Abiotic Catalysis Research Articles

Unraveling iron oxides as abiotic catalysts of organic phosphorus recycling in soil and sediment matrices

In biogeochemical phosphorus cycling, iron oxide minerals are acknowledged as strong adsorbents of inorganic and organic phosphorus. Dephosphorylation of organic phosphorus is attributed only to biological processes, but iron oxides could also catalyze this reaction. Evidence of this abiotic catalysis has relied on monitoring products in solution, thereby ignoring iron oxides as both catalysts and adsorbents. Here we apply high-resolution mass spectrometry and X-ray absorption spectroscopy to characterize dissolved and particulate phosphorus species, respectively. In soil and sediment samples reacted with ribonucleotides, we uncover the abiotic production of particulate inorganic phosphate associated specifically with iron oxides. Reactions of various organic phosphorus compounds with the different minerals identified in the environmental samples reveal up to twenty-fold greater catalytic reactivities with iron oxides than with silicate and aluminosilicate minerals. Importantly, accounting for inorganic phosphate both in solution and mineral-bound, the dephosphorylation rates of iron oxides were within reported enzymatic rates in soils. Our findings thus imply a missing abiotic axiom for organic phosphorus mineralization in phosphorus cycling.

Deciphering the underlying mechanism of MOF-808-based abiotic catalysis enhancing biodegradability of waste activated sludge: Insights from the effects on bioconversion of extracellular organic substances into methane

Extracellular organic substances (EOSs) usually control sludge biodegradability. Metal−organic framework-808 (MOF-808), a catalyst with a high ability of catalytic hydrolysis and proton transfer, has great potential to enhance biodegradability of EOSs. In this study, the underlying mechanism of MOF-808 enhancing the biodegradability of EOSs via abiotic catalysis was investigated. Experimental results showed that protein–like and humic acid–like substances were the main organic components in EOSs, and the MOF-808 enhanced the disintegration of protein-like substances rather than humic acid–like substances. Analyses of the changes in the functional group, the secondary structure of protein-like substances, and the electron transfer of catalytically degraded EOS samples revealed that the MOF-808 enhanced the hydrolysis of EOSs protein-like substances, loosened their secondary structure, and improved the electron transfer in EOSs. Further analyses of the MOF-808 before and after the catalysis reaction revealed that the coordination of Zr sites with protein-like substance-specific active sites (such as ZrN) in the MOF-808 substantially contributed to the high-efficiency catalysis. Biochemical methane potential assays confirmed that MOF-808–based abiotic catalysis promoted the generation efficiency of methane from the EOSs. These findings can elucidate the abiotic catalytic effect of MOF-808 on sludge biodegradability during the anaerobic digestion process.

Catalytic eDHFR Acylation in HEK293T Cells

Key words live-cell eDHFR acylation - abiotic catalysis - boronate-assisted hydroxamic acid

Live-Cell Protein Modification by Boronate-Assisted Hydroxamic Acid Catalysis.

Selective methods for introducing protein post-translational modifications (PTMs) within living cells have proven valuable for interrogating their biological function. In contrast to enzymatic methods, abiotic catalysis should offer access to diverse and new-to-nature PTMs. Herein, we report the boronate-assisted hydroxamic acid (BAHA) catalyst system, which comprises a protein ligand, a hydroxamic acid Lewis base, and a diol moiety. In concert with a boronic acid-bearing acyl donor, our catalyst leverages a local molarity effect to promote acyl transfer to a target lysine residue. Our catalyst system employs micromolar reagent concentrations and affords minimal off-target protein reactivity. Critically, BAHA is resistant to glutathione, a metabolite which has hampered many efforts toward abiotic chemistry within living cells. To showcase this methodology, we installed a variety of acyl groups in E. coli dihydrofolate reductase expressed within human cells. Our results further establish the well-known boronic acid-diol complexation as a bona fide bio-orthogonal reaction with applications in chemical biology and in-cell catalysis.

Front Cover: Enhancing Biosynthesis and Manipulating Flux in Whole Cells with Abiotic Catalysis (ChemBioChem 3/2021)

Front Cover: Enhancing Biosynthesis and Manipulating Flux in Whole Cells with Abiotic Catalysis (ChemBioChem 3/2021)

Integrating abiotic chemical catalysis and enzymatic catalysis in living cells.

Life emerges from networks of multiple chemical reactions mediated by enzymes. If abiotic chemical catalysis is implanted into the reaction network of life, such an integration would produce organisms generating unique secondary metabolites and value-added materials from feedstocks or even air, or new diagnostics and therapeutics against diseases. In this review, we introduce selected papers in this emerging field of catalysis research.

