Simulations of Liquid Ammonia Based on the Combined Quantum Mechanical/Molecular Mechanical (QM/MM) Approach

Abstract

Two combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations, namely, HF/MM and B3LYP/MM, have been performed to investigate the local structure and dynamics of liquid ammonia. The most interesting region, a sphere containing a central reference molecule and all its nearest surrounding molecules (first coordination shell), was treated by the Hartree-Fock (HF) and hybrid density functional B3LYP methods, whereas the rest of the system was described by the classical pair potentials. On the basis of both HF and B3LYP methods, it is observed that the hydrogen bonding in this peculiar liquid is weak. The structure and dynamics of this liquid are suggested to be determined by the steric packing effects, rather than by the directional hydrogen bonding interactions. Compared to previous empirical as well as Car-Parrinello (CP) molecular dynamics studies, our QM/MM simulations provide detailed information that is in better agreement with experimental data.

Exploring the conformational and reactive dynamics of biomolecules in solution using an extended version of the glycine reactive force field

“…On the one hand, this hybrid methodology is able to provide reliable results at a reasonable computational cost and has been established as a valuable tool for modeling, not only biomolecular compounds, [14][15][16][17][18][19][20][21] but also inorganic/organometallic complexes, [22][23][24][25][26] solid state systems [27][28][29][30] and mixed solvent solutions. [31][32][33][34] On the other hand, the level of theory and the basis set influence significantly simulation trends and energy values. 35,36 In addition, the method has also been found very sensitive to the definition of the boundary between the various subsystems.…”

Solvation structure and dynamics of K+ in aqueous ammonia solution: Insights from an ONIOM-XS MD simulation

“…In the recent ONIOM-XS MD simulation of Li + in aqueous ammonia solution [13], although the MRT values for first-shell ligands are significantly higher than those of pure solvents, it has been shown that the first solvation shell of Li + is somewhat flexible and that the 'structure-making' ability of Li + is not too strong. As compared to the case of Li + , it could be demonstrated that K + acts as a clear 'structure-breaking' ion, i.e., the MRT values for ligands in the first solvation shell of K + are not much different to the corresponding values observed in the pure solvent environments [12,31]. Interestingly, the MRT data of water molecules in the first solvation shell of K + are even less than the corresponding values for water molecules in the hydration shell of K + [10].…”

ND-stretching vibrational energy relaxation of NH2D in liquid-to-supercritical ammonia studied by femtosecond midinfrared spectroscopy

“…Since in light of these results, the relative number of neighboring H atoms ͑2 out of ϳ42͒ is much smaller than in liquid H 2 O ͑4 out of 8͒, it seems plausible to argue that liquid ammonia does not belong to the group of strongly associated liquids even at low temperatures. Modern computer simulations based on Car-Parinello ab initio molecular dynamics 20 and mixed quantum/classical molecular dynamics 21 support such an assignment of liquid NH 3 to weakly associated fluids.…”