{"title":"Exploring phytochemicals and marine natural products as alternative therapeutic agents targeting phosphotransacetylase (PTA) in Mycobacterium tuberculosis: An underexplored drug target","authors":"Sneha Subramaniyan, Manikandan Jayaraman, Jeyakanthan Jeyaraman","doi":"10.1016/j.jmgm.2025.109025","DOIUrl":"10.1016/j.jmgm.2025.109025","url":null,"abstract":"<div><div>Tuberculosis (TB), caused by <em>Mycobacterium tuberculosis</em> (MTB), remains a significant global health threat due to its widespread prevalence and increasing drug resistance. This study targets phosphotransacetylase (PTA), an essential enzyme in acetate metabolism, as a potential therapeutic target. A comprehensive multi-tiered virtual screening approach was employed to identify potent phytochemicals and marine natural products (MNPs) from five databases (AMMPDB, CMNPD, MNPD, Seaweed and SPECS). Five promising bioactive molecules (AMMPDB10473, CMNPD23347, CMNPD5918, MNPD6660, and SPECS-AK-693) were identified, showing high docking scores (−8.17 to −10.83 kcal/mol) and MM-GBSA binding energy scores (−47.51 to −59.14 kcal/mol). These molecules adhered to Lipinski's rule of five (Ro5) and demonstrated acceptable pharmacokinetic profiles. Density functional theory (DFT) calculations further validated the interaction potential of these molecules through HOMO and LUMO analysis. Long-range molecular dynamics simulations (MDS) over 300 ns confirmed the structural stability and enhanced hydrogen-bonding potential of the natural products-PTA complexes. Principal component analysis (PCA) and free energy landscape (FEL) contour plots revealed a single dominant energy basin, indicating structural stability and limited conformational flexibility of the complexes. Additionally, MMPBSA analysis corroborated the strong binding affinities of the identified hit molecules with PTA. Critical <strong>'hot spot'</strong> residues (Phe516, Cys530, Ala531, and Tyr639) were identified, contributing significantly to the structural stability and binding energy of the complexes. This computational study offers valuable insights into the potential of these lead molecules for combating TB, providing a foundation for experimental validation and innovative therapeutic development, and paving the way for future research and breakthroughs in TB treatment.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"138 ","pages":"Article 109025"},"PeriodicalIF":2.7,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143680349","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}
{"title":"Noncovalent guest-host interactions unlock the potential of MOFs for anesthetic xenon recovery: GCMC and DFT insights into real anesthetic conditions","authors":"Tuğçe Gökdemir, Yeliz Gurdal","doi":"10.1016/j.jmgm.2025.109015","DOIUrl":"10.1016/j.jmgm.2025.109015","url":null,"abstract":"<div><div>Innovative designs offering cost-effective and highly efficient methods for xenon (Xe) recovery are becoming important for developing sustainable applications. Recently, the use of metal–organic frameworks (MOFs) has shown promise as candidates for separating Xe from anesthetic gas mixtures, however, there are limited studies available. We conducted combined Grand Canonical Monte Carlo (GCMC) and Density Functional Theory (DFT) simulations to determine the Xe recovery capacities of 19 MOFs from the exhaled anesthetic gas mixture, Xe/CO<span><math><msub><mrow></mrow><mrow><mn>2</mn></mrow></msub></math></span>/O<span><math><msub><mrow></mrow><mrow><mn>2</mn></mrow></msub></math></span>/N<span><math><msub><mrow></mrow><mrow><mn>2</mn></mrow></msub></math></span>. COCMUE, GUHMIH, MAHCOQ, and PADKOK have demonstrated overall larger volumetric and gravimetric Xe uptake, demonstrating how ligand types can enhance selective Xe adsorption in MOFs. At low pressures, Xe atoms mainly adsorbed in close vicinity to the ligands, with tetrazole, phenyl, pyridyl, carboxamide, dicarboxylic acid, phenoxazine, and triazole ligands in the MOF structures acting as Xe trapping locations. Electronic structure analyses reveal that Xe-host interactions are primarily driven by charge-induced dipole and aerogen–<span><math><mi>π</mi></math></span> interactions. Our combined GCMC and DFT study shows that a relatively high amount of anesthetic Xe can be captured from real anesthetic exhale gas mixtures using MOFs with the proper chemical and geometrical characteristics. These characteristics maximize noncovalent Xe-host interactions and ultimately enable the utilization of Xe as an anesthetic gas in clinical applications.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"138 ","pages":"Article 109015"},"PeriodicalIF":2.7,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143680354","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}
