Journal of Chemical Physics最新文献_第10页

Accuracy, transferability, and computational efficiency of interatomic potentials for simulations of carbon under extreme conditions. 在极端条件下模拟碳的原子间势的准确性、可转移性和计算效率。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-08-28 DOI: 10.1063/5.0218705

Jonathan T Willman, Joseph M Gonzalez, Kien Nguyen-Cong, Sebastien Hamel, Vincenzo Lordi, Ivan I Oleynik

{"title":"Accuracy, transferability, and computational efficiency of interatomic potentials for simulations of carbon under extreme conditions.","authors":"Jonathan T Willman, Joseph M Gonzalez, Kien Nguyen-Cong, Sebastien Hamel, Vincenzo Lordi, Ivan I Oleynik","doi":"10.1063/5.0218705","DOIUrl":"https://doi.org/10.1063/5.0218705","url":null,"abstract":"Large-scale atomistic molecular dynamics (MD) simulations provide an exceptional opportunity to advance the fundamental understanding of carbon under extreme conditions of high pressures and temperatures. However, the fidelity of these simulations depends heavily on the accuracy of classical interatomic potentials governing the dynamics of many-atom systems. This study critically assesses several popular empirical potentials for carbon, as well as machine learning interatomic potentials (MLIPs), in their ability to simulate a range of physical properties at high pressures and temperatures, including the diamond equation of state, its melting line, shock Hugoniot, uniaxial compressions, and the structure of liquid carbon. Empirical potentials fail to accurately predict the behavior of carbon under high pressure-temperature conditions. In contrast, MLIPs demonstrate quantum accuracy, with Spectral Neighbor Analysis Potential (SNAP) and atomic cluster expansion (ACE) being the most accurate in reproducing the density functional theory results. ACE displays remarkable transferability despite not being specifically trained for extreme conditions. Furthermore, ACE and SNAP exhibit superior computational performance on graphics processing unit-based systems in billion atom MD simulations, with SNAP emerging as the fastest. In addition to offering practical guidance in selecting an interatomic potential with a fine balance of accuracy, transferability, and computational efficiency, this work also highlights transformative opportunities for groundbreaking scientific discoveries facilitated by quantum-accurate MD simulations with MLIPs on emerging exascale supercomputers.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142080434","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

GPU-accelerated on-the-fly nonadiabatic semiclassical dynamics. GPU 加速的即时非绝热半经典动力学。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-08-28 DOI: 10.1063/5.0223628

Christopher A Myers, Ken Miyazaki, Thomas Trepl, Christine M Isborn, Nandini Ananth

引用次数: 0

A quantitative theory and atomistic simulation study on the soft-sphere crystal-melt interfacial properties. I. Kinetic coefficients. 软球晶体-熔体界面特性的定量理论和原子模拟研究。I. 动力系数。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-08-28 DOI: 10.1063/5.0216556

Ya-Shen Wang, Xin Zhang, Zun Liang, Hong-Tao Liang, Yang Yang, Brian B Laird

{"title":"A quantitative theory and atomistic simulation study on the soft-sphere crystal-melt interfacial properties. I. Kinetic coefficients.","authors":"Ya-Shen Wang, Xin Zhang, Zun Liang, Hong-Tao Liang, Yang Yang, Brian B Laird","doi":"10.1063/5.0216556","DOIUrl":"https://doi.org/10.1063/5.0216556","url":null,"abstract":"By employing non-equilibrium molecular dynamics (NEMD) simulations and time-dependent Ginzburg-Landau (TDGL) theory for solidification kinetics [Cryst. Growth Des. 20, 7862 (2020)], we predict the kinetic coefficients of FCC(100) crystal-melt interface (CMI) of soft-spheres modeled with an inverse-sixth-power repulsive potential. The collective dynamics of the local interfacial liquid phase at the equilibrium FCC(100) CMIs are calculated based on a recently proposed algorithm [J. Chem. Phys. 157, 084 709 (2022)] and are employed as the resulting parameter that eliminates the discrepancy between the predictions of the kinetic coefficient using the NEMD simulations and the TDGL solidification theory. A speedup of the two modes of the interfacial liquid collective dynamics (at wavenumbers equal to the principal and the secondary reciprocal lattice vector of the grown crystal) is observed. With the insights provided by the quantitative predictive theory, the variation of the solidification kinetic coefficient along the crystal-melt coexistence boundary is discussed. The combined methodology (simulation and theory) presented in this study could be further applied to investigate the role of the inter-atomic potential (e.g., softness parameter s = 1/n of the inverse-power repulsive potential) in the kinetic coefficient.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142072873","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

