Force Field Model Research Articles

ReaxFF-based nonadiabatic dynamics method for azobenzene derivatives.

ReaxFF reactive force fields have been parameterized for the ground and first excited states of azobenzene and its derivatives. In addition, an extended set of ab initio reference data ensures wide applicability, including to azosystems in complex environments. Based on the optimized force fields, nonadiabatic surface hopping simulations produce photoisomerization quantum yields and decay times of azobenzene, both in the gas phase and in n-hexane solution, in reasonable agreement with higher level theory and experiment. The transferability to other azo-compounds is illustrated for different arylazopyrazoles as well as ethylene-bridged azobenzene. Moreover, it has been shown that the model can be easily extended to adsorbates on metal surfaces. The simulation of the ring-opening of cyclobutene triggered by the photoisomerization of azobenzene in a macrocycle highlights the advantages of a reactive force field model.

Revealing Morphology Evolution of Lithium Dendrites by Large‐Scale Simulation Based on Machine Learning Force Field

AbstractSolving the dendrite growth problem is critical for the development of lithium metal anode for high‐capacity batteries. In this work, a machine learning force field model in combination with a self‐consistent continuum solvation model is used to simulate the morphology evolution of dendrites in a working electrolyte environment. The dynamic evolution of the dendrite morphology can be described in two stages. In the first stage, the energy reduction of the surface atoms induces localized reorientation of the originally single‐crystal dendrite and the formation of multiple domains. In the second stage, the energy reduction of internal atoms drives the migration of grain boundaries and the slipping of crystal domains. The results indicate that the formation of multiple domains might help to stabilize the dendrite, as a higher temperature trajectory in a single crystal dendrite without domains shows a higher dendrite collapsing rate. Several possible modes of morphological evolutions are also investigated, including surface diffusion of adatoms and configuration twists from [100] exposed surfaces to [110] exposed surfaces. In summary, reducing the surface and grain boundary energy drives the morphology evolution. Based on the analysis of these driving forces, some guidelines are suggested for designing a more stable lithium metal anode.

Explaining the GeV Antiproton Excess, GeV γ -Ray Excess, and W -Boson Mass Anomaly in an Inert Two Higgs Doublet Model

For the newly discovered W-boson mass anomaly, one of the simplest dark matter (DM) models that can account for the anomaly without violating other astrophysical and experimental constraints is the inert two Higgs doublet model, in which the DM mass (m_{S}) is found to be within ∼54-74 GeV. In this model, the annihilation of DM via SS→bb[over ¯] and SS→WW^{*} would produce antiprotons and gamma rays, and may account for the excesses identified previously in both particles. Motivated by this, we reanalyze the AMS-02 antiproton and Fermi-LAT Galactic center γ-ray data. For the antiproton analysis, the novel treatment is the inclusion of the charge-sign-dependent three-dimensional solar modulation model as constrained by the time-dependent proton data. We find that the excess of antiprotons is more distinct than previous results based on the force-field solar modulation model. The interpretation of this excess as the annihilation of SS→WW^{*} (SS→bb[over ¯]) requires a DM mass of ∼40-80 (40-60)GeV and a velocity-averaged cross section of O(10^{-26}) cm^{3} s^{-1}. As for the γ-ray data analysis, besides adopting the widely used spatial template fitting, we employ an orthogonal approach with a data-driven spectral template analysis. The fitting to the GeV γ-ray excess yields DM model parameters overlapped with those to fit the antiproton excess via the WW^{*} channel. The consistency of the DM particle properties required to account for the W-boson mass anomaly, the GeV antiproton excess, and the GeV γ-ray excess suggests a common origin of them.

Sampling the Bulk Viscosity of Water with Molecular Dynamics Simulation in the Canonical Ensemble.

