Raman optical activity of a cyclic dipeptide analyzed by quantum chemical calculations combined with molecular dynamics simulations.
Raman optical activity of a cyclic dipeptide analyzed by quantum chemical calculations combined with molecular dynamics simulations.
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DOI：
10.1021/jp503874z
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发表时间：
2014-06
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影响因子：
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通讯作者：
Hiroyasu Urago;T. Suga;Taiki Hirata;H. Kodama;M. Unno
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作者：
Hiroyasu Urago;T. Suga;Taiki Hirata;H. Kodama;M. Unno
拉曼光学活性（ROA）测量了左右圆偏振拉曼散射光的不同强度，并提供了与振动模式相关的手性信息。由于对细微的结构和环境变化具有很高的敏感性，对ROA光谱的解释通常依赖于量子化学模拟。计算化学的最新进展使我们能够考虑从分子动力学（MD）模拟中得出的显式溶剂模型来计算拉曼和ROA光谱。显式溶剂模型的一个重要问题是导致观测光谱和计算光谱之间良好一致的MD快照的数量。在本研究中，我们测量了cyclo（L-Ala-Gly）的拉曼光谱和ROA光谱，然后利用密度泛函理论结合MD模拟对光谱进行了模拟。虽然环（L-Ala-Gly）是一种相对刚性的环状分子，但从MD计算中发现了船向上和船向下的构象。由于两种构象的拉曼光谱除了频率较低之外是相似的，所以~ 10 MD快照能够再现观测到的拉曼光谱的主要特征。相比之下，需要大量的MD快照来重现ROA光谱。在800-1580 cm（-1）的中频区域，平均约40个谱线使得观测谱线与计算谱线吻合良好。另一方面，低（0-800 cm(-1)）和高（1580-1800 cm(-1)）频率区域分别需要超过60和120 MD快照。低频区域的拉曼和ROA光谱相对较宽，这样的光谱特征需要较多的平均光谱数。光谱的高频区由酰胺I波段组成，主要是C = O拉伸振动。由于酰胺I波段的ROA强度和频率对结构和环境差异高度敏感，因此需要对大量光谱进行平均，以再现观测到的ROA光谱中的小负特征。
Raman optical activity (ROA) measures the different intensity of right- and left-circularly polarized Raman scattered light and provides information on chirality associated with vibrational modes. Because of a high sensitivity to subtle structural and environmental changes, interpretations of ROA spectra usually rely on quantum chemical simulations. Recent advances in computational chemistry allow us to consider explicit solvent models that are derived from molecular dynamics (MD) simulations to compute the Raman and ROA spectra. An important concern for the explicit solvent models is the number of MD snapshots that lead to a good agreement between the observed and calculated spectra. In the present study, we measured the Raman and ROA spectra of cyclo(L-Ala-Gly) and then simulated the spectra using density functional theory combined with MD simulations. Although cyclo(L-Ala-Gly) is a relatively rigid cyclic molecule, boat-up and boat-down conformations were found from the MD calculations. Because the Raman spectra of the two conformations are similar except for a lower frequency region, ∼10 MD snapshots are capable of reproducing the main features of the observed Raman spectra. In contrast, a larger number of MD snapshots was required to reproduce the ROA spectra. In the middle freqency region of 800-1580 cm(-1), an average of ∼40 spectra led to good agreement between the observed and calculated spectra. On the other hand, the low (0-800 cm(-1)) and high (1580-1800 cm(-1)) frequency regions require more than 60 and 120 MD snapshots, respectively. The Raman and ROA spectra in the low frequency region are relatively broad, and such spectral features require a larger number of averaged spectra. The high frequency region of the spectra consists of an amide I band, which is primarily a C═O stretching vibration. Since both the ROA intensity and frequency of the amide I band are highly sensitive to structural and environmental differences, a large number of the spectra need to be averaged to reproduce the small negative features in the observed ROA spectra.