Structure and dynamics of hydrated NH: An ab initio QM/MM molecular dynamics simulation

Abstract

A combined ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulation has been performed to investigate solvation structure and dynamics of NH(4) (+) in water. The most interesting region, the sphere includes an ammonium ion and its first hydration shell, was treated at the Hartree-Fock level using DZV basis set, while the rest of the system was described by classical pair potentials. On the basis of detailed QM/MM simulation results, the solvation structure of NH(4) (+) is rather flexible, in which many water molecules are cooperatively involved in the solvation shell of the ion. Of particular interest, the QM/MM results show fast translation and rotation of NH(4) (+) in water. This phenomenon has resulted from multiple coordination, which drives the NH(4) (+) to translate and rotate quite freely within its surrounding water molecules. In addition, a "structure-breaking" behavior of the NH(4) (+) is well reflected by the detailed analysis on the water exchange process and the mean residence times of water molecules surrounding the ion.

Molecular dynamics simulations of ion solvation by flexible‐boundary QM/MM: On‐the‐fly partial charge transfer between QM and MM subsystems

“…For example, the Car–Parrinello dynamics has been applied to examine the hydration of Cl − , Li + , and Na + ions. Other examples are the QM/MM dynamics simulations of the Cl − , Li + , Na + , and . Those theoretical investigations have contributed significantly to our understanding of those hydrated ions.…”

Ab initio QM/MM dynamics of H3O+ in water

“…In contrast, the B3LYP calculations, although they provide reasonable geometries, predict too strong ion-water interactions, most probably due to an overestimation of the correlation energy. 54,56 From the data shown in Table 1, the contributions of electron correlation to the binding energies were estimated to be about 5%. This can be expected to have a significant influence on structural and dynamical properties of hydrated H 3 O þ .…”

Effects of metal ion and solute conformation change on hydration of small amino acid

“…[44] that a complete understanding of the water exchange mechanisms requires information on both hydration structures and dynamics, which are closely related to the interactions and momentum transfer between water molecules in the first and second hydration shells. The influence of water molecules in the second hydration shell was also illustrated in our previous work on [NH 4 + ] aq [73] and [H 3 O + ] aq [74]. Especially in the case of [H 3 O + ] aq [74], it was shown that water molecules in the second hydration shell could help promote the proton transfer from H 3 O + to H 2 O, through the formation of the Zundel complex (H 5 O 2 + ).…”