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Computational targeting of iron uptake proteins in Covid-19 induced mucormycosis to identify inhibitors via molecular dynamics, molecular mechanics and density function theory studies

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In silico pharmacology 2024年第2期12卷 90页

作者： Manjima Sen B M Priyanka D Anusha S Puneetha Anagha S Setlur Chandrashekar Karunakaran Amulya Tandur C S Prashant Vidya Niranjan Department of Public Health Dentistry DAPM RV Dental College Bangalore 560078 India. Department of Oral Medicine and Diagnostic Radiology DAPM RV Dental College Bangalore 560078 India. Department of Periodontia DAPM RV Dental College Bangalore 560078 India. Department of Oral Pathology and Microbiology DAPM RV Dental College Bangalore 560078 India. Department of Biotechnology RV College of Engineering Bangalore 560059 India. Department of Orthodontics DAPM RV Dental College Bangalore 560078 India.

Mucormycosis is a concerning invasive fungal infection with difficult diagnosis, high mortality rates, and limited treatment options. Iron availability is crucial for fungal growth that causes this disease. This study aimed to computationally target iron uptake proteins in Rhizopus arrhizus, Lichtheimia corymbifera, and Mucor circinelloides to identify inhibitors, thereby halting fungal growth and intervening in mucormycosis pathogenesis. Seven important iron uptake proteins were identified, modeled, and validated using Ramachandran plots. An in-house antifungal library of ~ 15,401 compounds was screened in molecular docking studies with these proteins. The best small molecule-protein complexes were simulated at 100 ns using Maestro, Schrodinger. Toxicity predictions suggested all six molecules, identified as the best binding compounds to seven proteins, belonged to lower toxicity levels per GHS classification. A molecular mechanics GBSA study for all seven complexes indicated low standard deviations after calculating free binding energies every 10 ns of the 100 ns trajectory. density functional theory via quantum mechanics approaches highlighted the HOMO, LUMO, and other properties of the six best-bound molecules, revealing their binding capabilities and behaviour. This study sheds light on the molecular mechanisms and protein–ligand interactions, providing a multi-dimensional view towards the use of FDBD01920, FDBD01923, and FDBD01848 as stable antifungal ligands.

关键词： density function theory Iron uptake proteins MM-GBSA Molecular docking and simulations Mucormycosis Quantum mechanics

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Coupling computational thermodynamics with density-function-theory based calculations to design L12 precipitates in Fe-Ni based alloys

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MATERIALS & DESIGN 2020年 191卷

作者： Yang, Ying Samolyuk, German D. Chen, Tianyi Poplawsky, Jonathan D. Lupini, Andrew R. Tan, Lizhen Ken, Littrell Oak Ridge Natl Lab Mat Sci & Technol Div Oak Ridge TN 37831 USA Oak Ridge Natl Lab Ctr Nanophase Mat Sci Oak Ridge TN 37831 USA Oak Ridge Natl Lab Neutron Scattering Div Oak Ridge TN 37831 USA Oregon State Univ Corvallis OR 97331 USA

Achieving a high-volume fraction of thermodynamically stable L1(2)-type precipitates that are resistant to coarsening is of great importance for the development of low-cost Fe-Ni based austenitic steels. With the aid of computational thermodynamics, this work designed two model alloys: Fe-37.4Ni-6.1Al-2.9Ti (FNAT) and Fe-45.2Ni-5.9Al-8.5Si (FNAS). Both alloys were designed to contain a similar amount of L1(2) precipitate in Fe-Ni matrix with-out forming other precipitates. density-function-theory (DFT) calculation was coupled with computational thermodynamics to predict the critical radius at which the precipitates change shape from spherical to cuboidal. The calculation results suggest that critical radius for the FNAT alloy is about two orders of magnitude larger than that for the Fe-Ni-Al-Si alloy. Phase stability and morphology of the L1(2) precipitates in these two alloys were experimentally investigated through X-ray diffraction, atom probe tomography, and scanning and transmission electron microscopy. The L1(2) precipitates in the Fe-Ni-Al-Si system were found to be cuboidal and rod shaped, with much larger size than the spherical ones in the Fe-Ni-Al-Ti system, agreeing with the calculation results.

