The Journal of Physical Chemistry B最新文献

High-concentration aqueous electrolytes (hydrate-melts) have attracted significant attention for lithium-ion batteries due to their nonflammability and low toxicity. In these electrolytes, the static and dynamic structures of the solvent play a crucial role in determining various properties, such as the ionic conductivity, of the system. To clarify the solvent structure and ion diffusion mechanism, we conducted molecular dynamics simulations using a machine learning potential for Li and Na hydrate-melts. By analyzing the dynamical interaction between ions and their coordinating molecules, we found the ligand exchange of H₂O molecules coordinated to cations occurs frequently. As a result, it is considered that the kinetic energy of H₂O is transferred to cations and drives the diffusion of cations in the hydrate-melts. This ion transport mechanism is different from the conventionally understood vehicle-type or hopping-type ion transport mechanism. The comparison of Na hydrate-melts and Li hydrate-melts shows the higher diffusion of Na relative to Li. It was suggested that there exists an optimal value for the strength of interaction between cations and H₂O molecules, which influences ion diffusion, and that the interaction for Na is close to this optimal value compared to that of the Li.

The combined use of residual chemical shift anisotropy (RCSA) and residual dipolar coupling/residual dipole coupling (RDC) could provide highly complementary information about the structure and relative configuration of unknown organic molecules for their elucidation. However, tandem RCSA and RDC measurements in one sample remain a formidable challenge due to their varied testing requirements. Herein, a stimuli-responsive supramolecular liquid crystal self-assembled from an amphiphilic oligopeptide of C₁₉H₃₉-CONH-VVVVKKK-CONH₂ was constructed, which underwent a phasic transformation from anisotropy to isotropy when subjected to a thermal treatment. Both the anisotropic and isotropic phases exhibited good stability, facilitating tandem measurements of ¹³C-{¹H}-RCSA and (¹³C-¹H)-RDC in one sample with no need for special instruments or correction procedures. We expect that the joint use of RCSAs and RDCs will significantly improve data accuracy and utility for structural and configurational determination of small organic molecules and even biomacromolecules.

A complete understanding of aerosol formation remains elusive due to the microscopic scale and transient occurrence of nucleation. This process is further complicated by the multicomponent nature of atmospheric nucleating systems in which the properties of conucleating compounds influence the affinity of molecules to cluster. Molecular dynamics simulations were performed to investigate homogeneous vapor-liquid nucleation and growth of six binary mixtures composed of water, n-nonane, 1-butanol, and methanol. Structural analyses were performed to understand the dynamic configurations generated from binary nuclei. Geometric structure analysis revealed that clusters were found to be more spherical with increasing cluster size, while composition analysis revealed that more miscible species had less mole fraction variability from an equimolar composition. Radial density profiling and cluster snapshots revealed structural features that were dependent on the miscibility of the nucleating pairs. Homogeneous mixing was observed in n-nonane/1-butanol and water-methanol due to their miscibility. Meanwhile, systems with partial miscibility (water/1-butanol, water/methanol, 1-butanol/methanol, n-nonane/methanol), exhibited preferential ordering into core-shell structures. In water/n-nonane, simultaneous unary nucleation was observed, leading to lens-on-sphere configuration. Microstructure analysis also revealed internal fragmentation within core-shell motifs of water/1-butanol and 1-butanol/methanol. These findings have serious implications in nucleation theories, which lead to valuable insights for the nucleation of naturally occurring multicomponent systems in the atmosphere.

A rigorous thermodynamic modeling framework for a system of isomers in chemical equilibrium is developed and applied to the lactose-water system. Through the knowledge of the water activity and of the liquid phase composition, thermodynamically consistent expressions for the activity coefficients of lactose isomers have been derived and used in the context of solid-liquid equilibria to predict the dependence of the saturation concentration of α-lactose on the dissolved β-lactose concentration. We also developed a comprehensive first-principles model that accurately describes the dissolution dynamics of α-lactose monohydrate. The data support the hypothesis that the sugar activity coefficients are a stronger function of the total sugar content rather than of the sugar solution composition. The activity coefficient expressions have been used to quantitatively predict the effect of glucose, galactose, and sucrose on the solubility of α-lactose monohydrate.

Light-harvesting complexes (LHCs) are vital for photosynthesis, capturing light energy and transferring it to photosystems I and II. In diatoms, fucoxanthin chlorophyll (Chl) a/c-binding proteins (FCPs) function as unique LHCs. In this study, we examined the spectral properties of untreated and aggregated FCP complexes (Untreated-FCP and Aggregated-FCP, respectively) from the diatom Phaeodactylum tricornutum. Fluorescence quantum yields and excitation-energy transfer pathways were evaluated using absolute fluorescence spectroscopy and fluorescence decay-associated (FDA) spectra. Aggregation of FCPs significantly enhanced excitation-energy quenching, with a marked decrease in fluorescence quantum yield from 37.6% in Untreated-FCP to 4.8% in Aggregated-FCP. The FDA spectra of Aggregated-FCP showed prominent fluorescence decays with relatively high amplitudes with time constants of 310 ps and 1.6 ns, reflecting distinct alterations in excitation-energy transfer among Chls upon aggregation. These changes were accompanied by long-wavelength shifts and broadening of the fluorescence-emission spectra, characteristics typically observed in aggregated LHCs in land plants. Our results suggest that the structural rearrangement of pigment molecules, driven by changes in Chl-Chl and Chl-Car interactions, underlies the observed excitation-energy quenching upon aggregation. This study provides key insights into the quenching mechanisms of diatom FCPs, offering broader implications for understanding energy regulation in photosynthetic systems.

