首页 > 最新文献

Molecular Simulation最新文献

英文 中文
Molecular dynamic simulations of deformation behaviour of blended polyethylene 混合聚乙烯变形行为的分子动力学模拟
4区 化学 Q4 CHEMISTRY, PHYSICAL Pub Date : 2023-09-30 DOI: 10.1080/08927022.2023.2260496
Jingfu Shi, Jia Zhou, Lei Liu, Wenxiang Liu, Changqing Miao
ABSTRACTThe tensile deformation behaviour of blended polyethylene (PE) was studied using molecular dynamic methods. The blended PE was modeled by blending linear chains with different molecular weights based on a united atom model. The mechanical response and microscopic conformational behaviours of blended PE were investigated at different strain rates and temperatures. The interatomic energy evolution displayed a similar trend to the stress–strain curve showing the stiffness of blended PE increase with a higher fraction of chain with high molecular weight. The microstructure metrics associated with free volume, orientation, entanglement and crystallisation were recorded as a function of strain in detail to obtain insight into the role of PE chains with different molecular weights for blended PE during deformation. The conformation evolution indicates that orientation and disentanglement are more noticeable in the short chain with low molecular weight in a blended PE system, while the long chain promotes the crystallisation of the initial chain structure. The chain entanglement evolution clearly shows some new flexion nodes created to entangle short chains again, implying that re-entanglement might exist during the tensile deformation.KEYWORDS: Molecular dynamic simulationsblended polyethylenedeformation behaviour AcknowledgementsThe present work is supported by the Advanced Research Project of Manned Spaceflight under Grant Nos. 040101, and Science Foundation of the National Key Laboratory of Science and Technology on Advanced Composites in Special Environments.Disclosure statementNo potential conflict of interest was reported by the author(s).CRediT authorship contribution statementJingfu Shi: Conceptualisation, Methodology, Software, Formal analysis, Investigation, Writing – original draft. Jia Zhou: Validation, Investigation, Writing – review & editing. Lei Liu: Visualisation, Writing – review & editing. Wenxiang Liu: Writing – review & editing. Changqing Miao: Writing – review & editing, Supervision, Project administration, Funding acquisition.Declaration of competing interestThe authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
摘要采用分子动力学方法研究了共混聚乙烯(PE)的拉伸变形行为。在统一原子模型的基础上,通过共混不同分子量的线性链对共混聚乙烯进行建模。研究了混合聚乙烯在不同应变速率和温度下的力学响应和微观构象行为。原子间能演化与应力-应变曲线相似,表明随着高分子量链分数的增加,共混PE的刚度增加。与自由体积、取向、缠结和结晶相关的微观结构指标被详细记录为应变的函数,以深入了解不同分子量的PE链在混合PE变形过程中的作用。构象演化表明,在混合PE体系中,低分子量短链的取向和解缠更明显,而长链则促进了初始链结构的结晶。链缠结演化清楚地表明,短链在拉伸变形过程中可能存在重新缠结。致谢本工作得到载人航天先进研究计划(040101)和特殊环境下先进复合材料国家重点实验室科学基金的支持。披露声明作者未报告潜在的利益冲突。史景福:概念、方法、软件、形式分析、调查、写作-原稿。周佳:验证、调查、写作、评审、编辑。刘磊:视觉化,写作-评论与编辑。刘文祥:写作-评论与编辑。苗长青:写作审编、监督、项目管理、资金获取。竞争利益声明作者声明,他们没有已知的竞争经济利益或个人关系,可能会影响本文所报道的工作。
{"title":"Molecular dynamic simulations of deformation behaviour of blended polyethylene","authors":"Jingfu Shi, Jia Zhou, Lei Liu, Wenxiang Liu, Changqing Miao","doi":"10.1080/08927022.2023.2260496","DOIUrl":"https://doi.org/10.1080/08927022.2023.2260496","url":null,"abstract":"ABSTRACTThe tensile deformation behaviour of blended polyethylene (PE) was studied using molecular dynamic methods. The blended PE was modeled by blending linear chains with different molecular weights based on a united atom model. The mechanical response and microscopic conformational behaviours of blended PE were investigated at different strain rates and temperatures. The interatomic energy evolution displayed a similar trend to the stress–strain curve showing the stiffness of blended PE increase with a higher fraction of chain with high molecular weight. The microstructure metrics associated with free volume, orientation, entanglement and crystallisation were recorded as a function of strain in detail to obtain insight into the role of PE chains with different molecular weights for blended PE during deformation. The conformation evolution indicates that orientation and disentanglement are more noticeable in the short chain with low molecular weight in a blended PE system, while the long chain promotes the crystallisation of the initial chain structure. The chain entanglement evolution clearly shows some new flexion nodes created to entangle short chains again, implying that re-entanglement might exist during the tensile deformation.KEYWORDS: Molecular dynamic simulationsblended polyethylenedeformation behaviour AcknowledgementsThe present work is supported by the Advanced Research Project of Manned Spaceflight under Grant Nos. 040101, and Science Foundation of the National Key Laboratory of Science and Technology on Advanced Composites in Special Environments.Disclosure statementNo potential conflict of interest was reported by the author(s).CRediT authorship contribution statementJingfu Shi: Conceptualisation, Methodology, Software, Formal analysis, Investigation, Writing – original draft. Jia Zhou: Validation, Investigation, Writing – review & editing. Lei Liu: Visualisation, Writing – review & editing. Wenxiang Liu: Writing – review & editing. Changqing Miao: Writing – review & editing, Supervision, Project administration, Funding acquisition.Declaration of competing interestThe authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.","PeriodicalId":18863,"journal":{"name":"Molecular Simulation","volume":"129 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136279604","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
Size effects on dislocation starvation in Cu nanopillars: a molecular dynamic simulations study 铜纳米柱中位错饥饿的尺寸效应:分子动力学模拟研究
4区 化学 Q4 CHEMISTRY, PHYSICAL Pub Date : 2023-09-29 DOI: 10.1080/08927022.2023.2262045
G. Sainath, Vani Shankar, A. Nagesha
ABSTRACTSize plays an important role on the deformation mechanism of nanopillars. With decreasing size, many FCC nanopillars exhibit dislocation starvation which is responsible for their high strength. However, many details about the dislocation starvation like how often it occurs, and how much is its contribution to the total plastic strain, are still elusive. Similarly, the size below which the dislocation starvation occurs is not clearly established. In this context, atomistic simulations have been performed on the compression of <110> Cu nanopillars with size (d) ranging from 5 to 21.5 nm. Molecular dynamics (MD) simulation results indicate that the nanopillars deform by the slip of extended dislocations and exhibit dislocation starvation mainly at small sizes (<20 nm). The frequency of the occurrence of dislocation starvation is highest in small-sized nanowires and it decreases with increasing size. Above the size of 20 nm, no dislocation starvation has been observed. Furthermore, we define the dislocation starvation strain and based on this, it has been shown that the contribution of the dislocation starvation to the total plastic strain decreases from 70% in small-sized nanopillars to below 5% in large-sized pillars. The present results suggest that dislocation starvation is a dominant phenomenon in small-sized nanopillars.KEYWORDS: Nanopillarssize effectsdislocation starvationatomistic simulations Disclosure statementNo potential conflict of interest was reported by the author(s).Data availability statementThe data that support the findings in this paper are available from the corresponding author on request.
