C2 Carbon Research Articles

3,4-Dihalo-5-hydroxy-2(5H)-furanones: Highly Reactive Small Molecules.

3,4-Dichloro-5-hydroxy-2(5H)-furanone and its dibromo analog are highly reactive molecules. Both are members of the 2(5H)-furanone family, which are important as pharmacophores present in drugs and natural products. Compounds possessing the 2(5H)-furanone skeleton isolated from plants and marine organisms exhibit bioactivity against various microorganisms and viruses and can also be used in other medical treatments. The structures of these 3,4-dihalo-2(5H)-furanones cause their high reactivity due to the presence of a carbonyl group on the C2 carbon conjugated with a double bond and a hydroxyl group on the C5 carbon. Two labile halogen atoms on carbons 3 and 4 offer additional possibilities for the introduction of other substituents. These structural features make 3,4-dihalo-5-hydroxy-2(5H)-furanones versatile reactants in chemical synthesis. In this review, we present methods of 3,4-dihalo-5-hydroxy-2(5H)-furanone synthesis, their applications as substrates in various chemical transformations, and examples of their biologically active derivatives.

Iron (II) catalyzed cyclization of ketoxime acetates with triethyl orthoformate: An easy access to symmetrical pyridines

A simple and efficient iron (II) catalyzed approach to the synthesis of symmetrical pyridines has been demonstrated using ketoxime acetates and triethyl orthoformate in DMF at 120 °C under nitrogen environment. In this strategy, significantly, triethyl orthoformate functions as C1 carbon source and which is noteworthy. Other benefits of this process include good yields, high functional group tolerance, low cost of catalyst and avoiding of use of hazardous chemicals.

Catalytic Behavior of NHC–Silver Complexes in the Carboxylation of Terminal Alkynes with CO2

A number of N-heterocyclic carbene–silver compounds (NHCs)AgX were tested in the direct carboxylation of terminal alkynes using carbon dioxide as the C1 carbon feedstock. The reactions proceed at a pressure of 1 atm of CO2 at room temperature, in the presence of Cs2CO3, and using silver–NHC complexes as catalysts. Thus, phenylacetylene and several alkynes are converted to the corresponding propiolic acids in good to high conversions. The activity of the catalysts is strongly influenced by the substituents on the NHC backbone and the nature of the counterion. Specifically, the most active compound exhibits iodide as the counterion and is stabilized by a benzimidazole derivative. After 24 h of reaction, a quantitative conversion is obtained utilizing DMF as the solvent and phenylacetylene as the substrate.

Dynamic nuclear polarization solid-state NMR spectroscopy as a tool to rapidly determine degree of modification in dialcohol cellulose

AbstractDialcohol cellulose can be prepared by periodate-mediated oxidation of cellulose followed by reduction with borohydride. The two-step reaction creates a modified cellulose polymer which is ring-opened between the C2 and C3 carbons in the glucose unit. This material has attracted both scientific and commercial interest, due to its potential role in the transition towards a fossil-fuel-free society. In order to become a reliable component in the materials of tomorrow, chemical properties such as degree of modification must be accurately quantified. In this work we describe how solid-state NMR spectroscopy, enhanced by dynamic nuclear polarization (DNP), can be used for this purpose. Our results illustrate that it is possible to obtain high sensitivity enhancements in dialcohol cellulose with the DNP enhanced solid-state NMR technique. Enhancements above a factor of fifty, on a 400 MHz/263 GHz DNP system in the presence of 12 mM AMUPol radical were achieved. This allows us to quantify the degree of modification in dialcohol cellulose samples in time spans as short as 20 min using DNP enhanced multiple-contact cross polarization experiments. We also exemplify how DNP enhanced, 13C-13C dipolar recoupling experiments can be used for the same purpose and for studying chemical shift correlations in dialcohol cellulose. Graphical abstract

Xerogel synthesis from carbon materials and glue inspired by Japanese-solid-calligraphy ink

Abstract Japanese-solid-calligraphy ink is a xerogel made by mixing soot and glue followed by molding and drying. Herein, we prepare xerogels from glue and 1 or 2 carbon materials (fullerene C60, multiwalled and single-walled carbon nanotubes, nanodiamonds, graphite, graphene, and carbon nanohorns) and characterize their surface morphology, indentation hardness, surface resistivity, and other physical properties. Our ecofriendly and simple synthesis does not require special equipment and affords xerogels holding promise as electrode materials.

