Absolute and relative entropies from computer simulation with applications to ligand binding
Absolute and relative entropies from computer simulation with applications to ligand binding
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DOI：
10.1021/jp046022f
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发表时间：
2005-04-07
影响因子：
3.3
通讯作者：
Åqvist, J
中科院分区：
文献类型：
--
作者：
Carlsson, J;Åqvist, J
比较了Schlitter公式和准调和分析两种相关的方法，用分子动力学模拟从原子涨落协方差矩阵计算绝对熵。一组在气相中的有机化合物的计算相比，相应的统计热力学结果的平移和旋转熵和振动熵的实验数据。令人鼓舞的协议得到的平移熵，但对于旋转的贡献，这两种方法都未能再现理论计算值。绝对和相对振动熵被认为是更好地再现使用准谐波分析相比，Schlitter的公式。对于转动熵，我们提出了一种基于欧拉角方差的方法，该方法与理论吻合得很好。估计平移熵的基础上的主均方根（RMS）波动的质量中心的替代方法也提出了，这些再现理论计算值。这些方法被应用到苯的结合T4-溶菌酶，其中获得的平移和旋转熵与文献密切一致。
A comparison between two related methods, Schlitter's formula and quasiharmonic analysis, for calculating absolute entropies from the covariance matrix of atomic fluctuations using molecular dynamics (MD) simulations is presented. Calculations for a set of organic compounds in the gas phase are compared to the corresponding statistical thermodynamics results for translational and rotational entropies and to experimental data for vibrational entropies. Encouraging agreement is obtained for translational entropies, but for the rotational contribution, both methods fail to reproduce the theoretically calculated values. Absolute and relative vibrational entropies are found to be better reproduced using quasiharmonic analysis compared to Schlitter's formula. For rotational entropies, we propose a method based on the variances in Euler angles, which gives good agreement with theory. Alternative methods for estimating translational entropies based on principal root mean-square (rms) fluctuations of the center of mass are also presented, and these reproduce theoretically calculated values well. These methodologies are applied to the binding of benzene to T4-lysozyme, where close agreement with the literature is obtained for translational and rotational entropies.