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Unraveling the Intercalation-Mediated Phase Transformation and Epitaxy at the Mn/MoS2 Heterointerface. 揭示Mn/MoS2异质界面的插层介导相变和外延。
IF 8.2 2区 材料科学 Q1 MATERIALS SCIENCE, MULTIDISCIPLINARY Pub Date : 2026-03-23 DOI: 10.1021/acsami.6c01393
Mengling Yu, Junjie Ding, Zhuoya Zhang, Yashi Zhang, Yongqiang Li, Wenjun Lv, Wen Zhao, Xiahan Sang

The integration of functional oxides with two-dimensional (2D) transition metal dichalcogenides (TMDs) is pivotal for next-generation electronics yet remains constrained by aggressive interfacial reactions and interdiffusion. Herein, we resolve the atomic-scale reaction kinetics at the Mn/MoS2(0001) heterointerface by combining spherical aberration-corrected scanning transmission electron microscopy (STEM) with density functional theory (DFT) calculations. We identify a distinct temperature-dependent pathway that transforms destructive diffusion into precise phase engineering. At 500 °C, Mn cation intercalation serves as the primary driving force, inducing the nucleation of a metastable triclinic MnMoO5 phase while concurrently triggering a local 2H-to-1T polymorphic transition. Crucially, this intercalation is confined to a self-limiting skin layer, evidenced by a ∼4% c-axis expansion. Elevating the thermal treatment to 600 °C promotes thermodynamic equilibration, facilitating the crystallization of the polar magnetic hexagonal Mn2Mo3O8 phase and the reconstruction of an atomically sharp interface. These findings demonstrate a mechanism for exploiting reactive diffusion to synthesize high-quality, functional oxide/2D heterostructures with chemically distinct, sharp interfaces.

功能氧化物与二维(2D)过渡金属二硫族化合物(TMDs)的集成对于下一代电子产品至关重要,但仍然受到侵略性界面反应和相互扩散的限制。本文通过结合球差校正扫描透射电子显微镜(STEM)和密度泛函理论(DFT)计算,解析了Mn/MoS2(0001)异质界面的原子尺度反应动力学。我们确定了一种独特的温度依赖途径,将破坏性扩散转化为精确的相位工程。在500°C时,Mn阳离子插入是主要驱动力,诱导亚稳的三斜MnMoO5相成核,同时触发局部2h到1t的多晶转变。至关重要的是,这种嵌入被限制在一个自我限制的皮肤层,由约4%的c轴扩张证明。将热处理温度提高到600℃有助于热力学平衡,有利于极性磁性六方Mn2Mo3O8相的结晶和原子锐界面的重建。这些发现证明了一种利用反应扩散来合成高质量、功能氧化物/2D异质结构的机制,这些异质结构具有化学上独特的、尖锐的界面。
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引用次数: 0
Strong Metal-Support Interaction in Metal-Organic Framework (MOF)-Derived Multiphase TiO2 Supports for Durable Pt Catalysts in Acidic Hydrogen Evolution. 金属-有机骨架(MOF)衍生多相TiO2载体中强金属-载体相互作用在酸性析氢Pt催化剂中的应用
IF 8.2 2区 材料科学 Q1 MATERIALS SCIENCE, MULTIDISCIPLINARY Pub Date : 2026-03-23 DOI: 10.1021/acsami.5c24645
Yujin Son, Moonsu Kim, Gibaek Lee

