Modeling oceanic sedimentary methane hydrate growth through molecular dynamics simulation.

The crystallization process of methane hydrates in a confined geometry resembling seabed porous silica sedimentary conditions has been studied using molecular dynamics simulations. With this objective in mind, a fully atomistic quartz silica slit pore has been designed, and the temperature stability of a methane hydrate crystalline seed in the presence of water and guest molecule methane has been analyzed. NaCl ion pairs have been added in different concentrations, simulating salinity conditions up to values higher than average oceanic conditions. The structure obtained when the hydrate crystallizes inside the pore is discussed, paying special attention to the presence of ionic doping inside the hydrate and the subsequent induced structural distortion. The shift in the hydrate stability conditions due to the increasing water salinity is discussed and compared with the case of unconfined hydrate, concluding that the influence of the confinement geometry and pore hydrophilicity produces a larger deviation in the confined hydrate phase equilibria.

Molecular Simulation of SO2 Separation and Storage Using a Cryptophane-Based Porous Liquid.

A theoretical molecular simulation study of the encapsulation of gaseous SO2 at different temperature conditions in a type II porous liquid is presented here. The system is composed of cage cryptophane-111 molecules that are dispersed in dichloromethane, and it is described using an atomistic modelling of molecular dynamics. Gaseous SO2 tended to almost fully occupy cryptophane-111 cavities throughout the simulation. Calculations were performed at 300 K and 283 K, and some insights into the different adsorption found in each case were obtained. Simulations with different system sizes were also studied. An experimental-like approach was also employed by inserting a SO2 bubble in the simulation box. Finally, an evaluation of the radial distribution function of cryptophane-111 and gaseous SO2 was also performed. From the results obtained, the feasibility of a renewable separation and storage method for SO2 using porous liquids is mentioned.

Mechanisms of Listeria monocytogenes Disinfection with Benzalkonium Chloride: From Molecular Dynamics to Kinetics of Time-Kill Curves.

Unravelling the mechanisms of action of disinfectants is essential to optimise dosing regimes and minimise the emergence of antimicrobial resistance. In this work, we examined the mechanisms of action of a commonly used disinfectant-benzalkonium chloride (BAC)-over a significant pathogen-L. monocytogenes-in the food industry. For that purpose, we used modelling at multiple scales, from the cell membrane to cell population inactivation. Molecular modelling revealed that the integration of the BAC into the membrane requires three phases: (1) the approaching of BAC to the cellular membrane, (2) the absorption of BAC to its surface, and (3) the integration of the compound into the lipid bilayer, where it remains at least for several nanoseconds, probably destabilising the membrane. We hypothesised that the equilibrium of adsorption, although fast, was limiting for sufficiently large BAC concentrations, and a kinetic model was derived to describe time-kill curves of a large population of cells. The model was tested and validated with time series data of free BAC decay and time-kill curves of L. monocytogenes at different inocula and BAC dose concentrations. The knowledge gained from the molecular simulation plus the proposed kinetic model offers the means to design novel disinfection processes rationally.

Influence of Lennard-Jones Parameters in the Temperature Dependence of Real Gases Diffusion through Nanochannels.

Umbrella Sampling Molecular Dynamics has been used to determine transition energies for different guest molecules through hydroquinone ß-clathrate nanochannels, as well as their temperature trend. This clathrate has been shown to successfully enclathrate different types of small gases with remarkable selectivity, and thus it has been proposed as a potential gas separation and storage medium. Most of these potential guest gases can be successfully modeled as single Lennard-Jones spheres. Then, to obtain a general view of diffusion probabilities for different potential guest molecules, a comparative study for different virtual guest molecules described by different Lennard-Jones parameters has been performed. A regular temperature trend has been obtained for the transition energies for the molecular model characteristic parameter range explored. Finally, to locate the transition energy values of real gases within the space of phases explored, calculations have been repeated for molecular models of different noble gases and H2. The correlation results presented allow a wide interpolation ability for determining the transition energies of potential guest molecules stored or diffusing through the nanochannels of the studied clathrate structure.

