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Computational analysis of linear chain of holey nanographene and their molecular characterizations
IF 2.1 4区 化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-01-25 DOI: 10.1007/s00894-024-06261-z
S. Prabhu, M. Arulperumjothi, S. Salu, Bibin K. Jose

Context

Holey nanographene, an allotrope of carbon arranged in two dimensions, has gained remarkable attention as a nanomaterial with several potential uses in numerous industries, such as electronics, energy storage, healthcare, and environmental cleanup, because of its high carrier mobility, flexibility, transparency, high surface area, conductivity, and chemical stability. The fundamental holey nanographene is assembled in a linear form to create the holey nanographene chain (HNC) that is being discussed. To fully utilize it in various applications, it is essential to comprehend the basic ideas guiding its behavior at the nanoscale; for that, we find various topological indices for this holey nanographene chain using the cut method. Because topological indices are a robust mathematical tool that links molecular structure with chemical, physical, and biological properties, they are essential in diverse areas, namely chemistry, pharmaceutical research, environmental science, and materials science

Methods

The cut method is essential for calculating topological indices in large structures as standard definitions become increasingly complex for such computations. In this study, we apply the cut method to compute each topological index for holey nanographene structures, which involves extensive summations. MATLAB software is employed to simplify these calculations. To generate the DDSV (Distance Degree Sequence Vector) for each vertex within any dimension of holey nanographene, we utilize the NEWGRAPH interface. Python code is then used to analyze the DDSVs assigned to each vertex. Additionally, MATLAB code is applied to validate the numerical results derived from analytical formulae for the topological indices of the HNCs under consideration

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引用次数: 0
Synergizing Monte Carlo simulations and experimental insights for efficient cationic dye removal using natural fluorapatite 利用天然氟磷灰石高效去除阳离子染料的蒙特卡洛模拟与实验研究的协同作用。
IF 2.1 4区 化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-01-25 DOI: 10.1007/s00894-025-06277-z
Imane El Mrabet, Anouar Ameziane El Hassani, Abdelghni Hsini, Abdelali El Gaidoumi, Karim Tanji, Zineb Chaouki, Mohamed Ebn Touhami, Abdelillah Shaim, Hicham Zaitan

Context

Natural fluorapatite (FAP) has been investigated as an adsorbent for the removal of dyes such as methylene blue (MB) and crystal violet (CV) from aqueous solutions. Effective dye removal is crucial for water treatment, particularly for industrial wastewater containing toxic dyes. FAP, a naturally abundant material, was characterized using XRD, FTIR, and SEM analysis. The maximum adsorption efficiency achieved was 97% (23 mg/g) for CV and 95% (13 mg/g) for MB under optimal conditions within an equilibrium time of 50 min. The adsorption capacity increased with the ionic strength of the dye solution, reaching 35 mg/g for CV and 28 mg/g for MB. The kinetic study showed that the adsorption of CV and MB is well described by the pseudo-second-order kinetic model (R2 = 0.999) and fits the Freundlich model significantly, with an R2 = 0.99 for both studied molecules. The thermodynamic analysis (ΔH° = 22.647 and 14.907 kJ.mol−1, ΔS° = 88.627 and 47.330 J.mol−1.K−1 for CV and MB, respectively) revealed that the adsorption process is spontaneous and endothermic, with significant randomness at the adsorbent-adsorbate interface. However, desorption and regeneration tests showed that the efficiency of FAP decreases upon reuse. Despite this, the abundance of natural FAP balances its drawbacks. MD simulations confirmed that adsorption is exothermic and spontaneous, especially in basic conditions, where Van der Waals interactions dominate. These findings suggest that natural FAP has significant potential for dye removal in wastewater treatment applications.

Methods

The effects of various parameters, including dye concentration, temperature, adsorbent mass, and pH, on the adsorption capacity of FAP were studied. Experimental conditions included an initial dye concentration of 20 mg/L, adsorbent mass of 1 g/L, pH of 12, and temperature of 298 K. The Freundlich model was used to describe the adsorption process, while MD simulations provided insights into the adsorption mechanism.

