Bioinspired Catalysis E-Book

• Herausgeber: Wiley-VCH
• Kategorie: Wissenschaft und neue Technologien
• Sprache: Englisch

Seitenzahl: 820

Veröffentlichungsjahr: 2014

Beschreibung

This book provides an overview of bioinspired metal-sulfur catalysis by covering structures, activities and model complexes of enzymes exhibiting metal sulphur moieties in their active center.

Leseprobe

Table of Contents

Cover

Related Titles

Title Page

Copyright

List of Contributors

Preface

Part I: PrimordialMetal–Sulfur-Mediated Reactions

Chapter 1: From Chemical Invariance to Genetic Variability

1.1 Heuristic of Biochemical Retrodiction

1.2 Retrodicting the Elements of Life

1.3 Retrodicting Pioneer Catalysis

1.4 Retrodicting Metabolic Reproduction and Evolution

1.5 Retrodicting Pioneer-Metabolic Reactions

1.6 Early Evolution in a Spatiotemporal Flow Context

Acknowledgments

References

Chapter 2: Fe–S Clusters: Biogenesis and Redox, Catalytic, and Regulatory Properties

2.1 Introduction

2.2 Fe–S Cluster Biogenesis and Trafficking

2.3 Redox Properties of Fe–S Clusters

2.4 Fe–S Clusters and Catalysis

2.5 Fe–S Clusters and Oxidative Stress

2.6 Regulation of Protein Expression by Fe–S Clusters

2.7 Conclusion

References

Part II: Model Complexes of the Active Site of Hydrogenases – Proton and Dihydrogen Activation

Chapter 3: [NiFe] Hydrogenases

3.1 Introduction

3.2 Introduction to [NiFe] Hydrogenases

3.3 Nickel Thiolate Complexes as Analogs of [NiFe] Hydrogenase

3.4 [NiFe] Hydrogenase Model Complexes

3.5 Analogs of [NiFe] Hydrogenase Incorporating Proton Relays

3.6 Perspectives and Future Challenges

Acknowledgments

References

Chapter 4: [FeFe] Hydrogenase Models: an Overview

4.1 Introduction

4.2 Synthetic Strategies toward [FeFe] Hydrogenase Model Complexes

4.3 Properties of Model Complexes

4.4 Conclusion

References

Chapter 5: The Third Hydrogenase

5.1 Introduction

5.2 Initial Studies of Hmd

5.3 Discovery that Hmd Contains a Bound Cofactor

5.4 Discovery that Hmd is a Metalloenzyme

5.5 Crystal Structure Studies of [Fe] Hydrogenase

5.6 Mechanistic Models of [Fe] Hydrogenase

References

Chapter 6: DFT Investigation of Models Related to the Active Site of Hydrogenases

6.1 Introduction

6.2 QM Studies of Hydrogenases

6.3 QM Studies of Synthetic Complexes Related to the Active Site of Hydrogenases

6.4 Conclusions

References

Chapter 7: Mechanistic Aspects of Biological Hydrogen Evolution and Uptake

7.1 Introduction

7.2 [FeFe] Hydrogenases

7.3 [NiFe] Hydrogenases

7.4 [Fe] Hydrogenase

7.5 Nitrogenase

References

Part III: Nitrogen Fixation

Chapter 8: Structures and Functions of the Active Sites of Nitrogenases

8.1 Introduction

8.2 Properties of Mo Nitrogenase

8.3 Catalysis by Mo Nitrogenase

8.4 Unique Features of V Nitrogenase

8.5 Catalytic Properties of Isolated FeMo-co and FeVco

Acknowledgments

References

Chapter 9: Model Complexes of the Active Site of Nitrogenases: Recent Advances

9.1 Introduction

9.2 Structural Models of Metal–Sulfur Clusters in the Nitrogenases

9.3 Functional Modeling at a Single Molybdenum Center

9.4 Functional Modeling at a Single Iron Center

9.5 The Hydrogen and Homocitrate Issues in Nitrogenase Model Chemistry

9.6 Sulfur– and Metal–Metal Interaction in Functional Models of Nitrogenase

9.7 Surface Chemistry and the Supramolecular Protein Environment

9.8 Conclusion and Outlook

References

Chapter 10: A Unified Chemical Mechanism for Hydrogenation Reactions Catalyzed by Nitrogenase

