Carbohydrate and Trivalent Iron Ion Interactions in the Gas Phase and in Aqueous Solution - Metallic Systems: A Quantum Chemist's Perspective - page 88

long-range.interactions.[43]..Canonical.ensemble.simulations.were.performed.using.
Langevin.dynamics.at.300.K..Homogeneous.background.charge.was.applied.to.com-
pensate.for.the.net.ionic.charge..For.the.gas-phase.simulations,.separate.simulations.
with. cubic. cell. lattice. parameters. of. 25,. 35,. and. 45. Å. were. performed. and. results.
showed.that.these.various.lattice.parameters.do.not.impact.predicted.structural.and.
thermodynamic.properties.

3.2.3 d etermination of the P referred c onformation
for g lycoSidic l inkage
Figure.3.1.shows.the.torsional.angle.of.the.glycosidic.linkage.studied.in.this.work..
The. glycosidic. linkage. torsional. angle. φ.=.O5-C1-C7-O7. was. varied. between. 0°.
and. 360°. to. study. the. relative. torsional. energies. in. the. gas. phase. and. in. aqueous.
solution.. The. potential. of. mean. force. (PMF). method. (Equation. 3.1). was. used. for.
calculating.the.preferred.conformation.of.the.glycosidic.linkage.of.M,.M-Fe 3+ ,.and.
M-Fe 3+ .in.the.gas.phase.and.in.aqueous.solution.[46-48]:

. (3.1)

Δ G = − kT ln Z

.

where. Z . is. the. probability. of. the. torsional. angle. (φ). varying. between. 0°. and. 360°.
obtained.from.CPMD.and.CMD.simulations..For.the.PMF.calculations.with.CPMD.
simulations,.i.e.,.for.λ.=.0.→.λ.=.1.(λ.=.0.and.λ.=.1.represent.the.initial.and.inal.states.
of.the.system).each.window.was.simulated.for.80.ps.in.the.gas.phase..To.understand.
the.adequacy.and.convergence.of.PMF,.we.compared.the.PMF.values.calculated.for.
50,.60,.and.70.ps.simulations.for.each.window..Standard.deviations.were.computed.
using.results.obtained.at.these.different.simulation.times..For.PMF.calculations.with.
CMD.simulations,.the.systems.were.simulated.for.800.ps.for.each.window,.and.the.
convergence.was.tested.by.comparing.the.PMF.results.calculated.for.λ.=.0.→.λ.=.1.to.

O6

H4

O4

H3

H2

O3

O5

O2

C1

O1

ψ

C7

FIGURE 3.1 Methyl-α-mannopyranoside,.obtained.from.CPMD.simulations,.with.conven-
tional.numbering.of.speciic.atoms.