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引用次数: 0
In silico-based investigation of the molecular mechanism of Artocarpus communis seed hexane fraction against metabolic syndrome
IF 2.1 4区 化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-01-23 DOI: 10.1007/s00894-024-06274-8
Amel Elbasyouni, Dhamodharan Prabhu, Emmanuel Oluwatofunmi Akindoyin, Victor Gbolahan Adebiyi, Blessing Misturat Aremu, Cornelius Toluwase Ilori, Favour Inijesunimi Olagookun, Akingbolabo Daniel Ogunlakin, Enitan Omobolanle Adesanya

Context

The medications for metabolic syndromes are very minimal and the available are not effective and show adverse effects. There is a huge need for the development of effective and safe drugs to battle metabolic syndromes. In this context, our study aimed to decipher the key molecules from Artocarpus communis seed hexane fraction and their possible mechanism of action against metabolic syndrome. Network pharmacology and hub gene analysis revealed that STAT3 displayed the highest number of interactions with 56 genes compared to its counterparts HSP90AA1 (51 interactions) and EP300 (42 interactions). The molecular docking analysis revealed a suitable phytochemical with a higher binding affinity towards the three target genes (STAT3, HSP90AA1, and EP300), which were taken further for the molecular dynamic simulations. Overall, the simulation results depict that all the phytochemicals were stably bound within the cavity of the respective target proteins. Therefore, Artocarpus communis seed hexane fraction can potentially alleviate metabolic syndrome in humans.

Methods

Solvent-based extraction was performed in this study to extract the phytochemicals in Artocarpus communis seed powder. The hexane fraction was subjected to GCMS analysis to identify the constituents. ADMETlab 3.0 was used in ADME predictions. Gene databases (GeneCards, Pharos, NCBI-gene, and DisGe NET) were used to identify the genes for the study. STRING, DAVID, and KEGG pathways were utilized in this study. PubChem and Protein Databank were used to retrieve the structures of phytochemicals and protein structures. Schrodinger Suite was used for the molecular docking and Desmond 2021–4 was used to simulate the ligand-bound complexes.

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引用次数: 0
Computational investigation of the perylene-TCNQ complex: effects of chalcogen and fluorine substitutions 苝- tcnq配合物的计算研究:氯和氟取代的影响
IF 2.1 4区 化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-01-22 DOI: 10.1007/s00894-025-06283-1
Shubham Bajpai, Raghu Nath Behera

Context

Donor–acceptor (D-A) complexes, formed between two or more molecules held together by intermolecular forces, show interesting tunable properties and found applications in diverse fields, including semiconductors, catalysis, and sensors. In this study, we investigated the D-A complexes formed between perylene and 7,7,8,8-tetracyanoquinodimethane (TCNQ) and their chalcogen (S, Se) and fluorine derivatives. It was observed that interaction energies due to complex formation increase while the HOMO–LUMO gaps decrease with chalcogen substitutions. A redshift in the electronic absorption spectra of the complexes was observed with chalcogen substitutions. The substitution of fluorine further enhanced these changes without altering the trend. These changes were found to be more for substitution with selenium compared to that of sulfur.

Methods

The ωB97X-D/6–311+G(2df,p) level of theory was used to optimize the individual geometries, complexes, and for the frequency calculation. Atoms-in-molecule and reduced density gradient analyses were employed for the interaction study. Time-dependent density functional theory with the same level was used to analyze the electronic excitation for complexes.

Graphical abstract

供体-受体(D-A)复合物是由两个或多个分子通过分子间作用力结合在一起形成的,具有有趣的可调特性,并在半导体、催化和传感器等多个领域得到了应用。在本研究中,我们研究了苝与7,7,8,8-四氰喹诺二甲烷(TCNQ)之间形成的D-A配合物及其硫(S, Se)和氟衍生物。结果表明,配合物形成的相互作用能增加,而HOMO-LUMO间隙随着碳的取代而减小。在配合物的电子吸收光谱中观察到与硫取代的红移。氟的取代在不改变趋势的情况下进一步增强了这些变化。这些变化是由硒取代的,而不是硫取代的。方法采用ωB97X-D/ 6-311 +G(2df,p)理论水平对单个几何形状、复合体进行优化,并进行频率计算。分子内原子分析和降低密度梯度分析用于相互作用研究。采用同能级随时间密度泛函理论分析了配合物的电子激发。图形抽象
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引用次数: 0
Insights into the adsorption mechanisms of VOCs molecules on non-oxidized and oxidized SnO2 (110) monolayer: DFT analysis VOCs分子在未氧化和氧化SnO2(110)单层上的吸附机理:DFT分析
IF 2.1 4区 化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-01-22 DOI: 10.1007/s00894-025-06282-2
Mouad Soumane, Houda Lahlou, Nejma Fazouan

