A priori crystal structure prediction of native celluloses

Combining Computational Chemistry and Crystallography for a Better Understanding of the Structure of Cellulose

The approaches in this article seek to enhance understanding of cellulose at the molecular level, independent of the source and the particular crystalline form of cellulose. Four main areas of structure research are reviewed. Initially, the molecular shape is inferred from the crystal structures of many small molecules that have β-(1→4) linkages. Then, conformational analyses with potential energy calculations of cellobiose are covered, followed by the use of Atoms-In-Molecules theory to learn about interactions in experimental and theoretical structures. The last section covers models of cellulose nanoparticles. Controversies addressed include the stability of twofold screw-axis conformations, the influence of different computational methods, the predictability of crystalline conformations by studies of isolated molecules, and the twisting of model cellulose crystals.

Comparison of cellooligosaccharide conformations in complexes with proteins with energy maps for cellobiose

Shapes (conformations) of cellulose molecules are described by their glycosidic linkage torsion angles ϕ and ψ. Although the torsions are known for cellulose in crystals, amorphous shapes are also interesting for understanding reactivity and physical properties. ϕ and ψ determination for unorganized matter is difficult; one approach is to study their range in many related molecules. For example, linkage torsions of cellulose should be similar to those in cellobiose. Herein, torsions were measured for cellooligosaccharides and lactose moieties complexed with proteins in the Protein Data Bank (PDB). These torsions were compared with ϕ/ψ maps based on quantum mechanics energies for solvated cellobiose and analogs lacking hydroxyl groups. Most PDB conformations corresponded to low map energies. Amorphous cellulose should be generally extended with individual linkages that would give 2- to 3-fold helices. The map for an analog lacking hydrogen bonding ability was more predictive for PDB linkages than the cellobiose map.

Genomics review of holocellulose deconstruction by aspergilli

SUMMARY

Biomass is constructed of dense recalcitrant polymeric materials: proteins, lignin, and holocellulose, a fraction constituting fibrous cellulose wrapped in hemicellulose-pectin. Bacteria and fungi are abundant in soil and forest floors, actively recycling biomass mainly by extracting sugars from holocellulose degradation. Here we review the genome-wide contents of seven Aspergillus species and unravel hundreds of gene models encoding holocellulose-degrading enzymes. Numerous apparent gene duplications followed functional evolution, grouping similar genes into smaller coherent functional families according to specialized structural features, domain organization, biochemical activity, and genus genome distribution. Aspergilli contain about 37 cellulase gene models, clustered in two mechanistic categories: 27 hydrolyze and 10 oxidize glycosidic bonds. Within the oxidative enzymes, we found two cellobiose dehydrogenases that produce oxygen radicals utilized by eight lytic polysaccharide monooxygenases that oxidize glycosidic linkages, breaking crystalline cellulose chains and making them accessible to hydrolytic enzymes. Among the hydrolases, six cellobiohydrolases with a tunnel-like structural fold embrace single crystalline cellulose chains and cooperate at nonreducing or reducing end termini, splitting off cellobiose. Five endoglucanases group into four structural families and interact randomly and internally with cellulose through an open cleft catalytic domain, and finally, seven extracellular β-glucosidases cleave cellobiose and related oligomers into glucose. Aspergilli contain, on average, 30 hemicellulase and 7 accessory gene models, distributed among 9 distinct functional categories: the backbone-attacking enzymes xylanase, mannosidase, arabinase, and xyloglucanase, the short-side-chain-removing enzymes xylan α-1,2-glucuronidase, arabinofuranosidase, and xylosidase, and the accessory enzymes acetyl xylan and feruloyl esterases.

