Functional Groups In Organic Molecules Research Articles

Bio-organic adenosine with bilateral asymmetric units remodels definitive interfacial for highly reversible Zn anode

Functional groups of organic molecules play their respective advantages in the Zn deposition process, thus bringing significant improvements to the electrochemical performance even at trace additions. In this study, we introduced adenosine (ADS) bio-organic molecules into electrolyte to facilitate the uniform diffusion of Zn2+ and enable the in-situ construction of a zincophilic anode/electrolyte interface by preferential chemisorption of the ADS-amino group on the Zn anode. Automatically, the ADS-hydroxyl group towards the electrolyte bulk will coordinate free water molecules through hydrogen bonding, accelerating the process of Zn2+ extraction from the solvation structure. This interface not only has a strong affinity for promoting Zn2+ dynamic transport and uniform deposition but also acts as a suppressor for side reactions. Consequently, Zn||Zn symmetric cells with a trace amount of ADS additive (5 mM) exhibit an ultra-long lifespan of 3000 h at 2 mA cm−2 and 2 mAh cm−2 and 950 h at a harsh condition of 8.85 mA cm−2 and 8.85 mAh cm−2. A practical rechargeable Zn||NVO pouch cell is assembled, showing a capacity of 140 mAh g−1 and remarkable stability of 96 % retention for 300 cycles at 0.5 A g−1.

Generation and reactivity of the fragment ion [B12I8S(CN)]- in the gas phase and on surfaces.

Gaseous fragment ions generated in mass spectrometers may be employed as "building blocks" for the synthesis of novel molecules on surfaces using ion soft-landing. A fundamental understanding of the reactivity of the fragment ions is required to control bond formation of deposited fragments in surface layers. The fragment ion [B12X11]- (X = halogen) is formed by collision-induced dissociation (CID) from the precursor [B12X12]2- dianion. [B12X11]- is highly reactive and ion soft-landing experiments have shown that this ion binds to the alkyl chains of organic molecules on surfaces. In this work we investigate whether specific modifications of the precursor ion affect the chemical properties of the fragment ions to such an extent that attachment to functional groups of organic molecules on surfaces occurs and binding of alkyl chains is prevented. Therefore, a halogen substituent was replaced by a thiocyanate substituent. CID of the precursor [B12I11(SCN)]2- ion preferentially yields the fragment ion [B12I8S(CN)]-, which shows significantly altered reactivity compared to the fragment ions of [B12I12]2-. [B12I8S(CN)]- has a previously unknown structural element, wherein a sulfur atom bridges three boron atoms. Gas-phase reactions with different neutral reactants (cyclohexane, dimethyl sulfide, and dimethyl amine) accompanied by theoretical studies indicate that [B12I8S(CN)]- binds with higher selectivity to functional groups of organic molecules than fragment ions of [B12I12]2- (e.g., [B12I11]- and [B12I9]-). These findings were further confirmed by ion soft-landing experiments, which showed that [B12I8S(CN)]- ions attacked ester groups of adipates and phthalates, whereas [B12I11]- ions only bound to alkyl chains of the same reagents.

Palladium and copper co-catalyzed chloro-arylation of gem-difluorostyrenes - use of a nitrite additive to suppress β-F elimination.

The installation of fluorine and fluorinated functional groups in organic molecules perturbs the physicochemical properties of those molecules and enables the development of new therapeutics, agrichemicals, biological probes and materials. However, current synthetic methodologies cannot access some fluorinated functional groups and fluorinated scaffolds. One such group, the gem-difluorobenzyl motif, might be convergently synthesized by reacting a nucleophilic aryl precursor and an electrophilic gem-difluoroalkene. Previous attempts have relied on forming unstable anionic or organometallic intermediates that rapidly decompose through a β-F elimination process to deliver monofluorovinyl products. In contrast, we report a fluorine-retentive palladium and copper co-catalyzed chloro-arylation of gem-difluorostyrenes that takes advantage of a nitrite (NO2 -) additive to avoid the favorable β-F elimination pathway that forms monofluorinated products, instead delivering difluorinated products.

