We performed constant reservoir composition molecular dynamics (CRC-MD) simulations at 323 K and 124 bar to quantitatively study the partitioning of fluid species between the nano- and mesopores of clay and a bulk reservoir containing an equimolar mixture of CO2 and CH4. The results show that the basal (001) and protonated edge (010) surfaces of illite both demonstrate a strong preference for CO2 over CH4 adsorption; that the (001) surfaces show a stronger preference for CO2 than the (010) surfaces, especially with K+ as the exchangeable cation; and that the structuring of the near-surface CO2 by K+ is stronger than that by Na+. The protonated (010) surfaces have a somewhat greater preference for CH4, with the concentration near them close to that in the bulk fluid. The effects of the surfaces on the fluid composition extend to approximately 2.0 nm from them, with the fluid composition at the center of the pore becoming essentially the same as the bulk composition at a pore thickness of ~5.7 nm. The preference of nano- and mesopores bounded by clay minerals for CO2 over CH4 suggests that injection of CO2 into tight reservoirs is likely to displace CH4 into larger pores, thus enhancing its production.
Statistical information on the edge surface area and edge crystallographic orientation of clay nanoparticle surfaces is essential for proper accounting of the protonation-deprotonation reactions as a part of mechanistic surface complexation models. A combination of atomic-force microscopy (AFM) measurements and molecular dynamics computer simulations made it possible to quantify the relative contributions of the most frequently occurring montmorillonite edge surfaces to the total edge surface area. Edge surfaces normal to the  and  crystallographic directions are found to be the most abundant (~60% and ~20%, respectively), in agreement with previous estimations.
Non-turnover voltammetry is a sensitive tool to characterize the electrochemical properties of redox proteins. However, the catalytically competent oxidation states of most peroxidases do not display the required electrochemical reversibility. In this report, we circumvent this limitation and exploit the voltammetric response associated with the Fe(III)/Fe(II) redox couple of tobacco peroxidase to probe the energetics and electronic connectivity of the heme pocket. We have applied this approach to rationalize the previously reported influence of the immobilization protocol on the electrocatalytic activity of tobacco peroxidase. To decouple proton and electron transfer steps, measurements have been carried out over the 3 ≤ pH ≤ 9 range and a 1e − /2H + ladder scheme has been adopted for their analysis. At each pH, thermodynamic and kinetic parameters associated with the Fe(III)/Fe(II) redox conversion were determined as a function of temperature in the 0-30 °C range. Reduction entropies and reorganization energies displayed different values for covalently immobilized and physisorbed enzymes, pointing to a larger involvement of the solvent in the last case. These findings, together with a larger electronic coupling between the prosthetic group and the electrode, are indicative of a partial denaturation of the physisorbed enzymes as the origin of their lower electrocatalytic activity.
The carboxypeptidase T (CPT) from Thermoactinomyces vulgaris has an active site structure and 3D organization similar to pancreatic carboxypeptidases A and B (CPA and CPB), but differs in broader substrate specificity. The crystal structures of CPT complexes with the transition state analogs N-sulfamoyl-L-leucine and N-sulfamoyl-L-glutamate (SLeu and SGlu) were determined and compared with previously determined structures of CPT complexes with N-sulfamoyl-L-arginine and N-sulfamoyl-L-phenylalanine (SArg and SPhe). The conformations of residues Tyr255 and Glu270, the distances between these residues and the corresponding ligand groups, and the Zn-S gap between the zinc ion and the sulfur atom in the ligand's sulfamoyl group that simulates a distance between the zinc ion and the tetrahedral sp3-hybridized carbon atom of the converted peptide bond, vary depending on the nature of the side chain in the substrate's C-terminus. The increasing affinity of CPT with the transition state analogs in the order SGlu, SArg, SPhe, SLeu correlates well with a decreasing Zn-S gap in these complexes and the increasing efficiency of CPT-catalyzed hydrolysis of the corresponding tripeptide substrates (ZAAL > ZAAF > ZAAR > ZAAE). Thus, the side chain of the ligand that interacts with the primary specificity pocket of CPT, determines the geometry of the transition complex, the relative orientation of the bond to be cleaved by the catalytic groups of the active site and the catalytic properties of the enzyme. In the case of CPB, the relative orientation of the catalytic amino acid residues, as well as the distance between Glu270 and SArg/SPhe, is much less dependent on the nature of the corresponding side chain of the substrate. The influence of the nature of the substrate side chain on the structural organization of the transition state determines catalytic activity and broad substrate specificity of the carboxypeptidase T.
