A critical evaluation of DFT, including time-dependent DFT, applied to bioinorganic chemistry
A critical evaluation of DFT, including time-dependent DFT, applied to bioinorganic chemistry
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DOI：
10.1007/s00775-006-0138-1
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发表时间：
2006-09-01
影响因子：
3
通讯作者：
Neese, Frank
中科院分区：
文献类型：
--
作者：
Neese, Frank
在过去的十年里，量子化学方法在生物无机化学问题中的应用发生了爆炸性的变化。现在，将实验论文与量子化学计算一起发表几乎是司空见惯的。这些计算要么用来验证从实验分析中得出的结论，要么用来区分那些尚未确定的可能性。此外，有许多纯理论的研究，解决各种结构和机制方面的金属蛋白质的结构和功能。在这种情况下，术语“量子化学方法”几乎与密度泛函理论（DFT）同步应用。尽管密度泛函理论在生物无机化学中非常受欢迎，但实验界经常抱怨的一个问题是，计算往往很少或根本不注意现有的实验结果。例如，如果在反应中间体结构的建模中纳入了所提议物质的光谱数据作为限制条件，那么许多理论上提出的结构和机制可能会被完全排除在考虑之外。关于所研究的反应的实际动力学，应当指出，即使是测量不准确的速率常数对理论家也有很大帮助，因为速率常数是势垒高度的非常敏感的函数（见Siegbahn在本卷中的贡献）。然而，在许多情况下，研究的机制是很难解剖明确的动力学手段。在这种情况下，本评论中表达的中心观点如下：由于（1）生物无机电子结构问题的巨大复杂性和（2）适用于该领域的每种理论方法的有限准确性，有必要在理论研究中尽可能地寻找与实验数据的相似性。在试图将计算与已知的实验约束相匹配时，几十年来在生物无机化学中积累的大量光谱数据对于理论家衡量他或她的计算非常有用。与其他实验数据，如速率和平衡常数或动力学同位素效应一起，人们希望以最高的可能置信度成功地区分反应机制的替代制剂。由于光谱对捕获物种不产生速率常数，它是最富有成果的理论光谱方法研究的反应中间体的几何结构。考虑到这一点，这里试图总结我们小组在过去几年中使用DFT的经验。
The past decade has witnessed an explosive activity in the application of quantum chemical methods to problems of bioinorganic chemistry. It is now almost commonplace to publish an experimental paper together with quantum chemical calculations. The calculations serve either to validate the conclusions that have been reached from the analysis of the experiments or to distinguish between those possibilities that were left open. In addition, there are many purely theoretical investigations which address various structural and mechanistic aspects of metalloprotein structure and function. In this context the term ‘quantum chemical methods’ has been applied almost synonymously with density functional theory (DFT). Despite the enormous popularity of DFT in bioinorganic chemistry, one frequently voiced complaint from the experimental community is that the calculations often take too little or no notice of the available experimental results. For example, a number of theoretically proposed structures and mechanisms might have been excluded from consideration altogether if the spectroscopic data that are available for the species proposed had been included as constraints in the modelling of the structures of the reaction intermediates. Concerning the actual kinetics of the reactions investigated, it is to be noted that even an inaccurately measured rate constant is of much help to the theoretician since rate constants are very sensitive functions of the barrier height (see the contribution by Siegbahn in this volume). Nevertheless, in many cases the mechanisms investigated are difficult to dissect unambiguously by kinetics means. Given this situation, the central opinion voiced in this commentary is the following: owing to (1) the enormous complexity of bioinorganic electronic structure problems and (2) the limited accuracy of every theoretical method which is applicable in this area, it is necessary to search for as close a similarity to experimental data as possible in the theoretical investigations. In trying to match the computations with the known experimental constraints, the large body of spectroscopic data that has been accumulated in bioinorganic chemistry over the decades is extremely useful for the theoretician to gauge his or her calculations. Viewed together with other experimental data, such as rate and equilibrium constants or kinetic isotope effects, one hopes to successfully discriminate between alternative formulations of the reaction mechanisms with the highest possible degree of confidence. Since spectroscopy on trapped species does not yield rate constants, it is the geometric structure of the reaction intermediates which can most fruitfully be studied by the theoretical spectroscopy approach. With this in mind, an attempt is made here to summarize the experience that our group has had with DFT in the past few years.