Amide-imide tautomerism of acetohydroxamic acid in aqueous solution: quantum calculation and SMD simulations

Tolosa, S.; Mora‐Diez, Nelaine; Hidalgo, Antonio; Sansón, J.A.

doi:10.1039/c4ra06124a

Cited by 20 publications

(12 citation statements)

References 62 publications

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“…SMD simulations allow the calculation of Gibbs energy profiles. Hence, the standard Gibbs energies of activation (Δ G ‡ ) and reaction (Δ G ) can be determined by following the time evolution of the process as previously shown in several woks, that is, from the configuration of the reactant to the product (or vice versa) in an elementary step focusing on the reaction coordinate. The structures involved in the reaction mechanism can be visualized to represent the evolution of the system at each step of the process, especially intermediate and transition states.…”

Section: Computational Detailsmentioning

confidence: 99%

Theoretical thermodynamic study of the adenine-thymine tautomeric equilibrium: Electronic structure calculations and steered molecular dynamic simulations

2017

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Free energy of the tautomeric equilibrium A-T ! A*-T* between the canonical and noncanonical DNA base equilibrium in aqueous solution was theoretically determined by applying electronic structure methods (at the M06-2X-PCM/6-31111G(d,p) level) and steered molecular dynamic simulations. Concerted and stepwise mechanisms were considered for the double proton transfer in an effort to explain the anomalous behavior of this system where an unfavorable process without a transition state can be observed depending on the level of calculation used. Of the different mechanisms used in the simulations, the stepwise mechanism, in which the first step implies the transference of a proton from thymine to adenine, and a second step with the transference of a different proton from adenine to thymine, was the only one that showed two transition states and a reaction intermediate. However, a concerted and stepwise mechanism has similar kinetic and thermodynamic behavior, with similar reaction and activation energies. Simple proton transfer was more favorable for the transference of the hydrogen from the adenine to the thymine. The inclusion of an aqueous medium in this study only slightly modified these energies, but the barrier energy was higher when the solvent was described as a discrete medium. Transition states and intermediate structures were analyzed at molecular dynamic level. K E Y W O R D Sadenine-thymine, electronic structure calculation, proton transfer in solution, steered molecular dynamic simulations, tautomeric equilibrium, thermodynamic properties

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Section: Computational Detailsmentioning

confidence: 99%

Theoretical thermodynamic study of the adenine-thymine tautomeric equilibrium: Electronic structure calculations and steered molecular dynamic simulations

2017

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“…Long-range electrostatic interactions were considered by the Ewald summation (Ewald, 1921) and the Jarzynski's equality (Jarzynski, 1997) was used to calculate Gibbs energy differences between two equilibrium states. The activation and reaction energies were determined through the evolution of the process, as has been shown in several works (Tolosa et al, 2014, 2016, 2017a,b, 2018a,b; Tolosa et al, 2019).…”

Section: Methodsmentioning

confidence: 99%

Theoretical Study of Adenine to Guanine Transition Assisted by Water and Formic Acid Using Steered Molecular Dynamic Simulations

2019

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The free energy profile of the adenine to guanine transition in the gas and aqueous phases was obtained by applying steered molecular dynamic (SMD) simulations. Three processes were considered to explain the mechanism assisted by water and formic acid molecules. The first process is hydrolytic deamination of adenine, then oxidation of the hypoxanthine previously formed, and finally, the animation from xanthine to guanine. In the gas phase these processes indicate a slow and not spontaneous conversion (Δ G g = 4.07 kcal·mol −1 , k = 5.59·10 −40 s −1 ), and a lifetime for guanine of τ = 7.75·10 +22 s. The presence of solvent makes the transition more difficult by increasing the reaction energy to 26.90 kcal·mol −1 and decreasing the speed of the process to 1.63·10 −55 s −1 . However, it decreases the energy of the deamination process to −9.63 kcal·mol −1 and the lifetime of guanine base to τ = 6.85·10 +17 s when the surrounding medium used in the transition process is aqueous. The results show that the guanine could participate in genetic mutations based on the lifetimes obtained. Transition states and intermediates structures were analyzed at the molecular dynamic level. This allows to follow the mechanism over time and to calculate thermodynamic and kinetic properties.

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“…The standard Gibbs energies of activation (DG ‡ ) and reaction (DG) can be determined by following the time evolution of the process, as previously shown in several works, [66][67][68][69][70][71] i.e., from the conguration of the reactant to the product (or vice versa) in elementary steps focusing on the reaction coordinate. In a previous work, 66 several calculations at different postequilibrium simulation times (200, 400, 600, 800, and 1000 ps) were performed to verify the Gaussian distribution of W in eqn (2). Based on those results, long simulations have been used for each step of the deamination process in this work, verifying in each simulation that the variations of the chosen reaction coordinates do not deviate of the minimum of the harmonic restraint.…”

Section: Smd Simulationsmentioning

confidence: 99%

Theoretical study of mechanisms for the hydrolytic deamination of cytosine via steered molecular dynamic simulations

2018

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Amide-imide tautomerism of acetohydroxamic acid in aqueous solution: quantum calculation and SMD simulations

Abstract: The kinetics and the thermodynamics of the amide-imide tautomerizations of acetohydroxamic acid in aqueous solution are studied from a theoretical point of view.

Cited by 20 publications

References 62 publications

Theoretical thermodynamic study of the adenine-thymine tautomeric equilibrium: Electronic structure calculations and steered molecular dynamic simulations

Theoretical thermodynamic study of the adenine-thymine tautomeric equilibrium: Electronic structure calculations and steered molecular dynamic simulations

Theoretical Study of Adenine to Guanine Transition Assisted by Water and Formic Acid Using Steered Molecular Dynamic Simulations

Theoretical study of mechanisms for the hydrolytic deamination of cytosine via steered molecular dynamic simulations

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