Number Of Heteroatoms Research Articles

Tunable Activated Esters Enable Lysine-Selective Protein Labeling and Profiling.

Lysine residues on protein surfaces are abundant and often found in enzyme active sites, making them critical targets for studying undruggable proteins. However, the varied microenvironment surrounding lysine residues results in a wide range of pKa values, complicating site-specific covalent binding. In this study, we address the challenges posed by the diverse reactivity of amino side chains by modulating the amide reaction activity of heteroaromatic activated esters. By fine-tuning the type, position, and number of heteroatoms, we successfully rationalized the regulation of their amide reaction activity, leading to the design of probes for selective lysine labeling within the proteome for profiling purposes. Systematic optimization of these esters' reactivity and selectivity has yielded a series of effective probes suitable for both in vitro and cellular applications. These findings significantly enhance our understanding of protein functions and mechanisms, facilitated by the precise identification and analysis of protein labeling and profiling.

β-Ketoenamine Porous Organic Polymers for High-Efficiency Carbon Dioxide Adsorption and Separation.

To mitigate the greenhouse effect, a number of porous organic polymers (POPs) has been developed for carbon capture. Considering the permanent quadrupole of symmetrical CO2 molecules, the integration of electron-rich groups into POPs is a feasible way to enhance the dipole-quadrupole interactions between host and guest. To comprehensively explore the effect of pore environment, including specific surface area, pore size, and number of heteroatoms, on carbon dioxide adsorption capacity, we synthesized a series of microporous POPs with different content of β-ketoenamine structures via Schiff-base condensation reactions. These materials exhibit high BET specific surface areas, high stability, and excellent CO2 adsorption capacity. It is worth mentioning that the CO2 adsorption capacity and CO2/N2 selectivity of TAPPy-TFP reaches 3.87 mmol g-1 and 27. This work demonstrates that the introduction of β-ketoenamine sites directly through condensation reaction is an effective strategy to improve the carbon dioxide adsorption performance of carbon dioxide.

Nonmetal Doping Modulates Fe Single-Atom Catalysts for Enhancement in Peroxidase Mimicking via Symmetry Disruption, Distortion, and Charge Transfer.

Developing biomimetic catalysts with excellent peroxidase (POD)-like activity has been a long-standing goal for researchers. Doping nonmetallic atoms with different electronegativity to boost the POD-like activity of Fe-N-C single-atom catalysts (SACs) has been successfully realized. However, the introduction of heteroatoms to regulate the coordination environment of the central Fe atom and thus influence the activation of the H2O2 molecule in the POD-like reaction has not been extensively explored. Herein, the effect of different doping sites and numbers of heteroatoms (P, S, B, and N) on the adsorption and activation of H2O2 molecules of Fe-N sites is thoroughly investigated by density functional theory (DFT) calculations. In general, alternation in the catalytic efficiency directly depends on the transfer of electrons and the geometrical shifts near the Fe-N site. First, the symmetry disruption of the Fe-N4 site by P, S, and B doping is beneficial to the activation of H2O2 due to a significant reduction in the adsorption energies. In some cases, without Fe-N4 site disruption, the configurations fail to modulate the adsorption behavior of H2O2. Second, Fe-N-P/S configurations exhibit a stronger affinity for H2O2 molecules due to the significant out-of-plane distortions induced by larger atomic radii of P and S. Moreover, the synergistic effects of Fe and doping atoms P, S, and B with weaker electronegativity than that of N atoms promote electron donation to generated oxygen-containing intermediates, thus facilitating subsequent electron transfer with other substrates. This work demonstrates the critical role of tuning the coordinating environment of Fe-N active centers by heteroatom doping and provides theoretical guidance for controlling the types by breaking the symmetry of SACs to achieve optimal POD-like catalytic activity and selectivity.

