bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantum Chemical Molecular Dynamics Simulations for Methane‐Water Cages
Authors: Lanza Giuseppe 
Published: September 2024

ABSTRACTThe dynamic stability of various methane‐water clathrate‐like cages (CH4@(H2O)n, n = 16, 18, 20, 22), has been analyzed explicitly considering thermal effects by means of ab initio M06‐2X/6–31+G*/PCM calculations, which make use of Gaussian basis functions. Starting from the equilibrium filled cage structures, classical, dynamic reaction coordinate (DRC) on the Born–Oppenheimer surface, and semiclassical, Born–Oppenheimer plus harmonic zero‐point energy surface (BOMD), molecular dynamics have been carried out. Water molecules have a high tendency to orient covalent O–H bonds tangentially to the hydrophobic surface, thus clathrate‐like arrangements are an acceptable model to fully hydrate methane. If the cage size is such as to minimize core repulsion, due to electron cloud overlap, and to maximize host–guest van der Waals attractions, the clathrate‐like structures have a life‐time of two picoseconds in classical DRC simulations. The inclusion of quantum kinetic energy in BOMD simulations results in less structured cages with a reduced amount of hydrogen bond network. The preferential tangential orientation of the O‐H bonds is largely maintained, although few of them point toward the methane for a very short time in BOMD simulations. The reduced configurational space of water molecules hydrating hydrophobic moiety is highlighted, thus any satisfactory molecular modeling has to account for it.
Multiagent trajectory decision‐making for complex systems based on transformer large model structure
Authors: Ma Ziyuan , Gong Huajun , Wang Xinhua 
Published: September 2024

AbstractThe article explores the application of transformer‐based large models for trajectory decision‐making in complex decision systems, focusing on multiagent nodes in a topological structure. By leveraging the capabilities of large models, the proposed approach enhances decision‐making in model‐free control environments characterized by numerous agents, diverse internal tasks, and unknown conditions. The proposed framework integrates advanced transformer models with a sophisticated decision‐making framework to enhance the efficiency, safety, and reliability of multiagent operations in dynamic environments. The results demonstrate the superior performance of the transformer model, achieving a trajectory decision‐making accuracy of 97.8%, significantly outperforming other models such as long short‐term memory (LSTM), gate recurrent unit (GRU), and traditional approaches. The visualizations highlight the close alignment between the true and predicted outcomes of complex decision‐making systems, showcasing the model's ability to capture complex dependencies and interactions within the multiagent environment. High task completion rates and low collision rates further underscore the effectiveness of the decision‐making framework in optimizing agent coordination and ensuring safe operations.
Putting the soil health principles to the test in Iowa
Authors: McDaniel M. D. , Middleton T. A. 
Published: September 2024

AbstractOne of the most popular soil conservation campaigns is based on the USDA Natural Resource Conservation Service's Soil Health Principles (NRCS‐SHPs). The NRCS‐SHP program identifies four principles—maximize presence of living roots, minimize disturbance, maximize soil cover, and maximize biodiversity—with the underlying assumption that the more principles one follows, the greater improvements in soil health. Despite the popularity of the NRCS‐SHPs, this underlying assumption has not been rigorously tested. To do so, we used nine long‐term experiments all located in central Iowa, but with varying degree of NRCS‐SHP adoption, to determine if greater adoption increases three slow‐changing (maximum water holding capacity, bulk density [BD], and soil organic carbon) and three dynamic (microbial biomass carbon [MBC], potentially mineralizable carbon [PMC], and permanganate oxidizable carbon [POXC]) soil health indicators. We regressed these indicators with a soil health principle score that can scale soil management based on adoption of the NRCS‐SHPs. Of the slow‐changing soil properties, increased adoption of NRCS‐SHPs only decreased soil BD (R2 = 0.22, p = 0.024). On the other hand, increased adoption of NRCS‐SHPs strongly predicted increases in both MBC and PMC and across two sampling dates (R2 > 0.23, p < 0.015); POXC, however, did not increase with greater adoption. The consistent increases in MBC and PMC with greater adoption of NRCS‐SHPs supports their usefulness as sensitive indicators of positive soil health change. Our study provides scientific evidence to support the NRCS‐SHPs concept, improving its usefulness as an extension campaign, and stands as a step toward evidence‐based soil conservation.
Thermodynamic Study of Mehtylene Blue Adsorption and Photocatalytic Degradation on The N‐Doped TiO2 Thin Films: A DFT and Experimental Study
Authors: Duran (c) Freider , Díaz‐Uribe Carlos , Vallejo William , Vargas Ximena , Romero Bohorquez Arnold R. , Schott Eduardo , Zarate Ximena 
Published: September 2024

