Aromatic Core Structures Research Articles

Detailed Comparison of Xenon APPI (9.6/8.4 eV), Krypton APPI (10.6/10.0 eV), APCI, and APLI (266 nm) for Gas Chromatography High Resolution Mass Spectrometry of Standards and Complex Mixtures.

Photoionization schemes for mass spectrometry, either by laser or discharge lamps, have been widely examined and deployed. In this work, the ionization characteristics of a xenon discharge lamp (Xe-APPI, 9.6/8.4 eV) have been studied and compared to established ionization schemes, such as atmospheric pressure chemical ionization, atmospheric pressure photoionization with a krypton discharge lamp (Kr-APPI, 10.6/10 eV) and atmospheric pressure laser ionization (266 nm). Addressing the gas-phase ionization behavior has been realized by gas chromatography coupled to high-resolution mass spectrometry without the usage of a dopant. For standard substances, it has been found that Xe-APPI is able to ionize a broad range of polycyclic aromatic hydrocarbons as well as their heteroatom-containing and alkylated derivatives. However, thiol and ester compounds could not be detected. Moreover, Xe-APPI revealed a high tendency to generate oxygenated artifacts, most likely due to a VUV absorption band of oxygen at 148 nm. Beneficially, almost no chemical background, commonly caused by APCI or Kr-APPI due to column blood, plasticizers or impurities, is observed. This advantage is noteworthy for evolved gas analysis without preseparation or for chromatographic coelution. For the complex mixtures, Xe-APPI revealed the predominant generation of radical cations via direct photoionization with a high selectivity toward aromatic core structures with low alkylation. Interestingly, both Xe-APPI and Kr-APPI could sensitively detect sterane cycloalkanes, validated by gas chromatographic retention. The narrowly ionized chemical space could let Xe-APPI find niche applications, e.g., for strongly contaminated samples to reduce the background.

High-affinity binding at quadruplex-duplex junctions: rather the rule than the exception.

Quadruplex-duplex (Q-D) junctions constitute unique structural motifs in genomic sequences. Through comprehensive calorimetric as well as high-resolution NMR structural studies, Q-D junctions with a hairpin-type snapback loop coaxially stacked onto an outer G-tetrad were identified to be most effective binding sites for various polycyclic quadruplex ligands. The Q-D interface is readily recognized by intercalation of the ligand aromatic core structure between G-tetrad and the neighboring base pair. Based on the thermodynamic and structural data, guidelines for the design of ligands with enhanced selectivity towards a Q-D interface emerge. Whereas intercalation at Q-D junctions mostly outcompete stacking at the quadruplex free outer tetrad or intercalation between duplex base pairs to varying degrees, ligand side chains considerably contribute to the selectivity for a Q-D target over other binding sites. In contrast to common perceptions, an appended side chain that additionally interacts within the duplex minor groove may confer only poor selectivity. Rather, the Q-D selectivity is suggested to benefit from an extension of the side chain towards the exposed part of the G-tetrad at the junction. The presented results will support the design of selective high-affinity binding ligands for targeting Q-D interfaces in medicinal but also technological applications.

Engineering and optimization of the 2-phenylethylglucosinolate production in Nicotiana benthamiana by combining biosynthetic genes from Barbarea vulgaris and Arabidopsis thaliana.

2-Phenylethylglucosinolate (2PE) derived from homophenylalanine is present in plants of the Brassicales order as a defense compound. It is associated with multiple biological properties, including deterrent effects on pests and antimicrobial and health-promoting functions, due to its hydrolysis product 2-phenylethyl isothiocyanate, which confers 2PE as a potential application in agriculture and industry. In this study, we characterized the putative key genes for 2PE biosynthesis from Barbarea vulgaris W.T. Aiton and demonstrated the feasibility of engineering 2PE production in Nicotiana benthamiana Domin. We used different combinations of genes from B. vulgaris and Arabidopsis thaliana (L.) Heynh. to demonstrate that: (i) BvBCAT4 performed more efficiently than AtBCAT4 in biosynthesis of both homophenylalanine and dihomomethionine; (ii) MAM1 enzymes were critical for the chain-elongated profile, while CYP79F enzymes accepted both chain-elongated methionine and homophenylalanine; (iii) aliphatic but not aromatic core structure pathway catalyzed the 2PE biosynthesis; (iv) a chimeric pathway containing BvBCAT4, BvMAM1, AtIPMI and AtIPMDH1 resulted in a two-fold increase in 2PE production compared with the B. vulgaris-specific chain elongation pathway; and (v) profiles of chain-elongated products and glucosinolates partially mirrored the profiles in the gene donor plant, but were wider in N. benthamiana than in the native plants. Our study provides a strategy to produce the important homophenylalanine and 2PE in a heterologous host. Furthermore, chimeric engineering of the complex 2PE biosynthetic pathway enabled detailed understanding of catalytic properties of individual enzymes - a prerequisite for understanding biochemical evolution. The new-to-nature gene combinations have the potential for application in biotechnological and plant breeding.

