Quantum Chemical Insights into DNA Nucleobase Oxidation: Bridging Theory and Experiment

IF 5.7 1区化学 Q2 CHEMISTRY, PHYSICAL

Journal of Chemical Theory and Computation Pub Date : 2024-10-22 DOI:10.1021/acs.jctc.4c01045

Francesco Ambrosio, Alessandro Landi, Andrea Peluso, Amedeo Capobianco

引用次数: 0

Abstract

The oxidation free energies of DNA nucleobases in aqueous solution are still matter of extensive discussion because of the contrasting results reported so far. With the aim of settling a longstanding debate about the oxidation potentials of DNA constituents, herein we report the results of state-of-the-art DFT-based molecular dynamics simulations, in which the whole solvent environment is modeled at the atomistic level, by using DFT supercell calculations, with periodic boundary conditions. Calculated vertical ionization energies are very close to those observed by photoelectron spectroscopy both in the gas phase and in solution. One-electron oxidation free energies in aqueous solution agree well with the results of differential pulse voltammetry measurements and with those inferred by photoelectron spectroscopy with the aid of theoretical computations to estimate vibrational relaxation.

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DNA 核碱基氧化的量子化学启示：理论与实验的桥梁

DNA 核碱基在水溶液中的氧化自由能仍是一个需要广泛讨论的问题，因为迄今为止所报道的结果截然不同。为了解决有关 DNA 成分氧化电位的长期争论，我们在此报告了基于 DFT 的分子动力学模拟的最新结果，在该模拟中，通过使用 DFT 超级单元计算和周期性边界条件，在原子水平上模拟了整个溶剂环境。计算得出的垂直电离能与光电子能谱在气相和溶液中观测到的电离能非常接近。水溶液中的单电子氧化自由能与微分脉冲伏安测量的结果以及光电子能谱借助理论计算估算振动弛豫而推断出的结果十分吻合。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Journal of Chemical Theory and Computation 化学-物理：原子、分子和化学物理

CiteScore

9.90

自引率

16.40%

发文量

568

审稿时长

1 months

期刊介绍： The Journal of Chemical Theory and Computation invites new and original contributions with the understanding that, if accepted, they will not be published elsewhere. Papers reporting new theories, methodology, and/or important applications in quantum electronic structure, molecular dynamics, and statistical mechanics are appropriate for submission to this Journal. Specific topics include advances in or applications of ab initio quantum mechanics, density functional theory, design and properties of new materials, surface science, Monte Carlo simulations, solvation models, QM/MM calculations, biomolecular structure prediction, and molecular dynamics in the broadest sense including gas-phase dynamics, ab initio dynamics, biomolecular dynamics, and protein folding. The Journal does not consider papers that are straightforward applications of known methods including DFT and molecular dynamics. The Journal favors submissions that include advances in theory or methodology with applications to compelling problems.