Crystal and molecular structure of V-amylose complexed with ibuprofen.

Rectangular V-amylose single crystals were prepared by adding racemic ibuprofen to hot dilute aqueous solutions of native and enzymatically-synthesized amylose. The lamellar thickness increased with increasing degree of polymerization of amylose and reached a plateau at about 7 nm, consistent with a chain-folding mechanism. The CP/MAS NMR spectrum as well as base-plane electron and powder X-ray diffraction patterns recorded from hydrated specimens were similar to those of V-amylose complexed with propan-2-ol. Amylose was crystallized in an orthorhombic unit cell with parameters a = 2.824 ± 0.001 nm, b = 2.966 ± 0.001 nm, and c = 0.800 ± 0.001 nm. A molecular model was proposed based on structural analogies with the Vpropan-2-ol complex and on assumptions on the stoichiometry of ibuprofen. The unit cell would contain four antiparallel 7-fold amylose single helices with ibuprofen molecules distributed inside and between the helices.

Meaning of xylan acetylation on xylan-cellulose interactions: A quartz crystal microbalance with dissipation (QCM-D) and molecular dynamic study.

In plant cell walls, xylan chains present various substituents including acetate groups. The influence of the acetyl substitution on the organization of xylan-cellulose complexes remains poorly understood. This work combines in vitro and in silico approaches to decipher the functional role of acetyl groups on the xylan/cellulose interaction. Acetylated xylans were extracted from apple pomace with dimethyl sulfoxide-lithium chloride (DMSO-LiCl) and deacetylated using a mild alkali treatment. The adsorption behavior of acetylated and deacetylated xylan fractions was investigated using quartz crystal microbalance with dissipation (QCM-D) and molecular dynamics. Acetylated xylans form a dense and poorly hydrated and rigid layer on cellulose with xylan chains that have two residues per helical turn conformation, whereas the deacetylated fraction forms a swollen and more viscous layer in which only the xylan chains in direct contact with the cellulose surface have two residues per helical turn conformation. The other chains have three residues per turn conformation.

Cellulose crystals plastify by localized shear.

Cellulose microfibrils are the principal structural building blocks of wood and plants. Their crystalline domains provide outstanding mechanical properties. Cellulose microfibrils have thus a remarkable potential as eco-friendly fibrous reinforcements for structural engineered materials. However, the elastoplastic properties of cellulose crystals remain poorly understood. Here, we use atomistic simulations to determine the plastic shear resistance of cellulose crystals and analyze the underpinning atomic deformation mechanisms. In particular, we demonstrate how the complex and adaptable atomic structure of crystalline cellulose controls its anisotropic elastoplastic behavior. For perfect crystals, we show that shear occurs through localized bands along with noticeable dilatancy. Depending on the shear direction, not only noncovalent interactions between cellulose chains but also local deformations, translations, and rotations of the cellulose macromolecules contribute to the response of the crystal. We also reveal the marked effect of crystalline defects like dislocations, which decrease both the yield strength and the dilatancy, in a way analogous to that of metallic crystals.

Evaluation of hydrogen bond networks in cellulose Iß and II crystals using density functional theory and Car-Parrinello molecular dynamics.

Crystal models of cellulose Iß and II, which contain various hydrogen bonding (HB) networks, were analyzed using density functional theory and Car-Parrinello molecular dynamics (CPMD) simulations. From the CPMD trajectories, the power spectra of the velocity correlation functions of hydroxyl groups involved in hydrogen bonds were calculated. For the Iß allomorph, HB network A, which is dominant according to the neutron diffraction data, was stable, and the power spectrum represented the essential features of the experimental IR spectra. In contrast, network B, which is a minor structure, was unstable because its hydroxymethyl groups reoriented during the CPMD simulation, yielding a different crystal structure to that determined by experiments. For the II allomorph, a HB network A is proposed based on diffraction data, whereas molecular modeling identifies an alternative network B. Our simulations showed that the interaction energies of the cellulose II (B) model are slightly more favorable than model II(A). However, the evaluation of the free energy should be waited for the accurate determination from the energy point of view. For the IR calculation, cellulose II (B) model reproduces the spectra better than model II (A).

Translational Entropy and Dispersion Energy Jointly Drive the Adsorption of Urea to Cellulose.

