Molecular Theory Research Articles

Metal organic framework-derived porous Ni-doped In2O3 for highly sensitive and selective detection to hydrogen at low temperature

Achieving high sensitivity and selective detection at low temperature is of great significance for hydrogen leakage monitoring and early warning. As a very promising hydrogen sensitive material, In2O3 still faces great challenges in achieving high-performance hydrogen sensing at low temperatures due to inherent defects such as low specific surface area and limited active sites. Here, we prepared Ni-doped In2O3 mesoporous nanomaterials using metal organic framework (MOF) as sacrificial templates. The prepared Ni-doped In2O3 exhibited mesoporous structures with small diameters (2–3 nm), which could be used as effective molecular sieves for the selective detection of hydrogen. The high specific surface area (72.0 m²/g) provided numerous active sites for surface redox reactions, resulting in a remarkable hydrogen sensing response. Notably, gas sensitivity tests demonstrated that the Ni-doped In2O3 gas sensor achieved optimal hydrogen detection performance at 100°C. Particularly, the 3 at% Ni-doped In2O3 nanomaterials exhibited a high response of 12.5–100 ppm hydrogen, along with favorable response/recovery time and a practical limit of detection down to 5 ppm. Furthermore, the Ni-doped In2O3 sensor exhibited excellent reversibility, reproducibility, selectivity and long-term stability. In addition, simulation calculations based on molecular dynamics (MD) and density functional theory (DFT) show that molecular sieve effect is the main reason for the enhanced selectivity, and Ni doping induced oxygen vacancy (OV) defects could enhance gas adsorption. This work could provide technical support for leak detection and warning during hydrogen use, storage and transportation in the future.

Applications of magnesium iodide structure via modified-polynomials

A relatively recent approach in molecular graph theory for analyzing chemical networks and structures is called a modified polynomial. It emphasizes the characteristics of molecules through the use of a polynomial-based procedure and presents numerical descriptors in algebraic form. The Quantitative Structure-Property Relationship study makes use of Modified Polynomials (M-Polynomials) as a mathematical tool. M-Polynomials used to create connections between a material’s various properties and its structural characteristics. In this study, we calculated several modified polynomials and gave a polynomial description of the magnesium iodide structure. Particularly, we computed first, second and modified Zagreb indices based M-polynomials. Randić index, and inverse Randić indices based M-polynomials are also computed in this work.

Nucleoside Cation Radicals: Generation, Radical-Induced Hydrogen Atom Migrations, and Ribose Ring Cleavage in the Gas Phase.

Nucleoside ions that were furnished on ribose with a 2'-O-acetyl radical group were generated in the gas phase by multistep collision-induced dissociation of precursor ions tagged with radical initiator groups, and their chemistry was investigated in the gas phase. 2'-O-Acetyladenosine cation radicals were found to undergo hydrogen transfer to the acetoxyl radical from the ribose ring positions that were elucidated using specific deuterium labeling of 1'-H, 2'-H, and 4'-H and in the N-H and O-H exchangeable positions, favoring 4'-H transfer. Ion structures and transition-state energies were calculated by a combination of Born-Oppenheimer molecular dynamics and density functional theory and used to obtain unimolecular rate constants for competitive hydrogen transfer and loss of the acetoxyl radical. Migrations to the acetoxyl radical of ribose hydrogens 1'-H, 2'-H, 3'-H, and 4'-H were all exothermic, but product formation was kinetically controlled. Both Rice-Ramsperger-Kassel-Marcus (RRKM) and transition-state theory (TST) calculations indicated preferential migration of 4'-H in a qualitative agreement with the deuterium labeling results. The hydrogen migrations displayed substantial isotope effects that along with quantum tunneling affected the relative rate constants and reaction branching ratios. UV-vis action spectroscopy indicated that the cation radicals from 2'-O-acetyladenosine consisted of a mixture of isomers. Radical-driven dissociations were also observed for protonated guanosine, cytosine, and thymidine conjugates. However, for those nucleoside ions and cation radicals, the dissociations were dominated by the loss of the nucleobase or formation of protonated nucleobase ions.

Quantum Simulations and Experimental Insights into Glyphosate Adsorption Using Graphene-Based Nanomaterials.

