Journal of Molecular Modeling最新文献_第2页

Probing curcumin reactive conformers in keto-enol tautomerization enhanced by clustering with t-SNE 用t-SNE聚类增强酮-烯醇互变异构过程中姜黄素反应构象的探测。

IF 2.5 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2026-01-06 DOI: 10.1007/s00894-025-06621-3

Febdian Rusydi, Etika Dessi Susanti, Ira Puspitasari, Rizka Nur Fadilla, Roichatul Madinah, Wun F. Mark-Lee

Context

The extensive conformational space of flexible molecules poses a significant challenge for predicting chemical reactivity through quantum chemical methods. For curcumin, whose keto–enol tautomerization is crucial to its biological activity and associated with its therapeutic potential in conditions such as Alzheimer’s disease, selecting meaningful conformers is particularly challenging. Traditional strategies for conformer selection that rely on variations in torsion angles may result in an excessive number of conformers. Our previously developed fragmentation-based strategy addresses this issue but may overlook critical conformers in highly flexible molecules. In this study, we developed an integrated workflow and yielded a diverse yet manageable set of conformers, enabling a refined energy profile of curcumin tautomerization with reduced activation energy, thereby aligning the results more closely with the experimental values than our previous estimates. Beyond curcumin, our findings demonstrate that the integration of machine-learning-assisted clustering with electronic structure calculations provides an efficient and transferable strategy for capturing conformational diversity in flexible molecular systems.

Methods

Our workflow incorporates extended tight-binding (xTB) metadynamics for comprehensive conformer sampling, Coulomb matrix descriptors with t-SNE dimensionality reduction for structural encoding, clustering to identify representative structures, and DFT validation of ground and transition states. We used the second generation of xTB (GFN2-xTB) in the gas phase and implicit solvent with analytical linearized Poisson-Boltzmann (ALPB), which implemented in CREST. For the clustering algorithms, we utilized K-means and agglomerative clustering and monitored the Davies-Bouldin Index (DBI), Silhouette scores, and the elbow method to determine the optimal number of clusters. The exchange-correlation functional/basis set used for DFT calculations was APFD/6-311++G(d,p), which integrated into the Gaussian 16 software.

背景：柔性分子广泛的构象空间对通过量子化学方法预测化学反应性提出了重大挑战。姜黄素的酮烯醇互变异构化对其生物活性至关重要，并与其治疗阿尔茨海默病等疾病的潜力有关，因此选择有意义的构象尤其具有挑战性。传统的选择策略依赖于扭转角的变化，可能会导致过多的一致性。我们之前开发的基于片段的策略解决了这个问题，但可能忽略了高度柔性分子中的关键构象。在这项研究中，我们开发了一个集成的工作流程，并产生了一组多样化但易于管理的构象，从而实现了姜黄素互变异构化的精细能量分布，降低了活化能，从而使结果比我们之前的估计更接近实验值。除了姜黄素，我们的研究结果表明，将机器学习辅助聚类与电子结构计算相结合，为捕获灵活分子系统中的构象多样性提供了一种有效且可转移的策略。方法：我们的工作流程包括扩展紧密结合（xTB）元动力学，用于全面的一致性采样，具有t-SNE降维的库仑矩阵描述符，用于结构编码，聚类以识别代表性结构，以及基态和过渡态的DFT验证。我们使用了第二代xTB （GFN2-xTB）气相和隐式溶剂，并在CREST中实现了分析线性化泊松-玻尔兹曼（ALPB）。对于聚类算法，我们使用K-means和聚集聚类，并监测davis - bouldin指数（DBI）， Silhouette分数和肘部方法来确定最佳聚类数量。用于DFT计算的交换相关泛函/基集为APFD/6-311++G(d,p)，集成到高斯16软件中。

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引用次数: 0

Adsorption of dibenzothiophene on N-doped TiO₂ system: a DFT and molecular dynamics study 二苯并噻吩在n掺杂tio2体系上的吸附：DFT和分子动力学研究

IF 2.5 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2026-01-03 DOI: 10.1007/s00894-025-06550-1

Dilan Nawzad Mamakhan, Nabil Adil Fakhre

Context

This study examines the adsorption behavior of dibenzothiophene (DBT) on nitrogen-doped titanium dioxide (N-doped TiO₂) to evaluate its potential in photocatalytic desulfurization. The work focuses on structural stability, charge transfer, electronic properties, and dynamic interactions of the hybrid system. The findings show that nitrogen doping reduces the TiO₂ band gap, enhances charge redistribution, and improves adsorption affinity. Molecular dynamics simulations confirm the strong thermal stability of the DBT/N-doped TiO₂ composite, while recovery time calculations highlight its rapid sensing and reusability. These results underscore the promise of N-doped TiO₂ as an efficient material for sulfur pollutant removal.