关键词： CALPHAD density function theory Precipitates Morphology Fe-Ni based alloys

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Design, synthesis, biological activity and density function theory study of pyrazole derivatives containing 1,3,4- thiadiazole moiety

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Frontiers of Chemical Science and Engineering 2017年第3期11卷 379-386页

作者： Xiaoming Ding Zhiwen Zhai Luping Lv Zhaohui Sun2, Xinghai Liu Linjiang College Hangzhou Vocational & Technical College Hangzhou 310018 China College of Chemical Engineering Zhejiang University of Technology Hangzhou 3100 i4 China

A variety of pyrazole derivatives containing 1,3,4-thiadiazole moiety were synthesized under microwave irradiation, and their structures were confirmed by 1H NMR and HRMS. They were evaluated for herbicidal and antifungal activities, and the results indicated that two compounds with a phenyl group （6a） and 4-tert-butylphe- nyl group （6n） possess good herbicidal activity for dicotyledon Brassica campestris and Raphanus sativus with the inhibition of 90% for root and 80%-90% for stalk at 100 ppm respectively. The structure-activity relationship of compounds 6a and 6n was also studied by density function theory method.

关键词： pyrazole 1,3,4-thiadiazole antifungal activity herbicidal activity density function theory

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Microwave-accelerated ruthenium complex synthesis: Reaction modeling using dielectric measurement and density function theory 16

Microwave-accelerated ruthenium complex synthesis: Reaction ...

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16th International Conference on Microwave and High Frequency Heating, AMPERE 2017

作者： Matsumura, Takeko Yanagida, Shozo Minerva Light Laboratory L.L.C. United States Osaka University Japan

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Phosphorus incorporation-induced adsorption behavior modulation for carbon cathodes enables ultrastable and high-energy aqueous Zn-ion hybrid capacitors

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Science China Chemistry 2025年第3期68卷 900-907页

作者： Lai Yu Xiaoyue He Rong Liu Guanglin Wan Xinyi Ma Anqiang Pan Liang Shi Genqiang Zhang Hefei National Research Center for Physical Sciences at the Microscale CAS Key Laboratory of Material for Energy ConversionDepartment of Material Science and EngineeringUniversity of Science and Technology of ChinaHefei 230026China School of Materials and Engineering Xinjiang UniversityUrumqi 830046China

The aqueous zinc ions hybrid capacitors(ZHCs)have great potential for future energy storage devices by their high safety and low cost merits,more importantly,it could combine the advantages of batteries and supercapacitors with high energy density and power output,***,the development of reliable cathodes is still a challenge with the unsatisfactory cycling stability and limited reaction kinetic,severely restricting its further commercial ***,we present phosphorus functionalized nitrogen-doped hierarchical porous carbon nanosheets(PN-HPCNS),where the P incorporation could effectively enhance the electronic transfer kinetics and ion adsorption capability to achieve superior zinc-ion storage *** asprepared PN-HPCNS cathode-based ZHC exhibits a high energy and power density(169.1 Wh kg^(-1)/68 W kg^(-1),15,840 W kg^(-1)/30.8 Wh kg^(-1))and long cycling lifespans more than 20,000 cycles with 92.0%capacity *** characterizations coupled with kinetics studies indicate that phosphorus modification is crucial to superior zinc ion storage,enabling PN-HPCNS with favorable reaction kinetics,promoting ion adsorption by providing more active ***,the theoretical calculation reveals that the phosphorus modification could enhance the adsorption ability,contributing to the superior ZHCs performance of PN-HPCNS.

