Molecular dynamics simulation on the decomposition of type SII hydrogen hydrate and the performance of tetrahydrofuran as a stabiliser

Molecular dynamics simulation is used to study the decomposition and stability of SII hydrogen and hydrogen/tetrahydrofuran (THF) hydrates at 150 K, 220 K and 100 bar. The modelling of the microscopic decomposition process of hydrogen hydrate indicates that the decomposition of hydrogen hydrate is led by the diffusive behaviour of H₂ molecules. The hydrogen/THF hydrate presents higher stability, by comparing the distributions of the tetrahedral angle of H₂O molecules, radial distribution functions of H₂O molecules and mean square displacements or diffusion coefficients of H₂O and H₂ molecules in hydrogen hydrate with those in hydrogen/THF hydrate. It is also found that the resistance of the diffusion behaviour of H₂O and H₂ molecules can be enhanced by encaging THF molecules in the (5¹²6⁴) cavities. Additionally, the motion of THF molecules is restricted due to its high interaction energy barrier. Accordingly, THF, as a stabiliser, is helpful in increasing the stability of hydrogen hydrate.     

Analysis of dissociation process for gas hydrates by molecular dynamics simulation

The dissociation processes of methane and carbon dioxide hydrates were investigated by molecular dynamics simulation. The simulations were performed with 368 water molecules and 64 gas molecules using NPT ensembles. The TraPPE (single-site) and 5-site models were adopted for methane molecules. The EPM2 (3-site) and SPC/E models were used for carbon dioxide and water molecules, respectively. The simulations were carried out at 270 K and 5.0 MPa for hydrate stabilisation. Then, temperature was increased up to 370 K. The temperature increasing rates were 0.1–20 TK/s. The gas hydrates dissociated during increasing temperature or at 370 K. The potential models of methane molecule did not much influence the dissociation process of methane hydrate. The mechanisms of dissociation process were analysed with the coordination numbers and mean square displacements. It was found that the water cages break down first, then the gas molecules escape from the water cages. The methane hydrate was more stable than the carbon dioxide hydrate at the calculated conditions.     

Molecular simulation of cage occupancy and selectivity of binary THF–H2 sII hydrate

The hydrogen capacity of the binary THF–H₂ sII hydrate is determined by the cage occupancy and by the selectivity of guest molecules. Grand canonical Monte Carlo (GCMC) simulation is used to study the cage occupancy and selectivity of guest molecules from the equilibrium configuration of the binary sII hydrate. The cage framework is regarded as a rigid body and the number of guest molecules is varied to preserve the grand canonical ensemble. The occupancy and selectivity were investigated at a temperature of 270 K for pressures ranging from 0.1 to 200 MPa. It was found that most large cages select THF as guest molecules while small cages include only hydrogen molecules. Multiple occupancy of hydrogen, up to four molecules in large cages and two molecules in small cages, was found as the pressure increases. GCMC results show that the hydrogen capacity is approximately 1.1 wt% at 200 MPa.     

Decomposition of CH4 hydrate: effects of temperature and salt from molecular simulations

We report a molecular simulation study to investigate the decomposition of CH₄ hydrate. The decomposition is revealed to be stepwise from the outer to inner layers. Upon decomposition, the number of 5¹²6² cages drops faster than that of 5¹² cages. CH₄ molecules are released, dissolved in water, then enter gas phase; meanwhile, CH₄ bubbles may form particularly at a high temperature. Based on the variations of potential energy, order parameter, cage number and density profile of CH₄ at different temperatures (300, 330, 345 and 360 K) and NaCl concentrations (0, 0.6 and 1.8 M), the effects of temperature and salt are comprehensively examined. With increasing temperature, the decomposition in pure water is accelerated, whereas two opposite effects are observed in NaCl solution. At 330 K, the decomposition is retarded at a higher NaCl concentration, as attributed to the reduced CH₄ solubility in NaCl solution and the participation of ions in cage formation; at 360 K, however, the decomposition is accelerated when NaCl concentration increases due to bubble formation. This simulation study provides microscopic insights into hydrate decomposition, which might be useful towards the optimisation of operating conditions for CH₄ production from CH₄ hydrate.     

