Lehrstuhl für Biomolekulare Optik, Ludwig-Maximilians-Universität, Oettingenstr. 67, 80538 München, Germany.
J Phys Chem B. 2011 Mar 10;115(9):2117-23. doi: 10.1021/jp111334z. Epub 2011 Feb 10.
The functional reactions in blue light photoreceptors generally involve transiently reduced flavins exhibiting characteristic infrared (IR) spectra. To approach a theoretical understanding, here we apply density functional theory (DFT) to flavin radicals embedded in a molecular mechanics (MM) model of an aqueous solution. Combining a DFT/MM approach with instantaneous normal-mode analyses (INMA), we compute the IR solution spectra of anionic and neutral flavin radicals. For a set of mid-IR marker bands, we identify those changes of spectral locations, intensities, and widths, which are caused by sequentially adding an electron and a proton to the oxidized flavin. Comparisons with experimental IR solution spectra of flavin radicals show the accuracy of our DFT/MM-INMA approach and allow us to assign the observed bands. The room temperature ensembles of solvent cages required for the INMA calculations of the IR spectra are generated in an MM setting from molecular dynamics (MD) simulations. For the solvated flavin radicals, these MD simulations employ MM force fields derived from DFT/MM calculations.
蓝光光感受器中的功能反应通常涉及瞬态还原的黄素，其表现出特征性的红外（IR）光谱。为了达到理论理解，我们在这里将密度泛函理论（DFT）应用于水相溶液的分子力学（MM）模型中嵌入的黄素自由基。通过将 DFT/MM 方法与瞬时法向模式分析（INMA）相结合，我们计算了阴离子和中性黄素自由基的 IR 溶液光谱。对于一组中红外标记带，我们确定了光谱位置、强度和宽度的变化，这些变化是由于向氧化黄素中依次添加一个电子和一个质子引起的。与黄素自由基的实验 IR 溶液光谱的比较表明了我们的 DFT/MM-INMA 方法的准确性，并允许我们对观察到的带进行分配。为了进行 IR 光谱的 INMA 计算，需要生成室温溶剂笼的集合体，这是在 MM 设置中从分子动力学（MD）模拟生成的。对于溶剂化的黄素自由基，这些 MD 模拟使用从 DFT/MM 计算中得出的 MM 力场。
