Bonds In Organic Compounds Research Articles

Improving the generalization error and transparency of regression models to estimate soil organic carbon using soil reflectance data

Despite the success of using soil spectroscopy in studies to predict soil attributes, like soil organic carbon (SOC), recent work has revealed several limitations to this approach: a tendency for model overfitting and a lack of transparency of machine learning (ML) methods. Thus, we aimed to both test the ability to improve the generalizability of the models to predict SOC using a cross-validation (CV) strategy oriented to soil profiles and to test the gain in model interpretability by using the least absolute shrinkage and selection operator (LASSO) regression method instead of the commonly used partial least squares (PLS) method. We used one soil spectral library composed of 127 soil profiles (n = 701), from Northeast Brazil, containing reflectance data from the visible, near, and short-wave infrared (VNIR) and the mid-infrared (MIR) spectral regions. We tuned the ML models to predict SOC via two CV strategies: the standard k-fold CV and the leave-soil-profile-out (LSPO) CV. We found that LSPO CV can produce models with better generalizability, as they lose less accuracy than the ones trained with k-fold CV. We conclude that disregarding the autocorrelation of SOC within the soil profile can produce models that are prone to overfitting. In addition, LASSO used 105 covariables from VNIR and 190 from MIR for a total of 8604 and 13,336 covariables, respectively. Moreover, a few LASSO covariables correlated with SOC and are associated with both electronic transitions and vibrational bonds in organic compounds, so the possibility and ease of identifying spectral bands and their correlation with organic carbon indicate that the LASSO models presented more transparent models than the PLS models.

Experimental Study on the Degradation of Acaricides on the Surface of Kumquat Cuimi by Nonthermal Air Plasma

Nonthermal air plasma, which can be generated by air discharge, contains large amounts of reactive oxygen species (ROS), reactive nitrogen species (RNS) and high-energy particles. The ROS and RNS have strong oxidizing properties, and the high-energy particles can break chemical bonds in organic compounds, a process which can be used to degrade organic matter such as pesticides. In the present study, the effects of nonthermal air plasma on the degradation of several pesticides were investigated. An air plasma processing system was designed and constructed to produce nonthermal air plasma and to degrade five commonly used acaricides, namely, avermectin, bifenazate, spirodiclofen, etoxazole, and lufenuron, during the production of kumquat cuimi. The experimental results showed that nonthermal air plasma could degrade all the acaricides on the surface of the kumquat cuimi effectively. After 20 min of plasma treatment, the residues of avermectin, bifenazate, spirodiclofen, etoxazole and lufenuron on the surface of the kumquat cuimi were reduced by 80.67%, 79.52%, 62.40%, 48.93% and 23.11%, respectively. Further analysis indicated that the primary chemical bonds, hydrophobicity, and the pH value of the plasma-activated water can all affect the efficiency of pesticide degradation.

Photosystem I Inhibition, Protection and Signalling: Knowns and Unknowns.

Photosynthesis is the process that harnesses, converts and stores light energy in the form of chemical energy in bonds of organic compounds. Oxygenic photosynthetic organisms (i.e., plants, algae and cyanobacteria) employ an efficient apparatus to split water and transport electrons to high-energy electron acceptors. The photosynthetic system must be finely balanced between energy harvesting and energy utilisation, in order to limit generation of dangerous compounds that can damage the integrity of cells. Insight into how the photosynthetic components are protected, regulated, damaged, and repaired during changing environmental conditions is crucial for improving photosynthetic efficiency in crop species. Photosystem I (PSI) is an integral component of the photosynthetic system located at the juncture between energy-harnessing and energy consumption through metabolism. Although the main site of photoinhibition is the photosystem II (PSII), PSI is also known to be inactivated by photosynthetic energy imbalance, with slower reactivation compared to PSII; however, several outstanding questions remain about the mechanisms of damage and repair, and about the impact of PSI photoinhibition on signalling and metabolism. In this review, we address the knowns and unknowns about PSI activity, inhibition, protection, and repair in plants. We also discuss the role of PSI in retrograde signalling pathways and highlight putative signals triggered by the functional status of the PSI pool.

Direct Photocatalyzed Hydrogen Atom Transfer (HAT) for Aliphatic C-H Bonds Elaboration.

