Reactions Of Organic Molecules Research Articles

Redox conditions influence the chemical composition of iron-associated organic carbon in boreal lake sediments: A synchrotron-based NEXAFS study

The global carbon and iron cycles are intimately linked as redox-sensitive iron oxides readily bind organic carbon in a variety of environmental settings, including marine and lacustrine sediments. While these iron-organic carbon complexes sequester vast quantities of organic carbon, the composition of the organic matter within them remains unknown for lacustrine environments. Here we present C K1s and Fe L3,2 edge Near Edge X-ray Absorption Fine Structure (NEXAFS) spectra of surface sediments and authigenic iron complexes from adjacent basins of a pristine boreal lake located in Québec, Canada, with contrasting oxygen exposure regimes. We demonstrate differences in organic carbon speciation in sediments from both basins, as well as co-localization of organic carbon and iron on a sub-micron scale in 100 nm thick samples. Differences in redox cycling across these two basins allow for a direct comparison of the effect of oscillating redox conditions on the composition of organic carbon sequestered by iron. Our results suggest that reactive organic molecules, which may be polysaccharides, were found preferentially associated with iron in the perennially oxic sediments compared to more phenol rich organics in the seasonally anoxic sediments, highlighting the importance of iron oxides in the protection and preservation of labile organic compounds. Traces of aliphatic carbon were observed in sediments from the anoxic basin, alongside carboxyl and aromatic functionalities. This carboxyl-rich aliphatic material could possibly interact with the sediment mineral matrix either through a ligand exchange mechanism between the mineral phases and the carboxyl functionalities, or via non-specific hydrophobic interactions involving the aliphatic moieties. Finally, our work also shows that OC:Fe ratios should be used with caution when inferring a binding mechanism between OC and iron oxides.

Modeling of tubular membrane contactors for ozonation of water reveals reduced bromate formation with static mixers

Bromate formation and insufficient micropollutant degradation are two major problems in wastewater ozonation. The conventional process using bubble columns has the drawback of an inhomogeneous ozone distribution, causing increased bromate formation. Membrane contactors are a promising alternative as they can dissolve ozone bubble-free. This work presents a simulation of a tubular membrane contactor in COMSOL Multiphysics that includes flow, mass transfer, ozone decay, and reactions of organic molecules and bromide with ozone and hydroxyl radicals. Gaseous ozone and water flow on the lumen and shell side of the membrane, respectively. Static mixers are placed in the water channel, coaxial between the membrane and housing. The simulations show a 75% increase in ozone flux through the membrane, a homogenized ozone distribution, and 13 times higher degradation of a medium-oxidizable micropollutant in the presence of additional static mixers. Furthermore, static mixers enable the use of a lower gaseous ozone concentration, resulting in 31% lower bromate formation at the same ozone exposure without affecting micropollutant degradation. Overall, we demonstrate that membrane contactors with static mixers can be used as a strategy to reduce bromate formation.

Production and Reactions of Organic Molecules in Clouds of Venus

Production and Reactions of Organic Molecules in Clouds of Venus

Influence of hydrothermal asteroidal conditions on the molecular structure and isotopic compositions of polycyclic aromatic hydrocarbons

A variety of polycyclic aromatic hydrocarbons (PAHs) are reported in carbonaceous chondrites (CCs) and in the interstellar medium (ISM). Although PAHs in CCs are not as large as those detected in the ISM, their carbon isotope composition is interpreted as pinpointing an interstellar origin. In contrast, their hydrogen isotope composition can be related to the extent of secondary processes, as is the proportion of alkylated PAHs within CCs. Here, we experimentally investigate the molecular and isotopic evolution of PAHs under simulated asteroidal hydrothermal conditions at 150 °C. Results show that PAHs are chemically stable under these conditions whatever their size, i.e. no destruction, conjugation nor alkylation occurs, even in the presence of other reactive organic molecules. Plus, PAHs retain their carbon isotope compositions even in the presence of another carbon-rich reservoir, either organic or inorganic. On the other hand, their hydrogen isotope composition is modified through exchange with water. Of note, as shown by additional experiments, the presence of smectites, abundant in CCs, impacts the relative abundances of extractable PAHs, saponite trapping more efficiently the larger PAHs. Altogether, results of the present experiments show that PAHs of CCs can be used as tracers of both pre-accretion and secondary processes.

