The Journal of Physical Chemistry B最新文献

Water-lean solvents for point source carbon dioxide capture generally reveal an increase in polarity and viscosity with higher CO₂ loadings. Among these, N-(2-ethoxyethyl)-3-morpholinopropan-1-amine (2-EEMPA) exhibits notable CO₂ capture properties due to its formation of CO₂-dependent molecular tetramers. Wide-angle X-ray scattering (WAXS) was used to examine the evolution of nanoscale clusters at different CO₂ loadings ranging from 0 to 42 mol % CO₂ and from −17 to 90 °C. Computational and experimental data were used to estimate the solvent density, cluster size, and cluster–cluster correlations of various tetrameric species, enabling quantitative assessment of WAXS-derived structures. Particularly, the Teubner–Strey thermodynamical model was used to investigate the microphase separation of our system, while the molecular nearest-neighbor behavior was obtained through scattering- and molecular-dynamics-derived structure factor analysis. The experimentally derived correlation length (ξ) and periodicity (d) of the CO₂-bound clusters of 2-EEMPA grow as the concentration of CO₂ increases, reaching ξ = 5.0 Å and d = 11.6 Å, in agreement with simulation results. Our findings capture the detailed structural changes that occur with CO₂ variation and compare them with chemical process simulations and physical properties measurements. The structural insights derived from this study provide crucial input to the modeling and design of the CO₂ capture solvents.

Solid-state nanopore (SSN) sequencing has emerged as a revolutionary technique in genetic and proteomic analysis, offering low costs and long read-lengths. However, traditional SSN sequencing, which relies on an electric field to drive biomolecules, faces challenges in translocating nonuniformly charged proteins, limiting its application in single-molecule protein sequencing. In this work, molecular dynamics (MD) simulations were employed to investigate peptide translocation across a BC₃/C₃N van der Waals (vdW) heterostructure nanopore in the absence of external forces. Our results revealed that the peptide spontaneously translocates from the BC₃ surface to the C₃N surface due to stronger binding on the latter. However, the translocation is temporarily impeded by aromatic Phe residues, which experience strong π–π interactions with nanosurfaces, creating significant energy barriers for Phe desorption. These findings clarify the molecular-scale interactions that govern peptide motion across the BC₃/C₃N heterostructure interface and reveal how asymmetric adsorption energetics enable spontaneous, directional transport. Rather than assessing sequencing feasibility, this study provides mechanistic insights into heterostructure-mediated peptide motion and establishes a conceptual framework for future investigations of nanopore-based biomolecule manipulation.

Magnetic nanogels (MNGs)─deformable colloidal particles composed of cross-linked polymers with embedded magnetic nanoparticles (MNPs)─facilitate remote manipulation of their rheology and internal structure through biocompatible magnetic fields. This property renders MNGs particularly promising for applications in drug delivery and hyperthermia, although the rheological characteristics of these systems are not yet fully understood. In this research, we create an in silico planar rheometer by combining the solutions of Lattice–Boltzmann-based Navier–Stokes equations with molecular dynamics-tracked MNGs trajectories. Conducting steady shear experiments allows us to measure the viscosity of MNG suspensions by evaluating the effects of uniform external magnetic fields (H⃗) (in terms of strength and direction), concentration, and dipolar coupling interactions among MNPs within the MNGs. The application of H⃗ hinders colloid rotation and increases viscosity, while rotating H⃗ fields generate shear flow in otherwise stationary MNG suspensions. Differences in the rheological behavior between deformable and rigid colloids are highlighted.

Enhanced Linde Type A (LTA) zeolite-poly(methacrylic acid) (PMAA) composites are synthesized by incorporating high concentrations of LTA zeolite (35–52 mass%) into the PMAA hydrogel network. PMAA, LTA zeolite-PMAA composites in xerogel structure, and LTA zeolite are investigated by ¹³C, ²⁷Al, and ²⁹Si solid-state NMR. The interactions between LTA zeolite and PMAA in the xerogel structure are confirmed. Regularly aligned acid dimers with the carboxylic acids hydrogen-bonded to each other in LTA zeolite-PMAA composites are revealed. The ²⁹Si MAS NMR reveals the prevalent tetrahedral coordination of silicon atoms in composites and the presence of the hydrogen-bearing amorphous species. The ²⁷Al MAS NMR spectra of LTA zeolite and composites confirm predominant tetrahedrally coordinated aluminum atoms in a typical LTA zeolite framework and the presence of extraframework octahedral aluminum in composites.

