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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Ab initio free energies of liquid metal alloys: Application to the phase diagrams of Li-Na and K-Na

Comparison of free energies between different phases and different compositions underlies the prediction of alloy phase diagrams. To allow direct comparison, consistent reference points for the energies or enthalpies are required, and the entropy must be placed on an absolute scale, yielding absolute free energies. Here we derive absolute free energies of liquids from ab-initio molecular dynamics (AIMD) by combining the directly simulated enthalpies with an entropy derived from simulated densities and pair correlation functions. Additionally, as an example of the power of this method we calculate the phase diagrams of two binary alkali metal alloys, Li-Na and K-Na, revealing a critical point and liquid-liquid phase separation in the former case, and a deep eutectic in the latter. Good agreement with experimental data demonstrates the power of this simple method.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Ligand structure and adsorption free energy of nanocrystals on solid substrates

In this paper, we present an investigation on the absorption of alkylthiolated nanocrystals on a solid substrate. We calculate adsorption free energies and report a number of effects induced by the substrate. Nearest neighbor distances and bonding free energies are significantly different than for a free floating case, there is a weakening of bonding free energies among nanocrystals, and the adsorption is manifestly anisotropic, i.e., stronger along certain directions of the nanocrystal core. We contend that this last result accounts for the Bain transition (fcc → bcc) observed in experimental results. We report the presence of vortices induced by the substrate, which explain the increased nearest neighbor distance among nanocrystals, which is in excellent quantitative agreement with experimental results and with the predictions of the Orbifold Topological Model. Implications for the assembly of nanostructures and future experiments are also discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

The performance of ensemble-based free energy protocols in computing binding affinities to ROS1 kinase

Optimization of binding affinities for compounds to their target protein is a primary objective in drug discovery. Herein we report on a collaborative study that evaluates a set of compounds binding to ROS1 kinase. We use ESMACS (enhanced sampling of molecular dynamics with approximation of continuum solvent) and TIES (thermodynamic integration with enhanced sampling) protocols to rank the binding free energies. The predicted binding free energies from ESMACS simulations show good correlations with experimental data for subsets of the compounds. Consistent binding free energy differences are generated for TIES and ESMACS. Although an unexplained overestimation exists, we obtain excellent statistical rankings across the set of compounds from the TIES protocol, with a Pearson correlation coefficient of 0.90 between calculated and experimental activities.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Extraction of the spin-glass free-energy landscape from $1/f$ noise measurements

The 1/f resistance noise has been measured in thin CuMn (13.5 at.%) spin-glass films. The temperature and frequency dependence have been analyzed in terms of the landscape of free-energy barriers. Here this analysis provides the full barrier distribution for various thin film thicknesses between 10 nm and 80 nm. The free-energy barrier height distribution's width and energy position have been determined. Contrary to previous models with fixed shape and energy, the free-energy landscape is described by a distribution of barriers that both shifts and changes shape as the temperature is reduced. The dependence of this distribution is in contrast with recent predictions. Using the fluctuation dissipation theorem, the 1/f measurements connect with χ", displaying agreement with other direct measurements of the latter.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Impact of magnetic and electric fields on the free energy to form a calcium carbonate ion-pair

Electromagnetic fields are used in water treatment and desalination to regulate scale formation and extend the lifetime of membranes. External electric and magnetic fields can promote or suppress mineral nucleation and growth. However, the molecular-scale mechanisms of such processes remain unknown. Computing the free energies needed to form ion pairs under external fields provides important insights into understanding the elemental steps during the initial formation of mineral scales. In this paper, we used molecular dynamics combined with metadynamics simulations to investigate the free energies of forming the [Ca–CO 3 ] 0 ion pair, a fundamental building block of carbonate scales, under a range of magnetic (up to 10 T) and electric (up to 10 V m −1 ) fields in water. The presence of constant magnetic or electric fields favored the ion pairing reaction and lowered the free energies by up to 3% to 6%. The internal energy and entropic components of the free energy showed significant changes and exhibited non-linear behavior with increasing field strength. The [Ca–CO 3 ] 0 ion pairing is an entropy-driven process in the absence of an external field, but the mechanism shifts to an internal energy-driven process under selected external fields, suggesting possible changes in the nucleation pathways.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Large Scale Study of Ligand–Protein Relative Binding Free Energy Calculations: Actionable Predictions from Statistically Robust Protocols