摘要尺寸对纳米柱的变形机制起着重要的作用。随着尺寸的减小,许多FCC纳米柱表现出位错饥饿,这是其高强度的原因。然而,关于位错饥饿的许多细节,如它发生的频率,以及它对总塑性应变的贡献,仍然是难以捉摸的。同样,发生位错饥饿的尺寸也没有明确确定。在这种情况下,对尺寸(d)从5到21.5 nm的铜纳米柱的压缩进行了原子模拟。分子动力学(MD)模拟结果表明,纳米柱主要在小尺寸(<20 nm)处发生扩展位错滑移变形和位错饥饿。位错饥饿的发生频率在小尺寸纳米线中最高,随尺寸的增大而减小。在20nm以上,没有观察到位错饥饿现象。此外,我们定义了位错饥饿应变,并在此基础上表明,位错饥饿对总塑性应变的贡献从小尺寸纳米柱的70%下降到大尺寸纳米柱的5%以下。目前的研究结果表明,位错饥饿是小尺寸纳米柱中的主要现象。关键词:纳米微粒效应,错位,饥饿,原子模拟披露声明作者未报告潜在利益冲突。数据可用性声明支持本文研究结果的数据可应要求从通讯作者处获得。
{"title":"Size effects on dislocation starvation in Cu nanopillars: a molecular dynamic simulations study","authors":"G. Sainath, Vani Shankar, A. Nagesha","doi":"10.1080/08927022.2023.2262045","DOIUrl":"https://doi.org/10.1080/08927022.2023.2262045","url":null,"abstract":"ABSTRACTSize plays an important role on the deformation mechanism of nanopillars. With decreasing size, many FCC nanopillars exhibit dislocation starvation which is responsible for their high strength. However, many details about the dislocation starvation like how often it occurs, and how much is its contribution to the total plastic strain, are still elusive. Similarly, the size below which the dislocation starvation occurs is not clearly established. In this context, atomistic simulations have been performed on the compression of <110> Cu nanopillars with size (d) ranging from 5 to 21.5 nm. Molecular dynamics (MD) simulation results indicate that the nanopillars deform by the slip of extended dislocations and exhibit dislocation starvation mainly at small sizes (<20 nm). The frequency of the occurrence of dislocation starvation is highest in small-sized nanowires and it decreases with increasing size. Above the size of 20 nm, no dislocation starvation has been observed. Furthermore, we define the dislocation starvation strain and based on this, it has been shown that the contribution of the dislocation starvation to the total plastic strain decreases from 70% in small-sized nanopillars to below 5% in large-sized pillars. The present results suggest that dislocation starvation is a dominant phenomenon in small-sized nanopillars.KEYWORDS: Nanopillarssize effectsdislocation starvationatomistic simulations Disclosure statementNo potential conflict of interest was reported by the author(s).Data availability statementThe data that support the findings in this paper are available from the corresponding author on request.","PeriodicalId":18863,"journal":{"name":"Molecular Simulation","volume":"61 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135193132","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
Host–guest interactions of Crizotinib with natural and modified cyclodextrins: a combined molecular docking and molecular dynamics simulation approaches 克唑替尼与天然和修饰环糊精的主客体相互作用:结合分子对接和分子动力学模拟方法
4区 化学 Q4 CHEMISTRY, PHYSICAL Pub Date : 2023-09-28 DOI: 10.1080/08927022.2023.2259493
Elham Mohebbi, Leila Hokmabady, Fatemeh Ravari
ABSTRACTIn this work, molecular docking and molecular dynamics (MD) simulation were applied to investigate the ability of natural cyclodextrins (CDs; Alpha, Beta and Gamma Cyclodextrins) and modified CDs (hydroxypropyl, random methyl and amino Beta Cyclodextrins) to form the stable inclusion complexes (ICs) with Crizotinib, the oral small molecule kinase inhibitor as a chemotropic drug. Results of molecular docking and MD simulation studies demonstrated that Crizotinib forms stable ICs with all natural and modified CDs and in the presence of this drug, all six CDs become more rigid. The presence of Crizotinib and the release of water molecules result in a decrease in the number of hydrogen bonds between cyclodextrins (CDs) and solvent molecules within the encapsulated CDs, compared to the hydrogen bonds observed in free CDs. Additionally, HPBCD exhibited the strongest affinity for binding and established the highest quantity of hydrogen bonds with Crizotinib. Finally, all results of this paper demonstrated the potential of using this formulation to improve the bioavailability of the selected drug.KEYWORDS: Molecular dockingMolecular dynamics simulationNatural cyclodextrinsModified cyclodextrinsCrizotinib Disclosure statementNo potential conflict of interest was reported by the author(s).
