC, Klimov VV, Baranov SV, Kozlov YN, DasGupta J, Tyryshkin A (2001) The origin of atmospheric oxygen on Earth: The innovation of oxygenic photosynthesis. Proceedings of the National Academy of Sciences of the United States of America 98: 2170-2175

Du P, Kokhan O, Chapman KW, Chupas PJ, Tiede DM (2012) Elucidating the domain structure of the cobalt oxide water splitting catalyst by X-ray pair distribution function analysis. Journal of the American Chemical Society 134: 11096-11099

Duan L, Araujo CM, Ahlquist MSG, Sun L (2012) Highly efficient and robust molecular ruthenium catalysts for water oxidation. Proceedings of the National Academy of Sciences 109: 15584-15588

Duan L, Bozoglian F, Mandal S, Stewart B, Privalov T, Llobet A, Sun L (2012) A molecular ruthenium catalyst with water-oxidation activity comparable to that of photosystem II. Nat Chem 4: 418-423

70

Duan L, Fischer A, Xu Y, Sun L (2009) Isolated seven-coordinate Ru(IV) dimer complex with [HOHOH]− bridging ligand as an intermediate for catalytic water oxidation. Journal of the American Chemical Society 131: 10397-10399

Eaton-Rye J, Putnam-Evans C (2005) The CP47 and CP43 core antenna components. In T Wydrzynski, K Satoh, J Freeman, eds, Photosystem II, Vol 22. Springer Netherlands, pp 45-70

El Wakkad SES, Hickling A (1950) The anodic behaviour of metals. Part VI.-Cobalt. Transactions of the Faraday Society 46: 820-824

Elizarova GL, Matvienko LG, Lozhkina NV, Parmon VN, Zamaraev KI (1981) Homogeneous catalysts for dioxygen evolution from water. Water oxidation by trisbipyridylruthenium(III) in the presence of cobalt, iron and copper complexes. Reaction Kinetics and Catalysis Letters 16: 191-194

Esswein AJ, Surendranath Y, Reece SY, Nocera DG (2011) Highly active cobalt phosphate and borate based oxygen evolving catalysts operating in neutral and natural waters. Energy & Environmental Science 4: 499-504

Faller P, Debus RJ, Brettel K, Sugiura M, Rutherford AW, Boussac A (2001) Rapid formation of the stable tyrosyl radical in photosystem II. Proceedings of the National Academy of Sciences of the United States of America 98: 14368-14373

Ferreira KN, Iverson TM, Maghlaoui K, Barber J, Iwata S (2004) Architecture of the photosynthetic oxygen-evolving center. Science 303: 1831-1838

Forbush B, Kok B, McGloin MP (1971) Cooperation of charges in photosynthetic oxygen evolution. II. Damping of flash yield oscillation, deactivation. Photochemistry and Photobiology 14: 307-321

Fromme P (1996) Structure and function of photosystem I. Current Opinion in Structural Biology 6: 473-484

71

Gaudefroy C, Jouravsky G, Permingeat F (1963) La marokite, CaMn2O4 une nouvelle éspèce minérale. Bull. Soc. Fr. Miner. Crist.: 359-367

Geletii YV, Botar B, Kögerler P, Hillesheim DA, Musaev DG, Hill CL (2008) An all-inorganic, stable, and highly active tetraruthenium homogeneous catalyst for water oxidation. Angewandte Chemie International Edition 47: 3896-3899

Gersten SW, Samuels GJ, Meyer TJ (1982) Catalytic oxidation of water by an oxo-bridged ruthenium dimer. Journal of the American Chemical Society 104: 4029-4030

Gilbert JA, Eggleston DS, Murphy WR, Geselowitz DA, Gersten SW, Hodgson DJ, Meyer TJ (1985) Structure and redox properties of the water-oxidation catalyst [(Bpy)2(Oh2)Ruoru(Oh2)(Bpy)2]4+. Journal of the American Chemical Society 107: 3855-3864

Glöckner C, Kern J, Broser M, Zouni A, Yachandra V, Yano J (2013) Structural changes of the oxygen evolving complex in photosystem II during the catalytic cycle. J. Biol. Chem. 288: 22607-22620

Govindjee, Kern J, Messinger J, Whitmarsh J (2010) Photosystem II. In Encyclopedia of Life Sciences (ELS). John Wiley & Sons, Ltd., Chichester

Govindjee, Van Rensen JJS (1993) Photosystem II reaction centers and bicarbonate. In J Deisenhofer, JR Norris, eds, Photosynthetic Reaction Centers, Vol 1. Academic Press, Orlando, pp 357-389

Govindjee, Xu C, van Rensen JJS (1997) On the requirement of bound bicarbonate for photosystem II activity. Zeitschrift Fur Naturforschung 52: 24-32

Grabolle M, Haumann M, Müller C, Liebisch P, Dau H (2006) Rapid loss of structural motifs in the manganese complex of oxygenic photosynthesis by x-ray irradiation at 10-300 K. J. Biol. Chem. 281: 4580-4588

72

Grabolle M, Haumann M, Müller C, Liebisch P, Dau H (2006) Rapid loss of structural motifs in the manganese complex of oxygenic photosynthesis by x-ray irradiation at 10-300 K. Journal of Biological Chemistry 281: 4580-4588

Guskov A, Gabdulkhakov A, Broser M, Glöckner C, Hellmich J, Kern J, Frank M, Saenger W, Zouni A (2010) Recent progress in the crystallographic studies of photosystem II. ChemPhysChem 11: 1160-1171

Guskov A, Kern J, Gabdulkhakov A, Broser M, Zouni A, Saenger W (2009) Cyanobacterial photosystem II at 2.9-Angstrom resolution and the role of quinones, lipids, channels and chloride. Nature Structural & Molecular Biology 16: 334-342

Haber F, Weiss J (1934) The catalytic decomposition of hydrogen peroxide by iron salts. Proceedings of the Royal Society of London. Series A - Mathematical and Physical Sciences 147: 332-351

Hagfeldt A, Boschloo G, Sun L, Kloo L, Pettersson H (2010) Dye-sensitized solar cells. Chemical Reviews 110: 6595-6663

Han GY, Mamedov F, Styring S (2012) Misses during water oxidation in photosystem II are S state-dependent. Journal of Biological Chemistry 287: 13422-13429

Harriman A, Pickering IJ, Thomas JM, Christensen PA (1988) Metal oxides as heterogeneous catalysts for oxygen evolution under photochemical conditions. Journal of the Chemical Society, Faraday Transactions 1: Physical Chemistry in Condensed Phases 84: 2795-2806

Harriman A, Porter G, Walters P (1981) Photo-oxidation of water to oxygen sensitised by tris(2,2[prime or minute]-bipyridyl)ruthenium(II). Journal of the Chemical Society, Faraday Transactions 2: Molecular and Chemical Physics 77: 2373-2383

