Glycosidic Bond Breakage Research Articles

Characterization of Water-Soluble Intermediates from Slow Pyrolysis of Cellulose at Low Temperatures

This study reports the presence of both sugar and anhydro-sugar oligomers of a wide range of degrees of polymerization (1–10) as water-soluble intermediates in the solid residues produced from cellulose slow pyrolysis at low temperatures (100–350 °C) and a holding time of 30 min. These sugar and anhydro-sugar oligomers appear to be important precursors of volatiles formation during cellulose pyrolysis. Even at very low pyrolysis temperatures (e.g., 100 °C), sugar oligomers are found in the water-soluble intermediates. As the breakage of glycosidic bonds within cellulose chains is unlikely to take place under such low-temperature conditions, the results suggest that such sugar oligomers are likely to be produced from the short glucose chain segments that are hinged with crystalline cellulose via weak bonds (e.g., hydrogen bonds) in amorphous portions of microcrystalline cellulose. As the pyrolysis temperature increases, a wide range of anhydro-sugar oligomers start to appear while the sugar oligomers start...

Noncatalytic Hydrothermal Elimination of the Terminal d-Glucose Unit from Malto- and Cello-Oligosaccharides through Transformation to d-Fructose

Noncatalytic hydrothermolyses of malto- and cello-oligosaccharides (di-, tri-, tetraose), linked by α- and β-1,4-glycosidic bonds, respectively, were investigated at 100-140 °C. In situ (13)C NMR spectroscopy was applied to elucidate the position and pathways of the glycosidic bond breakage and the dependence of the hydrolysis rate on the bond type. Spectral analysis was carried out quantitatively as a function of time with the mass balance confirmed, and it was shown for both the malto- and the cello-oligosaccharides that the terminal D-glucose unit with a free anomeric carbon is selectively eliminated after transformation to D-fructose. Site-selective breakage of the glycosidic bonds proceeded on the order of hours. The initial apparent rates for terminal hydrolysis were found to be independent of the degree of oligomerization but dependent on the type of glycosidic bond. Rate constants were larger for the α-1,4-linked malto-oligosaccharides by a factor of 3-4 than for the β-1,4-linked cello-oligosaccharides. The pathways and mechanisms for the malto- and cello-oligosaccharide hydrothermolyses are common and can be understood in terms of the elementary reactions of the di- and monosaccharides.

Pyrolytic Sugars from Cellulosic Biomass

Depolymerization of cellulose offers the prospect of inexpensive sugars from biomass. Breaking the glycosidic bonds of cellulose to liberate glucose has usually been pursued by acid or enzymatic hydrolysis although a purely thermal depolymerization route to sugars is also possible. Fast pyrolysis of pure cellulose yields primarily the anhydrosugar levoglucosan (LG) whereas the presence of naturally occurring alkali and alkaline earth metals (AAEMs) in biomass strongly catalyzes ring-breaking reactions that favor formation of light oxygenates. Here, we show a method of significantly increasing the yield of sugars from biomass by purely thermal means through infusion of certain mineral acids (phosphoric and sulfuric acid) into the biomass to convert the AAEMs into thermally stable salts (particularly potassium sulfates and phosphates). These salts not only passivate AAEMs that normally catalyze fragmentation of pyranose rings, but also buffer the system at pH levels that favor glycosidic bond breakage. It appears that AAEM passivation contributes to 80 % of the enhancement in LG yield while the buffering effect of the acid salts contributes to the balance of the enhancement.

Theoretical insights into the catalytic mechanism of β-hexosaminidase

The enzyme (β-Hex) has a specific role in the degradation of a particular type of glycolipid, the GM2 ganglioside. This specificity is also manifested by its unusual mechanism of substrate-assisted catalysis, which is considered to be an alternative pathway for the breakage of glycosidic bonds. We have studied its catalytic mechanism using a small model of the enzyme: substrate Michaelis complex with DFT and MP2/MP3 methods. The results reflect the intrinsic chemical reactivity of the active site, decoupled from the long-range enzyme electrostatic field. The mechanism supports, and adds further atomic detail, on the earlier mechanistic suggestions based on experimental data. Moreover, we also have compared the geometry and full potential energy surface obtained with nine different exchange–correlation functionals. It was surprising that the B3LYP activation energies were lower than the ones from some of the hybrid meta functionals (known by their excellent performance on kinetics) by as much as 10 kcal/mol and lower than the MP2 energies by more than 12 kcal/mol. It is known that B3LYP underestimates barriers but underestimations of this extent are unusual and surprising. The effect of the theoretical method on the geometry, usually supposed to be less significant, had in some cases a relevant influence in the mechanism. Therefore, a more thoughtful choice should be made when choosing a methodology for geometry optimization.

Synergetic effect of DC air plasma and cellulase enzyme treatment on the hydrophilicity of cotton fabric

The effects of DC air plasma and cellulase enzyme treatments on the hydrophilicity of cotton fabric samples were investigated. Cotton fabric samples were treated with DC air plasma (P), cellulase enzyme (E), enzyme treatment preceded by plasma (PE) and plasma treatment preceded by enzyme (EP) to improve the hydrophilicity. The physico-chemical changes that occurred during the treatments were studied using dynamic wicking test, SEM, XRD, UATR-FTIR, weight loss and air permeability measurements. The UATR-FTIR results revealed that, for EP treated fabrics, there is a decrease in the intensity of C 1–O–C 4 peak (894 cm −1) indicating the glycosidic bond breakage with an increase in the intensity of C O peak (1734 cm −1) due to oxidation at C 6, C 1/C 4 carbon by enzyme and plasma treatments. SEM and XRD results reveal that, plasma and enzyme treatment leads to surface etching, removing the non-cellulosic compounds thereby increasing the hydrophilicity of the cotton fabrics. The synergetic effect of plasma and enzyme treatments on physical and chemical properties of the cotton fabric is studied and the results are discussed.

