Rezác Jan, Hobza Pavel
Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Flemingovo nám. 2, 16610 Prague 6, Czech Republic.
Chemistry. 2007;13(10):2983-9. doi: 10.1002/chem.200601120.
The unwinding free energy of 128 DNA octamers was correlated with the sum of interaction energies among DNA bases and their solvation energies. The former energies were determined by using the recently developed density functional theory procedure augmented by London dispersion energy (RI-DFT-D) that provides accurate hydrogen-bonding and stacking energies highly comparable with CCSD(T)/complete basis set limit benchmark data. Efficient tight-binding DFT covering dispersion energy was also used and yielded satisfactory results. The latter method can be used for extended systems. The solvation energy was determined by using a C-PCM continuum solvent at HF level calculations. Various models were adopted to correlate theoretical energies with experimental unwinding free energies. Unless all energy components (hydrogen-bonding, intra- and interstrand-stacking, and solvation energies) were included and weighted individually, no satisfactory correlation resulted. The most advanced model yielded very close correlation (RMSE=0.32 kcal mol(-1)) fully comparable with the entirely empirical correlation introduced in the original paper. Analysis of the theoretical results shows the importance of inter- and intramolecular stacking energies, and especially the latter term plays a key role in determining DNA-duplex stabilization.
128个DNA八聚体的解旋自由能与DNA碱基间相互作用能及其溶剂化能之和相关。前者的能量通过使用最近开发的密度泛函理论程序（该程序通过伦敦色散能增强，即RI-DFT-D）来确定，该程序提供的精确氢键和堆积能与CCSD(T)/完全基组极限基准数据高度可比。还使用了涵盖色散能的高效紧束缚DFT，结果令人满意。后一种方法可用于扩展体系。溶剂化能通过在HF水平计算中使用C-PCM连续介质溶剂来确定。采用了各种模型将理论能量与实验解旋自由能相关联。除非包含所有能量成分（氢键、链内和链间堆积以及溶剂化能）并分别加权，否则不会得到令人满意的相关性。最先进的模型产生了非常紧密的相关性（RMSE = 0.32 kcal mol⁻¹），与原始论文中引入的完全经验性相关性完全可比。对理论结果的分析表明了分子间和分子内堆积能的重要性，尤其是后一项在确定DNA双链稳定性中起关键作用。
