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

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 ra...

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Bibliographic Details
Published in:Journal of computational chemistry Vol. 41; no. 16; pp. 1509 - 1520
Main Authors: Šebesta, Filip, Šebera, Jakub, Sychrovský, Vladimír, Tanaka, Yoshiyuki, Burda, Jaroslav V.
Format: Journal Article
Language:English
Published: Hoboken, USA John Wiley & Sons, Inc 15.06.2020
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Subjects:
ab initio molecular dynamics (MD) simulations
Cations
Computer simulation
Dependence
Free energy
Mercury (metal)
Mercury compounds
metal–NA base interactions
NMR
Nuclear magnetic resonance
Perturbation
QM/MM calculations
Quantum mechanics
Thermodynamic properties
thermodynamics
Thymine
QM/MM calculations
thermodynamics
ab initio molecular dynamics (MD) simulations
metal-NA base interactions
ISSN:0192-8651, 1096-987X, 1096-987X
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Summary: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.
Bibliography:Funding information
Grant Agency of Czech Republic, Grant/Award Numbers: 16‐06240S, 18‐14990S; National Grid Infrastructure MetaCentrum, Grant/Award Number: LM2010005; Grant Agency of Charles University, Grant/Award Number: 1145016
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ISSN:0192-8651
1096-987X
1096-987X
DOI:10.1002/jcc.26194