The wetting of H2O by CO2. 二氧化碳对 H2O 的润湿。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-08-28 DOI: 10.1063/5.0224230

Samuel G H Brookes, Venkat Kapil, Christoph Schran, Angelos Michaelides

{"title":"The wetting of H2O by CO2.","authors":"Samuel G H Brookes, Venkat Kapil, Christoph Schran, Angelos Michaelides","doi":"10.1063/5.0224230","DOIUrl":"https://doi.org/10.1063/5.0224230","url":null,"abstract":"Biphasic interfaces are complex but fascinating regimes that display a number of properties distinct from those of the bulk. The CO2-H2O interface, in particular, has been the subject of a number of studies on account of its importance for the carbon life cycle as well as carbon capture and sequestration schemes. Despite this attention, there remain a number of open questions on the nature of the CO2-H2O interface, particularly concerning the interfacial tension and phase behavior of CO2 at the interface. In this paper, we seek to address these ambiguities using ab initio-quality simulations. Harnessing the benefits of machine-learned potentials and enhanced statistical sampling methods, we present an ab initio-level description of the CO2-H2O interface. Interfacial tensions are predicted from 1 to 500 bars and found to be in close agreement with experiment at pressures for which experimental data are available. Structural analyses indicate the buildup of an adsorbed, saturated CO2 film forming at a low pressure (20 bars) with properties similar to those of the bulk liquid, but preferential perpendicular alignment with respect to the interface. The CO2 monolayer buildup coincides with a reduced structuring of water molecules close to the interface. This study highlights the predictive nature of machine-learned potentials for complex macroscopic properties of biphasic interfaces, and the mechanistic insight obtained into carbon dioxide aggregation at the water interface is of high relevance for geoscience, climate research, and materials science.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142080439","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

Mechanical response of double-stranded DNA: Bend, twist, and overwind. 双链 DNA 的机械响应：弯曲、扭曲和过卷

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-08-28 DOI: 10.1063/5.0216585

Xuankang Mou, Kai Liu, Linli He, Shiben Li

引用次数: 0

The surface tension of Martini 3 water mixtures. Martini 3 水混合物的表面张力。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-08-28 DOI: 10.1063/5.0221199

Lorenzo Iannetti, Sonia Cambiaso, Fabio Rasera, Alberto Giacomello, Giulia Rossi, Davide Bochicchio, Antonio Tinti

{"title":"The surface tension of Martini 3 water mixtures.","authors":"Lorenzo Iannetti, Sonia Cambiaso, Fabio Rasera, Alberto Giacomello, Giulia Rossi, Davide Bochicchio, Antonio Tinti","doi":"10.1063/5.0221199","DOIUrl":"https://doi.org/10.1063/5.0221199","url":null,"abstract":"The Martini model, a coarse-grained forcefield for biomolecular simulations, has experienced a vast increase in popularity in the past decade. Its building-block approach balances computational efficiency with high chemical specificity, enabling the simulation of organic and inorganic molecules. The modeling of coarse-grained beads as Lennard-Jones particles poses challenges for the accurate reproduction of liquid-vapor interfacial properties, which are crucial in various applications, especially in the case of water. The latest version of the forcefield introduces refined interaction parameters for water beads, tackling the well-known artifact of Martini water freezing at room temperature. In addition, multiple sizes of water beads are available for simulating the solvation of small cavities, including the smallest pockets of proteins. This work focuses on studying the interfacial properties of Martini water, including surface tension and surface thickness. Employing the test-area method, we systematically compute the liquid-vapor surface tension across various combinations of water bead sizes and for temperatures from 300 to 350 K. These findings are of interest to the Martini community as they allow users to account for the low interfacial tension of Martini water by properly adjusting observables computed via coarse-grained simulations to allow for accurate matching against all-atom or experimental results. Surface tension data are also interpreted in terms of local enrichment of the various mixture components at the liquid-vapor interface by means of Gibbs' adsorption formalism. Finally, the critical scaling of the Martini surface tension with temperature is reported to be consistent with the critical exponent of the 3D Ising universality class.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142072917","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