Context

Designing efficient sensitive materials for the detection of volatile organic compounds (VOCs) such as ethanol, acetone, and benzene is stringent owing to the significant environmental and health risks induced by these compounds, in addition to their role as biomarkers for chronic diseases and food quality. This study investigates the adsorption mechanisms of VOC molecules (ethanol, acetone, and benzene) on both non-oxidized and oxidized SnO2 (110) monolayers and identifies the most suitable surface for gas sensing applications. For this, we examined structural properties, adsorption energies, density of states, gas responses, and recovery times. Additionally, we identified the most stable adsorption sites for each gas. Our results indicate that the oxidized SnO2 surface exhibits superior adsorption properties, response sensitivity, and recovery times, making it more effective for detecting VOC molecules, with particularly high sensitivity to ethanol. These findings are consistent with reported experimental results.

Methods

The calculations were performed using density functional theory (DFT), implemented in the Quantum ESPRESSO code. The Perdew-Burke-Ernzerhof (PBE) exchange–correlation functional was employed, along with a plane-wave basis set and a cutoff energy of 65 Ry. A comprehensive analysis of various VOC gas interactions with SnO2 surfaces was identified by examining the most stable adsorption sites for each gas.

设计用于检测挥发性有机化合物(voc)(如乙醇、丙酮和苯)的高效敏感材料是非常严格的,因为这些化合物除了作为慢性疾病和食品质量的生物标志物外,还会引起重大的环境和健康风险。本研究研究了VOC分子(乙醇、丙酮和苯)在未氧化和氧化的SnO2(110)单层上的吸附机理,并确定了最适合用于气敏应用的表面。为此,我们检查了结构性质、吸附能、状态密度、气体响应和恢复时间。此外,我们还确定了每种气体最稳定的吸附位点。我们的研究结果表明,氧化SnO2表面具有优越的吸附性能,响应灵敏度和恢复时间,使其更有效地检测VOC分子,特别是对乙醇具有很高的灵敏度。这些发现与报道的实验结果一致。方法采用密度泛函理论(DFT)进行计算,并在Quantum ESPRESSO代码中实现。使用Perdew-Burke-Ernzerhof (PBE)交换相关函数,以及平面波基集和65 Ry的截止能量。通过检查每种气体最稳定的吸附位点,确定了各种VOC气体与SnO2表面相互作用的综合分析。
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引用次数: 0
Prediction of endohedral borafullerenes X@B32C36 (X = CH4, BH4−, H2O, and NH3) with a B32C36 shell isovalent with C60 B32C36壳层与C60同价的内源性硼富勒烯X@B32C36 (X = CH4, BH4−,H2O和NH3)的预测
IF 2.1 4区 化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-01-21 DOI: 10.1007/s00894-024-06276-6
Ting Zhang, Cai-Yue Gao, Xiao-Ni Zhao, Gao-Yi Han, Si-Dian Li

Context

Inspired by the newly synthesized endohedral fullerene T CH4@C60 (1) and based on extensive density functional theory calculations, we predict herein a series of endohedral borafullerenes C3 CH4@B32C36 (4), T BH4@B32C36 (5), C1 H2O@B32C36 (6), C3 NH3@B32C36 (7), and T C8@B32C362– (8) which possess a B32C36 (3) shell isovalent with C60, with the neutral D2 C8@B24C44 (9) obtained from C8@B32C362– (8) by symmetric C─B substitutions. Detailed adaptive natural density partitioning (AdNDP) bonding analyses and iso-chemical shielding surfaces (ICSSs) calculations indicate that these core–shell species are spherically aromatic in nature, rendering high stability to the systems. More interestingly, based on the calculated effective donor–acceptor interaction between LP(O) → LV(B@B3C3) in H2O@B32C36 (6), we propose the concept of boron bond (BB) in chemistry which is defined as the in-phase orbital overlap between an electronegative atom A as lone-pair (LP) donor and an electron-deficient boron atom with a lone vacant (LV) orbital as LP acceptor. A boron bond appears to possess about 20 ~ 30% of the bond dissociation energy of a typical A-B covalent bond.

