Chapter31

Outline
y 1.Veryimportanttermsofcoordinationchemistry
y 2.Generalaspectsofbioinorganicchemistry
y
y
y
y
y

3.Coordinationforuptake,transportandstorage(Fe)
4.Hardions:Na+,K+,Mg2+,Ca2+5.Cobalamines
6.MetalsinPhotosynthesis
7.Feinbiosystems
8.FunctionofZn
9.Fixationofnitrogen

Coordinationcompound
(complex)complex)basics
y Centralatomisboundtounexpectedly

largenumberofligands
y Usuallydiscretespeciesinsolutionand
solid
y Examples:K4[Fe(CN)6],CoCl2*6H2O

Coordinationcompound
(complex)complex)basics
y Propertiesofcentralatoms(transition

metals):
y Largecharge/radiusratio
y Variableoxidationstates(delectrons
available)
y Metastablehighoxidationstates,s
electronsareremovedfirst

Coordinationcompound
(complex)complex)basics
y Compoundsareoftenparamagnetic(unpaired

electrons)
y Formationofcoloredionsandcompounds
y Compoundswithprofoundcatalyticactivity
y Formationofstablecomplexes(Lewisacids)
y Trendtometalmetalbonding(clusters,not
importantinbiology

Coordinationcompound
(complex)complex)basics
y Propertiesofligands
y Monodentateor
y polydentateligand
y Ambidentateligands(nitro,

nitrito)

CoordinationnumberCoordination
numberexamples
y HigherCNsarefavoured:
y Complexescontainingcentralatomsof

theperiods5and6,smallligands (size)
y Singlebondsmetalligand (seeMnO4)
y Ontheleftofarowofthedblock(size
andsmallnumberofdelectrons)
y Centralatomswithahighoxidation
number(sizeandsmallnumberofd
electrons)

y CN2:linear(Cu+,Ag+,Au+,Hg)
y CN3:trigonalplanar(HgI3,[Pt(P{C6H5}3]3)

trigonalpyramid
y CN4:tetrahedron([Al(OH)4],[Cd(CN)4]2)
squareplanar(d8,[PtCl4]2,[AuF4])
bisphenoidal(trigonalbipyramid,[AsF4]
[SbCl4])
y
tetragonalpyramid(octahedron)
y CN5:trigonalbipyramid(Fe(CO)5,[SnCl5])
y tetragonalpyramid

CoordinationNumberexamples

Coordinationnumberexamples
y Pseudorotation
y Exchangeofaandeligand,seeMgATpase
y [Ni(CN)5]3:b)anda)incrystalstructure
y Fe(CO)5:fastpseudorotationinsolution

Coordinationnumberexamples
y CN6:
y octahedron([Cr(H2O)6]3+,[Fe(CN)6]3)
y distortedoctahedron
y Trigonalprism

Coordinationnumberexamples

Isomerism
y Twoormoremoleculesorionshave

thesamemolecularformulabutthe
atomsarearrangeddifferently
y Thestructuresofisomersarenot
superimposable
y Isomershavedifferentphysical
(color)and/orchemicalproperties.

Isomerism
y Stereoisomerism
y Opticalisomerism:
y Enantiomers
y Geometricalisomerism:
y cis,trans;meridional,facial
y Structuralisomerism
y Ionizationisomerism([CoCl(NH3)5]SO4
/[CoSO4(NH3)5]Cl)
y Coordinationisomerism([Co(NH3)6]
[Cr(CN)6]/[Cr(NH3)6][Co(CN)6)
y Linkageisomerism(cyano/isocyano)

Periodictableoflife

Symptomsofdeficiency:
Mg(musclecramps),Fe(animea),Mn (infertility)
Toxiceffectsincaseofhighdoses(therapeuticwidth)
Occurrenceofnonessentialelements(e.g.Rb:1.1g/70kg)andof
contaminations(e.g.Hg)

Functionsofinorganicelements
y Assemblyofstructures(DNA,biomineralization),
y
y
y
y
y
y
y
y

endoandexoskeletons.Ca,Mg,Zn,Si
Informationcarriers(musclecontractions,nerve
function).Na,K,Ca,Mg
Activationofenzymes.Mg,Ca
Formation,metabolismanddegradagationof organic
compoundsbyLewisacid/basecatalysis.Zn,Mg
Transferofelectrons(energyconversion),
FeII/FeIII/FeIV,stableduetobioligands
Uptake,transport,storageandconversionofsmall
molecules
O2:Fe,Cu(conversion),Mn (generation)
N2:Fe,Mo,V(conversiontoammonia)
CO2:Ni,Fe(reductiontomethane)

