Université de Lyon, Université Claude Bernard Lyon1, Institut des Sciences Analytiques, CNRS UMR 5280, 43 Bd du 11 novembre 1918, 69622 Villeurbanne Cedex, France.
Phys Chem Chem Phys. 2012 Jul 28;14(28):9855-70. doi: 10.1039/c2cp40384f. Epub 2012 Jun 15.
The fragmentation process of the uracil RNA base has been investigated via DFT calculations in order to assign fragments to the ionisation mass spectrum obtained after dissociation induced by collision experiments. The analysis of the electronic distribution and geometry parameters of the cation allows selection of several bonds that may be cleaved and lead to the formation of various fragments. Differences are observed in the electronic behaviour of the bond breaking as well as the energy required for the cleavage. It is reported that N(3)-C(4) and N(1)-C(2) bonds are more easily cleaved than the C(5)-C(6) bond, since the corresponding energy barriers amount to ΔG = +1.627, +1.710, +5.459 eV, respectively, which makes the C(5)-C(6) bond cleavage almost prohibited. Among all possible formed fragments, the formation of the OCN(+) fragment for the peak at m/z = 42 Da is excluded because of an intermediate that was not observed experimentally and too a large free energy barrier. Based on the required free energy, it is observed that two fragment derivatives: C(2)H(4)N(+) and C(2)H(2)O˙(+) may be formed, with a small preference for C(2)H(4)N(+). This latter product is not formed through a retro Diels Alder reaction in contrast to C(2)H(2)O˙(+). The following sequence is proposed for the peak at 42 Da: C(2)H(4)N(+) (from N(1)-C(2), C(4)-C(5) cleavages) > C(2)H(2)O˙(+) (from N(3)-C(4), N(1)-C(2) and C(5)-C(6) cleavages) > C(2)H(4)N(+) (from N(1)-C(2), N(3)-C(4) and C(4)-C(5)) > C(2)H(2)O˙(+) (from C(5)-C(6), N(1)-C(2) and N(3)-C(4) cleavages) > NCO(+) (from N(1)-C(2), C(4)-C(5) and N(3)-C(4) cleavages). Finally the peak at 28 Da is assigned to CNH(2)(+) derivatives that can be formed through two different paths, the easiest one requiring 5.4 eV.
为了将碎片分配给通过碰撞实验诱导离解获得的离子质谱，通过 DFT 计算研究了尿嘧啶 RNA 碱基的碎片化过程。阳离子的电子分布和几何参数的分析允许选择可能断裂并导致各种碎片形成的几个键。在键断裂的电子行为以及断裂所需的能量方面存在差异。报告指出，N(3)-C(4)和 N(1)-C(2)键比 C(5)-C(6)键更容易断裂，因为相应的能量势垒分别为 ΔG = +1.627、+1.710 和 +5.459 eV，这使得 C(5)-C(6)键的断裂几乎不可能。在所有可能形成的碎片中，排除了形成 m/z = 42 Da 峰的 OCN(+) 片段，因为实验中未观察到中间产物，并且自由能势垒太大。基于所需的自由能，观察到可以形成两种碎片衍生物：C(2)H(4)N(+)和 C(2)H(2)O˙(+)，对 C(2)H(4)N(+)的偏好较小。与 C(2)H(2)O˙(+)相反，后一种产物不是通过逆行 Diels Alder 反应形成的。对于 42 Da 的峰，提出了以下顺序：C(2)H(4)N(+)（来自 N(1)-C(2)、C(4)-C(5)断裂）>C(2)H(2)O˙(+)（来自 N(3)-C(4)、N(1)-C(2)和 C(5)-C(6)断裂）>C(2)H(4)N(+)（来自 N(1)-C(2)、N(3)-C(4)和 C(4)-C(5)断裂）>C(2)H(2)O˙(+)（来自 C(5)-C(6)、N(1)-C(2)和 N(3)-C(4)断裂）>NCO(+)（来自 N(1)-C(2)、C(4)-C(5)和 N(3)-C(4)断裂）。最后，将 28 Da 的峰分配给可以通过两种不同路径形成的 CNH(2)(+)衍生物，最简单的路径需要 5.4 eV。
