Journal of Chemical Physics最新文献

Condensed phase explosives typically contain defects such as voids, bubbles, and pores; this heterogeneity facilitates the formation of hot spots and triggers decomposition reaction at low densities. The study of the thermal decomposition mechanisms of explosives at different densities has thus attracted considerable research interest. Gaining a deeper insight into these mechanisms would be helpful for elucidating the detonation processes of explosives. In this work, we developed an ab initio neural network potential for the FOX-7 system using machine learning method. Extensive large-scale (1008 atoms) and long-duration (nanosecond timescale) deep potential molecular dynamics simulations at different densities were performed to investigate the effect of the density on the thermal decomposition mechanism. The results indicate that the initial reaction pathway of the FOX-7 explosives is the cleavage of the C-NO2 bond at different densities, while the frequency of C-NO2 bond cleavage decreases at higher density. Increasing the initial density of FOX-7 significantly increases the reaction rate during the initial decomposition and the formation of final products. However, it leads to a decrease in released heat and has minimal impact on the decomposition temperature. In addition, by analyzing the molecular dynamics trajectories and conducting quantum chemical calculations, we identified two lower-barrier production pathways to produce the CO2 and N2.

Natural deep eutectic solvents (NADESs) are environmentally friendly green solvents and hold great promise in the pharmaceutical industry. The secondary structure of a protein, lysozyme, follows a non-monotonous behavior in aqueous glyceline (choline chloride + glycerol) as the wt. % of water is increased. However, it is unclear how the hydration affects the stability of the protein in a non-linear way. In this work, we have performed all-atom molecular dynamic simulations for 1 μs with the lysozyme protein in an aqueous glyceline deep eutectic solvent (DES) by varying the wt. % of water. The simulated radius of gyration, Rg, values can qualitatively reproduce the protein behavior such that the Rg increases initially with an increase in wt. % of water, reaches the peak at 40 wt. %, and then gradually decreases with dilution. Several other properties, including root mean square deviation, root-mean square fluctuation, secondary structure of the protein, and solvent accessible surface area, are examined to explore the NADES effect on the protein structure. Next, we analyze the hydrogen bond profile of intra-protein and among various interspecies, e.g., protein-DES, DES-DES, protein-water, and water-water. The variation in protein-protein hydrogen bonds with concentrations can qualitatively explain the non-linear conformational dependence of the protein. The radial distribution function analyses show various microscopic structures formed due to the DES and water interaction, which play a critical role in protein behavior. This study indicates that at lower wt. % of water, the protein is constrained in a strong hydrogen bond network formed by glycerol and water molecules, resulting in a lower Rg. As the wt. % of water increases, the protein-water interaction drives the protein to expand, reflecting an increasing Rg. At sufficiently higher wt. % of water, the DES constituent and the water molecules interact strongly with the protein, resulting in a decrease in Rg. Overall, the investigation offers a microscopic insight into the protein conformation in DES.

Electron spin resonance indicates that the unpaired electron in the methanol radical cation is delocalized, however, the molecular geometry has not been experimentally resolved. In this work, high level, state-of-the-art computations at the finite temperature density functional theory and highly correlated CCSD(T) levels indicate that a syn-periplanar conformation of the H-C-O-H bonds, in which the C-H and O-H bonds eclipse each other, is a three-fold global minimum in the potential energy surface for internal rotation of the O-H bond. We show that vicinal hyperconjugation between the orbitals in the C-H bonds and in the oxygen atom is responsible for this puzzling conformational preference. The transition state for the rotation yields an ≈0.6 kcal/mol rotational barrier, which matches the thermal energy at room conditions and, therefore, renders the O-H bond a free rotor. The molecular wave function has a moderate multireference character with the oxygen atom acting as the preferred spot for static correlation.

