Theoretical Studies on Artificial Water Splitting-Water

Oxidation and Proton Transfer

Ying Wang

Licentiate Thesis in Theoretical Chemistry and Biology

School of Biotechnology

Royal Institute of Technology

Stockholm, Sweden 2012

Theoretical Studies on Artificial Water Splitting-Water Oxidation and Proton Transfer
Thesis for Licentiate Degree
Division of Theoretical Chemistry & Biology
School of Biotechnology
Royal Institute of Technology (KTH)
Stockholm, Sweden 2012

© Ying Wang, 2012

ISBN 978-91-7501-490-6
ISSN 1654-2312
TRITA-BIO Report 2012:20
Printed by Universitetsservice US-AB
Stockholm, Sweden
To my family
 Abstract

Encouragement Can Work Miracles

The present thesis is concerned with the theoretical studies on artificial water
splitting process. As the quick development of research on utilizing of solar
energy, which is a green, clean, and renewable energy source, many research
groups focus their attention on artificial photo-synthesis systems inspired by the
photosystem I and II. The overall reaction in these artificial systems is water
splitting to oxygen and hydrogen. Artificial water splitting can generally be
divided into two half reactions, catalytic water oxidation and catalytic proton
reduction. There is an increasing interest and demand to understand the detailed
mechanism of these two key parts. Since DFT (density functional theory) in
particular, has proven to be a powerful and popular tool in exploring reaction
mechanisms, B3LYP and M06 functionals were employed to provide a theoretical
explanation of these two important reactions in this thesis.
For water oxidation reaction, many efficient Water Oxidation Catalysts
(WOCs) based on Ru, Ir, etc., have been reported over the last several years. The
discovery of mononuclear ruthenium WOCs carrying anionic ligands is one of the
major breakthroughs recently. WOCs bearing anionic ligands are able to
efficiently drive catalytic water oxidation with relatively higher Turnover
Numbers (TON) and Turnover Frequencies (TOF). Therefore the influence of
anionic ligands gained our attention. We decided to carry out a detailed
investigation on this effect, and try to propose a full mechanism of this catalytic
water oxidation as well. We found that 1) The anionic ligands exert a promoting
influence on the ligand exchange between picoline and water, which facilitates the
formation of aqua-Ru complex, 2) The anionic ligands facilitate the complex
access to higher oxidation states, which is necessary for the OO bond formation,
and 3) The work of OO bond formation is in progress.
For the proton reduction reaction, the transport or movement of protons is
vital and interesting in many biological and chemical processes, including the
hydrogen uptake/production, the reduction of CO2 to formate, and the reduction of
O2 to water. It is often related to energy storage and utilization. However, the
details of these processes are still ambiguous. In most natural hydrogenase
enzymes or synthetic catalysts based on iron or nickel, the incorporation of a
pendant amine is a frequently occurring feature. This internal amine base seems to
facilitate this proton transfer by acting as a proton relay. Our calculated results

i
showed that the internal base allows for a splitting of one high enthalpy-high
entropy barrier into two: one with a high enthalpy-low entropy barrier and the
other with a low enthalpy-high entropy barrier, resulting in a low free energy of
activation for proton transfer. Our results can serve as a guideline in the
development of new catalysts, not only for proton reduction catalysts, but also for
any process that involves proton transfer from a metal hydride to an external base,
such as C-H activation and functionalization catalysts.
A thorough understanding on the mechanism of water splitting can help
generate a strategy to enhance the catalytic performance on both water oxidation
and proton reduction. We can tune or modify the synthetic complex by
accelerating the slow step (rate-determining step) in the overall catalytic cycle,
and can construct artificial water splitting systems with improved performance.

ii
 The work presented in the thesis was carried out at the Department of
Theoretical Chemistry & Biology, School of Biotechnology, Royal Institute of
Technology (KTH), Sweden.

List of papers included in the thesis

Paper I. Pendant Amine Bases Speed up Proton Transfers to Metals by Splitting

the Barriers.

Ying Wang, Mei Wang, Licheng Sun, and Mårten S. G. Ahlquist.

Chem. Commun., 2012, 48, 4450-4452.

Paper II. Water Oxidation Catalysis: Influence of Anionic Ligands upon the
Redox Properties and Catalytic Performance of Mononuclear Ruthenium
Complexes.
Lianpeng Tong, Ying Wang, Lele Duan, Yunhua Xu, Xiao Cheng, Andreas
Fischer, Mårten S. G. Ahlquist, and Licheng Sun.
Inorg. Chem., 2012, 51 (6), pp 3388–3398
Paper III. The Ligand Returns – Theoretical Evidence for Direct Involvement of
a Dissociated Picoline in Catalyst Decay.
Ying Wang and Mårten S. G. Ahlquist.

(Manuscript)

Comments on my contribution to the papers included.

As the first author, I was responsible for the calculations and the writing of
the first draft for Paper I. As the co-author, I was responsible for the theoretical
calculations, discussion and revision of Paper II.

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iv
Abbreviations and acronyms

bpp bis(2-pyridyl)-3,5-pyrazolate
bpy bipyridine
dpp 2,9-dipyrid-2’-yl-1,10-phenanthroline
isoq isoquinoline
pbn 2,2’-[4-(tert-butyl)pyridine-2,6-diyl]bis(1,8-naphthyridine)
pic 4-picoline
py pyridine
tpy 2,2′:6′,2′′-terpyridine
B3LYP Becke, three-parameter, Lee-Yang-Parr
BLYP Becke-Lee-Yang-Parr
CAES Compressed Air Energy Storage
CCSD Coupled Cluster Singles and Doubles
CI Configuration Interaction
CpI Clostridium pasteurianum I
DdH Desulfovibrio desulfuricans Hildenborough
DFT Density Functional Theory
GGAs Generalized gradient approximations
OEC Oxygen Evolving Complex
H2bda 2,2’-bipyridine-6,6’-dicarboxylic acid
H2hqc 8-hydroxyquinoline-2-carboxylic acid
H2pdc 2,6-pyridine-dicarboxylic acid
HF Hartree-Fock
I2M Interaction Between Two M-O Units
LDA local density approximation
MCSCF Multi-Configuration Self-Consistent Field
MPn Many-body Perturbation theory
M06 Minnesota density functional
NHE Normal Hydrogen Electrode
P680 Triad composed of a multimer of Chlorophylls
PBE Gradient-corrected correlation functional of Perdew, Burke and
Ernzerhof

v
PCET Proton-Coupled Electron Transfer
TOF TurnOver Frequency
TON TurnOver Number
PRC Proton Reduction Catalyst
PS-II PhotoSystem II
TST Transition State Theory
Tyrz D1-tyrosine 161
WNA Water Nucleophilic Attack
WOC Water Oxidation Catalyst
XC Exchange-Correlation
ZPE Zero Point Energy

vi
 Acknowledgments
First of all, I would like to express my sincere gratitude to my supervisor Dr.
Mårten Ahlquist, thanks a lot for his guidance, insightful suggestions, the work of
this thesis would not have been completed without the great help of him and I
really appreciated it. I really learned a lot of things which are new to me before.
Great thanks to Prof. Hans Ågren, for giving me this precious opportunity
studying in this department, and creating such a wonderful and nice enviroment
for us. Great thanks to Prof Yi Luo, for his kind help when I firstly came to this
department, and valuable advices all the time.
Many thanks to Prof. Licheng Sun, Prof. Mei Wang, Dr Lele Duan, Lianpeng
Tong and Xiao Cheng for their pleasant cooperation and useful discussion.
Many thanks to Prof. Boris Minaev, Prof. Ying Fu, Prof. Faris Gel’mukhanov,
Prof. Yaoquan Tu, Prof. Zilvinas Rinkevicius, Prof. Olav Vahtras for their
wonderful lectures.
Many thanks to Dr Rocío Sánchez, Dr Liqin Xue and Irina Osadchuk for
their useful discussion and pleasant time we spent together.
Many thanks to my colleagues in this department, they are Dr Weijie Hua,
Chunze Yuan, Dr Yuejie Ai, Wei Hu, Dr Xiuneng Song, Dr Peng Cui, Yan Wang,
Xianqiang Sun, Li Gao, Quan Miao, Dr. Xin Li, Guangjun Tian, Li Li, Xinrui Cao,
Bogdan Frecus, Junfeng Li, Dr Zhihui Chen, Dr Xiangjun Shang, Dr Xifeng Yang,
Hongbao Li, Fuming Ying, Dr. Arul Murugan, Dr. Kestutis Aidas, Dr Johannes
Niskanen and Kayathri Rajarathinam.
Special thanks are sent to Dr Qiang Fu and Dr Xing Chen for their patient
instruction on the basic knowledge of theoretical chemistry, and persistent
encouragement as well, this is quite helpful and important for me to carry on.
Special thanks to Dr Lili Lin, Yong Ma, Dr Qiong Zhang, Lu Sun, Dr Sai
Duan, Dr Junkuo Gao, Ce Song, Yongfei Ji and Lijun Liang for their kind help
and pleasant cooperation on courses I attended.
Special thanks to Dr Liqin Xue, Dr Rocío Sánchez and Dr Qiang Fu for
proof reading of this thesis.
I would also like to thank the Erasmus Mundus Tandem for financial support.
Last but not least, great thanks to my family, I could not make this if lack of
your endless love and confirmed support all the time, I will love you always and
forever, and keep following my dream no matter whatever comes along.