Direct photocatalyzed hydrogen atom transfer (d-HAT) can be considered a method of choice for the elaboration of aliphatic C–H bonds. In this manifold, a photocatalyst (PCHAT) exploits the energy of a photon to trigger the homolytic cleavage of such bonds in organic compounds. Selective C–H bond elaboration may be achieved by a judicious choice of the hydrogen abstractor (key parameters are the electronic character and the molecular structure), as well as reaction additives. Different are the classes of PCsHAT available, including aromatic ketones, xanthene dyes (Eosin Y), polyoxometalates, uranyl salts, a metal-oxo porphyrin and a tris(amino)cyclopropenium radical dication. The processes (mainly C–C bond formation) are in most cases carried out under mild conditions with the help of visible light. The aim of this review is to offer a comprehensive survey of the synthetic applications of photocatalyzed d-HAT.

Direct Observation of the Microscopic Reverse of the Ubiquitous Concerted Metalation Deprotonation Step in C-H Bond Activation Catalysis.

The ability of carboxylate groups to promote the direct functionalization of C-H bonds in organic compounds is unquestionably one of the most important discoveries in modern chemical synthesis. Extensive computational studies have indicated that this process proceeds through the deprotonation of a metal-coordinated C-H bond by the basic carboxylate, yet experimental validation of these predicted mechanistic pathways is limited and fraught with difficulty, mainly as rapid proton transfer is frequently obscured in ensemble measures in multistep reactions (i.e., a catalytic cycle consisting of several steps). In this paper, we describe a strategy to experimentally observe the microscopic reverse of the key C-H bond activation step underpinning functionalization processes (viz. M-C bond protonation). This has been achieved by utilizing photochemical activation of the thermally robust precursor [Mn(ppy)(CO)4] (ppy = metalated 2-phenylpyridine) in neat acetic acid. Time-resolved infrared spectroscopy on the picosecond-millisecond time scale allows direct observation of the states involved in the proton transfer from the acetic acid to the cyclometalated ligand, providing direct experimental evidence for the computationally predicted reaction pathways. The power of this approach to probe the mechanistic pathways in transition-metal-catalyzed reactions is demonstrated through experiments performed in toluene solution in the presence of PhC2H and HOAc. These allowed for the observation of sequential displacement of the metal-bound solvent by the alkyne, C-C bond formation though insertion in the Mn-C bond, and a slower protonation step by HOAc to generate the product of a Mn(I)-catalyzed C-H bond functionalization reaction.

Recent advance in the C–F bond functionalization of trifluoromethyl-containing compounds

The C–F bond is the strongest single bond in organic compounds.

Relationship Investigation between C(sp2)-X and C(sp3)-X Bond Energies Based on Substituted Benzene and Methane.

The C–X bonds of organic compounds between group X and a saturated or unsaturated carbon atom differ in bond energy. To identify the causes of variation is of great significance in terms of bond nature understanding and bond energy estimation. In this paper, the electronegativity χ[X] of group X was calculated by the “valence electron equalized electronegativity” method. Then, χ[X] and the electronic effect constant of the substituent were taken as variables to establish equations for quantitative correlation between C(sp3)–X and C(sp2)–X for the calculation of C–X bond energies. The aim is make comparison between substituted methane, Me–X, and substituted benzene, Ph–X, as well as that between Me–X and substituted ethylene, C2H3–X. We conducted calculation over 40 compounds that contain different X groups, and the results reveal that the C(sp3)–X and C(sp2)–X bond energies are under the influence of a number of factors. In addition to the covalent properties of C and X atoms and χ[X], the bond energies of C(sp2)–X (i.e., D[C(sp2)–X]) are under the influence of the field/inductive effect (σF[X]) and conjugated effect (σR[X]) of group X, with the former causing a decrease while the latter an increase of D[C(sp2)–X]. Using the acquired quantitative correlation equations and on the basis of a relatively rich set of measured D[Me–X] data, we estimated D[Ph–X] of Ph–X and D[C2H3–X] of C2H3–X, and the estimation accuracy is within experimental uncertainty. Employing the above method, the D[C(sp2)–X] of 33 substituted benzenes, 53 substituted ethenes, and 82 α-substituted naphthalenes was estimated with satisfactory outcomes.

