Bende Attila, Muntean Cristina M
Molecular and Biomolecular Physics Department, National Institute for Research and Development of Isotopic and Molecular Technologies, Donath Street, No. 65-103, 400293, Cluj-Napoca, Romania.
J Mol Model. 2014 Mar;20(3):2113. doi: 10.1007/s00894-014-2113-z. Epub 2014 Feb 25.
The theoretical IR and Raman spectra of the guanine-cytosine DNA base pairs in Watson-Crick and Hoogsteen configurations were computed using DFT method with M06-2X meta-hybrid GGA exchange-correlation functional, including the anharmonic corrections and solvent effects. The results for harmonic frequencies and their anharmonic corrections were compared with our previously calculated values obtained with the B3PW91 hybrid GGA functional. Significant differences were obtained for the anharmonic corrections calculated with the two different DFT functionals, especially for the stretching modes, while the corresponding harmonic frequencies did not differ considerable. For the Hoogtseen case the H⁺ vibration between the G-C base pair can be characterized as an asymmetric Duffing oscillator and therefore unrealistic anharmonic corrections for normal modes where this proton vibration is involved have been obtained. The spectral modification due to the anharmonic corrections, solvent effects and the influence of sugar-phosphate group for the Watson-Crick and Hoogsteen base pair configurations, respectively, were also discussed. For the Watson-Crick case also the influence of the stacking interaction on the theoretical IR and Raman spectra was analyzed. Including the anharmonic correction in our normal mode analysis is essential if one wants to obtain correct assignments of the theoretical frequency values as compared with the experimental spectra.
采用含M06 - 2X元杂化广义梯度近似（GGA）交换关联泛函的密度泛函理论（DFT）方法，计算了鸟嘌呤 - 胞嘧啶DNA碱基对在沃森 - 克里克（Watson - Crick）和 hoogsteen构型下的理论红外光谱和拉曼光谱，包括非谐校正和溶剂效应。将谐波频率及其非谐校正的结果与我们之前用B3PW91杂化GGA泛函计算得到的值进行了比较。用两种不同的DFT泛函计算得到的非谐校正存在显著差异，特别是对于伸缩模式，而相应的谐波频率差异不大。对于Hoogtseen情况，G - C碱基对之间的H⁺振动可表征为非对称杜芬振荡器，因此对于涉及该质子振动的简正模式得到了不切实际的非谐校正。还分别讨论了非谐校正、溶剂效应以及糖 - 磷酸基团对沃森 - 克里克和Hoogsteen碱基对构型光谱的影响。对于沃森 - 克里克情况，还分析了堆积相互作用对理论红外光谱和拉曼光谱的影响。如果要获得与实验光谱相比正确的理论频率值归属，在我们的简正模式分析中包含非谐校正是必不可少的。
