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  • PROGRESS IN

    INORGANIC CHEMISTRY

    Edited by

    KENNETH D. KARLIN

    Department of Chemistry

    Johns Hopkins University

    Baltimore, Maryland

    VOLUME 55

    WILEY-INTERSCIENCE

    A John Wiley & Sons, Inc., Publication

  • This Page Intentionally Left Blank

  • Progress in Inorganic Chemistry

    Volume 55

  • Advisory Board

    JACQUELINE K. BARTON

    CALIFORNIA INSTITUTE OF TECHNOLOGY, PASADENA, CALIFORNIA

    THEODORE J. BROWN

    UNIVERSITY OF ILLINOIS, URBANA, ILLINOIS

    JAMES P. COLLMAN

    STANFORD UNIVERSITY, STANFORD, CALIFORNIA

    F. ALBERT COTTON�

    TEXAS A & M UNIVERSITY, COLLEGE STATION, TEXAS

    ALAN H. COWLEY

    UNIVERSITY OF TEXAS, AUSTIN, TEXAS

    RICHARD H. HOLM

    HARVARD UNIVERSITY, CAMBRIDGE, MASSACHUSETTS

    EIICHI KIMURA

    HIROSHIMA UNIVERSITY, HIROSHIMA, JAPAN

    NATHAN S. LEWIS

    CALIFORNIA INSTITUTE OF TECHNOLOGY, PASADENA, CALIFORNIA

    STEPHEN J. LIPPARD

    MASSACHUSETTS INSTITUTE OF TECHNOLOGY, CAMBRIDGE,

    MASSACHUSETTS

    TOBIN J. MARKS

    NORTHWESTERN UNIVERSITY, EVANSTON, ILLINOIS

    EDWARD I. STIEFEL�

    PRINCETON UNIVERSITY, PRINCETON, NEW JERSEY

    KARL WIEGHARDT

    MAX-PLANCK-INSTITUT, MÜLHEIM, GERMANY

    �Deceased

  • PROGRESS IN

    INORGANIC CHEMISTRY

    Edited by

    KENNETH D. KARLIN

    Department of Chemistry

    Johns Hopkins University

    Baltimore, Maryland

    VOLUME 55

    WILEY-INTERSCIENCE

    A John Wiley & Sons, Inc., Publication

  • Copyright � 2007 by John Wiley & Sons, Inc. All rights reserved

    Published by John Wiley & Sons, Inc., Hoboken, New Jersey

    Published simultaneously in Canada

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    10 9 8 7 6 5 4 3 2 1

  • Contents

    Chapter 1 Elucidation of Electron- Transfer Pathways

    in Copper and Iron Proteins by Pulse Radiolysis

    Experiments 1

    OLE FARVER AND ISRAEL PECHT

    Chapter 2 Peptide- or Protein-Cleaving Agents Based on

    Metal Complexes 79

    WOO SUK CHEI AND JUNGHUN SUH

    Chapter 3 Coordination Polymers of the Lanthanide Elements:

    A Structural Survey 143

    DANIEL T. dE LILL AND CHRISTOPHER L. CAHILL

    Chapter 4 Supramolecular Chemistry of Gases 205

    DMITRY M. RUDKEVICH

    Chapter 5 The Organometallic Chemistry of Rh-,

    Ir-, Pd-, and Pt-Based Radicals:

    Higher Valent Species 247

    BAS dE BRUIN,

    DENNIS G. H. HETTERSCHEID,

    ARJAN J. J. KOEKKOEK,

    AND HANSJÖRG GRÜTZMACHER

    Chapter 6 Unique Metal–Diyne, –Enyne, and –Enediyne Complexes:

    Part of the Remarkably Diverse World of

    Metal–Alkyne Chemistry 355

    SIBAPRASAD BHATTACHARYYA, SANGITA,

    AND JEFFREY M. ZALESKI

    Chapter 7 Oxygen Activation Chemistry of Pacman

    and Hangman Porphyrin Architectures Based

    on Xanthene and Dibenzofuran Spacers 483

    JOEL ROSENTHAL AND DANIEL G. NOCERA

    v

  • Chapter 8 Metal-Containing Nucleic Acid Structures Based

    on Synergetic Hydrogen and

    Coordination Bonding 545

    WEI HE, RAPHAEL M. FRANZINI,

    AND CATALINA ACHIM

    Chapter 9 Bispidine Coordination Chemistry 613

    PETER COMBA, MARION KERSCHER,

    AND WOLFGANG SCHIEK

    Subject Index 705

    Cumulative Index, Volumes 1–55 743

    vi CONTENTS

  • CHAPTER 1

    Elucidation of Electron- Transfer Pathways in Copper

    and Iron Proteins by Pulse Radiolysis Experiments

    OLE FARVER

    Institute of Analytical Chemistry, University of Copenhagen,

    2100 Copenhagen, Denmark

    ISRAEL PECHT

    Department of Immunology, The Weizmann Institute of Science,

    76100 Rehovot, Israel

    CONTENTS

    I. INTRODUCTION 2

    A. Biological Electron Transfer / 2

    B. Electron-Transfer Theory / 3

    II. PULSE RADIOLYSIS 6

    III. COPPER PROTEINS 8

    A. Azurin, a Model System / 8

    B. Copper-Containing Oxidases and Reductases / 24

    1. Ascorbate Oxidase / 25

    2. Ceruloplasmin / 30

    3. Copper Nitrite Reductase / 38

    Progress in Inorganic Chemistry, Vol. 55 Edited by Kenneth D. Karlin

    Copyright # 2007 John Wiley & Sons, Inc.

    1

  • IV. IRON-CONTAINING PROTEINS 44

    A. cd1 Nitrite Reductase / 44

    V. COPPER VERSUS IRON NITRITE REDUCTASES: FINAL COMMENTS 57

    VI. PROTEINS WITH MIXED METAL ION CONTENT 58

    A. Cytochrome c Oxidase / 58

    B. Xanthine Dehydrogenase and Oxidase / 66

    VII. CONCLUSIONS 69

    ACKNOWLEDGMENTS 71

    ABBREVIATIONS 71

    REFERENCES 72

    I. INTRODUCTION

    A. Biological Electron Transfer

    Electron-transfer (ET) reactions play a central role in all biological systems

    ranging from energy conversion processes (e.g., photosynthesis and respiration)

    to the wide diversity of chemical transformations catalyzed by different

    enzymes (1). In the former, cascades of electron transport take place in the

    cells where multicentered macromolecules are found, often residing in mem-

    branes. The active centers of these proteins often contain transition metal ions

    [e.g., iron, molybdenum, manganese, and copper ions] or cofactors as nicoti-

    namide adenine dinucleotide (NAD) and flavins. The question of evolutionary

    selection of specific structural elements in proteins performing ET processes is

    still a topic of considerable interest and discussion. Moreover, one key question

    is whether such structural elements are simply of physical nature (e.g., separa-

    tion distance between redox partners) or of chemical nature (i.e., providing ET

    pathways that may enhance or reduce reaction rates).

    Biological ET is characterized by the use of redox centers that are spatially

    fixed in macromolecules and thus separated by the protein matrix and usually

    prevented from coming in direct contact with solvent. Therefore intramolecular

    ET becomes a central part of the biological function of the redox proteins, and

    the ET rates are expected to decrease exponentially with the separation distance

    of the redox centers that is generally quite large (>1.0 nm). Further, usually only very modest structural changes of the active centers accompany the redox

    changes, thus minimizing the activation energy required for ET.

    2 OLE FARVER AND ISRAEL PECHT

  • During the last decades there has been a remarkable progress in determina-

    tion of three-dimensional (3D) structures of proteins, including many involved

    in ET, which has opened the way for a detailed study of the relationship between

    structure and reactivity of this large and diverse group of molecules (2).

    A key challenge in studies of biological redox processes is trying to define and

    understand the parameters that control the rates of ET. These parameters include

    (a) driving force (i.e., change in free energy of the reaction); (b) the reorganiza-

    tion energy (i.e., the energy of the reactants

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