Journal of molecular graphics & modelling最新文献_第10页

First-principles calculation on electronic properties of hydrogen evolution reaction of Ni-based electrode surfaces with different monatomic doping 不同单原子掺杂的镍基电极表面氢进化反应电子特性的第一性原理计算。

IF 2.9 4区生物学

Journal of molecular graphics & modelling Pub Date : 2024-05-10 DOI: 10.1016/j.jmgm.2024.108790

Jianping Zeng , Yan Zhang , Shuyu Zeng , Jingwen Li , Yuchen Fang , Ling Qian , Luobu Pubu , Song Chen

{"title":"First-principles calculation on electronic properties of hydrogen evolution reaction of Ni-based electrode surfaces with different monatomic doping","authors":"Jianping Zeng , Yan Zhang , Shuyu Zeng , Jingwen Li , Yuchen Fang , Ling Qian , Luobu Pubu , Song Chen","doi":"10.1016/j.jmgm.2024.108790","DOIUrl":"10.1016/j.jmgm.2024.108790","url":null,"abstract":"<div><p>At present, the hydrogen evolution reaction (HER) of Ni-based electrode has an important influence on water electrolysis hydrogen production technology, involving complex electrochemical process of electrode. In this project, Materials Studio (MS) software was used to design and construct Ni-based electrode surface (NES) models with monatomic Mo, Co, Fe, Cr doping, and the NES models attached 1 H atom and 2H atoms were denoted as the NES-H models and NES-2H model, respectively. Then the first-principles calculation was carried out.</p><p>The results showed that the doping of different atoms can effectively change the work function of the pure Ni. In the charge transfer process of the four NES-2H models, the distance between the two H atoms is most affected by Mo doping, and they leave the Ni electrode surface as a single H ion, respectively, while the effect on Co, Fe and Cr doping is relatively consistent, and they leave the Ni electrode surface with H<sub>2</sub> molecules, respectively. The doping of four single atoms changes the distance of valence band (VB) top and conduction band (CB) bottom from Fermi level in NES, NES-H and NES-2H models, and affects the HER, in which Mo doping has the greatest effect. The TDOS of the above models is mainly derived from the PDOS of the d orbitals of the doped atoms and Ni atoms. The results will provide a theoretical basis for the research and development of Ni-based electrode materials in HER.</p></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"130 ","pages":"Article 108790"},"PeriodicalIF":2.9,"publicationDate":"2024-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140945302","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","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 modelling of ciprofloxacin specific aptamer for the development of high-performance biosensor 为开发高性能生物传感器建立环丙沙星特异性适配体的硅学模型

IF 2.9 4区生物学

Journal of molecular graphics & modelling Pub Date : 2024-05-05 DOI: 10.1016/j.jmgm.2024.108787

Misgana Mengistu Asmare , Chandran Krishnaraj , Sivaprakasam Radhakrishnan , Byoung-Sukh Kim , June-Sun Yoon , Soon-Il Yun