Amit Dubey , Hamad A. Al-Lohedan , Mohd Sajid Ali , Andrea Ragusa
{"title":"Integrative in silico analysis to explore the potential of Zingiberaceae compounds to inhibit estrogen receptor alpha activity in breast cancer","authors":"Amit Dubey , Hamad A. Al-Lohedan , Mohd Sajid Ali , Andrea Ragusa","doi":"10.1016/j.jmgm.2025.109023","DOIUrl":"10.1016/j.jmgm.2025.109023","url":null,"abstract":"<div><div>The estrogen receptor alpha (ERα) is a critical player in breast cancer progression, making it a key target for therapeutic development. This study employed an advanced computational method to discover potential inhibitors of ERα from a library of compounds from the Zingiberaceae family. The workflow includes virtual screening, re-docking, molecular dynamics (MD) simulations, radius of gyration (RG), and root mean-square deviation (RMSD)-based free energy landscape (FEL) analysis. This multifaceted strategy led to the selection of four compounds with superior docking scores compared to established control molecules. The MD simulation assessments confirmed that these selected compounds exhibited robust stability and favorable binding interactions within the ERα binding pocket. Notably, the pocket volume analysis of the minimum energy structures obtained from FEL analysis indicated a significant reduction in volume compared to the initial docking poses, suggesting a more compact and potentially more effective binding conformation. These findings highlight the potential of Zingiberaceae family-derived compounds as promising candidates for ERα inhibition. The stability of these interactions and the observed compactness of the binding pocket, as demonstrated by our comprehensive computational analysis, underscore the potential of these compounds for further preclinical evaluation.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"138 ","pages":"Article 109023"},"PeriodicalIF":2.7,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143705180","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}
{"title":"Exploring the catalytic performance of ligand-functionalized Cu-BTC paddlewheels in carboxylative cyclization of propargyl alcohol with CO2: DFT and SISSO insights","authors":"Jakkapan Sirijaraensre","doi":"10.1016/j.jmgm.2025.109022","DOIUrl":"10.1016/j.jmgm.2025.109022","url":null,"abstract":"<div><div>The M06-L functional with the 6-31G(d,p) and SDD ECP basis sets, was used to investigate the structure and electronic properties of defective linker-coordinated paddlewheel complexes (Cu-BTC(L1–L4)) in the catalytic conversion of propargyl alcohol (PA) and CO<sub>2</sub> into cyclic carbonate. Two catalytic processes are proposed based on the different PA adsorption modes at the Cu center. The reaction proceeds via adsorption by the hydroxyl group in two sequential steps: PA/CO<sub>2</sub> activation and cyclization. This pathway is proposed as the dominant process in the Cu-BTC and Cu-BTC(L1–L3) systems. However, only Cu-BTC(L3) and Cu-BTC(L4), which exhibit stronger electron back-donation compared to the other systems, effectively promote the catalytic process via PA adsorption through its alkyne bond. In this latter mode, the reaction proceeds through three consecutive steps: PA/CO<sub>2</sub> activation, ring closure, and H-transfer. Compared to pristine Cu-BTC, Cu-BTC(L3) and Cu-BTC(L4) are proposed as more efficient catalysts for the carboxylative cycloaddition of CO<sub>2</sub> with PA. The rate-determining step for the reaction on these two systems is the PA/CO<sub>2</sub> activation via the latter mechanism. This step has an activation free energy of 16.7 kcal/mol and 15.0 kcal/mol for the Cu-BTC(L3) and Cu-BTC(L4). The SISSO model reveals the role of the Cu center in activating PA and stabilizing the generated intermediate, thereby lowering the activation free energy for PA/CO<sub>2</sub> activation.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"138 ","pages":"Article 109022"},"PeriodicalIF":2.7,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143680353","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}