The instant crystallization of semi-crystalline polymers has become possible following the recent advances in Fast Scanning Calorimetry (FSC) and enables us to make a bridge between the time scale available experimentally with those accessible with computer simulations. Although the FSC observations have provided new information on the crystallization kinetics and evolution of the crystals, the molecular details on the chain exchange events between the ordered and disordered domains of crystals have remained elusive. Using molecular dynamics simulations, we examined the detailed chain dynamics and thermodynamics of polyamide 6 (PA6) system under two heating treatments: (i) quenching PA6 melt deeply below the melting temperature Tm and (ii) annealing the resulting quenched system to a temperature close to Tm. We categorized the chains into mobile amorphous fraction (MAF) and rigid amorphous fraction (RAF), based on the length of consecutive chain's bond angles in the trans state. In the deep quenched system close to the glass transition temperature Tg, the mobility of the MAF chains is strongly suppressed and they remain in the glassy state. However, upon rising the temperature close to melting temperature, the system undergoes recrystallization, leading to the coexistence of RAF and supercooled liquid MAF chains. The highly mobile unentangled MAF chains explore the interphase domains, and during the late-stage of crystallization, they are thermally translocated into the lamella by reducing the fold number of RAF chains. The chain mobility in the annealed system could potentially lead to improved biodegradation in semi-crystalline chains.

The release of Ag+ ions into the environment through silica layers is a promising strategy for the development of anti-microbial surface coating devices. The aim of the present study is to provide some insight into the elementary mechanisms of diffusion of Ag+ ions through silica with the objective of proposing control strategies. Thanks to the development of interaction potentials based on neural networks, the diffusion processes were studied via molecular dynamics simulations. Silver diffusion was found to be anomalous and sub-diffusive, the origin of which could be attributed to deceleration and temporal anti-correlations. This sub-diffusion has been attributed primarily to the disordered nature of the silica matrix. Furthermore, it is magnified by the presence of coordination defects within the silica matrix. These defects, in particular the under-coordinated oxygen atoms, act as traps for Ag+ by forming O-Ag bonds, thereby limiting the jump length and retaining the ion for long duration. By comparison with existing diffusion models, the diffusion mechanism in the absence of defects appears to be of the fractional Brownian motion type, substantially modified by the presence of defects. Two possible approaches have emerged to tune the release of Ag+ ions through the silica layer: the monitoring of the number of defects and the opening/closing of diffusion paths via, e.g., a modification of the silica density.

Manganese is one of the most intriguing elements showing multiple magnetic phases. In order to shed some light on the complex behavior, the manganese dimer has been the focus of extensive interest in theoretical research. Various quantum techniques have been utilized to comprehend the characteristics of the Mn dimer. Several approaches and functionals have been employed that suggest that the ferromagnetic (FM) state is its lowest energy configuration. Nevertheless, these findings are inconsistent with the experimental results showing that Mn2 has an antiferromagnetic (AFM) Σg+1 configuration at an interatomic Mn-Mn distance of dMn-Mn = 3.40 Å. This work presents a comparative assessment of outcomes obtained through several levels of the exchange-correlation functional: generalized gradient approximation (GGA), meta-GGA, GGA+U, and the hybrid Heyd-Scuseria-Ernzerhof (HSE06), the Perdew-Burke-Ernzerhof 0, and the Becke, 3-parameter, Lee-Yang-Parr. The results of our investigation are discussed based on previous theoretical and experimental reports. We found that the best description is obtained with the hybrid HSE06 functional. The Mn2 has a FM coupling at short distances and the characteristic AFM Σg+1 state at dMn-Mn = 3.27 Å. Furthermore, we obtained a magnetic moment (μ) per Mn atom of μ = 4.527 μB, a stretching frequency of ω = 80 cm-1, and a binding energy of Eb = -195 meV, which is in good agreement with the experimental results.

