Hydrogen Atoms Research Articles

Unlocking the potential of Allium dictyoprasum C.A. Meyer ex Kunth: quantum chemical insights into radical scavenging, chemical composition, phenolic content, and antimicrobial activity

ABSTRACT Allium dictyoprasum C.A. Meyer ex Kunth (A. dictyoprasum) underwent comprehensive analysis, encompassing quantum chemical computations to assess its radical scavenging potential, chemical and elemental composition, total phenolic content, and antimicrobial activity. Experimental and theoretical investigations focused on elucidating the radical scavenging properties of polyhydroxy phenolic compounds present in the plant. Quantum chemical calculations were employed to evaluate the antioxidants employed to evaluate selected polyhydroxy phenolic molecules including flavonoids, hydrocinnamic acid derivatives, and hydroxybenzoic acid derivatives from natural sources. Thermochemical parameters of these compounds were calculated by the B3LYP/6–311 G++(d,p) level in both gas and solvent phases to elucidate the radical scavenging mechanism including hydrogen atom transfer (HAT), single electron transfer followed by proton transfer (SET-PT) and sequential proton loss electron transfer (SPLET). Analysis of A. dictyoprasum extracts obtained via various extraction methods revealed the presence of several major compounds, including dimethyl trisulfide, 3,5-Dihydroxy-6-methyl-2,3-dihydro-4 H-pyran-4-one, 2-Methoxy-4-vinylphenol, Dimethyl phthalate, Methyl palmitate, Methyl oleate, Methyl stearate, (9Z)-9-Octadecenamide. Notably, Malic acid and Quinic acid were identified as major compounds, with concentrations of 43.31 and 17.47 mg kg−1 extract, respectively, based on LC-MS/MS analysis. The total phenolic content of the extract was measured as 17.83 mg gallic acid/mL, while its free radical scavenging activity was 80.89% per mg/mL. Elemental analysis revealed significant levels of Mg, K, Na, Fe, and P, with minor concentrations of elements such as Ti, Tl, B, and Be. Furthermore, A. dictyoprasum exhibited notable antibacterial activity against various bacteria strains, surpassing the efficacy of some commercial antibiotics.

Unraveling the Structural and Vibrational Response of Zharchikhite to Pressure (II): Insights from First Principles Calculations

The halide mineral Zharchikhite with the chemical formula AlF(OH)2 is studied using first-principles methods of density functional theory with the local functional VBH, generalized gradient functionals PBE, BLYP, PBEsol, with an empirical dispersion correction in the form of D3(BJ) PBE-D3, BLYP-D3, global hybrid functionals PBE0, B3LYP, PBEsol0, hybrid functionals with range separation HSE06, SC-BLYP. It is shown that all functionals overestimate O-H and underestimate O-H∙∙∙O distances. The best values are provided by SC-BLYP, B3LYP. The bulk modulus, determined from the Birch-Murnaghan equation of state, is 72.32GPa. The axes compress unevenly and the fastest is the longest one with a modulus of 217.3GPa. The linear compressibility modulus of the Al-F bond has a similar value and is twice as large for the Al-O bond. Under pressure, the lengths of H∙∙∙O hydrogen bonds decrease faster and, conversely, O-H bonds slowly increase. Also, at a rate of 0.289°/GPa, the monoclinic angle also increases with pressure. The spectra of infrared absorption and Raman scattering of light have been calculated, in which vibrations of Al-F and Al-O atoms will be active in the region up to 600cm−1; above 700cm−1 there are translational vibrations of O-H with a dominant contribution of H1 (Au symmetry) or H2 (Bu symmetry) and above 3200cm−1 100% hydrogen atoms. For them, with increasing pressure, the wave numbers decrease and the Grüneisen parameters change from −0.36 to −0.54. The large value of the derivative dν/dP can be used to solve the inverse problem - finding the pressure P from the known wave number ν(P).

