Multistate lambda-local-elevation umbrella-sampling (MS-lambda-LEUS): method and application to the complexation of cations by crown ethers.
Multistate lambda-local-elevation umbrella-sampling (MS-lambda-LEUS): method and application to the complexation of cations by crown ethers.
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DOI：
10.1021/acs.jctc.5b00118
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发表时间：
2015-06-09
影响因子：
5.5
通讯作者：
Hunenberger, Philippe H
中科院分区：
文献类型：
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作者：
Bieler, Noah S;Tschopp, Jan P;Hunenberger, Philippe H
Lambda-Local-Elevation伞采样（Lambda-Leus）方案的扩展[Bieler等。 J. Chem。理论计算。提出了2014，10，3006]来处理多态（MS）情况，即基于单个模拟的多个物理状态的相对自由能的计算。 MS-Lambda-Leus方法的关键要素是使用单个耦合变量lambda以环状方式控制感兴趣状态之间的连续成对突变。 lambda变量被动态传播作为扩展系统变量，使用与lambda-leus中的坐标转换和基于内存的偏置潜力。与其他可用的MS方案（一步扰动，包裹分布采样和常规lambda-demanics）相比，提出的方法具有许多重要的优势，即：（i）物理状态被明确访问，并在有限的时间段内访问； （ii）确保过渡所需的非物理空间的程度，尤其是一维； （iii）设置协议仅需要物理状态的拓扑； （iv）该方法仅需要在能够处理两州突变的模拟代码中进行有限的修改。作为初始应用，计算了三种不同溶剂中五个碱阳离子与三个冠状醚的绝对结合自由能。发现该结果是在定性上重现的主要实验趋势，尤其是水和甲醇中K（+）的18c6的实验选择性，这是用阳离子沿阳离子循环序列的相反趋势来解释的。阳离子和复合物内的直接静电相互作用。
An extension of the lambda-local-elevation umbrella-sampling (lambda-LEUS) scheme [ Bieler et al. J. Chem. Theory Comput. 2014 , 10 , 3006 ] is proposed to handle the multistate (MS) situation, i.e. the calculation of the relative free energies of multiple physical states based on a single simulation. The key element of the MS-lambda-LEUS approach is to use a single coupling variable Lambda controlling successive pairwise mutations between the states of interest in a cyclic fashion. The Lambda variable is propagated dynamically as an extended-system variable, using a coordinate transformation with plateaus and a memory-based biasing potential as in lambda-LEUS. Compared to other available MS schemes (one-step perturbation, enveloping distribution sampling and conventional lambda-dynamics) the proposed method presents a number of important advantages, namely: (i) the physical states are visited explicitly and over finite time periods; (ii) the extent of unphysical space required to ensure transitions is kept minimal and, in particular, one-dimensional; (iii) the setup protocol solely requires the topologies of the physical states; and (iv) the method only requires limited modifications in a simulation code capable of handling two-state mutations. As an initial application, the absolute binding free energies of five alkali cations to three crown ethers in three different solvents are calculated. The results are found to reproduce qualitatively the main experimental trends and, in particular, the experimental selectivity of 18C6 for K(+) in water and methanol, which is interpreted in terms of opposing trends along the cation series between the solvation free energy of the cation and the direct electrostatic interactions within the complex.