Chemistry Reference
In-Depth Information
the.QM.and.MM.region,.a.“link.atom,”.usually.a.hydrogen.atom,.is.placed.between.
the.two.bonded.atoms.and.bonds.to.this.atom.are.computed.in.both.the.QM.and.MM.
regions.. The. combination. of. QM. and. MM. has. been. widely.applied.to. study. reac-
tion.mechanisms.in.biological.systems,.and.especially.to.biological.compounds.and.
metal.ion.coordination.chemistry.
To.study.the.coordination.of.a.transition.metal.ion.to.the.protein,.we.performed.
QM/MM.simulations..The.gradient.corrected.Becke-Lee-Yang-Parr.(BLYP).func-
tional.was.used.to.treat.the.active.part.of.the.protein.(histidine,.according.to.experi-
ment). and. the. Fe
3+
. ion. using. ab. initio. MD. simulations. with. the. CPMD. approach..
The. CPMD. method. permits. eficient. evaluation. of. the. dynamical. evolution. of. the.
molecular. system.. The. observation. of. the. dynamics. of. a. molecule. provides. a. dis-
tinct. advantage. over. the. more. common. use. of. static. (ixed. geometry). electronic.
structure.calculations.for.studies.of.the.type.reported.here..Nevertheless,.static.irst.
principles.calculations.in.the.gas.phase.and.in.water.using.implicit.and.explicit.sol-
vent.molecules.have.been.widely.used.for.studies.of.biometallic.species.since.these.
calculations.are.less.expensive.than.the.CPMD.simulations..Such.calculations.may.
encompass.a.few.points.of.dynamical.interest,.but.are.no.substitute.for.a.dynamical.
trajectory..The.remainder.of.the.protein.outside.the.QM.region,.the.water.molecules.
and.the.counter.ions.were.treated.using.classical.MD.
Recently,. we. predicted. a. mechanism. for. water. dissociation. in. aqueous. solution.
that.is.induced.by.the.presence.of.a.Fe
3+
.ion.and.the.impact.of.the.dissociated.states.
of.water.on.the.hydration.structure.of.the.Fe
3+
.in.water.using.CPMD.simulations.cou-
pled.with.transition.path.sampling.(TPS).calculations..(TPS.is.a.specialized.method.
for.simulating.rare.events.and.is.critical.to.the.study.of.metal.ions.in.water.).The.ini-
tial.geometry.of.the.Fe(OH)
3
(H
2
O)
6
.complex.and.of.the.surrounding.water.molecules.
and.aqua.ions.(H
3
O
+
.and.OH
−
.complexes).were.taken.from.the.CPMD/TPS.study.to.
investigate.the.coordination.chemistry.of.the.hydrated.Fe
3+
.ion.with.the.proteins.and.
the.impact.of.dissociated.states.of.water.on.the.coordination.chemistry..For.details.
see.Chapter.in.this.topic.entitled.
Metal Ions in Aqueous Solution
.
The.details.of.the.QM/MM.studies.are.as.follows..Dangling.bonds.were.termi-
nated. with. hydrogen. bonds.. A. plane-wave. basis. cutoff. of. 76. Ry. was. used. in. the.
DFT.calculations..Troullier-Martin.pseudopotentials.for.core.electrons.along.with.
a.double.zeta.quality.valence.basis.set.were.used.on.all.atoms..The.CPMD.method.
was. used. to. perform. dynamical. calculations. of. the. metal. ion. binding. site. of. the.
protein..A.time.step.of.0.2.fs.and.a.ictitious.electron.mass.of.600.au.were.used..The.
temperature.was.controlled.using.a.Nosé-Hoover.thermostat..A.cutoff.value.of.12.Å.
was. used. for. nonbonded. interactions. and. the. PME. method. was. used. for. treating.
long-range.interactions..The.temperature.was.ixed.at.310.K.
When.simulating.proteins.in.aqueous.solution,.it.is.often.necessary.to.ascertain.
structural. properties. of. the. protein. by. calculating. a. root-mean-square. deviation.
(RMSD).from.a.reference.set.of.atomic.coordinates
∑
N
(
)
2
r t
( )
−
r
i
ref
i
=
1
RMSD
=
(2.20)
N
.
.
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