Complete Study of Nature and Importance of Spectral Bands Contained in Infrared Spectra of Leaves of Maize Inbred Lines with Significant Breeding Properties

In this article we used the method of IR spectroscopy to identify bioactive organic compounds and their structural characteristics in the leaves of maize inbred lines ZPPL 186, ZPPL 225 and M1-3-3 Sdms based on a standard study of high intensity high-amplitude spectral bands and based on attempt-study of hypothetically influential low intensity low-amplitude spectral bands. The made assumption was that numerous spectral bands, not analyzed yet, but occurring in different kinetic forms should be systematically analyzed and the dynamics of their formation caused by different oscillations and vibrations of molecular bonds of organic compounds and their functional groups should be proven. Low intensity spectral bands imply unstable state of the biological system (leaf), which is a consequence of the excited state of molecules, radicals, atoms or ions in tissues, cells or biomembranes. Similar transport processes occur when biological systems are rhythmically stimulated, as well as in the case of a complex ion transport across the excited thylakoid membrane. These bands most frequently occurred in the wave number range of 500–1600 cm–1; they appeared in several spots in wave number ranges up to 3000 cm–1. Amines, primary and secondary amides, proteins, amino acids, alkanes, alkenes, aldehydes, ketones, aromatic compounds, carbohydrates, carboxylic acids, ethers, alcohols, sulfides, mono- and polysaccharides were identified in leaves of inbred lines. The analysis of spectral bands showed that the most intensive was the inbred line ZPPL 186, then the ZPPL M1-3-3 Sdms, while the lowest intensity was detected in ZPPL 225. Thus, by overall study it is possible to identify not only organic compounds and their structures in leaves of inbred lines, but also to indicate the possibility of causing an unstable and conformational state in them.

Хиральные комплексы переходных металлов с хелатными азотными лигандами в асимметрическом гидрировании с переносом водорода

The reaction of catalytic hydrogenation involving hydrogen transfer through unsaturated C = C and C = O bonds in organic compounds in the presence of optically active soluble complexes of transition metals with nitrogen-containing multidentate ligands has recently gained increased popularity. This review is aimed at generalising available information on the most effective and promising metal complex catalysts for asymmetric hydrogenation involving hydrogen transfer, which have been proposed in the past 10–15 years. Since the activity and selectivity of catalysts based on transition metal complexes are largely dependent on their composition and structure, the design of ligands, the presence or absence of stereogenic centres, the stability and configuration of the chelating ligand system, the nature of the dentate atoms present therein are extremely important. Researchers worldwide have been largely focused on the synthesis and use such ligands, as optically active diamines and aminoalcohols with sp3 -hybridized dentate atoms. These compositions are not oxidized in the coordination sphere of transition metals compared to phosphine ligands, at the same time as maintaining a high level of stereogenicity. Optically active ligands with sp2 nitrogen atoms containing the C = N azomethine bond and oxazoline fragments have been considered as a separate group. In complexes with transition metals, these ligands exhibit a high stability in the catalytic hydrogenation reaction with hydrogen transfer. The stereoselectivity of catalysts in some cases increases with an increase in the denticity of nitrogen-containing ligands. Among them are N-heterocyclic N, H, C–ligands in the Rh (III) complexes; Ru (II) complexes with tridentate N, N, N–ligands with chiral oxazoline fragments; C, N, N–ruthenium complexes. In this review, we grouped catalysts by ligand denticity (from 2 to 6). Comparative data on the activity of various catalysts and the stereoselectivity of respective reactions is provided. The effect of the structure of chiral ligands on the catalytic characteristics of metal complexes is discussed. The authors declare no conflict of interests regarding the publication of this article.

Effect of Stacking Microbial Fuel Cells on Electricity Generation from Sludge

Microbial fuel cells (MFCs) are bioreactors that convert energy in the chemical bonds of organic compounds into electrical energy through catalytic activity of electrogenic micro-organisms, under anaerobic conditions. In this study, a stacked MFC consisting of 4 single MFCs was assembled using microbial sludge and connected in series. 1.0 V of electricity was generated in each cell and as much as 4.0V of electricity was generated in the four stacked cells. The stacked MFC was used to power a flashlight and a 4.0-volt LED light bulb. The electricity generated decreased with time due to a decrease in microbial activity and increased with increase in the number of stacked cells.

