Highly enantioselective Michael addition of cyclohexanone to nitroolefins catalyzed by pyrrolidine‐based bifunctional benzoylthiourea in water

Organocatalysis and aqueous reactions are identified as the focus of the greening of chemistry. Combining these two strategies effectively remains an interesting challenge in organic synthesis. Herein, we used pyrrolidine‐based benzoylthiourea 1c to catalyze the asymmetric Michael addition of cyclohexanone to various nitroolefins in water to afford the corresponding compounds in moderate to good yields, and with excellent diastereoselectivities (up to >99:1 dr) and enantioselectivities (up to 99% ee).     

Scaling‐up of complex whole‐cell bioconversions in conventional and non‐conventional media

The use of whole cells is becoming a more common approach in pharmaceutical and agrochemical industries in order to obtain pure compounds with fewer production steps, higher yields, and cleaner processes, as compared to those achieved with traditional strategies. Whole cells are often used as enzymes pools, in particular when multi‐step reactions and/or co‐factor regeneration are envisaged. Nonetheless, published information on the scale‐up of such systems both in aqueous and in two‐phase aqueous–organic systems is relatively scarce. The present work aims to evaluate suitable scale‐up criteria in conventional and non‐conventional medium for a whole‐cell bioconversion that uses resting cells of Mycobacterium sp. NRRL B‐3805 to cleave the side chain of β‐sitosterol, a poorly water‐soluble substrate. The experiments were performed in 24‐well microtiter plates and in 250 mL shaken flasks as orbital stirred systems, and in 300 mL stirred tanks as mechanically stirred systems. Results show that productivity yields were similar in all scales tested, when maintaining oxygen mass transfer coefficients constant in aqueous systems, or when maintaining constant volumetric power consumption in aqueous–organic two‐phase systems. Biotechnol. Bioeng. 2010;106: 619–626. © 2010 Wiley Periodicals, Inc.     

Organic synthesis by quench reactions.

The effects of chemical quench reactions on the formation of organic compounds at a water surface under simulated primordial earth conditions were investigated for the study of chemical evolution. A mixture of gaseous methane and ammonia over a water surface was exposed to an arc discharge between an electrode and the water surface. This discharge served as a source of dissociated, ionized and excited atomic and molecular species. Various organic molecules were formed in the gaseous, aqueous, and solid states by a subsequent quenching of these reactive species on the water surface. The effects of these water-surface quench reactions were assessed by comparing the amounts of synthesized molecules to the amounts which formed during the discharge of an arc above the water level. The results showed that: (1) the water-surface quench reaction permitted faster rates of formation of an insoluble solid and (2) the quench discharge yielded twice as much amino acids and 17 times more insoluble solids by weight than the other discharge. The highest yield of amino acids with the quench reaction was 9 x 10-7 molecules per erg of input energy. These observations indicate that quench reactions on the oceans, rain, and clouds that would have followed excitation by lightning and shock waves may have played an important role in the prebiotic milieu. Furthermore, the possibility exists that quench reactions can be exploited for the synthesis of organic compounds on a larger scale from simple starting materials.     

Biomimicry of volatile‐based microbial control for managing emerging fungal pathogens

Volatile organic compounds (VOCs) are known to be produced by a wide range of micro‐organisms and for a number of purposes. Volatile‐based microbial inhibition in environments such as soil is well‐founded, with numerous antimicrobial VOCs having been identified. Inhibitory VOCs are of interest as microbial control agents, as low concentrations of gaseous VOCs can elicit significant antimicrobial effects. Volatile organic compounds are organic chemicals typically characterized as having low molecular weight, low solubility in water, and high vapour pressure. Consequently, VOCs readily evaporate to the gaseous phase at standard temperature and pressure. This contact‐independent antagonism presents unique advantages over traditional, contact‐dependent microbial control methods, including increased surface exposure and reduced environmental persistence. This approach has been the focus of our recent research, with positive results suggesting it may be particularly promising for the management of emerging fungal pathogens, such as the causative agents of white‐nose syndrome of bats and snake fungal disease, which are difficult or impossible to treat using traditional approaches. Here, we review the history of volatile‐based microbial control, discuss recent progress in formulations that mimic naturally antagonistic VOCs, outline the development of a novel treatment device, and highlight areas where further work is needed to successfully deploy VOCs against existing and emerging fungal pathogens.     

