QM and QM/MM umbrella sampling MD study of the formation of Hg(II)–thymine bond: Model for evaluation of the reaction energy profiles in solutions with constant pH

0523810 - ÚOCHB 2021 RIV US eng J - Journal Article
Šebesta, F. - Šebera, Jakub - Sychrovský, Vladimír - Tanaka, Y. - Burda, J. V.
QM and QM/MM umbrella sampling MD study of the formation of Hg(II)–thymine bond: Model for evaluation of the reaction energy profiles in solutions with constant pH.
Journal of Computational Chemistry. Roč. 41, č. 16 (2020), s. 1509-1520. ISSN 0192-8651. E-ISSN 1096-987X
R&D Projects: GA ČR(CZ) GA18-14990S
Institutional support: RVO:61388963
Keywords : ab initio molecular dynamics (MD) simulations * metal–NA base interactions * QM/MM calculations * thermodynamics
OECD category: Physical chemistry
Impact factor: 3.376, year: 2020
Method of publishing: Limited access
https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.26194

The formation of the Hg–N3(T) bond between the 1-methylthymine (T) molecule and the hydrated Hg2+ cation was explored with the combined quantum mechanics/molecular mechanics (QM/MM) method including Free Energy Perturbation corrections. The thermodynamic properties were determined in the whole pH range, when these systems were explicitly investigated and considered as the QM part: (1) T + [Hg(H2O)6]2+, (2) T + [Hg(H2O)5(OH)]+, (3) T + Hg(H2O)4(OH)2, and (4) N3-deprotonated T + Hg(H2O)4(OH)2. The MM part contained only solvent molecules and counterions. As a result, the dependence of Gibbs-Alberty reaction free energy on pH was obtained along the reaction coordinate. We found that an endoergic reaction in acidic condition up to pH < 4–5 becomes exoergic for a higher pH corresponding to neutral and basic solutions. The migration of the Hg2+ cation between N3 and O4/2 positions in dependence on pH is discussed as well. For the verification, DFT calculations of stationary points were performed confirming the qualitative trends of QM/MM MD simulations and NMR parameters were determined for them.
Permanent Link: http://hdl.handle.net/11104/0308102