The Journal of Physical Chemistry B最新文献

We report the interactions and dynamics of chemically powered soft swimmers that undergo autonomous oscillatory motion. The interaction of autonomous entities is the basis for the development of collective behaviors among biological organisms. Collective behaviors enable organisms to efficiently attain food and coordinate against threats. The basis of these behaviors is the interaction between nearest neighbors. Mimicking these interactions in artificial systems would enable their organization for the performance of complex tasks. Oscillatory phenomena are also ubiquitous in nature. Hence artificial oscillatory systems can serve as the most direct mimics and models of many biological systems. In this work, we report the interactions and dynamics of oscillatory swimmers propelled by the nonlinear oscillatory Belousov-Zhabotinsky (BZ) reaction. Individually, these swimmers displace by undergoing nonfully reciprocal oscillatory motion in conjunction with the BZ reaction. We find that, in addition to their individual oscillatory motion, multiple BZ swimmers exhibit successive oscillatory changes in their inter swimmer distance. This oscillatory attraction and repulsion between adjacent swimmers occurs in conjunction with the BZ waves and oxidation state of the catalyst. The effect of swimmer size and number on these dynamic interactions is interrogated. The level of chemical synchronization between multiple swimmers is determined. This work is a starting point for the design of collective behaviors utilizing autonomous chemically propelled soft swimmers.

The effects of alkali-metal ions (Li⁺, Na⁺, K⁺, Rb⁺, and Cs⁺) on the vibrational dynamics of the DNA ion-hydration shell were studied through classical molecular dynamics simulations. As a result, the vibrational spectra of the DNA-water-salt systems were calculated within the framework of two approaches, using dipole-dipole and velocity-velocity autocorrelation functions. We dissect the effect of the individual compartments of the DNA double helix (minor groove, major groove, and phosphate groups) on the behavior of the systems. The obtained spectra have a different shape in the case of structure-making and structure-breaking ions. This difference becomes more prominent for the ions interacting with DNA, especially in the case of structure-breaking ions in the minor groove of the double helix. The obtained spectra of DNA do not show a significant effect of counterion type, except for Li⁺, which influences the vibrational modes of the DNA phosphates. The analysis of the spectra of water vibrations around ions revealed an isosbestic point at ∼70 cm^-1, which appears as a response to the confinement induced by interaction with the DNA double helix and counterions. The obtained results are important for understanding the structural and dynamical organization of the DNA ion-hydration shell.

In this work, we carry out a systematic computer simulation investigation of the single particle dynamics at the free surface of imidazolium-based room temperature ionic liquids by applying intrinsic surface analysis. Besides assessing the effect of the potential model and temperature, we focus in particular on the effect of changing the anion type, and, hence, their shape and size. Further, we also address the role of the length of the cation alkyl chains, known to protrude into the vapor phase, on the surface dynamics of the ions. We observe that the surface dynamics of ionic liquids, being dominated by strong electrostatic interactions, is about 2 orders of magnitude slower than that for common molecular liquids. Furthermore, the free energy driving force for exposing apolar chains to the vapor phase "pins" the cations at the surface layer for much longer than anions, allowing them to perform noticeable lateral diffusion at the liquid surface during their stay there. On the other hand, anions, accumulated in the second layer beneath the liquid surface, stay considerably longer here than in the surface layer. The ratio of the mean surface residence time of the cations and anions depends on the relative size of the two ions: larger size asymmetry typically corresponds to larger values of this ratio. We also find, in a clear contrast with the bulk liquid phase behavior, that anions typically diffuse faster at the liquid surface than cations. Finally, our results show that the surface dynamics of the ions is largely determined by the apolar layer of the cation alkyl chains at the liquid surface, as in the absence of such a layer, cations and anions are found to behave similarly with respect to their single particle dynamics.

