A theoretical study on the water structure for nucleic acids bases and base pairs in solution at T=300 K
A theoretical study on the water structure for nucleic acids bases and base pairs in solution at T=300 K
复制标题
T=300 K溶液中核酸碱基和碱基对水结构的理论研究
DOI：
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发表时间：
1980
期刊：
影响因子：
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通讯作者：
G. Corongiu
中科院分区：
文献类型：
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作者：
E. Clementi;G. Corongiu
蒙特卡罗模拟的碱基A，C，G，T，和U封闭在一个集群的40个水分子和碱基对A-T，G-C，和A-U封闭在一个集群的50个水分子。这些计算是在300 K的模拟温度下进行的。通过对T=100 K时腺嘌呤的MC模拟，说明了温度效应的重要性。分子间的相互作用是用从水-水和水基复合物的量子力学计算中获得的原子-原子对势计算的。通过氢原子和氧原子的概率分布图，确定了水分子在第一层水化壳层中的位置和取向。初步提出了碱基和碱基对周围的水结构与B‐DNA双螺旋大、小沟水结构之间的关系。
Monte Carlo simulations are presented for the bases A, C, G, T, and U enclosed in a cluster of forty water molecules and for the base pairs A–T, G–C, and A–U enclosed in a cluster of fifty water molecules. These computations are carried out at a simulated temperature of 300 K. The importance of the temperature effect is shown by carrying the MC simulation for adenine at T=100 K. The intermolecular interactions are computed with atom–atom pair potentials obtained from quantum‐mechanical calculations on the water–water and water–base complexes. The identification of the positions and orientations for the water molecules in the first hydration shell is obtained from hydrogen and oxygen atoms probability distribution maps. Relations between the water structure around the bases and base pairs and the water structure in the major and minor groove of B‐DNA double helix are preliminarily presented.