Molecular dynamics simulation of replacement of methane hydrate with carbon dioxide

Molecular dynamics simulation was performed to analyse the phenomena of replacement of methane hydrate with carbon dioxide (CO₂) at 270 K and 5.0 MPa for 5300 ps. The methane hydrate phase was constructed with 16 unit cells of hydrate. Every cage in the hydrate was occupied by one methane molecule. The methane hydrate phase was sandwiched between two CO₂ phases. During the simulation the hydrate partially melted and liquid water phase appeared, and CO₂ dissolved in the liquid water phase. The replacements were observed three times at the hydrate–liquid water interface during the simulation. In the first case, the replacement occurred at a S-cage without changing the structure. In the second case, an M-cage of methane hydrate partially collapsed, and methane and CO₂ molecules exchanged. After the exchange, the cage occupied by CO₂ remained in the M-cage structure. In the third case, a S-cage of methane hydrate partially collapsed, and methane and CO₂ molecules exchanged. After the exchange, the cage occupied by CO₂ changed to an M-cage-like structure.     

Density functional study of H<Subscript>2</Subscript>O molecule adsorption on α-U(001) surface

Periodic density functional theory (DFT) calculations were performed to investigate the adsorption of H₂O on U(001) surface. The metallic nature of uranium atom and different adsorption sites of U(001) surface play key roles in the H₂O molecular dissociate reaction. The long-bridge site is the most favorable site of H₂O-U(001) adsorption configuration. The triangle-center site of the H atom is the most favorable site of HOH-U(001) adsorption configuration. The interaction between H₂O and U surface is more evident on the first layer than that on any other two sub-layers. The dissociation energy of one hydrogen atom from H₂O is ?1.994 to ?2.215 eV on U(001) surface, while the dissociating energy decreases to ?3.351 to ?3.394 eV with two hydrogen atoms dissociating from H₂O. These phenomena also indicate that the O_ads can promote the dehydrogenation of H₂O. A significant charge transfer from the first layer of the uranium surface to the H and O atoms is also found to occur, making the bonding partly ionic.     

On the Approximation of Solvent Effects on the Conformation and Dynamics of Cyclosporin A by Stochastic Dynamics Simulation Techniques

Abstract

The molecular simulation technique of stochastic dynamics (SD) is tested by application to the immunosuppressive drug cyclosporin A (CPA). Two stochastic dynamics simulations are performed, one (SD_CCl4 ) with atomic friction coefficients proportional to the viscosity of the nonpolar solvent CCl₄, and one (SD_H2O) with atomic friction coefficients corresponding to an aqueous solution. The atomic friction coefficients are also taken proportional to an approximate expression for the atomic accessible surface area. The properties of both stochastic dynamics simulations are compared to those of two full molecular dynamics (MD) simulations of cyclosporin A, one in a box with 591 CCl₄ molecules, and one in a box with 632 H₂O molecules.

The properties of cyclosporin A as found in the molecular dynamics simulation in CCl₄ are well reproduced by the SD_CCl4 simulation. This indicates that the neglect of a mean force reresenting the average solvent effects on the solute is justified in the case of nonpolar solvents. For polar solvents, like water, this mean force may not be neglected. The SD_H2O simulation of cyclosporin A clearly fails to reproduce the amount of hydrogen bonding found in the molecular dynamics stimulation of cyclosporin A in water.

A comparison with a molecular dynamics simulation of cyclosporin A in vacuo shows that both the SD_CCl4 and the SD_H2O simulation come closer to the properties of the molecular dynamics simulations in CCl₄ and in H₂O than a molecular dynamics simulation in vacuo.     

Theoretical studies on the structures,intra- and inter-molecular hydrogen bonding interactions in HNF and HNF–H2O clusters in the gaseous,aqueous and solid phases

Hydrazimium nitroformate ([N₂H₅]⁺[C(NO₂)₃]^? , HNF) is an ionic oxidiser used in solid propellants. Its properties are easily affected by H₂O because of its hygroscopicity. In this article, density functional theory (DFT) and molecular dynamics (MD) were employed to study the isolated HNF molecule and the HNF–H₂O cluster in gas phase and in the aqueous solution. Three stable conformations were obtained for HNF in the gas phase and in the aqueous solution, respectively, and each conformation can form several different HNF–H₂O clusters. Irrespective of whether it is in gas phase or in solution, intramolecular hydrogen bond interactions and other interactions (e.g. the binding energy, the dispersion energy, the second-order perturbation energy and the energy gap between frontier orbitals) of HNF are weaker in the clusters than in the isolated state. The initial decomposition energy of the cluster is lower than that of the isolated HNF molecule in both gaseous and aqueous phases, while the dissociation processes are the same. Molecular dynamic simulations showed that the clustered H₂O elongates and weakens the C–NO₂ bond in the solid HNF–H₂O cluster compared with that in the solid HNF. H₂O reduces and weakens intramolecular N–HΛO bonds too, and O–HΛN is the dominant intermolecular hydrogen bond between HNF and H₂O.     

