Studying cellulose hydrolysis

8.7.1 Work to date

The questions researchers have tried to answer over the last two decades using molecular mechanics and molecular dynamics have been, what are the structures of cellulose isotypes Ia, Ip, and II, and, can the uncertainties and irregularities in the experimental data be clarified? Many insights have been gained from simulations using multiple force fields, models, and programs. The structure of Ia has been robust in its behavior across several of the force fields as evidenced by the average structures after sufficient equilibration (37, 50-54, 56, 57, 71, 72). These simulations have been able to show the details of the tilting of sugar rings in alternating layers, the right-handed twist in the cellulose fiber, and the stable hydrogen bonding and changes in hydrogen bonding (53) over nanosecond time scales. Analysis of the water structure (57,73,74) and simulations of smaller bundles of cellodextrin chains suggest that the structure is more gel-like (72) in contrast to the simulations of larger bundles in which highly crystalline structure is found to be stable below the first layer. The study of the free energy surface of the alpha-(1-4)-glycosidic linkage including the effects of water (75) provides insight into the contribution of this linkage to more complex cellulosic structures using umbrella sampling to produce the surface.

More recently, MD tools have been used to study interactions between cellulose and other non-cellulosic molecules. The binding domains of cellulases have been docked onto the [100] surface of cellulose Ia resulting in observation of interesting and possibly important behavior in multi-nanosecond MD simulations (58). The entire CBH I enzyme was docked onto the cellulose surface and simulated for 1.5 ns. The complex was found to be stable and have significant water structuring around the interaction regions (76).