Diffusion and dynamics of noble gases in hydroquinone clathrate channels.

In the present work, we study the behavior of the noble gases He, Ne, Ar, and Kr inside a hydroquinone clathrate (HQC) by using all-atom molecular dynamics. Larger elements of the same group were not considered due to their inability to fit inside the HQC cavities. By using the umbrella sampling technique, we have obtained the following inter-cage transition barriers-which are arguably the main factor determining the type of diffusion of the gases-at 310 K and 0.1 MPa: 1192; 2204; 6450; 10 730 kJ mol-1 for the guests He, Ne, Ar, and Kr, respectively. These energy barriers were found to have a linear relation with atomic radii (σ). We have tested this tendency with CH4, due to its intermediate size between Ar and Kr, obtaining a barrier of 8926 kJ mol-1, in excellent agreement with the results for noble gases.

Molecular Simulation of CO2 and H2 Encapsulation in a Nanoscale Porous Liquid.

In this study we analyse from a theoretical perspective the encapsulation of both gaseous H2 and CO2 at different conditions of pressure and temperature in a Type II porous liquid, composed by nanometric scale cryptophane-111 molecules dispersed in dichloromethane, using atomistic molecular dynamics. Gaseous H2 tends to occupy cryptophane-111's cavities in the early stages of the simulation; however, a remarkably greater selectivity of CO2 adsorption can be seen in the course of the simulation. Calculations were performed at ambient conditions first, and then varying temperature and pressure, obtaining some insight about the different adsorption found in each case. An evaluation of the host molecule cavities accessible volume was also performed, based on the guest that occupies the pore. Finally, a discussion between the different intermolecular host-guest interactions is presented, justifying the different selectivity obtained in the molecular simulation calculations. From the results obtained, the feasibility of a renewable separation and storage method for CO2 using these nanometric scale porous liquids is pointed out.

Ionogels Derived from Fluorinated Ionic Liquids to Enhance Aqueous Drug Solubility for Local Drug Administration.

Gelatin is a popular biopolymer for biomedical applications due to its harmless impact with a negligible inflammatory response in the host organism. Gelatin interacts with soluble molecules in aqueous media as ionic counterparts such as ionic liquids (ILs) to be used as cosolvents to generate the so-called Ionogels. The perfluorinated IL (FIL), 1-ethyl-3-methylpyridinium perfluorobutanesulfonate, has been selected as co-hydrosolvent for fish gelatin due to its low cytotoxicity and hydrophobicity aprotic polar structure to improve the drug aqueous solubility. A series of FIL/water emulsions with different FIL content and their corresponding shark gelatin/FIL Ionogel has been designed to enhance the drug solubility whilst retaining the mechanical structure and their nanostructure was probed by simultaneous SAXS/WAXS, FTIR and Raman spectroscopy, DSC and rheological experiments. Likewise, the FIL assisted the solubility of the antitumoural Doxorubicin whilst retaining the performing mechanical properties of the drug delivery system network for the drug storage as well as the local administration by a syringe. In addition, the different controlled release mechanisms of two different antitumoral such as Doxorubicin and Mithramycin from two different Ionogels formulations were compared to previous gelatin hydrogels which proved the key structure correlation required to attain specific therapeutic dosages.

Tailoring Nanofluid Thermophysical Profile through Graphene Nanoplatelets Surface Functionalization.

In this study, the effect of chemical surface functionalization through oxidation of exfoliated graphite nanoplatelets in the transport properties of their aqueous nanofluids has been analyzed. With this objective, thermal conductivity and viscoelastic properties have been determined for original and oxidized nanoplatelets. The results show that the functionalization completely changes the internal structure of the suspension, which is reflected in shifts of even orders of magnitude on viscosity, yield stress, or storage or loss moduli. It is evident that this influences thermal conduction properties as well, as it has been also demonstrated. This shows that nanostructure surface functionalization can be a useful strategy to tune nanofluid thermophysical properties.

Simulation of Capture and Release Processes of Hydrogen by ß-Hydroquinone Clathrate.

