The properties of higher n-alkanes and their mixtures is a topic of significant interest for the oil and chemical industry. However, the experimental data at high temperatures are scarce. The present ...study focuses on simulating n-dodecane, n-octacosane, their binary mixture at a n-dodecane mole fraction of 0.3, and a model mixture of the commercially available hydrocarbon wax SX-70 to evaluate the performance of several force fields on the reproduction of properties such as liquid densities, surface tension, and viscosities. Molecular dynamics simulations over a broad temperature range from 323.15 to 573.15 K were employed in examining a broad set of atomistic molecular models assessed for the reproduction of experimental data. The well-established united atom TraPPE (TraPPE-UA) was compared against the all atom optimized potentials for liquid simulations (OPLS) reparametrization for long n-alkanes, L-OPLS, as well as Lipid14 and MARTINI force fields. All models qualitatively reproduce the temperature dependence of the aforementioned properties, but TraPPE-UA was found to reproduce liquid densities most accurately and consistently over the entire temperature range. TraPPE-UA and MARTINI were very successful in reproducing surface tensions, and L-OPLS was found to be the most accurate in reproducing the measured viscosities as compared to the other models. Our simulations show that these widely used force fields originating from the world of biomolecular simulations are suitable candidates in the study of n-alkane properties, both in the pure and mixture states.
Shale gas is an unconventional source of energy, which has attracted a lot of attention during the last years. Kerogen is a prime constituent of shale formations and plays a crucial role in shale gas ...technology. Significant experimental effort in the study of shales and kerogen has produced a broad diversity of experimentally determined structural and thermodynamic properties even for samples of the same well. Moreover, proposed methods reported in the literature for constructing realistic bulk kerogen configurations have not been thoroughly investigated. One of the most important characteristics of kerogens is their porosity, due to its direct connection with their transport properties and its potential as discriminating and classifying metric between samples. In this study, molecular dynamics (MD) simulations are used to study the porosity of model kerogens. The porosity is controlled effectively with systematic variations of the number and the size of dummy LJ particles that are used during the construction of system’s configuration. The porosity of each sample is characterized with a newly proposed algorithm for analyzing the free space of amorphous materials. It is found that, with moderately sized configurations, it is possible to construct percolated pores of interest in the shale gas industry.
Kerogen is a microporous amorphous solid, which is the major component of the organic matter scattered in the potentially lucrative shale formations hosting shale gas. A deeper understanding of the ...way kerogen porosity characteristics affect the transport properties of hosted gas is important for the optimal design of the extraction process. In this work, we employ molecular simulation techniques to investigate the role of porosity on the adsorption and transport behavior of shale gas in overmature type II kerogen found in many currently productive shales. To account for the wide range of porosity characteristics present in the real system, a large set of 60 kerogen structures that exhibit a diverse set of void space attributes was used. Grand canonical Monte Carlo simulations were performed for the study of the adsorption of CH4, C2H6, n-C4H10, and CO2 at 298.15 and 398.15 K and a variety of pressures. The amount adsorbed is found to correlate linearly with the porosity of the kerogen. Furthermore, the adsorption of a quaternary mixture of CH4, C2H6, CO2, and N2 was investigated under the same conditions, indicating that a composition resembling that of the shale gas is achieved under higher temperature and pressure values, i.e., conditions closer to those prevailing in the hosting shale field. The diffusion of CH4, C2H6, and CO2, both as pure components and as components of the quaternary mixture, was investigated using equilibrium molecular dynamics simulations at temperatures of 298.15 and 398.15 K and pressures of 1 and 250 atm. In addition to the effect of temperature and pressure, the importance of limiting pore diameter (LPD), maximum pore diameter (MPD), accessible volume (V acc), and accessible surface (S acc) on the observed adsorbed amount and diffusion coefficient was revealed by qualitative relationships. The diffusion across the models was found to be anisotropic and the maximum component of the diffusion coefficient to correlate linearly with LPD, indicating that the controlling step of the transport process is the crossing of the limiting pore region. Finally, the transport behavior of the pure compounds was compared with their transport properties when in mixture and it was found that the diffusion coefficient of each compound in the mixture is similar to the corresponding one under pure conditions. This observation agrees with earlier studies in different kerogen models comprising wider pores that have revealed negligible cross-correlation Onsager coefficients.
