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Plos One : Mapping Enzymatic Catalysis Using the Effective Fragment Molecular Orbital Method ; Towards All Ab Initio Biochemistry, Volume 8

By Salsbury, Freddie

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Book Id: WPLBN0003951724
Format Type: PDF eBook :
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Reproduction Date: 2015

Title: Plos One : Mapping Enzymatic Catalysis Using the Effective Fragment Molecular Orbital Method ; Towards All Ab Initio Biochemistry, Volume 8  
Author: Salsbury, Freddie
Volume: Volume 8
Language: English
Subject: Journals, Science, Medical Science
Collections: Periodicals: Journal and Magazine Collection (Contemporary)
Historic
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Publisher: Plos

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Salsbury, F. (n.d.). Plos One : Mapping Enzymatic Catalysis Using the Effective Fragment Molecular Orbital Method ; Towards All Ab Initio Biochemistry, Volume 8. Retrieved from http://www.worldlibrary.org/


Description
Description : 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 18:3+3:5 kcal mol21 for MP2/cc-pVDZ and 19:3+3:6 for MP2/ccpVTZ in an ONIOM approach using EFMO-RHF/6-31G(d) for the high and low layers, respectively

 

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