Vibrational spectra of deuterated methane and water molecules in structure I clathrate hydrate from ab initio MD simulation

The deuteration of the lattice molecules in clathrate hydrates is a widely used experimental technique to clearly separate the vibrational modes. However, the effect of the deuteration on the vibrational spectra and molecular motions is not fully understood. Since the guest–host coupling may change the vibrational spectra, a detailed analysis of the vibrational spectra of deuterated clathrate hydrate is significant in the understanding of the mechanism of the vibrational shift. In this study, the vibrational spectra of the deuterated methane hydrates were calculated by ab initio molecular dynamics simulation. The intramolecular vibrational frequency of the methane in D₂O lattice and deuterated methane in H₂O lattice was calculated and compared with the pure methane hydrate. The bending, rocking and overtone of the bending mode was also reported. The effect of coupling of the rattling motions of guest and host molecules on the vibrational spectra was revealed.     

Proton reduction at surface of transition metal nanocatalysts

Catalytic activities of neutral and charged palladium (Pd) nanoparticles are compared for hydrogen reduction half-reaction. In this work the sequential H₂ dissociation from the surface of a Pd₁₃H₂₄ cluster is systematically studied by ab initio molecular dynamics (AIMD) at the density functional theory level. AIMD simulation is launched by preparing initial values of momenta of all nuclei in the model corresponding to a temperature range of 0–1700 K. AIMD simulation provides the trajectories of all the atoms in the cluster. A sequential H₂ desorption up to seven molecules is observed from the cluster surface due to thermal motion of nuclei. Modifications of total charge on the neutral Pd₁₃H₂₄ cluster model are found to affect surface H₂ desorption behaviour. A desorption rate of H₂ molecule on both neutral and charged Pd₁₃H₂₄ clusters is compared to the data of Pt₁₃H₂₄ cluster reported previously. The H₂ desorption energy on all the investigated clusters is also determined. The results reveal that Pd₁₃ cluster presents a higher catalytic activity than Pt₁₃ cluster.     

Low-frequency spectroscopy of four-photon scattering in aqueous solutions of biopolymers

The novel method of nonlinear laser spectroscopy — low frequency spectroscopy of four-photon scattering of laser radiation was applied to detect a considerable growth of ortho-H₂O spin isomer and also H₂O₂ molecule concentration in a hydrate layer at the interface between water and DNA, denatured DNA molecules and α-chymotrypsin. Spectra of rotational resonances of ortho/para-H₂O spin isomers were observed in aqueous solutions of different biopolymers and also in distilled water in the range from zero to 100 cm^?1 with the spectral resolution of 0.05–0.1 cm^?1. The fitting of four-wave mixing spectra shows notable growth of the H₂O₂ concentration and rotational line’s amplitude by a factor of ～3 in DNA solutions due to denaturizing. Besides, we studied the four-photon scattering spectra of α-chymotrypsin aqueous solutions at protein concentrations between 0 and 20 mg/cm³ in the range of ±7 cm^?1. We found that the velocity of sound in the protein aqueous solution measured by the shift of the Mandelstam-Brillouin scattering spectrum components was a cubic dependence on the protein concentration and reached the value of about 3000 m/s at 20 mg/cm³.     

DFT studies of the adsorption and dissociation of H2O on the Al13 cluster: origins of this reactivity and the mechanism for H2 release

A theoretical study of the chemisorption and dissociation pathways of water on the Al₁₃ cluster was performed using the hybrid density functional B3LYP method with the 6-311+G(d, p) basis set. The activation energies, reaction enthalpies, and Gibbs free energy of activation for the reaction were determined. Calculations revealed that the H₂O molecule is easily adsorbed onto the Al₁₃ surface, forming adlayers. The dissociation of the first H₂O molecule from the bimolecular H₂O structure via the Grotthuss mechanism is the most kinetically favorable among the five potential pathways for O–H bond breaking. The elimination of H₂ in the reaction of an H₂O molecule with a hydrogen atom on the Al cluster via the Eley–Rideal mechanism has a lower activation barrier than the elimination of H₂ in the reaction of two adsorbed H atoms or the reaction of OH and H. Following the adsorption and dissociation of H₂O, the structure of Al₁₃ is distorted to varying degrees.