AbstractN‐Doped TiO2 coatings (N‐TiO2) were synthesized and characterized. The effect of the doping process on the physical‐chemical properties and photocatalytic efficiency of Methylene Blue (MB) under visible light irradiation were studied. The bare TiO2 showed only anatase crystalline structure. Furthermore, after the doping process, a slight transition from anatase to rutile was verified. The HRXPS confirmed that the doping process was effective. The N2 sorption using the BET assay showed a slight increase in surface area after the doping process. MB adsorption kinetic showed also a slight increase for doped TiO2 films, showing as best fitting the Langmuir model. Furthermore, a modification on the electronic structure was observed, showed by the modification of the optical absorption profile in the doped material. The results showed that the MB adsorption on N‐TiO2 thin films was endothermic (▵H=11 kJ mol−1) and a spontaneous process (▵G=−6.45 kJ mol−1). We performed DFT calculations to three simulated doped‐structures. The Gap value, the global reactivity indexes and, the Fukui function isosurfaces are presented. Finally, the scavenger tests suggested that
and OH⋅ could be the main ROS driving the photocatalytic process.
Synthesis, Spectral Analysis, Antimicrobial Evaluation, Molecular Modelling, DFT, TD‐DFT and SAR Studies of Novel 4,5,6,7‐Tetrabromo‐1H‐benzo[d][1,2,3]triazole Derivatives
Authors: Maiti Nigam Jyoti , Ganguly Swastika 
Published: September 2024

AbstractThis study evaluated 14 new 4,5,6,7‐tetrabromo‐1H‐benzo[d][1,2,3]triazole derivatives (3a‐n) for their antimicrobial activities, identifying compound 3k as the most effective. In vivo oral toxicity tests confirmed its non‐toxic nature. Predictive ADME analysis indicated favorable drug development properties. Molecular docking and dynamics studies were performed to investigate the interactions of compound 3k with Mycobacterium TB (PDB ID 2X22) and glucosamine‐6‐phosphate synthase (PDB ID 2VF5). The reactivity properties and reactive sites were determined using DFT‐derived HOMO and LUMO orbitals, along with MEP, and ESP maps, providing insights into the electron density, electrophilicity, and nucleophilicity. The electronic properties of the TD‐DFT and IEFPCM models were analyzed in solvents such as acetonitrile, ethanol, and DMSO and results were compared using UV‐Vis spectroscopy. Structural–activity relationship (SAR) investigations elucidated biological activities.
In Silico Screening of Sulfonamide Derivatives against Glycolytic Enzymes Reveals Mutation‐Independent Interactions of Sulfisoxazole and Sulfamethazine
Authors: Dasgupta Jayashis , Malla Avirup , Gupta Suvroma , Sur Runa 
Published: September 2024

AbstractGlycolysis is a highly conserved biochemical process that involves the sequential conversion of glucose to pyruvate and the generation of adenosine triphosphate (ATP), generating energy for cellular functions. This is carried out by several enzymes that play an important role in glucose metabolism. The sulfonamide group of drugs is commonly used as an antibiotic that inhibits the bacterial folic acid production pathway, although its effects on glycolytic enzymes are unclear. Since altered glycolytic enzyme expression is linked to a variety of metabolic disorders as well as cancer, the quest for new ligands against glycolytic enzymes is never over. We revealed that different sulfonamide derivatives interact with glycolytic enzymes with varying binding affinities. Among the selected sulfonamides, sulfisoxazole and sulfamethazine had greater binding scores to certain glycolytic enzymes than others. In silico point mutation analysis predicts that sulfisoxazole and sulfamethazine interact with certain glycolytic enzymes in a residue‐independent manner. This research generates a repository of the 2D interactions of sulfonamide derivatives with glycolytic enzymes, binding energies, impacts of induced point mutations on the local environment, and changes in protein structural flexibility. In the future, sulfisoxazole and sulfamethazine may be repurposed as specific glycolytic enzyme inhibitors to combat a variety of glycolysis‐related metabolic disorders.
Ligand Backbone Influenced Luminescent Properties of Mononuclear Zn(II)‐N3Py2 Compounds: Synthesis, Structures and Nitroaromatics Detection
Authors: Viegas Jeffrey L. , Chari Vishnu R. , Dhuri Sunder N. 
Published: September 2024