Interactions binding mineral and organic phases in nanocomposites based on bacterial cellulose and calcium phosphates

The interactions responsible for the adhesion of calcium phosphate (CP) nanocrystals and bacterial cellulose (BC) nanofibrils in the composite material obtained by mixing aqueous suspensions of presynthesized CP and BC and the dependence of these interactions on the CP morphology and chemical structure have been elucidated by molecular mechanics calculations of the CP-BC interfacial structures. The interactions between the superficial CP and BC crystal layers have been simulated. Two crystalline CP structures (i.e., hydroxyapatite (HAP) and whitlockite) with two morphologies (plate-shaped and rod-shaped) were considered. Electrostatics has been found to be the major contributor to the adhesion of the CP crystallites and BC nanofibers, and the formation of interfacial hydrogen bonds makes a minor contribution to the interaction energy. It has also been found that, in general, the energy gain resulting from whitlockite-BC binding is greater than that for HAP-BC binding, and the binding of the rod-shaped crystallites of whitlockite with BC is the most profitable. The energy loss and entropy gain upon replacement of the BC-water and CP-water contacts by the BC-CP contacts have been estimated.

Cellulose nanomaterials review: structure, properties and nanocomposites

This critical review provides a processing-structure-property perspective on recent advances in cellulose nanoparticles and composites produced from them. It summarizes cellulose nanoparticles in terms of particle morphology, crystal structure, and properties. Also described are the self-assembly and rheological properties of cellulose nanoparticle suspensions. The methodology of composite processing and resulting properties are fully covered, with an emphasis on neat and high fraction cellulose composites. Additionally, advances in predictive modeling from molecular dynamic simulations of crystalline cellulose to the continuum modeling of composites made with such particles are reviewed (392 references).

Increased crystalline cellulose activity via combinations of amino acid changes in the family 9 catalytic domain and family 3c cellulose binding module of Thermobifida fusca Cel9A

Amino acid modifications of the Thermobifida fusca Cel9A-68 catalytic domain or carbohydrate binding module 3c (CBM3c) were combined to create enzymes with changed amino acids in both domains. Bacterial crystalline cellulose (BC) and swollen cellulose (SWC) assays of the expressed and purified enzymes showed that three combinations resulted in 150% and 200% increased activity, respectively, and also increased synergistic activity with other cellulases. Several other combinations resulted in drastically lowered activity, giving insight into the need for a balance between the binding in the catalytic cleft on either side of the cleavage site, as well as coordination between binding affinity for the catalytic domain and CBM3c. The same combinations of amino acid variants in the whole enzyme, Cel9A-90, did not increase BC or SWC activity but did have higher filter paper (FP) activity at 12% digestion.

Spontaneous adsorption on a hydrophobic surface governed by hydrogen bonding

Spontaneous adsorption from solution onto solid surface is a common phenomenon in nature, but the force that governs adsorption is still a matter of considerable debate. (1, 2) We found that surfactants and cellulose adsorb from solution onto a poly(methyl methacrylate) (PMMA) surface in an ordered and cooperative way governed by hydrogen bonding. The glucose rings of n-dodecyl-beta-D-maltoside (DDM) and hydroxyethylcellulose (HEC) stand perpendicular to the surface, H-bond to the surface COOMe groups with their C=O and Me-O bonds parallel to the surface, and form a tight monolayer. The non-H-bonded COOMe groups orient their C=O bonds perpendicular to the surface. In contrast, the glucose rings of hydrophobically modified hydroxyethylcellulose (HMHEC) lie flat with the side chains perpendicular to the surface and H-bond to the perpendicular-oriented C=O groups. The non-H-bonded COOMe groups orient their C=O bonds parallel but Me-O bonds near-perpendicular to the surface for stabilizing HMHEC. The current work provides a detailed picture of how surface-active molecules interact with a solid surface and self-assemble into greatly different architectures.

Thermal Response in Crystalline Iβ 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.

Exhaustive crystal structure search and crystal modeling of β-chitin

An exhaustive search of the crystal structure of beta-chitin was carried out by simultaneously optimizing all the structural parameters based on published X-ray diffraction data and stereochemical criteria. The most probable structure was characterized by a parallel-up chain polarity, a gg orientation of hydroxymethyl groups and an intermolecular hydrogen bond along the a-axis, which essentially reproduced the original structure proposed by Gardner and Blackwell. The proposed crystal structure was subsequently subjected to crystal modeling using the AMBER force field. The probable orientation of hydroxyl groups and their motional behaviors is proposed based on calculations for the crystal models identified. Solvated crystal models exhibited a slightly deformed structure with the formation of appreciable numbers of hydrogen bonds along the b-axis.