{"title":"In silico modelling of ciprofloxacin specific aptamer for the development of high-performance biosensor","authors":"Misgana Mengistu Asmare , Chandran Krishnaraj , Sivaprakasam Radhakrishnan , Byoung-Sukh Kim , June-Sun Yoon , Soon-Il Yun","doi":"10.1016/j.jmgm.2024.108787","DOIUrl":"https://doi.org/10.1016/j.jmgm.2024.108787","url":null,"abstract":"<div><p>Ciprofloxacin (CFX), a widely used fluoroquinolone antibiotic, is critical in healthcare settings for treating patients. However, improper treatment of wastewater from these facilities can lead to environmental contamination with CFX. This underscores the need for an efficient, straightforward method for early detection. In this study, a DNA aptamer was selected through a hierarchical docking workflow, and the stability and interactions were assessed by Molecular Dynamics (MD) simulation. The aptamer-CFX complex that showed the most promise had a docking score of −8.596 kcal/mol and was further analyzed using MD simulation and MM/PBSA. Based on the overall results, the identified ssDNA sequence length of 60 nt (CAGCGCTAGGGCTTTTAGCGTAATGGGTAGGGTGGTGCGGTGCAGATATCGGAATTGGTG) was immobilized over a gold transducer surface through the self-assembled monolayer (SAM; Au–S-ssDNA) method. The ssDNA-modified surface has demonstrated a high affinity towards CFX, which is confirmed by cyclic voltammogram (CV) and electrochemical impedance spectroscopy measurements (EIS). The DNA-aptamer modified electrode demonstrated a good linear range (10 × 10<sup>−9</sup> – 200 × 10<sup>−9</sup> M), detection limit (1.0 × 10<sup>−9</sup> M), selectivity, reproducibility, and stability. The optimized DNA-aptamer-based CFX sensor was further utilized for the accurate determination of CFX with good recoveries in real samples.</p></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"130 ","pages":"Article 108787"},"PeriodicalIF":2.9,"publicationDate":"2024-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140917915","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Computational insights into allosteric inhibition of focal adhesion kinase: A combined pharmacophore modeling and molecular dynamics approach 通过计算深入了解病灶粘附激酶的异位抑制作用：药效学建模与分子动力学相结合的方法

IF 2.9 4区生物学

Journal of molecular graphics & modelling Pub Date : 2024-05-04 DOI: 10.1016/j.jmgm.2024.108789

Vikas Kumar , Pooja Singh , Shraddha Parate , Rajender Singh , Hyeon-Su Ro , Kyoung Seob Song , Keun Woo Lee , Yeong-Min Park

{"title":"Computational insights into allosteric inhibition of focal adhesion kinase: A combined pharmacophore modeling and molecular dynamics approach","authors":"Vikas Kumar , Pooja Singh , Shraddha Parate , Rajender Singh , Hyeon-Su Ro , Kyoung Seob Song , Keun Woo Lee , Yeong-Min Park","doi":"10.1016/j.jmgm.2024.108789","DOIUrl":"https://doi.org/10.1016/j.jmgm.2024.108789","url":null,"abstract":"<div><p>Focal adhesion kinase (FAK) is a non-receptor tyrosine kinase that modulates integrin and growth factor signaling pathways and is implicated in cancer cell migration, proliferation, and survival. Over the past decade various, FAK kinase, FERM, and FAT domain inhibitors have been reported and a few kinase domain inhibitors are under clinical consideration. However, few of them were identified as multikinase inhibitors. In kinase drug design selectivity is always a point of concern, to improve selectivity allosteric inhibitor development is the best choice. The current research utilized a pharmacophore modeling (PM) approach to identify novel allosteric inhibitors of FAK. The all-available allosteric inhibitor bound 3D structures with PDB ids 4EBV, 4EBW, and 4I4F were utilized for the pharmacophore modeling. The validated PM models were utilized to map a database of 770,550 compounds prepared from ZINC, EXIMED, SPECS, ASINEX, and InterBioScreen, aiming to identify potential allosteric inhibitors. The obtained compounds from screening step were forwarded to molecular docking (MD) for the prediction of binding orientation inside the allosteric site and the results were evaluated with the known FAK allosteric inhibitor (REF). Finally, 14 FAK-inhibitor complexes were selected from the docking study and were studied under molecular dynamics simulations (MDS) for 500 ns. The complexes were ranked according to binding free energy (BFE) and those demonstrated higher affinity for allosteric site of FAK than REF inhibitors were selected. The selected complexes were further analyzed for intermolecular interactions and finally, three potential allosteric inhibitor candidates for the inhibition of FAK protein were identified. We believe that identified scaffolds may help in drug development against FAK as an anticancer agent.</p></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"130 ","pages":"Article 108789"},"PeriodicalIF":2.9,"publicationDate":"2024-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140878989","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Wettability behavior of DTMS modified SiO2: Experimental and molecular dynamics study DTMS 改性二氧化硅的润湿行为：实验和分子动力学研究

