Search NASA⌕ Search

SEARCH · Search NASA

Results for “Free energy calculations”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Large-scale application of free energy perturbation calculations for antibody design

Abstract Alchemical free energy perturbation (FEP) is a rigorous and powerful technique to calculate the free energy difference between distinct chemical systems. Here we report our implementation of automated large-scale FEP calculations, using the Amber software package, to facilitate antibody design and evaluation. In combination with Hamiltonian replica exchange, our FEP simulations aim to predict the effect of mutations on both the binding affinity and the structural stability. Importantly, we incorporate multiple strategies to faithfully estimate the statistical uncertainties in the FEP results. As a case study, we apply our protocols to systematically evaluate variants of the m396 antibody for their conformational stability and their binding affinity to the spike proteins of SARS-CoV-1 and SARS-CoV-2. By properly adjusting relevant parameters, the particle collapse problems in the FEP simulations are avoided. Furthermore, large statistical errors in a small fraction of the FEP calculations are effectively reduced by extending the sampling, such that acceptable statistical uncertainties are achieved for the vast majority of the cases with a modest total computational cost. Finally, our predicted conformational stability for the m396 variants is qualitatively consistent with the experimentally measured melting temperatures. Our work thus demonstrates the applicability of FEP in computational antibody design.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Alchemical Free Energy Estimators and Molecular Dynamics Engines: Accuracy, Precision, and Reproducibility

The binding free energy between a ligand and its target protein is an essential quantity to know at all stages of the drug discovery pipeline. Assessing this value computationally can offer insight into where efforts should be focused in the pursuit of effective therapeutics to treat a myriad of diseases. In this work, we examine the computation of alchemical relative binding free energies with an eye for assessing reproducibility across popular molecular dynamics packages and free energy estimators. The focus of this work is on 54 ligand transformations from a diverse set of protein targets: MCL1, PTP1B, TYK2, CDK2, and thrombin. These targets are studied with three popular molecular dynamics packages: OpenMM, NAMD2, and NAMD3 alpha. Trajectories collected with these packages are used to compare relative binding free energies calculated with thermodynamic integration and free energy perturbation methods. The resulting binding free energies show good agreement between molecular dynamics packages with an average mean unsigned error between them of 0.50 kcal/mol. The correlation between packages is very good, with the lowest Spearman’s, Pearson’s and Kendall’s tau correlation coefficients being 0.92, 0.91, and 0.76, respectively. Agreement between thermodynamic integration and free energy perturbation is shown to be very good when using ensemble averaging.

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

High-Precision Calculation of Nanoparticle (Nanocrystal) Potentials of Mean Force and Internal Energies

Thermodynamic stability assessment of nanocrystal systems requires precise free energy calculations. This study highlights the importance of meticulous control over various factors, including the thermostat, time step, potential cutoff, initial configuration, sampling method, and overall simulation duration. Free energy computations in dry (solvent-free) systems are on the order of several hundred $k_BT$ but can be obtained with consistent accuracy. However, calculation of internal energies becomes challenging, as they are typically much larger in magnitude than free energies and exhibit significant noise and reduced reliability. To address this limitation, we propose a new internal energy estimate that drastically reduces the noise. Here, we also present formulas that enable the optimization of the parameters of the harmonic bias potential for optimal convergence. Finally, we discuss the implications of these findings for the computation of free energies in nanocrystal clusters and superlattices.

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

Potent Noncovalent Inhibitors of the Main Protease of SARS-CoV-2 from Molecular Sculpting of the Drug Perampanel Guided by Free Energy Perturbation Calculations

Starting from our previous finding of 14 known drugs as inhibitors of the main protease (M pro ) of SARS-CoV-2, the virus responsible for COVID-19, we have redesigned the weak hit perampanel to yield multiple noncovalent, nonpeptidic inhibitors with ca. 20 nM IC 50 values in a kinetic assay. Free-energy perturbation (FEP) calculations for M pro -ligand complexes provided valuable guidance on beneficial modifications that rapidly delivered the potent analogues. The design efforts were confirmed and augmented by determination of high-resolution X-ray crystal structures for five analogues bound to M pro . Results of cell-based antiviral assays further demonstrated the potential of the compounds for treatment of COVID-19. In addition to the possible therapeutic significance, the work clearly demonstrates the power of computational chemistry for drug discovery, especially FEP-guided lead optimization.