The accurate and reliable prediction of protein–ligand binding affinities can play a central role in the drug discovery process as well as in personalized medicine. Of considerable importance during lead optimization are the alchemical free energy methods that furnish an estimation of relative binding free energies (RBFE) of similar molecules. Recent advances in these methods have increased their speed, accuracy, and precision. This is evident from the increasing number of retrospective as well as prospective studies employing them. However, such methods still have limited applicability in real-world scenarios due to a number of important yet unresolved issues. Here, we report the findings from a large data set comprising over 500 ligand transformations spanning over 300 ligands binding to a diverse set of 14 different protein targets which furnish statistically robust results on the accuracy, precision, and reproducibility of RBFE calculations. We use ensemble-based methods which are the only way to provide reliable uncertainty quantification given that the underlying molecular dynamics is chaotic. These are implemented using TIES (Thermodynamic Integration with Enhanced Sampling). Results achieve chemical accuracy in all cases. Ensemble simulations also furnish information on the statistical distributions of the free energy calculations which exhibit non-normal behavior. We find that the “enhanced sampling” method known as replica exchange with solute tempering degrades RBFE predictions. We also report definitively on numerous associated alchemical factors including the choice of ligand charge method, flexibility in ligand structure, and the size of the alchemical region including the number of atoms involved in transforming one ligand into another. Our findings provide a key set of recommendations that should be adopted for the reliable application of RBFE methods.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes

Understanding the impact of extractant functionalization on metal-binding energetics in liquid-liquid extraction is essential to guide the development of better separation processes. Traditionally, computational extractant design uses electronic structure calculations on metal-ligand clusters to determine the metal-binding energy of the lowest energy state. Although highly accurate, this approach does not account for all of the relevant physics encountered under experimental conditions. Such methodologies often neglect entropic contributions such as temperature effects and ligand flexibility, in addition to approximating solvent-extractant interactions with implicit solvent models. In this study, we use classical molecular dynamics simulations with an advanced sampling method, metadynamics, to map out extractant molecule conformational free energies in the condensed phase. Here we generate the complete conformational landscape in solution for a family of bidentate malonamide-based extractants with different functionalizations of the headgroup and the side chains. In particular, we show how such alkyl functionalization reshapes the free energy landscape, affecting the free energy penalty of organizing the extractant into the cis-like metal-binding conformation from the trans-like conformation of the free extractant in solution. Specifically, functionalizing alkyl tails to the center of the headgroup has a greater influence on increasing molecular rigidity and disfavoring the binding conformation than functionalizing side chains. These findings are consistent with trends in metal-binding energetics based on experimentally reported distribution ratios. We also consider a different bidentate extractant molecule, carbamoylmethylphosphine oxide, and show how the choice of solvent can further reshape the conformational energetic landscape. This study demonstrates the feasibility of using molecular dynamics simulations with advanced sampling techniques to investigate extractant conformational energetics in solution, which, more broadly, will enable extractant design that accounts for entropic effects and explicit solvation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Ensemble Simulations and Experimental Free Energy Distributions: Evaluation and Characterization of Isoxazole Amides as SMYD3 Inhibitors

Optimization of binding affinities for ligands to their target protein is a primary objective in rational drug discovery. Herein, we report on a collaborative study that evaluates various compounds designed to bind to the SET and MYND domain-containing protein 3 (SMYD3). SMYD3 is a histone methyltransferase and plays an important role in transcriptional regulation in cell proliferation, cell cycle, and human carcinogenesis. Experimental measurements using the scintillation proximity assay show that the distributions of binding free energies from a large number of independent measurements exhibit non-normal properties. We use ESMACS (enhanced sampling of molecular dynamics with approximation of continuum solvent) and TIES (thermodynamic integration with enhanced sampling) protocols to predict the binding free energies and to provide a detailed chemical insight into the nature of ligand-protein binding. Our results show that the 1-trajectory ESMACS protocol works well for the set of ligands studied here. Although one unexplained outlier exists, we obtain excellent statistical ranking across the set of compounds from the ESMACS protocol and good agreement between calculations and experiments for the relative binding free energies from the TIES protocol. ESMACS and TIES are again found to be powerful protocols for the accurate comparison of the binding free energies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Tunable noninteracting free-energy density functionals for high-energy-density physics applications