Unraveling the structure-property relationship of pyrimidine-derivatives as CO2 corrosion inhibitors: Experimental and periodic DFT investigations

CO2-containing environments commonly cause corrosion of carbon steel (CS) pipelines used in the oil and gas industry. In this work, the inhibition of corrosion by three derivatives of pyrimidine, namely 2-mercaptopyrimidine (MPY), 4-hydroxy-2-mercapto-6-methylpyrimidine (HMMP), and 4,5-Diamino-2,6-dimercaptopyrimidine (DDMP) for C1018 CS in CO2 saturated 3.5% NaCl brine was investigated. The corrosion rates and inhibition efficiency were investigated at 25 and 70 °C using open circuit potential, linear polarization resistance, potentiodynamic polarization and electrochemical impedance measurements. The post-immersion surface characterization of the exposed C1018 CS with and without the three molecules was carried out using SEM and 3D surface optical profilometer. Theoretical computation using DFT was further utilized to examine the role of the molecular structures and the mechanism of inhibition of the three molecules on steel surface at the atomic level. The experimental results indicate the following order of inhibition efficiency: MPY > DDMP > HMMP. Our experimental work proved that MPY molecule (the smaller one with the least number of heteroatoms) as the most efficient corrosion inhibitor. Surface characterization analysis confirmed the order of inhibition efficiency. The theoretical results revealed that the stability of molecules adsorbed on Fe (110) surface in the parallel orientation and on FeCO3 (104) is identical on both surfaces, which is completely consistent with the experiment. Our study provides a feasible strategy for developing new corrosion inhibitors by understanding how similar organic inhibitors work.

Multi-cavity molecular descriptor interconnections: Enhanced protocol for prediction of serum albumin drug binding

The role of human serum albumin (HSA) in the transport of molecules predicates its involvement in the determination of drug distribution and metabolism. Optimization of ADME properties are analogous to HSA binding thus this is imperative to the drug discovery process. Currently, various in silico predictive tools exist to complement the drug discovery process, however, the prediction of possible ligand-binding sites on HSA has posed several challenges. Herein, we present a strong and deeper-than-surface case for the prediction of HSA-ligand binding sites using multi-cavity molecular descriptors by exploiting all experimentally available and crystallized HSA-bound drugs. Unlike previously proposed models found in literature, we established an in-depth correlation between the physicochemical properties of available crystallized HSA-bound drugs and different HSA binding site characteristics to precisely predict the binding sites of investigational molecules. Molecular descriptors such as the number of hydrogen bond donors (nHD), number of heteroatoms (nHet), topological polar surface area (TPSA), molecular weight (MW), and distribution coefficient (LogD) were correlated against HSA binding site characteristics, including hydrophobicity, hydrophilicity, enclosure, exposure, contact, site volume, and donor/acceptor ratio. Molecular descriptors nHD, TPSA, LogD, nHet, and MW were found to possess the most inherent capacities providing baseline information for the prediction of serum albumin binding site. We believe that these associations may form the bedrock for establishing a solid correlation between the physicochemical properties and Albumin binding site architecture. Information presented in this report would serve as critical in provisions of rational drug designing as well as drug delivery, bioavailability, and pharmacokinetics.

Investigating multifaceted action of ibuprofen derivatives towards cox isozymes and interleukin-6 (IL-6) site correlating with various target sites

The multifaceted action of new ibuprofen analogs has been investigated against inflammation, neurological and pro-inflammation factors. On the basis of ADMET (absorption, distribution, metabolism, excretion, and toxicity) analysis, molecular docking as well as molecular dynamics simulation, compound 3 was thought to have good anti-inflammatory activity. As the presence of structural interactions such as conventional hydrogen bonds and electrostatic interactions through the nitrogen atoms of the linker in compound 3 gave strong evidence of its potency. The major finding of the current work is that the presence of appropriate number of hetero atoms (NH, OH) in a compound makes it more efficient than the number of labile groups (i.e., hydroxyl groups). Additionally, the position of hetero atoms in a compound and orientation also play a vital role in its efficacy. It was also screened for in vitro anti-inflammatory activity by membrane stability method, where it has shown 90.8% protection of RBC hemolysis. Thus, compound 3 with effective structural features may have good anti-inflammatory activity. Communicated by Ramaswamy H. Sarma