AbstractMononuclear Zn(II) compounds, [Zn(L1)](ClO4)2 (1) and [Zn(L2)](ClO4)2 (2), embedded with ligands, L1=N1‐(pyridin‐2‐ylmethyl)‐N2‐(2‐((pyridin‐2‐ylmethyl)amino)ethyl)ethane‐1,2‐diamine and L2=N1‐(pyridin‐2‐ylmethyl)‐N3‐(3‐((pyridin‐2‐ylmethyl)amino)propyl)propane‐1,3‐diamine are synthesized. Compound 1 is revisited, and structure‐function relation is compared with new compound 2. Single crystal X‐ray analysis revealed that compound 1 crystallizes in the tetragonal non‐centrosymmetric P41 space group while 2 crystallizes in a centrosymmetric monoclinic space group P21/c. The asymmetric unit consists of a crystallographically independent [Zn(L1)]2+cation in 1 while [Zn(L2)]2+cation in 2 and two unique perchlorate anions in both. IR spectra of 1 and 2 confirmed the vibrations due to organic ligands and tetrahedral perchlorates. PXRD confirmed the phase purity of powdered samples compared with theoretical PXRD patterns obtained from single‐crystal X‐ray diffraction data. NMR and ESI‐MS data suggested the phase purity and stability of compounds 1 and 2 in solution. Photoluminescence properties of compounds 1 and 2 have been investigated, considering their application in sensing explosive nitroaromatic compounds. Our results suggest that compound 1 is very selective in the chemical sensing of trinitrophenol (TNP) and dinitrophenol (DNP) in an aqueous medium compared to the reactivity of compound 2. The existence of spectral overlap in the absorption spectra of 2,4‐dinitrophenol (DNP) and 2,4,6‐trinitrophenol (TNP) with the emission spectrum of 1 or 2 indicates the operation of the resonance electron transfer (RET) mechanism.
In Silico Prediction of Antibacterial Activity of Quinolone Derivatives
Authors: Karim Tafsir , Almatarneh Mansour H. , Rahman Shofiur , Alodhayb Abdullah N. , Albrithen Hamad , Hossain Md. Mainul , Kawsar Sarkar M. A. , Poirier Raymond A. , Uddin Kabir M. 
Published: September 2024

AbstractThe rising antimicrobial resistance crisis has diminished the effectiveness of traditional antibiotics against pathogenic bacteria. This study addresses this urgent challenge by exploring the antibacterial potential of novel quinolone derivatives (1–33). Using computational in silico modeling to simulate biological interactions, we aimed to identify candidates with potent antibacterial activity. A total of 33 quinolone derivatives were assessed for their physicochemical properties and effectiveness against a range of clinically relevant pathogens, including methicillin‐resistant Staphylococcus aureus (MRSA), Klebsiella pneumoniae, Streptococcus pneumoniae, and Enterococcus faecalis. Molecular docking studies identified compounds 28, 29, 32, and 33 as having notable binding affinities, particularly against MRSA. Further molecular dynamics simulations of compound 29 confirmed its favorable stability and potential for disrupting MRSA, reinforcing the docking results and showing strong alignment with in vitro findings. These findings position compound 29 as a promising lead for developing alternative MRSA therapies and underscore the need for further in vivo studies to evaluate its therapeutic potential.
Oxygen‐Doped Graphitic Carbon Nitride for Electrochemical Uric Acid Sensing: Method Without Metals
Authors: Thakur Palak , Bhardwajj Vineet , Taunk Manish , Kumar Sunil , Seo Yongho , Fouad Dalia , Ataya Farid S. , Thakur Kamal Kishor 
Published: September 2024

AbstractThe present study examined potential benefits of heteroatom doping to manipulate the electrical structure and to enhance the efficiency of the sensor, with an emphasis on developing inexpensive, metal‐free electrochemical sensors. Melamine and ammonium oxalate were used as precursors in a one‐step thermal polymerization technique yielding oxygen‐doped graphitic carbon nitride (O‐gCN). Following synthesis, the material's structural and morphological properties were thoroughly examined using a multitude of analytical techniques, including EIS. A notable decrease in impedance was observed, suggesting improved conductivity. Additionally, the doping approach exhibited a noticeable improvement in reduction current receptivity and surface area as compared to unmodified graphitic carbon nitride (g‐CN). Utilizing both differential pulse voltammetry (DPV) and the classical cyclic voltammetry (CV) methods, we investigated the electro oxidation of uric acid (UA) as well as concentration dependence and selectivity studies using oxygen‐doped graphitic carbon nitride modified glassy carbon electrode (O‐gCN@GCE). O‐gCN@GCE demonstrated remarkable performance, allowing the detection of UA concentrations as low as 7.784 µAµM−1cm−2. Its low detection limit of 0.57 µM and wider linear range (5–120 µM) further highlighted its potential for extremely sensitive assays and its remarkable capacity to operate over a broad UA concentration range.
Engineering of (−)‐Limonene‐3‐Hydroxylase to Enhance Its Regioselectivity for Biosynthesis of (−)‐Menthol
Authors: Yan Jun‐Chi , Shou Chao , Pan Jiang , Xu Jian‐He , Li Chun‐Xiu 
Published: September 2024

