QM/MM studies of cisplatin complexes with DNA dimer and octamer

Gkionis, Konstantinos and Platts, James Alexis ORCID: https://orcid.org/0000-0002-1008-6595 2012. QM/MM studies of cisplatin complexes with DNA dimer and octamer. Computational and Theoretical Chemistry 993 , pp. 60-65. 10.1016/j.comptc.2012.05.034

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Abstract

Hybrid QM/MM calculations on adducts of cisplatin with DNA dimer and octamer are reported. Starting from the crystal structure of a cisplatin–DNA dimer complex and an NMR structure of a cisplatin–DNA octamer complex, several variants of the ONIOM approach are tested, all employing BHandH for the QM part and AMBER for MM. We demonstrate that a generic set of molecular mechanics parameters for description of Pt-coordination can be used within the subtractive ONIOM scheme without loss of accuracy, such that dedicated parameters for new platinum complexes may not be required. Comparison of optimised structures obtained with different strategies indicates that electrostatic embedding is vital for proper description of the complex, while inclusion of water molecules as explicit solvent further improves performance. The resulting DNA structural parameters are in good general agreement with the experimental structure obtained, particularly when the inherent variability in NMR-derived parameters is taken into account.

Item Type:	Article
Date Type:	Publication
Status:	Published
Schools:	Advanced Research Computing @ Cardiff (ARCCA) Chemistry
Subjects:	Q Science > QD Chemistry
Uncontrolled Keywords:	DNA; Cisplatin; Density functional theory; QM/MM; ONIOM
ISSN:	2210-271X
Related URLs:	Publisher
Last Modified:	24 Oct 2022 10:55
URI:	https://orca.cardiff.ac.uk/id/eprint/46398

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