Carbohydrate and Trivalent Iron Ion Interactions in the Gas Phase and in Aqueous Solution - Metallic Systems: A Quantum Chemist's Perspective - page 87

3.2.1 c ar -P arrinello m olecular d ynamicS S imulationS
The.Becke-Lee-Yang-Parr.(BLYP).gradient.corrected.functional,.which.was.found.
to.be.reliable.in.the.studies.of.glucose,.was.used.along.with.Troullier-Martins.pseu-
dopotentials. and. a. double-ζ. basis. set. in. the. CPMD. simulations. [41,42].. The. elec-
tronic.wave.functions.were.expanded.in.a.plane.wave.basis.set.with.a.kinetic.energy.
cutoff.of.114.Ry..A.homogeneous.background.charge.was.applied.to.compensate.for.
the.ionic.charge..The.time.step.for.the.CPMD.simulations.was.0.1.fs..The.electronic.
mass.was.900.a.u..The.isotopic.mass.of.deuterium.was.used.for.hydrogen..CPMD.
simulations.of.80.ps.were.performed.for.methyl-α-d-mannopyranoside.(M),.M-Fe 3+ ,.
and. M-Fe 3+ . in. the. gas. phase.. Statistics. were. collected. for. 70.ps.. Separate. CPMD.
simulations.were.performed.in.cubic.cells.with.lattice.parameters.of.25,.35,.and.45.Å.
using.periodic.boundary.conditions..It.was.found.that.these.lattice.parameters.do.not.
have.a.signiicant.impact.on.predicted.structural.and.thermodynamic.properties.in.
the.gas.phase..Canonical.ensemble.CPMD.simulations.were.performed.at.room.tem-
perature. using. the. Nose-Hoover. thermostat.. Long-range. interactions. were. treated.
with.the.Ewald.sum.method.[43].
For.simulations.in.aqueous.solution,.M.was.solvated.by.58.water.molecules.in.a.
cubic.cell.with.lattice.parameters.of.16.6.Å.and.a.homogeneous.background.charge.
was. applied. to. compensate. for. the. ionic. charge.. CPMD. simulations. of. 80.ps. were.
performed.for.M,.M-Fe 3+ ,.and.M-Fe 3+ .in.aqueous.solution..To.assess.the.effects.of.
the.chosen.number.of.water.molecules,.we.performed.another.set.of.CPMD.simu-
lations. with. 92. water. molecules.. The. structures. and. conformations. obtained. from.
these.simulations.showed.that.the.impact.of.additional.water.molecules.is.extremely.
small.with.a.carbohydrate.conformational.difference.of.1.6%..Canonical.ensemble.
simulations.using.the.periodic.boundary.conditions.at.room.temperature.were.per-
formed.. The. Nose-Hoover. thermostat. was. used. to. control. the. temperature.. The.
Ewald. sum. method. was. used. to. treat. long-range. interactions. in. aqueous. solution.
simulations.of.these.compounds.[43].
3.2.2 c laSSical m olecular d ynamicS S imulationS
The.OPLS-AA.and.UFF.force.ield.parameters.were.used.for.M.and.the.Fe 3+ .ion,.
respectively.[44,45]..Our.recent.studies.on.methyl-α-mannopyranoside.in.aqueous.
solution. using. TIP3P,. TIP4P,. and. TIP5P. models. for. water. showed. that. simulation.
results.with.the.TIP5P.model.for.water.are.closer.to.the.results.obtained.via.CPMD.
simulations.[29,30]..Thus,.we.chose.the.TIP5P.potential.function.for.water.in.this.
work.to.study.the.impact.of.water.on.the.predicted.conformation.of.M,.M-Fe 3+ ,.and.
M-Fe 3+ .complexes.in.aqueous.solution.[29,30]..Lorentz-Berthelot.mixing.rules.were.
used.for.calculating.the.cross.parameters..Separate.simulations.of.60.and.50.ns.were.
performed.for.M.and.its.complexes.with.the.Fe 3+ .ion.in.the.gas.phase.and.in.aqueous.
solution,.respectively..Statistics.were.sampled.for.50.and.40.ns.in.the.gas.phase.and.
in.water,.respectively..For.the.simulations.in.aqueous.solution,.M.was.solvated.by.
470.water.molecules.in.a.cubic.box.with.a.box.length.of.24.4.Å..Periodic.boundary.
conditions.were.used..A.cutoff.distance.of.12.Å.was.applied.for.treating.solute.and.
solvent. long-range. interactions.. The. Ewald. sum. method. was. used. for. treating. the.