Abstract
The impact of the dispersion and electron correlation effects on describing quantum mechanics/molecular mechanics (QM/MM) interactions in QM/MM molecular dynamics (MD) simulations was explored by performing a series of up to 2 ns QM/MM MD simulations on the B states of the myoglobin–carbon monoxide (MbCO) system. The results indicate that both dispersion and electron correlations play significant roles in the simulation of the ratios of two B states (B1/B2), which suggests that the inclusion of the electron correlation effects is essential for accurately modeling the interactions between QM and MM subsystems. We found that the QM/MM interaction energies between the CO and the surroundings statistically present a linear correlation with the electric fields along the CO bond. This indicates that QM/MM interactions can be described by a simple physical model of a dipole with constant moment under the action of the electric fields. The treatment provides us with an accurate and effective approach to account for the electron correlation effects in QM/MM MD simulations.
Highlights
Mixed multiscale QM/MM1–5 models are routinely utilized in studies exploring the structure, reactivity, and electronic properties of proteins and other biological molecules[6,7,8,9,10,11]
The predicted locations of the B state in the 2 ns quantum mechanics/ molecular mechanics (QM/MM) molecular dynamics (MD) simulation were at the edge of the distal heme pocket adjacent to the porphyrin ring c, which is in good agreement with the X-ray experiment
The CO molecule lay approximately parallel to the heme plane in the 2 ns QM/MM MD simulation, which is in good agreement with the X-ray experiment
Summary
Mixed multiscale QM/MM1–5 models are routinely utilized in studies exploring the structure, reactivity, and electronic properties of proteins and other biological molecules[6,7,8,9,10,11] In such models, the part of a large system that is of primary interest (e.g., the active site of an enzyme) is treated using an electronic structure method for capturing more accurate interaction energies, with the surroundings treated using an MM approach. The QM/MM treatment of the interactions is not exactly the same as that of the QM method, the change in the interactions (e.g., during a reaction or the dynamics of a biomolecular hydrogen bond) are modeled www.nature.com/scientificreports well by the QM/MM method using the electrostatic embedding approach[16] This is as expected, because most of the protein functions are primarily achieved by the electrostatic[17,18,19,20,21]. Great efforts have been made to account for the dispersion effects in QM methods over the past decade, with a number of empirical dispersion methods routinely used for the QM calculations[45,51,52,53]
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