The increasing global demand for food and agrarian development brings to light a dual issue concerning the use of substances that are crucial for increasing productivity yet can be harmful to human health and the environment when misused. Herein, we combine insights from high-level quantum simulations and experimental findings to elucidate the fundamental physicochemical mechanisms behind developing graphene-based nanomaterials for the adsorption of emerging contaminants, with a specific focus on pesticide glyphosate (GLY). We conducted a comprehensive theoretical and experimental investigation of graphene-based supports as promising candidates for detecting, sensing, capturing, and removing GLY applications. By combining ab initio molecular dynamics and density functional theory calculations, we explored several chemical environments encountered by GLY during its interaction with graphene-based substrates, including pristine and punctual defect regions. Our results unveiled distinct interaction behaviors: physisorption in pristine and doped graphene regions, chemisorption leading to molecular dissociation in vacancy-type defect regions, and complex transformations involving the capture of N and O atoms from impurity-adsorbed graphene, resulting in the formation of new GLY-derived compounds. The theoretical findings were substantiated by FTIR and Raman spectroscopy, which proposed a mechanism explaining GLY adsorption in graphene-based nanomaterials. The comprehensive evaluation of adsorption energies and associated properties provides valuable insights into the intricate nature of these interactions, shedding light on potential applications and guiding future experimental investigations of graphene-based nanofilters for water decontamination.

Renewed spectroscopic and theoretical research of hydrogen bonding in ascorbic acid

The studies of two isomers of ascorbic acid and their deuteroanalogues, presented in the paper, have been accomplished by vibrational spectroscopy methods and quantum-chemical simulations. The spectroscopic research of L-ascorbic and D-isoascorbic acids have been carried out by the infrared (IR) and Raman (R) techniques. On the basis of the obtained results the spectral interpretation of the hydrogen bonded groups of ascorbic acids has been performed. Car-Parrinello Molecular Dynamics (CPMD) and Density Functional Theory (DFT) have been employed to support spectroscopic experimental findings and shed light onto the bridged proton dynamics in the L- and D- isomers of ascorbic acids. The accurate assignments of the hydrogen bond modes have been accomplished with the application of deuterosubstitution, CPMD-solid state simulations and Potential Energy Distribution (PED) analysis. The spectral and structural results have shown that dependency ν(OH) = f(γ(OH)) is the most common for the OHO hydrogen bond, whereas dependency d(OO) = f(γ(OH)) differs as for the ionic and resonance assisted hydrogen bonds.

Charge block-driven liquid-liquid phase separation - mechanism and biological roles.

Liquid-liquid phase separation (LLPS) has increasingly been found to play pivotal roles in a number of intracellular events and reactions, and has introduced a new paradigm in cell biology to explain protein-protein and enzyme-ligand interactions beyond conventional molecular and biochemical theories. LLPS is driven by the cumulative effects of weak and promiscuous interactions, including electrostatic, hydrophobic and cation-π interactions, among polypeptides containing intrinsically disordered regions (IDRs) and describes the macroscopic behaviours of IDR-containing proteins in an intracellular milieu. Recent studies have revealed that interactions between 'charge blocks' - clusters of like charges along the polypeptide chain - strongly induce LLPS and play fundamental roles in its spatiotemporal regulation. Introducing a new parameter, termed 'charge blockiness', into physicochemical models of disordered polypeptides has yielded a better understanding of how the intrinsic amino acid sequence of a polypeptide determines the spatiotemporal occurrence of LLPS within a cell. Charge blockiness might also explain why some post-translational modifications segregate within IDRs and how they regulate LLPS. In this Review, we summarise recent progress towards understanding the mechanism and biological roles of charge block-driven LLPS and discuss how this new characteristic parameter of polypeptides offers new possibilities in the fields of structural biology and cell biology.

Differential Performance of Xanthophylls in Combination with Phenol Classes against H2O2-Induced Oxidative Stress: An In Vitro Analysis Using Retinal Pigment Epithelial Cells.