Development of Novel Mitochondrial Pyruvate Carrier Inhibitors to Treat Hair Loss.

Herein, we report the synthesis and evaluation of novel analogues of UK-5099 both in vitro and in vivo for the development of mitochondrial pyruvate carrier (MPC) inhibitors to treat hair loss. A comprehensive understanding of the structure-activity relationship was obtained by varying four positions of the hit compound, namely, the alkyl group on the N1 position, substituents on the indole core, various aromatic and heteroaromatic core structures, and various Michael acceptors. The major discovery was that the inhibitors with a 3,5-bis(trifluoromethyl)benzyl group at the N1 position were shown to have much better activity than JXL001 (UK-5099) to increase cellular lactate production. Additionally, analogue JXL069, possessing a 7-azaindole heterocycle, was also shown to have significant MPC inhibition activity, which further increases the chemical space for drug design. Finally, more than 10 analogues were tested on shaved mice by topical treatment and promoted obvious hair growth on mice.

Front Cover: Rigid Multidimensional Alkoxyamines: A Versatile Building Block Library (Eur. J. Org. Chem. 2/2021)

Since the discovery of the “living” free‐radical polymerization, alkoxyamines were widely used in nitroxide‐mediated polymerization (NMP). Most of the known alkoxyamines bear just one functionality with only a few exceptions bearing two or more alkoxyamine units. Herein, we present a library of novel multidimensional alkoxyamines based on commercially available, rigid, aromatic core structures. A versatile approach allows the introduction of different sidechains which have an impact on the steric hindrance and dissociation behavior of the alkoxyamines. The reaction to the alkoxyamines was optimized by implementing a mild and reliable procedure to give all target compounds in high yields. Utilization of biphenyl, p‐terphenyl, 1,3,5‐triphenylbenzene, tetraphenylethylene, and tetraphenyl‐methane results in linear, trigonal, square planar, and tetrahedral shaped alkoxyamines. These building blocks are useful initiators for multifold NMP leading to star‐shaped polymers or as a linker for the nitroxide exchange reaction (NER), to obtain dynamic frameworks with a tunable crosslinking degree and self‐healing abilities.

Rigid Multidimensional Alkoxyamines: A Versatile Building Block Library

AbstractSince the discovery of the “living” free‐radical polymerization, alkoxyamines were widely used in nitroxide‐mediated polymerization (NMP). Most of the known alkoxyamines bear just one functionality with only a few exceptions bearing two or more alkoxyamine units. Herein, we present a library of novel multidimensional alkoxyamines based on commercially available, rigid, aromatic core structures. A versatile approach allows the introduction of different sidechains which have an impact on the steric hindrance and dissociation behavior of the alkoxyamines. The reaction to the alkoxyamines was optimized by implementing a mild and reliable procedure to give all target compounds in high yields. Utilization of biphenyl, p‐terphenyl, 1,3,5‐triphenylbenzene, tetraphenylethylene, and tetraphenyl‐methane results in linear, trigonal, square planar, and tetrahedral shaped alkoxyamines. These building blocks are useful initiators for multifold NMP leading to star‐shaped polymers or as a linker for the nitroxide exchange reaction (NER), to obtain dynamic frameworks with a tunable crosslinking degree and self‐healing abilities.