In this work, we introduce the concept of a tunable noninteracting free-energy density functional and present two examples realized: (i) via a simple one-parameter convex combination of two existing functionals and (ii) via the construction of a generalized gradient approximation (GGA) enhancement factor that contains one free parameter and is designed to satisfy a set of incorporated constraints. Functional (i), constructed as a combination of the local Thomas–Fermi and a pseudopotential-adapted GGA for the noninteracting free-energy, has already demonstrated its practical usability for establishing the high temperature end of the equation of state of deuterium [Phys. Rev. B 104, 144104 (2021)] and CHON resin [Phys. Rev. E 106, 045207 (2022)] for inertial confinement fusion applications. Hugoniot calculations for liquid deuterium are given as another example of how the application of computationally efficient orbital-free density functional theory (OF-DFT) can be utilized with the employment of the developed functionals. Once the functionals have been tuned such that the OF-DFT Hugoniot calculation matches the Kohn–Sham solution at some low-temperature point, agreement with the reference Kohn–Sham results for the rest of the high temperature Hugoniot path is very good with relative errors for compression and pressure on the order of 2% or less.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

Entropic control of the free-energy landscape of an archetypal biomolecular machine

Biomolecular machines are complex macromolecular assemblies that utilize thermal and chemical energy to perform essential, multistep, cellular processes. Despite possessing different architectures and functions, an essential feature of the mechanisms of action of all such machines is that they require dynamic rearrangements of structural components. Surprisingly, biomolecular machines generally possess only a limited set of such motions, suggesting that these dynamics must be repurposed to drive different mechanistic steps. Although ligands that interact with these machines are known to drive such repurposing, the physical and structural mechanisms through which ligands achieve this remain unknown. Using temperature-dependent, single-molecule measurements analyzed with a time-resolution-enhancing algorithm, here, we dissect the free-energy landscape of an archetypal biomolecular machine, the bacterial ribosome, to reveal how its dynamics are repurposed to drive distinct steps during ribosome-catalyzed protein synthesis. Specifically, we show that the free-energy landscape of the ribosome encompasses a network of allosterically coupled structural elements that coordinates the motions of these elements. Moreover, we reveal that ribosomal ligands which participate in disparate steps of the protein synthesis pathway repurpose this network by differentially modulating the structural flexibility of the ribosomal complex (i.e., the entropic component of the free-energy landscape). Here, we propose that such ligand-dependent entropic control of free-energy landscapes has evolved as a general strategy through which ligands may regulate the functions of all biomolecular machines. Such entropic control is therefore an important driver in the evolution of naturally occurring biomolecular machines and a critical consideration for the design of synthetic molecular machines.

Science & Technology - Other Topics↗
DOE OSTI2020

Universal free-energy landscape produces efficient and reversible electron bifurcation

For decades, it was unknown how electron-bifurcating systems in nature prevented energy-wasting short-circuiting reactions that have large driving forces, so synthetic electron-bifurcating molecular machines could not be designed and built. The underpinning free-energy landscapes for electron bifurcation were also enigmatic. We predict that a simple and universal free-energy landscape enables electron bifurcation, and we show that it enables high-efficiency bifurcation with limited short-circuiting (the EB scheme). The landscape relies on steep free-energy slopes in the two redox branches to insulate against short-circuiting using an electron occupancy blockade effect, without relying on nuanced changes in the microscopic rate constants for the short-circuiting reactions. The EB scheme thus unifies a body of observations on biological catalysis and energy conversion, and the scheme provides a blueprint to guide future campaigns to establish synthetic electron bifurcation machines.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Free Energies of Hydrated Halide Anions: High Through-Put Computations on Clusters to Treat Rough Energy-Landscapes

