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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 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 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 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
Boron-modified phenolic resin: thermal stability and decomposition mechanisms via experiments and simulations 硼改性酚醛树脂:热稳定性及分解机理的实验与模拟。
IF 2.5 4区 化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-12-16 DOI: 10.1007/s00894-025-06602-6
Xiao-Feng Qing, Xiao Liu, Qing Han, Jia-Jun Ma, Li-Juan Ran, Fei Zhou, Hongli Wang, Bo Dai, Ni-Na Ge

Context

Currently, boron modification represents a significant strategy for enhancing the thermal stability of phenolic resins. However, existing boron modification methods generally suffer from synthetic complexity, and the mechanism of boron’s effect on phenolic resins at the molecular level remains incompletely understood. This study investigated how 4-hydroxyphenylboronic acid pinacol ester (4-HPBAPE) doping regulates the glass transition temperature (Tg), thermal conductivity, and pyrolysis behavior of phenolic resin. Results showed that 4-HPBAPE doping increased the glass transition temperature (162 → 187 ℃), while thermal conductivity testing revealed a 10% reduction (0.2154 → 0.1920 W/(m·K)). The errors between the results obtained from MD simulation and the experimental results were all less than 10%. The char yield decreased with increasing 4-HPBAPE doping ratio. ReaxFF MD simulations demonstrated that boron modification of phenolic resins enhanced the production of light hydrocarbons (C1–C5) during pyrolysis, resulting in higher mass loss. This occurred via boron-mediated ring-opening and suppression of large aromatic cluster formation. Future efforts could focus on controlling the bonding form of boron to suppress ring-opening reactions, thereby enhancing the char yield.

Methods

The materials were characterized using Fourier transform infrared spectrometer (FTIR) and nuclear magnetic resonance spectroscopy (NMR). Thermal conductivity was measured using a DRE-2C thermal conductivity meter. Thermogravimetric analysis (TGA) and differential scanning calorimetry (DSC) were performed using a synchronous thermal analyzer. Simulations were carried out with the LAMMPS and Materials Studio software package. Classical molecular dynamics (MD) simulations employed the COMPASS force field, while the reaction force field files containing C, H, O and B element were used. The post-processing of the results was implemented using OVITO and self-programmed Python scripts.

背景:目前,硼改性是提高酚醛树脂热稳定性的重要策略。然而,现有的硼改性方法普遍存在合成复杂的问题,并且硼在分子水平上对酚醛树脂的作用机理尚不完全清楚。本研究考察了4-羟基苯基硼酸松醇酯(4- hpape)掺杂对酚醛树脂玻璃化 转变 温度(Tg)、导热系数和热解行为的调节。结果表明,4- hpape掺杂提高了玻璃化 转变 温度(162→187℃),导热系数降低了10%(0.2154→0.1920 W/(m·K))。MD仿真结果与实验结果的误差均小于10%。炭产率随4- hpape掺杂比的增加而降低。ReaxFF MD模拟表明,硼改性酚醛树脂在热解过程中增加了轻烃(C1-C5)的生成,导致更高的质量损失。这是通过硼介导的开环和抑制大芳香团簇形成而发生的。未来的研究可以集中在控制硼的成键形式来抑制开环反应,从而提高炭的产率。方法:采用傅里叶红外光谱(FTIR)和核磁共振光谱(NMR)对材料进行表征。采用DRE-2C导热仪测量导热系数。采用同步热分析仪进行热重分析(TGA)和差示扫描量热分析(DSC)。利用LAMMPS和Materials Studio软件包进行了仿真。经典分子动力学(MD)模拟采用COMPASS力场,反作用力文件采用C、H、O、B元素。使用OVITO和自编程的Python脚本实现了结果的后处理。
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引用次数: 0
Enhanced quantum capacitance of near valence doped stanene nanosheets for asymmetric supercapacitors 非对称超级电容器中近价掺杂stanene纳米片的量子电容增强。
IF 2.5 4区 化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-12-16 DOI: 10.1007/s00894-025-06600-8
Akash Moi, Md. Shahzad Khan, Anurag Srivastava, Boddepalli SanthiBhushan