Hydrogen peroxide mediated thermo-catalytic conversion of carbon dioxide to C1-C2 products over Cu (0)

The global challenge concerning CO2 conversion to valuable products is anticipated to execute an essential task towards net zero carbon emissions. Thermal CO2 reduction is advantageous in terms of higher conversion rates, selectivity, and already-established industrial thermal instruments for scalability. However, the method is energy-intensive, a hindrance to sustainably practical adoption. Herein, we present a comprehensive study of H2O2-mediated thermal CO2 conversion in the presence of dendritic zerovalent copper (d-ZCu) in a batch-type reactor, yielding C1 and C2 carbon products, with acetic acid (AcOH) as the major product (achieving an optimized yield of approximately 0.98 M and a selectivity of around 97 % at near ambient conditions of 25–150 °C and 1–15 bar), along with trace amounts of methanol and ethanol, and carbon monoxide (CO) as a gaseous product. The reaction parameters, including temperature, time, pressure, and concentrations, were optimized to gain better insight into the reaction. To further explore the feasibility of the process, experiments were conducted in a continuous flow-packed bed reactor using similar parameters as those in the batch reactor, where CO was identified as the primary product of CO2 reduction. For advanced real-life applicability, the as-emitted exhaust gases from diesel and petrol engines, as sources of anthropogenic CO2, were utilized to establish the practical applicability of the proposed method.

Metabolomics of related C3 and C4 Flaveria species indicate differences in the operation of photorespiration under fluctuating light.

C3 photosynthesis can be complemented with a C4 carbon concentrating mechanism (CCM) to minimize photorespiratory losses. C4 photosynthesis is often more efficient than C3 under steady-state conditions. However, the C4 CCM depends on inter-cellular metabolite concentration gradients, which must increase following increases in light intensity and could decrease rates of C4 photosynthesis under fluctuating light. Additionally, incomplete flux through photorespiration could prove beneficial to C4 assimilation during light induction of the CCM. Here, we compare metabolic profiles in the closely related C3 Flaveria robusta and C4 Flaveria bidentis during a light transient from low to high light to determine if these non-steady state accumulation patterns provide insight to the induction of the metabolite gradients needed to drive C4 intermediate transport and if there is incomplete cycling of photorespiratory intermediates. In these C3 and C4 species, metabolite steady-state pool sizes suggest that C4 transport acids maintain concentration gradients across the bundle sheath and mesophyll cell types under these light fluctuations. However, there was incomplete flux through photorespiration in the C4 F. bidentis, which could reduce photorespiratory CO2 loss via glycine decarboxylation and help maintain higher rates of assimilation during following induction periods.

Novel Approach of Tackling Wax Deposition Problems in Pipeline Using Enzymatic Degradation Process: Challenges and Potential Solutions

