The Journal of Physical Chemistry B最新文献

Studying ionic liquids (ILs) through computational methods is one of the ways to accelerate progress in the design of novel and potentially green materials optimized for task-specific applications. Therefore, it is essential to develop simple and cost-effective computational procedures that are able to replicate and predict experimental data. Among these, spectroscopic measurements are of particular relevance since they are often implicated in structure-property relationships, especially in the infrared spectral region, where characteristic absorption and scattering processes due to molecular vibrations are ultimately influenced by the surrounding environment in the condensed phase. In this frame, we validate, vis-à-vis experimental data, an efficient theoretical method to compute the Raman spectra in the liquid phase of four especially synthesized dicationic ionic liquids and to assess the conformational cation/anion contributions to the experimental bands. The computational procedure is based on the assessment of the most probable conformations as evaluated by a computational protocol involving both molecular dynamics and ab initio methods.

Barrier-crossing rates of biophysical processes, ranging from simple conformational changes to protein folding, often deviate from the Kramers prediction of an inverse viscosity dependence. In many recent studies, this has been attributed to the presence of internal friction within the system. Previously, we showed that memory-dependent friction arising from the nonequilibrium solvation of a single particle crossing a smooth one-dimensional barrier can also cause such a deviation and be misinterpreted as internal friction. Here we introduce a simple diatom model and show that even in the absence of explicit solvent, internal memory effects arise due to coupling of the reaction coordinate motion with frictionally orthogonal degrees of freedom. This results in a fractional viscosity dependence and a deviation from Kramers' theory, typically attributed to the presence of internal friction. This model therefore mimics several biological processes where a local conformational change of a biomolecule is often influenced by its surroundings. This gives rise to an apparent "internal friction" commonly measured in terms of empirical fitting parameters α and σ. We propose a microscopic measure of this internal friction using Grote-Hynes theory which employs memory-dependent friction. We use butane to demonstrate the effect of coupling strength on the internal friction in realistic systems. This model therefore can serve the purpose of understanding internal friction in biological systems in terms of such coupling.

Brownian dynamics simulations have been performed to investigate the structural dependence of the first epitaxial layer in colloidal heteroepitaxy. When the epitaxial particles were larger than the substrate particles and the interactions were dominated by the depletion force, a hexagonal structure formed on a closely packed hexagonal substrate. The orientation of this hexagonal structure varied with the size ratio of the epitaxial to substrate particles to make the interaction between the substrate and epitaxial particles strong. When the sizes of the substrate and epitaxial particles were similar, long-period structures formed instead of hexagonal structures to strengthen the interaction between the substrate and epitaxial layer at the expense of the interaction between particles in the first epitaxial layer.

The spleen tyrosine kinase (Syk) is a key regulator in immune cell signaling and is linked to various mechanisms in cancer and neurodegenerative diseases. Although most computational research on Syk focuses on novel drug design, the molecular-level regulatory dynamics remain unexplored. In this study, we utilized 5 × 1 μs all-atom molecular dynamics simulations of the Syk kinase domain, examining it in combinations of activation segment phosphorylated/unphosphorylated (at Tyr525, Tyr526) and the "DFG"-Asp protonated/deprotonated (at Asp512) states to investigate conformational variations and regulatory dynamics of various loops and motifs within the kinase domain. Our findings revealed that the formation and disruption of several electrostatic interactions among residues within and near the activation segment likely influenced its dynamics. The protein structure network analysis indicated that the N-terminal and C-terminal anchors were stabilized by connections with the nearby stable helical regions. The P-loop showed conformational variation characterized by movements toward and away from the conserved "HRD"-motif. Additionally, there was a significant correlation between the movement of the β3-αC loop and the P-loop, which controls the dimensions of the adenine-binding cavity of the C-spine region. Overall, understanding these significant motions of the Syk kinase domain enhances our knowledge of its functional regulatory mechanism and can guide future research.

Ionic liquids (ILs) have proven extremely useful for a wide variety of roles, including as propellants for electrospray thrusters (ETs), due to their unique physical and chemical properties, as well as the potential tunability of those properties, through chemical engineering. However, there is a lack of literature exploring the effects of IL properties on ET operation. This paper presents experimental results investigating key physical properties of the common ILs 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide (EMI-TFSI), 1-butyl-3-methylimidazolium trifluoromethanesulfonate (BMI-TFO), EAN, and Bmpyr-DCA not provided by manufacturers or reported in the literature, namely, their electrochemical stability windows (ESWs) and contact angles. Cyclic voltammetry experiments were employed to define the ESW of each IL, which is necessary for long-term ET operation while avoiding chemical breakdown. Contact-angle measurements were also conducted to study the wettability of the ILs on glass surfaces to be used for ET thruster substrates [Howell, J. H.; . J. Electrost. 2023, 122, 103799]. In addition, an analytical discussion is presented using established parametric relationships and scaling laws to examine the effects of relevant IL physical properties, such as surface tension and ion molecular weights, on ET performance. The results demonstrate the relative impact of IL properties on important ET figures of merit such as thrust density, power density, and specific impulse, which provide key insights into the future development of novel ILs specifically tailored for use as ET propellants.