Haumann M, Grundmeier A, Zaharieva I, Dau H (2008) Photosynthetic water oxidation at elevated dioxygen partial

73

pressure monitored by time-resolved X-ray absorption measurements. Proceedings of the National Academy of Sciences of the United States of America 105: 17384-17389

Haumann M, Liebisch P, Müller C, Barra M, Grabolle M, Dau H (2005) Photosynthetic O2 formation tracked by time-resolved X-ray experiments. Science 310: 1019-1021

Hayes SA, Yu P, O’Keefe TJ, O’Keefe MJ, Stoffer JO (2002) The phase stability of cerium species in aqueous systems: I. E-pH diagram for the Ce HClO4 H2O system. Journal of The Electrochemical Society 149: C623-C630

Hendry G, Wydrzynski T (2002) The Two Substrate−Water Molecules Are Already Bound to the Oxygen-Evolving Complex in the S2 State of Photosystem II. Biochemistry 41: 13328-13334

Hendry G, Wydrzynski T (2003) 18O Isotope Exchange Measurements Reveal that Calcium Is Involved in the Binding of One Substrate-Water Molecule to the Oxygen-Evolving Complex in Photosystem II. Biochemistry 42: 6209-6217

Henry RP (1996) Multiple roles of carbonic anhydrase in cellular transport and metabolism. Annual Review of Physiology 58: 523-538

Hersleth H-P, Andersson KK (2011) How different oxidation states of crystalline myoglobin are influenced by X-rays. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 1814: 785-796

Hervás M, Navarro JA, De la Rosa MA (2003) Electron transfer between membrane complexes and soluble proteins in photosynthesis. Accounts of Chemical Research 36: 798-805

Hienerwadel R, Berthomieu C (1995) Bicarbonate binding to the non-heme iron of photosystem II investigated by Fourier transform infrared difference spectroscopy and 13C-labeled bicarbonate. Biochemistry 34: 16288-16297

Hillier W, McConnell I, Badger MR, Boussac A, Klimov VV, Dismukes GC, Wydrzynski T (2006) Quantitative assessment

74

of intrinsic carbonic anhydrase activity and the capacity for bicarbonate oxidation in photosystem II. Biochemistry 45: 2094-2102

Hillier W, Messinger J, Wydrzynski T (1998) Kinetic determination of the fast exchanging substrate water molecule in the S3 state of photosystem II. Biochemistry 37: 16908-16914

Hillier W, Wydrzynski T (2000) The Affinities for the Two Substrate Water Binding Sites in the O2 Evolving Complex of Photosystem II Vary Independently during S-State Turnover. Biochemistry 39: 4399-4405

Hoch G, Kok B (1963) A mass spectrometer inlet system for sampling gases dissolved in liquid phases. Archives of Biochemistry and Biophysics 101: 160-170

Hocking RK, Brimblecombe R, Chang L-Y, Singh A, Cheah MH, Glover C, Casey WH, Spiccia L (2011) Water-oxidation catalysis by manganese in a geochemical-like cycle. Nat Chem 3: 461-466

Hoffert MI, Caldeira K, Benford G, Criswell DR, Green C, Herzog H, Jain AK, Kheshgi HS, Lackner KS, Lewis JS, Lightfoot HD, Manheimer W, Mankins JC, Mauel ME, Perkins LJ, Schlesinger ME, Volk T, Wigley TML (2002) Advanced technology paths to global climate stability: Energy for a greenhouse planet. Science 298: 981-987

Hoffert MI, Caldeira K, Jain AK, Haites EF, Harvey LDD, Potter SD, Schlesinger ME, Schneider SH, Watts RG, Wigley TML, Wuebbles DJ (1998) Energy implications of future stabilization of atmospheric CO2 content. Nature 395: 881-884

Hu XL, Piccinin S, Laio A, Fabris S (2012) Atomistic structure of cobalt-phosphate nanoparticles for catalytic water oxidation. ACS Nano 6: 10497-10504

Huang P, Hogblom J, Anderlund MF, Sun LC, Magnuson A, Styring S (2004) Light-induced multistep oxidation of dinuclear

75

manganese complexes for artificial photosynthesis. Journal of Inorganic Biochemistry 98: 733-745

Huang P, Magnuson A, Lomoth R, Abrahamsson M, Tamm M, Sun L, van Rotterdam B, Park J, Hammarstrom L, Akermark B, Styring S (2002) Photo-induced oxidation of a dinuclear Mn2(II,II) complex to the Mn2(III,IV) state by inter- and intramolecular electron transfer to RuIII tris-bipyridine. Journal of Inorganic Biochemistry 91: 159-172

Hunter MS, DePonte DP, Shapiro DA, Kirian RA, Wang X, Starodub D, Marchesini S, Weierstall U, Doak RB, Spence JCH, Fromme P (2011) X-ray dffraction from membrane protein nanocrystals. Biophysical journal 100: 198-206

Isgandarova S, Renger G, Messinger J (2003) Functional differences of photosystem II from Synechococcus elongatus and spinach characterized by flash-induced oxygen evolution patterns. Biochemistry 42: 8929-8938

Jiao F, Frei H (2010) Nanostructured cobalt and manganese oxide clusters as efficient water oxidation catalysts. Energy & Environmental Science 3: 1018-1027

Johansson LC, Arnlund D, White TA, Katona G, DePonte DP, Weierstall U, Doak RB, Shoeman RL, Lomb L, Malmerberg E, Davidsson J, Nass K, Liang M, Andreasson J, Aquila A, Bajt S, Barthelmess M, Barty A, Bogan MJ, Bostedt C, Bozek JD, Caleman C, Coffee R, Coppola N, Ekeberg T, Epp SW, Erk B, Fleckenstein H, Foucar L, Graafsma H, Gumprecht L, Hajdu J, Hampton CY, Hartmann R, Hartmann A, Hauser G, Hirsemann H, Holl P, Hunter MS, Kassemeyer S, Kimmel N, Kirian RA, Maia FRNC, Marchesini S, Martin AV, Reich C, Rolles D, Rudek B, Rudenko A, Schlichting I, Schulz J, Seibert MM, Sierra RG, Soltau H, Starodub D, Stellato F, Stern S, Struder L, Timneanu N, Ullrich J, Wahlgren WY, Wang X, Weidenspointner G, Wunderer C, Fromme P, Chapman HN, Spence JCH, Neutze R (2012)

76

Lipidic phase membrane protein serial femtosecond crystallography. Nat Meth 9: 263-265

Joliot P (1972) Modulated light source use with the oxygen electrode. In A San Pietro, ed, Photosynthesis and Nitrogen Fixation, Vol 24 B. Academic Press, New York, pp 123-134

Joliot P, Barbieri G, Chabaud R (1969) Un nouveau modele des centres photochimiques du systeme II. Photochemistry and Photobiology 10: 309-329