The bulk viscosity, a transport coefficient in the Navier-Stokes equation, is often neglected in the continuum mechanics of Newtonian fluids. Recently, however, the role of the bulk viscosity is highlighted in the area of surface and interface-related phenomena, in systematic model up-scaling and as an important quantity for the interpretation of acoustic sensor data. The prediction of the bulk viscosity usually employs molecular dynamics and the Green-Kubo linear response theory, which is used to sample transport properties in general from molecular trajectories. Since simulations are usually carried out at specified state points in concert with the evaluation of other thermodynamic properties, the role of thermostats in molecular dynamics needs to be explored systematically. In this work, we carefully investigate the role of thermostatting schemes and numerical implementations of the Green-Kubo formalism, in particular in the canonical ensemble, using two popular water force field models. It turns out that the sampling of the bulk and shear viscosities is a delicate challenge since details of thermostatting and numerical subtleties may have an influence on the results beyond statistical uncertainties. Based on the present findings, we conclude with hints on how to construct robust sampling in the canonical ensemble for the bulk viscosity.

SAFT-[formula omitted] force field for the simulation of molecular fluids 9: Coarse-grained models for polyaromatic hydrocarbons describing thermodynamic, interfacial, structural, and transport properties

Coarse-grained models of polyaromatic hydrocarbons parametrized by employing the SAFT-γ Mie approach are presented and assessed by comparison with experimental data and all-atom models in their ability to describe liquid densities, isothermal compressibilities, thermal expansivities, viscosities, and interfacial tensions. The structural behaviour characterized by the center of mass and angular radial distribution functions are also benchmarked. The SAFT-γ Mie force field models are shown to deliver quantitatively accurate predictions while promising significant speedups in the computational cost of performing molecular dynamics simulations.

Structure and bonding in cryolitic melts a combined study by density functional theory and ionic model calculations

Present study aims to analyze the nature of the bonding of ion pairs and formation of Al(III) fluorocomplexes by discussing the detailed ion pair interactions for various microclusters on AlF3/NaF solutions (cryolitic melts). Using a comparative study between the density functional theory and an interionic force-field model calculations developed in our group, the structure of neutral micro clusters in cryolitic melts are analyzed to reveal their bonding characteristics of the ion pairs. Quantum Theory of Atoms in Molecules (QTAIM) analyses were perfomed in order to understand the molecular or ionic interactions both in vacuo and in dielectric continuum. This study provides detailed information about the local structure in cryolitic melts in terms of the bonding interactions between the ions.

The Application of Deep Learning on Room Temperature Conductivity of Li10GeP2S12 Type Solid State Electrolyte

Room temperature ionic conductivity of the solid-state electrolyte is the essencial element of the commercialization of solid-state lithium-ion batteries. First-principles method is a good tool as it simulates the atomic level dynamics, and provides accurate insides of the ion moving velocity, path, and the microscopic environment. However, the first-principles method is time and computational resources-consuming. It is usually applied to systems with hundreds of atoms and the simulation time is less than 100 picoseconds. The classical molecular dynamics method applies to systems containing thousands of atoms and the simulation time can reach the scale of nanoseconds. However, it is based on the experimental force-field parameters and can only be applied to limited systems with experimentally-proofed good parameters. The method used in this paper is a combination of the first-principles simulation and classical dynamics. Deep-learning tool Deepmd-kit is used to train the first-principles simulation data of the targeted system into a tailor-made force-field model. The verified model for the specific system will then be used in the classical molecular dynamics simulation. With the first-principles precise and classical efficiency, the molecular dynamics simulation of ion movement at room temperature is achieved. The results of Li10GeP2S12 and Li10SiP2S12 showed good agreement with the experiments.

Molecular dynamics simulations of the adsorption of an intrinsically disordered protein: Force field and water model evaluation in comparison with experiments.

