Journal of Chemical Physics最新文献

This work presents a comprehensive theoretical investigation of key isomers of C2H4N2 using state-of-the-art quantum chemical methods. The objective is to characterize their molecular structures, spectroscopic constants, and electronic energies and to elucidate plausible formation and destruction pathways, providing data critical for astrochemical and atmospheric detection. High-accuracy ab initio methods were employed, notably CCSD(T)-F12/cc-pVTZ-F12 for optimized geometries. Additional calculations were performed at the CCSD(T)/aug-cc-pVTZ, CCSD(T)/cc-pVTZ, MP2/aug-cc-pVTZ, and CIS levels. Intrinsic reaction coordinate calculations were performed at the B3LYP/6-31G(d,p) level to explore reaction pathways. The Zero-Point Energy (ZPE)-corrections were determined for all the isomers considered. Six low-energy C2H4N2 isomers were identified, all within 1 eV of the global minimum. Among them, methylcyanamide (MCA) exhibits the lowest relative energy (∼0.2 eV) and a significant electric dipole moment of 5.00 D, making it a strong candidate for detection in gas-phase environments. The rotational constants for MCA, computed at the level of CCSD(T)-F12/cc-pVTZ-F12, are Ae = 34 932.44 MHz, Be = 4995.31 MHz, and Ce = 4520.30 MHz. The V3 torsional barrier was found to be 631.19 cm-1. Centrifugal distortion constants were computed up to sextic order for all isomers. Formation pathways for MCA-such as CH3N + HCN → CH3NHCN-and related isomers were characterized. The combination of large dipole moments and distinct rotational signatures supports the detectability of MCA and related C2H4N2 isomers via radioastronomy, IR, and MW spectroscopy. Isomerization and reaction pathways involving radical-neutral and neutral-neutral processes were found to be key to their formation in gas-phase environments. These results offer a robust foundation for future observational and modeling efforts.

The energetic plausibility of photoinduced Penning-type ionization in collisional complexes between high-n Rydberg carbon atoms (C*s) and small molecules, such as CO and OH, is assessed. Experimental ionization potentials and vibrational constants of CO yield two transitions at 450.23 ± 0.04 nm and 498.33 ± 0.05 nm, for v = 0 and 1, respectively, while the ionization potential and spectroscopic constants of OH give rise to transitions at 705.57 ± 0.15 nm and 712.56 ± 0.15 nm, corresponding to the 2Π3/2 and 2Π1/2 states of OH. These predicted wavelengths closely match diffuse interstellar bands observed at 450.18, 498.47, 706.08, and 711.99 nm, suggesting that C* collisional complexes with interstellar molecules may contribute to selected astrophysical absorption features. Taken together, these results suggest an energetically plausible and physically motivated connection between Rydberg-mediated interactions and selected spectroscopic features under interstellar conditions, particularly in regions where C+ recombination and CO or OH coexist. Although direct experimental detection of such transient complexes has not yet been achieved, the convergence of energetic feasibility, spectral alignment, and environmental plausibility defines a testable framework. Continued progress in many-body theory, ultrahigh-resolution spectroscopy, and astronomical observations will be essential to further constrain the role of Rydberg complexes in interstellar chemistry.

A disordered quasi-liquid layer of water is thought to cover the ice surface, but many issues, such as its onset temperature, its thickness, or its actual relation to bulk liquid water, have been a matter of unsettled controversy for more than a century. In this perspective article, current computer simulations and experimental results are discussed under the light of a suitable theoretical framework. It is found that using a combination of wetting physics, the theory of intermolecular forces, statistical mechanics, and out-of-equilibrium physics, a large number of conflicting results can be reconciled and collected into a consistent description of the ice surface. This helps understand the crucial role of surface properties in a range of important applications, from the enigmatic structure of snow crystals to the slipperiness of ice.

Motivated by a recently synthesizable class of active interfaces formed by linked self-propelled colloids, we investigate the dynamics and fluctuations of a phoretically (chemically) interacting active interface with roto-translational coupling. We enumerate all steady-state shapes of the interface across parameter space and identify a regime where the interface acquires a finite curvature, leading to a characteristic "C-shaped" topology, along with persistent self-propulsion. In this phase, the interface height fluctuations obey Family-Vicsek scaling but with novel exponents: a dynamic exponent zh ≈ 0.5, a roughness exponent αh ≈ 0.9, and a super-ballistic growth exponent βh ≈ 1.7. In contrast, the orientational fluctuations of the colloidal monomers exhibit a negative roughness exponent, reflecting a surprising smoothness law, where steady-state fluctuations diminish with increasing system size. Together, these findings point toward a unique non-equilibrium universality class associated with self-propelled interfaces of non-standard shape.

Understanding how specific molecular substructures control chemical behavior is central to rational molecular design and the development of new materials. However, most current predictive models offer limited mechanistic resolution at the fragmental level. We present a conceptually novel use of fragment-based structure-activity reasoning, based on systematically perturbing a parent molecule, to quantify fragment-level contributions to both a specific mechanistic action and a broader functional outcome. As a case study, we investigated local structural contributions to pyronaridine (PY), a clinically used antimalarial drug with a mechanistically distinctive mode of inhibition of hematin crystal growth via step-bunching. Chemically plausible PY molecular analogs have been computationally generated by selectively removing or substituting functional groups hypothesized to influence either step-bunching mechanisms or whole-parasite blood-stage activity. For each analog, we predicted the probability of four different crystal-growth inhibition mechanisms using a centroid-based similarity model based on a small dataset of experimentally verified crystal-growth inhibitors. The blood-stage antimalarial activity has also been estimated using the MAIP platform. A systematic comparison of molecular analogs revealed that step-bunching mechanisms depend primarily on two protonated pyrrolidines, with chlorobenzene as a strong secondary contributor. In contrast, antimalarial activity is more distributed, relying on coordinated interactions between aromatic-heteroatom scaffolds and an amine linker. The obtained results demonstrate that our approach can disentangle position-specific and cooperative fragmental effects, offering mechanistically interpretable guidance for the design of mechanism-optimized inhibitors. The framework might be broadly applicable across chemical and materials domains where linking local structure to specific mechanisms is essential.

