Free Energy Curves Research Articles

Rate Constants of the H + HCF3 → H2 + CF3 Reaction from Ring Polymer Molecular Dynamics on a Highly Accurate Potential Energy Surface.

The reaction between H and HCF3 is the primary consumption pathway of HCF3 in the atmosphere and combustion. In this work, ring polymer molecular dynamics (RPMD) calculations are performed to calculate the rate constants of the reaction on a recently developed accurate potential energy surface. 36, 20, and 8 beads are used to compute the rate constants at 350 K ≤ T < 800 K, 800 K ≤ T ≤ 1000 K, and T > 1000 K, respectively. The obtained RPMD rate constants agree well with the experimental measurements. In addition, a detailed analysis of the free-energy curves and transmission coefficients reveals that the quantum tunneling significantly affects the reaction dynamics, even at high temperatures.

Free Energy Evaluation of Cavity Formation in Metastable Liquid Based on Stochastic Thermodynamics.

Nucleation is a fundamental and general process at the initial stage of first-order phase transition. Although various models based on the classical nucleation theory (CNT) have been proposed to explain the energetics and kinetics of nucleation, detailed understanding at nanoscale is still required. Here, in view of the homogeneous bubble nucleation, we focus on cavity formation, in which evaluation of the size dependence of free energy change is the key issue. We propose the application of a formula in stochastic thermodynamics, the Jarzynski equality, for data analysis of molecular dynamics (MD) simulation to evaluate the free energy of cavity formation. As a test case, we performed a series of MD simulations with a Lennard-Jones (LJ) fluid system. By applying an external spherical force field to equilibrated LJ liquid, we evaluated the free energy change during cavity growth as the Jarzynski's ensemble average of required works. A fairly smooth free energy curve was obtained as a function of bubble radius in metastable liquid of mildly negative pressure conditions.

Role of Solvents in Oriented Attachment of Ag Nanoparticles: Insights from Molecular Dynamics Simulations and Topological Analysis.

Although the solvation force is considered one of the key forces behind the oriented attachment (OA), the precise roles of solvents in this process remain incompletely elucidated. In this study, we examined the effect of solvent polarities (water, acetone, and chloroform) on the attachment of silver nanoparticles by calculating the free energy curves for the OA process. The observed magnitudes of the binding energies and approaching and dissociation energy barriers are commensurate with the respective solvent polarities. Consequently, OA is more likely to occur in acetone with an intermediate permittivity relative to that of water and chloroform. Additionally, we identified a topological descriptor, namely, the Euler characteristic, of the solvent network, especially the water network, between two approaching surfaces, which manifests a linear correlation with the observed free energy profiles. This descriptor holds promise as a quantitative tool for predicting interactions between nanoparticles in solvent environments featuring hydrogen bond networks.

Elucidating Heavy-Atom-Tunneling Kinetics in the Cope Rearrangement of Semibullvalene.

In this work, we characterize the temperature dependence of kinetic properties in heavy atom tunneling reactions by means of molecular dynamics simulations, including nuclear quantum effects (NQEs) via Path Integral theory. To this end, we consider the prototypical Cope rearrangement of semibullvalene. The reaction was studied in the 25-300 K temperature range observing that the inclusion of NQEs modifies the temperature behavior of both free energy barriers and dynamical recrossing factors with respect to classical dynamics. Notably, while in classical simulations the activation free energy shows a very weak temperature dependence, it becomes strongly dependent on temperature when NQEs are included. This temperature behavior shows a transition from a regime where the quantum effects are limited and can mainly be traced back to zero point energy, to a low temperature regime where tunneling plays a dominant role. In this regime, the free energy curve tunnels below the potential energy barrier along the reaction coordinate, allowing much faster reaction rates. Finally, the temperature dependence of the rate constants obtained from molecular dynamics simulations was compared with available experimental data and with semi-classical transition state theory calculations, showing comparable behaviors and similar transition temperatures from thermal to (deep) tunneling regime.