Anthropogenic activities have led to hydrocarbon spills, and while traditional bioremediation methods are costly and time-consuming, recent research has focused on engineered enzymes for managing pollutant. The potential of enzymes for resolving wax flow problems in the petroleum industry remains unexplored. This paper offers a comprehensive review of the current state of research activities related to the bioremediation of petroleum-polluted sites and the biodegradation of specific petroleum hydrocarbons. The assayed enzymes that took part in the degradation were discussed in detail. Lipase, laccase, alkane hydroxylase, alcohol dehydrogenase, esterase, AlkB homologs and cytochrome P450 monooxygenase are among the enzymes responsible for the degradation of more than 50% of the hydrocarbons in contaminated soil and wastewater and found to be active on carbon C8 to C40. The possible biodegradation mechanism of petroleum hydrocarbons was also elucidated. The enzymes’ primary metabolic pathways include terminal, subterminal, and ω-oxidation. Next, given the successful evidence of the hydrocarbon treatment efficiency, the authors analyzed the opportunity for the enzymatic degradation approach if it were to be applied to a different scenario: managing wax deposition in petroleum-production lines. With properties such as high transformation efficiency and high specificity, enzymes can be utilized for the treatment of viscous heavy oil for transportability, evidenced by the 20 to 99% removal of hydrocarbons. The challenges associated with the new approach are also discussed. The production cost of enzymes, the characteristics of hydrocarbons and the operating conditions of the production line may affect the biocatalysis reaction to some extent. However, the challenges can be overcome by the usage of extremophilic enzymes. The combination of technological advancement and deployment strategies such as the immobilization of a consortium of highly thermophilic and halotolerant enzymes is suggested. Recovering and reusing enzymes offers an excellent strategy to improve the economics of the technology. This paper provides insights into the opportunity for the enzymatic degradation approach to be expanded for wax deposition problems in pipelines.

The effect of plant alkaloid Chelidonin with fullerene C60 carbon nanoparticles on the permeability of hERG potassium channels

The effect of plant alkaloid Chelidonin with fullerene C60 carbon nanoparticles on the permeability of hERG potassium channels

Molecular modelling of luciferyl adenylate deprotonation in the active site of Photinus pyralis luciferase

Firefly bioluminescence is a product of chemical reactions that involve luciferin chromophore oxidation in the active site of luciferase proteins. We perform a series of classical molecular dynamic simulations and combined quantum and molecular mechanics (QM/MM) calculations to expose the molecular mechanism of C4 carbon atom deprotonation in luciferyl adenylate molecule. QM/MM calculations confirm that ND-protonated His245 residue is a suitable proton acceptor in the wild-type Photinus pyralis luciferase. Classical molecular dynamic simulations reveal oxygen-binding cavities inside the protein including the one located close to the C4 atom of luciferin. In mutant forms that lack direct interactions with the His245 side chain, a proton wire comprising water molecules stimulates either protonation of the phosphate group of the luciferyl adenylate forming an unstable intermediate or keto–enol tautomerisation of luciferin. The comparison of the ionisation potentials of molecular systems with the ‘deprotonated’ C4 carbon atom revealed that the ionisation energy for the enol tautomeric form is close to the system with the His245 proton acceptor. Thus, the existence of the keto–enol tautomerisation channel might explain bioluminescence in case of the absence of the amino acid proton acceptor.

QuEChERS-HPLC-MS for the determination of coronatine residues in paddy field environment and five common fruits and vegetables

The residue of coronatine in the paddy field environment, as well as five common fruits and vegetables, was analyzed using the QuEChERS pre-treatment technique combined with HPLC-MS in this experiment. Acetonitrile was used as the extractant, while C18 and multi-walled carbon nanotubes served as adsorbents for sample extraction and purification. Subsequently, the samples were filtered through a 0.2 μm organic filter membrane before detection on the machine. The limits of detection (LOD) and quantification (LOQ) for coronatine in the paddy field environment and five common fruits and vegetables were determined to be 0.0005–0.0035 mg/kg and 0.0018–0.0118 mg/kg, respectively, exhibiting good linear correlation coefficients (R2≥0.9900) at spiked levels ranging from 0.01 to 1 mg/kg. The average intra-day recoveries ranged from 75.19 % to 107.9 %, with relative standard deviations (RSDs) of 1.24 %-12.66 % at spiked levels of 0.05–0.5 mg/kg.