Boronation of Biomass-Derived Materials for Hydrogen Storage

In spite of the widespread range of hydrogen applications as one of the greenest energy vectors, its transportation and storage still remain among the main concerns to be solved in order to definitively kickstart a rapid takeoff of a sustainable H2 economy. The quest for a simple, efficient, and highly reversible release storage technique is a very compelling target. Many studies have been undertaken to increase H2 storage efficiency by exploiting either chemisorption or physisorption processes, or through entrapment on different porous solid materials as sorbent systems. Among these, biomass-derived carbons represent a category of robust, efficient, and low-cost materials. One question that is still open-ended concerns the correlation of H2 uptake with the kind and number of heteroatoms as dopant of the carbonaceous sorbent matrix, such as boron, aiming to increase whenever possible bonding interactions with H2. Furthermore, the preferred choice is a function of the type of hydrogen use, which may involve a short- or long-term storage option. In this article, after a brief overview of the main hydrogen storage methods currently in use, all the currently available techniques for the boronation of activated carbonaceous matrices derived from recycled biomass or agricultural waste are discussed, highlighting the advantages and drawbacks of each of them.

Aza-Oxa-Triazole Based Macrocycles with Tunable Properties: Design, Synthesis, and Bioactivity.

A modular platform for the synthesis of tunable aza-oxa-based macrocycles was established. Modulations in the backbone and the side-chain functional groups have been rendered to achieve the tunable property. These aza-oxa-based macrocycles can also differ in the number of heteroatoms in the backbone and the ring size of the macrocycles. For the proof of concept, a library of macrocycles was synthesized with various hanging functional groups, different combinations of heteroatoms, and ring sizes in the range of 17–27 atoms and was characterized by NMR and mass spectrometry. In light of the importance of the copper-catalyzed azide-alkyne cycloaddition (CuAAC) reaction and the significance of triazole groups for various applications, we employed the click-reaction-based macrocyclization. The competence of the synthesized macrocycles in various biomedical applications was proven by studying the interactions with the serum albumin proteins; bovine serum albumin and human serum albumin. It was observed that some candidates, based on their hanging functional groups and specific backbone atoms, could interact well with the protein, thus improving the bioactive properties. On the whole, this work is a proof-of-concept to explore the backbone- and side-chain-tunable macrocycle for different properties and applications.

Characterization and Structural Classification of Heteroatom Components of Vacuum-Residue-Derived Asphaltenes Using APPI (+) FT-ICR Mass Spectrometry

Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) has been widely used as a major breakthrough to investigate the structure of asphaltenes in heavy oils. In this study, saturates, aromatics, resins, and asphaltenes (SARA) fractions derived from vacuum residue were analyzed using FT-ICR MS, and, particularly, the asphaltenes were examined in detail. Basically, the mass-to-charge ratio spectra, double bond equivalents (DBE) distribution, and heteroatom classes of SARA fractions were checked. After that, we delved into the asphaltenes with very high aromaticity and classified the asphaltenes according to heteroatom classes to understand their structural diversity. This classification disclosed that the DBE distribution of asphaltenes exhibited different trends, depending on heteroatom classes and the number of heteroatoms, which could not be identified by DBE distribution of whole asphaltenes. Based on the relative abundance peaks of the DBE and carbon number distribution, the compositional space of DBE and carbon number was separated into four groups in various heteroatom classes. The structure types of asphaltenes corresponding to each group are maltene-like components (DBE 5–15, carbon number 20–60), archipelago-type asphaltenes (DBE 10–25, carbon number 25–70), island-type asphaltenes (DBE 15–35, carbon number 25–60), and larger island-type asphaltenes (DBE 35–50, carbon number 40–75), which are highly aromatic and independent of the normal island-type asphaltenes. The classification results are expected to be applied to develop a structural model of asphaltenes.

