All-atom molecular dynamics simulations with explicit water solvent were used to investigate the microstructure and conformational dynamics of cellulose Iβ microfibrils as a function of microfibril length and cross-sectional size and shape. Cellulose microfibrils quickly develop a right-handed twist, which then remains stable over the entire 10 ns simulation time. The helical angle is independent of microfibril length and inversely proportional to its cross-sectional area, in accord with the expectations of continuum theory for an intrinsic chiral twist that is opposed by torsional shear. These calculations provide-to our knowledge-the first estimates of the shear modulus of a cellulose microfibril from MD simulations. The internal strains caused by this helical twist, propagated indefinitely along the microfibril axis, could be relaxed by periodic regions of amorphous structure along the axis of the cellulose microfibrils.

Periodic planewave and molecular cluster density functional theory (DFT) calculations were performed on Ia and Ib cellulose in four different conformations each. The results are consistent with the previous interpretation of experimental X-ray and neutron diffraction data that both Ia and Ib cellulose are dominantly found in the tg conformation of the hydroxymethyl group with a H-bonding conformation termed ''Network A''. Structural and energetic results of the periodic DFT calculations with dispersion corrections (DFT-D2) are consistent with observation suggesting that this methodology is accurate to within a few percent for modeling cellulose. The structural and energetic results were confirmed by comparison of calculated vibrational frequencies against observed infrared and Raman frequencies of Ia and Ib cellulose. Structures extracted from the periodic DFT-D2 energy minimizations were used to calculate the 13 C nuclear magnetic resonance chemical shifts (d 13 C), and the tg/Network A conformations of both Ia and Ib cellulose produced excellent correlations with observed d 13 C values.

Cellulose nanowhiskers (CNWs) were used in conjunction with phage display technology to identify polypeptides which bind the crystalline region of cellulose. A consensus peptide WHWTYYW was identified to efficiently bind the CNWs. The binding affinities of specific phage particles were assessed using biopanning assays and enzyme-linked immunosorbent assay (ELISA). The WHWTYYW peptide was synthesized and isothermal titration calorimetry (ITC) analysis showed that the peptide exhibited a binding constant of ∼10(5) M(-1) toward the crystalline CNWs. In order to understand how the affinity of this peptide differs for noncrystalline cellulose, binding properties were characterized using cello-oligosaccharides as substrates. Binding analysis was performed using UV spectroscopy and fluorescence quenching experiments. The specific molecular interactions of the WHWTYYW peptide with cellohexaose were examined using nuclear magnetic resonance (NMR). Interactions of this peptide with crystalline cellulose were also investigated using classical molecular modeling and quantum mechanical calculations of (13)C NMR chemical shifts. The NMR experiments and calculations indicate that the WHWTYYW peptide exhibits a bent structure when bound, allowing the Y5 amino acid to form a CH/π stacking interaction and H-bond with the glucose ring of cellulose.

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Coniferyl alcohol is a monomeric building block of lignin, the second most abundant biopolymer. During lignification, the monomer forms a variety of linkages through free radical additions. A large NMR database has been constructed that reports the (1)H and (13)C chemical shifts for thousands of lignin oligomers. Herein, Boltzmann averaged (1)H and (13)C GIAO NMR calculations were performed on coniferyl alcohol and four of its dimers, β-O-4, β-β, β-5, and 5-5, to compare the calculated chemical shifts with experiment. Six B3LYP/6-311++G(d,p) energy-minimized conformational isomers of coniferyl alcohol were subjected to single-point GIAO NMR calculations. Initially, four NMR shift calculation methods were compared: three were performed using the TMS-standard method at the HF/6-311+G(2d,p), B3LYP/6-311+G(2d,p), and mPW1PW91/6-31G(d) theory levels, and the fourth was performed with a multistandard approach using a mPW1PW91/6-31G(d) theory level. For the multistandard method, benzene was used as the standard for aromatic C and H atoms and methanol was used for aliphatic C and H atoms. The hydroxyl-H of methanol was used as the standard for hydroxyl-H atoms. The Boltzmann averaged results for six conformers showed that the multistandard method is more accurate for coniferyl alcohol and its dimers than the often used TMS-standard method, based on the mean unsigned, root-mean-squared, and maximum errors, as well as linear correlations between observed and calculated values. The (13)C results were more accurate than the (1)H results, due to poorer agreement between calculated hydroxyl-H results and observed data. Further Boltzmann-averaged, multistandard NMR calculations compared the (13)C and (1)H chemical shifts with experiment for the four stereoisomers of the β-O-4 dimer, as well as the 5-5, β-5, and β-β dimers of coniferyl alcohol. The (13)C results correlated well with experiment (r(2)>0.99) for all dimers and showed small statistical errors, compared with experiment. The correlation with experiment for (1)H NMR was generally inferior to the (13)C NMR results for the dimers.