Context

Ever since the experimental realization of the first free-standing layers of stanene by researchers in 2016, this potential wonder material is widely being explored for various applications. This work analyzes the implication of this novel 2D material for supercapacitor electrodes and ways to enhance its quantum capacitance and charge storage capacity via first principles simulations. The stanene nanosheet is subjected to single vacancy (SV) defect and near valence (In and Sb) doping (direct doping at the SV site, independent doping at the SV edges, and co-doping at the SV edges). The results reveal the zero band gap nature of pristine stanene similar to graphene, yet at least 7 times enhancement in quantum capacitance in comparison to pristine graphene. The incorporation of a single vacancy (SV) defect in stanene has improved its quantum capacitance and charge storage capacity by 1.54 times, at the expense of compromised thermodynamic stability. Thus, to preserve the thermodynamic stability with minimal lattice distortions and enhance the quantum capacitance as well as charge storage of SV stanene, near valence dopants are introduced at the SV site and SV edges. Our results confirm that antimony doping in stanene offers better thermodynamic stability than Indium. Moreover, the independent doping of 3 antimony atoms at SV edges offers the highest quantum capacitance of 134.21 μF/cm2 at 0.6 V, which is about 1.47 times higher than the maximum value (91 μF/cm2 for N and Ni co-doping) reported in the literature for any doping. All the SV and near valence doped stanene configurations are observed to be better suitable for the anode electrode of asymmetric supercapacitors owing to their quantum capacitance and charge storage peaks on the positive side of the electrochemical window, except for one particular configuration, i.e., the direct antimony doping at the SV site, which is better suitable for the cathode electrode of the asymmetric supercapacitor.

Methods

The DFT-based first principle simulations combined with MATLAB programming are performed to study the capacitive behavior of the electrodes. A k-point sampling of 7 × 7 × 1 is found to be sufficient for sampling the Brillouin zone in reciprocal space, and a density mesh cutoff of 80 Hartree is used to define the fineness of real space effective potential and electron density grids for solving Poisson’s equation. The Generalized Gradient Approximation (GGA) with Perdew-Burke-Ernzerhof parameterization is used as the exchange correlation functional.