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viii
Contents

1. Introduction 1

2. Theoretical Background 5
2.1 Brief Introduction of Quantum Chemistry……………………………….5
2.2 Wave-function Based Method……………………………………………6
2.3 Density Functional Theory (DFT) ……………………………………….8
2.3.1 Hohenberg and Kohn THEOREM……………………………...8
2.3.2 Kohn-Sham Equation…………………………………………...9
2.3.3 Hybrid DFT Method-B3LYP………………………………….10
2.3.3.1 Accuracy on Geometries…………………..…………10
2.3.3.2 Accuracy on Energies…………………..…….………11
2.3.4 Recently Developed Hybrid DFT Methods……………...…....12
2.3.4.1 The Minnesota Density Functionals………..…...……12
2.3.4.2 The Family of “Double-Hybrid” Density Functionals.13
2.3.4.3 Density Functional Theory Including Dispersion
Corrections ……………………………………..……13
2.4 Transition State Theory…………………………………………………14
2.5 Solvation Model………………………………………………………...15
2.6 Theoretical Studies…………………………………………………...…15

3. Experimental and Theoretical Studies on Water Oxidation Catalysts 17

3.1 Brief Introduction……………………………………………………….17
3.2 Introduction of Proton-Coupled Electron Transfer (PCET)…………….19
3.3 Water Oxidation Catalysts………………………………………………21
3.3.1 Ruthenium-Based WOCs……………………………………...21
3.3.1.1 Dimeric Ruthenium-Based WOCs…..……………….21
3.3.1.2 Monomeric Ruthenium-Based WOCs Carrying
Neutral Ligand…………………………………..…...22
3.3.1.3 Monomeric Ruthenium-Based WOCs Carrying
Anionic Ligands………………..……………..……...24

ix
 3.3.2 Iridium-Based WOCs……………………………………….…24
3.3.3 First-Row Transition Metal Based WOCs………….…………25
3.3.3.1 Manganese-Based WOCs…………..……………..…25
3.3.3.2 Cobalt-Based WOCs…………………………………26
3.4 A Hydrogen-Bonding Network Effect………………………………….26
3.5 OO Bond Formation (O2 Evolution).…………………………………...27
3.5.1 Water Nucleophilic Attack (WNA) …………………………...27
3.5.2 Interaction Between Two M-O Units (I2M).………………….30
3.5.2.1 Intramolecular Approach……………………….……31
3.5.2.2 Intermolecular Approach………………….…………31

4. Natural Hydrogenases and Synthetic Mimic Complexes 35

4.1 Brief Introduction……………………………………………………….35
4.2 Hydrogenases Enzymes………………………………………………...36
4.2.1 Ni-Fe Hydrogenases………………………………………...…36
4.2.2 Fe-Fe Hydrogenases…………………………………………...37
4.3 Homogeneous Light-Driven Catalytic Systems………………………...38
4.4 Effect of the Pendant Amine Base in Iron-Complexes…………………39
4.4.1 Pendant Amine Base Effect on Proton Transfer in
Iron-Complex………………………………………………….39
4.4.2 Pendant Amine Base Effect on Heterolytic Activation of
Hydrogen in Iron-Complex……………………………...…….41

References 43

x
Chapter 1

Introduction

The sun will play an irreplaceable role in sustainable energy production, which is
the original source of most of the energy we are using now. Energy consumption
demand is predicted to rise significantly, up to 28-35 TW by 2050, from the
present state of about 13 TW,[1,2] Hence the access to sustainable energy will
clearly be a crucial problem already in the next decades.
In order to solve the future energy supply problem, it is necessary to find and
develop new technologies for generation of sustainable and environmentally
benign energy. As solar energy, an abundant and sustainable form of energy, is
gaining attention we need to find ways to store the energy efficiently.
To utilize the solar energy effectively, nature shows a perfect example,
namely Photosynthesis.[3,4] Photosynthesis, which occurs in plants and some algae,
is a chemical process of converting the solar energy into chemical forms and
storing it in the bonds of carbohydrates. The entire process needs the energy from
sunlight, carbon dioxide and water, all of them are abundant and easy to fetch. The
products of the photosynthesis are carbohydrates and oxygen, which are essential
and vital to the survival and development of mankind.
Although photosynthesis takes place in many different ways in different
environments, the key features of the process are similar.[5] From these features
we can make a general conclusion about this important process (Figure 1.1).

hv e- e- e- e-
Further
P680 Pheo QA QB Reduction
e-

Tyrz
Mn4 = Cluster including four Manganese atoms (Mn4CaO5)
e - P680 = Triad composed of a multimer of Chlorophylls
Pheo = Pheophytin
Mn4 Tyrz = D1-tyrosine 161
QA = Permanently bound Plastoquinone, secondary electron acceptor
O2 +H+ 2H2O QB = Exchangeable Plastoquinone, a two electron gate
- 4e- S = S states the Mn4 carries, the subscript means the number of
oxidizing equivalent stored

S0 S1 S2 S3 S4
e- e- e- e-

Figure 1.1 A Brief overview of Photosynthesis in nature.

1
 Photosynthesis starts with the absorption of energy from the sunlight by the
photosensitizer P680, which is a triad composing of a multimer of chlorophylls.
Once the energy is absorbed, P680 reaches its excited state of P680* and it
transfers electrons to a permanently bound plastoquinone molecule, QA, via a
pheophytin molecule. By binding a plastoquinone molecule at the QB site, the
transferring electrons finally go to the plastoquinone molecules in the membrane,
where a two-electron reduction from plastoquinone to plastoquinol occurs, here
QB functions as a two-electron gate. On the other side, after transferring one
electron to the electron acceptor part, the oxidized P680+ becomes one of nature’s
strongest oxidizing species, with a potential of 1.2V vs. NHE. It can oxidize the
tyrosine residue Tyrz in a multiphasic process, and the oxidized Tyrz will be
reduced by the manganese cluster quickly, which is the oxygen-evolving complex
(OEC) [6,7] of photosystem II. The oxidized manganese cluster which includes four
manganese atoms can in turn oxidize the water nearby. By four successive charge
separations the manganese cluster accumulates the four oxidizing equivalents,
which are named as S1 to S4, (the subscript means the number of oxidizing
equivalents it stored), and it is able to split two water molecules into oxygen and
protons. In general, the electrons are originally from water.
Inspired by nature (Photosynthesis), many artificial photo-synthesis systems
have been constructed recently.[8-11] The overall reaction in these systems is water
splitting (Figure 1.2), which is breaking water into hydrogen and oxygen assisted
by corresponding catalysts. The reaction of water splitting is typically separated
into its two half reactions: catalytic water oxidation and catalytic proton reduction.

hv
hv
PRC H2

Photosensitizer e H+
H2O H2 + O2 H2+O2 H2O +ENERGY
WOC/PRC meet humanity's needs
O2
WOC
WOC = Water Oxidation Catalyst
PRC = Proton Reduction Catalyst H2O

Figure 1.2 Light-driven catalytic water splitting.

1) Catalytic water oxidation:
hv, WOC
2H2O Photo-sensitizer O2 + 4e- + 4H+

This reaction is an essential part of water splitting, the net half reaction is
water oxidation to produce oxygen, and electrons and protons are generated as
“by-products”. This reaction can convert solar energy into chemical energy, and is

2
completed with an involvement of photo-sensitizer and Water Oxidation Catalysts.
[Ru(bpy)3]2+ (bpy is 2, 2’-bipyridine) is often used as photo-sensitizer. After
absorption of energy from sunlight, it reaches its excited state [Ru(bpy)3]2+*, a
strong oxidant, it can oxidize the corresponding water oxidation catalysts (Ru, Ir,
Co complexes), which complete water oxidation afterwards.
2) Catalytic proton reduction:
hv, PRC
2H+ + 2e- Photo-sensitizer H2

The generated protons from catalytic water oxidation are reduced to produce
hydrogen using the reducing power of the electrons generated from catalytic water
oxidation. The process is assisted by Proton Reduction Catalysts. Here
[Ru(bpy)3]2+ can be also used as a photo-sensitizer, after being exposed to sunlight,
it reaches its excited state [Ru(bpy)3]2+* and is reduced to [Ru(bpy)3]1+ quickly by
sacrificial electron donor such as ascorbate. After transferring electrons to proton
reduction catalysts, such as hydrogenases, it returns to [Ru(bpy)3]2+ and the
electrons transferred to the catalysts are used to reduce protons to produce
hydrogen.
In this thesis, density functional theory is employed in mechanistic studies of
these two key reactions:
1) Catalytic water oxidation using ruthenium based catalysts. In order to
design water oxidation catalysts with higher efficiency, a thorough mechanistic
understanding for water oxidation is necessary, and we need to provide an
explanation for the promoting effects of anionic ligand.
2) Proton transfer in iron complexes. Since the proton transfer or movement
in the complex is a vital part of the mechanistic study of hydrogen generation and
uptake, a thorough understanding of the mechanism of proton transfer or
movement could serve as a guideline for designing new catalysts for proton
reduction.
This thesis is organized in the following manner. A brief introduction of the
mechanism of photosystem-II and purpose of our research is given in this chapter,
followed by a description of theoretical background and the adopted methodology
in our calculations (chapter 2). An introduction to water oxidation catalysts and
related basic concepts is given in chapter 3. Then a description about proton
transfer or movement in natural and synthetic complexes is presented in chapter 4,
accompanied with an explanation about the pendant base effect in iron complexes.
A summary of included papers is presented at the end of this thesis.

3
4
Chapter 2
Theoretical Background

2.1 Brief Introduction of Quantum Chemistry

Quantum chemistry is usually taken as an important subfield of theoretical

chemistry. It aims to calculate the various structures and properties of molecules,
such as geometry, electronic energy, electric dipole moment, charge distribution,
vibrational frequency, etc. by using the principles of theoretical chemistry and the
tools of computer science. It aims at explaining the chemical problems
specifically.[12] Efficient computer programs are therefore indispensable to
accomplish this target, and are constructed by theoretical chemists and physicists.
Since we focus on investigating chemical reactions, which include
bond-forming and bond-breaking via transition states, a good description of the
electronic distribution is necessary. Usually, quantum chemical methods, which
are electronic structure methods ranging from ab initio to semi-empirical methods,
are used to calculate the corresponding molecular properties. From ab initio
methods, the solutions are obtained from purely theoretical calculations. It works
well for small systems, however, the computational cost increases dramatically to
get accurate results for large systems. On the contrary, semi-empirical methods
reduce the computational demand for calculation of large systems, however, the
accuracy becomes its limitation.
The time-independent Schrödinger equation[13,14] is shown in Eq. 2-1.