Theoretical screening of electrocatalytic performance of Fe@BNC materials in lithium-sulfur batteries

Advanced cathode materials can suppress the shuttle effect and improve the slow sulfur reduction kinetics during discharge in lithium-sulfur batteries. The catalytic performance of Fe@BNC single-atom catalysts as cathode materials was evaluated through simulations based on density functional theory in this article. By calculating the Gibbs free energy curve and adsorption energy of polysulfides on the substrate, it was found that Fe@BNC has a reasonable adsorption energy range and good catalytic activity. Moreover, calculations of reaction energy barriers indicate that Fe@B1N3 performs well in delithiation when charged. The Research investigates in detail the electrocatalytic properties and electronic structure properties of Fe@BNC as a cathode material for lithium-sulfur batteries. This paper highlights its potential to improve battery performance by reducing the shuttle effect and accelerating the redox kinetics.

Trade Off between Hydrodynamic and Thermodynamic Forces at the Liquid-Liquid Interface.

Viscous fingering (VF) instability has been investigated in the case of a partially miscible binary system by nonlinear numerical simulations. Partially miscible fluid systems offer the possibility of phase separation coupled with VF instability. The thermodynamics of such systems are governed by the Margules parameter (interaction parameter) as well as the fluid concentrations. Kinetics of the decomposition is also influenced by dynamical parameters such as the viscosity of the fluid, which incidentally also affects the hydrodynamic forces. Here, we explore the effects of concentration and Margules parameter in order to ascertain the trade-offs incurred between hydrodynamic and thermodynamic effects at the interface as well as the thermodynamics of the bulk. Based on the Gibb's free energy versus concentration curve, we select concentrations (i) outside spinodal and binodal regions, (ii) within binodal but outside the spinodal, and (iii) within the spinodal curve. We solve the modified Cahn-Hilliard-Hele-Shaw equation employing the COMSOL Multiphysics software. Applying high-resolution numerical simulations, we show a strong dependence of the thermodynamic forces on the concentration of the mixtures. Rapid phase separation and hence a faster rate of droplet formation have been found when the concentration lies inside the spinodal region. Further, we have investigated the correlation between the fractal dimension and dynamics of the system. The spatiotemporal studies presented in this work clearly illustrate the competition between hydrodynamic and thermodynamic forces and provide insights on the kinetics of decomposition and growth of interfacial instabilities.

Free energy curves for the Volmer reaction obtained from molecular dynamics simulation based on quantum chemistry

Hydrogen desorption from Au(111) at a constant electrode charge has been studied by a DFT-based tight binding theory (DFTB). Free energy curves have been obtained from molecular dynamics with umbrella sampling. The activation energy increases linearly with the applied negative charge and decreases with temperature, so that the Butler-Volmer law does not hold in its strict form. The activation energy is determined by the reorganization of the accepting water molecule and its surroundings, which becomes more facile with temperature. A separation of the free energy curves into a constant chemical part and an electrostatic part, which varies with the charge, does not hold. Because of its speed DFTB is very suitable for the investigation of electrochemical reactions, but is presently hampered by a lack of sets of interaction parameters.

Correlated translational motions in pseudo-rotaxane complexes controlled by a single chemical stimulus.

Coordinated motions are essential in the operation of molecular machines. This feature can be achieved by landscaping the energy surface along the movement coordinates. Herein, we present an approach of using a single stimulus to modify the free energy curve describing the threading and shuttling of a ring along a linear molecule. This approach has been realized by locating two identical ring-binding sites near the axle termini.

Understanding ion-transfer reactions in silver electrodissolution and electrodeposition from first-principles calculations and experiments.

The electrified aqueous/metal interface is critical in controlling the performance of energy conversion and storage devices, but an atomistic understanding of even basic interfacial electrochemical reactions challenges both experiment and computation. We report a combined simulation and experimental study of (reversible) ion-transfer reactions involved in anodic Ag corrosion/deposition, a model system for interfacial electrochemical processes generating or consuming ions. With the explicit modeling of the electrode potential and a hybrid implicit-explicit solvation model, the density functional theory calculations produce free energy curves predicting thermodynamics, kinetics, partial charge profiles, and reaction trajectories. The calculated (equilibrium) free energy barriers (0.2 eV), and their asymmetries, agree with experimental activation energies (0.4 eV) and transfer coefficients, which were extracted from temperature-dependent voltage-step experiments on Au-supported, Ag-nanocluster substrates. The use of Ag nanoclusters eliminates the convolution of the kinetics of Ag+(aq.) generation and transfer with those of nucleation or etch-pit formation. The results indicate that the barrier is controlled by the bias-dependent competition between partial solvation of the incipient ion, metal-metal bonding, and electrostatic stabilization by image charge, with the latter two factors weakened by stronger positive biases. We also report simulations of the bias-dependence of defect generation relevant to nucleating corrosion by removing an atom from a perfect Ag(100) surface, which is predicted to occur via a vacancy-adatom intermediate. Together, these experiments and calculations provide the first validated, accurate, molecular model of the central steps that govern the rates of important dissolution/deposition reactions broadly relevant across the energy sciences.

