The fragment-based polarizable embedding (PE) model combined with an appropriate electronic structure method constitutes a highly efficient and accurate multiscale approach for computing spectroscopic properties of a central moiety including effects from its molecular environment through an embedding potential. There is, however, a comparatively high computational overhead associated with the computation of the embedding potential, which is derived from first-principles calculations on individual fragments of the environment. To reduce the computational cost associated with the calculation of embedding potential parameters, we developed a set of amino acid-specific transferable parameters tailored for large-scale PE-based calculations that include proteins. The amino acid-based parameters are obtained by simultaneously fitting to a set of reference electric potentials based on structures derived from a backbone-dependent rotamer library. The developed cost-effective polarizable protein potential (CP3) consists of atom-centered charges and isotropic dipole-dipole polarizabilities of the standard amino acids. In terms of reproduction of electric potentials, the CP3 is shown to perform consistently and with acceptable accuracy across both small tripeptide test systems and larger proteins. We show, through applications on realistic protein systems, that acceptable accuracy can be obtained by using a pure CP3 representation of the protein environment, thus altogether omitting the cost associated with the calculation of embedding potential parameters. High accuracy comparable to that of the full fragment-based approach can be achieved through a mixed description where the CP3 is used only to describe amino acids beyond a threshold distance from the central quantum part.

中文翻译：

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在蛋白质环境中进行准确的可极化嵌入计算的具有成本效益的潜力。

基于片段的可极化嵌入（PE）模型与适当的电子结构方法相结合，构成了一种高效，准确的多尺度方法，用于计算中心部分的光谱特性，包括通过嵌入电位从其分子环境产生的影响。但是，与嵌入潜力的计算相关的计算开销相对较高，这是根据对环境的各个片段的第一性原理计算得出的。为了减少与嵌入潜在参数的计算相关的计算成本，我们开发了一套针对氨基酸的可转移参数，这些参数是为包含蛋白质的大规模基于PE的计算量身定制的。基于氨基酸的参数是通过基于源自骨架的旋转异构体库的结构同时拟合一组参考电势而获得的。已开发的具有成本效益的可极化蛋白电势（CP3）由原子中心电荷和标准氨基酸的各向同性偶极-偶极极化率组成。就电位的再现而言，CP3在小型三肽测试系统和大型蛋白质中均表现出一致的性能和可接受的精度。我们显示，通过在实际蛋白质系统上的应用，可以通过使用蛋白质环境的纯CP3表示来获得可接受的准确性，从而完全省去与嵌入潜在参数的计算有关的成本。