The Journal of Physical Chemistry B最新文献

The rapid development of the natural gas hydrate industry has put forward higher requirements for hydrate promotion technology. The exploration of methods that can simultaneously enhance both the hydrate formation rate and the final gas and water conversion efficiency has become a critical research focus. This study systematically investigated the synergistic effects of electric field (EF) signals, including three distinct waveforms (square, sine, ramp wave) at six different voltage levels, combined with four concentration gradients of the cationic surfactant called hexadecyl trimethylammonium bromide (CTAB) on the CH₄ hydrate formation process. Experimental results demonstrated that the application of external EF significantly enhanced the gas storage capacity of hydrate, with different waveforms exhibiting varying degrees of promotional effects. Notably, square wave and ramp wave, which allow for instantaneous changes in the EF direction, exhibited superior performance in improving hydrate formation rates and gas and water conversion efficiency and enhancing hydrate fluidity. Furthermore, a kinetic model for hydrate formation was developed, which showed excellent agreement with the observed results. These findings not only advance the theoretical framework of EF-assisted hydrate formation but also provide valuable insights and practical guidance for the development of natural gas hydrate technologies.

The von Willebrand factor (VWF), a multimeric plasma glycoprotein, binds to the platelet glycoprotein (GPIbα) to initiate the process of primary hemostasis as a response to blood flow alteration in the site of vascular injury. The GPIbα binding site located on the A1 domain of VWF is exposed during the activation of the VWF multimer when it changes from a coiled form to a thread-like, extended form. Though experimental studies have demonstrated that the autoinhibitory module (AIM) connected to the N-/C-termini of the A1 domain is a regulator of VWF activity, the molecular mechanism underlying the regulation of A1-GPIbα binding remains unclear. We modeled the structures of the A1 domain having full-length N-terminal AIM (NAIM) and C-terminal AIM (CAIM) with different types of O-linked glycans. The conventional and steered molecular dynamics simulations were conducted to investigate the dynamics of the AIM and O-glycans under different conditions and elucidate how they affect the binding of GPIbα. Our results indicate that the NAIM alone with no glycan is sufficient to shield the GPIbα binding site under static conditions. However, when the AIM is unfolded with external forces applied, the O-glycans on both NAIM and CAIM increase the shielding of the binding site. These findings suggest a potential mechanism by which the AIM and O-glycans regulate the interaction of the VWF A1 domain and GPIbα.

Hydrogen bonds and metal-ligand interactions catalyze the epoxy-amine cross-linking reactions. Through a detailed quantum chemical study, it was demonstrated that water, through hydrogen bond formations, acts as a better catalyst than amines in the epoxy-amine cross-linking reactions. The presence of various solvated metal cations (Na⁺, Mg²⁺, and Al³⁺) results in the formation of metal-ligand interactions with both epoxy and amine moieties. A comprehensive investigation of these interactions has been performed in the study to demonstrate that the presence of these cations in small quantities effectively catalyzes the epoxy-amine reactions. The energetic analysis of different metal-epoxy-amine complexes suggests the inhibitory nature of Al³⁺ toward the extent of cross-linking.

Poly(vinyl alcohol) (PVA) films have been widely used as flexible matrixes in advanced optical materials. Most studies concern the rigidification strategy of PVA films, while the physicochemical properties of inside bound water are ignored. In this study, we have employed lumichrome as the fluorescent probe to explore the acid-base property of bound water, which was demonstrated to exhibit an enhanced proton-accepting ability than bulk water, evidenced by the promoted deprotonation of lumichrome in the ground state. Decreasing the water content in a PVA film is demonstrated to further improve the proton-accepting ability. Different from that in bulk solution, a selective prototropism of lumichrome is determined in PVA films, which is induced by the formation of an anchored lumichrome-PVA complex through three hydrogen bonds. This work first points out the enhanced proton-accepting ability of bound water in PVA films, opening a new avenue for the development of flexible optical materials based on proton transfer.