Intra/extracellular electron transfer for aerobic denitrification mediated by in-situ biosynthesis palladium nanoparticles

The slow electron transfer rate is the bottleneck to the biological wastewater treatment process, and the nanoparticles (NPs) has been verified as a feasible strategy to improve the biological degradation efficiency by accelerating the electron transfer. Here, we employed the Gram-positive Bacillus megaterium Y-4, capable of synthetizing Pd(0), to investigate the intra/extracellular electron transfer (IET/EET) mechanisms mediated by NPs in aerobic denitrification for the first time. Kinetic and thermodynamic results showed that the bio-Pd(0) could significantly promote the removal of both nitrate and nitrite by improving affinity and decreasing activation energy. The enzymic activity and the respiration chain inhibition experiment indicated that the bio-Pd(0) could facilitate the nitrate biotic reduction by improving the Fe-S center activity and serving as parallel H carriers to replace coenzyme Q to selectively increase the electron flux toward nitrate in IET, while promoting the nitrite reduction by abiotic catalysis. Most importantly, the detection of DPV peak at -226~-287 mV proved that the one-electron EET via multiheme cytochrome-bound flavins also occurred in Gram-positive bacteria and enhanced in Pd-loaded cells. In addition, the remarkable increase of the formal charge in EPS indicated that the bio-Pd(0) could act as an electron shuttle to increase the redox site in EPS, eventually accelerating the electron hopping in long-distance electron transfer. Overall, this study expanded our understanding of the roles of bio-Pd(0) on the aerobic denitrification process and provided an insight into the IET/EET of Gram-positive strains.

Enhancing Biosynthesis and Manipulating Flux in Whole Cells with Abiotic Catalysis.

Metabolic engineering uses genetic strategies to drive flux through desired pathways. Recent work with electrochemical, photochemical, and chemocatalytic setups has revealed that these systems can also expand metabolic pathways and manipulate flux in whole cells. Electrochemical systems add or remove electrons from metabolic pathways to direct flux to more- or less-reduced products. Photochemical systems act as synthetic light-harvesting complexes and yield artificial photosynthetic organisms. Biocompatible chemocatalysis increases product scope, streamlines syntheses, and yields single-flask processes to deliver products that would be challenging to synthesize through biosynthetic means alone. Here, we exclusively highlight systems that combine abiotic systems with living whole cells, taking particular note of strategies that enable the merger of these typically disparate systems.

Catalytic activity of water molecules in gas‐phase glycine dimerization

AbstractThe dimerization of glycine is the simplest oligomerization of amino acids and plays an important role in biology. Although this reaction is thermodynamically unfavorable in the aqueous phase, it has been shown to be spontaneous in the gas phase and proceeds via two different concerted reaction mechanisms known as cis and trans. This may have profound implications in prebiotic chemistry as common atmospheric prenucleation clusters are thought to have participated in gas‐phase reactions in the early Earth's atmosphere. We hypothesize that particular arrangements of water molecules in these clusters could lead to lowering of the reaction barrier of amino acid dimerization and could lead to abiotic catalysis toward polypeptides. We test our hypothesis on a system of the cis transition state of glycine dimerization solvated by one to five water molecules using a combination of a genetic algorithm‐based configurational sampling, density functional theory geometries, and domain‐based local pair natural orbital coupled‐cluster electronic structure. First, we discuss the validity of the model chemistries used to obtain our results. Then, we show that the Gibbs free energy barrier for the concerted cis mechanism can indeed be lowered by the addition of up to five water molecules, depending on the temperature.

Orthogonal Expression of an Artificial Metalloenzyme for Abiotic Catalysis.

A cytochrome P450 was engineered to selectively incorporate Ir(Me)-deuteroporphyrin IX (Ir(Me)-DPIX), in lieu of heme, in bacterial cells. Cofactor selectivity was altered by introducing mutations within the heme-binding pocket to discriminate the deuteroporphyrin macrocycle, in combination with mutations to the P450 axial cysteine to accommodate a pendant methyl group on the Ir(Me) center. This artificial metalloenzyme was investigated for activity in non-native metallocarbenoid-mediated olefin cyclopropanation reactions and showed enhanced activity for aliphatic and electron-deficient olefins when compared to the native heme enzyme. This work provides a general strategy to augment the chemical functionality of heme enzymes in cells with application towards abiotic catalysis.