99 GENERAL AND MISCELLANEOUS↗
NASA NTRS2005

Optimal Sampling of a Reaction Coordinate in Molecular Dynamics

Estimating how free energy changes with the state of a system is a central goal in applications of statistical mechanics to problems of chemical or biological interest. From these free energy changes it is possible, for example, to establish which states of the system are stable, what are their probabilities and how the equilibria between these states are influenced by external conditions. Free energies are also of great utility in determining kinetics of transitions between different states. A variety of methods have been developed to compute free energies of condensed phase systems. Here, I will focus on one class of methods - those that allow for calculating free energy changes along one or several generalized coordinates in the system, often called reaction coordinates or order parameters . Considering that in almost all cases of practical interest a significant computational effort is required to determine free energy changes along such coordinates it is hardly surprising that efficiencies of different methods are of great concern. In most cases, the main difficulty is associated with its shape along the reaction coordinate. If the free energy changes markedly along this coordinate Boltzmann sampling of its different values becomes highly non-uniform. This, in turn, may have considerable, detrimental effect on the performance of many methods for calculating free energies.

Pohorille, Andrew↗
DOE OSTI2023

Revisiting the pseudo-supercritical path method: An improved formulation for the alchemical calculation of solid–liquid coexistence

Alchemical free energy calculations via molecular dynamics have been applied to obtain thermodynamic properties related to solid–liquid equilibrium conditions, such as melting points. In recent years, the pseudo-supercritical path (PSCP) method has proved to be an important approach to melting point prediction due to its flexibility and applicability. In the present work, we propose improvements to the PSCP alchemical cycle to make it more compact and efficient through a concerted evaluation of different potential energies. The multistate Bennett acceptance ratio (MBAR) estimator was applied at all stages of the new cycle to provide greater accuracy and uniformity, which is essential concerning uncertainty calculations. In particular, for the multistate expansion stage from solid to liquid, we employed the MBAR estimator with a reduced energy function that allows affine transformations of coordinates. Free energy and mean derivative profiles were calculated at different cycle stages for argon, triazole, propenal, and the ionic liquid 1-ethyl-3-methyl-imidazolium hexafluorophosphate. Comparisons showed a better performance of the proposed method than the original PSCP cycle for systems with higher complexity, especially the ionic liquid. Furthermore, a detailed study of the expansion stage revealed that remapping the centers of mass of the molecules or ions is preferable to remapping the coordinates of each atom, yielding better overlap between adjacent states and improving the accuracy of the methodology.

25 ENERGY STORAGE↗
DOE OSTI2025

Binding Free Energy Analysis of Colicin D, E3 and E8 to Their Respective Cognate Immunity Proteins Using Computational Simulations

Colicins are antimicrobial proteins produced by bacteria for the purpose of destroying neighboring bacteria. Colicin activity is neutralized by a specific cognate immunity protein in order to protect the host. This study investigates the structural and binding mechanisms underlying the interaction of colicin-D, -E3 and -E8 to their respective immunity proteins (ImD, Im3 and Im8) using structure prediction, molecular dynamics (MD) simulations and MM-PBSA approach of free energy calculations. High-confidence colicin-immunity (Col-Im) complex structures predicted using AlphaFold2 were subjected to MD simulations of 150 ns with GROMACS and were analyzed for the binding free energy calculation using gmx_MMPBSA. Results showed that the complex of Col_E3-Im3 exhibited the most favorable binding free energy, driven by strong van der Waals and electrostatic interactions. Col_D-ImD and Col_E8-Im8 also showed the favorable binding. Electrostatics and hydrogen bonding emerged as a key factor driving binding and stability, while polar solvation acted as a destabilizing factor across all systems. These outcomes provide an understanding of the molecular mechanisms of Col-Im systems, with potential applications for developing natural antimicrobials for food safety.

