The Journal of Physical Chemistry B最新文献

The structure H (sH) of methane hydrate, which has a distinctive structure with large (LL) cages capable of encapsulating multiple methane molecules, has been suggested as a methane reservoir in large icy bodies such as Titan, making it important in planetary science. This high-pressure phase, which exists in the GPa range, lends itself to the study of methane states and dynamics using powerful experimental techniques such as IR and Raman spectroscopy. However, the interpretation of the vibrational spectra of methane in the sH structure has been challenging because of the spectral complexities. The signals attributed to the methane molecules in the LL cage, as well as those of the other two cage types, overlap in the spectra. In this study, we investigated the microscopic origins of the shape of the C–H stretching vibration spectrum of methane in the LL cage using ab initio molecular dynamics (AIMD) simulations. For a single methane molecule in the LL cage, the ν₃ band of the C–H stretching mode was observed at a higher frequency typical of isolated molecules in vacuum due to the large size of the LL cage. As the number of methane molecules in the LL cage increased beyond one, a tendency to blue-shift with increasing methane occupancy was observed, consistent with a loose-cage–tight-cage model. By characterizing the time correlation function of methane stretching vibrations based on the solvation number of methane and water molecules proximal to methane within the LL cage, we showed that the complicated spectral line shape observed in cases of higher methane occupancy in the LL cage resulted from the wider variation of the solvation shell states. Analysis of the solvation structures of the AIMD trajectories provided interpretations of the experimental spectral line shape, demonstrating the complementary nature of AIMD to the experiment and its effectiveness in analysis.

An in-depth understanding and characterization of molten salt properties are necessary for the optimized design, efficient operation, and safety assurance of molten salt reactors (MSRs). Investigating molten salt properties in experimental settings can be challenging and time-consuming due to the high temperatures of interest, the salt’s corrosiveness, purity and composition control, and health and safety concerns. Therefore, it is beneficial to perform computational screening to assist in the ultimate experimental measurements. Herein, we used first-principles molecular dynamics simulations to calculate several thermophysical, structural, and dynamic properties of eutectic LiF–NaF with fuel additives UF₄ and ThF₄. We found that with the incorporation of uranium or thorium, a prepeak appears in the structure factor, indicative of a medium-range structural ordering. Furthermore, we explore the mechanism through which these structural changes enhance shear stress correlations, thereby increasing the salt’s viscosity. This work highlights the importance of studying the atomic-scale structure of molten salts and how the addition of fuel elements can substantially affect it.

This study investigates the role of alkali cations in modulating the interaction between deoxyribonucleic acid (DNA) and Thioflavin T (ThT) in dilute and condensed phases. The emission characteristics of ThT were analyzed in the presence of double-stranded DNA and G-quadruplex structures with a focus on the effects of four cations: sodium, potassium, calcium, and magnesium. The ThT emission in double-stranded DNA was influenced by direct DNA binding and steric hindrance within the hydration shell of DNA, which was modulated by the presence of alkali cations. Lasing spectroscopy experiments further highlighted ThT sensitivity to the spatial arrangement of water molecules in the DNA hydration shell. Lasing was exclusively observed in the presence of Mg²⁺ in the G-quadruplex structure, suggesting that the parallel propeller configuration of G4 provides an optimal environment for ThT light amplification. This study highlights the critical role of cations in DNA-dye interactions and reaffirms the significance of ThT in biophysical studies.

Interactions of the cations Li⁺, Na⁺, Mg²⁺, and Ca²⁺ with L-glutamate (Glu^–) in aqueous solution were studied at room temperature with dielectric relaxation spectroscopy in the gigahertz region. Spectra of ∼0.4 M NaGlu with added LiCl, NaCl, MgCl₂, or CaCl₂ (c(MCl_n) ≤ 1.5 M) were evaluated and experiments supplemented by density functional theory and 3D reference interaction site model (3D-RISM) calculations. In addition to the modes found for aqueous NaGlu, namely, the reorientation of free Glu^– ions (peaking at ∼1.6 GHz), of moderately retarded H₂O molecules hydrating the carboxylate moieties of Glu^– (∼8.4 GHz), of the cooperative resettling of the H-bond network of bulk water (∼20 GHz), and its preceding fast H-bond flip (∼400 GHz), an additional low-frequency relaxation at ∼0.4 GHz was detected upon the addition of the four salts. In the case of NaGlu + MgCl₂(aq) and NaGlu + CaCl₂(aq), this mode could be unequivocally assigned to an ion pair formed by the cation and the side-chain carboxylate moiety of Glu^–. For NaGlu + LiCl(aq), either this species or a backbone-[Li⁺–H₂O–Cl^––Glu^–] triple ion is formed. Binding constants increase in the order Li⁺<Mg²⁺<Ca²⁺. For NaGlu + NaCl(aq), an assignment of the ∼0.4 GHz mode to ion pairs or triples was not plausible. Accordingly, its origin remains speculative here.