Temperature dependent magnetic properties of crystallographically amorphous TbCo: An atomistic simulation study

Due to interesting properties such as perpendicular magnetic anisotropy (PMA), ferrimagnetism, etc., rare earth-transition metal(RE-TM) alloys attract considerable attention in ultrafast and terahertz spintronics applications. The magnetic properties of RE-TM alloys strongly depend on their composition and vary with temperature. Here, we model crystallographically amorphous ferrimagnetic TbCo using atomistic spin dynamics(ASD) simulations to study their temperature dependence on magnetic properties by varying the compositions. In this study, we investigate the temperature dependence of magnetisation, uniaxial anisotropy, and coercivity values of amorphous TbxCo100−x for the composition range Tb18Co82 to Tb36Co64. The monte carlo method is used to calculate the temperature dependence of magnetisation and calculate the magnetisation compensation temperature(TM) and curie temperature(Tc) values for different compositions. The temperature dependence of uniaxial anisotropy is calculated from the angular dependence of free energy curves calculated at different temperatures using constrained monte carlo methods. Further, we evaluate the temperature dependence of coercivity values by calculating the magnetic hysteresis at different temperatures using the LLG Heun method. The results show the magnetic properties of amorphous TbCo can be easily tuned by varying their composition and have a strong temperature dependence. These highly tunable magnetic properties make them promising candidates for spintronics applications.

Nucleation by a charged particle in fluids containing salt

We present a model to describe ion-induced nucleation in fluids. Nucleation is induced by a charged molecular aggregate, a large ion, a charged colloid, or an aerosol particle. This model generalizes the Thomson model to polar environments. Solving the Poisson-Boltzmann equation, we find the potential profiles around the charged core and calculate the energy. Our results are analytical in the Debye-Hückel limit and numerical otherwise. From the Gibbs free energy curve vs. nucleus size, we find the metastable and stable states and the energy barrier between them, for varying saturation values, core's charge, and amount of salt. The nucleation barrier decreases with increasing core charge or Debye length. We calculate the phase lines in the phase diagram of supersaturation and core charge. We find regions of one phase, electro-prewetting, spontaneous nucleation, ion-induced nucleation, and classical-like nucleation.

Phase field modeling and computation of vesicle growth or shrinkage.

We present a phase field model for vesicle growth or shrinkage induced by an osmotic pressure due to a chemical potential gradient. The model consists of an Allen-Cahn equation describing the evolution of the phase field parameter that describes the shape of the vesicle and a Cahn-Hilliard-type equation describing the evolution of the ionic fluid. We establish conditions for vesicle growth or shrinkage via a common tangent construction using free energy curves. During the membrane deformation, the model ensures total mass conservation of the ionic fluid, and we weakly enforce a surface area constraint of the vesicle. We develop a stable numerical scheme and an efficient nonlinear multigrid solver to evolve the phase and concentration fields, and we use this to evolve the fields to near equilibrium for 2D vesicles. Convergence tests confirm an [Formula: see text] accuracy for our scheme and near-optimal convergence for our multigrid solver. Numerical results reveal that the diffuse interface model captures the main features of cell shape dynamics: for a growing vesicle, there exist circle-like equilibrium shapes if the concentration difference across the membrane and the initial osmotic pressure are large enough; while for a shrinking vesicle, there exists a rich collection of finger-like equilibrium morphologies.

Effects of temperature and microwave on the stability of the blast effector complex APikL2A/sHMA25 as determined by molecular dynamics analyses.