The hydrophilicity of two-dimensional (2D) transition-metal carbides, carbonitrides, and nitrides (MXene) nanochannels plays a critical role in water transport during filtration, yet its specific effects on MXene membranes remain inadequately understood. Herein, we systematically investigated water transport through Ti₃C₂T_X MXene nanochannels using molecular dynamics simulations coupled with experimental validation, addressing a significant knowledge gap in MXene-based separation membranes. Our simulations demonstrated that strong interactions between water molecules and hydrophilic nanochannel MXene surfaces (Ti₃C₂(OH)₂ MXene or Ti₃C₂(NH)₂ MXene) facilitated the formation of ordered molecular arrangements, substantially improving water permeability. Conversely, hydrophobic nanochannels (Ti₃C₂O₂ MXene or Ti₃C₂F₂ MXene) exhibited disordered water molecule distributions, leading to reduced permeability. Experimental validation corroborated these simulation results, demonstrating a direct correlation between the hydrophilicity of the Ti₃C₂T_X surface and the water flux. The highly hydrophilic Ti₃C₂(OH)₂ MXenes exhibited water flux maximum, whereas the more hydrophobic Ti₃C₂F₂ MXenes had the lowest water flux. By integrating molecular dynamics simulations with experimental analyses, we gained comprehensive insights into the influence of nanochannel hydrophilicity on water transport mechanisms in MXene membranes. These findings provide critical guidelines for designing high-performance MXene-based membranes for advanced water treatment and separation applications.

Passive and targeted delivery of peptides to cells and organelles is a fundamental biophysical process controlled by membranes surrounding biological compartments. Embedded proteins, phospholipid composition, and solution conditions contribute to targeted transport. An anticancer peptide, NAF-1^44-67, permeates to cancer cells but not to normal cells. The mechanism of this selectivity is of significant interest. However, the complexity of biomembranes makes pinpointing passive targeting mechanisms difficult. To dissect contributions to selective transport by membrane components, we constructed simplified phospholipid vesicles as plasma membrane (PM) models of cancer and normal cells and investigated NAF-1^44-67 permeation computationally and experimentally. We use atomically detailed simulations with enhanced sampling techniques to study kinetics and thermodynamics of the interaction. Experimentally, we study the interaction of the peptide with large and giant unilamellar vesicles. The large vesicles were investigated with fluorescence spectroscopy and the giant vesicles with confocal microscopy. Peptide permeation across a model of cancer PM is more efficient than permeation across a PM model of normal cells. The investigations agree on the mechanism of selectivity, which consists of three steps: (i) early electrostatic attraction of the peptide to the negatively charged membrane, (ii) the penetration of the peptide hydrophobic N-terminal segment into the lipid bilayer, and (iii) exploiting short-range electrostatic forces to create a defect in the membrane and complete the permeation process. The first step is kinetically less efficient in a normal membrane with fewer negatively charged phospholipids. The model of a normal membrane is less receptive to defect creation in the third step.

Mitochondrial neurogastrointestinal encephalopathy (MNGIE) is a rare metabolic disorder caused by missense mutations in the TYMP gene, leading to the loss of human thymidine phosphorylase (HTP) activity and subsequent mitochondrial dysfunction. Despite its well-characterized biochemical basis, the molecular mechanisms by which MNGIE-associated mutations alter HTP's structural stability, dynamics, and substrate (thymidine) binding remain unclear. In this study, we employ a multiscale computational approach, integrating AlphaFold2-based structural modeling, all-atom and coarse-grained molecular dynamics (MD) simulations, protein-ligand (HTP-thymidine) docking, HTP-thymidine complex simulations, binding free-energy landscape analysis, and systematic mutational profiling to investigate the impact of key MNGIE-associated mutations (R44Q, G145R, G153S, K222S, and E289A) on HTP function. Analyses of our long-duration multiscale simulations (comprising 9 μs coarse-grained, 1.2 μs all-atom apo HTP, and 1.2 μs HTP-thymidine complex MD simulations) and physicochemical properties reveal that while wild-type HTP maintains structural integrity and strong thymidine-binding affinity, MNGIE-associated mutations induce substantial destabilization, increased flexibility, and reduced enzymatic efficiency. Free-energy landscape analysis highlights a shift toward less stable conformational states in mutant HTPs, further supporting their functional impairment. Additionally, the G145R mutation introduces steric hindrance at the active site, preventing thymidine binding and causing off-site interactions. These findings not only provide fundamental insights into the physicochemical and dynamic alterations underlying HTP dysfunction in MNGIE but also establish a computational framework for guiding future experimental studies and the rational design of therapeutic interventions aimed at restoring HTP function.

