BINDING FREE ENERGIES & EXTRACTION SELECTIVITY CALCULATIONS

在我们的研究项目自由能微扰分子 在AMBER 4.1和AMBER 5.0中实施的动力学模拟 包用于估计主机-来宾相对绑定空闲 三个球状体的能量（球状有机分子预组织 用于结合）和碱金属离子（Li+、Na+、K+）。 成果 研究可以用来提高我们预测自由能的能力， 绑定，这可能是有用的计算机辅助药物设计。 的 在水和氯仿中进行模拟。 分子 图形用于准备输入结构以及评估 这些过程涉及阳离子结合。 是非常重要 将阳离子放置在球体空腔的中间。 在一些 在某些情况下，我们还尝试向空腔中加入不同数量的水。 分子图谱是正确定位客体的必要工具 进入宿主体腔

In our research project free energy perturbation molecular dynamics simulations as implemented in AMBER 4.1 and AMBER 5.0 packages are used 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 are performed both in water and chloroform. Molecular graphics is used to prepare the input structure as well as to evaluate the processes invoved in cation binding. It is very 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. Molecular graphcs is a necessary tool to correctly position the guests into the host cavity.