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.

Ether-Functionalized Pyrrolidinium-Based Room Temperature Ionic Liquids: Physicochemical Properties, Molecular Dynamics, and the Lithium Ion Coordination Environment.

The physicochemical properties of room temperature ionic liquids (RTILs) consisting of bis(trifluoromethanesulfonyl)amide (TFSA- ) combined with 1-hexyl-1-methylpyrrolidinium (Pyr1,6+ ), 1-(butoxymethyl)-1-methylpyrrolidinium (Pyr1,1O4+ ), 1-(4-methoxybutyl)-1-methyl pyrrolidinium (Pyr1,4O1+ ), and 1-((2-methoxyethoxy)methyl)-1-methylpyrrolidinium (Pyr1,1O2O1+ ) were investigated using both experimental and computational approaches. Pyr1,1O2O1 TFSA, which contains two ether oxygen atoms, showed the lowest viscosity, and the relationship between its physicochemical properties and the position and number of the ether oxygen atoms was discussed by a careful comparison with Pyr1,1O4 TFSA and Pyr1,4O1 TFSA. Ab initio calculations revealed the conformational flexibility of the side chain containing the ether oxygen atoms. In addition, molecular dynamics (MD) calculations suggested that the ion distributions have a significant impact on the transport properties. Furthermore, the coordination environments of the Li ions in the RTILs were evaluated using Raman spectroscopy, which was supported by MD calculations using 1000 ion pairs. The presented results will be valuable for the design of functionalized RTILs for various applications.

The effects of the position of the ether oxygen atom in pyrrolidinium-based room temperature ionic liquids on their physicochemical properties.

Room temperature ionic liquids (RTILs) containing ether oxygen atoms have been investigated for a gamut of science and technology applications owing to their superior physicochemical properties. However, the effect of the position of the ether oxygen atom in the side chain on their physicochemical properties is not clearly understood. This study investigates, using both experimental and computational approaches, the effect of ether oxygen atoms on the physicochemical properties of RTILs consisting of bis(trifluoromethylsulfonyl)amide (TFSA-) with 1-methyl-1-propylpyrrolidinium (MPP+), 1-butyl-1-methylpyrrolidinium (BMP+), 1-methoxymethyl-1-methylpyrrolidinium (MOMMP+), 1-ethoxymethyl-1-methylpyrrolidinium (EOMMP+), and 1-methoxyethyl-1-methylpyrrolidinium (MOEMP+). The viscosity of the RTILs containing the ether oxygen atom was lower than that of the alkyl analogues. Moreover, the viscosity of EOMMPTFSA was lower than that of MOEMPTFSA, albeit EOMMPTFSA and MOEMPTFSA have the same molecular weight with ether oxygen atoms at different positions. Ab initio calculations reveal that the number of methylene groups between nitrogen and oxygen atoms in the cation structure profoundly impacts the local stable structure of the cation. Furthermore, we discussed the relationship between the transport properties and the spatial distribution of ions obtained by MD simulations. This result will be valuable in the design of functionalized RTILs, via the judicious tuning of the conformational flexibility of ether oxygen atoms in related ionic liquids.

Correction: The effects of the position of the ether oxygen atom in pyrrolidinium-based room temperature ionic liquids on their physicochemical properties.

Correction for 'The effects of the position of the ether oxygen atom in pyrrolidinium-based room temperature ionic liquids on their physicochemical properties' by Kazuki Yoshii et al., Phys. Chem. Chem. Phys., 2020, DOI: .

Understanding dissolution process of chitin crystal in ionic liquids: theoretical study.

Chitin is a promising biomass resource and has high potential for industrial applications owing to its huge annual production in nature. However, it exhibits poor processability and solubility due to its very stable and crystalline character. Recently, ionic liquids (ILs) have attracted attention as solvents for structural polysaccharides - for example, 1-allyl-3-methylimidazolium bromide (AMIMBr) has been found to dissolve chitin. As few ILs are known to dissolve chitin, little research has been conducted on the dissolution mechanism involved. In this study, we have adopted a molecular dynamics (MD) approach to study the dissolution of chitin crystals in imidazolium-based ILs. The MD simulation in AMIMBr has demonstrated that the dissolution process involved peeling of chitin chains from the crystal surface, with Br- cleaving the chitin hydrogen bonds, and AMIM+ preventing a return to the crystalline phase after the peeling. By contrast, in imidazolium acetates, which has also been reported to dissolve chitin, although the molecular chains are peeled off, the peeled chains occasionally return to the crystalline phase. Furthermore, the MD trajectory analysis has revealed that the solubility of chitin is well correlated with the number of intermolecular hydrogen bonds by acetamido groups in the chitin crystal. It has been experimentally proven that mixing a small amount of 2-bromoethyl acetate, as a bromide generator, with 1-allyl-3-methylimidazolium chloride can enhance chitin solubility, which supports the dissolution mechanism indicated by the above theoretical results.