Methods

Density functional theory (DFT) was employed to analyze adsorption energies, band structures, charge density, and non-covalent interactions, supported by Bader charge analysis. Molecular dynamics (MD) simulations were carried out to evaluate the thermal stability and dynamic behavior of the DBT/N-doped TiO₂ system.

本研究考察了二苯并噻吩（DBT）在氮掺杂二氧化钛（n掺杂TiO 2）上的吸附行为，以评价其在光催化脱硫中的潜力。研究的重点是结构稳定性、电荷转移、电子特性和混合系统的动态相互作用。结果表明，氮的掺杂减小了tio2的带隙，增强了电荷的再分配，提高了吸附亲和力。分子动力学模拟证实了DBT/ n掺杂TiO 2复合材料具有较强的热稳定性，而恢复时间计算则强调了其快速传感和可重用性。这些结果强调了n掺杂二氧化钛作为一种高效的硫污染物去除材料的前景。方法采用密度泛函理论（DFT）分析吸附能、能带结构、电荷密度和非共价相互作用，并辅以Bader电荷分析。通过分子动力学（MD）模拟来评价DBT/ n掺杂tio2体系的热稳定性和动力学行为。

引用次数: 0

Comment on: Energy and momentum eigenspectrum of the Hulthèn-screened cosine Kratzer potential using proper quantization rule and SUSYQM method 用适当的量化规则和SUSYQM方法讨论hulth<s:1>屏蔽余弦Kratzer势的能量和动量特征谱

IF 2.5 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2026-01-03 DOI: 10.1007/s00894-025-06616-0

Francisco M. Fernández

引用次数: 0

Exploration on thermal behavior of synthetic ester with antioxidant based on thermodynamic analysis and molecular simulations 基于热力学分析和分子模拟的含抗氧化剂合成酯的热行为探讨。

IF 2.5 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2025-12-29 DOI: 10.1007/s00894-025-06601-7

Mengke Zhang, Qin Zhao, Junming Liu, Bingbing Lai, Gaiqing Zhao, Xiaobo Wang

Context

Synthetic ester is a high-quality lubricating base oil, and its antioxidant stability and high-temperature service life are greatly affected by antioxidants. For a considerable period, a significant number of researchers have utilized a variety of conventional methodologies, including the rotating oxygen bomb test, for the selection and evaluation of antioxidants. However, there is little systematic research on the thermal stability and antioxidant performance of these antioxidants through a combination of experiments and calculations. In this study, a range of investigative approaches, including experimental, calculation, and molecular simulation methods, were employed to assess the impact of synthetic esters (PE5) with antioxidants (1010, L57, and hybrid). Compared with PE5 base oil, the thermodynamic analysis showed the value of activation energy for PE5 samples was probably PE5 + 2% L57 ≥ PE5 + 1% 1010 + 1% L57 > PE5 + 2% 1010 ≥ PE5. These results were in consistent with the acid number changes and viscosity changes for PE5 samples. The IOT results obtained from PDSC also proved the validity of this trend. Especially, PE5 containing 1% 1010 and 1% L57 showed good antioxidant properties, indicating that the hybrid antioxidants have excellent high-temperature antioxidant performance. The molecule simulation results show L57 can effectively and quickly reach the protected point without rapid volatilization and loss, thereby achieving excellent antioxidant performance. In addition, the movement rate of the hybrid antioxidant system (1wt% 1010 + 1wt% L57) can also achieve similar results compared with L57.