Hydrocarbons to carboxyl-rich alicyclic molecules: A continuum model to describe biodegradation of petroleum-derived dissolved organic matter in contaminated groundwater plumes

Relationships between dissolved organic matter (DOM) reactivity and chemical composition in a groundwater plume containing petroleum-derived DOM (DOMHC) were examined by quantitative and qualitative measurements to determine the source and chemical composition of the compounds that persist downgradient. Samples were collected from a transect down the core of the plume in the direction of groundwater flow. An exponential decrease in dissolved organic carbon concentration resulting from biodegradation along the transect correlated with a continuous shift in fluorescent DOMHC from shorter to longer wavelengths. Moreover, ultrahigh resolution mass spectrometry showed a shift from low molecular weight (MW) aliphatic, reduced compounds to high MW, unsaturated (alicyclic/aromatic), high oxygen compounds that are consistent with carboxyl-rich alicyclic molecules. The degree of condensed aromaticity increased downgradient, indicating that compounds with larger, conjugated aromatic core structures were less susceptible to biodegradation. Nuclear magnetic resonance spectroscopy showed a decrease in alkyl (particularly methyl) and an increase in aromatic/olefinic structural motifs. Collectively, data obtained from the combination of these complementary analytical techniques indicated that changes in the DOMHC composition of a groundwater plume are gradual, as relatively low molecular weight (MW), reduced, aliphatic compounds from the oil source were selectively degraded and high MW, alicyclic/aromatic, oxidized compounds persisted.

Efficient Fused-Ring Extension of A-D-A-Type Non-Fullerene Acceptors by a Symmetric Replicating Core Unit Strategy.

The extension of fused aromatic ring core structures is beneficial for enhancing intramolecular charge transfer and effective π conjugation in A-D-A-type (A=acceptor; D=donor) non-fullerene acceptors (NFAs). In this work, a novel strategy involving the extension of a fused-ring core by symmetrically replicating the core unit has been developed, and a novel symmetric fused-12-ring NFA, LC81, has been synthesized. When paired with the wide-bandgap polymer donor PBT1-C, the corresponding organic solar cells (OSCs) showed a high power conversion efficiency of 12.71 %, much higher than that of the device based on the reference NFA, TPTT-4F. Moreover, the LC81-based OSC displayed a lower energy loss and a better ambient stability than the TPTT-4F-based device. Our results indicate that the extension of the fused-ring core by the symmetric replicating core unit strategy is an effective approach to promoting the photovoltaic characteristics of A-D-A-type NFAs.

Characterization of Arabidopsis CYP79C1 and CYP79C2 by Glucosinolate Pathway Engineering in Nicotiana benthamiana Shows Substrate Specificity Toward a Range of Aliphatic and Aromatic Amino Acids.

Glucosinolates (GLSs) are amino acid-derived defense compounds characteristic of the Brassicales order. Cytochromes P450s of the CYP79 family are the entry point into the biosynthetic pathway of the GLS core structure and catalyze the conversion of amino acids to oximes. In Arabidopsis thaliana, CYP79A2, CYP79B2, CYP79B3, CYP79F1, and CYP79F2 have been functionally characterized and are responsible for the biosynthesis of phenylalanine-, tryptophan-, and methionine-derived GLSs, respectively. However, the substrate(s) for CYP79C1 and CYP79C2 were unknown. Here, we investigated the function of CYP79C1 and CYP79C2 by transiently co-expressing the genes together with three sets of remaining genes required for GLS biosynthesis in Nicotiana benthamiana. Co-expression of CYP79C2 with either the aliphatic or aromatic core structure pathways resulted in the production of primarily leucine-derived 2-methylpropyl GLS and phenylalanine-derived benzyl GLS, along with minor amounts of GLSs from isoleucine, tryptophan, and tyrosine. Co-expression of CYP79C1 displayed minor amounts of GLSs from valine, leucine, isoleucine, and phenylalanine with the aliphatic core structure pathway, and similar GLS profile (except the GLS from valine) with the aromatic core structure pathway. Additionally, we co-expressed CYP79C1 and CYP79C2 with the chain elongation and aliphatic core structure pathways. With the chain elongation pathway, CYP79C2 still mainly produced 2-methylpropyl GLS derived from leucine, accompanied by GLSs derived from isoleucine and from chain-elongated mono- and dihomoleucine, but not from phenylalanine. However, co-expression of CYP79C1 only resulted in GLSs derived from chain-elongated amino acid substrates, dihomoleucine and dihomomethionine, when the chain elongation pathway was present. This shows that CYP79 activity depends on the specific pathways co-expressed and availability of amino acid precursors, and that description of GLS core structure pathways as “aliphatic” and “aromatic” pathways is not suitable, especially in an engineering context. This is the first characterization of members of the CYP79C family. Co-expression of CYP79 enzymes with engineered GLS pathways in N. benthamiana is a valuable tool for simultaneous testing of substrate specificity against multiple amino acids.