Using molecular simulation techniques, we investigate the storage capabilities of H2 gas by the clathrate of hydroquinone (HQ). Quantum mechanics calculations have been used to assess structure and interactions at the atomic scale and molecular dynamics to model the HQ clathrate at successive equilibriums during the processes of capture and release of H2, as well as the diffusion of H2 inside the clathrate structure. The thermodynamic conditions of the simulations performed try to reproduce closely the corresponding experimental procedures, with results that are in good agreement with literature observed trends. The results obtained contribute to depict a more complete and better substantiated image of the mechanisms involved in stability and in the processes of capture and release of H2 by the HQ clathrate.

Evidence of viscoplastic behavior of exfoliated graphite nanofluids.

The rheological behavior of ethylene glycol-based nanofluids containing exfoliated graphite nanoplatelets has been carried out using a cone-plate Physica MCR rheometer. Initial experiments based on flow curves were carried out, the flow curves were based on the controlled shear stress model, these tests show that the studied nanofluids present non-Newtonian shear thinning behavior with yield stress. Furthermore, linear viscoelastic experiments were conducted in order to determine the viscoelastic behavior: using strain sweep and frequency sweep tests the storage and loss modulus were determined. The fractal dimension (Df) was estimated from the suspension static yield-stress and volume fraction (ϕ) dependence, and was determined to be Df = 2.36, a value consistent with a process of aggregation of RLCA type (reaction limited cluster aggregation). This value is unusual if compared with other nanofluids, and can be regarded as a result of the bidimensionality of the suspended nanoplatelets. Finally, creep-recovery tests and mechanical models confirm the viscoplastic nature of our nanofluids, a feature never shown so far for this type of systems, increasing the solid-like character in the range of concentrations studied if compared with other nanofluids reported in the literature. This is a result of the combination of a remarkable internal structure and strong interactions, which evidence an unexpected behaviour sharing many solid-like features.

DFT calculation of the potential energy landscape topology and Raman spectra of type I CH4 and CO2 hydrates.

CO2 and CH4 clathrate hydrates of type I were studied by means of DFT and QTAIM, in order to better understand their properties at the molecular level. Sub-cells of type I hydrates were modeled as independent rigid cages, both empty and containing guest molecules. Interaction potentials of guest molecules inside each cage, and moving from a cell to the adjacent one, were calculated using the DFT approximation B3LYP/6-311+g(d,p), considering the cases with and without long range Coulombic corrections. The selected theory level was validated by comparison of the simulated Raman spectra with the experimental ones, for the case of type I lattice at full occupation of CO2 and CH4, respectively. For this comparison, Fermi resonances of CO2 were taken into account by transforming experimental bands to the corresponding theoretical non-mixed states. On the one hand, our results confirm the validity of the theory level selected for the model. We have shown the high anisotropy of the guest-cell interaction potential of the molecules analyzed, which has implications in the formulation and use of equations of state, and in the study of transport properties as well. On the other hand, our results suggest that the concentration of guest species inside type I hydrates could be computed from the comparison of experimental and predicted Raman spectra, although there are non-trivial experimental limitations to get over for that purpose.

Molecular dynamics simulations of the structure of the graphene-ionic liquid/alkali salt mixtures interface.

We performed molecular dynamics simulations of mixtures of 1-butyl-3-methylimidazolium tetrafluoroborate with lithium tetrafluoroborate and potassium tetrafluoroborate between two charged and uncharged graphene walls, in order to analyze the structure of the well-known formation of layers that takes place on liquids under confinement. For this purpose, we studied the molecular density profiles, free energy profiles for bringing lithium and potassium cations from the bulk mixture to the graphene wall and the orientational distributions of imidazolium rings within the first adsorbed layer as a function of salt concentration and electrode potential. The charge densities in the electrodes were chosen to be zero and ±1 e nm(-2), and the salt molar percentages were %salt = 0, 10 and 25. We found that the layered structure extends up to 1-2 nm, where the bulk behaviour is recovered. In addition, whereas for the neutral surface the layers are composed of both ionic species, increasing the electrode potential, the structure changes to alternating cationic and anionic layers leading to an overcompensation of the charge of the previous layer. We also calculated the distribution of angles of imidazolium rings near neutral and charged graphene walls, finding a limited influence of the added salt. In addition, the average tilt of the imidazolium ring within the first layer goes from 36° with respect to a normal vector to the uncharged graphene wall to 62° in the presence of charged walls. The free energy profiles revealed that lithium and potassium ions are adsorbed on the negative surface only for the highest amount of salt, since the free energy barriers for approaching this electrode are considerably higher than kBT.