Methods

The thermal stability of antioxidants was investigated by TG/DTG analysis, and the corresponding decomposition kinetic parameters were evaluated by Flynn–Wall–Ozawa (FWO) and Kissinger–Akahira–Sunose (KAS) methods. The optimization of the geometry of related molecules was performed via Gaussian 16 package at B3LYP/def2-SVP level. The single point energy was then calculated at B3LYP/def2-TZVP level. The ACPEPY script was employed to obtain the GAF force field topology file of them. Molecular dynamics simulations were performed using the GROMACS software package.

背景：合成酯是一种优质的润滑基础油，抗氧化剂对其抗氧化稳定性和高温使用寿命影响很大。在相当长的一段时间里，大量的研究人员使用了各种传统的方法，包括旋转氧弹试验，来选择和评估抗氧化剂。然而，通过实验和计算相结合的方法对这些抗氧化剂的热稳定性和抗氧化性能进行系统的研究却很少。在本研究中，采用了一系列调查方法，包括实验，计算和分子模拟方法，来评估合成酯（PE5）与抗氧化剂（1010，L57和杂交）的影响。与PE5基础油相比，热力学分析表明PE5样品的活化能值可能为PE5 + 2% L57≥PE5 + 1% 1010 + 1% L57 > PE5 + 2% 1010≥PE5。这些结果与PE5样品的酸值变化和粘度变化一致。从PDSC获得的物联网结果也证明了这一趋势的有效性。其中含有1% 1010和1% L57的PE5表现出良好的抗氧化性能，表明该杂化抗氧化剂具有优异的高温抗氧化性能。分子模拟结果表明，L57能有效、快速地到达保护点，不会快速挥发和损失，从而获得优异的抗氧化性能。此外，混合抗氧化体系（1wt% 1010 + 1wt% L57）的移动速率也可以达到与L57相似的结果。方法：采用TG/DTG分析考察抗氧化剂的热稳定性，采用Flynn-Wall-Ozawa （FWO）法和Kissinger-Akahira-Sunose （KAS）法评价其分解动力学参数。在B3LYP/def2-SVP水平上通过高斯16封装对相关分子的几何结构进行优化。然后在B3LYP/def2-TZVP水平上计算单点能量。利用ACPEPY脚本获取它们的GAF力场拓扑文件。使用GROMACS软件包进行分子动力学模拟。

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引用次数: 0

Regulatory mechanism of interface adhesion and moisture damage in aged SBS-modified asphalt–aggregate systems modified with waste plastic and oxidized graphene 废塑料和氧化石墨烯改性sbs改性沥青-骨料老化体系界面粘结和水分损伤的调控机制

IF 2.5 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2025-12-27 DOI: 10.1007/s00894-025-06594-3

Tengfei Nian, Haowen Sun, Wei Li, Piyi Li

Context

Waste plastics have a significant impact on natural resources and the environment. The focus is on the interfacial adhesion behavior of three types of waste plastics—polyethylene (PE), polypropylene (PP), and Poly acrylic (PA)—with neutral silica (SiO₂) aggregates, as well as the influence of graphene oxide (GO) on the asphalt-water-aggregate interface performance. The validity of the molecular dynamics simulations was assessed based on fundamental thermodynamic properties of asphalt, including density, glass transition temperature, cohesive energy density, and solubility parameters. The diffusion patterns of the four asphalt components on the SiO₂ aggregate surface were analyzed using the mean square displacement (MSD), diffusion coefficient, and relative concentration distribution. The bonding strength between various waste plastics and the asphalt-aggregate interface was quantified by calculating the adhesion work. The results indicate that van der Waals forces and electrostatic forces play a crucial role in the adhesion between asphalt and minerals. The adhesion work between aged asphalt and aggregates is highest when PE plastic is added, lowest when PP plastic is added, and intermediate when PA plastic added. Upon introducing water molecules at the asphalt-aggregate interface, the interfacial adhesion work decreased significantly, indicating that water molecules exert a substantial negative impact on interfacial adhesion performance. However, after coating the aggregate surface with graphene oxide, the adhesion work at the asphalt-water-aggregate interface increased significantly, suggesting that graphene oxide enhances water damage resistance by improving interfacial polarity. This study provides molecular-level theoretical support for the recycling of waste plastics in asphalt-based materials and for the optimization of interfaces.