Molecular-dynamic simulation of phospholipid bilayers: Ion distribution at the surface of neutral and charged bilayer in the liquid crystalline state

The electric field and ion distribution at the surface of neutral and charged lipid bilayers (BeCl₂ and dipalmitoyl phosphatidylcholine/dipalmitoyl phosphatidylserine (DPPC/DPPS) + KCl) were studied with molecular dynamic (MD) methods. It is shown that the contributions of lipid molecules, water and ions to the electric potential compensate each other in the region of the diffuse double layer and decrease the potential value close to zero. It is also demonstrated that the ion distribution at the charged surface is determined not only by the electrostatic ion-medium interaction. The total energy of this interaction was compared with the potential of mean ion force. It was shown that cations and anions have a different effect on the state of water molecules at the surface. The order parameter of water in the system DPPC + BeCl₂ and the Clion distribution have the extremum at the distance of 10 α atoms of the phospholipid glycerol. This position was chosen as the “electrical” interface of the electrical double layer (EDL) for all lipid systems studied. The potential of mean force of counter ions in EDL allows us to obtain the value of potential at the lipid surface suitable for experimental test of the MD data. This surface potential and surface charge density was found from MD simulation different electrolyte concentrations and DPPS content of 20, 40 and 60% in the mixture with DPPC and was shown to be in a good agreement with the Gouy-Chapman-Stern model upon fitting parameters close to their experimental values.     

Dissociation mechanism of gas hydrates (I,II, H) of alkane molecules: a comparative molecular dynamics simulation

Employing NPT molecular dynamics method with consistent valence force field, the dissociation processes of sI, sII and sH gas hydrates are simulated at different temperatures and at a constant pressure of 100 MPa. The dissociation mechanisms of gas hydrates are revealed by analysing the structural snapshots, radial distribution functions and diffusion coefficients at different temperatures. As temperature increases, the diffusion rates of water molecules and guest molecules increase; thus the clathrate skeleton formed by water molecules with hydrogen bonds distorts and breaks down; meanwhile the guest molecules encapsulated in the water cavities are released. The size of guest molecules affects the dissociation behaviour of gas hydrate. In addition, the dissociation behaviour also relies on the structural phase of gas hydrates.     

DFT study of CO<Subscript>2</Subscript> and H<Subscript>2</Subscript>O co-adsorption on carbon models of coal surface

The moisture content of coal affects the adsorption capacity of CO₂ on the coal surface. Since the hydrogen bonds are formed between H₂O and oxygen functional group, the H₂O cluster more easily adsorbs on the coal micropore than CO₂ molecule. The coal micropores are occupied by H₂O molecules that cannot provide extra space for CO₂ adsorption, which may leads to the reduction of CO₂ adsorption capacity. However, without considering factors of micropore and oxygen functional groups, the co-adsorption mechanisms of CO₂ and adsorbed H₂O molecule are not clear. Density functional theory (DFT) calculations were performed to elucidate the effect of adsorbed H₂O to CO₂ adsorption. This study reports some typical coal-H₂O···CO₂ complexes, along with a detailed analysis of the geometry, energy, electrostatic potential (ESP), atoms in molecules (AIM), reduced density gradient (RDG), and energy decomposition analysis (EDA). The results show that H₂O molecule can more stably adsorb on the aromatic ring surface than CO₂ molecule, and the absolute values of local ESP maximum and minimum of H₂O cluster are greater than CO₂. AIM analysis shows a detailed interaction path and strength between atoms in CO₂ and H₂O, and RDG analysis shows that the interactions among CO₂, H₂O, and coal model belong to weak van der Waals force. EDA indicates that electrostatic and long-range dispersion terms play a primary role in the co-adsorption of CO₂ and H₂O. According to the DFT calculated results without considering micropore structure and functional group, it is shown that the adsorbed H₂O can promote CO₂ adsorption on the coal surface. These results demonstrate that the micropore factor plays a dominant role in affecting CO₂ adsorption capacity, the attractive interaction of adsorbed H₂O to CO₂ makes little contribution.     

