Mulliken Center for Theoretical Chemistry, University of Bonn , D-53115 Bonn, Germany.
J Am Chem Soc. 2017 Aug 30;139(34):11682-11685. doi: 10.1021/jacs.7b05833. Epub 2017 Aug 18.
A fully quantum mechanical (QM) treatment to calculate electronic absorption (UV-vis) and circular dichroism (CD) spectra of typical biomolecules with thousands of atoms is presented. With our highly efficient sTDA-xTB method, spectra averaged along structures from molecular dynamics (MD) simulations can be computed in a reasonable time frame on standard desktop computers. This way, nonequilibrium structure and conformational, as well as purely quantum mechanical effects like charge-transfer or exciton-coupling, are included. Different from other contemporary approaches, the entire system is treated quantum mechanically and neither fragmentation nor system-specific adjustment is necessary. Among the systems considered are a large DNA fragment, oligopeptides, and even entire proteins in an implicit solvent. We propose the method in tandem with experimental spectroscopy or X-ray studies for the elucidation of complex (bio)molecular structures including metallo-proteins like myoglobin.
本文提出了一种完全量子力学（QM）方法，用于计算具有数千个原子的典型生物分子的电子吸收（UV-vis）和圆二色性（CD）光谱。通过我们高效的 sTDA-xTB 方法，可以在标准台式计算机上合理的时间内计算出沿分子动力学（MD）模拟结构平均的光谱。这样，就可以包括非平衡结构和构象，以及电荷转移或激子耦合等纯量子力学效应。与其他现代方法不同，整个系统都被量子力学处理，不需要进行碎片处理或针对系统的调整。所考虑的系统包括大的 DNA 片段、寡肽，甚至是在隐溶剂中的完整蛋白质。我们提出了这种方法，与实验光谱学或 X 射线研究相结合，用于阐明包括肌红蛋白等金属蛋白在内的复杂（生物）分子结构。