Microbial production of 1, 3-propanediol: a transition of feedstocks from C6 to C3 and C1 carbon sources

1, 3-propanediol (1, 3-PDO) is an important diol with wide applications in the pharmaceutical, food, and cosmetics industries. In addition, 1, 3-PDO serves as a crucial monomer in the synthesis of polytrimethylene terephthalate, an important synthetic fiber material. Microbial conversion of renewable resources such as glucose into 1, 3-PDO has been industrialized due to its environmentally friendly, energy-efficient, safe, and sustainable characteristics. It serves as a successful case in the design and application of microbial cell factories for biochemicals. However, concerns such as food scarcity and climate change are driving the exploration of non-food, low-cost, and sustainable alternatives as biomanufacturing feedstocks. The biosynthesis of 1, 3-PDO from the C3 feedstock glycerol by microorganisms has been well studied. In recent years, increasing attention has been paid to the synthesis of 1, 3-PDO from C1 feedstocks such as methanol, which has higher energy density than glucose and glycerol. Several new artificial biosynthetic pathways have been proposed and validated, laying a foundation for the sustainable bioproduction of 1, 3-PDO. This article reviews the feedstock transition from C6 to C3 and C1 carbon sources for the microbial synthesis of 1, 3-PDO and discusses the strategies for reprogramming metabolic pathway to enhance 1, 3-PDO biosynthesis from different feedstocks. Finally, the development prospects of 1, 3-PDO bioproduction from C1 feedstocks are forecasted.

Molecular Electrochemical Catalysis of CO-to-Formaldehyde Conversion with a Cobalt Complex.

Formox, a highly energy-intensive process, currently serves as the primary source of formaldehyde (HCHO), for which there is a crucial and steadily growing chemical demand. The alternative electrochemical production of HCHO from C1 carbon sources such as CO2 and CO is still in its early stages, with even the few identified cases lacking mechanistic rationalization. In this study, we demonstrate that cobalt phthalocyanine (CoPc) immobilized on multiwalled carbon nanotubes (MW-CNTs) constitutes an excellent electrocatalytic system for producing HCHO with productivity through the direct reduction of CO, the two-electron reduction product of CO2. By carefully adjusting both the pH and the applied potential, we identified conditions that enable the production of HCHO with a partial current density of 0.64 mA cm-2 (17.5% Faradaic efficiency, FE) and a total FE of 61.2% for the liquid products (formaldehyde and methanol). A reduction mechanism is proposed.

Novel Superhard Tetragonal Hybrid sp3/sp2 Carbon Allotropes Cx (x = 5, 6, 7): Crystal Chemistry and Ab Initio Studies

Novel superhard tetragonal carbon allotropes C5, C6, and C7, characterized by the presence of sp3- and sp2-like carbon sites, have been predicted from crystal chemistry and extensively studied by quantum density functional theory (DFT) calculations. All new allotropes were found to be cohesive, with crystal densities and cohesive energies decreasing along the C5-C6-C7 series due to the greater openness of the structures resulting from the presence of C=C ethene and C=C=C propadiene subunits, and they were mechanically stable, with positive sets of elastic constants. The Vickers hardness evaluated by different models qualifies all allotropes as superhard, with Hv values ranging from 90 GPa for C5 to 79 GPa for C7. Phonon band structures confirm that the new allotropes are also dynamically stable. The electronic band structures reveal their metallic-like behavior due to the presence of sp2-hybridized carbon.

Nitrogen form mediates sink strength and resource allocation of a C3 root crop under elevated CO2