Confined-pyrolysis as an experimental method for hydrothermal organic synthesis

A closed pyrolysis system has been developed as a tool for studying the reactions of organic compounds under extreme hydrothermal conditions. Small high pressure stainless steel vessels in which the ratio of sediment or sample to water has been adjusted to eliminate the headspace at peak experimental conditions confines the organic components to the bulk solid matrix and eliminates the partitioning of the organic compounds away from the inorganic components during the experiment. Confined pyrolysis experiments were performed to simulate thermally driven catagenetic changes in sedimentary organic matter using a solids to water ratio of 3.4 to 1. The extent of alteration was measured by monitoring the steroid and triterpenoid biomarkers and polycyclic aromatic hydrocarbon distributions. These pyrolysis experiments duplicated the hydrothermal transformations observed in nature. Molecular probe experiments using alkadienes, alkenes and alkanes in H₂O and D₂O elucidated the isomerization and hydrogenation reactions of aliphatic compounds and the competing oxidative reactions occurring under hydrothermal conditions. This confined pyrolysis technique is being applied to test experiments on organic synthesis of relevance to chemical evolution for the origin of life.     

Aqueous pathways dominate permeation of solutes across Pisum sativum seed coats and mediate solute transport via diffusion and bulk flow of water

The permeability of seed coats to solutes either of biological or anthropogenic origin plays a major role in germination, seedling growth and seed treatment by pesticides. An experimental set‐up was designed for investigating the mechanisms of seed coat permeation, which allows steady‐state experiments with isolated seed coats of Pisum sativum. Permeances were measured for a set of organic model compounds with different physicochemical properties and sizes. The results show that narrow aqueous pathways dominate the diffusion of solutes across pea seed coats, as indicated by a correlation of permeances with the molecular sizes of the compounds instead of their lipophilicity. Further indicators for an aqueous pathway are small size selectivity and a small effect of temperature on permeation. The application of an osmotic water potential gradient across isolated seed coats leads to an increase in solute transfer, indicating that the aqueous pathways form a water‐filled continuum across the seed coat allowing the bulk flow of water. Thus, the uptake of organic solutes across pea testae has two components: (1) by diffusion and (2) by bulk water inflow, which, however, is relevant only during imbibition.     

Inhibitory effect of dissolved organic matter on triplet-induced oxidation of aquatic contaminants.

Excited triplet states of organic chromophores, in particular aromatic ketones, are capable of inducing oxidation of a variety of organic compounds. These reactions probably play an important role in the degradation of organic contaminants in sunlit natural waters. The effect of dissolved natural organic matter (DOM) on the oxidation rate of twenty-two aquatic organic contaminants, including phenols, anilines, phenylurea and s-triazine herbicides, and some pharmaceuticals, was investigated using photoexcited benzophenone-4-carboxylate (CBBP) as the oxidant. For about half of the studied compounds, a decrease in depletion rate was observed in the presence of Suwannee River fulvic acid, used as a reference DOM. Also, depletion rates decreased with increasing DOM concentration, as verified for five selected compounds. Such an inhibitory effect of DOM on oxidation is attributed to its antioxidant properties, whereby oxidation intermediates of the contaminants are supposed to be reduced back to their parent compounds. The presented screening study shows that DOM may be a relevant factor for inhibiting the oxidation of many organic contaminants in surface waters and possibly in engineered water treatment systems.     

