ct0c00127_si_001.pdf (2.57 MB)
Semiclassical Vibrational Spectroscopy of Biological Molecules Using Force Fields
journal contribution
posted on 2020-05-20, 16:45 authored by Fabio Gabas, Riccardo Conte, Michele CeottoSemiclassical spectroscopy is a practical
way to get an accurately
approximate quantum description of spectral features starting from ab initio molecular dynamics simulations. The computational
bottleneck for the method is represented by the cost of ab
initio potential, gradient, and Hessian matrix estimates.
This drawback is particularly severe for biological systems due to
their unique complexity and large dimensionality. The main goal of
this manuscript is to demonstrate that quantum dynamics and spectroscopy,
at the level of semiclassical approximation, are doable even for sizable
biological systems. To this end, we investigate the possibility of
performing semiclassical spectroscopy simulations when ab
initio calculations are replaced by computationally cheaper
force field evaluations. Both polarizable (AMOEBABIO18) and nonpolarizable
(AMBER14SB) force fields are tested. Calculations of some particular
vibrational frequencies of four nucleosides, i.e., uridine, thymidine,
deoxyguanosine, and adenosine, show that ab initio simulations are accurate and widely applicable. Conversely, simulations
based on AMBER14SB are limited to harmonic approximations, but those
relying on AMOEBABIO18 yield acceptable semiclassical values if the
investigated conformation has been included in the force field parametrization.
The main conclusion is that AMOEBABIO18 may provide a viable route
to assist semiclassical spectroscopy in the study of large biological
molecules for which an ab initio approach is not
computationally affordable.
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dynamicforce field evaluationsab initio simulationsapproximationquantumAMOEBABIO 18Force Fields Semiclassical spectroscopyforce field parametrizationSemiclassical Vibrational Spectroscopyab initio approachab initio calculationscomputationallysemiclassical spectroscopy simulationsab initioHessian matrix estimatesAMBER 14SB force fields
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