Preparation of Contiguous Bisaziridines for Regioselective Ring-Opening Reactions.

Aziridines, a class of reactive organic molecules containing a three-membered ring, are important synthons for the synthesis of a large variety of functionalized nitrogen-containing target compounds through the regiocontrolled ring-opening of C-substituted aziridines. Despite the tremendous progress in aziridine synthesis over the past decade, accessing contiguous bisaziridines efficiently remains difficult. Therefore, we were interested in synthesizing contiguous bisaziridines bearing an electronically diverse set of N-substituents beyond the single aziridine backbone for regioselective ring-opening reactions with diverse nucleophiles. In this study, chiral contiguous bisaziridines were prepared by organocatalytic asymmetric aziridination of chiral (E)-3-((S)-1-((R)-1-phenylethyl)aziridin-2-yl)acrylaldehyde with N-Ts-O-tosyl or N-Boc-O-tosyl hydroxylamine as the nitrogen source in the presence of (2S)-[diphenyl(trimethylsilyloxy)methyl]pyrrolidine as a chiral organocatalyst. Also demonstrated here are representative examples of regioselective ring-opening reactions of contiguous bisaziridines with a variety of nucleophiles such as sulfur, nitrogen, carbon, and oxygen, and the application of contiguous bisaziridines to the synthesis of multi-substituted chiral pyrrolidines by Pd-catalyzed hydrogenation.

Metal-free one-pot oxidative conversion: Molecular Iodine Mediated Oxidation Organic Reactions

Various oxidative compounds such as aldehyde, ketone ester, and acids can be produced in large yields by an effective iodine-mediated oxidative reaction of organic molecules. Molecular iodine is a generally available and commercially extremely inexpensive substance that induces oxidative esterification. With the comparison with different Brønsted acid catalysis, molecular iodine or iodophilic activations proceed the reaction onto a deoxygenation pathway. With only a few mol% of I2, the oxidation occurs very quickly at room temperature. This approach could also be used to transport different benzil derivatives from nonactivated alkynes, such as diaryl acetylenes. Molecular iodine with several mild reagents such as aq. NH3, ∼30% aq. H2O2 and DMSO might be used to convert various one degree alcohols, particularly benzylic alcohols, into the corresponding aromatic amides in suffiently high yields in a one-pot method. Similarly, by treating different benzylic chloride, bromide and iodide with a molecular iodine oxidation medium, the corresponding aromatic amides may be prepared in a one-pot method. The reactions in this section include transformation of several compounds into their respective oxidative products with the metal-free one-pot oxidative.

Using Physical Organic Chemistry Knowledge to Predict Unusual Metabolites of Synthetic Phenolic Antioxidants by Cytochrome P450.

Biotransformation, especially by human CYP450 enzymes, plays a crucial role in regulating the toxicity of organic compounds in organisms, but is poorly understood for most emerging pollutants, as their numerous "unusual" biotransformation reactions cannot retrieve examples from the textbooks. Therefore, in order to predict the unknown metabolites with altering toxicological profiles, there is a realistic need to develop efficient methods to reveal the "unusual" metabolic mechanism of emerging pollutants. Combining experimental work with computational predictions has been widely accepted as an effective approach in studying complex metabolic reactions; however, the full quantum chemical computations may not be easily accessible for most environmentalists. Alternatively, this work practiced using the concepts from physical organic chemistry for studying the interrelationships between structure and reactivity of organic molecules, to reveal the "unusual" metabolic mechanism of synthetic phenolic antioxidants catalyzed by CYP450, for which the simple pencil-and-paper and property-computation methods based on physical organic chemistry were performed. The phenol-coupling product of butylated hydroxyanisole (BHA) (based on spin aromatic delocalization) and ipso-addition quinol metabolite of butylated hydroxytoluene (BHT) (based on hyperconjugative effect) were predicted as two "unusual" metabolites, which were further confirmed by our in vitro analysis. We hope this easily handled approach will promote environmentalists to attach importance to physical organic chemistry, with an eye to being able to use the knowledge gained to efficiently predict the fates of substantial unknown synthesized organic compounds in the future.