{"title":"Molecular property prediction based on graph contrastive learning with partial feature masking","authors":"Kunjie Dong, Xiaohui Lin, Yanhui Zhang","doi":"10.1016/j.jmgm.2025.109014","DOIUrl":"10.1016/j.jmgm.2025.109014","url":null,"abstract":"<div><div>Molecular representation learning facilitates multiple downstream tasks such as molecular property prediction (MPP) and drug design. Recent studies have shown great promise in applying self-supervised learning (SSL) to cope with the data scarcity in MPP. Contrastive learning (CL) is a typical SSL method used to learn prior knowledge so that the trained model has better generalization performance on various downstream tasks. One important issue of CL is how to generate enhanced samples that preserve the molecular core semantics for each training sample, which may significantly impact the earnings of the CL strategy. To address this issue, we propose the partial <u>F</u>eature <u>M</u>asking-based molecular <u>G</u>raph <u>C</u>ontrastive <u>L</u>earning model (FMGCL). FMGCL constructs the masked molecular graph by masking partial features of each atom and bond in the featured molecular graph. Since the masking molecular graphs preserve the chemical structure of the molecules, they do not violate the chemical semantics of molecules, which is beneficial for capturing valuable prior knowledge of molecules during pre-training. Then, FMGCL fine-tunes the well-trained encoder on the featured molecular graph for downstream tasks. Moreover, we propose using the relative distance between samples within a batch to enhance the performance in regression tasks. Experiments on the 12 benchmark datasets from MoleculeNet and ChEMBL showed the superiority of FMGCL.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"138 ","pages":"Article 109014"},"PeriodicalIF":2.7,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143680351","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}
Shoaib Khan , Mujaddad Ur Rehman , Tayyiaba Iqbal , Zanib Fiaz , Parham Taslimi , Hany W. Darwish , Muhammad Adnan
{"title":"Experimental and computational analysis of benzothiophene as a selective inhibitors of diabetes mellitus","authors":"Shoaib Khan , Mujaddad Ur Rehman , Tayyiaba Iqbal , Zanib Fiaz , Parham Taslimi , Hany W. Darwish , Muhammad Adnan","doi":"10.1016/j.jmgm.2025.109010","DOIUrl":"10.1016/j.jmgm.2025.109010","url":null,"abstract":"<div><div>Diabetes mellitus results in chronic hyperglycemia, affecting more than one hundred million people over the world. To treat diabetes mellitus, novel benzothiophene-derived thiadiazole analogues <strong>(1-17)</strong> were synthesized to biological assess their potential as lead inhibitors of both diabetic enzymes (α-amylase and α-glucosidase). These compounds showed quite remarkable potency against both enzymes and emerged as anti-diabetic agents. As a reference for their biological assessment, acarbose (<strong>5.90 ± 0.30</strong> μM, <strong>6.50 ± 1.80</strong> μM) were used and in comparison to it analogue <strong>3 having IC<sub>50</sub> of 4.20 ± 0.50 μM, 4.90 ± 1.50 μM</strong>, <strong>6 with IC<sub>50</sub> of 3.10 ± 1.20 μM, 4.10 ± 0.80 μM</strong>, <strong>10</strong> with <strong>IC<sub>50</sub> of 5.20 ± 1.20 μM, 6.10 ± 2.10 μM</strong> and <strong>16 having IC<sub>50</sub> of 3.90 ± 2.20 μM, 4.10 ± 1.20 μM</strong> emerged as most active analogues among the synthesized derivatives. Versatile attached functionalities such as CF<sub>3</sub>, F, OH and Cl bind with the target proteins in order to inhibit their normal activity or function. Binding potency (interactive properties) of the leading compounds was also revealed under molecular docking. ADME analysis further unveiled that the potent compounds exhibit drug properties. Moreover, reactivity of these analogues with leading potential was also explored via density functional theory (DFT), revealing their molecular electrostatic potential, electrophilic, nucleophilic, HOMO and LUMO sites.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"138 ","pages":"Article 109010"},"PeriodicalIF":2.7,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143714503","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}