摘要:本文采用分子对接和分子动力学(MD)模拟的方法研究了天然环糊精(CDs;α、β和γ环糊精)和修饰的CDs(羟丙基、随机甲基和氨基β环糊精)与口服小分子激酶抑制剂克唑替尼形成稳定的包合物(ICs)。分子对接和MD模拟研究的结果表明,克唑替尼与所有天然和修饰的CDs形成稳定的ic,并且在该药物存在下,所有六种CDs都变得更加刚性。与游离cd中观察到的氢键相比,克唑替尼的存在和水分子的释放导致封装cd内环糊精(cd)和溶剂分子之间的氢键数量减少。此外,HPBCD表现出最强的结合亲和力,并与克唑替尼建立了最多的氢键。最后,本文的所有结果都证明了使用该配方可以提高所选药物的生物利用度。关键词:分子对接分子动力学模拟天然环糊精改性环糊精斯克唑替尼披露声明作者未报告潜在利益冲突。
{"title":"Host–guest interactions of Crizotinib with natural and modified cyclodextrins: a combined molecular docking and molecular dynamics simulation approaches","authors":"Elham Mohebbi, Leila Hokmabady, Fatemeh Ravari","doi":"10.1080/08927022.2023.2259493","DOIUrl":"https://doi.org/10.1080/08927022.2023.2259493","url":null,"abstract":"ABSTRACTIn this work, molecular docking and molecular dynamics (MD) simulation were applied to investigate the ability of natural cyclodextrins (CDs; Alpha, Beta and Gamma Cyclodextrins) and modified CDs (hydroxypropyl, random methyl and amino Beta Cyclodextrins) to form the stable inclusion complexes (ICs) with Crizotinib, the oral small molecule kinase inhibitor as a chemotropic drug. Results of molecular docking and MD simulation studies demonstrated that Crizotinib forms stable ICs with all natural and modified CDs and in the presence of this drug, all six CDs become more rigid. The presence of Crizotinib and the release of water molecules result in a decrease in the number of hydrogen bonds between cyclodextrins (CDs) and solvent molecules within the encapsulated CDs, compared to the hydrogen bonds observed in free CDs. Additionally, HPBCD exhibited the strongest affinity for binding and established the highest quantity of hydrogen bonds with Crizotinib. Finally, all results of this paper demonstrated the potential of using this formulation to improve the bioavailability of the selected drug.KEYWORDS: Molecular dockingMolecular dynamics simulationNatural cyclodextrinsModified cyclodextrinsCrizotinib Disclosure statementNo potential conflict of interest was reported by the author(s).","PeriodicalId":18863,"journal":{"name":"Molecular Simulation","volume":"8 1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135385846","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
Exploration of anti-tumour inhibitors from colchicine derivatives based on 3D-QSAR, molecular docking and molecular dynamics simulations 基于3D-QSAR、分子对接和分子动力学模拟的秋水仙碱衍生物抗肿瘤抑制剂研究
4区 化学 Q4 CHEMISTRY, PHYSICAL Pub Date : 2023-09-25 DOI: 10.1080/08927022.2023.2259499
Jian-Bo Tong, Yuan Liu, Xue-chun Xiao, Peng Gao, Hai-yin Xu
ABSTRACTMicrotubulin is an important research target for anti-tumour drugs, which can be used to inhibit microtubulin polymerisation and improve the efficacy of tumour therapy. In this paper, 61 microtubule protein inhibitors with anticancer activity are selected as the data set for building a stable and effective QSAR (Topomer CoMFA) model, resulting in a Topomer CoMFA model with validation coefficients of q2 = 0.737 and r2 = 0.922. Fifteen new inhibitors with theoretically high activity are designed by screening the zinc database for new fragments with good activity through the contribution descriptors obtained by Topomer CoMFA. After simulating the binding affinity and interaction of the inhibitors with the proteins by molecular docking, all these compounds formed strong interactions such as hydrogen bonds with multiple amino acids in the receptor proteins. Furthermore, molecular dynamics results show that the predicted highly active compounds exhibited stable and favourable binding patterns to the active pocket. In addition, these new compounds exhibit good ADMET properties. The present work establishes a reliable QSAR model for computational simulation screening of microtubulin drug development and provides a basis for further access to novel microtubulin inhibitors.KEYWORDS: Microtubule protein inhibitorColchicineTopomer coMFAMolecular dockingMolecular dynamics Disclosure statementThe authors declare that they have no conflict of interest.(s).Additional informationFundingThis work was supported by National Natural Science Foundation of China: [Grant Number 21475081]; Graduate Innovation Fund of Shaanxi University of Science and Technology; The National Natural Science Foundation of China (22373062).
摘要微管蛋白是抗肿瘤药物的重要研究靶点,可用于抑制微管蛋白的聚合,提高肿瘤治疗的疗效。本文选取61个具有抗癌活性的微管蛋白抑制剂作为数据集,构建稳定有效的QSAR (Topomer CoMFA)模型,得到验证系数q2 = 0.737, r2 = 0.922的Topomer CoMFA模型。通过Topomer CoMFA获得的贡献描述符筛选锌数据库中具有良好活性的新片段,设计了15种理论上具有高活性的新抑制剂。通过分子对接模拟抑制剂与蛋白质的结合亲和力和相互作用后,这些化合物均与受体蛋白中的多个氨基酸形成氢键等强相互作用。此外,分子动力学结果表明,预测的高活性化合物与活性口袋具有稳定和良好的结合模式。此外,这些新化合物还具有良好的ADMET性能。本研究为微管蛋白药物开发的计算模拟筛选建立了可靠的QSAR模型,为进一步获得新型微管蛋白抑制剂提供了基础。关键词:微管蛋白抑制剂;秋水仙碱;聚物;分子对接;本研究由国家自然科学基金资助:[批准号21475081];陕西科技大学研究生创新基金;国家自然科学基金项目(22373062);
{"title":"Exploration of anti-tumour inhibitors from colchicine derivatives based on 3D-QSAR, molecular docking and molecular dynamics simulations","authors":"Jian-Bo Tong, Yuan Liu, Xue-chun Xiao, Peng Gao, Hai-yin Xu","doi":"10.1080/08927022.2023.2259499","DOIUrl":"https://doi.org/10.1080/08927022.2023.2259499","url":null,"abstract":"ABSTRACTMicrotubulin is an important research target for anti-tumour drugs, which can be used to inhibit microtubulin polymerisation and improve the efficacy of tumour therapy. In this paper, 61 microtubule protein inhibitors with anticancer activity are selected as the data set for building a stable and effective QSAR (Topomer CoMFA) model, resulting in a Topomer CoMFA model with validation coefficients of q2 = 0.737 and r2 = 0.922. Fifteen new inhibitors with theoretically high activity are designed by screening the zinc database for new fragments with good activity through the contribution descriptors obtained by Topomer CoMFA. After simulating the binding affinity and interaction of the inhibitors with the proteins by molecular docking, all these compounds formed strong interactions such as hydrogen bonds with multiple amino acids in the receptor proteins. Furthermore, molecular dynamics results show that the predicted highly active compounds exhibited stable and favourable binding patterns to the active pocket. In addition, these new compounds exhibit good ADMET properties. The present work establishes a reliable QSAR model for computational simulation screening of microtubulin drug development and provides a basis for further access to novel microtubulin inhibitors.KEYWORDS: Microtubule protein inhibitorColchicineTopomer coMFAMolecular dockingMolecular dynamics Disclosure statementThe authors declare that they have no conflict of interest.(s).Additional informationFundingThis work was supported by National Natural Science Foundation of China: [Grant Number 21475081]; Graduate Innovation Fund of Shaanxi University of Science and Technology; The National Natural Science Foundation of China (22373062).","PeriodicalId":18863,"journal":{"name":"Molecular Simulation","volume":"52 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135816003","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 insights into the corrosion inhibition mechanism of omeprazole and tinidazole: a theoretical investigation 奥美拉唑和替硝唑缓蚀机理的分子洞察:理论研究