MD simulations of the formation of stable clusters in mixtures of alkaline salts and imidazolium-based ionic liquids.

Structural and dynamical properties of room-temperature ionic liquids containing the cation 1-butyl-3-methylimidazolium ([BMIM](+)) and three different anions (hexafluorophosphate, [PF6](-), tetrafluoroborate, [BF4](-), and bis(trifluoromethylsulfonyl)imide, [NTf2](-)) doped with several molar fractions of lithium salts with a common anion at 298.15 K and 1 atm were investigated by means of molecular dynamics simulations. The effect of the size of the salt cation was also analyzed by comparing these results with those for mixtures of [BMIM][PF6] with NaPF6. Lithium/sodium solvation and ionic mobilities were analyzed via the study of radial distribution functions, coordination numbers, cage autocorrelation functions, mean-square displacements (including the analysis of both ballistic and diffusive regimes), self-diffusion coefficients of all the ionic species, velocity and current autocorrelation functions, and ionic conductivity in all the ionic liquid/salt systems. We found that lithium and sodium cations are strongly coordinated in two different positions with the anion present in the mixture. Moreover, [Li](+) and [Na](+) cations were found to form bonded-like, long-lived aggregates with the anions in their first solvation shell, which act as very stable kinetic entities within which a marked rattling motion of salt ions takes place. With very long MD simulation runs, this phenomenon is proved to be on the basis of the decrease of self-diffusion coefficients and ionic conductivities previously reported in experimental and computational results.

C-C reductive elimination in palladium complexes, and the role of coupling additives. A DFT study supported by experiment.

A DFT study of R-R reductive elimination (R = Me, Ph, vinyl) in plausible intermediates of Pd-catalyzed processes is reported. These include the square-planar tetracoordinated systems cis-[PdR(2)(PMe(3))(2)] themselves, possible intermediates cis-[PdR(2)(PMe(3))L] formed in solution or upon addition of coupling promoters (L = acetonitrile, ethylene, maleic anhydride (ma)), and tricoordinated intermediates cis-[PdR(2)(PMe(3))] (represented as L = empty). The activation energy ranges from 0.6 to 28.6 kcal/mol in the gas phase, increasing in the order vinyl-vinyl < Ph-Ph < Me-Me, depending on R, and ma < "empty" < ethylene < PMe(3) approximately MeCN, depending on L. The effect of added olefins was studied for a series of olefins, providing the following order of activation energy: p-benzoquinone < ma < trans-1,2-dicyanoethylene < 3,5-dimethylcyclopent-1-ene < 2,5-dihydrofuran < ethylene < trans-2-butene. Comparison of the calculated energies with experimental data for the coupling of cis-[PdMe(2)(PPh(3))(2)] in the presence of additives (PPh(3), p-benzoquinone, ma, trans-1,2-dicyanoethylene, 2,5-dihydrofuran, and 1-hexene) reveals that: (1) There is no universal coupling mechanism. (2) The coupling mechanism calculated for cis-[PdMe(2)(PMe(3))(2)] is direct, but PPh(3) retards the coupling for cis-[PdMe(2)(PPh(3))(2)], and DFT calculations support a switch of the coupling mechanism to dissociative for PPh(3). (3) Additives that would provide intermediates with coupling activation energies higher than a dissociative mechanism (e.g., common olefins) produce no effect on coupling. (4) Olefins with electron-withdrawing substituents facilitate the coupling through cis-[PdMe(2)(PR(3))(olefin)] intermediates with much lower activation energies than the starting complex or a tricoordinated intermediate. Practical consequences are discussed.