The Journal of Physical Chemistry B最新文献

We investigated the temperature dependence of the intermolecular dynamics, including intermolecular vibrations and collective orientational relaxation, of one of the most typical deep eutectic solvents, reline, using femtosecond Raman-induced Kerr effect spectroscopy (fs-RIKES), subpicosecond optical Kerr effect spectroscopy (ps-OKES), and molecular dynamics (MD) simulations. According to fs-RIKES results, the temperature-dependent intermolecular vibrational band peak at ∼90 cm^-1 exhibited a redshift with increasing temperature. The density-of-state (DOS) spectrum of reline by MD simulations reproduced this fs-RIKES spectral feature. The decomposition analysis of the DOS spectra showed that all constituent components, including urea, cholinium cation, and chloride anion, also exhibited similar magnitudes of redshifts upon heating, indicating that the three species intermolecularly interact one another. The temperature sensitivity of the intermolecular vibrational frequency was high compared to that of ionic liquids. According to ps-OKES results, the slow orientational relaxation rate increased with increasing temperature; however, this phenomenon was not well explained by the Stokes-Einstein-Debye hydrodynamic model. Analysis of the orientational relaxation time based on the Stokes-Einstein-Debye model indicates that the decoupling between the orientational relaxation time and viscosity occurs at temperatures below ∼330 K. Quantum chemistry calculations of urea and the cholinium cation based on the MP2/6-311++G(d,p) level of theory confirmed that the contribution of intramolecular vibrational bands to low-frequency bands below 200 cm^-1 was minimal. The densities, viscosities, electrical conductivities, and surface tensions of reline at various temperatures were also estimated and compared with the dynamics data.

Energetic composite systems with uniform particle distributions are of considerable interest, but sedimentation is a persisting challenge. Tungsten carbide (WC, density: 15.36 g/cm³) particles are promising cemented carbide particles owing to their desirable properties. In this study, we investigated the mitigation of sedimentation in a polymer-bonded explosive (PBX) energetic composite by optimizing the viscosity and particle distribution using WC particles and a hydroxyl-terminated polybutadiene-based binder. A simulation based on a modified version of Stokes' law is used to study the sedimentation behaviors of the system at different viscosities, and the resistance coefficient of particle sedimentation is estimated. The PBX energetic composite system loaded with the WC particles is prepared and analyzed. In the early curing stages, when the resistance coefficient is 0.65-1.95 (×10⁹), the sedimentation rate is low, but increases rapidly as the viscosity of the system increases. When the effective viscosity is ≥11,510 MPa·s, the particle sedimentation is improved. The energetic components are tightly entangled within the binder, with no exposure or agglomeration, and the WC particles are evenly distributed. The system can reach a solid content of 91% and retain its pourability. Thus, an energetic composite system loaded with high-density metal particles is prepared, providing a reference for use in PBX formulation.

Fermi resonance is a common phenomenon, and a hidden caveat exists in the applications of infrared probes, causing spectral complication and shorter vibrational lifetime. In this work, using the cyanotryptophan (CNTrp) side chain model compound 5-cyanoindole (CN-5CNI), we performed Fourier transform infrared spectroscopy (FTIR) and two-dimensional infrared (2D-IR) spectroscopy on unlabeled ¹²C¹⁴N-5CNI and its isotopically labeled substituents (¹²C¹⁵N-5CNI, ¹³C¹⁴N-5CNI, ¹³C¹⁵N-5CNI) and demonstrated the existence of Fermi resonance in 5CNI. By constructing the Hamiltonian and simulating 2D-IR spectra, we show that the distinct Fermi resonance 2D-IR patterns in various isotope substituents are determined by the quantum mixing consequences at the v = 1 state, as well as the v = 2 state, where the Fermi coupling and anharmonicity play a crucial role. Our work provides important insights into the elusive type of Fermi resonance, where the coupling is much smaller than the anharmonicity, which is termed the weak coupling case.

Solid-state polymer electrolytes (SPEs) are increasingly favored over liquid electrolytes for emerging energy storage devices due to their safety features, enhanced stability, and multifunctionality. Minor solvents (such as water) are often introduced unintentionally or intentionally into SPEs. Although it can significantly affect SPEs' electrochemical and mechanical properties, the fundamental role of such solvent content has rarely been studied. Here, we investigate the effects of minor water content on two representative SPEs through molecular dynamics simulations. Focusing on SPEs composed of different base polymers, namely, poly(ethylene oxide) (PEO) and poly(lactic acid) (PLA), and the same salt, lithium perchlorate (LiClO₄), our simulations reveal that slight hydration facilitates an increase in ionic conductivity while preserving the mechanical integrity of the SPEs. Notably, these water contents appear to affect ionic conductivity more effectively in certain systems than others, which is attributed to the unique interactions among ions, water, and the polymer matrix. Moreover, small amounts of water can maintain the stiffness of SPEs rather than reducing it. Such results suggest a facile approach to developing SPEs with balanced ionic conductivity and mechanical properties, suitable for a range of energy storage applications.

