Molecular dynamics simulation of diffusion coefficients and structural properties of some alkylbenzenes in supercritical carbon dioxide at infinite dilution

Single-Point Mutant Inverts the Stereoselectivity of a Carbonyl Reductase toward β-Ketoesters with Enhanced Activity

Enzyme stereoselectivity control is still a major challenge. To gain insight into the molecular basis of enzyme stereo-recognition and expand the source of antiPrelog carbonyl reductase toward β-ketoesters, rational enzyme design aiming at stereoselectivity inversion was performed. The designed variant Q139G switched the enzyme stereoselectivity toward β-ketoesters from Prelog to antiPrelog, providing corresponding alcohols in high enantiomeric purity (89.1-99.1 % ee). More importantly, the well-known trade-off between stereoselectivity and activity was not found. Q139G exhibited higher catalytic activity than the wildtype enzyme, the enhancement of the catalytic efficiency (k_cat /K_m ) varied from 1.1- to 27.1-fold. Interestingly, the mutant Q139G did not lead to reversed stereoselectivity toward aromatic ketones. Analysis of enzyme-substrate complexes showed that the structural flexibility of β-ketoesters and a newly formed cave together facilitated the formation of the antiPrelog-preferred conformation. In contrast, the relatively large and rigid structure of the aromatic ketones prevents them from forming the antiPrelog-preferred conformation.

Theoretical insight on effect of DMSO-acetonitrile co-solvent on the formation of CL-20/HMX cocrystal explosive

CL-20/HMX-solvent interface models were established to understand the effect of DMSO-acetonitrile co-solvent on the formation of CL-20/HMX cocrystal. The molecular dynamics simulations were applied to theoretically investigate the interactions of CL-20/HMX cocrystal surfaces and dimethyl sulfoxide/acetonitrile co-solvents. The binding energies were calculated, and the interaction between solvent molecules and CL-20/HMX cocrystal faces was analyzed. The results show that molecular interactions would be affected by the mole ratios of solvent, and the comparison of the binding energies with different mole ratios revealed that dimethyl sulfoxide/acetonitrile with mole ratio of 1:3 favors the formation of CL-20/HMX cocrystal.

Diffusivity and hydrophobic hydration of hydrocarbons in supercritical CO2 and aqueous brine

CO₂ injection (EOR and sequestration technique) creates the amalgamation of hydrocarbons, CO₂, and aqueous brine in the subsurface. In this study, molecular dynamics (MD) simulations were used to investigate the diffusivity of hydrocarbon molecules in a realistic scenario of supercritical CO₂ (SC-CO₂) injection in the subsurface over a wide range of pressures (50 < P < 300 bar) and aqueous brine concentrations (0, 2, and 5% brine). To overcome existing challenges in traditional diffusivity calculation approaches, we took advantage of fundamental molecular-based methods, along with further verification of results by previously published experimental data. In this regard, computational methods and MD simulations were employed to compute diffusion coefficients of hydrocarbons (benzene and pentane). It was found that the presence of water and salt affects the thermodynamic properties of molecules where the intermolecular interactions caused the hydrophobic hydration of hydrocarbons coupled with ionic hydration due to hydrogen bond and ion-dipole interactions. Based on these results, it is demonstrated that the formation of water clusters in the SC-CO₂ solvent is a major contributor to the diffusion of hydrophobic molecules. The outcome at different pressure conditions showed that hydrocarbons always would diffuse less in the presence of water. The slopes of linearly fitted MSD of benzene and pentane infinitely diluted in SC-CO₂ is around 13 to 20 times larger than the slope with water molecules (4 wt%). When pressure increases (100–300 bar), the diffusion coefficients (D) of benzene and pentane decreases (around 1.2 × 10⁻⁹ to 0.4 × 10⁻⁹ and 2 × 10⁻⁹ to 1 × 10⁻⁹ m² s⁻¹, respectively). Furthermore, brine concentration generally plays a negative role in reducing the diffusivity of hydrocarbons due to the formation of water clusters as a result of hydrophobic and ionic hydration. Under the SC-CO₂ rich (injection) system in the shale reservoir, the diffusion of hydrocarbon is correlated to the efficiency of hydrocarbon flow/recovery. Ultimately, this study will guide us to better understand the phenomena that would occur in nanopores of shale that undergo EOR or are becoming a target of CO₂ sequestration.