Tautomeric equilibrium, proton affinity and mass spectrometry fragmentation of flexible hydrogen-bonded precursors and rigid hbox {N}longrightarrow hbox {BF}_2 fluorescent dyes

The stability of two groups of conformationally locked molecules, similar in topology, but differing only by the type of the bridge rigidifying their structure, is studied. The series of the less-rigid 2-phenacylheterocyclic compounds and their stiff difluoroboranyl derivatives are investigated for the determination of the effect of hbox {NCH}_3/S/O replacement in a five-membered heterocyclic ring and the presence of a strong electron-donating group on the tautomeric equilibrium, protonation affinity, and fragmentation pattern observed in the structural elucidation by means of mass spectrometry technique. The results of the omega B97X-D/6-311++G(d,p) calculations, the topological analysis of electron density as well as the experimental MS measurements show the importance of the number of heteroatoms, their properties, and location in the molecule for the rational design of the systems of desired stable tautomers or the favorable protonation sites. The obtained data allow for the understanding of the fundamentals of the novel highly fluorescent difluoroborates fragmentation behavior, vital for their structural elucidation with the application of high-resolution tandem mass spectrometry methods.

Comprehensive molecular scale modeling of anionic surfactant-asphaltene interactions

Asphaltene is the heaviest fraction of oil sands/bitumen, which is also the leading cause of these oil resources' high viscosity value. Nowadays, steam with additives is used to make oil sands/bitumen mobile through a reservoir by lowering their viscosity. Additives can be air, solvent, non-condensable gas (NCG), and surfactants. Surfactants can be used not only as a chemical additive in thermal oil recovery but also as an asphaltene inhibitor or dispersant. Formulating surfactants needs thorough and reliable knowledge about molecular interactions between asphaltene and surfactants. This paper has used molecular dynamics (MD) simulation to evaluate these interactions at thermodynamic conditions close to thermal-based oil recovery conditions. Three different asphaltene architectures observed in Athabasca oil-sands are used to examine the molecular interactions between asphaltenes and anionic surfactants.Moreover, the effect of a benzene ring on inter-molecular interactions at different temperatures is thoroughly investigated. Various analyses, including a radial distribution function (RDF), hydrogen bonds, and interaction energies, are employed to support the outcomes. Based on MD simulation results, the presence of a benzene ring in a surfactant structure can increase the interactions, especially van der Waals interactions. Moreover, the position and number of heteroatoms in asphaltene architecture play a vital role in asphaltene behavior in a solution. Results of this work give solid knowledge regarding asphaltene and surfactant interactions and provide helpful information for formulating surfactants, whether as an asphaltene inhibitor/dispersant or a steam additive for in-situ bitumen recovery.

Understanding the 1,3-Dipolar Cycloadditions of Allenes.

We have quantum chemically studied the reactivity, site‐, and regioselectivity of the 1,3‐dipolar cycloaddition between methyl azide and various allenes, including the archetypal allene propadiene, heteroallenes, and cyclic allenes, by using density functional theory (DFT). The 1,3‐dipolar cycloaddition reactivity of linear (hetero)allenes decreases as the number of heteroatoms in the allene increases, and formation of the 1,5‐adduct is, in all cases, favored over the 1,4‐adduct. Both effects find their origin in the strength of the primary orbital interactions. The cycloaddition reactivity of cyclic allenes was also investigated, and the increased predistortion of allenes, that results upon cyclization, leads to systematically lower activation barriers not due to the expected variations in the strain energy, but instead from the differences in the interaction energy. The geometric predistortion of cyclic allenes enhances the reactivity compared to linear allenes through a unique mechanism that involves a smaller HOMO–LUMO gap, which manifests as more stabilizing orbital interactions.

Synthesis of Medium-Sized Heterocycles by Transition-Metal-Catalyzed Intramolecular Cyclization.

Medium-sized heterocycles (with 8 to 11 atoms) constitute important structural components of several biologically active natural compounds and represent promising scaffolds in medicinal chemistry. However, they are under-represented in the screening of chemical libraries as a consequence of being difficult to access. In particular, methods involving intramolecular bond formation are challenging due to unfavorable enthalpic and entropic factors, such as transannular interactions and conformational constraints. The present review focuses on the synthesis of medium-sized heterocycles by transition-metal-catalyzed intramolecular cyclization, which despite its drawbacks remains a straightforward and attractive synthesis strategy. The obtained heterocycles differ in their nature, number of heteroatoms, and ring size. The methods are classified according to the metal used (palladium, copper, gold, silver), then subdivided according to the type of bond formed, namely carbon–carbon or carbon–heteroatom.