Biochemistry & Molecular Biology↗
DOE OSTI2021

Ab initio anharmonic thermodynamic properties of cubic Ca Si O 3 perovskite

We present an ab initio study of the thermodynamic properties of cubic CaSiO 3 perovskite (CaPv) over the pressure and temperature range of the Earth's lower mantle. We compute the anharmonic phonon dispersions throughout the Brillouin zone by utilizing the phonon quasiparticle approach, which characterizes the intrinsic temperature dependence of phonon frequencies and, in principle, captures full anharmonicity. Such temperature-dependent phonon dispersions are used to calculate ab initio free energy in the thermodynamic limit (N → ∞) within the framework of the phonon gas model. Accurate free energy calculations enable us to investigate cubic CaPv's thermodynamic properties, e.g., thermal expansivity, Grüneisen parameter, bulk modulus, heat capacity and thermal equation of state, where anharmonic effects are demonstrated. Furthermore, the present methodology provides an important theoretical approach for exploring phase boundaries, thermodynamic, and thermoelastic properties of strongly anharmonic materials at high pressures and temperatures.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Comparison of Equilibrium and Nonequilibrium Approaches for Relative Binding Free Energy Predictions

Alchemical relative binding free energy calculations have recently found important applications in drug optimization. A series of congeneric compounds are generated from a preidentified lead compound, and their relative binding affinities to a protein are assessed in order to optimize candidate drugs. While methods based on equilibrium thermodynamics have been extensively studied, an approach based on nonequilibrium methods has recently been reported together with claims of its superiority. However, these claims pay insufficient attention to the basis and reliability of both methods. Here we report a comparative study of the two approaches across a large data set, comprising more than 500 ligand transformations spanning in excess of 300 ligands binding to a set of 14 diverse protein targets. Ensemble methods are essential to quantify the uncertainty in these calculations, not only for the reasons already established in the equilibrium approach but also to ensure that the nonequilibrium calculations reside within their domain of validity. If and only if ensemble methods are applied, we find that the nonequilibrium method can achieve accuracy and precision comparable to those of the equilibrium approach. Compared to the equilibrium method, the nonequilibrium approach can reduce computational costs but introduces higher computational complexity and longer wall clock times. There are, however, cases where the standard length of a nonequilibrium transition is not sufficient, necessitating a complete rerun of the entire set of transitions. This significantly increases the computational cost and proves to be highly inconvenient during large-scale applications. Our findings provide a key set of recommendations that should be adopted for the reliable implementation of nonequilibrium approaches to relative binding free energy calculations in ligand-protein systems.

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

Excited state electron transfer in A 2 and A 2 B 2 functionalized zinc porphyrins carrying rigid and flexible β -pyrrole π-extended substituents

Optical absorption and emission, electrochemical, and photochemical properties of peripherally functionalized with flexible and rigid π-extended substituents on A 2 and A 2 B 2 type zinc porphyrins is investigated. The significance of rigid π-substituents over flexible ones in governing the spectral properties is unraveled. Flexible π-substituents on the porphyrin ring caused appreciable spectral broadening compared to porphyrin carrying rigid π-substituents. Further, supramolecular dyads are formed by coordinating phenyl imidazole functionalized fullerene, C 60 Im. Here, the calculated binding constants for the 1:1 complexes is in the order of 2–7 × 10 5 M −1 suggesting stable complex formation. Free-energy calculations performed according to the Rehm–Weller approach suggested possibility of excited state electron transfer in these dyads. Femtosecond transient absorption studies of the dyads performed in o-dichlorobenzene showed evidence of occurrence of electron transfer from the singlet-excited state that was in competition with the intersystem crossing process to populate the triplet-excited state of porphyrins.