Xanthophylls, vital for ocular defense against blue light and reactive oxygen species, are prone to oxidative degradation; however, they may be regenerated antioxidant-rich plant phenols. Despite certain in vitro evidence, clinical studies show inconsistent findings and this may be due to varying phenolic reduction potentials. Therefore, the current study aims to investigate the ocular protective effect of various plant phenols combined with xanthophyll. Human retinal pigment epithelial cells (ARPE-19) are subjected to oxidative stress induced by hydrogen peroxide (H2O2) after xanthophyll and phenol pretreatment. Assessments include xanthophyll uptake, total antioxidant capacity, cell viability, intracellular reactive oxygen species levels, apoptosis, phagocytosis, and vascular endothelial growth factor formation. The study finds that while the combination of lutein with phenols does not show significant protective effects compared to lutein-only, zeaxanthin combined with phenols exhibits enhanced protection compared to both the zeaxanthin-only and control groups. The research reveals the complex relationship between xanthophylls and phenols, suggesting that the advantageous effects of their combination might vary among different xanthophylls. Caution is necessary when applying molecular theories to ocular health, and this necessitates further research, serving as a basis for proposing clinical trials to evaluate the efficacy of specific xanthophyll and phenol combinations.

Discovery of 1,2,3–triazoles incorporated benzoxazinones as potent antimicrobial agents: Synthesis, in vitro biological evaluation, DFT interactions and molecular docking

The study of the chemical and biological properties of molecules simultaneously comprising various heterocycles, such as fused 1,2,3–triazoles and benzoxazinones have been conducted as part of our ongoing research in the field of medicinal and organic chemistry. Two classes of 1,2,3–triazoles linked benzoxazinone derivatives were prepared from 2-((prop‑2-yn-1-ylamino) methyl)-4H-benzo[d][1,3]oxazin-4-one 4 and substituted azides successfully CuAAC reaction and more efficient approach. The structures of these new triazole derivatives have been confirmed by Mass, 1H NMR, 13C NMR, and IR spectral data. From antibacterial studies, benzoxazinone–linked 1,2,3–triazoles 5a, 5d, and 6e were found to be most effective against P. aeruginosa was measuring MICs of 4.15 ± 0.03, 4.23 ± 0.02, and 4.43 ± 0.04 μg mL−1, whereas 5a and 6d displayed excellent activity against B. subtilis with MICs 5.33 ± 0.01, and 3.91 ± 0.02 μg mL−1 respectively. In particular, the prepared scaffolds 5b, 6d, and 5a showed remarkable antifungal activity against C. albicans with MICs 4.18 ± 0.04, 4.70 ± 0.01, and 5.10 ± 0.02 μg mL−1 accordingly. Initially, all of the synthesized compounds were evaluated in silico docking against antifungal drug candidate (5TZ1) and further evaluated for their ADMET properties by SwissADME and ADMETlab2.0. The computational modelling of benzoxazinone–1,2,3–triazole 6d revealed better hydrogen bonding patterns with amino acids Arg381(A) [O2—NH] (2.98 Å), Try132(A) [N22—OH] (2.61 Å), Ile471(A) [O28—NH] (3.16 Å) and has predicted to show remarkable affinity with C. albicans. Theoretical evaluation provides an insight about ligand interaction with proteins, highest occupied molecular orbital (HOMO), lowest unoccupied molecular orbital (LUMO), electronegativity, hardness, softness, electrophilicity and neucleophilicity of the ligands via molecular docking and density functional theory (DFT) studies; this presents probable evidence for the biological activity of the derivatives.

Revealing the mechanism, Regio- and stereo selectivity and solvent effects of [3 + 2] cycloaddition reactions involving N-benzyl fluoro nitrone and electron-deficient alkynes

The [3 + 2] cycloaddition reactions (32CA) between N-benzyl fluoro nitrone and electron-deficient dipolarophiles alkynes have been studied using molecular electron density theory at the B3LYP-D3/6-31G(d) level. The findings indicate that, in these 32CA reactions, a one-step mechanism is in play with asynchronous transition states. The topological analyses of these transition states are consistent with the presence of non-covalent interactions at the bonding regions between atoms. The analysis of the energy profile in gas phase and in the presence of solvents indicates a preference for a specific site addition over the others. Parr functions were thus used to justify such regioselectivity. In addition, we show that solvents do not modify the regioselectivity achieved, but it increases the activation energies and reduces the exothermic nature of this 32CA reaction. The present findings are in agreement with the experimental results.