Diffusion of mobile charge carriers, such as ferredoxin and plastocyanin, often constitutes a rate-determining step in photosynthetic energy conversion. The diffusion time scales typically exceed that of other primary bioenergetic processes and remain beyond the reach of direct simulation at the molecular level. We characterize the diffusive kinetics of ferredoxin and plastocyanin upon the photosystem I-rich domain of Prochlorococcus, the most abundant phototroph on Earth by mass. A modeling approach for ferredoxin and plastocyanin diffusion is presented that uses ensembles of coarse-grained molecular dynamics simulations in Martini 2.2P with GROMACS 2021.2. The simulation ensembles are used to construct the diffusion coefficient and drift for ferredoxin and plastocyanin as spatial functions in the photosystem I domain of the MIT9313 ecotype. Four separate models are constructed, corresponding to ferredoxin and plastocyanin in reduced and oxidized states. A single scaling constant of 0.7 is found to be sufficient to adjust the diffusion coefficient obtained from the Martini simulation ensemble to match the in vitro values for both ferredoxin and plastocyanin. A comparison of Martini versions (2.2P, 2.2, 3) is presented with respect to diffusion scaling. The diffusion coefficient and drift together quantify the inhomogeneity of diffusive behavior. Notably, a funnel-like convergence toward the corresponding putative binding positions is observed for both ferredoxin and plastocyanin, even without such a priori foreknowledge supplied in the simulation protocol. The approach presented here is of relevance for studying diffusion kinetics in photosynthetic and other bioenergetic processes.

Members of the KCNE family are accessory subunits that modulate voltage-gated potassium channels. One member, KCNE4, has been shown to inhibit the potassium ion current in these channels. However, little is known about the structure, dynamics, and mode of inhibition of KCNE4, likely due to challenges in overexpressing and purifying the protein. In this study, an alternative expression and purification protocol has been developed and validated to obtain overexpressed KCNE4 for in vitro studies. This protocol was validated through SDS-PAGE, CW-EPR, CW-EPR power saturation, and CD experiments. The SDS-PAGE and CD data reveal that this protocol produces relatively pure and properly folded KCNE4 in large quantities at a lower cost. The CW-EPR and EPR power saturation spectra show that KCNE4 consists of extracellular, transmembrane, and intracellular regions. Together, these techniques indicate that this alternative protocol produces structurally and dynamically native KCNE4 without the need for mammalian cell lines. This study provides guidance for characterizing the structure and dynamics of KCNE4 in a lipid bilayer environment.

We investigated oscillatory motion of a camphor disk floating on water containing 5 mM hexylethylenediaminium trifluoroacetate (HHexen-TFA) as an ionic liquid (IL). The frequency of the oscillatory motion increased with increasing concentrations of the transition metal ions Cu²⁺ and Ni²⁺ but was insensitive to Na⁺, Ca²⁺, and Mg²⁺, the typical metal ions in the water phase. The surface tension of the water phase containing 5 mM HHexen-TFA also increased with increasing concentrations of Cu²⁺ and Ni²⁺ but was insensitive to Na⁺, Ca²⁺, and Mg²⁺. Based on density functional theory, metal-ion species-dependent frequency response is discussed with regard to surface tension as the force of self-propulsion and complex formation between HHexen-TFA and metal ions. These results suggest that complex formation between the transition metal ions (Cu²⁺, Ni²⁺) and the ethylenediamine group in the IL increases the surface tension around the camphor disk, resulting in an increase in the frequency of oscillatory motion with increasing concentrations of Cu²⁺ or Ni²⁺. The present study suggests that the nature of self-propulsion can be created by complexation, which changes the force of self-propulsion.

We reassess the modeling of amorphous silica bilayers as a 2D classical system whose particles interact with an effective pairwise potential. We show that it is possible to reparametrize the potential developed by Roy, Heyde, and Heuer to quantitatively match the structural details of the experimental samples. We then study the glassy dynamics of the reparametrized model at low temperatures. Using appropriate cage-relative correlation functions, which suppress the effect of Mermin-Wagner fluctuations, we highlight the presence of two well-defined Arrhenius regimes separated by a narrow crossover region, which we connect to the thermodynamic anomalies and changes in the local structure. We find that the bond-orientational order grows steadily below the crossover temperature and is associated with transient crystalline domains of nanometric size. These findings raise fundamental questions about the nature of the glass structure in two dimensions and provide guidelines to interpret the experimental data.

