Geometry Optimization, Transition State Search, and Reaction Path Mapping Accomplished with the Fragment Molecular Orbital Method

Hiroya Nakata; Dmitri G Fedorov

doi:10.1007/978-1-0716-0282-9_6

Geometry Optimization, Transition State Search, and Reaction Path Mapping Accomplished with the Fragment Molecular Orbital Method

Methods Mol Biol. 2020:2114:87-103. doi: 10.1007/978-1-0716-0282-9_6.

Authors

Hiroya Nakata¹, Dmitri G Fedorov²

Affiliations

¹ Kyocera Corporation, Research Institute for Advanced Materials and Devices, Seika-cho, Soraku-gun, Kyoto, Japan. nakata.hiro07@gmail.com.
² CD-FMat, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan.

PMID: 32016888
DOI: 10.1007/978-1-0716-0282-9_6

Abstract

Recent development of the fragment molecular orbital (FMO) method related to energy gradients, geometry optimization, transition state search, and chemical reaction mapping is summarized. The frozen domain formulation of FMO is introduced in detail, and the structure of related GAMESS input files for FMO is described.

Keywords: DFT; DFTB; FMO; FMO-DFTB; FMO/FD; FMO/MD; FMO/MM; Fragment molecular orbital method; GAMESS; Geometry optimization; OPTFMO; OPTIMIZE; SADPOINT; Transition state search.

Publication types

Review

MeSH terms

Drug Discovery / methods*
Pharmaceutical Preparations / chemistry*

Substances

Pharmaceutical Preparations