First Principles DFT Studies of Metal-Based Biological and Biomimetic Systems - Metallic Systems: A Quantum Chemist's Perspective - page 19

ES TS EP

CEF '

CEF '

CEF

Asn233

N5 C8

N5 C8

His196
Zn1

OH -

His263

WAT '
Zn1

WAT

RC
OH -

Zn1

OH - '

Zn2

Zn2

OH '

Zn2

Cys221

His118

Asp120 His116

FIGURE 1.7 (See color insert.) QM/MM.structural.insights.into.the.reaction.mechanism.
of.di-Zn.MβL.CcrA.from. B. fragilis .(atoms.shown.in.licorice.are.included.in.the.QM.cell,.see.
also.Schemes.1.1.and.1.2)..(Adapted.from.Dal.Peraro,.M.,.Vila,.A.J.,.Carloni,.P.,.and.Klein,.
M.L.,. J. Am. Chem. Soc. ,.129,.2808,.2007.)

It.is.striking.that.these.common.minimal.features.are.suficient.to.accommodate.
different.β-lactams.creating.productive.conformations.for.the.enzymatic.reaction.in.
all. complexes;. indeed,. the. putative. reaction. coordinate. (i.e.,. the. distance. between.
the.nucleophilic.carbonyl.oxygen.and.β-lactam.carbonyl.carbon).ranges.from.3.2.to.
3.5.Å,.giving.plausible.models.for.the.Michaelis.complexes. 194,195
We.used.classical.MD.and.hybrid.QM/MM.calculations.within.the.DFT/BLYP.
framework. to. investigate. the. hydrolysis. of. a. commonly. used. cephalosporin. (cefo-
taxime),.which.is.actively.degraded.by.mono-Zn.and.di-Zn.species. 194,195 .BcII.from.
B. cereus .shows.that.the.metal.ion.is.bound.in.the.3H.zinc.site,.whereas.CcrA.from.
B. fragilis .has.both.the.3H.and.DCH.sites.occupied.(Scheme.1.2)..Calculations.show.
that.both.enzymes.are.able.(1).to.promote.the.nucleophilic.attack.by.a.metal-bound.
hydroxide.and.(2).to.catalytically.activate.a.water.(WAT).which.eventually.triggers.
the.C-N.bond.cleavage.of.the.β-lactam.ring..Nonetheless,.the.chemistry.and.kinetics.
of.the.two.reactions.strongly.depends.on.the.Zn.architecture.and.content.(Figure.1.7,.
Scheme.1.2).
In. di-zinc. CcrA. MβL,. the. nucleophile. OH − . approaches. the. β-lactam. carbonyl.
carbon.maintaining.its.coordination.with.the.metal.ions..When.the.transition.state.
(TS).is.reached.(reaction.coordinate.RC = 2.0.Å,.where.RC.is.the.distance.between.
the. β-lactam. carbonyl. carbon. and. the. nucleophilic. oxygen),. a. cascade. of. almost.
simultaneous. events. occurs. (Figures. 1.6,. 1.7. and. Scheme. 1.2).. (i). OH − . moves. out.
from.the.Zn1-Zn2.plane.attacking.C8.while.the.Zn1-OH − .bond.is.elongated.(2.2.Å)..
(ii).The.OH − -Zn2.bond.is.lost.upon.nucleophilic.attack.and.the.Zn1-Zn2.distance.
increases.(3.8.Å)..A.hydroxide.simultaneously.bound.to.Zn1.and.Zn2.is.expected.to.
be.a.poor.nucleophile.and.thus.it.is.reasonable.that.OH − .attacks.while.detaching.from.
at.least.one.Zn.ion..As.a.consequence,.the.Zn2.coordination.number.changes.from.5.
to.4..(iii).The.WAT.ligand.bonds.tightly.to.Zn2.forming.a.bipyramidal.polyhedron..
The.WAT-Zn2.distance.gradually.decreases,.thus.lowering.the.WAT.pK a ..(iv).The.
Zn2-bound.WAT.gets.closer.to.the.β-lactam.ring,.consequently.increasing.the.C-N.
distance.. The. partial. negative. charge. on. N. together. with. the. enhanced. nucleophi-
licity.of.WAT.produces.a.proton.shuttle.from.WAT.to.the.N5.atom.that.ultimately.
triggers.the.C8-N5.bond.cleavage..(v).Deprotonated.water.binds.Zn1,.completing.the.
tetrahedral.coordination.sphere.of.Zn2.and.replacing.the.position.of.the.OH − .nucleo-
phile.in.ES.state..Zn1.then.switches.to.a.penta-coordinated.bipyramidal.coordination.