Abstract
In this paper, we demonstrate the possibility to perform spectroscopy simulations of solvated biological species taking into consideration quantum effects and explicit solvation. We achieve this goal by interfacing our recently developed divide-and-conquer approach for semiclassical initial value representation molecular dynamics with the polarizable AMOEBABIO18 force field. The method is applied to the study of solvation of the thymidine nucleoside in two different polar solvents, water and N,N-dimethylformamide. Such systems are made of up to 2476 atoms. Experimental evidence concerning the different behavior of thymidine in the two solvents is well reproduced by our study, even though quantitative estimates are hampered by the limited accuracy of the classical force field employed. Overall, this study shows that semiclassically approximate quantum dynamical studies of explicitly solvated biological systems are both computationally affordable and insightful.
Highlights
In this paper, we demonstrate the possibility to perform spectroscopy simulations of solvated biological species taking into consideration quantum effects and explicit solvation
Several works, based on different experimental techniques such as nuclear magnetic resonance (NMR), high-performance liquid chromatography (HPLC), and neutron scattering, show that, in the presence of an apolar solute, water rearranges its hydrogen bond network creating a cavity.[7−10] Interactions between the solute and the solvent, for nonpolar solvation, derive mainly from weak dispersion forces originating from the fluctuation of induced dipoles within solvent and solute molecules rather than from the electrostatics of charge distributions as in the polar solutes case.[11−15] water can interact with solutes in a site-specific and “nonbulk” manner
Simulating biological molecules using explicit water molecules requires high computational costs and resources. These requirements entirely exclude the possibility of using accurate ab initio molecular dynamics methods (AIMD), in which the potential energy is evaluated adopting an ab initio quantum method, such as MP2, Coupled Cluster, or the family of DFT functionals
Summary
We demonstrate the possibility to perform spectroscopy simulations of solvated biological species taking into consideration quantum effects and explicit solvation. The most common type of potential employed in explicit solvation is obtained from classical molecular mechanics (MM) carried out by using popular and well-tested force fields, such as AMBER,[21,22] CHARMM,[23,24] or AMOEBABIO18.25,26 This approach permits even dynamical studies of large dimensional systems, because the quantum electronic structure is not calculated and polarization effects are quite approximated.
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