Joliot P, Joliot A (1968) A polarographic method for detection of oxygen production and reduction of Hill reagent by isolated chloroplasts. Biochimica et Biophysica Acta 153: 625-&

Junge W, Nelson N (2005) Nature's rotary electromotors. Science 308: 642-644

Junge W, Sielaff H, Engelbrecht S (2009) Torque generation and elastic power transmission in the rotary FOF1-ATPase. Nature 459: 364-370

Jursinic P (1981) Investigation of double turnovers in photosystem II charge separation and oxygen evolution with excitation flashes of different duration. Biochimica et Biophysica Acta 635: 38 - 52

Jursinic P, Govindjee (1977) Temperature dependence of delayed light emission in the 6 to 340 microsecond range after a single flash in chloroplasts. Photochemistry and Photobiology 26: 617-628

Kamiya N, Shen J-R (2003) Crystal structure of oxygen-evolving photosystem II from Thermosynechococcus vulcanus at 3.7 Å resolution. Proceedings of the National Academy of Sciences of the United States of America 100: 98-103

Kanan MW, Nocera DG (2008) In situ formation of an oxygen-evolving catalyst in neutral water containing phosphate and Co2+. Science 321: 1072-1075

77

Kanan MW, Yano J, Surendranath Y, Dincă M, Yachandra VK, Nocera DG (2010) Structure and valency of a cobalt−phosphate water oxidation catalyst determined by in situ X-ray spectroscopy. Journal of the American Chemical Society 132: 13692-13701

Kargul J, Barber J (2012) Structure and function of photosynthetic reaction centres. In T Wydrzynski, W Hillier, eds, Molecular Solar Fuels. RSC Publishing, Cambridge, pp 107-142

Karlsson EA, Lee B-L, Åkermark T, Johnston EV, Kärkäs MD, Sun J, Hansson Ö, Bäckvall J-E, Åkermark B (2011) Photosensitized water oxidation by use of a bioinspired manganese catalyst. Angewandte Chemie International Edition 50: 11715-11718

Karlsson J, Hiltonen T, Husic HD, Ramazanov Z, Samuelsson G (1995) Intracellular carbonic anhydrase of chlamydomonas reinhardtii. Plant Physiology 109: 533-539

Kawakami K, Umena Y, Kamiya N, Shen J-R (2009) Location of chloride and its possible functions in oxygen-evolving photosystem II revealed by X-ray crystallography. Proceedings of the National Academy of Sciences 106: 8567-8572

Kern J, Alonso-Mori R, Hellmich J, Tran R, Hattne J, Laksmono H, Glöckner C, Echols N, Sierra RG, Sellberg J, Lassalle-Kaiser B, Gildea RJ, Glatzel P, Grosse-Kunstleve RW, Latimer MJ, McQueen TA, DiFiore D, Fry AR, Messerschmidt M, Miahnahri A, Schafer DW, Seibert MM, Sokaras D, Weng T-C, Zwart PH, White WE, Adams PD, Bogan MJ, Boutet S, Williams GJ, Messinger J, Sauter NK, Zouni A, Bergmann U, Yano J, Yachandra VK (2012) Room temperature femtosecond X-ray diffraction of photosystem II microcrystals. Proceedings of the National Academy of Sciences 109: 9721-9726

Kern J, Alonso-Mori R, Tran R, Hattne J, Gildea RJ, Echols N, Glöckner C, Hellmich J, Laksmono H, Sierra RG, Lassalle-Kaiser B, Koroidov S, Lampe A, Han G, Gul S, DiFiore D, Milathianaki D, Fry AR, Miahnahri A,

78

Schafer DW, Messerschmidt M, Seibert MM, Koglin JE, Sokaras D, Weng T-C, Sellberg J, Latimer MJ, Grosse-Kunstleve RW, Zwart PH, White WE, Glatzel P, Adams PD, Bogan MJ, Williams GJ, Boutet S, Messinger J, Zouni A, Sauter NK, Yachandra VK, Bergmann U, Yano J (2013) Simultaneous femtosecond X-ray spectroscopy and diffraction of photosystem II at room temperature. Science 340: 491-495

Kern J, Loll B, Lüneberg C, DiFiore D, Biesiadka J, Irrgang KD, Zouni A (2005) Purification, characterisation and crystallisation of photosystem II from Thermosynechococcus elongatus cultivated in a new type of photobioreactor. Biochimica et Biophysica Acta (BBA) - Bioenergetics 1706: 147-157

Kirch M, Lehn JM, Sauvage JP (1979) Hydrogen generation by visible-light irradiation of aqueous-solutions of metal-complexes - Approach to the photo-chemical conversion and storage of solar-energy. Helvetica Chimica Acta 62: 1345-1384

Kirian RA, White TA, Holton JM, Chapman HN, Fromme P, Barty A, Lomb L, Aquila A, Maia FRNC, Martin AV, Fromme R, Wang X, Hunter MS, Schmidt KE, Spence JCH (2011) Structure-factor analysis of femtosecond microdiffraction patterns from protein nanocrystals. Acta Crystallographica Section A 67: 131-140

Klauss A, Haumann M, Dau H (2012) Alternating electron and proton transfer steps in photosynthetic water oxidation. Proceedings of the National Academy of Sciences of the United States of America

Klevanik AV, Klimov VV, Shuvalov VA, Krasnovskii AA (1977) Reduction of pheophytin in light reaction of Photosystem II of higher plants. Doklady Akademii Nauk SSSR 236: 241-244

Klimov VV, Allakhverdiev SI, Baranov SV, Feyziev YM (1995) Effects of bicarbonate and formate on the donor side of photosystem 2. Photosynthesis Research 46: 219-225

79

Klimov VV, Allakhverdiev SI, Feyziev YM, Baranov SV (1995) Bicarbonate requirement for the donor side of photosystem II. FEBS Letters 363: 251-255

Klimov VV, Allakverdiev SI, Demeter S, Krasnovsky AA (1979) Photoreduction of pheophytin in photosystem II of chloroplasts as a function of redox potential of the medium. Doklady Akademii Nauk SSSR 249: 227-230

Klimov VV, Klevanik AV, Shuvalov VA, Krasnovsky AA (1977) Reduction of pheophytin in primary light reaction of Photosystem 2. FEBS Letters 82: 183-186

Kok B, Forbush B, McGloin M (1970) Cooperation of charges in photosynthetic O2 evolution. Photochemistry and Photobiology 11: 457-476

Konermann L, Messinger J, Hillier W (2008) Mass spectrometry based methods for studying kinetics and dynamics in biological systems. In J Amesz, AJ Hoff, eds, Biophysical Techniques in Photosynthesis, Vol 26. Springer, Dordrecht, pp 167-190

