ACS Physical Chemistry Au最新文献

Measuring nanoscale local temperatures, particularly in vertically integrated and multicomponent systems, remains challenging. Spectroscopic techniques like X-ray absorption and core-loss electron energy-loss spectroscopy (EELS) are sensitive to lattice temperature, but understanding thermal effects is nontrivial. This work explores the potential for nanoscale and element-specific core-loss thermometry by comparing the Si L_2,3 edge's temperature-dependent redshift against plasmon energy expansion thermometry (PEET) in a scanning TEM. Using density functional theory (DFT), time-dependent DFT, and the Bethe-Salpeter equation, we ab initio model both the Si L_2,3 and plasmon redshift. We find that the core-loss redshift occurs due to bandgap reduction from electron-phonon renormalization. Our results indicate that despite lower core-loss signal intensity compared to plasmon features, core-loss thermometry has key advantages and can be more accurate through standard spectral denoising. Specifically, we show that the Varshni equation easily interprets the core-loss redshift for semiconductors, which avoids plasmon spectral convolution for PEET in complex junctions and interfaces. We also find that core-loss thermometry is more accurate than PEET at modeling thermal lattice expansion in semiconductors, unless the specimen's temperature-dependent dielectric properties are fully characterized. Furthermore, core-loss thermometry has the potential to measure nanoscale heating in multicomponent materials and stacked interfaces with elemental specificity at length scales smaller than the plasmon's wave function.

We have performed Quantum Monte Carlo (QMC) simulations on Na-intercalated bilayer graphene to study the evolution of electronic and optical properties upon Na intercalation into hard carbon layers. The objective was to model the optimal configuration of Na intercalation into a hard carbon matrix containing graphene regions. Our study showed that Na intercalation can be energetically stabilized at large interlayer distances (over 6 Å) in both AA- and AB-stacked bilayer graphene. In the QMC results, we found a significant band gap opening at the equilibrium interlayer distance of Na-intercalated bilayer graphene, while corresponding density functional theory (DFT) results showed no gap. This difference between DFT and QMC results indicates that the gap opening induced by Na intercalation into a hard carbon is underestimated within the DFT framework. In addition, a zigzag configuration of Na atoms was found to be energetically stable at interlayer distances up to 10 Å, leading us to predict the existence of a local minimum of Na intercalation at large interlayer distance. These computation and modeling results can provide guidance on how to synthesize and optimize hard carbon with bilayer graphene regions that permit a zigzag intercalation configuration that will maximize and stabilize sodium hosting.

Competitive binding between metal cofactors and functional groups of polypeptides results in a diversity of structures and chemistries in metalloproteins. Herein, we examined elements of this competitive binding using [metal-(auxiliary ligand)-(peptide)] complexes, where the metal-(auxiliary ligand) combinations are Cu^II(terpy)²⁺, Co^III(salen)⁺, and Fe^III(salen)⁺ and the peptides are either the dipeptide arginine-tyrosine (RY) or the tripeptide arginine-tyrosine-glycine (RYG). Structural diversity was established and substantiated via tandem mass spectrometry, with and without peptide derivatization and substitution. All the complexes dissociated to give high abundances of the peptide radical cations, but the structures of these ions differ depending on the composition of the preceding metal complex. Density functional theory calculations provided insights into different binding modes within the complexes and also provided details of the mechanisms by which different [RY]^•+ and [RYG]^•+ ions fragment. Infrared multiple-photon dissociation spectroscopy established that [Cu-(terpy)-RYG]²⁺ is bound through the carboxylate group, but calculations showed that it can convert to the phenolate-bound structure under a low-energy barrier. Despite the variety and apparent complexity in binding, the overall chemistry could be characterized using intrinsic acid-base chemistry and the concept of hard/soft Lewis acids/bases. The resulting complex structures were experimentally probed and were found to be in accordance with predictions. For the complexes, the drive toward energy minimization can take several pathways that involve multiple functional groups, thereby leading to a rich chemistry.

The process of water clustering in the interparticle gaps of hydrophilic (A-300) and hydrophobic (AM1) silicas in different media was studied using ¹H NMR spectroscopy. It has been established that when equal amounts (100 mg/g) of water and oil are introduced into the interparticle gaps of compacted hydrophilic or hydrophobic silica by grinding under the influence of mechanical load, the water transforms into a nanosized state with cluster radii in the range of 1-50 nm. In air, the main part of water is in a strongly associated state with a network of hydrogen bonds similar to liquid water. Replacing air with a chloroform medium leads to the stabilization of weakly associated forms of water, which are observed in the NMR spectra in the form of one or several signals with chemical shifts δ_H = 1-2 ppm. A comparison of the intensities of the NMR signals of water and oil allows us to conclude that the oil is partially frozen not only in air, but also in chloroform, which has unlimited solubility in relation to oil. In the medium of acetone, which is capable of dissolving both water and oil, in the interparticle gaps of hydrophobic silica, the formation of several types of clusters of strongly and weakly associated water is observed, existing as spatially separated nanodroplets, slowly (on the NMR time scale) exchanging protons or molecules with each other. It has been shown that the hydrophobic walls of silica particles have such an ordering effect on clusters of water and acetone, oil or TMS located in the interparticle gaps that a significant part of it turns into a solid state at temperatures (up to 287 K), which is several tens of degrees higher than the bulk freezing temperature.