This study investigates possible structural changes of an intrinsically disordered protein (IDP) when it adsorbs to a solid surface. Experiments on IDPs primarily result in ensemble averages due to their high dynamics. Therefore, molecular dynamics (MD) simulations are crucial for obtaining more detailed information on the atomistic and molecular levels. An evaluation of seven different force field and water model combinations have been applied: (A) CHARMM36IDPSFF + CHARMM-modified TIP3P, (B) CHARMM36IDPSFF + TIP4P-D, (C) CHARMM36m + CHARMM-modified TIP3P, (D) AMBER99SB-ILDN + TIP3P, (E) AMBER99SB-ILDN + TIP4P-D, (F) AMBERff03ws + TIP4P/2005, and (G) AMBER99SB-disp + disp-water. The results have been qualitatively compared with those of small-angle X-ray scattering, synchrotron radiation circular dichroism spectroscopy, and attenuated total reflectance Fourier transform infrared spectroscopy. The model IDP corresponds to the first 33 amino acids of the N-terminal of the magnesium transporter A (MgtA) and is denoted as KEIF. With a net charge of +3, KEIF is found to adsorb to the anionic synthetic clay mineral Laponite® due to the increase in entropy from the concomitant release of counterions from the surface. The experimental results show that the peptide is largely disordered with a random coil conformation, whereas the helical content (α- and/or 310-helices) increased upon adsorption. MD simulations corroborate these findings and further reveal an increase in polyproline II helices and an extension of the peptide conformation in the adsorbed state. In addition, the simulations provided atomistic resolution of the adsorbed ensemble of structures, where the arginine residues had a high propensity to form hydrogen bonds with the surface. Simulations B, E, and G showed significantly better agreement with experiments than the other simulations. Particularly noteworthy is the discovery that B and E with TIP4P-D water had superior performance to their corresponding simulations A and D with TIP3P-type water. Thus, this study shows the importance of the water model when simulating IDPs and has also provided an insight into the structural changes of surface-active IDPs induced by adsorption, which may play an important role in their function.

The thermodynamics of pressurized methanol: A simple hydrogen-bonded liquid as a touchstone for experiment and computer simulations.

Methanol as a basic liquid and the simplest alcohol is widely used in industry and scientific experiments. However, there are still no reliable data on the thermodynamic properties of methanol at high pressure. Here, we present an experimental and computational study of the thermodynamic properties of liquid methanol under high pressure up to 15 kbar, which significantly exceeds previously reported pressures. A temperature response to a small adiabatic change in pressure has been measured using a piston-cylinder apparatus. We have compared our experimental results with the literature data for lower pressures and NIST approximations. We find that all existing experimental data do not agree with each other and with our experiments. The NIST approximations are mainly based on low pressure data and appear to be unreliable in the high pressure region, giving even qualitatively wrong results. OPLS and COMPASS force field models have been used in the method of molecular dynamics. The agreement of molecular simulation with our experimental data is definitely unsatisfactory, which means that the most common computational models of methanol are not sufficiently good. We hope that these experimental data and approximations will help in developing better computational models.

Molecular Dynamics Investigation of Hyaluronan in Biolubrication.

Aqueous solution of strongly hydrophilic biopolymers is known to exhibit excellent lubrication properties in biological systems, such as the synovial fluid in human joints. Several mechanisms have been proposed on the biolubrication of joints, such as the boundary lubrication and the fluid exudation lubrication. In these models, mechanical properties of synovial fluid containing biopolymers are essential. To examine the role of such biopolymers in lubrication, a series of molecular dynamics simulations with an all-atom classical force field model were conducted for aqueous solutions of hyaluronan (hyaluronic acid, HA) under constant shear. After equilibrating the system, the Lees-Edwards boundary condition was imposed, with which a steady state of uniform shear flow was realized. Comparison of HA systems with hydrocarbon (pentadecane, PD) solutions of similar mass concentration indicates that the viscosity of HA solutions is slightly larger in general than that of PDs, due to the strong hydration of HA molecules. Effects of added electrolyte (NaCl) were also discussed in terms of hydration. These findings suggest the role of HA in biolubirication as a load-supporting component, with its flexible character and strong hydration structure.

A new framework for frequency-dependent polarizable force fields.