   (2-1)

where Ψ is the wave function which determines the given physical system, H
is the Hamiltonian operator that represents the energy of the system, which
includes kinetic and potential energy, and E is the energy of the given system
obtained as an eigenvalue to the Hamiltonian.
The Hamiltonian of the time-independent Schrödinger equation within the
non-relativistic approximation can be expressed in Eq. 2-2,

 tot  n   e (2-2)

5
 1
where n    a 2  e  e  Vne  Vee  Vnn
a 2M a

Where Tn is the nuclear kinetic energy, He is the electronic Hamiltonian

operator, Te means the electron kinetic energy, Vne denotes the attraction between
nuclei and electron, Vee is the electron-electron repulsion and Vnn is the
nuclei-nuclei repulsion.
Employment of the Born-Oppenheimer approximation further reduces the
computational cost of solving the time-independent Schrödinger equation. In this
approximation the coupling interaction between the nuclei and electron is
neglected. The electronic part of the Schrödinger equation is solved with the
nuclear positions as parameters. The potential energy surface which results from
electronic part solution is used as a basis to solve the nuclear movement. Hence,
for a given set of nuclear coordinates, the large part of the computational cost will
lie on the electronic Schrödinger equation solution (Eq. 2-3).

 e  e  Vne  Vee  Vnn (2-3)

N elec N elec
1 Za
where e     a 2 Vne    
a 2 a i Ra  ri
N elec N elec N elec N elec
1 Z a Zb
Vee    Vnn   
i j i ri  rj a ba Ra  Rb

The fundamental methodologies for investigating the properties of a system

are divided into two main categories: wave-function based methods and electron
density based methods, depending on the different bases.

2.2 Wave-Function Based Methods

Although we have adopted the Born-Oppenheimer approximation to solve the
time-independent Schrödinger equation, the electronic Schrödinger equation is
still too complicated to solve, since the interactions between electrons need to be
considered.
In Hartree-Fock theory,[15] which takes the interaction between the electrons
as an average, the electrons are assumed to move independently under a mean
potential field generated by the remaining electrons. Their movements can be
written as spin-orbital wave functions separately, and an expression of all the

6
occupied spin-orbital wave functions can be defined as the total electronic wave
function for the system. The Hartree Fock theory includes the exchange
interaction between two electrons, which comes from the anti-symmetric property
of the wavefunction.
The HF equation can be described as in Eq. 2-4,

Fi   ii (2-4)

Where F means the Fock operator, εi means the energy of orbital, and φi the
Hartree–Fock molecular orbitals.

The Fock operator includes three terms, and can be expressed as in Eq. 2-5,

F  h   ( J i  Ki ) (2-5)
i

Where h denotes the Hamiltonian of a single electron, which includes its

kinetic energy and the attraction interaction with the nuclei, and J and K denote
the Coulomb operator and exchange operator, respectively.
In general, the Hartree-Fock method cannot give satisfactory accuracy due to
the lack of description of correlation interaction. The lack of this correlation
interaction always results in a higher energy than the real one. The energy
difference between the real energy and HF energy is defined as correlation energy.
Although the correlation energy in a system is quite small, it is often important in
a chemical reaction. This correlation interaction should be taken into account
especially when calculating reaction barriers.
Therefore, many kinds of more accurate methods based on the Hartree-Fock
method, usually referred as post-Hartree-Fock methods such as Configuration
Interaction method[16] (CI), Multi-Configuration Self-Consistent Field method[17]
(MCSCF), Many-body Perturbation theory method[18] (MPn), etc. are developed to
improve the performance. The correlation energy is considered in different ways
with different methods, which improves the results systematically.
The computational cost of those accurate methods is usually huge, especially
for large systems, which clearly sets a limitation for broad applications.
Fortunately, taken as an improvement in HF method, the Density Functional
Theory (DFT) method includes the correlation interaction part, and provides a
better balance between computational cost and accuracy. It has therefore become
popular in the chemical community in recent years.

7
2.3 Density Functional Theory (DFT)
As early as 1927, the first attempt of describing the property of a system with
electron density was made by Thomas and Fermi. One year later, Dirac added one
more term, which described the exchange energy between electrons. Therefore,
the Thomas-Fermi-Dirac model is considered a breakthrough in the development
of electron density based approaches.[19-21] Different from the wave-function
based methods, DFT incorporated the conception of electron density, which
indicates that the electronic energy of ground state is determined by the electron
density entirely. The relationship between the electron density and the energy for a
given system is a one to one correspondence.
In fact, density functional theory (DFT) has become one of the most popular
tools in investigation in chemistry and material science now. The Nobel prize in
chemistry was awarded to Kohn and Pople in 1998 for their contribution to DFT
and computational methods development, respectively.
A general description of its broad application[22] is shown in Figure 2.1.

7 DFT
B3LYP
6

5
kilopapers

0
2001 2005 2010

Figure 2.1 Numbers of papers in Web of Knowledge from 2001 to 2011. (grey bar:
“DFT” is searched as a topic; blue bar: B3LYP citations).

2.3.1 Hohenberg and Kohn THEOREM

DFT is based on the proof by Hohenberg and Kohn,[23] a theorem formulated in
1964 that is the basis of Density Functional Theory. The first theorem describes
that an external potential vext is uniquely determined by the electron density,
therefore, the total energy of one system, specifically the ground state energy, can
be written as a functional of the electron density. This theorem states that the
electron density determines the properties of a system exclusively. The second
theorem describes that we could calculate the electron density of one system by

8
using a variational method, which means we can obtain the true electron density
ρ0 of the system by finding the minimum of the energy functional E[ρ0].
According to these two theorems, the energy of ground state can be
expressed as in Eq. 2-6,

E     F      ext  dr (2-6)

Where ρ means the electron density of system, E means the energy of ground
state, F means the universal functional composed of electron-electron repulsion
energy and electron kinetic energy, and vext means external potential.

2.3.2 Kohn-Sham Equation

The expression of Kohn-Sham equation is shown in Eq. 2-7,

 1 2 
  2   eff (r )  i (r )   i i (r ) (2-7)

 (r ')
eff (r )   (r )   dr '  xc (r ) (2-8)
rr'

The first term on the left hand side of Eq. 2-7 is the kinetic energy, υeff(r) means
effective local potential and υ(r) means the external potential, including the
electron-nuclei interaction. The second term on the right hand side of Eq. 2-8 is
the electrostatic interaction between electrons, and υxc(r) denotes the
exchange-correlation potential.
The exchange-correlation (XC) energy is approximated in practical
calculations. Different types of approximations have been introduced into this
exchange-correlation term, therefore, many different density functional methods
have been proposed and developed.
The simplest exchange-correlation energy approximation is the local density
approximation (LDA),[24] which was popular in the 1970s and 1980s. Generalized
gradient approximations (GGAs)[25] was introduced in the late 1980s, and it can
be used well in chemical reactions with an acceptable accuracy. The most popular
approximation in chemistry B3LYP currently was introduced by Becke in the
early 1990s. He adopted the Hartree-Fock (HF) exchange instead of a fraction of
GGA exchange. Recently, the Minnesota density functionals, especially the M06
family of functionals, were developed by Truhlar’s group, and it shows a broad

9
accuracy in many research fields.

2.3.3 Hybrid DFT Method-B3LYP.

There are many DFT methods available at present, the difference between them
lies on the difference choice of functional form related to the exchange and
correlation energy. B3LYP as one of the hybrid DFT methods has become very
popular, due to its reliable performance.
The exchange-correlation term of B3LYP[26,27] is shown in Eq. 2-9,

ExcB 3 LYP  aExHF  (1  a) ExSlater  bExB 88  (1  c) EcVWN  cEcLYP (2-9)

For the exchange part, it introduces exact Hartree-Fock exchange in the

functional, Slater local functional and Becke 1988 nonlocal gradient correction.
For the correlation it includes the Vosko-Wilk-Nusair (VWN) local functional, and
the Lee-Yang-Parr local and nonlocal functional.
We have found that density functional theory (DFT) gives highly accurate
results, and it can be used for the mechanistic studies in our projects. We adopted
B3LYP and M06 to study the mechanism of our target reactions, namely water
oxidation and proton transfer.

2.3.3.1 Accuracy on Geometries

The errors in the calculation of geometrical parameters were analyzed by
Charles W. Bauschlicher Jr,[28] standard G2 are used as the benchmark, and
consists of 55 molecules containing first and second row atoms. A series of 55
molecules including 71 bond lengths, 26 bond angles and 2 dihedral angles is
tested for this purpose.
As shown in Table 2.1, comparing to other approaches the hybrid B3LYP
functional has the lowest average error (0.013) when applied to the calculation of
bond lengths. The error for B3LYP functional could be further reduced by using a
large basis set.
The average absolute deviation on bond angles displays a similar trend, the
hybrid functional B3LYP has the smallest error (0.62). Improving the basis set can
slightly decrease the error (0.61) at the B3LYP level.

10
Table 2.1 The average absolute deviation for geometrical parameters.

Bond length (Å) Angle (deg) Dihedral angle (deg)

(average absolute error) (average absolute error) (average absolute error)
HFa 0.020 1.16 1.92
MP2a 0.015 0.67 1.24
BLYPa 0.026 1.03 0.89
BPa 0.020 0.91 0.27
BP86a 0.022 0.96 0.24
B3P86a 0.010 0.62 0.86
B3LYPa 0.013 0.62 0.35
B3LYP (big)b 0.008 0.61 3.66
a
The 6-31G* basis set is used
b
The 6-311 + G(3df, 2p) basis set is used
Different from the bond angles and bond lengths, B3LYP does not have the
smallest error when calculating dihedral angles, however, it is acceptable. Since
the analysis only includes two dihedral angles, it is not likely to accurately
describe the reliability of dihedral calculation using the approaches mentioned
above.

2.3.3.2 Accuracy on Energies

In order to test the B3LYP accuracy on various energy calculations, which

includes atomization energy, electron affinity, barrier height, etc., many reports
have been published by various groups. One of them is the atomization energy
calculations reported by Charles W. Bauschlicher Jr.
Table 2.2 The average absolute deviation for atomization energy calculation.

Atomization energy (kcal/mol) Atomization energy (kcal/mol)

(average absolute error) a (average absolute error) b
HF 80.52 74.50
MP2 16.04 7.43
BP 8.21 11.81
BLYP 5.31 4.95
BP86 7.23 10.32
B3P86 5.87 7.82
B3LYP 5.18 2.20
a
The 6-31G* basis set is used
b
The 6-311 + G(3df, 2p) basis set is used
From Table 2.2, it is clear that the hybrid functional B3LYP demonstrates
superior performance over other approaches. The average absolute error is 5.18

11
kcal/mol using a small basis set. Improving the basis set lead to a decrease to 2.2
kcal/mol.
In 2005 a new extensive set[29] based on G3/05 containing a total of 454
energies was used to test for validation of quantum chemical methods. After
comparison, B3LYP still stands out of other approaches within a mean unsigned
error of 4.14 kcal/mol. Furthermore, the results indicate that B3LYP performs as
well or even better than B98, which is considered as the most accurate functional
in this G3/05 test set for smaller molecules.