Polyuronates are polyelectrolytes widely distributed in nature with a broad range of practical applications. Linear polysaccharide molecules, such as polyglucuronates, polygalacturonates, and alginates, despite having similar chemical character, exhibit distinct conformational properties due to several details in their molecular structure. This study focuses on the detailed conformational analysis of individual polyuronate chains, including alginates of heterogeneous composition. The research employed molecular dynamics atomistic simulations and Monte Carlo simulations based on a coarse-grained model, enabling the consideration of chains with lengths of up to hundreds of monomers. The results obtained for all polyuronates allowed us to rank the local rigidity of their chains and interpret these data in the context of the available conformational space for rotations around glycosidic linkages. The descriptors of local chain stiffness (persistence length and characteristic ratio) are strongly correlated with the average number of consecutive linkages in a polyuronate chain that remain in the dominant syn-exo conformation. Surprisingly, the block composition of the alginate chain does not significantly affect the global conformation of the longer chains. The only significant factor is the content of mannuronate (M) and guluronate (G) monomers. This observation was used to establish relationships among the fractions of MM, GG, and MG blocks in the alginate chain and its conformational properties. The differences in the persistence length of alginates under standard ionic strength conditions are not drastically large, reaching at most 6 nm when comparing the most (MM) and least (MG) flexible blocks. However, applying the Odijk–Skolnick–Fixman model and simulation data revealed a significant increase in both the persistence length values (for all polyuronates studied) and the differences between the corresponding values for alginates with varying compositions (they can reach hundreds of nanometers). This suggests the theoretical possibility of estimating the composition of an alginate chain through conformational measurements under conditions of extremely low ionic strength.

The isomerization of the chromophore is a central photoactivated process in the functioning of a class of proteins called the bacteriophytochrome. This isomerization is affected by the protein environment and leads to the specific activity of the proteins. We have studied the reverse direction (conversion of the far-red light absorbing form to the red light absorbing form) of the photoisomerization process for phytochrome. Our study reveals two different pathways that may lead to this photoisomerization, and we have identified one of them as the preferred one on the basis of energy criteria. We compared this pathway with that of the forward direction of the photoisomerization. Furthermore, we explored that the electrostatic interaction of the protein environment has a pivotal role in favoring one of the pathways for this photoconversion.

Poor water solubility of many active pharmaceutical ingredients limits their bioavailability and therapeutic efficacy. Surface-active ionic liquids (SAILs), with their tunable physicochemical properties and strong self-aggregation behavior, offer a promising strategy for drug delivery by forming mixed assemblies with drug molecules that influence micellar structure, morphology, and interactions. In the current study, a coarse-grained molecular dynamics (CG) simulation was carried out to investigate the mechanism of loading of an antidepressant drug, imipramine (IMP), with 1-decyl-3-methylimidazolium bromide (DMI) in aqueous medium at a concentration range. Mixing soluble DMI surface-active ionic liquids with hydrophobic IMP drugs modulates the encapsulation of drug molecules by influencing aggregation behavior. The molar fraction determined the loading and distribution of imipramine in mixed micelles. Due to the synergistic interaction from the incorporation of IMP among DMI monomers, larger and more compact mixed micelles with higher aggregation numbers were formed. At lower concentrations, IMP monomers capture inside DMI micelles, while, at higher concentrations, they self-assemble alongside DMI molecules. The IMP weakens the electrostatic repulsive interaction between DMI monomers. The strong synergistic interactions between the SAIL and drug molecules in the mixed micelles are attributed to the formation of cationic mixtures.

Correlated vibrational spectroscopy (CVS) is a hyper-Raman-based vibrational spectroscopy that retrieves separate spectra of individual (self-correlated, SC) and interacting (cross-correlated, CC) molecules. The spectra are recorded in the >40 cm^–1 THz/mid-IR frequency range and contain modes that are IR and/or Raman active. Here, we further develop CVS and apply it to investigate intra- and intermolecular interactions using room temperature liquid carbon tetrachloride (CCl₄), a nonpolar liquid, and acetonitrile (CH₃CN), a polar liquid, as case studies. CVS spectra of CCl₄ display no intermolecular coupling, confirming the isotropy and short-range nature of the molecular interactions. Strong intramolecular coupling is observed on the Fermi resonance, and the relative phase between the participating modes is determined based on the intensities in the experimental spectra. CVS spectra of acetonitrile display intermolecular coupling of the C≡N mode vibrations, whose cross-correlated out-of-phase signature is evidence for near-perpendicular pair arrangements. Performing a theoretical analysis of the CVS response, an equation for the effective average orientational angle between C≡N groups of adjacent liquid molecules is developed and solved. The effective average orientational angle between adjacent acetonitrile dipoles is ∼102° ± 2°, which is close to a head-to-tail arrangement.

Allostery, the intriguing phenomenon of long-range communication between distant sites in proteins, plays a central role in biomolecular regulation and signal transduction. While it is commonly attributed to conformational rearrangements, the underlying dynamical mechanisms remain poorly understood. The contact cluster model of allostery [J. Chem. Theory Comput. 2024, 20, 10731–10739] identifies localized groups of highly correlated contacts that mediate interactions between secondary structure elements. This framework proposes that allostery proceeds through a multistep process involving cooperative contact changes within clusters and communication between distant clusters, transmitted through rigid secondary structures. To demonstrate the validity and generality of the model, this Perspective employs extensive molecular dynamics simulations (∼1 ms total simulation time) of four different photoswitchable PDZ domains and studies how different domains, ligands, and perturbations influence both the contact clusters and their dynamical evolution. These analyses reveal several recurring clusters that represent shared flexible structural modules, such as loops connecting β-sheets, and show that the characteristic time scales of the nonequilibrium protein response can be directly associated with the motions of individual contact clusters. Thus, the dynamic decomposition of PDZ domains into contact clusters uncovers a modular, dynamics-based architecture that underlies and facilitates long-range allosteric communication.