A2 and A2B2 functionalized zinc↗
DOE OSTI2025

gRASPA

GPU Monte Carlo Simulation Code with a taste of RASPA We present enhancements in Monte Carlo simulation speed and functionality within an open-source code, gRASPA, which uses graphical processing units (GPUs) to achieve significant performance improvements compared to serial, CPU implementations of Monte Carlo. The code supports a wide range of Monte Carlo simulations, including canonical ensemble (NVT), grand canonical, NVT Gibbs, Widom test particle insertions, and continuous-fractional component Monte Carlo. Implementation of grand canonical transition matrix Monte Carlo (GC-TMMC) and a novel feature to allow different moves for the different components of metal-organic framework (MOF) structures exemplify the capabilities of gRASPA for precise free energy calculations and enhanced adsorption studies, respectively. The introduction of a High-Throughput Computing (HTC) mode permits many Monte Carlo simulations on a single GPU device for accelerated materials discovery. The code can incorporate machine learning (ML) potentials. The open-source nature of gRASPA promotes reproducibility and openness in science, and users may add features to the code and optimize it for their own purposes. The code is written in CUDA/C++ and SYCL/C++ to support different GPU vendors. The gRASPA code is publicly available at https://github.com/snurr-group/gRASPA.

Li, Zhao [Purdue/Northwestern/Notre Dame Universit↗
DOE OSTI2025

Confinement-controlled selective CO 2 insertion into a dicopper dihydride core: A multiscale mechanistic study

CO 2 is an abundant C 1 feedstock for fuel and chemical synthesis. We have previously demonstrated experimentally a stepwise insertion of CO 2 into a [Cu 2 H 2 ] core via a solid–gas in crystallo reaction, forming formate species that are unstable and inaccessible under solution-phase conditions. This work elucidates how structural confinement within the crystal lattice enables such selective reactivity. In particular, co-crystallized tetrahydrofuran molecules induce site asymmetry around the [Cu 2 H 2 ] unit, modulating both the local electronic environment and CO 2 diffusion pathways. Using a multiscale computational approach that combines classical molecular mechanics, hybrid quantum mechanics/molecular mechanics molecular dynamics, and enhanced-sampling free energy calculations, we demonstrate how site asymmetry affects CO 2 binding affinities and reaction pathways. These results provide detailed mechanistic insight into CO 2 insertion and hydride transfer, highlighting key differences between crystal- and solution-phase pathways and offering a general framework for understanding how lattice confinement shapes chemical reactivity.

Chemical bonding↗
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↗
NASA NTRS1984

Quantum chemical studies of a model for peptide bond formation. 3. Role of magnesium cation in formation of amide and water from ammonia and glycine

The SN2 reaction between glycine and ammonia molecules with magnesium cation Mg2+ as a catalyst has been studied as a model reaction for Mg(2+)-catalyzed peptide bond formation using the ab initio Hartree-Fock molecular orbital method. As in previous studies of the uncatalyzed and amine-catalyzed reactions between glycine and ammonia, two reaction mechanisms have been examined, i.e., a two-step and a concerted reaction. The stationary points of each reaction including intermediate and transition states have been identified and free energies calculated for all geometry-optimized reaction species to determine the thermodynamics and kinetics of each reaction. Substantial decreases in free energies of activation were found for both reaction mechanisms in the Mg(2+)-catalyzed amide bond formation compared with those in the uncatalyzed and amine-catalyzed amide bond formation. The catalytic effect of the Mg2+ cation is to stabilize both the transition states and intermediate, and it is attributed to the neutralization of the developing negative charge on the electrophile and formation of a conformationally flexible nonplanar five-membered chelate ring structure.