Koopmann R, Cupelli K, Redecke L, Nass K, DePonte DP, White TA, Stellato F, Rehders D, Liang M, Andreasson J, Aquila A, Bajt S, Barthelmess M, Barty A, Bogan MJ, Bostedt C, Boutet S, Bozek JD, Caleman C, Coppola N, Davidsson J, Doak RB, Ekeberg T, Epp SW, Erk B, Fleckenstein H, Foucar L, Graafsma H, Gumprecht L, Hajdu J, Hampton CY, Hartmann A, Hartmann R, Hauser G, Hirsemann H, Holl P, Hunter MS, Kassemeyer S, Kirian RA, Lomb L, Maia FRNC, Kimmel N, Martin AV, Messerschmidt M, Reich C, Rolles D, Rudek B, Rudenko A, Schlichting I, Schulz J, Seibert MM, Shoeman RL, Sierra RG, Soltau H, Stern S, Struder L, Timneanu N, Ullrich J, Wang X, Weidenspointner G, Weierstall U, Williams GJ, Wunderer CB, Fromme P, Spence JCH, Stehle T, Chapman HN, Betzel C, Duszenko M (2012) In vivo protein crystallization opens new routes in structural biology. Nat Meth 9: 259-262

80

Kraatz H-B, Metzler-Nolte N (2006) Concepts and models in bioinorganic chemistry. Wiley

Kremer ML, Stein G (1959) The catalytic decomposition of hydrogen peroxide by ferric perchlorate. Transactions of the Faraday Society 55: 959-973

Krishnamurthy VM, Kaufman GK, Urbach AR, Gitlin I, Gudiksen KL, Weibel DB, Whitesides GM (2008) Carbonic anhydrase as a model for biophysical and physical-organic studies of proteins and protein-ligand binding. Chemical Reviews 108: 946-1051

Kudo A (2011) Z-scheme photocatalyst systems for water splitting under visible light irradiation. MRS Bulletin 36: 32-38

Kurz P, Anderlund MF, Shaikh N, Styring S, Huang P (2008) Redox reactions of a dinuclear manganese complex – the influence of water. European Journal of Inorganic Chemistry 2008: 762-770

Lassali TAF, De Castro SC, Boodts JFC (1998) Structural, morphological and surface properties as a function of composition of Ru+Ti+Pt mixed-oxide electrodes. Electrochimica Acta 43: 2515-2525

Lavorel J (1976) Matrix analysis of the oxygen evolving system of photosynthesis. Journal of Theoretical Biology 57: 171-185

Lee S-HA, Zhao Y, Hernandez-Pagan EA, Blasdel L, Youngblood WJ, Mallouk TE (2012) Electron transfer kinetics in water splitting dye-sensitized solar cells based on core-shell oxide electrodes. Faraday Discussions 155: 165-176

Lewis NS, Nocera DG (2006) Powering the planet: Chemical challenges in solar energy utilization. Proceedings of the National Academy of Sciences of the United States of America 103: 15729-15735

Li G, Sproviero EM, Snoeberger Iii RC, Iguchi N, Blakemore JD, Crabtree RH, Brudvig GW, Batista VS (2009)

81

Deposition of an oxomanganese water oxidation catalyst on TiO2 nanoparticles: computational modeling, assembly and characterization. Energy & Environmental Science 2: 230-238

Li L, Duan L, Wen F, Li C, Wang M, Hagfeldt A, Sun L (2012) Visible light driven hydrogen production from a photo-active cathode based on a molecular catalyst and organic dye-sensitized p-type nanostructured NiO. Chemical Communications 48: 988-990

Li X, Siegbahn PEM (2013) Water Oxidation Mechanism for Synthetic Co–Oxides with Small Nuclearity. Journal of the American Chemical Society 135: 13804-13813

Limburg J, Vrettos JS, Liable-Sands LM, Rheingold AL, Crabtree RH, Brudvig GW (1999) A functional model for O–O bond formation by the O2 evolving complex in photosystem II. Science 283: 524-527

Loll B, Kern J, Saenger W, Zouni A, Biesiadka J (2005) Towards complete cofactor arrangement in the 3.0 Å resolution structure of photosystem II. Nature 438: 1040-1044

Lomb L, Barends TRM, Kassemeyer S, Aquila A, Epp SW, Erk B, Foucar L, Hartmann R, Rudek B, Rolles D, Rudenko A, Shoeman RL, Andreasson J, Bajt S, Barthelmess M, Barty A, Bogan MJ, Bostedt C, Bozek JD, Caleman C, Coffee R, Coppola N, DePonte DP, Doak RB, Ekeberg T, Fleckenstein H, Fromme P, Gebhardt M, Graafsma H, Gumprecht L, Hampton CY, Hartmann A, Hauser G, Hirsemann H, Holl P, Holton JM, Hunter MS, Kabsch W, Kimmel N, Kirian RA, Liang M, Maia FRNC, Meinhart A, Marchesini S, Martin AV, Nass K, Reich C, Schulz J, Seibert MM, Sierra R, Soltau H, Spence JCH, Steinbrener J, Stellato F, Stern S, Timneanu N, Wang X, Weidenspointner G, Weierstall U, White TA, Wunderer C, Chapman HN, Ullrich J, Strüder L, Schlichting I (2011) Radiation damage in protein serial femtosecond crystallography using an x-ray free-electron laser. Physical Review B 84: 214111

82

Lubitz W (2006) EPR Studies of the Primary Electron Donor P700 in Photosystem I. In JH Golbeck, ed, Photosystem I. The Light-Driven Plastocyanin:Ferredoxin Oxidoreductase, Vol 24. Springer, Dordrecht, pp 245-269

Lubitz W, Reijerse EJ, Messinger J (2008) Solar water-splitting into H2 and O2: design principles of photosystem II and hydrogenases. Energy & Environmental Science 1: 15-31

Luthi D, Le Floch M, Bereiter B, Blunier T, Barnola J-M, Siegenthaler U, Raynaud D, Jouzel J, Fischer H, Kawamura K, Stocker TF (2008) High-resolution carbon dioxide concentration record 650,000-800,000 years before present. Nature 453: 379-382

Lutterman D, Surendranath Y, Nocera D (2009) A self-healing oxygen-evolving catalyst. Journal of the American Chemical Society 131: 3838-3839

Maeda K, Domen K (2010) Photocatalytic water splitting: recent progress and future challenges. The Journal of Physical Chemistry Letters 1: 2655-2661

Maeda K, Domen K (2011) Oxynitride materials for solar water splitting. MRS Bulletin 36: 25-31

Maeda K, Xiong A, Yoshinaga T, Ikeda T, Sakamoto N, Hisatomi T, Takashima M, Lu D, Kanehara M, Setoyama T, Teranishi T, Domen K (2010) Photocatalytic overall water splitting promoted by two different cocatalysts for hydrogen and oxygen evolution under visible light. Angewandte Chemie International Edition 49: 4096-4099

