Spectroscopic identification of fragment ions of DNA/RNA building blocks: the case of pyrimidine.,Physical Chemistry Chemical Physics

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Spectroscopic identification of fragment ions of DNA/RNA building blocks: the case of pyrimidine.
Physical Chemistry Chemical Physics ( IF 2.9 ) Pub Date : 2020-07-07 , DOI: 10.1039/d0cp02919j
Kuntal Chatterjee ₁ , Otto Dopfer ₁

Affiliation

Pyrimidine (Pym, 1,3-diazine, 1,3-diazabenzene) is an important N-heterocyclic building block of nucleobases. Understanding the structures of its fragment and precursor ions provides insight into its prebiotic and abiotic synthetic route. The long-standing controversial debate about the structures of the primary fragment ions of the Pym⁺ cation (C₄H₄N₂⁺, m/z 80) resulting from loss of HCN, C₃H₃N⁺ (m/z 53), is closed herein with the aid of a combined approach utilizing infrared photodissociation (IRPD) spectroscopy in the CH and NH stretch ranges (ν_CH/NH) and density functional theory (DFT) calculations. IRPD spectra of cold Ar/N₂-tagged fragment ions reveal that the C₃H₃N⁺ population is dominated by cis-/trans-HCCHNCH⁺ ions (∼90%) along with a minor contribution of the most stable H₂CCCNH⁺ and cis-/trans-HCCHCNH⁺ isomers (∼10%). We also spectroscopically confirm that the secondary fragment resulting from further loss of HCN, C₂H₂⁺ (m/z 26), is the acetylene cation (HCCH⁺). The spectroscopic characterization of the identified C₃H₃N⁺ isomers and their hydrogen-bonded dimers with Ar and N₂ provides insight into the acidity of their CH and NH groups. Finally, the vibrational properties of Pym⁺ in the 3 μm range are probed by IRPD of Pym⁺-(N₂)_1–2 clusters, which shows a high π-binding affinity of Pym⁺ toward a nonpolar hydrophobic ligand. Its ν_CH spectrum confirms the different acidity of the three nonequivalent CH groups.

中文翻译：

光谱鉴定DNA / RNA结构单元的碎片离子：嘧啶的情况。

嘧啶（Pym，1,3-二嗪，1,3-二氮杂苯）是重要的N杂环核碱基。了解其碎片和前体离子的结构可深入了解其益生元和非生物合成途径。关于由HCN，C ₃ H ₃ N ⁺（m / z的损失）引起的Pym ⁺阳离子的主要碎片离子（C ₄ H ₄ N ₂⁺，m / z 80）的结构的长期争论53），与利用红外光解（IRPD）光谱在CH和NH伸缩范围相结合的办法的助剂（本文关闭ν _{CH / NH}）和密度泛函理论（DFT）计算。冷的Ar / N ₂标记碎片离子的IRPD光谱表明，C ₃ H ₃ N ⁺种群主要是顺式-/反式-HCCHNCH ⁺离子（约90％），而少量的最稳定的H ₂ CCCNH ⁺和顺- /反式-HCCHCNH ⁺异构体（〜10％）。我们还通过光谱确认了由HCN的进一步损失C ₂ H ₂⁺（m / z 26）引起的第二个片段是乙炔阳离子（HCCH ⁺）。鉴定出的C ₃ H ₃ N ⁺异构体及其与Ar和N ₂氢键结合的二聚体的光谱表征提供了对其CH和NH基团酸度的了解。最后，通过Pym ⁺ -（N ₂）_1–2团簇的IRPD探测了3μm范围内Pym ⁺的振动特性，这表明Pym ⁺具有很高的π结合亲和力⁺朝向非极性疏水配体。它ν_CH频谱肯定了这三个不等价CH群体的不同酸度。

更新日期：2020-08-05

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