Magnaporthe oryzae is the causal agent of rice blast, and understanding how abiotic stress affects the resistance of plants to this disease is useful for designing disease control strategies. In this paper, the effects of temperature and microwave irradiation on the effector complex comprising APikL2A from M. oryzae and sHMA25 from foxtail millet were investigated by molecular dynamics simulations using the GROMACS software package. While the structure of APikL2A/sHMA25 remained relatively stable in a temperature range of 290K (16.85°C) to 320K (46.85°C), the concave shape of the temperature-dependent binding free energy curve indicated that there was maximum binding affinity between APikL2A and sHMA25 at 300K-310K. This coincided with the optimum infectivity temperature, thus suggesting that coupling of the two polypeptides may play a role in the infection process. A strong oscillating electric field destroyed the structure of APikL2A/sHMA25, although it was stable and not susceptible to weak electric fields.

Structural mechanism of Fab domain dissociation as a measure of interface stability

Therapeutic antibodies should not only recognize antigens specifically, but also need to be free from developability issues, such as poor stability. Thus, the mechanistic understanding and characterization of stability are critical determinants for rational antibody design. In this study, we use molecular dynamics simulations to investigate the melting process of 16 antigen binding fragments (Fabs). We describe the Fab dissociation mechanisms, showing a separation in the VH–VL and in the CH1–CL domains. We found that the depths of the minima in the free energy curve, corresponding to the bound states, correlate with the experimentally determined melting temperatures. Additionally, we provide a detailed structural description of the dissociation mechanism and identify key interactions in the CDR loops and in the CH1–CL interface that contribute to stabilization. The dissociation of the VH–VL or CH1–CL domains can be represented by conformational changes in the bend angles between the domains. Our findings elucidate the melting process of antigen binding fragments and highlight critical residues in both the variable and constant domains, which are also strongly germline dependent. Thus, our proposed mechanisms have broad implications in the development and design of new and more stable antigen binding fragments.

Understanding microstructure evolution and corrosion behavior of wire arc cladding inconel 625 Superalloy by thermodynamic approaches

Ni-based superalloys have excellent corrosion and oxidation resistance and are often used to make coatings on engineering components or steel materials. The free energy of the melt of Inconel 625 and multiple mixed Ni-based alloy were calculated by the optimized molecular interaction volume model (MIVM), and the cladding material composition is designed according to the composition - free energy curve. The corrosion resistance of the single and double deposited Ni-based layers with different Fe content were studied and compared. Potentiodynamic polarization and electrochemical impedance spectroscopy(EIS) analyses show that the corrosion resistance of the single deposited layers increases with the increase of Fe element, which Component is designed by thermodynamic calculation. Because of the thermodynamic stability of alloy melt is improved by the increase of Fe element, and reducing element segregation and formation of Laves phase. The pitting potential of the single deposited layer increase with the increase of Fe content, and the passivation film of the double deposited layers are more stable.

The Rate Constant - Reaction Free Energy Dependence for the Electron Transfer Reactions in Solutions. The Way to Interpret the Experimental Data Correctly

The relative influences of the reorganization energies of the classical and quantum modes on the maximum position of the rate constant – reaction free energy curve have been studied. In the framework of the continuum electrostatics, the electron transfer reorganization energies in methyltetrahydrofurane solutions for the system biphenylyl – spacer – acceptor were calculated. For different acceptors the solvent reorganization energy varies from 1.0 to 1.1 eV. When added with the rather small reorganization energies for classical intra-molecular modes we obtain 1.13 - 1.34 eV. With account of possible errors this coincides practically with the experimental estimate of the energy at the maximum of the rate–free energy curve DGmax ? -1.2 eV. Hence, we can conclude that the reorganization of quantum modes does not influence substantially the position of this maximum. To the contrary, in a non-polar solvent isooctane were the solvent reorganization does not play any role the reorganization of the quantum intra-reactants modes becomes determinant. These conclusions agree fully with the results of the general theoretical analysis and should be accounted for in the experimental data interpretation.

Chitin and Chitosan Binding to the α-Chitin Crystal: A Molecular Dynamics Study.