Azhar Iqbal , Muhammad Sajid , Guendouzi Abdelkrim , Ammara Riaz , Umar Farooq , Shabana Bibi , Ghadeer M. Albadrani , Muath Q. Al-Ghadi , Amany A. Sayed , Mohamed M. Abdel-Daim
{"title":"Targeting OPA1 protein for therapeutic intervention in autosomal dominant optic atrophy: In silico drug discovery","authors":"Azhar Iqbal , Muhammad Sajid , Guendouzi Abdelkrim , Ammara Riaz , Umar Farooq , Shabana Bibi , Ghadeer M. Albadrani , Muath Q. Al-Ghadi , Amany A. Sayed , Mohamed M. Abdel-Daim","doi":"10.1016/j.jmgm.2025.109013","DOIUrl":"10.1016/j.jmgm.2025.109013","url":null,"abstract":"<div><div>Autosomal dominant hereditary optic atrophy (ADOA) is a prevalent hereditary condition characterized by the gradual and simultaneous deterioration of vision. Mutations in Optic atrophy 1 (<em>OPA1</em>) have been linked to ADOA, the prevailing form of inherited optic neuropathy. However, the current therapeutic options are limited. This study aimed to identify a drug-like molecule that can serve as an activator of the <em>OPA1</em> GTPase domain, using in silico virtual screening and molecular dynamic simulation pipeline. A ligand-based pharmacophore model was generated to identify the important biological entities in natural compounds, followed by virtual screening pipeline. Total 55,96,00 drug-like compounds were screened and then subsequently proceed for molecular docking, molecular dynamics simulation (200ns), MM-PBSA analysis, and ADMET (Swiss ADME server) studies. Virtual screening revealed the top-ranked compound ZINC000009190697 (−8 kcal/mol). Furthermore, the stability of the top hit compound at the active site of <em>OPA1</em> was demonstrated using molecular dynamics simulations and MM-PBSA calculations. ADMET analysis assisted in the identification of the top hit compound as possible activators of <em>OPA1</em> with optimal drug-like properties. These results indicated that there is need of further experimental assessment of the top-hit compound ZINC000009190697 in wet lab to confirm its efficacy as a potential <em>OPA1</em> activator in both in vitro and in vivo studies.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"138 ","pages":"Article 109013"},"PeriodicalIF":2.7,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143680350","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}
Blanca Alicia Guardado Villegas , Roberto García Carrillo , Nora Aleyda García , Paul Horley , Mario Sánchez
{"title":"Hydrogen storage in graphitic carbon nitride coordinated with boron clusters: A DFT study","authors":"Blanca Alicia Guardado Villegas , Roberto García Carrillo , Nora Aleyda García , Paul Horley , Mario Sánchez","doi":"10.1016/j.jmgm.2025.109021","DOIUrl":"10.1016/j.jmgm.2025.109021","url":null,"abstract":"<div><div>The search for novel materials capable of adsorbing molecular hydrogen is of great interest due to the urgent need to replace polluting fossil fuels with clean energy sources. This study evaluates the adsorption of hydrogen molecules using computational methods, specifically density functional theory (M06-2X) combined with the def2-TZVP basis set, in complexes formed with graphitic carbon nitride, gC<sub>3</sub>N<sub>4</sub>, and boron clusters (B<sub>n</sub>, n = 1–6). The average adsorption energy values for the B–H<sub>2</sub> interactions range from −0.11 to −0.08 eV. To assess the spontaneity of these adsorption processes, Gibbs free energies were calculated for the temperatures 50–400 K. The results indicate that gC<sub>3</sub>N<sub>4</sub>B<sub>n</sub> complexes can adsorb from 2 to 7 hydrogen molecules. Calculations confirm that adsorption remains spontaneous across the temperature range studied, which makes the gC<sub>3</sub>N<sub>4</sub>B<sub>n</sub> complexes promising for hydrogen storage applications.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"138 ","pages":"Article 109021"},"PeriodicalIF":2.7,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143680352","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}