Fused Heteroaromatic Organic Compounds for High‐Power Electrodes of Rechargeable Lithium Batteries

Organic redox compounds are emerging electrode materials for rechargeable lithium batteries. However, their electrically insulating nature plagues efficient charge transport within the electroactive bulk. Alternative to the popular solution of elaborating nanocomposite materials, herein we report on a molecular‐level engineering strategy towards high‐power organic electrode materials with multi‐electron reactions. Systematic comparisons of anthraquinone analogues incorporating fused heteroaromatic structures as cathode materials in rechargeable lithium batteries reveal that the judicious incorporation of heteroaromatics improves the cell performance in terms of specific gravimetric capacity, working potential, rate capability, and cyclability. Combination studies with morphological observation, electrochemical impedance characterization, and theoretical modeling provide insight into the advantage of heteroaromatic building blocks. In particular, benzofuro[5,6‐b]furan‐4,8‐dione ( BFFD ) bearing furan moeities shows a reversible capacity of 181 mAh g^?1 when charged/discharged at 100C, corresponding to a power density of 29.8 kW kg^?1. These results have pointed to a general design route of high‐rate organic electrode materials by rational functionalization of redox compounds with appropriate heteroaromatic units as versatile structural tools.     

Recent Development of Zeolitic Imidazolate Frameworks (ZIFs) Derived Porous Carbon Based Materials as Electrocatalysts

Development of effective, stable, and economic electrocatalysts is critical for further implementation of fuel cells, water electrolysis, and metal–air batteries in clean energy conversion technologies. As a subfamily of metal–organic frameworks (MOFs), zeolitic imidazolate frameworks (ZIFs) possess the characteristics of both MOFs and zeolites, showing highly porous structures, large surface area, and open catalytic active sites. This review presents materials design strategies for constructing improved electrocatalysts based on ZIF precursors/templates, with special emphasis on the varieties of derivatives, controllable building of active sites, the construction of macroscopic structure, and the favored electrocatalytic reactions based on these materials. These ZIF‐derived N‐doped carbon‐based composites or compounds have exhibited remarkable activity and stability for a broad electrocatalysis application, displaying great potential to replace noble‐metal‐based catalysts. The challenges and perspectives regarding ZIF‐derived electrocatalysts are also discussed for better development of ZIF‐derived electrocatalysts.     

Early diagenesis of organic matter in lacustrine sediments in terms of methane fermentation

The amounts of organic compounds such as amino acids (proteinaceous substances), fatty acids, and sterols in lacustrine sediments were found to decrease greatly from the mud‐water interface to depths of 20 cm and less at greater core depths. The amounts of methane produced by microbial activity in subsamples incubated for 40 days at 27°C were also found to decrease with core depth, apparently limited by the exhaustion of organic substrates subject to methane fermentation. Decomposition rates of certain organic compounds added to sediment samples were determined by incubation experiments at different temperatures for 40 to 450 days. Experimental results with mixed cultures of microorganisms in lacustrine sediments indicated the following: (a) The marked decomposition of organic compounds such as amino acids, fatty acids, and sterols in the lacustrine sediments resulted mainly in the formation of methane, (b) Unsaturated compounds were more readily decomposed with the ultimate formation of methane than saturated compounds, (c) The susceptibility of saturated fatty acids to methane formation decreased in proportion to their molecular weights.     

Organic synthesis by quench reactions

The effects of chemical quench reactions on the formation of organic compounds at a water surface under simulated primordial earth conditions were investigated for the study of chemical evolution. A mixture of gaseous methane and ammonia over a water surface was exposed to an arc discharge between an electrode and the water surface. This discharge served as a source of dissociated, ionized and excited atomic and molecular species. Various organic molecules were formed in the gaseous, aqueous, and solid states by a subsequent quenching of these reactive species on the water surface. The effects of these water-surface quench reactions were assessed by comparing the amounts of synthesized molecules to the amounts which formed during the discharge of an arc above the water level. The results showed that: (1) the water-surface quench reaction permitted faster rates of formation of an insoluble solid and (2) the quench discharge yielded twice as much amino acids and 17 times more insoluble solids by weight than the other discharge. The highest yield of amino acids with the quench reaction was 9×10⁷ molecules per erg of input energy. These observations indicate that quench reactions on the oceans, rain, and clouds that would have followed excitation by lightning and shock waves may have played an important role in the prebiotic milieu. Furthermore, the possibility exists that quench reactions can be exploited for the synthesis of organic compounds on a larger scale from simple startng materials.     

