Reha D, Valdés H, Vondrásek J, Hobza P, Abu-Riziq Ali, Crews Bridgit, de Vries Mattanjah S
Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Center for Biomolecules and Complex Molecular Systems, Prague, Czech Republic.
Chemistry. 2005 Nov 18;11(23):6803-17. doi: 10.1002/chem.200500465.
We investigated the potential-energy surface (PES) of the phenylalanyl-glycyl-glycine tripeptide in the gas phase by means of IR/UV double-resonance spectroscopy, and quantum chemical and statistical thermodynamic calculations. Experimentally, we observed four conformational structures and we recorded their IR spectra in the spectral region of 3000-4000 cm(-1). Computationally, we investigated the PES by a combination of molecular dynamics/quenching procedures with high-level correlated ab initio calculations. We found that neither empirical potentials nor various DFT functionals provide satisfactory results. On the other hand, the approximative DFT method covering the dispersion energy yields a reliable set of the most stable structures, which we subsequently investigated with an accurate, correlated ab initio treatment. The global minimum contains three moderately strong intramolecular hydrogen bonds and is mainly stabilized by London dispersion forces between the phenyl ring, the carboxylic acid group, and various peptide bonds. A proper description of the last type of interaction requires accurate correlated ab initio calculations, including the complete basis set limit of the MP2 method and CCSD(T) correction terms. Since in our beam experiments the conformations are frozen by cooling from a higher temperature, it is necessary to localize the most stable structures on the free-energy surface rather than on the PES. We used two different procedures (rigid rotor/harmonic oscillator/ideal gas approximation based on ab initio characteristics and evaluation of relative populations from the molecular dynamic simulations using the AMBER potential) and both yield four structures, the global minimum and three local minima. These four structures were among the 15 most energetically stable structures obtained from accurate ab initio optimization. The calculated IR spectra for these four structures agree well with the experimental frequencies, which validates the localization procedure.
我们通过红外/紫外双共振光谱法以及量子化学和统计热力学计算，研究了气相中苯丙氨酰 - 甘氨酰 - 甘氨酸三肽的势能面（PES）。实验上，我们观测到了四种构象结构，并记录了它们在3000 - 4000 cm⁻¹光谱区域的红外光谱。计算方面，我们通过分子动力学/猝灭程序与高水平相关从头算相结合的方法研究了PES。我们发现经验势和各种密度泛函理论（DFT）泛函都不能提供令人满意的结果。另一方面，涵盖色散能的近似DFT方法产生了一组可靠的最稳定结构，随后我们用精确的相关从头算处理对其进行了研究。全局最小值包含三个中等强度的分子内氢键，并且主要通过苯环、羧酸基团和各种肽键之间的伦敦色散力得以稳定。对最后一种相互作用类型的恰当描述需要精确的相关从头算计算，包括MP2方法的完整基组极限和CCSD(T)校正项。由于在我们的束流实验中，构象是通过从较高温度冷却而冻结的，因此有必要在自由能面上而不是在PES上定位最稳定的结构。我们使用了两种不同的程序（基于从头算特征的刚性转子/谐振子/理想气体近似以及使用AMBER势从分子动力学模拟中评估相对丰度），两者都产生了四种结构，即全局最小值和三个局部最小值。这四种结构在通过精确从头算优化得到的15个能量最稳定的结构之中。这四种结构的计算红外光谱与实验频率吻合得很好，这验证了定位程序。
