Jan Jensen edited section_Introduction_Semiempirical_electronic_structure__.tex  over 8 years ago

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The Yalmazer and Korth study \cite{Yilmazer_2013} raises a similar question about whether benchmark results for semiempirical barrier height-predictions on small systems, such as the BH76 and BHPERI subsets of GMTK24/30, are transferable to barrier height predictions for enzymes. This towards answering this question is to create a benchmark set barriers computed for systems that are relatively large and representative to enzymatic reactions. This is a considerable challenge because, unlike for ligand-protein complexes, there is no large database of corresponding transition state (TS) structures (or even substrate-enzyme structures) to start from. Thus, TS structures must be computed which is time-consuming and hard to automate. There are a significant number of such structures in the literature but many are not computed at a high enough level of theory to serve as benchmarks. Furthermore, TS structures are known to dependent significantly on the level of theory used and it is therefore important that the benchmark set is computed using identical or very similar levels of theory. Creating such a benchmark set is this a considerable challenge for any one research group but can be addressed by a concerted effort from the community. This paper represents the first step in this process.   We have collected barrier heights and reaction energies (and associated structures) for five enzymes from studies published by Himo and co-workers \cite{Chen_2007,Georgieva_2010,Hopmann_2008,Liao_2011,Sevastik_2007} on a Gitbub repository (github.com/jensengroup/db-enzymes). Using this data, obtained at the same level of theory, we then benchmark PM6, PM7,  DFT2, and DFTB3 and discuss the influence of system size. bulk solvation, and geometry re-optimization on the error. We end by discuss steps needed to expand and improve the data set and how other researchers can contribute to the process.