Cytochrome P450 compound I in the plane wave pseudopotential framework: GGA electronic and geometric structure of thiolate-ligated iron(IV)-oxo porphyrin.
Cytochrome P450 compound I in the plane wave pseudopotential framework: GGA electronic and geometric structure of thiolate-ligated iron(IV)-oxo porphyrin.
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DOI：
10.1002/jcc.23311
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发表时间：
2013-07-15
影响因子：
3
通讯作者：
Hackett, John C.
中科院分区：
文献类型：
--
作者：
Elenewski, Justin E.;Hackett, John C.
细胞色素P450构成普遍存在的金属酶家族，通过表示为化合物I（Cpd I）的硫醇盐连接的铁-氧代（IV）卟啉自由基物质催化生物学和合成重要性的多种反应。实验研究表明，这种中间体在广谱的生物药理学有趣的现象，进一步增加了一个化合物I模型系统的重要性。从头算分子动力学（AIMD），包括Car-Parrinello（CP）和路径积分（PI）方法，结合电子结构理论与有限温度模拟，提供最有价值的工具来接近这样的酶。这些方法通常由密度泛函理论（DFT）在平面波赝势框架驱动，然而，现有的研究Cpd I已被限制到本地化高斯基组。因此，对于这样的模拟，密度泛函和赝势的适当选择并不明显。为了补救这种情况，硫醇连接的化合物I的系统基准进行使用几个广义梯度近似（GGA）的功能在Martins-Troullier和范德比尔特超软赝势计划。由此产生的电子和结构参数进行比较，使用GGA和混合密度泛函局域化的基础DFT计算。每种方案的优点和缺点的复制现有的实验和理论结果的范围内，我。
The cytochromes P450 constitute a ubiquitous family of metalloenzymes, catalyzing manifold reactions of biological and synthetic importance via a thiolate–ligated iron–oxo (IV) porphyrin radical species denoted Compound I (Cpd I). Experimental investigations have implicated this intermediate in a broad spectrum of biophysically interesting phenomena, further augmenting the importance of a Cpd I model system. Ab initio molecular dynamics (AIMD), including Car—Parrinello (CP) and path integral (PI) methods, conjoin electronic structure theory with finite temperature simulation, affording tools most valuable to approach such enzymes. These methods are typically driven by density functional theory (DFT) in a plane–wave pseudopotential framework, however, existing studies of Cpd I have been restricted to localized Gaussian basis sets. The appropriate choice of density functional and pseudopotential for such simulations is accordingly not obvious. To remedy this situation, a systematic benchmarking of thiolate–ligated Cpd I is performed using several generalized gradient approximation (GGA) functionals in the Martins—Troullier and Vanderbilt ultrasoft pseudopotential schemes. The resultant electronic and structural parameters are compared to localized–basis DFT calculations using GGA and hybrid density functionals. The merits and demerits of each scheme are presented in the context of reproducing existing experimental and theoretical results for Cpd I.
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