An evaluation of the structures of cellulose generated by the CHARMM force field: comparisons to in planta cellulose

Molecular dynamics simulations of cellulose regularly sample a conformational space different to the crystal structures they were initiated from, with changes to the tilt of chains, expansion of the unit cell and variation in exocyclic group conformations. Given the differences in the structures sampled the question presents itself as to whether these simulations are sampling structures that resemble cellulose in planta. To investigate this question, we have performed MD simulations on different size and shaped Iα and Iβ cellulose microfibrils with the structures generated characterized with regards to changes in expansion, chain shift along the polymerization axis, tilt, exocyclic conformation and H-bonding. Structures were then input into a quantum mechanical NMR chemical shift calculation protocol with the resulting ¹³C chemical shifts compared to experimental data. Chemical shifts were shown to be strongly dependent on the exocyclic group conformation with the structures of Iα simulations more closely replicating experimental data than the Iβ simulations, especially at the C4 and C6 positions which suggests that the conformational space was not being accurately represented for the Iβ microfibrils. Despite this, peak sizes based on the sampling occupancy of exocyclic conformations from unrestrained simulations were found to replicate experimental peak sizes better than simulations where exocyclic groups of interior chains were restrained to the tg conformation, suggesting that exocyclic groups have greater freedom to sample different conformations than suggested by their crystal structures.