4区 化学 Q4 CHEMISTRY, PHYSICAL Pub Date : 2023-09-25 DOI: 10.1080/08927022.2023.2256888
Savaş Kaya, Hassane Lgaz, Abhinay Thakkur, Ashish Kumar, Dilara Özbakır Işın, Nihat Karakuş, Samia Ben Ahmed
ABSTRACTIn many studies published in recent years, corrosion scientists proved that various drug molecules can exhibit high inhibition performance against the corrosion of metal surfaces and alloys. This study presents the adsorption behaviour and inhibition mechanism of Omeprazole and Tinidazole on steel surface in gas phase and aqueous acidic conditions using quantum chemical calculations and molecular dynamics simulations. Well-known quantum chemical parameters such as EHOMO, ELUMO, energy gaps, dipole moment, global hardness, softness, electrophilicity, electrodonating power, electroaccepting power and the fraction of electron transfer, were calculated to understand the corrosion inhibition properties and interactions with the steel surface of the studied molecules. Fukui indices analysis was performed to identify the local reactivities of the molecules. Additionally, Monte Carlo simulations were used to determine the optimal adsorption configuration of the inhibitors onto a Fe (1 1 0) surface. The study's findings provide valuable insights into preventing corrosion of steel surfaces in aqueous acidic environments. The theoretical data obtained was evaluated in terms of Maximum Hardness, Minimum Polarizability and Minimum Electrophilicity Principles.KEYWORDS: Corrosioninhibitioncomputational analysisMCSFukui indices Disclosure statementNo potential conflict of interest was reported by the author(s).AcknowledgementsThe authors extend their appreciation to the Deanship of Scientific Research at King Khalid University, Saudi Arabia for funding this work through Large Research Groups Programme under grant number L.R.G.P2/3/44.
在近年来发表的许多研究中,腐蚀科学家证明了各种药物分子对金属表面和合金的腐蚀具有很高的抑制性能。采用量子化学计算和分子动力学模拟研究了奥美拉唑和替硝唑在气相和水酸性条件下在钢表面的吸附行为和抑制机理。计算了已知的量子化学参数,如EHOMO、ELUMO、能隙、偶极矩、整体硬度、柔软度、亲电性、供电功率、电接受功率和电子转移分数,以了解所研究分子的缓蚀性能及其与钢表面的相互作用。用福井指数分析来鉴定分子的局部反应性。此外,蒙特卡罗模拟确定了抑制剂在Fe(110)表面的最佳吸附构型。该研究的发现为防止钢表面在酸性水环境中的腐蚀提供了有价值的见解。根据最大硬度、最小极化率和最小亲电性原则对所得理论数据进行了评价。关键词:缓蚀计算分析mcsfukui指数披露声明作者未报告潜在利益冲突。作者感谢沙特阿拉伯哈立德国王大学科学研究主任通过大型研究小组计划资助本工作,资助号为L.R.G.P2/3/44。
{"title":"Molecular insights into the corrosion inhibition mechanism of omeprazole and tinidazole: a theoretical investigation","authors":"Savaş Kaya, Hassane Lgaz, Abhinay Thakkur, Ashish Kumar, Dilara Özbakır Işın, Nihat Karakuş, Samia Ben Ahmed","doi":"10.1080/08927022.2023.2256888","DOIUrl":"https://doi.org/10.1080/08927022.2023.2256888","url":null,"abstract":"ABSTRACTIn many studies published in recent years, corrosion scientists proved that various drug molecules can exhibit high inhibition performance against the corrosion of metal surfaces and alloys. This study presents the adsorption behaviour and inhibition mechanism of Omeprazole and Tinidazole on steel surface in gas phase and aqueous acidic conditions using quantum chemical calculations and molecular dynamics simulations. Well-known quantum chemical parameters such as EHOMO, ELUMO, energy gaps, dipole moment, global hardness, softness, electrophilicity, electrodonating power, electroaccepting power and the fraction of electron transfer, were calculated to understand the corrosion inhibition properties and interactions with the steel surface of the studied molecules. Fukui indices analysis was performed to identify the local reactivities of the molecules. Additionally, Monte Carlo simulations were used to determine the optimal adsorption configuration of the inhibitors onto a Fe (1 1 0) surface. The study's findings provide valuable insights into preventing corrosion of steel surfaces in aqueous acidic environments. The theoretical data obtained was evaluated in terms of Maximum Hardness, Minimum Polarizability and Minimum Electrophilicity Principles.KEYWORDS: Corrosioninhibitioncomputational analysisMCSFukui indices Disclosure statementNo potential conflict of interest was reported by the author(s).AcknowledgementsThe authors extend their appreciation to the Deanship of Scientific Research at King Khalid University, Saudi Arabia for funding this work through Large Research Groups Programme under grant number L.R.G.P2/3/44.","PeriodicalId":18863,"journal":{"name":"Molecular Simulation","volume":"53 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135815126","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
In-silico and in-vitro identification of triazole based compounds as potential EGFR inhibitors targeting lung cancer 基于三唑的化合物作为潜在的肺癌EGFR抑制剂的硅内和体外鉴定
4区 化学 Q4 CHEMISTRY, PHYSICAL Pub Date : 2023-09-15 DOI: 10.1080/08927022.2023.2256624
Sunil Kumar, Monu Kumar Shukla, Iqra Ali, Faheem Abbas, Rachna Verma, Girish Chandra, Deepak Kumar
