Chemistry Reference
In-Depth Information
indicated the limitation of the classical approach, the classical dynamics
dataset was used rather than the quantum chemistry approach (CPMD),
in order to provide a complete distribution of the conformational states
visited. The aim here is to compare different representations of the
conformational behaviours of the furanose ring.
As previously explained with respect to the puckering concept, the local
endocyclic coordinates are not independent, but are coupled to each
other. In the previous models (Altona, Rao, Cremer-Pople), the pseudo-
rotational concept reduces the 5-dimensional (y
1
, y
2
, y
3
, y
4
, y
5
) problem
of the furanose system to a 2-dimension problem, i.e. P and y
m
variables.
However, very often, only the puckering is considered to describe the
energy landscape of the ring, thus considering that the puckering amp-
litude y
m
remains nearly constant along the lowest energy path. While
this can be acceptable when considering individual minimum energy
conformations, it is clearly inadequate when considering an energy well,
as the width of the well in the y
m
dimension is as relevant as in the P
dimension. Therefore, a polar representation including both P and y
m
is
eminently preferable.
30
This provides a more complete view of the energy
landscape. We present on the left side of Fig. 8 the complete 2D-free
energy map of the ring conformations of the dihydroxylated compound
IV in polar coordinates based on the two-dimensional probability dis-
tribution function of the coordinates P and y
m
(see computational de-
tails) with P, the angular coordinate, increasing in a counter-clockwise
sense from a horizontal value of P
=
01, and y
m
, the puckering amplitude
(in degrees), increasing radially. The classical vacuum simulation data
were used in this case (charge set 1). The solid circle corresponds to a
pseudo-rotational pathway with fixed y
m
=
36.11 (mean value of y
m
during
the simulation). This two-dimensional graphic clearly brings more in-
formation on ring flexibility than the one-dimensional one: the apparent
tight well in the 1D-plot G
=
f (P) about P
=
591 (on the right side of Fig. 8,
solid line) now appears as a broad basin in the polar representation. It
shows that
the resulting energy landscape in a vacuum is rather
Fig. 8 Left side: 2D-free energy map of the ring conformations of the dihydroxylated
compound IV in polar coordinates; minimum free energy pathway (MEP, white dashed);
right side: 1D-free energy profile as a single function of P (as previously seen on Fig. 6)
compared to the free energy obtained along the minimum energy pathway of the 2D-
representation; 1 ns classical simulation in vacuum with charge set 1.
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