Molecular dynamics studies of the Nafion®, Dow® and Aciplex® fuel-cell polymer membrane systems

The Nafion, Dow and Aciplex systems – where the prime differences lies in the side-chain length – have been studied by molecular dynamics (MD) simulation under standard pressure and temperature conditions for two different levels of hydration: 5 and 15 water molecules per (H)SO₃ end-group. Structural features such as water clustering, water-channel dimensions and topology, and the dynamics of the hydronium ions and water molecules have all been analysed in relation to the dynamical properties of the polymer backbone and side-chains. It is generally found that mobility is promoted by a high water content, with the side-chains participating actively in the H₃O⁺/H₂O transport mechanism. Nafion, whose side-chain length is intermediate of the three polymers studied, is found to have the most mobile polymer side-chains at the higher level of hydration, suggesting that there could be an optimal side-chain length in these systems. There are also some indications that the water-channel network connectivity is optimal for high water-content Nafion system, and that this could explain why Nafion appears to exhibit the most favourable overall hydronium/water mobility. Figure The simulation box for Aciplex with 5 water molecules per sulphonate end-group (yellow spheres). The polymer backbone is black; while side-chains are brown. The water-channel iso-surfaces are represented as blue clouds     

Monte Carlo study of sI hydrogen hydrates

In this study, we perform grand canonical Monte Carlo simulations to evaluate the hydrogen storage capacity of structure I (sI) hydrogen hydrates at pressures up to 500 MPa. Initially, we calculate the upper limit of H₂ content of sI hydrates by studying the hypothetical sI hydrate, where H₂ is the single guest component. It is found that the storage capacity of the hypothetical pure H₂ sI hydrate could reach 3.5 wt% at 500 MPa and 274 K. Depending on pressure, the large cavities of the pure H₂ hydrate can accommodate up to three H₂ molecules while the small ones are singly occupied at most, even at pressures as high as 500 MPa, without any double occupancy being observed. Subsequently, the binary H₂–ethylene oxide (EO) hydrate is examined. In this case, the large cavities are occupied by a single EO molecule while the small cavities can accommodate at most a single H₂ molecule. Such configuration results in a maximum H₂ content of only 0.37 wt%. The hydrogen storage capacity does not improve significantly even in case when EO is replaced by a component with smaller molecular weight.     

New horizons of adenosinetriphosphate energetics arising from interaction with magnesium cofactor

MD DFT:B3LYP (6-31G** basis set, T = 310 K) method is used to study interactions [singlet (S) and triplet (T) reaction paths] between adenosinetriphosphate, ATP⁴⁻, and [Mg(H₂O)₆]²⁺ in water environment, modeled with 78 water molecules. Computations reveal the appearance of low and high-energy states (stable, quasi-stable, and unstable), assigned to different spin symmetries. At the initial stage of interaction, ATP donates a part of its negative charge to the Mg complex making the Mg slightly charged. As a result, the original octahedral Mg complex loses two (S state) or four (T state) water molecules. Moving along S or T potential energy surfaces (PESs), Mg(H₂O)₄ or Mg(H₂O)₂ display different ways of complexation with ATP. S path favors the formation of a stable chelate with the O1–O2 fragment of ATP triphosphate tail, whereas T path favors producing a single-bonded complex with the O2. The latter, being unstable, undergoes a further conversion into a spin-separated complex, also unstable, and two metastable S complexes, which finally arise in two stable, low-energy and high-energy, chelates. The spin-separated complex experiences rapid decomposition resulting in the production of a highly reactive adenosinemonophosphate ion-radical •AMP, early observed in the CIDNP experiment (Tulub 2006). Biological consequences of the findings are discussed.     

First Principles Modeling of Dissociative Adsorption at Crystal Surfaces: Hydrogen on Pt(111)

Multiscale simulation has the potential of becoming the new modeling paradigm in chemical sciences. An important class of multiscale models involves the mapping of a finer scale model into an approximate surface that is used by a coarser scale model. As a specific example of this class we present the case of the adsorption dynamics of diatomic molecules on single crystal catalyst surfaces. The prototype system studied is the dissociative adsorption of H₂ on Pt(111). The finer scale model consists of density functional theory (DFT) periodic slab calculations that provide a small dataset for training an atomistic scale potential energy surface. The coarser scale model uses a semi-classical molecular dynamics (MD) algorithm to obtain the sticking coefficient as a function of the incident energy. Comparison to experimental data and published simulation work is presented. Finally, major challenges in multiscale modeling of chemical reactivity in coupled DFT/MD simulations are discussed, specifically the need for a systematic method of assessing the accuracy of the coarse graining process.