Infrared Spectroscopy of Fluxional Molecules from (ab Initio) Molecular Dynamics: Resolving Large-Amplitude Motion, Multiple Conformations, and Permutational Symmetries.
Infrared Spectroscopy of Fluxional Molecules from (ab Initio) Molecular Dynamics: Resolving Large-Amplitude Motion, Multiple Conformations, and Permutational Symmetries.
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从头开始分子动力学的流动分子红外光谱：解决大振幅运动、多重构象和排列对称性
DOI：
10.1021/ct2006665
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发表时间：
2012
影响因子：
5.5
通讯作者：
D. Marx
中科院分区：
文献类型：
--
作者：
G. Mathias;S. D. Ivanov;A. Witt;M. D. Baer;D. Marx
由从头算分子动力学模拟生成的时间相关函数计算复杂分子的振动谱，近年来取得了可喜的进展。然而，这种光谱的分析，即原子运动的振动带的分配，绝不是直截了当的。在最近的一篇文章[J]。化学。Mathias和Baer提出了一种相应的分析方法，该方法从分子动力学轨迹中导出广义法向坐标（GNCs），该方法提供了分离振动模式的能带位置、能带形状和红外强度。这种振动分析技术依赖于通常的准刚度假设；也就是说，原子运动是通过围绕一个参考结构的小振荡来描述的。然而，如果分子经历大幅度运动并沿着轨迹访问不同的构象，或者如果原子的不同顺序可以采用相同的构象，即，如果必须考虑排列对称性，则该假设就会失效。在这里，我们提出了GNC方法的扩展，通过考虑不同构象和排列对称的多个参考结构来处理这种情况。通过引入投影技术和计算概率，将轨迹的时间框架分配给这些参考结构，振动谱通过一致的时间相关形式划分为构象贡献。对于每个构象，排列对称性被解决，这允许一个确定构象局部GNCs波段分配。对于甲基旋转的简单情况，证明了这种概括的工作原理和优点。随后应用于一个更复杂的情况：在质子化甲烷CH5+中用氘核取代一个质子后，由于CH4D+同位素具有五种不同的同位素体，因此观察到其红外光谱发生了显著变化。在这里，投影方案中总共需要120个构象和排列参考，以捕捉这个小而最松软的分子的频繁和多样的结构转变，并分配其红外光谱。扩展的GNC方法是通用的。因此，它可以很容易地应用于需要多个参考结构的系统，并且可以转移到用时间相关函数表示的其他理论光谱。
The computation of vibrational spectra of complex molecules from time correlation functions generated by ab initio molecular dynamics simulations has made lively progress in recent years. However, the analysis of such spectra, i.e., the assignment of vibrational bands to atomic motions, is by no means straightforward. In a recent article [J. Chem. Theory Comput.2011,7, 2028–2039], Mathias and Baer presented a corresponding analysis method that derives generalized normal coordinates (GNCs) from molecular dynamics trajectories, which furnish band positions, band shapes, and infrared intensities of the separated vibrational modes. This vibrational analysis technique relies on the usual quasi-rigidity assumption; i.e., atomic motions are described by small oscillations around a single reference structure. This assumption, however, breaks down if the molecule undergoes large-amplitude motion and visits different conformations along the trajectory or if the same conformation can be adopted by a different ordering of the atoms, i.e., if permutational symmetries have to be considered. Here, we present an extension of the GNC method that handles such cases by considering multiple reference structures, both for different conformations and for permutational symmetries. By introducing a projection technique and computing probabilities that assign the time frames of the trajectories to these reference structures, the vibrational spectra are split into conformational contributions via a consistent time correlation formalism. For each conformation, the permutational symmetries are resolved, which permits one to determine conformation-local GNCs for the band assignment. The working principle and the virtues of this generalization are demonstrated for the simple case of a methyl group rotation. This is followed by an application to a more intricate case: Upon replacing one proton by a deuteron in protonated methane, CH5+, significant changes of its infrared spectrum have been observed since the CH4D+isotopologue features five different isotopomers. Here, a total of 120 conformational and permutational references are required in the projection scheme in order to capture the frequent and versatile structural transitions of this small but utmost floppy molecule and to assign its infrared spectrum. The extended GNC method is general. Thus, it can be applied readily to systems that require more than one reference structure, and it can be transferred to other theoretical spectroscopies that are formulated in terms of time correlation functions.
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质子化甲烷超快时间尺度和红外光谱的量子分子动力学计算：量化同位素特定寿命
影响因子：
5.7
作者：
Alexander Witt;S. Ivanov;G. Mathias;D. Marx
通讯作者：
D. Marx
DOI：
--
发表时间：
1968
期刊：
影响因子：
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作者：
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DOI：
--
发表时间：
2009
期刊：
影响因子：
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作者：
D. Marx;J. Hutter
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J. Hutter
振动光谱作为探测蛋白质功能的工具。
影响因子：
7.8
作者：
R. Vogel;F. Siebert
通讯作者：
F. Siebert
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DOI：
--
发表时间：
1969
期刊：
影响因子：
--
作者：
S. Hsu;M. Kemp;J. M. Pochan;R. C. Benson;W. Flygare
通讯作者：
W. Flygare