ABSTRACTThe use of FDA-approved drugs for the therapy of lung cancer through drug repurposing is a noteworthy approach. We retrieved all the FDA-approved triazole-based drugs from Drugbank and conducted docking-based virtual screening of the triazole-based FDA-approved drugs against the EGFR target. Deferasirox demonstrated hydrogen bonding interactions with residues Thr 830, Asp 831, Lys 721 and Met 769 of the EGFR-TKD receptor (PDB ID: 1M17) and Posaconazole showed hydrogen bonding with residues Met 769 and Glu 734 of the similar EGFR receptor along with the binding energies of −9.60, −9.50, kcal/mol respectively. The dock score for reference molecule found to be −6.70 (kcal/mol). Best two ligands (Deferasirox and Posaconazole) were selected on the basis of dock score from the virtual screening results for in vitro NRU assay using A549 cells to determine their cytotoxicity and cell viability. During the in vitro NRU experiment, Deferasirox and Posaconazole demonstrated IC50 values of 114.9 and 910.2 µM, respectively. MD simulations were performed to investigate the dynamic behaviour and stability, and interactions were compared to the standard inhibitor for the EGFR target. DFT studies were carried out to determine their molecular properties, including their electronic structure, bond lengths and bond energies. The results of the in silico and in vitro studies were analysed to assess the potential of Deferasirox and Posaconazole for use as anticancer agents in the mitigation of lung cancer symptoms. This study focused on repurposing FDA-approved triazole-based compounds to identify their potential as effective lung cancer treatments with anticancer properties.KEYWORDS: Lung cancerin-silicoin-vitrodrug repurposingEGFR AcknowledgmentsThe authors express their gratitude to the Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Shoolini University, Solan, Himachal Pradesh 173 229, India, for the support.Disclosure statementNo potential conflict of interest was reported by the author(s).
摘要通过药物再利用的方式使用fda批准的药物治疗肺癌是一个值得注意的途径。我们从Drugbank检索了所有fda批准的三唑类药物,并对fda批准的三唑类药物针对EGFR靶点进行了基于对接的虚拟筛选。去铁唑与EGFR- tkd受体(PDB ID: 1M17)的残基Thr 830、Asp 831、Lys 721和Met 769表现出氢键作用,Posaconazole与类似EGFR受体的残基Met 769和Glu 734表现出氢键作用,结合能分别为- 9.60、- 9.50 kcal/mol。参考分子的dock分数为- 6.70 (kcal/mol)。根据虚拟筛选结果的dock评分,选择最佳的两个配体(去铁宁和泊沙康唑)进行体外NRU实验,以A549细胞为实验对象,测定其细胞毒性和细胞活力。在体外NRU实验中,去铁呋司和泊沙康唑的IC50值分别为114.9和910.2µM。进行了MD模拟以研究其动态行为和稳定性,并将其与EGFR靶标的标准抑制剂的相互作用进行了比较。DFT研究确定了它们的分子性质,包括它们的电子结构、键长和键能。对计算机和体外研究的结果进行了分析,以评估去铁沙精和泊沙康唑作为抗癌剂在缓解肺癌症状方面的潜力。这项研究的重点是重新利用fda批准的基于三唑的化合物,以确定它们作为具有抗癌特性的有效肺癌治疗方法的潜力。作者感谢印度喜马偕尔邦索兰173 229肖利尼大学药学院药物化学系的支持。披露声明作者未报告潜在的利益冲突。
{"title":"<i>In-silico</i> and <i>in-vitro</i> identification of triazole based compounds as potential EGFR inhibitors targeting lung cancer","authors":"Sunil Kumar, Monu Kumar Shukla, Iqra Ali, Faheem Abbas, Rachna Verma, Girish Chandra, Deepak Kumar","doi":"10.1080/08927022.2023.2256624","DOIUrl":"https://doi.org/10.1080/08927022.2023.2256624","url":null,"abstract":"ABSTRACTThe use of FDA-approved drugs for the therapy of lung cancer through drug repurposing is a noteworthy approach. We retrieved all the FDA-approved triazole-based drugs from Drugbank and conducted docking-based virtual screening of the triazole-based FDA-approved drugs against the EGFR target. Deferasirox demonstrated hydrogen bonding interactions with residues Thr 830, Asp 831, Lys 721 and Met 769 of the EGFR-TKD receptor (PDB ID: 1M17) and Posaconazole showed hydrogen bonding with residues Met 769 and Glu 734 of the similar EGFR receptor along with the binding energies of −9.60, −9.50, kcal/mol respectively. The dock score for reference molecule found to be −6.70 (kcal/mol). Best two ligands (Deferasirox and Posaconazole) were selected on the basis of dock score from the virtual screening results for in vitro NRU assay using A549 cells to determine their cytotoxicity and cell viability. During the in vitro NRU experiment, Deferasirox and Posaconazole demonstrated IC50 values of 114.9 and 910.2 µM, respectively. MD simulations were performed to investigate the dynamic behaviour and stability, and interactions were compared to the standard inhibitor for the EGFR target. DFT studies were carried out to determine their molecular properties, including their electronic structure, bond lengths and bond energies. The results of the in silico and in vitro studies were analysed to assess the potential of Deferasirox and Posaconazole for use as anticancer agents in the mitigation of lung cancer symptoms. This study focused on repurposing FDA-approved triazole-based compounds to identify their potential as effective lung cancer treatments with anticancer properties.KEYWORDS: Lung cancerin-silicoin-vitrodrug repurposingEGFR AcknowledgmentsThe authors express their gratitude to the Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Shoolini University, Solan, Himachal Pradesh 173 229, India, for the support.Disclosure statementNo potential conflict of interest was reported by the author(s).","PeriodicalId":18863,"journal":{"name":"Molecular Simulation","volume":"17 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135393416","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
Identification of small-molecule glucokinase activator for type-2-diabetes treatment: a structure-based virtual screening approach 鉴定用于2型糖尿病治疗的小分子葡萄糖激酶激活剂:基于结构的虚拟筛选方法
4区 化学 Q4 CHEMISTRY, PHYSICAL Pub Date : 2023-09-14 DOI: 10.1080/08927022.2023.2256425
Manokaran Malini, Ramasamy Thilagavathi, Jannet Vennila, Beutline Malgija, Gandhi Praveena, Chelliah Selvam
ABSTRACTGlucokinase (GK, EC 2.7.1.2) is a crucial enzyme that catalyses the conversion of glucose to glucose-6-phosphate. It is used to treat type-2 diabetes (T2D), a serious metabolic disorder that is still at the forefront without proper medication. Fast Rigid Exhaustive Docking (FRED) was carried out for 400,000 compounds from the Zinc database to identify novel glucokinase activators. The hit compounds ZINC69775727, ZINC9114647, ZINC91773667, ZINC9305321, and ZINC96165848 interacted strongly with allosteric site residues and, formed hydrogen bonds with ARG 63. The hit compounds met the criterion for drug-likeness, according to the ADME prediction. The compounds were then subjected to 100 ns of molecular dynamics simulation and MM-GBSA calculation using DESMOND. The findings demonstrated that the compounds had good stability and minimal fluctuation throughout the course of the simulation, pointing to the potential of the chosen compounds for glucokinase activation. The compound ZINC69775727 in particular has the lowest binding energy of −111.1 kcal/mol, which is lower than the native ligand’s binding energy of −102.84 kcal/mol and the binding energies of the control compounds PSN-GK1 and Piragliatin, which are −102.49 kcal/mol and −107.767 kcal/mol, respectively. Therefore, the information from this work may be useful in finding novel small molecules as GKAs.KEYWORDS: Glucokinase (GK)glucokinase activators (GKA)FREDDESMONDzinc database AcknowledgementChelliah Selvam thanks the Openeye Inc for providing the academic license to use the docking tools.Disclosure statementNo potential conflict of interest was reported by the author(s).
