Journal of Chemical Physics最新文献

{"title":"Boron-based B3Zn6- alloy cluster as a hybrid between prismatic and sandwich-like structures: Stabilization of a linear B3 chain motif using electronic transmutation.","authors":"Fang-Lin Liu, Shu-Juan Gao, Hua-Jin Zhai","doi":"10.1063/5.0257359","DOIUrl":"https://doi.org/10.1063/5.0257359","url":null,"abstract":"<p><p>Doping boron clusters with metallic elements can tune the structural, electronic, and bonding properties. We report on the computational design of a zinc-rich D3h (1A1') B3Zn6- alloy cluster, whose global-minimum structure is a hybrid between prismatic, sandwich-like, and core-shell tubular geometries. The binary cluster features a linear B3 chain along its C3 axis, as well as three lateral Zn-Zn dimers, in which a central B atom is sandwiched by two quasi-planar BZn3 units in an eclipsed form. Chemical bonding analyses show that the B3 chain motif has Lewis-type B-B σ single bonds and a pair of orthogonal three-center two-electron (3c-2e) π bonds, collectively leading to a B-B bond order of two. Stabilizing a boron single chain is scarce in the literature, as is observing a series of double B=B bonds in a monoatomic chain fashion. The triangular pyramid BZn3 units are each in a unique triplet σ2σ*1σ*1 configuration, thus rendering σ aromaticity to the cluster according to the reversed 4n Hückel rule. It is proposed that the alloy cluster can be rationalized using the concept of electronic transmutation, wherein a close chemical analogy to the carbon dioxide (CO2) molecule is established.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 11","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143657284","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Reaction-limited evaporation for the color-gradient lattice Boltzmann model.","authors":"Gaurav Nath, Othmane Aouane, Jens Harting","doi":"10.1063/5.0253799","DOIUrl":"https://doi.org/10.1063/5.0253799","url":null,"abstract":"<p><p>We propose a reaction-limited evaporation model within the color-gradient lattice Boltzmann (LB) multicomponent framework to address the lack of intrinsic evaporation mechanisms. Unlike diffusion-driven approaches, our method directly enforces mass removal at the fluid interface in a reaction-limited manner while maintaining numerical stability. Using the inherent color-gradient magnitude and a single adjustable parameter, evaporation sites are chosen in a computationally efficient way with seamless mass exchange between the components, with no change to the core algorithm. Extensive validation across diverse interface geometries and evaporation flux magnitudes demonstrates high accuracy, with errors below 5% for unit density ratios. For density contrasts, the method remains robust in the limit of smaller evaporation flux magnitudes and density ratios. Our approach extends the applicability of the color-gradient LB model to scenarios involving reaction-limited evaporation, such as droplet evaporation on heated substrates, vacuum evaporation of molten metals, and drying processes in porous media.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 11","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143657396","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"What have the XH4+ (X = C, Si, Ge) ions in common? An updated summary.","authors":"Tanmoy Mondal, Alberto Guerra-Barroso, Jianjun Fang, Jing Li, António J C Varandas","doi":"10.1063/5.0252880","DOIUrl":"https://doi.org/10.1063/5.0252880","url":null,"abstract":"<p><p>A high level quantum mechanical study has been performed to explore the structural rearrangement and relative stability of the XH4+ (X = C, Si, Ge) radical cations at their X̃2T2 ground electronic states. All the stationary points located on the lowest adiabatic sheet of the Jahn-Teller (JT) split X̃2T2 state are fully optimized and characterized by performing harmonic vibrational frequency calculations. Five JT distorted stationary points with D2d(B22), C3v(A12), C2v(B22), and Cs(A'2) symmetries are located on the CH4+ ground state potential energy surface (PES), whereas four such structures are found on each of the SiH4+ and GeH4+ PESs. While the C2v(B22) isomer is found to be a global minimum and the Cs(A'2) one as a transition state for CH4+, the nature of them is reversed for SiH4+ and GeH4+. In particular, the Cs(A'2) stationary points are now global minima for the latter pair of radical cations, and C2v(B22) represents the transition state. Attempts are being made to understand such inconsistent findings via a combination of JT and epikernel principles. The barriers between equivalent C2v(B22) global minimum structures for CH4+ are found to be low, and thus CH4+ undergoes rapid interconversion along cyclic exchange of three hydrogen atoms via Cs transition state. The general features of the ground state PESs of SiH4+ and GeH4+ are similar. The pseudorotation between the Cs lowest energy structures undergoes along SiH2 and GeH2 wagging motions via C2v(B22) transition state for SiH4+ and GeH4+, respectively.