The adsorption of urea on cellulose at room temperature has been studied using adsorption isotherm experiments and molecular dynamics (MD) simulations. The immersion of cotton cellulose into bulk urea solutions with concentrations between 0.01 and 0.30 g/mL led to a decrease in urea concentration in all solutions, allowing the adsorption of urea on the cellulose surface to be measured quantitatively. MD simulations suggest that urea molecules form sorption layers on both hydrophobic and hydrophilic surfaces. Although electrostatic interactions accounted for the majority of the calculated interaction energy between urea and cellulose, dispersion interactions were revealed to be the key driving force for the accumulation of urea around cellulose. The preferred orientation of urea and water molecules in the first solvation shell varied depending on the nature of the cellulose surface, but urea molecules were systematically oriented parallel to the hydrophobic plane of cellulose. The translational entropies of urea and water molecules, calculated from the velocity spectrum of the trajectory, are lower near the cellulose surface than in bulk. As urea molecules adsorb on cellulose and expel surface water into the bulk, the increase in the translational entropy of the water compensated for the decrease in the entropy of urea, resulting in a total entropy gain of the solvent system. Therefore, the cellulose-urea dispersion energy and the translational entropy gain of water are the main factors that drive the adsorption of urea on cellulose.

Linear, non-linear and plastic bending deformation of cellulose nanocrystals.

The deformation behaviour of cellulose nanocrystals under bending loads was investigated by using atomistic molecular dynamics (MD) simulations and finite element analysis (FEA), and compared with electron micrographs of ultrasonicated microfibrils. The linear elastic, non-linear elastic, and plastic deformation regions were observed with increasing bending displacements. In the linear elastic region, the deformation behaviour was highly anisotropic with respect to the bending direction. This was due to the difference in shear modulus, and the deformation could be approximated by standard continuum mechanics using the corresponding elastic tensors. Above the linear elastic region, the shear deformation became a dominant factor as the amplitude of shear strain drastically increased. Plastic deformation limit was observed at the bending angle above about 60°, independent of the bending direction. The morphology of the atomistic model of plastically deformed cellulose crystals showed a considerable similarity to the kinked cellulose microfibrils observed by transmission electron microscopy. Our observations highlight the importance of shear during deformation of cellulose crystals and provide an understanding of basic deformations occurring during the processing of cellulose materials.

A coarse-grain force-field for xylan and its interaction with cellulose.

We have built a coarse-grain (CG) model describing xylan and its interaction with crystalline cellulose surfaces. Each xylosyl or glucosyl unit was represented by a single grain. Our calculations rely on force-field parameters adapted from the atomistic description of short xylan fragments and their adsorption on cellulose. This CG model was first validated for xylan chains both isolated and in the bulk where a good match was found with its atomistic counterpart as well as with experimental measurements. A similar agreement was also found when short xylan fragments were adsorbed on the (110) surface of crystalline cellulose. The CG model, which was extended to the (100) and (1-10) surfaces, revealed that the adsorbed xylan, which was essentially extended in the atomistic situation, could also adopt coiled structures, especially when laying on the hydrophobic cellulose surfaces.

The hygroscopic power of amorphous cellulose: a modeling study.

The relationship between cellulose and water was studied by building dense amorphous cellulose models and subjecting them to increasing moisture contents. When starting from completely dry cellulose, the first diffused water molecules were essentially individualized and hydrogen bonded exclusively to the O6 and O2 hydroxyl groups of cellulose. Upon continued hydration increase, the hydroxyl at O3 and then the acetal oxygens of cellulose also started to attract the upcoming water molecules, which were no longer isolated. They progressively became aggregated, first into clusters and then at high hydration content, into continuous capillary channels. A benefit of this study was to allow predicting a number of physical parameters of amorphous cellulose and their variation under hydration. With some parameters, the calculated values matched rather well the experimental literature determinations. This was the case for the hydration dependence of Tg, the stereoselectivity of the cellulose oxygen atoms for water molecules, together with the diffusion coefficients of water into cellulose. An estimate of the hygro-expansion of amorphous cellulose was provided.

Probing the helical forms of Ca2+ -guluronan junction zones in alginate gels by molecular dynamics 1: Duplexes.

A molecular dynamics investigation of the helical forms adopted by (1→4)-α-L-guluronan in explicit water environment was carried out. Single chains and duplexes were modeled at 300 K starting both from 21 or 32 helical conformations and in the presence of a neutralizing amount of Ca(2+) ions. All systems were allowed full conformational freedom. The initial perfect helices with integral screw symmetries were lost at the very beginning of simulations and two distinct behaviors were observed: At equilibrium the 21 models mostly retained the 21 local helical conformations while exploring the 32 ones the rest of the time. In duplexes the two chains, which behaved similarly, were well extended and slightly twisted. By contrast, the chains in 32 duplex models were dissimilar and explored a much broader conformational space in which 21 and 32 local helical conformations were dominant and equally represented but the 31 and other conformations were also present. The wide variety of conformations revealed in this study is consistent with the general difficulty in obtaining crystals of Ca(2+)-guluronate with suitable lateral dimensions for crystallographic studies.