10.1 Introduction

10.2 Investigations of Mechanism

10.3 Hydrogen Supply for the Reactions of Nitrogenase

10.4 FeMo-co in Nitrogenase as a General Hydrogenating Machine

10.5 Chemical Mechanisms for the Catalysis of Substrate Hydrogenation at FeMo-co

10.6 Hydrogen Tunneling in the Nitrogenase Mechanism

10.7 Intramolecular Hydrogenation of Other Substrates

10.8 Interpretation of the Structure of FeMo-co and Its Surrounds

10.9 Mimicking Nitrogenase

10.10 Summary and Epilog

Acknowledgments

References

Chapter 11: Binding Substrates to Synthetic Fe–S-Based Clusters and the Possible Relevance to Nitrogenases

11.1 Introduction

11.2 Mechanism of Nitrogenases

11.3 Studies on Synthetic Clusters

11.4 Studies on Extracted FeMo-Cofactor

11.5 The Future

References

Part IV: Miscellaneous: CO, RCN Activation, DMSO Reduction

Chapter 12: Sulfur-Oxygenation and Functional Models of Nitrile Hydratase

12.1 Introduction

12.2 Nitrile Hydratase

12.3 Small-Molecule Mimics

12.4 Early S-Oxygenation Studies

12.5 Sulfur-Oxygenation of Co(III) NHase Mimics

12.6 Sulfur-Oxygenation of Fe(III) NHase Mimics

12.7 Ruthenium Complexes

12.8 Conclusions/Challenges

Abbreviations

References

Chapter 13: Molybdenum and Tungsten Oxidoreductase Models

13.1 Introduction

13.2 Classification of Molybdenum- and Tungsten-Dependent Enzymes

13.3 Ligand Systems Commonly Used in Model Studies

13.4 Selected Molybdenum-Containing Enzymes and Relevant Modeling Chemistry

13.5 Selected Tungsten-Containing Enzymes and Relevant Model Chemistry

References

Part V: Applicative Perspectives

Chapter 14: Electrode Materials and Artificial Photosynthetic Systems

14.1 Introduction

14.2 Electrode Materials for Hydrogen Evolution

14.3 Photoelectrode Materials for Hydrogen Evolution

14.4 Artificial Photosynthetic Systems

14.5 Toward Photoelectrode Materials for CO

2

Reduction

14.6 Conclusion and Perspective

References

Index

End User License Agreement

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Guide

Cover

Table of Contents

Preface

Part I: PrimordialMetal–Sulfur-Mediated Reactions

Chapter 1: From Chemical Invariance to Genetic Variability

List of Illustrations

Figure 1.1

Figure 1.2

Figure 1.3

Figure 1.4

Figure 1.5

Figure 1.6

Figure 1.7

Figure 2.1

Figure 2.2

Figure 2.3

Figure 2.4

Figure 2.5

Scheme 3.1

Figure 3.1

Figure 3.2

Figure 3.3

Figure 3.4

Figure 3.5

Figure 3.6

Figure 3.7

Figure 3.8

Figure 3.9

Figure 3.10

Figure 3.11

Figure 3.12

Figure 3.13

Figure 3.14

Figure 3.15

Figure 3.16

Figure 3.17

Figure 3.18

Figure 3.19

Figure 3.20

Scheme 3.2

Figure 3.21

Figure 3.22

Figure 3.23

Scheme 3.3

Figure 3.24

Figure 3.25

Figure 3.26

Figure 3.27

Figure 3.28

Figure 3.29

Figure 3.30

Figure 3.31

Figure 4.1

Scheme 4.1

Scheme 4.2

Figure 4.1

Figure 4.2

Figure 4.3

Figure 4.4

Scheme 4.3

Scheme 4.4

Figure 4.5

Scheme 4.5

Figure 4.2

Scheme 4.6

Figure 4.6

Scheme 4.7

Figure 4.7

Figure 4.8

Figure 4.9

Figure 4.10

Figure 5.1

Figure 5.2

Figure 5.3

Figure 5.4

Figure 5.5

Figure 5.6

Figure 5.7

Figure 5.8

Scheme 5.1

Figure 5.9

Scheme 5.2

Scheme 5.3

Scheme 5.4

Figure 5.10

Figure 5.11

Scheme 5.5

Scheme 5.6

Figure 5.12

Scheme 5.7

Figure 5.13

Figure 5.14

Scheme 5.8

Scheme 5.9

Figure 5.15

Figure 5.16

Figure 5.17

Figure 5.18

Scheme 5.10

Figure 5.19

Figure 5.20

Figure 5.21

Figure 5.22

Figure 5.23

Scheme 5.11

Scheme 5.12

Scheme 5.13

Scheme 5.14