Hemoglobin-oxygen equilibrium is normally studied within the grand-canonical ensemble, which assumes that each hemoglobin molecule is immersed in a reservoir of unbound oxygen molecules in the plasma. We show that this assumption is incorrect inside the RBC (red blood cell or erythrocyte), where the hemoglobin concentration is larger than the concentration of unbound oxygen in plasma. We suggest a better model, where a single hemoglobin and a few oxygen molecules around it reach a canonical equilibrium at a fixed volume (determined from the RBC structure) and a fixed temperature. The basic models of hemoglobin-oxygen equilibrium-Pauling's model and the Monod-Wyman-Changeux model-can be reformulated for this canonical situation. They predict cooperative interaction energies that are significantly lower than predictions of the same models in the grand-canonical ensemble. Larger cooperative energies, in particular, those predicted by the grand-canonical ensemble, lead to instabilities (cascade processes) in oxygen release within the canonical approach. Oxygen-binding fluctuations within this approach are sizably smaller than those in the grand-canonical situation. These results suggest that the hopping diffusion of oxygen from one hemoglobin to another may play a role in oxygen diffusion within the RBC.

We present an open-source, graphics processing unit (GPU)-accelerated software implementation of the Uneyama-Doi model (UDM) for studying the collective dynamics of block copolymer blends and solutions. The UDM provides a field-theoretic framework that includes the entropy of mixing, binary interactions between segment species, and molecular connectivity, thereby capturing interfacial properties even in the strong-segregation regime. Our implementation utilizes a semi-implicit time-stepping scheme, incorporates thermal noise, and employs a concentration-conserving regularization algorithm that maintains non-negative concentrations. Spatial derivatives and convolutions are computed via optimized CUDA-based pseudo-spectral methods, enabling simulations of systems spanning tens of polymer end-to-end distances and thousands of molecular relaxation times within hours on a single GPU. We validate the implementation against established results, including the mean-field phase diagram of diblock copolymers, structure factors of disordered systems, and the fluctuation-induced order-disorder transition for symmetric copolymers. Dynamic simulations reproduce experimentally observed amphiphilic morphologies, including micellar lattices, vesicles, and phase-separated structures. The software provides an efficient and versatile tool for investigating equilibrium and nonequilibrium behavior of complex polymer systems.

We propose the powerful integration of the Hybrid Monte Carlo (hybridMC) algorithm and well-tempered metadynamics. This new algorithm, hybridMC-MetaD, enhances the flexibility and applicability of metadynamics by allowing for the utilization of a wider range of collective variables (CVs), namely non-differentiable CVs. We demonstrate the usage of hybridMC-MetaD through five examples of rare events in molecular dynamics (MD) simulations, including a rare transition in a model potential system, condensation of the argon system, crystallization in a nearly hard sphere system, a nearly hard bipyramid system, and a colloidal suspension. By taking advantage of hybridMC, which combines MD and MC, we are able to bias the transitions along non-differentiable CVs for all five cases, which would be unfeasible with conventional MD simulations. Enabled by metadynamics, we observed significant acceleration of the phase transitions and calculated free energy barriers using the hybridMC-MetaD simulation data. For the nearly hard bipyramid system, whose crystallization is primarily driven by entropy, we report the free energy surface for the first time. Through our case studies, we show that our hybridMC-MetaD scheme reduces the complexity of using metadynamics and increases its accessibility. We believe the hybridMC-MetaD algorithm will stimulate greater interest in and foster broader applications of metadynamics.

We combine differential scanning calorimetry, broadband dielectric spectroscopy, and 1H and 2H nuclear magnetic resonance (NMR) for component-selective studies of molecular reorientation and diffusion in mixtures comprising the dipeptide N-acetyl-glycine-methylamide (NAGMA), which is commonly considered as a protein-backbone model, and deuterated water in a broad temperature range of 140-340 K. For a 7.5 m NAGMA-D2O mixture, crystallization is largely avoided, revealing a separation of the dipeptide-dominated α process, which describes the glassy slowdown, from the water-caused ν process. The latter shows a dynamical crossover at Tg = 175 K and thermally activated motion governed by a temperature-independent Gaussian-like distribution of activation energies with a mean value of Em = 0.49 eV and a standard deviation of σE = 0.035 eV in the glassy state. Detailed NMR analyses show that, despite the time-scale separation, rotational-translational coupling is found for water dynamics at least down into the weakly supercooled regime. Moreover, NMR reveals that the ν process involves a quasi-isotropic reorientation of basically all water molecules even below Tg, while slow or restricted water reorientation does not occur. Based on our findings, we discuss the temperature-dependent coupling of the dipeptide and water motions. For a 2 m NAGMA-D2O mixture, partial crystallization leads to an enhanced temperature dependence. Disentangling the rotational motions of the liquid and crystalline water fractions, we find that the liquid fraction exhibits Arrhenius behavior with Ea = 0.89 eV until a dynamical crossover again occurs upon cooling, while the reorientation of the ice fraction highly resembles that in hexagonal bulk ice.