Campus Units

Chemistry, Ames Laboratory

Document Type

Article

Publication Version

Published Version

Publication Date

2011

Journal or Book Title

Journal of Chemical Physics

Volume

134

First Page

1

Last Page

12

DOI

10.1063/1.3517110

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.

Comments

The following article appeared in Journal of Chemical Physics 134 (2011): 034110, and may be found at doi:10.1063/1.3517110.

Rights

Copyright 2011 American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics.

Copyright Owner

American Institute of Physics

Language

en

File Format

application/pdf

Included in

Chemistry Commons

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