Methods

Molecular dynamics simulations were performed using Materials Studio software with the COMPASS II force field. The Nose thermostat and Berendsen isobaric thermostat were used to control temperature and pressure, respectively, to maintain constant temperature and pressure conditions throughout the simulation. In non-bonded interaction calculations, electrostatic forces were calculated using the Ewald method, and van der Waals forces were calculated using the Atom Based method, with a cutoff radius of 15.5 Å. The simulations were conducted using NVT and NPT ensembles, with all simulations set to fine computational precision. The constructed model was first subjected to geometric optimization (100,000 iterations), followed by annealing treatment (10 cycles with a temperature change gradient of 100 K), and then the ideal molecular structure of the model was obtained through NPT ensemble simulations.

废旧塑料对自然资源和环境有重大影响。重点研究了三种废塑料——聚乙烯（PE）、聚丙烯（PP）和聚丙烯酸（PA）——与中性二氧化硅（SiO2）骨料的界面粘附行为，以及氧化石墨烯（GO）对沥青-水-骨料界面性能的影响。基于沥青的基本热力学性质，包括密度、玻璃化转变温度、内聚能密度和溶解度参数，评估了分子动力学模拟的有效性。采用均方位移（MSD）、扩散系数和相对浓度分布分析了4种沥青组分在SiO2集料表面的扩散规律。通过计算黏附功，量化了各种废塑料与沥青-骨料界面的黏附强度。结果表明，范德华力和静电力对沥青与矿物的粘结起着至关重要的作用。老化沥青与骨料的粘接强度以PE塑料最高，PP塑料最低，PA塑料居中。在沥青-骨料界面处引入水分子后，界面黏附功显著降低，说明水分子对界面黏附性能有较大的负面影响。然而，在骨料表面涂覆氧化石墨烯后，沥青-水-骨料界面的粘附工作显著增加，表明氧化石墨烯通过改善界面极性来增强抗水损伤能力。本研究为废塑料在沥青基材料中的回收利用和界面优化提供了分子水平的理论支持。方法采用Materials Studio软件，采用COMPASS II力场进行分子动力学模拟。使用Nose恒温器和Berendsen等压恒温器分别控制温度和压力，以在整个模拟过程中保持恒定的温度和压力条件。在非键相互作用计算中，静电力采用Ewald法计算，范德华力采用Atom Based法计算，截断半径为15.5 Å。模拟使用NVT和NPT组合进行，所有模拟都设置为良好的计算精度。首先对构建的模型进行几何优化（10万次迭代），然后进行退火处理（10次循环，温度变化梯度为100 K），然后通过NPT系综模拟获得模型的理想分子结构。

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引用次数: 0

Mechanistic studies on a biomimetic cycloaddition between phloroglucinol and 2-hydroxyethyl-α,β-unsaturated ketone 间苯三酚与2-羟乙基-α，β-不饱和酮间仿生环加成反应机理研究。

IF 2.5 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2025-12-22 DOI: 10.1007/s00894-025-06611-5

Wen-Bin Wu, Qian Hu, Hua-Kang Zhou, Kai Chen

Context

The biomimetic domino cycloaddition between acylphloroglucinol and 2-hydroxyethyl-cyclohexenone has been previously established as an efficient strategy for constructing tricyclic ketal scaffolds and synthesizing the bioactive natural products, Myrtucommulone J and Myrtucommuacetalone. In this study, density functional theory (DFT) calculations were performed to elucidate the plausible reaction mechanism. The transformation proceeds via a tandem sequence involving hemiacetalization, dehydration, electrophilic attack, re-aromatization, protonation of the C = C bond, and annulation. The rate-determining step was identified as the electrophilic attack of an allylic cation on the aromatic ring of acylphloroglucinol, with an overall free energy barrier of approximately 23.5 kcal/mol. These mechanistic insights not only advance our understanding of this biomimetic cascade but also provide a foundation for the rational design of novel synthetic methodologies.

Methods

In this work, density functional theory (DFT) calculations were carried out using the Gaussian 16 software package. Geometry optimizations and vibrational frequency analyses for all stationary points were performed at the M06-2X/def2-SVP level of theory. The intrinsic reaction coordinate (IRC) calculations were employed to verify the connectivity between each transition state and its corresponding minima. Single-point energy calculations were subsequently conducted using the M06-2X functional in conjunction with the def2-TZVP basis set for all atoms. Solvent effects of toluene were incorporated through Truhlar’s SMD continuum solvation model. All optimized structures and transition states were visualized with CYLview.