Platinum-based electrocatalysts exhibit exceptional intrinsic activity toward the hydrogen evolution reaction (HER), but their practical deployment in water electrolysis is hindered by nanoparticle agglomeration, carbon-support degradation, and weak metal-support interaction (MSI). Here, porous TiO2 supports with systematically tunable anatase-rutile composition were synthesized using MIL-125 (Ti) as a metal-organic framework (MOF) template, followed by controlled calcination and chemical reduction to anchor uniformly dispersed Pt nanoparticles. Precise phase engineering strengthened MSI, most notably in Pt/TiO2-500, which displayed a distinct negative shift in Pt 4f (-0.7 eV) and a positive shift in Ti 2p (+0.5 eV), indicating strong interfacial electronic coupling. This optimized interaction reduced charge-transfer resistance, yielded overpotentials of 34 mV and 84 mV at 10 and 50 mA cm-2, and produced a Tafel slope of 32.6 mV dec-1, comparable to or better than many state-of-the-art TiO2-supported Pt electrocatalysts. Pt/TiO2-500 also preserved 96.5% of its activity after 2000 potential cycles and maintained stable operation for over 100 h at 10 mA cm-2, confirming its structural and electrochemical robustness. These results demonstrate that phase-engineered MOF-derived TiO2 significantly reinforces MSI, suppresses Pt agglomeration, and accelerates interfacial charge-transfer kinetics. This work establishes a generalizable strategy for designing durable and high-performance Pt-based electrocatalysts for sustainable hydrogen production.

铂基电催化剂在析氢反应(HER)中表现出优异的内在活性,但其在水电解中的实际应用受到纳米颗粒团聚、碳载体降解和弱金属载体相互作用(MSI)的阻碍。本文以MIL-125 (Ti)为金属有机骨架模板,通过煅烧和化学还原法制备均匀分散的Pt纳米颗粒,合成了具有系统可调锐钛矿-金红石组成的多孔TiO2载体。精确的相位工程增强了MSI,特别是在Pt/TiO2-500中,在Pt 4f (-0.7 eV)中表现出明显的负位移,在Ti 2p (+0.5 eV)中表现出明显的正位移,表明界面电子耦合强。这种优化的相互作用降低了电荷转移电阻,在10和50 mA cm-2下产生了34 mV和84 mV的过电位,并产生了32.6 mV的Tafel斜率(12 / 1),与许多最先进的tio2负载Pt电催化剂相当或更好。Pt/TiO2-500在2000个电位循环后仍保持96.5%的活性,并在10 mA cm-2下稳定运行100小时以上,证实了其结构和电化学稳健性。这些结果表明,相工程mof来源的TiO2显著增强了MSI,抑制了Pt团聚,加速了界面电荷转移动力学。这项工作为设计耐用和高性能的pt基电催化剂的可持续制氢建立了一个可推广的策略。
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引用次数: 0
A Non-Peptidic Fluorescent Probe for In Vitro Detection of Chymotrypsin. 一种体外检测凝乳胰蛋白酶的非肽类荧光探针。
IF 4.7 Q2 MATERIALS SCIENCE, BIOMATERIALS Pub Date : 2026-03-23 DOI: 10.1021/acsabm.5c02288
Ramakrishnan AbhijnaKrishna, Yu-Tung Fu, Shu-Pao Wu, Sivan Velmathi

The work presents the development of a non-peptide fluorescent probe, NQ , for in vitro detection of chymotrypsin (Chy). Unlike traditional peptide-based probes that suffer from instability and enzymatic degradation, NQ incorporates hydrocinnamoyl chloride as a recognition group, offering enhanced stability under physiological conditions. Upon enzymatic cleavage by Chy, the probe releases a fluorogenic product (NQOH), generating a turn-on fluorescence signal. NQ exhibits a rapid initial response, with a distinguishable fluorescence signal generated within 10 min, and a low detection limit of 7.64 ng/mL. Although the enzymatic reaction reaches saturation over a period of 30-60 min, the rapid initial turn-on allows for rapid qualitative screening. A notable feature is the probe's large Stokes shift (177nm) combined with an efficient non-peptidic recognition group. This synergistic design significantly improves detection accuracy by minimizing background interference and resisting non-specific degradation in complex biological environments. The probe showed effective performance in HepG2 cell models, confirming its suitability for biological applications. This study underscores the value of non-peptide probe designs for fast and precise enzyme detection in complex biological environments.

