Multiscale Modeling of Phosphate···π Contacts in RNA U‑Turns Exposes Differences between Quantum-Chemical and AMBER Force Field Descriptions

Phosphate···π, also called anion···π,
contacts occur between nucleobases and anionic phosphate oxygens (OP2)
in r(GNRA) and r(UNNN) U-turn motifs (N = A,G,C,U; R = A,G). These
contacts were investigated using state-of-the-art quantum-chemical
methods (QM) to characterize their physicochemical properties and
to serve as a reference to evaluate AMBER force field (AFF) performance.
We found that phosphate···π interaction energies
calculated with the AFF for dimethyl phosphate···nucleobase
model systems are less stabilizing in comparison with double-hybrid
DFT and that minimum contact distances are larger for all nucleobases.
These distance stretches are also observed in large-scale AFF vs QM/MM
computations and classical molecular dynamics (MD) simulations on
several r(gcGNRAgc) tetraloop hairpins when compared to experimental
data extracted from X-ray/cryo-EM structures (res. ≤ 2.5 Å)
using the WebFR3D bioinformatic tool. MD simulations further revealed
shifted OP2/nucleobase positions. We propose that discrepancies between
the QM and AFF result from a combination of missing polarization in
the AFF combined with too large AFF Lennard-Jones (LJ) radii of nucleobase
carbon atoms in addition to an exaggerated short-range repulsion of
the r–12 LJ repulsive term. We
compared these results with earlier data gathered on lone pair···π
contacts in CpG Z-steps occurring in r(UNCG) tetraloops. In both instances,
charge transfer calculations do not support any significant n → π* donation effects. We also investigated
thiophosphate···π contacts that showed reduced
stabilizing interaction energies when compared to phosphate···π
contacts. Thus, we challenge suggestions that the experimentally observed
enhanced thermodynamic stability of phosphorothioated r(GNRA) tetraloops
can be explained by larger London dispersion.