Molecular Structure Research Articles

Hydrogen Bonding Analysis of Structural Transition-Induced Symmetry Breaking and Spin Splitting in a Hybrid Perovskite Employing a Synergistic Diffraction-DFT Approach.

Two-dimensional (2D) hybrid organic-inorganic perovskites (HOIPs) offer an outstanding opportunity for spin-related technologies owing in part to their tunable structural symmetry breaking and distortions driven by organic-inorganic hydrogen (H) bonds. However, understanding how H-bonds tailor inorganic symmetry and distortions and therefore enhance spin splitting for more effective spin manipulation remains imprecise due to challenges in measuring H atom positions using X-ray diffraction. Here, we report a thermally induced structural transition (at ∼209 K) for a 2D HOIP, (2-BrPEA)2PbI4 [2-BrPEA = 2-(2-bromophenyl)ethylammonium], which induces inversion asymmetry and a strong spin splitting (ΔE > 30 meV). While X-ray diffraction generally establishes heavy atom coordinates, we utilize neutron diffraction for accurate H atom position determination, demonstrating that the structural transition-induced rearrangement of H-bonds with distinct bond strengths asymmetrically shifts associated iodine atom positions. Consequences of this shift include an increased structural asymmetry, an enhanced difference between adjacent interoctahedra distortions (i.e., Pb-I-Pb bond angles), and therefore significant spin splitting. We further show that H-only density-functional theory (DFT) relaxation of the X-ray structure shifts H atoms to positions that are consistent with the neutron experimental data, validating a convenient pathway to more generally improve upon HOIP H-bonding analyses derived from quicker/less-expensive X-ray data.

Pharmacoinformatics and quantum chemicals‐based analysis of aromatic molecule decanal as a potent drug against breast cancer

AbstractThis study's primary goal is to perform density functional theory and molecular docking simulation to determine decanal's structural stability and biological activity against proteins allied to breast cancer in order to validate its anti‐cancer potential. Initially, the drug‐likeness features of decanal was predicted and the outcomes confirmed that it is non‐toxic and follows Lipinski's rule. Through basis set 6‐311++G (d, p), the structural optimization was performed and molecular geometry was investigated. The FT‐IR and UV–Visible spectroscopic analysis was theoretically performed and validated via experimental analysis. The reactive surface of decanal was further investigated using a calculated molecular electrostatic potential surface. The molecular structural stability and bio‐reactivity of decanal was determined by using the HOMO‐LUMO energies and energy gap calculated is 6.215 eV. The charge distribution among the atoms of decanal was ascertained through the analysis of Mulliken and natural population distribution. To look at the decanal molecule's topological properties, electron localization function and localized orbital locator were used. The decanal's weak interactions were investigated via reduced density gradient assessment. The docking evaluation was performed against the proteins involved in breast cancer and the highest binding ability was calculated against the protein Bcl‐2 with the score of −6.5 kcal/mol. These theoretical findings will pave a way to understand the decanal's structural stability, reactivity and breast cancer inhibitory property and can be used as a drug candidate against tumor after in vitro and clinical evaluation.

Investigating the Star-forming Sites in the Outer Galactic Arm

We aim to investigate the global star formation scenario in star-forming sites AFGL 5157, [FSR2007] 0807 (hereafter FSR0807), [HKS2019] E70 (hereafter E70), [KPS2012] MWSC 0620 (hereafter KPS0620), and IRAS 05331+3115 in the outer Galactic arm. The distribution of young stellar objects in these sites coincides with a higher extinction and H2 column density, which agrees with the notion that star formation occurs inside the dense molecular cloud cores. We have found two molecular structures at different velocities in this direction; one contains AFGL 5157 and FSR0807, and the other contains E70, [KPS2012] MWSC 0620, and IRAS 05331+3115. All these clusters in our target region are in different evolutionary stages and might form stars through different mechanisms. The E70 cluster seems to be the oldest in our sample; AFGL 5157 and FSR0807 formed later, and KPS0620 and IRAS 05331+3115 are the youngest sites. AFGL 5157 and FSR0807 are physically connected and have cold filamentary structures and dense hub regions. Additionally, the near-infrared photometric analysis shows signatures of massive star formation in these sites. KPS0620 also seems to have cold filamentary structures with the central hub but lacks signatures of massive stars. Our analysis suggests molecular gas flow and the hub filamentary star formation scenario in these regions. IRAS 05331+3115 is a single clump of molecular gas favoring low-mass star formation. Our study suggests that the selected area is a menagerie of star-forming sites where the formation of the stars happens through different processes.