Theoretical Studies of Damage to 3′-Uridine Monophosphate Induced by Electron Attachment

Low-energy electrons (LEE) are well known to induce nucleic acid damage. However, the damage mechanisms related to charge state and structural features remain to be explored in detail. In the present work, we have investigated the N1-glycosidic and C3'-O(P) bond ruptures of 3'-UMP (UMP=uridine monophosphate) and the protonated form 3'-UMPH with -1 and zero charge, respectively, based on hybrid density functional theory (DFT) B3 LYP together with the 6-31+G(d,p) basis set. The glycosidic bond breakage reactions of the 3'UMP and 3'UMPH electron adducts are exothermic in both cases, with barrier heights of 19-20 kcal mol(-1) upon inclusion of bulk solvation. The effects of the charge state on the phosphate group are marginal, but the C2'-OH group destabilizes the transition structure of glycosidic bond rupture of 3'-UMPH in the gas phase by approximately 5.0 kcal mol(-1). This is in contrast with the C3'-O(P) bond ruptures induced by LEE in which the charge state on the phosphate influences the barrier heights and reaction energies considerably. The barrier towards C3'-O(P) bond dissociation in the 3'UMP electron adduct is higher in the gas phase than the one corresponding to glycosidic bond rupture and is dramatically influenced by the C2'-OH group and bulk salvation, which decreases the barrier to 14.7 kcal mol(-1). For the C3'-O(P) bond rupture of the 3'UMPH electron adduct, the reaction is exothermic and the barrier is even lower, 8.2 kcal mol(-1), which is in agreement with recent results for 3'-dTMPH and 5'-dTMPH (dTMPH=deoxythymidine monophosphate). Both the Mulliken atomic charges and unpaired-spin distribution play significant roles in the reactions.

Electron attachment to DNA single strands: gas phase and aqueous solution

The 2′-deoxyguanosine-3′,5′-diphosphate, 2′-deoxyadenosine-3′,5′-diphosphate, 2′-deoxycytidine-3′,5′-diphosphate and 2′-deoxythymidine-3′,5′-diphosphate systems are the smallest units of a DNA single strand. Exploring these comprehensive subunits with reliable density functional methods enables one to approach reasonable predictions of the properties of DNA single strands. With these models, DNA single strands are found to have a strong tendency to capture low-energy electrons. The vertical attachment energies (VEAs) predicted for 3′,5′-dTDP (0.17 eV) and 3′,5′-dGDP (0.14 eV) indicate that both the thymine-rich and the guanine-rich DNA single strands have the ability to capture electrons. The adiabatic electron affinities (AEAs) of the nucleotides considered here range from 0.22 to 0.52 eV and follow the order 3′,5′-dTDP > 3′,5′-dCDP > 3′,5′-dGDP > 3′,5′-dADP. A substantial increase in the AEA is observed compared to that of the corresponding nucleic acid bases and the corresponding nucleosides. Furthermore, aqueous solution simulations dramatically increase the electron attracting properties of the DNA single strands. The present investigation illustrates that in the gas phase, the excess electron is situated both on the nucleobase and on the phosphate moiety for DNA single strands. However, the distribution of the extra negative charge is uneven. The attached electron favors the base moiety for the pyrimidine, while it prefers the 3′-phosphate subunit for the purine DNA single strands. In contrast, the attached electron is tightly bound to the base fragment for the cytidine, thymidine and adenosine nucleotides, while it almost exclusively resides in the vicinity of the 3′-phosphate group for the guanosine nucleotides due to the solvent effects. The comparatively low vertical detachment energies (VDEs) predicted for 3′,5′-dADP− (0.26 eV) and 3′,5′-dGDP− (0.32 eV) indicate that electron detachment might compete with reactions having high activation barriers such as glycosidic bond breakage. However, the radical anions of the pyrimidine nucleotides with high VDE are expected to be electronically stable. Thus the base-centered radical anions of the pyrimidine nucleotides might be the possible intermediates for DNA single-strand breakage.

Hypocrea jecorina (Trichoderma reesei) Cel7A as a molecular machine: A docking study

Hypocrea jecorina (formerly Trichoderma reesei) Cel7A has a catalytic domain (CD) and a cellulose-binding domain (CBD) separated by a highly glycosylated linker. Very little is known of how the 2 domains interact to degrade crystalline cellulose. Based on the interaction energies and forces on cello-oligosaccharides computationally docked to the CD and CBD, we propose a molecular machine model, where the CBD wedges itself under a free chain end on the crystalline cellulose surface and feeds it to the CD active site tunnel. Enzyme-substrate interactions produce the forces required to pull cellulose chains from the surface and also to help the enzyme move on the cellulose chain for processive hydrolysis. The energy to generate these forces is ultimately derived from the chemical energy of glycosidic bond breakage.

M-Fluorotyrosine substitution in β-galactosidase; Evidence for the existence of a catalytically active tyrosine

The pH profiles of β-galactosidase, having tyr replaced by m-fluorotyrosine, were compared to those of normal enzyme. The inflection point on the alkaline side was lowered about 1.5 pH units in the fluoro-enzyme, corresponding to the difference in the phenolic pKa values of m-fluorotyrosine and tyr. When glycosidic bond breakage was rate-limiting, the Vm at pH 7.0 was higher for the fluoro-enzyme. When hydrolysis was rate-limiting or when acceptors which made transgalactosylis rate-limiting were used, the Vm was lower for the fluoro-enzyme. This shows that a tyr in β-galactosidase is a general-acid catalyst in the glycosidic bond breaking reaction and a tyr (probably the same one) is a general-base catalyst in the hydrolytic reaction.