该工作提出了一种非肽荧光探针NQ的发展,用于体外检测凝乳胰蛋白酶(Chy)。与传统的肽类探针不稳定和酶降解不同,NQ将氢肉桂酰氯作为识别基团,在生理条件下提供更高的稳定性。在Chy的酶切作用下,探针释放出荧光产物(NQOH),产生开启荧光信号。NQ初响应迅速,10 min内可产生可识别的荧光信号,检出限较低,为7.64 ng/mL。虽然酶促反应在30-60分钟内达到饱和,但快速初始启动允许快速定性筛选。一个显著的特点是探针的大斯托克斯位移(177nm)与有效的非肽识别基团相结合。这种协同设计通过最大限度地减少背景干扰和抵抗复杂生物环境中的非特异性降解,显著提高了检测精度。该探针在HepG2细胞模型中表现出有效的性能,证实了其生物学应用的适用性。这项研究强调了非肽探针设计在复杂生物环境中快速精确检测酶的价值。
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引用次数: 0
Near-Unity-Efficiency Charge Transfer and Quantum Confinement-Regulated Long-Lifetime Charge Recombination in 2D Perovskite/Atomically Thin Semiconductor Heterostructures. 二维钙钛矿/原子薄半导体异质结构中的近单位效率电荷转移和量子约束调控长寿命电荷复合。
IF 8.2 2区 材料科学 Q1 MATERIALS SCIENCE, MULTIDISCIPLINARY Pub Date : 2026-03-23 DOI: 10.1021/acsami.6c00254
Chi Zhang, Xingtao Wang, Yao Zhang, Congbo Shi, Dongming Zhao, Zhiguo Zhao, Xiaojun Qin, Menglei Li, Lichuang Wang, Xiongfei Chen, Zizhen Lin, Feng Gao, Yuan Xia, Fengyi Fu

Transition metal dichalcogenides (TMDs) have shown great potential in optoelectronic devices, such as phototransistors and photodetectors. However, TMD-based optoelectronic devices face notable limitations, primarily weak light absorption due to their atomically thin structure and short exciton-carrier lifetimes caused by strong excitonic effects. Constructing heterostructures (HSs) with TMDs and perovskites is an important strategy to overcome these challenges. Understanding charge transfer dynamics and interlayer recombination at the TMD/2D perovskite interface is essential but still lacking. Here, we prepared monolayer WS2/2D perovskite HSs with varying n-values (n = 1, 2, and 4, n represents the number of inorganic octahedral layers between two adjacent organic spacers within the 2D perovskite structure) and systematically investigated the photogenerated carrier transfer and interlayer electron-hole recombination process. By employing the n = 1 2D perovskite film and selectively exciting monolayer WS2, we observed ultrafast photogenerated hole transfer from monolayer WS2 to the n = 1 2D perovskite film within 200 fs. Further, in the HS formed with the n = 4 2D perovskite film, upon selectively exciting the n = 4 2D perovskite film, we observed an ultrafast photogenerated electron transfer from the n = 4 2D perovskite film to monolayer WS2, occurring within 2.5 ps. Finally, we found that as the n value increased, the reduced quantum confinement led to a significant increase in the interlayer electron-hole recombination lifetime within the 2D perovskite/monolayer WS2 HSs, extending from 0.2 ns at n = 1 to 8.6 ns at n = 4. This study demonstrates that in TMD/2D perovskite HSs, ultrafast hole transfer from TMD to the 2D perovskite and efficient electron transfer from the 2D perovskite to TMD can both occur. Additionally, the interlayer electron-hole recombination lifetime can be modulated by quantum confinement effects. Our findings provide critical guidance for optimizing optoelectronic devices based on TMD/2D perovskite HSs.