背景:自2016年研究人员实验实现第一个独立的stanene层以来,这种潜在的神奇材料被广泛探索用于各种应用。这项工作分析了这种新型二维材料对超级电容器电极的意义,以及通过第一性原理模拟增强其量子电容和电荷存储容量的方法。研究了单空位(SV)缺陷和近价(In和Sb)掺杂(SV位直接掺杂、SV边缘独立掺杂和SV边缘共掺杂)对纳米片结构的影响。结果表明,原始stanene具有与石墨烯相似的零带隙特性,但量子电容比原始石墨烯至少提高了7倍。单空位(SV)缺陷的加入使其量子电容和电荷存储能力提高了1.54倍,但牺牲了热力学稳定性。因此,为了在最小晶格畸变的情况下保持热力学稳定性,增强SV烯的量子电容和电荷存储,在SV位点和SV边缘引入近价掺杂剂。我们的研究结果证实,在stanene中掺杂锑比掺杂铟具有更好的热力学稳定性。此外,在SV边缘独立掺杂3个锑原子的量子电容在0.6 V时最高,为134.21 μF/cm2,是文献报道的任何掺杂的最大值(N和Ni共掺杂为91 μF/cm2)的1.47倍。所有SV和近价掺杂stanene构型都更适合于非对称超级电容器的阳极电极,因为它们的量子电容和电荷存储峰都在电化学窗口的正侧,除了一个特殊的构型,即在SV位点直接掺杂锑,它更适合于非对称超级电容器的阴极电极。方法:采用基于dft的第一性原理模拟,结合MATLAB编程对电极的电容特性进行研究。发现7 × 7 × 1的k点采样足以对倒易空间中的布里渊区进行采样,并使用80 Hartree的密度网格截断来定义实空间有效势和电子密度网格的精细度,以求解泊松方程。采用Perdew-Burke-Ernzerhof参数化的广义梯度近似(GGA)作为交换相关泛函。
{"title":"Enhanced quantum capacitance of near valence doped stanene nanosheets for asymmetric supercapacitors","authors":"Akash Moi,&nbsp;Md. Shahzad Khan,&nbsp;Anurag Srivastava,&nbsp;Boddepalli SanthiBhushan","doi":"10.1007/s00894-025-06600-8","DOIUrl":"10.1007/s00894-025-06600-8","url":null,"abstract":"<div><h3>Context</h3><p>Ever since the experimental realization of the first free-standing layers of stanene by researchers in 2016, this potential wonder material is widely being explored for various applications. This work analyzes the implication of this novel 2D material for supercapacitor electrodes and ways to enhance its quantum capacitance and charge storage capacity via first principles simulations. The stanene nanosheet is subjected to single vacancy (SV) defect and near valence (In and Sb) doping (direct doping at the SV site, independent doping at the SV edges, and co-doping at the SV edges). The results reveal the zero band gap nature of pristine stanene similar to graphene, yet at least 7 times enhancement in quantum capacitance in comparison to pristine graphene. The incorporation of a single vacancy (SV) defect in stanene has improved its quantum capacitance and charge storage capacity by 1.54 times, at the expense of compromised thermodynamic stability. Thus, to preserve the thermodynamic stability with minimal lattice distortions and enhance the quantum capacitance as well as charge storage of SV stanene, near valence dopants are introduced at the SV site and SV edges. Our results confirm that antimony doping in stanene offers better thermodynamic stability than Indium. Moreover, the independent doping of 3 antimony atoms at SV edges offers the highest quantum capacitance of 134.21 μF/cm<sup>2</sup> at 0.6 V, which is about 1.47 times higher than the maximum value (91 μF/cm<sup>2</sup> for N and Ni co-doping) reported in the literature for any doping. All the SV and near valence doped stanene configurations are observed to be better suitable for the anode electrode of asymmetric supercapacitors owing to their quantum capacitance and charge storage peaks on the positive side of the electrochemical window, except for one particular configuration, i.e., the direct antimony doping at the SV site, which is better suitable for the cathode electrode of the asymmetric supercapacitor.</p><h3>Methods</h3><p>The DFT-based first principle simulations combined with MATLAB programming are performed to study the capacitive behavior of the electrodes. A <i>k-point</i> sampling of 7 × 7 × 1 is found to be sufficient for sampling the Brillouin zone in reciprocal space, and a density mesh cutoff of 80 Hartree is used to define the fineness of real space effective potential and electron density grids for solving Poisson’s equation. The Generalized Gradient Approximation (GGA) with Perdew-Burke-Ernzerhof parameterization is used as the exchange correlation functional.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145761783","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Investigation into the performance characteristics of N,N′-bonded bis-triazole derivatives N,N键双三唑衍生物的性能研究。
IF 2.5 4区 化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-12-16 DOI: 10.1007/s00894-025-06604-4
Die Gao, Qi Gao, Jianguo Zhang, Jinting Wu, Tingxing Zhao, Hongbo Li

Context

Substituents including -NH2, -NO2, -NHNO2, and -CH(NO2)2 were introduced into the N,N′-linked bis-triazole scaffold to design 72 derivatives. Density functional theory (DFT) calculations at the B3LYP/6-311+G(d, p) level were performed using the Gaussian 09 software package to evaluate critical parameters such as density, heat of formation (HOF), detonation pressure (P), detonation velocity (D), explosive energy release (Q), sensitivity, and molecular orbital energies (HOMO–LUMO) for all 72 derivatives. The results indicate that compound C3 (ρ = 1.86 g.cm−3, D = 8.77 km.s−1, P = 34.83 GPa, h50% = 39.27 cm), C12 (ρ = 1.86 g.cm−3, D = 9.11 km.s−1, P = 37.45 GPa, h50% = 29.97 cm), and D15 (ρ = 1.80 g.cm−3, D = 9.03 km.s−1, P = 36.11 GPa, h50% = 31.47 cm) exhibit potential as substitute explosive candidates for 1,3,5-trinitro-1,3,5-triazinane (RDX) (ρ = 1.80 g.cm−3, D = 8.75 km.s−1, P = 34 GPa, h50% = 26 cm).

