ArticlePloS one2013
Mapping enzymatic catalysis using the effective fragment molecular orbital method: towards all ab initio biochemistry.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed, 37 citations in OpenAlex.
- Quantum computational study of chloride attack on chloromethane for chemical accuracy and quantum noise effects with UCCSD and k-UpCCGSD ansatzes.Scientific reports · 2022Article
- Effective Fragment Potentials for Flexible Molecules: Transferability of Parameters and Amino Acid Database.Journal of chemical theory and computation · 2020Article
- Ambient Ionization Mass Spectrometry Measurement of Aminotransferase Activity.Journal of the American Society for Mass Spectrometry · 2017Article
- Hybrid RHF/MP2 geometry optimizations with the effective fragment molecular orbital method.PloS one · 2014Article
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We extend the Effective Fragment Molecular Orbital (EFMO) method to the frozen domain approach where only the geometry of an active part is optimized, while the many-body polarization effects are considered for the whole system. The new approach efficiently mapped out the entire reaction path of chorismate mutase in less than four days using 80 cores on 20 nodes, where the whole system containing 2398 atoms is treated in the ab initio fashion without using any force fields. The reaction path is constructed automatically with the only assumption of defining the reaction coordinate a priori. We determine the reaction barrier of chorismate mutase to be [Formula: see text] kcal mol(-1) for MP2/cc-pVDZ and [Formula: see text] for MP2/cc-pVTZ in an ONIOM approach using EFMO-RHF/6-31G(d) for the high and low layers, respectively.
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