Figure 5.24

Figure 5.25

Scheme 6.1

Scheme 6.2

Figure 6.1

Scheme 6.3

Scheme 6.4

Scheme 6.5

Scheme 6.6

Scheme 6.7

Scheme 6.8

Scheme 6.9

Scheme 6.10

Scheme 6.11

Scheme 7.1

Figure 7.1

Figure 7.2

Figure 7.3

Figure 7.4

Figure 7.5

Figure 7.6

Figure 7.7

Scheme 7.2

Figure 7.8

Figure 7.9

Figure 7.10

Figure 7.11

Scheme 7.3

Scheme 7.4

Figure 7.12

Figure 7.13

Figure 7.14

Figure 7.15

Scheme 7.5

Scheme 7.6

Scheme 7.7

Scheme 7.8

Scheme 7.9

Figure 7.16

Figure 7.17

Figure 7.18

Figure 7.19

Scheme 7.10

Figure 7.20

Scheme 7.11

Scheme 7.12

Figure 7.21

Scheme 7.13

Figure 7.22

Scheme 7.14

Scheme 7.15

Scheme 7.16

Figure 7.23

Figure 7.24

Scheme 7.17

Figure 7.25

Figure 7.26

Figure 8.1

Figure 8.2

Figure 8.3

Figure 8.4

Figure 8.5

Figure 8.6

Figure 8.7

Figure 8.8

Figure 8.9

Figure 8.10

Figure 8.11

Figure 9.1

Figure 9.2

Figure 9.3

Figure 9.4

Figure 9.5

Figure 9.6

Figure 9.7

Figure 10.1

Figure 10.2

Figure 10.3

Figure 10.4

Figure 10.5

Scheme 10.1

Scheme 10.2

Figure 10.6

Figure 10.7

Scheme 10.3

Scheme 10.4

Figure 10.8

Scheme 10.5

Figure 10.9

Figure 10.10

Figure 10.11

Scheme 10.6

Figure 10.12

Figure 10.13

Figure 11.1

Figure 11.2

Figure 11.3

Figure 11.4

Figure 11.5

Figure 11.6

Figure 11.7

Figure 11.8

Figure 11.9

Figure 11.10

Figure 11.11

Figure 11.12

Figure 11.13

Figure 11.14

Figure 11.18

Figure 11.15

Figure 11.16

Figure 11.17

Figure 11.19

Figure 11.20

Figure 11.21

Figure 11.22

Scheme 12.1

Scheme 12.2

Scheme 12.3

Scheme 12.4

Scheme 12.5

Scheme 12.6

Scheme 12.7

Scheme 12.8

Scheme 12.9

Scheme 12.10

Scheme 12.11

Scheme 12.12

Figure 13.1

Figure 13.2

Figure 13.3

Figure 13.4

Figure 13.5

Figure 13.6

Scheme 13.1

Figure 13.7

Scheme 13.2

Figure 13.8

Scheme 13.3

Figure 13.9

Scheme 13.4

Scheme 13.5

Scheme 13.6

Scheme 13.7

Figure 13.10

Scheme 13.8

Figure 13.11

Figure 13.12

Scheme 13.9

Figure 14.1

Figure 14.2

Figure 14.3

Figure 14.4

Figure 14.5

Figure 14.6

Figure 14.7

Figure 14.8

Figure 14.9

Figure 14.10

Figure 14.11

Figure 14.12

Figure 14.13

Figure 14.14

Figure 14.15

Figure 14.16

Figure 14.17

List of Tables

Table 3.1

Table 3.2

Table 5.1

Table 7.1

Table 10.1

Table 12.1

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Edited by Wolfgang Weigand and Philippe Schollhammer

Bioinspired Catalysis

Metal-Sulfur Complexes

Editors

Wolfgang Weigand

Friedrich-Schiller-Universität

Inst.f.Anorg.+ Analyt.Chemie

August-Bebel-Str. 2

07743 Jena

Germany

Prof. Philippe Schollhammer

Université de Bretagne

Occidentale

Avenue Victor le Gorgeu 6

29285 Brest

France

Cover

The structures shown on the cover have the PDB ID SF4 and 3U7Q (DOI:10.1126/SCIENCE.1214025) and were visualized using VMD (Humphrey, W., Dalke, A. and Schulten, K., ‘VMD - Visual Molecular Dynamics’, J. Molecular Graphics, 1996, vol. 14, pp. 33–38)

All books published by Wiley-VCH are carefully produced. Nevertheless, authors, editors, and publisher do not warrant the information contained in these books, including this book, to be free of errors. Readers are advised to keep in mind that statements, data, illustrations, procedural details or other items may inadvertently be inaccurate.

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The Deutsche Nationalbibliothek lists this publication in the Deutsche Nationalbibliografie; detailed bibliographic data are available on the Internet at <http://dnb.d-nb.de>.