Molecular modeling of the structural and dynamical properties of secondary plant cell walls: influence of lignin chemistry.

A modeling of lignified secondary plant cell walls adapted to grass has been achieved, using molecular dynamics for time up to 180 ns, applied to systems composed of cellulose, xylan, water, and lignin. The overall model, which was 70 nm thick for a volume of 74.4 nm(3), consisted of two crystalline cellulose layers, each being two molecules deep, separated by an interlayer space where the three other components were located. Whereas the cellulose and xylan chemistry was fixed, 18 lignin systems were considered that varied not only in guaiacyl, syringyl, and p-hydroxyphenyl composition, but also in chain length, linkage types, and the presence or absence of coumaryl units. The stabilized models showed a well-defined interface between xylan and cellulose, but some interpenetration of xylan into the lignin part of the models. A survey of the 18 models showed that their lignin component was amorphous and that their density profile was very variable and essentially model dependent. This variability was also reflected in the co-orientation of the lignin phenyl rings with respect to the cellulose surfaces, some systems showing some orientation whereas others did not. The pattern of void distribution accessible to water varied from one system to the next, but the overall void volume was systematically established at around 3%, accepting around 200 water molecules. The estimated mobility of the water molecules interacting with lignin was 1.5 times greater than that interacting with carbohydrates.

The molecular structure and solution conformation of an acidic heteropolysaccharide from Auricularia auricula-judae.

A water soluble acidic heteropolysaccharide named WAF was isolated from Auricularia auricula-judae by extracting with 0.9% NaCl solution. By using gas chromatography, gas chromatography-mass spectrometry, and NMR, its chemical structure was determined to be composed of a backbone of α-(1→3)-linked D-mannopyranose residues with pendant side groups of ß-D-xylose, ß-D-glucose, or ß-D-glucuronic acid at position O6 or O2. Six fractions prepared from WAF with a weight-average molecular mass (M(w)) between 5.9 × 104 and 64.7 × 104 g/mol were characterized with laser light scattering and viscometry in 0.1M NaCl at 25°C. The dependence of intrinsic viscosity ([η]) and radius of gyration (R(g)) on M(w) for this polysaccharide were found to be [η] = 1.79 × 10⁻³ M(w) °.96 cm³ g⁻¹ and R(g) = 6.99 × 10⁻² M(w) (0.54) nm. The molar mass per unit contour length (M(L)) and the persistence length (L(p)) were estimated to be 1124 nm⁻¹ and 11 nm, respectively. The WAF exhibited a semirigid character typical of linear polysaccharides. Molecular modeling was then used to predict the ordered and disordered states of WAF; the simulated M(L) and L(p) were however much smaller than the experimental values. Taken altogether, the results suggested that WAF formed a duplex in solution.

Dynamics of cellulose-water interfaces: NMR spin-lattice relaxation times calculated from atomistic computer simulations.

Solid-state nuclear magnetic resonance (CP/MAS 13C NMR) spectroscopy has often been used to study cellulose structure, but some features of the cellulose NMR spectrum are not yet fully understood. One such feature is a doublet around 84 ppm, a signal that has been proposed to originate from C4 atoms at cellulose fibril surfaces. The two peaks yield different T1, differing by approximately a factor of 2 at 75 MHz. In this study, we calculate T1 from C4-H4 vector dynamics obtained from molecular dynamics computer simulations of cellulose I beta-water interfacial systems. Calculated and experimentally obtained T1 values for C4 atoms in surface chains fell within the same order of magnitude, 3-20 s. This means that the applied force field reproduces relevant surface dynamics for the cellulose-water interface sufficiently well. Furthermore, a difference in T1 of about a factor of 2 in the range of Larmor frequencies 25-150 MHz was found for C4 atoms in chains located on top of two different crystallographic planes, namely, (110) and (10). A previously proposed explanation that the C4 peak doublet could derive from surfaces parallel to different crystallographic planes is herewith strengthened by computationally obtained evidence. Another suggested basis for this difference is that the doublet originates from C4 atoms located in surface anhydro-glucose units with hydroxymethyl groups pointing either inward or outward. This was also tested within this study but was found to yield no difference in calculated T1.

Thermal response in crystalline Ibeta cellulose: a molecular dynamics study.