With a longer-term goal of addressing the comparative behavior of the aqueous halides F−, Cl−, Br−, and I− on the basis of quasi-chemical theory (QCT), here we study structures and free energies of hydration clusters for those anions. We confirm that energetically optimal (H2O)nX clusters, with X = Cl−, Br−, and I−, exhibit surface hydration structures. Computed free energies, based on optimized surface hydration structures utilizing a harmonic approximation, typically (but not always) disagree with experimental free energies. To remedy the harmonic approximation, we utilize single-point electronic structure calculations on cluster geometries sampled from an AIMD (ab initio molecular dynamics) simulation stream. This rough-landscape procedure is broadly satisfactory and suggests unfavorable ligand crowding as the physical effect addressed. Nevertheless, this procedure can break down when n≳4, with the characteristic discrepancy resulting from a relaxed definition of clustering in the identification of (H2O)nX clusters, including ramified structures natural in physical cluster theories. With ramified structures, the central equation for the present rough-landscape approach can acquire some inconsistency. Extension of these physical cluster theories in the direction of QCT should remedy that issue, and should be the next step in this research direction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Predicting Small Molecule Transfer Free Energies by Combining Molecular Dynamics Simulations and Deep Learning

Accurately predicting small molecule partitioning and hydrophobicity is critical in the drug discovery process. There are many heterogeneous chemical environments within a cell and entire human body. For example, drugs must be able to cross the hydrophobic cellular membrane to reach their intracellular targets, and hydrophobicity is an important driving force for drug–protein binding. Atomistic molecular dynamics (MD) simulations are routinely used to calculate free energies of small molecules binding to proteins, crossing lipid membranes, and solvation but are computationally expensive. Machine learning (ML) and empirical methods are also used throughout drug discovery but rely on experimental data, limiting the domain of applicability. We present atomistic MD simulations calculating 15,000 small molecule free energies of transfer from water to cyclohexane. This large data set is used to train ML models that predict the free energies of transfer. We show that a spatial graph neural network model achieves the highest accuracy, followed closely by a 3D-convolutional neural network, and shallow learning based on the chemical fingerprint is significantly less accurate. A mean absolute error of ~4 kJ/mol compared to the MD calculations was achieved for our best ML model. We also show that including data from the MD simulation improves the predictions, tests the transferability of each model to a diverse set of molecules, and show multitask learning improves the predictions. This work provides insight into the hydrophobicity of small molecules and ML cheminformatics modeling, and our data set will be useful for designing and testing future ML cheminformatics methods.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Vibrational Entropy Contribution to Mixing Free Energy of Ni-Rich LiNi 1- y Co y O 2

First principles density-functional-theory calculations are performed of the mixing free energy of the layered oxide LiNi 1-y Co y O 2 , a model Li-ion-battery cathode material, at 1000 K. Analysis of internal energy, LN exchange, configurational entropy and vibrational entropy are combined to obtain the net mixing free energy. The vibrational entropy requires a more indirect treatment than the other terms; analysis based on heat capacity is presented here, to show that the vibrational entropy is of comparable magnitude to the configurational entropy, and it tends to promote solid-solution behavior in LiNi 1-y Co y O 2 .

25 ENERGY STORAGE↗
DOE OSTI2021

Computing Free Energies with Fluctuation Relations on Quantum Computers

One of the most promising applications for quantum computers is the dynamic simulation of quantum materials. Current hardware, however, sets stringent limitations on how long such simulations can run before decoherence begins to corrupt results. The Jarzynski equality, a fluctuation theorem that allows for the computation of equilibrium free energy differences from an ensemble of short, non-equilibrium dynamics simulations, can make use of such short-time simulations on quantum computers. Here, we present a quantum algorithm based on the Jarzynski equality for computing free energies of quantum materials. We demonstrate our algorithm using the transverse field Ising model on both a quantum simulator and real quantum hardware. As the free energy is a central thermodynamic property that allows one to compute virtually any equilibrium property of a physical system, the ability to perform this algorithm for larger quantum systems in the future has implications for a wide range of applications including the construction of phase diagrams, prediction of transport properties and reaction constants, and computer-aided drug design.