Iron‐Silicate Chemical Garden Morphology and Silicate Reactivity with Alpha‐Keto Acids

AbstractChemical gardens, which are self‐organizing, abiotic, inorganic precipitates in far‐from‐equilibrium systems, are of interest for prebiotic chemistry/origin of life research and, under certain reaction systems, can be considered hydrothermal vent analogs. While the presence of different additives to chemical gardens, including phosphate and amino acids, have been explored, the reactivity of organic molecules in chemical garden systems is not well understood. Here we explored the reactivity of two metabolically important alpha‐keto acids (pyruvic acid and glyoxylic acid) and ammonia in the presence of iron‐silicate chemical gardens. While reactivity was not observed in the case of pyruvic acid, we found that glyoxylic acid formed alpha‐hydroxy acids and amino acids. We found that the observed organic reactivity can be attributed to the silicate in the exterior solution as opposed to the solid iron‐containing chemical garden structure. These results have implications for the reactivity of hydrothermal vent chimneys and their surrounding environments in iron‐ and silica‐rich systems.

Humic substances as electron acceptors for anaerobic oxidation of methane driven by ANME-2d

Humic substances (humics) are ubiquitous in terrestrial and aquatic environments where they can serve as electron acceptors for anaerobic oxidation of organic compounds. Methane is a powerful greenhouse gas, as well as the least reactive organic molecule. Anaerobic oxidation of methane (AOM) coupled to microbial reduction of various electron acceptors plays a crucial role in mitigating methane emissions. Here, we reported that humics could serve as terminal electron acceptors for AOM using enriched nitrate-reducing AOM microorganisms. AOM coupled to the reduction of humics was demonstrated based on the production of 13C-labelled carbon dioxide, and AOM activity was evaluated with different methane partial pressures and electron acceptor concentrations. After three-cycle reduction, both AOM activity and copy numbers of the archaea 16S rRNA and mcrA genes were the highest when anthraquinone-2,6-disulfonic acid and anthraquinone-2-sulfonic acid were electron acceptors. The high-throughput sequencing results suggested that ANME-2d were the dominant methane oxidation archaea after humics reduction, although the partner bacteria NC10 trended downward, other reported humics reduction bacteria (Geobactor and Anammox) appeared. The potential electron transfer models from ANME-2d to humics were proposed. These results enable a better understanding of available electron acceptors for AOM in natural environments and broaden our insight into the significant role of ANME-2d.

Biochar efficiency in copper removal from Haplic soils

The main aim of the study was to examine the biochar efficiency in copper (Cu) ion removal from Haplic (Luvisol, Podzol) soils. In other words, the most effective biochar dose and the most favorable environment pH value were proposed. The copper removal was carried out based on the adsorption process. The results of kinetics measurements were modeled using Richie equation, whereas the adsorption isotherms using Langmuir–Freundlich and Dubinin–Radushkevich equations. The copper removal is a strongly pH-dependent process which is associated with variability of chemical Cu forms and various reactivities of organic molecules. The Cu adsorption amount was higher on silty Haplic Luvisol than on sandy Haplic Podzol mainly due to higher content of organic carbon, functional groups, clay and silt fractions as well as larger surface area. Moreover, the biochar addition increased linearly the soil surface charge and contributed to higher copper adsorption in the whole range of investigated ion concentrations. The higher the biochar dose added, the more Cu ions were adsorbed.