Density functional theory model for carbon dot surfaces and their interaction with silver nanoparticles

Abstract Density functional theory (DFT) and time dependent density functional theory (TDDFT) calculations were performed to represent carbon dots surfaces. The addition of different oxygen functional groups to the aromatic carbon core structure and the stability in the interaction with silver nanoparticles was also investigated. Adsorption energies were evaluated in order to compare the competition for adsorption sites on silver surface with d -glucose and d -gluconate ion molecules. The –COOH and –COO groups and the interaction of the latter with silver were proposed to explain some features of the UV–visible absorption spectra , which could also contribute to an explanation for the charge observed on carbon dot surfaces.

Studying the fragmentation mechanism of selected components present in crude oil by collision-induced dissociation mass spectrometry.

Structural characterization of individual compounds in very complex mixtures is difficult to achieve. One important step in structural elucidation is understanding the mass spectrometric fragmentation mechanisms of the compounds present in such mixtures. Here, different individual compounds presumed to be present in a complex crude oil mixture have been synthesized and structurally characterized by tandem mass spectrometry (MS/MS) studies. Model compounds with different aromatic cores and various substitutents were synthesized. Major effort has been put into producing isomerically pure compounds to better understand the fragmentation pattern. Each synthesized compound has been subjected to MSn studies using either a triple quadrupole or a linear ion trap mass spectrometer with electrospray or atmospheric pressure photoionization. The results are used to analyze individual compounds from a complex vacuum gas oil (VGO). The synthesized compounds and a chromatographically simplified vacuum gas oil were used for structural analysis. The major fragmentation mechanism is the benzylic cleavage of the aliphatic side chain. Each side chain can be separately removed from the aromatic core by using MSn methods. At the end of a series of fragmentations, the base aromatic core structure remains and can be chararcterized. By defining the fragmentation mechanism in complex oil samples it was possible to structurally characterize individual compounds present in a chromatographically simplified VGO. The compounds consist of an aromatic core with aliphatic side chains. Cleavage of all side chains can be achieved by MSn measurements, allowing characterization of the remaining core structure.

Molecular Motors in Aqueous Environment.

Molecular motors are Nature’s solution for (supra)molecular transport and muscle functioning and are involved in most forms of directional motion at the cellular level. Their synthetic counterparts have also found a myriad of applications, ranging from molecular machines and smart materials to catalysis and anion transport. Although light-driven rotary molecular motors are likely to be suitable for use in an artificial cell, as well as in bionanotechnology, thus far they are not readily applied under physiological conditions. This results mainly from their inherently aromatic core structure, which makes them insoluble in aqueous solution. Here, the study of the dynamic behavior of these motors in biologically relevant media is described. Two molecular motors were equipped with solubilizing substituents and studied in aqueous solutions. Additionally, the behavior of a previously reported molecular motor was studied in micelles, as a model system for the biologically relevant confined environment. Design principles were established for molecular motors in these media, and insights are given into pH-dependent behavior. The work presented herein may provide a basis for the application of the remarkable properties of molecular motors in more advanced biohybrid systems.