过渡金属二硫族化合物(TMDs)在光电器件,如光电晶体管和光电探测器中显示出巨大的潜力。然而,基于tmd的光电器件面临着明显的局限性,主要是由于其原子薄结构导致的弱光吸收和强激子效应导致的短激子载流子寿命。利用tmd和钙钛矿构建异质结构(HSs)是克服这些挑战的重要策略。了解TMD/2D钙钛矿界面的电荷转移动力学和层间复合是必要的,但仍然缺乏。本文制备了不同n值的单层WS2/2D钙钛矿HSs (n = 1、2和4,n表示二维钙钛矿结构中相邻有机间隔层之间的无机八面体层数),并系统地研究了光生载流子转移和层间电子-空穴复合过程。利用n = 1的二维钙钛矿薄膜和选择性地激发单层WS2,我们观察到在200 fs内从单层WS2到n = 1的二维钙钛矿薄膜的超快光生空穴转移。此外,在由n = 4 2D钙钛矿膜形成的HS中,通过选择性激发n = 4 2D钙钛矿膜,我们观察到从n = 4 2D钙钛矿膜到单层WS2的超快光电子转移,发生在2.5 ps内。最后,我们发现随着n值的增加,量子约束的减少导致二维钙钛矿/单层WS2 HS中层间电子-空穴复合寿命显著增加。从n = 1时的0.2 ns扩展到n = 4时的8.6 ns。本研究表明,在TMD/2D钙钛矿高温超导中,可以实现TMD向2D钙钛矿的超快空穴转移和2D钙钛矿向TMD的高效电子转移。此外,层间电子-空穴复合寿命可以通过量子约束效应进行调制。我们的研究结果为优化基于TMD/2D钙钛矿HSs的光电器件提供了重要的指导。
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引用次数: 0
Fourier Plane Tomographic Spectroscopy Reveals Orientation-Dependent Multipolar Plasmon Modes in Micrometer-Scale Janus Particles. 傅里叶平面层析光谱揭示了微米尺度Janus粒子中取向相关的多极等离子体模式。
IF 16 1区 材料科学 Q1 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2026-03-23 DOI: 10.1021/acsnano.6c01771
Felix H Patzschke, Frank Cichos

Precise control of light-matter interactions is a cornerstone of next-generation technologies, from ultrasensitive biosensing and single-molecule tracking to the development of adaptive metamaterials. While small, symmetric nanostructures are well-understood, micrometer-scale plasmonic Janus particles (pJPs), comprising dielectric cores with thin metallic caps, exhibit complex optical properties due to their asymmetric structure. Despite widespread applications in active matter research, their orientation-dependent scattering properties remain largely unexplored. We introduce Fourier plane tomographic spectroscopy for simultaneous four-dimensional characterization of scattering from individual micrometer-scale particles across wavelength, incident angle, and scattering angle. Combining measurements with finite-element simulations, we identify discrete spectral markers in visible and near-infrared regions that evolve predictably with cap orientation. Spherical-harmonics decomposition reveals that these markers arise from three distinct multipolar modes up to fifth order: axial-propagating transverse-electric, transverse-propagating transverse-electric, and transverse-propagating axial-electric, with retardation-induced splitting. We observe progressive red-shifts and line width narrowing of higher-order resonances, demonstrating curvature's influence on mode dispersion. Orientation-specific scattering patterns exhibit polarization-dependent features enabling optical tracking of particle rotation. Beyond pJPs, this methodology establishes a general framework for characterizing asymmetric nanostructures of diverse material combinations and geometries, offering a toolkit for designing orientation-responsive nanoantennas, reconfigurable metasurfaces, active colloidal systems with tailored light-matter interactions, and high-precision optical tracking of particle rotation.

