Progress in Inorganic Chemistry, Volume 55

771 Pages·54.493 MB·English

Progress in
Inorganic Chemistry
Volume 55
Advisory Board
JACQUELINE K.BARTON
CALIFORNIAINSTITUTEOF TECHNOLOGY,PASADENA,CALIFORNIA
THEODOREJ.BROWN
UNIVERSITYOFILLINOIS,URBANA,ILLINOIS
JAMES P.COLLMAN
STANFORD UNIVERSITY,STANFORD,CALIFORNIA
F.ALBERTCOTTON(cid:1)
TEXASA&MUNIVERSITY,COLLEGE STATION,TEXAS
ALANH.COWLEY
UNIVERSITYOFTEXAS,AUSTIN,TEXAS
RICHARDH.HOLM
HARVARDUNIVERSITY,CAMBRIDGE, MASSACHUSETTS
EIICHIKIMURA
HIROSHIMAUNIVERSITY,HIROSHIMA,JAPAN
NATHANS.LEWIS
CALIFORNIAINSTITUTEOF TECHNOLOGY,PASADENA,CALIFORNIA
STEPHENJ.LIPPARD
MASSACHUSETTSINSTITUTEOFTECHNOLOGY,CAMBRIDGE,
MASSACHUSETTS
TOBINJ.MARKS
NORTHWESTERN UNIVERSITY,EVANSTON,ILLINOIS
EDWARDI.STIEFEL(cid:1)
PRINCETONUNIVERSITY,PRINCETON,NEWJERSEY
KARLWIEGHARDT
MAX-PLANCK-INSTITUT,MU¨LHEIM,GERMANY
(cid:1)Deceased
PROGRESS IN
INORGANIC CHEMISTRY
Edited by
KENNETH D. KARLIN
DepartmentofChemistry
Johns Hopkins University
Baltimore, Maryland
VOLUME 55
WILEY-INTERSCIENCE
A John Wiley & Sons, Inc., Publication
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Contents
Chapter 1 Elucidation of Electron- Transfer Pathways
in Copper and Iron Proteins by Pulse Radiolysis
Experiments 1
OLE FARVERAND ISRAEL PECHT
Chapter 2 Peptide- or Protein-Cleaving Agents Based on
Metal Complexes 79
WOO SUK CHEIAND JUNGHUN SUH
Chapter 3 Coordination Polymers of the Lanthanide Elements:
A Structural Survey 143
DANIEL T. dE LILLAND 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 HANSJO¨RG GRU¨TZMACHER
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 ROSENTHALAND DANIEL G. NOCERA
v
vi CONTENTS
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
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. BiologicalElectronTransfer / 2
B. Electron-TransferTheory / 3
II. PULSERADIOLYSIS 6
III. COPPERPROTEINS 8
A. Azurin,aModelSystem / 8
B. Copper-ContainingOxidasesandReductases / 24
1. AscorbateOxidase / 25
2. Ceruloplasmin / 30
3. CopperNitriteReductase / 38
ProgressinInorganicChemistry,Vol.55 Edited byKenneth D.Karlin
Copyright#2007JohnWiley&Sons,Inc.
1
2 OLEFARVERANDISRAELPECHT
IV. IRON-CONTAININGPROTEINS 44
A. cd NitriteReductase / 44
1
V. COPPERVERSUSIRONNITRITEREDUCTASES:FINALCOMMENTS 57
VI. PROTEINSWITHMIXEDMETALIONCONTENT 58
A. CytochromecOxidase / 58
B. XanthineDehydrogenaseandOxidase / 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
rangingfromenergyconversionprocesses(e.g.,photosynthesisandrespiration)
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
stillatopicofconsiderableinterestanddiscussion.Moreover,onekeyquestion
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
preventedfromcomingindirectcontactwithsolvent.Thereforeintramolecular
ET becomes a central part of the biological function of the redox proteins, and
theETratesareexpectedtodecreaseexponentiallywiththeseparationdistance
oftheredoxcentersthatisgenerallyquitelarge(>1.0nm).Further,usuallyonly
very modest structural changes of the active centers accompany the redox
changes, thus minimizing the activation energy required for ET.
ELUCIDATIONOFELECTRON-TRANSFERPATHWAYSINCOPPER 3
During the last decades there has been a remarkable progress in determina-
tion of three-dimensional (3D) structures of proteins, including many involved
inET,whichhasopenedthewayforadetailedstudyoftherelationshipbetween
structure and reactivity of this large and diverse group of molecules (2).
Akeychallengeinstudiesofbiologicalredoxprocessesistryingtodefineand
understandtheparametersthatcontroltheratesofET.Theseparametersinclude
(a)drivingforce(i.e.,changeinfreeenergyofthereaction);(b)thereorganiza-
tion energy (i.e., the energy of the reactants at the equilibrium nuclear config-
urationoftheproducts);(c)thedistanceseparatingelectrondonorandacceptor;
and finally (d) the nature ofthe mediumseparating the tworedox centers.