All-atom molecular dynamics (MD) calculations of the crystalline polymeric p-hydroxybenzoic acid (pHBA) were conducted at various temperatures to investigate its thermal response. The calculated structure factor equivalent to the X-ray diffraction pattern of pHBA clearly showed two phase transitions occurring at 600 and 650 K. The first transition at 600 K occurred from the orthorhombic phase to the pseudohexagonal phase, identified by the presence of the 211-peak. This peak disappeared during the second transition at 650 K, indicating that the phase at 650 K was hexagonal. The structure of the pseudohexagonal phase was anisotropic with respect to the ab plane but isotropic in the hexagonal phase. Discontinuous changes in the calculated unit cell volume and unit cell length were observed at 600 K, associated with the first phase transition. We also calculated the linear expansion coefficients in three directions. An anisotropic expansion was observed in three directions for the orthorhombic crystal. In particular, the linear expansion coefficient in the c-direction was negative. In contrast to this, an isotropic expansion was found in the a- and b-directions for the hexagonal crystal, while the expansion in the c-direction is still negative. This study provides valuable insights into the thermal behavior of polymeric pHBA, which is essential for understanding its structural transformations and designing crystalline polymers with tailored thermal properties.

Light-harvesting complexes (LHCs) play a critical role in modulating energy flux within photosynthetic organisms in response to fluctuating light. Under high light conditions, they activate quenching mechanisms to mitigate photodamage. Despite their importance, the molecular mechanisms underlying these photoprotective processes remain incomplete. Herein, we present a computational protocol to model the energy pathways in the LHC, focusing specifically on the minor CP29 antenna complex of plants. We explore the factors that modulate the switch between the light-harvesting and quenched states. The protocol includes modeling the exciton Hamiltonian of the chlorophylls/lutein aggregate and calculating population dynamics using a kinetic model based on the Redfield-Förster approach. Our analysis reveals a highly tunable excited-state lifetime for the complex, that can switch between quenched and unquenched state depending on the excitation energy of the lutein, which acts as a final quencher, in accordance with recent experiments. Moreover, we observe that the s-trans lutein conformers are more likely to exhibit characteristics of the quencher.

The high activity of water in aqueous battery electrolytes can trigger side reactions, limiting their large-scale application. Additives that form contact pairs (CPs) with cations by coordinating with them can effectively reduce water's activity. However, due to the complex interactions between ions, additives, and solvent molecules and the fact that current strategies for additive screening primarily rely on static physical parameters, the dynamic mechanisms that govern the modulation of ion solvation sheaths are still poorly understood. In this study, we introduce butyramide (BUT) as a molecular additive and employ molecular simulations to demonstrate its regulatory effect on the hydration sheath of Ca²⁺, which is more pronounced than that for Na⁺. The dynamic process by which BUT replaces water molecules in the tight hydration sheath of Ca²⁺ is elucidated by forming a stable [BUT-Ca²⁺(H₂O)₇] complex that suppresses water molecule activity. At a 2 M concentration, the free energy barrier for the transition from contact pair (CP) to solvent-shared pair (SP) for Ca²⁺ is 11.7 kJ/mol higher than that for Na⁺ at 8.5 kJ/mol, consistent with the cationic Hofmeister series. Furthermore, the stability and dynamic fluctuations among solvent-separated pair (SSP), SP, and CP states are attributed to the balance between electrostatic attractive potential energy and hydration repulsive potential energy, supported by quantum chemical calculations of the ion desolvation process. Using BUT as an additive presents a promising strategy to enhance battery performance by modulating the solvation environment of metal ions, addressing the growing demand for safer and more sustainable energy storage solutions.