The Journal of Physical Chemistry B最新文献

In this article, we present three mesoscopic models for water. All three models make use of local density-dependent interaction potentials, as employed within the Pagonabarraga-Frenkel framework [Pagonabarraga, I.; Frenkel, D. J. Chem. Phys. 2001, 115, 5015-5026]. The forms of these three interaction potentials are based on the free energy function of the SAFT-VR Mie equation of state (EoS) [Lafitte, T. J. Chem. Phys. 2013, 139, 154504]. Two of these models represent the water-water interaction as a spherically symmetric Mie interaction with temperature-dependent parameters, while the third model works with a temperature-independent Mie potential and explicitly models the effect of hydrogen bonding using an association term. All three models provide good predictions of the vapor-liquid equilibrium of water over a wide temperature range. They also give accurate predictions of the isothermal compressibility for both sub- and supercritical conditions. To model the interfacial tension of the vapor-liquid interface with our mesoscale simulations, we added a square-gradient term to our potential energy function. We show that the addition of this term has a minimal effect on the bulk properties of water. However, by parametrizing the coefficient of this term as a function of temperature, all three models again provide excellent predictions of water's interfacial tension over a wide temperature range. Of the three models, our preference is for the model that includes an association term, as this model can operate successfully over a wider range of conditions.

Operando electron paramagnetic resonance is used to monitor the light-initiated generation of the diethylnitroxyl radical from diethylhydroxylamine (DEHA) and its decay kinetics, thereby unveiling solvent effects on both the electronic structure and stability of the nitroxyl radical. The observed trends in hyperfine coupling constants (A_N and A_H) across different solvents align with previously reported values of the 4-amino-2,2,6,6-tetramethylpiperidoxyl radical (ATEMPO). Regarding the stability of the DEHA radical in various solvents, the obtained decay-kinetic constants (k) correlated more strongly with A_N than with the permittivity of the solvents. Moreover, distinguishing between protic and aprotic solvents leads to a better relationship between A_N and k, and a positive and constant correction of the nitroxyl radical's A_N supports the hydrogen-bonding effect in protic solvents. These findings indicate that mere hydrogen-bonding interaction does not enhance the stability of radicals. A_N of ATEMPO may serve as a superior metric for assessing the impact of solvent effects on both the electronic structure and stability of nitroxyl radicals. The data presented in this study will offer substantiation for the judicious selection of suitable solvents in reactions involving radicals.

Direct air capture of CO₂ using amino acid absorbents, such as glycine or sarcosine, is constrained by the relatively slow mass transfer of CO₂ through the air-aqueous interface. Our recent study showed a marked improvement in CO₂ capture by introducing CO₂-permeable oligo-dimethylsiloxane (ODMS-MIM⁺) oligomers with cationic (imidazolium, MIM⁺) headgroups. In this work, we have employed all-atom molecular dynamics simulations in combination with subensemble analysis using network theory to provide a detailed molecular picture of the behavior of CO₂ and the glycinate anions (Gly^-) at the ODMS-MIM⁺ decorated air-aqueous interfaces. We show that the cationic head groups of the surfactants enhance the concentration and lifetime of Gly^- in the interfacial region, while ODMS tails promote the physisorption of CO₂ in the interfacial region. Together, these two factors increase the effective region of contact and the probability of interactions between CO₂ and Gly^- compared to that of the pure air-aqueous interface. The fundamental insights gained in this work establish essential foundations for developing hybrid systems with oligomer-decorated interfaces to maximize the overall CO₂ capture rates.