Sustained Water Oxidation by Direct Electrosynthesis of Ultrathin Organic Protection Films on Silicon

Artificial photosynthesis allows exceeding the efficiency and stability limits of natural photosynthesis. Based on the use of semiconducting absorbers, high efficiency in water photolysis has been achieved in various photoelectrode configurations. However, integrated systems are limited in their stability, and more stable half‐cell electrodes use protection films prepared by laborious methods. Herein, the facile low‐temperature preparation of ultrathin organic protection coatings is demonstrated. The formation is based on the catalytic properties of water oxidation catalysts toward alcohol‐polymerization reactions, which results in the formation of hitherto unknown protection layers on silicon. The interfacial layers are generated via iodine‐mediated electro‐reductive polymerization of ethanol, concomitantly forming during electrophoretic transport of RuO₂ onto silicon supports. Reaction chemistry analyses show that the RuO₂‐induced catalysis introduces E2‐elimination reactions which result in a carbon sp³–sp² transformation of the film. For the two modes of photoelectrochemical operation, the photovoltaic and the photoelectrocatalytic mode, 20 and 15 mA cm^?2 photocurrent densities, respectively, are obtained with unaltered output for 8 and 24 h. The interfacial layer enables Si photovoltages of 500 mV, demonstrating extraordinary electronic interface quality. Since only hydrogen termination of the surface is a prerequisite for growth of the organic protection layer, the method is applicable to a wide range of semiconductors.     

Biodegradation of the Water‐Soluble Gasoline Components in a Novel Hybrid Bioreactor

A novel hybrid bioreactor was designed to remove volatile organic compounds from water contaminated with water‐soluble gasoline components, and the performance of this new bioreactor was investigated. It was composed of two biotrickling filter sections and one biofilter section. The liquid phase pollutants were removed by a mixed culture in the biotrickling filter sections and the gas phase pollutants stripped by air injection in the biofilter section. The specific rates of chemical oxygen demand (COD) removal obtained in the reactor were directly proportional to the pollutant‐loading rate. A stable operation of the hybrid bioreactor was attained for long periods of time. The bioreactor had the potential to simultaneously treat a complex mixture of volatile organic compounds, e.g., those present in the water‐soluble fraction of gasoline, as well as the capacity to readily adapt to changing operational conditions, such as an increased contaminant loading, and variations in the airflow rate.     

Grafting under water stress in tomato cherry: improving the fruit yield and quality

As the concentrations of essential vitamins and minerals and a number of other health‐promoting compounds are often low in stable crops, research is under way to understand and increase synthesis of phytochemicals in order to improve crop nutritional quality. The question addressed in this study is whether shoot genotypes or root genotypes with tolerant drought character are able to increase the fruit quality and production under moderate water stress. Zarina (drought tolerant) and Josefina (drought sensitive) were grafted self and reciprocally. The results showed that the use of cv. Zarina (drought tolerant) as rootstock (Zar × Jos) results in a greater number of fruits under water‐stress conditions, a moderate increase in some antioxidant compounds, such as ascorbic acid, phenols and flavonoids and lycopene and β‐carotene, and Zar × Jos showed high levels of sugars and organic acids, sweetness index and sugars : acids ratio, as well as important minerals, such as K and Mg, which could increase its nutritional quality under stress conditions. Overall, the use of drought‐tolerant rootstock could provide a useful tool to improve fruit yield and quality of cherry tomato fruit under moderate water stress, which in turn could mean lower costs in the use of irrigation water.     

