Jonathan T Willman, Joseph M Gonzalez, Kien Nguyen-Cong, Sebastien Hamel, Vincenzo Lordi, Ivan I Oleynik
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.
{"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":"<p><p>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.</p>","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}
Christopher A Myers, Ken Miyazaki, Thomas Trepl, Christine M Isborn, Nandini Ananth
GPU-accelerated on-the-fly nonadiabatic dynamics is enabled by interfacing the linearized semiclassical dynamics approach with the TeraChem electronic structure program. We describe the computational workflow of the "PySCES" code interface, a Python code for semiclassical dynamics with on-the-fly electronic structure, including parallelization over multiple GPU nodes. We showcase the abilities of this code and present timings for two benchmark systems: fulvene solvated in acetonitrile and a charge transfer system in which a photoexcited zinc-phthalocyanine donor transfers charge to a fullerene acceptor through multiple electronic states on an ultrafast timescale. Our implementation paves the way for an efficient semiclassical approach to model the nonadiabatic excited state dynamics of complex molecules, materials, and condensed phase systems.
{"title":"GPU-accelerated on-the-fly nonadiabatic semiclassical dynamics.","authors":"Christopher A Myers, Ken Miyazaki, Thomas Trepl, Christine M Isborn, Nandini Ananth","doi":"10.1063/5.0223628","DOIUrl":"https://doi.org/10.1063/5.0223628","url":null,"abstract":"<p><p>GPU-accelerated on-the-fly nonadiabatic dynamics is enabled by interfacing the linearized semiclassical dynamics approach with the TeraChem electronic structure program. We describe the computational workflow of the \"PySCES\" code interface, a Python code for semiclassical dynamics with on-the-fly electronic structure, including parallelization over multiple GPU nodes. We showcase the abilities of this code and present timings for two benchmark systems: fulvene solvated in acetonitrile and a charge transfer system in which a photoexcited zinc-phthalocyanine donor transfers charge to a fullerene acceptor through multiple electronic states on an ultrafast timescale. Our implementation paves the way for an efficient semiclassical approach to model the nonadiabatic excited state dynamics of complex molecules, materials, and condensed phase systems.</p>","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":"142080435","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}
Ya-Shen Wang, Xin Zhang, Zun Liang, Hong-Tao Liang, Yang Yang, Brian B Laird
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.
{"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":"<p><p>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.</p>","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}
Samuel G H Brookes, Venkat Kapil, Christoph Schran, Angelos Michaelides
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.
{"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":"<p><p>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.</p>","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}
We employed all-atom molecular dynamics simulations to explore the mechanical response of bending, twisting, and overwinding for double-stranded DNA (dsDNA). We analyzed the bending and twisting deformations, as well as their stiffnesses, using the tilt, roll, and twist modes under stretching force. Findings indicate that the roll and twist angles vary linearly with the stretching force but show opposite trends. The tilt, roll, and twist elastic moduli are considered constants, while the coupling between roll and twist modes slightly decreases under stretching force. The effect of the stretching force on the roll and twist modes, including both their deformations and elasticities, exhibits sequence-dependence, with symmetry around the base pair step. Furthermore, we examined the overwinding path and mechanism of dsDNA from the perspective of the stiffness matrix, based on the tilt, roll, and twist modes. The correlations among tilt, roll, and twist angles imply an alternative overwinding pathway via twist-roll coupling when dsDNA is stretched, wherein entropic contribution prevails.
{"title":"Mechanical response of double-stranded DNA: Bend, twist, and overwind.","authors":"Xuankang Mou, Kai Liu, Linli He, Shiben Li","doi":"10.1063/5.0216585","DOIUrl":"10.1063/5.0216585","url":null,"abstract":"<p><p>We employed all-atom molecular dynamics simulations to explore the mechanical response of bending, twisting, and overwinding for double-stranded DNA (dsDNA). We analyzed the bending and twisting deformations, as well as their stiffnesses, using the tilt, roll, and twist modes under stretching force. Findings indicate that the roll and twist angles vary linearly with the stretching force but show opposite trends. The tilt, roll, and twist elastic moduli are considered constants, while the coupling between roll and twist modes slightly decreases under stretching force. The effect of the stretching force on the roll and twist modes, including both their deformations and elasticities, exhibits sequence-dependence, with symmetry around the base pair step. Furthermore, we examined the overwinding path and mechanism of dsDNA from the perspective of the stiffness matrix, based on the tilt, roll, and twist modes. The correlations among tilt, roll, and twist angles imply an alternative overwinding pathway via twist-roll coupling when dsDNA is stretched, wherein entropic contribution prevails.</p>","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":"142035975","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}
Lorenzo Iannetti, Sonia Cambiaso, Fabio Rasera, Alberto Giacomello, Giulia Rossi, Davide Bochicchio, Antonio Tinti
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.