Assessment of molecular diversity of lignin products by various ionization techniques and high-resolution mass spectrometry

Lignin is a highly complex, plant-derived natural biomass component, the analysis of which requires significant demands on the analytical platform. Fourier transform ion cyclotron mass spectrometry (FT-ICR MS) has been shown to be able to readily assess the complexity of lignin and lignin degradation products by assigning tens of thousands of compounds with elemental formulae. Nevertheless, many experimental and instrumental parameters introduce discrimination towards certain components, which limits the comprehensive MS analysis. As a result, a complete characterization of the lignome remains a challenge. The present study investigated a degraded lignin sample using FT-ICR MS and compared several atmospheric pressure ionization methods, e.g., electrospray ionization, atmospheric-pressure chemical ionization, and atmospheric-pressure photoionization. The results clearly show that the number of heteroatoms (e.g., N, S, P) in the sample greatly increases the chemical diversity of lignin, while at the same time also providing potentially useful biomarkers. We demonstrate here that FT-ICR MS was able to directly isolate isotopically pure single components from the ultra-complex mixture for subsequent structural analysis, without the time-consuming chromatographic separation. CapsuleVarious ionization techniques coupled to FT-ICR MS provide a powerful tool to assess the lignome coverage.

Heteroatom-bridged heterofluorenes: a theoretical study on molecular structures and optoelectronic properties

Heteroatom incorporation is highly effective in tuning the molecular structures and optoelectronic properties of conjugated organic molecules. Here, we performed systematic theoretical studies on heteroatom-bridged heterofluorenes (BXFs) constructed by double heteroatom bridges of biphenyl to reveal the effects of heavily incorporated heteroatoms on molecular architecture and π-conjugation for different optoelectronic properties. Nine novel BXFs in three series were investigated and all of them exhibit promising potential optoelectronic properties owing to their highly fused molecular structure with heavy π-conjugation, although the introduction of different types and numbers of heteroatoms will lead to varied properties. Moreover, spiropolymers of BSiF and BGeF polymerized at the bridging position were also designed for the first time and found to have attractive optoelectronic properties of poly(BXF)s inherited from their monomers, demonstrating further the effectiveness of the bis-heteroatom introduction strategy in the construction of high-performance optoelectronic polymers. This heteroatom introduction strategy in constructing highly rigid π-conjugated materials could be applicable to other systems, representing a new concept advance to design novel conjugated small molecules and polymers for high-performance optoelectronic applications.

Thermodynamic and kinetic studies of the retro-Diels-Alder reaction of 1,4-cyclohexadiene, 4H-pyran 4H-thiopyran, 1,4-dioxine, and 1,4-dithiine: a theoretical investigation

Theoretical studies of the retro-Diels-Alder reaction of 1,4-cyclohexadiene, 4H-pyran 4H-thiopyran, 1,4-dioxine, and 1,4-dithiine in the gas phase were carried out using DFT methods at the B3LYP/6–311 + G(d,p) levels of theory. The barrier height (ΔE‡) and thermodynamic parameters (ΔG‡ and ΔH‡) were estimated. The progress of the reactions was followed by means of the Wiberg bond indices. The synchronicity values of the reactions were calculated. The kinetic parameters were calculated for both reactions in 300–1200-K temperature range. Also, fitted equations to the gas phase Arrhenius equation were determined. Effect of the character and number of heteroatoms were illustrated on the thermodynamic and kinetic parameters.