A Polarizable Forcefields for Glyoxal Acetals as Electrolyte Components for Lithium-Ion Batteries.

In this work we have derived the parameters of an AMOEBA-like polarizable forcefield for electrolytes based on tetramethoxy and tetraethoxy-glyoxal acetals, and propylene carbonate. The resulting forcefield has been validated using both ab-initio data and the experimental properties of the fluids. Using molecular dynamics simulations, we have investigated the structural features and the solvation properties of both the neat liquids and of the corresponding 1 M LiTFSI electrolytes at the molecular level. We present a detailed analysis of the Li ion solvation shells, of their structure and highlight the different behavior of the solvents in terms of their molecular structure and coordinating features.

Molecular dynamics simulations study on structure and mechanical properties of Na2O–CaO-Al2O3-B2O3-SiO2 glasses with different Al2O3/B2O3 ratio

The structure and mechanical properties of Na2O–CaO-Al2O3-B2O3-SiO2 glass were simulated using molecular dynamics simulations, with Al2O3 replacing B2O3. The simulated elastic modulus (E) increases while the fracture toughness (KIc) decreases, consistent with the experimental findings. The increase in Al2O3/B2O3 enhances the proportion of [AlO4] in the glass network, while reducing the proportion of [BO4] and [BO3], thereby increasing dissociation energy and atomic packing density, ultimately improving the E of the glass. The fracture process of glasses involves both elastic and plastic deformations. Elastic deformation primarily includes bond length extension, bond angle bending, and changes in coordination numbers of Ca2+ and Na+. Plastic deformation primarily results from changes in coordination numbers of B3+ and Al3+ during stretching, with reduced [BO3] and [BO4] decreasing the plastic region and subsequently reducing KIc. This study will provide a theoretical basis for adjusting E and KIc values for aluminoborosilicate glass.

Structural, Thermal, Optical, Electrical, and Dielectric Properties of Complex Lead-Free Compound: [Bi1∕2Na1∕2][Fe1∕2W1∕2]O3

Some physical properties (structural, dielectric and optical) of a complex lead-free ceramic [[Formula: see text][Formula: see text]][[Formula: see text][Formula: see text]]O3 have been thoroughly examined in different experimental conditions in this study. It was fabricated via a solid-state reaction method. The crystal structure is monoclinic, according to the detailed analysis of the X-ray diffraction pattern. Also, the functional vibrational bands can be observed in the FT-IR and Raman spectra, which support the creation of the molecular structure. Scanning electron microscope (SEM) images of the sample clearly show the effects of [Formula: see text] and [Formula: see text] incorporation in morphology, and energy dispersive X-ray spectroscopy (EDX) indicates the existence of all constituents. The non-overlapping small polaron tunneling (NSPT) and correlated barrier hopping (CBH) model conduction mechanisms are examined through Jonscher’s power law. The contribution of the grain and grain boundary to the capacitive behavior is shown by Nyquist plots. According to a leakage current analysis, the compound exhibits Ohmic and space charge limited conduction (SCLC) conduction mechanisms. Electric field polarization was used to study the ferroelectric nature. The findings of this study show that the inclusion of [Formula: see text] and [Formula: see text] is an efficient technique to improve its dielectric and optical characteristics.

