Chemistry, Ames Laboratory
Journal or Book Title
Journal of Chemical Physics
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.
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American Institute of Physics
Nagata, Takeshi; Fedorov, Dmitri G.; Sawada, Toshihiko; Kitaura, Kazuo; and Gordon, Mark S., "A Combined Effective Fragment Potential–Fragment Molecular Orbital Method. II. Analytic Gradient and Application to the Geometry Optimization of Solvated Tetraglycine and Chignolin" (2011). Ames Laboratory Publications. 344.