Protein Cryoprotectant Ability of the Aqueous Zwitterionic Solution.

Protein cryopreservation is important for the long-term storage of unstable proteins. Recently, we found that N-acetylglucosaminyltransferase-V (GnT-V) can be cryopreserved in a deep freezer without temperature control using a dilute binary aqueous solution of 3-(1-(2-(2-methoxyethoxy)ethyl)imidazol-3-io)butane-1-carboxylate (OE2imC3C) [10 wt %, mole fraction of solute (x) = 7.75 × 10-3], an artificial zwitterion. However, it is unclear which solvent properties are required in these media to preserve unstable proteins, such as GnT-V. In this study, we investigated the melting phenomena and solution structure of dilute binary aqueous OE2imC3C solutions [x = 0-2.96 × 10-2 (0-30 wt %)] using differential scanning calorimetry (DSC) and Raman and Fourier transform infrared (FTIR) spectroscopies combined with molecular dynamics (MD) simulation to compare the cryoprotectant ability of OE2imC3C with two general cryoprotectants (CPAs), glycerol and dimethyl sulfoxide. DSC results indicated that aqueous OE2imC3C solutions can be melted at lower temperatures with less energy than the control CPA solution, with increasing x, primarily due to OE2imC3C having a higher content of unfrozen water molecules. Moreover, Raman and FTIR results showed that the high content of unfrozen water molecules in aqueous OE2imC3C solutions was due to the hydration around the ionic parts (the COO- group and imidazolium ring) and the OCH2CH2O segment. In addition, the MD simulation results showed that there were fewer structured water molecules around the OCH2CH2O segment than the hydration water molecules around the ionic parts. These solvent properties suggest that dilute aqueous OE2imC3C solutions are effective in preventing freezing, even in a deep freezer. Therefore, this medium has the potential to act as a novel cryoprotectant for proteins in biotechnology and biomedical fields.

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.

Strong attractive interaction between finite element models of twisted cellulose nanofibers by intermeshing of twists.

Analysis of the attractive interaction between intrinsically twisted cellulose nanofibers (CNFs) is essential to control the physical properties of the higher-order structures of CNFs, such as paper and spun fiber. In this study, a finite element model reflecting the typical morphology of a twisted CNF was used to analyze the attractive interaction forces between multiple approaching CNF models. For two parallel CNF models, when one of the CNF models was rotated 90° around the long-axis direction, the twisting periods meshed, giving the maximum attraction force. Conversely, when the two CNF models were approaching diagonally, the CNF models were closest at an angle of -3.2° (i.e., in left-handed chirality) to give the most stable structure owing to the right-handed twist of the CNF models themselves. Furthermore, the two nematic layers were closest when one nematic layer was approached at an angle of -2° (i.e., in left-handed accumulation chirality), resulting in the greatest attraction. The results characterize the unique distribution of the attractive interaction forces between twisted CNF models, and they underscore the importance of chiral management in CNF aggregates, especially intermeshing of twists.

Cell-compatible isotonic freezing media enabled by thermo-responsive osmolyte-adsorption/exclusion polymer matrices.

During the long-term storage of cells, it is necessary to inhibit ice crystal formation by adding cryoprotectants. Non-cell-permeable cryoprotectants have high osmotic pressure which dehydrates cells, indirectly suppressing intracellular ice crystal formation. However, the high osmotic pressure and dehydration often damage cells. Emerging polymer-type non-cell-permeable cryoprotectants form matrices surrounding cells. These matrices inhibit the influx of extracellular ice nuclei that trigger intracellular ice crystal formation. However, these polymer-type cryoprotectants also require high osmotic pressure to exert an effective cryoprotecting effect. In this study, we designed a poly(zwitterion) (polyZI) that forms firm matrices around cells based on their high affinity to cell membranes. The polyZI successfully cryopreserved freeze-vulnerable cells under isotonic conditions. These matrices also controlled osmotic pressure by adsorbing and desorbing NaCl depending on the temperature, which is a suitable feature for isotonic cryopreservation. Although cell proliferation was delayed by the cellular matrices, washing with a sucrose solution improved proliferation.

