Elliott R J, Goodfellow J M
Department of Crystallography, Birkbeck College, London, U.K.
J Theor Biol. 1987 Sep 7;128(1):121-5. doi: 10.1016/s0022-5193(87)80035-8.
Monte Carlo computer simulation techniques may be used to predict structural properties of solvent networks in helical fragments of nucleic acids, provided that suitable potential functions are available to describe the interactions between nucleic acid atoms, water and counterions. Previous studies have shown that simple non-bonded and point charge parameters are adequate for mononuclear ions such as sodium and calcium. In this study a model interaction potential for the polynuclear ammonium ion is evaluated. The parameters used take account of the distribution of charge over the constituent atoms in the ion. Simulations are carried out on the ammonium salt of a small nucleic acid crystal hydrate and a comparison is made between the predicted and experimental results. It is shown that the simulated structure is in reasonable agreement with experiment. It is therefore feasible to use this potential in studies of ammonium-containing bimolecular systems.
蒙特卡罗计算机模拟技术可用于预测核酸螺旋片段中溶剂网络的结构特性，前提是有合适的势能函数来描述核酸原子、水和抗衡离子之间的相互作用。先前的研究表明，简单的非键合和点电荷参数适用于钠和钙等单核离子。在本研究中，评估了多核铵离子的模型相互作用势。所使用的参数考虑了离子中组成原子上电荷的分布。对一种小核酸晶体水合物的铵盐进行了模拟，并对预测结果与实验结果进行了比较。结果表明，模拟结构与实验结果合理吻合。因此，在含铵双分子体系的研究中使用这种势能是可行的。
