Ring dihedral Principal Component Analysis of furanose conformation - Carbohydrate Chemistry: Chemical and Biological Approaches - page 385

Fig. 6 Potential energy profile during the pseudo-rotation circuit of the dichlorinated
derivative II at fixed y m = 40 1 (same intensity difference scale as in Fig. 5; gas-phase cal-
culations performed at the B3LYP/6-311 þþ G** level of theory).
could not be adequately rationalised on this basis. A very recent
topological approach, precisely developed to highlight spatial regions of
weak interactions (Non Covalent Interaction analysis), 28 provides an
interesting clue to get a deeper insight into the attractive/repulsive con-
tributions appearing along the pseudo-rotational pathway. This analysis
is currently in progress in our laboratory.
Based on this first series of results, the conformational energy profiles
of furanose rings seem far from featureless, and the conformation of the
b- D -xylosyl derivatives, for example, can be reasonably described as
vibrating within the pseudo-rotational cycle around 4 E. However, two
important caveats remain: first, determination of the conformational
energy profile required setting an arbitrary constraint (y m = 401) that may
significantly distort the results; second, the very description of furanose
conformation in terms of two parameters, P and y m , excludes portions of
conformational space from our description by limiting the search to
pseudo-symmetrical conformations.
4 Results for classical and quantum molecular
dynamics investigations for b - D -xylosyl derivatives
The potential energy profile in Fig. 6 above was obtained with a fixed y m
value throughout the geometry relaxations, as a P value cannot be defined
without a y m value, and vice versa. A more realistic approach to study the
conformation of carbohydrates, without constraining either P or y m ,
involves molecular dynamics experiments. Only classical molecular dy-
namics are usually realized in the literature because of the prohibitive
cost of a quantum evaluation of the potential energy. For such molecular
mechanics calculations, a force field must previously be parameterized to
describe the potential energy of a given molecular family, every par-
ameter then remaining fixed over the course of the simulation. 29 One of
the key ingredients of such simulations is the choice of atomic partial
charges governing the electrostatic interactions, which remain constant
in the approximation of non-polarisable force fields. However, one may
ask whether or not the conformation affects these partial charges, and
consequently whether using a fixed charge set in a classical molecular
dynamics is a good approximation. Using a quantum-chemistry based