Cerný Jirí, Hobza Pavel
Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic.
Phys Chem Chem Phys. 2005 Apr 21;7(8):1624-6. doi: 10.1039/b502769c.
The performance of the recently introduced X3LYP density functional which was claimed to significantly improve the accuracy for H-bonded and van der Waals complexes was tested for extended H-bonded and stacked complexes (nucleic acid base pairs and amino acid pairs). In the case of planar H-bonded complexes (guanine...cytosine, adenine...thymine) the DFT results nicely agree with accurate correlated ab initio results. For the stacked pairs (uracil dimer, cytosine dimer, adenine...thymine and guanine...cytosine) the DFT fails completely and it was even not able to localize any minimum at the stacked subspace of the potential energy surface. The geometry optimization of all these stacked clusters leads systematically to the planar H-bonded pairs. The amino acid pairs were investigated in the crystal geometry. DFT again strongly underestimates the accurate correlated ab initio stabilization energies and usually it was not able to describe the stabilization of a pair. The X3LYP functional thus behaves similarly to other current functionals. Stacking of nucleic acid bases as well as interaction of amino acids was described satisfactorily by using the tight-binding DFT method, which explicitly covers the London dispersion energy.
对最近引入的X3LYP密度泛函进行了测试，该泛函据称能显著提高氢键和范德华复合物的精度，测试对象为扩展的氢键和堆积复合物（核酸碱基对和氨基酸对）。对于平面氢键复合物（鸟嘌呤……胞嘧啶、腺嘌呤……胸腺嘧啶），密度泛函理论（DFT）结果与精确的相关从头算结果吻合良好。对于堆积对（尿嘧啶二聚体、胞嘧啶二聚体、腺嘌呤……胸腺嘧啶和鸟嘌呤……胞嘧啶），DFT完全失效，甚至无法在势能面的堆积子空间中定位任何最小值。所有这些堆积簇的几何优化系统地导致了平面氢键对。在晶体几何结构中研究了氨基酸对。DFT再次严重低估了精确的相关从头算稳定能，通常无法描述一对的稳定性。因此，X3LYP泛函的表现与其他当前泛函类似。通过使用明确涵盖伦敦色散能的紧束缚DFT方法，可以令人满意地描述核酸碱基的堆积以及氨基酸的相互作用。