关键词： carbon zinc ion hybrid capacitors cathode nanosheet density function theory

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Computational insights into the adsorption of lung cancer biomarkers on graphene-based materials and interfacial phenomena

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APPLIED SURFACE SCIENCE 2025年 696卷

作者： Shtepliuk, Ivan Puglisi, Donatella Eriksson, Jens Linkoping Univ Dept Phys Chem & Biol S-58183 Linkoping Sweden

An artificial intelligence-enhanced electronic nose (AI-enhanced e-nose) targeting lung cancer biomarkers-volatile organic compounds (VOCs) present in human breath-represents a revolutionary technology capable of transforming early-stage lung cancer detection. In this context, the choice of sensor materials for the enose plays a critical role in ensuring the necessary discriminatory power of the device. This selection must be based on a deep understanding of the physicochemical properties of potential candidate materials and their adsorption characteristics with respect to lung cancer biomarkers. The density functional theory (DFT) method is a powerful tool for achieving this understanding. This study presents the results of a comprehensive DFT investigation of the adsorption of 22 VOC lung cancer biomarkers on five different types of graphene using vdWBH functional combined with double-zeta plus polarization basis set. The 22 VOCs were classified based on their dipole moments. We demonstrate the importance of applying energy decomposition methods for VOC adsorption, along with coupled charge population analysis and charge density difference analysis approaches, for a more profound understanding of the interactions between VOCs and graphene-based materials. This variability in responses could serve as the foundation for creating an e-nose capable of providing diverse signal outputs when combining these materials.

关键词： Lung cancer Volatile organic compounds Biomarkers density function theory Graphene Electronic nose

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Surface/interface regulation of Ni0.85Se via tungsten-doping for enhanced oxygen evolution reaction

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JOURNAL OF ALLOYS AND COMPOUNDS 2025年 1011卷

作者： Fu, Xiao Liu, Xu Wang, Yi Wang, Yujia Yin, Xiaoxiao Liu, Zhongqing Sichuan Univ Sch Chem Engn Chengdu 610065 Peoples R China Sichuan Univ Sci & Engn Sch Chem Engn Zigong 643000 Peoples R China

Transition metal selenides have attracted wide attention due to their excellent electrocatalytic activity and stability in the oxygen evolution reaction (OER). Doping effectively regulates surface and interface electronic structure, thereby enhancing activity and optimizing kinetic properties. In this study, tungsten (W) was doped into Ni0.85Se through a one-step electrodeposition method, producing a self-supported W-Ni0.85Se electrode prepared on a stainless steel mesh substrate. The W introduction significantly improved the conductivity, electron transfer ability, and electrochemically active surface area of Ni0.85Se, greatly enhancing electrocatalytic performance for OER. In 1 M KOH solution, the electrode exhibited excellent OER activity, with overpotentials of 222 mV and 273 mV at current densities of 50 mA center dot cm-2 and 100 mA center dot cm- 2, respectively, and a Tafel slope of 51.2 mV center dot dec- 1 fitted in the current density range of 60 mA center dot cm- 2 to 140 mA center dot cm- 2. Moreover, after testing for 48 hours at a current density of 100 mA center dot cm- 2, the catalyst showed almost no significant performance degradation. density functional theory (DFT) calculations revealed that W doping enhances electron transport, adjusts adsorption/desorption of intermediates, and accelerates OER kinetics. This study provides a new approach for designing efficient, stable, and cost-effective transition metal selenide OER electrocatalysts.

关键词： One step electrodeposition W -doped Ni 0.85 Se Surface/interface regulation density function theory

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Stress-mediated copper-molybdenum alloy enables boosted hydrogen evolution activity

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ACTA MATERIALIA 2025年 286卷

作者： Xie, Yuming Dong, Jianing Li, Yifan Ma, Xiaotian Wang, Naijie Meng, Xiangchen Huang, Yongxian Harbin Inst Technol State Key Lab Precis Welding &Joining Mat & Struct Harbin 150001 Peoples R China Harbin Inst Technol Zhengzhou Res Inst Zhengzhou 450046 Peoples R China