A study to identify S-S and S-S-S bonds in organic compounds by mass spectrometry and ultraviolet and Raman spectroscopy techniques

ABSTRACTIn the present study, after an investigation and study of organic di- and trisulfide characters, a method for the identification of S–S and S–S–S bonds using some common spectroscopy techniques, including ultraviolet (UV) spectroscopy, Raman, mass spectrometry (MS) and thin-layer chromatography (TLC), has been introduced and developed. It is worth mentioning that only the reported literature data and our own results have been used.

Effects of Nonthermal Plasma Technology on Functional Food Components.

Understanding the impact of nonthermal plasma (NTP) technology on key nutritional and functional food components is of paramount importance for the successful adoption of the technology by industry. NTP technology (NTPT) has demonstrated marked antimicrobial efficacies with good retention of important physical, chemical, sensory, and nutritional parameters for an array of food products. This paper presents the influence of NTPT on selected functional food components with a focus on low-molecular-weight bioactive compounds and vitamins. We discuss the mechanisms of bioactive compound alteration by plasma-reactive species and classify their influence on vitamins and their antioxidant capacities. The impact of NTP on specific bioactive compounds depends both on plasma properties and the food matrix. Induced changes are mainly associated with oxidative degradation and cleavage of double bonds in organic compounds. The effects reported to date are mainly time-dependent increases in the concentrations of polyphenols, vitamin C, or increases in antioxidant activity. Also, improvement in the extraction efficiency of polyphenols is observed. The review highlights future research needs regarding the complex mechanisms of interaction with plasma species. NTP is a novel technology that can both negatively and positively affect the functional components in food.

Reduction of α,ω-Dihalohexanes with Electrogenerated Nickel(I) Salen

A recent study has described the electrocatalytic reduction of 1,6-dibromohexane at a silver electrode.1 To mitigate the costs of silver electrodes, glassy carbon electrodes can be used in the presence of a solution-phase catalyst. [[2,2′-[1,2-Ethanediylbis-(nitrilomethylidyne)]bis[phenolato]-N,N′,O,O′]nickel(I), further referred to as nickel(I) salen, has been used as an electrogenerated catalyst in tandem with glassy carbon electrodes due to its ability to reductively cleave carbon—halogen bonds in organic compounds. Previous studies at glassy carbon electrodes with nickel(I) salen or at silver electrodes have primarily focused on reduction of monohalogenated compounds or linear hydrocarbons substituted at both primary positions with mixed halogens. Catalytic reduction of such straight-chain alkyl halides with electrogenerated nickel(I) salen yielded both straight-chain monomeric and dimeric products in high yields.2 In this study, electrogenerated nickel(I) salen was used to reduce 1,6-dibromohexane, 1,6-diiodohexane, and 1-bromo-6-iodohexane catalytically. These substrates were electrolyzed in the presenece of 0.10 M tetramethylammonium tetrafluoroborate (TMABF4) in N,N-dimethylformamide at a glassy carbon electrode. Cyclic voltammetry indicated that direct reduction of 1,6-dibromohexane and 1,6-diiodohexane occurs respectively at –1.64 and –1.56 V vs. a cadmium mercury amalgam reference electrode (Cd(Hg)) with a potential of –0.76 V vs. an aqueous saturated calomel electrode. In contrast, catalytic cathodic peaks are at –0.92 and –0.97 V vs. Cd(Hg) for 1,6-dibromohexane and 1,6-diiodohexane, respectively, indicating that nickel(I) salen does indeed reduce these substrates electrocatalytically. Controlled-potential (bulk) electrolyses of the halogenated substrates led to minor conversion to cyclohexane and halogenated dimers with significant amounts of starting material remaining in solution. This drastic decrease in yield compared to previous studies is hypothesized to be the result of alkylation of the imino bond on the salen ligand.2,3 Though nickel(II) salen can undergo a reversible, one-electron reduction to form nickel(I) salen, reduction of nickel(II) salen can also create a ligand-reduced radical at the imino bond, thus resulting in alkylation of both imino bonds on the salen ligand during electrolysis.3 This dialkylation is responsible for the decreased yield of reaction products and was confirmed with the aid of liquid chromatography—mass spectrometry. A mechanism is proposed with radical intermediates which result in dialkylated nickel(II) salen. Martin, E. T.; Strawsine, L. M.; Mubarak, M. S.; Peters, D. G., Direct Reduction of 1,2- and 1,6-Dibromohexane at Silver Cathodes in Dimethylformamide. Electrochim. Acta 2015, 186, 369–376.Mubarak, M. S.; Peters, D. G., Homogeneous Catalytic Reduction of α,ω-Dihaloalkanes with Electrogenerated Nickel(I) Salen. J. Electroanal. Chem. 1995, 388, 195–198.Martin, E. T.; McGuire, C. M.; Peters, D. G., Catalytic Reduction of Organic Halides by Electrogenerated Nickel(I) Salen. Electrochem. Soc. Interface 2016, 25, 41–45. Figure 1