Computational Investigation of LiF Formation at Graphite-Electrolyte Interfaces.

The performance of rechargeable batteries is strongly influenced by the solid-electrolyte interphase (SEI), and a comprehensive understanding of SEI formation from the atomic level is crucial for effective battery design. The dynamics of the electrode-electrolyte interface is important and needs to be considered when evaluating the mechanism of the SEI formation. Here, we employed ab initio molecular dynamics (AIMD) and density functional theory (DFT) calculations to examine interfacial behaviors and LiF formation. Through molecular dynamics and structure sampling, we successfully constructed an electrochemical stability diagram correlating the thermodynamic free energy with the potential, which is determined by the work function of electrode surfaces. DFT calculations revealed that LiF formation at the graphite-electrolyte interfaces occurs easily via the intermediate LiHF complex. Interestingly, LiF tends to be solvated by solvents rather than directly deposited onto electrode surfaces (e.g., the Au electrode), a phenomenon we identify as a critical determinant of the porous and uneven nature of the LiF layer observed on graphite electrodes. Our finding offers new mechanistic insights into LiF formation at graphite-electrolyte interfaces.

Exploring structures of small anionic nickel-ethanol clusters with infrared spectroscopy.

Small anionic nickel clusters with ethanol are investigated with a combination of mass-selective infrared photodissociation spectroscopy in a molecular beam and density functional theory simulations at the BLYP/6-311g(d,p) and TPSSh/def2-TZVPP level. In this context, the O-H stretching vibration of the ethanol is analyzed to obtain information about the structural motif, the geometry of the metal core, and the spin state of the clusters. For the [Ni2(EtOH)]- and [Ni3(EtOH)]- clusters, we assign quartet states of motifs with a hydrogen bond from the ethanol to the linear nickel core. The aggregation of a further ethanol molecule, yielding the [Ni3(EtOH)2]- cluster, results in the formation of a cooperative hydrogen bond network between the nickel core and the two ethanol molecules.

Thermodynamic properties of TPAC-EG deep eutectic solvents: A study based on the IGC method with molecular simulations

The study of thermodynamic properties and intermolecular interactions in deep eutectic solvents (DES) is an important innovative step in the development of DES. This research focuses on the synthesis of DES using a 1:2 M ratio of tetrapropylammonium chloride and ethylene glycol. Inverse gas chromatography (IGC) techniques are used to investigate DES of thermodynamics in the temperature range of 303.15–333.15 K. Additionally, molecular dynamics (MD) simulations and density functional theory (DFT) are used to explore intermolecular interactions in DES at both molecular and atomic levels. The research findings yield crucial insights, including the successful determination of infinite dilution activity coefficients, Flory-Huggin’s interaction parameters, solubility parameters, and Abraham solvation parameters of DES through IGC techniques. A careful study of the temperature-dependent trends in these parameters is provided. Analyses of structural properties, including radial distribution functions, hydrogen bond counts, and thermal fluctuation indices, reveal that, at experiments temperatures, the amount and nature of intermolecular hydrogen bonds in binary mixtures are the main factors influencing the thermodynamic properties of DES. Finally, based on DFT calculations, a quantitative assessment of the molecular interaction mechanisms of DES at the atomic level confirms the predominant role of hydrogen bonding in DES formation, with multicenter hydrogen bonds characterized by stronger hydrogen bond strengths emerging as the primary type.

Employing molecular dynamics simulations and DFT calculations to elucidate the energetic, structural, and spectroscopic attributes of (poly)valines in water solution

In this study, we explored how the growth of peptide chains containing valines impacts nuclear magnetic resonance (NMR) and optical absorption spectra. Results stem from equilibrated configurations in water, reflecting solvent influence and valine vibration. Utilizing fully atomistic molecular dynamics (MD), simulations, and density functional theory (DFT) including TD-DFT, we observe a notable shift in optical absorption towards longer wavelengths with increased valine count. Additionally, carbon atom magnetic signatures unveil distinct peptide bond characteristics. This work sheds light on the spectroscopic behavior of valine-rich peptide chains, crucial for understanding structural and functional properties, particularly in biomolecular contexts.

Effect of Condensed Water at an Alumina/Epoxy Resin Interface on Curing Reaction.