Bridging classical nucleation theory and molecular dynamics simulation for homogeneous ice nucleation. 衔接经典成核理论与分子动力学模拟的均质冰成核。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-08-28 DOI: 10.1063/5.0216645

Min Lin, Zhewen Xiong, Haishan Cao

{"title":"Bridging classical nucleation theory and molecular dynamics simulation for homogeneous ice nucleation.","authors":"Min Lin, Zhewen Xiong, Haishan Cao","doi":"10.1063/5.0216645","DOIUrl":"https://doi.org/10.1063/5.0216645","url":null,"abstract":"Water freezing, initiated by ice nucleation, occurs widely in nature, ranging from cellular to global phenomena. Ice nucleation has been experimentally proven to require the formation of a critical ice nucleus, consistent with classical nucleation theory (CNT). However, the accuracy of CNT quantitative predictions of critical cluster sizes and nucleation rates has never been verified experimentally. In this study, we circumvent this difficulty by using molecular dynamics (MD) simulation. The physical properties of water/ice for CNT predictions, including density, chemical potential difference, and diffusion coefficient, are independently obtained using MD simulation, whereas the calculation of interfacial free energy is based on thermodynamic assumptions of CNT, including capillarity approximation among others. The CNT predictions are compared to the MD evaluations of brute-force simulations and forward flux sampling methods. We find that the CNT and MD predicted critical cluster sizes are consistent, and the CNT predicted nucleation rates are higher than the MD predicted values within three orders of magnitude. We also find that the ice crystallized from supercooled water is stacking-disordered ice with a stacking of cubic and hexagonal ices in four representative types of stacking. The prediction discrepancies in nucleation rate mainly arise from the stacking-disordered ice structure, the asphericity of ice cluster, the uncertainty of ice-water interfacial free energy, and the kinetic attachment rate. Our study establishes a relation between CNT and MD to predict homogeneous ice nucleation.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142107859","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

Dynamics of the Cl + CH3CN reaction on an automatically-developed full-dimensional ab initio potential energy surface. 自动开发的全维 ab initio 势能面上 Cl + CH3CN 反应的动力学。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-08-28 DOI: 10.1063/5.0220917

Petra Tóth, Tímea Szűcs, Tibor Győri, Gábor Czakó

{"title":"Dynamics of the Cl + CH3CN reaction on an automatically-developed full-dimensional ab initio potential energy surface.","authors":"Petra Tóth, Tímea Szűcs, Tibor Győri, Gábor Czakó","doi":"10.1063/5.0220917","DOIUrl":"https://doi.org/10.1063/5.0220917","url":null,"abstract":"A full-dimensional analytical potential energy surface (PES) is developed for the Cl + CH3CN reaction following our previous work on the benchmark ab initio characterization of the stationary points. The spin-orbit-corrected PES is constructed using the Robosurfer program and a fifth-order permutationally invariant polynomial method for fitting the high-accuracy energy points determined by a ManyHF-based coupled-cluster/triple-zeta-quality composite method. Quasi-classical trajectory simulations are performed at six collision energies between 10 and 60 kcal mol-1. Multiple low-probability product channels are found, including isomerization to isonitrile (CH3NC), but out of the eight possible channels, only the H-abstraction has significant reaction probability; thus, detailed dynamics studies are carried out only for this reaction. The cross sections and opacity functions show that the probability of the H-abstraction reaction increases with increasing collision energy (Ecoll). Scattering angle, initial attack angle, and product relative translational energy distributions indicate that the mechanism changes with the collision energy from indirect/rebound to direct stripping. The distribution of initial attack angles shows a clear preference for methyl group attack but with different angles at different Ecoll values. Post-reaction energy distributions show that the energy transfer is biased toward the products' relative translational energy instead of their internal energy. Rotational and vibrational energy have about the same amount of contribution to the internal energy in the case of both products (HCl and CH2CN), i.e., both of them are formed with high rotational excitations. HCl is produced mostly in the ground vibrational state, while a notable fraction of CH2CN is formed with vibrational excitation.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142107860","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

