Leading coordinate analysis of reaction pathways in proton chain transfer: Application to a two-proton transfer model for the green fluorescent protein |
| |
Authors: | Sufan Wang Sean C. Smith |
| |
Affiliation: | Centre for Computational Molecular Science, The University of Queensland, Chemistry Building #68, Brisbane, Qld 4072, Australia |
| |
Abstract: | The ‘leading coordinate’ approach to computing an approximate reaction pathway, with subsequent determination of the true minimum energy profile, is applied to a two-proton chain transfer model based on the chromophore and its surrounding moieties within the green fluorescent protein (GFP). Using an ab initio quantum chemical method, a number of different relaxed energy profiles are found for several plausible guesses at leading coordinates. The results obtained for different trial leading coordinates are rationalized through the calculation of a two-dimensional relaxed potential energy surface (PES) for the system. Analysis of the 2-D relaxed PES reveals that two of the trial pathways are entirely spurious, while two others contain useful information and can be used to furnish starting points for successful saddle-point searches. Implications for selection of trial leading coordinates in this class of proton chain transfer reactions are discussed, and a simple diagnostic function is proposed for revealing whether or not a relaxed pathway based on a trial leading coordinate is likely to furnish useful information. |
| |
Keywords: | Proton transfer Proton chain transfer Green fluorescent protein Leading coordinate Driving coordinate Reaction pathway |
本文献已被 ScienceDirect 等数据库收录! |
|