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.

Irregular and suppressed elastic deformation by a structural twist in cellulose nanofibre models.

The elastic responsiveness of single cellulose nanofibres is important for advanced analysis of biological tissues and their use in sophisticated functional materials. However, the mechanical responsiveness derived from the twisted structure of cellulose nanofibres (CNFs) has remained unexplored. In this study, finite element simulations were applied to characterize the deformation response derived from the torsional structure by performing tensile and bending tests of an unconventionally very long and twisted rod model, having the known dimensional parameters and properties of CNFs. The antagonistic action of two types of structural elements (a contour twist and a curvilinear coordinate) was found to result in an irregular deformation response but with only small fluctuations. The contour twist generated rotational displacements under tensile load, but the curvilinear coordinate suppressed rotational displacement. Under bending stress, the contour twist minimized irregular bending deformation because of the orthotropic properties and made the bending stress transferability a highly linear response.

Molecular and Crystal Structure of a Chitosan-Zinc Chloride Complex.

We determined the molecular and packing structure of a chitosan-ZnCl2 complex by X-ray diffraction and linked-atom least-squares. Eight D-glucosamine residues-composed of four chitosan chains with two-fold helical symmetry, and four ZnCl2 molecules-were packed in a rectangular unit cell with dimensions a = 1.1677 nm, b = 1.7991 nm, and c = 1.0307 nm (where c is the fiber axis). We performed exhaustive structure searches by examining all of the possible chain packing modes. We also comprehensively searched the positions and spatial orientations of the ZnCl2 molecules. Chitosan chains of antiparallel polarity formed zigzag-shaped chain sheets, where N2···O6, N2···N2, and O6···O6 intermolecular hydrogen bonds connected the neighboring chains. We further refined the packing positions of the ZnCl2 molecules by theoretical calculations of the crystal models, which suggested a possible coordination scheme of Zn(II) with an O6 atom.

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.

Synthetic zwitterions as efficient non-permeable cryoprotectants.

Cryopreservation of cells is necessary for long periods of storage. However, some cell lines cannot be efficiently cryopreserved, even when optimized commercial cryoprotectants are employed. Previously, we found that a low-toxic synthetic zwitterion aqueous solution enabled good cryopreservation. However, this zwitterion solution could not cryopreserve some cells, such as human kidney BOSC cells, with good efficiency. Therefore, details of the cryoprotective effect of the zwitterions and optimization based on its mechanisms are required. Herein, we synthesized 18 zwitterion species and assessed the effects of the physical properties of water/zwitterion mixtures. Non-cell-permeable zwitterions can inhibit ice crystal formation extracellularly via direct interaction with water and intracellularly via dehydration of cells. However, cells that could not be cryopreserved by zwitterions were insufficiently dehydrated in the zwitterion solution. Dimethyl sulfoxide (DMSO) was combined as a cell-permeable cryoprotectant to compensate for the shortcomings of non-cell-permeable zwitterions. The water/zwitterion/DMSO (90/10/15, v/w/w) could cryopreserve different cells, for example freezing-vulnerable K562 and OVMANA cells; yielding ~1.8-fold cell viability compared to the case using a commercial cryoprotectant. Furthermore, molecular dynamics simulation indicated that the zwitterions protected the cell membrane from the collapse induced by DMSO.

Molecular Dynamics Simulation of Cellulose I-Ethylenediamine Complex Crystal Models.

Cellulose I fibrils swell on exposure to ethylenediamine (EDA), which forms the cellulose I-EDA complex. These are regarded as host materials with guest intercalation. The present study reports molecular dynamics (MD) simulations of cellulose I-EDA crystal models with finite fiber to reproduce desorption of EDA molecules. The force field parameters for EDA were improved. Part of the EDA molecules was desorbed only from the surfaces of the crystal models, not from their interiors. The EDA molecules diffused through a hydrophilic channel composed of the hydrophilic edges of the cellulose chains, and their conformations and orientations changed. With the configuration of the cellulose chains being held, the vacant hydrophilic channel was immediately filled with water molecules. The innermost part of the crystal models, defined as a core unit, was partly deformed from the initial crystal structure, including the changes in the exocyclic group conformations of the cellulose chains and the orientations of the EDA molecules, coupled with partial reconfiguration of the intermolecular hydrogen bonding scheme. A possible crystalline conversion scheme after complete desorption of EDA has been discussed based on the present findings.