A frequency-dependent extension of the polarizable force field "Atom-Condensed Kohn-Sham density functional theory approximated to the second-order" (ACKS2) [Verstraelen et al., J. Chem. Phys. 141, 194114 (2014)] is proposed, referred to as ACKS2ω. The method enables theoretical predictions of dynamical response properties of finite systems after partitioning of the frequency-dependent molecular response function. Parameters in this model are computed simply as expectation values of an electronic wavefunction, and the hardness matrix is entirely reused from ACKS2 as an adiabatic approximation is used. A numerical validation shows that accurate models can already be obtained with atomic monopoles and dipoles. Absorption spectra of 42 organic and inorganic molecular monomers are evaluated using ACKS2ω, and our results agree well with the time-dependent DFT calculations. Also for the calculation of C6 dispersion coefficients, ACKS2ω closely reproduces its TDDFT reference. When parameters for ACKS2ω are derived from a PBE/aug-cc-pVDZ ground state, it reproduces experimental values for 903 organic and inorganic intermolecular pairs with an MAPE of 3.84%. Our results confirm that ACKS2ω offers a solid connection between the quantum-mechanical description of frequency-dependent response and computationally efficient force-field models.

Balanced Force Field ff03CMAP Improving the Dynamics Conformation Sampling of Phosphorylation Site.

Phosphorylation plays a key role in plant biology, such as the accumulation of plant cells to form the observed proteome. Statistical analysis found that many phosphorylation sites are located in disordered regions. However, current force fields are mainly trained for structural proteins, which might not have the capacity to perfectly capture the dynamic conformation of the phosphorylated proteins. Therefore, we evaluated the performance of ff03CMAP, a balanced force field between structural and disordered proteins, for the sampling of the phosphorylated proteins. The test results of 11 different phosphorylated systems, including dipeptides, disordered proteins, folded proteins, and their complex, indicate that the ff03CMAP force field can better sample the conformations of phosphorylation sites for disordered proteins and disordered regions than ff03. For the solvent model, the results strongly suggest that the ff03CMAP force field with the TIP4PD water model is the best combination for the conformer sampling. Additional tests of CHARMM36m and FB18 force fields on two phosphorylated systems suggest that the overall performance of ff03CMAP is similar to that of FB18 and better than that of CHARMM36m. These results can help other researchers to choose suitable force field and solvent models to investigate the dynamic properties of phosphorylation proteins.

Simultaneous Prediction of Equilibrium, Interfacial, and Transport Properties of CO2-Brine Systems Using Molecular Dynamics Simulation: Applications to CO2 Storage

This study aims to provide accurate simultaneous predictions of crucial properties affecting CO2 storage in saline aquifers with deep microstructural insights using comprehensive molecular dynamics (MD) simulations under actual operating conditions ranges. We investigated the effects of pressure, temperature, and salinity on mutual solubility, interfacial tension (IFT), density, and viscosity of a CO2-brine system over the temperature range of 323.15–393.15 K, pressures up to 30 MPa, and salinity range of 0.98–2.97 mol/kg. Brine was resembled by employing different brine systems like actual reservoirs, including mixed electrolyte solutions containing monovalent and divalent ions. MD model configurations and force fields were validated by experimental data of a CO2-water/NaCl aqueous solution. The maximum average absolute deviations for the solubility, density, and IFT were 5.50, 6.95, and 7.136%, respectively. The simulation results indicated that mutual solubilities of CO2 and water in the CO2-NaCl + KCl solution system are higher than those of CO2-NaCl + CaCl2, while for IFT, the opposite trend is observed. Unlike pressure, salt concentration variations result in considerable density and viscosity changes for all systems. The maximum density and viscosity values are obtained for the brine-containing divalent cations. This study gives insight into the storage process and relates the microstructure effects to solubility, IFT, and viscosity of CO2-brine systems using a single MD model.

Force-Field-Dependent DNA Breathing Dynamics: A Case Study of Hoogsteen Base Pairing in A6-DNA.