2.3.4 Recently Developed Hybrid DFT Methods

Recently, many new approximate density functionals in the framework of

Kohn-Sham density functional theory have been developed to improve the
performance of DFT, such as the Minnesota density functionals, the family of
“double-hybrid” density functionals, density functional theory including
dispersion corrections, etc. These improved DFT methods meet the two
fundamental conditions required by a good density functional approach. Firstly,
they can produce a high accuracy for basic physical and chemical properties, such
as geometry and energy. Secondly, these improved methods can be applied to a
general research field (including organometallic chemistry, inorganic and organic
chemistry, and biochemistry) and provide a better description.

2.3.4.1 The Minnesota Density Functionals

The Truhlar group has developed several approximate functionals, named as the
Minnesota density functionals, or the M06 family.[30,31] These functionals show a
successful applications in many fields, such as organometallic, inorganic, organic
and biological chemistry. Compared to B3LYP, M06 family shows a better
performance for organic chemistry due to the improved treatment of
medium-range correlation energy. We choose this method to give a more accurate
electronic energy in our system.
10 functionals were tested against the dissociation energies of four
16T-isobutene complexes (four possible models of the dissociation of isobutene
from 16T zeolite model cluster).[32] Two of them (π-complex and tert-butyl
carbenium ion) are non-covalent, while the other (tert-butoxide and isotutoxide)
two are covalent. The results (Table 2.3) showed that, M05-2X and M06-2X gave
the best performance, followed by M06-L and M06. All these four functionals
gave a small MAD value. However, the other six functionals did not give an

12
acceptable result. The M06 family produces a satisfactory result for both covalent
and non-covalent cases.

Table 2.3 A benchmark data of dissociation energies (kcal/mol) in four complexes

involving the dissociation of isobutene from a 16T Zeolite cluster model.
π-complex ter-butyl carbenium tert-butoxide isotutoxide mean error
(non-covalent) ion (non-covalent) (covalent) (covalent)
methoda De-Cp De-Cp De-Cp De-Cp MAD-Cp
Best estimate 15.1 -9.8 13.9 13.9
M05-2X 11.7 -8.1 14.9 14.0 1.6
M06-2X 12.7 -9.1 16.6 15.6 1.9
M06-L 14.4 -2.3 15.6 13.5 2.6
M06 13.3 -3.9 16.0 14.4 2.6
M06-HF 12.4 -12.5 18.6 18.8 3.7
PBEh 2.9 -15.6 4.7 4.7 9.1
PBE 3.2 -12.8 2.3 2.0 9.6
B97-1 3.9 -14.3 2.2 2.9 9.6
TPSSh -0.9 -17.7 1.8 1.6 12.1
B3LYP -2.5 -20.7 -5.5 -4.8 16.6
a
The 6-311+G (2df, 2p) basis set is used for all density functionals in this table. MAD denotes mean absolute

deviation, and De-Cp denotes dissociation energy calculation with counterpoise correction

2.3.4.2 The Family of “Double-Hybrid” Density Functionals

A new family of “double-hybrid” density functionals is proposed by Grimme in
2006,[33] the performance of B2-PLYP (one of these new functionals) is assessed
by the G2/97 standard benchmark test (including a suite of atoms, molecules and
reactions). The accuracy of B2-PLYP for many vital aspects of chemistry
(including transition-metal compound, reaction barriers and weakly bonded
complexes) is satisfactory. B2-PLYP is taken as a reliable and efficient quantum
chemical method for general purpose.

2.3.4.3 Density Functional Theory Including Dispersion

Corrections
Non-covalent interactions, such as the ubiquitous attractive long-range van der
Waals (dispersion) interactions, are playing an increasingly vital role in the
theoretical description of chemical research, especially in organic chemistry,
supramolecular chemistry and biochemistry. Several density functional

13
approximations have been developed to include this weak interaction. Density
functional Theory- Dispersion (DFT-D), which means the developments of
dispersion corrections in Kohn-Sham density functional theory, is one method and
is applied successfully in various fields.
The common G3/99 set of heat of formation (HOF) is chosen by the Grimme
group to test the general applicability.[34] The G3/99 set includes relatively large
molecules, therefore, intramolecular dispersion makes a significant contribution.
Three density functionals (B3LYP, B2PLYP and mPW2PLYP) with and without
the dispersion correction were adopted for comparison. The results with the
dispersion correction improved remarkably for all three functionals. A statistical
summary of their results is shown in Table 2.4.
Table 2.4 Performance of three functionals (B3LYP, B2PLYP and mPW2PLYP)
with and without the dispersion corrections. All values are in kcal/mol.
Functional MDa MADb
B3LYP -4.6 5.6
B3LYP-D -1.3 3.1
B2PLYP -1.7 2.4
B2PLYP-D 0.0 1.7
mPW2PLYP -1.4 2.1
mPW2PLYP-D -0.2 1.7
a
MD means the Mean Deviation.
b
MAD means the Mean Absolute Deviation.

2.4 Transition State Theory

Transition state theory, which was developed by Eyring and coworkers in 1935,[35]
has been proven to be a considerable success in the application of a wide variety
of processes. This theory is generally used to calculate the reaction rates of
chemical reactions, and describe qualitatively how a chemical reaction occurs,[36]
especially important for catalytic reactions.
As reactant A converting to product B in the reaction, a bond breaking and a
new bond forming is often involved. The transition state forms or activated
complex A* are usually assumed to exist as intermediate states during the reaction.
(Figure 2.2).
K* k
A A* B
Figure 2.2

14
The rate constant k of a reaction can be described as follows,


k BT RTG
k e
h (2-10)

where kB denotes the Boltzmann’s constant (1.38×10-23J/K), h is Plank’s

constant (6.63× 10-34J s), △G≠ is the difference in Gibbs free energy between
reactant and the transition state, R is the gas constant (8.314 J K-1 mol-1), and T is
the temperature in Kelvin.
From the formula above, we can derive that a rate of 1 s-1, which indicates one
unit of reaction per second, corresponds to a barrier of 17.4 kcal/mol at room
temperature (298.15K). A change of 1.4 kcal/mol in activation barrier depicts an
approximate raise or fall in reaction rate by one order of magnitude. These useful
relationships can serve as a guideline for our mechanistic research, and help us
assess the feasibilities of related reaction and compare different mechanistic
proposals.

2.5 Solvation Model

In this thesis, the reactions we are interested in were carried out in a certain
solvent, either in water or in dichloromethane. In order to describe solvated
molecular systems we use a self-consistent reaction field method, here we choose
a Poisson-Boltzman solver. To consider the solvation effect in our research, the
solvation free energies corrections, which is the difference between the energy of
optimized geometry in gas phase and the optimized geometry in a certain solvent,
were calculated using Poisson-Boltzman Solvation Model.[37]

2.6 Theoretical Studies

All Density Functional Theory (DFT) calculations were performed with Jaguar
7.6 program package of Schrödinger LLC. Becke’s three-parameter hybrid
functional and the LYP correlation functional (B3LYP) was employed with the
LACVP** core potential and basis set for geometry optimizations, frequency and
solvation energy calculations, while the M06 functional using the LACV3P**++
basis set (augmented with two f-polarization functions on M (Fe or Ru) as
suggested by Martin[38]) was used for single point energy corrections. In order to
confirm whether the geometries correspond to minima or first-order saddle points
(transition states) or not on the potential energy surface (PES), frequency

15
calculations were performed using the optimized geometries. The expression for
Gibbs free energies were presented as the following equation G =
E(M06/LACV3P**++ 2f on M) + Gsolv + ZPE + H298 - TS298 + 1.9 (1.9 denotes
the concentration correction to the free energy of solvation from 1 M(g) → 1
M(aq) to 1 atm(g) → 1 M(aq)). The solvation model adopted was the
Poisson-Bolzmann reactive field (PBF) implemented in Jaguar 7.6. For free
energy of solvating proton, we chose the experimental number by Tissandier[39] et
al. of −264 kcal mol−1 (for the free energy of 1M proton in water the value of
−270.3 kcal mol−1 was adopted).

16
Chapter 3
Experimental and Theoretical Studies on Water
Oxidation Catalysts.
3.1 Brief Introduction
Searching and building a renewable and sustainable energy system is probably
one of the greatest challenges facing the world. Trying to find a sustainable fuel to
change our current energy consumption infrastructure is one of the key points in
such a system. The conversion of solar energy into electricity or other forms of
energy, which is one of the manners of energy storage, is a very promising way to
solve this problem. Energy storage plays a critical role in balancing the supply and
demand of energy and therefore securing our energy future. The development of
storage technologies is therefore crucial to achieve this target. Generally, energy
storage systems [40] can be categorized into four sectors, which are mechanical,
bio-chemical, electrical and thermal forms.
1) Mechanical form. Compressed Air Energy Storage (CAES) system was
constructed recently. In the form of compressed air it stores energy in a deep
underground geological vessel or reservoir. Electricity from the grid powers
compressors is used to drive air into the storage vessel underground during
off-peak hours. When peak hours come, the stored air is released and heated with
natural gas to expand its velocity. This air-gas mixture then can be used in a
combustion turbine which can generate power for use.
2) Bio-Chemical form. Biofuels are gaining increased attention of both public
and scientific recently. This kind of fuel is formed by biological carbon fixation
and can be derived from biomass conversion. A considerable amount of solar
energy is stored as chemical energy in this process, and the stored energy then can
be released in a straightforward way. The widely utilization of biofuels such as
bioethanol, biodiesel, biogas, etc., would increase energy security. This is the class
of sunlight-to-bio-chemical energy storage.
3) Electrical form. Many kinds of rechargeable batteries such as Lead-acid,
Carbon-zinc, Lithium-ion etc., are usually used to store spare electricity, and the
stored electricity can be used at times when a demand comes. As the stored energy
in battery is used up, it is easy to recharge.