Methods

Extensive density functional theory investigations at the hybrid M06-2X-D3 and PBE0-D3 levels with the basis set 6-311 + G(d) were employed to fully optimize the structures of endohedral C3 CH4@B32C36 (4), T BH4@B32C36 (5), C1 H2O@B32C36 (6), C3 NH3@B32C36 (7), T C8@B32C362– (8), and D2 C8@B24C44 (9), with natural bonding orbital (NBO) and adaptive natural density partitioning (AdNDP) analyses performed to analyze the bonding patterns of the concerned species and the non-covalent interactions reduced density gradient (NCI-RDG) approach utilized to identify the types of the intramolecular non-covalent bonding interactions.

Graphical abstract

受新合成的内嵌富勒烯T CH4@C60(1)的启发,基于广泛的密度泛函理论计算,我们在此预测了一系列内嵌富勒烯C3 CH4@B32C36(4)、T BH4@B32C36 -(5)、C1 H2O@B32C36(6)、C3 NH3@B32C36(7)和T C8@B32C362 -(8),它们与C60具有B32C36(3)的壳价,并通过对称的C─B取代从C8@B32C362 -(8)得到中性的D2 C8@B24C44(9)。详细的自适应自然密度分配(AdNDP)键合分析和等化学屏蔽面(icss)计算表明,这些核-壳物质本质上是球形芳香的,使系统具有很高的稳定性。更有趣的是,基于H2O@B32C36(6)中计算的LP(O)→LV(B@B3C3)之间的有效供体-受体相互作用,我们提出了化学中硼键(BB)的概念,将其定义为电负性原子A作为孤对(LP)供体与具有孤空(LV)轨道的缺电子硼原子作为LP受体之间的相轨道重叠。硼键似乎具有典型的A- b共价键的键解离能的20 ~ 30%。方法在M06-2X-D3和PBE0-D3杂交水平上,以6-311 + G(d)为基集,进行密度泛函理论研究,充分优化内源性C3 CH4@B32C36(4)、T BH4@B32C36 -(5)、C1 H2O@B32C36(6)、C3 NH3@B32C36(7)、T C8@B32C362 -(8)和D2 C8@B24C44(9)的结构。利用自然成键轨道(NBO)和自适应自然密度分配(AdNDP)分析了相关物种的成键模式,并利用非共价相互作用降低密度梯度(NCI-RDG)方法鉴定了分子内非共价相互作用的类型。图形抽象
{"title":"Prediction of endohedral borafullerenes X@B32C36 (X = CH4, BH4−, H2O, and NH3) with a B32C36 shell isovalent with C60","authors":"Ting Zhang,&nbsp;Cai-Yue Gao,&nbsp;Xiao-Ni Zhao,&nbsp;Gao-Yi Han,&nbsp;Si-Dian Li","doi":"10.1007/s00894-024-06276-6","DOIUrl":"10.1007/s00894-024-06276-6","url":null,"abstract":"<div><h3>Context</h3><p>Inspired by the newly synthesized endohedral fullerene<i> T</i> CH<sub>4</sub>@C<sub>60</sub> (<b>1</b>) and based on extensive density functional theory calculations, we predict herein a series of endohedral borafullerenes <i>C</i><sub>3</sub> CH<sub>4</sub>@B<sub>32</sub>C<sub>36</sub> (<b>4</b>), <i>T</i> BH<sub>4</sub>@B<sub>32</sub>C<sub>36</sub><sup>–</sup> (<b>5</b>), <i>C</i><sub>1</sub> H<sub>2</sub>O@B<sub>32</sub>C<sub>36</sub> (<b>6</b>), <i>C</i><sub>3</sub> NH<sub>3</sub>@B<sub>32</sub>C<sub>36</sub> (<b>7</b>), and <i>T</i> C<sub>8</sub>@B<sub>32</sub>C<sub>36</sub><sup>2–</sup> (<b>8</b>) which possess a B<sub>32</sub>C<sub>36</sub> (<b>3</b>) shell isovalent with C<sub>60</sub>, with the neutral <i>D</i><sub><i>2</i></sub> C<sub>8</sub>@B<sub>24</sub>C<sub>44</sub> (<b>9</b>) obtained from C<sub>8</sub>@B<sub>32</sub>C<sub>36</sub><sup>2–</sup> (<b>8</b>) by symmetric C─B substitutions. Detailed adaptive natural density partitioning (AdNDP) bonding analyses and iso-chemical shielding surfaces (ICSSs) calculations indicate that these core–shell species are spherically aromatic in nature, rendering high stability to the systems. More interestingly, based on the calculated effective donor–acceptor interaction between LP(O) → LV(B@B<sub>3</sub>C<sub>3</sub>) in H<sub>2</sub>O@B<sub>32</sub>C<sub>36</sub> (<b>6</b>), we propose the concept of boron bond (BB) in chemistry which is defined as the in-phase orbital overlap between an electronegative atom A as lone-pair (LP) donor and an electron-deficient boron atom with a lone vacant (LV) orbital as LP acceptor. A boron bond appears to possess about 20 ~ 30% of the bond dissociation energy of a typical A-B covalent bond.