© 2015 Wiley-VCH Verlag GmbH & Co. KGaA, Boschstr. 12, 69469 Weinheim, Germany

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Print ISBN: 978-3-527-33308-0

ePDF ISBN: 978-3-527-66419-1

ePub ISBN: 978-3-527-66418-4

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List of Contributors

Ulf-Peter Apfel

Ruhr-University Bochum

Inorganic Chemistry I/Bioinorganic Chemistry

Universitätsstrasse 150

Bochum

Germany

Vincent Artero

Université Grenoble Alpes

CNRS, CEA Life Science Division

Laboratoire de Chimie et Biologie des Métaux

Av. des Martyrs

Grenoble Cedex 9

France

Frédéric Barrière

Université de Rennes I

Institut des Sciences Chimiques de Rennes

UMR CNRS 6226 – Campus de Beaulieu – Bâtiment 10 C

Rennes Cedex

France

Ian Dance

University of New South Wales

School of Chemistry

Sydney 2052

Australia

Joe Dawson

The University of Nottingham

School of Chemistry

University Park

Nottingham NG7 2RD

UK

Luca De Gioia

University of Milano-Bicocca

Department of Biotechnology and Biosciences

Piazza della Scienza, 2

Milan

Italy

Marc Fontecave

Université Grenoble Alpes

CNRS, CEA Life Science Division

Laboratoire de Chimie et Biologie des Métaux

Av. des Martyrs

Grenoble Cedex 9

France

and

Collège de France

CNRS

Laboratoire de Chimie des Processus Biologiques

place Marcelin Berthelot

Paris

France

Juan C. Fontecilla-Camps

Institut de Biologie Structurale ‘Jean-Pierre Ebel’

Metalloproteins Unit

71, Avenue des Martyrs

CS 10090, 38044

Grenoble Cedex 9

France

Ashta Chandra Ghosh

Institut für Biochemie

Bioorganische Chemie

Felix-Hausdorffstr 4

Greifswald

Germany

Craig A. Grapperhaus

University of Louisville

Department of Chemistry

South Brook Street

Louisville

KY 40292

USA

Claudio Greco

University of Milano-Bicocca

Department of Earth and Environmental Sciences

Piazza della Scienza, 1

Milan

Italy

Richard A. Henderson

Newcastle University

School of Chemistry

Newcastle upon Tyne, NE1 7RU

UK

Yilin Hu

University of California

Irvine, Department of Molecular Biology and Biochemistry

McGaugh Hall

Irvine

CA 92697-3900

USA

Davinder Kumar

University of Louisville

Department of Chemistry

South Brook Street

Louisville

KY 40292

USA

Chi Chung Lee

University of California

Irvine, Department of Molecular Biology and Biochemistry

McGaugh Hall

Irvine

CA 92697-3900

USA

Jonathan McMaster

The University of Nottingham

School of Chemistry

University Park

Nottingham NG7 2RD

UK

John A. Murphy

University of Strathclyde

Department of Pure and Applied Chemistry

Thomas Graham Building

Cathedral Street

Glasgow

G1 1XL Scotland

UK

Yvain Nicolet

Institut de Biologie Structurale ‘Jean-Pierre Ebel’

Metalloproteins Unit

71, Avenue des Martyrs

CS 10090, 38044

Grenoble Cedex 9

France

Carlo Perotto

The University of Nottingham

School of Chemistry

University Park

Nottingham NG7 2RD

UK

François Y. Pétillon

Université de Bretagne Occidentale

UMR CNRS 6521 “Chimie, Electrochimie Moléculaires et Chimie Analytique”

UFR Sciences et Techniques

avenue Le Gorgeu

CS 93837

Brest-Cedex 3

France

Christopher J. Pickett

University of East Anglia

Energy Materials Laboratory

School of Chemistry

Norwich Research Park

Norwich NR4 7TJ

UK

Markus W. Ribbe

University of California

Irvine, Department of Molecular Biology and Biochemistry

McGaugh Hall

Irvine

CA 92697-3900

USA

Philippe Schollhammer

Université de Bretagne Occidentale

UMR CNRS 6521 “Chimie, Electrochimie Moléculaires et Chimie Analytique”

UFR Sciences et Techniques

avenue Le Gorgeu

CS 93837

Brest-Cedex 3

France

Martin Schröder

The University of Nottingham

School of Chemistry

University Park

Nottingham NG7 2RD

UK

Carola Schulzke

Institut für Biochemie

Bioanorganische Chemie

Felix-Hausdorffstr 4

Greifswald

Germany

Callum Scullion

University of Strathclyde

Department of Pure and Applied Chemistry

Thomas Graham Building

Cathedral Street

Glasgow G1 1XL Scotland

UK

Jean Talarmin

Université de Bretagne Occidentale

UMR CNRS 6521 “Chimie, Electrochimie Moléculaires et Chimie Analytique”