Molecular Dynamics Simulations of Solvated Crystal Models of Cellulose Iα and IIII

Swelling behaviors of cellulose I(alpha) and III(I) crystals have been studied using molecular dynamics simulations of the solvated finite-crystal models. The typical crystal models consisted of 48 x 10-mer chains. For the cellulose I(alpha) crystal, models consisting of different numbers of chains and chain lengths were also studied. The structural features of the swollen crystal models, including the cellulose I(beta) crystal model reported previously, were compared. A distinct right-handed twist was observed for models of the native cellulose crystals (cellulose I(alpha) and I(beta)), with a greater amount of twisting observed for the I(alpha) crystal model. Although the amount of twist decreased with increasing dimensions of the cellulose I(alpha) crystal model, the relative changes in twist angle suggest that considerable twist would arise in a crystal model of the actual dimensions. In contrast to the swelling behavior of crystal models of the native cellulose, the cellulose III(I) crystal model exhibited local, gradual disordering at the corner of the reducing end. Comparison of the lattice energies indicated that the cellulose chains of the I(beta) crystal were packed in the most stable fashion, whereas those of the I(alpha) and III(I) crystals were in a metastable state, which is consistent with the crystallization behaviors observed. Upon heating of the native cellulose crystal models, the chain sheets of the I(alpha) model showed a continuous increase in twist angle, suggesting weaker intersheet interactions in this model. The swollen crystal models of cellulose I(alpha) and III(I) reproduce well the representative structural features observed in the corresponding crystal structures. The crystal model twist thus characterizes the swelling behavior of the native cellulose crystal models, which seems to be related to the insolubility of the crystals.

Swelling behavior of the cellulose Iβ crystal models by molecular dynamics

The various crystal models of cellulose Ibeta, each differing in crystal size, have been studied by computer simulation using the amber molecular-dynamics package and the GLYCAM parameters. The four types of crystal model were constructed by a combination of two base-plane sizes, consisting of either 24 or 48 chains and two chain lengths having either 10 or 20 residues. The base planes of the crystal models were composed by the edges of the [1,1,0], [1,-1,0], and [1,0,0] crystal planes, where the [1,1,0] plane was assigned to the longest edge. The crystal models were soaked in water boxes to investigate their swelling behavior. Unexpectedly, the crystal models twisted quickly to form a slightly right-handed shape during the initial approximately 50 ps and that, in a steady, swollen state, the twisted forms remained for the rest of the simulation time. In spite of such overall deformation, the inner part of the swollen model fairly reproduced the important structural features of the original crystal structure, such as the rotational positions of the substituent groups and the hydrogen-bonding scheme. On heating the crystal model up to 550 K, the twisted shape was conserved in most of the temperature range, while the initial conformations of the substituent groups deviated above approximately 430 K, followed by appreciable disordering in chain sheets at higher temperatures. It is suggested that some internal tensions are involved within a chain sheet of the initial structure. In the course of swelling, some of these tensions were released to introduce a twisted shape in the crystal models.

Review of Recent Research into Cellulosic Whiskers, Their Properties and Their Application in Nanocomposite Field

There are numerous examples where animals or plants synthesize extracellular high-performance skeletal biocomposites consisting of a matrix reinforced by fibrous biopolymers. Cellulose, the world's most abundant natural, renewable, biodegradable polymer, is a classical example of these reinforcing elements, which occur as whisker-like microfibrils that are biosynthesized and deposited in a continuous fashion. In many cases, this mode of biogenesis leads to crystalline microfibrils that are almost defect-free, with the consequence of axial physical properties approaching those of perfect crystals. This quite "primitive" polymer can be used to create high performance nanocomposites presenting outstanding properties. This reinforcing capability results from the intrinsic chemical nature of cellulose and from its hierarchical structure. Aqueous suspensions of cellulose crystallites can be prepared by acid hydrolysis of cellulose. The object of this treatment is to dissolve away regions of low lateral order so that the water-insoluble, highly crystalline residue may be converted into a stable suspension by subsequent vigorous mechanical shearing action. During the past decade, many works have been devoted to mimic biocomposites by blending cellulose whiskers from different sources with polymer matrixes.