The Mechanism of Adsorption, Diffusion, and Photocatalytic Reaction of Organic Molecules on TiO2 Revealed by Means of On-Site Scanning Tunneling Microscopy Observations

The interaction of organic molecules and titanium dioxide (TiO2) plays a crucial role in many industry-oriented applications and an understanding of its mechanism can be helpful for the improvement of catalytic efficiency of TiO2. Scanning tunneling microscopy (STM) has been proved to be a powerful tool in characterizing reaction pathways due to its ability in providing on-site images during the catalytic process. Over the past two decades, many research interests have been focused on the elementary reaction steps, such as adsorption, diffusion, and photocatalytic reaction, occurring between organic molecules and model TiO2 surfaces. This review collects the recent studies where STM was utilized to study the interaction of TiO2 with three classes of representative organic molecules, i.e., alcohols, carboxylic acids, and aromatic compounds. STM can provide direct evidence for the adsorption configuration, diffusion route, and photocatalytic pathway. In addition, the combination of STM with other techniques, including photoemission spectroscopy (PES), temperature programmed desorption (TPD), and density functional theory (DFT), have been discussed for more insights related to organic molecules-TiO2 interaction.

Porous Organic Polymers for CO2 Storage and Conversion Reactions

AbstractTo overcome the challenges of global warming and environmental pollution it is mandatory to reduce the concentration of atmospheric carbon dioxide (CO2), which is largely accumulated in air through the combustion of fossil fuels. Thus, sequestration of CO2 through physisorption on solid adsorbents and their successful conversion into value added fine chemicals are the major priority areas of research today. Innovation of efficient solid CO2‐philic adsorbents together with their high mechanical/chemical stability and regeneration efficiency are the most challenging objectives to achieve this goal. In this context, porous organic polymers (POPs) owing to their high specific surface area, chemical stability, nanoscale porosity and structural diversity have huge potential to play as selective CO2 adsorbent. POPs synthesized through large varieties of reactive monomers via simple and convenient chemical routes can be the ideal adsorbents for the CO2 storage and fixation reactions. A wide range of POPs can be synthesized from different multidentate amines, aldehydes, carboxylic acids or triazine monomers through the polycondensation reactions or solid state condensation reactions. Ease of synthesis, uniform pore width together with high surface area and surface basic sites (nitrogen and other heteroelements) play crucial role in the CO2 absorption and conversion reactions. This review provides a concise account in designing POPs and their application in CO2 adsorption and fixation into reactive organic molecules for the synthesis of fuels and value added fine chemicals.

Hyperconjugation

This review outlines the role of hyperconjugative interactions in the structure and reactivity of organic molecules. After defining the common hyperconjugative patterns, we discuss the main factors controlling the magnitude of hyperconjugative effects, including orbital symmetry, energy gap, electronegativity, and polarizability. The danger of underestimating the contribution of hyperconjugative interactions are illustrated by a number of spectroscopic, conformational, and structural effects. The stereoelectronic nature of hyperconjugation offers useful ways for control of molecular stability and reactivity. New manifestations of hyperconjugative effects continue to be uncovered by theory and experiments.This article is categorized under:Structure and Mechanism > Molecular StructuresSoftware > Molecular ModelingStructure and Mechanism > Reaction Mechanisms and Catalysis

Materials with Nanoscale Porosity: Energy and Environmental Applications.