Taylor-Aris (T-A) dispersion of a solute in a flowing solvent is a fundamental phenomenon in most mass-transfer processes. Despite its significance and numerous applications in microreactors, colloidal transport in confined media, chromatographic separation, and transport in biological tissues, the effect of the slip length and the topology of surface potential landscapes on T-A dispersion in nanostructured channels has not been studied in detail. We propose a novel methodology for molecular dynamics (MD) simulation of T-A dispersion in such systems, derive an analytical expression for the dispersion coefficient in them, and report on the results of extensive MD simulations of the phenomenon in carbon nanotubes and hexagonal carbon nanochannels. By broadening the topology of the surface energy landscape, we vary the slip lengths, making it possible to distinguish between the effects of confinement, the topology of the energy landscape, and the slip length on the T-A dispersion coefficient. It is demonstrated that measuring the T-A dispersion coefficient in laminar flow is a straightforward and reliable approach for estimating the slip length in nanotubes and other nanostructured materials.

We study the influence of tyrosine phosphorylation on PTP-PEST, a cytosolic protein tyrosine phosphatase. Utilizing a combination of experimental data and computational modeling, specific tyrosine sites, notably, Y64 and Y88, are identified for potential phosphorylation. Phosphorylation at these sites affects loop dynamics near the catalytic site, altering interactions among key residues and modifying the size of the binding pocket. This, in turn, impacts substrate binding, as indicated by changes in the binding energy. Our findings provide insights into the structural and functional consequences of tyrosine phosphorylation on PTP-PEST, enhancing our understanding of its effects on substrate binding and catalytic conformation.

The measured surface tension of a binary liquid is found to depend strongly on the constituents of the adjacent vapor and on whether equilibrium has been achieved, giving insight into the complex interfacial configuration. This dependence is quantified by three techniques that offer complementary insights: surface tension measurements with a constrained sessile drop surrounded by different vapors, surface tension measurements by surface light scattering spectroscopy in a sealed cell at equilibrium, and molecular dynamics simulations of the equilibrium surface tension and excess surface concentration. Ensuring homogeneity of the binary liquid, which is essential for surface light scattering, was found to be nontrivial and was assured by high-sensitivity Schlieren imaging. Two pairs of liquids, n-pentane with 2-methylpentane and n-pentane with n-hexane, were investigated. The first pair was motivated by the observed improvement in the effectiveness of binary fluids versus a single constituent in wickless heat pipes studied in microgravity. The second pair was used for comparison. Experimental evaluation of different volume fractions of the two liquids showed strong dependence of surface tension on the relative concentration of different molecules near the interfacial region. For the above pairs of liquids, which appear to form ideal mixtures in bulk, we present sufficiently precise surface tension measurements to indicate unexpectedly complex behaviors at interfaces.

Several antiviral therapeutic approaches have been targeted toward the RNA-dependent RNA polymerase (RdRp) complex that is involved in viral genome replication. In SARS-CoV-2, although the RdRp is a multiprotein complex, the focus has been on the ligand binding catalytic core (nonstructural protein nsp12), and not the multiprotein functional dynamics. In this study, we focus on the conformational ensembles of the RdRp complex and their modulation by the presence of RNA, performing comprehensive microsecond-scale atomistic simulations of the apo- and RNA-bound complex. We delineate the differential impact of RNA on the constituent proteins, such as conformational polymorphisms, dominant segment-specific fluctuations, and the switch in dynamical crosstalk within the complex. We distinguish dynamical signatures of nsp7, nsp8, and nsp12 in the apo-state that are reduced in the presence of the RNA and appear to "prime" the complex for activity. Importantly, we identify a unique structural malleability of the nsp8 protein with high conformational heterogeneity in the apo state, especially at three sites (Y71 for nsp8A, and D52 and A66 for nsp8B). Our work highlights the functional implications of the polymorphism of nsp8 structures and reveals possibilities for the development of allosteric inhibitors.