Methods

The structural optimization, volume calculations, and electrostatic potential energy analyses were conducted using the Gaussian 09 and Multiwfn 3.8 software packages, employing the B3LYP method within density functional theory (DFT). The structures of 72 derivatives were optimized at the 6-311+G(d, p) basis set level, followed by an investigation into their detonation performance and stability characteristics.

背景:将-NH2、-NO2、-NHNO2、-CH(NO2)2等取代基引入N,N'链双三唑支架中,设计72个衍生物。使用Gaussian 09软件包进行B3LYP/6-311+G(d, p)水平的密度泛函数理论(DFT)计算,以评估所有72个衍生物的密度、形成热(HOF)、爆轰压力(p)、爆轰速度(d)、爆炸能量释放(Q)、灵敏度和分子轨道能(HOMO-LUMO)等关键参数。结果表明,复合C3(ρ= 1.86 g.cm-3, km.s-1 D = 8.77, P = 34.83的绩点,h50% = 39.27厘米),C12(ρ= 1.86 g.cm-3, km.s-1 D = 9.11, P = 37.45的绩点,h50% = 29.97厘米),和D15(ρ= 1.80 g.cm-3, km.s-1 D = 9.03, P = 36.11的绩点,h50% = 31.47厘米)表现出潜在的替代炸药候选人1,3,5-trinitro-1, 3, 5-triazinane (RDX)(ρ= 1.80 g.cm-3, km.s-1 D = 8.75, P = 34 GPa, h50% = 26厘米)。方法:采用密度泛函理论(DFT)中的B3LYP方法,利用Gaussian 09和Multiwfn 3.8软件包进行结构优化、体积计算和静电势能分析。在6-311+G(d, p)基集水平上对72种衍生物进行了结构优化,并对其爆轰性能和稳定性进行了研究。
{"title":"Investigation into the performance characteristics of N,N′-bonded bis-triazole derivatives","authors":"Die Gao,&nbsp;Qi Gao,&nbsp;Jianguo Zhang,&nbsp;Jinting Wu,&nbsp;Tingxing Zhao,&nbsp;Hongbo Li","doi":"10.1007/s00894-025-06604-4","DOIUrl":"10.1007/s00894-025-06604-4","url":null,"abstract":"<div><h3>Context</h3><p>Substituents including -NH<sub>2</sub>, -NO<sub>2</sub>, -NHNO<sub>2</sub>, and -CH(NO<sub>2</sub>)<sub>2</sub> were introduced into the <i>N,N</i>′-linked bis-triazole scaffold to design 72 derivatives. Density functional theory (DFT) calculations at the B3LYP/6-311+G(d, p) level were performed using the Gaussian 09 software package to evaluate critical parameters such as density, heat of formation (HOF), detonation pressure (<i>P</i>), detonation velocity (<i>D</i>), explosive energy release (<i>Q</i>), sensitivity, and molecular orbital energies (HOMO–LUMO) for all 72 derivatives. The results indicate that compound C3 (<i>ρ</i> = 1.86 g.cm<sup>−3</sup>, <i>D</i> = 8.77 km.s<sup>−1</sup>, <i>P</i> = 34.83 GPa, <i>h</i><sub>50%</sub> = 39.27 cm), C12 (<i>ρ</i> = 1.86 g.cm<sup>−3</sup>, <i>D</i> = 9.11 km.s<sup>−1</sup>, <i>P</i> = 37.45 GPa, <i>h</i><sub>50%</sub> = 29.97 cm), and D15 (<i>ρ</i> = 1.80 g.cm<sup>−3</sup>, <i>D</i> = 9.03 km.s<sup>−1</sup>, <i>P</i> = 36.11 GPa, <i>h</i><sub>50%</sub> = 31.47 cm) exhibit potential as substitute explosive candidates for 1,3,5-trinitro-1,3,5-triazinane (RDX) (<i>ρ</i> = 1.80 g.cm<sup>−3</sup>, <i>D</i> = 8.75 km.s<sup>−1</sup>, <i>P</i> = 34 GPa, <i>h</i><sub>50%</sub> = 26 cm).</p><h3>Methods</h3><p>The structural optimization, volume calculations, and electrostatic potential energy analyses were conducted using the Gaussian 09 and Multiwfn 3.8 software packages, employing the B3LYP method within density functional theory (DFT). The structures of 72 derivatives were optimized at the 6-311+G(d, p) basis set level, followed by an investigation into their detonation performance and stability characteristics.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145761763","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Effects of Si-doped and shear strain on the optoelectronic properties of WSe2: A first principles study si掺杂和剪切应变对WSe2光电性能影响的第一性原理研究。
IF 2.5 4区 化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-12-16 DOI: 10.1007/s00894-025-06608-0
Zilian Tian, Lu Yang, Jianlin He