The adhesion of epoxy adhesives to aluminum materials is an important issue in assembling parts for lightweight mobility. Aluminum surfaces typically possess an oxide layer, which readily adsorbs water. In this study, the aggregation states of water and its effect on the curing reaction were examined by placing a water layer between an amorphous alumina surface and a mixture of epoxy and amine components. This study used molecular dynamics simulations and density functional theory calculations. Before the reaction, water molecules strongly adsorbed onto the alumina surface, aggregating excess water. Some water diffused into the epoxy/amine mixture, accelerating the diffusion of unreacted substances. This led to faster reaction kinetics, particularly in proximity to the alumina surface. The adsorption of water molecules onto the alumina surface and the aggregation of excess water were similarly observed even after the curing process. Subsequently, the interaction between the alumina surface and various functional groups of the epoxy/amine mixture was evaluated before and after the reaction. Epoxy monomers had little interaction with the alumina surface before the reaction, whereas hydroxy groups formed by the ring-opening reaction of epoxy groups exhibited notable interaction. Conversely, sulfonyl and amino groups in amine compounds formed hydrogen bonds with OH groups on the alumina surface before the reaction. However, after the reaction, amino groups weakened their interaction with the alumina OH groups as they transformed from primary to tertiary during the curing reaction. Both epoxy and amine monomers/fragments similarly interacted with water molecules, both before and after the reaction. The insights gained from this study are expected to contribute to a better understanding of the impact of moisture absorption on the application of epoxy resins.

Unveiling [3 + 2] cycloaddition reactions of diphenyl diazomethane to thiobenzophenone and cycloaliphatic thioketones in the light of molecular electron density theory

The reactivity, regiochemistry and substituent effects observed in the [3 + 2] cycloaddition (32CA) reactions of diphenyldiazomethane (PDM) with thiobenzophenone and a series of cycloaliphatic thioketones (TKs) have been studied within the molecular electron density theory at the ωB97XD/6-311G(d,p) computational level. The cycloaliphatic TK series shows remarkable substituent effects, changing from a non-polar 32CA reaction to a highly polar one, with the electron density flowing from PDM to the corresponding TK in a reaction classified as a forward electron density flux (FEDF). These 32CA reactions follow a one-step mechanism through earlier asynchronous transition state structures in which the formation of the two new single bonds has not yet begun, and the energetically predicted regiochemistry towards the generation of 1,3,4-thiadiazole is in complete agreement with the experimental outcome.

Development of a novel polydopamine-imprinted MOFs targeted for removal of refractory organic pollutants: Synergistic mechanisms of adsorption and degradation

In this study, a novel dopamine-imprinted MOFs (metal organic frameworks) was developed for the first time to achieve targeted degradation of refractory organic pollutants (ROPs) in advanced oxidation process. The targeted adsorption and degradation capacity of sulfamethoxazole (SMX) by molecularly imprinted catalyst (Fe-MOFs@MIP) was 3.17 times and 5.47 times that of Fe-MOFs, respectively. The results showed that the polydopamine (PDA) imprinted layer not only enhanced the targeted adsorption of SMX, but also improved the activity of the catalyst by promoting electron transfer. The physicochemical properties of Fe-MOFs@MIP were investigated. In situ Fourier transform infrared spectroscopy and molecular dynamics theory were used to investigate targeted adsorption mechanism. The active species were identified by quenching experiments and electron paramagnetic resonance (EPR). The reaction sites of SMX were predicted using density functional theory (DFT) and the possible degradation pathways of SMX were proposed. Finally, the targeted degradation mechanism of Fe-MOFs@MIP was elucidated. This study has a guiding significance for the deep removal of refractory organic pollutants in wastewater.

Surface-Enriched Room-Temperature Liquid Bismuth for Catalytic CO2 Reduction.