Bassman, Lindsay↗
DOE OSTI2021

Free Energies of Proton-Coupled Electron Transfer Reagents and Their Applications

Here, we present an update and revision to our 2010 review on the topic of proton- coupled electron transfer (PCET) reagent thermochemistry. Over the past decade, the data and thermochemical formalisms presented in that review have been of value to multiple fields. Concurrently, there have been advances in the thermochemical cycles and experimental methods used to measure these values. This Review (i) summarizes those advancements, (ii) corrects systematic errors in our prior review that shifted many of the absolute values in the tabulated data, (iii) provides updated tables of thermochemical values, and (iv) discusses new conclusions and opportunities from the assembled data and associated techniques. We advocate for updated thermochemical cycles that provide greater clarity and reduce experimental barriers to the calculation and measurement of Gibbs free energies for the conversion of X to XHn in PCET reactions. In particular, we demonstrate the utility and generality of reporting potentials of hydrogenation, E°(V vs H 2 ), in almost any solvent and how these values are connected to more widely reported bond dissociation free energies (BDFEs). The tabulated data demonstrate that E°(V vs H 2 ) and BDFEs are generally insensitive to the nature of the solvent and, in some cases, even to the phase (gas versus solution). This Review also presents introductions to several emerging fields in PCET thermochemistry to give readers windows into the diversity of research being performed. Some of the next frontiers in this rapidly growing field are coordination-induced bond weakening, PCET in novel solvent environments, and reactions at material interfaces.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Linear Correlations of Gibbs Free Energy of REE Phosphates (Monazite, Xenotime, and Rhabdophane) and Internally Consistent Binary Mixing Properties

Rare Earth Elements (REE) phosphates (monazite, xenotime, and rhabdophane) are critical REE-bearing minerals typically formed in hydrothermal and magmatic ore deposits. The thermodynamic properties of those REE minerals are crucial to understanding the solubility, speciation, and transport of REE complexes. However, the standard-state Gibbs free energy of formation (∆G°f) values reported for these minerals in the literature vary by up to 25 kJ mol−1. Here, we present linear free energy relationships that allow the evaluation and estimation of the ∆G°f values at 25 °C and 1 bar for the three minerals from the ionic radius (rREE3+) and the non-solvation Gibbs free energy contribution to the REE3+ aqua ion (∆G°n, REE3+): ∆G°f,monazite − 399.71 rREE3+ = 1.0059 ∆G°n,REE3+ − 2522.51; ∆G°f,xenotime − 344.08 rREE3+ = 0.9909 ∆G°n,REE3+ − 2451.53; and ∆G°f,rhabdophane − 416.17 rREE3+ = 1.0067 ∆G°n, REE3+ − 2688.86. Moreover, based on the new dataset derived for REE end-members, we re-fitted the binary Margules parameter (W) from previous theoretical calculations into linear correlations: W + 0.00204 ∆G°’n,monazite = 39.3549 ∆V + 0.0641; W + 0.00255 ∆G°’n,xenotime = 25.4885 ∆V − 0.0062. The internally consistent thermodynamic properties of these REE phosphates are incorporated into the computer program Supcrtbl, which is available online at Zhu’s research website.

Pan, Ruiguang (ORCID:0000000324896545)↗
DOE OSTI2022

$T\overline{T}$-deformed free energy of the Airy model

Sharpening the correspondence of Jackiw-Teitelboim (JT) gravity and its dual matrix model description at a finite radial cutoff λ through the $T\overline{T}$ deformation is of interest. To proceed, we simplify the problem by considering the Airy model and deform Airy correlators in the same way as in $T\overline{T}$ -deformed JT gravity. We use those correlators to compute the annealed and quenched free energies for both λ > 0 and λ < 0 from an integral representation of the replica trick. At the leading order in λ and low temperatures, we confirm that the genus-zero quenched free energy monotonically decreases as a function of temperature when perturbation theory is valid. We then study the all-genus quenched free energy at low temperatures, where we discover and discuss subtleties due to non-perturbative effects in the Airy model, as well as the contributions from the non-perturbative branch under the $T\overline{T}$ deformation.

2D gravity↗