C Atoms Research Articles

Synthesis of Boronates with a Protoilludane Skeleton

AbstractNaturally occurring sesquiterpenes with a protoilludane skeleton are frequently oxygenated at carbon atoms C4 and C8. Boronic acid pinacol esters (BPin) are potential precursors for hydroxy groups at these positions and synthetic methods have now been developed for their preparation. Introduction of a boronate in position C4 was achieved by Cu-catalyzed hydroboration of a photochemically generated cyclobutene precursor, which displayed the complete C15-carbon skeleton of protoilludanes. Introduction of BPin at carbon atom C8 was possible by starting with an alkenyl boronate as precursor in a photochemical transformation. A two-photon reaction cascade allowed for creation of the complete protoilludane skeleton with BPin selectively positioned at C8. Subsequent reactions were studied and the oxidative transformation of the boronates into the respective alcohols was shown.

Investigating the physicochemical properties, structural attributes, and molecular dynamics of organic–inorganic hybrid [NH3(CH2)2NH3]2CdBr4·2Br crystals

An in-depth understanding of the physicochemical properties of the organic–inorganic hybrid [NH3(CH2)2NH3]2CdBr6 whose structure corresponds to the formulation [NH3(CH2)2NH3]2CdBr4· 2Br is essential for its application in batteries, supercapacitors, and fuel cells. Therefore, this study aimed to determine the crystal structure, phase transition, structural geometry, and molecular dynamics of these complexes. Considering its importance, a single crystal of [NH3(CH2)2NH3]2CdBr6 was grown; the crystal structure was found to be monoclinic. The phase transition temperatures were determined to be 443, 487, 517, and 529 K, and the crystal was thermally stable up to 580 K. Furthermore, the 1H, 13C, 14N, and 113Cd NMR chemical shifts caused by the local field surrounding the resonating nucleus of the cation and anion varied with increasing temperature, along with the surrounding environments of their atoms. In addition, 1H spin–lattice relaxation time T1ρ and 13C T1ρ, which represent the energy transfer around the 1H and 13C atoms of the cation, respectively, varied significantly with temperature. Consequently, changes in the coordination geometry of Br around Cd in the CdBr6 anion and the coordination environment around N (in the cation) were associated with changes in the N–H···Br hydrogen bond. The structural geometry revealed critical information regarding their basic mechanism of organic–inorganic hybrid compounds.

Synthesis, Crystal structure, Hirshfeld surface interactions, anti-corrosion analysis, DFT calculations, Docking studies and evaluation of the antioxidant activity of a new zwitterion Schiff base

The title compound Schiff base (SB) named: (6E)-3-benzyloxy-6- [ [ [2‑hydroxy-1,1-bis(hydroxymethyl)ethyl]amino]methylene]cyclohexa-2,4‑dien-1-one(I) (C18 H21 N O5), was synthesized via the reaction of 4-benzyloxy-2‑hydroxy-benzaldehyde with 2-amino-2-(hydroxymethyl)propane-1,3-diol (Trizma)and characterized by single-crystal diffraction XRD, infrared spectra, 1H and 13C NMR spectroscopy. It crystallizes as a zwitterion, (E)-5-(benzyloxy)-2-(((1,3-dihydroxy-2-(hydroxymethyl)propan-2-yl)iminio)methyl)phenolate (II), with the phenolic H atom having migrated to the imino group. Additionally,Hirshfeld surface analysis (HS), two-dimensional fingerprint plots and energy frameworks of II were calculated to quantify the interatomic interactions present in the crystal.The antioxidant activity of the synthesized compound was evaluated by five tests: ABTS, DPPH, O-pH, SNP and reducing power activity. Furthermore, molecular docking calculations were performed for SB compound at the active site of mushroom tyrosinase (PDB ID:2Y9X) to determine the binding affinity between the title compound and receptor protein. Results reveal a great affinity (-6.16 kcal/mol) of the SB to the protein that is mainly dominated by hydrogen bonds. In this work, experimentally, the assessment of the anti-corrosion ability of this compound by different methods showed excellent inhibition. On the other hand, anti-corrosion potentials of title compound have been investigated using density functional theory (DFT) in gas and solvent phases. Chemical reactivity descriptors like global hardness (η), chemical potential (u), electronegativity (χ), electrophilicity (ω) and number of transferred electrons (ΔN) were computed at ωB97XD with 6–311+g(d) basis set. The local reactive sites on this compound were studied using Fukui indices, local philicity index and dual descriptor. The quantum chemical calculation suggests a good charge transfer tendency from the title compound to the low-lying vacant d-orbitals of iron (The average value of charge transfer is ΔNIII/Fe.≈ 2.21 and ΔNIII/Cu.≈ 0.07). The C7 atom is the nucleophilic sites (Δf(r)C7 ≈ 0.25) on the inhibitor for effective interaction on the metal surface as shown by local reactive descriptor in gas and solvent. Furthermore, the results obtained from DFT and TD-DFT studies are in excellent agreement with experimental data (structure geometry (RMS Error ≈ 0.3 Å), optical properties (λexp-Cal ≈18 nm) and inhibition efficiencies).

