A Coarse-Grained SPICA Makeover for Solvated and Bare Sodium and Chloride Ions.

Aqueous ionic solutions are pivotal in various scientific domains due to their natural prevalence and vital roles in biological and chemical processes. Molecular dynamics has emerged as an effective methodology for studying the dynamic behavior of these systems. While all-atomistic models have made significant strides in accurately representing and simulating these ions, the challenge persists in achieving precise models for coarse-grained (CG) simulations. Our study introduces two optimized models for sodium and chloride ions within the nonpolarizable surface property fitting coarse-grained force field (SPICA-FF) framework. The two models represent solvated ions, such as the original FF model, and unsolvated or bare ions. The nonbonded Lennard-Jones interactions were reparameterized to faithfully reproduce bulk properties, including density and surface tension, in sodium chloride solutions at varying concentrations. Notably, these optimized models replicate experimental surface tensions at high ionic strengths, a property not well-captured by the ions of the original model in the SPICA-FF. The optimized unsolvated model also proved successful in reproducing experimental osmotic pressure. Additionally, the newly reparameterized ion models capture hydrophobic interactions within sodium chloride solutions and show qualitative agreement when modeling structural changes in phospholipid bilayers, aligning with experimental observations. For aqueous solutions, these optimized models promise a more precise representation of the ion behavior.

An in silico osmotic pressure approach allows characterization of pressure-area isotherms of lipid monolayers at low molecular areas.

Surface pressure-area isotherms of lipid monolayers at the air-water interface provide essential information about the structure and mechanical behaviour of lipid membranes. These curves can be readily obtained through Langmuir trough measurements and, as such, have been collected for decades in the field of membrane biochemistry. However, it is still challenging to directly observe and understand nanoscopic features of monolayers through such experiments, and molecular dynamics (MD) simulations are generally used to provide a molecular view of such interfaces. In MD simulations, the surface pressure-area (Π-A) isotherms are generally computed using the Kirkwood-Irving formula, that relies on the evaluation of the pressure tensor. This approach, however, has intrinsic limitations when the molecular area in the monolayer is low (typically < 60 Å2 per lipid). Recently, an alternative method to compute Π-A isotherms of surfactants, based on the calculation of the three-dimensional osmotic pressure via the implementation of semipermeable barriers was proposed. In this work, we investigate the feasibility of this approach for long-chain surfactants such as phospholipids. We identify some discrepancies between the computed values and experimental results, and we propose a semi-empirical correction based on the molecular structure of the surfactants at the monolayer interface. To validate the potential of this new approach, we simulate several phosphatidylcholine and phosphatidylethanolamine lipids at various temperatures using all-atom and coarse-grained force fields, and we compute the corresponding Π-A isotherms. Our results show that the Π-A isotherms obtained using the new method are in very good agreement with experiments and far superior to the canonical pressure tensor-based method at low molecular areas. This corrected osmotic pressure method allows for accurate characterization of the molecular packing in monolayers in various physical phases.

Recharging your fats: CHARMM36 parameters for neutral lipids triacylglycerol and diacylglycerol.

Neutral lipids (NLs) are an abundant class of cellular lipids. They are characterized by the total lack of charged chemical groups in their structure, and, as a consequence, they play a major role in intracellular lipid storage. NLs that carry a glycerol backbone, such as triacylglycerols (TGs) and diacylglycerols (DGs), are also involved in the biosynthetic pathway of cellular phospholipids, and they have recently been the subject of numerous structural investigations by means of atomistic molecular dynamics simulations. However, conflicting results on the physicochemical behavior of NLs were observed depending on the nature of the atomistic force field used. Here, we show that current phospholipid-derived CHARMM36 parameters for DGs and TGs cannot adequately reproduce interfacial properties of these NLs because of excessive hydrophilicity at the glycerol-ester region. By following a CHARMM36-consistent parameterization strategy, we develop improved parameters for both TGs and DGs that are compatible with both cutoff-based and particle mesh Ewald schemes for the treatment of Lennard-Jones interactions. We show that our improved parameters can reproduce interfacial properties of NLs and their behavior in more complex lipid assemblies. We discuss the implications of our findings in the context of intracellular lipid storage and NLs' cellular activity.

Magnetic Co-Doped MoS2 Nanosheets for Efficient Catalysis of Nitroarene Reduction.

Co-doped MoS2 nanosheets have been synthesized through the hydrothermal reaction of ammonium tetrathiomolybdate and hydrazine in the presence of cobalt acetate. These nanosheets exhibit a dominant metallic 1T phase with cobalt ion-activated defective basal planes and S-edges. In addition, the nanosheets are dispersible in polar solvents like water and methanol. With increased active sites, Co-doped MoS2 nanosheets exhibit exceptional catalytic activity in the reduction of nitroarenes by NaBH4 with impressive turnover frequencies of 8.4, 3.2, and 20.2 min-1 for 4-nitrophenol, 4-nitroaniline, and nitrobenzene, respectively. The catalyst is magnetic, enabling its easy separation from the reaction mixture, thus making its recycling and reusability simple and efficient. The enhanced catalytic activity of the Co-doped 1T MoS2 nanosheets in comparison to that of undoped 1T MoS2 nanosheets suggests that incorporation of cobalt ions in the MoS2 lattice is the major reason for the efficiency of the catalyst. The dopant, Co, plays a dual role. In addition to providing active sites where electron transfer is assisted through redox cycling, it renders the nanosheets magnetic, enabling their easy removal from the reaction mixture.