Molten salts are promising candidates in numerous clean energy applications, where knowledge of thermophysical properties and vapor pressure across their operating temperature ranges is critical for safe operations. Due to challenges in evaluating these properties using experimental methods, fast and scalable molecular simulations are essential to complement the experimental data. In this study, we developed machine learning interatomic potentials (MLIP) to study the AlCl₃ molten salt across varied thermodynamic conditions (T = 473-613 K and P = 2.7-23.4 bar), which allowed us to predict temperature-surface tension correlations and liquid-vapor phase diagram from direct simulations of two-phase coexistence in this molten salt. Two MLIP architectures, a Kernel-based potential and neural network interatomic potential (NNIP), were considered to benchmark their performance for AlCl₃ molten salt using experimental structure and density values. The NNIP potential employed in two-phase equilibrium simulations yields the critical temperature and critical density of AlCl₃ that are within 10 K (∼3%) and 0.03 g/cm³ (∼7%) of the reported experimental values. An accurate correlation between temperature and viscosities is obtained as well. In doing so, we report that the inclusion of low-density configurations in their training is critical to more accurately represent the AlCl₃ system across a wide phase-space. The MLIP trained using PBE-D3 functional in the ab initio molecular dynamics (AIMD) simulations (120 atoms) also showed close agreement with experimentally determined molten salt structure comprising Al₂Cl₆ dimers, as validated using Raman spectra and neutron structure factor. The PBE-D3 as well as its trained MLIP showed better liquid density and temperature correlation for AlCl₃ system when compared to several other density functionals explored in this work. Overall, the demonstrated approach to predict temperature correlations for liquid and vapor densities in this study can be employed to screen nuclear reactors-relevant compositions, helping to mitigate safety concerns.

Liquid phase-separating proteins can form condensates that play an important role in spatial and temporal organization of biological cells. The understanding of the mechanisms that lead to the formation of protein condensates and their interactions with other biomolecules may lead to processing routes for soft materials with tailored geometry and function. Fused in sarcoma (FUS) is an example of a nuclear protein that forms stable complexes, and recent studies have highlighted its ability to wet actin filaments and bundle them into networks. We perform coarse-grained molecular dynamics simulations to investigate the wetting and spreading of FUS droplets on actin filaments. We employ the Martini model and rescale the protein-protein and protein-actin interactions to tune the interfacial and wetting properties of FUS droplets. By measuring the molecular displacements in the three-phase region, we are able to relate contact angle, contact line velocity, and contact line friction in terms of a linear approximation of molecular kinetic theory. The results show that the rescaled Martini model can be used to study the molecular mechanisms of dynamic wetting at the nanoscale and to obtain quantitative predictions of the contact line friction and contact angles during dynamic wetting.

This study employs first-principles molecular dynamics (FPMD) simulations combined with the Voronoi tessellation method to explore the microstructure, transport properties, electronic properties, and Raman spectra of the NaF-AlF₃-CaF₂/LiF/KF systems with varying cryolite ratios, additive types, and concentrations. The results indicate that Na⁺, Ca²⁺, Li⁺, and K⁺ exist in a free state in the molten salts, while Al³⁺ forms complex ion groups in the form of [AlF_x]^3-x with F^-, and free F^- also exists in the molten salts. In the NaF-AlF₃-CaF₂ system, the average Al-F distance is slightly shorter than that in the other two systems, while the Al-F coordination number is higher in NaF-AlF₃-LiF. Cryolite ratios and additive concentrations have little effect on the average Al-F distance. The diffusion abilities of different ions follow the order: Li⁺ > Na⁺ > F^- > Al³⁺, with the diffusion ability of K⁺ being close to that of Li⁺. In Al-F chemical bonds, both ionic and covalent bonds coexist and double bonds can be observed in certain transient structures. The Al-F complex ion groups mainly consist of [AlF₄]^-, [AlF₅]^2-, and [AlF₆]^3-, with the concentration of [AlF₆]^3- being higher in the NaF-AlF₃-LiF system compared to the other two systems. This study establishes the relationship between the microscopic properties and the composition of aluminum electrolytes, demonstrating the suitability of FPMD combined with Voronoi tessellation for probing the microstructural properties of aluminum electrolytes.