Mattioli G, Giannozzi P, Amore BA, Guidoni L (2013) Reaction pathways for oxygen evolution promoted by cobalt catalyst. Journal of the American Chemical Society 135: 15353-15363

McAlpin J, Surendranath Y, Dincǎ M, Stich T, Stoian S, Casey W, Nocera D, Britt RD (2010) EPR evidence for Co(IV) species produced during water oxidation at neutral pH. Journal of the American Chemical Society 132: 6882-6883

83

McAlpin JG, Stich TA, Ohlin CA, Surendranath Y, Nocera DG, Casey WH, Britt RD (2011) Electronic structure description of a [Co(III)3Co(IV)O4] cluster: A model for the paramagnetic intermediate in cobalt-catalyzed water oxidation. Journal of the American Chemical Society 133: 15444-15452

McCarty RE, Evron Y, Johnson EA (2000) The chloroplast ATP synthase: A rotary enzyme? Annual Review of Plant Physiology and Plant Molecular Biology 51: 83-109

McConnell IL, Eaton-Rye JJ, Van Rensen JJS (2012) Regulation of photosystem II electron transport by bicarbonate. In JJ Eaton-Rye, BC Tripathy, TD Sharkey, eds, Photosynthesis: Plastid Biology, Energy Conversion and Carbon Assimilation. Springer, Dordrecht, pp 475-500

McDaniel ND, Coughlin FJ, Tinker LL, Bernhard S (2007) Cyclometalated iridium(III) aquo complexes:  efficient and tunable catalysts for the homogeneous oxidation of water. Journal of the American Chemical Society 130: 210-217

Meharenna YT, Doukov T, Li H, Soltis SM, Poulos TL (2010) Crystallographic and single-crystal spectral analysis of the peroxidase ferryl intermediate. Biochemistry 49: 2984-2986

Messinger J (1993) Untersuchungen über die reaktiven Eigenschaften der verschiedenen Redoxzustände der Wasseroxidase Höherer Pflanzen. TU Berlin, Berlin

Messinger J, Badger MR, Wydrzynski T (1995) Detection of one slowly exchanging substrate water molecule in the S3 state of photosystem II. Proceedings of the National Academy of Sciences of the United States of America 92: 3209-3213

Messinger J, Noguchi T, Yano J (2012) Photosynthetic O2 Evolution. In T Wydrzynski, W Hillier, eds, Molecular Solar Fuels. RSC Publishing, Cambridge, pp 163-207

Messinger J, Renger G (1993) Generation, oxidation by the oxidized form of the tyrosine of polypeptide D2, and possible electronic configuration of the redox States S0, S-1 and S-2 of the water

84

oxidase in isolated spinach thylakoids. Biochemistry 32: 9379-9386

Messinger J, Renger G (2008) Photosynthetic Water Splitting. In G Renger, ed, Primary Processes of Photosynthesis, Part 2 Principles and Apparatus, Vol 9. RSC Publishing, Cambridge, pp 291-351

Messinger J, Schröder WP, Renger G (1993) Structure-function relations in photosystem II. Effects of temperature and chaotropic agents on the period four oscillation of flash induced oxygen evolution. Biochemistry 32: 7658-7668

Messinger J, Wacker U, Renger G (1991) Unusual low reactivity of the water oxidase in the redox state S3 toward exogenous reductants. Analysis of the NH2OH and NH2NH2 induced modifications of flash induced oxygen evolution in isolated spinach thylakoids. Biochemistry 30: 7852-7862

Meyer TJ (2008) Catalysis: The art of splitting water. Nature 451: 778-779

Meyer TJ, Huynh MHV, Thorp HH (2007) The possible role of proton-coupled electron transfer (PCET) in water oxidation by photosystem II. Angewandte Chemie-International Edition 46: 5284-5304

Millet P, Ngameni R, Grigoriev SA, Mbemba N, Brisset F, Ranjbari A, Etiévant C (2010) PEM water electrolyzers: From electrocatalysis to stack development. International Journal of Hydrogen Energy 35: 5043-5052

Mills GA, Urey HC (1940) The Kinetics of Isotopic Exchange between Carbon Dioxide, Bicarbonate Ion, Carbonate Ion and Water. Journal of the American Chemical Society 62: 1019-1026

Mojzsis SJ, Arrhenius G, McKeegan KD, Harrison TM, Nutman AP, Friend CRL (1996) Evidence for life on Earth before 3,800 million years ago. Nature 384: 55-59

85

Moroney JV, Bartlett SG, Samuelsson G (2001) Carbonic anhydrases in plants and algae. Plant Cell and Environment 24: 141-153

Morris ND, Mallouk TE (2002) A high-throughput optical screening method for the optimization of colloidal water oxidation catalysts. Journal of the American Chemical Society 124: 11114-11121

Müh F, Glöckner C, Hellmich J, Zouni A (2012) Light-induced quinone reduction in photosystem II. Biochimica et Biophysica Acta - Bioenergetics 1817: 44-65

Mukhopadhyay S, Mandal SK, Bhaduri S, Armstrong WH (2004) Manganese clusters with relevance to photosystem II. Chemical Reviews 104: 3981-4026

Mullineaux CW (1992) Excitation energy transfer from phycobilisomes to Photosystem I in a cyanobacterium. Biochimica et Biophysica Acta - Bioenergetics 1100: 285-292

Mullins CS, Pecoraro VL (2008) Reflections on small molecule manganese models that seek to mimic photosynthetic water oxidation chemistry. Coordination Chemistry Reviews 252: 416-443

Najafpour MM, Ehrenberg T, Wiechen M, Kurz P (2010) Calcium manganese(III) oxides (CaMn2O4 xH2O) as biomimetic oxygen-evolving catalysts. Angewandte Chemie International Edition 49: 2233-2237

Nelson N, Yocum CF (2006) Structure and function of photosystems I and II. Annual Review of Plant Biology 57: 521-565

Neutze R, Wouts R, van der Spoel D, Weckert E, Hajdu J (2000) Potential for biomolecular imaging with femtosecond X-ray pulses. Nature 406: 752-757

Nixon P, Sarcina M, Diner B (2005) The D1 and D2 Core Proteins. In T Wydrzynski, K Satoh, J Freeman, eds, Photosystem II, Vol 22. Springer Netherlands, pp 71-93

86

Nocera DG (2012) The artificial leaf. Accounts of Chemical Research 45: 767-776

Noguchi T (2008) Fourier transform infrared analysis of the photosynthetic oxygen-evolving center. Coordination Chemistry Reviews 252: 336-346

Noguchi T (2008) FTIR detection of water reactions in the oxygen-evolving centre of photosystem II. Philosophical Transactions of the Royal Society B: Biological Sciences 363: 1189-1195

