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
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Published simultaneously in Canada
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Wiley Bicentennial Logo: Richard J. Pacifico
Library of Congress Catalog Card Number 59-13035
ISBN 978-0-471-68242-4
Printed in the United States of America
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