17
 4) Thermal form. This means the temporary storage of heat or cold for later
use, ice-storage for air conditioning on hot summer days is one example, water is
frozen into ice at night, when electricity consumption cost is lower, then the cool
of the ice can be used in the afternoon to meet conditioning demand as well as
reduce the electricity consumption in daytime when cost is higher. This ice storage
is produced with a lower electrical utility rate.
Recently, much effort has been put to convert solar energy into electricity,
and the discovery of the new type device showed that low cost materials can be
used in the construction of solar cells. Another way to utilize solar energy is water
splitting with production of molecular oxygen and hydrogen.[41]
The function of Photosynthesis sets an almost perfect example to solar
energy utilization including solar capture, conversion and storage. This process
provides energy for nearly all life on the earth. The generation of oxygen[42] from
water takes place at an active site in Photosystem II (PS-II). This active center
contains four manganese ions, which is a binuclear bis(μ-oxo) dimanganese unit..
This cluster containing four manganese ions is named the Oxygen Evolving
Complex (OEC).[43,44]
O MnII
O2 IV
O Mn O OH2 O
O
O -e-, -H+
O
MnIV O OH2
O
2OH2 O MnIII

S0 O MnIII
O MnIV O MnIV O OH
O MnIV O O
O
O O
O O
O MnIV O OH2
O O
MnIV O O MnIII
O
O MnIII
S1
S4

-e-, -H+
O MnIV
O MnIV -e-, -H+
IV
O MnIV O OH O Mn O OH
O
O O
O
O
O MnIV O OH
MnIV O O O
O O MnIII
O MnIV
S2
S3
- +
-e , -H

Figure 3.1 Proposed mechanism on water oxidation at the OEC in photosystem II.
Many papers reported the possible mechanism[45] related to oxygen evolution
at this active center. One general proposal is show in Figure 3.1. It is recognized
that the release of oxygen from water takes place via a stepwise proton-coupled

18
electron transfer, resulting in the manganese complex from the sequentially
oxidized state S0 to S4. At state S4, O2 is generated while two water molecules
come in, and finally the complex returns to the state S0.
Inspired by the function of PS-II, many artificial photosynthesis systems
aiming at producing oxygen by light-driven water splitting have been built
recently. In order to mimic the function of the oxygen evolving complex (OEC) in
PS II, much effort has been devoted to the development of molecular catalysts in
order to be able to oxidize water. The design of qualified water oxidation
catalysts[46-54] (WOCs) is one of the keys for an artificial photosynthesis system
with high efficiency. However, only a few artificial bioinspired complexes display
a satisfactory performance on catalytic O2 generation from water. Several series of
efficient WOCs based on the Ru, Ir and other transition metals, have been
reported over the last years.

3.2 Introduction to Proton-Coupled Electron Transfer (PCET).

Charge separation is the basis of photosynthetic energy utilization which carried

out in biological systems. The electron transfer, which occurs in the charge
separation, is frequently accompanied with proton transfer, such as in
Photosystem II (PS-II), and this is called as Proton-Coupled Electron Transfer
(PCET) reactions.[55,56] The theory on PCET reaction has been developed over
several years. It is depicted as[57] the nonadiabatic transitions between the
reactant and product electron-proton vibronic states. Actually, this kind of
reaction plays a vital role in a wide range of biological processes, such as
respiration and photosynthesis.
In PS II, upon the absorption of a photon, P680 is excited and becomes
strongly reducing and transfers an electron to the acceptor and form P680+. Then a
tyrosine group (Tyrz) donates one electron to the P680+, and simultaneously
dissociates its phenolic proton to a base nearby.
In order to mimic the proton coupled electron transfer function in PS II,
Hammarström and coworkers used a synthetic compound[58,59] to investigate the
electron transferring of tyrosine (Figure 3.2). They took ruthenium-tris-bipyridine
(Ru(bpy)3) as a photosensitizer, after exposure to sunlight, the Ru(bpy)3 reaches
its excited state and loses one electron. The oxidized Ru(bpy)3 can receive one
electron from the tyrosine, which transfers one electron and is deprotonated
simultaneously.

19
 hv
Oxidative
Quenching
N N e
O
EtOOC N Ru N MV2+
NH
HO N N
Deprotonation
e
Electron Transfer
Figure 3.2 Proton coupled electron transfer from tyrosine. The supramolecular system
RuII(bpy)2(4-Me-4’-CONH-L-tyrosine etyl ester-2,2’-bpy)2+.

In fact, PCET processes are important for oxygen evolution in artificial

photosynthetic systems as well. Water is required to be oxidized to produce
oxygen, however, this is not straight forward. The thermodynamic potentials
decrease as the number of electrons transferred increase (Table 3.1).[60,61] The
required thermodynamic potential for oxygen evolution from water is 1.23 V vs.
NHE at pH 1.0, and this water oxidation involves the loss of four protons and four
electrons. The designed catalysts should have the property of multiple electron
transfer. Therefore, transition metal complexes are considered as suitable
candidates to perform this reaction in a catalytic manner since they often have
many accessible oxidation states. Among them, ruthenium aqua complexes meet
these requirements, since the Ru complexes has the ability of losing protons and
electrons to reach their higher oxidation states.
Table 3.1
Redox couple E, V (vs. NHE)
pH = 1.0
+ -
•OH + 1H +1e — H2O 2.81
HO-OH + 2H+ +2e-—2H2O 1.78
HOO• + 3H+ +3e- — 2H2O 1.51
O=O + 4H+ +4e- — 2H2O 1.23

0.67 V 0.78 V
(a) cis-[RuII(bpy)2(py)(H2O)]2+ cis-[RuIII(bpy)2(py)(OH)]2+ cis-[RuIV(bpy)2(py)(O)]2+

V vs NHE, u=0.1M, pH=7

1.7 V
(b) cis-[RuII(bpy)2(Cl)2]0 0.0 V cis-[RuIII(bpy)2(Cl)2]1+ cis-[RuIV(bpy)2(Cl)2]2+

V vs NHE, 0.1M [N(n-Bu4)PF6/CH3CN]

Scheme 3.2 Oxidation potentials for two sets of ruthenium polypyridyl based
redox couples.

20
 Without involving high energy intermediates, the type of PCET provides a
plausible reaction pathway to access the higher state for ruthenium aqua
complexes.[62-64] The comparison in Scheme 3.2 provides an explanation for the
advantage of ruthenium aqua complex. The redox potential difference between
Ru(IV/III) and Ru(III/II) is only 0.11V for ruthenium aqua complex (Scheme 3.2
a), while this difference jumps to 1.7V for ruthenium chloride complex (Scheme
3.2 b). The smaller difference in oxidation of the ruthenium aqua complex
indicates that the coordination of water stabilizes Ru(IV) dramatically. The main
reason for this stabilization of higher oxidation state is the oxo formation. It also
indicates that the conditions required for oxidation from Ru(II) to Ru(IV) are
relatively mild for ruthenium aqua complexes.
One specific example[65] of PCET is for the “blue dimer”. The initial
oxidation state H2O-RuIII-O-RuIII-OH2 also undergoes oxidative activation via
proton-coupled electron transfer pathway, which means a sequential loss of
protons and electron occurs. PCET is important for the blue dimer to build up
multiple oxidative equivalents without increasing positive charge.

3.3 Water Oxidation Catalysts

3.3.1 Ruthenium-Based WOCs.

3.3.1.1 Dimeric Ruthenium-Based WOC.

H2O
OH2 N
N
O Ru N
N Ru
N N
N
N

3-1
(13, 0.004 s-1)
Figure 3.3 Structure of cis,cis-[(bpy)2(H2O)RuIII-O-RuIII-(H2O)(bpy)2]4+. TON and
TOF values are given in parentheses, respectively.

Complex 3-1 cis,cis-[(bpy)2(H2O)RuIII-O-RuIII-(H2O)(bpy)2]4+ (bpy = bipyridine)

normally referred to as the blue dimer[66] due to its deep blue color, was first
reported by Meyer’s group. The feature of this dimer is two Ru-OH2 units are
connected by a dianionic oxido ligand (Figure 3.3), which results in an electronic

21
coupling between the two metal centers, and therefore shows interesting
electrochemical properties, such as redox behaviors and its catalytic property by
extension.

The X-ray structure[67] of this blue dimer is shown in Figure 3.4:

Figure 3.4 X-ray structure of complex 3-1 cis,cis-[(bpy)2(H2O)RuIII-O-RuIII-

(H2O)(bpy)2]4+. Hydrogen atoms are omitted for clarity. (purple for Ru, grey for C,
red for O and blue for N).
When adding CeIV into the acidic solutions containing the blue dimer, the gas
is released from the solution. After gas chromatographic and mass spectrometric
measurements, the released gas was confirmed to be oxygen. The turnover
number (TON) is around 13 and the turnover frequency (TOF) is 0.004 s-1. This
ruthenium complex was taken as a landmark in water splitting since it is the first
synthetic molecular catalyst for water oxidation. The mechanistic and kinetic
studies of CeIV oxidation of this blue dimer will be discussed in detail later in this
chapter.
Since the first water oxidation catalyst ‘blue dimer’ carries a dimeric
structure. The two Ru fragments are connected via an oxo bridge that tends to
cleave, which limits the lifetime of the catalysts. The discussion about the
requirement for dimeric or higher order structures was in debate at that time until
the discovery of monomeric ruthenium-based WOCs.

3.3.1.2 Monomeric Ruthenium-Based WOCs Carrying Neutral

Ligands.
Several monomeric complexes based on Ru were presented by Thummel’s
group.[68-70] These complexes also displayed a good performance on catalytic
water oxidation. This demonstrated that one site is enough for catalytic water
oxidation. In fact, the discovery of mononuclear ruthenium WOCs is one of the

22
major recent breakthroughs.

In 2005, the hydrogen-bonded aqua complex 3-2 trans-[Ru(pbn)(4-R-py)2

(OH2)]2+ (pbn = 2,2’-[4-(tert-butyl)pyridine-2,6-diyl]bis(1,8-naphthyridine); py =
pyridine)[71] (Figure 3.5), which contains only one Ru center was reported by
Thummel’s group. It was encouraging that this mononuclear catalyst also could
perform water oxidation, which provides a qualitative evidence for catalytic
activity of mono-nuclear catalyst.

