Atomistic Simulation of Water Incorporation and Mobility in Bombyx mori Silk Fibroin.

Bombyx mori silk fibroin (SF) is a biopolymer that can be processed into materials with attractive properties (e.g., biocompatibility and degradability) for use in a multitude of technical and medical applications (including textiles, sutures, drug delivery devices, tissue scaffolds, etc.). Utilizing the information from experimental and computational SF studies, a simplified SF model has been produced (alanine-glycine [Ala-Gly] n crystal structure), enabling the application of both molecular dynamic and density functional theory techniques to offer a unique insight into SF-based materials. The secondary structure of the computational model has been evaluated using Ramachandran plots under different environments (e.g., different temperatures and ensembles). In addition, the mean square displacement of water incorporated into the SF model was investigated: the diffusion coefficients, activation energies, most and least favorable positions of water, and trajectory of water diffusion through the SF model are obtained. With further computational study and in combination with experimental data, the behavior/degradation of SF (and similar biomaterials) can be elucidated. Consequently, greater control of the aforementioned technologies may be achieved and positively affect their potential applications.

Structural behaviour of 2-hydroxypropyl-beta-cyclodextrin in water: molecular dynamics simulation studies.

PURPOSE: To investigate the effect of 2-hydroxypropyl side group substitutions on the structure of beta-cyclodextrin (CD) in water. METHODS: Molecular dynamics simulations were carried out on four HPBCDs that broadly represent a range of degree of substitutions in order to investigate the effect of substitution of beta-cyclodextrin with 2-hydroxypropyl groups at various O2 and O6 positions of the glucose units. RESULTS: The 2-hydroxypropyl side groups located at the O2 positions widen the cavity entrance at the secondary OH position of the CD molecule. These groups are spatially more spread out but dynamically more restricted, due to the formation of a hydrogen bond network between the hydroxyl groups of the side chains and the glucose units. On the other hand, the 2-hydroxypropyl groups at the O6 positions are dynamically more flexible. CONCLUSIONS: The extent and the location of the substitution can affect the cavity structure of the CD molecule, and thus possibly the molecular encapsulation capabilities.