Hydrogen penetration into the NiTi superelastic alloy investigated in-situ by synchrotron diffraction experiments

Microstructural changes induced by a hydrogen permeation into the NiTi superelastic alloy were investigated in-situ using the X-ray synchrotron diffraction. A new design of an electrochemical cell enabled to uncover time and position dependent processes under a flat alloy surface exposed to the cathodic hydrogen. The diffraction data supported by thermo-elastic FEM calculations helped to quantify an evolution of compressive stresses in the B2 austenitic phase hosting hydrogen atoms. The compressive stress state initiates a formation of martensitic phases starting from the exposed surface layer and advancing into the alloy volume with increasing time of hydrogen charging. We have performed the ab-initio DFT study in order to rationalize volumetric changes associated with variations in the B2 austenite and B19’ martensite lattice parameters. The numerical results also contributed to the identification of a new hydride phase with orthorhombic crystal structure and lattice parameters a=0.8505 nm, b=0.7366 nm and c=0.4722 nm.

Unraveling the Mechanism of Hydrogen Atom Transfer by a Nickel-Hypochlorite Species and the Influence of Electronic Effects.

The oxidation of hydrocarbons is an important chemical transformation with relevance to biology and industry. Ni-catalyzed transformations are more scarce compared to Mn or Fe but have gained attention in recent years, affording efficient oxidations. Understanding the mechanism of action of these catalysts, including the detection and characterization of the active nickel-oxygen species, is of interest to design better catalysts. In this work, we undertake a theoretical study to unravel the mechanism of formation of the previously reported [Ni(OCl)(HL)]+ (H2) and how it activates C-H bonds. We disclose that the active species is indeed compound [Ni(O)(HL)]+, formed after homolytic cleavage of the O-Cl bond in H2 assisted by a chlorine radical. [Ni(O)(HL)]+ mediates C-H activation through an asynchronous concerted mechanism, in which the transition state is given by hydrogen atom transfer. Moreover, the electronic tuning of the ligand has a very modest impact on the stability and reactivity of the corresponding X2 species. Effective oxidation state analysis reveals an intriguing electronic structure of H2 and [Ni(O)(HL)]+, in which both the macrocycic HL ligand and the OCl and O ligands behave as redox noninnocent. Such redox activity leads to a fully ambiguous oxidation state assignation.

Hydrogen Atom Abstraction and Reduction Study of 21-Thiaporphyrin and 21,23-Dithiaporphyrin

The metal-free porphyrins protonation has gained interest over five decades because its structure modification and hardly monoacid intermediate isolation. Here, upon the hydrogen atom abstraction processes, one step diproptonated H2STTP(BF4)2 (STTP = 5,10,15,20-tetraphenyl-21-thiaporphyrin) (3) and stepwise protonated HS2TTPSbCl6 (5) and diprotonated H2S2TTP(BF4)2 (6) (S2TTP = 5,10,15,20-tetraphenyl-21,23-thiaporphyrin) compounds were obtained using HSTTP and S2TTP with oxidants. The closed-shell protonated compounds were fully characterized using XRD, UV-vis, IR and NMR spectra. In addition, the reduced 19π compounds [K(2,2,2)]HSTTP (2) and [K(2,2,2)]S2TTP (7) were synthesized by the ligands with reductant KC8 in THF solution. These two open-shell compounds were characterized with UV-vis, IR and EPR spectroscopies. The semiempirical ZINDO/S method was employed to analyze the HOMO/LUMO gap lever and identify the electronic transitions of the UV-vis spectra of the closed- and open-shell porphyrin compounds.

Time evolution as an optimization problem: The hydrogen atom in strong laser fields in a basis of time-dependent Gaussian wave packets.

