平面DNA碱基对的密度泛函计算
Density functional calculations of planar DNA base-pairs
摘要：
本文用密度泛函理论对核酸DNA碱基（鸟嘌呤、腺嘌呤、胞嘧啶和胸腺嘧啶）和30种不同的DNA碱基对的几何构型和能量进行了系统的研究。我们使用最近开发的线性标度DFT计划，这是特别适合于大量的原子系统。作为研究大DNA系统的第一步，在这项工作中：（i）我们建立我们的方法（包括赝势和基组）的近似的可靠性的氢键碱基对的描述，通过比较我们的结果与以前的计算。结果表明，在Hartree-Fock几何构型下的相互作用能与二阶Møller-Plesset（MP2）微扰理论（目前对碱基对大小的体系最精确的微扰理论）的相互作用能非常一致. (ii)我们对30种不同的DNA碱基对进行DFT结构优化，其中只有三种是以前用DFT研究过的。我们的研究结果提供了信息的相关性对其他27个碱基对的结构的影响，只有Hartree-Fock几何形状以前可用。
英文摘要：
We present a systematic Density Functional Theory (DFT) study of geometries and energies of the nucleic acid DNA bases (guanine, adenine, cytosine and thymine) and 30 different DNA base-pairs. We use a recently developed linear-scaling DFT scheme, which is specially suited for systems with large numbers of atoms. As a first step towards the study of large DNA systems, in this work: (i) We establish the reliability of the approximations of our method (including pseudopotentials and basis sets) for the description of the hydrogen-bonded base pairs, by comparing our results with those of former calculations. We show that the interaction energies at Hartree-Fock geometries are in very good agreement with those of second order Møller-Plesset (MP2) perturbation theory (the most accurate technique that can be applied at present for system of the sizes of the base-pairs). (ii) We perform DFT structural optimizations for the 30 different DNA base-pairs, only three of which had been previously studied with DFT. Our results provide information on the effect of correlation on the structure of the other 27 base pairs, for which only Hartree-Fock geometries were formerly available.
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