We present a mechanistic study of hole spin dynamics in colloidal cadmium selenide (CdSe) nanosheets, aiming to gain insights into the elusive interplay between two counteracting surface effects, i.e., hole-trapping interaction [between the valence-band heavy-hole (HH) state and its nearby localized surface trap (LST) state] vs spin-exchange interaction [between the HH spin state and the surface dangling-bond spin (DBS) state]. Differently from our previous work adopting a strategy of ligand engineering [see Wu et al., Adv. Opt. Mater. 12, 2400583 (2024)], we here implement an alternative strategy of element doping to regulate the LST and DBS states in the Ag+-doped CdSe nanosystem. It is observed that the hole spin-flip lifetime is shortened when the Ag+-doping level is elevated, demonstrating that the hole-DBS exchange interaction can effectively compete against the coexisting hole-LST trapping interaction, mainly due to the doping-induced increase in the density of the DBS state. Markedly, this observation is contrary to that in the ligand-engineering case, where the hole-trapping interaction plays a predominant role due to the strong ligand/CdSe orbital hybridization. This work elucidates the interplay between the two surface effects and enriches the understanding about the subtle DBS-related effect, providing valuable mechanistic information for rational design and optimization of spintronic applications based on colloidal nanostructures.

The binding behavior of 3-methylcyclopentane-1,2-dione, a cyclic α-diketone with a caramel-like aroma, was investigated to elucidate molecular mechanisms of olfactory recognition. Using Fourier-transform microwave spectroscopy complemented with quantum chemical calculations, the structures of 3-methylcyclopentane-1,2-dione and its monohydrate were determined, revealing the preferred conformation of the monomer and structural changes upon complexation with water. Intramolecular hydrogen bond weakening was observed, indicating significant rearrangements, as further supported by non-covalent interaction and quantum theory analyses. Molecular docking demonstrates how these structural adaptations facilitate ligand-protein interactions, providing a microscopic framework for understanding diketone binding within odorant-binding proteins.

Membrane protein folding in the viscous microenvironment of a lipid bilayer is an inherently slow process that challenges experiments and computational efforts alike. The folding kinetics is moreover associated with topological modulations of the biological milieu. Studying such structural changes in membrane-embedded proteins and understanding the associated topological signatures in membrane leaflets, therefore, remain relatively unexplored. Herein, we first aim to estimate the free energy barrier and the minimum free energy path (MFEP) connecting the membrane-embedded fully and partially inserted states of the bacteriorhodopsin fragment. To achieve this, we have considered independent sets of simulations from membrane-mimicking and membrane-embedded environments, respectively. An autoencoder model is used to elicit state-distinguishable collective variables for the system utilizing membrane-mimicking simulations. Our in-house Expectation Maximized Molecular Dynamics algorithm is initially used to deduce the barrier height between the two membrane-embedded states. Next, we develop the Geometry Optimized Local Direction search as a post-processing algorithm to identify the MFEP and the corresponding peptide conformations from the autoencoder-projected trajectories. Finally, we apply a graph attention neural network (GAT) model to learn the membrane surface topology as a function of the associated peptide structure, supervised by the membrane-embedded simulations. The resultant GAT model is then utilized to predict the membrane leaflet topology for the peptide structures along MFEP, obtained from membrane-mimicking simulations. The combined framework is expected to be useful in capturing key phenomena accompanying folding transitions in membranes. We discuss opportunities and avenues for further development.

Accurate prediction of polymer properties using molecular dynamics (MD) simulations requires a properly relaxed starting structure. Polymer models built from scratch by specialized algorithms (self-avoiding random walk, Monte Carlo, etc.) are far from relaxed and, moreover, often possess a large number of structural defects: close contacts between atoms, wrong bond distances, voids, unfavorable molecular conformations or packing, etc. This is especially problematic for ring-containing polymers whose initial structures also include ring spearing (bonds passing through cycles, including benzene rings). All these defects must be eliminated before running an MD simulation to correctly predict polymer properties. Short MD simulations can be enough to remove close contacts; however, ring spearing elimination and general structure relaxation cannot be achieved this way. In this work, we propose α-Replica Exchange MD (α-REMD)-a Hamiltonian replica-exchange MD protocol that reliably eliminates ring spearing defects and performs a general relaxation of the system. Its efficiency is demonstrated on five polyethersulfones whose initial geometries contained numerous ring intersections that were completely removed by α-REMD.