Recent advances in attosecond science have made it increasingly important to develop stable, reliable, and accurate algorithms and methods to model the time evolution of atoms and molecules in intense laser fields. A key process in attosecond science is high-harmonic generation, which is challenging to model with fixed Gaussian basis sets, as it produces high-energy electrons, with a resulting rapidly varying and highly oscillatory wave function that extends over dozens of ångström. Recently, Rothe's method, where time evolution is rephrased as an optimization problem, has been applied to the one-dimensional Schrödinger equation. Here, we apply Rothe's method to the hydrogen wave function and demonstrate that thawed, complex-valued Gaussian wave packets with time-dependent width, center, and momentum parameters are able to reproduce spectra obtained from essentially exact grid calculations for high-harmonic generation with only 50-181 Gaussians for field strengths up to 5 × 1014 W/cm2. This paves the way for the inclusion of continuum contributions into real-time, time-dependent electronic-structure theory with Gaussian basis sets for strong fields and eventually accurate simulations of the time evolution of molecules without the Born-Oppenheimer approximation.

Photocatalyzed Cascade Hydrogen Atom Transfers for Assembly of Multi-Substituted α-SCF3 and α-SCF2H Cyclopentanones.

A photocatalyzed formal (3+2) cycloaddition has been developed to construct original polysubstituted α-SCF3 cyclopentanones in a regio- and diastereoselective manner. This building block approach leverages trifluoromethylthio alkynes and branched/linear aldehydes, as readily available reaction partners, in consecutive hydrogen atom transfers and C-C bond formations. Difluoromethylthio alkynes are also compatible substrates. Furthermore, the potential for telescoped reaction starting from alcohols instead of aldehydes was demonstrated, as well as process automatization and scale-up under continuous microflow conditions. This prompted density functional theory (DFT) calculations to support a radical-mediated cascade process.

Photocatalyzed Cascade Hydrogen Atom Transfers for Assembly of Multi‐Substituted α‐SCF3 and α‐SCF2H Cyclopentanones

AbstractA photocatalyzed formal (3+2) cycloaddition has been developed to construct original polysubstituted α‐SCF3 cyclopentanones in a regio‐ and diastereoselective manner. This building block approach leverages trifluoromethylthio alkynes and branched/linear aldehydes, as readily available reaction partners, in consecutive hydrogen atom transfers and C−C bond formations. Difluoromethylthio alkynes are also compatible substrates. Furthermore, the potential for telescoped reaction starting from alcohols instead of aldehydes was demonstrated, as well as process automatization and scale‐up under continuous microflow conditions. This prompted density functional theory (DFT) calculations to support a radical‐mediated cascade process.

Photoinduced Lignin C α -C β Bond Cleavage and Chemodivergent Functionalization via Iron Catalysis.

The photocatalytic conversion of lignin into value-added chemicals especially those functionalized molecules represent one of the most important strategies for sustainable and environmental-friendly development. Cleavage of C-C bonds in lignin under mild photocatalytic conditions for refining lignin into useful molecules is meaningful but challenging. Meanwhile, the assembly of diverse functional groups into active lignin fragments during the depolymerization is of great challenging. Herein, using cheap iron catalysts under visible light irradiation, the highly selective and efficient cleavage of Cα-Cβ bond in lignin is realized via ligand-to-metal charge transfer (LMCT) and hydrogen atom transfer (HAT) processes. The subsequent divergent functionalization of generated lignin fragment-based radical intermediates enables an efficient formation of diverse functionalized molecules. This method is also effective for cleavage of Cα-Cβ bond in native lignin, yielding two identified benzaldehyde monomers in a total yield of 8.7 wt%.

Desorption of atomic hydrogen from graphene on hexagonal boron nitride

Desorption of atomic hydrogen from graphene on hexagonal boron nitride

Probing Short-Range Interactions in Isostructural Hydrate and Perhydrate of Dabrafenib by Magic-Angle Spinning Solid-State NMR.