Molecular dynamics (MD) simulations are employed to study the effect of chain length and temperature on the density and conformational properties of regioregular poly(3-hexylthiophene), also denoted ...as RR-P3HT, in its pure amorphous phase. First, several widely used all-atom force fields (FFs) currently available in the literature are evaluated by comparing their predictions for the density, mean-square chain end-to-end distance, mean-square chain radius-of-gyration, and persistence length of RR-P3HT oligomers at temperatures above their melting point with the limited available experimental data in the literature. Then, with one of the most promising from these FFs, we extend the MD simulations to higher-chain-length P3HT systems (containing up to 150 monomers per chain) at various temperatures. The MD results indicate that the density and persistence length of amorphous P3HT increase slightly with chain length approaching limiting asymptotic values equal to 0.788 ± 0.003 g cm–3 and 21 ± 0.4 Å, respectively, at temperature T = 700 K and pressure P = 1 atm. This is attributed to excess chain end free volume effects that are significant at low molecular weights. On the contrary, the effective conjugation length, which is found to become larger than the persistence length only above a certain molecular weight, shows a stronger dependence on chain length. Both of these characteristic lengths are found to increase with decreasing temperature due to the increasing relative population of planar (cis and trans) conformational states of the inter-ring torsion angle. The probability distribution of the maximum length of conjugated segments along a P3HT chain coincides with the theoretical distribution of a longest run of “heads” in a coin-flip experiment. Our MD results suggest that short-chain-length RR-P3HT chains in their bulk amorphous phase are semiflexible but, as their molecular weight increases, they adopt more and more random coil conformations, especially at higher temperatures.
Natural gas production from shale formations is one of the most recent and fast growing developments in the oil and gas industry. The accurate prediction of the adsorption and transport of shale gas ...is essential for estimating shale gas production capacity and improving existing extractions. To realistically represent heterogeneous shale formations, a composite pore model was built from a kaolinite slit mesopore hosting a kerogen matrix. Moreover, empty slabs (2, 3, and 4 nm) were added between the kerogen matrix and siloxane surface of kaolinite. Using Grand–Canonical Monte Carlo (GCMC) and molecular dynamics (MD) simulations, the adsorption and diffusion of pure methane, pure ethane, and a shale gas mixture were computed at various high pressures (100, 150, and 250 atm) and temperature of 298.15 K. The addition of an inner slit pore was found to significantly increase the excess adsorption of methane, as a pure component and in the shale gas mixture. The saturation of the composite pore with methane was observed to be at a higher pressure compared to ethane. The excess adsorption of carbon dioxide was not largely affected by pressure, and the local number density profile showed its strong affinity to kerogen micropores and the hydroxylated gibbsite surface under all conditions and pore widths. Lateral diffusion coefficients were found to increase with increasing the width of the empty slab inside the composite pore. Statistical errors of diffusion coefficients were found to be large for the case of shale gas components present at low composition. A larger composite pore configuration was created to investigate the diffusion of methane in different regions of the composite pore. The calculated diffusion coefficients and mean residence times were found to be indicative of the different adsorption mechanisms occurring inside the pore.
The adsorption behavior inside kaolinite mesopores of aqueous solutions of various salts and additives is investigated using Molecular Dynamics simulations. In particular, we examine the various ...combinations of water + salt, water + additive, and water + salt + additive mixtures, where the salts are NaCl, CsCl, SrCl2, and RaCl2 and the additives are methanol and citric acid. Citric acid is modeled in two forms, namely, fully protonated (H3A) and fully deprotonated (A3–), the latter being prevalent in neutral pH conditions, in accordance with the kaolinite structure employed. The force fields used for the individual system components include CLAYFF for the kaolinite mesopores, SPC/E for water, parameters optimized for the SPC/E water model based on hydration free energies (HFE) for ions, and general Amber force field (GAFF) for the additives. The spatial distributions along the kaolinite pore are delineated and reveal the preferential adsorption behavior of the various species with respect to the gibbsite and siloxane surface, as well as the effect on this behavior of the interactions between the various species. Furthermore, we examine the hydrogen bonds formed between the kaolinite surfaces and water molecules as well as the additives. For the case of citric acid, which tends to aggregate, a cluster analysis is also carried out, in order to examine the effect of the various ions on the cluster formation. Finally, through the calculation of lateral diffusion coefficients and mean residence times, we provide insights on the mobility of the various species inside the kaolinite mesopores.