Surface Polarity Induced Simultaneous Enhancement of Nanopore Accessibility and Metal Utilization in Metal and Nitrogen Co-Doped Carbon Electrocatalysts for CO2 Reduction

The efficient utilization of active centers for the emerging class of metal (M) and nitrogen (N) co-doped carbon (M–N–C) catalysts remains a research hotspot for electrochemical synthesis such as the reduction reactions of CO2, O2, N2, or functional groups in organic molecules. However, keeping sufficient accessibility to these active centers upon thermal treatment at high temperatures can be challenging due to possible nanopore blocking issues. To tackle this limitation, this work presents a precise surface modulation approach based on a kind of porous carbon support with an ultrapolar surface, over which the unusual enhancement of nanopore accessibility and metal utilization is achieved. The strategy is well applicable to transition metals, precious metals, and rare earth metals. Experimental evidence revealed that the ultrapolar pore walls can be spontaneously wetted by hydrated metal ions. The unprecedented wettability ensured a unique metal-support interaction, which not only warrants the anchoring metal species in a dispersed manner but also induces the development of transport nanopores by dynamical etching of the polar carbon walls during thermal treatment. By this way, this strategy addresses the trade-off issue between metal utilization efficiency and accessibility to the active centers for the M–N–C type catalysts.

Automatic materials characterization from infrared spectra using convolutional neural networks.

Infrared spectroscopy is a ubiquitous technique used to characterize unknown materials in the form of solids, liquids, or gases by identifying the constituent functional groups of molecules through the analysis of obtained spectra. The conventional method of spectral interpretation demands the expertise of a trained spectroscopist as it is tedious and prone to error, particularly for complex molecules which have poor representation in the literature. Herein, we present a novel method for automatically identifying functional groups in molecules given the corresponding infrared spectra, which requires no recourse to database-searching, rule-based, or peak-matching methods. Our model employs convolutional neural networks that are capable of successfully classifying 37 functional groups which have been trained and tested on 50 936 infrared spectra and 30 611 unique molecules. Our approach demonstrates its practical relevance in the autonomous analytical identification of functional groups in organic molecules from infrared spectra.

Drug Molecular Immobilization and Photofunctionalization of Calcium Phosphates for Exploring Theranostic Functions.

Theranostics (bifunction of therapeutics and diagnostics) has attracted increasing attention due to its efficiency that can reduce the physical and financial burden on patients. One of the promising materials for theranostics is calcium phosphate (CP) and it is biocompatible and can be functionalized not only with drug molecules but also with rare earth ions to show photoluminescence that is necessary for the diagnostic purpose. Such the CP-based hybrids are formed in vivo by interacting between functional groups of organic molecules and inorganic ions. It is of great importance to elucidate the interaction of CP with the photofunctional species and the drug molecules to clarify the relationship between the existing state and function. Well-designed photofunctional CPs will contribute to biomedical fields as highly-functional ormultifunctional theranostic materials at the nanoscales. In this review, we describe the hybridization between CPs and heterogeneous species, mainly focusing on europium(III) ion and methylene blue molecule as the representative photofunctional species for theranostics applications.

Ispitivanje strukturnih delova zrna hibrida kukuruza ZP 677 metodom IC ometene totalne refleksije

In this paper, the grain and structural parts of the grain of maize hybrid ZP 677 were studied, using Infrared Spectroscopy - Attenuated Total Reflectance (ATR). The ATR spectra of grain, endosperm, pericarp and germ of maize hybrid are characterized by a number of bands, band intensity, band kinetics and band location distribution in the wavelength range 400 cm-1 to 4000 cm-1. These parameters were specifically tested for both, the grain and the endosperm, pericarp and germ. Spectral bands that are very high and high intensity usually range from 3 to 5, characterized by different intensity, kinetic forms, as well as by the distribution of origin in the wavelength range. These spectral bands enable the identification of the following organic compounds: proteins, carotenoids, ethers, cellulose, lipids, carboxylic acids, amino acids, protein amides, alkanes, sugars, carbohydrates, ketones, alcohols, phenols, aldehydes and amines. Spectral bands of grains, endosperm, pericarp and germs that are low and very low intensity are also characterized by the number of bands, low bandwidth, distribution of the place of origin, and especially by the oscillation frequency of valence bonds of functional groups of organic molecules. Spectral bands that are low and very low intensity enable the identification of organic molecules, compounds and their fragments, as well as the identification of various forms of excited states of molecular structures and excited states of valence bonds of organic molecules. The excited state of molecular structures and the excited state of valence bonds of functional groups of organic molecules are manifested in various forms of oscillatory motion. Examples of functional groups of organic molecules in which all the mentioned excited states of molecular structures and excited states of valence bonds occur are alcohols, amines, alkynes, ketones, alkenes, ester, lipids, carbonyl group (ester), amides, nitrogen-hydrogen group, (NH), primary amines, carboxylic acids, amides, acid chlorides, nitrites, amides, carbonyl group (amide), aliphatic carbon-hydrogen bond and aldehydes.