</p><h3>Methods</h3><p>Extensive density functional theory investigations at the hybrid M06-2X-D3 and PBE0-D3 levels with the basis set 6-311 + G(d) were employed to fully optimize the structures of endohedral <i>C</i><sub>3</sub> CH<sub>4</sub>@B<sub>32</sub>C<sub>36</sub> (<b>4</b>), <i>T</i> BH<sub>4</sub>@B<sub>32</sub>C<sub>36</sub><sup>–</sup> (<b>5</b>), <i>C</i><sub>1</sub> H<sub>2</sub>O@B<sub>32</sub>C<sub>36</sub> (<b>6</b>), <i>C</i><sub>3</sub> NH<sub>3</sub>@B<sub>32</sub>C<sub>36</sub> (<b>7</b>), <i>T</i> C<sub>8</sub>@B<sub>32</sub>C<sub>36</sub><sup>2–</sup> (<b>8</b>), and <i>D</i><sub><i>2</i></sub> C<sub>8</sub>@B<sub>24</sub>C<sub>44</sub> (<b>9</b>), with natural bonding orbital (NBO) and adaptive natural density partitioning (AdNDP) analyses performed to analyze the bonding patterns of the concerned species and the non-covalent interactions reduced density gradient (NCI-RDG) approach utilized to identify the types of the intramolecular non-covalent bonding interactions.</p><h3>Graphical abstract</h3>\u0000<div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 2","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142995614","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
Molecular dynamics simulation of CL-20 based high temperature resistant PBX 基于CL-20的耐高温PBX的分子动力学模拟
IF 2.1 4区 化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-01-21 DOI: 10.1007/s00894-025-06287-x
Ya-fang Chen, Bao-guo Wang, Chun-guang Wang

Context

To address the issue that the output charge in existing Deflagration to Detonation Transition (DDT) detonators cannot withstand high temperatures of 200 °C, and to improve the output performance of the detonator, a CL-20 (Hexanitrohexaazaisowurtzitane) based polymer bonded explosive (PBX) was investigated as the primary charge material for the detonator. To select the most suitable binder for thermal resistance, molecular dynamics (MD) simulations were employed to evaluate the performance of different binders at various crystal planes and temperatures. The results indicate that among the five PBXs models, CL-20/F2602 exhibits the highest binding energy and the shortest bond initiation length at both ambient and elevated temperatures. CL-20/F2611 demonstrates stronger hydrogen bonding interactions and superior thermal stability at high temperatures. CL-20/PCTFE shows the best ductility, while CL-20/F2602 possesses the second-best ductility. Therefore, PBXs containing F2602 possess the best stability, compatibility, and satisfactory ductility, while PBXs with F2611 exhibit the best thermal stability. Both F2602 and F2611 are suitable as binders for CL-20.

