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ensembles for a 48 waters
รพ
carbohydrate system. Two other interesting
trends are available from Fig. 7 for compound IV. First, quantum-chem-
istry simulation has a tendency to yield a slightly larger barrier to con-
formational change, as seen in the well-sampled vacuum simulations.
Secondly, in water, the slope value appears more abrupt compared to the
simulations under vacuum, either under classical or quantum conditions,
highlighting the modulating role of the solvent on the conformational
vibration. Examination of the molecular dynamics snapshots actually
emphasizes strong hydrogen bonding between explicit water molecules
and endocyclic oxygen atom as well as extracyclic hydroxyl groups of IV.
This effect clearly contributes to hinder ring degrees of freedom, and
consequently, solvent influences the ring puckering behaviour.
One important point was to measure how well P and y
m
were able to
capture all the non-equilibrium and non-symmetrical situations explored
by molecular dynamics. Analysing our simulation data, each visited ring
geometry characterized by its set (y
1
, y
2
, y
3
, y
4
, y
5
) was back-calculated
using equation 1 from the set (P, y
m
) associated to this geometry. First,
as previously highlighted, situations where P is in the range 88-92 or 268-
272 lead to outlier values of y
m
. Furthermore, for plausible values of y
m
,
derived y
j
may deviate from their original value (Dy
j
=
2to41). Though
these correspond to relatively small variations, they can represent large
deviations in term of potential energy, even more so when the ring bears
substituents. It is therefore important to emphasize that (a) a continuum
of conformations can lead to a given value of P and y
m
,and(b)pseudo-
symmetrical geometries generated from a given P and y
m
value by the
Altona equations 1 and 2 do not necessarily correspond to any reality.
From a dynamic point of view, examination of the molecular dynamics
data shows that the ring puckering fluctuates constantly. It takes less
than 2 ps for the molecule to make a full ''P-revolution'' on the graph.
Small fluctuations are observed in the range DP
=
2-301 at relatively high
frequencies (800 cm
1
), which can be analogized to a vibration within a
conformational well. However, analysis of puckering fluctuations also
reveals lower frequencies (1-10 cm
1
). Since the amplitude of a mode is
inversely proportional to the frequency, the most significant ring motion
is thus produced by these low frequency modes. However, the sole con-
sideration of puckering in studying these large amplitude motions of the
ring is inadequate, as the degree of puckering (y
m
) also has essential
implications in the definition of flexibility. Therefore, there remains one
critical caveat: Fig. 7 describes only one conformational parameter P, and
while y
m
is not constrained, we do not have the width of the well in the y
m
dimension.
5 Dihedral PCA on the five endocyclic angles of the
dihydroxylated
b
-
D
-xylosyl derivatives: an orientation
table to fully explore the conformational landscape
In this section, various representations of the free energy landscape of IV
are explored using statistical analyses. Though our previous study has
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