光-物质相互作用的精确控制是下一代技术的基石,从超灵敏生物传感和单分子跟踪到自适应超材料的开发。虽然人们已经很好地理解了小而对称的纳米结构,但微米尺度的等离子体Janus粒子(pJPs),由带有薄金属帽的电介质芯组成,由于其不对称结构而表现出复杂的光学特性。尽管在活性物质研究中得到了广泛的应用,但它们的定向散射特性仍未得到充分的研究。我们引入傅里叶平面层析光谱来同时表征单个微米尺度粒子在波长、入射角和散射角上的四维散射。结合测量和有限元模拟,我们确定了可见光和近红外区域的离散光谱标记,这些标记可预测地随帽的方向演变。球谐波分解表明,这些标记来自三种不同的多极模式,最高可达五阶:轴向传播横向电、横向传播横向电和横向传播轴向电,并伴有延迟诱导分裂。我们观察到高阶共振的渐进红移和线宽变窄,证明了曲率对模色散的影响。定向散射模式表现出与偏振相关的特征,能够光学跟踪粒子旋转。除了pJPs,该方法还为表征不同材料组合和几何形状的不对称纳米结构建立了一个总体框架,为设计定向响应纳米天线、可重构超表面、具有定制光物质相互作用的活性胶体系统以及粒子旋转的高精度光学跟踪提供了一个工具包。
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引用次数: 0
Origin of Bright Quantum Emissions with a High Debye-Waller Factor in Silicon Nitride. 氮化硅中高德拜-沃勒因子亮量子发射的起源。
IF 9.1 1区 材料科学 Q1 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2026-03-23 DOI: 10.1021/acs.nanolett.5c06190
Shibu Meher, Manoj Dey, Abhishek Kumar Singh

Silicon nitride has emerged as a promising photonic platform for integrated single-photon sources, yet the microscopic origin of the recently observed bright quantum emissions remains unclear. Using hybrid density functional theory, we show that the negatively charged NSiVN center (NV-) in the C1h configuration exhibits a linearly polarized zero phonon line (ZPL) at 2.46 eV, with a radiative lifetime of 9.01 ns and a high Debye-Waller (DW) factor of 33%. We further find that the C1h configuration is prone to a pseudo-Jahn-Teller distortion, yielding two symmetrically equivalent defect structures that emit bright, linearly polarized ZPL at 1.80 eV with a lifetime of 10.17 ns and an increased DW factor of 41%. These nitrogen-vacancy-related defects explain the origins of visible quantum emissions, paving the way for deterministic and monolithically integrated silicon nitride quantum photonics.

氮化硅已经成为集成单光子源的一个有前途的光子平台,然而最近观测到的明亮量子发射的微观起源仍然不清楚。利用杂化密度函数理论,我们发现带负电荷的NSiVN中心(NV-)在2.46 eV下呈现线性极化零声子线(ZPL),辐射寿命为9.01 ns, DW系数高达33%。我们进一步发现C1h结构容易发生伪jahn - teller畸变,产生两个对称等效的缺陷结构,在1.80 eV下发射明亮的线极化ZPL,寿命为10.17 ns, DW因子增加了41%。这些与氮空位相关的缺陷解释了可见量子发射的起源,为确定性和单片集成氮化硅量子光子学铺平了道路。
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引用次数: 0
Iodosobenzene-Mediated Synthesis of 1-Benzothiazolyl-o-Carboranes. 碘苯介导的1-苯并噻唑基-邻碳硼烷的合成。
IF 3.6 2区 化学 Q1 CHEMISTRY, ORGANIC Pub Date : 2026-03-23 DOI: 10.1021/acs.joc.5c03227
Huijin Guo, Ji Wu, Ke Cao, Chunguang Zhu, Quanli Zhang, Qiuxia Peng, Zejun Pu, Jiachun Zhong

The innovation of synthetic strategies for incorporating heterocycles into carborane is a significant objective in the realm of carborane chemistry on account of the fact that heterocyclic skeletons are widespread among natural products as well as bioactive molecules and the versatility applications of carboranes in medicinal chemistry and materials science. This method disclosed a facile and practical protocol for the synthesis of 1-benzothiazolyl-o-carboranes through an iodosobenzene-mediated intramolecular oxidative annulation process of C(1)-N-arylthioaacylamino-o-carborane. A series of 1-benzothiazolyl-o-carboranes have been synthesized in good to excellent yields. This work would be an important reference for the synthesis of aromatic heterocycle-carborane derivatives and promote their applications in designing drug candidates and functional materials.