The influence of temperature on structure and properties of the cellulose Ibeta crystal was studied by molecular dynamics simulations with the GROMOS 45a4 force-field. At 300 K, the modeled crystal agreed reasonably with several sets of experimental data, including crystal density, corresponding packing and crystal unit cell dimensions, chain conformation parameters, hydrogen bonds, Young's modulus, and thermal expansion coefficient at room temperature. At high-temperature (500 K), the cellulose chains remained in sheets, despite differences in the fine details compared to the room-temperature structure. The density decreased while the a and b cell parameters expanded by 7.4% and 6%, respectively, and the c parameter (chain axis) slightly contracted by 0.5%. Cell angles alpha and beta divided into two populations. The hydroxymethyl groups mainly adopted the gt orientation, and the hydrogen-bonding pattern thereby changed. One intrachain hydrogen bond, O2'H2'...O6, disappeared and consequently the Young's modulus decreased by 25%. A transition pathway between the low- and high-temperature structures has been proposed, with an initial step being an increased intersheet separation, which allowed every second cellulose chain to rotate around its helix axis by about 30 degrees . Second, all hydroxymethyl groups changed their orientations, from tg to gg (rotated chains) and from tg to gt (non-rotated chains). When temperature was further increased, the rotated chains returned to their original orientation and their hydroxymethyl groups again changed their conformation, from gg to gt. A transition temperature of about 450 K was suggested; however, the transition seems to be more gradual than sudden. The simulated data on temperature-induced changes in crystal unit cell dimensions and the hydrogen-bonding pattern also compared well with experimental results.

A hydrophilic cyclodextrin duplex forming supramolecular assemblies by physical cross-linking of a biopolymer.

New beta-cyclodextrin (beta-CD) dimeric species have been synthesised in which the two CD moieties are connected by one or two hydrophilic oligo(ethylene oxide) spacers. Their complexation with sodium adamantylacetate (free adamantane) and adamantane-grafted chitosan (AD-chitosan) was then studied by different complementary techniques and compared with their hydrophobic counterparts that contain an octamethylene spacer. Isothermal titration calorimetry experiments have demonstrated that the use of hydrophilic spacers between the two CDs instead of aliphatic chains makes almost all of the CD cavities available for the inclusion of free adamantane. Investigation of the interaction of the CDs with AD-chitosan by viscosity measurements strongly suggests that the molecular conformation of the CD dimeric species plays a crucial role in their cross-linking with the biopolymer. The derivative doubly linked with hydrophilic arms, also called a duplex, has been shown to be a more efficient cross-linking agent than its singly bridged counterpart, referred to as a dimer. Hence, only 0.5 molar equivalents of the hydrophilic duplex with respect to adamantane was required to obtain the maximum viscosity, whereas in the case of the duplex with aliphatic spacers, the maximum viscosity was achieved with a [duplex]/[AD] ratio of about 1.7 (corresponding to a [CD]/[AD] ratio of 2.5), but with a higher value. To clarify the relationships between the molecular architecture and complexation properties, computational studies were also performed that clearly confirmed the importance of double bridging.

The xyloglucan-cellulose assembly at the atomic scale.

The assembly of cell wall components, cellulose and xyloglucan (XG), was investigated at the atomistic scale using molecular dynamics simulations. A molecular model of a cellulose crystal corresponding to the allomorph Ibeta and exhibiting a flexible complex external morphology was employed to mimic the cellulose microfibril. The xyloglucan molecules considered were the three typical basic repeat units, differing only in the size of one of the lateral chain. All the investigated XG fragments adsorb nonspecifically onto cellulose fiber; multiple arrangements are equally probable, and every cellulose surface was capable of binding the short XG molecules. The following structural effects emerged: XG molecules that do not have any long side chains tended to adapt themselves nicely to the topology of the microfibril, forming a flat, outstretched conformation with all the sugar residues interacting with the surface. In contrast, the XG molecules, which have long side chains, were not able to adopt a flat conformation that would enable the interaction of all the XG residues with the surface. In addition to revealing the fundamental atomistic details of the XG adsorption on cellulose, the present calculations give a comprehensive understanding of the way the XG molecules can unsorb from cellulose to create a network that forms the cell wall. Our revisited view of the adsorption features of XG on cellulose microfibrils is consistent with experimental data, and a model of the network is proposed.

Conformational analysis of xylan chains.