Reduced defects and enhanced Vbi in perovskite absorbers through synergetic passivating effect using 4-methoxyphenylacetic acid

Surface defect-assisted non-radiative recombination is one of major detrimental factors limiting the development of efficient and stable perovskite solar cells (PSCs). The ionic characteristic of perovskite absorbers facilitates passivation of diverse defects through the interaction of specific ending functional groups of organic molecules. Here, the passivation mechanism of a bifunctional organic molecule, 4-methoxyphenylacetic acid (MPA), on the defects within perovskite absorbers is systematically investigated. Density functional theory and X-ray photoelectric spectroscopy confirm that the keto-oxygen atom of carboxylic acid in the MPA mainly passivates Pb–I antisite through Lewis base-acid interaction, while the O-donor of the methoxy group from MPA heals the undercoordinated Pb2+ on the perovskite absorbers surface via a coordination bond. The synergetic passivation of two functional groups significantly reduces the defect density and thus recombination loss, which is confirmed by the space charge limited current, time-resolved photoluminescence (PL) spectroscopy and PL mapping. The capacitance-voltage measurement proves that MPA treatment enhances the built-in potential to accelerate the separation of photogenerated charges within perovskite absorbers. As a result, MPA-treated PSCs achieve a champion efficiency of 22.32% (relatively to 20.97% of the control) coupled with improved environmental tolerance for PSCs on ITO/glass and 19.34% for PSCs on flexible ITO/polyethylene terephthalate.

Thiol-Ene “Click Reactions” as a Promising Approach to Polymer Materials

This review is devoted to relatively new and promising approach to the synthesis of novel organic compounds and polymer materials, based on the “click chemistry” concept. Several types of the “click reactions” (cycloaddition, nucleophilic ring opening, non-aldol carbonyl chemistry, and addition to multiple carbon-carbon bonds) have been described, and the relevant examples have been provided. The “thiol-ene” reactions based on the addition of thiol to unsaturated functional groups of organic molecules have been mostly considered in this review, including their conditions and mechanisms. Diverse and wide range of applications of the thiol-ene “click chemistry” has been demonstrated, including the preparation of biocompatible materials and materials for culture and encapsulation of cells; the synthesis of block copolymers; the development of degradable materials as well as novel homogeneous and hybrid network structures; chromatography, glycopolymer synthesis, immobilization of proteins, stabilization/functionalization of capsules and multilayer systems, functionalized micro- and nanogels, nanomedicine, and development of antitumor drugs.

Effect of Gelation Temperature on the Molecular Structure and Physicochemical Properties of the Curdlan Matrix: Spectroscopic and Microscopic Analyses.

In order to determine the effect of different gelation temperatures (80 °C and 90 °C) on the structural arrangements in 1,3-β-d-glucan (curdlan) matrices, spectroscopic and microscopic approaches were chosen. Attenuated total reflection Fourier transform infrared spectroscopy (ATR FT-IR) and Raman spectroscopy are well-established techniques that enable the identification of functional groups in organic molecules based on their vibration modes. X-ray photoelectron spectroscopy (XPS) is a quantitative analytical method utilized in the surface study, which provided information about the elemental and chemical composition with high surface sensitivity. Contact angle goniometer was applied to evaluate surface wettability and surface free energy of the matrices. In turn, the surface topography characterization was obtained with the use of atomic force microscopy (AFM) and scanning electron microscopy (SEM). Described techniques may facilitate the optimization, modification, and design of manufacturing processes (such as the temperature of gelation in the case of the studied 1,3-β-d-glucan) of the organic polysaccharide matrices so as to obtain biomaterials with desired characteristics and wide range of biomedical applications, e.g., entrapment of drugs or production of biomaterials for tissue regeneration. This study shows that the 1,3-β-d-glucan polymer sample gelled at 80 °C has a distinctly different structure than the matrix gelled at 90 °C.