The Hoogsteen (HG) base pairing conformation, commonly observed in damaged and mutated DNA helices, facilitates DNA repair and DNA recognition. The free energy difference between HG and Watson-Crick (WC) base pairs has been computed in previous studies. However, the mechanism of the conformational transition is not well understood. A detailed understanding of the process of WC to HG base pair transition can provide a deeper understanding of DNA repair and recognition. In an earlier study, we explored the free energy landscape for this process using extensive computer simulation with the CHARMM36 force field. In this work, we study the impact of force field models in describing the WC to HG base pairing transition using meta-eABF enhanced sampling, quasi-harmonic entropy calculation, and nonbonded energy analysis. The secondary structures of both base pairing forms and the topology of the free energy landscapes were consistent over different force field models, although the relative free energy, entropy, and the interaction energies tend to vary. The relative stability of the WC and HG conformations is dictated by a delicate balance between the enthalpic stabilization and the reduced entropy of the structurally rigid HG structure. These findings highlight the impact that subtleties in force field models can have on accurately modeling DNA base pair dynamics and should stimulate further computational investigations into other dynamically important motions in DNA.

Galactic Cosmic-Ray Propagation in the Inner Heliosphere: Improved Force-field Model

A key goal of heliophysics is to understand how cosmic rays propagate in the solar system’s complex, dynamic environment. One observable is solar modulation, i.e., how the flux and spectrum of cosmic rays change as they propagate inward. We construct an improved force-field model, taking advantage of new measurements of magnetic power spectral density by Parker Solar Probe to predict solar modulation within the Earth’s orbit. We find that modulation of cosmic rays between the Earth and Sun is modest, at least at solar minimum and in the ecliptic plane. Our results agree much better with the limited data on cosmic-ray radial gradients within Earth’s orbit than past treatments of the force-field model. Our predictions can be tested with forthcoming direct cosmic-ray measurements in the inner heliosphere by Parker Solar Probe and Solar Orbiter. They are also important for interpreting the gamma-ray emission from the Sun due to scattering of cosmic rays with solar matter and photons.

Impact of Side-Chain Hydrophilicity on Packing, Swelling, and Ion Interactions in Oxy-Bithiophene Semiconductors.

Exchanging hydrophobic alkyl-based side chains to hydrophilic glycol-based side chains is a widely adopted method for improving mixed-transport device performance, despite the impact on solid-state packing and polymer-electrolyte interactions being poorly understood. Presented here is a molecular dynamics (MD) force field for modeling alkoxylated and glycolated polythiophenes. The force field is validated against known packing motifs for their monomer crystals. MD simulations, coupled with X-ray diffraction (XRD), show that alkoxylated polythiophenes will pack with a "tilted stack" and straight interdigitating side chains, whilst their glycolated counterpart will pack with a "deflected stack" and an s-bend side-chain configuration. MD simulations reveal water penetration pathways into the alkoxylated and glycolated crystals-through the π-stack and through the lamellar stack respectively. Finally, the two distinct ways triethylene glycol polymers can bind to cations are revealed, showing the formation of a metastable single bound state, or an energetically deep double bound state, both with a strong side-chain length dependence. The minimum energy pathways for the formation of the chelates are identified, showing the physical process through which cations can bind to one or two side chains of a glycolated polythiophene, with consequences for ion transport in bithiophene semiconductors.

JAX-ReaxFF: A Gradient-Based Framework for Fast Optimization of Reactive Force Fields.

The reactive force field (ReaxFF) model bridges the gap between traditional classical models and quantum mechanical (QM) models by incorporating dynamic bonding and polarizability. To achieve realistic simulations using ReaxFF, model parameters must be optimized against high fidelity training data which typically come from QM calculations. Existing parameter optimization methods for ReaxFF consist of black box techniques using genetic algorithms or Monte Carlo methods. Due to the stochastic behavior of these methods, the optimization process oftentimes requires millions of error evaluations for complex parameter fitting tasks, thereby significantly hampering the rapid development of high quality parameter sets. Rapid optimization of the parameters is essential for developing and refining Reax force fields because producing a force field which exhibits empirical accuracy in terms of dynamics typically requires multiple refinements to the training data as well as to the parameters under optimization. In this work, we present JAX-ReaxFF, a novel software tool that leverages modern machine learning infrastructure to enable fast optimization of ReaxFF parameters. By calculating gradients of the loss function using the JAX library, JAX-ReaxFF utilizes highly effective local optimization methods that are initiated from multiple guesses in the high dimensional optimization space to obtain high quality results. Leveraging the architectural portability of the JAX framework, JAX-ReaxFF can execute efficiently on multicore CPUs, graphics processing units (GPUs), or even tensor processing units (TPUs). As a result of using the gradient information and modern hardware accelerators, we are able to decrease ReaxFF parameter optimization time from days to mere minutes. Furthermore, the JAX-ReaxFF framework can also serve as a sandbox environment for domain scientists to explore customizing the ReaxFF functional form for more accurate modeling.

