New Insight into Uracil Stacking in Water from ab Initio Molecular Dynamics

Area of Science:

• Biochemistry
• Physical Chemistry
• Computational Chemistry

Background:

• Nucleobases spontaneously aggregate in aqueous solutions.
• Hydrophobic and base-base dispersion forces are primary drivers of aggregation.
• Understanding these interactions is crucial for biological systems.

Purpose of the Study:

• To investigate the aggregation mechanism of uracil in water.
• To analyze the structural and energetic changes upon uracil dimerization.
• To correlate these changes with spectroscopic properties.

Main Methods:

• First-principle molecular dynamics simulations of uracil monomer and dimer in water.
• Analysis of dimer structure, hydrogen bonding, and hydration shell.
• Simulation of infrared absorption spectra.

Main Results:

• Uracil stacking enhances uracil-water hydrogen bonding strength.
• Dimerization alters the hydration structure around uracil.
• Simulated IR spectra show significant changes in the carbonyl stretching band due to stacking.

Conclusions:

• Stacking interactions significantly influence uracil's behavior in water.
• Hydrogen bonding and hydration changes are key factors in nucleobase association.
• Findings provide microscopic insights into heteroaromatic association in biological contexts.