School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States.
J Chem Theory Comput. 2023 Aug 22;19(16):5481-5490. doi: 10.1021/acs.jctc.2c01309. Epub 2023 Jul 29.
Low-frequency molecular vibrations at far-infrared frequencies are thermally excited at room temperature. As a consequence, thermal fluctuations are not limited to the immediate vicinity of local minima on the potential energy surface, and anharmonic properties cannot be ignored. The latter is particularly relevant in molecules with multiple conformations, such as proteins and other biomolecules. However, existing theoretical and computational frameworks for the analysis of molecular vibrations have so far been limited by harmonic or quasi-harmonic approximations, which are ill-suited to describe anharmonic low-frequency vibrations. Here, we introduce a fully anharmonic analysis of molecular vibrations based on a time correlation formalism that eliminates the need for harmonic or quasi-harmonic approximations. We use molecular dynamics simulations of a small protein to demonstrate that this new approach, in contrast to harmonic and quasi-harmonic normal modes, correctly identifies the collective degrees of freedom associated with molecular vibrations at any given frequency. This allows us to unambiguously characterize the anharmonic character of low-frequency vibrations in the far-infrared spectrum.
在室温下，远红外频率的低频分子振动被热激发。因此，热涨落并不仅限于势能表面局部极小值的紧邻区域，非谐性质也不容忽视。在具有多种构象的分子中，如蛋白质和其他生物分子，后者尤为重要。然而，迄今为止，用于分析分子振动的现有理论和计算框架一直受到谐波或准谐波近似的限制，这些近似不适用于描述非谐低频振动。在这里，我们基于时间相关形式主义引入了一种完全非谐的分子振动分析方法，该方法无需谐波或准谐波近似。我们使用小蛋白的分子动力学模拟证明，与谐波和准谐正则模式相比，这种新方法可以正确识别与任何给定频率的分子振动相关的集体自由度。这使我们能够明确地描述远红外光谱中低频振动的非谐特性。