Understanding the binding of chitosan oligomers to the surface of a chitin nanocrystal is important for improving the enzymatic deacetylation of chitin and for the design of chitin/chitosan composite films. Here, we study the binding of several chito-oligomers to the (100) surface of an α-chitin crystal using molecular dynamics (MD), steered MD, and umbrella sampling. The convergence of the free energy was carefully considered and yielded a binding energies of -12.5 and -2 kcal mol-1 for 6-monomer-long chitin and uncharged chitosan oligomers, respectively. We also found that the results for the umbrella sampling were consistent with the force profile from the steered MD and with classical MD simulations of the adsorption process. Our results give insight into the molecular-scale interactions, which can be helpful for the design of new chitin composite films. Furthermore, the free energy curves we present can be used to validate coarse-grained models for chitin and chitosan, which are necessary to study the self-assembly of chitin crystals due to the long time scale of the process.

Synergistic Effects of IMX-104 Components in Membrane Absorption: A Computational Study.

New insensitive munitions such as IMX-104 formulations are being developed to improve the safety suffering from accidental stimulations. Experimental data indicated the synergistic toxicity of 2,4-dinitroanisole (DNAN) and hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) in IMX-104, which increased the concern about its environmental and health threats. Indeed, little is known about the synergistic mechanism. Here, we investigated the membrane absorption of DNAN and RDX as the first step toward uncovering synergistic toxicity. The permeability coefficient, transmembrane time, and liposome-water partition coefficient were calculated by the umbrella sampling technique. The results show that component RDX in the IMX-104 formulation promotes the membrane absorption of another more toxic component DNAN, suggesting that the synergistic toxicity effect of IMX-104 may emerge from their membrane adsorption stage. In detail, the integrating free-energy curves show that DNAN, RDX, or their mixture in membranes would promote subsequent molecules passing through membranes. For the mixture of DNAN and RDX, RDX was absorbed by the membrane before DNAN. Postabsorbed DNAN tends to stay around RDX, which is due to the strong van der Waals (VDW) interaction between them. RDX stabilized under phospholipid headgroups limits the overflow of DNAN from the membrane, which results in 11% more absorption of DNAN by the membrane than in the case of the pure DNAN system.

Calcite Kinks Grow via a Multistep Mechanism.

The classical model of crystal growth assumes that kinks grow via a sequence of independent adsorption events where each solute transitions from the solution directly to the crystal lattice site. Here, we challenge this view by showing that some calcite kinks grow via a multistep mechanism where the solute adsorbs to an intermediate site and only transitions to the lattice site upon the adsorption of a second solute. We compute the free energy curves for Ca and CO3 ions adsorbing to a large selection of kink types, and we identify kinks terminated both by Ca ions and by CO3 ions that grow in this multistep way.

Obtaining Consistent Free Energies for Ion Binding at Surfaces from Solution: Pathways versus Alchemy for Determining Kink Site Stability.

Ion incorporation or removal from a solid at the interface with solution is a fundamental part of crystal growth. Despite this, there have been few quantitative determinations of the thermodynamics for such processes from atomistic molecular dynamics due to the associated technical challenges. In this study, we compute the free energies for ion removal from kink sites at the interface between NaCl and water as an illustrative example. To examine the influence of the free energy technique used, we compare methods that follow an explicit pathway for dissolution with those that focus on the thermodynamics of the initial and final states using metadynamics and free energy perturbation, respectively. While the initial results of the two approaches are found to be completely different, it is demonstrated that the thermodynamics can be reconciled with appropriate corrections for the standard states, thus illustrating the need for caution in interpreting raw free energy curves for ion binding as widely found in the literature. In addition, a new efficient approach is introduced to correct for the system size dependence of kink site energies both due to the periodic interaction of charges in an inhomogeneous dielectric system and due to the dipolar interactions between pairs of kinks along a row. Ultimately, it is shown that with suitable care, both classes of free energy techniques are capable of producing kink site stabilities that are consistent with the solubility of the underlying bulk solid. However, the precise values for individual kink sites exhibit a small systematic offset, which can be ascribed to the contribution of the interfacial potential to the pathway-based results. For the case of NaCl, the free energies of the kink sites relative to a 1 M aqueous solution for Na+ and Cl- are found to be surprisingly different and of opposite sign, despite the ions having very similar hydration free energies.