Intramolecular Ynamide-Benzyne (3+2) Cycloadditions.

We report herein intramolecular (3+2) cycloadditionreactions between ynamides as three-atom components and benzyne. In theseintramolecularreactions, the two-bond formation is realized by exploiting benzyne precursors thatcontain a chlorosilyl group as alinking functionality. This method thushighlights the ambivalent character of the intermediate indolium ylide, which exhibitsboth nucleophilic and electrophilic properties at its C2 atom.

Intramolecular Ynamide–Benzyne (3+2) Cycloadditions

AbstractWe report herein intramolecular (3+2) cycloaddition reactions between ynamides as three‐atom components and benzyne. In these intramolecular reactions, the two‐bond formation is realized by exploiting benzyne precursors that contain a chlorosilyl group as a linking functionality. This method thus highlights the ambivalent character of the intermediate indolium ylide, which exhibits both nucleophilic and electrophilic properties at its C2 atom.

A new tetragonal superhard carbon allotrope with unusual stress-strain behavior

We identified a carbon allotrope with tetragonal symmetry (P42/nnm, 12 atoms/cell), termed TC12. Unusual tensile behavior characterized by an enormous deformation was observed, leading to a phase transition from superhard TC12 to metallic T6 carbon. This could be related to planar recovery of the C2 atom during stretching of twisted six-membered rings along the crystal direction [100]. The tensile limit of TC12 along the [100] crystal direction is up to 62.5%, corresponding to the tensile strength of 129.96 GPa. The phonon dispersion spectra and elastic constant verified its dynamical and mechanical stabilities. TC12 is a metastable 3D carbon allotrope possessing remarkable mechanical properties: bulk modulus of 339 GPa together with hardness of 56.8 GPa. Electronic structure prediction showed that semiconductor TC12 has an indirect bandgap of 2.247 eV. The findings establish a unique type of carbon phase, which is suggested as a potential material for electronic and machining applications.

Bidirectional selection of the functional properties and environmental friendliness of organophosphorus (OP) pesticide derivatives: Design, screening, and mechanism analysis

Organophosphorus pesticides (OPs) are widely used in agricultural production, but the resulting pollution and drug resistance have sparked widespread concern. Therefore, this paper built a model to design OP substitute molecules with high functionality and environmental friendliness, as well as conducted various human health and ecological environment evaluations, synthetic accessibility screening, and easy detection screening. The functionality of the two OP substitute molecules, DIM-100 and DIM-164, increased by 22.79 % and 22.18 %, respectively, and the environmental friendliness increased by 18.07 % and 24.02 %, respectively. The human health risk and ecological, environmental risks were significantly reduced. Both molecules are easy to synthesize, and their detection sensitivity is 9.85 % and 11.24 % higher than that of the target molecule, respectively. Furthermore, significant changes in the distribution of electrons and holes near the C8 and S1 atoms of the OP substitute molecule resulted in easier breakage of the C8-S1 bond, enhancing its photodegradation ability. The charge transfer ability between the atoms of the molecule (as increasing the electron-withdrawing group led to an increase in charge of the P atom) and the volume of the cholinesterase active pocket both affect the functionality of the DIM substitute molecule. That is, the volume of the cholinesterase active pocket of the bee is smaller than that of the brown planthopper and is more affected by the volume of the OP molecule. Furthermore, the mutual verification analysis of the bidirectional selectivity effect of OP substitute molecules between the BayesianRidge model and the 3D-QS(A2 + ∀3)R model reveals that the overall charge transfer degree of DIM substitute molecules is the main reason for the increase in the bidirectional selectivity effect.