IF 2.9 4区生物学

Journal of molecular graphics & modelling Pub Date : 2024-05-02 DOI: 10.1016/j.jmgm.2024.108786

Chen-Xiang Wang , Ning Wang , Xu-Sheng Li , Xue-Fen Zhang

{"title":"Wettability behavior of DTMS modified SiO2: Experimental and molecular dynamics study","authors":"Chen-Xiang Wang , Ning Wang , Xu-Sheng Li , Xue-Fen Zhang","doi":"10.1016/j.jmgm.2024.108786","DOIUrl":"https://doi.org/10.1016/j.jmgm.2024.108786","url":null,"abstract":"<div><p>In this research, the wetting behavior of SiO<sub>2</sub> modified with dodecyltrimethoxysilane (DTMS) was explored using both experimental and molecular dynamics (MD) simulation approaches. The experimental results reveal that DTMS can chemically bond to the SiO<sub>2</sub> surface, and the contact angle (CA) reaches the maximum value of 157.7° when the mass of DTMS is twice that of SiO<sub>2</sub>. The different wetting behaviors caused by DTMS grafting were analyzed by CA fitting, ionic pairs, concentration distribution, molecule orientation, and interfacial interaction energy. The results demonstrate that a 25 % DTMS grafting rate resulted in a maximum CA of 158.2°, which is ascribed to the disruption of interfacial hydrogen bonding and changes in the hydration structure caused by DTMS grafting. Moreover, the above hydrophobic SiO<sub>2</sub> model shows a slight decrease in CA as the water temperature increases, which is consistent with the experimental findings. In contrast, an opposite change was observed for the pristine SiO<sub>2</sub> model. Although the higher water temperature enhances the diffusion capacity of water molecules in both models, the difference in interfacial interactions is responsible for the change in CA. We hope this finding will contribute to a deeper understanding of the wetting adjustment of SiO<sub>2</sub>.</p></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"130 ","pages":"Article 108786"},"PeriodicalIF":2.9,"publicationDate":"2024-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140825355","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Aptamer biosensor design for the detection of endocrine-disrupting chemicals small organic molecules using novel bioinformatics methods 利用新型生物信息学方法设计用于检测干扰内分泌的化学物质和小分子有机物的 Aptamer 生物传感器

IF 2.9 4区生物学

Journal of molecular graphics & modelling Pub Date : 2024-05-02 DOI: 10.1016/j.jmgm.2024.108785

Imren Bayıl , Md. Sarowar Hossain , Sonia Tamanna , Md Jamir Uddin , F.M. Mashood Ahamed , Yousef A. Bin Jardan , Mohammed Bourhia , Tugba Taskin Tok

{"title":"Aptamer biosensor design for the detection of endocrine-disrupting chemicals small organic molecules using novel bioinformatics methods","authors":"Imren Bayıl , Md. Sarowar Hossain , Sonia Tamanna , Md Jamir Uddin , F.M. Mashood Ahamed , Yousef A. Bin Jardan , Mohammed Bourhia , Tugba Taskin Tok","doi":"10.1016/j.jmgm.2024.108785","DOIUrl":"10.1016/j.jmgm.2024.108785","url":null,"abstract":"<div><p>Endocrine-disrupting chemicals (EDCs) are substances that can disrupt the normal functioning of hormones.Using aptamers, which are biological recognition elements, biosensors can quickly and accurately detect EDCs in environmental samples. However, the elucidation of aptamer structures by conventional methods is highly challenging due to their complexity.</p><p>This has led to the development of three-dimensional aptamer structures based on different models and techniques. To do this, we developed a way to predict the 3D structures of the SS DNA needed for this sequence by starting with an aptamer sequence that has biosensor properties specific to bisphenol-A (BPA), one of the chemicals found in water samples that can interfere with hormones. In addition, we will elucidate the intermolecular mechanisms and binding affinity between aptamers and endocrine disruptors using bioinformatics techniques such as molecular docking, molecular dynamics simulation, and binding energies. The outcomes of our study are to compare modeling programs and force fields to see how reliable they are and how well they agree with results found in the existing literature, to understand the intermolecular mechanisms and affinity of aptamer-based biosensors, and to find a new way to make aptamers that takes less time and costs less.</p></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"131 ","pages":"Article 108785"},"PeriodicalIF":2.9,"publicationDate":"2024-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141047504","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Interaction between hydroxymethanesulfonic acid and several organic compounds and its atmospheric significance 羟甲基磺酸与几种有机化合物的相互作用及其对大气的意义

