Molecular Dynamics Simulations of Nitrate Complexes with Polyammonium Macrocycles: Insight on Phosphoryl Transfer Catalysis

Nitrate complexes of two different polyammonium macrocycles, the
tetrahydrogen nitrate salts of 1,4,7,16,19,21-hexaaza-10,13-dioxacyclotetracosane
[24]N6O2·4HNO3,
1, and
1,4,10,13-tetraaza-7,16-dioxacyclooctadecane,
[18]N4O2·4HNO3,
2, have been isolated and their structures determined by
X-ray crystallographic methods. Compound
1 crystallizes in the orthorhombic space group
Imma with unit cell dimensions a =
22.692(3) Å, b = 19.563(3) Å,
c = 7.005(1) Å, V = 3110(1)
Å3, and Z = 4. Compound 2
crystallizes in the orthorhombic space group Pbca
with
a = 13.877(1) Å, b = 15.553(1) Å,
c = 10.742(1) Å, V = 2314.6(5)
Å3, and Z = 8. Full-matrix
least-squares
refinement resulted in R = 0.051 and
Rw = 0.067 for 1 and R
= 0.063 and Rw = 0.072 for 2.
Compound 1 has a
boat-shaped geometry, and one of the four nitrates is situated in the
macrocyclic cavity. Compound 2 is
relatively
flat with two nitrates above and two below the plane of the molecule.
Molecular dynamics simulations were performed
for the two molecules using the structural coordinates obtained from
the crystal structures and the CHARMM molecular
model. Simulations were carried out to 400 ps for 1 and
200 ps for 2 using 2 fs time steps. The average
temperature
during the simulation was 302 ± 5 K and the average total energy was
−7805.9 ± 0.5 kcal mol-1 for 1 and
−7851.9
± 0.5 kcal mol-1 for 2. The
conformation of 2 did not change appreciably during the
simulations, whereas 1 flattened
out considerably due to hydration effects.