In-source collision activated dissociation for coal/biomass-based model compounds and structural characterization of a coal extract

In-source collision activated dissociation (ISCAD) is an effective method to obtain molecular structure of coal and biomass and provide basic knowledge for coal/biomass conversion. Twenty two coal/biomass-based model compounds and one coal extract were studied via ISCAD to understand the relationship between collision energy and molecular structure and the application of ISCAD in the characterization of coal. Model compounds showed different fragmentation patterns with the increase of collision energy and the detailed fragmentation pathways in context of collision energies were proposed. According to the ISCAD results of coal extract, the weighted mean molecular weight (MW) and weighted mean double-bond equivalent (DBE) values of ionized coal molecules decreased over collision energy of 80 eV. The decrease of weighted mean MW and DBE were mainly caused by the cleavage of alkyl chains, bridged bonds, and minor cracking of small aromatic cores from precursor ions upon fragmentation. Therefore, the optimal ISCAD collision energy for the investigation of aromatic core structures of the coal extract should be around 80 eV.

A Novel High-Capacity Anode Material Derived from Aromatic Imides for Lithium-Ion Batteries.

A novel anode material for lithium-ion batteries derived from aromatic imides with multicarbonyl group conjugated with aromatic core structure is reported, benzophenolne-3,3',4,4'-tetracarboxylimide oligomer (BTO). It could deliver a reversible capacity of 829 mA h g-1 at 42 mA g-1 for 50 cycles with a stable discharge plateaus ranging from 0.05-0.19 V versus Li+ /Li. At higher rates of 420 and 840 mA g-1 , it can still exhibit excellent cycling stability with a capacity retention of 88% and 72% after 1000 cycles, delivering capacity of 559 and 224 mA h g-1 . In addition, a rational prediction of the maximum amount of lithium intercalation is proposed and explored its possible lithium storage mechanism.

Separation and Characterization of Organic Chlorides in a Chinese Crude Oil

A crude oil from Shengli oilfield of China was extracted with N,N‐dimethylformamide (DMF) for separation and enrichment of organic chlorides. The resulting extract with relatively higher chlorine concentration was analyzed with gas chromatography–mass spectrometry (GC/MS). Among the identified heteroatom compounds in the extract sample, nitrogen‐containing compounds were most abundant in the extract sample, followed by chlorine‐, sulfur‐, and oxygen‐containing compounds, respectively. Four organochlorines with an aromatic core structure, i.e., 5‐chloro‐2‐methylaniline, 2‐chloro‐6‐methylaniline, 4‐chloro‐2‐nitrotoluene, and 1‐(5‐chloro‐2‐hydroxyphenyl)ethanone, were identified from crude oil extract. The dominant abundant organic chloride is 5‐chloro‐2‐methylaniline with relative content of 65.1% in the total of identified organic chlorides, followed by 1‐(5‐chloro‐2‐hydroxyphenyl)ethanone of 16.3%, 2‐chloro‐6‐methylaniline of 14.5%, and 4‐chloro‐2‐nitrotoluene of 4.1%, respectively.

Effects of aromatic core and flexible terminal chain structures on the properties of luminous liquid-crystalline gold(i) complexes for functional materials

ABSTRACTLuminescent liquid-crystalline (LC) Au complexes with various aromatic cores and flexible terminal chains were synthesized. The aromatic core aspect ratio crucially affected the LC temperature range and melting point of the complexes. Moreover, branched flexible chains reduced the melting point, thus expanding the LC temperature range. In the crystalline and LC phases of the complexes, fluorescence was quenched by the aggregation-caused quenching effect, but phosphorescence was enhanced by the crystallization-induced phosphorescence effect. However, no phosphorescence was observed in the isotropic phase. Thus, not only aggregation but also regularity of molecular aggregates is necessary for the observed crystallization-induced phosphorescence effect.

Advances in Asphaltene Petroleomics. Part 1: Asphaltenes Are Composed of Abundant Island and Archipelago Structural Motifs

For decades, discussion of asphaltene structure focused primarily on molecular weight. Now that it is widely accepted that asphaltene monomers are between ∼250 and 1200 g/mol, disagreement has turned to asphaltene architecture. The classic island model depicts asphaltenes as single core aromatic molecules with peripheral alkyl side chains, whereas the less widely accepted archipelago model, includes multiple aromatic cores that are alkyl-bridged with multiple polar functionalities. Here, we analyze asphaltene samples by positive-ion atmospheric pressure photoionization Fourier transform ion cyclotron resonance mass spectrometry and perform infrared multiphoton dissociation to identify their aromatic core structures to shed light on the abundance of island and archipelago structural motifs. Our results indicate that island and archipelago motifs coexist in petroleum asphaltenes, and unlike readily accessible island motifs, asphaltene purification is required to detect and characterize archipelago species b...