Cooperative Catalysis: A New Development in Heterogeneous Catalysis

Whereas cooperative effect in catalysis, in which multiple chemical interactions participate cooperatively to achieve significant enhancement in catalytic activity and/or selectivity, is common in enzymatic reactions, it has been sparingly employed in heterogeneous catalytic systems. Here, some recent literature examples of abiotic catalysis, with emphasis on heterogeneous systems, that employ cooperation between acid and base and two metal centers are briefly described to demonstrate the principles involved. Since effective cooperation places strict demand on the positions of the different functional groups, new synthetic methods and strategies are needed to design and construct structures useful for cooperative catalysis. Recent progress in our laboratory in synthesizing new nanocage structures that possess molecular-size cavities, atomic layer thick, porous shells with internal functional groups is described. These recent developments suggest possibilities of new catalytic transformations that have not been attempted before. This is illustrated with two speculative examples utilizing cooperative catalysis: oxidative hydrolytic desulfurization and terminal carbon activation of hydrocarbon molecules.

Organic matter humification in olive oil mill wastewater by abiotic catalysis with manganese(IV) oxide

The chemical changes occurring in an olive oil mill wastewater (OMW) sample digested catalytically with MnO 2 for 30 and 60 days were evaluated comparatively with those occurring in the same OMW left standing for the same time in an open-air lagoon. Both treatments increased the pH and electrical conductivity and decreased the contents of dry matter, total organic C and total N, and C/N ratio of OMW. The humic acid (HA)-like fraction isolated from the fresh OMW was characterized by a marked aliphatic character, small O and acidic functional group contents, marked presence of proteinaceous materials, partially modified lignin moieties and polysaccharides-like structures, extended molecular heterogeneity, and small degrees of aromatic ring polycondensation, polymerization and humification. With increasing the time of either lagooning or catalytic digestion, a loss of aliphatic materials and an increase of extraction yield, oxygenation, acidic functional groups, carbohydrates and aromaticity occurred in the HA-like fractions. The more evident changes measured for the HA-like fractions from catalytically-digested OMW, with respect to those from lagooned OMW, indicated that MnO 2 was able to catalyze organic matter humification in OMW.

A mineral support and biotic catalyst are essential in the formation of highly polymeric soil humic substances

The hypothesis was proposed that highly polymeric humic substances in the mineral horizons of soils in a temperate humid climate originate from polymerization of water-soluble structural precursors directly on mineral surfaces under the catalytic effect of immobilized phenoloxidases (heterophasic biocatalysis). This hypothesis was confirmed by a laboratory experiment using a mixture of monomeric phenols and nitrogenous compounds as structural precursors, fungal laccase as a biotic catalyst, and a hydroxyaluminum-kaolinite complex as a mineral support. Enzymic oxidation of phenolic precursors on the mineral surface was substantially more rapid than abiotic oxidation and led to synthesis of a highly polymeric fraction with a molecular weight over 75 kDa. These products were not produced on the mineral with an absence of laccase (abiotic catalysis) or in solution without the mineral matrix (homogeneous catalysis).

Significance of the Henri–Michaelis–Menten theory in abiotic catalysis: catechol oxidation by δ-MnO 2

The Henri–Michaelis–Menten theory, for more than eight decades, was only restricted to homogeneous enzymatic catalysis. A mimic of an enzymatic kinetics based on the Henri–Michaelis–Menten concept was experimentally observed in heterogeneous catalysis in the present study with δ-MnO 2 as an abiotic catalyst in the oxidation of catechol (1,2-dihydroxybenzene). Using the derived linear forms of Lineweaver–Burk or Hofstee, the data show that similar to the enzyme tyrosinase, the kinetics of the catechol oxidation catalyzed by δ-MnO 2 can be described by the Henri–Michaelis–Menten equation, V 0= V max S/( K m+ S), where V max is the maximum velocity and K m the concentration of the substrate ( S) corresponding to an initial velocity ( V 0) half of V max. By analogy to the enzymatic kinetics, the parameters V max and K m for an heterogeneous abiotic catalysis were derived for the first time. Further, based on the concentration of the active centers of the mineral oxide, the kinetic constants k cat and k cat/ K m, respectively, representing the turnover frequency and the efficiency of the mineral catalyst, were also determined from the derived general rate equation of Briggs and Haldane. As an abiotic catalyst, δ-MnO 2 has a paramount role in the oxidation of phenolic compounds in soil, sediment and water environments. Therefore, the present observation is of fundamental and practical significance in elucidating the affinity between an abiotic catalyst and a substrate based on the Henri–Michaelis–Menten theory.

Role of hydroxy-aluminosilicate ions (proto-imogolite sol) in the formation of humic substances

Little is known of the role of solution species of soil aluminosilicates in the formation of humic substances. Catalysis by hydroxy-aluminosilicate (HAS) ions, one of the major forms of soluble aluminum and silicon and the precursor of noncrystalline aluminosilicates in acidic natural environments, in catechol humification was investigated in this study by using UV-visible, FTIR, and solid state 13C CP–MAS NMR spectroscopies, X-ray diffractometry, atomic force microscopy, and elemental analysis. Hydroxy-aluminosilicate ions substantially promoted the oxidative polymerization and ring cleavage of catechol, resulting in the formation of black precipitates of humic macromolecules. This abiotic catalysis by HAS ions merits close attention in understanding the formation and related geochemistry of humic substances especially in acidic environments in temperate and subtropical regions.