N N
N Ru N
HO
H N
N
(PF6)2

3-2

(260, 0.014 s-1)

Figure 3.5 Structure of complex 3-2, trans-[Ru(pbn)(4-Me-py)2(OH2)]2+. TON
and TOF values are given in parentheses, respectively.

N 2+
OH2 2+ N
N N 2+
II II
N Ru N Ru N N
N II
N N N Ru N
N N
N

3-3 3-4 3-5

(310, 0.029 s-1) (89, ---) (416, 0.028 s-1)

Figure 3.6 Molecular structures of mono-nuclear Ru (II) catalysts. TON and TOF
values are given in parentheses, respectively.

Afterwards, a series of monomeric ruthenium WOCs were synthesized, as

shown in Figure 3.6. All those complexes, 3-3 Ru(tpy)(bpy)OH2 (tpy = terpyridine;
bpy = bipyridine), 3-4 Ru(tpy)(pic)3 (pic = 4-picoline) and 3-5 Ru(dpp)(py)2 (dpp
= 2,9-dipyrid-2’-yl-1,10-phenanthroline; py = pyridine) are active catalysts for

23
water oxidation, although their activities are different between different series.

3.3.1.3 Monomeric Ruthenium-Based WOCs Carrying Anionic

Ligands .
Recent research shows that the introduction of anionic (negatively charged)
ligands,[72-75] as in complexes 3-6 Ru(bda)(pic)2 (H2bda =
2,2’-bipyridine-6,6’-dicarboxylic acid; pic = 4-picoline) and 3-7 Ru(bda)(isoq)2
(isoq = isoquinoline), and 3-8 Ru(pdc)(pic)3 (H2pdc = 2,6-pyridine-dicarboxylic
acid; pic = 4-picoline.) (Figure 3.7), yields significantly improved catalytic
activity compared to complexes bearing neutral ligands. This is because the
introduction of negatively charged ligands results in destabilization of the filled d
orbitals of ruthenium complexes with lower-valence, due to dπ-pπ repulsion. When
the ruthenium complexes reach high-valent states, these negatively charged
ligands provide stabilization by favorable interaction between the empty d-orbitals
of the ruthenium and filled p-orbitals of the oxygen atoms.
CH3 Me

N N O N
O
N N N N N RuII N Me
O Ru II O O Ru II O O
O O O O O N
N N

Me
CH3
3-6 3-7 3-8

(2000, 18 s-1) (8440, 469 s-1) (550, 0.23 s-1)

Figure 3.7 Molecular structures of complexes 3-6, 3-7, 3-8. TON and TOF values
are given in parentheses, respectively.

3.3.2 Iridium-Based WOCs

Several complexes based on iridium display water oxidation activity. The

cyclometalated iridium-based complex 3-9 [Ir(5-F,4’-F-phenylpyridine)2(OH2)2]+
has been synthesized by Bernhard’s group.[76,77]

24
 Me OH2 Me
N
Ir
N
F OH2 F
3-9
(2760, 0.004 s-1)

Figure 3.8 Molecular structure of Ir catalyst. TON and TOF values are given in
parentheses, respectively.
This kind of water oxidation catalyst (Figure 3.8) shows some impressive
properties, such as robustness, high-efficiency, and easy-modification. However,
the low catalytic rate limits its broad application. Usually it takes a long time
(around one week) to complete the reaction.

3.3.3 First-Row Transition Metal Based WOCs

Artificial water oxidation catalysts using first row transition metals such as
manganese, cobalt and so forth, usually suffers from both low turnover numbers
and low turnover frequencies, even though a manganese cluster is central to the
OEC in photosynthesis. Few of complexes based on the first-row transition metals
have been reported as efficient water oxidation catalysts.
3.3.3.1 Manganese-Based WOCs
Synthetic water oxidation catalysts based on manganese have come into
notice since complex 3-10 [(tpy)(H2O)Mn(-O)2Mn(tpy)(H2O)]3+ (tpy =
2,2’:6’,2’’-terpyridine) (Figure 3.9) was reported by Brudvig’s group.[78] The TON
reaches a moderate number of 17 using CeIV as an oxidant.

OH2
N O N
N Mn Mn N
O
N N
H2O

3-10
(17, ---)

Figure 3.9 Molecular structure of [(tpy)(H2O)Mn(-O)2Mn(tpy)(H2O)]3+, TON

and TOF values are given in parentheses, respectively.

25
3.3.3.2 Cobalt-Based WOCs
Complex 3-11 Cobalt-based –octa-fluoro hangman corrole was reported by
Nocera’s group in 2011.[79] It contains meso-pentafluorophenyl and –octa-fluoro
substituents (Figure 3.10), and shows a satisfactory performance on water
oxidation. This complex is so far confirmed as the most active catalyst among
cobalt corroles.
t-Bu
O
C OH

O F C6F5 F
F F
N N
Co
N N
F F
t-Bu F C6F5 F

3-11

(---, 1 s-1)

Figure 3.10 Molecular structure of cobalt-based –octa-fluoro hangman corrole.

TON and TOF values are given in parentheses, respectively.
The TOFs per Co atom for 3-11 can approach around 1 s-1 (at pH 7) when
immobilized in Nafion films, which is higher than other cobalt-based water
oxidation complexes.

3.4 A Hydrogen-Bonding Network Effect

Hydrogen bonds which are involving multiple peptide carbonyl groups to water
form a network around the oxygen-evolving complex (OEC) in photosystem II.
Some research results demonstrate that this hydrogen bonding network could be
involved in the catalytic water oxidation and play a key role in this process.
The position of bound water molecules has been confirmed by the Kamiya
research group.[80] There are approximately 1300 water molecules per monomer of
PS-II, four water molecules are proposed to be placed at the active reaction center
OEC. Two of them were predicted to bind to manganese, and another two waters
are bound to calcium (Figure 3.11). This structure confirmation suggests that at
the OEC water forms wide hydrogen-bonding network.

26
Figure3.11 Hydrogen bonding network at oxygen evolving complex, two of them
were bound to manganese, and another two waters bound calcium. (Reprinted
with permission from Nature Publishing Group).

In fact, this water hydrogen-bonding network at the OEC is necessary and

important for water oxidation.[81] Experiments show that disruption of this
network destroys the steady state rate of S1 to S4 in water oxidation.
Hydrogen bonding networks are important in our calculated systems as well.
In a realistic medium of water, the protic solvation effect is obvious and quite
strong. In order to reproduce this effect accurately, we add two additional explicit
water molecules to the aqua-Ru complex (L)(pic)2RuIII-OH2 (L = hqc, pdc, H2hqc
= 8-hydroxyquinoline-2-carboxylic acid) in our calculations.[82] Two optimized
geometries are shown in Figure 3.12:

a) b)

Figure 3.12 Calculated geometries of [RuIII(hqc)(pic)2−OH2]+ (a) and

[RuIII(pdc)(pic)2−OH2]+ (b) in aqueous medium. Hydrogen atoms except those
bonding to oxygen atoms are omitted for clarity. (purple for Ru, grey for C, blue
for N, red for O and green for H).

27
 One of the water molecules serves as both a hydrogen-bond donor and
acceptor at the same time, the other one acts only as a hydrogen-bond acceptor.
This hydrogen-bonding network could function as a channel for proton transfer
and facilitate the Proton-Coupled Electron Transfer (PCET).

3.5 OO Bond Formation (O2 Evolution)

The O-O bond formation is one of the most important steps in the oxygen
evolution mechanism. After a stepwise and simultaneous loss of electrons and
protons, the complexes are able to reach their higher oxidation states, which is
required for the OO bond formation.
Generally, there are two main proposals for the key O-O bond formation
event.[83-85] One is coupling between one terminal oxo and the oxygen atom of the
incoming water substrate or possibly a hydroxide ion (WNA). The other one is
oxo-oxo coupling between two M=O units (I2M). The difference between these
two pathways is whether a solvent water molecule is involved in the formation of
OO bond or not. The two proposed OO bond formation pathways are shown in
Table 3.2.
Table 3.2

M O
WNA H M + O-O +2H+
O
H

M O
I2M 2M + O-O
O M

3.5.1 Water Nucleophilic Attack (WNA).

Water attack on the oxo group to give a terminal peroxide in the key OO
bond forming step
When the transition metal complex reaches its higher oxidation state, it could
undergo a water nucleophilic attack, forming a peroxidic intermediate, and finally
release the oxygen while the empty position is coordinated by an incoming
water.[86-89] The whole mechanistic proposal of WNA for water oxidation using
Ru-based WOC is represented in Figure 3.13.

28
 (L)RuII OH2
O-O
-2e-
+ OH2 -2H+

O
(L)RuIV O (L)RuIV O

-e-
-e-
+
-H

OH + OH2
(L)RuIII O (L)RuV O
-H+

Figure 3.13 Proposed OO bond formation mechanism based on the water

nucleophilic attack.
The complex RuII-OH2 undergoes a sequential removal of electrons and
protons to form RuIV-O, and it can reach an even higher oxidation state RuV-O.
Once the RuV-O is formed, which is a highly reactive species, it undergoes a
nucleophilic attack from a solvent water, then forms the terminal hydroperoxidic
complex RuIII-OOH, which contains the key feature of the O-O bond. The formed
RuIII-OOH intermediate can lose one more electron accompanied with one proton
loss to form RuIV-OO, then releasing oxygen and finally coordinate a solvent
water molecule. This WNA route was identified to be feasible for the well-known
blue dimer (Figure 3.14).[90]
RuV-O-RuIV
-e- O O -e-
-2H+

RuIV-O-RuIV RuV-O-RuV
OH OH O O
- RuIII-O-RuIII H2O
-e
OH2 OH2 pa
-H+ -e- th
-H+ a
O2
III IV
Ru -O-Ru RuIV-O-RuIV
H2O
OH2 OH
OH OOH

b
th
O2 pa -e-
RuIV-O-RuV
H2O
OH OOH
Figure 3.14 Mechanistic proposal for O2 generation using the blue dimer as
catalyst. bpy ligands are omitted for clarity.