ModeHunter is a modular Python software package for the simulation of 3D biophysical motion across spatial resolution scales using modal analysis of elastic networks. It has been curated from our in-house Python scripts over the last 15 years, with a focus on detecting similarities of elastic motion between atomic structures, coarse-grained graphs, and volumetric data obtained from biophysical or biomedical imaging origins, such as electron microscopy or tomography. With ModeHunter, normal modes of biophysical motion can be analyzed with various static visualization techniques or brought to life by dynamics animation in terms of single or multimode trajectories or decoy ensembles. Atomic structures can also be refined against volumetric densities with flexible fitting strategies. The software consists of multiple stand-alone programs for the preparation, analysis, visualization, animation, and refinement of normal modes and 3D data sets. At its core, two spatially reductionist elastic motion engines are currently supported: elastic network models (typically for a Cα level of detail and rectangular meshes) and bend-twist stretch (for trigonal or tetrahedral meshes or trees resulting from spatial clustering). The programs have recently been modernized to Python 3, requiring only the common numpy and scipy external libraries for numerical support. The main advantage of our modular design is that the tools can be combined by the end users for specific modeling applications, either standalone or with complementary tools from our C/C++-based Situs modeling package. The modular design and consistent look and feel facilitate the maintenance of individual programs and the development of novel application workflows. Here, we provide the first complete overview of the ModeHunter package as it exists today, with an emphasis on functionality and workflows supported by version 1.4.

Dry skin is a common condition that is experienced by many. Besides being particularly present during the cold season, various diseases exist all year round, leading to localized xerosis. To prevent it, the skin is provided with natural moisturizing factors (NMFs). They are small amino acids or derivatives found in the outermost layer of the skin, the stratum corneum (SC). They are often claimed to be highly efficient humectants, increasing the water content to maintain the fluidity of the skin. However, alternative mechanisms have been proposed, suggesting that NMFs themselves may act as lipid mobility amplifiers. This work aims at investigating the role of three NMFs, namely, urea (URE), glycerol (GLY), and urocanic acid/urocanate (UCA/UCO) in SC in silico models, considering two different levels of humidity. Molecular dynamic simulations showed an increase in the diffusion of different lipid components, mainly free fatty acids (FFAs) and ceramide acyl chain moieties, in the presence of either high water content or NMFs. The membrane properties were modified, as seen by an increased thickness and greater lateral stiffness. All NMFs exhibited a similar impact, whereas UCA revealed slight differences according to its charged state. By studying NMF-water intermolecular interactions, we highlighted the role of NMF as a regulator of membrane perturbations while ensuring membrane fluidity. This role allows NMFs to prevent destabilization of the skin membrane in the presence of high water content. This study, performed at an atomistic resolution, highlighted a strong H-bond network between lipids involving mainly ceramides but also all other components. This network can be modified in the presence of a high water concentration or NMFs, resulting in modifications of membrane properties, rationalizing hydration effects.

The ion binding to the lipid/water interface can substantially influence the structural, functional, and dynamic properties of the cell membrane. Despite extensive research on ion-lipid interactions, the specific effects of ion binding on the polarity and hydration at the lipid/water interface remain poorly understood. This study explores the influence of three biologically relevant divalent cations─Mg²⁺, Ca²⁺, and Zn²⁺─on the depth-dependent interfacial polarity and hydration of zwitterionic DPPC lipid in its gel phase at room temperature. To measure these depth-dependent properties, we use a series of solvatochromic fluorescent probes synthesized based on 4-aminophthalimide with varying alkyl chain lengths (4AP-Cn; n = 5, 7, and 9). Employing steady-state fluorescence experiments and all-atom molecular dynamics (MD) simulations, we quantify changes in interfacial polarity and hydration induced by the cations binding to the lipid/water interface. Our results reveal that Zn²⁺ induces a significant blue shift in the fluorescence spectra of all 4AP-Cn dyes, indicating a marked decrease in local polarity (E_T^N ≤ 0.05) at the lipid/water interface compared to Mg²⁺ and Ca²⁺, which results in a higher polarity (E_T^N ≥ 0.2). The depth-dependent fluorescence spectra of dyes at the interface in the presence of Mg²⁺ and Ca²⁺ remain similar to those in the absence of cations, with only a minor red shift observed for Mg²⁺, implying a slight hydration effect. MD simulations show that cations primarily bind to the headgroup and glycerol regions of lipid. Simulations also reveal that Zn²⁺ causes substantial dehydration at the lipid/water interface, as detected by the 4AP-Cn dyes, while Mg²⁺ and Ca²⁺ have less pronounced effects, with only slight hydration induced by Mg²⁺. This study highlights the distinct positional effects of cations probed by 4AP-Cn probes at the lipid-water interface, underscoring the potential of 4AP-Cn dyes for monitoring depth-dependent changes in membrane properties induced by external agents or environmental conditions.