Dynamics simulation of the interaction between serine and water

Area of Science:

• Computational Chemistry
• Biophysics
• Materials Science

Background:

• Serine hydration dynamics are crucial for biochemical processes.
• Previous studies suggest water molecules interact differently with serine's functional groups based on hydration levels.

Purpose of the Study:

• To simulate and analyze the neutron scattering spectra of serine hydration dynamics.
• To elucidate the specific hydrogen bonding interactions between water and serine functional groups (-OH and -NH3+).

Main Methods:

• First-principles density functional theory (DFT) simulations were employed.
• Neutron scattering spectra were calculated for hydrated serine models.
• Simulated phonon signals were compared with experimental data.

Main Results:

• Water molecules preferentially form hydrogen bonds with the -OH group at lower hydration and shift to the -NH3+ group at higher hydration.
• DFT simulations accurately reproduced experimental spectra when combining -OH···H2O and -NH3(+)···H2O signals in a 3:1 ratio.
• Specific spectral peaks at 423 cm⁻¹ (-OH···H2O) and 367 cm⁻¹ (-NH3(+)···H2O) were identified and validated.

Conclusions:

• Water can disrupt existing serine intermolecular hydrogen bonds to form new structures.
• Serine's flexible structure facilitates stronger hydrogen bonding with the -NH3+ group, indicating a dynamic hydration mechanism.