In this personal account, several key inventions on designing novel microporous and mesoporous materials, and their applications in energy and environmental research are reviewed. Although, crystalline materials with sub-nanometer pore size regime like zeolites, AlPOs, MOFs, ZIFs etc. are known over the years, silicious and non-silicious mesoporous materials have revolutionized the research on the materials with nanoscale porosity in last two and half decades. A wide range of inorganic, organic-inorganic hybrid as well as purely organic mesoporous materials with either periodic or disordered mesopores are known. Apart from conventional hydrothermal syntheses involving soft templating route, hard templating, evaporation induced self-assembly (EISA), electrochemical or solvothermal (using hydrophilic solvents) synthetic routes are often employed in designing a large spectrum of mesoporous materials. Ease of synthesis using available cheap raw chemicals and versatility in the framework compositions together with the unique surface properties like exceptionally high surface area, pore volume and tunability in pore dimensions have made these materials very exciting to a wide range of researchers working on materials chemistry. Nanoscale porosity in the semiconductor nanomaterials is highly beneficial for the photocatalytic, optoelectronic and related light-harvesting applications. Their high chemical stability has been explored intensively in designing novel heterogeneous catalysts for the synthesis of biofuels from biomass or CO2 fixation to reactive organic molecules for the synthesis of fine chemicals and fuels, which has a large impact on energy and environmental research for the years to come. Diversity in mesoporous frameworks and their potential applications related to light harvesting, generation of renewable energy and synthesis of value added fine chemicals and fuels through environment friendly routes are mostly focused in this review.

Supported Porous Nanomaterials as Efficient Heterogeneous Catalysts for CO2 Fixation Reactions.

CO2 is a major greenhouse gas responsible for global warming and can act as an abundant and inexpensive C1 source for enhancing the chain length/functionalization of a wide range of reactive organic molecules. It is moderately reactive, nontoxic and renewable. Thus, CO2 fixation reactions are important to meet the global challenges, that is, to mitigate the concentration of CO2 in the atmosphere through its fruitful utilization, which is of great interest from economic and environmental perspectives. Various metallic nanoparticles as well as metal oxides can be supported over high surface area porous materials and the resulting nanomaterial can act as heterogeneous and reusable solid catalyst for CO2 fixation reactions for the synthesis of a large number of fuels, natural products agrochemicals, and pharmaceutical compounds. Here we present an overview of the recent progress as well as promising future of metal/metal oxide nanoparticles supported over porous nanomaterials as heterogeneous catalysts for a wide spectrum of these CO2 fixation reactions.

Spin polarization and magnetic characteristics at C6H6/Co2MnSi(001) spinterface.

Organic materials with mechanical flexibility, low cost, chemical engineering, and long spin lifetime attract considerable attention for building spintronic devices. Here, a C6H6/Co2MnSi(001) spinterface is investigated by first-principles calculations and spin-polarized scanning tunneling microscopy simulations. Several high symmetry adsorption sites are discussed, together with two possible surface terminations of Co2MnSi(001). An inversion of the spin polarization is induced near EF even in the case of an external electric field, indicating that C6H6 can act as a spin filter to exploit the spin injection efficiency in organic spintronic devices. Unlike previous studies on molecule/ferromagnet interfaces, this inversion is closely related to the electronic structure of the atoms in the subsurface layer of Co2MnSi according to the orbital symmetry analysis. Furthermore, the magnetic moment and magnetic anisotropic energy (MAE) in the outermost Co2MnSi layer are studied. Particularly, in the most stable configuration, the sign of MAE is inversed due to hybridization between C p and Co dz2 orbitals, which suggests that a greater modification on MAE can be achieved by the use of a highly chemically reactive organic molecule. These findings improve the study on the engineering of magnetic properties at molecule/ferromagnetic interfaces through a single π-conjugated organic molecule.

Radiolysis of the Glycolaldehyde-Na+Montmor- illonite and Glycolaldehyde-Fe3+Montmorillonite Systems in Aqueous Suspension under Gamma Radiation Fields: Implications in Chemical Evolution