Confinement and heating promoted RTP of flumequine, oxolinic acid and levofloxacin on papers for their detection and discrimination

Developing simple assays to identify and discriminate quinolones are highly desired for food safety, which remain a great challenge due to the interferences from food matrices and the minor variation on the molecular structure of massive quinolones. We proposed a room-temperature phosphorescence (RTP) assay for the quantitative detection and discrimination of quinolones, aided by a confinement and heating strategy. Quinolones were loaded into the porous framework of paper, which provided confinement effects on the molecular motions of quinolones. The heating process further removed the solvents, eliminating their quenching effects on excitons. These synergistic effects improved the RTP intensity and emission lifetime by 1144-fold and from nanoseconds to seconds, respectively. Three types of quinolones were quantitatively detected and discriminated through pattern recognition methods. The proposed assay showed excellent detection performance in complicated meat samples, aided by the delayed signal collecting of RTP. The reported results provided a clue to modulate the RTP properties of organic molecules, showing great potential for application prospect in food safety analysis, environmental and healthy monitoring.

Small, Fluorinated Mn2+ Chelate as an Efficient 1H and 19F MRI Probe.

We explore the potential of fluorine-containing small Mn2+ chelates as alternatives to perfluorinated nanoparticles, widely used as 19F MRI probes. In MnL1, the cyclohexanediamine skeleton and two piperidine rings, involving each a metal-coordinating amide group and an appended CF3 moiety, provide high rigidity to the complex. This allows for good control of the Mn-F distance (rMnF = 8.2±0.2 Å determined from 19F relaxation data), as well as for high kinetic inertness (a dissociation half-life of 1285 h is estimated for physiological conditions). The paramagnetic Mn2+ leads to a ~150-fold acceleration of the longitudinal 19F relaxation, with moderate line-broadening effect, resulting in T2/T1 ratios of 0.8 (9.4 T). Owing to its inner sphere water molecule, MnL1 is a good 1H relaxation agent as well (r1 = 5.36 mM-1s-1 at 298K, 20MHz). MnL1 could be readily visualized in 19F MRI by using fast acquisition techniques, both in phantom images and living mice following intramuscular injection, with remarkable signal-to-noise ratios and short acquisition times. While applications in targeted imaging or cell therapy monitoring require further optimisation of the molecular structure, these results argue for the potential of such small, monohydrated and fluorinated Mn2+ complexes for combined 19F and 1H MRI detection.

A Human Feedback Strategy for Photoresponsive Molecules in Drug Delivery: Utilizing GPT-2 and Time-Dependent Density Functional Theory Calculations

Photoresponsive drug delivery stands as a pivotal frontier in smart drug administration, leveraging the non-invasive, stable, and finely tunable nature of light-triggered methodologies. The generative pre-trained transformer (GPT) has been employed to generate molecular structures. In our study, we harnessed GPT-2 on the QM7b dataset to refine a UV-GPT model with adapters, enabling the generation of molecules responsive to UV light excitation. Utilizing the Coulomb matrix as a molecular descriptor, we predicted the excitation wavelengths of these molecules. Furthermore, we validated the excited state properties through quantum chemical simulations. Based on the results of these calculations, we summarized some tips for chemical structures and integrated them into the alignment of large-scale language models within the reinforcement learning from human feedback (RLHF) framework. The synergy of these findings underscores the successful application of GPT technology in this critical domain.

Tailoring the Molecular Structure of 6-Gingerol for Targeting the Phase Separation in Human Lysozyme.

Human lysozyme undergoes a phase-separation process to form insoluble amyloid-architects that cause several pathologies including systemic amyloidosis. Here we have tailored 6-gingerol by extending its molecular framework with active functional groups to specifically target lysozyme phase-transition events. Aggregation assay revealed that tailored 6-gingerol with 4-aromatic moieties (MTV4) substantially suppressed the conversion of the lysozyme low-density liquid phase (LDLP) to solid-phase structured amyloids. The data obtained from biophysical, computational, and microscopic imaging tools suggest direct intervention of MTV4 with the liquid-liquid phase separation. The CD data suggest that MTV4 was able to retain the native conformation of lysozyme. Both biomolecular and computational data reveal the interference of MTV4 with the aggregation-prone hydrophobic stretches within the lysozyme, thereby retaining the native structure and reversing the misfolded intermediates to active monomers. Also, MTV4 was able to induce rapid dissolution of preformed-toxic amyloid fibrils. These results reinforce the importance of the aromatic-aromatic interaction in preventing human lysozyme phase separation.

