Prediction of nitroxide hyperfine coupling constants in solution from combined nanosecond scale simulations and quantum computations.
Prediction of nitroxide hyperfine coupling constants in solution from combined nanosecond scale simulations and quantum computations.
复制标题
通过结合纳秒级模拟和量子计算来预测溶液中氮氧自由基超精细耦合常数。
DOI：
10.1063/1.2939121
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发表时间：
2008
期刊：
影响因子：
--
通讯作者：
D. Siri
中科院分区：
文献类型：
--
作者：
C. Houriez;N. Ferré;M. Masella;D. Siri
我们提出了一个组合的理论方法的基础上分析分子动力学轨迹（在纳秒级）通过使用经典的极化力场和量子计算计算平均超精细耦合常数。该方法用于估计原型氮氧化物的常数：二甲基氮氧化物。在模拟过程中，分子被嵌入一个含有大约500个水分子的立方体盒子中，分子动力学是使用周期性条件生成的。一旦实现的轨迹，氮氧化物和它的第一个水化壳分子被提取，并通过考虑后者的聚集体通过量子计算的耦合常数进行计算。然而，所有的水分子的散装也占在这些计算过程中通过静电势拟合方法。我们的研究结果表明，为了预测准确和可靠的耦合常数，需要仔细描述的平面外运动的氮氧化物氮和采样轨迹的时间间隔为400 fs至少产生一个不相关的大组氮氧化物结构。与Car-Parrinello分子动力学技术相比，我们的方法可以很容易地用于计算大系统的超精细耦合常数，例如与蛋白质或聚合物等大分子相互作用的大尺寸氮氧化物。
We present a combined theoretical approach based on analyzing molecular dynamics trajectories (at the nanosecond scale) generated by use of classical polarizable force fields and on quantum calculations to compute averaged hyperfine coupling constants. That method is used to estimate the constant of a prototypical nitroxide: the dimethylnitroxide. The molecule is embedded during the simulations in a cubic box containing about 500 water molecules and the molecular dynamics is generated using periodic conditions. Once the trajectories are achieved, the nitroxide and its first hydration shell molecules are extracted, and the coupling constants are computed by considering the latter aggregates by means of quantum computations. However, all the water molecules of the bulk are also accounted for during those computations by means of the electrostatic potential fitted method. Our results exhibit that in order to predict accurate and reliable coupling constants, one needs to describe carefully the out-of-plane motion of the nitroxide nitrogen and to sample trajectories with a time interval of 400 fs at least to generate an uncorrelated large set of nitroxide structures. Compared to Car-Parrinello molecular dynamics techniques, our approach can be used readily to compute hyperfine coupling constants of large systems, such as nitroxides of great size interacting with macromolecules such as proteins or polymers.
影响因子：
2.9
作者：
Mchaourab, HS;Lietzow, MA;Hubbell, WL
通讯作者：
Hubbell, WL