A New Perspective on the Apparent Solubility of Dissolved Black Carbon

Black carbon (BC), pyrogenic organic matter generated from the incomplete combustion of biomass, is ubiquitous in the environment. The molecular structures which comprise the BC pool of compounds are defined by their condensed aromatic core structures polysubstituted with O-containing functionalities (e.g., carboxyl groups). Despite the apparent hydrophobicity of BC molecules, a considerable portion of BC is translocated from terrestrial to aquatic systems in the form of dissolved BC (DBC). However, the specific biogeochemical mechanisms which control the transfer of BC from the land to the water remain elusive. In the current study, the apparent solubility of DBC was inferred from octanol-water partition coefficients (Kow) modeled for proposed DBC structures with varying degrees of polycondensation and polar functionality. Modeled Kow values indicated that DBC molecules with small aromatic ring systems and high degrees of hydrophilic functionality may be truly solubilized in the aqueous phase. However, large and highly condensed DBC structures yielded high Kow values, which suggested that a considerable portion of the DBC pool which has been quantified in aquatic environments is not truly dissolved. We hypothesized that other DOM components may act as mediators in the solubilization of condensed aromatic molecules and serve to increase the solubility of DBC via hydrophobic, intermolecular associations. This hypothesis was tested through controlled leaching experiments to determine whether the mobilization of DBC from particulate soils and chars became enhanced in the presence of DOM. However, we observed that characteristics inherent to each sample type had a greater influence than added DOM on the apparent solubility of DBC. In addition, the direct comparison of molecular marker (benzenepolycarboxylic acids) and ultrahigh resolution mass spectral data (FT-ICR/MS) on leachates obtained from the same set of soils and char did not show a clear overlap in DBC quantification or characterization between the two analytical methods. Correlations between FT-ICR/MS results and BPCA were not significant possibly due to differences in the methodological windows and/or small sample size. Our results were unable to provide evidence in support of proposed hydrophobic interactions between DOM and DBC, suggesting that other physical/chemical mechanisms play important roles in the dissolution of BC.

Unique Reversible Crystal-to-Crystal Phase Transition—Structural and Functional Properties of Fused Ladder Thienoarenes

Donor–acceptor type molecules based on fused ladder thienoarenes, indacenodithiophene (IDT), and dithienocyclopenta–thienothiophene (DTCTT), coupled with benzothiadiazole, are prepared, and their solid-state structures are investigated. They display a rich variety of solid phases ranging from amorphous glass states to crystalline states, upon changes in the central aromatic core and side group structures. Most notably, the DTCTT-based derivatives showed reversible crystal-to-crystal phase transitions in heating and cooling cycles. Unlike what has been seen in π-conjugated molecules, variable temperature XRD revealed that structural change occurs continuously during the transition. A columnar self-assembled structure with slip-stacked π–π interaction is proposed to be involved in the solid state. This research provides the evidence of unique structural behavior of the DTCTT-based molecules through the detailed structural analysis. This unique structural transition paves the way for these materials to have ...

Fast switching negative dielectric anisotropic multicomponent mixtures for vertically aligned liquid crystal displays

Negative dielectric anisotropic nematic multicomponent mixtures are particularly attractive in vertically aligned mode liquid crystal displays for achieving faster response time. In this work, we report the mesomorphic and physical properties (e.g. birefringence, dielectric anisotropy, bend elastic constant, relaxation time and rotational viscosity) of three nematic multicomponent mixtures based solely on laterally fluorinated aromatic rigid core structures. A nine component Base mixture was prepared and further modified into two different ten component mixtures using suitable laterlally fluorinated tolane dopants. These mixtures exhibit reasonably large values of dielectric anisotropy, low values of rotational viscosity as well as a high figure of merit which is desirable for reducing the device response time. The mixtures emerged to be promising candidate for their applicability in vertically aligned mode display devices.