Investigating on crystal structure, thermodynamic, and molecular dynamic of lead-free organic-inorganic hybrid [NH3(CH2)2NH3]ZnBr4 crystals

In this study, lead-free organic-inorganic hybrid [NH3(CH2)2NH3]ZnBr4 crystals were grown by slow evaporation and analyzed. The crystals showed orthorhombic structure with the P212121 space group, and the following lattice constants: a = 8.3818 (2) Å, b = 10.8880 (4) Å, c = 11.8175 (4) Å, and Z = 4. The crystals were stable up to 584 K, with two phase transitions at 468 K (TC1) and 503 K (TC2), as indicated by differential scanning calorimetry and differential thermal analysis. The structural environments of the atoms were analyzed by 1H and 13C NMR. On increasing the temperature, the spin-lattice relaxation time, T1ρ, decreased rapidly due to large energy transfer at high temperatures, as indicated by large thermal displacements of the 1H and 13C atoms of the cation. Additionally, the activation energy, Ea, at high and low temperatures was found to be 49.23 and 1.44 kJ/mol, respectively, for the molecular motion of 1H, and 37.93 and 2.13 kJ/mol, respectively, for that of 13C. Analyzing the physiochemical properties of [NH3(CH2)2NH3]ZnBr4 could facilitate its application in stable and environment-friendly solar cells.

Analysis of the Electron Density of a Water Molecule Encapsulated by Two Cholic Acid Residues

Cholic acid is a trihydroxy bile acid with a nice peculiarity: the average distance between the oxygen atoms (O7 and O12) of the hydroxy groups located at C7 and C12 carbon atoms is 4.5 Å, a value which perfectly matches with the O/O tetrahedral edge distance in Ih ice. In the solid phase, they are involved in the formation of hydrogen bonds with other cholic acid units and solvents. This fact was satisfactorily used for designing a cholic dimer which encapsulates one single water molecule between two cholic residues, its oxygen atom (Ow) being exactly located at the centroid of a distorted tetrahedron formed by the four steroid hydroxy groups. The water molecule participates in four hydrogen bonds, with the water simultaneously being an acceptor from the 2 O12 (hydrogen lengths are 2.177 Å and 2.114 Å) and a donor towards the 2 O7 (hydrogen bond lengths are 1.866 Å and 1.920 Å). These facts suggest that this system can be a nice model for the theoretical study of the formation of ice-like structures. These are frequently proposed to describe the water structure found in a plethora of systems (water interfaces, metal complexes, solubilized hydrophobic species, proteins, and confined carbon nanotubes). The above tetrahedral structure is proposed as a reference model for those systems, and the results obtained from the application of the atoms in molecules theory are presented here. Furthermore, the structure of the whole system allows a division into two interesting subsystems in which water is the acceptor of one hydrogen bond and the donor of another. The analysis of the calculated electron density is performed through its gradient vector and the Laplacian. The calculation of the complexation energy used correction of the basis set superposition error (BSSE) with the counterpoise method. As expected, four critical points located in the H…O bond paths were identified. All calculated parameters obey the proposed criteria for hydrogen bonds. The total energy for the interaction in the tetrahedral structure is 54.29 kJ/mol, while the summation obtained of the two independent subsystems and the one between the alkyl rings without water is only 2.5 kJ/mol higher. This concordance, together with the calculated values for the electron density, the Laplacian of the electron density, and the lengths of the oxygen atom and the hydrogen atom (involved in the formation of each hydrogen bond) to the hydrogen bond critical point, suggests that each pair of hydrogen bonds can be considered independent of each other.