由于杂环骨架在天然产物和生物活性分子中广泛存在,以及杂环烷在药物化学和材料科学中的广泛应用,杂环烷合成策略的创新是碳硼烷化学领域的一个重要目标。本方法通过碘苯介导的C(1)- n -芳基硫酰基氨基-o-碳硼烷分子内氧化环化反应,公开了一种简便实用的合成1-苯并噻唑基-o-碳硼烷的方案。以优异的收率合成了一系列1-苯并噻唑基-邻碳硼烷。本研究为芳香族杂环碳硼烷衍生物的合成提供了重要参考,并促进其在候选药物和功能材料设计中的应用。
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引用次数: 0
Correction to "Direct Ink Writing of Skin-Mountable Free-Form Thermoelectric Sensors Based on Ag2Te Composites". 更正“基于Ag2Te复合材料的可贴合皮肤的自由形式热电传感器的直接墨水书写”。
IF 8.2 2区 材料科学 Q1 MATERIALS SCIENCE, MULTIDISCIPLINARY Pub Date : 2026-03-23 DOI: 10.1021/acsami.6c05418
Sooyeon Moon, Joo-Won Lee, Sungju Jun, Hoon Yeub Jeong, Hyejin Jang, Min-Seok Kim, Sohee Jeong, Seungjun Chung
{"title":"Correction to \"Direct Ink Writing of Skin-Mountable Free-Form Thermoelectric Sensors Based on Ag<sub>2</sub>Te Composites\".","authors":"Sooyeon Moon, Joo-Won Lee, Sungju Jun, Hoon Yeub Jeong, Hyejin Jang, Min-Seok Kim, Sohee Jeong, Seungjun Chung","doi":"10.1021/acsami.6c05418","DOIUrl":"https://doi.org/10.1021/acsami.6c05418","url":null,"abstract":"","PeriodicalId":5,"journal":{"name":"ACS Applied Materials & Interfaces","volume":" ","pages":""},"PeriodicalIF":8.2,"publicationDate":"2026-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147496889","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Bifunctional Analgesic-Pro-Healing Hydrogel Dressing for Postoperative Analgesia and Wound Healing in Mice. 双功能镇痛促愈合水凝胶敷料在小鼠术后镇痛和伤口愈合中的应用。
IF 5.5 2区 医学 Q2 MATERIALS SCIENCE, BIOMATERIALS Pub Date : 2026-03-23 DOI: 10.1021/acsbiomaterials.5c01418
Yuting Rong, Ayang Zhao, Ao Zhang, Siqi Sun, Yueyue Gao, Guibo Fan, Sihua Qi

Incision dressings play a crucial role in postoperative care, while hydrogel, as a commonly used polymeric material, can effectively maintain wound moisture and promote wound healing. The present study aims to fabricate a dual-functional hydrogel dressing, carboxymethyl chitosan hydrogel loaded with the nonsteroidal anti-inflammatory drug flurbiprofen (hCMPG-FP), for alleviating postoperative acute pain and promoting incision healing. hCMPG-FP exhibits excellent properties such as gelation, drug release, and degradation, and, in particular, possesses good incision conformability after secondary lyophilization. In vitro and in vivo experiments have confirmed that hCMPG-FP can exert dual functions of wound healing promotion and analgesia, which is associated with the antibacterial activity, coagulation-promoting effect, and cell migration-promoting ability of carboxymethyl chitosan hydrogel, as well as the analgesic and anti-inflammatory properties of flurbiprofen. In conclusion, when acting on incisions, hCMPG-FP regulates multiple pathways such as wound healing and inflammation modulation, exerts ideal dressing functions, and provides a theoretical basis and experimental evidence for the further development of innovative wound treatment strategies.