Context

Two-dimensional transition-metal dichalcogenides such as WSe2 are promising platforms for tunable optoelectronic devices. Here, first-principles molecular modeling is used to examine how substitutional Si doping combined with shear strain tunes the electronic and optical properties of monolayer WSe2. Si dopants introduce localized states that reduce the band gap from 1.599 to 1.029 eV and enhance low-energy absorption. Shear strain applied along orthogonal in-plane directions (xy and yx) further induces direction-dependent electronic localization and band-gap renormalization, giving rise to anisotropic optical absorption. These results provide mechanistic insight and a simple strategy for tailoring the optoelectronic response of WSe2-based materials.

Methods

Density functional theory calculations within the generalized-gradient approximation are performed using the Perdew–Burke–Ernzerhof functional and Gaussian-type basis sets as implemented in the Materials Studio package. Substitutional Si doping is modeled in a WSe2 supercell, and shear strain is introduced by distorting the in-plane lattice vectors along the xy and yx directions. For each configuration, fully relaxed geometries are used to evaluate the electronic band structures, charge redistribution, and complex dielectric function. Optical absorption spectra are obtained from the frequency-dependent dielectric tensor within the independent-particle approximation.

背景:二维过渡金属二硫族化合物如WSe2是可调谐光电器件的有前途的平台。本文采用第一性原理分子模型研究了取代Si掺杂与剪切应变的结合如何调节单层WSe2的电子和光学性质。Si掺杂剂引入局域态,使带隙从1.599 eV减小到1.029 eV,增强了低能吸收。沿正交面内方向(xy和yx)施加的剪切应变进一步诱导方向相关的电子局域化和带隙重整化,产生各向异性光吸收。这些结果为调整wse2基材料的光电响应提供了机制见解和简单策略。方法:密度泛函理论计算在广义梯度近似中使用Perdew-Burke-Ernzerhof泛函和高斯型基集执行,这些基集在Materials Studio软件包中实现。在WSe2超级单体中模拟了取代Si掺杂,并通过沿xy和yx方向扭曲平面内晶格矢量引入了剪切应变。对于每种结构,完全放松的几何形状被用来评估电子能带结构、电荷再分配和复杂的介电函数。光吸收光谱由频率相关的介电张量在独立粒子近似下得到。
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引用次数: 0
Competitive adsorption mechanisms of CO2 in hydrous silica-alumina clay shale nanopores: a comprehensive exploration 二氧化硅-氧化铝粘土页岩纳米孔中CO2竞争吸附机制的综合探讨。
IF 2.5 4区 化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-12-16 DOI: 10.1007/s00894-025-06597-0
Zhichao Zhang, Liehui Zhang, Yulong Zhao, Peiming Bian, Xin Chen

Context

High carbon emissions have become a major problem perplexing human society, and the use of shale for CO2 storage has a broad application prospect and significance. In this paper, a SiO2- Al2O3 heterostructure model representing clay shale is established, and the adsorption mechanisms of CO2 in clay shale are studied systematically by means of grand canonical Monte Carlo (GCMC), molecular dynamics (MD) and density functional theory (DFT). The findings indicate that the system's equilibrium shifts toward adsorption as pressure increases, enhancing gas uptake. Conversely, rising temperature favors the desorption equilibrium, thereby reducing the overall adsorption capacity. Higher water content reduces CO2 adsorption capacity in hydrous SiO2-Al2O3 nanopores. For every 5 wt% increment in water content, the CO2 adsorption amount decreases by approximately 18.6%. The density profiles show that the interaction between H2O and adsorption sites on the shale surface is stronger than that of CO2. The radial distribution functions indicate the difference of CO2 distribution between SiO2 region and Al2O3 region and reveal the effect of water on Al2O3 region is greater than that of SiO2 region. This study has an in-depth exploration of the adsorption rule and migration mechanism of CO2 in clay shale, which may contribute preliminary theoretical insights for optimizing CO2 adsorption and storage.