Methods

Molecular dynamics (MD) simulations were carried out using the Materials Studio software to calculate the binding energies, trigger bond lengths, and mechanical properties of five PBX models at different crystal planes at 298 K, and at various temperatures on the (0 1 1) crystal plane after a 1 ns NPT dynamics simulation. The total MD simulation time was 1 ns, with a time step of 1 fs, and the COMPASS force field was employed throughout the simulation.

为解决现有爆燃转爆轰(DDT)雷管输出装药不能承受200℃高温的问题,提高雷管的输出性能,研究了CL-20 (Hexanitrohexaazaisowurtzitane)基聚合物粘结炸药(PBX)作为雷管的主装药材料。为了选择最合适的热阻粘结剂,采用分子动力学(MD)模拟方法评估了不同粘结剂在不同晶面和温度下的性能。结果表明,在5种PBXs模型中,CL-20/F2602在常温和高温下均表现出最高的结合能和最短的键起始长度。CL-20/F2611在高温下表现出更强的氢键相互作用和优异的热稳定性。CL-20/PCTFE的延展性最好,CL-20/F2602的延展性次之。因此,含F2602的PBXs具有最好的稳定性、相容性和良好的延展性,而含F2611的PBXs具有最好的热稳定性。F2602和F2611都适合作为CL-20的粘结剂。方法利用Materials Studio软件进行分子动力学(MD)模拟,计算5种PBX模型在298 K和(0 1 1)晶面不同温度下的结合能、触发键长和力学性能。MD仿真总时间为1 ns,时间步长为1 fs,仿真全程采用COMPASS力场。
{"title":"Molecular dynamics simulation of CL-20 based high temperature resistant PBX","authors":"Ya-fang Chen,&nbsp;Bao-guo Wang,&nbsp;Chun-guang Wang","doi":"10.1007/s00894-025-06287-x","DOIUrl":"10.1007/s00894-025-06287-x","url":null,"abstract":"<div><h3>Context</h3><p>To address the issue that the output charge in existing Deflagration to Detonation Transition (DDT) detonators cannot withstand high temperatures of 200 °C, and to improve the output performance of the detonator, a CL-20 (Hexanitrohexaazaisowurtzitane) based polymer bonded explosive (PBX) was investigated as the primary charge material for the detonator. To select the most suitable binder for thermal resistance, molecular dynamics (MD) simulations were employed to evaluate the performance of different binders at various crystal planes and temperatures. The results indicate that among the five PBXs models, CL-20/F<sub>2602</sub> exhibits the highest binding energy and the shortest bond initiation length at both ambient and elevated temperatures. CL-20/F<sub>2611</sub> demonstrates stronger hydrogen bonding interactions and superior thermal stability at high temperatures. CL-20/PCTFE shows the best ductility, while CL-20/F<sub>2602</sub> possesses the second-best ductility. Therefore, PBXs containing F<sub>2602</sub> possess the best stability, compatibility, and satisfactory ductility, while PBXs with F<sub>2611</sub> exhibit the best thermal stability. Both F<sub>2602</sub> and F<sub>2611</sub> are suitable as binders for CL-20.</p><h3>Methods</h3><p>Molecular dynamics (MD) simulations were carried out using the Materials Studio software to calculate the binding energies, trigger bond lengths, and mechanical properties of five PBX models at different crystal planes at 298 K, and at various temperatures on the (0 1 1) crystal plane after a 1 ns NPT dynamics simulation. The total MD simulation time was 1 ns, with a time step of 1 fs, and the COMPASS force field was employed throughout the simulation.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 2","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142995612","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
Computational insight into the formation of cation-π/cation-lone pair complexes between 3d-metal (II) ions and furan 三维金属(II)离子与呋喃之间形成阳离子-π/阳离子-孤对配合物的计算洞察力
IF 2.1 4区 化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-01-21 DOI: 10.1007/s00894-025-06279-x
Bapan Saha