Noyes AA, Deahl TJ (1937) Strong oxidizing agents in nitric acid solution. III. Oxidation potential of cobaltous-cobaltic salts, with a note on the kinetics of the reduction of cobaltic salts by water. Journal of the American Chemical Society 59: 1337-1344

O'Regan B, Gratzel M (1991) A low-cost, high-efficiency solar cell based on dye-sensitized colloidal TiO2 films. Nature 353: 737-740

Olson JM, Blankenship RE (2004) Thinking about the evolution of photosynthesis. Photosynthesis Research 80: 373-386

Pace R, Krausz E (2012) Chapter 2. Solar energy utilisation. In Molecular Solar Fuels. The Royal Society of Chemistry, pp 20-38

Parent AR, Crabtree RH, Brudvig GW (2013) Comparison of primary oxidants for water-oxidation catalysis. Chemical Society Reviews 42: 2247-2252

Pearce JM (2002) Photovoltaics — a path to sustainable futures. Futures 34: 663-674

Petit JR, Jouzel J, Raynaud D, Barkov NI, Barnola JM, Basile I, Bender M, Chappellaz J, Davis M, Delaygue G, Delmotte M, Kotlyakov VM, Legrand M, Lipenkov VY, Lorius C, Pepin L, Ritz C, Saltzman E, Stievenard M (1999) Climate and atmospheric history of the past 420,000 years from the Vostok ice core, Antarctica. Nature 399: 429-436

87

Petrouleas V, Crofts AR (2005) The iron-quinone acceptor complex In T Wydrzynski, K Satoh, eds, Photosystem II. The Light-Driven Water:Plastoquinone Oxidoreductase, Vol 22. Springer, Dordrecht, pp 177-206

Petrouleas V, Deligiannakis Y, Diner BA (1994) Binding of carboxylate anions at the nonheme FeII of PSII. 2. Competition with bicarbonate and effects on the QA/QB electron-transfer rate. Biochimica et Biophysica Acta 1188: 271-277

Porra RJ, Thompson WA, Kriedemann PE (1989) Determination of accurate extinction coefficients and simultaneous equations for assaying chlorophyll-a and chlorophyll-b extracted with 4 different solvents - verification of the concentration of chlorophyll standards by atomic absorption spectroscopy. Biochimica et Biophysica Acta 975: 384-394

Post JE (1999) Manganese oxide minerals: Crystal structures and economic and environmental significance. Proceedings of the National Academy of Sciences 96: 3447-3454

Pushkar YL, Yano J, Sauer K, Boussac A, Yachandra VK (2008) Structural changes in the Mn4Ca cluster and the mechanism of photosynthetic water splitting. Proceedings of the National Academy of Sciences of the United States of America 105: 1879-1884

Ramaraj R, Kira A, Kaneko M (1987) Heterogeneous water oxidation by a dinuclear manganese complex. Chemistry Letters 16: 261-264

Rapatskiy L, Cox N, Savitsky A, Ames WM, Sander J, Nowaczyk MM, Rögner M, Boussac A, Neese F, Messinger J, Lubitz W (2012) Detection of the water-binding sites of the oxygen-evolving complex of photosystem II using W-band 17O electron–electron double resonance-detected NMR spectroscopy. Journal of the American Chemical Society 134: 16619-16634

Rappaport F, Guergova-Kuras M, Nixon PJ, Diner BA, Lavergne J (2002) Kinetics and pathways of charge recombination in photosystem II. Biochemistry 41: 8518-8527

88

Reece SY, Hamel JA, Sung K, Jarvi TD, Esswein AJ, Pijpers JJH, Nocera DG (2011) Wireless solar water splitting using silicon-based semiconductors and earth-abundant catalysts. Science 334: 645-648

Renger G (2011) Light induced oxidative water splitting in photosynthesis: Energetics, kinetics and mechanism. Journal of Photochemistry and Photobiology B: Biology 104: 35-43

Renger G, Hanssum B (1988) Studies on the deconvolution of flash induced absorption changes into the difference spectra of individual redox steps within the water oxidizing enzyme system. Photosynthesis Research 16: 243-259

Renger G, Hanssum B (2009) Oxygen detection in biological systems. Photosynthesis Research 102: 487-498

Renger G, Renger T (2008) Photosystem II: The machinery of photosynthetic water splitting. Photosynthesis Research 98: 53-80

Renger T (2012) Photophysics of photosynthetic reaction centres. In T Wydrzynski, W Hillier, eds, Molecular Solar Fuels. RSC Publishing, Cambridge, pp 143-162

Risch M, Khare V, Zaharieva I, Gerencser L, Chernev P, Dau H (2009) Cobalt-oxo core of a water-oxidizing catalyst film. Journal of the American Chemical Society 131: 6936

Risch M, Klingan K, Ringleb F, Chernev P, Zaharieva I, Fischer A, Dau H (2012) Water oxidation by electrodeposited cobalt oxides—role of anions and redox-inert cations in structure and function of the amorphous catalyst. ChemSusChem 5: 542-549

Robinson HH, Crofts AR (1983) Kinetics of the oxidation reduction reactions of the photosystem II quinone acceptor complex, and the pathway for deactivation. FEBS Letters 153: 221-226

Rutherford AW, Inoue Y (1984) Oscillation of delayed luminescence from PS II: recombination of S2QB

- and S3QB-. FEBS Letters 165:

163-170

89

Sartorel A, Carraro M, Scorrano G, Zorzi RD, Geremia S, McDaniel ND, Bernhard S, Bonchio M (2008) Polyoxometalate embedding of a tetraruthenium(IV)-oxo-core by template-directed metalation of [γ-SiW10O36]8−: A totally inorganic oxygen-evolving catalyst. Journal of the American Chemical Society 130: 5006-5007

Sauer K, Yachandra VK (2002) A possible evolutionary origin for the Mn4 cluster of the photosynthetic water oxidation complex from natural MnO2 precipitates in the early ocean. Proceedings of the National Academy of Sciences of the United States of America 99: 8631-8636

Schidlowski M (1988) A 3,800-million-year isotopic record of life from carbon in sedimentary rocks. Nature 333: 313-318

Schopf JW (1993) Microfossils of the early Archean apex chert: new evidence of the antiquity of life. Science 260: 640-646

Seidler A (1996) The extrinsic polypeptides of photosystem II. Biochimica et Biophysica Acta 1277: 35-60

Shafirovich VY, Khannanov NK, Strelets VV (1980) Chemical and light-induced catalytic water oxidation. . Nouv. J. Chim. 4: 81-84

Shafirovich VY, Strelets VV (1978) New J. Chem. 2: 199-201

Shevchenko D, Anderlund MF, Thapper A, Styring S (2011) Photochemical water oxidation with visible light using a cobalt containing catalyst. Energy & Environmental Science 4: 1284-1287