The oxidation from H2O-RuIII-O-RuIII-OH2 to O-RuV-O-RuV-O was

completed by a stepwise electron-proton removal. This product is a reactive and

29
transient intermediate which is responsible for releasing oxygen when reacting
with the solvent water. Once complex O-RuV-O-RuV-O was generated, it
underwent a water nucleophilic attack immediately to form
IV IV
HO-Ru -O-Ru -OOH intermediate. The following oxygen releasing step is
dependent on the amount of CeIV oxidant.
If there is a stoichiometric amount of the CeIV oxidant, following path a
HO-RuIV-O-RuIV-OOH intermediate generates oxygen and reforms the complex
H2O-RuIII-O-RuIII-OH2, which is the initial form of blue dimer. However, the
generation rate is relatively slow. If an excess of the CeIV oxidant is used, as path
b shows, intermediate HO-RuIV-O-RuIV-OOH will be further oxidized to
O-RuV-O-RuIV-OOH, which releases oxygen much more rapidly, and then forms
H2O-RuIII-O-RuIV-OH.

3.5.2 Interaction Between Two M-O Units (I2M).

Oxidative coupling of the two terminal oxo atoms of M=O.

The OO bond formation from the interaction between two M-O complexes
includes two different manners, 1) Intramolecular approach, which means two
M-O units are situated in one complex; 2) Intermolecular approach, which
indicates that it is a bimolecular process, each complex contains only one M-O
unit. Both pathways using Ru-based WOCs can be concluded in Figure 3.15.

Ru Ru
O O

RuIV RuIV RuIII RuIII

O O O O
-4e- Two Ru units are either + OH2
-4H+ linked or separated

RuII RuII Ru Ru
O
OH2 OH2 O O
H H
O2

H2O RuIII RuIII

O O
H
OH

Figure 3.15 General proposed OO bond formation mechanism based on

interaction of two Ru-O units. (Both intramolecular and intermolecular pathways)

30
3.5.2.1 Intramolecular Approach

For the complex in, in-{[RuII(trpy)(OH2)]2(bpp)}3+ (in, in- Ru-Hbpp) (trpy is

2,2′:6′,2′′-terpyridine, bpp is bis(2-pyridyl)-3,5-pyrazolate),[91] which contains two
Ru-O units in one same complex, calculations show that the only OO bond
formation mechanism occurring in this system is an intramolecular pathway
(Figure 3.16), whereas the water nucleophilic attack manner is excluded.

N N N N
In
- RuIV RuIV tra
-4e m
O O ol
ec
-4H+ ul
ar

N N N N N N N N
RuII RuII RuIII RuIII
OH2 OH2 O O

H2O
O2
N N N N
H2O
RuIII RuIII
OOH OH

Figure 3.16 Potential water oxidation mechanism for the in, in-Ru-Hbpp complex,
and the trpy ligands are omitted for clarity.

The complex H2O-RuII-Hbpp-RuII-OH2 is stepwise oxidized by Ce(IV) up to

O-RuIV-Hbpp-RuIV-O. It then generates a Hbpp-1,2-peroxo intermediate via an
intramolecular interaction between two oxygen atoms, and this coupling reduces
the Ru oxidation state from IV to III. A hydroperoxdic intermediate
HOO-RuIII-Hbpp-RuIII-OH is then formed when one water molecule enters and it
release oxygen finally with one more water coming in.

3.5.2.2 Intermolecular Approach.

To the best of our knowledge, OO bond formation via intermolecular coupling
proposal was first reported by Privalov and Sun in 2010.[92, 93]

31
 N N

N N N N
O Ru O O Ru O
O O O O
N N

3-6 3-7

Figure 3.17 Structures of complexes 3-6 and 3-7.

Two different mono-ruthenium complexes 3-6 Ru(bda)(pic)2 (H2bda =

2,2’-bipyridine-6,6’-dicarboxylic acid; pic = 4-picoline) and 3-7 Ru(bda)(isoq)2
(isoq = isoquinoline) were synthesized by Sun and coworkers (Figure 3.17).
Especially complex 3-7 demonstrates superior catalytic performance on water
oxidation using CeIV as the oxidant. It reaches to an amazingly high reaction rate
with a TOF of more than 400 s-1. The performance of complex 3-7 is comparable
to the oxygen-evolving complex in photosystem II, where the oxygen generation
rate[94] in OEC is estimated at 100-400s-1(light-driven).
The kinetic studies provide insight into the mechanism of OO bond
formation. The kinetics of the catalytic reaction for water oxidation was identified
as second order, which indicates the reaction proceeds in a bimolecular manner. A
radical coupling between two Ru-O units[95-98] was proposed to be involved in this
key process.
Now we focus complex 3-6 for a detailed discussion. Normally the ideal
angle for an octahedron configuration is 90º, however, for complex 3-6, the
O-Ru-O angle is expanded to 122.99º. It therefore can generate a
seven-coordinated complex by accepting one incoming water molecule. After
reaching its high oxidation state, it forms a seven-coordinate RuIV dimer
–(HOHOH)-[RuIV(bda)(pic)2]2. The crystal structure of this dimer is shown in
Figure 3.18.

32
Figure 3.18 Crystal structure of seven-coordinate Ru(IV) dimeric complex.
Hydrogen atoms except those bonding to oxygen atoms are omitted for clarity.
(purple for Ru, grey for C, red for O, blue for N, and green for H).

The calculated free energy barrier via a low-spin antiferromagnetic transition

state is only 11.9 kcal/mol by taking the encounter complex as a reference. From
the former computational study by Yang and Baik,[99] the dissociation of oxygen
does not demand a high-energy ligand exchange from a peroxo intermediate. The
general inter-molecular OO bond formation proposal is shown in Figure 3.19.

RuII - 2e- RuIII - 2e- RuIV - 2e- RuV

2 2 2 2
OH2 OH2 -2H+ OH -2H+ O

O2 O
RuIV RuIV
O
+2OH2

Figure 3.19 General description of oxygen evolution with inter-molecular

coupling pathway.
Both electronic and geometrical properties of bda ligand make a contribution
on the formation of a seven-coordinate complex, which is essential for generation
of seven-coordinate dimer afterwards. OO bond formation is proposed from the
bi-nuclear coupling for the first time.

33
34
Chapter 4
Natural Hydrogenases and Synthetic Mimic Complexes

4.1 Brief Introduction

Providing a non-polluting, abundant and renewable energy source is one of the

main scientific challenges we are facing. As an energy carrier and potential
transportation fuel, hydrogen (H2), a closed-shell molecule has been
envisioned.[100,101] Hydrogen is an ideal fuel, which can be generated from water,
and the only product of the reaction is water when combustion of hydrogen is
made with pure oxygen. It can therefore conform to the requirement of
sustainability, energy security and environmental-benign character. Furthermore,
hydrogen is one of the fuels which has highest specific energy. The energy density
of hydrogen can reach 33.3 kWh/kg (30 MPa),[102] this indicates it can release 33.3
kWh/kg of energy for every one kilogram. The energy density of hydrogen is
much higher than that of gasoline (12.7 kWh/kg) which is frequently used in our
daily life. However, gasoline (8.76 kWh/kg) shows a much better performance
than hydrogen (0.75 kWh/kg, 30 MPa) if we compare these fuels in energy per
unit volume. Finding new ways to store hydrogen is therefore one of the main
targets we are facing now.
Hydrogen is also involved in several key chemical processes, such as
hydrogenation of inorganic and organic compounds which affects our daily life
greatly. For example, ammonia fertilizer is necessary for human society to survive
and develop since we need to feed the growing population by increasing the
production of agricultural products.[103,104] In addition, there is a need to remove
sulfur and nitrogen from hundreds of million tons of crude oil to keep a high
quality,[105] and hydrogen is used for this purpose.
Although hydrogen is playing and continues to play an important role in our
daily life, the economical production or the uptake of molecular hydrogen is
limited by the intrinsic kinetic properties. Usually hydrogen does not react with
other chemicals at room temperature. It can react with oxygen to form water,
however, this reaction is extraordinarily slow at ambient temperature. The
hydrogen was even used as an “inert” gas in early air-free chemistry because of its
stable chemical properties although it is now replaced by N2 or Argon.

35
 The following physical and chemical properties[106] could provide part of the
explanation for the unreactive property of hydrogen:

(1) Hydrogen is a completely nonpolar molecule;

(2) The bond between H-H is remarkably strong, and the required energy for
homolytic cleavage of an H-H bond is 103 Kcal/Mol;
(3) Due to the high basicity of hydride (H-) hydrogen is a poor acid.

Since the H-H bond is generally stronger than most new H-X bonds,
chemists place the H-H bond into the strongest single bond category. The design
of effective catalysts for hydrogen oxidation and proton reduction becomes a
challenge. Because of the intrinsic thermodynamic limitations, molecular
hydrogen production/uptake is currently only economically viable under high
temperature condition or in presence of a platinum catalyst.[107,108]

4.2 Hydrogeneases Enzymes

The natural hydrogeneases[109-113] serve as good models for hydrogen
uptake/production. Hydrogeneases are billion-year old redox enzymes and
frequently present in microorganisms belonging to the Archaea and Bacteria
domains of life, a few of them are found in Eukarya as well.[114] They display a
remarkable performance on the reversible inter-conversion between protons and
hydrogen, since the purpose of hydrogeneases enzymes is to set a charge
separation or combination. Consequently, synthetic catalysts with simpler
structure based on these hydrogenase enzymes have been studied.
Most of the hydrogenase enzymes[115] can be divided into two major classes
by specifying the transition metal they carry: Ni-Fe and Fe-only hydrogenases.
Ni-Fe hydrogenases are primarily used for hydrogen uptake, whereas the Fe-Fe
hydrogenases are usually used for proton reduction.

4.2.1 Ni-Fe Hydrogenases

The Ni-Fe hydrogenases[116,117] are mainly used for the heterolytic cleavage of
hydrogen. The X-ray crystal structure of the oxidized form of Desulfovibrio gigas
of a Ni-Fe hydrogenase was obtained at a resolution of 2.85 Å for the first time in
1995,[118] and from then on X-ray crystal structures from other organisms have
been obtained.[119-121]

36
Figure 4.1 The crystal structure of nickel-iron hydrogenases purified from D.
gigas. (Reprinted with permission from ACS Publications )

As shown in Figure 4.1, a nickel atom is situated in the active site, a chain of
three iron-sulfur clusters consists of one [3Fe-4S] cluster and two cubane type
clusters contain eleven iron atoms.[122]

4.2.2 Fe-Fe Hydrogenase

Iron-iron hydrogenases[123-126] are generally found capable of reducing protons,
although some of them are used for hydrogen oxidation and bi-directional
occasionally. For molecular structures of Fe-Fe hydrogenases, there are many
different sources, scientists still found many structural similarities among them
although the structures of them are even slightly different from each other under
different crystallization states. The main structures were concluded from the X-ray
crystallographic information of Desulfovibrio desulfuricans Hildenborough (DdH)
and Clostridium pasteurianum I (CpI)[127-129] (Figure 4.2), which are hydrogen
uptake and hydrogen production enzymes, respectively.