马蒂尼模型是一种用于生物分子模拟的粗粒度力场,在过去十年中大受欢迎。它的积木式方法兼顾了计算效率和高化学特异性,能够模拟有机和无机分子。作为伦纳德-琼斯粒子的粗粒珠子建模对准确再现液体-蒸汽界面特性提出了挑战,而这些特性在各种应用中都至关重要,尤其是在水的情况下。最新版本的力场引入了细化的水珠相互作用参数,解决了众所周知的马蒂尼水在室温下冻结的问题。此外,还提供了多种尺寸的水珠,用于模拟小空腔(包括蛋白质的最小口袋)的溶解。这项工作的重点是研究马天尼水的界面特性,包括表面张力和表面厚度。我们采用测试区域法,系统地计算了不同水珠尺寸组合和 300 至 350 K 温度下的液体-蒸汽表面张力。这些发现引起了马天尼社区的兴趣,因为它们允许用户通过适当调整粗粒度模拟计算的观测值来解释马天尼水的低界面张力,以便与全原子或实验结果准确匹配。表面张力数据还可以通过吉布斯吸附形式主义,从液气界面各种混合物成分的局部富集角度进行解释。最后,报告了马尔蒂尼表面张力随温度变化的临界比例与三维伊辛普遍性类的临界指数相一致。
{"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":"<p><p>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.</p>","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}
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.
{"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":"<p><p>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.</p>","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}
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.
{"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":"<p><p>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.</p>","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}
John Strahan, Chatipat Lorpaiboon, Jonathan Weare, Aaron R Dinner
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.
分子动力学模拟的一个问题是,感兴趣的事件所涉及的时间尺度往往比模拟时间步长得多,而模拟时间步是由模型的最快时间尺度设定的。由于这种时标分离,直接模拟许多事件的计算成本过高。要解决这个问题,可以从许多相对较短的模拟中汇总信息,对涉及相关事件的轨迹片段进行采样。这是马尔可夫状态模型(MSM)和相关方法的策略,但由于定义状态的变量通常不能完全捕捉动态,因此这类方法存在近似误差。相比之下,加权集合(WE)方法一旦收敛,就会汇总来自轨迹片段的信息,从而对热力学和动力学统计进行无偏估计。遗憾的是,在最初制定和普遍采用的加权集合法中,误差衰减的速度并不比无偏模拟快。在这里,我们介绍了一种描述 WE 的理论框架,它表明在分层之上引入近似静态分布(如非平衡伞状采样(NEUS))可加速收敛。基于 MSMs 和相关方法的思想,我们对 NEUS 方法进行了概括,从而系统地减少了近似误差。我们的研究表明,改进后的算法可以将达到理想精度所需的模拟时间减少几个数量级。
{"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":"<p><p>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.</p>","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}
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.
有机-无机混合型过氧化物太阳能电池因其卓越的光伏和光电特性而在光电领域备受关注。虽然以铅(Pb)为基础的包晶体具有最高的功率转换效率,但人们对其毒性和环境影响的担忧促使人们开展了大量研究活动,探索替代成分。在这方面,人们特别关注锡(Sn)和锗(Ge)基的包晶石。为了揭示锡-锗基包晶石的全部潜力,我们在密度泛函理论水平上,特别是利用 HSE06 混合函数,对通式为 A0.5A0.5'SnyGe1-yX3(y = 0.00、0.25、0.50、0.75、1.00)的包晶石进行了计算筛选。通过使用 18 个 A/A'阳离子、4 个 X 阴离子和 5 种不同的 y 成分,共考虑了立方(C)、正交(O)和四方(T)相中的 7695 种包晶石,并根据其形成能和带隙筛选出了最有前途的包晶石。更具体地说,已经确定了 596、525 和 542 个 C 相、O 相和 T 相包晶石,其 HSE06 带隙范围为 1.0-2.0 eV。虽然在 C 相和 O 相中,Sn1.00Ge0.00 成分占主导地位,但在 T 相中,Sn0.75Ge0.25 成分的包晶石数量更多。研究还发现,与富含 Ge 的包晶石相比,富含 Sn 的包晶石表现出更有利的带隙特性。FA、MS、MA、K、Cs 和 Rb 是这些前景广阔的包晶石中最受欢迎的 A/A'- 阳离子。此外,I- 作为主要的阴离子占据了压倒性的优势。进一步的实验验证可能会揭示这些前景广阔的包晶的真正能力和实际应用性。
{"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":"<p><p>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.</p>","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}