Heat of formation prediction by G4MP2-SFM schemes: An application to various nitroazole derivatives

Abstract Our G4MP2-SFM parameterization schemes have been applied to the various azole derivatives including imidazole, triazole, tetrazole, imidazolidine, [1,2,4]triazolo[4,3-a][1,3,5]triazine, tetrazine and pyrimidine, in order to establish a set of parameters for the reliable and fast heat of formation ( Δ H f o ) predictions. It is shown that a parameterization on such complex systems is possible, yielding an overall mean absolute deviation (MAD) and root mean square deviation (RMSD) to be 3.5 kcal/mol and 4.3 kcal/mol, respectively compared to full G4MP2. During the development of the parameters, we have found that nonbonded interactions are very important to predict the Δ H f o of high energy materials (HEMs). While both molecular weight and the number of NO2 substituents rarely affect the Δ H f o magnitude, the geometric configurations and the number of heteroatoms in the azole ring significantly change it.

Characterization of Asphaltenes Precipitated at Different Solvent Power Conditions Using Atmospheric Pressure Photoionization (APPI) and Laser Desorption Ionization (LDI) Coupled to Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR MS)

In the present work, asphaltenes obtained using different n-heptane/crude oil ratios (HCORs) were analyzed using atmospheric pressure photoionization (APPI) and laser desorption ionization (LDI) coupled to Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). The main objective was to improve the understanding of the components of the crude oil that precipitate under different solvent power conditions. Analysis of the compositional distribution of the asphaltenes reveals that the decrease in solvent power produces an increase in double bond equivalent (DBE) and the number of heteroatoms per molecule, while the carbon number remains almost unaltered. This finding seems to indicate that one of the main drivers for precipitation is aromaticity as HCOR increases and, consequently, the solvent power decreases. Both APPI and LDI FT-ICR MS produce average values that describe the general tendencies obtained using other techniques. Additionally, APPI FT-ICR MS closely matches bulk data of the m...

Enhanced electrochemical properties of boron functional groups on porous carbon nanofiber/MnO2 materials

Heteroatoms (B, N, O)-containing porous manganese oxide (MnO2)/carbon nanofiber (MnB-CNF) materials are prepared by one-step electrospinning method via polyacrylonitrile (PAN) and manganese(II) chloride (MnCl2) in dimethylformamide (DMF) solution containing different concentrations of B2O3. The MnB-CNF electrode exhibits optimized electrochemical behavior with a high energy density of 22.6Whkg−1 at a power density of 400Wkg−1 and a specific capacitance range of 210–160Fg−1 in the discharge current density range of 1.0 to 20mAcm−2 in aqueous KOH electrolyte. The higher electrochemical performance of MnB-CNF as a result of the electrochemical double-layer capacitor (EDLC), compared to regular Mn-CNF without B-based functional groups, is attributed to well-balanced meso- and micropores affecting the easy adsorption and transport of electrolyte ions, in addition to the pseudocapacitive redox reactions from MnO2, N, O, and extra numerous B in alkaline electrolytes. Thus, tailoring the pore structures with proper specific surface area, pore size, and number of heteroatoms is crucial for optimizing their electrochemical properties in the combined efforts to develop EDLCs and pseudocapacitance.

Substituent effect on structure, stability, and aromaticity of novel BnNmC20–(n+m) heterofullerenes

AbstractWe are focusing our calculations on the structural stabilities and electronic properties of 26 novel BnNmC20–(n+m) heterofullerenes, with n, m = 1 − 5, at B3LYP/6‐311++G** and B3LYP/AUG‐cc‐pVTZ levels of theory. Vibrational frequency calculations on C20 and its analogues show that except B2N2C16 (1) and B2N2C16 (2), all other heterofullerenes are true minima. The heats of atomization energies, binding energy, band gaps (ΔEHOMO‐LUMO), aromaticity, nucleus‐independent chemical shifts, thermodynamic stability, kinetic stability against electronic excitation, binding energy as a stability criterion of different configurations, geometrical parameters, conformational structures, conductivity, charge transfer, and possibility for hydrogen storage of these heterofullerenes strongly depend on their number of heteroatoms, topology, filling patterns, and locations as well as “B‐site and N‐site attachments.” B5N5C10 contains 5 alternating boron and nitrogen atoms in the equatorial position. It is predicted to be thermodynamically and kinetically the most stable against electron excites. Thus, it is energetically favorable and its electronic properties as well as stabilities make it perhaps a good candidate for an experimental investigation and testing verification.