Mostprominentbioelements
y Na+,K+:Electrolytes
y Mg2+:Chlorophyll,energyproduction(ATP
y
y
y
y

ADP),skeleton
Ca2+:musclefunctions,
HydroxylapatiteCa5(PO4)3(OH),CaCO3
VIV/V,MoIV/VI,WIV/VI,MnII/III/IV,FeII/III,
NiI/II/III,CuI/II:electrontransfer
FeandCu:transportandstorageofoxygen
FeII,FeIII:Magnetite(Fe3O4)

Roleofthemetallicelements
y Themetallicelementsplayavarietyofrolesinbiochemistry.Severalofthe

mostimportantrolesarethefollowing:

y 1.RegulatoryactionisexercisedbyNa+,K+,Mg2+,andCa2+.Thefluxofthese

ionsthroughcellmembranesandotherboundarylayerssendssignalsthatturn
metabolicreactionsonandoff.

y 2.Thestructuralroleofcalciuminbonesandteethiswellknown,butmany

proteinsowetheirstructuralintegritytothepresenceofmetalionsthattie
togetherandmakerigidcertainportionsoftheselargemolecules,portionsthat
wouldotherwisebeonlylooselylinked.Metalionsparticularlyknowntodothis
areCa2+andZn2+.

y 3.Anenormousamountofelectrontransferchemistrygoesoninbiological

systems,andnearlyallofitcriticallydependsonmetalcontainingelectron
transferagents.Theseincludecytochromes (Fe),ferredoxins (Fe),andanumber
ofcoppercontaining"blueproteins,"suchasazurin,plastocyanin,and
stellacyanin.

Mostprominentbioelements
y Co:Cobalamine,e.g.VitaminB12
y Zn2+:Enzymes,zincfinger(gen.transcription),
y
y
y
y

stabilizationofproteins
SiIV:bones;SiO2/silicagel
PV:Hydroxylapatite,ATP,cellmembrane,DNA
SeII:Selenocysteine
F:Fluorapatit(Ca5(PO4)3F)teeth;Cl:besides
HCO3mostimportantfreeanion,I:hormonesof
thethyroid,radiationtherapy

Termsrelatedtobioinorganic
chemistry
y Activecenter:Locationinanenzymewherethespecificreactiontakes
y
y
y
y
y
y
y
y
y
y
y

place
Allosteric enzyme:
Canbindasmallregulatorymoleculethatinfluencescatalyticactivity
Apoenzyme:
Anenzymethatlacksitsmetalcenterorprostheticgroups
ATP: Adenosine5triphosphate
Biomembrane:Sheetlikeassembliesofproteinsandlipids(bilayer)
Calmodulin: Cabindingproteininvolvedinmetabolicregulation
Carbonicanhydrase:Zncontainingenzymethatcatalyzesthereversible
decompositionofcarbonicacidtocarbondioxideandwater
Chargetransfercomplex:Anaggregateoftwoormoremoleculesin
whichchargeistransferredfromadonortoanacceptor.
Chlorin: 2,3Dihydroporphyrin,reducedporphyrin withtwononfused
saturatedcarbonatoms(C2,C3)inoneofthepyrrolerings.
Chlorophyll:Magnesiumcomplexofaporphyrin inwhichadoublebond
inoneofthepyrrole rings(1718)hasbeenreduced.Afused
cyclopentanonering isalso present

y Cluster:Metalcentersgroupedclosetogetherwhichcanhavedirect
y
y
y

y
y

metalbondingorthroughabridgingligand,e.g.ferredoxin
Cobalamin:VitaminB12,substitutedcorrinCo(III)complex
Coenzyme:Alowmolecularweight,nonproteinorganiccompound
(oftenanucleotide)participatinginenzymaticreactions
Cofactor: Anorganicmoleculeorion(usuallyametalion)thatis
requiredbyanenzymeforitsactivity.Itmaybeattachedeitherloosely
(coenzyme)ortightly(prostheticgroup).
Cooperativity: Thephenomenonthatbindingofaneffector moleculeto
abiologicalsystemeitherenhancesordiminishesthebindingof
successivemolecules,e.g.hemoglobin
Corrin: Ringcontractedporphyrinderivative thatismissingacarbon
Cytochrome: Hemeprotein thattransferselectrons,andexhibitsintense
absorptionbands.Theironundergoesoxidationreductionbetween
oxidationstatesFe(II)andFe(III).
Cytochrome Coxidase:Themajorrespiratoryproteinofanimaland
plantmitochondria.ItcatalyzestheoxidationofFe(II)cytochromec,
andthereductionofdioxygento water.Containstwohemes andthree
copperatoms,arrangedinthreecenters.

