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Theoretical Spectroscopic Studies on Chemical and Electronic Structures of Selenocysteine and Pyrrolysine
The Journal of Physical Chemistry A ( IF 2.7 ) Pub Date : 2020-03-05 , DOI: 10.1021/acs.jpca.9b10756 Hongbao Li 1, 2 , Weijie Hua 3 , Zhiqiang Wang 1 , Axue Liu 1 , Jun Jiang 2 , Yi Luo 2
The Journal of Physical Chemistry A ( IF 2.7 ) Pub Date : 2020-03-05 , DOI: 10.1021/acs.jpca.9b10756 Hongbao Li 1, 2 , Weijie Hua 3 , Zhiqiang Wang 1 , Axue Liu 1 , Jun Jiang 2 , Yi Luo 2
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The chemical and electronic structures of the 21st and 22nd proteinogenic amino acid selenocysteine (Sec), pyrrolysine (Pyl), and their derivatives (deprotonated and protonated ions) were extensively characterized for the first time. Through the fragment based step-by-step research on their potential energy surface (PES), electronic energies of the most stable conformers of Sec, Pyl and the related ions were finally determined at the advanced CBS-QB3 and DSD-PBEP86-D3(BJ)/aug-cc-pVTZ levels, respectively, with the identification of many new low-energy conformers. The infrared spectra (IR) at 298 K of the most abundant conformers in different forms were scaled by comparison with the anharmonic frequency calculations and analyzed comparing with the experimental spectra of similar molecules. The characteristic soft X-ray spectra (including X-ray photoelectron spectra (XPS) and near-edge X-ray absorption fine-structure spectra (NEXAFS)) of the most stable conformers at 498 K were also simulated. In particular, the two possible protonated configurations of Pyl can be clearly distinguished by their different spectral features. Furthermore, a small binding energy intersection appeared around 293 eV at the C 1s edge between the canonical and protonated Pyl conformers, which is different from all the previous studies. This work thus filled the gap in our knowledge by providing detailed information on the chemical and electronic structures of Sec and Pyl and will be a useful guidance for future experimental research.
中文翻译：
硒代半胱氨酸和吡咯赖氨酸的化学和电子结构的理论光谱研究
首次广泛表征了第21和第22个蛋白原氨基酸硒代半胱氨酸（Sec），吡咯赖氨酸（Pyl）及其衍生物（去质子化和质子化离子）的化学和电子结构。通过对片段的势能面（PES）进行逐步研究，最终在高级CBS-QB3和DSD-PBEP86-D3上确定了Sec，Pyl和相关离子的最稳定构象的电子能（ BJ）/ aug-cc-pVTZ水平，并鉴定了许多新的低能耗构象体。通过与非谐频率计算进行比较，缩放了不同形式的最丰富构象异构体在298 K时的红外光谱（IR），并与相似分子的实验光谱进行了比较。还模拟了最稳定构象物在498 K时的特征性软X射线光谱（包括X射线光电子能谱（XPS）和近边缘X射线吸收精细结构能谱（NEXAFS））。特别是，Pyl的两种可能的质子化构型可以通过其不同的光谱特征清楚地区分开。此外，在典范质子化和质子化Pyl构象异构体之间的C 1s边缘处，一个小的结合能交点出现在293 eV附近，这与之前的所有研究均不同。因此，这项工作通过提供有关Sec和Pyl的化学和电子结构的详细信息，填补了我们知识的空白，并将为将来的实验研究提供有用的指导。
更新日期：2020-03-05
中文翻译：
硒代半胱氨酸和吡咯赖氨酸的化学和电子结构的理论光谱研究
首次广泛表征了第21和第22个蛋白原氨基酸硒代半胱氨酸（Sec），吡咯赖氨酸（Pyl）及其衍生物（去质子化和质子化离子）的化学和电子结构。通过对片段的势能面（PES）进行逐步研究，最终在高级CBS-QB3和DSD-PBEP86-D3上确定了Sec，Pyl和相关离子的最稳定构象的电子能（ BJ）/ aug-cc-pVTZ水平，并鉴定了许多新的低能耗构象体。通过与非谐频率计算进行比较，缩放了不同形式的最丰富构象异构体在298 K时的红外光谱（IR），并与相似分子的实验光谱进行了比较。还模拟了最稳定构象物在498 K时的特征性软X射线光谱（包括X射线光电子能谱（XPS）和近边缘X射线吸收精细结构能谱（NEXAFS））。特别是，Pyl的两种可能的质子化构型可以通过其不同的光谱特征清楚地区分开。此外，在典范质子化和质子化Pyl构象异构体之间的C 1s边缘处，一个小的结合能交点出现在293 eV附近，这与之前的所有研究均不同。因此，这项工作通过提供有关Sec和Pyl的化学和电子结构的详细信息，填补了我们知识的空白，并将为将来的实验研究提供有用的指导。
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