Effects of Nitro-Oxidative Stress on Biomolecules: Part 2—Reactive Molecular Dynamics Simulations
In this review article, statistical mechanisms of oxidative modification reactions in various organic compounds under the influence of reactive oxygen species (ROS) generated by cold atmospheric plasma (CAP) are investigated and analyzed based on reactive molecular dynamics (MD) simulations. As an e...
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2025-06-01
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| author | Zhaonan Chai Yawei Feng Tong Zhao Xiaolong Wang Maksudbek Yusupov Maryam Ghasemitarei Tayebeh Ghorbi Annemie Bogaerts Yuantao Zhang |
| author_facet | Zhaonan Chai Yawei Feng Tong Zhao Xiaolong Wang Maksudbek Yusupov Maryam Ghasemitarei Tayebeh Ghorbi Annemie Bogaerts Yuantao Zhang |
| author_sort | Zhaonan Chai |
| collection | DOAJ |
| description | In this review article, statistical mechanisms of oxidative modification reactions in various organic compounds under the influence of reactive oxygen species (ROS) generated by cold atmospheric plasma (CAP) are investigated and analyzed based on reactive molecular dynamics (MD) simulations. As an efficient and hygienic advanced oxidation technology, CAP demonstrates tremendous potential in fields such as biomedicine and environmental protection. Through simulations, this paper provides a detailed analysis of the interaction mechanisms between ROS and components of biological tissues and environmental toxins. In this paper, we review the reactions involving four major ROS (OH radicals, O atoms, <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msub><mi mathvariant="normal">O</mi><mn>3</mn></msub></semantics></math></inline-formula> molecules, and <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mrow><msub><mi mathvariant="normal">H</mi><mn>2</mn></msub><msub><mi mathvariant="normal">O</mi><mn>2</mn></msub></mrow></semantics></math></inline-formula> molecules) and organic compounds, including proteins, DNA, polysaccharides, fatty acids, antibiotics, and mycotoxins. Atomic-level analysis reveals various oxidative modification reactions induced by ROS and their resulting products, including dehydrogenation reactions, bond-formation reactions, oxygen-addition reactions, and bond-cleavage reactions. Additionally, the study elucidates the role of active functional groups in various organic compounds, the presence of special elements, and the specific reactive nature of <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mrow><msub><mi mathvariant="normal">H</mi><mn>2</mn></msub><msub><mi mathvariant="normal">O</mi><mn>2</mn></msub></mrow></semantics></math></inline-formula>. Furthermore, the influence of different ROS species and concentrations on reaction types is explored, aiming to provide a solid theoretical foundation for the application of CAP technology in biomedicine and environmental remediation. |
| format | Article |
| id | doaj-art-e3d3b44fb6d644d698a1be061f4dd3b8 |
| institution | DOAJ |
| issn | 2218-273X |
| language | English |
| publishDate | 2025-06-01 |
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| series | Biomolecules |
| spelling | doaj-art-e3d3b44fb6d644d698a1be061f4dd3b82025-08-20T03:07:57ZengMDPI AGBiomolecules2218-273X2025-06-0115795210.3390/biom15070952Effects of Nitro-Oxidative Stress on Biomolecules: Part 2—Reactive Molecular Dynamics SimulationsZhaonan Chai0Yawei Feng1Tong Zhao2Xiaolong Wang3Maksudbek Yusupov4Maryam Ghasemitarei5Tayebeh Ghorbi6Annemie Bogaerts7Yuantao Zhang8School of Electrical Engineering, Shandong University, Jinan 250061, ChinaSchool of Electrical Engineering, Shandong University, Jinan 250061, ChinaSchool of Electrical Engineering, Shandong University, Jinan 250061, ChinaSchool of Electrical Engineering, Shandong University, Jinan 250061, ChinaInstitute of Fundamental and Applied Research, National Research University TIIAME, Tashkent 100000, UzbekistanDepartment of Applied Physics, Aalto University, FI-00076 Espoo, FinlandLaboratory of Experimental Biophysics, Centre for Advanced Technologies, Tashkent 100174, UzbekistanResearch Group PLASMANT, Department of Chemistry, University of Antwerp, 2610 Antwerp, BelgiumSchool of Electrical Engineering, Shandong University, Jinan 250061, ChinaIn this review article, statistical mechanisms of oxidative modification reactions in various organic compounds under the influence of reactive oxygen species (ROS) generated by cold atmospheric plasma (CAP) are investigated and analyzed based on reactive molecular dynamics (MD) simulations. As an efficient and hygienic advanced oxidation technology, CAP demonstrates tremendous potential in fields such as biomedicine and environmental protection. Through simulations, this paper provides a detailed analysis of the interaction mechanisms between ROS and components of biological tissues and environmental toxins. In this paper, we review the reactions involving four major ROS (OH radicals, O atoms, <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msub><mi mathvariant="normal">O</mi><mn>3</mn></msub></semantics></math></inline-formula> molecules, and <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mrow><msub><mi mathvariant="normal">H</mi><mn>2</mn></msub><msub><mi mathvariant="normal">O</mi><mn>2</mn></msub></mrow></semantics></math></inline-formula> molecules) and organic compounds, including proteins, DNA, polysaccharides, fatty acids, antibiotics, and mycotoxins. Atomic-level analysis reveals various oxidative modification reactions induced by ROS and their resulting products, including dehydrogenation reactions, bond-formation reactions, oxygen-addition reactions, and bond-cleavage reactions. Additionally, the study elucidates the role of active functional groups in various organic compounds, the presence of special elements, and the specific reactive nature of <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mrow><msub><mi mathvariant="normal">H</mi><mn>2</mn></msub><msub><mi mathvariant="normal">O</mi><mn>2</mn></msub></mrow></semantics></math></inline-formula>. Furthermore, the influence of different ROS species and concentrations on reaction types is explored, aiming to provide a solid theoretical foundation for the application of CAP technology in biomedicine and environmental remediation.https://www.mdpi.com/2218-273X/15/7/952cold atmospheric plasmabiological tissuesenvironmental toxinsreactive MD simulationreactive oxygen species52.80Pi |
| spellingShingle | Zhaonan Chai Yawei Feng Tong Zhao Xiaolong Wang Maksudbek Yusupov Maryam Ghasemitarei Tayebeh Ghorbi Annemie Bogaerts Yuantao Zhang Effects of Nitro-Oxidative Stress on Biomolecules: Part 2—Reactive Molecular Dynamics Simulations Biomolecules cold atmospheric plasma biological tissues environmental toxins reactive MD simulation reactive oxygen species 52.80Pi |
| title | Effects of Nitro-Oxidative Stress on Biomolecules: Part 2—Reactive Molecular Dynamics Simulations |
| title_full | Effects of Nitro-Oxidative Stress on Biomolecules: Part 2—Reactive Molecular Dynamics Simulations |
| title_fullStr | Effects of Nitro-Oxidative Stress on Biomolecules: Part 2—Reactive Molecular Dynamics Simulations |
| title_full_unstemmed | Effects of Nitro-Oxidative Stress on Biomolecules: Part 2—Reactive Molecular Dynamics Simulations |
| title_short | Effects of Nitro-Oxidative Stress on Biomolecules: Part 2—Reactive Molecular Dynamics Simulations |
| title_sort | effects of nitro oxidative stress on biomolecules part 2 reactive molecular dynamics simulations |
| topic | cold atmospheric plasma biological tissues environmental toxins reactive MD simulation reactive oxygen species 52.80Pi |
| url | https://www.mdpi.com/2218-273X/15/7/952 |
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