Context

Cation-π and cation-lone pair interactions between 3d-metal (II) ions [Fe(II), Co(II), Ni(II) and Cu(II)] and furan are explored in the formation of 1:1 and 1:2 type complexes. Both cation-π (IEgas= −192.27 to −312.65 kcal mol−1) and cation-lone pair (IEgas= −163.13 to −271.76 kcal mol−1) interactions are reasonably strong and lead to the formation of stable 1:1 and 1:2 type complexes in gas phase. The complexes are also stable in solvent phase, but their stability is reduced significantly in presence of solvent dielectrics, especially in ethanol, DMSO and water. Formation of the complexes is thermodynamically favourable (exothermic and spontaneous). Charge transfer (Δq = 0.62 to 1.92 e), Laplacian of electron density (∇2ρ = 0.1435 to 0.6628 au) and total electron energy density (H(r) = −0.0019 to −0.0436 au) analysis have argued in favour of partial ionic and partial covalent character of the interactions.

Methods

Density functional theory (DFT) is exclusively used for the study. Polarizable continuum model (PCM) is used to perform solvent phase study. Natural bond orbital (NBO), quantum theory of atoms in molecules (QTAIM) and non-covalent interaction (NCI) analyses are performed for understanding other aspects of complex formation.

研究了三维金属(II)离子[Fe(II), Co(II), Ni(II)和Cu(II)]与呋喃形成1:1和1:2型配合物时的阳离子-π和阳离子-孤对相互作用。阳离子-π (IEgas=−192.27 ~−312.65 kcal mol−1)和阳离子-孤对(IEgas=−163.13 ~−271.76 kcal mol−1)的相互作用都相当强,在气相中形成稳定的1:1和1:2型配合物。该配合物在溶剂相中也很稳定,但在溶剂介质存在时,特别是在乙醇、二甲二甲砜和水中,其稳定性明显降低。配合物的形成在热力学上是有利的(放热和自发的)。电荷转移(Δq = 0.62 ~ 1.92 e−)、电子密度拉普拉斯函数(∇2ρ = 0.1435 ~ 0.6628 au)和总电子能量密度(H(r) = - 0.0019 ~ - 0.0436 au)分析表明,相互作用具有部分离子和部分共价的特征。方法采用密度泛函理论(DFT)进行研究。采用极化连续介质模型(PCM)进行溶剂相研究。自然键轨道(NBO),分子中原子的量子理论(QTAIM)和非共价相互作用(NCI)分析用于理解复杂形成的其他方面。
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引用次数: 0
A coarse-grained molecular dynamics simulation on the mechanical and thermal properties of natural rubber composites reinforced by fullerene nanoparticles 纳米富勒烯增强天然橡胶复合材料力学和热性能的粗粒度分子动力学模拟
IF 2.1 4区 化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-01-21 DOI: 10.1007/s00894-025-06278-y
Qing Li, Fanlin Zeng, Jianzheng Cui, Hongyu Guo

Context

The influence of fullerene C60 on the mechanical and thermal properties of natural rubber was systematically investigated using coarse-grained molecular dynamics simulations. The tensile results demonstrate that systems with longer NR chains exhibit reduced tensile strength. Moreover, the addition of C60 nanoparticles significantly enhanced the mechanical properties, with Young's modulus, yield strength, and tensile strength increasing by approximately 24.03%, 23.21%, and 51.61%, respectively, at a C60 concentration of 0.2 phr under a strain rate of 1e-6. Furthermore, the mechanical response was found to be strain rate-dependent, with higher strain rates leading to increased Young's modulus, yield strength, and tensile strength. Therefore, excessively high strain rates should be avoided in simulations to ensure consistency with real conditions. In terms of thermal properties, the addition of C60 nanoparticles was shown to significantly improve the thermal conductivity of natural rubber, with the optimal enhancement of 17.17% achieved at an inclusion level of approximately 0.1 phr. A comprehensive microstructural analysis, including mean square displacement, radial distribution function, coordination number, and interaction energy, revealed the reinforcement mechanisms of C60 on the mechanical and thermal properties of the nanocomposites. This study provides valuable insights into the rational design and fabrication of fullerene-reinforced natural rubber nanocomposites with superior mechanical and thermal performance.