Evaluation of artificial crystalline structure from amylose analog polysaccharide without hydroxy groups at C-2 position.

In this study, we found that a new artificial crystalline structure was fabricated from an amylose analog polysaccharide without hydroxy groups at the C-2 position, i.e., 2-deoxyamylose. The polysaccharide with a well-defined structure was synthesized by facile thermostable α-glucan phosphorylase-catalyzed enzymatic polymerization. Powder X-ray diffraction (XRD) analysis of the product indicated the formation of a specific crystalline structure that was completely different from the well-known double helix of the natural polysaccharide, amylose. Molecular dynamics simulations showed that the isolated chains of 2-deoxyamylose spontaneously assembled to a novel double helix based on building blocks with controlled hydrophobicity arising from pyranose ring stacking. The simulation results corresponded with the XRD patterns.

Nanocellulose enriches enantiomers in asymmetric aldol reactions.

Cellulose nanofibers obtained from wood pulp by TEMPO-mediated oxidation acted as a chiral enhancer in direct aldol reactions of 4-nitrobenzaldehyde and cyclopentanone with (S)-proline as an organocatalyst. Surprisingly, catalytically inactive TEMPO-oxidized cellulose nanofibers enriched the (R,R)-enantiomer in this reaction, affording 89% ee in the syn form with a very high yield (99%). Conversely, nanocellulose-free (S)-proline catalysis resulted in poor selectivity (64% ee, syn form) with a low yield (18%). Green organocatalysis occurring on nanocellulose solid surfaces bearing regularly aligned chiral carbons on hydrophobic crystalline facets will provide new insight into asymmetric synthesis strategies for interfacial catalysis.

Non-aqueous, zwitterionic solvent as an alternative for dimethyl sulfoxide in the life sciences.

Dimethyl sulfoxide (DMSO) is widely used as a solvent in the life sciences, however, it is somewhat toxic and affects cell behaviours in a range of ways. Here, we propose a zwitterionic liquid (ZIL), a zwitterion-type ionic liquid containing histidine-like module, as a new alternative to DMSO. ZIL is not cell permeable, less toxic to cells and tissues, and has great potential as a vehicle for various hydrophobic drugs. Notably, ZIL can serve as a solvent for stock solutions of platinating agents, whose anticancer effects are completely abolished by dissolution in DMSO. Furthermore, ZIL possesses suitable affinity to the plasma membrane and acts as a cryoprotectant. Our results suggest that ZIL is a potent, multifunctional and biocompatible solvent that compensates for many shortcomings of DMSO.

DFT Optimization of Isolated Molecular Chain Sheet Models Constituting Native Cellulose Crystal Structures.

Because of high crystallinity and natural abundance, the crystal structures of the native cellulose allomorphs have been theoretically investigated to elucidate the cellulose chain packing schemes. Here, we report systematic structure optimization of cellulose chain sheet models isolated from the cellulose Iα and Iß crystals by density functional theory (DFT). For each allomorph, the three-dimensional chain packing structure was partitioned along each of the three main crystal planes to construct either a flat chain sheet model or two stacked chain sheet models, each consisting of four cello-octamers. Various combinations of the basis set and DFT functional were investigated. The flat chain sheet models constituting the cellulose Iα (110) and Iß (100) planes, where the cellulose chains are mainly linked by intermolecular hydrogen bonds, exhibit a right-handed twist. More uniform and symmetrical sheet twists are observed when the flat chain sheet models are optimized using a basis set with diffuse functions (6-31+G(d,p)). The intermolecular interactions are more stable when the chain sheet models are optimized with the two hybrid functionals CAM-B3LYP and M06-2X. Optimization of the two stacked chain sheet models, where van der Waals interactions predominated between adjacent chains, gave differing results; those retaining the initial structures and those losing the sheet appearance, corresponding to the cellulose Iα/Iß (010)/(11̅0) and (100)/(110) chain sheet models, respectively. The cellulose Iß (11̅0) chain sheet model is more stable using the M06-2X functional than using the CAM-B3LYP functional.

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.