摘要葡萄糖激酶(glucokinase, GK, EC 2.7.1.2)是催化葡萄糖转化为葡萄糖-6-磷酸的关键酶。它被用于治疗2型糖尿病(T2D),这是一种严重的代谢紊乱,在没有适当的药物治疗的情况下仍然处于最前沿。快速刚性穷举对接(FRED)对锌数据库中的400,000种化合物进行了快速刚性穷举对接(FRED),以鉴定新的葡萄糖激酶激活剂。命中的化合物ZINC69775727、ZINC9114647、ZINC91773667、ZINC9305321和ZINC96165848与变构位点残基强相互作用,并与ARG 63形成氢键。根据ADME的预测,命中的化合物符合药物相似的标准。然后用DESMOND进行100 ns的分子动力学模拟和MM-GBSA计算。研究结果表明,这些化合物在整个模拟过程中具有良好的稳定性和最小的波动,这表明所选化合物具有葡萄糖激酶激活的潜力。其中,ZINC69775727的结合能最低,为- 111.1 kcal/mol,低于天然配体的- 102.84 kcal/mol,也低于对照化合物PSN-GK1和Piragliatin的- 102.49 kcal/mol和- 107.767 kcal/mol。因此,这项工作的信息可能有助于寻找新的小分子作为gka。关键词:葡萄糖激酶(GK)葡萄糖激酶激活剂(GKA)FREDDESMONDzinc数据库致谢chelliah Selvam感谢Openeye公司提供使用对接工具的学术许可。披露声明作者未报告潜在的利益冲突。
{"title":"Identification of small-molecule glucokinase activator for type-2-diabetes treatment: a structure-based virtual screening approach","authors":"Manokaran Malini, Ramasamy Thilagavathi, Jannet Vennila, Beutline Malgija, Gandhi Praveena, Chelliah Selvam","doi":"10.1080/08927022.2023.2256425","DOIUrl":"https://doi.org/10.1080/08927022.2023.2256425","url":null,"abstract":"ABSTRACTGlucokinase (GK, EC 2.7.1.2) is a crucial enzyme that catalyses the conversion of glucose to glucose-6-phosphate. It is used to treat type-2 diabetes (T2D), a serious metabolic disorder that is still at the forefront without proper medication. Fast Rigid Exhaustive Docking (FRED) was carried out for 400,000 compounds from the Zinc database to identify novel glucokinase activators. The hit compounds ZINC69775727, ZINC9114647, ZINC91773667, ZINC9305321, and ZINC96165848 interacted strongly with allosteric site residues and, formed hydrogen bonds with ARG 63. The hit compounds met the criterion for drug-likeness, according to the ADME prediction. The compounds were then subjected to 100 ns of molecular dynamics simulation and MM-GBSA calculation using DESMOND. The findings demonstrated that the compounds had good stability and minimal fluctuation throughout the course of the simulation, pointing to the potential of the chosen compounds for glucokinase activation. The compound ZINC69775727 in particular has the lowest binding energy of −111.1 kcal/mol, which is lower than the native ligand’s binding energy of −102.84 kcal/mol and the binding energies of the control compounds PSN-GK1 and Piragliatin, which are −102.49 kcal/mol and −107.767 kcal/mol, respectively. Therefore, the information from this work may be useful in finding novel small molecules as GKAs.KEYWORDS: Glucokinase (GK)glucokinase activators (GKA)FREDDESMONDzinc database AcknowledgementChelliah Selvam thanks the Openeye Inc for providing the academic license to use the docking tools.Disclosure statementNo potential conflict of interest was reported by the author(s).","PeriodicalId":18863,"journal":{"name":"Molecular Simulation","volume":"43 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134910703","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
Nanoindentation simulation study on mechanical properties and microstructure evolution of twin γ-TiAl alloy 孪晶γ-TiAl合金力学性能及组织演变的纳米压痕模拟研究
4区 化学 Q4 CHEMISTRY, PHYSICAL Pub Date : 2023-09-11 DOI: 10.1080/08927022.2023.2254845
Junye Li, Jiaxu Tang, Junwei Li, Rongxian Qiu, Fujun Xiao, Xiwei Dong, Lei Zhang
ABSTRACT To explore the mechanical properties and deformation mechanism of twin γ-TiAl alloy under load and impact, based on the special interface structure in polycrystals, twinning at room temperature is established in this paper simulation of nanoindentation response of twin γ-TiAl alloy. Through the load-displacement curve, the hardness and Young's modulus of the workpiece are obtained. By analysing the microstructure evolution behaviour under the action of the indenter, it is found that during the loading process, multiple dislocation rings are generated in the grain and slip to the lower part of the workpiece, resulting in the hardness decreasing with the increase of the indentation depth, which is consistent with the indentation size effect; The dislocation lock generated during the unloading process delayed the annihilation of the defect structure, but the dislocation and stacking fault structure disappeared completely and the stress concentrated at the defect residue; in the stress relaxation stage, the dislocation ring structure in the grain extends and annihilates away from the grain boundary, releasing a large amount of stress to reduce the indentation load, and then the defect structure around the indenter is stable to keep the load stable, with high stress at the defect.
