论文标题
实现溶液中生物分子的结构波动：广义Langevin模式分析
Realization of the structural fluctuation of biomolecules in solution: Generalized Langevin Mode Analysis
论文作者
论文摘要
提出了一种新的理论方法，称为广义Langevin模式分析（GLMA），以分析溶液中生物分子的结构波动模式。该方法结合了统计力学中的两种理论，即广义的Langevin理论和RISM/3D-RISM理论，以计算水溶液中生物分子的自由分子的自由能表面的第二个衍生物或Hessian矩阵，该溶液中的生物分子的自由能表面由生物分子溶液中的分子相互作用组成。该方法用于计算水中丙氨酸二肽的波数光谱，可与光学杂项探测的拉曼诱导的光谱（Rikes）光谱相比，可以与之进行比较。 The theoretical analysis reproduced the main features of the experimental spectrum with respect to the peak positions of the four bands around ~90 cm-1, ~240 cm-1, ~370 cm-1, and 400 cm-1, observed in the experimental spectrum, in spite that the physics involved in the two spectrum was not exactly the same: the experimental spectrum includes the contributions from the dipeptide and the water molecules interacting with the溶质，而理论上只是与溶质分子有关，受溶剂的影响。理论和实验光谱之间的两个主要差异，一个在〜100 cm-1左右的频带强度中，另一个在约370 cm-1左右的峰位置中，另一个是根据与二肽相互作用的波动模式讨论的，在理论分析中没有明确考虑。
A new theoretical method, referred to as Generalized Langevin Mode Analysis (GLMA), is proposed to analyze the mode of structural fluctuations of a biomolecule in solution. The method combines the two theories in the statistical mechanics, or the Generalized Langevin theory and the RISM/3D-RISM theory, to calculate the second derivative, or the Hessian matrix, of the free energy surface of a biomolecule in aqueous solution, which consists of the intramolecular interaction among atoms in the biomolecule and the solvation free energy. The method is applied to calculate the wave-number spectrum of an alanine dipeptide in water for which the optical heterodyne-detected Raman-induced spectroscopy (RIKES) spectrum is available to compare with. The theoretical analysis reproduced the main features of the experimental spectrum with respect to the peak positions of the four bands around ~90 cm-1, ~240 cm-1, ~370 cm-1, and 400 cm-1, observed in the experimental spectrum, in spite that the physics involved in the two spectrum was not exactly the same: the experimental spectrum includes the contributions from the dipeptide and the water molecules interacting with the solute, while the theoretical one is just concerned with the solute molecule, influenced by solvation. Two major discrepancies between the theoretical and experimental spectra, one in the band intensity around ~100 cm-1, and the other in the peak positions around ~370 cm-1, are discussed in terms of the fluctuation mode of water molecules interacting with the dipeptide, which is not taken explicitly into account in the theoretical analysis.
