Combining computational chemistry and crystallography for a better understanding of the structure of cellulose

Optimization of Liquid Hot Water Pretreatment and Fermentation for Ethanol Production from Sugarcane Bagasse Using Saccharomyces cerevisiae

Sugarcane bagasse can be considered a potential raw material in terms of quantity and quality for the production of alternative biofuels. In this research, liquid hot water (LHW) was studied as a pretreatment process to enhance the digestibility of pretreated material for further conversion into bioethanol. Different variables (temperature, residual time, and acid concentration) were determined to predict the optimized condition. LHW pretreatment showed an impact on the hemicellulose structure. The optimized condition at 160 °C for 60 min with 0.050 M acid concentration reached the highest glucose yield of 96.86%. Scanning electron microscopy (SEM) showed conspicuous modification of the sugarcane bagasse structure. The effect of LHW pretreatment was also demonstrated by the changes in crystallinity and surface area analysis. FTIR techniques revealed the chemical structure changes of pretreated sugarcane bagasse. The prepared material was further converted into ethanol production with the maximized ethanol concentration of 19.9 g/L.

Theoretical study of cellulose II nanocrystals with different exposed facets

Derived from the most abundant natural polymer, cellulose nanocrystal materials have attracted attention in recent decades due to their chemical and mechanical properties. However, still unclear is the influence of different exposed facets of the cellulose nanocrystals on the physicochemical properties. Herein, we first designed cellulose II nanocrystals with different exposed facets, the hydroxymethyl conformations distribution, hydrogen bond (HB) analysis, as well as the relative structural stability of these models (including crystal facets {A, B, O} and Type-A models vary in size) are theoretically investigated. The results reveal that the HB network of terminal anhydroglucose depends on the adjacent chain's contact sites in nanocrystals exposed with different facets. Compared to nanocrystals exposed with inclined facet, these exposed with flat facet tend to be the most stable. Therefore, the strategy of tuning exposed crystal facets will guide the design of novel cellulose nanocrystals with various physicochemical properties.

Computerized Molecular Modeling of Carbohydrates

Computerized molecular modeling continues to increase in capability and applicability to carbohydrates. This chapter covers nomenclature and conformational aspects of carbohydrates, perhaps of greater use to computational chemists who do not have a strong background in carbohydrates, and its comments on various methods and studies might be of more use to carbohydrate chemists who are inexperienced with computation. Work on the intrinsic variability of glucose, an overall theme, is described. Other areas of the authors' emphasis, including evaluation of hydrogen bonding by the atoms-in-molecules approach, and validation of modeling methods with crystallographic results are also presented.

Energy maps for glycosidic linkage conformations

Glycosidic linkage conformations are the main factors in determining the shapes of disaccharide, oligosaccharide, and polysaccharide molecules. The conformations are expressed in terms of the torsion angles about the bonds from each ring of the disaccharide moiety to its glycosidic oxygen atom, and the probability of a given conformation is often expressed in terms of its free or potential energy. The energy surface or map for a disaccharide is a display of the energy plotted against the two torsion angles. Successful mapping allows a particular kind of energy calculation to provide the energy values for each conformation and avoids possible pitfalls. Although different methods are discussed, the main emphasis of this chapter is on the technical production of the maps and their exploitation in further understanding the shape of the molecule in question.

Carbohydrate-protein interactions: molecular modeling insights

The article reviews the significant contributions to, and the present status of, applications of computational methods for the characterization and prediction of protein-carbohydrate interactions. After a presentation of the specific features of carbohydrate modeling, along with a brief description of the experimental data and general features of carbohydrate-protein interactions, the survey provides a thorough coverage of the available computational methods and tools. At the quantum-mechanical level, the use of both molecular orbitals and density-functional theory is critically assessed. These are followed by a presentation and critical evaluation of the applications of semiempirical and empirical methods: QM/MM, molecular dynamics, free-energy calculations, metadynamics, molecular robotics, and others. The usefulness of molecular docking in structural glycobiology is evaluated by considering recent docking- validation studies on a range of protein targets. The range of applications of these theoretical methods provides insights into the structural, energetic, and mechanistic facets that occur in the course of the recognition processes. Selected examples are provided to exemplify the usefulness and the present limitations of these computational methods in their ability to assist in elucidation of the structural basis underlying the diverse function and biological roles of carbohydrates in their dialogue with proteins. These test cases cover the field of both carbohydrate biosynthesis and glycosyltransferases, as well as glycoside hydrolases. The phenomenon of (macro)molecular recognition is illustrated for the interactions of carbohydrates with such proteins as lectins, monoclonal antibodies, GAG-binding proteins, porins, and viruses.

Supramolecular stacking motifs in the solid state of amide and triazole derivatives of cellobiose

1-Acetamido-1-deoxy-(4-O-β-d-glucopyranosyl-β-d-glucopyranose) (5) and 1-deoxy-1-(4-phenyl-1,2,3-triazolyl)-(4-O-β-d-glucopyranosyl-β-d-glucopyranose) (7) were synthesised from 1-azido-1-deoxy-(4-O-β-d-glucopyranosyl-β-d-glucopyranose) (2) and crystallised as dihydrates. Crystal structural analysis of 5·2H2O displayed an acetamide C(4) chain and stacked cellobiose residues. The structure of 7·2H2O featured π-π stacking and stacking of the cellobiose residues.

Effect of distal sugars and interglycosidic linkage on the N-glycoprotein linkage region conformation: synthesis and X-ray crystallographic investigation of β-1-N-alkanamide derivatives of cellobiose and maltose as disaccharide analogs of the conserved chitobiosylasparagine linkage

The linkage region constituents, 2-deoxy-2-acetamido-β-D-glucopyranose (GlcNAc) and L-asparagine (Asn) are conserved in the N-glycoproteins of all eukaryotes. Elucidation of the structure and conformation of the linkage region of glycoproteins is important to understand the presentation and dynamics of the carbohydrate chain at the protein/cell surface. Earlier crystallographic studies using monosaccharide models and analogs of N-glycoprotein linkage region have shown that the N-glycosidic torsion, ϕN, is more influenced by the structural variation in the sugar part than that of the aglycon moiety. To access the influence of distal sugar as well as interglycosidic linkage (α or β) on the N-glycosidic torsion angles, cellobiosyl and maltosyl alkanamides have been synthesized and structural features of seven of these analogs have been characterized by X-ray crystallography. Comparative analysis of the seven disaccharide analogs with the reported monosaccharide analogs showed that the ϕN value of cellobiosyl analogs deviate ~9° with respect to GlcβNHAc. In the case of maltosyl analogs, deviation is more than 18°. These deviations indicate that the N-glycosidic torsion is influenced by addition of distal sugar as well as with respect to inter glycosidic linkage (α or β); it is less influenced by changes occurring at the aglycon. The χ₂ value of alkanamide derived from glucose, cellobiose and maltose exhibit a large range of variations (from 1.6° to -109.9°). This large span of χ₂ value suggests the greater degree of rotational freedom around C1'-C2' bond which is restricted in GlcNAc alkanamides. The present finding explicitly proved the importance of molecular architecture in the N-glycoproteins linkage region to maintain the linearity, planarity and rigidity. These factors are necessary for N-glycan to serve role in inter- as well as intramolecular carbohydrate-protein interactions.