Evidence for organic synthesis in high temperature aqueous media — Facts and prognosis

Hydrothermal systems are common along the active tectonic areas of the earth. Potential sites being studied for organic matter alteration and possible organic synthesis are spreading ridges, off-axis systems, back-arc activity, hot spots, volcanism, and subduction. Organic matter alteration, primarily reductive and generally from immature organic detritus, occurs in these high temperature and rapid fluid flow hydrothermal regimes. Hot circulating water (temperature range — warm to >400 °C) is responsible for these molecular alterations, expuslion and migration. Compounds that are obviously synthesized are minor components because they are generally masked by the pyrolysis products formed from contemporary natural organic precursors. Heterocyclic sulfur compounds have been identified in high temperature zones and hydrothermal petroleums of the Guaymas Basin vent systems. They can be interpreted as being synthesized from formaldehyde and sulfur or HS _x ^– in the hydrothermal fluids.Other products from potential synthesis reactions have not yet been found in the natural systems but are expected based on known industrial processes and inferences from experimental simulation data. Various industrial processes have been reviewed and are of relevance to hydrothermal synthesis of organic compounds. The reactivity of organic compounds in hot water (200–350 °C) has been studied in autoclaves, and supercritical water as a medium for chemistry has also been evaluated. This high temperature aqueous organic chemistry and the strong reducing conditions of the natural systems suggest this as an important route to produce organic compounds on the primitive earth. Thus a better understanding of the potential syntheses of organic compounds in hydrothermal systems will require investigations of the chemistry of condensation, autocatalysis, catalysis and hydrolysis reactions in aqueous mineral buffered systems over a range of temperatures from warm to >400 °C.Presented in part at the International Society for the Study of the Origin of Life Meeting, Barcelona, Spain, July 1993.     

Synthesis of organic compounds from carbon monoxide and water by UV photolysis

The photolysis of water vapor with carbon monoxide at 1849 Å yields alcohols, aldehydes and organic acids, with an overall quantum yield of 3.3×10^–2. This rather high quantum yield could have led to a contribution of 10¹¹ organic molecules cm^–2 sec^–1 to the pool of organic material on the primitive Earth. The reactions are initiated by the photolysis of water molecules and the resulting hydrogen atoms reduce the carbon monoxide to a variety of one and two carbon compounds. The organic molecules are dissolved in water and thus escape destruction by photolysis. Photolysis of water vapor with carbon dioxide did not yield organic compounds under these conditions.     

Tools for Selective Enzyme Reaction Steps in the Synthesis of Laboratory Chemicals

The need for more selective reactions steps and the compatibility between process steps which follow on from each other has been a major driving force for organic synthesis. The synthesis of chiral compounds, metabolites, new chemical entities and natural products by a combination of chemical and enzyme reaction steps has become well established, due the existence of stable enzymes as selective catalysts which are inherently chiral by nature. Auxiliary tools such as suitable transfer reagents for reaching complete conversion, easy and robust reaction control as well as tools for straightforward workup and purification of the final product have been developed. Selective enzyme reaction steps in the area of hydrolyses, oxidation steps including hydroxylation and the Baeyer‐Villiger oxidation, carbon‐carbon bond formation and glycosylation reactions have compared favorably with existing methods of classical organic synthesis. The tools developed during optimization and scale‐up of these enzyme reaction steps have the potential to shorten development time. The introduction of selective enzyme reactions into an entire synthetic process has resulted in harmonization of improvements in economic efficiency with resultant solutions to health, safety and environment problems. This will become even more important in industrial synthetic chemistry in the future, for convenient solutions to certain intractable synthetic problems and for expanding the repertoire of chemistry by modular biocatalysts. Efficient isolation procedures for the final product are essential to take full advantage of the biocatalytic conversion to obtain high product yields.     