Potassium single cation ionic liquids (K-SCILs), which solely contain K⁺ as the cationic species, realize exceptionally high K⁺ concentrations and exhibit unique physicochemical and electrochemical properties. However, K-SCILs tend to have high melting points due to the smaller size of K⁺ than those of bulky organic cations, resulting in high operating temperatures for battery applications. In this study, a K-SCIL with a melting point below that of K metal (64 °C) was developed by evolving a binary system to a ternary one. The resulting K-SCIL, K[FSA]_0.33[FTA]_0.33[TfO]_0.33 (FSA^-: bis(fluorosulfonyl)amide, FTA^-: (fluorosulfonyl)(trifluoromethanesulfonyl)amide, and TfO^-: trifluoromethanesulfonate), has a low melting point of 50 °C with a high K⁺ concentration of 9.3 mol dm^-3 at 55 °C. It allows the safe handling of K metal and exhibits improved solid K metal deposition/dissolution compared to a conventional organic electrolyte. The K-SCIL does not involve the formation of a K⁺ concentration gradient near the electrode surface, which is demonstrated by the applicability of large currents exceeding a limiting current density assumed by calculation. Furthermore, stable K⁺ intercalation/deintercalation into/from graphite was successfully demonstrated at 55 °C, highlighting the potential of this K-SCIL for advanced potassium battery applications.

This article presents experimental characterization information and synchrotron X-ray scattering measurements on a set of novel O- and S-substituted phosphonium-based ionic liquids (ILs) all coupled with the bis(fluorosulfonyl)imide (FSI^-) anion. The ILs include the ethoxyethyltriethylphosphonium (P_222(2O2)⁺) and triethyl[2-(ethylthio)ethyl]phosphonium (P_222(2S2)⁺) cations, and we contrast results on these with those for unsubstituted triethylpentylphosphonium (P₂₂₂₅⁺). The article also introduces a physics-based protocol that combines classical force field studies on larger simulation boxes with classical and first-principles studies on smaller boxes. The method produces significantly improved S(q) functions in the regime which in prior publications we have associated with inter- and intraionic adjacency correlations. By understanding which shorter-range structural changes improve S(q) in the q-regime of interest, we are also able to pinpoint specific deficiencies in the classical force field model. The approach we take should be quite general and could help study other complex liquids on different length scales.

Molecular insight into amyloid aggregation is crucial for understanding the details of protein fibril nucleation and growth, which play a significant role in a wide range of proteinopathies. The length and time scales for fibrillization make its computational study an intrinsically multiscale problem, necessitating the use of coarse-grained modeling. A wide variety of coarse-grained models for peptides have been proposed, often parametrized with a combination of top-down and bottom-up approaches. Here, we present a predictive, sequence-transferable bottom-up coarse-grained model, systematically developed using only information from atomistic simulations by applying an extended-ensemble relative entropy minimization technique. The resulting model is capable of accurately recovering conformational properties of peptides constructed from a reduced alphabet of amino acids, of predicting secondary structures of isolated and interacting peptides from their sequences alone, and of simulating aggregation of peptides that have been experimentally characterized as amyloidogenic. Finally, we couple such coarse-grained simulations with a genetic algorithm to characterize the sequence space of the reduced alphabet and identify features of sequences for which ordered fibrillar states are both thermodynamically favorable and kinetically accessible.

Computational approaches can provide details of molecular mechanisms in a crowded environment inside cells. Protein docking predicts stable configurations of molecular complexes, which correspond to deep energy minima. Systematic docking approaches, such as those based on fast Fourier transform (FFT), also map the entire intermolecular energy landscape by determining the position and depth of the full spectrum of the energy minima. Such mapping allows speeding up simulations by precalculating the intermolecular energy values. Our earlier study combined FFT docking with the Monte Carlo protocol, enabling simulation of cell-size, crowded protein systems with seconds, and longer trajectories at atomic resolution, several orders of magnitude longer than those achievable by alternative approaches. In this study, we present a further drastic extension of the modeling capabilities by parallelized implementation of the simulation protocol. The procedure was applied to a panel of Death Fold Domains that form nucleated polymers in human innate immune signaling, recapitulating their homooligomerization tendencies and providing insights into the molecular mechanisms of polymer nucleation. The parallelized protocol allows extension of the simulation trajectories by orders of magnitude beyond the previously reported implementation, reaching into the uncharted territory of atomic resolution simulation of cell-sized systems.

Perceiving a suitably tuned aqueous solution to unravel water's liquid-liquid critical point (LLCP) has become challenging. In this work, we investigated the structures of light and heavy water in the presence of MgCl₂ using excess infrared spectroscopy and density functional theory calculations. The excess spectroscopy enabled us to differentiate the low-density liquid (LDL) water from the other liquid domains of pure water and reveal the new interaction modes between water and the ions. The addition of salt decreases and then increases the population of LDL in aqueous solutions. At the concentrations of 0.4 M in H₂O and 0.6 M in D₂O, the LDL structures undergo the most significant disruption under ambient conditions in the bulk phase. Furthermore, threshold concentrations of 1 and 1.3 M for light and heavy water, respectively, were found to induce higher LDL populations. The current investigation sheds light on the intriguing liquid-liquid phase transition (LLPT) and the LLCP of water.