Method

The simulation software employed in this study is Materials Studio, and the associated force field utilized is COMPASS III. The adsorption configurations are obtained from the Sorption module and molecular dynamics simulations are performed on it by using the Forcite module with the NVT ensemble. Based on the DFT, molecular optimization and performance metrics analysis are all calculated using the DMol3 module.

背景:高碳排放已成为困扰人类社会的重大问题,利用页岩进行CO2封存具有广阔的应用前景和意义。本文建立了代表粘土页岩的SiO2- Al2O3异质结构模型,并利用大正则蒙特卡罗(GCMC)、分子动力学(MD)和密度泛函理论(DFT)对粘土页岩中CO2的吸附机理进行了系统研究。研究结果表明,随着压力的增加,系统的平衡向吸附方向转移,从而增强了气体的吸收率。相反,温度升高有利于解吸平衡,从而降低了总吸附容量。较高的含水量降低了含水SiO2-Al2O3纳米孔对CO2的吸附能力。含水量每增加5 wt%, CO2吸附量减少约18.6%。密度分布表明,H2O与页岩表面吸附位点的相互作用强于CO2。径向分布函数反映了SiO2区和Al2O3区CO2分布的差异,表明水对Al2O3区的影响大于SiO2区。本研究深入探索了CO2在粘土页岩中的吸附规律和运移机理,为优化CO2的吸附和储存提供了初步的理论见解。方法:本研究采用的仿真软件为Materials Studio,使用的联合力场为COMPASS III。通过吸附模块得到了吸附构型,并利用具有NVT系综的Forcite模块对其进行了分子动力学模拟。在DFT的基础上,利用DMol3模块计算分子优化和性能指标分析。
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引用次数: 0
`Theoretical study of the enhancement of the photoconversion eficiency on zinc porphyrin dyes by combining electron donor–acceptor theory with the Barrera-Crivelli-Loeb (BCL) model 结合电子供体-受体理论和Barrera-Crivelli-Loeb (BCL)模型提高卟啉锌染料光转换效率的理论研究。
IF 2.5 4区 化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-12-16 DOI: 10.1007/s00894-025-06591-6
Mauricio Barrera, Irma Crivelli

Context

In order to increase the efficiency of dye-sensitized solar cells (DSSC), we propose to study the influence of maximizing the push–pull effect by quantifying the donor force (Ds) and the acceptor capacity (Ap) calculated as functions of the Electrophilicity, Orbital Hardness, and Polarizability. The sum of the donor force and the acceptor capacity is the inductive force, which allows the push–pull effect to be maximized. With this approach, we applied the Barrera-Crivelli-Loeb (BCL) model to a series of eleven Zinc Porphyrins to correlate the Global Efficiency Index (GEI) with the experimental measurement of Photo Conversion Efficiency (PCE). The use of this strategy together with the use of siloles and siloxanes allows the design of two new dyes, BCL 516 and BCL 520, with theoretically calculated efficiencies of 10.64% and 10.61%.

Methods

In this work, all calculations were performed with the Amsterdam Density Functional 2023 package. For geometry optimization (ground state and first singlet), the optimized Perdew-Becke-Ernzerhof exchange correlation functional was employed with a DZP basis set for H, C, N, O, S, and a Zeroth Order Regular Approximation (ZORA) – TZP basis set for Ti and Zn. Time-Dependent Density Functional Theory (TDDFT) calculations were achieved with the Statistical Average Orbital model exchange correlation potential (SAOP), including solvent effects with the Conductor-like Screening Model (COSMO). Calculations of molecular properties like electrophilicity, orbital hardness, and polarizability were carried out in the gas phase with the SAOP potential model after optimization of the target molecule with the OPBE exchange correlation functional. To determine the orbital hardness of the HOMO and LUMO, the occupation number of the frontier orbital was modified by 0.3 units.