Controlling the valency of directional interactions of patchy particles is insufficient for the selective formation of target crystalline structures due to the competition between phases of similar free energy. Examples of such are stacking hybrids of interwoven hexagonal and cubic diamonds with (i) its liquid phase, (ii) arrested glasses, or (iii) clathrates, all depending on the relative patch size, despite being within the one-bond-per-patch regime. Herein, using molecular dynamics simulations, we demonstrate that although tetrahedral patchy particles with narrow patches can assemble into clathrates or stacking hybrids in the bulk, this behavior can be suppressed by the application of external surface potential. Depending on its strength, the selective growth of either cubic diamond crystals or empty sII clathrate cages can be achieved. The formation of a given ordered network depends on the structure of the first adlayer, which is commensurate with the emerging network.

Mixing two solvents can sometimes make a much better solvent than expected from their weighted mean. This phenomenon, called synergistic solvation, has commonly been explained via the Hildebrand and Hansen solubility parameters, yet their inability in other solubilization phenomena, most notably hydrotropy, necessitates an alternative route to elucidating solubilization. While, recently, the universal theory of solubilization was founded on the statistical thermodynamic fluctuation theory (as a generalization of the Kirkwood–Buff theory), its demand for experimental data processing has been a hindrance for its wider application. This can be overcome by the solubility isotherm theory, which is founded on the fluctuation theory yet reduces experimental data processing significantly to the level of isotherm analysis in sorption. The isotherm analysis identifies the driving force of synergistic solvation as the enhancement of solvent mixing around the solute, opposite in behavior to hydrotropy (characterized by the enhancement of demixing or self-association around the solute). Thus, the fluctuation theory, including its solubility isotherms, provides a universal language for solubilization across the historic subcategorization of solubilizers, for which different (and often contradictory) mechanistic models have been proposed.

Precise characterization of the supercritical CO₂–water interface under high pressure and temperature conditions is crucial for the geological storage of carbon dioxide (CO₂) in deep saline aquifers. Molecular dynamics (MD) simulations offer a valuable approach to gaining insight into the CO₂–water interface at a microscopic level. However, no attempt has been made to characterize the CO₂–water interface with the accuracy afforded by ab initio calculations. In this study, we performed ab initio MD (AIMD) simulations to investigate the structural and dynamical properties of the CO₂–water interface, comparing the results with those obtained from classical force-field MD (FF-MD) simulations. Molecular orientation at the interface was well reproduced in both AIMD and FF-MD simulations. Characteristic structural fluctuations of water at the interface were unveiled by applying multidimensional scaling and time-dependent principal component analysis to the AIMD trajectories; however, they were not prominent in the FF-MD simulations. Furthermore, our study demonstrated a marked difference in the residence time of molecules in the interface region between AIMD and FF-MD simulations, indicating that time-dependent properties of the CO₂–water interface strongly depend on the description of the intermolecular forces.

While GLP-1 and its analogues are important pharmaceutical agents in the treatment of type 2 diabetes and obesity, their susceptibility to aggregate into amyloid fibrils poses a significant safety issue. Many factors may contribute to the aggregation propensity, including pH. While it is known that the monomeric structure of GLP-1 has a strong impact on primary nucleation, probing its diverse structural ensemble is challenging. Here, we investigated the monomer structural ensembles at pH 3, 4, and 7.5 using state-of-the-art computational methods in combination with experimental data. We found significant stabilization of β-strand structures and destabilization of helical structures at lower pH, correlating with observed aggregation lag times, which are lower under these conditions. We further identified helical defects at pH 4, which led to the fastest observed aggregation, in agreement with our far-UV circular dichroism data. The detailed atomistic structures that result from the computational studies help to rationalize the experimental results on the aggregation propensity of GLP-1. This work provides a new insight into the pH-dependence of monomeric structural ensembles of GLP-1 and connects them to experimental observations.

Elastin-like polymers are a class of stimuli-responsive protein polymers that hold immense promise in applications such as drug delivery, hydrogels, and biosensors. Yet, understanding the intricate interplay of factors influencing their stimuli-responsive behavior remains a challenging frontier. Using temperature-controlled dynamic light scattering and zeta potential measurements, we investigate the interactions between buffer, pH, salt, water, and protein using an elastin-like polymer containing ionizable lysine residues. We observed the elevation of transition temperature in the presence of the common buffering agent HEPES at low concentrations, suggesting a “salting-in” effect of HEPES as a cosolute through weak association with the protein. Our findings motivate a more comprehensive investigation of the influence of buffer and other cosolute molecules on elastin-like polymer behavior.

Hydrogen sulfide (H₂S) is an important endogenous gas transmitter that plays a critical role in various physiological and pathological processes and can also cause a negative impact on foodstuffs. In this study, we designed and synthesized a simple, easily available, high-yield, and low-cost near-infrared (λ_em = 710 nm) fluorescent probe, DEM-H₂S, with a substantial Stokes shift (205 nm) for the detection of H₂S. DEM-H₂S features high selectivity and sensitivity (LOD = 80 nM) toward H₂S, accompanied by a noticeable color change. Upon interaction with H₂S, DEM-H₂S exhibits a restored ICT (Intramolecular Charge Transfer) process, thereby manifesting near-infrared fluorescence. DEM-H₂S has been successfully utilized to detect H₂S in actual water samples and to monitor the spoilage of food items, such as pork, shrimp, and eggs. Furthermore, DEM-H₂S enables the imaging of endogenous and exogenous H₂S in living MCF-7 cells and zebrafish. Hence, DEM-H₂S provides an attractive method for the detection of H₂S in environmental, food, and biological systems, holding potential value in physiological and pathological research.