UFR Sciences et Techniques

avenue Le Gorgeu

CS 93837

Brest-Cedex 3

France

Phong D. Tran

Nanyang Technological University

Energy Research Institute ERI@N

Nanyang Drive 637553

Singapore

Gönter Wächtershäuser

Weinstr. Munich

80333

Gemany

and

Mill Race Drive

Chapel Hill

NC 27512

USA

Wolfgang Weigand

Friedrich-Schiller Universität Jena

Institut für Anorganische und Analytische Chemie

Humboldtstraße 8

Jena

Germany

Jared A. Wiig

University of California

Irvine, Department of Molecular Biology and Biochemistry

McGaugh Hall

Irvine

CA 92697-3900

USA

Joseph A. Wright

University of East Anglia

Energy Materials Laboratory

School of Chemistry

Norwich Research Park

Norwich NR4 7TJ

UK

Preface

In nature, metal–sulfur clusters provide the active sites of several enzymes which catalyze important reactions such as, for example, H+/H2 conversion by hydrogenases and nitrogen fixation by the nitrogenases. The understanding of the functioning of these metalloenzymes and the design of active bioinspired molecules are great challenges for chemists, and they require a multidisciplinary approach at the interface of chemistry and biology.

The focus of this book is to highlight the more recent developments in metal–sulfur complexes involved in bioinspired catalysis.

As an introductory part, the first chapter shows the possible importance of metal-sulfides in the chemautotrophic origin of life. In this context, the iron–sulfur world theory is emphasized. This introductory part is completed by the second chapter concerning biogenesis and redox, catalytic, and regulatory properties of Fe–S clusters. The second part deals with impressive advances that have been reported during the past 15 years in the molecular chemistry of models of the active sites of the different classes of hydrogenases. Advances into the electrocatalytic H2 production and uptake are reported. A third part is intended to provide recent insights concerning N2-fixation by nitrogenases for which understanding their functioning is still one of the most exciting and intricate modern challenges in bioinorganic chemistry. Recent X-ray analyses of the structure of the FeMo cofactor have led to a kind of renaissance of this field. In the two previous parts, syntheses as well as analytical and theoretical aspects of structural and functional models of these enzymes are described. The fourth part deals with metal–sulfur-containing enzymes activating nitriles (nitrile hydratase) of molybdenum and tungsten enzymes, which contain the pyranopterin cofactor and perform a wide variety of biological functions. They catalyze a diversity of mostly two-electron oxidation–reduction reactions crucial in the metabolism of nitrogen, sulfur, and carbon (xanthine oxidase, dimethyl sulfoxide reductase, sulfite oxidase, and nitrate reductases). In the final chapter, some applicative perspectives of bioinspired complexes, as electrode materials, and artificial photosynthetic systems, are illustrated.

Finally, we thank the authors for their contributions to this book and their efforts and we hope that the readers will find in it a source of recent knowledge in this area of chemistry and of inspiration.

Wolfgang Weigand

Friedrich-Schiller-Universität

Institut für Anorganische &

Analytische Chemie

Jena, Germany

and

Philippe Schollhammer

Université de Bretagne Occidentale

France

Part IPrimordialMetal–Sulfur-Mediated Reactions

1From Chemical Invariance to Genetic Variability

Günter Wächtershäuser

The archaeologist of nature is at liberty to go back to the traces that remain of nature's earliest revolutions, and, appealing to all he knows or can conjecture about its mechanism, to trace the origin of that great family of creatures…down even to mosses and lichens, and finally down to the lowest perceivable stage of nature, to crude matter. From this and from the forces within, by mechanical laws, like those that are at work in the formation of crystals, seems to be derived the whole technique of nature.

Immanuel Kant [1]

1.1 Heuristic of Biochemical Retrodiction

Darwin (1863) wrote in a letter to Hooker [2]: “It is mere rubbish, thinking at present of the origin of life; one might as well think of the origin of matter.” Studies of nucleosynthesis are now quite advanced, but research into the origin of life is still an immature science. The problem of early evolution of life is unique and requires its own heuristic. A commonly used heuristic consists of one-to-one back-extrapolations of individual biochemical features (a), for which Lipmann [3] coined the term . More and more backward projections add evermore ingredients to the recipe. Inevitably, this way of thinking leads to the notion of a “primordial broth.” No one has ever spelled out all that what would or would not have been in the broth and how precisely the organization of life could have come about within such a chaotic situation.