Kubelka Jan, Huang Rong, Keiderling Timothy A
Department of Chemistry (M/C 111), University of Illinois at Chicago, 845 W. Taylor Street, room 4500 SES, Chicago, Illinois 60607-7061, USA.
J Phys Chem B. 2005 Apr 28;109(16):8231-43. doi: 10.1021/jp0506078.
Simulations of IR and VCD spectra are carried out for model alpha-helical, 3(10)-helical, and 3(1)-helical (polyProII-like) oligopeptides, with up to 21 amide groups, and including explicit consideration of effects of directly hydrogen-bonded solvent (water). Parameters used were obtained from ab initio density functional theory (DFT) computations of force field, atomic polar and axial tensors for oligopeptides of 5 to 7 amides, whose structures were constrained in (phi,psi) to target the secondary structure type but otherwise fully optimized. By comparison with experimental data as well as with calculations for identical but isolated (gas phase) peptides, the computed effects of an inner shell of aqueous solvent on the vibrational spectra of helical oligopeptides are illustrated. The interaction with solvent causes significant frequency shifts of the amide bands, but only minor changes in the characteristic IR intensity distributions and splittings and the VCD band shapes. Better agreement with experimental band shapes is achieved for the alpha-helical amide I' (N-deuterated) VCD by inclusion of explicit solvent in the calculations. Some improvements are also observed in theoretical VCD predictions for 13C labeled alpha-helical peptides when solvated models are used. However, the qualitative isotopic splitting patterns are preserved and just shifted in frequency due to consistent, solvent independent interamide coupling constants. The critical match of experiment and theory for relative positions of transitions in peptides with specifically separated 13C=O labels, including and neglecting solvent, confirms the stability of the coupling interactions. Despite these solvation effects, the calculated VCD band shape of the amide I mode is shown to be a reliable conformational probe, since it remains basically insensitive to frequency shifts caused by environment. Thus theoretical VCD simulations, even vacuum calculations, are shown to provide useful spectral predictions for solution-phase peptides.
对含有多达21个酰胺基团的α-螺旋、3(10)-螺旋和3(1)-螺旋（类聚脯氨酸II）寡肽模型进行了红外（IR）和振动圆二色性（VCD）光谱模拟，其中明确考虑了直接氢键合溶剂（水）的影响。所使用的参数来自对5至7个酰胺的寡肽的力场、原子极化张量和轴向张量的从头算密度泛函理论（DFT）计算，这些寡肽的结构在(φ,ψ)中受到约束以靶向二级结构类型，但在其他方面进行了完全优化。通过与实验数据以及相同但孤立的（气相）肽的计算结果进行比较，说明了水溶剂内壳层对螺旋寡肽振动光谱的计算影响。与溶剂的相互作用导致酰胺带发生显著的频率位移，但对特征红外强度分布、分裂以及VCD带形状的影响较小。通过在计算中包含明确的溶剂，α-螺旋酰胺I'（N-氘代）VCD与实验带形状的一致性更好。当使用溶剂化模型时，在13C标记的α-螺旋肽的理论VCD预测中也观察到了一些改进。然而，定性的同位素分裂模式得以保留，只是由于一致的、与溶剂无关的酰胺间耦合常数而在频率上发生了偏移。对于具有特定分离的13C=O标记的肽，包括和忽略溶剂时，实验与理论在跃迁相对位置上的关键匹配证实了耦合相互作用的稳定性。尽管存在这些溶剂化效应，但酰胺I模式的计算VCD带形状被证明是一种可靠的构象探针，因为它对环境引起的频率位移基本不敏感。因此，理论VCD模拟，甚至真空计算，都被证明可为溶液相肽提供有用的光谱预测。
