Parameterization for molecular Gaussian surface and a comparison study of surface mesh generation.

Area of Science:

• Computational chemistry
• Molecular modeling and simulation

Background:

• Molecular Gaussian surfaces are crucial in computational chemistry, typically defined by decay rate and isovalue parameters.
• Existing methods lack systematic approaches for optimizing these parameters based on geometric features.

Purpose of the Study:

• To develop a systematic method for parameterizing molecular Gaussian surfaces.
• To ensure Gaussian surfaces accurately approximate solvent-excluded surfaces (SES) and van der Waals (VDW) surfaces.

Main Methods:

• Utilized surface area, enclosed volume, and Hausdorff distance as criteria for Gaussian surface parameterization.
• Performed parameter space searches to find optimal values for approximating SES.
• Analyzed explicit expressions to approximate VDW surfaces, with applicability to solvent-accessible surfaces (SAS).

Main Results:

• Optimal parameters derived from different geometric criteria were found to be close, yielding similar molecular properties.
• The parameterized Gaussian surface accurately approximates SES and VDW surfaces.
• The TMSmesh software, utilizing these parameters, demonstrated superior mesh quality and fidelity compared to other programs.
• Poisson-Boltzmann solvation energies calculated using TMSmesh-generated surfaces showed high accuracy.

Conclusions:

• The developed systematic parameterization method provides accurate Gaussian molecular surfaces.
• The parameterized Gaussian surface is applicable for approximating SES, VDW, and SAS.
• TMSmesh software offers a reliable tool for generating high-quality molecular surface meshes for computational chemistry applications.