IF 2.9 4区生物学

Journal of molecular graphics & modelling Pub Date : 2024-04-26 DOI: 10.1016/j.jmgm.2024.108782

Dong-Ping Chen , Wen Ma , Chun-Hong Yang, Ming Li, Zhao-Zhen Zhou, Yang Zhang, Zheng-Jun Quan

{"title":"Interaction between hydroxymethanesulfonic acid and several organic compounds and its atmospheric significance","authors":"Dong-Ping Chen , Wen Ma , Chun-Hong Yang, Ming Li, Zhao-Zhen Zhou, Yang Zhang, Zheng-Jun Quan","doi":"10.1016/j.jmgm.2024.108782","DOIUrl":"https://doi.org/10.1016/j.jmgm.2024.108782","url":null,"abstract":"<div><p>The interactions of the micro-mechanism of hydroxymethanesulfonic acid (HMSA) with the typical small organic molecule in atmospheric (X = methanol, formaldehyde, formic acid, methyl formate, dimethyl ether, acetone) has been investigated by density functional theory (DFT), quantum theory of atoms in molecules (QTAIM), Generalized Kohn-Sham Enery Decomposition Analysis (GKS−EDA) and the atmospheric clusters dynamic code (ACDC). The results of DFT show that the stable six− to eight−membered ring structures are easily formed in HMSA−X clusters. According to the topological analysis results of the AIM theory and the IRI method, a strong hydrogen bonding interaction is present in the complex. GKS−EDA results show that electrostatic energy is the main contributor to the interaction energy as it accounts for 51 %–55 % of the total attraction energy. The evaporation rates of HMSA−HMSA and HMSA−HCOOH clusters were much lower than those of the other HMSA complexes. In addition, the Gibbs energy of formation (Δ<em>G</em>) of HMSA−X dimers is investigated under atmosphere temperature <em>T</em> = 217–298 K and <em>p</em> = 0.19–1.0 atm, the Δ<em>G</em> decreased with decreasing of the atmosphere temperature and increased with the decrease of atmospheric pressure, indicating that the low temperature and high pressure may significantly facilitate to the formation of dimers.</p></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"130 ","pages":"Article 108782"},"PeriodicalIF":2.9,"publicationDate":"2024-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140807453","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","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 simulations of choline chloride and ascorbic acid deep eutectic solvents: Investigation of structural and dynamics properties 氯化胆碱和抗坏血酸深度共晶溶剂的分子动力学模拟：结构和动力学特性研究

IF 2.9 4区生物学

Journal of molecular graphics & modelling Pub Date : 2024-04-26 DOI: 10.1016/j.jmgm.2024.108784