Methods

In this study, coarse-grained molecular dynamics simulations were performed using the LAMMPS software. The system used the real unit system with periodic boundary conditions. The interatomic interactions were described using the lj/expand model. The simulations were conducted at a temperature of 300 K with a time step of 1 fs.

采用粗粒度分子动力学模拟方法,系统研究了富勒烯C60对天然橡胶力学性能和热性能的影响。拉伸结果表明,NR链较长的体系的拉伸强度降低。此外,C60纳米颗粒的加入显著提高了材料的力学性能,当C60浓度为0.2 phr,应变速率为1e-6时,杨氏模量、屈服强度和抗拉强度分别提高了约24.03%、23.21%和51.61%。此外,力学响应与应变率有关,应变率越高,杨氏模量、屈服强度和抗拉强度越高。因此,在模拟中应避免过高的应变率,以保证与实际情况的一致性。在热性能方面,C60纳米颗粒的加入显著提高了天然橡胶的导热性,当掺入量约为0.1 phr时,其导热性提高了17.17%。通过均方位移、径向分布函数、配位数和相互作用能等微观组织分析,揭示了C60对复合材料力学和热性能的增强机制。该研究为富勒烯增强天然橡胶纳米复合材料的合理设计和制造提供了有价值的见解。方法采用LAMMPS软件进行粗粒度分子动力学模拟。系统采用具有周期边界条件的实单位制。原子间的相互作用用lj/expand模型来描述。模拟在300 K的温度下进行,时间步长为1 fs。
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引用次数: 0
A prediction model for electrical strength of gaseous medium based on molecular reactivity descriptors and machine learning method 基于分子反应描述符和机器学习方法的气体介质电强度预测模型
IF 2.1 4区 化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-01-18 DOI: 10.1007/s00894-024-06254-y
Lingyun Luo, Shuai Yang, Zhao Yang, Hanyi Xia, Jixiong Xiao, Hang Wang

Context

Ionization and adsorption in gas discharge are similar to electrophilic and nucleophilic reactions. The molecular descriptors characterizing reactions such as electrostatic potential descriptors are useful in predicting the electrical strength of environmentally friendly gases. In this study, descriptors of 73 molecules are employed for correlation analysis with electrical strength. These molecular descriptors are categorized into two types: area-related descriptors and reactivity-related descriptors. Furthermore, the predictive performance between statistical models and machine learning models is compared. The statistical models include multiple linear regression, and polynomial regression, while machine learning models consist of K-nearest neighbors, random forest, and gradient boosting decision trees. The results indicate that machine learning models are generally better than statistical models in terms of predictive accuracy and stability, with gradient boosting decision trees demonstrating the best performance. Specifically, the coefficient of determination and mean squared error on the testing set after 1000 training iterations are 0.864 and 0.105, respectively. Therefore, the application of molecular reactivity descriptors and machine learning methods can effectively predict the electrical strength of gaseous medium.

Methods

The Gaussian 16 software is employed to optimize the molecular structure with the M06-2X functional and def2 series basis sets in this study. Then, the Multiwfn is utilized for wavefunction analysis to obtain molecular surface descriptors.

气体排放中的环境化和吸附类似于亲电和亲核反应。描述反应的分子描述符,如静电势描述符,在预测环境友好气体的电强度方面是有用的。本研究采用73个分子的描述符与电强度进行相关性分析。这些分子描述符分为两类:与面积相关的描述符和与反应性相关的描述符。此外,还比较了统计模型和机器学习模型的预测性能。统计模型包括多元线性回归和多项式回归,而机器学习模型由k近邻、随机森林和梯度增强决策树组成。结果表明,机器学习模型在预测精度和稳定性方面通常优于统计模型,其中梯度增强决策树表现出最好的性能。其中,经过1000次训练迭代后,测试集的决定系数为0.864,均方误差为0.105。因此,应用分子反应性描述符和机器学习方法可以有效地预测气体介质的电强度。方法采用Gaussian 16软件,以M06-2X功能基集和def2系列基集对分子结构进行优化。然后,利用Multiwfn进行波函数分析,得到分子表面描述符。
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Journal of Molecular Modeling
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