CHARACTERISTICS OF PYROGALLOL-DERIVED POLYMERS FORMED BY CATALYSIS OF OXIDES

The influence of the nature and properties of oxides in soil and sediment environments on the characteristics of polyphenol-derived humic polymers formed by abiotic catalysis is not fully understood. The objective of this study was to investigate the catalytic power of Mn(IV), Fe(III), Al, and Si oxides in the transformation of pyrogallol and the development of carboxylic and aliphatic groups in the resulting humic polymers. The metal oxides differed significantly in their effectiveness for catalyzing pyrogallol humification. The results indicate that the carboxylic group of humic polymers developed as a result of ring cleavage of pyrogallol catalyzed by the oxides. The ability of short-range ordered oxides of Al, Si, and especially Fe and Mn, in enhancing the formation of aliphatic and carboxylic groups in humic polymers derived from polyphenol humification may, in part, contribute to the origin of aliphaticity of humic substances and the variation of their characteristics, including carboxylic group contents with soils from different climatic zones.

Catalytic science and technology for environmental issues

In the first part of the lecture, it is demonstrated how knowledge that comes from studies of catalysis at the molecular level helps to design new, more efficient catalysts and catalytic processes. In the second part, the importance of catalytic technologies for solving environmental issues and providing sustainable development is discussed. In the third part, the role of the natural abiotic catalysis in the chemistry of the troposphere is discussed.

Deamination of aspartic acid by aspartase—Ca-montmorillonite complex

Aspartase was adsorbed by Ca-montmorillonite at an initial pH of 7.0 and 25°C; the equilibrium adsorption isotherm was of L (Langmuir) type with a maximum adsorption of 0.22 mg aspartase protein/mg clay. The d 001 spacing of the aspartase—Ca-montmorillonite complex was 26.5 Å when 0.20 mg aspartase protein was adsorbed per mg clay, indicating the intercalation of the aspartase in the clay structure. After washing, the amount of aspartase protein remaining immobilized on the clay surfaces was 0.0073 mg/mg clay. The activity of free and immobilized aspartase in the deamination of aspartic acid was studied in unbuffered systems at pH of 7.0 to avoid the effect of the buffer on the surface reactivity of montmorillonite. During the first 2 h of the reaction no ammonium was released from aspartic acid in the presence of aspartase—Ca-montmorillonite complex, probably because there was insufficient time for the expansion and swelling of the mineral and/or the diffusion of the aspartase molecules to the interlayer edges and external surfaces of montmorillonite or the infusion of the substrate (aspartic acid). After 3 days, the specific activity of the aspartase immobilized on Ca-montmorillonite was slightly higher than that of free aspartase in homogenous solution. This was evidently due to the preservation of the activity of the adsorbed aspartase, the contribution of the catalytic power of the montmorillonite to the deamination of aspartic acid, and the complementary effects of the enzymatic and abiotic catalysis. The purification treatment of the montmorillonite did not show a significant effect on either the adsorption or the activity of the immobilized aspartase.

Catalytic science and technology for environmental issues

Abstract

Micro-organisms and manganese cycling in a seasonally stratified freshwater dam

This work describes investigations into the role that biotic and abiotic mechanisms play in the manganese redox cycle in a freshwater dam over a twelve month period. Enzymatic control of manganese oxidation was taking place with a temperature optimum of approx. 30°C. Manganese oxidation was only significant above about 19°C. The temperature and season play vital roles in determining the extent to which abiotic and microbial mechanisms contribute to manganese oxidation. Results showed that microbial catalysis is overwhelmingly responsible for manganese oxidation in the lower epilimnion from November to May. Significant abiotic catalysis (up to 25%) can occur in late summer/autumn when the water temperature is greatest. Mn(II) oxidation, pseudo-first order rate constants to 1.12 × 10 22 M −4 · d −1 were measured while poisoned sample experiments confirmed the role of biological mediation. In winter, biological control could not occur because of the lower temperature of the water column. The measurement of “ x” in MnO x showed that higher manganese oxidation states were expected when the manganese oxidation rate was at a maximum and therefore when microbial activity was greatest. Direct microbial reduction of MnO x in the water column was of much less significance. However, indirect reduction may have taken place through the reaction of MnO x with sulfide. The results of this work have important implications for the design and operation of artificial destratification units for the control of manganese speciation.