Kexin Cheng, Xuchen Xu, Jilun Song, Yu Chen, Zigui Kan, Caolong Li

{"title":"Molecular dynamics simulations of choline chloride and ascorbic acid deep eutectic solvents: Investigation of structural and dynamics properties","authors":"Kexin Cheng, Xuchen Xu, Jilun Song, Yu Chen, Zigui Kan, Caolong Li","doi":"10.1016/j.jmgm.2024.108784","DOIUrl":"https://doi.org/10.1016/j.jmgm.2024.108784","url":null,"abstract":"<div><p>Deep eutectic solvents (DESs) composed of choline chloride (ChCl) and ascorbic acid (AA) were investigated using the molecular dynamics (MD) simulations. The analyses of the configuration, radial distribution function (RDFs), coordination number, spatial distribution function (SDFs), interaction energies, hydrogen bond number, and self-diffusion coefficient of the ChCl/AA binary systems of different concentrations showed that the stability of the hydrogen bond network and the mutual attraction between systems were the strongest at the experimental eutectic concentration (molar ratio of 2:1). In our simulated temperature range from 303.15 to 353.15 K, the hydrogen bonding network of ChCl/AA DES does not undergo considerable alterations, indicating that its stability was insensitive to temperature. In addition, the influence of the water content on the ChCl/AA DES system was further investigated. The simulated results revealed that the water molecules could disrupt the formation of the hydrogen bonding network by occupyin positions that are essential for the formation of hydrogen bonds within the DES system.</p></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"130 ","pages":"Article 108784"},"PeriodicalIF":2.9,"publicationDate":"2024-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140815747","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Atomistic understanding of Ti3C2 MXene membrane performance for separation of nitrate ions from aqueous solutions 从原子论角度理解从水溶液中分离硝酸根离子的 Ti3C2 MXene 膜性能

IF 2.9 4区生物学

Journal of molecular graphics & modelling Pub Date : 2024-04-25 DOI: 10.1016/j.jmgm.2024.108781

Zahra Tavakkoli , Peyman Mohammad Valizadeh Maleki , Jafar Azamat , Esmaeil Zaminpayma , Hamid Erfan-Niya

{"title":"Atomistic understanding of Ti3C2 MXene membrane performance for separation of nitrate ions from aqueous solutions","authors":"Zahra Tavakkoli , Peyman Mohammad Valizadeh Maleki , Jafar Azamat , Esmaeil Zaminpayma , Hamid Erfan-Niya","doi":"10.1016/j.jmgm.2024.108781","DOIUrl":"10.1016/j.jmgm.2024.108781","url":null,"abstract":"<div><p>Water desalination, which is a reliable method for providing drinking water and a suitable solution, as well as the membrane filtration method in wastewater treatment, has increased significantly in recent years. In this research, the separation of nitrite and nitrate ions from aqueous solutions was done using the MXene membrane of the Ti<sub>3</sub>C<sub>2</sub> type using molecular dynamics simulation. In this study, various parameters, such as pore size MXene structure, characteristics of cavities, applied pressure, and flux were investigated. To investigate the removal of toxic pollutants from water, water flux, potential mean force, distribution of water molecules, and density were investigated. The results showed that the amount of penetration through the membrane increased with the increase in pressure. It was observed that by applying pressure to the system, the number of water molecules accumulated in front of the membrane decreases because they quickly pass through the membrane, which indicates the positive effect of increasing pressure on the separation rate of molecules. The permeability of this membrane was several times higher than the existing membranes in the industry. So that Mexene membranes, which consist of at least two layers, can repel ions with 100 % success.</p></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"130 ","pages":"Article 108781"},"PeriodicalIF":2.9,"publicationDate":"2024-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140762007","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

DRTerHGAT: A drug repurposing method based on the ternary heterogeneous graph attention network DRTerHGAT：基于三元异质图注意网络的药物再利用方法

IF 2.9 4区生物学

Journal of molecular graphics & modelling Pub Date : 2024-04-24 DOI: 10.1016/j.jmgm.2024.108783

Hongjian He , Jiang Xie , Dingkai Huang , Mengfei Zhang , Xuyu Zhao , Yiwei Ying , Jiao Wang

