Polarizable empirical force field for nitrogen-containing heteroaromatic compounds based on the classical Drude oscillator.
Polarizable empirical force field for nitrogen-containing heteroaromatic compounds based on the classical Drude oscillator.
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DOI：
10.1002/jcc.21183
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发表时间：
2009-09
影响因子：
3
通讯作者：
Mackerell, Alexander D., Jr.
中科院分区：
文献类型：
--
作者：
Lopes, Pedro E. M.;Lamoureux, Guillaume;Mackerell, Alexander D., Jr.
关键词：
基于经典Drude振子的可极化经验ChARMM力场被推广到含氮杂环化合物吡啶、嘧啶、吡咯、咪唑、吲哚和嘌呤。六元环的初始参数是以苯为基础的，非键参数的优化主要集中在氮原子和邻近的碳以及连接的氢上。在5元环的情况下，首先开发了咪唑的参数并将其转移到吡咯。根据大量的量子力学和实验数据，对所有参数进行了优化。通过计算模型化合物的二聚体相互作用、模型化合物与水的相互作用以及稀有气体与模型化合物的相互作用，利用从头算数据确定了初始静电参数、振动分析和优化了Lennard-Jones参数的相对大小。以实验的汽化热、分子体积、升华热、晶格参数和水化自由能为指标，确定了Lennard-Jones参数的绝对值。从气相值到极化率0.85的最终定标是由吡啶和吡咯的介电常数的重现决定的。开发的参数集与其他实验数据进行了广泛的验证，如扩散常数、热容和等温压缩系数，包括作为温度函数的数据。
The polarizable empirical CHARMM force field based on the classical Drude oscillator has been extended to the nitrogen-containing heteroaromatic compounds pyridine, pyrimidine, pyrrole, imidazole, indole and purine. Initial parameters for the 6-membered rings were based on benzene with non-bond parameter optimization focused on the nitrogen atoms and adjacent carbons and attached hydrogens. In the case of 5-member rings, parameters were first developed for imidazole and transferred to pyrrole. Optimization of all parameters was performed against an extensive set of quantum mechanical and experimental data. Ab initio data was used for determination of the initial electrostatic parameters, the vibrational analysis, and in the optimization of the relative magnitudes of the Lennard-Jones parameters, through computations of the interactions of dimers of model compounds, model compound-water interactions and interactions of rare gases with model compounds. The absolute values of the Lennard-Jones parameters were determined targeting experimental heats of vaporization, molecular volumes, heats of sublimation, crystal lattice parameters and free energies of hydration. Final scaling of the polarizabilities from the gas phase values by 0.85 was determined by reproduction of the dielectric constants of pyridine and pyrrole. The developed parameter set was extensively validated against additional experimental data such as diffusion constants, heat capacities and isothermal compressibilities, including data as a function of temperature.
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