Valence-Bound and Diffuse-Bound Anions of 5-Azauracil

Corzo, Héctor H.; Dolgounitcheva, O.; Zakrzewski, V. G.; Ortiz, J. V.

doi:10.1021/jp505307m

Cited by 5 publications

(3 citation statements)

References 52 publications

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“…Anionic fragments of nucleic acids and other molecules of biochemical importance have been frequent targets of electron propagator methodology. Photoelectron spectra of anions of the purine and pyrimidine bases that occur in the multiply charged anions known as DNA and RNA have been interpreted with electron propagator methods. − Predictions of the electron detachment energies of deprotonated bases have been made . Photoelectron spectra of an anion of a uracil–water complex with a hydrogen bond between the molecules have been assigned .…”

Section: Introductionmentioning

confidence: 99%

Electron Propagator Theory of Vertical Electron Detachment Energies of Anions: Benchmarks and Applications to Nucleotides

2023

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A new generation of ab initio electron-propagator self-energy approximations that are free of adjustable parameters is tested on a benchmark set of 55 vertical electron detachment energies of closed-shell anions. Comparisons with older self-energy approximations indicate that several new methods that make the diagonal self-energy approximation in the canonical Hartree−Fock orbital basis provide superior accuracy and computational efficiency. These methods and their acronyms, mean absolute errors (in eV), and arithmetic bottlenecks expressed in terms of occupied (O) and virtual (V) orbitals are the opposite-spin, non-Dyson, diagonal second-order method (os-nD-D2, 0.2, OV 2 ), the approximately renormalized quasiparticle third-order method (Q3+, 0.15, O 2 V 3 ) and the approximately renormalized, non-Dyson, linear, third-order method (nD-L3+, 0.1, OV 4 ). The Brueckner doubles with triple field operators (BD-T1) nondiagonal electron-propagator method provides such close agreement with coupled-cluster single, double, and perturbative triple replacement total energy differences that it may be used as an alternative means of obtaining standard data. The new methods with diagonal self-energy matrices are the foundation of a composite procedure for estimating basis-set effects. This model produces accurate predictions and clear interpretations based on Dyson orbitals for the photoelectron spectra of the nucleotides found in DNA.

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Section: Introductionmentioning

confidence: 99%

Electron Propagator Theory of Vertical Electron Detachment Energies of Anions: Benchmarks and Applications to Nucleotides

2023

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“…Recently, investigations on the tautomerism of 5‐azauracil and 6‐azauracil anions were published. However, there are not studies on tautomeric conversions in solution (particularly, water) of neutral azauracils.…”

Section: Introductionmentioning

confidence: 99%

A Hybrid statistical mechanics—quantum chemical model for proton transfer in 5‐azauracil and 6‐azauracil in water solution

Маркова

Pejov

Enchev

2015

Int J of Quantum Chemistry

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A hybrid statistical physics—quantum‐chemical methodology was implemented to study the water‐assisted intramolecular proton‐transfer processes in 5‐ and 6‐azauracils in aqueous solutions. The solvent effects were included in the model by explicit inclusion of two pairs of water molecules, which model the relevant part of the first hydration shell around the solute. The position of these water molecules was initially estimated by carrying out a classical Metropolis of dilute water solutions of the title compounds and subsequently analyzing solute–solvent intermolecular interactions in the Monte Carlo‐generated configurations. Sequentially to the statistical physics simulation, ab initio quantum mechanical (QM) level of theory was implemented. The effects of the water as solvent (at ab initio QM level) were introduced at two different levels—using solute–solvent clusters (four‐water molecules) and using the same clusters embedded in an external continuum. Full geometry optimizations of these complexes were carried out at MP2/6–31 + G(d, p) and conductor‐polarizable continuum model (C‐PCM)/MP2/6–31 + G(d, p). Single point calculations were performed at CCSD(T)/6–31 + G(d, p)//MP2/6–31 + G(d, p) computational level to obtain more accurate energies. According to our calculations hydrated azauracils should exist in three forms: mainly dioxo form and two hydroxy forms. The calculated proton transfer activation energies for tautomeric reactions of 5‐azauracil and 6‐azauracil show different pictures for these two compounds. According to C‐PCM/MP2/6–31 +G(d, p) data, water‐assisted proton transfer in 5‐azauracil realizes through two parallel reactions: 1,3,5‐triazine‐2,4(1H,3H)‐dione → 6‐hydroxy‐1,3,5‐triazin‐2(1H)‐one and 1,3,5‐triazine‐2,4(1H,3H)‐dione → 4‐hydroxy‐1,3,5‐triazin‐2(1H)‐one. Tautomeric equilibrium in 6‐azauracil in water could occur by two contiguous reactions: 1,2,4‐triazine‐3,5(2H,4H)‐dione → 5‐hydroxy‐1,2,4‐triazin‐3(2H)‐one and 5‐hydroxy‐1,2,4‐triazin‐3(2H)‐one → 3‐hydroxy‐1,2,4‐triazin‐5(2H)‐one. The proton transfer investigated reactions in 5‐ and 6‐azauracils involve concerted atomic movement. © 2015 Wiley Periodicals, Inc.

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“…We chose this level of theory given the lower computational cost and the good reproduction of the energy barriers with respect to the DLPNO-CCSD(T), CASPT2 and DFT/ωB97-XD methods (see Figure S17). Analysis of the spin-density representations and spatial extensions of the electron density (⟨ r 2 ⟩) of the anionic solutions (Table S1) indicate that the anion states are mostly of valence-bound nature; , hence, no diffuse functions are needed to describe the C7–N8 dissociation process.…”

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confidence: 99%

Hypoxia-Selective Dissociation Mechanism of a Nitroimidazole Nucleoside in a DNA Environment

Francés‐Monerris

Tuñón

Monari

2019

J. Phys. Chem. Lett.

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Photodynamic therapy is a promising approach to treat a variety of superficial tumors and other diseases. One of its major limitations arises from its dependence on molecular oxygen, which decreases the efficiency of the therapy in hypoxia conditions commonly developed by solid tumors. The present contribution reveals the molecular mechanism of a modified thymine bearing a nitroimidazole substituent, a photosensitizer able to produce highly harmful interstrand cross-links in the DNA double strand after irradiation selectively in absence of oxygen. The mechanism is resolved at a fully atomistic and electronic level relying on quantum mechanics (CASPT2, coupledcluster, DFT, and TD-DFT methods), classical molecular dynamics, and advanced biased QM/MM simulations, revealing an energy penalty of ∼8 kcal/mol for the anionic nitromidazole release. Our findings indicate that the global interstrand cross-link production is driven by a combination of multiple factors, namely, the reverse energy penalty, the diffusion of the nitroimidazole anion, and the further reactivity of the formed thymine radical. On the basis of these results, we also suggest some possible strategies to improve the efficiency of interstrand cross-link production.

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Valence-Bound and Diffuse-Bound Anions of 5-Azauracil

Cited by 5 publications

References 52 publications

Electron Propagator Theory of Vertical Electron Detachment Energies of Anions: Benchmarks and Applications to Nucleotides

Electron Propagator Theory of Vertical Electron Detachment Energies of Anions: Benchmarks and Applications to Nucleotides

A Hybrid statistical mechanics—quantum chemical model for proton transfer in 5‐azauracil and 6‐azauracil in water solution

Hypoxia-Selective Dissociation Mechanism of a Nitroimidazole Nucleoside in a DNA Environment

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