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.

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.

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

Crystal models of cellulose Iβ 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 Iβ 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.

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.

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.

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.

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.

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.

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.

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 β-D-xylose, β-D-glucose, or β-D-glucuronic acid at position O6 or O2.

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.

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.

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 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.

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.

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.

Theoretical and experimental studies on the adsorption of aromatic compounds onto cellulose.

The adsorption of several aromatic compounds over microcrystalline cellulose was studied by molecular modeling and experimentally using gas chromatography. Experimental adsorption enthalpies were obtained from an equation based on Clausius-Clapeyron formalism and the temperature dependence of retention volume at infinite dilution. Four different cellulose surfaces (three crystalline (110, 100, and 010) and one amorphous) were modeled.

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 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.

Conformational study of a guaiacyl beta-O-4 lignin model compound by NMR. Examination of intramolecular hydrogen bonding interactions and conformational flexibility in solution.

Intramolecular H-bonding interactions were investigated in solution for the threo and erythro diastereomeric forms of a guaiacyl beta-O-4 lignin model compound by using the NMR data obtained from hydroxyl protons. Temperature coefficients of the chemical shifts (ddelta/dT) and coupling constants (3J(HCOH)) were measured in aprotic and protic solutions: DMSO-d6, acetone-d6 and acetone-d6-water. The NMR parameters do not support the existence of strong and persistent intramolecular H-bonds that could participate in the stabilization of the guaiacyl beta-O-4 structure in solution, but instead indicate that intermolecular H-bonds to solvent predominate.

Molecular dynamics simulations of a guaiacyl beta-O-4 lignin model compound: examination of intramolecular hydrogen bonding and conformational flexibility.

The dynamical conformational behavior of a guaiacyl beta-O-4 lignin model compound has been investigated by molecular simulations. The potential energy surface of the molecule in vacuum has been examined by means of an adiabatic map, showing a large accessible conformational space with multiple energy minima separated by low barriers. Molecular dynamics simulations have been performed in vacuum and with explicit solvent molecules for 10 and 2.

Structure and properties of a bacterial polysaccharide named Fucogel.

The chemical structure of a polysaccharide named Fucogel was characterized and the position of acetylation was identified by NMR. A conformational analysis was performed on this 3-sugar repeating unit. From this, the persistence length, characterizing the stiffness of the polysaccharide, was determined and the role of the presence of acetyl group, reducing the stiffness, was pointed out.

Conformational analysis of the exopolysaccharide from Burkholderia caribensis strain MWAP71: impact on the interaction with soils.

The strain MWAP71 of Burkholderia caribensis produces a branched charged exopolysaccharide (EPS) that is responsible for soil aggregation. Understanding the conformational properties of the isolated polysaccharide is a prerequisite for proper investigation of the interactions between the polysaccharide and the soil at the atomic level. The aim of this study is first to have an overall view of the flexibility of the backbone and then to ascertain the role played by side groups in the conformational properties of the main chain.