Chemical scanning of atomic oxygen at the gas-liquid interface of a NaCl solution via quantum mechanics/molecular mechanics molecular dynamics simulations

Atmospheric pressure plasmas can serve as double phase reactors to produce plasma activated water for water treatment. However, the physical-chemical processes involving plasma-supplied atomic oxygen and reactive oxygen species in an aqueous solution remain unclear. In this work, quantum mechanics (QM)/molecular mechanics (MM) molecular dynamics simulations (MDs) have been performed to directly observe the chemical reactions occurring between atomic oxygen and a NaCl solution at the gas-liquid interface using a model containing 10,800 atoms. During simulations, the atoms in the QM and MM Parts are dynamically adjusted. To examine the effects of local microenvironments on the chemical processes, atomic oxygen is used as a chemical probe to scan the gas-liquid interface. The excited atomic oxygen reacts with water molecules and Cl- ions to produce H2O2, OH, HOCl, ClO-, and HO2-/H3O+ species. The ground-state atomic oxygen is significantly more stable than the excited atomic oxygen, although it can react with water molecules to produce OH radicals. However, the branch ratio of ClO- computed for triplet atomic oxygen is significantly larger than that determined for singlet atomic oxygen. This study can help achieve a better understanding of the fundamental chemical processes during plasma-treated solution experiments and promotes advances in applications of QM/MM calculations at the gas-liquid interface.

A comparative study of trypsin specificity based on QM/MM molecular dynamics simulation and QM/MM GBSA calculation

Hydrogen bonding and polar interactions play a key role in identification of protein-inhibitor binding specificity. Quantum mechanics/molecular mechanics molecular dynamics (QM/MM MD) simulations combined with DFT and semi-empirical Hamiltonian (AM1d, RM1, PM3, and PM6) methods were performed to study the hydrogen bonding and polar interactions of two inhibitors BEN and BEN1 with trypsin. The results show that the accuracy of treating the hydrogen bonding and polar interactions using QM/MM MD simulation of PM6 can reach the one obtained by the DFT QM/MM MD simulation. Quantum mechanics/molecular mechanics generalized Born surface area (QM/MM-GBSA) method was applied to calculate binding affinities of inhibitors to trypsin and the results suggest that the accuracy of binding affinity prediction can be significantly affected by the accurate treatment of the hydrogen bonding and polar interactions. In addition, the calculated results also reveal the binding specificity of trypsin: (1) the amidinium groups of two inhibitors generate favorable salt bridge interaction with Asp189 and form hydrogen bonding interactions with Ser190 and Gly214, (2) the phenyl of inhibitors can produce favorable van der Waals interactions with the residues His58, Cys191, Gln192, Trp211, Gly212, and Cys215. This systematic and comparative study can provide guidance for the choice of QM/MM MD methods and the designs of new potent inhibitors targeting trypsin.