This chapter reviews results and current insights emerging primarily from
pulse radiolysis (PR) studies ofintramolecular ETin multisite proteins, mainly
iron- and copper-containing redox enzymes, with emphasis on interactions
between the different redox centers.
B. Electron-Transfer Theory
Rates of ETare expected to depend on the energy required for bond-length and
bond-angle changes of the reactants, as well as solvent reorganization accom-
panying the ET process. In proteins, however, these processes involve the
polypeptide matrix as part of the medium that is far less homogeneous than
solvent molecules surrounding small molecule ET partners. Further, conforma-
tionalchangesprecedingorfollowingETinmacromoleculesmayaffectthefree
energy changes of the reaction. Moreover, while small molecules exchange
electrons in solutions where they are in close, sometimes direct contact, in
proteins the redox reaction partners are held in fixed positions by and within
thepolypeptidematrix.Hence,theyarepreventedfromcomingintodirectinner-
spherecontact.Therefore,thedistancebetweenelectrondonorandacceptorisone
decisive parameter affecting long-range ET (LRET) rates. Considerable efforts
havebeendevotedtostudiesoftheseprocesses,andthecomprehensionofintra-
andinterproteinmediatedETreactionshasadvancedsignificantly,largelydueto
thedeterminationof3Dstructuresofanever-increasingnumberofredoxproteins.
In addition,the theoretical models for analyzing LRET havealso advanced toa
stagewheretheycanmorereadilybeemployedandtestedexperimentally.Still,
someveryinterestingquestionsremaintobeanswered:(1)HowdoestheETrate
dependonthenatureofthemediumseparatingthetworedoxpartnersinaprotein
system? (2) To what extent did the structures of redox proteins undergo evolu-
tionaryselectioninordertooptimizetheirfunctionforspecificityandcontrolof
biologicalET,andifso,whatarethestructuralcorollariesofthisselection?These
aresomeoftheissuesthatwillbeaddressedinthischapter.
Several excellent reviews on ET theory are available (3–5). Here only an
outline, necessary for the discussion of this topic, is presented. Long-range ET
4 OLEFARVERANDISRAELPECHT
in proteins is characterized by a weak interaction between electron donor, D,
andacceptor,A,andinthenonadiabaticlimit,where theD–Adistanceislarge
(>1.0nm), the rate constant is proportional to the square of the electronic
coupling between the electronic states of reactant and product, represented in
the form of a tunneling matrix element, H . For intramolecular ET the rate
DA
constant is given by Fermi’s golden rule (3):
2p
k¼ H2 (cid:2)ðFCÞ ð1Þ
(cid:1)h DA
TheFranck–Condonfactor(FC)fornuclearmovementscanforrelativelysmall
vibrationalfrequencies,wherek T >hn,betreatedclassically,aconditionthat
B
often applies to biological ET. In polar solvents likewater, the reorientation of
solvent molecules contributes considerably to the total reorganization energy,
l , in response to changes in charge distribution of the reaction partners. The
tot
reorganization energy can be defined as the energy of the reactants at the
equilibrium nuclear configuration ofthe products (3,4). If D and Aareviewed
as conducting spheres, the dielectric model illustrates an important feature,
namely,thatthemorepolarthemedium,thelargerbecomesl (3).Therefore,
tot
reorganizationenergyrequirementsareexpectedtodecreasedramaticallywhen
the redox centers reside in a low-dielectric medium, (e.g., the hydrophobic
interior of a protein). In a nonpolar environment, the reorganization energy
requirement for the surrounding medium vanishes. Another contribution to
thereorganizationenergycomesfromchangesinbondlengthsandanglesofthe
coordination sphere that accompany ET. The nuclear factor also expresses the
relationship between reorganization energy and driving force that further
influences the ET rate (cf. Eq. 2). The other factor included in the FC term is
the driving force of the ETreaction that is givenby the difference in reduction
potentialsofelectronacceptoranddonor.Thesepotentialsarerathersensitiveto
thestructureandenvironmentofthemetalsiteandmaythusbetunedbysubtle
conformational changes.
The electronic motion, however, requires a quantum mechanical approach,
and the semiclassical Marcus equation may be expressed as (3):
2p H2
k¼ DA e(cid:5)ð(cid:2)G(cid:6)þltotÞ2=ð4ltotRTÞ ð2Þ
(cid:1)h ð4pltotRTÞ12
where(cid:2)G(cid:6) isthereactionfreeenergyandlthenuclearreorganizationenergy.
Since wave functions decay exponentially with distance, the tunneling matrix
element, H will decrease with the distance, (r(cid:5)r ), as:
DA 0
H ¼H0 (cid:2)e(cid:5)bðr(cid:5)r0Þ=2 ð3Þ
DA DA