y CytochromeP450: Generaltermforagroupofhemecontaining
y
y
y
y

y
y

monooxygenases Thereactionwithdioxygenappears toinvolve

higheroxidationstatesofiron,suchasFe(IV)=O
Desferrioxamine(dfo):Chelatingagentusedworldwideinthe
treatmentofironoverloadconditions,suchashemochromatosis
andthalassemia.
Dismutase: Enzymethatcatalyzesadisproportionation reaction
Entaticstate:Astateofanatomorgroupwhichhasitsgeometric
orelectronicconditionadaptedforfunction.Derivedfrom
entasis(Greek)meaningtension
Enzyme:Amacromoleculethatfunctionsasabiocatalystby
increasingthereactionrateFeMocofactor:Aninorganiccluster
foundintheFeMo proteinofthemolybdenumnitrogenase,
essentialforthecatalyticreductionofN2toammonia
Ferredoxin: Aproteincontainingmorethanoneironandacid
labilesulfur,thatdisplayselectrontransferactivitybut not
classicalenzymefunction
Ferritin: Anironstorageproteinconsistingofashellof24
proteinsubunits,encapsulatingupto4500ironatomsinthe
formofahydratediron(III)oxide.

y Heme: Anearplanarcoordinationcomplexobtainedfromironand
y
y
y
y
y
y

y
y

dianionicporphyrin
Hemerythrin: Adioxygencarryingproteinfrommarineinvertebrates,containing
anoxobridgeddinucleariron center
Hemocyanin: Adioxygencarryingprotein(frominvertebrates,e.garthropods and
molluscs),containingdinucleartype 3coppersites
Hemoglobin:Adioxygencarryinghemeprotein ofredbloodcells
HiPIP:HighPotentialIronsulfurProtein(ferredoxin).Clusterwhichundergoes
oxidationreductionbetweenthe[4Fe4S]2+and[4Fe4S]3+states
Holoenzyme: Anenzymecontainingitscharacteristicprostheticgroup(s)and/or
metal(s)
Ionchannel:Enableionstoflowrapidlythroughmembranesina
thermodynamicallydownhilldirectionafteranelectricalorchemicalimpulse.
Theirstructuresusuallyconsistof46membranespanningdomains.Thisnumber
determinesthesizeoftheporeandthusthesizeoftheiontobetransported
Ionophore:Acompoundwhichcancarryspecificionsthroughmembranes
Ionpumps:Enableionstoflowthroughmembranesinathermodynamically
uphilldirectionbytheuseofanenergysource.Theyopenandcloseuponthe
bindingandsubsequenthydrolysisofATP,usuallytransportingmorethanoneion
towardstheoutsideortheinsideofthemembrane

Termsrelatedtobioinorganic
chemistry
y Metalloenzyme: Anenzymethat,intheactivestate,

containsoneormoremetalionsMitochondria:
Cytoplasmic organelles,produceATPbyoxidative
phosphorylation
y Myoglobin: Amonomeric dioxygenbindingheme
proteinofmuscletissue,structurallysimilartoa
subunitofhemoglobin
y Photosynthesis:Ametabolicprocessinplantsand
certainbacteria,usinglightenergyabsorbedby
chlorophyllandotherphotosyntheticpigmentsfor
thereductionofCO2,followedbytheformationof
organiccompounds

Termsrelatedtobioinorganic
chemistry
y Plastocyanin: Anelectrontransferprotein,containingatype1copper

y
y
y
y
y

site,involvedinplantandcyanobacterialphotosynthesis,which
transferselectronstoPhotosystem1
IronSulfurprotein:Anironsulfurproteinofthemitochondrial
respiratorychain,containinga[2Fe2S]cluster
Rubredoxin:Ansingleironsulfurprotein,functionasanelectron
carrier
SOD: superoxidedismutase,cataysisofdisproportionationofsuperoxide
Substrates:Acompoundthatistransformedundertheinfluenceofa
catalyst
Traceelements:Elementsrequiredforphysiologicalfunctionsinvery
smallamounts,e.g.Co,Cu,F,Fe,I,Mn,Mo,Ni,Se,V,W,andZn

