ct400832r_si_001.pdf (1.9 MB)
Benchmark Study of the SCC-DFTB Approach for a Biomolecular Proton Channel
journal contribution
posted on 2014-01-14, 00:00 authored by Ruibin Liang, Jessica M. J. Swanson, Gregory A. VothThe self-consistent charge density
functional tight binding (SCC-DFTB)
method has been increasingly applied to study proton transport (PT)
in biological environments. However, recent studies revealing some
significant limitations of SCC-DFTB for proton and hydroxide solvation
and transport in bulk aqueous systems call into question its accuracy
for simulating PT in biological systems. The current work benchmarks
the SCC-DFTB/MM method against more accurate DFT/MM by simulating
PT in a synthetic leucine–serine channel (LS2), which emulates
the structure and function of biomolecular proton channels. It is
observed that SCC-DFTB/MM produces overcoordinated and less structured
pore water, an overcoordinated excess proton, weak hydrogen bonds
around the excess proton charge defect, and qualitatively different
PT dynamics. Similar issues are demonstrated for PT in a carbon nanotube,
indicating that the inaccuracies found for SCC-DFTB are not due to
the point charge based QM/MM electrostatic coupling scheme, but rather
to the approximations of the semiempirical method itself. The results
presented in this work highlight the limitations of the present form
of the SCC-DFTB/MM approach for simulating PT processes in biological
protein or channel-like environments, while providing benchmark results
that may lead to an improvement of the underlying method.