Journal of Chemical Physics最新文献_第7页

How the choice of exchange-correlation functional affects DFT-based simulations of the hydrated electron.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-21 DOI: 10.1063/5.0253369

William R Borrelli, Xiaoyan Liu, Benjamin J Schwartz

{"title":"How the choice of exchange-correlation functional affects DFT-based simulations of the hydrated electron.","authors":"William R Borrelli, Xiaoyan Liu, Benjamin J Schwartz","doi":"10.1063/5.0253369","DOIUrl":"https://doi.org/10.1063/5.0253369","url":null,"abstract":"Hydrated electrons are anionic species that are formed when an excess electron is introduced into liquid water. Building an understanding of how hydrated electrons behave in solution has been a long-standing effort of simulation methods, of which density functional theory (DFT) has come to the fore in recent years. The ability of DFT to model the reactive chemistry of hydrated electrons is an attractive advantage over semi-classical methodologies; however, relatively few density functional approximations (DFAs) have been used for the hydrated electron simulations presented in the literature. Here, we simulate hydrated electron systems using a series of exchange-correlation (XC) functionals spanning Jacob's ladder. We calculate a variety of experimental and other observables of the hydrated electron and compare the XC functional dependence for each quantity. We find that the formation of a stable localized hydrated electron is not necessarily limited to hybrid XC functionals and that some hybrid functionals produce delocalized hydrated electrons or electrons that react with the surrounding water at an unphysically fast rate. We further characterize how different DFAs impact the solvent structure and predicted spectroscopy of the hydrated electron, considering several methods for calculating the hydrated electron's absorption spectrum for the best comparison between structures generated using different density functionals. None of the dozen or so DFAs that we investigated are able to correctly predict the hydrated electron's spectroscopy, vertical detachment energy, or molar solvation volume.","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":"143657355","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}

引用次数: 0

Adaptive-precision potentials for large-scale atomistic simulations.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-21 DOI: 10.1063/5.0245877

David Immel, Ralf Drautz, Godehard Sutmann

{"title":"Adaptive-precision potentials for large-scale atomistic simulations.","authors":"David Immel, Ralf Drautz, Godehard Sutmann","doi":"10.1063/5.0245877","DOIUrl":"https://doi.org/10.1063/5.0245877","url":null,"abstract":"Large-scale atomistic simulations rely on interatomic potentials, providing an efficient representation of atomic energies and forces. Modern machine-learning (ML) potentials provide the most precise representation compared to electronic structure calculations, while traditional potentials provide a less precise but computationally much faster representation and, thus, allow simulations of larger systems. We present a method to combine a traditional and a ML potential into a multi-resolution description, leading to an adaptive-precision potential with an optimum of performance and precision in large, complex atomistic systems. The required precision is determined per atom by a local structure analysis and updated automatically during simulation. We use copper as demonstrator material with an embedded atom model as classical force field and an atomic cluster expansion (ACE) as ML potential, but, in principle, a broader class of potential combinations can be coupled by this method. The approach is developed for the molecular-dynamics simulator LAMMPS and includes a load-balancer to prevent problems due to the atom dependent force-calculation times, which makes it suitable for large-scale atomistic simulations. The developed adaptive-precision copper potential represents the ACE-forces with a precision of 10 me V/Å and the ACE-energy exactly for the precisely calculated atoms in a nanoindentation of 4 × 106 atoms calculated for 100 ps and shows a speedup of 11.3 compared with a full ACE simulation.","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":"143663596","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}

引用次数: 0

Transition path and interface sampling of stochastic Schrödinger dynamics. 随机薛定谔动力学的过渡路径和界面采样

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-21 DOI: 10.1063/5.0246727

Robson Christie, Peter G Bolhuis, David T Limmer

引用次数: 0

What have the XH4+ (X = C, Si, Ge) ions in common? An updated summary.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-21 DOI: 10.1063/5.0252880

Tanmoy Mondal, Alberto Guerra-Barroso, Jianjun Fang, Jing Li, António J C Varandas

{"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":"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.","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}