BAD-NEUS: Rapidly converging trajectory stratification. BAD-NEUS：快速收敛的轨迹分层。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-08-28 DOI: 10.1063/5.0215975

John Strahan, Chatipat Lorpaiboon, Jonathan Weare, Aaron R Dinner

{"title":"BAD-NEUS: Rapidly converging trajectory stratification.","authors":"John Strahan, Chatipat Lorpaiboon, Jonathan Weare, Aaron R Dinner","doi":"10.1063/5.0215975","DOIUrl":"10.1063/5.0215975","url":null,"abstract":"An issue for molecular dynamics simulations is that events of interest often involve timescales that are much longer than the simulation time step, which is set by the fastest timescales of the model. Because of this timescale separation, direct simulation of many events is prohibitively computationally costly. This issue can be overcome by aggregating information from many relatively short simulations that sample segments of trajectories involving events of interest. This is the strategy of Markov state models (MSMs) and related approaches, but such methods suffer from approximation error because the variables defining the states generally do not capture the dynamics fully. By contrast, once converged, the weighted ensemble (WE) method aggregates information from trajectory segments so as to yield unbiased estimates of both thermodynamic and kinetic statistics. Unfortunately, errors decay no faster than unbiased simulation in WE as originally formulated and commonly deployed. Here, we introduce a theoretical framework for describing WE that shows that the introduction of an approximate stationary distribution on top of the stratification, as in nonequilibrium umbrella sampling (NEUS), accelerates convergence. Building on ideas from MSMs and related methods, we generalize the NEUS approach in such a way that the approximation error can be reduced systematically. We show that the improved algorithm can decrease the simulation time required to achieve the desired precision by orders of magnitude.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11349377/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142055708","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Exploring the potential of Sn-Ge based hybrid organic-inorganic perovskites: A density functional theory based computational screening study. 探索锡-锗基混合有机-无机过氧化物的潜力：基于密度泛函理论的计算筛选研究。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-08-21 DOI: 10.1063/5.0220297

Adem Tekin, Merve Kalpar, Emine Tekin

{"title":"Exploring the potential of Sn-Ge based hybrid organic-inorganic perovskites: A density functional theory based computational screening study.","authors":"Adem Tekin, Merve Kalpar, Emine Tekin","doi":"10.1063/5.0220297","DOIUrl":"https://doi.org/10.1063/5.0220297","url":null,"abstract":"Hybrid organic-inorganic perovskite solar cells have attracted significant attention in the field of optoelectronics due to their exceptional photovoltaic and optoelectronic properties. Although lead (Pb)-based perovskites exhibit the highest power conversion efficiencies, concerns about their toxicity and environmental impact have prompted significant research activities to explore alternative compositions. In this regard, a special emphasis has been devoted to tin (Sn) and germanium (Ge) based perovskites. In order to reveal the full potential of Sn-Ge based perovskites, we computationally screened perovskites with a general formula of A0.5A0.5'SnyGe1-yX3 (y = 0.00, 0.25, 0.50, 0.75, 1.00) at the density functional theory level, particularly using the HSE06 hybrid functional. By using 18 A/A'-cations, four X-anions, and five different y compositions, a total of 7695 perovskites in cubic (C), orthogonal (O), and tetragonal (T) phases were considered, and the most promising ones have been filtered out based on their formation energy and bandgap. More specifically, 596, 525, and 542 C-, O-, and T-phase perovskites have been identified with a HSE06 bandgap range of 1.0-2.0 eV. While the Sn1.00Ge0.00 composition was dominated for both C- and O-phases, for the T-phase, a higher number of promising perovskites were obtained with the Sn0.75Ge0.25 composition. It has also been found that Sn-rich perovskites exhibit more favorable bandgap characteristics compared to Ge-rich ones. FA, MS, MA, K, Cs, and Rb are the most favored A/A'-cations in these promising perovskites. Moreover, I- overwhelmingly prevails as the dominant anion. Further experimental validation may uncover the true capabilities and practical applicability of these promising perovskites.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142017617","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