Systematic Literature Review: A Fun Organic Chemistry Learning Experience with Educational Games

This article examines organic chemistry educational games developed between 2017-2023. The purpose of this study is to find out the types of educational games that are most developed, organic chemistry materials that have been developed in the form of educational games, and the positive impact of educational games in studying organic chemistry. The method used in this study is a systematic literature review. The systematic literature review is carried out in three stages, namely the planning stage, the implementation stage, and the reporting stage. Based on the results of the study, 38 articles were obtained by the criteria and further analysis was carried out. The results of the analysis show that organic chemistry educational games are developed with various types of games both in digital and non-digital forms. The most developed organic chemistry educational games are strategy video games and card games. The most developed material in the form of educational games is the molecular structure of organic compounds which is shown to deepen students' understanding in organic chemistry courses.

Molecular structure regulation and herbicidal activity of dibutyltin aryloxyacetate complexes

Six dibutyltin aryloxyacetate complexes [(X-C6H4OCH2COO)(SnBu2)2(μ3O)(OMe)]2 (A1, B1), [(X-C6H4OCH2COO)2(SnBu2)2(μ3O)]2 (A2, B2), and [(X-C6H4OCH2COO)2SnBu2] (A3, B3) were synthesized and characterized by IR, NMR, HRMS, and TGA techniques. The molecular structure of complexes A1, A3 and B1-B3 was confirmed by single-crystal X-ray crystallography. Complexes A1, B1, A2, and B2 are dimeric carboxylate tetraorganodistannoxanes, displaying a "ladder-like" molecular arrangement. The aryloxyacetate ligands in A1 and B1 adopt a monodentate mode, while they function as bridging coordination ligands in A2 and B2. Complexes A3 and B3 represent dibutyltin carboxylates with crystallographically imposed two-fold symmetry, with the aryloxyacetate ligands adopting a bidentate mode. Aryloxyacetic acids demonstrate a propensity for assuming various coordination modes, leading to the formation of diverse molecular architectures in organotin carboxylates. In addition, complex B1 exhibits polymorphism. Echinochloa crus-galli and Portulaca oleracea L. were used as target organisms for herbicidal activity testing using a petri dish method. It was found that they have a significant inhibitory effect on weed roots and stems at 200 μmol/L, and the structure-activity relationship analysis revealed the important influence of substituent types and complex structures on their activity.

Ultrasound and enzyme treatments on morphology, structures, and adsorption properties of cassava starch

Porous starch materials are environmentally friendly and renewable and exhibit high adsorption performances. Ultrasound and compound enzyme (α-amylase and glucoamylase) treatments were applied to prepare modified cassava starch. The granules, crystal morphology, crystal structure, and molecular structure of starch were investigated. The hydrolysis degree, solubility, swelling, and adsorption properties of cassava starch were analyzed. After the cassava starch was modified by ultrasound and enzyme treatments, the granule size of the starch decreased, and the surfaces were eroded to form pits, grooves and cavity structure. The starch spherulites weakened or even disappeared. The functional groups of starch did not change significantly, but the degree of crystal order decreased. The double-helix structure was reduced, and the crystal structure was composed of A + V-type crystals, with a decrease in crystallinity. The gelatinization temperature and thermal degradation temperatures enhanced. The enzymatic hydrolysis degree and solubility of the modified cassava starch increased. The swelling degree decreased, and oil adsorption, water adsorption improved. MB adsorption behavior of modified cassava starch closely followed a pseudo-second-order kinetics model and the Langmuir isotherm equation. These findings could help to understand the relationship between the structure and properties of modified starch, and guide its application in the field of adsorption.

