Cellulosic ethanol: progress towards a simulation model of lignocellulosic biomass;
- ORNL
A CHARMM molecular mechanics force field for lignin is derived. Parameterization is based on reproducing quantum mechanical data of model compounds. Partial atomic charges are derived by the examination of methoxybenzene:water interactions. Dihedral parameters are optimized by fitting to critical rotational potentials, and bonded parameters are obtained by optimizing vibrational frequencies and normal modes. The force field is validated by performing a molecular dynamics simulation of a crystal of a lignin fragment molecule and comparing simulation-derived structural features with experimental results. Together with the existing force field for polysaccharides, this work will enable full simulations of lignocellulose. This work presents a molecular mechanics force field for lignin that is compatible with the CHARMM potential energy function. The parameterization was based on reproducing quantum-mechanically derived target data. Special care was taken to correctly describe the most common lignin linkage: the {beta}-O-4{prime} bond. The partial atomic charge of the oxygen and carbon atoms participating in the linkage were derived by examining interactions between a lignin fragment model compound and a water molecule. Dihedral parameters were obtained by reproducing QM potential energy profiles, with emphasis placed on reproducing accurately the thermally sampled low energy regions. The remaining bond and angle parameters were derived using the AFMM method. In order to test the validity of the force field a simulation of a lignin-dimer crystal was performed. The overall good agreement between the structural properties of the MD run and the experiment provide confidence that the force field can be used in simulation of biomass. The accurate computer simulation of lignin in lignocellulose will present significant challenges. Unlike many biological macromolecules that have been studied with molecular simulation, both the chemical and three-dimensional structures of lignin are relatively poorly researched. However, the present force field provides a basis for constructing molecular models of lignin systems, and, in combination with a range of biophysical measurements, significant progress in determining structures of lignocellulosic biomass can be expected in the near future.
- Research Organization:
- Oak Ridge National Laboratory (ORNL)
- Sponsoring Organization:
- SC USDOE - Office of Science (SC)
- DOE Contract Number:
- AC05-00OR22725
- OSTI ID:
- 1018666
- Country of Publication:
- United States
- Language:
- English
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