Guided by the Sabatier volcano principle, we designed a severe plastic deformation-based strategy to obtain high-performance metallic electrocatalysts with boosted hydrogen evolution activity. Cu-Mo system was selected due to their opposite Gibbs free energies of adsorbed hydrogen and surface mechanical treatment was utilized to fine-tune the adsorption energy. A surface compressive stress layer with high values of -464+37 MPa was realized under the cryogenic severe plastic deformation process. The treated metallic catalysts exhibit ultra-low overpotential (79+3 mV at 10 mA cm-2 at the alkaline condition and 31+2 mV at 10 mA cm-2 at the acidic condition). The effective Tafel slope of acidic hydrogen evolution treated in the cryogenic environment is 141.2 mV decade-1, showing a fast Tafel-dominated Volmer-Tafel reaction mechanism. The density function theory calculation showed a transformation of the hydrogen adsorption site with increased external compressive stress, which contributed to the adsorption site adjacent to the supersaturated solid solution Mo atom. Bader charge analyses showed that the Mo atom lost more electrons, causing the surrounding Cu atoms to enter a stronger electronegative state, which significantly enhanced the adsorption capacity of Cu atoms for hydrogen with nearzero adsorption energy.

关键词： CU-Mo alloys Compressive stress Surface mechanical treatment density function theory Hydrogen evolution reaction

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Computational insights into the Ir-catalyzed hydrolysis dehydrogenation of ammonia borane: A carbene-assisted proton transfer mechanism

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INTERNATIONAL JOURNAL OF HYDROGEN ENERGY 2025年 99卷 85-92页

作者： Qian, Kehan Peng, Cheng Wang, Yong Soochow Univ Coll Chem Chem Engn & Mat Sci Suzhou 215123 Peoples R China

Ammonia borane (NH3BH3, AB), owing to its high theoretical hydrogen generation capacity, has garnered significant attention. In this article, we employed density functional theory (DFT) to investigate the hydrolysis dehydrogenation mechanism of AB catalyzed by an Ir cyclometalated carbene complex. Two potential mechanisms for the production of three equivalents of hydrogen were proposed: one involves B-N bond cleavage, and the other does not involve B-N bond cleavage. Our computational results indicate that the proton transfer pathway, which does not involve B-N bond cleavage, has the lowest activation barrier of 27.7 kcal/mol. Moreover, carbene ligands play dual roles in stabilizing the intermediate and assisting in proton transfer.

关键词： Ammonia borane Hydrolysis mechanism density function theory

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Tailoring redox couples of Li-rich Mn-based cathode materials by in-situ surface reconstruction for high-performance lithium-ion batteries

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NANO ENERGY 2025年 134卷

作者： Zhu, Xutao Xie, Xujia Lin, Jie Liu, Yuanyuan Gao, Guiyang Yang, Yong Zhang, Yinggan Xiong, Weicheng Jiang, Yidi Li, Qiyuan Peng, Dong-Liang Xiamen Univ Coll Mat State Key Lab Phys Chem Solid Surfaces Fujian Key Lab Surface & Interface Engn High Perfo Xiamen 361005 Fujian Peoples R China Xiamen Univ Collaborat Innovat Ctr Chem Energy Mat Xiamen 361005 Fujian Peoples R China

Li-rich Mn-based layered oxides (LLOs) are promising cathode materials due to their high capacity derived from the unique cation and anion redox couples. However, the poor cycling stability and drastic voltage decay impede their practical application. Despite the covalency theory is proposed to understand the redox activity of LLOs, comprehensive design guidelines are still lacking. Inspired by the covalency theory of polyanion cathodes, highperformance LLOs are developed through an in-situ surface reconstruction strategy of near-surface doping and surface coating. density function theory (DFT) calculations show that through the introduction of Ni2+ and PO43-, the energy bands of the transition metal (TM) 3d-O 2p and non-bonding O-2p shift to lower energy, resulting in the elevated working potential, reduced activity of lattice oxygen, and enhanced reversibility of redox oxygen. Meanwhile, the Li3PO4 coating can prevent electrolyte corrosion and mitigate surface degradation of LLOs upon cycling. As a result, the capacity retention of the modified LLOs is increased from 35.9 % to 77 %, and the voltage retention is raised from 68.6 % to 75.1 % after 700 cycles at 1 C. Furthermore, at 55 degrees C the capacity retention of the modified LLOs is also elevated from 32.1 % to 85.9 %, and the voltage retention is improved from 67.9 % to 82.3 % after 120 cycles at 1 C. The proposed strategy could advance the application of high-performance LLOs and their high-energy-density Li-ion batteries.

关键词： Li-rich Mn-based layered oxide Near-surface doping Surface coating Energy band density function theory

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