Physical Insight into the Conditions Required in the Solid-Phase Molecular Self-Assembly of SDS Revealed by Coarse-Grained Molecular Dynamics Simulation.

Molecular self-assembled materials have attracted considerable interest in recent years. As part of the efforts to overcome the shortcoming that the solution-based methods were hardly applicable in preparing bulk macroscopic molecular self-assemblies, Yan [ CCS Chem. 2020, 2, 98-106] developed a strategy of solid-phase molecular self-assembly (SPMSA) that allows scaling up the generation of massive supramolecular films. It is highly desired to understand the physical insight into the SPMSA at a molecular level. Here, in combination with the experimental study, we report molecular dynamics (MD) simulations on the SPMSA of the surfactant sodium dodecyl sulfate (SDS) using a coarse-grained method with the Martini force field model. The MD simulations clearly manifest that a small amount of water is required to endow the SDS molecules with sufficient mobility to self-assemble, and the smaller size of the preassembled SDS particles favors their further fusion into mesophases by reducing the total surface Gibbs free energy, while the smaller interparticle distance decreases the time for the particle fusion. The simulation results agree well with the conditions required in the experiment, confirming that SMPSA is a free-energy-favored process leading to bulk self-assembled materials.

Gecko Adhesion on Flat and Rough Surfaces: Simulations with a Multi‐Scale Molecular Model

A multiscale modeling approach is used to develop a particle-based mesoscale gecko spatula model that is able to link atomistic simulations and mesoscale (0.44 µm) simulations. It is used to study the detachment of spatulae from flat as well as nanostructured surfaces. The spatula model is based on microscopical information about spatulae structure and on atomistic molecular simulation results. Target properties for the coarse-graining result from a united-atom model of gecko keratin in periodic boundary conditions (PBC), previously developed by the authors. Pull-off forces necessary to detach gecko keratin under 2D PBC parallel to the surface are previously overestimated when only a small region of a spatula is examined. It is shown here that this is due to the restricted geometry (i.e., missing peel-off mode) and not model parameters. The spatula model peels off when pulled away from a surface, both in the molecular picture of the pull-off process and in the force-extension curve of non-equilibrium simulations mimicking single-spatula detachment studied with atomic force microscopy equipment. The force field and spatula model can reproduce experimental pull-off forces. Inspired by experimental results, the underlying mechanism that causes pull-off forces to be at a minimum on surfaces of varying roughnesses is also investigated. A clear sigmoidal increase in the pull-off force of spatulae with surface roughness shows that adhesion is determined by the ratio between spatula pad area and the area between surface peaks. Experiments showed a correlation with root-mean-square roughness of the surface, but the results of this work indicate that this is not a causality but depends on the areaaccessible.

Electronic structure calculations of the fundamental interactions in solvent extraction desalination

Solvent extraction desalination (SED) is a promising membrane-free desalination technology, but new solvents are still needed that can improve the molecular-level water selectivity, while minimizing solvent contamination in the aqueous phase. Improvements in solvent design for SED require a fundamental understanding of the molecular interactions governing solvation behavior. Herein, quantum chemical calculations are used to delineate different fundamental interactions in water-solvent systems involving 38 different solvents, with a particular focus on the role of the electrostatic potential characteristics. These interactions are rigorously analyzed using the independent gradient model based on Hirshfeld partition (IGMH), Symmetry-Adapted Perturbation Theory (SAPT), as well as the energy decomposition analysis based on force field (EDA-FF) to compare against a standard force field model. The solvation free energies and partition coefficients are also calculated to estimate water extraction performance in a bulk solvent system.