BINDING FREE ENERGIES & EXTRACTION SELECTIVITY CALCULATIONS

在这个研究项目中，我们使用自由能微扰 分子动力学模拟在Amber 4.1和Amber中的实现 5.0程序包估算主-客体相对结合自由能 三个球体(为结合而预先组织的球形有机分子) 碱金属离子(Li、Na、K)。这项研究的结果可能是 用来提高我们预测结合自由能的能力，这 对计算机辅助药物设计有一定的参考价值。这些模拟是 在水和氯仿中都可以进行。访问分子图形 在计算机图形学讲堂，这项研究是必不可少的。在.期间 在数据准备阶段，重要的是将阳离子放置在 球腔的中间。在某些情况下，我们还尝试添加 不同数量的水进入洞穴。苦味酸根阴离子相互作用 并引入球体来模拟实验条件。 将这些客人正确定位和对接到东道主中将是 在没有3D图形洞察的情况下，这是一个非常痛苦的过程。

In this research project we are using free energy perturbation molecular dynamics simulations as implemented in AMBER 4.1 and AMBER 5.0 packages to estimate host-guest relative binding free energies of three spherands (spherical organic molecules preorganized for binding) and alkali metal ions (Li+, Na+, K+). Results of this study may be used to improve our ability to predict free energies of binding, which may be useful for computer aided drug design. The simulations were performed both in water and chloroform. Access to molecular graphics at the Computer Graphics Laoratory is essential in this study. During the data preparation stage it is important to position the cation in the middle of the spherand cavity. In some cases we also tried to add various amounts of water into the cavity. Picrate anion interacting with the spherand was introduced to simulate experimental conditions. Proper positioning and docking of these guests into the host would be a very painful process without 3D graphical insight.