The Journal of Physical Chemistry B最新文献

Ion pair aggregates (IPAs) in olefin polymerization catalysts have attracted growing attention due to their potential influence on catalytic activity and selectivity. In this study, employing (pyridylamido)Hf(IV) as a model system, we investigated the destabilization and structural diversity of IPAs by using the molecular dynamics method. The potential of mean force (PMF) analysis indicates that the growing polymer chains, ethylene, and ZnEt₂ destabilize the IPAs. In addition, the energy decomposition analysis demonstrated that not only the dominant electrostatic interaction but also relatively small yet qualitatively different contributions from dispersion and coordination interactions play an essential role in the structures of IPAs. These findings can be regarded as a piece of evidence that chemical species other than the catalyst itself in the reaction medium, through relatively small interactions, should modulate catalytic behaviors. Furthermore, we also found that the growing polymer chains, ethylene, and ZnEt₂ induce structural diversity of IPAs, and classified IPAs' structures into three distinct classes: (1) inner-sphere ion pair aggregate (ISIPA), (2) bridged ion pair aggregate (BIPA), and (3) outer-sphere ion pair aggregate (OSIPA). Our findings have laid the groundwork for a broader understanding of IPAs' behaviors in olefin polymerization catalysts across diverse catalytic environments.

The long-time scale behavior of hydrogels is still a core problem in material design, especially due to the limitation of computational cost and accessibility time scale of molecular dynamics (MD) simulations. So, this study offered a combined model, which integrates both MD and artificial intelligence (AI) models to truly predict the dynamics of structural and transport characteristics of thiol-norbornene click cross-linked carboxymethyl cellulose (CMC) hydrogels. All-atom MD portrays a consistent network of hydrogen bonds, a measurable swelling ratio, and restricted polymer mobility, and these are indicators of a strong gel. To extrapolate these properties, the gated recurrent unit (GRU), long short-term memory (LSTM), and transformer-based LAG-LLAMA are trained and compared with an echo state network (ESN). The GRU, LSTM, and LAG-LLAMA models have not been successful in explaining the nonlinear oscillations of hydrogen bonding, obtaining insignificant values of R² (0.05), whereas ESN has demonstrated outstanding predictive power (R² = 0.99) with only 200 MD trajectory frames of initial information. In addition to this, despite the deep learning models achieving a high accuracy, via optimization, for mean-squared displacement (R² = 0.95), the training sets are much larger (40-70%) than the ESN. In this way, the present work shows that reservoir computing models are more efficient and reachable in data efficiency and stability compared to the traditional recurrent and transformer models when applied to modeling the time-dependent transformation of complex molecular systems. This methodology will provide a generalizable methodology of fastening the computational design of soft materials bridging atomistic fidelity and AI-based temporal extrapolation.

The effect of asymmetry in supported lipid bilayers on their electrochemical phase behavior has been studied using in situ Polarization Modulation Infrared Reflection Absorption Spectroscopy (PM-IRRAS). Dimyristoylphosphatidylcholine (DMPC) and dimyristoylphosphatidylethanolamine (DMPE), which have the same tails and different headgroups, have been used to construct asymmetric bilayers on Au(111) electrodes. The organization and orientation of the hydrocarbon tails in each leaflet of the asymmetric bilayers have been characterized separately by deuterating the tails in the opposing leaflet. The vibrational frequencies of the chain methylene stretching modes show that DMPC is relatively ordered in asymmetric bilayers, and DMPE is relatively disordered, compared with their respective symmetric bilayers. The tail orientations in the as-deposited asymmetric bilayers are similar, showing the two monolayers influence each other, but the changes induced in each bilayer by the application of a potential difference across the bilayer are different and indicate that the bilayers decouple, with each monolayer responding separately to the imposed field. The results suggest that the behavior of previously reported symmetric systems may be more strongly influenced by the properties of the electrolyte-facing leaflet and highlight the value of using electrochemical perturbation of lipid bilayers in structural studies to provide additional insights into lipid-lipid interactions.