Mechanism investigation for anoin-assisted nickel catalyzed C–F bond functionalization reaction: a DFT study

C–F bond functionalization still faces with great challenges in synthetic chemistry due to the inert nature of C–F bond in organic compounds. Herein, the newly reported DFT method M11-L was used to determine the mechanism of nickel catalyzed C–F/C–H bond cross coupling involving the C–F bond cleavage of flouroarenes and C–H bond functionalization of oxazoles. DFT calculations revealed that fluoride would stabilize the nickel(0) compound to afford an active nickel(0) ate-complex. With the assistance of fluoride, the oxidative addition of C–F bond to nickel(0) ate-complex would yield an active nickel(II) species, which is the rate-determining step in this catalytic cycle. The following C–H bond cleavage step would proceed via a direct deprotonation step under the attack of Bronsted base, to generate diarylnickel(II) species. Finally, reductive elimination step would occur to give the coupling product with regeneration of active nickel(0) ate-complex. In this pathway, we found that the relative free energies of nickel ate-complex species are more stable than commonly assumed neutral-nickel intermediates. This work could provide a new way for the mechanism study of inert C--F bond activation reactions.

Free Catalyzed Synthesis of 2,2′-Bipyridine via Ozonolysis Technique

ABSTRACTThe ozonation of a triple bond in organic compounds is rare in industry. The reaction is much more complicated to run, because ozone is an electrophilic agent and more likely to bind to the double bond compared to the triple bond in an organic compound. This may be a problem because some fine organic substances are very hard to synthesize and can only be solved by the ozonolysis technique of a triple-bond organic compound. In addition, oxidation by using ozone is also preferred because of the cleanliness and effectiveness of the reaction. A novel method for the synthesis of 2,2ʹ-bipyridine was described, which involves ozonolysis of a 2-ethynylpyridine and is supported by a high-pressure reactor. The reaction proceeds via ozone attack on the acetylenic triple bond, cleavage, and free radical formation. The present study establishes the conditions for selective ozonolysis of 2-ethynylpyridine, leading to 2,2ʹ-bipyridine. The 2,2ʹ-bipyridine was characterized by gas chromatography flame ionization detector (GC-FID) and mass spectroscopy techniques. A novel suggested mechanism was used to explain the oxidation process. Analysis showed that the formation of oxidized product is shown when ozone is supplied in excess, which shows that the reaction between 2-ethynylpyridine and ozone is a first-order reaction, whe reby the result of the relationship only depends on the concentration of the starting material, which is 2-ethynylpyridine acts as the limiting reactant.

A review of design, operational conditions and applications of microbial fuel cells

ABSTRACTThe exploitation of fossil fuels, mainly oil and gas, has increased and is causing a worldwide energy crisis. Because of global environmental concerns and energy uncertainty, sustainable and clean energy resources with minimum or zero use of hydrocarbons are being investigated. Microbial fuel cell (MFC) technology changes the energy stored in chemical bonds in organic compounds to electrical energy through catalytic reactions by microorganisms and may be an alternative fuel for energy generation. It offers an opportunity for the sustainable production of energy from biodegradable, reduced compounds. MFCs have applications as biosensors, wastewater treatment and biohydrogen production. The present review article discusses the microorganisms used for MFCs, and their design, components, effect of operational conditions and applications.

