Theoretical studies on sulfur and metal cation (Cu(II), Ni(II), Pd(II), and Pt(II))-containing artificial DNA.
Theoretical studies on sulfur and metal cation (Cu(II), Ni(II), Pd(II), and Pt(II))-containing artificial DNA.
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DOI：
10.1021/jp9045319
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发表时间：
2009-08
期刊：
影响因子：
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通讯作者：
Toru Matsui;Hideaki Miyachi;Yasuyuki Nakanishi;Y. Shigeta;Takeshi Sato;Y. Kitagawa;M. Okumura;K. Hira
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文献类型：
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作者：
Toru Matsui;Hideaki Miyachi;Yasuyuki Nakanishi;Y. Shigeta;Takeshi Sato;Y. Kitagawa;M. Okumura;K. Hira
我们用密度泛函理论（DFT）研究了[S-M（II）-S]（M=Ni，Pd，Pt，S：hydroxypyridinethione）的稳定性、紫外-可见光谱和堆积的可能性。我们计算了硫族元素原子和金属阳离子的可能组合的改性碱的形成能。结果证实，[H-Ni（II）-H]（H：羟基吡啶酮）、[H-Cu（II）-H]和[S-Cu（II）-S]将形成稳定的金属-碱基配对;另一方面，[H-Zn（II）-H]、[S-Zn（II）-S]和[H-Pt（II）-H]将不形成稳定的金属-碱基配对。我们预测了400-410 nm处的紫外-可见光激发，主要由[S-M（II）-S]中的d-pi * 跃迁伴随pi-pi * 跃迁主导，其中金属到配体的电荷转移移动了S的峰（没有金属阳离子）通过执行时间依赖性密度泛函理论（TDDFT）计算。通过对杂化DFT结果进行Anderson-Langreth-Lundqvist货车der Waals修正，估算了[S-M（II）-S]碱基对间的相互作用能.根据这些结果，[S-M（II）-S]单体之间的相互作用对于所有情况都是有吸引力的，使得含金属DNA的形成的选择性主要由水相中碱基对的形成和仅轻微地由修饰的碱基之间的π-π堆积相互作用来控制。
We evaluated the stability, UV-vis spectra, and possibility of stacking of [S-M(II)-S] (M=Ni, Pd, Pt, S: hydroxypyridinethione) using density functional theory (DFT). We calculated the formation energies of modified bases with possible combinations of chalcogen atoms and metal cations. The results confirmed that [H-Ni(II)-H] (H: hydroxypyridone), [H-Cu(II)-H], and [S-Cu(II)-S] would form stable metal-base pairing; on the other hand, [H-Zn(II)-H], [S-Zn(II)-S], and [H-Pt(II)-H] would not. We predicted UV-vis excitations at 400-410 nm, mainly dominated by a d-pi* transition accompanied by a pi-pi* transition in [S-M(II)-S], where a metal-to-ligand charge transfer shifts the peak of S (without metal cations) by performing time-dependent density functional theory (TDDFT) calculations. By adding the Andersson-Langreth-Lundqvist van der Waals correction to the hybrid DFT results, we estimated the interaction energy between base pairs of [S-M(II)-S]. According to the results, the interaction between [S-M(II)-S] monomers for all cases is attractive, so that the selectivity of formation of the metal-containing DNA is governed mainly by the formation of the base pair in the aqueous phase and only slightly by the pi-pi stacking interaction between the modified bases.