Exploiting Fruit Waste Grape Pomace for Silver Nanoparticles Synthesis, Assessing Their Antioxidant, Antidiabetic Potential and Antibacterial Activity Against Human Pathogens: A Novel Approach.

Grape pomace, a most abundant and renewable wine industry waste product was utilized as a suitable reducing, capping, and stabilizing biomolecules for green synthesis of silver nanoparticles (AgNPs). The physicochemical properties of biosynthesized grape pomace extract (GPE)-AgNPs were duly appraised via UV–Visible spectroscopy, X-ray diffractometer (XRD), Fourier-transform infrared spectroscopy (FTIR), and transmission electron microscopy. The analytical studies revealed that the GPE-AgNPs were well formed and stable in nature. The functional groups of organic molecules of GPE are present on the surface of AgNPs with average NPs diameter in the range of 20–35 nm. GPE-AgNPs exhibited significant free radical scavenging activity mainly DPPH radical (IC50, 50.0 ± 2.25 μg/mL) and ABTS radical (IC50, 38.46 ± 1.14 μg/mL). Additionally, the synthesized AgNPs showed noticeable inhibition of carbohydrate hydrolyzing enzymes mainly, α-amylase (IC50, 60.2 ± 2.15 μg/mL) and α-glucosidase (IC50, 62.5 ± 2.75 μg/mL). The GPE fabricated AgNPs showed noteworthy antibacterial potential against infectious bacteria viz., Escherichia coli and Staphylococcus aureus. The reaction mechanism of antibacterial activity was studied by measuring the bacterial cell membrane breakage and cytoplasmic contents, mainly, nucleic acid, proteins, and reducing sugar. Therefore, this research attempt illustrated the potential of GPE as a novel source intended for the biosynthesis of AgNPs that may open up new horizons in the field of nanomedicine.

Experimental methods in chemical engineering: Fourier transform infrared spectroscopy—FTIR

AbstractWhen molecules absorb infrared radiation (IR), their vibrational mode—stretching and bending of the electric dipole—changes to an excited state. Functional groups in organic molecules absorb IR related to their characteristic vibrational modes. A Fourier transform infrared absorption (FTIR) analyzer measures the absorbed IR to identify molecular composition of surfaces, structural and geometric isomers, orientation in polymers and solutions, and quantify impurities. We describe the power of FTIR instruments and their basic operating principles, including the main experimental setups available: transmission, diffuse reflectance (DRIFTS), reflection adsorption infrared spectroscopy (RAIRS), and attenuated total reflection (ATR), including the recent advances related to time‐resolved and operando applications. In catalytic studies, FTIR spectroscopy has demonstrated its versatility over the last several decades to understand reaction mechanisms, measure gas phase composition, and identify active sites. Over 3000 articles include catalysis and FTIR as keywords but 50 000 articles per year mention IR. We generated a bibliometric map of keywords in articles that Web of Science indexed in 2016 and 2017. The map identified four broad clusters of research related to or applying FTIR: nano‐composites, composites, and mechanical properties; nano‐particles, degradation, graphene oxide, and photo‐catalysis; adsorption, aqueous solutions, and waste water; and drug delivery, silver and gold nano‐particles, green synthesis, and antibacterial activity. Together with a synopsis of the principals of IR spectroscopy and a review of the applications, we discuss uncertainties and limitations of the technique.

On the occasion of the 100th anniversary: Ernst Sp\xe4th and his mescaline synthesis of 1919

Characterizing plant ingredients has been the main topic of chemical research at the University of Vienna since the beginning of the last half of the nineteenth century, especially at the IInd Chemical Institute (founded in 1870). The remarkable success in many fields of natural organic product structure elucidation was in part the result of the discovery of important identifying reactions of functional groups in organic molecules by Austrian chemists, e.g., Lieben´s iodoform test, the Herzig–Meyer´s method for the determination of methylamino groups or Zeisel´s method for the determination of methoxy groups in organic compounds. Ernst Späth was the most prominent exponent of the Viennese school of phytochemistry. He and his coworkers identified more than 120 phytochemical substances. His mescaline synthesis of 1919 has marked a milestone in the chemistry of organic natural products.Graphical abstract

Using differential ion mobility spectrometry to perform class-specific ion-molecule reactions of 4-quinolones with selected chemical reagents.