Peptoids are structural analogs of peptides in which side chains are appended to the backbone nitrogen rather than the α-carbon. The sequence-defined modularity of peptoids enables precise control over structure-function relationships, enabling applications in energy storage and biomedical materials. Despite recent progress, the role of sequence and conformation on electron transport in peptoid molecules is not fully understood. Here, we synthesize a library of peptoid oligomers and characterize their molecular electronic properties using the scanning tunneling microscope-break junction (STM-BJ) technique. Our results show well-defined electron transport behavior for peptoid sequences containing aromatic side groups lacking hydrogen bonds (H-bonds) and without chemical substitutions at the N-C_α position. This behavior fundamentally differs from electron transport in peptides, where H-bond interactions give rise to higher conductance states. All-atom molecular dynamics (MD) simulations are used to understand the conformational heterogeneity of peptoids, and molecular conformations obtained from MD simulations are used in quantum mechanical calculations based on the nonequilibrium Green's function-density functional theory (NEGF-DFT) formalism. In all cases, computational results are in reasonable qualitative agreement with experiments. Our work demonstrates that the conductance behavior of peptoids depends on monomer identity, including side-chain aromaticity and substitution at the N-C_α position. Overall, this work provides new insights into the structure-function relationships governing electron transport in peptoid-based materials and establishes design rules for peptoid-based molecular junctions.

The present study investigates the potential of dicationic ionic liquids (DILs) and monocationic ionic liquids (MoIL), with and without metal in the anion, for CO₂ capture applications. The structures of the samples were confirmed by FTIR, ¹H NMR spectroscopy, and Raman spectroscopy, while their physicochemical properties, density, viscosity, and thermal stability were evaluated. A series of computational simulations were conducted by using density functional theory (M11/def2-TZVP) to ascertain the multiplicity of the ground state of the magnetic anion [FeCl₄]^-. These simulations determined the multiplicity to be a sextet and furthermore identified the trans conformation as the most energetically favorable for cation [E(MIM)₂]²⁺. This finding demonstrates a correlation between the structural conformations and the experimental Raman spectra. The findings of CO₂ sorption and kinetic tests, conducted under postcombustion conditions (40 °C, 4 bar), indicated that DILs exhibited superior performance in comparison to MoILs. The DIL [E(MIM)₂][2Cl] exhibited the highest sorption capacity (110.20 μmol/g), which is almost three times higher than that of the best MoIL (BMIM FeCl₄). These enhancements can be ascribed to reduced viscosities and an augmented number of active interaction sites in the dicationic structures. Furthermore, [E(MIM)₂][2Cl] exhibited a high degree of selectivity for CO₂ over N₂ and demonstrated stability over five recycling cycles, suggesting the potential of DILs as candidates for the development of CO₂ capture technologies.

Proteins in complex with small-molecule ligands represent the core of structure-based drug discovery. However, three-dimensional representations are absent from most deep-learning-based generative models. Here, we present a graph-based generative modeling technology that encodes explicit 3D protein-ligand contacts within a relational graph architecture and evaluate its behavior using the dopamine D2 receptor (DD2R) as a model system. The models combine a conditional variational autoencoder that allows for activity-specific molecule generation with putative contact generation that provides predictions of molecular interactions within the target-binding pocket. We show that molecules generated with our 3D procedure are more compatible with the DD2R-binding pocket than those produced by a comparable ligand-based 2D generative method, as measured by docking scores, expected stereochemistry, and recoverability in commercial chemical databases. Predicted protein-ligand contacts were found to be among the highest-ranked docking poses with a high recovery rate. Overall, this work shows how the structural context of a protein target can enhance the generation of small molecules within a realistic binding environment.

Nonphotochemical spectral hole burning (NPHB) experiments were performed on the modified LH2 complex from Rbl. acidophilus, in which some but not all B800 Bchl a molecules have been replaced with Chl a, with the initial goal of utilizing Chl a as a local thermometer. The focus of the work eventually shifted to exploring low-temperature protein dynamics. Different sample batches contained different proportions of Chl a capable and incapable of excitation energy transfer (EET) to the Bchl a molecules. This indicates that there were at least two subpopulations of Chl a, with only one of them featuring proper reconstitution of Chl a into the original B800 protein pocket and fast EET. Nevertheless, the other, EET-incapable Chl a molecules were clearly associated with the LH2 complex and were not located in solution. NPHB and hole recovery experiments reveal that relevant protein energy landscapes do not differ much between different subsets of Chl a despite different environments but they both differ from those of the original B800 Bchl a. This suggests that small structural changes responsible for NPHB and shifts of spectral lines in single-complex experiments may involve the pigment molecule itself or that structural changes in the immediate protein environment of the pigment are constrained differently by different pigment molecules. The NPHB dynamics did not depend much on the deuteration of the solvent, except that the slowdown of NPHB with the increase of light intensity was much more prominent. Attributing this effect to triplets alone would be unrealistic. This observation lends support to the hypothesis that local heating of the protein complexes plays a role in spectroscopy experiments, particularly single-molecule spectroscopy experiments, where excitation intensities are higher.

