Extended Ensemble Molecular Dynamics Study of Ammonia-Cellulose I Complex Crystal Models: Free-Energy Landscape and Atomistic Pictures of Ammonia Diffusion in the Crystalline Phase.

Here, we report extended ensemble molecular dynamics simulations of ammonia-cellulose I complex crystal models to evaluate the diffusion behavior of the guest ammonia molecules and the potential of mean force (PMF), namely, the free energy change along the chosen reaction coordinate, for migration of an ammonia molecule in the crystal models. Accelerated molecular dynamics simulations confirmed that ammonia molecules almost exclusively diffused through the hydrophilic channel even when the crystal framework was retained. Adaptive steered molecular dynamics simulations detected distinct PMF peaks with heights of approximately 7 kcal/mol as the ammonia molecule passed through the cellulose-chain layers. Introducing hybrid quantum mechanical and molecular mechanics theory to the adaptive steered molecular dynamics simulation effectively lowered the heights of the PMF peaks to approximately 5 kcal/mol, accompanied by a slight decrease in the baseline. Removal of the ammonia molecules in the neighboring channels resulted in a continuous increase in the baseline for the migration of an ammonia molecule in the hydrophilic channel. When the halves of the crystal model were separated to widen the hydrophilic channel to 0.2 nm, the PMF profiles exhibited an unexpected increase. This resulted from water structuring in the expanded hydrophilic channel, which disappeared with further expansion of the hydrophilic channel to 0.3 nm.

Optimization of Zwitterionic Polymers for Cell Cryopreservation.

Cryopreservation techniques are valuable for the preservation of genetic properties in cells, and the development of this technology contributes to various fields. In a previous study, an isotonic freezing medium composed of poly(zwitterion) (polyZI) has been reported, which alleviates osmotic shock, unlike typical hypertonic freezing media. In this study, the primitive freezing medium composed of emerging polyZI is optimized. Imidazolium/carboxylate-type polyZI (VimC3C) is the optimal chemical structure. The molecular weight and degree of ion substitution (DSion) are not significant factors. There is an impediment with the primitive polyZI freezing media. While the polyZI forms a matrix around the cell membrane to protect cells, the matrix is difficult to remove after thawing, resulting in low cell proliferation. Unexpectedly, increasing the poly(VimC3C) concentration from 10% to 20% (w/v) improves cell proliferation. The optimized freezing medium, 20% (w/v) poly(VimC3C)_DSion(100%)/1% (w/v) NaCl aqueous solution, exhibited a better cryoprotective effect.

Tunability of the thermal diffusivity of cellulose nanofibril films by addition of multivalent metal ions.

Discovering principles to tune the heat-transport properties of cellulose nanofibril (CNF) films will open the door for the development of biomass-derived heat-transfer materials and break away from existing petroleum-based polymer composites. In this study, we added various multivalent metal ions to CNF films with surface carboxy groups formed by 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO) oxidation and measured their thermal diffusivities in the dry state by an original method to verify the tunability of the thermal diffusivity. We found that the in-plane thermal diffusivity of the film is inversely proportional to the ionic radius and directly proportional to the Pauling electro-negativity. The CNF film with proton-neutralized carboxyl groups showed the highest level of thermal diffusivity among the films with various metal ions. Molecular dynamics simulations clarified that the spatial distribution of the introduced ions is determined by the closest distance between the cation and carboxylate oxygen atom of the TEMPO-oxidized CNF surface.

Molecular Dynamics Simulation of Cellulose Synthase Subunit D Octamer with Cellulose Chains from Acetic Acid Bacteria: Insight into Dynamic Behaviors and Thermodynamics on Substrate Recognition.

The present study reports the building of a computerized model and molecular dynamics (MD) simulation of cellulose synthase subunit D octamer (CesD) from Komagataeibacter hansenii. CesD was complexed with four cellulose chains having DP = 12 (G12) by model building, which revealed unexpected S-shaped pathways with bending regions. Combined conventional and accelerated MD simulations of CesD complex models were carried out, while the pyranose ring conformations of the glucose residues were restrained to avoid undesirable deviations of the ring conformation from the 4C1 form. The N-terminal regions and parts of the secondary structures of CesD established appreciable contacts with the G12 chains. Hybrid quantum mechanical (QM) and molecular mechanical (MM) simulations of the CesD complex model were performed. Glucose residues located at the pathway bends exhibited reversible changes to the ring conformation into either skewed or boat forms, which might be related to the function of CesD in regulating microfibril production.

Cellulose Crystal Dissolution in Imidazolium-Based Ionic Liquids: A Theoretical Study.

The highly crystalline nature of cellulose results in poor processability and solubility, necessitating the search for solvents that can efficiently dissolve this material. Thus, ionic liquids (ILs) have recently been shown to be well suited for this purpose, although the corresponding dissolution mechanism has not been studied in detail. Herein, we adopt a molecular dynamics (MD) approach to study the dissolution of model cellulose crystal structures in imidazolium-based ILs and gain deep mechanistic insights, demonstrating that dissolution involves IL penetration-induced cleavage of hydrogen bonds between cellulose molecular chains. Moreover, we reveal that in ILs with high cellulose dissolving power (powerful solvents, such as 1-allyl-3-methylimidazolium chloride and 1-ethyl-3-methylimidazolium chloride), the above molecular chains are peeled from the crystal phase and subsequently dispersed in the solvent, whereas no significant structural changes are observed in poor-dissolving-power solvents. Finally, we utilize MD trajectory analysis to show that the solubility of microcrystalline cellulose is well correlated with the number of intermolecular hydrogen bonds in cellulose crystals. The obtained results allow us to conclude that both anions and cations of high-dissolving-power ILs contribute to the stepwise breakage of hydrogen bonds between cellulose chains, whereas this breakage does not occur to a sufficient extent in poorly solubilizing ILs.

Theoretical study of the structural stability of molecular chain sheet models of cellulose crystal allomorphs.

The structural stabilities of the molecular chain sheets constituting the crystal structures of the cellulose allomorphs Iα, Iß, II, and IIII were investigated by density functional theory (DFT) optimization of the isolated chain sheet models with finite dimensions. The DFT-optimized chain sheet models of the two native cellulose crystals developed a right-handed twist with a similar amount of twisting. The DFT-optimized cellulose II (010) and (020) models twisted in opposite directions with right- and left-handed chirality, respectively. The cellulose IIII (1-10) model retained the initial flat structure after the DFT-optimization. The structural features of the DFT-optimized chain sheet models were reflected in the structures of the parent crystal models observed in solvated molecular dynamics (MD) simulations. The minor conformations of the hydroxymethyl groups proposed in the real crystal structures were detected in the MD crystal models and the DFT-optimized (010) model of cellulose II. The crystal chain packing and crystal conversions are interpreted in terms of principal chain sheet stacking.