Gas phase ion/molecule reactions are often used in analytical applications to support the analysis of isomers or to identify specific functional groups of organic molecules. Until now, deliberate chemical reactions have not been performed in differential ion mobility spectrometry (DMS) devices except for hydrogen exchange and cluster formation. The present work extends that of Colorado and Brodbelt (Anal Chem 66:2330-5, 1994) on ion/molecule reactions in an ion trap mass spectrometer. In this study, class-specific chemical reactions of 4-quinolone antibiotics with various chemical reagents were used to demonstrate the analytical utility of ion/molecule reactions in a DMS drift cell. For these reactions, dehydrated reactive precursor ions were initially formed and made to undergo annulation reactions with selected reagents within the timescale of the DMS separation. Careful study of the energies required for dissociation of the adducts confirmed the covalent nature of the newly formed bond; thus demonstrating the analytical utility of this approach. Graphical abstract.

Generation of Phosphoranyl Radicals via Photoredox Catalysis Enables Voltage-Independent Activation of Strong C-O Bonds.

Despite the prevalence of alcohols and carboxylic acids as functional groups in organic molecules and the potential to serve as radical precursors, C-O bonds remain difficult to activate. We report a synthetic strategy for direct access to both alkyl and acyl radicals from these ubiquitous functional groups via photoredox catalysis. This method exploits the unique reactivity of phosphoranyl radicals, generated from a polar/SET crossover between a phosphine radical cation and an oxygen-centered nucleophile. We show the desired reactivity in the reduction of benzylic alcohols to the corresponding benzyl radicals with terminal H atom trapping to afford the deoxygenated products. Using the same method, we demonstrate access to synthetically versatile acyl radicals, which enables the reduction of aromatic and aliphatic carboxylic acids to the corresponding aldehydes with exceptional chemoselectivity. This protocol also transforms carboxylic acids to heterocycles and cyclic ketones via intramolecular acyl radical cyclizations to forge C-O, C-N, and C-C bonds in a single step.

Impact of microbial activity on the mobility of metallic elements (Fe, Al and Hg) in tropical soils

Dissolved organic carbon (DOC), especially low molecular mass organic acids (LMMOAs) derives principally from biota degradation process in which soil microorganisms are the main actors and from roots exudates. The presence of LMMOAs led to an increase of availability and mobility of metallic elements through the formation of organo-metallic complex. In tropical soils, very few information about LMMOAs quantification and their role in the biogeochemical process related to trace metals cycling was available. Quantification of LMMOAs is limited due to their low concentration and rapid degradation. Until now, the role of microbial activity as well as LMMOAs in the biogeochemical cycle of metallic elements in tropical soils has not been investigated. The present study was conducted to evaluate the effect of microbial activity and biomass on the availability and mobility of metallic elements (Fe, Al and Hg) in two tropical soils, Ferralsol and Acrisol. We also quantified LMMOAs contents in soil solutions and addressed to their role in the mobilization of metals.Utilization of Diffuse Gradient in Thin film (DGT) method permits to analyze bioavailable metal in both fractions: organically complexed and free metals. The results show that the quantity of Fe, Al and Hg labile were higher in Ferralsol than Acrisol soils. This was more accentuated for the 50 cm-depth of soils where the microbial activities and the organic carbon content were important. Concentration of LMMOAs of Ferralsol and Acrisol were lower in compare to coniferous and deciduous forest soils. Proportions of LMMOAs in DOC were very small at 10.5% and 6.85% in the Ferralsol and Acrisol soils, respectively. The mobilization of Fe, Al and Hg in Ferralsol and Acrisol soils appeared to vary depending on the soil physico-chemical characteristics (sorption capacities and metals content) and also on the microbial biomass and activity. Soil pH influences the acidity of the functional groups in organic molecules and consequently their speciation. In addition, low pH increase proton competition within acidic functional groups involved in coordinate bond. The content of CEC in Ferralsol is higher than Acrisol that is related to the high contents of clay and organic carbon. Low CEC content can result in a decrease of retain of the cationic trace metals. Low CEC content led to a decrease of the capacity of retaining of metallic elements in tropical soils in compare to temperate soils.