Crystal Structure and Hydrogen Bonding System in Cellulose Iα from Synchrotron X-ray and Neutron Fiber Diffraction

The crystal and molecular structure, together with the hydrogen-bonding system in cellulose I(alpha), has been determined using atomic-resolution synchrotron and neutron diffraction data recorded from oriented fibrous samples prepared by aligning cellulose microcrystals from the cell wall of the freshwater alga Glaucocystis nostochinearum. The X-ray data were used to determine the C and O atom positions. The resulting structure is a one-chain triclinic unit cell with all glucosyl linkages and hydroxymethyl groups (tg) identical. However, adjacent sugar rings alternate in conformation giving the chain a cellobiosyl repeat. The chains organize in sheets packed in a "parallel-up" fashion. The positions of hydrogen atoms involved in hydrogen-bonding were determined from a Fourier-difference analysis using neutron diffraction data collected from hydrogenated and deuterated samples. The differences between the structure and hydrogen-bonding reported here for cellulose I(alpha) and previously for cellulose I(beta) provide potential explanations for the solid-state conversion of I(alpha) --> I(beta) and for the occurrence of two crystal phases in naturally occurring cellulose.

Molecular basis of C(2+)-induced gelation in alginates and pectins: the egg-box model revisited

For many ionic polysaccharides, the ability to form gels in the presence of divalent cations such as calcium is the key to biological functions and technological applications. This is particularly true for alginates and pectins, where the regular occurrence of respectively alpha-L-(1-4)-guluronate residues and alpha-D-galacturonate residues generates ordered templates for polymer chain associations that are involved in physical gels. The molecular basis responsible for the strength and the stereospecificity of calcium interactions for the two polysaccharides were investigated in a previous paper (Braccini; et al. Carbohydr. Res. 1999, 119). In the present work, a novel molecular modeling procedure has been developed; it involves a pairing procedure that evaluates all the possible associations of the ordered polyuronate chains with calcium ions to form dimers. Starting from the stable ordered forms of polygalacturonate and polyguluronate, all possible ways to form Ca(2+)-bridged dimers were computed; the parallel and antiparallel relative arrangements of the chains were also considered. Despite the structural analogy between polyguluronate and polygalacturonate chains, significant differences at the level of chain-chain associations are found. The popular "egg box model" can still be referred to in the case of polyguluronate. However, it cannot be used to describe a pectate junction zone as the unique feature of two consecutive chelation site per repeat, that provides a favorable entropic contribution to the interchain association is not reproduced by this pioneering model. The body of these results corroborates the two-stage process in the mechanism of calcium gelation, where the formation of strongly linked dimer associations is followed by the formation of weak inter-dimer associations mainly governed by electrostatic interactions.

Crystal structure and hydrogen-bonding system in cellulose Ibeta from synchrotron X-ray and neutron fiber diffraction

The crystal and molecular structure together with the hydrogen-bonding system in cellulose Ibeta has been determined using synchrotron and neutron diffraction data recorded from oriented fibrous samples prepared by aligning cellulose microcrystals from tunicin. These samples diffracted both synchrotron X-rays and neutrons to better than 1A resolution (>300 unique reflections; P2(1)). The X-ray data were used to determine the C and O atom positions. The resulting structure consisted of two parallel chains having slightly different conformations and organized in sheets packed in a "parallel-up" fashion, with all hydroxymethyl groups adopting the tg conformation. The positions of hydrogen atoms involved in hydrogen-bonding were determined from a Fourier-difference analysis using neutron diffraction data collected from hydrogenated and deuterated samples. The hydrogen atoms involved in the intramolecular O3...O5 hydrogen bonds have well-defined positions, whereas those corresponding to O2 and O6 covered a wider volume, indicative of multiple geometry with partial occupation. The observation of this disorder substantiates a recent infrared analysis and indicates that, despite their high crystallinity, crystals of cellulose Ibeta have an inherent disorganization of the intermolecular H-bond network that maintains the cellulose chains in sheets.