Fischer–Tropsch synthesis (FTS) is used extensively in the gas-to-liquids (GTL) process to produce clean, high-quality low emission transportation fuels from synthesis gas. In order to gain a better ...understanding of the phase behavior of the produced wax–water mixtures at reaction conditions by accounting for confinement effects of either hydrophilic or hydrophobic characteristics and catalyst nanoparticles (NPs), one needs to closely examine the validity of incorporating coarse grained approaches in the context of FTS. The present study focuses on simulating by means of atomistic (AA) and coarse-grained (CG) molecular dynamics (MD; CGMD) simulations the n-octacosane (n-C28)–water mixture inside graphene (G) and graphene oxide (GO) mesopores under low-temperature FTS conditions (473.15 K) with the inclusion of a Co NP. Graphene derivatives were selected as they are emerging catalyst support materials in the FTS reaction and allow for direct comparisons between the AA and CG methodologies. We also evaluated the presence of long-chain alcohols such as dodecan-1-ol at 7 wt % on the n-C28–H2O mixture phase behavior. The AA simulations involved the use of the united atom TraPPE (TraPPE-UA) force field for n-C28 and the alcohols and the TIP4P/2005 force field for water, while the MARTINI force field was used for the CG description. With regard to the mixtures inside the G pore, both AA and CG simulation methods capture the phase separation of the mixture, with water molecules occupying the center of the pore and n-C28 forming layers at the pore walls; inside GO, both methodologies show that water separates near the surface and the model wax lies at the pore center. Both AA and CG simulations accurately capture the n-C28 and H2O diffusivity as a function of the distance from the G and GO pore centers, respectively, being lower closer to the pore surface. Dodecan-1-ol is mostly located at the n-C28–H2O interface showing a higher preference toward the wax as a consequence of increased van der Waals intermolecular interactions, slightly reducing the mobility of water. The agreement between AA and CG MD simulations paved the way for novel CGMD simulations with DFT-derived parameters for Co, to study the n-C28–H2O behavior in its presence. Our results show that the Co NP does not affect phase separation of the n-C28–H2O mixture inside the pores; however, water at such high concentrations covers the Co NP surface extensively. Given the experimental difficulties in exploring the relevant mechanisms at this scale, our results showcase that CGMD using the MARTINI force field can be employed to study FTS-related processes at this level and are expected to open new pathways in the investigation of confined mixtures relevant to the FTS reaction in the presence of supported catalyst NPs.
Lipoprotein(a) Lp(a) plays an important role in atherosclerosis. The biological effects of Lp(a) have been attributed either to apolipoprotein(a) or to its low-density lipoprotein-like particle. ...Lp(a) contains platelet-activating factor acetylhydrolase, an enzyme that exhibits a Ca2+-independent phospholipase A2 activity and is complexed to lipoproteins in plasma; thus, it is also referred to as lipoprotein-associated phospholipase A2. Substrates for lipoprotein-associated phospholipase A2 include phospholipids containing oxidatively fragmented residues at the sn-2 position (oxidized phospholipids; OxPLs). OxPLs may play important roles in vascular inflammation and atherosclerosis. Plasma levels of OxPLs present on apolipoprotein B-100 particles (OxPL/apolipoprotein B) are correlated with coronary artery, carotid, and peripheral arterial disease. Furthermore, OxPL/apolipoprotein B levels in plasma are strongly correlated with Lp(a) levels, are preferentially sequestered on Lp(a), and thus are potentially subjected to degradation by the Lp(a)-associated lipoprotein-associated phospholipase A2. The present review article focuses specifically on the characteristics of the lipoprotein-associated phospholipase A2 associated with Lp(a) and discusses the possible role of this enzyme in view of emerging data showing that OxPLs in plasma are preferentially sequestered on Lp(a) and may significantly contribute to the increased atherogenicity of this lipoprotein.
DFT functionals are of paramount importance for an accurate electronic and structural description of transition metal systems. In this work, a systematic analysis using some well-known and commonly ...used DFT functionals is performed. A comparison of the structural and energetic parameters calculated with the available experimental data is made in order to find the adequate functional for an accurate description of the TiO
bulk and surface of both anatase and rutile structures. In the absence of experimental data on the surface energy, the theoretical predictions obtained using the high-accuracy HSE06 functional were used as a reference to compare against the surface energy values calculated with the other DFT functionals. A clear improvement in the electronic description of both anatase and rutile was observed by introducing the Hubbard U correction term to PBE, PW91, and OptPBE functionals. The OptPBE-U4 functional was found to offer a good compromise between accurately describing the structural and electronic properties of titania.
The use of rate models for networks of stochastic reactions is frequently used to comprehend the macroscopically observed dynamic properties of finite size reactive systems as well as their ...relationship to the underlying molecular events. Τhis particular approach usually stumbles on parameter derivation associated with stochastic kinetics, a quite demanding procedure. The present study incorporates a novel algorithm, which infers kinetic parameters from the system’s time evolution, manifested as changes in molecular species populations. The proposed methodology reconstructs distributions required to infer kinetic parameters of a stochastic process pertaining to either a simulation or experimental data. The suggested approach accurately replicates rate constants of the stochastic reaction networks, which have evolved over time by event-driven Monte Carlo (MC) simulations using the Gillespie algorithm. Furthermore, our approach has been successfully used to estimate rate constants of association and dissociation events between molecular species developing during molecular dynamics (MD) simulations. We certainly believe that our method will be remarkably helpful for considering the macroscopic characteristic molecular roots related to stochastic physical and biological processes.
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