the effective fragment molecular orbital method for fragments connected by covalent bonds有效片段片段分子轨道方法通过共价键连接.pdf

The Effective Fragment Molecular Orbital Method for Fragments Connected by Covalent Bonds 1 2 1 Casper Steinmann *, Dmitri G. Fedorov , Jan H. Jensen 1 Department of Chemistry, University of Copenhagen, Copenhagen, Denmark, 2 NRI, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan Abstract We extend the effective fragment molecular orbital method (EFMO) into treating fragments connected by covalent bonds. The accuracy of EFMO is compared to FMO and conventional ab initio electronic structure methods for polypeptides including proteins. Errors in energy for RHF and MP2 are within 2 kcal/mol for neutral polypeptides and 6 kcal/mol for charged polypeptides similar to FMO but obtained two to five times faster. For proteins, the errors are also within a few kcal/mol of the FMO results. We developed both the RHF and MP2 gradient for EFMO. Compared to ab initio, the EFMO ˚ optimized structures had an RMSD of 0.40 and 0.44 A for RHF and MP2, respectively. Citation: Steinmann C, Fedorov DG, Jensen JH (2012) The Effective Fragment Molecular Orbital Method for Fragments Connected by Covalent Bonds. PLoS ONE 7(7): e41117. doi:10.1371/journal.pone.0041117 ¨ Editor: Jorg Langowski, German Cancer Research Center, Germany Received February 22, 2012; Accepted June 19, 2012; Published July 23, 2012 Copyright: 2012 Steinmann et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This work was funded by a Schou Fellowship to JHJ from the Danish research Co