Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, MI, 48202, USA.
Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7c, 6525 ED, Nijmegen, Netherlands.
J Am Soc Mass Spectrom. 2019 Sep;30(9):1758-1767. doi: 10.1007/s13361-019-02274-8. Epub 2019 Jul 8.
Gas-phase conformations of the sodium-cationized forms of the 2'-deoxycytidine and cytidine mononucleotides, [pdCyd+Na] and [pCyd+Na], are examined by infrared multiple photon dissociation action spectroscopy. Complimentary electronic structure calculations at the B3LYP/6-311+G(2d,2p)//B3LYP/6-311+G(d,p) level of theory provide candidate conformations and their respective predicted IR spectra for comparison across the IR fingerprint and hydrogen-stretching regions. Comparisons of the predicted IR spectra and the measured infrared multiple photon dissociation action spectra provide insight into the impact of sodium cationization on intrinsic mononucleotide structure. Further, comparison of present results with those reported for the sodium-cationized cytidine nucleoside analogues elucidates the impact of the phosphate moiety on gas-phase structure. Across the neutral, protonated, and sodium-cationized cytidine mononucleotides, a preference for stabilization of the phosphate moiety and nucleobase orientation is observed, although the details of this stabilization differ with the state of cationization. Several low-energy conformations of [pdCyd+Na] and [pCyd+Na] involving several different orientations of the phosphate moiety and sugar puckering modes are observed experimentally.
通过红外多光子解离作用光谱研究了 2'-脱氧胞苷和胞苷单核苷酸的钠离子加合形式[pdCyd+Na]和[pCyd+Na]的气相构象。在 B3LYP/6-311+G(2d,2p)//B3LYP/6-311+G(d,p)理论水平上进行的补充电子结构计算提供了候选构象及其各自在红外指纹区和氢键伸缩区的预测红外光谱，用于比较。预测的红外光谱与测量的红外多光子解离作用光谱的比较提供了对钠离子加合对固有单核苷酸结构影响的深入了解。此外，将本研究结果与已报道的胞苷核苷类似物的钠离子加合结果进行比较，阐明了磷酸部分对气相结构的影响。在中性、质子化和钠离子加合的胞苷单核苷酸中，观察到稳定磷酸部分和碱基取向的偏好，尽管这种稳定化的细节随阳离子化状态而变化。实验中观察到[pdCyd+Na]和[pCyd+Na]的几种低能构象，涉及磷酸部分和糖环构象的几种不同取向。