Figure 4.2 The crystal structure of Clostridium pasteurianum I (CpI) iron-iron

hydrogenase. (Reprinted with permission from ACS Publications)

37
 The consensus structure[130] of the active site of Fe-Fe hydrogenase is shown
in Figure 4.3,

X
4Fe-4S
L S S
S Cys
OC Fe Fe CN
NC C CO
O
X = CH2, NH or O.

Figure 4.3 The consensus structure of the active site of Fe-Fe Hydrogenase.

Furthermore, the Fe-Fe hydrogenases are well known for their abilities to
reduce protons to hydrogen, at nearly Nernstian potentials the turnover
frequencies of Fe-Fe hydrogenase enzymes can reach a value of around 6000 mol
of H2/mol per hydrogenase enzyme per second. Many scientists are inspired by
the amazing catalytic performance of proton reduction/hydrogen uptake with
hydrogenases. Therefore, many variations of electrochemical and photochemical
hydrogen production/uptake systems based on Fe-complexes have been created.
Numerous studies both experimentally and theoretically focus on these artificial
systems.

4.3 Homogeneous Light-Driven Catalytic Systems

After studying the structures of hydrogenase enzymes, we found that the first-row
transition metals, such as iron and nickel, are usually present in catalysts for a
catalytic hydrogen uptake/production. This discovery results in a fast development
of hydrogenase modelization, therefore many studies have been devoted to
synthesize much smaller molecular complexes to mimic the structure and function
of these hydrogenase enzymes.
In addition, hydrogen generation using renewable energy such as solar
energy could be an ideal method for sustainable production and storage of energy,
and many scientific groups has focused their attention on water splitting during
last 30 years.[131-138] It is important to emphasize that most of work in this field
was devoted to heterogeneous photocatalytic systems,[139-141] while homogeneous
ones were poorly developed. However, during the past few years much progress
has been achieved in developing and understanding homogeneous photocatalytic
systems.[142-146]
Recently, Mei Wang and coworkers designed a system[147] (Figure 4.4)
comprising of 1) Photosensitizer, usually based on the ruthenium tris-bpy moiety;

38
2) A catalytic center based on a transition metal complex; 3) A redox mediator.

X
hv 2+

Y X H2
- N e-
e N
N N
(a) (b) (c)
Ru S
Donor S
N N OC CO
H+
N OC Fe Fe CO
Y X H
OC CO

X
(a) reductive quenching; (b) intermolecular ET; (c) catalytic proton reduction

Figure 4.4 Homogeneous light-driven catalytic systems based on Fe for hydrogen

production using ruthenium-polypyridine as photosensitizer.

However, homogeneous light-driven catalytic systems for hydrogen

production remain relatively rare in experimental phase. A practical technology
for hydrogen generation derived from solar energy remains a goal to be achieved.

4.4 Effect of the Pendant Base in Iron-Complexes.

The transport or movement of proton is vital[148-151] in many biological and
chemical processes including the hydrogen oxidation/production, the reduction of
CO2 to formate and the reduction of O2 to water. It is often related to energy
storage and utilization, however the details of these processes are still ambiguous.
Internal amine base is a reoccurring feature of hydrogenases. It is likely to
facilitate the proton transfer to the metal center. For natural hydrogenase enzymes
or synthetic catalysts based on iron or nickel, we found that the incorporation of a
pendant amine is a frequently occurring feature, the pendant amine base is located
in proximity of the metal and forms a weak interaction with the metal since it is
too far away to form a strong bond.[152] Many research groups have also reported
aza and oxadithiolates as probable proton relays[153-158] in functional models for
the Fe-Fe hydrogenases, and are dedicating their efforts to this process, aiming at
providing understanding for their functions.

4.4.1 Pendant Base Effect on Proton Transfer in Iron-Complex

Three complexes 4-1 Fe2(pdt)(CO)2(dppv)2, 4-2 Fe2(adt)(CO)2(dppv)2 and 4-3
Fe2(odt)(CO)2(dppv)2 (dppv = cis-1,2-bis(diphenylphosphino)ethylene; pdt =
1,3-propanedithiolate; adt = 2-azapropane-1,3-dithiolate; odt =

39
2-oxopropane-1,3-dithiolate) were synthesized, and all these complexes are with a
dithiolate moiety which acts as a bridge between the two iron subunits.[159]
Rauchfuss and coworkers proposed that the functionality of amine in complex 4-2
could act as a proton relay that transfers the proton from and to the bridging site
between the two Fe atoms.

X XH 1+

Ph2 Ph2 Ph2 Ph2

S S H+ S
P P P S P
X = NH, O
OC Fe Fe P OC Fe Fe P
P CO Ph2 CO Ph2
P
Ph2 4-1. X = CH2 Ph2
sl
ow

4-2. X = NH
fo

4-3. X = O
r X

H+
=
C
H2

X 1+ X 1+

Ph2 Ph2
S S CO S S H Ph2
P Ph2 P
Fe P
OC Fe Fe P OC Fe
H P C P
P P O
Ph2 Ph2 Ph2
Ph2

[4-1(μ-H)]+; [4-2(μ-H)]+; [4-3(μ-H)]+ [4-1(t-H)]+; [4-2(t-H)]+; [4-3(t-H)]+

Scheme 4.1 Proton relay effect of heteroatom in the dithiolate.

Scheme 4.1 demonstrates how a heteroatom in the dithiolate shuffles proton

to and from the metal iron. All these complexes 4-1, 4-2 and 4-3 were found to be
protonated with a strong acid [H(Et2O)2]BArF4 quickly at -90℃, however, only
complex 4-2 can be protonated if a billion-fold weaker acid [HPMe2Ph]BF4 was
used instead, even though these diiron complexes have similar basicities. This
difference indicates that the presence of a heteroatom N exerts a strong effect on
the rate of protonation. Their results suggested that in complex 4-2 the protonation
initially happens at the amine base, then transfers to the terminal site, and finally
reaches the bridging site. In contrast, for complex 4-1 that contains nonbasic
propanedithiolate or complex 4-3 with a weakly basic oxadithiolate, the initial
protonation on the internal base is blocked.
They also compared the deprotonation of all terminal hydride complex
[4-1(t-H)]+, [4-2(t-H)]+, [4-3(t-H)]+. For complex [4-1(t-H)]+, even at room
temperature it is impossible deprotonate using any organic base, and it isomerizes
to bridging complex eventually. For complex [4-3(t-H)]+, it is inert toward base at
-78℃, however it will generate two products 4-3 and [4-3(μ-H)]+ slowly when the

40
temperature increase to around 0℃. Neither the concentration nor the pKa of the
base has any influence on the proportion of these two products. It is quite different
in the case of [4-2(t-H)]+, the deprotonation of it occurs immediately with a base
of PBu3[HPBu3] BF4 even at a rather low temperature of -90℃, and the only
observed product is complex 4-2.
Since there is almost no difference in the υCO region among these three
complexes in the IR spectra, the thermodynamic acidities of them should be the
similar. This demonstrates that the big difference of the deprotonation rate among
them lies in the presence of the heteroatom.
In summary, complex 4-2 shows that the heteroatom N facilitates the
protonation and relay the proton to Fe immediately, and complex 4-3 which
contains a relatively weakly basic oxadithiolate shows a moderate performance
although inferior of complex 4-2. Complex 4-1 with non-basic propanedithiolate
is inert to both protonation and deprotonation.

4.4.2 Pendant Amine Base Effect on Heterolytic Activation of

Hydrogen in Iron-Complex
The pendant amine base is not only involved in the intramolecular proton transfer
but also related to the heterolytic activation of hydrogen. Computational and
experimental studies were used to provide insight into the details of heterolytic
splitting of hydrogen, which takes place at the incorporated pendant amine and the
metal core (Scheme 4.2).

CH2Ph CH2Ph
N NH 2+
1+

S S S S
H2 (1atm) H
Cp*2Fe+
4-4 (PMe3)(CO)2Fe Fe(dppv) Cp*2Fe+, rm (PMe3)(CO)2Fe Fe(dppv)

C C
O O
[4-4]+

CH2Ph CH2Ph
N NH
+ 2+

S S S S
CO HP(o-tol)3+ P(o-tol)3 CO

(PMe3)(CO)2Fe Fe(dppv) (PMe3)(CO)2Fe Fe(dppv)

H H

[4-4H] + [4-4HH]2+

Scheme 4.2 The pendant amine base facilitates the heterolytic activation of
hydrogen.

41
 Complex 4-4[160] Fe2[(SCH2)2NBn](CO)3-(dppv)(PMe3) first loses one
electron to generate [4-4]+ to the mild oxidant [Fe(C5Me5)2]+, then [4-4]+
participates in the heterolytic activation of hydrogen, one situated at the pendant
amine base N position, while another one is located at the Fe atom. This internal
base makes a contribution to the stabilization of the heterolytically splitted species.
The cleavage first generates a terminal hydride intermediate, which isomerizes to
a more stable form the bridging hydride complex [4-4HH]2+. The proton at the N
site is trapped by P(o-tol)3, and yields [4-4H]+ as the final product.
The two cases we described above indicate that pendant amine bases are
important in proton transfer or movement. In fact, this proton transfer or
movement in complex is a vital part of the mechanistic study of hydrogen
generation and uptake, and pendant amine base plays an important role in this
kind of proton movement or transfer. It is worth for a detailed investigation.
However, the need for this proton relay function has not been clearly explained. It
is therefore necessary for us to study and provide further explanation on the role
the pendant base. We believe that a thorough understanding of proton relays will
be crucial for developing efficient hydrogen production and hydrogen oxidation
catalysts.

42
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