EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9ST, United Kingdom.
J Comput Chem. 2012 Oct 15;33(27):2161-72. doi: 10.1002/jcc.23052. Epub 2012 Jun 25.
The potential energy surfaces of stacked uracil dimer (U/U) and stacked thymine dimer (T/T) have been explored at the counterpoise (CP)-corrected M06-2X/6-31+G(d) level of theory, in the gas phase and in solution (with water and, for U/U, 1,4-dioxane as the solvents) modeled by a continuum solvent using the polarizable continuum model. Potential energy scans were created by rotation of one monomer around its center-of-mass, whereas the other monomer remained still. Both face-to-back (one molecule exactly on top of the other) and face-to-face (one base molecule flipped by 180°) structures were considered. Five or six (dependent on whether CP correction is included or not) stacked uracil dimer minima and six stacked thymine dimer minima were located. A number of transition states on the U/U and T/T potential energy surfaces were likewise identified. The general effect of the continuum solvent is a flattening of the potential energy surface. Comparison of the gas-phase M06-2X/6-31+G(d) U/U interaction energies with estimated CCSD(T)/complete basis set values (where available) show the excellent performance of this functional for stacking energies.
已在气相和溶液（以水和 1,4-二恶烷作为溶剂，通过极化连续模型模拟）中，在 CP 校正的 M06-2X/6-31+G(d)理论水平上，对堆积尿嘧啶二聚体（U/U）和堆积胸腺嘧啶二聚体（T/T）的势能面进行了研究。通过一个单体绕质心的旋转来创建势能扫描，而另一个单体保持静止。同时考虑了面对面（一个碱基分子翻转 180°）和面对面（一个分子完全在另一个分子的顶部）两种结构。确定了五个或六个（取决于是否包括 CP 校正）堆积尿嘧啶二聚体的极小值和六个堆积胸腺嘧啶二聚体的极小值。同样在 U/U 和 T/T 势能表面上识别了一些过渡态。连续溶剂的一般影响是使势能面变平。气相 M06-2X/6-31+G(d) U/U 相互作用能与估计的 CCSD(T)/完全基组值（在可用的情况下）的比较表明，该函数在堆积能方面具有出色的性能。