背景:为了提高染料敏化太阳能电池(DSSC)的效率,我们提出通过量化供体力(Ds)和受体容量(Ap)作为亲电性、轨道硬度和极化率的函数来研究最大化推挽效应的影响。供体力和受体容量的总和是感应力,这使得推挽效应得到最大化。利用这种方法,我们将Barrera-Crivelli-Loeb (BCL)模型应用于一系列11种锌卟啉,以将全球效率指数(GEI)与光转换效率(PCE)的实验测量相关联。该策略与硅孔和硅氧烷的使用一起允许设计两种新的染料,BCL 516和BCL 520,理论计算效率为10.64%和10.61%。方法:采用阿姆斯特丹密度泛函2023软件包进行计算。对于几何优化(基态和第一单重态),采用优化后的Perdew-Becke-Ernzerhof交换相关泛函,H、C、N、O、S采用DZP基集,Ti和Zn采用零阶正则逼近(ZORA) - TZP基集。利用统计平均轨道模型交换相关势(SAOP)计算了时间依赖密度泛函理论(TDDFT),包括溶剂效应和类导体筛选模型(COSMO)。利用OPBE交换相关泛函对目标分子进行优化后,利用SAOP电位模型在气相中计算了分子的亲电性、轨道硬度和极化率等分子性质。为了确定HOMO和LUMO的轨道硬度,将前沿轨道的占用数修改0.3个单位。
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引用次数: 0
Chain rigidity of 3D-ladder polymers quantified by molecular simulations 分子模拟量化三维阶梯聚合物的链刚性。
IF 2.5 4区 化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-12-16 DOI: 10.1007/s00894-025-06609-z
Chaofu Wu

Context

Due to the versatile properties, the hydrocarbon ladder polymers developed recently represent a class of promising materials for membrane separations of industrially relevant gas mixtures. The excellent thermomechanical properties and ultrahigh permselectivity are generally attributed to the chain rigidity of the three-dimensional (3D) ladder structures, which are not readily accessible via experiments. Therefore, this work takes advantage of molecular simulations to quantify the chain rigidity of such polymers, which exhibit quite different behaviors from the conventional polymers. It is first identified that the characteristic segments and repeating units behave like bows that are easy to press but difficult to pull. Furthermore, it is demonstrated that the subtle influences of side groups and temperature on the end-to-end distance (Re) can be well captured by these all-atomistic (AA) simulations. As suggested by the fluctuation in Re, the configuration provides an effective way to tune overall chain morphology and thus its rigidity, resulting from both the rigidity and shape of characteristic segments. These results highlight the unique rigidity of such polymers, which should inspire further development of new robust polymer membranes of gas separations.

Methods

The software named Materials Studio 4.0 was employed to construct the all-atomistic structures of model systems and to perform all the energy minimizations and molecular dynamics simulations with the Deriding force field and QEq charges, and to analyze the structural and energetic properties.

背景:由于其多用途的特性,最近开发的碳氢阶梯聚合物代表了一类有前途的材料,用于工业相关气体混合物的膜分离。优异的热机械性能和超高的过电选择性通常归因于三维(3D)阶梯结构的链刚性,这是不易通过实验获得的。因此,这项工作利用分子模拟来量化这种聚合物的链刚性,它表现出与传统聚合物完全不同的行为。首先确定了特征段和重复单元的行为像弓,容易按,但很难拉。此外,这些全原子(AA)模拟可以很好地捕捉到侧基和温度对端到端距离(Re)的微妙影响。正如Re的波动所表明的那样,该构型提供了一种有效的方法来调整整体链的形态,从而调整其刚度,这是由特征段的刚度和形状产生的。这些结果突出了这种聚合物的独特刚性,这应该激发进一步开发新的坚固的气体分离聚合物膜。方法:采用Materials Studio 4.0软件构建模型体系的全原子结构,并利用Deriding力场和QEq电荷进行全能量最小化和分子动力学模拟,分析其结构和能量性质。
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引用次数: 0
期刊
Journal of Molecular Modeling
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