The stability and reactivity of organic molecules with biological and pre-biological significance in primitive conditions are of paramount importance in chemical evolution studies. Sugars are an essential component in biological systems for the different roles that they play in living beings. The objective of the present work is to study the gamma radiolysis of aqueous solutions of glycolaldehyde, the simplest sugar and aqueous suspensions of glycolaldehyde-Na+-montmorillonite and glycolaldehyde-Fe3+Montmorillonite. Our results indicate that the radiolysis of the aqueous solutions of glycolaldehyde (0.03M), oxygen free, mainly produce the linear dimer known as eritriol (122 g/mol) and a sugar-like compound with six carbon atoms (180 g/mol). The experiments with the clay suspensions show that clays can adsorb glycolaldehyde and protect it from gamma irradiation. Additionally, it was observed that depending on the cation present in the clay, the percentage and the product (monomer or cyclic dimer) adsorption was different. In the case of Fe3+ Montmorillonite, this clay catalyzed the decomposition of glycolaldehyde, forming small amounts non-identified products. The analysis of these systems was performed by ATR-FTIR, UV spectroscopy, liquid chromatography (UHPLC-UV), and HPLC coupled to a mass spectrometry.

Stability of Flow Battery Organic and Organometallic Reactant Molecules

Flow batteries for grid scale energy storage have been proposed as a technological solution to the intermittency of renewable energy sources. Aqueous-soluble organic reactant molecules composed of earth abundant elements, such as quinones, show promise for reducing system cost. In addition to low cost, sufficient capacity retention is also a prerequisite for the practical success of any flow battery chemistry. For inorganic systems, capacity retention is often determined by crossover of reactant species, whereas organic reactant crossover is typically lower due to a larger molecular size. Instead of crossover, reactant molecule stability can become the limiting factor for organic flow battery lifetime. In an operating battery, the lifetime of the reactant molecules depends on their chemical stability within the electrolyte as well as on their electrochemical stability during reduction and oxidation. We report here some of the results pertaining to the chemical and electrochemical stability of several organic and organometallic redox reactants in aqueous electrolytes. Chemical stability of molecules is monitored by detection of potential decomposition products by NMR spectroscopy during long duration storage at room temperature and at 60 °C. Electrochemical stability is determined by monitoring oxidation and reduction peak currents during standard three-electrode cyclic voltammetry in addition to capacity measurements in a custom designed two-electrode cell.

Site-Specific Reactivity of Ethylene at Distorted Dangling-Bond Configurations on Si(001).

Differences in adsorption and reaction energetics for ethylene on Si(001) are reported with respect to distorted dangling-bond configurations induced by hydrogen precoverage, as obtained by DFT calculations. This can help to understand the influence of surface defects and precoverage on the reactivity of organic molecules on semiconductor surfaces in general. The results show that the reactivity of surface dimers fully enclosed by hydrogen-covered atoms is essentially unchanged compared to the clean surface. This is confirmed by scanning tunneling microscopy measurements. On the contrary, adsorption sites with partially covered surface dimers show a drastic increase in reactivity. This is due to a lowering of the reaction barrier by more than 50 % relative to the clean surface, which is in line with previous experiments. Adsorption on dimers enclosed by molecule (ethylene)-covered surface atoms is reported to have a strongly decreased reactivity, as a result of destabilization of the intermediate state due to steric repulsion; this is quantified through periodic energy decomposition analysis. Furthermore, an approach for the calculation of Gibbs energies of adsorption based on statistical thermodynamics considerations is applied to the system. The results show that the loss in molecular entropy leads to a significant destabilization of adsorption states.

External electric field control: driving the reactivity of metal-free azide-alkyne click reactions.

Recent reports have suggested that an external electric field (EEF) can assist and even control product selectivity. In this work, we have shown that the barrier for the Huisgen reaction between alkyl (aryl) azide and cyclooctyne(biflurocyclooctyne) is reduced by ∼3-4 kcal mol-1 when an oriented EEF is applied along the reaction axis. As a consequence of their inherently polar transition-states (TSs), a parallel orientation of the EEF results in enhancement of the charge transfer (CT) between the fragments and concomitant increase in the dipole moment along the reaction axes. This leads to an increase in the reaction rate for moderate EEFs in the range of 0.3-0.5 V Å-1. Since highly polar and directional environments are omnipresent in biological environments, metal-free click reactions can be further accelerated for non-invasive imaging of live-cells. Conceptually, electric field control appears to be a novel tool (catalyst) to drive, and possibly even tune, the reactivity of organic molecules.