Dabrafenib (DBF), an anticancer drug, exhibits isostructural properties in its hydrate (DBF⊃H2O) and perhydrate (DBF⊃H2O2) forms, as revealed by single-crystal X-ray diffraction. Despite the H2O and H2O2 solvent molecules occupying identical locations, the two polymorphs have different thermal behaviors. In general, determination of stoichiometry of H2O in the perhydrate crystals is difficult due to the presence of both H2O and H2O2 in the same crystal voids. This study utilizes magic-angle spinning (MAS) solid-state NMR (SSNMR) combined with gauge-included projector augmented wave calculations to characterize the influence of solvent molecules on the local environment in pseudopolymorphs. SSNMR experiments were employed to assign 1H, 13C, and 15N peaks and identify spectral differences in the isostructural pseudopolymorphs. Proton spectroscopy at fast MAS was used to identify and quantify H2O2/H2O in DBF⊃H2O2 (mixed hydrate/perhydrate). 1H-1H dipolar-coupling-based experiments were recruited to confirm the 3D molecular packing of solvent molecules in DBF⊃H2O and DBF⊃H2O2. Homonuclear (1H-1H) and heteronuclear (1H-14N) distance measurements, in conjunction with diffraction structures and optimized hydrogen atom positions by density functional theory, helped decipher local interactions of H2O2 with DBF and their geometry in DBF⊃H2O2. This integrated X-ray structure, quantum chemical calculations, and NMR study of pseudopolymorphs offer a practical approach to scrutinizing crystallized solvent interactions in the crystal lattice even without high-resolution crystal structures or artificial sample enrichment.

Unraveling the Geometry-Driven C═C Epoxidation and C-H Hydroxylation Reactivity of Tetra-Coordinated Nonheme Iron(IV)-Oxo Complexes.

The electronic structure and reactivity of tetra-coordinated nonheme iron(IV)-oxo complexes have remained unexplored for years. The recent synthesis of a closed-shell iron(IV)-oxo complex [(quinisox)FeIV(O)]+ (1) has set up a platform to understand how such complexes compare with the celebrated open-shell iron-oxo chemistry. Herein, using density functional theory and ab initio calculations, we present an in-depth electronic structure investigation of the C═C epoxidation [oxygen atom transfer (OAT)] and C-H hydroxylation [hydrogen atom transfer (HAT)] reactivity of 1. Using a solvent-coordinated geometry of 1 (1') and other potential tetra-coordinated iron(IV)-oxo complexes bearing rigid ligands (2 and 3), we established the geometric origin of spin-state energetics and reactivity of 1. Complex 1 featuring a strong Fe-O bond exhibits OAT and HAT reactivity in its quintet state. The lowest quintet OAT pathway has a lower barrier by ∼4 kcal/mol than the quintet HAT pathway, corroborating the experimentally observed gas-phase OAT reactivity preference. A conventional HAT reactivity preference for 2 and a comparable OAT and HAT reactivity for 3 are observed. This further supports the geometry-driven reactivity preference for 1. Noncovalent interaction analyses reveal a pronounced π-π interaction between the substrate and ligand in the OAT transition state, rationalizing the origin of the observed reactivity preference for 1.

Ultrahigh Pt-mass-activity catalyst for alkaline hydrogen evolution synthesized by microwave method in air

Platinum (Pt) metal is widely acknowledged as a highly efficient electrocatalyst for hydrogen evolution reaction (HER) in acidic electrolyte. However, its performance in alkaline environments is significantly lower owing to the sluggish water dissociation step. Herein, we synthesized an ultrahigh Pt-mass-activity alkaline HER catalyst using microwave reduction method in air. Our catalyst, PtRu@CNT, comprises PtRu alloy nanoparticles uniformly loaded on carbon nanotubes, with Pt and Ru contents of 12.3 wt% and 4.5 wt%, respectively. The PtRu alloy nanoparticles have an average diameter of about 3 nm and a face-centered cubic structure, and the introduction of Ru has led to a modified electronic structure in Pt. As a result, an impressively low HER overpotential of 13 mV was achieved, significantly lower than commercial 20 wt% Pt/C (61 mV). PtRu@CNT exhibited a high turnover frequency based on metal mass of 3.06 s−1 at 100 mV, about 6 times higher than commercial Pt/C (0.46 s−1 at 100 mV), highlighting its excellent intrinsic activity. The HER mechanism of PtRu@CNT is a Volmer-Tafel mechanism, where the rate-limiting step changed to the recombination of hydrogen atoms from initial water dissociation, attributed to the presence of Ru. The alkaline HER activity of PtRu@CNT ranks among the best of currently reported Pt-based catalysts.