{"title":"Efficient TF-IDF method for alignment-free DNA sequence similarity analysis","authors":"Emre Delibaş","doi":"10.1016/j.jmgm.2025.109011","DOIUrl":"10.1016/j.jmgm.2025.109011","url":null,"abstract":"<div><div>This study proposes a pioneering alignment-free approach for the analysis of DNA sequence similarity. The method employs the representation of DNA sequences as <em>n</em>-grams, a technique that involves the adaptation of the Term Frequency-Inverse Document Frequency (TF-IDF) algorithm to genomic data. The primary objective of this approach is to enhance the accuracy of the results while concomitantly reducing the computational costs of the process, by ascertaining the most informative <em>n</em>-grams. The approach adopted in this study successfully circumvents the limitations of both traditional alignment-based and alignment-free methods, thereby demonstrating a commendable level of performance. The proposed method was tested on three different datasets and achieved high agreement with reference phylogenetic trees in the AFProject benchmark system. The results demonstrate that TF-IDF-based similarity matrices effectively capture phylogenetic relationships and significantly reduce processing time. The high accuracy rates obtained prove that the method offers a scalable and robust alternative in large genomic datasets. The method demonstrates considerable potential in DNA sequence similarity analysis, exhibiting high accuracy and low computational cost.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"137 ","pages":"Article 109011"},"PeriodicalIF":2.7,"publicationDate":"2025-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143662477","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}
Chen Manjiao , Jiang Qianxi , Yu Jinlong , Lin Zhoujun , Hu Xinjun , Tian Jianping
{"title":"Effect of metal ions in Baijiu on cluster formation of water, ethanol, acetic acid and ethyl acetate molecules: Molecular dynamics and density functional theory studies","authors":"Chen Manjiao , Jiang Qianxi , Yu Jinlong , Lin Zhoujun , Hu Xinjun , Tian Jianping","doi":"10.1016/j.jmgm.2025.109020","DOIUrl":"10.1016/j.jmgm.2025.109020","url":null,"abstract":"<div><div>Metal ions in Baijiu play an important role in the formation of liquor flavor, but their molecular mechanism has not been studied yet. In this study, molecular dynamics was used to calculate the radial distribution function (RDF), coordination number, and mean square displacement (MSD) of K<sup>+</sup>, Ca<sup>2+</sup>, and Fe<sup>2+</sup> in water, ethanol, acetic acid, and ethyl acetate systems. Density functional theory was used to determine the binding energy, geometric configuration, and charge distribution of different clusters. The results of the MSD and RDF indicate that Ca<sup>2+</sup> and Fe<sup>2+</sup> are easily encapsulated by water or ethanol molecules in the system, resulting in weaker diffusion ability than K<sup>+</sup>. The interaction energy between K<sup>+</sup>, Ca<sup>2+</sup>, and Fe<sup>2+</sup> and each molecule in the system increases sequentially, especially for Fe<sup>2+</sup>, which significantly changes the charge of molecules in the cluster. There are hydrogen bonds between molecules in clusters formed with K<sup>+</sup> as the core, but there are no hydrogen bonds between molecules in clusters formed with Ca<sup>2+</sup> and Fe<sup>2+</sup> as the core. The cohesion of clusters formed with K<sup>+</sup>, Ca<sup>2+</sup>, and Fe<sup>2+</sup> as the core increased in that order. The results of this study lay a theoretical foundation for understanding the molecular mechanism of metal ions in Baijiu.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"137 ","pages":"Article 109020"},"PeriodicalIF":2.7,"publicationDate":"2025-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143670132","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}