Zhang Chao, Raugei Simone, Eisenberg Bob, Carloni Paolo
German Research School for Simulation Sciences, FZ-Juelich/RWTH Aachen University, Aachen, Germany, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington 99352, Rush University Medical Center, 1653 W. Congress Parkway, Chicago, Illinois 60612, and SISSA, CNR-INFN-DEMOCRITOS, and Italian Institue of Technology (IIT), SISSA Unit, Trieste, Italy.
J Chem Theory Comput. 2010 Jul 13;6(7):2167-75. doi: 10.1021/ct9006579.
The monovalent ions Na(+) and K(+) and Cl(-) are present in any living organism. The fundamental thermodynamic properties of solutions containing such ions is given as the excess (electro-)chemical potential differences of single ions at finite ionic strength. This quantity is key for many biological processes, including ion permeation in membrane ion channels and DNA-protein interaction. It is given by a chemical contribution, related to the ion activity, and an electric contribution, related to the Galvani potential of the water/air interface. Here we investigate molecular dynamics based predictions of these quantities by using a variety of ion/water force fields commonly used in biological simulation, namely the AMBER (the newly developed), CHARMM, OPLS, Dang95 with TIP3P, and SPC/E water. Comparison with experiment is made with the corresponding values for salts, for which data are available. The calculations based on the newly developed AMBER force field with TIP3P water agrees well with experiment for both KCl and NaCl electrolytes in water solutions, as previously reported. The simulations based on the CHARMM-TIP3P and Dang95-SPC/E force fields agree well for the KCl and NaCl solutions, respectively. The other models are not as accurate. Single cations excess (electro-)chemical potential differences turn out to be similar for all the force fields considered here. In the case of KCl, the calculated electric contribution is consistent with higher level calculations. Instead, such agreement is not found with NaCl. Finally, we found that the calculated activities for single Cl(-) ions turn out to depend clearly on the type of counterion used, with all the force fields investigated. The implications of these findings for biomolecular systems are discussed.
单价离子Na⁺、K⁺和Cl⁻存在于任何生物体内。含有此类离子的溶液的基本热力学性质表现为在有限离子强度下单离子的过量（电）化学势差。这个量对于许多生物过程至关重要，包括膜离子通道中的离子渗透以及DNA与蛋白质的相互作用。它由与离子活度相关的化学贡献和与水/空气界面的伽伐尼电位相关的电贡献组成。在此，我们使用生物模拟中常用的各种离子/水势场，即AMBER（新开发的）、CHARMM、OPLS、带TIP3P的Dang95以及SPC/E水，来研究基于分子动力学对这些量的预测。将其与有相应数据的盐的实验值进行比较。如先前报道的那样，基于新开发的带TIP3P水的AMBER势场的计算结果与水溶液中KCl和NaCl电解质的实验结果吻合良好。基于CHARMM - TIP3P和Dang95 - SPC/E势场的模拟分别与KCl和NaCl溶液的实验结果吻合良好。其他模型则没那么准确。对于此处考虑的所有势场，单个阳离子的过量（电）化学势差结果相似。在KCl的情况下，计算得到的电贡献与更高水平的计算结果一致。相反，NaCl的情况则未发现这种一致性。最后，我们发现，在所研究的所有势场中，单个Cl⁻离子的计算活度明显取决于所使用的抗衡离子类型。讨论了这些发现对生物分子系统的影响。
