Effects of Long-Range Electrostatics on Time-Dependent Stokes Shift Calculations

Area of Science:

• Computational Chemistry
• Biophysical Chemistry
• Spectroscopy

Background:

• Time-dependent Stokes shift (TDSS) experiments probe fluorescent molecules in biological systems.
• Interpreting TDSS data requires accurate molecular dynamics (MD) simulations.
• Solute-environment electrostatic interactions significantly influence TDSS response.

Purpose of the Study:

• To systematically investigate the impact of long-range electrostatic treatments in MD simulations on TDSS response calculations.
• To compare various electrostatic calculation protocols against a standard reference (PME).
• To identify efficient and accurate methods for TDSS simulations.

Main Methods:

• Utilized MD simulations to model fluorescent probes (diatomic, coumarin 102, Hoechst 33258) in aqueous solution.
• Compared nine different electrostatic treatment protocols, including Particle Mesh Ewald (PME) as a reference.
• Evaluated the damped shifted force method as a computationally efficient alternative.

Main Results:

• The damped shifted force method accurately reproduced TDSS responses calculated using PME for all tested probes.
• Ignoring long-range electrostatics in MD simulations led to artifacts in TDSS response calculations.
• The choice of electrostatic treatment significantly affects the accuracy of TDSS predictions.

Conclusions:

• The damped shifted force method is a viable and efficient alternative to PME for calculating TDSS responses in MD simulations.
• Accurate treatment of long-range electrostatics is crucial for reliable interpretation of TDSS experimental data.
• MD simulations with appropriate electrostatic handling are essential for understanding fluorescent probe behavior in biological environments.