PyQM/MM: a Python Interface for ONIOM(QM:MM) Calculations with the AMOEBA09 Polarizable Force Field to Study the Chemical Processes in the Interstellar Medium

Abstract

We have developed a Python interface, PyQM/MM, to perform ONIOM(QM:MM) calculations with the AMOEBA09 polarizable force field. The ONIOM(QM:MM) implementation in PyQM/MM uses the Gaussian16 program for quantum mechanical (QM) computations and the Tinker program for molecular mechanics (MM) computations with the AMOEBA09 polarizable force field. We have used PyQM/MM, employing ONIOM(QM:AMOEBA09) method, to calculate binding energy of SH and OH radicals on amorphous solid water (ASW). Computed binding energies of SH radical are in the range of 0.10-0.36 eV, where the average binding energy is 0.22 eV. Compared to SH radical, OH radical binding energies are stronger (0.21 – 0.52 eV, and the average value is 0.36 eV). We propose that both SH and OH radicals adsorb on ASW, and SH radical binding preference is smaller than OH radical. Also, we have rationalized the mechanism for the reaction between OH anion and CO in ice using ONIOM(wB97X-D:AMOEBA09) method. The computed reaction mechanism showed a relatively low energy path to form HC(O)OH, where the OH anion is recovered during the reaction. In contrast, the reaction between OH radical CO gives rise to HOCO radical. We propose that OH anions and OH radicals in interstellar ices can react with the molecules trapped in ices to synthesize complex organic molecules. These examples evidence that PyQM/MM is a user-friendly strategy to perform ONIOM(wB97XD:AMOEBA09) calculations to study chemical processes in the interstellar medium.

A systematic mechanistic survey on the reactions between OH radical and CH3OH on ice

“…The ASW model has 162 Geometry optimizations were performed using the two-layer ONIOM method as implemented in the PyQM/MM interface. 31 The uB97X-D, 32 functional and def2-TZVP, 33 basis sets were used for the ONIOM, 34,35 high-layer. The AMOEB09 [36][37][38] polarizable force eld was used for the ONIOM low-layer.…”

Methanol Formation through Reaction of Low-energy CH3 + Ions with an Amorphous Solid Water Surface at Low Temperature

“…The total initial nuclear kinetic energy of the system was set to 0.1952 eV (0.00129 eV atom −1 ) so that the value per atom corresponds to 3k B T/2 at the initial temperature of T = 10 K, and the target temperature for nuclear motion of the whole system was kept at 10 K with an allowed deviation from the target temperature of ±3 K. To study the relaxed potential energy surface for the reaction between + CH 3 and ice surface, an ice cluster model consisting of 240 H 2 O molecules was prepared (density 0.94 g cm −3 ). The ONIOM(ωB97X-D/6-31G(d):AMOEBA09) method, as implemented in the PyQM/MM interface (Rathnayake et al 2022), was used for structure optimizations, where 50 H 2 O molecules are in the QM region and the remaining 190 H 2 O molecules are in the MM region. A + CH 3 ion was then placed at a distance of 10.0 Å above the surface (Figure A2), and a relaxed potential energy surface was calculated.…”