AbstractThere is high market demand for (−)‐menthol because of its unique aroma and cooling properties. The first bottleneck encountered in the biosynthesis of (−)‐menthol in Escherichia coli is the low hydroxylation efficiency of (−)‐limonene‐3‐hydroxylase. Few known enzymes can hydroxylate the third carbon atom of (−)‐limonene. In this work, initially, we searched for new enzymes and screened a library of cytochrome P450BM3 variants aiming to improve catalysis of this reaction, but did not identify any variants with improved activity or regioselectivity. Then, through protein engineering of a cytochrome P450 monooxygenase variant from Pseudomonas putida (PpcamY96F/V247L), we obtained variant PpcamF87W/Y96F/L244I/V247L/V396A with regioselectivity of 93% (starting from 70%) toward (−)‐limonene without losing activity. Because of the improvement in regioselectivity, its turnover number was 1.5 times that of the starting enzyme. We analyzed the reasons for the improvement through molecular dynamics simulations. The new variant also exhibited 95% regioselectivity toward (+)‐limonene. This enzyme variant can be applied in biosynthesis of (−)‐menthol.
A Novel Structured Si‐Based Composite with 2D Structured Graphite for High‐Performance Lithium‐Ion Batteries
Authors: Kim Min Ji , Lee Inuk , Lee Jin Woong , Yoon Dowoong , Kim Jung Hyun , Lee Seungho , Kim Kwanghyun , Kim Patrick Joohyun , Choi Junghyun , Kang Yun Chan , Jung Dae Soo 
Published: September 2024

AbstractSilicon is a promising alternative to graphite anodes for achieving high‐energy‐density in lithium‐ion batteries (LIBs) because of its high theoretical capacity (3579 mAh g−1). However, silicon anode must be developed to address its disadvantages, such as volume expansion and low electronic conductivity. Therefore, the use of silicon as composed with graphite and carbon anode materials is investigated, which requires properties such as a spherical morphology for high density and encapsulation of silicon particles in the composite. Herein, a graphite@silicon@carbon (Gr@Si@C) micro‐sized spherical anode composite is synthesized by mechanofusion process. This composite comprises an outer surface, middle layer, and core pore, which are formed by the capillary force arising from 2D structured graphite and pitch properties. This structure effectively addresses the intrinsic issues associated with Si. Gr@Si@C exhibits a high capacity of 1622 mAh g−1 and capacity retention of 72.2% after 100 cycles, with a high areal capacity 4.2 mAh cm−2. When Gr@Si@C is blended with commercial graphite, the composite exhibits high capacity retention and average Coulombic efficiency after cycling. The Gr@Si@C blended electrode exhibits a high energy density of 820 Wh L−1 with ≈16% metallic Si in the electrode (40 wt.% composite), enabling the realization of practical commercial LIBs.
Microheater Controlled Crystal Phase Engineering of Nanowires Using In Situ Transmission Electron Microscopy
Authors: Andersen Christopher R. Y. , Tornberg Marcus , Lehmann Sebastian , Jacobsson Daniel , Dick Kimberly A. , Mølhave Kristian S. 
Published: September 2024

AbstractCrystal Phase Quantum Dots (CPQDs) offer promising properties for quantum communication. How CPQDs can be formed in Au‐catalyzed GaAs nanowires using different precursor flows and temperatures by in situ environmental transmission electron microscopy (ETEM) experiments is studied. A III‐V gas supply system controls the precursor flow and custom‐built micro electro‐mechanical system (MEMS) chips with monocrystalline Si‐cantilevers are used for temperature control, forming a micrometer‐scale metal–organic vapor phase epitaxy (µMOVPE) system. The preferentially formed crystal phases are mapped at different precursor flows and temperatures to determine optimal growth parameters for either crystal phase. To control the position and length of CPQDs, the time scale for crystal phase change is investigated. The micrometer size of the cantilevers allows temperature shifts of more than 100 °C within 0.1 s at the nanowire growth temperature, which can be much faster than the growth time for a single lattice layer. For controlling the crystal phase, the temperature change is found to be superior to precursor flow, which takes tens of seconds for the crystal phase formation to react. This µMOVPE approach may ultimately provide faster temperature control than bulk MOVPE systems and hence enable engineering sequences of CPQDs with quantum dot lengths and positions defined with atomic precision.
Characterization and spatial distribution of microplastics in Surma river, Bangladesh: Assessing water and sediment dynamics
Authors: Izlal Saif , Ruhad Fahim Mahafuz , Islam Tariqul , Rahman Md. Hafizur , Tania Hafsa Akter 
Published: September 2024

