Molecular Dynamics Simulations of Hydrogen Bonding in Clathrate Hydrates with Ammonia and Methanol Guest Molecules

Abstract

We performed molecular dynamics simulations of the ammonia and methanol-based clathrate hydrates with the emphasis on characterizing hydrogen-bonding interactions of these guest molecules with the water lattice. Systems studied include structure II (sII) binary clathrate hydrates of tetrahydrofuran (THF) (large cage, L) + NH3 (small cage, S) and THF (L) + CH3OH (S), the structure I (sI) pure NH3 (L), pure CH3OH (L), the binary NH3 (L) + CH4 (S), and binary CH3OH (L) + CH4 (S) clathrate hydrates. We simulated these clathrate hydrates with the transferable intermolecular potential with four point changes (TIP4P) water potential and the TIP4P/ice water potential to determine the effect of the water potential on the predicted hydrogen bonding of the guest molecules. Simulations show that, despite strongly hydrogen bonding with the framework water molecules, clathrate hydrate phases with NH3 and CH3OH can be stable within temperatures ranges up to 240 K. Indeed, a limited number of thermodynamic integration free energy calculations show that both NH3 and CH3OH molecules give more stable guest–host configurations in the large sI clathrate hydrate cages than methane guests. Predictions of hydrogen bonding from simulations with the two different water potentials used can differ substantially. To study the effect of proton transfer from water to the basic NH3 guests, simulations were performed on a binary NH3 + CH4 sI clathrate hydrate where less than 10 % of the ammonia guests in the large cages were converted to NH4 + and a water molecule of the hydrate lattice in the same large cage was converted to OH–. The small percentage of proton transfer to ammonia guests in the large cages did not affect the stability of the resultant hydrate. The structural perturbations in the lattice that result from this proton transfer are characterized.

Hydrogen Inter-Cage Hopping and Cage Occupancies inside Hydrogen Hydrate: Molecular-Dynamics Analysis

“…A Lennard-Jones 12-6 with a 6.8 Å cut-off was implemented, whilst the smooth particle-mesh Ewald method [26] was used to handle the long-range electrostatics. The selected four-site water model, TIP4P/2005, was also used in many simulation studies on hydrate structures [27,28]. The velocity Verlet algorithm was used for the molecular dynamics (MD) simulations with a time step of 3.33 fs using the canonical NVT ensemble, featuring a Nosé-Hoover relaxation time of 5 ps, for a total time of 50 ns [29].…”

Inclusion complexes of norepinephrine with β-cyclodextrin, 18-crown-6 and cucurbit[7]uril: experimental and molecular dynamics study

“…6,[25][26][27][28][29][30] Furthermore, theoretical molecular modeling calculations, such as density functional theory calculations and molecular dynamics are usually used to shed the light on the molecular recognition mechanism and to delineate the structure of these complexes. 23,[31][32][33][34][35][36] Norepinephrine, NP, is a member of the catecholamine family of compounds known to possess pharmacological activities as neurotransmitters and hormones. It is used to treat cases of low blood pressure because as a stimulant of the sympathetic nervous system it increases the heart rate and blood pressure.…”

Structural Identification of Binary Tetrahydrofuran + O2 and 3-Hydroxytetrahydrofuran + O2 Clathrate Hydrates by Rietveld Analysis with Direct Space Method

“…THF hydrate exists, the number of small guest molecules occupying the large cages is usually ignorable when a stoichiometric amount of large guest molecules for sII hydrate is used. The hydroxyl group capable of hydrogen bonding is usually allowed to approach the host water molecules more closely than other hydrophobic groups in the guest molecules [15,20,30,31]; this may explain the 3-OH THF formation of the sII hydrate, while 2-methyl THF, which is similar in size, forms the sH hydrate with the assistance of CH4 or Xe gases [32]. Figures 3 and 4 show the crystal structures and guest positions of the THF + O2 and 3-OH THF + O2 hydrates as obtained by Rietveld refinement.…”

“…Figures 3 and 4 show the crystal structures and guest positions of the THF + O2 and 3-OH THF + O2 hydrates as obtained by Rietveld refinement. The hydroxyl group capable of hydrogen bonding is usually allowed to approach the host water molecules more closely than other hydrophobic groups in the guest molecules [15,20,30,31]; this may explain the 3-OH THF formation of the sII hydrate, while 2-methyl THF, which is similar in size, forms the sH hydrate with the assistance of CH 4 or Xe gases [32]. As shown in Figure 3a, THF molecules are spherically distributed in the 5 12 6 4 cages.…”