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The crystal structure of the native Iβ-allomorph of cellulose [Nishiyama et al. 2002. J. Am. Chem. Soc. 124: 9074–9082] reveals subtle but significant conformational differences between the two different chains and also a multiplicity of positions of the hydrogen atoms of the HO2 and HO6 hydroxyl groups. Two structures differing in the hydrogen bonding networks were then proposed, however, the static...
By use of 9.7 GHz and 94 GHz ESR spectra and electron spin echo (ESE)-detected spectra the six radical centres produced by γ-irradiation of cellobiose were identified. The radicals are localized on different carbon atoms. Use of high-frequency ESR spectra with computer resolution enhancement methods enabled unique radical identification and determination of g-factors and proton hyperfine splitting,...
We describe the construction of a model complex of the cellobiohydrolase I (CBH I) cellulase from Trichoderma reesei bound to a cellulose microfibril in an aqueous environment for use in molecular dynamics (MD) simulations. Preliminary characterization from the initial phases of an MD simulation of this complex is also described. The linker sequence between the two globular domains was found to be...
Molecular dynamics (MD) simulations of cellulose IIII crystal models have been carried out. The crystal models were composed by either 24 or 48 cellooligomers consisting of either 20 or 40 residues and were surrounded by waters in a periodic boundary box. Two base plane types differing in a constituent crystal lattice plane, (0 −1 0) × (0 1 0) and (1 0 0) × (0 1 0), were additionally considered. Among...
This paper re-examines our previous molecular dynamics (MD) study on cellulose IIII crystal models with finite dimensions solvated in explicit water molecules. Eight crystal models, differing in a constituent lattice plane and dimensions, were studied. One calculation allowed for O–H and C–H bond stretching, and had a small time step of 0.5 fs. The other calculation adopted non-scaling factors of...
The hydrogen bond arrangement in a complex of cellulose with ammonia has been studied using neutron crystallography in combination with molecular dynamics simulations. The O6 atom of the hydroxymethyl group is donor in a highly occupied hydrogen bond to an ammonia molecule. This rotating ammonia molecule is donor in partially occupied and transient hydrogen bonds to the O2, O3 and O6 atoms of the...
Molecular dynamics simulations were performed to better understand the atomic details of thermal induced transitions in cellulose Iβ. The latest version of the GLYCAM force field series (GLYCAM06) was used for the simulations. The unit cell parameters, density, torsion angles and hydrogen-bonding network of the crystalline polymer were carefully analyzed. The simulated data were validated against...
In order to model the adsorption of xylan on cellulose, we have simulated, at the atomic level, the gas phase adsorption of small xylan fragments having 5 skeletal β (1 → 4) xylosyl residues (X5), using molecular dynamics simulations. A first regime was considered, corresponding to a low surface coverage, with the adsorption of isolated X5 in various initial orientations. In this regime, the simulation...
A computer docking study was carried out on the (110) crystal surface of the cellulose Iα crystal model for the carbohydrate binding module (CBM) of cellobiohydrolase Cel6A, which is produced by the filamentous fungus Trichoderma reesei. Three-dimensional structures of the CBM were constructed by the homology modeling method using the Cel7A CBM, which is another cellobiohydrolase from T. reesei, as...
An in-depth analysis was performed of the molecular deformation mechanisms in cellulose during axial stretching. For the first time, it was demonstrated that entropy affects the stiffness of cellulose nanocrystals significantly. This was achieved through Molecular Dynamics simulations of model nanocrystals subject to constant stress in the axial direction, for nanocrystals of varying lateral dimensions...
The elastic modulus of cellulose Iβ in the axial and transverse directions was obtained from atomistic simulations using both the standard uniform deformation approach and a complementary approach based on nanoscale indentation. This allowed comparisons between the methods and closer connectivity to experimental measurement techniques. A reactive force field was used that explicitly describes hydrogen...
In hot-water molecular dynamics simulation at 370 K, four cellulose IIII crystal models, with different lattice planes and dimensions, exhibited partial crystalline transformations of (1 −1 0) chain sheets, in which hydroxymethyl groups were irreversibly rotated from gt into tg conformations, accompanied by hydrogen-bond exchange from the original O3–O6 to cellulose-I-like O2–O6 bonds. The final hydrogen-bond...
Inorganic salts are a natural component of biomass which have a significant effect on the product yields from a variety of biomass conversion processes. Understanding their effect on biomass at the microscopic level can help discover their mechanistic role. We present a study of the effect of aqueous sodium chloride on the largest component of biomass, cellulose, focused on the thermodynamic and structural...
We report the generation of a nano-scale tubular structure of cellulose molecules (CelNT), through density functional theory (DFT) calculations. When a cellulose IIII (1 0 0) chain sheet model is optimized by DFT calculations, the sheet models spontaneously roll into tubes. The oligomers arrange in a right-handed, four-fold helix with one-quarter chain staggering, oriented with parallel polarity similar...
The Family 7 cellobiohydrolase (Cel7A) from Trichoderma reesei consists of a carbohydrate-binding module (CBM) joined by a linker to a catalytic domain. Cellulose hydrolysis is limited by the accessibility of Cel7A to crystalline substrates, which is perceived to be primarily mediated by the CBM. Here, the binding of CBM to the cellulose Iβ fiber is characterized by combined Brownian dynamics (BD)...
We have performed molecular dynamics calculations using a revised version of the Gromos56Acarbo force field to understand the consequences of the different potential hydrogen bonding patterns on the structural stability and thermal behavior of the Iα and Iβ forms of native cellulose. For each allomorph, we considered three patterns of hydrogen bonds: two patterns obtained from neutron diffraction...
Previous studies of calculated diffraction patterns for cellulose crystallites suggest that distortions that arise once models have been subjected to molecular dynamics (MD) simulation are the result of both microfibril twisting and changes in unit cell dimensions induced by the empirical force field; to date, it has not been possible to separate the individual contributions of these effects. To provide...
The influence of the non-bonded parameters, i.e., Lennard-Jones and the partial atomic charges, on the predicted unit cell dimensions of different allomorphs of cellulose were studied in the framework of the GROMOS force field. Systematic variation of partial atomic charges revealed the particular importance of charge distribution at the proximity of glycosidic linkage to the monoclinic angles. Furthermore,...
The mechanical properties of Iβ crystalline cellulose are studied using molecular dynamics simulation. A model Iβ crystal is deformed in the three orthogonal directions at three different strain rates. The stress–strain behaviors for each case are analyzed and then used to calculate mechanical properties. The results show that the elastic modulus, Poisson’s ratio, yield stress and strain, and ultimate...
We used molecular dynamics simulation to model the effect of urea and thiourea on the solvent quality of aqueous solutions with respect to cellulose. A model system consisting of a periodically replicated cellulose molecule of effectively infinite degree of polymerization immersed in aqueous (thio-)urea solution was considered. Kirkwood-Buff theory, which relates the pair distribution functions to...
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