Fuentes-Cabrera Miguel, Zhao Xiongce, Kent P R C, Sumpter Bobby G
Center for Nanophase Materials Sciences and Computer Science and Mathematics Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, Tennessee 37831-6494, USA.
J Phys Chem B. 2007 Aug 2;111(30):9057-61. doi: 10.1021/jp0729056.
xDNA is an artificial duplex made of natural and benzo-homologated bases. The latter can be seen as a fusion between benzene and a natural base. We have used two different ab initio techniques, one based on B3LYP and a Gaussian expansion of the wave functions, and the other on GGA and plane-waves, to investigate the electronic properties of an xDNA duplex and a natural one with an analogous sequence. The calculations were performed in dry conditions, i.e., H atoms were used to neutralize the charge. It is found that the HOMO-LUMO gap of xDNA is about 0.5 eV smaller than that of B-DNA, independent of the technique used. The pi-pi* gap of xDNA is 1.3 or 1.0 eV smaller than that of B-DNA, depending on whether one uses B3LYP/6-31G or GGA/plane-waves, respectively. An analysis of how saturation changes the electronic properties of the nucleotide pairs that make up these duplexes suggests that different saturation schemes significantly affect the HOMO-LUMO gap value of xDNA and B-DNA. The same is not true for the pi-pi* gap. That xDNA has a smaller pi-pi* gap than B-DNA suggests that xDNA could be a plausible candidate for molecular-wire applications.
xDNA是一种由天然碱基和苯并同系物碱基构成的人工双链体。后者可视为苯与天然碱基的融合体。我们使用了两种不同的从头算技术，一种基于B3LYP和波函数的高斯展开，另一种基于广义梯度近似（GGA）和平面波，来研究xDNA双链体和具有相似序列的天然双链体的电子性质。计算是在干燥条件下进行的，即使用氢原子来中和电荷。结果发现，xDNA的最高占据分子轨道（HOMO）-最低未占据分子轨道（LUMO）能隙比B-DNA的小约0.5电子伏特，与所使用的技术无关。xDNA的π-π能隙比B-DNA的小1.3或1.0电子伏特，这取决于分别使用的是B3LYP/6-31G还是GGA/平面波。对饱和度如何改变构成这些双链体的核苷酸对的电子性质的分析表明，不同的饱和方案会显著影响xDNA和B-DNA的HOMO-LUMO能隙值。对于π-π能隙则并非如此。xDNA的π-π*能隙比B-DNA的小，这表明xDNA可能是分子导线应用的一个合理候选者。