背景：酰基间苯三酚和2-羟乙基环己酮之间的仿生多米诺环加成已被证实是构建三环酮支架和合成具有生物活性的天然产物桃金娘共酮J和桃金娘共酮的有效策略。在本研究中，密度泛函理论（DFT）计算来阐明合理的反应机理。转化通过串联顺序进行，包括半缩化、脱水、亲电攻击、重芳构化、C = C键的质子化和环化。决定速率的步骤被确定为烯丙基阳离子对酰基间苯三酚芳香环的亲电攻击，总自由能垒约为23.5 kcal/mol。这些机制的见解不仅促进了我们对这种仿生级联的理解，而且为合理设计新的合成方法提供了基础。方法：采用Gaussian 16软件包进行密度泛函理论（DFT）计算。在M06-2X/def2-SVP理论水平上对各驻点进行几何优化和振动频率分析。本征反应坐标（IRC）计算验证了每个过渡态与其对应的最小值之间的连通性。随后使用M06-2X泛函结合所有原子的def2-TZVP基集进行单点能量计算。通过Truhlar的SMD连续溶剂化模型纳入了甲苯的溶剂效应。利用CYLview对所有优化后的结构和过渡态进行可视化。

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引用次数: 0

Accelerating the search for carbon cluster isomers via machine learning potential 通过机器学习潜力加速寻找碳簇异构体。

IF 2.5 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2025-12-22 DOI: 10.1007/s00894-025-06613-3

Huy Duy Nguyen, Phong Hai Nguyen, Giang Huong Bach, Oanh Kim Thi Nguyen

Context

Trivalent C(_{22}) cages are explored with the recent generation of Gaussian approximation potential (GAP-20) and density functional theory (DFT) calculations. Using the GAP-20 to approximate the energy landscape significantly reduces the search time and provides superior starting structures for DFT optimization. The GAP-20, however, fails to capture the Jahn-Teller distortion. The relative GAP-20 energies are overestimated, and the vibrational modes/frequencies are poorly characterized.

Methods

Via the CALYPSO package, particle swarm optimization is employed to explore the configuration space. Energies/forces are calculated via the QUIP/LAMMPS module, employing the GAP-20. Structural relaxation follows the conjugate gradient method to a force precision of (10^{-7} text { eV}/)Å. Cage isomers are further optimized by DFT, utilizing BFGS optimization scheme, until forces are below 0.05 eV/Å. The (text {B3LYP/6-31+G}*) level of theory is applied, as implemented in the NWChem software. Vibrational analysis is performed to study the stability/infrared spectra.

背景：用最近一代的高斯近似势（GAP-20）和密度泛函理论（DFT）计算探索了三价c22笼。使用GAP-20近似能量格局显著减少了搜索时间，并为DFT优化提供了优越的起始结构。然而，GAP-20未能捕捉到扬-泰勒扭曲。相对GAP-20能量被高估，振动模式/频率特征不佳。方法：利用CALYPSO软件包，采用粒子群算法对构型空间进行寻优。能量/力通过QUIP/LAMMPS模块计算，采用GAP-20。结构松弛遵循共轭梯度法，力精度为10 - 7 eV / Å。利用BFGS优化方案对笼形异构体进行进一步的DFT优化，直至作用力小于0.05 eV/Å。在NWChem软件中，应用了B3LYP/6-31+G *水平的理论。通过振动分析研究其稳定性和红外光谱。

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引用次数: 0

Structural, electronic, thermodynamic, and thermal properties of zinc-blende AlP, BP, and their Al₁₋ₓBₓP ternary alloy 锌-闪锌矿AlP、BP及其Al₁j.p.ₓBₓP三元合金的结构、电子、热力学和热性能。

IF 2.5 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2025-12-22 DOI: 10.1007/s00894-025-06607-1

K. Boubendira, A. Saoudi

Context

III–V semiconductors such as aluminum phosphide (AlP) and boron phosphide (BP) are promising materials for high-power and high-temperature optoelectronic applications due to their wide band gaps, excellent thermal stability, and strong covalent bonding. However, their ternary alloys, particularly Al₁₋ₓBₓP, remain scarcely investigated in terms of their structural, electronic, thermodynamic, and thermal properties. Understanding these characteristics is essential to assess the alloy’s potential for device applications and to establish reliable theoretical data for future experimental validation.