AbstractMicroplastics (MPs), or tiny pieces of plastic, have become a major global environmental problem because of their ubiquitous availability and possible risks to aquatic ecosystems. Surma is one of the vital rivers in Bangladesh located in the northeast part, with higher chances of MP pollution due to different anthropogenic reasons. In this instance, we carried out the investigation on the abundance, distribution, and characteristics of MPs in the sediment and surface water of the river. Samples were collected from 15 major locations of the Surma river flowing through Sylhet municipality. MPs particles were isolated from sediments and water samples utilizing techniques like sieve analysis, wet peroxide oxidation, density separation, and filtration and then characterized using a stereomicroscope. The abundance of MPs recorded 8 to 18 items/L in water samples (mean ± SD: 12.33 ± 2.98 items/L) and 360 to 1120 items/kg in sediment samples (mean ± SD: 522.67 ± 197.84 items/kg). The prominent size, shape, and color of MPs isolated from sediments were 1–2 mm sizes (24.49%), fragments (47.71%), and black (30.65%). However, for water samples, 1–2 mm sizes (37.22%), fiber shapes (48.48%), and transparent colors (38.46%) were dominant features. Conspicuously, in both sediment and water samples, there was a higher prevalence of smaller sized particles, posing a significant threat to the ecosystem. This heightened risk stems from the increased likelihood of ingestion by microorganisms, as well as the larger surface area of these particles, which may serve as vectors for other pollutants like organic pollutants and heavy metals. A greater abundance of fibers suggests an increased presence of lightweight particles in the water and sediment. Furthermore, the transparent color of the MPs in water might be impacted by prolonged weathering in the river, while the presence of black‐colored MPs in sediment points to the existence of plastic pellets originating from industrial and diverse sources. Future studies should concentrate on long‐term and broad monitoring, ecological effects, and practical mitigation techniques for MPs, providing essential baseline data to guide the formulation of policies in developing nations.Practitioner points
12.33 items/L in surface water and 522.67 items/kg in sediment were observed.
High correlation indicates a single MP source in mainstream water, differing from sediment.
Fiber shapes, black, and transparent colored MPs are dominant.
Higher prevalence of smaller sized MPs, posing a significant threat to the aquatic ecosystem.
Molecular Transformations for Direct Synthesis of Thorium Dioxide Films
Authors: Lichtenberg Andreas , Altuntas Kemal , Fischer Thomas , Karimpour Touraj , Diel Simon , Aytuna Ziyaad , Amadi Chijioke Kingsley , Mathur Sanjay 
Published: September 2024

AbstractNew Th(IV) complexes with high volatility were synthesized and applied as molecular single‐source precursors for chemical vapor deposition (CVD) of ThO2 thin films. The change in the steric profile of alkoxide ligands and concomitant reduction in the molecular weight of [Th(L)2(OR)2] (1‐OR, R=iso‐propyl (1‐OiPr) or tert‐butyl (1‐OtBu), L=N‐(4,4,4‐trifluorobut‐1‐ene‐3‐one)‐methoxyethylamide)) had a profound effect on the vapor pressure (at 10−5 mbar) evident in the drop in sublimation temperature to 100 °C for the iso‐propoxide derivative against 130 °C observed for the tert‐(1‐OtBu). Hirshfeld surface analysis of both complexes showed different degrees of intermolecular H⋅⋅⋅F interactions responsible for the observed differences in the volatilities of the two complexes. Both mixed‐ligand compounds (1‐OiPr, 1‐OtBu) were applied in the CVD process to deposit thorium oxide thin films without any carrier or reactive gas that verified their suitability as single‐source precursors to ThO2 coatings. Thin films of ThO2 were grown at 500 °C and 600 °C on Si/SiO2 substrates, which showed presence of C, N, and F presumably originating from the incorporation of ligand fragments in the growing CVD deposits. Subsequent calcination of CVD‐grown ThO2 films at 800 °C in air led to phase pure ThO2 coatings with uniform morphology.