Squalamine is an aminosterol from dogfish shark which has drawn attention, besides its antimicrobial activity, as a drug candidate in the treatment of Parkinson's disease due to its ability to prevent binding of α-synuclein to lipid membranes. To get insight into the mode of action of this steroid, we studied the influence of squalamine on lipid bilayers and whether it could inhibit the binding of a model peptide. Solid-state ¹⁹F NMR of labeled [KIGAKI]₃ indicated that, indeed, this peptide no longer binds as a flexible chain to the bilayer in the presence of squalamine. When the cationic squalamine was added to lipid vesicles containing phosphatidylglycerol lipids, the aminosterol was found in differential scanning calorimetry and solid-state ³¹P NMR experiments to lower the gel-to-fluid phase transition and cause the phase separation of domains enriched in anionic lipids. Squalamine had only a little influence on ²H NMR relaxation and on the order parameters of the chains. These findings indicate that the aminosterol does not affect the molecular mobility of the hydrophobic core of the bilayer; hence, it does not insert into the membrane, nor causes thinning as found for molecules inserting in the headgroup region. On the other hand, squalamine was found to interact with lipid headgroups through electrostatic interactions, as seen by solid-state ²H NMR on headgroup-labeled lipids. Furthermore, ³¹P NMR showed that squalamine shifted the lamellar-to-hexagonal phase transition of phosphatidylethanolamine lipids to higher temperatures, indicating a preference for positively curved membranes. Altogether, our experiments indicate a strong interaction of the cationic squalamine with lipid headgroups, in particular with anionic lipids. This affinity for membranes is strong enough to efficiently displace cationic polypeptides, confirming the proposed action mechanism in Parkinson treatment. Notably, supported by ¹H-¹H NOESY experiments, it was found that squalamine does not insert into the bilayer, but rather acts as facial amphiphile binding to the membrane surface. The binding to membranes may be envisaged in the form of oligomeric or micellar assemblies, which can disrupt the membrane at high concentrations, thereby explaining the antimicrobial and antifungal activities of squalamine.

Mycobacterium tuberculosis (Mtb) contains potential G-quadruplex (PGQ) motifs in the genes espK and cyp51, which are crucial for the bacteria's virulence within host cells. Aminoglycoside molecules are commonly used as antibiotics for ribosomal targets. This study provides insight into the interactions between these aminoglycosides and Mtb-PGQ sequences (espK and cyp51), shedding light on the structural and thermodynamic dynamics of their binding. This study demonstrates the stability, affinity, and conformation of Mtb-PGQ in the presence of neomycin and streptomycin. Ultraviolet-visible spectroscopy (UV-vis), circular dichroism spectroscopy (CD), CD thermal melting, isothermal titration calorimetry (ITC), and fluorescence intercalator displacement (FID) assays were used to comprehensively examine these interactions. Our results reveal that neomycin with Mtb-PGQexhibits hypochromism accompanied by a 4-5 nm red shift in the UV-visible absorption titration, whereas streptomycin exhibits a hypochromic shift without changes in the maximum wavelength. Notably, neomycin shows a nonlinear binding isotherm, suggesting the involvement of more than one binding process in the formation of neomycin.Mtb-PGQ complexes. Scatchard plot analysis indicates higher binding affinity values for neomycin compared with weaker affinity of streptomycin. CD studies reveal that neomycin decreases the ellipticity of Mtb-PGQ with a red shift while retaining the parallel topology, ultimately enhancing the thermal stability of both espK and cyp51. In contrast, streptomycin destabilizes the cells. ITC analysis reveals that neomycin exhibits the strongest binding affinity for cyp51, with the relative order being NEO-cyp51 > NEO-espk > STR-cyp51 > STR-espk. Moreover, thermodynamic analysis reveals that neomycin possesses a unique dual mode of binding through grooves as well as stacking. FID studies further confirm a lower DC₅₀ value for neomycin than for streptomycin, suggesting that neomycin is a strong displacer of thiazole orange. Thus, the results show that neomycin with amino groups selectively recognizes the grooves of cyp51 over espK.

Molecular dynamics simulations were performed to investigate the properties of the ice/quartz interface. The premelting liquid at the interface, which behaves as a nanofluid, plays an important role in both the compression and shearing processes. The results reveal that the sliding velocity, compression, and temperature are crucial factors in analyzing the shear process at the interface and quantifying shear stress. The microscopic mechanisms underlying these effects are closely tied to the formation and evolution of the premelting layer. Specifically, the effect of sliding velocity shows a logarithmic relationship between shear stress and shear rate in the premelting liquid, which is attributed to the shear thinning behavior of the premelting layer. Compression and temperature affect the thickening of the premelting layer, leading to a decrease in shear stress as the normal stress increases. Furthermore, when the premelting layer is sufficiently thick, shear stress is observed to act in the direction opposite to sliding. This study offers an atomic-scale understanding of the ice/quartz interface and connects the findings to tribological and hydrodynamic theory.