Methylene activation reached new heights

An organic synthesis method that took flight this year could prove to have an unusually wide wingspan. Developed by Jin-Quan Yu and coworkers at Scripps Research Institute California after a 14-year effort, the reaction advances a long-standing goal: activating specific C–H bonds in organic compounds and converting them catalytically and enantioselectively into C–C bonds or other derivatives. Since there’s no shortage of C–H bonds in organic compounds, the technique has lots of potential for widespread applicability. Specifically, the new reaction uses a palladium catalyst and quinoline-based ligand to convert β-methylenes—CH2 groups two carbon atoms away from amides or carboxylic acids—into chiral centers (Science 2016, DOI: 10.1126/science.aaf4434). Synthetic organic chemists had previously developed ways to activate several types of C–H bonds, such as by preinstalling activating groups in substrates. But the ability to target C–H bonds of unactivated methylene groups and then derivatize them catalytica...

Iodine catalysis: A green alternative to transition metals in organic chemistry and technology

Iodine and compounds of iodine in higher oxidation states have emerged as versatile and environmentally benign reagents for organic chemistry. One of the most impressive recent achievements in this area has been the discovery of catalytic activity of iodine in numerous oxidative transformations leading to the formation of new C—O, C—N, and C—C bonds in organic compounds. These catalytic transformations in many cases are very similar to the transition metal-catalyzed reactions, but have the advantage of environmental sustainability and efficient utilization of natural resources. Iodine is an environmentally friendly and a relatively inexpensive element, which is currently underutilized in industrial applications. One of the main goals of this review is presenting to industrial researchers the benefits of using catalytic iodine in chemical technology as an environmentally sustainable alternative to transition metals. The present review summarizes catalytic applications of iodine and compounds of iodine in organic synthesis. The material is organized according to the nature of active catalytic species (hypoiodite, trivalent, or pentavalent hypervalent iodine species) generated in these reactions from appropriate pre-catalysts. Numerous synthetic procedures based on iodine(III) or iodine(V) catalytic species in the presence of hydrogen peroxide, Oxone, peroxyacids or other stoichiometric oxidants are summarized. A detailed discussion of catalytic cycles involving hypervalent iodine, hypoiodites, and other active intermediates is presented.

Iodine catalysis: A green alternative to transition metals in organic chemistry and technology

Abstract Iodine and compounds of iodine in higher oxidation states have emerged as versatile and environmentally benign reagents for organic chemistry. One of the most impressive recent achievements in this area has been the discovery of catalytic activity of iodine in numerous oxidative transformations leading to the formation of new C O, C N, and C C bonds in organic compounds. These catalytic transformations in many cases are very similar to the transition metal-catalyzed reactions, but have the advantage of environmental sustainability and efficient utilization of natural resources. Iodine is an environmentally friendly and a relatively inexpensive element, which is currently underutilized in industrial applications. One of the main goals of this review is presenting to industrial researchers the benefits of using catalytic iodine in chemical technology as an environmentally sustainable alternative to transition metals. The present review summarizes catalytic applications of iodine and compounds of iodine in organic synthesis. The material is organized according to the nature of active catalytic species (hypoiodite, trivalent, or pentavalent hypervalent iodine species) generated in these reactions from appropriate pre-catalysts. Numerous synthetic procedures based on iodine(III) or iodine(V) catalytic species in the presence of hydrogen peroxide, Oxone, peroxyacids or other stoichiometric oxidants are summarized. A detailed discussion of catalytic cycles involving hypervalent iodine, hypoiodites, and other active intermediates is presented.

Chalcogen and pnicogen bonds in complexes of neutral icosahedral and bicapped square-antiprismatic heteroboranes.

A systematic quantum mechanical study of σ-hole (chalcogen, pnicogen, and halogen) bonding in neutral experimentally known closo-heteroboranes is performed. Chalcogens and pnicogens are incorporated in the borane cage, whereas halogens are considered as exo-substituents of dicarbaboranes. The chalcogen and pnicogen atoms in the heteroborane cages have partial positive charge and thus more positive σ-holes. Consequently, these heteroboranes form very strong chalcogen and pnicogen bonds. Halogen atoms in dicarbaboranes also have a highly positive σ-hole, but only in the case of C-bonded halogen atoms. In such cases, the halogen bond of heteroboranes is also strong and comparable to halogen bonds in organic compounds with several electron-withdrawing groups being close to the halogen atom involved in the halogen bond.