{"title":"DRTerHGAT: A drug repurposing method based on the ternary heterogeneous graph attention network","authors":"Hongjian He , Jiang Xie , Dingkai Huang , Mengfei Zhang , Xuyu Zhao , Yiwei Ying , Jiao Wang","doi":"10.1016/j.jmgm.2024.108783","DOIUrl":"https://doi.org/10.1016/j.jmgm.2024.108783","url":null,"abstract":"<div><p>Drug repurposing is an effective method to reduce the time and cost of drug development. Computational drug repurposing can quickly screen out the most likely associations from large biological databases to achieve effective drug repurposing. However, building a comprehensive model that integrates drugs, proteins, and diseases for drug repurposing remains challenging. This study proposes a drug repurposing method based on the ternary heterogeneous graph attention network (DRTerHGAT). DRTerHGAT designs a novel protein feature extraction process consisting of a large-scale protein language model and a multi-task autoencoder, so that protein features can be extracted accurately and efficiently from amino acid sequences. The ternary heterogeneous graph of drug-protein-disease comprehensively considering the relationships among the three types of nodes, including three homogeneous and three heterogeneous relationships. Based on the graph and the extracted protein features, the deep features of the drugs and the diseases are extracted by graph convolutional networks (GCN) and heterogeneous graph node attention networks (HGNA). In the experiments, DRTerHGAT is proven superior to existing advanced methods and DRTerHGAT variants. DRTerHGAT's powerful ability for drug repurposing is also demonstrated in Alzheimer's disease.</p></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"130 ","pages":"Article 108783"},"PeriodicalIF":2.9,"publicationDate":"2024-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140649246","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Mechanistic studies of adsorption and ion exchange of Si(OH)4 molecules on the surface of scorodites 蝎石表面 Si(OH)4 分子的吸附和离子交换机理研究

IF 2.9 4区生物学

Journal of molecular graphics & modelling Pub Date : 2024-04-22 DOI: 10.1016/j.jmgm.2024.108779

Manjiao Chen , Wang Guo , Xinjun Hu , Jianping Tian

{"title":"Mechanistic studies of adsorption and ion exchange of Si(OH)4 molecules on the surface of scorodites","authors":"Manjiao Chen , Wang Guo , Xinjun Hu , Jianping Tian","doi":"10.1016/j.jmgm.2024.108779","DOIUrl":"https://doi.org/10.1016/j.jmgm.2024.108779","url":null,"abstract":"<div><p>Scorodites are commonly used for arsenic immobilization, and it is also the main component of arsenic bearing tailings. Alkali-activated geopolymers are commonly used to landfill arsenic-bearing minerals. However, there no previous studies have explored the interaction between geopolymer molecules and the surface of scorodite. In this paper, Si(OH)<sub>4</sub> as a monomer molecule of geopolymer, the mechanism of adsorption and ‘ion exchange’ between Si(OH)<sub>4</sub> molecule and the surface of scorodite during alkali-activation is studied. Results show that the Fe-terminated scorodite (010) surface has high stability. Si(OH)<sub>4</sub> are more easily adsorbed on the hollow site of an Fe-terminated scorodite (010) surface, which is described as chemisorption. Compared with Si(OH)<sub>4</sub>, NaOH is easier to adsorb on an Fe-terminated scorodite (010) surface. The co-adsorption of NaOH and Si(OH)<sub>4</sub> on the Fe-terminated scorodite (010) surface was studied, and also belongs to chemical adsorption. When the hydroxyl binds to the As atom, the adsorbed Si(OH)<sub>4</sub> is more likely to undergo an ‘ion exchange’ reaction with the surface, and the reaction is barrierless. The intermediate As(OH)<sub>4</sub> produced by the ‘ion exchange’ reaction can be deprotonated to form an arsenate molecule, which can occur spontaneously. This work reveals that the interaction mechanism of geopolymer molecules on surface of scorodite.</p></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"130 ","pages":"Article 108779"},"PeriodicalIF":2.9,"publicationDate":"2024-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140638416","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0