Magnesium/chemistry↗
DOE OSTI2021

Formic Acid Electrooxidation on Pt or Pd Monolayer on Transition-Metal Single Crystals: A First-Principles Structure Sensitivity Analysis

Here, we present a density functional theory analysis of trends for the electrooxidation of formic acid (FAO) on a single Pt or Pd monolayer supported on the close-packed (111) facet of transition metals (Pt*/M or Pd*/M): Au, Ag, Cu, Pt, Pd, Ir, and Rh, the close-packed (0001) facet of Os, Ru, and Re, and the open (100) facet of Au, Ag, Pt, Pd, Ir, and Rh. We show that the deposition of Pt or Pd pseudomorphic monolayers on these single crystals modifies the electronic structure of the Pt or Pd monolayer. Specifically, we found a direct correlation between the d-band center of the Pt and Pd monolayer and the free energy of adsorbed CO*, the latter being a reactivity descriptor for FAO. Together with the free energy of adsorbed OH* as a second reactivity descriptor, we depict the thermochemistry of the reaction network as phase diagrams showing calculated free energies across regions of rate-determining steps. We found that FAO is structure-sensitive on most surfaces studied. Pt*/Au(111) is predicted to be the most active among all Pt*/M(111/0001) surfaces studied, despite binding CO*, the strongest among the close-packed facets. This is the case because of its superiority in activating water to OH*, thus removing CO* at lower potentials than other surfaces. On similar grounds, Pt*/Pd(100), Pd*/Re(0001), Pd*/Au(111), Pd*/Ag(111), and Pd*/Pt(111) are predicted to show higher FAO activity than the corresponding monometallic Pt and Pd surfaces.

(100) facets↗
DOE OSTI2025

The importance of accounting for the Tolman correction to surface tension for nucleation and growth modeling of Fe clusters

Gibbs free energies of clusters are required for predictive modeling of cluster growth during condensation of a cooling vapor. Here, we present a straightforward method of calculating free energies of cluster formation using the data from molecular dynamics (MD) simulations. We apply this method to iron clusters having from 2 to 100 atoms. The energies obtained are verified by comparing to an MD-simulated equilibrium cluster size distribution in a sub-saturated vapor. We show that these free energies differ significantly from those obtained with a commonly used spherical cluster approximation, which relies on a surface tension coefficient of a flat surface, as it is used in the classical nucleation theory (CNT). We show that the spherical cluster approximation in CNT can be improved by using a cluster-size-dependent Tolman correction for the surface tension. The Tolman length and effective surface tension values were derived for iron clusters, and they significantly differ from the commonly used experimentally measured values. This improved approximation does not account for geometric magic number effects responsible for spikes and troughs in densities of neighbor cluster sizes. Nonetheless, it allows to more accurately model cluster formation from a cooling vapor. It better reproduces the condensation timeline, overall shape of the cluster size distribution, average cluster size, and the distribution width. In contrast, using a constant surface tension coefficient (as done in CNT) resulted in incorrect condensation dynamics and cluster size distributions. The analytical expression for cluster nucleation rate from CNT was updated to account for the size-dependence of cluster surface tension.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

ML-AMD/exa-pd

Exa-pd is a highly parallelizable workflow for constructing multi-element phase diagrams (PDs). It uses standard sampling techniques—molecular dynamics (MD) and Monte Carlo (MC)—as implemented in the LAMMPS package, to simultaneously sample multiple phases on a fine temperature–composition mesh for free-energy calculations. The workflow uses Parsl as a global controller to manage the MD/MC jobs to achieve massive parallelization with almost ideal scalability. The resulting free energies of both liquid and solid phases (including solid solutions) are then fed to CALPHAD modeling using the PYCALPHAD package for the construction of a multi-element PD.

Zhang, Feng [Ames Laboratory (AMES), Ames, IA (Uni↗