The Journal of Physical Chemistry B最新文献

Single-molecule Förster resonance energy transfer (smFRET) experiments have greatly contributed to the understanding of the conformational dynamics of proteins and other biomolecules. Generating high-fidelity simulated data for smFRET experiments is an important step toward developing and examining accurate and efficient smFRET data analysis techniques. Here, we use distributions of interdye distances generated using Langevin dynamics to simulate freely diffusing smFRET timestamp data for proteins and biomolecules that have conformational flexibility. We then compare analysis techniques for smFRET data to validate the new module. The Langevin dynamics is used here as an illustrative example to demonstrate how modeling conformational dynamics can be integrated with molecular diffusion and photon emission statistics, all of which are essential for realistic simulation of freely diffusing smFRET data. We also discuss different ways to generalize our approach to make the simulated data more realistic including the employment of molecular dynamics (MD) simulations that is illustrated with an example. The Langevin dynamics module provides a framework for generating timestamp data for systems with a known underlying conformational heterogeneity as a step toward the development of new analysis techniques for smFRET data dealing with flexible proteins or other biomolecular systems.

CP2K is a versatile open-source software package for simulations across a wide range of atomistic systems, from isolated molecules in the gas phase to low-dimensional functional materials and interfaces, as well as highly symmetric crystalline solids, disordered amorphous glasses, and weakly interacting soft-matter systems in the liquid state and in solution. This review highlights CP2K’s capabilities for computing both static and dynamical properties using quantum-mechanical and classical simulation methods. In contrast to the accompanying theory and code paper [J. Chem. Phys. 152, 194103 (2020)], the focus here is on the practical usage and applications of CP2K, with underlying theoretical concepts introduced only as needed.

Interfacial environments are highly sensitive to changes in composition. The addition of trace solutes or cosolvent mixtures can dramatically alter the surface composition, by altering the energetics of adsorption and solvation, or by creating nanoenvironments where chemistry is enhanced or suppressed. Prior aerosol experiments show that the addition of oxygenated spectator molecules accelerates the heterogeneous chlorination rate of squalene without altering the mechanism. Using molecular dynamics simulations and kinetic models, we find that long-chain alcohols are enriched in a subsurface layer and enhance reactivity both at the interface and in the bulk. The bulk reaction rate increases by an order of magnitude relative to pure squalene, while the interfacial rate is accelerated by 2 orders of magnitude compared to that bulk value. These findings illustrate how modest compositional changes reshape the interfacial environment to catalyze multiphase chemistry.

Accurate modeling of self-diffusivity in deep eutectic solvents (DESs) is critical for understanding mass transport in electrochemical and separation applications. However, the complex hydrogen-bonding networks and heterogeneous charge distributions in DESs present major challenges for molecular simulations. We investigated translational self-diffusion in five choline chloride-based DESs using the polarizable AMOEBA force field with targeted monopole scaling, validated against quantum mechanics and experiments. Although AMOEBA’s explicit polarization captured key features of DES hydrogen-bond networks, quantitative agreement with experiment required charge scaling. For nonhydroxyl DESs, excellent agreement was achieved by scaling only the monopoles of choline chloride by +10%, whereas hydroxyl-rich DESs required uniform −10% scaling of ions and hydrogen bond donors to capture hydrogen bonding accurately and polyhydroxyl differences. AMOEBA thereby captures the influence of donor identity on diffusivity. Structural properties are also well reproduced. These findings establish a transferable modeling strategy and provide benchmarks for future polarizable force fields.

An interface between a solution and air could attract or dispel ions and thus alter its own thermodynamic properties. One major source of the force is the electrostatic interaction. We solve a different model from previous models on this subject where an ion represented by a point charge at the center of a hollow sphere sits on or close to the dielectric interface. Two numerical methods are developed to solve the corresponding Poisson equations to get the electrostatic self-energy. One is based on expanding the electric potential function by spherical and cylindrical harmonic functions. The other self-consistently calculates the induced charge on the air–solution interface and the shell of the ion. The numerical results support, in certain regions, some simple analytical approximations and some simple physical pictures behind them. The results may help to improve the understanding of complex ion–interface interactions in biological and electrochemical systems.

Biomolecular condensates, a type of subcellular or membraneless organelle, form through liquid–liquid phase separation (LLPS) driven by multivalent interactions. As an RNA-binding protein, FUS participates in biological processes by forming dynamic liquid condensates via LLPS, with its abnormal fibrous aggregation associated with neurodegenerative disorders such as amyotrophic lateral sclerosis (ALS). Experiments show that phosphorylation inhibits LLPS of the FUS low-complexity domain (LCD) under low salt conditions, whereas for full-length FUS, phosphorylation does not block initial LLPS but inhibits the conversion of liquid droplets to toxic aggregates. The molecular mechanism underlying the difference between the two remains unknown. In this molecular dynamics simulation study, we examined condensate structural characteristics and compared wild-type (WT) versus phosphorylated condensates, revealing the molecular details of how full-length FUS avoids LLPS impairment through synergistic compensatory regulation among various domains. As for the FUS-LCD system, the extent to which their LLPS is reduced by phosphorylation is associated with the number of phosphorylation sites. Moreover, we have developed a model for analyzing the viscoelasticity of the condensates, which revealed that altered interaction patterns impact condensate viscoelasticity. This study characterizes the postphosphorylation architecture of FUS condensates and elucidates the molecular mechanisms by which phosphorylation regulates condensate formation and properties.

Anthracene-based dyes are widely known to be impressive emitters, whereas triphenylamine-based dyes are notable for sensory applications. This work focuses on compiling these two building blocks by connecting them through a triple bond to ensure maximum planarity and high fluorescence quantum yield. Three anthracene-triphenylamine based dyes were synthesized, one of which is a basic 4-(anthracen-9-ylethynyl)-N,N-diphenylaniline [AnTPA]. The other two molecules are 4-(10-((4-(diphenylamino)phenyl)ethynyl)anthracen-9-yl)benzonitrile [sTPA] and 4-((10-((4-(diphenylamino)phenyl)ethynyl)anthracen-9-yl)ethynyl)benzonitrile [tTPA], where the electron-withdrawing benzonitrile group is added via one single bond and triple bond, respectively. The photophysical properties of these molecules are compared with the help of experimental and theoretical studies. These dyes exhibit intramolecular charge transfer (ICT) in their excited states resulting in high Stokes shifts, with their emission covering a broad spectrum ranging from blue to orange-red region. sTPA shows the highest ICT characteristics among these three molecules despite having an orthogonal benzonitrile unit. Emission of the synthesized molecules in polar media is sensitive to the fluctuations in solvent temperature, with tTPA being the most sensitive one. The ratiometric fluorescence increment displays a linear relationship with temperature. Fluorescence anisotropy values of these dyes are very sensitive to the medium viscosity and rotational constraint. Additionally, AnTPA was found to be a good candidate to study protein molecules, as evident by its good binding efficiency with human serum albumin. These fluorophores penetrate and stay within lipid bilayers and can be used for fluorescence imaging of giant unilamellar vesicles. They sense the phase transition temperature of liposomes. In mammalian cell-imaging experiments, AnTPA shows negligible cytotoxicity in HEK293T and HeLa cells and remains inside the cells for up to 36 h with a strong signal, highlighting its potential as a long-term cell-tracing dye.

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.