{"title":"Nanoindentation simulation study on mechanical properties and microstructure evolution of twin γ-TiAl alloy","authors":"Junye Li, Jiaxu Tang, Junwei Li, Rongxian Qiu, Fujun Xiao, Xiwei Dong, Lei Zhang","doi":"10.1080/08927022.2023.2254845","DOIUrl":"https://doi.org/10.1080/08927022.2023.2254845","url":null,"abstract":"ABSTRACT\u0000 To explore the mechanical properties and deformation mechanism of twin γ-TiAl alloy under load and impact, based on the special interface structure in polycrystals, twinning at room temperature is established in this paper simulation of nanoindentation response of twin γ-TiAl alloy. Through the load-displacement curve, the hardness and Young's modulus of the workpiece are obtained. By analysing the microstructure evolution behaviour under the action of the indenter, it is found that during the loading process, multiple dislocation rings are generated in the grain and slip to the lower part of the workpiece, resulting in the hardness decreasing with the increase of the indentation depth, which is consistent with the indentation size effect; The dislocation lock generated during the unloading process delayed the annihilation of the defect structure, but the dislocation and stacking fault structure disappeared completely and the stress concentrated at the defect residue; in the stress relaxation stage, the dislocation ring structure in the grain extends and annihilates away from the grain boundary, releasing a large amount of stress to reduce the indentation load, and then the defect structure around the indenter is stable to keep the load stable, with high stress at the defect.","PeriodicalId":18863,"journal":{"name":"Molecular Simulation","volume":"39 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135981918","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
Atomistic and molecular level portrayal of DNA – 1,8-napthalimide interaction DNA - 1,8-萘酰亚胺相互作用的原子和分子水平表征
IF 2.1 4区 化学 Q4 CHEMISTRY, PHYSICAL Pub Date : 2023-09-07 DOI: 10.1080/08927022.2023.2249122
R. Radhika, R. Shankar
ABSTRACT The present work reports the physicochemical interaction between DNA and 1,8-napthalimide drugs to enlighten the field of drug discovery. Molecular dynamic studies of 1,8-napthalimide interacted DNA revealed distortions and destabilisation of the DNA. Among the drugs (Amonafide Azonafide and NNM-25), NNM-25 is found to have a strong interaction with DNA in gas and water phases by using the ONIOM method by investigating deformation and interaction energies. The reason for the higher interaction energy is attributed to the higher deformation of DNA during the interaction with NNM-25. Furthermore, the complex is investigated by the quantum chemical method to find the detailed observation of the direct Interaction of the 1,8-napthalimides with the DNA base pairs. NBO analysis is done to understand the charge transfer mechanism of 1,8-napthalimides’ interacted DNA and also it is observed that highly stabilised complexes are found to have the highest interaction energies. The density functional theory is used to calculate the chemical reactivity and site selectivity of the molecular system to explore the results that may call for further experimental studies.
摘要本文报道了DNA与1,8-萘酰亚胺类药物之间的物理化学相互作用,以期对药物发现领域有所启发。分子动力学研究1,8-萘酰亚胺相互作用的DNA揭示了DNA的扭曲和不稳定。在这些药物(Amonafide Azonafide和NNM-25)中,通过对变形和相互作用能的研究,利用ONIOM方法发现NNM-25在气相和水相与DNA有很强的相互作用。相互作用能较高的原因是DNA在与NNM-25相互作用过程中变形较大。此外,利用量子化学方法对配合物进行了研究,详细观察了1,8-萘酰亚胺与DNA碱基对的直接相互作用。通过NBO分析了解1,8-萘酰亚胺与DNA相互作用的电荷转移机制,并观察到高度稳定的配合物具有最高的相互作用能。利用密度泛函理论计算了分子体系的化学反应性和位点选择性,以探索可能需要进一步实验研究的结果。
{"title":"Atomistic and molecular level portrayal of DNA – 1,8-napthalimide interaction","authors":"R. Radhika, R. Shankar","doi":"10.1080/08927022.2023.2249122","DOIUrl":"https://doi.org/10.1080/08927022.2023.2249122","url":null,"abstract":"ABSTRACT The present work reports the physicochemical interaction between DNA and 1,8-napthalimide drugs to enlighten the field of drug discovery. Molecular dynamic studies of 1,8-napthalimide interacted DNA revealed distortions and destabilisation of the DNA. Among the drugs (Amonafide Azonafide and NNM-25), NNM-25 is found to have a strong interaction with DNA in gas and water phases by using the ONIOM method by investigating deformation and interaction energies. The reason for the higher interaction energy is attributed to the higher deformation of DNA during the interaction with NNM-25. Furthermore, the complex is investigated by the quantum chemical method to find the detailed observation of the direct Interaction of the 1,8-napthalimides with the DNA base pairs. NBO analysis is done to understand the charge transfer mechanism of 1,8-napthalimides’ interacted DNA and also it is observed that highly stabilised complexes are found to have the highest interaction energies. The density functional theory is used to calculate the chemical reactivity and site selectivity of the molecular system to explore the results that may call for further experimental studies.","PeriodicalId":18863,"journal":{"name":"Molecular Simulation","volume":"49 1","pages":"1542 - 1551"},"PeriodicalIF":2.1,"publicationDate":"2023-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45001268","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
Effect of endohedral nickel atoms on the hydrophilicity of carbon nanotubes 镍原子对碳纳米管亲水性的影响
IF 2.1 4区 化学 Q4 CHEMISTRY, PHYSICAL Pub Date : 2023-09-06 DOI: 10.1080/08927022.2023.2254393
Shakhrizoda Matnazarova, U. Khalilov, M. Yusupov
ABSTRACT Carbon nanotubes (CNTs) have been successfully used in biomedicine, including cancer therapy, due to their unique physico-chemical properties. Because pristine CNTs exhibit hydrophobic behaviour, they can have a cytotoxic effect on cells, which limits their practical use in biomedicine. The toxicity of CNTs can be reduced by adding water-soluble functional radicals to their surface, i.e. by increasing their hydrophilicity. Another possibility for increasing the hydrophilicity of CNTs is probably filling them with endohedral metal atoms, which has not yet been studied. Thus, in this study, we use computer simulations to investigate the combined effect of endohedral nickel atoms and functional groups on the hydrophilicity of CNTs. Our simulation results show that the introduction of endohedral nickel atoms into CNTs increases their binding energy with functional groups. We also find that the addition of functional groups to the surface of CNT, along with filling it with endohedral nickel atoms, leads to an increase in the dipole moment of the CNT as well as its interaction energy with water, thereby increasing the hydrophilicity of the CNT and, consequently, its solubility in water. This, in turn, can lead to a decrease in CNT toxicity.
