Electronic Spectroscopy of Isolated DNA Polyanions

低能电子在DNA和RNA基底上的散射：形状共振和辐射损伤

Low energy electron scattering from DNA and RNA bases: shape resonances and radiation damage

进行计算，以确定弹性散射截面和共振能量的低能量电子的影响尿嘧啶和每个DNA碱基（胸腺嘧啶，胞嘧啶，腺嘌呤，鸟嘌呤），孤立的分子在其平衡几何形状。我们的计算与现有的理论和实验进行了比较。我们还试图通过分析形状共振中电子捕获形成的临时阴离子结构，将这些信息与实验解离模式相关联。

Aqueous Contact Ion Pairs of Phosphate Groups with Na$^+$, Ca$^{2+}$ and Mg$^{2+}$ -- Structural Discrimination by Femtosecond Infrared Spectroscopy and Molecular Dynamics Simulations

The extent of contact and solvent shared ion pairs of phosphate groups with Na$^+$, Ca$^{2+}$ and Mg$^{2+}$ ions in aqueous environment and their relevance for the stability of polyanionic DNA and RNA structures is highly debated. Employing the asymmetric phosphate stretching vibration of dimethyl phosphate (DMP), a model system of the sugar-phosphate backbone of DNA and RNA, we present linear infrared, femtosecond infrared pump-probe and absorptive 2D-IR spectra that report on contact ion pair formation via the presence of blue shifted spectral signatures. Compared to the linear infrared spec…

On the interaction between gold and silver metal atoms and DNA/RNA nucleobases -- a comprehensive computational study of ground state properties

The interaction between metal atoms and nucleobases has been a topic of high interest due to the wide scientific and technological implications. Combining density functional theory simulations with a literature overview, we achieved an exhaustive study of the ground state electronic properties of DNA/RNA nucleobases interacting with gold and silver atoms at three charge states: neutral, cationic, and anionic. We describe the nature of the stability and electronic properties in each hybrid metallic structure. In addition to the metal interacting with the five isolated nucleobases, we included t…

从计算角度看碱基的激发II：动力学

Excitation of Nucleobases from a Computational Perspective II: Dynamics

本章致力于从时间依赖性的角度阐明气相中分离的DNA/RNA核碱基在光激发后发生的弛豫过程。为了达到这个目的，有几种方法，从全量子动力学到各种各样的半经典或从头算分子动力学，每种方法都有其优点和局限性。正如这一贡献所示，最常见的方法采用了最新的了解在气相中的核碱基的失活的Tully表面跳跃算法与飞行CASSCF计算相结合。不同的方法，或者更引人注目的是，不同的电子结构方法可以提供不同的动力学。提供了一个全面的审查，建议为每个核碱基的不同机制，并比较可用的实验时间尺度。结果进行了讨论，在一般情况下，涉及不同的应用电子结构和动力学方法的影响。阐明了两组核碱基-嘌呤衍生物（腺嘌呤和鸟嘌呤）和嘧啶衍生物（胸腺嘧啶、尿嘧啶和胞嘧啶）之间的机制相似性和差异。最后，在核碱基弛豫的背景下的动力学模拟的未来的前景。