Shevela D (2008) Photosynthtic Water Oxidation. Role of Inorganic Cofactors and Species Differences. VDM Verlag Dr. Müller, Saarbrücken

Shevela D, Beckmann K, Clausen J, Junge W, Messinger J (2011) Membrane-inlet mass spectrometry reveals a high driving force for oxygen production by photosystem II. Proceedings of the National Academy of Sciences of the United States of America 108: 3602-3607

90

Shevela D, Eaton-Rye JJ, Shen J-R, Govindjee (2012) Photosystem II and the unique role of bicarbonate: A historical perspective. Biochimica et Biophysica Acta - Bioenergetics 1817: 1134-1151

Shevela D, Koroidov S, Najafpour MM, Messinger J, Kurz P (2011) Calcium manganese oxides as oxygen evolution catalysts: O2 formation pathways indicated by 18O-labelling studies. Chemistry - A European Journal 17: 5415-5423

Shevela D, Messinger J (2013) Studying the oxidation of water to molecular oxygen in photosynthetic and artificial systems by time-resolved membrane-inlet mass spectrometry. Frontiers in Plant Science 4

Shevela D, Nöring B, Koroidov S, Shutova T, Samuelsson G, Messinger J (2013) Efficiency of photosynthetic water oxidation at ambient and depleted levels of inorganic carbon. Photosynthesis Research 117: 401-412

Shevela D, Su JH, Klimov V, Messinger J (2008) Hydrogencarbonate is not a tightly bound constituent of the water-oxidizing complex in photosystem II. Biochimica et Biophysica Acta - Bioenergetics 1777: 532-539

Shinkarev V, Wraight CA (1993) Oxygen evolution in photosynthesis: from unicycle to bicycle. Proceedings of the National Academy of Sciences of the United States of America 90: 1834-1838

Shutova T, Kenneweg H, Buchta J, Nikitina J, Terentyev V, Chernyshov S, Andersson B, Allakhverdiev SI, Klimov VV, Dau H, Junge W, Samuelsson G (2008) The photosystem II-associated Cah3 in Chlamydomonas enhances the O2 evolution rate by proton removal. EMBO Journal 27: 782-791

Siegbahn PEM (2009) Structures and energetics for O2 formation in photosystem II. Accounts of Chemical Research 42: 1871-1880

91

Siegbahn PEM (2009) Water oxidation in photosystem II: oxygen release, proton release and the effect of chloride. Dalton Transactions: 10063-10068

Sigfridsson KGV, Chernev P, Leidel N, Popović-Bijelić A, Gräslund A, Haumann M (2013) Rapid X-ray photoreduction of dimetal-oxygen cofactors in ribonucleotide reductase. Journal of Biological Chemistry 288: 9648-9661

Silverman DN (1982) Carbonic anhydrase: Oxygen-18 exchange catalyzed by an enzyme with rate-contributing proton-transfer steps. Methods in Enzymology 87: 732-752

Siuzdak G, Bothner B, Yeager M, Brugidou C, Fauquet CM, Hoey K, Chang CM (1996) Mass spectrometry and viral analysis. Chemistry & Biology 3: 45-48

Song S, Zhang H, Ma X, Shao Z, Baker RT, Yi B (2008) Electrochemical investigation of electrocatalysts for the oxygen evolution reaction in PEM water electrolyzers. International Journal of Hydrogen Energy 33: 4955-4961

Stemler A, Babcock GT, Govindjee (1974) Effect of bicarbonate on photosynthetic oxygen evolution in flashing light in chloroplast fragments. Proceedings of the National Academy of Sciences of the United States of America 71: 4679-4683

Stemler A, Govindjee (1973) Bicarbonate ion as a critical factor in photosynthetic oxygen evolution. Plant Physiology 52: 119-123

Styring S, Rutherford AW (1987) In the oxygen evolving complex of photosystem II the S0 state is oxidized to the S1 State by YD

+ (Signal IIslow). Biochemistry 26: 2401-2405

Surendranath Y, Dinca M, Nocera DG (2009) Electrolyte-Dependent Electrosynthesis and Activity of Cobalt-Based Water Oxidation Catalysts. Journal of the American Chemical Society 131: 2615-2620

Surendranath Y, Kanan MW, Nocera DG (2010) Mechanistic studies of the oxygen evolution reaction by a cobalt-phosphate

92

catalyst at neutral pH. Journal of the American Chemical Society 132: 16501-16509

Suzuki H, Sugiura M, Noguchi T (2012) Determination of the miss probabilities of Individual S-state transitions during photosynthetic water oxidation by monitoring electron flow in photosystem II using FTIR spectroscopy. Biochemistry 51: 6776-6785

Swanson RM (2009) Photovoltaics Power Up. Science 324: 891-892

Thapper A, Mamedov F, Mokvist F, Hammarström L, Styring S (2009) Defining the far-red limit of photosystem II in spinach. The Plant Cell Online 21: 2391-2401

Thomson JJ (1910) LXXXIII. Rays of positive electricity. Philosophical Magazine Series 6 20: 752-767

Thomson JJ (1912) XIX. Further experiments on positive rays. Philosophical Magazine Series 6 24: 209-253

Thomson JJ (1913) Rays of positive electricity and their application to chemical analyses. . Longmans, Green and Co. in London

Tseng H-W, Zong R, Muckerman JT, Thummel R (2008) Mononuclear ruthenium(II) complexes that catalyze water oxidation. Inorganic Chemistry 47: 11763-11773

Tsui EY, Tran R, Yano J, Agapie T (2013) Redox-inactive metals modulate the reduction potential in heterometallic manganese–oxido clusters. Nat Chem 5: 293-299

U.S. Energy Information Administration, What is Energy: Energy Basics, (2011), http://www.eia.gov/kids/energy.cfm?page=about_home-basics

Ulas G, Olack G, Brudvig GW (2008) Evidence against bicarbonate bound in the O2-evolving complex of photosystem II. Biochemistry 47: 3073-3075

93

Umena Y, Kawakami K, Shen J-R, Kamiya N (2011) Crystal structure of oxygen-evolving photosystem II at a resolution of 1.9 Å. Nature 473: 55-60

Umena Y, Kawakami K, Shen JR, Kamiya N (2011) Crystal structure of oxygen-evolving photosystem II at a resolution of 1.9 angstrom. Nature 473: 55-60

Van Rensen JJS (2002) Role of bicarbonate at the acceptor side of photosystem II. Photosynthesis Research 73: 185-192

Van Rensen JJS, Klimov VV (2005) Bicarbonate interactions. In T Wydrzynski, K Satoh, eds, Photosystem II. The Light-Driven Water:Plastoquinone Oxidoreductase, Vol 22. Springer, Dordrecht, pp 329-346

Van Rensen JJS, Xu C, Govindjee (1999) Role of bicarbonate in photosystem II, the water-plastoquinone oxido-reductase of plant photosynthesis. Physiologia Plantarum 105: 585-592