Methods

The present study employs first-principles calculations based on density functional theory (DFT) within the generalized gradient approximation (GGA–PBE) to investigate the structural, electronic, thermodynamic, and thermal properties of zinc-blende AlP, BP, and their ternary alloy Al₁₋ₓBₓP (x = 0.25, 0.50, 0.75). The equilibrium lattice parameters, band structures, density of states (DOS), formation energies, and thermodynamic parameters were systematically analyzed to evaluate alloy stability and temperature-dependent behavior.

背景：III-V型半导体，如磷化铝（AlP）和磷化硼（BP），由于其宽带隙、优异的热稳定性和强的共价键，是高功率和高温光电应用的有前途的材料。然而，它们的三元合金，特别是Al₁瞪ₓBₓP，在其结构、电子、热力学和热性能方面仍然很少被研究。了解这些特性对于评估合金在设备应用中的潜力以及为未来的实验验证建立可靠的理论数据至关重要。方法：本研究采用基于广义梯度近似（GGA-PBE）内密度泛函理论（DFT）的第一性原理计算来研究锌-闪锌矿AlP， BP及其三元合金Al₁ₓₓBₓP （x = 0.25, 0.50, 0.75）的结构，电子，热力学和热性能。系统分析了平衡晶格参数、能带结构、态密度（DOS）、形成能和热力学参数，以评价合金的稳定性和温度依赖行为。

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引用次数: 0

Computational screening of natural phenolic compounds as potential EGFR inhibitors against triple negative breast cancer 计算筛选天然酚类化合物作为潜在的EGFR抑制剂对抗三阴性乳腺癌。

IF 2.5 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2025-12-22 DOI: 10.1007/s00894-025-06589-0

Prashant Kurkute, Sakshi Wagh, Komal Nandode, Amit Gangwal, Sumit Sonawane, Vedant Shimpi, Azim Ansari, Yogeeta O. Agrawal, Mrunali Patil, Mohd Usman MohdSiddique MS

Context

Overexpression of Epidermal Growth Factor Receptor (EGFR) is commonly found in triple negative breast cancer. This subtype does not contain the oestrogen receptors (ER), progesterone receptors (PR), and HER2 amplification. The wide scope of biological activities and varied structural classes of natural phenolic compounds paves significant opportunities for drug discovery. The modern drug discovery process combines natural phenolic compounds and computational or AI techniques to develop novel drugs. Considering this fact, EGFR inhibitors were designed based upon the multiscale computational studies of natural phenolic compounds to identify the potent anticancer molecules for triple negative breast cancer (TNBC).

Method

Preliminary screening of all natural phenolic compounds (containing 440 phenolic compounds) was done by molecular docking studies using the glide utility of Maestro tools. The top scoring molecules were further subjected to MD simulation studies by using Desmond software. The obtained trajectory files were processed through R Studio software for data analysis employing PCA analysis, cluster analysis, and DCCM calculation. Then, binding free energies of complexes were determined by MMGBSA calculation, and drug likeliness of molecules were checked by in silico ADME calculation. These obtained in silico generated data were analysed, and it was concluded that the identified molecules bearing phenolic compounds would be a promising scaffold for EGFR inhibitors and anticancer drugs for TNBC. However, experimental results are needed to prove the obtained results.

背景：表皮生长因子受体（EGFR）过表达常见于三阴性乳腺癌。该亚型不含雌激素受体（ER）、孕激素受体（PR）和HER2扩增。天然酚类化合物广泛的生物活性和多样的结构类别为药物发现提供了重要的机会。现代药物发现过程结合了天然酚类化合物和计算或人工智能技术来开发新药。考虑到这一事实，EGFR抑制剂是基于天然酚类化合物的多尺度计算研究来设计的，以确定三阴性乳腺癌（TNBC）的有效抗癌分子。方法：利用Maestro工具的滑动实用程序进行分子对接研究，初步筛选所有天然酚类化合物（含440种酚类化合物）。使用Desmond软件对得分最高的分子进行进一步的MD模拟研究。通过R Studio软件对得到的轨迹文件进行数据分析，采用PCA分析、聚类分析、DCCM计算。然后通过MMGBSA计算确定配合物的结合自由能，通过计算机ADME计算检查分子的药物可能性。我们分析了这些用硅合成的数据，并得出结论，所鉴定的含有酚类化合物的分子将是一个很有希望的EGFR抑制剂和TNBC抗癌药物的支架。然而，得到的结果需要实验结果来证明。