碳纳米管(CNTs)由于其独特的物理化学性质,已成功地应用于生物医学,包括癌症治疗。由于原始碳纳米管表现出疏水行为,它们可能对细胞具有细胞毒性作用,这限制了它们在生物医学中的实际应用。通过在其表面添加水溶性功能自由基,即增加其亲水性,可以降低碳纳米管的毒性。增加碳纳米管亲水性的另一种可能性可能是在碳纳米管中填充内嵌金属原子,这一点尚未得到研究。因此,在本研究中,我们使用计算机模拟来研究内嵌镍原子和官能团对CNTs亲水性的联合影响。我们的模拟结果表明,在碳纳米管中引入内嵌镍原子增加了碳纳米管与官能团的结合能。我们还发现,在碳纳米管表面添加官能团,以及用内嵌镍原子填充碳纳米管,会增加碳纳米管的偶极矩以及与水的相互作用能,从而增加碳纳米管的亲水性,从而提高其在水中的溶解度。这反过来又可以导致碳纳米管毒性的降低。
{"title":"Effect of endohedral nickel atoms on the hydrophilicity of carbon nanotubes","authors":"Shakhrizoda Matnazarova, U. Khalilov, M. Yusupov","doi":"10.1080/08927022.2023.2254393","DOIUrl":"https://doi.org/10.1080/08927022.2023.2254393","url":null,"abstract":"ABSTRACT\u0000 Carbon nanotubes (CNTs) have been successfully used in biomedicine, including cancer therapy, due to their unique physico-chemical properties. Because pristine CNTs exhibit hydrophobic behaviour, they can have a cytotoxic effect on cells, which limits their practical use in biomedicine. The toxicity of CNTs can be reduced by adding water-soluble functional radicals to their surface, i.e. by increasing their hydrophilicity. Another possibility for increasing the hydrophilicity of CNTs is probably filling them with endohedral metal atoms, which has not yet been studied. Thus, in this study, we use computer simulations to investigate the combined effect of endohedral nickel atoms and functional groups on the hydrophilicity of CNTs. Our simulation results show that the introduction of endohedral nickel atoms into CNTs increases their binding energy with functional groups. We also find that the addition of functional groups to the surface of CNT, along with filling it with endohedral nickel atoms, leads to an increase in the dipole moment of the CNT as well as its interaction energy with water, thereby increasing the hydrophilicity of the CNT and, consequently, its solubility in water. This, in turn, can lead to a decrease in CNT toxicity.","PeriodicalId":18863,"journal":{"name":"Molecular Simulation","volume":"49 1","pages":"1575 - 1581"},"PeriodicalIF":2.1,"publicationDate":"2023-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45165737","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
期刊
Molecular Simulation
全部 Acc. Chem. Res. ACS Applied Bio Materials ACS Appl. Electron. Mater. ACS Appl. Energy Mater. ACS Appl. Mater. Interfaces ACS Appl. Nano Mater. ACS Appl. Polym. Mater. ACS BIOMATER-SCI ENG ACS Catal. ACS Cent. Sci. ACS Chem. Biol. ACS Chemical Health & Safety ACS Chem. Neurosci. ACS Comb. Sci. ACS Earth Space Chem. ACS Energy Lett. ACS Infect. Dis. ACS Macro Lett. ACS Mater. Lett. ACS Med. Chem. Lett. ACS Nano ACS Omega ACS Photonics ACS Sens. ACS Sustainable Chem. Eng. ACS Synth. Biol. Anal. Chem. BIOCHEMISTRY-US Bioconjugate Chem. BIOMACROMOLECULES Chem. Res. Toxicol. Chem. Rev. Chem. Mater. CRYST GROWTH DES ENERG FUEL Environ. Sci. Technol. Environ. Sci. Technol. Lett. Eur. J. Inorg. Chem. IND ENG CHEM RES Inorg. Chem. J. Agric. Food. Chem. J. Chem. Eng. Data J. Chem. Educ. J. Chem. Inf. Model. J. Chem. Theory Comput. J. Med. Chem. J. Nat. Prod. J PROTEOME RES J. Am. Chem. Soc. LANGMUIR MACROMOLECULES Mol. Pharmaceutics Nano Lett. Org. Lett. ORG PROCESS RES DEV ORGANOMETALLICS J. Org. Chem. J. Phys. Chem. J. Phys. Chem. A J. Phys. Chem. B J. Phys. Chem. C J. Phys. Chem. Lett. Analyst Anal. Methods Biomater. Sci. Catal. Sci. Technol. Chem. Commun. Chem. Soc. Rev. CHEM EDUC RES PRACT CRYSTENGCOMM Dalton Trans. Energy Environ. Sci. ENVIRON SCI-NANO ENVIRON SCI-PROC IMP ENVIRON SCI-WAT RES Faraday Discuss. Food Funct. Green Chem. Inorg. Chem. Front. Integr. Biol. J. Anal. At. Spectrom. J. Mater. Chem. A J. Mater. Chem. B J. Mater. Chem. C Lab Chip Mater. Chem. Front. Mater. Horiz. MEDCHEMCOMM Metallomics Mol. Biosyst. Mol. Syst. Des. Eng. Nanoscale Nanoscale Horiz. Nat. Prod. Rep. New J. Chem. Org. Biomol. Chem. Org. Chem. Front. PHOTOCH PHOTOBIO SCI PCCP Polym. Chem.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术
文献互助 智能选刊 最新文献 互助须知 联系我们:info@booksci.cn
Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。
Copyright © 2023 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1