Adsorption desulfurization is a potential new method for deep desulfurization of fuel oil. The development of adsorbents with high adsorption capacity and selectivity is the core of deep adsorption desulfurization. The adsorption behavior of thiophene in MCM-41 mesoporous materials modified by various metal ions was studied in order to understand the adsorption desulfurization process of molecular sieves. The Fe-, Co-, and Zn-modified MCM-41 materials were prepared using a one-step in situ hydrothermal synthesis method. The modified MCM-41 molecular sieves maintained the mesoporous structure, and the metal ions had specific dispersion on the surface of the molecular sieves. Adsorption of thiophene on the surfaces of molecular sieves had both physical and chemical characteristics. The adsorption desulfurization performance of the modified molecular sieve was superior to that of the pure silica molecular sieve. In the simulated gasoline with sulfur content of 220 μg/g, when the amount of adsorbent used was 100 mg, the adsorptive desulfurization performance tended to be in equilibrium, and the optimum adsorption temperature was 30°C. Fe-MCM-41 and MCM-41 molecular sieves reached adsorption equilibrium after ~60 min, but the desulfurization rate of Co-MCM-41 and Zn-MCM-41 still increased slightly. The kinetic simulation results indicated that the pseudo-second-order kinetics adsorption model described well the adsorption process of thiophene on molecular sieves. The molecular sieve Fe-MCM-41 had the best desulfurization performance with an equilibrium adsorption capacity of 14.02 mg/g and the desulfurization rate was ~90%.

Iron oxides and oxyhydroxides are commonly of considerable importance in the sorption of ions onto rocks, soils and sediments. They can be the controlling sorptive phases even if they are present in relatively small quantities. In common with other oxides and clay minerals, the sorptionpH-edge of metals is directly linked to their hydrolysis: the higher the residual charge on the metal ion, the lower the pH-edge. Modelling of this process has been successfully carried out using different microscopic or macroscopic definitions of the interface (e.g. surface complexation orion exchange models that may or may not include mineralogical descriptions). The influence of organic material on the sorption of many metals is of significant. This organic material includes simple organic molecules and more complex exopolymeric substances (e.g. humic substances) producedby the decay of natural organic matter. Sorption of this organic material to mineral surfaces has been the subject of a large body of work. The various types of organic substances do not share the same affinities for mineral surfaces in general, and for iron oxides and oxyhydroxides in particular.In those cases in which successful models of the component binary systems (i.e. metal–surface, metal–organic, organic–surface) have been developed, the formation of mixed surface complexes, the evolution of the surface itself, the addition order in laboratory systems, andthe evolution of natural organic matter fractions during sorption, have often precluded a satisfactory description of metal–surface–organic ternary systems over a sufficiently wide range of parameter values (i.e. pH, ionic strength, concentration of humic substances). This manuscriptdescribes the reasons for some successes and failures in the modelling of the ternary systems. Promising recent advances and possible methods of providing more complete descriptions of these intricate systems are also discussed.

Previously, it has been suggested that metal ions complexed to humic acid in the environment might show slower dissociation than those added to humic substances in the laboratory, which has serious implications for the transport of radionuclides in the environment. The dissociation of lanthanide and anthropogenic actinide ions from humic substance complexes has been studied as a function of humic concentration and metal ion:humic concentration ratio. The results suggest that the apparently slower kinetics observed for metal ions complexed in the environment are probably due to the large humic concentrations that are used in those studies. Further, there is no evidence that the dissociation rate constant varies at very low metal ion concentrations. Although humic samples size-fractionated by ultrafiltration showed that more metal may be bound non-exchangeably, there was no evidence for different rate constants. Ultrafiltration of Eu(III)/humic acid mixtures did show a shift in Eu from smaller to larger fractions over a period of two days. Therefore, the results suggest that dissociation rate constants determined in the laboratory at metal ion concentrations higher than those expected in the environment may be used in predicting radionuclide mobility, provided that the humic acid concentration is in the range expected at the site.

Lysozyme, a low-molecular weight basic protein, is an important component of the antibacterial system in milk. Lysozyme activity is higher in buffalo milk (60±3·9×10−3 units/ml) than in bovine milk (29·1±1·5×10−3 units/ml). Buffalo colostrum contains five-times more lysozyme activity than mature milk (Priyadarshini & Kansal, 2002a). Lysozyme activity in buffalo milk is not influenced by the parity of animal or stage of lactation, but it increases during extreme weather (winter and summer). Lysozyme in buffalo milk is more stable than in cow milk during storage and heat treatment. A sharp increase in milk lysozyme has been observed in buffaloes with sub-clinical mastitis (Priyadarshini & Kansal, 2002a).

Although the hammerhead reaction proceeds most efficiently in divalent cations, cleavage in 4 M LiCl is only ∼10-fold slower than under standard conditions of 10 mM MgCl2 (Murray et al., Chem Biol, 1998, 5:587–595; Curtis & Bartel, RNA, 2001, this issue, pp. 546–552). To determine if the catalytic mechanism with high concentrations of monovalent cations is similar to that with divalent cations, we compared the activities of a series of modified hammerhead ribozymes in the two ionic conditions. Nearly all of the modifications have similar deleterious effects under both reaction conditions, suggesting that the hammerhead adopts the same general catalytic structure with both monovalent and divalent cations. However, modification of three ligands previously implicated in the binding of a functional divalent metal ion have substantially smaller effects on the cleavage rate in Li+ than in Mg2+. This result suggests that an interaction analogous to the interaction made by this divalent metal ion is absent in the monovalent reaction. Although the contribution of this divalent metal ion to the overall reaction rate is relatively modest, its presence is needed to achieve the full catalytic rate. The role of this ion appears to be in facilitating formation of the active structure, and any direct chemical role of metal ions in hammerhead catalysis is small.

