LignAmb25: A comprehensive AMBER force field addressing lignin's structural and chemical diversity

Area of Science:

• Computational chemistry
• Biomolecular modeling
• Polymer science

Background:

• Lignin, a complex biopolymer, presents challenges for accurate molecular dynamics simulations due to its heterogeneous structure.
• Existing force fields often lack comprehensive coverage of diverse lignin units and linkages, limiting simulation capabilities.

Purpose of the Study:

• To develop and validate LignAmb25, a novel, comprehensive force field for lignin molecular dynamics simulations.
• To ensure LignAmb25 is compatible with the AMBER molecular dynamics suite and other major biomolecular force fields.

Main Methods:

• Parameterization derived from GAFF2 and optimized using quantum mechanical calculations (ωB97X-D4/def2-TZVPP).
• Conformational sampling via CREST/CENSO and partial atomic charge derivation using RESP methodology.
• Validation against experimentally measured crystal structures and calculation of enthalpy of vaporization and hydration free energy.

Main Results:

• LignAmb25 accurately reproduces lignin crystal structure packing, outperforming existing CHARMM force fields.
• The force field reliably estimates thermodynamic properties like enthalpy of vaporization and hydration free energy.
• Two variants, LignAmb25^Solo and LignAmb25^HF, are provided for different simulation needs, with LignAmb25^HF ensuring compatibility with protein, carbohydrate, and lipid force fields.

Conclusions:

• LignAmb25 offers a significant advancement for simulating complex softwood and hardwood lignin structures.
• Its compatibility with other AMBER force fields broadens its applicability in multi-component biomolecular systems.
• The force field is set to be distributed with AMBER 26, making it widely accessible to the research community.