Sources of organic nitrogen at the serpentinite‐hosted Lost City hydrothermal field

The reaction of ultramafic rocks with water during serpentinization at moderate temperatures results in alkaline fluids with high concentrations of reduced chemical compounds such as hydrogen and methane. Such environments provide unique habitats for microbial communities capable of utilizing these reduced compounds in present‐day and, possibly, early Earth environments. However, these systems present challenges to microbial communities as well, particularly due to high fluid pH and possibly the availability of essential nutrients such as nitrogen. Here we investigate the source and cycling of organic nitrogen at an oceanic serpentinizing environment, the Lost City hydrothermal field (30°N, Mid‐Atlantic Ridge). Total hydrolizable amino acid (THAA) concentrations in the fluids range from 736 to 2300 nm and constitute a large fraction of the dissolved organic carbon (2.5–15.1%). The amino acid distributions, and the relative concentrations of these compounds across the hydrothermal field, indicate they most likely derived from chemolithoautotrophic production. Previous studies have identified the presence of numerous nitrogen fixation genes in the fluids and the chimneys. Organic nitrogen in actively venting chimneys has δ¹⁵N values as low as 0.1‰ which is compatible with biological nitrogen fixation. Total hydrolizable amino acids in the chimneys are enriched in ¹³C by 2–7‰ compared to bulk organic matter. The distribution and absolute δ¹³C_THAA values are compatible with a chemolithoautotrophic source, an attribution also supported by molar organic C/N ratios in most active chimneys (4.1–5.5) which are similar to those expected for microbial communities. In total, these data indicate nitrogen is readily available to microbial communities at Lost City.     

The role of microorganisms in mobilization and fixation of phosphorus in sediments

Cycling of phosphorus (P) at the sediment/water interface is generally considered to be an abiotic process. Sediment bacteria are assumed to play only an indirect role by accelerating the transfer of electron from electron donors to electron acceptors, thus providing the necessary conditions for redox-and pH-dependent, abiotic sorption/desorption or precipitation/dissolution reactions. Results summarized in this review suggest that

1. in eutrophic lakes, sediment bacteria contain as much P as settles with organic detritus during one year
2. in oligotrophic lakes, P incorporated in benthic bacterial biomass may exceed the yearly deposition of bioavailable P several times
3. storage and release of P by sediment bacteria are redox-dependent processes
4. an appreciable amount of P buried in the sediment is associated with the organic fraction
5. sediment bacteria not only regenerate PO₄, they also contribute to the production of refractory, organic P compounds, and
6. in oligotrophic lakes, a larger fraction of the P settled with organic detritus is converted to refractory organic compounds by benthic microorganisms than in eutrophic lakes.

From this we conclude that benthic bacteria do more than just mineralize organic P compounds. Especially in oligotrophic lakes, they also may regulate the flux of P across the sediment/water interface and contribute to its terminal burial by the production of refractory organic P compounds.     

Self-assembly processes in the prebiotic environment

An important question guiding research on the origin of life concerns the environmental conditions where molecular systems with the properties of life first appeared on the early Earth. An appropriate site would require liquid water, a source of organic compounds, a source of energy to drive polymerization reactions and a process by which the compounds were sufficiently concentrated to undergo physical and chemical interactions. One such site is a geothermal setting, in which organic compounds interact with mineral surfaces to promote self-assembly and polymerization reactions. Here, we report an initial study of two geothermal sites where mixtures of representative organic solutes (amino acids, nucleobases, a fatty acid and glycerol) and phosphate were mixed with high-temperature water in clay-lined pools. Most of the added organics and phosphate were removed from solution with half-times measured in minutes to a few hours. Analysis of the clay, primarily smectite and kaolin, showed that the organics were adsorbed to the mineral surfaces at the acidic pH of the pools, but could subsequently be released in basic solutions. These results help to constrain the range of possible environments for the origin of life. A site conducive to self-assembly of organic solutes would be an aqueous environment relatively low in ionic solutes, at an intermediate temperature range and neutral pH ranges, in which cyclic concentration of the solutes can occur by transient dry intervals.