Biosynthesis of the Non-canonical C17 Sesquiterpenoids Chlororaphen A and B from Pseudomonas chlororaphis.

Chlororaphens A and B are structurally unique non-canonical C17 sesquiterpenoids from Pseudomonas chlororaphis that are made by two SAM-dependent methyltransferases and a type I terpene synthase. This study addresses the mechanism of their formation in isotopic labelling experiments and DFT calculations. The results demonstrate an astonishing complexity with distribution of labellings within a cyclopentane core that is reversely connected to two acyclic fragments in chlororaphen A and B. In addition, the uptake of up to 14 deuterium atoms from D2O was observed. These findings are explainable by a repeated late stage multistep rearrangement sequence. The absolute configurations of the chlororaphens and their biosynthetic intermediates were elucidated in stereoselective labelling experiments.

Flavonoid as a Potent Antioxidant: Quantitative Structure-Activity Relationship Analysis, Mechanism Study, and Molecular Design by Synergizing Molecular Simulation and Machine Learning.

In this work, a quantitative structure-antioxidant activity relationship of flavonoids was performed using a machine learning (ML) method. To achieve lipid-soluble, highly antioxidant flavonoids, 398 molecular structures with various substitute groups were designed based on the flavonoid skeleton. The hydrogen dissociation energies (ΔG1, ΔG2, and ΔG3) related to multiple hydrogen atom transfer processes and the solubility parameter (δ) of flavonoids were calculated using molecular simulation. The group decomposition results and the calculated antioxidant parameters constituted the ML data set. The artificial neural network and random forest models were constructed to predict and analyze the contribution of the substitute groups and positions to the antioxidant activity. The results showed the hydroxyl group at positions B4', B5', and B6' and the branched alkyl group at position C3 in the flavonoid skeleton were the optimal choice for improving antioxidant activity and compatibility with apolar organic materials. Compared to the pyrogallol group-grafted flavonoid, the designed potent flavonoid decreased ΔG1 and δ by 2.2 and 15.1%, respectively, while ΔG2 and ΔG3 kept the favorable lower values. These findings suggest that an efficient flavonoid prefers multiple ortho-phenolic hydroxyl groups and suitable sites with hydrophobic groups. The combination of molecular simulation and the ML method may offer a new research approach for the molecular design of novel antioxidants.

Deuterium Editing of Small Molecules: A Case Study on Antitumor Activity of 1,4-Benzodiazepine-2,5-dione Derivatives.

Substituting hydrogen with deuterium in drug molecules is an appealing bioisosteric strategy for the generation of novel chemical entities in drug development. Optimizing lead compounds through deuteration has proven to be challenging and unpredictable, particularly for compounds with multiple metabolic sites. This study presents the pioneering achievement of substituting up to 19 hydrogen atoms with deuterium on 1,4-benzodiazepine-2,5-dione derivatives, shedding light on the structure-metabolism relationship and the impact of multiple deuterations on drug-like properties. Notably, the deuterated compound 3f exhibited remarkable antitumor activity in vivo and demonstrated favorable drug-like properties as a drug candidate.

