Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States.
J Phys Chem B. 2012 Oct 18;116(41):12522-34. doi: 10.1021/jp308218m. Epub 2012 Oct 5.
The implementation of the solvent macromolecule boundary potential (SMBP) by Benighaus and Thiel (J. Chem. Theory Comput. 2009, 5, 3114) into the program package CHARMM is presented. The SMBP allows for the efficient calculation of solvent effects for large macromolecules using irregularly shaped dielectric boundaries. In contrast to the generalized solvent boundary potential (GSBP) by Roux et al. (J. Chem. Phys. 2001, 114, 2924) from which it is derived, the SMBP is targeted for quantum mechanical/molecular mechanical (QM/MM) setups using ab initio methods for the QM part. After presenting benchmark results for simple model systems, applications of the SMBP for the calculation of geometries, reaction energy barriers, and vibrational frequencies for an alkaline phosphatase (AP) enzyme are discussed. Although the effect of the boundary potential on optimized structures (including the transition state) and vibrational frequencies is relatively small, the energetics of the phosphoryl transfer catalyzed by AP depend significantly on the boundary potential. Finally, to emphasize a unique feature of our implementation, we apply both SMBP and GSBP to the calculation of the energy barrier for a proton transfer reaction in a simple model channel, where the effect of an external transmembrane potential is studied. Due to the dipolar response of the polar environment, the effective charge displacement estimated based on the effect of the membrane potential on the proton transfer energetics deviates from the net charge that passes the membrane.
本尼豪斯和泰尔（Benighaus and Thiel）在《J. Chem. Theory Comput. 2009, 5, 3114》中提出了将溶剂大分子边界势（SMBP）应用于 CHARMM 程序包中的方法。SMBP 允许使用不规则形状的介电边界有效地计算大分子的溶剂效应。与 Roux 等人（Roux et al.）提出的广义溶剂边界势（GSBP）不同，SMBP 是为使用从头算方法进行 QM 部分的量子力学/分子力学（QM/MM）设置而设计的。在给出简单模型系统的基准结果后，讨论了 SMBP 在计算几何形状、反应能垒和碱性磷酸酶（AP）酶的振动频率方面的应用。尽管边界势对优化结构（包括过渡态）和振动频率的影响相对较小，但 AP 催化的磷酸转移的能量学却显著依赖于边界势。最后，为了强调我们实现的独特功能，我们将 SMBP 和 GSBP 应用于计算简单模型通道中质子转移反应的能垒，其中研究了跨膜电势的影响。由于极性环境的偶极响应，基于膜电势对质子转移能学的影响估计的有效电荷位移与穿过膜的净电荷不同。