引用次数: 0

Boron-based B3Zn6- alloy cluster as a hybrid between prismatic and sandwich-like structures: Stabilization of a linear B3 chain motif using electronic transmutation. 硼基 B3Zn6- 合金簇是棱柱形结构和三明治状结构的混合体：利用电子嬗变稳定线性 B3 链图案。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-21 DOI: 10.1063/5.0257359

Fang-Lin Liu, Shu-Juan Gao, Hua-Jin Zhai

{"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":"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.","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}

引用次数: 0

Reaction-limited evaporation for the color-gradient lattice Boltzmann model.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-21 DOI: 10.1063/5.0253799

Gaurav Nath, Othmane Aouane, Jens Harting

引用次数: 0

Pareto-based optimization of sparse dynamical systems.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-21 DOI: 10.1063/5.0249780

Gianmarco Ducci, Maryke Kouyate, Karsten Reuter, Christoph Scheurer

引用次数: 0

Unraveling cation-cation "attraction" in argentophilic interaction in 2,2'-bipydine coordinated silver complex.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-21 DOI: 10.1063/5.0258704

Yuan Xu

{"title":"Unraveling cation-cation \"attraction\" in argentophilic interaction in 2,2'-bipydine coordinated silver complex.","authors":"Yuan Xu","doi":"10.1063/5.0258704","DOIUrl":"https://doi.org/10.1063/5.0258704","url":null,"abstract":"The nature of argentophilic interaction in the 2,2'-bipyridine-coordinated silver complex, which manifests counterintuitive cation-cation \"attraction,\" is attributed to ligand stacking and solvation effects in the present article. While charged closed-shell transition metal complexes aggregating spontaneously to form oligomers has long been observed experimentally, the interpretation of the nature of so-called metallophilicity is still ongoing. For the dimer [(2,2'-bpy)2Ag]22+, qualitative electrostatic potential, non-covalent interaction, atoms-in-molecules analyses, and quantitative energy decomposition analysis calculations indicate that the electrostatic repulsion between two like formal charges at silver centers can be overcome by long-range dispersion attraction and short-range electronic correlation from ligands. In addition, delocalizing the net charges on silvers over the whole ligands can decrease electrostatic repulsion of metal centers to stabilize oligomers. The vital role of the screening effect of solvent has also been realized in the bound binding of the title system. Overall, this research highlights the importance of ligand stacking to argentophilicity, while d10-d10 attraction of silver centers presents quite little contribution.","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":"143657453","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}

引用次数: 0

Correlation between entropy fluctuations and the dielectric relaxation of glass-forming systems: The central role of dipolar-dipolar cross correlations.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-21 DOI: 10.1063/5.0250974

S Arrese-Igor

{"title":"Correlation between entropy fluctuations and the dielectric relaxation of glass-forming systems: The central role of dipolar-dipolar cross correlations.","authors":"S Arrese-Igor","doi":"10.1063/5.0250974","DOIUrl":"https://doi.org/10.1063/5.0250974","url":null,"abstract":"The premise that the dielectric α relaxation has a one-to-one correspondence with entropy fluctuations in equilibrium near the glass transition was experimentally verified in a systematic and quantitative manner for glass-forming systems in general. Validation of this relation was structured at different levels, taking into account various ingredients as the apolar-polar character, macromolecular structure, the presence of hydrogen bonds, or complex structure and dynamics. The results reclaim the suitability of dielectric spectroscopy to echo the primary structural relaxation of glass-forming systems, demonstrating that the dielectric response effectively captures the structural relaxation by reliably correlating with entropy fluctuations. The correlation with entropy fluctuations holds even when the dielectric strength of the systems is high and the dielectric response is narrow and dominated by cross correlations, proving that dipolar intermolecular interactions are fundamental to the structural relaxation and not a particularity of the dielectric probe. This one-to-one correspondence between structural and dielectric α relaxation does not support the existence of a generic spectral shape for the primary structural relaxation valid for all kinds of susceptibility functions.","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":"143674054","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}

引用次数: 0

A comparison of probabilistic generative frameworks for molecular simulations.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-21 DOI: 10.1063/5.0249683

Richard John, Lukas Herron, Pratyush Tiwary

{"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":"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.","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}

引用次数: 0