Plant physiological processes alter with elevated carbon dioxide concentrations in the atmosphere (eCO2), which affects the growth and yield potential of crops. Among plants with C3 carbon fixation, root crops show highest yield response under eCO2 which is suggested to be linked to their large carbon (C) sink strength. The high C gain under eCO2 can be limited by processes that constrain sink capacity, such as nitrogen (N) supply. Different N sources may interact with eCO2 and thus have variable impacts on carboxylation activity, N uptake efficiency and plant development. This study aims at contributing to a better understanding of sink-driven assimilation, re-allocation and finally growth processes under eCO2 as a function of N-form. Radish (Raphanus sativus L. var. sativus), a C3 tuber plant with strong sink strength, was used. The plants were grown in pots in climate chambers at 400 ppm (aCO2) and 1000 ppm CO2 (eCO2) with either pure nitrate or ammonium-dominated nutrition. A split plot design was applied. Plants were harvested after four weeks and physiological, morphological and chemical parameters in leaves and tubers were assessed. The N-form had no effect on N acquisition, but affected C and N partitioning into plant organs differently under eCO2. N assimilation processes of nitrate-fed plants were focussed on leaves being both source and sink, and those of ammonium-fed plants on tubers, the strongly pronounced sink. Acclimation of CO2 fixation due to eCO2 did not occur for both N forms, probably due to altered sink strength and low N content in leaves. The N-form influences the sink-driven C and N balance and thus enables unrestricted carbon gain as well as the variation of organ development under future eCO2 conditions. These processes can be utilized in cultivation and breeding.

Deuteration of non-labile protium in starch: Biosynthesis and characterisation from yeast-derived starch granules

Deuterium labelling of the non-labile protium atoms in starch granules has been achieved for the first time, by growing genetically modified yeast on deuterated media. Mass spectrometry of the glucose monomers from digested starch showed 44 % average deuteration of the non-labile protium when grown on partially deuterated raffinose (with average deuteration 48 %); yielding starch with 26 % average overall deuteration. Non-labile deuteration was also demonstrated using D2O solvent in the culture medium. Solid-state NMR revealed that deuteration was not evenly distributed across the monomer, being highest at the C6 carbon and lowest at the C1 carbon. SANS revealed two structural features at q = 0.05 Å−1 and 0.4 Å−1, the first corresponding to a lamellar repeat of approximately 12–13 nm while the latter is consistent with B-type crystalline polymer packing. Furthermore, solvent contrast variation SANS analysis yielded a contrast match point of 66 mol% D2O indicative of approximately 30–35 % average deuteration of the bulk granules, consistent with mass spectroscopy. When coupled with the more traditional process of exchange of labile protium in the hydroxyl groups by D2O solvent exchange, the biosynthesis of highly deuterated starch opens new opportunities for neutron scattering experiments involving multicomponent starch-based systems.

Endogeic earthworms mediate aggregate formation and carbon storage in an Ultisol

The role of soil fauna in the incorporation of carbon into soil aggregates of tropical soils has been understudied. We conducted a field experiment within a secondary forest and a microcosm experiment at the University of Puerto Rico in Mayagüez to test soil aggregate formation and carbon incorporation by earthworm activity. Using 13C natural abundance in vegetation and the difference in δ13C between C3 and C4 plants, carbon sources in the soil were tracked. Maize leaves (C4 carbon isotopic signal) were used to track the carbon incorporation into soil aggregates (C3 carbon isotopic signal). Earthworms and soil samples (Typic Haplohumults) were collected at 0 to 10 cm soil depth. The treatments for microcosms were: (I) soil, (II) soil + C4 leaves, (III) soil + C4 leaves + two earthworms (low density), and (IV) soil + C4 leaves + three earthworms (high density). Aggregate size classes were separated by the wet sieving method. At the study site, we found two earthworm species belonging to epigeic and endogeic ecological categories. Over six months, our field data suggested that endogeic P. corethrurus can reorganize small macroaggregates to form large macroaggregates. The microcosm experiment corroborated that P. corethrurus consumes soil and transfers soil-derived carbon from microaggregates to macroaggregates. The treatment with the highest earthworm density did not show higher carbon incorporation (0.23 g C/kg sand-free aggregates) into the soil compared to low earthworm density (0.25 g C/kg sand-free aggregates). Our results suggest that P. corethrurus prefers consuming soil-derived carbon and can translocate it from microaggregates to macroaggregates by restructuring soil aggregates.

