ArticleJournal of molecular modeling2024
Binding energies and hydrogen bonds effects on DNA-cisplatin interactions: a DFT-xTB study.
Article in Journal of molecular modeling, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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Who cites it
3 citing papers in PubMed.
- The Excess Polarizability of Single-Stranded DNA Molecules in Solution: A Linear Response Theory in the Polarizable Continuum Model with an Application to Biosensing.The journal of physical chemistry. A · 2025Article
- Developing a Machine Learning Model for Hydrogen Bond Acceptance Based on Natural Bond Orbital Descriptors.The Journal of organic chemistry · 2025Article
- Article
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Authors and funding
4 authors.
Funding
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Abstract
contextA systematic study of hydrogen bonds in base pairs and the interaction of cisplatin with DNA fragments was carried out. Structure, binding energies, and electron density were analyzed. xTB has proven to be an accurate method for obtaining structures and binding energies in DNA structures. Our xTB values for DNA base binding energy were in the same order and in some cases better than CAM-B3LYP values compared to experimental values. Double-stranded DNA-cisplatin structures have been calculated and the hydrogen bonds of water molecules are a decisive factor contributing to the preference for the cisplatin-Guanine interaction. Higher values of the water hydrogen bonding energies were obtained in cisplatin-Guanine structures. Furthermore, the electrostatic potential was used to investigate and improve the analysis of DNA-cisplatin structures.
methodsWe applied the xTB method and the CAM-B3LYP functional combined with def2-SVP basis set to perform and analyze of the bonding energies of the cisplatin interaction and the effects of the hydrogen bonds. Results were calculated employing the xTB and the ORCA software.
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