The present study provides a theoretical description of the different levels of structural organization that characterize the xylan polysaccharide in its native and hydrophobic lauroyl esterified forms. The goal of this study was to ascertain the role played by the hydroxyl or lauroyl side groups on the conformational flexibility of the xylan chain backbone. The results reported provide a detailed description of the low-energy conformers of the dimer segments, a complete characterization of the helical structures, an insight into the disordered state of the polysaccharide chains and an estimation of the cohesion of the amorphous solids. Esterification of xylan hydroxyl groups by lauric acid has a large effect on the conformational properties of the glycosidic bonds linking two repeat units. Both the location and the relative energies of the low energy areas of the potential energy surfaces strongly differ: extended and coiled conformations are preferred for the native and hydrophobic forms, respectively. Consequently, the predicted unperturbed polymer chain extension strongly depends on the structure, predicted Lp of the native xylan of 35 A compares favourably well with the experimental ones, this characteristic dramatically decreases to 9A for the hydrophobically modified chain. Curiously, only extended 2(1) and left-handed 3(1) helical structures are calculated stable for both polymers. The estimated cohesive parameters of amorphous bulks reveal that inter-chain interactions are stronger for the xylan chain than that for modified one, the former being stabilized by hydrogen bonds whereas hydrophobic interactions play a determinant role for the latter.

Cellulose poly(ethylene-co-vinyl acetate) nanocomposites studied by molecular modeling and mechanical spectroscopy.

Structure property relationships have been established at two different scales to examine reinforcing effects of nanocomposites made of cellulose whiskers and polyethylene-vinyl acetate (EVA) matrixes with different vinyl acetate contents. The role of the polymer structure on the work of adhesion as predicted by molecular modeling at the atomic scale and on the mechanical performance of nanocomposites observed by dynamic mechanical analysis at the macroscopic level is reported. Concordant results were obtained by the two approaches; both demonstrated a reinforcing effect that increases with the acetate content of the polymer. However, a leveling of this effect was observed at high acetate contents. A detailed picture of the interactions at the interface between the two species accessed by modeling gives a reasonable explanation of this unexpected phenomenon.

The cellulose/lignin assembly assessed by molecular modeling. Part 2: Seeking for evidence of organization of lignin molecules at the interface with cellulose.

We have extended our previous computational investigation of the cellulose lignin assembly by considering more complex systems. Surface coverage of cellulose, structural parameters such as molecular mass and structural features of the lignin models and the presence of an explicit hydrated environment have been taken into account to examine their influence on the associative interactions between cellulose and lignin. To this end, different lignin molecular models, from beta-O-4 dimers up to a 20-units oligomer, were considered. Independently of the system studied, the key feature of the adsorption is globally preserved: aromatic rings of lignin adopt a preferential parallel orientation relative to the cellulose surface. Such structural order appears to be limited to the first shell of lignin units adsorbed on the cellulose. The pre-organization of the lignin monolayer at the surface of cellulose is not significantly changed at the interface with water. However, adsorption significantly depends on the molecular mass and the structure of lignin. The structural order is significantly hindered by the presence of branching or some particular inter-units linkages in the structure of lignin. Such results rationalize the apparent contradiction between the available experimental results.

The cellulose/lignin assembly assessed by molecular modeling. Part 1: adsorption of a threo guaiacyl beta-O-4 dimer onto a Ibeta cellulose whisker.

The assembly of the two major cell wall components, cellulose and lignin, were investigated at the atomistic scale using molecular dynamics simulations. To this end, a molecular model of a cellulose crystal corresponding to the allomorph Ibeta and exhibiting different surfaces was considered to mimic the carbohydrate matrix present in native wood cell wall. The lignin model compound considered here is a threo guaiacyl beta-O-4 dimer. The dynamical process of adsorption of the lignin dimer onto the different surfaces of the cellulose crystal was examined. The modes of association between the two constituents were analyzed; energies of adsorption of the dimer are calculated favorable and of the same order of magnitude on all sides of the cellulosic model, suggesting that the deposition of lignin precursors onto cellulose fibers is non-specific from an enthalpic point of view. Interestingly, geometrical characteristics and energetical details of the adsorption are surface-dependent. Computed data have underlined the predominant contribution of van der Waals interactions for adsorption onto the (200) face, as well as the major influence of H-bonding interactions in the dynamical process of adsorption onto (110) and (1-10) faces. A large number of adsorption sites have been identified and a noticeable "flat" geometry of adsorption of the lignin dimer has been observed, as a consequence of the stacking interactions between lignin aromatic rings and C-H groups of cellulose. Importantly, these dispersive interactions lead to a preferential parallel orientation of lignin aromatic rings relative to the cellulose surface, notably on the (200) face. Such a parallel orientation is consistent with previously reported experimental observations.