Solid-Surface Modification with Two-Dimensionally Ordered Oriented Molecular Films

The surface properties of solid substrates have a considerable impact on many physical, chemical, and electrochemical events occurring at a materials interface, and thus the control of chemical and physical properties of solid surfaces (e.g., surface morphology and energy, wettability, and adhesiveness) provides a key technology in many practical applications. As a useful approach for this purpose, the formation of self-assembled monolayers (SAMs) has widely been used, which relies on specific bonding between polar functional groups of organic molecules and outermost surface elements of inorganic substrates. However, this approach cannot be applied for the modification of polymer substrate surfaces, which are devoid of any effective binding site against polar functional groups. Here we report a new type of organic surface modifier consisting of a paraffinic tripodal triptycene, which undergoes controlled self-assembly not only on inorganic substrates but also on polymer substrates, resulting in a completely oriented molecular thin film like SAMs. The formation of this molecular film does not rely on specific chemical bonding but on a unique assembling property of the molecular building block capable of forming 2D (hexagonal triptycene array) + 1D (layer stacking) structure regardless of the types of substrates. In this presentation, an application of this molecular film to organic electronic devices, which can enhance device performances, will also be described.

Dehydrogenative desaturation-relay via formation of multicenter-stabilized radical intermediates

In organic molecules, the reactivity at the carbon atom next to the functional group is dramatically different from that at other carbon atoms. Herein, we report that a versatile copper-catalyzed method enables successive dehydrogenation or dehydrogenation of ketones, aldehydes, alcohols, α,β-unsaturated diesters, and N-heterocycles to furnish stereodefined conjugated dienecarbonyls, polyenecarbonyls, and nitrogen-containing heteroarenes. On the basis of mechanistic studies, the copper-catalyzed successive dehydrogenation process proceeds via the initial α,β-desaturation followed by further dehydrogenative desaturation of the resultant enone intermediate, demonstrating that the reactivity at α-carbon is transferred through carbon–carbon double bond or longer π-system to the carbon atoms at the positions γ, ε, and η to carbonyl groups. The dehydrogenative desaturation–relay is ascribed to the formation of an unusual radical intermediate stabilized by 5- or 7,- or 9-center π-systems. The discovery of successive dehydrogenation may open the door to functionalizations of the positions distant from functional groups in organic molecules.

Controllable Sulfoxidation and Sulfenylation with Organic Thiosulfate Salts via Dual Electron- and Energy-Transfer Photocatalysis

Sulfoxides and sulfides are two important functional groups in organic molecules, containing different valence states of sulfur. Both sulfoxidation and sulfenylation with common sulfurating reagents were successfully tuned via a facile variation of the atmosphere under photocatalyzed conditions. The sulfoxidation and sulfenylation transformations involved tandem electron-/energy-transfer and single-electron-transfer processes, respectively. Late-stage sulfoxidation for pharmaceuticals and sugar derivatives was established to be highly compatible. Divergent formal syntheses of sulfoxide/sulfide-containing marketed pharmaceuticals were switchably implemented. Gram-scale operations further demonstrated the practicability of the protocol.

An algorithm to identify functional groups in organic molecules

BackgroundThe concept of functional groups forms a basis of organic chemistry, medicinal chemistry, toxicity assessment, spectroscopy and also chemical nomenclature. All current software systems to identify functional groups are based on a predefined list of substructures. We are not aware of any program that can identify all functional groups in a molecule automatically. The algorithm presented in this article is an attempt to solve this scientific challenge.ResultsAn algorithm to identify functional groups in a molecule based on iterative marching through its atoms is described. The procedure is illustrated by extracting functional groups from the bioactive portion of the ChEMBL database, resulting in identification of 3080 unique functional groups.ConclusionsA new algorithm to identify all functional groups in organic molecules is presented. The algorithm is relatively simple and full details with examples are provided, therefore implementation in any cheminformatics toolkit should be relatively easy. The new method allows the analysis of functional groups in large chemical databases in a way that was not possible using previous approaches.Graphical abstract.