Explicitly Correlated Gaussians with Tensor Pre-factors: Analytic Matrix Elements

We consider a specific form of explicitly correlated Gaussians—with tensor pre-factors—which appear naturally when dealing with certain few-body systems in nuclear and particle physics. We derive analytic matrix elements with these Gaussians—overlap, kinetic energy, and Coulomb potential—to be used in variational calculations of those systems. We also perform a quick test of the derived formulae by applying them to p- and d-waves of the hydrogen atom.

1,3-Difunctionalization of [1.1.1]propellane through iron-hydride catalyzed hydropyridylation

Current methodologies for the functionalization of [1.1.1]propellane primarily focus on achieving 1, 3-difunctionalized bicyclo[1.1.1]pentane or ring-opened cyclobutane moiety. Herein, we report an innovative approach for the 1, 3-difunctionalization of [1.1.1]propellane, enabling access to a diverse range of highly functionalized cyclobutanes via nucleophilic attack followed by ring opening and iron-hydride hydrogen atom transfer. To enable this method, we developed an efficient iron-catalyzed hydropyridylation of various alkenes for C − H alkylation of pyridines at the C4 position, eliminating the need for stoichiometric quantities of oxidants or reductants. Mechanistic investigations reveal that the resulting N-centered radical serves as an effective oxidizing agent, facilitating single-electron transfer oxidation of the reduced iron catalyst. This process efficiently sustains the catalytic cycle, offering significant advantages for substrates with oxidatively sensitive functionalities that are generally incompatible with alternative approaches. The strategy presented herein is not only mechanistically compelling but also demonstrates broad versatility, highlighting its potential for late-stage functionalization.

A broad-spectrum oxidation capability Ru-CeO2 catalyst for efficient synergistic selective oxidation of benzyl alcohol

Selective oxidation of alcohols to aldehydes by molecular oxygen is one of the most important transformations in multiphase catalysis. In this paper, a catalyst with selective oxidation ability was designed and synthesized for the selective catalytic oxidation of benzyl alcohol. N-doped carbon materials were prepared by high-temperature calcination using hydrothermal reaction products of citric acid and melamine as a carbon source, and a bimetallic catalyst supported by Ru-CeO2 was constructed using the mixture as the carrier for the selective oxidation of benzyl alcohol to benzaldehyde. The results showed that the introduction of CeO2 could effectively improve the oxidizing ability and catalytic activity of the catalyst. The Ru-Ce0.05/NC170–600 catalyst was able to convert 85.5 % benzyl alcohol into benzaldehyde at 140 °C, 6 h, and 2 MPa, and the selectivity for benzaldehyde was 100 %. It was demonstrated by DFT that it was theoretically feasible to generate benzaldehyde by extracting hydrogen atoms from benzyl alcohol molecules. Further, the selective oxidation experiments on other alcohols showed that the catalyst has high activity for the oxidation of various alcohols to generate the corresponding carbonyl products, and it is a catalyst with broad-spectrum selective oxidation ability. In this study, a green synthesis route of benzaldehyde was proposed to solve the problems in the traditional process. Meanwhile, it provides a new idea for the synthesis of carbonyl products by selective oxidation of alcohols.

Direct Functionalization of Polyethylene Surfaces with High-Density Polymer Brushes.

Introducing functionality onto PE surfaces is a longstanding challenge in polymer science, driven by the need for polymer materials with improved adhesion and antifouling properties. Herein, we report surface-initiated hydrogen atom transfer-reversible addition-fragmentation chain transfer (SI HAT-RAFT) as a robust method to grow high-density brush polymers from PE surfaces. We demonstrate that, under mild conditions, direct initiation from the C-H bonds of PE surfaces allows for the graft polymerization of a variety of (meth)acrylate monomers. The resulting polymer brushes reached several hundred nanometers in thickness with densities of ca. 0.62 chains/nm2, compared to the current standard of ∼0.28 chains/nm2. Finally, we show that our method is capable of dramatically improving the adhesive properties of PE surfaces. This work enables the preparation of PE with diverse surface functionalities for potential use in biomedical, industrial, and battery applications.