Vass I, Styring S (1991) pH dependent charge equilibria between tyrosine D and the S states in photosystem II. Estimation of relative midpoint potentials. Biochemistry 30: 830-839

Vass I, Styring S, Hundal T, Koivuniemi A, Aro E, Andersson B (1992) Reversible and irreversible intermediates during photoinhibition of photosystem II: stable reduced QA species promote chlorophyll triplet formation. Proceedings of the National Academy of Sciences 89: 1408-1412

Vermaas WEJ, Renger G, Dohnt G (1984) The reduction of the oxygen evolving system in chloroplasts by thylakoid components. Biochimica et Biophysica Acta 764: 194-202

Vermaas WFJ (2001) Photosynthesis and respiration in cyanobacteria. In Encyclopedia of Life Sciences (ELS). John Wiley & Sons, Ltd, London

Vermaas WFJ, Rutherford AW, Hansson O (1988) Site directed mutagenesis in photosystem II of the cyanobacterium Synechocystis sp. PCC 6803: donor D is a tyrosine residue in the

94

D2 protein. Proceedings of the National Academy of Sciences of the United States of America 85: 8477-8481

Wada T, Tsuge K, Tanaka K (2000) Electrochemical oxidation of water to dioxygen catalyzed by the oxidized form of the Bis(ruthenium – hydroxo) complex in H2O. Angewandte Chemie International Edition 39: 1479-1482

Wada T, Tsuge K, Tanaka K (2001) Syntheses and redox properties of Bis(hydroxoruthenium) complexes with quinone and bipyridine ligands. Water-oxidation catalysis. Inorganic Chemistry 40: 329-337

Warburg O, Krippahl G (1958) Hill-reaktionen. Zeitschrift Fur Naturforschung Part B-Chemie Biochemie Biophysik Biologie Und Verwandten Gebiete 13: 509-514

Weakley TJR, Evans HT, Showell JS, Tourne GF, Tourne CM (1973) 18-Tungstotetracobalto(II)diphosphate and related anions: a novel structural class of heteropolyanions. Journal of the Chemical Society, Chemical Communications: 139-140

Wiechen M, Berends H-M, Kurz P (2012) Water oxidation catalysed by manganese compounds: from complexes to 'biomimetic rocks'. Dalton Transactions 41: 21-31

Wydrzynski T, Satoh K, eds (2005) Photosystem II. The light-driven water : plastoquinone oxidoreductase, Vol 22. Springer, Dordrecht

Xiong J, Fischer WM, Inoue K, Nakahara M, Bauer CE (2000) Molecular evidence for the early evolution of photosynthesis. Science 289: 1724-1730

Xu Y, Fischer A, Duan L, Tong L, Gabrielsson E, Åkermark B, Sun L (2010) Chemical and light-driven oxidation of water catalyzed by an efficient dinuclear ruthenium complex. Angewandte Chemie International Edition 49: 8934-8937

Yachandra VK, Yano J (2011) Calcium in the oxygen-evolving complex: Structural and mechanistic role determined by X-ray

95

spectroscopy. Journal of Photochemistry and Photobiology B: Biology 104: 51-59

Yagi M, Kaneko M (2001) Molecular catalysts for water oxidation. Chemical Reviews 101: 21 -36

Yagi M, Narita K (2004) Catalytic O2 evolution from water induced by adsorption of [(OH2)(Terpy)Mn(μ-O)2Mn(Terpy)(OH2)]3+ complex onto clay compounds. Journal of the American Chemical Society 126: 8084-8085

Yagi M, Narita K, Maruyama S, Sone K, Kuwabara T, Shimizu K-i (2007) Artificial model of photosynthetic oxygen evolving complex: Catalytic O2 production from water by di-μ-oxo manganese dimers supported by clay compounds. Biochimica et Biophysica Acta (BBA) - Bioenergetics 1767: 660-665

Yano J, Kern J, Irrgang KD, Latimer MJ, Bergmann U, Glatzel P, Pushkar Y, Biesiadka J, Loll B, Sauer K, Messinger J, Zouni A, Yachandra VK (2005) X-ray damage to the Mn4Ca complex in single crystals of photosystem II: a case study for metalloprotein crystallography. Proceedings of the National Academy of Sciences of the United States of America 102: 12047-12052

Yano J, Kern J, Irrgang KD, Latimer MJ, Bergmann U, Glatzel P, Pushkar Y, Biesiadka J, Loll B, Sauer K, Messinger J, Zouni A, Yachandra VK (2005) X-ray damage to the Mn4Ca complex in single crystals of photosystem II: A case study for metalloprotein crystallography. Proc Natl Acad Sci U S A 102: 12047-12052

Yano J, Kern J, Sauer K, Latimer MJ, Pushkar Y, Biesiadka J, Loll B, Saenger W, Messinger J, Zouni A, Yachandra VK (2006) Where water is oxidized to dioxygen: structure of the photosynthetic Mn4Ca cluster. Science 314: 821-825

Yano J, Robblee J, Pushkar Y, Marcus MA, Bendix J, Workman JM, Collins TJ, Solomon EI, DeBeer George S, Yachandra VK (2007) Polarized X-ray absorption spectroscopy of single-crystal Mn(V) complexes relevant to the oxygen-

96

evolving complex of photosystem II. Journal of the American Chemical Society 129: 12989-13000

Yano J, Yachandra VK (2008) Where water is oxidized to dioxygen: structure of the photosynthetic Mn4Ca cluster from X-ray spectroscopy. Inorganic Chemistry 47: 1711-1726

Yeagle GJ, Gilchrist ML, McCarrick RM, Britt RD (2008) Multifrequency pulsed electron paramagnetic resonance study of the S2 state of the photosystem II manganese cluster. Inorganic Chemistry 47: 1803-1814

Yin Q, Tan JM, Besson C, Geletii YV, Musaev DG, Kuznetsov AE, Luo Z, Hardcastle KI, Hill CL (2010) A fast soluble carbon-free molecular water oxidation catalyst based on abundant metals. Science 328: 342-345

Youngblood WJ, Lee S-HA, Maeda K, Mallouk TE (2009) Visible light water splitting using dye-sensitized oxide semiconductors. Accounts of Chemical Research 42: 1966-1973

Zeng K, Zhang D (2010) Recent progress in alkaline water electrolysis for hydrogen production and applications. Progress in Energy and Combustion Science 36: 307-326

Zong R, Thummel RP (2005) A new family of Ru complexes for water oxidation. Journal of the American Chemical Society 127: 12802-12803

Zouni A, Witt HT, Kern J, Fromme P, Krauß N, Saenger W, Orth P (2001) Crystal structure of photosystem II from Synechococcus elongatus at 3.8 Å resolution. Nature 409: 739-743