Toxic oligomeric species are suspected in the etiology of Alzheimer's disease. The full-length Aβ₄₂ can be studied by the fragment Aβ_25-35 as it retains neurotoxicity. According to experimental studies, amidation of the Aβ_25-35 carboxyl terminal decreases fibrillation activity while retaining its neurotoxic properties. Our molecular dynamics simulation studied the aggregation of the Aβ_25-35 trimer from two initial structures (fibril and randomized helical structures) in their amidated and nonamidated forms. Comparing the amidated and nonamidated systems, the results suggest that antiparallel chains are dominant in nonamidated systems, while the amide group leads to parallel chains. In terms of secondary structures, a higher helix content with a corresponding decrease in β-sheet content is observed as a consequence of amidation. Despite the variation in secondary structures, the chain-chain contacts are still mediated by the Gly motif (GxxxG) and Ile residues in both amidated and nonamidated systems. As neurotoxicity does not change upon amidation, our results imply that clumping of peptides sustained by the Gly motif is a greater contributing factor to toxicity than secondary and quaternary structures.

The oxidation of human sebum, a lipid mixture covering our skin, generates a range of volatile and semivolatile carbonyl compounds that contribute largely to indoor air pollution in crowded environments. Kinetic models have been developed to gain a deeper understanding of this complex multiphase chemistry, but they rely partially on rough estimates of kinetic and thermodynamic parameters, especially those describing skin permeation. Here, we employ atomistic molecular dynamics simulations to study the translocation of selected skin oil oxidation products through a model stratum corneum membrane. We find these simulations to be nontrivial, requiring extensive sampling with up to microsecond simulation times, in spite of employing enhanced sampling techniques. We identify the high degree of order and stochastic, long-lived temporal asymmetries in the membrane structure as the leading causes for the slow convergence of the free energy computations. We demonstrate that statistical errors due to insufficient sampling are substantial and propagate to membrane permeabilities. These errors are independent of the enhanced sampling technique employed and very likely independent of the precise membrane model.

Two nearly universal and anomalous properties of glasses, the peak in the specific heat and plateau of the thermal conductivity, occur around the same temperature. This coincidence suggests that the two phenomena are related. Both effects can be rationalized by assuming Rayleigh scaling of sound attenuation and this scaling leads one to consider scattering from defects. Identifying defects in glasses, which are inherently disordered, is a long-standing problem that was approached in several ways. We examine candidates for defects in glasses that represent areas of strong sound damping. We show that some defects are associated with quasi-localized excitations, which may be associated with modes in excess of the Debye theory. We also examine generalized Debye relations, which relate sound damping and the speed of sound to excess modes. We derive a generalized Debye relation that does not resort to an approximation used by previous authors. We find that our relation and the relation given by previous authors are almost identical at small frequencies and also reproduce the independently determined density of states. However, the different generalized Debye relations do not agree around the boson peak. While generalized Debye relations accurately predict the boson peak in two-dimensional glasses, they underestimate the boson peak in three-dimensional glasses.

Fe₃O₄ core Gd shell nanoparticles are interesting candidates as multimodal MRI/MPI contrast agents/tracers that can potentially provide MPI signal from the magnetic iron component while still achieving positive MRI contrast from the Gd shell. However, a current challenge in synthesizing these NPs is controlling the uniformity of the Gd shell while maintaining the particle size. In this study, we show that by using thermal decomposition of mixed metal oleate precursors, the iron oxide nanoparticle core with Gd shell coating can be varied from 7% to 27% while maintaining a high level of control over the particle size, producing highly uniform particles of d = 13.5 nm. Iron oxide nanoparticles with moderate Gd coating have resulted in improved MPI signal and MRI relaxation compared with commercial tracers, indicating that iron oxide core Gd shell nanoparticles are effective materials for both MPI and MRI applications. These results demonstrate the ability to synthetically control both the amount of the Gd shell and the size of the core-shell iron oxide nanoparticles, which can be applied to other magnetic nanomaterials.