Ali Kadhim Wadday , Sukaina Tuama Ghafel , Suraa Reaad , Mustafa M. Kadhim
{"title":"金属-卟啉与微量土臭素选择性相互作用的理论设计","authors":"Ali Kadhim Wadday , Sukaina Tuama Ghafel , Suraa Reaad , Mustafa M. Kadhim","doi":"10.1016/j.compbiolchem.2025.108604","DOIUrl":null,"url":null,"abstract":"<div><div>Geosmin, even at minuscule concentrations, can significantly compromise the taste and odor of drinking water, making its removal a critical challenge. In this study, an integrated computational strategy encompassing DFT, QTAIM, NCI analysis, RDG, DOS, and Molecular Dynamics simulations was used to probe how geosmin interacts with both pristine Porphin and its copper-coordinated variant. The findings clearly show that copper coordination markedly enhances geosmin adsorption. Specifically, the average isosteric heat increases from 18.66 to 20.67 kcal/mol, while the energy distribution narrows, suggesting more consistent interaction strength. Mulliken charge and electrostatic potential analyses indicate a partial charge transfer involving the hydroxyl group of geosmin, supporting the conclusion that van der Waals and hydrogen-bonding interactions play a significant role. Additionally, copper coordination dramatically reduces the HOMO–LUMO gap from 0.0756 eV to 0.00083 eV signaling increased electronic reactivity and a shift towards semi-metallic character. Molecular Dynamics simulations confirm that these frameworks are both structurally and thermally stable, with total energy fluctuations remaining within ±0.17 kcal/mol. Altogether, these results highlight copper-modified Porphin as a highly promising platform for geosmin adsorption, offering robust thermal stability, enhanced selectivity, and notable electronic property modulation. Such frameworks are potential candidates for next-generation VOC sensors and advanced water purification technologies.</div></div>","PeriodicalId":10616,"journal":{"name":"Computational Biology and Chemistry","volume":"119 ","pages":"Article 108604"},"PeriodicalIF":3.1000,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Theoretical design of metal–porphin systems for selective interaction with trace geosmin\",\"authors\":\"Ali Kadhim Wadday , Sukaina Tuama Ghafel , Suraa Reaad , Mustafa M. Kadhim\",\"doi\":\"10.1016/j.compbiolchem.2025.108604\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><div>Geosmin, even at minuscule concentrations, can significantly compromise the taste and odor of drinking water, making its removal a critical challenge. In this study, an integrated computational strategy encompassing DFT, QTAIM, NCI analysis, RDG, DOS, and Molecular Dynamics simulations was used to probe how geosmin interacts with both pristine Porphin and its copper-coordinated variant. The findings clearly show that copper coordination markedly enhances geosmin adsorption. Specifically, the average isosteric heat increases from 18.66 to 20.67 kcal/mol, while the energy distribution narrows, suggesting more consistent interaction strength. Mulliken charge and electrostatic potential analyses indicate a partial charge transfer involving the hydroxyl group of geosmin, supporting the conclusion that van der Waals and hydrogen-bonding interactions play a significant role. Additionally, copper coordination dramatically reduces the HOMO–LUMO gap from 0.0756 eV to 0.00083 eV signaling increased electronic reactivity and a shift towards semi-metallic character. Molecular Dynamics simulations confirm that these frameworks are both structurally and thermally stable, with total energy fluctuations remaining within ±0.17 kcal/mol. Altogether, these results highlight copper-modified Porphin as a highly promising platform for geosmin adsorption, offering robust thermal stability, enhanced selectivity, and notable electronic property modulation. Such frameworks are potential candidates for next-generation VOC sensors and advanced water purification technologies.</div></div>\",\"PeriodicalId\":10616,\"journal\":{\"name\":\"Computational Biology and Chemistry\",\"volume\":\"119 \",\"pages\":\"Article 108604\"},\"PeriodicalIF\":3.1000,\"publicationDate\":\"2025-08-05\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Computational Biology and Chemistry\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S1476927125002658\",\"RegionNum\":4,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Computational Biology and Chemistry","FirstCategoryId":"99","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S1476927125002658","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"BIOLOGY","Score":null,"Total":0}
Theoretical design of metal–porphin systems for selective interaction with trace geosmin
Geosmin, even at minuscule concentrations, can significantly compromise the taste and odor of drinking water, making its removal a critical challenge. In this study, an integrated computational strategy encompassing DFT, QTAIM, NCI analysis, RDG, DOS, and Molecular Dynamics simulations was used to probe how geosmin interacts with both pristine Porphin and its copper-coordinated variant. The findings clearly show that copper coordination markedly enhances geosmin adsorption. Specifically, the average isosteric heat increases from 18.66 to 20.67 kcal/mol, while the energy distribution narrows, suggesting more consistent interaction strength. Mulliken charge and electrostatic potential analyses indicate a partial charge transfer involving the hydroxyl group of geosmin, supporting the conclusion that van der Waals and hydrogen-bonding interactions play a significant role. Additionally, copper coordination dramatically reduces the HOMO–LUMO gap from 0.0756 eV to 0.00083 eV signaling increased electronic reactivity and a shift towards semi-metallic character. Molecular Dynamics simulations confirm that these frameworks are both structurally and thermally stable, with total energy fluctuations remaining within ±0.17 kcal/mol. Altogether, these results highlight copper-modified Porphin as a highly promising platform for geosmin adsorption, offering robust thermal stability, enhanced selectivity, and notable electronic property modulation. Such frameworks are potential candidates for next-generation VOC sensors and advanced water purification technologies.
期刊介绍:
Computational Biology and Chemistry publishes original research papers and review articles in all areas of computational life sciences. High quality research contributions with a major computational component in the areas of nucleic acid and protein sequence research, molecular evolution, molecular genetics (functional genomics and proteomics), theory and practice of either biology-specific or chemical-biology-specific modeling, and structural biology of nucleic acids and proteins are particularly welcome. Exceptionally high quality research work in bioinformatics, systems biology, ecology, computational pharmacology, metabolism, biomedical engineering, epidemiology, and statistical genetics will also be considered.
Given their inherent uncertainty, protein modeling and molecular docking studies should be thoroughly validated. In the absence of experimental results for validation, the use of molecular dynamics simulations along with detailed free energy calculations, for example, should be used as complementary techniques to support the major conclusions. Submissions of premature modeling exercises without additional biological insights will not be considered.
Review articles will generally be commissioned by the editors and should not be submitted to the journal without explicit invitation. However prospective authors are welcome to send a brief (one to three pages) synopsis, which will be evaluated by the editors.