N-heterocyclic carbene-mediated oxidation of copper(I) in an imidazolium ionic liquid

Abstract The aerobic oxidation of copper(I) to copper(II) was studied in the ionic liquid (IL) 1-n-butyl-3-methylimidazolium acetate [BMIm][OAc]. Temperatures above 100 °C promote the deprotonation of the C2 atom of the imidazolium ring and the dissolution of CuCl. 1H and 13C NMR spectra indicate the formation of the N-heterocyclic carbene (NHC) complex [NHC] CuICl under inert conditions. Upon aerobic oxidation, air-stable blue-green crystals of [BMIm]2[CuII 2(OAc)4Cl2] precipitate in high yield and the NHC is recovered. X-ray diffraction on a single-crystal of the complex salt revealed a monoclinic structure with space group P21/n. The centrosymmetric dinuclear acetate complex [Cu2(OAc)4Cl2]2– has the paddle-wheel motif and is weakly paramagnetic.

Backbone NMR assignment of the yeast expressed Fab fragment of the NISTmAb reference antibody.

The monoclonal antibody (mAb) protein class has become a primary therapeutic platform for the production of new life saving drug products. MAbs are comprised of two domains: the antigen-binding fragment (Fab) and crystallizable fragment (Fc). Despite the success in the clinic, NMR assignments of the complete Fab domain have been elusive, in part due to problems in production of properly folded, triply-labeled 2H,13C,15N Fab domain. Here, we report the successful recombinant expression of a triply-labeled Fab domain, derived from the standard IgG1κ known as NISTmAb, in yeast. Using the 2H,13C,15N Fab domain, we assigned 94% of the 1H, 13C, and 15N backbone atoms.

Adsorption of 3d transition-metal atoms on two-dimensional penta-graphene: A first-principles study

The adsorption of single 3d transition metal (TM) atoms (from Sc to Zn) on a (3 × 3) penta-graphene (PG) sheet has been systematically studied by means of density-functional theory calculations. We particularly study the effect of the TM adatom on the structural, electronic, and magnetic properties when adsorbed on the PG sheet. Our calculations have shown that most of the TM adatoms are preferably adsorbed on the T2 site (i.e., the top of the C2 atom located at the bottom layer), while Cr, Zn, and Ni are preferably adsorbed on different B sites. The calculated band structures demonstrate that all TM-PG systems remain semiconductors such that the gap between the valence and conduction bands moves to a lower energy state relative to the Fermi level. For this reason, an apparent narrowing in the band gap values for the TM-PG systems has been predicted (0.11 – 0.97 eV) compared to the band gap of the isolated PG sheet (2.23 eV). Additionally, our results indicate that most of the TM-PG systems are magnetic, with the exception of Ni-PG and Zn-PG systems. Consequently, the engineering of the electronic properties of the TM-PG systems implies that such systems might be promising candidates for different applications.

Mid-Infrared Photothermal-Fluorescence In Situ Hybridization for Functional Analysis and Genetic Identification of Single Cells.

Simultaneous identification and metabolic analysis of microbes with single-cell resolution and high throughput are necessary to answer the question of "who eats what, when, and where" in complex microbial communities. Here, we present a mid-infrared photothermal-fluorescence in situ hybridization (MIP-FISH) platform that enables direct bridging of genotype and phenotype. Through multiple improvements of MIP imaging, the sensitive detection of isotopically labeled compounds incorporated into proteins of individual bacterial cells became possible, while simultaneous detection of FISH labeling with rRNA-targeted probes enabled the identification of the analyzed cells. In proof-of-concept experiments, we showed that the clear spectral red shift in the protein amide I region due to incorporation of 13C atoms originating from 13C-labeled glucose can be exploited by MIP-FISH to discriminate and identify 13C-labeled bacterial cells within a complex human gut microbiome sample. The presented methods open new opportunities for single-cell structure-function analyses for microbiology.

Irreversible inactivation of lactate racemase by sodium borohydride reveals reactivity of the nickel-pincer nucleotide cofactor.