切口敷料在术后护理中起着至关重要的作用,而水凝胶作为一种常用的高分子材料,可以有效地保持伤口水分,促进伤口愈合。本研究旨在制备一种双功能水凝胶敷料,羧甲基壳聚糖水凝胶负载非甾体抗炎药氟比洛芬(hCMPG-FP),以减轻术后急性疼痛,促进切口愈合。hCMPG-FP具有良好的凝胶、药物释放和降解性能,特别是在二次冻干后具有良好的切口相容性。体外和体内实验证实,hCMPG-FP具有促进创面愈合和镇痛的双重功能,这与羧甲基壳聚糖水凝胶的抗菌活性、促凝作用和细胞迁移能力以及氟比洛芬的镇痛和抗炎作用有关。综上所述,hCMPG-FP作用于切口时,可调控创面愈合、炎症调节等多种通路,发挥理想的敷料功能,为进一步开发创新创面治疗策略提供理论基础和实验依据。
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引用次数: 0
LigandExplorer: An Automated Tool for Ligand Extraction from PDB Structures. LigandExplorer:一个从PDB结构中提取配体的自动化工具。
IF 5.3 2区 化学 Q1 CHEMISTRY, MEDICINAL Pub Date : 2026-03-23 Epub Date: 2026-02-28 DOI: 10.1021/acs.jcim.5c02921
Yaqi Li, Rongfeng Zou, Maohua Yang, Ying Wang, Zhonghua Liu, Hang Zheng

The structural information on protein-ligand complexes is crucial for small-molecule design and drug discovery. Yet primary resources often have heterogeneous annotations, lack machine-ready ligand categorization, and require substantial postprocessing before large-scale modeling. Here, we present LigandExplorer, an open-source, automated postprocessing pipeline that identifies and extracts covalent and noncovalent ligands from biomolecular complex structures and standardizes outputs for downstream use. Using residue-level graphs built solely from atomic coordinates, LigandExplorer is robust to missing or inconsistent metadata and integrates LightGBM models to classify ligands (peptides, nucleic acids, phospholipids, carbohydrates, organics, and ions) and assess interaction relevance. Because the pipeline is rerunnable, it can be applied to each new databases release to keep derived, categorized data sets current without altering source records. On the PDBbind v2020 refined set, LigandExplorer achieved a 98.38% raw structural agreement under harmonized comparison criteria prior to any manual reconciliation; the remaining discrepancies were analyzed separately and were dominated by divergences between raw RCSB entries and curated PDBBind records. On the PepBDB, LigandExplorer successfully processed 4881 of 5005 complexes, achieving a 97.52% success rate. Most failures reflected upstream record errors, where complex cyclic peptides constituted the primary algorithmic boundary. LigandExplorer thus mitigates data-cleaning burdens and enables rapidly refreshed, standardized data sets for computational modeling and molecular design.

蛋白质配体复合物的结构信息对小分子设计和药物发现至关重要。然而,初级资源通常具有异构注释,缺乏机器就绪的配体分类,并且在大规模建模之前需要大量的后处理。在这里,我们提出了LigandExplorer,这是一个开源的自动化后处理管道,可以从生物分子复杂结构中识别和提取共价和非共价配体,并将输出标准化以供下游使用。LigandExplorer使用仅由原子坐标构建的残基级图,对缺失或不一致的元数据具有很强的健壮性,并集成了LightGBM模型来分类配体(肽、核酸、磷脂、碳水化合物、有机物和离子)并评估相互作用的相关性。由于管道是可重新运行的,因此可以将其应用于每个新的数据库版本,以便在不更改源记录的情况下保持派生的、分类的数据集是最新的。在pdbinding v2020精化集上,LigandExplorer在协调的比较标准下实现了98.38%的原始结构一致性。其余差异被单独分析,主要是原始RCSB条目和整理PDBBind记录之间的差异。在PepBDB上,LigandExplorer成功处理了5005个配合物中的4881个,成功率为97.52%。大多数失败反映了上游记录错误,其中复杂的环状肽构成了主要的算法边界。因此,LigandExplorer减轻了数据清理的负担,并为计算建模和分子设计提供了快速更新、标准化的数据集。
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引用次数: 0
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