Graphite paper is widely used in energy storage systems such as batteries and supercapacitors due to its availability, cost, and excellent chemical and thermal stability. However, its hydrophobic surface and dense structure limit electrolytic ion diffusion in aqueous supercapacitors, reducing electrochemical performance. To address these issues, graphite paper was treated with mild acid solution and electrochemically oxidized for varying durations to enhance its properties for high-performance supercapacitors. Acid treatment not only expanded the graphite but also functionalized its surface, making it more hydrophilic, as confirmed by FTIR and contact angle measurements. This modification improved the electrode’s electrochemical performance by facilitating better ion diffusion and insertion, resulting in increased specific capacitance. After 5 min of treatment, the graphite layers enlarged from 35 to 469 μm, resulting in an enhanced specific capacitance of 219 F g^–1 at 10 mV s^–1 but poor cycling stability with 80% capacitance retention after 500 cycles. In contrast, the 3 min treatment achieved a specific capacitance of 113 F g^–1 with excellent cycling stability without significant capacitance fading. These results highlight the importance of optimizing both the structural and chemical properties of graphite for achieving high performance and long cycling stability.

The lipid composition of membrane systems plays a critical role in regulating their structural dynamics and curvature, particularly in the biological context of matrix vesicles (MVs) formation during bone mineralization. Recent evidence suggests that the lipid composition of MVs, particularly the balance between sphingomyelin (SM) and ceramide (CER), influences their curvature and stability. We report on the impact of SM and CER ratios on membrane curvature through surface pressure-area isotherm measurements and molecular dynamics (MD) simulations at atomistic and coarse-grained levels. Our findings reveal that increasing the CER content up to 25% significantly enhances membrane curvature, as demonstrated by changes in experimental compressibility moduli and lateral pressure profiles. The lateral pressure profiles and spontaneous bending moments calculated from MD simulations of osteoblast-mimetic membrane models suggest a strong propensity for curvature, particularly in asymmetrical bilayers. It also reveals the role of CER-rich domains in the stabilization of membrane curvature, potentially facilitating the budding processes critical for MVs formation in osteoblasts. These findings underscore the critical role of lipid composition in the mechanisms driving MVs biogenesis.

Nine structures of the ALX/FPR2 receptor are currently deposited in the PDB. In seven structures, the receptor is complexed with formylated peptides. In all seven structures, residue D106 is indicated as acting in the ALX/FPR2 receptor activation in addition to residues R201 and R205. Here, we performed docking simulations and long-term molecular dynamics simulations to investigate the ALX/FPR2 receptor activation using two pro-resolution agonists (lipoxin A4 (LXA₄) and resolvin D3 (RvD3)) and a formylated peptide pro-inflammatory agonist (fMLFII). We have analyzed the receptor’s activation state, electrostatic interactions, and the binding affinities of the complexes receptor-agonist using the MM/PBSA approach. The results showed that LXA₄ and fMLFII kept the receptor in an active state by a higher simulation time when compared to RvD3. Only R201 and R205 were considered key residues in the ALX/FPR2 receptor activation by all agonists. The electrostatic interaction analysis confirmed the importance of these residues in ALX/FPR2 receptor activation. Furthermore, only fMLLII showed interactions with residue D106. The binding free energy calculations indicated that the electrostatic component significantly binds the agonists to the receptor. Overall, the results from this study provide new insights into the ALX/FPR2 receptor activation mechanisms, reinforcing the role of critical residues and interactions in the binding of pro-resolution and inflammatory agonists.

The three-dimensional (3D) atomistic-resolution structure and dynamics of RNA kissing complexes (KCs) and extended duplexes (EDs), homodimers formed through palindromic base pairing, are crucial for understanding viral replication and structure-informed therapeutic design. Polyacrylamide gel electrophoresis (PAGE) evidence suggests KC and ED dimer formation between stem-loop II motif (s2m) elements in SARS-CoV, SARS-CoV-2, and Delta SARS-CoV-2, which may regulate host immune response. However, the absence of 3D structural data on s2m dimers limits structural interpretation needed to explain differences in stability indicated by native PAGE and biophysical implications. In this work, we evaluate the VFold3D/LA-IsRNA pipeline for resolving 3D structures of s2m KCs and EDs by validating its accuracy with blind and referenced predictions against experimental HIV-1 DIS KC and ED structures. Engendering confidence in the approach for blind prediction of KC and ED structures, HIV-1 DIS predictions achieved an average RMSD of 3.28 Å relative to crystal structures, while local interactions, such as palindrome-flanking purine stack orientations in the terminal loops, were in closer agreement with reported solution-phase NMR (RMSD ∼ 2.5 Å), cryo-EM maps, and previous molecular dynamics (MD) simulations. We find that the predicted 3D dimer structures of s2m resulted in kinked or linear shapes of s2m KC complexes that provide an interpretation consistent with native PAGE migration differences, where KCs are more kinked (63° to 133°) than linear ED dimers (127° to 156°). Following MD refinement, the SARS-CoV s2m KC adopts stacking palindromic basepair triplets, whereas SARS-CoV-2 and Delta s2m only form canonical palindrome basepairs, explaining their relative dimer instability suggested by PAGE band intensity. Ultimately, our results support the use of the VFold3D/LA-IsRNA pipeline for KC and ED generation, yielding predictions consistent with experimental data and providing an atomistic foundation for data-driven design of antiviral therapies to disrupt the lifecycle or immune response of viruses.

Neutral gabapentin has been vaporized by laser ablation and supersonically expanded to record its rotational spectrum using Fourier transform microwave spectroscopy. We report the detection of five stable conformers, which differ in the intramolecular interactions between the different functional groups (OH, C=O, and NH). Two configurations, axial and equatorial, are possible depending on the chair form of the cyclohexane ring, and both forms are detected, with the latter being predominant. The conformational landscape of gabapentin is compared with that of GABA, and significant differences are observed. One of the most meaningful results of such a comparison is that the relationship between the intramolecular interactions and the relative abundance within each type is reversed from GABA to gabapentin. It could explain the distinction in the mechanism of action of GABA and gabapentin, despite being structurally similar.