Semiclassical Vibrational Spectroscopy of Biological Molecules Using Force Fields.
Fabio Gabas1, Riccardo Conte1, Michele Ceotto1
1Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, 20133 Milano, Italy.
Journal of Chemical Theory and Computation
|May 7, 2020
Summary
Semiclassical spectroscopy for large biological systems is computationally intensive. Replacing ab initio calculations with the AMOEBABIO18 force field offers a viable, cost-effective alternative for quantum dynamics and spectroscopy.
Area of Science:
- Computational chemistry
- Quantum dynamics
- Spectroscopy
Background:
- Semiclassical spectroscopy provides approximate quantum descriptions of spectral features from ab initio molecular dynamics.
- Computational cost of ab initio calculations (potential, gradient, Hessian) is a bottleneck, especially for complex biological systems.
Purpose of the Study:
- To assess the feasibility of semiclassical spectroscopy for sizable biological systems by replacing ab initio calculations with force field evaluations.
- To investigate the performance of polarizable (AMOEBABIO18) and nonpolarizable (AMBER14SB) force fields for this purpose.
Main Methods:
- Semiclassical spectroscopy simulations were performed on four nucleosides (uridine, thymidine, deoxyguanosine, adenosine).
- Ab initio calculations were compared against force field evaluations using AMOEBABIO18 and AMBER14SB.
Main Results:
- Ab initio simulations demonstrated accuracy and broad applicability for vibrational frequencies.
- AMBER14SB simulations were restricted to harmonic approximations.
- AMOEBABIO18 simulations provided acceptable semiclassical values when the conformation was included in parametrization.
Conclusions:
- AMOEBABIO18 offers a computationally affordable route for semiclassical spectroscopy of large biological molecules.
- This approach can aid the study of systems where ab initio methods are not feasible.
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