Small, Fluorinated Mn2+ Chelate as an Efficient 1H and 19F MRI Probe

We explore the potential of fluorine‐containing small Mn2+ chelates as alternatives to perfluorinated nanoparticles, widely used as 19F MRI probes. In MnL1, the cyclohexanediamine skeleton and two piperidine rings, involving each a metal‐coordinating amide group and an appended CF3 moiety, provide high rigidity to the complex. This allows for good control of the Mn‐F distance (rMnF = 8.2±0.2 Å determined from 19F relaxation data), as well as for high kinetic inertness (a dissociation half‐life of 1285 h is estimated for physiological conditions). The paramagnetic Mn2+ leads to a ~150‐fold acceleration of the longitudinal 19F relaxation, with moderate line‐broadening effect, resulting in T2/T1 ratios of 0.8 (9.4 T). Owing to its inner sphere water molecule, MnL1 is a good 1H relaxation agent as well (r1 = 5.36 mM‐1s‐1 at 298K, 20MHz). MnL1 could be readily visualized in 19F MRI by using fast acquisition techniques, both in phantom images and living mice following intramuscular injection, with remarkable signal‐to‐noise ratios and short acquisition times. While applications in targeted imaging or cell therapy monitoring require further optimisation of the molecular structure, these results argue for the potential of such small, monohydrated and fluorinated Mn2+ complexes for combined 19F and 1H MRI detection.

Regulation of Dihedral Angle on Molecular Engineering for Enhancing Triboelectric Performance

AbstractThe performance of triboelectric polymers relies on their molecular structure. Therefore, investigating how to construct high‐performance molecular structures of triboelectric polymers becomes imperative, yet the relationship between microscopic structural parameters and triboelectric performance remains unclear. In this study, the relationship is studied between dihedral angles of adjacent conjugated planes and triboelectric performance. Various polyimide monomers are synthesized to manipulate the conjugated dihedral angles within the molecular chains. Introducing larger dihedral angles in polyimides (PIs) reduces the conjugation between molecular chains, suppressing the formation of charge transfer complexes (CTCs), and widening the energy gap between molecular orbitals. With the increase in dihedral angles, the output performance improved by 100%. The surface charge density of 335 µC·m−2 is achieved through the synergistic effect of the high charge retention capability of the PI film and the high triboelectric properties of the corona‐polarized fluorinated ethylene propylene (FEP). A large dihedral angle can form numerous deep traps and effectively prevent charge escaping while ensuring stable output. This study provides a feasible strategy for investigating the construction of high triboelectric performance molecular structures, enriching the understanding of how molecular structures influence the triboelectric properties of polymer materials and promote high‐performance fluorine‐free and environmentally friendly polymers.

On the Emergence of Ferromagnetism in LaCoO3 Ultrathin Films

AbstractIt is well known that the properties of a crystal evolve as it increases in size from a single atomic plane to that of the bulk. Such size‐dependent transitions can stem from many different origins and depend on minute changes to crystal bonding and composition. A model example is that of LaCoO3, which is non‐magnetic in the bulk but can display ferromagnetism at the nanoscale. Here, the evolution of structure‐property relationships is studied in the LaCoO3−δ/SrTiO3 (001) system as the thickness of LaCoO3−δ is increased from a single plane to 10 unit cells. In situ synchrotron X‐ray studies are performed during and post‐deposition to probe changes in the interactions between structure, stoichiometry, and magnetic behavior. Structural quantification indicates that the oxygen octahedral rotation pattern evolves with thickness, due to inherent differences in crystal symmetry between the film and substrate. The change in rotation modifies the required energy barrier for the spin state transition via the Co–O bond length and Co–O–Co bond angle, affecting the appearance of ferromagnetism. Our results highlight the contributions of high spin Co2+ and/or high spin Co3+ to respective weak and robust ferromagnetism and the evolution of properties with size in ultrathin LaCoO3−δ heterostructures.