Bismuth-based electrocatalysts are effective for carbon dioxide (CO2) reduction to formate. However, at room temperature, these materials are only available in solid state, which inevitably suffers from surface deactivation, declining current densities, and Faradaic efficiencies. Here, the formation of a liquid bismuth catalyst on the liquid gallium surface at ambient conditions is shown as its exceptional performance in the electrochemical reduction of CO2 (i.e., CO2RR). By doping a trace amount of bismuth (740ppm atomic) in gallium liquid metal, a surface enrichment of bismuth by over 400 times (30 at%) in liquid state is obtained without atomic aggregation, achieving 98% Faradic efficiency for CO2 conversion to formate over 80 h. Ab initio molecular simulations and density functional theory calculations reveal that bismuth atoms in the liquid state are the most energetically favorable sites for the CO2RR intermediates, superior to solid Bi-sites, as well as joint GaBi-sites. This study opens an avenue for fabricating high-performing liquid-state metallic catalysts that cannot be reached by elementary metals under electrocatalytic conditions.

Tuning the Electronic Characteristics of Monolayer MoS2‐Based Transistors by Ion Irradiation: The Role of the Substrate

AbstractThis study explores defect engineering in 2D materials using ion beam irradiation to modify the electrical and optical properties with potential in advancing quantum electronics and photonics. Helium and neon ions ranging from 5 to 7.5 keV are employed to manipulate charge transport in monolayer molybdenum disulfide (MoS2). In situ electrical characterization occurs without vacuum breakage post‐irradiation. Raman and photoluminescence spectroscopy quantify ion irradiation's impact on MoS2. Small doses of helium ion irradiation enhance monolayer MoS2 conductivity in field‐effect transistor geometry by inducing doping and substrate charging. Findings reveal a strong correlation between the electrical properties of MoS2 and the primary ion used, as well as the substrate on which the irradiation occurred. Using hexagonal boron nitride (h‐BN) as a buffer layer between MoS2 flake and SiO2 substrate yields distinct alterations in electrical behavior subsequent to ion irradiation compared to the MoS2 layer directly interfacing with SiO2. Molecular dynamics simulations and density functional theory provide insight into experimental results, emphasizing substrate influence on measured electrical properties post‐ion irradiation.

Solvent constraints for biopolymer folding and evolution in extraterrestrial environments

We propose that spontaneous folding and molecular evolution of biopolymers are two universal aspects that must concur for life to happen. These aspects are fundamentally related to the chemical composition of biopolymers and crucially depend on the solvent in which they are embedded. We show that molecular information theory and energy landscape theory allow us to explore the limits that solvents impose on biopolymer existence. We consider 54 solvents, including water, alcohols, hydrocarbons, halogenated solvents, aromatic solvents, and low molecular weight substances made up of elements abundant in the universe, which may potentially take part in alternative biochemistries. We find that along with water, there are many solvents for which the liquid regime is compatible with biopolymer folding and evolution. We present a ranking of the solvents in terms of biopolymer compatibility. Many of these solvents have been found in molecular clouds or may be expected to occur in extrasolar planets.

Effects and molecular mechanisms of jet ablation and fuel corrosion on separation failure of the asphalt-aggregate interface in airport asphalt pavements

To guide the improvement of asphalt pavement durability in airports, the effects and molecular mechanisms of jet ablation and fuel corrosion on separation failure of the asphalt-aggregate interface were investigated in this study using molecular dynamics simulations and density functional theory method. Firstly, tensile separation behaviors of the virgin, aged, and fuel-corroded asphalt-aggregate interfaces were simulated under different loading rates to evaluate their tensile strength and fatigue cracking resistance, and the experimental data were also used to verify the reliability of the simulation results. Subsequently, the molecular mechanisms of jet ablation and fuel corrosion on the separation failure of the asphalt-aggregate interface were analyzed by calculating the work of adhesion, work of cohesion, flowability parameters, and intermolecular binding energy. The results show that the aged specimen has higher ultimate tensile strength and fracture energy, but its flexibility and fatigue cracking resistance are significantly reduced. This is because the polar oxygen-containing groups generated during high-temperature aging enhance the intermolecular binding energy of the asphalt, but this also restricts the diffusion of asphalt molecules, resulting in greater frictional resistance and viscosity of asphalt during shear deformation, and thus loss of mobility and self-healing properties. On the contrary, since the light and medium oils soften and dilute the asphalt, and also weaken the intermolecular binding energy of asphalt, the fuel corrosion reduces the ultimate tensile strength and fracture energy of the asphalt-aggregate interface system, resulting in insufficient overall strength and load-bearing capacity.