Termsrelatedtobioinorganic
chemistry
y Type1,2,3copper:Differentclassesofcopperbinding

sitesinproteins,classifiedbytheirspectroscopic
propertiesasCu(II).Type1,orbluecoppercentersthe
copperiscoordinatedtoatleasttwoimidazole
nitrogensfromHisandonesulfurfromCys.Intype2,
ornonbluecoppersites,thecopperismainlybound
toimidazolenitrogensfromHis.Type3coppercenters
comprisetwospincoupledcopperions,boundto
imidazolenitrogens
y Zinc finger:Adomain,foundincertainDNAbinding
proteins,comprisingahelixloopstructureinwhicha
zincioniscoordinatedto24Cyssulfurs,the
remainingligandsbeingHis

Principleofcomplementarity
y Theactivesitesofenzymestendtobemore

complementarytothetransitionstatesthanthey
y aretotheactualsubstrates
y Preformation ofthetransitionstatebystrained
y
y
y
y

enzyme(entactic state)
Energyaspect:smallactivationenergy,
statisticalaspect:moreproductiveencounters
betweenreactionpartners,
Kineticaspect:fasterreaction

CyclicligandsligandsPorphyrin
complexes
y Unsaturatedtetradentatemacrocyclicligands
y Coordinationofotherwiselabiledivalentmetalions
y Porphyrincomplexes:chelateeffectandsizeselectiveashost
y Porphyrin:verystable,Hckelaromatic(18el=4n+2),

colored

Porphyrins

CyclicligandsligandsPorphyrin
complexes

Feinproteins
y Transport:Transferrin
y CoordinationofFebycaboxyand
y
y
y
y
y

phenolate groupsofresidues
UptakeoftwoFe(III)andoneHCO3
Stabilityofcomplexesdecreasewith
decreasingpH
HighaffinityofApotransferrin,protection
againstinfections
Notveryspecific(Cr3+,Al3+,Cu2+,Mn2+)
ReleaseofFe(III):ReductiontoFe(II)and
bindingbyporphyrine

Feinproteins
y Storage:Ferritin
y HighsymmetryofApoferritin:F432
y Hollowspherebuiltfromproteins(innerdia.:~7
y
y
y
y

nm,outerdia.~13nm)
Capacity:upto4500Fe3+,biomineralization(?)
CarboxylategroupsforFe(III)binding,core
structurerelatedtoFerrihydriteFe10O6(OH)18
Exchangeviachannels(dia.1nm),tuningof
hydrophilic/hydrophobiccharacterviaresidues
ReleaseofFeasFe(II)viahydrophilicchannels

Feinproteins
y Hemoglobin

Hemoglobin Myoglobin
y Bohreffect

BohrEffect

TheBioinorganicchemistryof
Cobalt
y Thebestknownbiologicalfunctionofcobaltisitsintimateinvolvementinthe

coenzymesrelatedtovitaminB12
y Itconsistsoffourprincipalcomponents:
y 1.Acobaltatom.

y 2.Amacrocyclic ligand calledthecorrin ring,whichbearsvarioussubstituents.

Theessentialcorrin ringsystemisshowninboldlines.Itresemblestheporphine
ring,butdiffersinvariousways,notablyintheabsenceofonemethine (=CH)
bridgebetweenapairofpyrrole rings.

y 3.Acomplexorganicportionconsistingofaphosphategroup,asugar,andan

organicbase,thelatterbeingcoordinatedtothecobaltatom.

y 4.Asixthligand maybecoordinatedtothecobaltatom.Thisligand canbe

varied,andwhenthecobaltatomisreducedtotheoxidationstate+1,itis
evidentlyabsent.

StructureofCobalamin

Cobalamine
y Thecobalamins canbereducedinneutraloralkaline

y
y
y
y

solutiontogivecobalt(Il)andcobalt(I)species,often
calledBI2randBI2srespectively.
powerfulreducingagent
decomposingwatertogivehydrogenandB12r
reductionscanapparentlybecarriedoutinvivoby
reducedferredoxin.
cyanoor hydroxocobalamin isreduced,theligand
(CNorOH)islost,andtheresultingfivecoordinate
cobalt(I)species reactswithATPinthepresenceofa
suitableenzymetogeneratetheB12coenzyme.

Nitrogenfixation
y Nitrogenases
y Consistof2proteins
y AFeprotein
y AMoFeprotein
y Eachofthemisinactive
y Mixingthemmakesthemactive
y TheFeproteinconsistsoftwoidenticalsubunitsthat

claspaferredoxin unit(Fe4S4)betweenthemby
formingFeSbondstotwocysteine residuesineach
subunit.

Nitrogenfixation
y TheMoFeprotein,socalledbecauseitcontainsboth

molybdenumandiron.
y Xraycrystallographicstudyrevealedametalcluster
arrangement
y Thestructureisstillsomewhatinaccurateandoneof
thebridginggroups(Y)hasnotyetbeenconclusively
identified.