Effect of functional groups in strawberry flavoring on pea protein-flavor interactions: Potential applicable in flavor formulation for plant-based protein aqueous foods

This research aimed to explore binding interactions between pea protein isolate (PPI) and selected strawberry flavorings including vanillin, γ-decalactone, furaneol, and (Z)-3-hexen-1-ol within an aqueous system. The results showed that binding affinities of PPI with all various functional group of flavor compounds decreased as temperature increased from 5 °C to 25 °C. Notably, at 25 °C, γ-decalactone displayed the highest binding affinity, followed by vanillin, (Z)-3-hexen-1-ol, and furaneol. Lowest binding was observed for furaneol, explained by its greater lipophilicity (lower partition coefficient values or LogP value) and molecular structure in each functional group in the flavor compounds. Thermodynamically, the interaction between PPI and each selected flavor compound was spontaneous, with evidence suggesting primary forces being hydrophobic interactions or hydrogen bonding/van der Waals forces. Computational molecular docking further confirmed these interaction types. This research provides insights into the interactions between PPI and strawberry flavorings, aiding in the selection of optimal flavor compound proportion for protein-rich products.

Investigation of tribological behavior of polytetrafluoroethylene/graphene composite

AbstractIn this study, we constructed molecular friction models for polytetrafluoroethylene (PTFE)/graphene composites with various defect ratios to represent their different wear stages and simulated their friction processes under different load conditions. The friction and wear mechanisms were revealed by analyzing the variations in their molecular architectures and energies during friction. The results indicate that the friction coefficient decreased with increasing load. When the load was constant, the friction coefficients of the composites containing defections were resemble, indicating that they remained unchanged in the different wear stages. The composite wear continued to increase during friction. However, the wear increment decreased gradually. In addition, by analyzing the changes in MSD, wear can be divided into initial, stable, and accelerated wear stages.Highlights Construct PTFE/Gr molecular models to represent their different wear stages. Simulate the dynamic changes of PTFE/Gr molecular structure during friction. The influence of PTFE/Gr dynamic structural changes was revealed. Reveal the normal force variation from an energy perspective.

Design Strategy for the Synthesis of Self-Doped n-Type Molecules.

n-Type organic conductive molecules play a significant role in organic electronics. Self-doping can increase the carrier concentration within the materials to improve the conductivity without the need for additional intentional dopants. This review focuses on the various strategies employed in the synthesis of self-doped n-type molecules, and provides an overview of the doping mechanisms. By elucidating these mechanisms, the review aims to establish the relationship between molecular structure and electronic properties. Furthermore, the review outlines the current applications of self-doped n-type molecules in the field of organic electronics, highlighting their performance and potential in various devices. It also offers insights into the future development of self-doped materials.

Effect of Li2O on the structure and properties of low‐boron aluminosilicate fiber glasses from molecular dynamics simulations and quantitative structure–property relationship analysis

AbstractMixed alkaline earth (MgO, CaO) aluminosilicate glass fibers (MCAS) with and without boron are commonly used as reinforcements in plastic composites, and the fundamental understanding of the thermal and mechanical properties is essential to the design of new glass compositions to satisfy the growing demands in applications from renewable energy to lightweight structural components. In this work, a series of Li2O containing low‐boron MCAS fiber glasses have been studied by using molecular dynamic (MD) simulations with recently developed effective partial charge composition dependent boron potentials. Structural characteristics, such as pair distribution function, bond angle distribution, and neutron/X‐ray diffraction structure factors, were calculated, as well as properties such as elastic moduli and vibrational density of states. The addition of Li2O was found to improve the elastic moduli of the fiber glasses in excellent agreement with experimental results we reported earlier. The simulation results showed that the weakened network connectivity and decrease of tri‐/bridging oxygen have positively affected the lowering of liquid temperature, owing to the transformation to more boron Q2 and silicon/aluminon Q3. It is found that higher oxygen packing density, coordinated aluminum/boron species such as [AlO5] and [BO4] units, larger‐membered oxide rings, and intensified connections of [AlOx] and [SiO4] are the main reasons that lead to improved mechanical properties. MD‐based quantitative structure–property relationship analyses were performed and showed excellent correlations to measured properties, indicating that it is a promising approach to understand glass properties and design new glass compositions for functional applications.