The nickel-pincer nucleotide (NPN) cofactor discovered in lactate racemase from Lactiplantibacillus plantarum (LarALp) is essential for the activities of racemases/epimerases in the highly diverse LarA superfamily. Prior mechanistic studies have established a proton-coupled hydride-transfer mechanism for LarALp, but direct evidence showing that hydride attacks the C4 atom in the pyridinium ring of NPN has been lacking. Here, we show that sodium borohydride (NaBH4) irreversibly inactivates LarALp accompanied by a rapid color change of the enzyme. The altered ultraviolet-visible spectra during NaBH4 titration supported hydride transfer to C4 of NPN, and the concomitant Ni loss unraveled by mass spectrometry experiments accounted for the irreversible inactivation. High resolution structures of LarALp revealed a substantially weakened C-Ni bond in the metastable sulfite-NPN adduct where the NPN cofactor is in the reduced state. These findings allowed us to propose a mechanism of LarALp inactivation by NaBH4 that provides key insights into the enzyme-catalyzed reaction and sheds light on the reactivity of small molecule NPN mimetics.

Synthesis of fluorescent chalcones, photophysical properties, quantitative structure-activity relationship and their biological application

The development of fluorescent pigments is an area of interest in several research fields due to their high sensitivity. In the current study-eight known and three new N,N-dimethylamino-chalcones (12a-k) were synthesized with good yields using the Claisen-Schmidt reaction. For each molecular system, the photophysical properties, including the maximum absorption wavelength (λAbsorption), molar absorption coefficient (ε), maximum excitation wavelength (λExcitation), maximum emission wavelength (λEmission), Stokes Shift (Δλ), fluorescence quantum yield (Φfl), fluorescence lifetime (τfl), radiative and non-radiative rate constants (kR and kNR, respectively) were evaluated. Variations in each of these properties were analyzed depending on the substituents present on each compound. To relate the chemical structures of the synthesized compounds to their photophysical properties, Hansch analysis (2D-QSPR) was applied. As a result of Hansch analysis, we found different photophysical properties related to molecular orbitals and the energy of their derivatives (Highest Occupied Molecular Orbital-HOMO, Lowest Unoccupied Molecular Orbital-LUMO, Difference between LUMO-HOMO-ΔLH, Chemical potential-µ, Hardness-η, Softness-S, and electrophilic global index-ω) as well as to the atomic charges on atoms C5, Cα, Cβ, and CO. The application of this type of analysis has made it possible to understand and subsequently design new molecules with defined photophysical properties. Finally, the compounds were use as fluorescent pigment to get living cell imaging on breast cancer cells, obtaining the compound 12a as promissory alternative.

Stereoselective Epoxidation of Triterpenic Allylic Alcohols and Cytotoxicity Evaluation of Synthesized Compounds.

The epoxidation process of semi-synthetic triterpenoids 2-methyl-3-oxo-19β,28-epoxy- 18α-olean-1-ene, and its allylic alcohol derivatives were examined. 1,2α-epoxide, as the main product, was found to be formed from the starting enone exposed to m-chloroperbenzoic acid (mCPBA). In the case of hydroxy-directed mCPBA-oxidation of triterpenic allyl alcohols and their 3α-alkyl-substituted derivatives, inversion of C1 and C2 asymmetric centers with the formation of 1,2β-epoxyalcohols took place. The synthesis of 2,3α-epoxides was fulfilled from 2,3-dialkyl-substituted C(3) allyl alcohols by the action of pyridinium chlorochromate under [1,3]-oxidative rearrangement conditions. The transformations brought about enabled chiral oleanane derivatives with an oxygen-containing substituent at the C1, C2, and C3 atoms to be obtained. The study also provides information on in silico PASS prediction of pharmacological effects and in vitro evaluation of the cytotoxic activity of the synthesized compounds.

Ab initio chemical kinetics of Isopropyl acetate oxidation with OH radicals

ABSTRACT Global reactivity descriptors of isopropyl acetate (IPA) and thermo-kinetic aspects of its oxidation via OH radicals have been studied. Transition state theory (TST) was utilized to estimate the bimolecular rate constants. Ten oxidation pathways have been investigated, and all of them are exothermic. The potential energy diagram has been sketched using different pre- and post-reactive complexes for all reaction pathways. Rate coefficient calculations were obtained directly by connecting the separated reactants with different transition states. The results indicate that the reaction of IPA with OH radicals occurs in the ground state rather than the excited state, and the rate constants obtained directly and from the effective approach are the same, which confirmed the accuracy of the estimated pre-reactive complexes and the reaction mechanism. Rate constants and branching ratios show that hydrogen atom abstraction from the iso C − H (C2 atom) bond is the most kinetically preferable route up to 1000 K, while at higher temperatures, H-atom abstraction from the out-of-plane CH3 group (C3 atom) became the most dominant route with high competition with that of the in-plane CH3 group (C4 atom).