2-Azidomethyl-5-ethynylfuran, a new ambivalent compound with both azide and alkyne moieties that can be used as a self-clickable monomer, is synthesized starting directly from renewable biomass. The reactivity of the azide group linked to furfural is tested via the efficient preparation of a broad range of furfural-containing triazoles in good to excellent yields using a ‘green’ copper(I)-catalyzed azide–alkyne cycloaddition procedure. Access to new bio-based chemicals and oligomeric materials via a click-chemistry approach is also demonstrated using this bio-derived building block.
Oxidative esterification of biomass-derived 5-(hydroxymethyl) furfural (HMF) and furfural and their derivatives has been performed using a simple MnO2/NaCN system. The developed method allows the selective one-pot transformation of HMF to dimethyl furan-2,5-dicarboxylate (FDME) in 83% isolated yield without the formation of a free acid. Simplification of FDME production provides the missing link for manufacturing sustainable value-added materials from biomass. Addition of water to the oxidative system allows finetuning of reaction selectivity to obtain the previously difficult-to-access pure methyl 5-(hydroxylmethyl) furan-2-carboxylate in one step directly from the unprotected HMF without chromatographic separation.
The effect of mild pyrolysis methods (hydrothermal carbonization and torrefaction) on the physi-cochemical properties of biocoal was studied. It was established that biocoal obtained by hydrothermal car-bonization has a large specific surface area and exerts an exothermic effect upon decomposition; as comparedwith the samples obtained by torrefaction, it has a more dispersed structure and lower ash content.
Toward the development of classical force fields for the accurate modeling of clay mineral-water systems, we have extended the use of metalâ€“Oâ€“H (Mâ€“Oâ€“H) angle bending terms to describe surface Siâ€“Oâ€“H bending for hydrated kaolinite edge structures. Kaolinite, comprising linked octahedral Al and tetrahedral Si sheets, provides a rigorous test by combining aluminol and silanol groups with water molecules in hydrated edge structures. Periodic density functional theory and classical force fields were used with molecular dynamics to evaluate the structure, dynamics, hydrogen bonding, and power spectra for deriving optimum bending force constants and optimal equilibrium angles. Cleavage energies derived from density functional theory molecular dynamics calculations indicate the relative stabilities of both AC1 and AC2 edge terminations of kaolinite where Siâ€“OH and Alâ€“(OH2) or Siâ€“OH, Alâ€“OH, and Alâ€“(OH2) groups exist, respectively. Although not examined in this study, the new Siâ€“Oâ€“H angle bending parameter should allow for improved modeling of hydroxylated surfaces of silica minerals such as quartz and cristobalite, as well as amorphous silica-based surfaces and potentially those of other silicate and aluminosilicate phases.
A comparison was made between two plant peroxidases, cationic horseradish peroxidase (HRP) and anionic tobacco peroxidase (TOP), combined with a highly cationic osmium polymer [Os(4,4′-dimethyl-2,2′-bipyridine)2poly(N-vinylimidazole)10Cl]+ 2/+ ([Os(dmp)PVI]+/2 +) to develop highly sensitive, stable and selective hydrogen peroxide biosensors. The two different plant peroxidases were individually immobilized onto graphite rod (G) electrodes by a three steps drop-casting procedure consisting of the subsequent deposition of an aqueous solution of ([Os(dmp)PVI]+/2 +), followed by a solution of poly(ethyleneglycol) diglycidyl ether (PEGDGE), used as a cross linking agent and finally an aliquot of a solution of cationic HRP or anionic TOP to make HRP/PEGDGE/[Os(dmp)PVI]+/2 +/G and TOP/PEGDGE/[Os(dmp)PVI]+/2 +/G based electrodes, respectively. Electrochemical experiments were carried out to investigate the influence of the surface charge of the enzyme and the charge of the polymer on the efficiency of the electron transfer (ET) between the enzyme and the wiring redox polymer and the efficiency for electrocatalytic reduction of H2O2. In the case of HRP a decrease in the ET rate was observed due to the repulsion between this enzyme and the polymer, both positively charged, whereas with TOP there was an enhanced ET rate due to the attraction between the anionic enzyme and the cationic polymer. The effects of enzyme loading and pH were investigated. Both peroxidase modified electrodes exhibited a wide dynamic response range (1–500 μM H2O2) and a low detection limit (0.3 μM H2O2). The TOP based electrode showed a higher sensitivity (470 nA μM− 1 cm− 2) compared to that of the HRP based electrode (300 nA μM− 1 cm− 2) and an improved long-term stability (decrease in 17.3% upon 30 days compared with 50% for HRP). Both enzyme electrodes showed a response time of 3 s. The HRP based sensor was more sensitive to the presence of phenolic compounds acting as alternative electron donors, whereas the TOP based sensor was virtually interference free. Both HRP and TOP based electrodes were successfully tested in contact lens cleaning samples and real “spiked” samples from different sources such as tap water, milk and dairy products.