Nanopore sensing relies on associating the measured current signals with specific features of the target molecules. The diversity of amino acids presents significant challenges in detecting and sequencing peptides and proteins. The hollow and uniform tubular structure of single-walled carbon nanotubes (SWCNTs) makes them ideal candidates for nanopore sensors. Here, we demonstrate by molecular dynamics simulations the discrimination and translocation of charged proteinogenic amino acids through the nanopore sensor formed by inserting a SWCNT into lipid bilayers. Moreover, our analysis suggests that the current blockade is influenced not only by excluded atomic volume but also by noncovalent interactions between amino acids and SWCNT during similar helical translocation. The presence of noncovalent interactions enhances the understanding of current differences in nanopore translocation of molecules with similar excluded atomic volume. This finding provides new perspectives and applications for the optimal design of SWCNT nanopore sensors.

Conjugated polymers are indispensable building blocks in a variety of organic electronics applications such as solar cells, light-emitting diodes, and field-effect transistors. Poly[N-9'-heptadecanyl-2,7-carbazole-alt-5,5-(4',7'-di-2-thienyl-2',1',3'-benzothiadiazole)] (PCDTBT) is a carbazole-benzothiadiazole-based copolymer with a donor-acceptor structure, consisting of electron-donating and electron-withdrawing subunits and featuring a low band gap. In this work, the General Amber Force Field is extended in two ways, specifically for modeling PCDTBT. First, a set of partial atomic charges is derived that mimic a long chain and adequately describe different conformations that may be encountered in a bulk environment. Second, torsional terms are reparametrized for all dihedral angles in the backbone via ab initio computations. Subsequently, a series of large-scale Molecular Dynamics simulations are employed to construct and equilibrate bulk ensembles of three PCDTBT oligomers using different starting conformations of the oligomer chains. Several structural properties are computed, namely mass density, chain stiffness (through persistence length and Kuhn segment length), and glass transition temperature. Our results are in good agreement with available literature data, demonstrating the suitability of the new parametrization.

Pterin (Ptr) is the model compound of aromatic pterins, which are efficient photosensitizers present in human skin and are able to oxidize biomolecules upon UVA irradiation. Photosensitization involves chemical alteration of a biomolecule as a result of the initial absorption of radiation by another chemical species, the photosensitizer. Under anaerobic conditions, Ptr reacts with thymine (T) to form photoadducts (T-Ptr). In this work, we present a method to prepare and purify T-Ptr adducts, using 2'-deoxythymidine 5'-monophosphate (dTMP) and single stranded oligonucleotide 5'-d(TTTTT)-3' (dT₅), and investigate their photosensitizing properties. Interestingly, the Ptr moiety, when attached to T, retains its photophysical properties. The adduct dTMP-Ptr, upon excitation, forms singlet and triplet excited states, the latter being capable of transferring energy to dissolved O₂ and generating singlet oxygen, with an efficiency similar to Ptr. In air-equilibrated solutions, both dTMP-Ptr and dT₅-Ptr adducts can photosensitize the oxidation of tryptophan and 2'-deoxyguanosine 5'-monophosphate, two of the main targets of photosensitization in biological systems, with efficiencies close to that of free Ptr. The mechanisms involved in the oxidation of biomolecules can be either type I (electron transfer) or type II (singlet oxygen).