NDLI: A combined effective fragment potential-fragment molecular orbital method. II. Analytic gradient and application to the geometry optimization of solvated tetraglycine and chignolin.

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A combined effective fragment potential-fragment molecular orbital method. II. Analytic gradient and application to the geometry optimization of solvated tetraglycine and chignolin.

Content Provider	Semantic Scholar
Author	Nagata, Takeshi Fedorov, Dmitri G. Sawada, Toshihiko Kitaura, Kazuo Gordon, Mark S.
Copyright Year	2011
Abstract	The gradient for the fragment molecular orbital (FMO) method interfaced with effective fragment potentials (EFP), denoted by FMO∕EFP, was developed and applied to polypeptides solvated in water. The structures of neutral and zwitterionic tetraglycine immersed in water layers of 2.0, 2.5, 3.0, 3.5, 4.0, and 4.5 Å are investigated by performing FMO∕EFP geometry optimizations at the RHF∕cc-pVDZ level of theory for the solutes. The geometries optimized with FMO-RHF∕EFP are compared to those from the conventional RHF∕EFP and are found to be in very close agreement. Using the optimized geometries, the stability of the hydrated zwitterionic and neutral structures is discussed structurally and in terms of energetics at the second-order Møller-Plesset theory (MP2)∕cc-pVDZ level. To demonstrate the potential of the method for proteins, the geometry of hydrated chignolin (protein data bank ID: 1UAO) was optimized, and the importance of the inclusion of water was examined by comparing the solvated and gas phase structures of chignolin with the experimental NMR structure.
Starting Page	034110
Ending Page	034110
Page Count	1
File Format	PDF HTM / HTML
DOI	10.1063/1.3517110
PubMed reference number	21261333
Journal	Medline
Volume Number	134
Issue Number	3
Alternate Webpage(s)	http://lib.dr.iastate.edu/cgi/viewcontent.cgi?amp%3Bcontext=ameslab_pubs&article=1345
Alternate Webpage(s)	https://doi.org/10.1063/1.3517110
Journal	The Journal of chemical physics
Language	English
Access Restriction	Open
Content Type	Text
Resource Type	Article

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