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 11","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143663600","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An ab initio deep neural network potential to study the effect of density on the thermal decomposition mechanism of FOX-7.","authors":"Yinhua Ma, Nan Wang, Zhiyang Chen, Li Zhao, Runze Liu, Danna Song, Huaxin Liu, Jianyong Liu","doi":"10.1063/5.0256140","DOIUrl":"https://doi.org/10.1063/5.0256140","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 11","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143657283","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Hydrogen-bond induced non-linear size dependence of lysozyme under the influence of aqueous glyceline.","authors":"Ivy Das Sarkar, Arnab Sil, Biswajit Guchhait, Suman Das","doi":"10.1063/5.0251283","DOIUrl":"https://doi.org/10.1063/5.0251283","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 11","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143657359","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The puzzling structure and bonding of the methanol radical cation.","authors":"Santiago Gómez, Jhoan Londoño-Restrepo, Albeiro Restrepo","doi":"10.1063/5.0250493","DOIUrl":"https://doi.org/10.1063/5.0250493","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 11","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143657448","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ultrafast fragmentation dynamics of carbon dioxide trication induced by an intense laser field: Transient deformation route vs direct Coulomb repulsion.","authors":"Weiqing Xu, Ruichao Dong, Xincheng Wang, Ahai Chen, Yuhai Jiang","doi":"10.1063/5.0255127","DOIUrl":"https://doi.org/10.1063/5.0255127","url":null,"abstract":"<p><p>We present a combined experimental and theoretical study of the detailed fragmentation process of CO23+→ CO2+ + O+ induced by an intense laser field. Through multicoincidence fragment measurements together with ab initio molecular dynamics (AIMD) simulations, we find that a transient deformation route appears in competition with the expected Coulomb explosion. The AIMD simulations visually demonstrate that CO23+ undergoes several bending vibrations in ∼50-480 fs, and in the final dissociation stages, the electron density distribution in three-dimensional space migrates from the O ion to the C ion, while the bond strength rapidly decreases to 0, resulting in bond breaking assisted by the asymmetric stretching vibrations. The measured kinetic energy releases are in general agreement with AIMD simulations, and the deduced amount of energy transfer into the vibrational and rotational degrees of freedom of CO2+ is about 3 eV less than that estimated by the Coulomb potential.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 11","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143673978","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A comparison of probabilistic generative frameworks for molecular simulations.","authors":"Richard John, Lukas Herron, Pratyush Tiwary","doi":"10.1063/5.0249683","DOIUrl":"https://doi.org/10.1063/5.0249683","url":null,"abstract":"<p><p>Generative artificial intelligence is now a widely used tool in molecular science. Despite the popularity of probabilistic generative models, numerical experiments benchmarking their performance on molecular data are lacking. In this work, we introduce and explain several classes of generative models, broadly sorted into two categories: flow-based models and diffusion models. We select three representative models: neural spline flows, conditional flow matching, and denoising diffusion probabilistic models, and examine their accuracy, computational cost, and generation speed across datasets with tunable dimensionality, complexity, and modal asymmetry. Our findings are varied, with no one framework being the best for all purposes. In a nutshell, (i) neural spline flows do best at capturing mode asymmetry present in low-dimensional data, (ii) conditional flow matching outperforms other models for high-dimensional data with low complexity, and (iii) denoising diffusion probabilistic models appear the best for low-dimensional data with high complexity. Our datasets include a Gaussian mixture model and the dihedral torsion angle distribution of the Aib9 peptide, generated via a molecular dynamics simulation. We hope our taxonomy of probabilistic generative frameworks and numerical results may guide model selection for a wide range of molecular tasks.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 11","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143674053","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Laser spectroscopic study of the electronic states of palladium monoxide (PdO).","authors":"Lei Zhang, Chaofan Li, Wenli Zou, Xianhong Wang, Jianhuang Lv, Jie Yang","doi":"10.1063/5.0256862","DOIUrl":"https://doi.org/10.1063/5.0256862","url":null,"abstract":"<p><p>Among the group 10 transition metal monoxides, only the palladium monoxide (PdO) radical has hitherto eluded detection in optical spectra. In this study, we report the first optical spectra of the gas-phase PdO molecule using the laser-induced fluorescence excitation and single-vibronic-level (SVL) emission spectroscopies. Eight rotationally resolved excitation spectra were observed in 17 800-23 650 cm-1, allowing the determination of the vibrational frequencies and rotational constants for the ground and five highly excited electronic states. Six low-energy Ω states below 3500 cm-1 were identified from the SVL emission spectra and assigned to six spin-orbit components of the X 3Σ- and A 3Π electronic states. Furthermore, high-level ab initio calculations were performed on numerous Λ-S and Ω electronic states to support the assignments from the experimental observations. The spectral results elucidate the bonding characteristics of PdO and provide support for verifying the significant relativistic effect on the bonding of PtO.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 11","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143674065","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular insights into odorant recognition: Rotational and docking studies of 3-methylcyclopentane-1,2-dione and its monohydrate.","authors":"Meng Li, Juan Wang, Sven Herbers, Xiujuan Wang, Hao Wang, Qian Gou, Jens-Uwe Grabow, Geng Zhong","doi":"10.1063/5.0257066","DOIUrl":"https://doi.org/10.1063/5.0257066","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 10","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143624797","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}