Improving the stability of catechins against autoxidation and simultaneously exerting their biological activity to scavenge reactive oxygen species (ROS) are essential for achieving their efficient utilization in healthcare and drug therapy. Focusing on this important objective, a feasible strategy for modifying catechins with arylboronic acid has been proposed as they have good biocompatibility and also controllable release at specific sites. We developed three catechin-diarylboronate (DiarylBA) ester self-assembly carriers, in which DiarylBA serves as the receptor molecules of catechins, including a coupled benzyl ammonium boronic acid (BTEAB) or two coupled pyridinium boronic acids (PyBBA and PyPBA) linked by a spacer, and (-)-epicatechin (EC) is taken as the representative catechin molecule. Specifically, the inhibition of the auto-oxidation and the antioxidant activities for both EC and EC-DiarylBA esters were characterized sufficiently by combining spectroscopies (UV-vis, NMR), and ROS scavenging assessment. The relevant binding thermodynamics and interaction mechanism, as well as their aggregation behavior, were also studied by ITC, NMR, and light scattering. The thermodynamic and spectroscopic results all confirm the generation of EC-DiarylBA esters in a range from a weak acid of pH 6.5 to an alkaline one of pH 8.5. It was found that the esterification of EC with DiarylBA can effectively inhibit the auto-oxidation of EC even at pH 8.5 and still retain the excellent antioxidant activity of the original EC. Furthermore, the EC-BTEAB ester exhibits a favorable H₂O₂ responsiveness in the H₂O₂-overexpressed site, while EC-PyBBA and EC-PyPBA esters need to first release the EC component to effectively eliminate H₂O₂. Therefore, the comprehensive results of stability and antioxidant activity indicate that the EC-DiarylBA ester would be a promising candidate for enhancing EC's medicinal and health care effects.

Microplastics (MPs) and per- and polyfluoroalkyl substances (PFAS) are two classes of highly persistent contaminants that frequently co-occur in the environment, raising concern about potential synergistic effects. To better understand their interactions, we investigated the adsorption of perfluorooctanoic acid (PFOA) and perfluorooctanesulfonic acid (PFOS) on polyethylene (PE) through molecular dynamics (MD) simulations. The potential of mean force (PMF) at infinite dilution was calculated for both the semicrystalline and crystalline PE models. For semicrystalline PE systems, the PMF minima were -26.5 ± 4.8 kJ mol^-1 for PFOA and -43.9 ± 4.3 kJ mol^-1 for PFOS, whereas, for crystalline PE, the values were -26.6 ± 5.2 and -42.0 ± 7.7 kJ mol^-1, respectively. These results indicate that, within statistical uncertainty, no significant differences are observed between the two PE morphologies for either PFAS when considering the depth of the free-energy minimum. Moreover, PFOS exhibited stronger interactions with PE than PFOA. This behavior reflects not only differences in fluoroalkyl chain length but also the distinct chemical nature of the functional groups, with the larger and more hydrophobic sulfonate headgroup of PFOS compared to the carboxylate group of PFOA. In addition to adsorption strength, molecular orientation at the PE-water interface was characterized. PFAS tails showed a general tendency to align parallel to PE chains within the polymer slab, but this alignment was disrupted upon the transition into water. Notably, PFOS interacting with semicrystalline PE exhibited orientation changes with transitions between parallel and perpendicular alignment associated with local PMF barriers. These orientation-dependent interactions highlight the importance of both chain packing and functional group chemistry in driving PFAS-polymer affinity. Taken together, these findings provide molecular-scale evidence that microplastics can act as reservoirs for PFAS, potentially enhancing their environmental persistence and transport.