Connecting detailed photosynthetic kinetics to crop growth and yield: a coupled modelling framework

Abstract Photosynthesis and crop growth are inseparable processes that govern plant carbon assimilation and allocation. An accurate model description of these processes can bridge dynamics at the leaf and canopy levels, assisting in identifying potential photosynthetic improvements that can be converted into increased yield. Integrating multiscale biophysical processes and achieving computational effectiveness for seasonal simulations, however, are challenging. Here, we present a fully coupled modelling framework that integrates a metabolic model of C3 photosynthesis (ePhotosynthesis) and a semi-mechanistic crop growth model (BioCro). We replaced the leaf-level Farquhar photosynthesis model in BioCro with the ePhotosynthesis model that mechanistically describes the photosystem electron transport processes and the C3 carbon metabolism including the Calvin–Benson–Bassham cycle and the photorespiratory pathway. The coupled BioCro-ePhotosynthesis model was calibrated to represent a soybean cultivar and developed to be operationally fast for seasonal simulations. As an example of model application, we conducted a global sensitivity analysis of 26 enzymes under an average daytime intercepted radiation of 400 µmol m−2 s−1, identifying 2 enzymes, phosphoglycerate kinase (PGK) and phosphoribulokinase (PRK), which had the largest impact on the leaf-level assimilation. Increasing PGK and PRK by 2-fold was predicted to increase the leaf-level assimilation by 8.3 % and the final seed yield by 6.75 % ± 0.5 % over 4 years of observed field climate data. The coupled BioCro-ePhotosynthesis model provides a seamless and efficient integration between the leaf-level metabolism and the field-level yield over a full growing season. The coupled model could be further applied to investigate non-steady-state photosynthetic processes such as non-photochemical quenching.

The Influence of Clustered DNA Damage Containing Iz/Oz and OXOdG on the Charge Transfer through the Double Helix: A Theoretical Study.

The genome-the source of life and platform of evolution-is continuously exposed to harmful factors, both extra- and intra-cellular. Their activity causes different types of DNA damage, with approximately 80 different types of lesions having been identified so far. In this paper, the influence of a clustered DNA damage site containing imidazolone (Iz) or oxazolone (Oz) and 7,8-dihydro-8-oxo-2'-deoxyguanosine (OXOdG) on the charge transfer through the double helix as well as their electronic properties were investigated. To this end, the structures of oligo-Iz, d[A1Iz2A3OXOG4A5]*d[T5C4T3C2T1], and oligo-Oz, d[A1Oz2A3OXOG4A5]*d[T5C4T3C2T1], were optimized at the M06-2X/6-D95**//M06-2X/sto-3G level of theory in the aqueous phase using the ONIOM methodology; all the discussed energies were obtained at the M06-2X/6-31++G** level of theory. The non-equilibrated and equilibrated solvent-solute interactions were taken into consideration. The following results were found: (A) In all the discussed cases, OXOdG showed a higher predisposition to radical cation formation, and B) the excess electron migration toward Iz and Oz was preferred. However, in the case of oligo-Oz, the electron transfer from Oz2 to complementary C4 was noted during vertical to adiabatic anion relaxation, while for oligo-Iz, it was settled exclusively on the Iz2 moiety. The above was reflected in the charge transfer rate constant, vertical/adiabatic ionization potential, and electron affinity energy values, as well as the charge and spin distribution. It can be postulated that imidazolone moiety formation within the CDL ds-oligo structure and its conversion to oxazolone can significantly influence the charge migration process, depending on the C2 carbon hybridization sp2 or sp3. The above can confuse the single DNA damage recognition and removal processes, cause an increase in mutagenesis, and harm the effectiveness of anticancer therapy.

Domino reactions of chromones with activated carbonyl compounds.

Domino reactions of chromones with activated carbonyl compounds, such as dimethyl acetone-1,3-dicarboxylate and 1,3-diphenylacetone, and with 1,3-bis(silyloxy)-1,3-butadienes, electroneutral equivalents of 1,3-dicarbonyl dianions, allow for a convenient synthesis of a great variety of products. The regioselectivity and course of the reaction depends of the substituent located at carbon C3 of the chromone moiety and also on the type of nucleophile employed.