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引用次数: 0

Tuning the band gap and optical characteristics of NiO nanoparticles via tin (Sn) doping: a combined experimental and DFT investigation 通过锡掺杂调整NiO纳米颗粒的带隙和光学特性：实验和DFT相结合的研究。

IF 2.5 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2025-12-17 DOI: 10.1007/s00894-025-06610-6

Habtamu F. Etefa, Francis B. Dejene

Context

The structural and electronic modifications induced by tin (Sn) doping in cubic nickel oxide (NiO) were investigated through a combined computational and experimental approach. Sn incorporation into the NiO lattice is of significant interest for tailoring its optoelectronic properties toward enhanced energy conversion and photocatalytic applications. Experimentally synthesized NiO nanoparticles confirmed the theoretical predictions, showing that increasing Sn concentration (0–12.5%) leads to lattice distortion and bandgap narrowing. The observed bandgap reduction, from 2.89 eV (pure NiO) to 2.56 eV (12.5% Sn-NiO), was attributed to a Fermi level shift and the introduction of defect states, demonstrating that Sn doping effectively tunes the electronic structure of NiO.

Methods

Theoretical investigations were conducted using spin-polarized density functional theory with Hubbard correction (DFT + U) within the Quantum ESPRESSO (v7.2) framework to elucidate the electronic properties. The cubic NiO (a = 4.22 Å) was modeled with a 2 × 2 × 2 supercell using the Perdew–Burke–Ernzerhof (PBE) functional under generalized gradient approximation (GGA) and ultrasoft pseudopotentials from PSLibrary 1.0.0. Convergence tests yielded cutoffs of 50 Ry (wavefunction) and 400 Ry (charge density) with a 7 × 7 × 7 Monkhorst–Pack grid. A Hubbard U of 6.0 eV was applied to Ni 3d orbitals to correct correlation effects. Sn doping (3.125–12.5%) was introduced by substituting Ni atoms, and all structures were optimized using the Broyden–Fletcher–Goldfarb–Shanno (BFGS) algorithm. Electronic band structures and density of states (DOS) were calculated along high-symmetry paths to analyze the doping-induced modifications in NiO’s electronic properties.

背景：采用计算和实验相结合的方法研究了锡（Sn）掺杂在立方氧化镍（NiO）中的结构和电子修饰。在NiO晶格中加入Sn对于调整其光电性能以增强能量转换和光催化应用具有重要意义。实验合成的NiO纳米颗粒证实了理论预测，表明增加Sn浓度（0-12.5%）会导致晶格畸变和带隙缩小。观察到的带隙减小，从2.89 eV（纯NiO）到2.56 eV (12.5% Sn-NiO)，归因于费米能级位移和缺陷态的引入，表明Sn掺杂有效地调节了NiO的电子结构。方法：在Quantum ESPRESSO （v7.2）框架下，利用带Hubbard校正的自旋极化密度泛函理论（DFT + U）进行理论研究，以阐明其电子性质。利用广义梯度近似（GGA）下的Perdew-Burke-Ernzerhof （PBE）泛函和来自plibrary 1.0.0的ultrasoft伪势，用2 × 2 × 2超级单体对立方NiO （a = 4.22 Å）进行建模。收敛测试的截止值为50ry（波函数）和400ry（电荷密度），采用7 × 7 × 7 Monkhorst-Pack网格。在Ni三维轨道上应用6.0 eV的Hubbard U修正相关效应。通过Ni原子取代引入Sn掺杂（3.125 ~ 12.5%），采用BFGS （Broyden-Fletcher-Goldfarb-Shanno）算法对所有结构进行优化。通过计算高对称路径下的电子能带结构和态密度（DOS）来分析掺杂对NiO电子性质的影响。

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引用次数: 0