Design of N-11-Azaartemisinins Potentially Active against <i>Plasmodium falciparum</i> by Combined Molecular Electrostatic Potential, Ligand-Receptor Interaction and Models Built with Supervised Machine Learning Methods

N-11-azaartemisinins potentially active against Plasmodium falciparum are designed by combining molecular electrostatic potential (MEP), ligand-receptor interaction, and models built with supervised machine learning methods (PCA, HCA, KNN, SIMCA, and SDA). The optimization of molecular structures was performed using the B3LYP/6-31G* approach. MEP maps and ligand-receptor interactions were used to investigate key structural features required for biological activities and likely interactions between N-11-azaartemisinins and heme, respectively. The supervised machine learning methods allowed the separation of the investigated compounds into two classes: cha and cla, with the properties εLUMO+1 (one level above lowest unoccupied molecular orbital energy), d(C6-C5) (distance between C6 and C5 atoms in ligands), and TSA (total surface area) responsible for the classification. The insights extracted from the investigation developed and the chemical intuition enabled the design of sixteen new N-11-azaartemisinins (prediction set), moreover, models built with supervised machine learning methods were applied to this prediction set. The result of this application showed twelve new promising N-11-azaartemisinins for synthesis and biological evaluation.

ОКИСЛЕНИЕ ХИРАЛЬНЫХ БИС-ТИОЭФИРОВ РЯДА 2(5Н)-ФУРАНОНА ДО ДИСУЛЬФОКСИДОВ

Novel disulfinyl derivatives based on 3,4-dichloro-2(5H)-furanone, aliphatic dithiols, and monoterpene alcohols were synthesized. Chiral bis-thioethers in the molecules of which the dithiol fragment links two five-membered cycles at C4 atoms were obtained in the reactions of 5(S)-(l-menthyloxy)- and 5(S)-(l-bornyloxy)-2(5H)-furanones with ethane-1,2-dithiol and propane-1,3-dithiol in acetone in basic medium. The action of an excess of m-chloroperoxybenzoic acid (2.0–3.2 equiv.) on bis-thioethers led to the formation of the corresponding mono- and disulfoxides bearing l-menthol or l-borneol fragments at the 5th position of the lactone ring. The methods of column chromatography and fractional recrystallization were used for the isolation of individual products. The structure of the synthesized heterocycles was proved by IR and NMR spectroscopy, and their composition was confirmed by high-resolution mass spectrometry. The molecular structure of the three disulfoxides was characterized by X-ray diffraction analysis.

Investigation of the structure, phase transitions, molecular dynamics, and ferroelasticity of organic-inorganic hybrid NH(CH3)3CdCl3 crystals.

Understanding the physical and chemical properties of the organic-inorganic hybrid NH(CH3)3CdCl3 is essential for its application. Considering its importance, a single crystal of NH(CH3)3CdCl3 was grown with an orthorhombic structure at 300 K. The phase transition temperatures were determined to be 345 (TC3), 376 (TC2), and 452 K (TC1) (phases IV, III, II, and I, respectively, starting from a low temperature). The partial decomposition temperature was 522 K (Td). Furthermore, the NMR chemical shifts of the 1H, 13C, and 113Cd atoms of the cation and anion varied with increasing temperature. Consequently, a significant change in the coordination geometry of Cl around Cd in CdCl6 and a change in the coordination geometry of H in NH was associated with changes in the N-H⋯Cl hydrogen bond near the phase transition temperature. The 13C activation energy Ea obtained from the spin-lattice relaxation time was smaller than that of 1H Ea, suggesting that energy transfer around 13C is easier. Additionally, a comparison of the twin domain walls measured via optical polarizing microscopy and Sapriel's theory indicated that the crystal structure in phase III was more likely to be orthorhombic than hexagonal.