Proteins often require cofactors to perform their biological functions and must fold in the presence of their cognate ligands. Using circular dichroism spectroscopy, we investigated the effects of divalent metal binding upon the folding pathway of Escherichia coli RNase HI. This enzyme binds divalent metal in its active site, which is proximal to the folding core of RNase HI as defined by hydrogen/deuterium exchange studies. Metal binding increases the apparent stability of native RNase HI chiefly by reducing the unfolding rate. As with the apo-form of the protein, refolding from high denaturant concentrations in the presence of Mg2+ follows three-state kinetics: formation of a rapid burst phase followed by measurable single exponential kinetics. Therefore, the overall folding pathway of RNase HI is minimally perturbed by the presence of metal ions. Our results indicate that the metal cofactor enters the active site pocket only after the enzyme reaches its native fold, and therefore, divalent metal binding stabilizes the protein by decreasing its unfolding rate. Furthermore, the binding of the cofactor is dependent upon a carboxylate critical for activity (Asp10). A mutation in this residue (D10A) alters the folding kinetics in the absence of metal ions such that they are similar to those observed for the unaltered enzyme in the presence of metal.

The hairpin ribozyme catalyzes RNA cleavage in partially hydrated RNA films in the absence of added divalent cations. This reaction exhibits the characteristics associated with the RNA cleavage reaction observed under standard conditions in solution. Catalysis is a site-specific intramolecular transesterification reaction, requires the 2′-hydroxyl group of substrate nucleotide A−1, and generates 2′,3′-cyclic phosphate and 5′-hydroxyl termini. Mutations in both ribozyme and substrate abolish catalysis in hydrated films. The reaction is accelerated by cations that may enhance binding, conformational stability, and catalytic activity, and is inhibited by Tb3+. The reaction has an apparent temperature optimum of 4 °C. At this temperature, cleavage is slow (kobs: 2 d−1) and progressive, with accumulation of cleavage products to an extent of 40%. The use of synthetic RNAs, chelators, and analysis of all reaction components by inductively coupled plasma-optical spectrophotometry (ICPOES) effectively rules out the possibility of contaminating divalent metals in the reactions. Catalysis is minimal under conditions of extreme dehydration, indicating that the reaction requires hydration of RNA by atmospheric water. Our results provide a further caution for those studying the biochemical activity of ribozymes in vitro and in cells, as unanticipated catalysis could occur during RNA manipulation and lead to misinterpretation of data.

In the natural form of the hairpin ribozyme the two loop-carrying duplexes that comprise the majority of essential bases for activity form two adjacent helical arms of a four-way RNA junction. In the present work we have manipulated the sequence around the junction in a way known to perturb the global folding properties. We find that replacement of the junction by a different sequence that has the same conformational properties as the natural sequence gives closely similar reaction rate and Arrhenius activation energy for the substrate cleavage reaction. By comparison, rotation of the natural sequence in order to alter the three-dimensional folding of the ribozyme leads to a tenfold reduction in the kinetics of cleavage. Replacement with the U1 four-way junction that is resistant to rotation into the antiparallel structure required to allow interaction between the loops also gives a tenfold reduction in cleavage rate. The results indicate that the conformation of the junction has a major influence on the catalytic activity of the ribozyme. The results are all consistent with a role for the junction in the provision of a framework by which the loops are presented for interaction in order to create the active form of the ribozyme.

The two transesterification reactions catalyzed by self-splicing group II introns take place in either two active sites or two conformations of a single active site involving rearrangements of the positions of the reacting groups. We have investigated the effects on the rates of the chemical steps of the two reactions due to sulfur substitution of nonbridging oxygens at both the 5′ and 3′ splice sites as well as the deoxyribose substitution of the ribose 2′ hydroxyl group at the 5′ splice site. The data suggest that the two active sites differ in their interactions with several of these groups. Specifically, sulfur substitution of the pro-Sp nonbridging oxygen at the 5′ splice site reduces the chemical rate of the step one branching reaction by at least 250-fold, whereas substitution of the pro-Sp oxygen at the 3′ splice site has only a 4.5-fold effect on the chemical rate of step two. Previous work demonstrated that the Rp phosphorothioate substitutions at both the 5′ and 3′ splice sites reduced the rate of both steps of splicing to an undetectable level. These results suggest that either two distinct active sites catalyze the two steps or that more significant alterations must be made in a single bifunctional active site to accommodate the two different reactions.

Four-way helical junctions are found widely in natural RNA species. In this study, we have studied the conformation of two junctions by fluorescence resonance energy transfer. We show that the junctions are folded by pairwise coaxial helical stacking, forming one predominant stacking conformer in both examples studied. At low magnesium ion concentrations, the helical axes of both junctions are approximately perpendicular. One junction undergoes a rotation into a distorted antiparallel structure induced by the binding of a single magnesium ion. By contrast, the axes of the four-way junction of the U1 snRNA remain approximately perpendicular under all conditions examined, and we have determined the stacking conformer adopted.