CO₂ injection (EOR and sequestration technique) creates the amalgamation of hydrocarbons, CO₂, and aqueous brine in the subsurface.

Evolution of diffusion and structure of six n-alkanes in carbon dioxide at infinite dilution over wide temperature and pressure ranges: a molecular dynamics study

Over wide temperature and pressure ranges, the molecular dynamics simulation is performed to study the mass transfer of six n-alkanes from n-C₅H₁₂ to n-C₁₀H₂₂ in CO₂ at infinite dilution by calculating the diffusion coefficients, which have not yet been measured by experiment. Meanwhile, the structural properties of these systems are explored. It is found that under different temperature and pressure conditions, the variation trends of the radial distribution functions of n-alkanes are quite different, while the variation trends of the average coordination number of n-alkanes can be divided into three types. The radius of gyration and the solvent accessible surface area are both affected by temperature and carbon chain length, but their variation trends are different, and it could explain the abnormal variation trends of the radial distribution functions and the average coordination number. Graphical abstract Over wide temperature and pressure ranges, the variation trends of the average coordination number of n-alkanes can be divided into three types.

Diffusion of Benzene and Alkylbenzenes in Nonpolar Solvents

The translational diffusion constants, D, of benzene and a series of alkylbenzenes have been determined in n-pentadecane, 2,6,10,14-tetramethylpentadecane (pristane), 2,2,4,4,6,8,8-heptamethylnonane (isocetane), and 2,6,10,15,19,23-hexamethyltetracosane (squalane) using capillary flow techniques. The solutes' D values are compared with the predictions of a cylinder diffusion model as are those for (a) benzene and alkylbenzenes in n-nonane, n-decane, n-dodecane, and supercritical CO₂ and (b) n-alkanes and 1-alkenes in n-hexane, n-heptane, n-octane, benzene, and toluene. The D values for benzene and the alkylbenzenes also are compared with the predictions of lollipop diffusion for which the phenyl ring is the candy and the alkyl chain is the handle. Both models give an average difference of less than 4% between experimental and calculated diffusion constants in solvents whose viscosities vary by a factor of more than 600 when benzene and toluene (as solutes) are omitted; the comparisons include 150 and 85 D values for the cylinder and lollipop models, respectively. The differences increase when benzene and toluene are included and are most likely because of their shapes and the shapes assumed by the models. The agreement with the models indicates that the chains of the alkylbenzenes and 1-alkenes, like those of the n-alkanes, are relatively extended. The D values for several of the solutes also are fitted to a modification of the Stokes-Einstein relation that varies their dependence on viscosity instead of chain dimensions.

Modeling Solvation in Supercritical CO2

In recent decades, a microscopic understanding of solute-solvent intermolecular interactions has been key to advances in technologies based on supercritical carbon dioxide. In many cases, computational work has provided the impetus for new discoveries, shedding new light on important concepts such as the local structure around the solute in the supercritical medium, the influence of the peculiar properties of the latter on the molecular behavior of dissolved substances and, importantly, CO₂ -philicity. In this Review, the theoretical work that has been relevant to these developments is surveyed and, by presenting some crucial open questions, the possible routes to achieving further progress based on the interplay between theory and experiments is discussed.

MD simulation study of the diffusion and local structure of n-alkanes in liquid and supercritical methanol at infinite dilution

The diffusion coefficients of 14 n-alkanes (ranging from methane to n-tetradecane) in liquid and supercritical methanol at infinite dilution (at a pressure of 10.5 MPa and at temperatures of 299 K and 515 K) were deduced via molecular dynamics simulations. Values for the radial distribution function, coordination number, and number of hydrogen bonds were then calculated to explore the local structure of each fluid. The flexibility of the n-alkane (as characterized by the computed dihedral distribution, end-to-end distance, and radius of gyration) was found to be a major influence and hydrogen bonding to be a minor influence on the local structure. Hydrogen bonding reduces the flexibility of the n-alkane, whereas increasing the temperature enhances its flexibility, with temperature having a greater effect than hydrogen bonding on flexibility. Graphical abstract The flexibility of the alkane is a major influence and the hydrogen bonding is a minor influence on the first solvation shell; the coordination numbers of long-chain n-alkanes in the first solvation shell are rather low.