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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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8 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Extending quantum-mechanical benchmark accuracy to biological ligand-pocket interactions

Predicting the binding affinity of ligands to protein pockets is key in the drug design pipeline. The flexibility of ligand-pocket motifs arises from a range of attractive and repulsive electronic interactions during binding. Accurately accounting for all interactions requires robust quantum-mechanical (QM) benchmarks, which are scarce for ligand-pocket systems. Additionally, disagreement between “gold standard” Coupled Cluster (CC) and Quantum Monte Carlo (QMC) methods casts doubt on many benchmarks for larger non-covalent systems. We introduce the “QUantum Interacting Dimer” (QUID) benchmark framework containing 170 non-covalent (non-)equilibrium systems modeling chemically and structurally diverse ligand-pocket motifs. Symmetry-adapted perturbation theory shows that QUID broadly covers non-covalent binding motifs and energetic contributions. Robust binding energies are obtained using complementary CC and QMC methods, achieving agreement of 0.5 kcal/mol. The benchmark data analysis reveals that several dispersion-inclusive density functional approximations provide accurate energy predictions, though their atomic van der Waals forces differ in magnitude and orientation. Contrarily, semiempirical methods and empirical force fields require improvements in capturing non-covalent interactions (NCIs) for out-of-equilibrium geometries. The wide span of NCIs, highly accurate interaction energies, and analysis of molecular properties take QUID beyond the “gold standard” for QM benchmarks of ligand-protein systems.

Puleva, Mirela [University of Luxembourg, Luxembou↗
DOE OSTI2025

Convergent Protocols for Computing Protein–Ligand Interaction Energies Using Fragment-Based Quantum Chemistry

Fragment-based quantum chemistry methods offer a way to sidestep the steep nonlinear scaling of electronic structure calculations so that large molecular systems can be investigated using high-level methods. Here, we use fragmentation to compute protein–ligand interaction energies in systems with several thousand atoms, using a new software platform for managing fragment-based calculations that implements a screened many-body expansion. Convergence tests using a minimal-basis semiempirical method (HF-3c) indicate that two-body calculations, with single-residue fragments and simple hydrogen caps, are sufficient to reproduce interaction energies obtained using conventional supramolecular electronic structure calculations, to within 1 kcal/mol at about 1% of the computational cost. We also demonstrate that the HF-3c results are illustrative of trends obtained with density functional theory in basis sets up to augmented quadruple-ζ quality. Strategic deployment of fragmentation facilitates the use of converged biomolecular model systems alongside high-quality electronic structure methods and basis sets, bringing ab initio quantum chemistry to systems of hitherto unimaginable size. This will be useful for generation of high-quality training data for machine learning applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Quick-and-Easy Validation of Protein–Ligand Binding Models Using Fragment-Based Semiempirical Quantum Chemistry

Electronic structure calculations in enzymes converge very slowly with respect to the size of the model region that is described using quantum mechanics (QM), requiring hundreds of atoms to obtain converged results and exhibiting substantial sensitivity (at least in smaller models) to which amino acids are included in the QM region. As such, there is considerable interest in developing automated procedures to construct a QM model region based on well-defined criteria. However, testing such procedures is burdensome due to the cost of large-scale electronic structure calculations. Here, we show that semiempirical methods can be used as alternatives to density functional theory (DFT) to assess convergence in sequences of models generated by various automated protocols. The cost of these convergence tests is reduced even further by means of a many-body expansion. We use this approach to examine convergence (with respect to model size) of protein–ligand binding energies. Fragment-based semiempirical calculations afford well-converged interaction energies in a tiny fraction of the cost required for DFT calculations. Two-body interactions between the ligand and single-residue amino acid fragments afford a low-cost way to construct a “QM-informed” enzyme model of reduced size, furnishing an automatable active-site model-building procedure. This provides a streamlined, user-friendly approach for constructing ligand binding-site models that needs neither a priori information nor manual adjustments. Extension to model-building for thermochemical calculations should be straightforward.

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

High-Performance Semiempirical Excited-State Molecular Dynamics Powered by Graphics Processing Units

Here, this Letter introduces excited-state molecular dynamics in PYSEQM, a GPU-accelerated semiempirical quantum chemistry engine implemented in PyTorch. The new module enables Born–Oppenheimer molecular dynamics (BOMD) using configuration-interaction singles and random phase approximation for excited states, allowing long trajectories and large statistical ensembles to be simulated efficiently on a single GPU. We also implement an extended Lagrangian excited-state BOMD (XL-ESMD) scheme that propagates auxiliary electronic variables, enabling relaxed ground and excited-state convergence thresholds without compromising energy conservation. The excited-state BOMD implementation scales smoothly from small chromophores to a nearly 900-atom dendrimer (taking 6.5 s per MD step). PYSEQM also supports batched execution, allowing many geometries or trajectories to be evaluated in a single GPU launch, substantially increasing throughput and making ensemble-based protocols routine. As a demonstration, we compute absorption, emission, and infrared spectra from trajectories propagated on the ground and first excited states. The XL-ESMD scheme yields identical spectra at significantly lower computational cost, establishing the role of extended Lagrangian based dynamics for efficient excited-state BOMD simulations. Beyond raw performance, PYSEQM’s PyTorch foundation provides automatic differentiation for forces, efficient GPU batching, and seamless interfacing with machine learning models. These capabilities position PYSEQM as a practical platform for machine learning-augmented excited-state dynamics and lay the foundation for future data-driven nonadiabatic excited-state dynamics modeling of ultrafast spectroscopic probes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Computationally Guided and Experimentally Validated Design of Custom Chelators for Critical Mineral Recovery

Selective, high throughput separation of target critical metals from complex environments such as fly ash leachates and mining process streams presents a significant challenge for economical production. Custom chelators and sorbents are an attractive technology for selective metal extraction, however it can be difficult to predict their performance, and significant experimental efforts are often required to develop chelating technologies. Here, we present a computational strategy focused on modelling chelator-metal binding interactions and benchmark these results versus experimental data. A computational pipeline combining forcefield, semiempirical, and meta-GGA methods with a thermodynamic framework optimized for error cancellation has been developed to predict binding energies of chelator complexes towards critical mineral recovery applications. This approach, originally validated on [2.2.2] cryptates binding mono- and divalent cations, demonstrated robust predictive capabilities with an R2 of 0.850 against experimental aqueous binding energies. The workflow includes metadynamics for exploring high-dimensional potential energy surfaces and a cluster-continuum model for accurate yet computationally efficient solvation modeling. Error cancellation between solvation energies of free and chelator-coordinated ions enables faster convergence, even with finite cluster sizes. Initial studies on the cryptates revealed consistent metal-ligand coordination patterns, with systematic variations influenced by ion size and charge, highlighting key structural features linked to binding selectivity. Further studies of a proprietary chelator have resulted in identification of previously unreported selectivity towards economically significant metals, which in-house experiments have confirmed, demonstrating the feasibility of this approach. By applying this methodology to new chelators targeting critical minerals such as lithium, cobalt, nickel and other strategic metals, we aim to accelerate the discovery of next-generation chelators for efficient recovery, recycling, and separation processes. This computational framework serves as the backbone of a high-throughput design pipeline tailored for sustainable resource utilization and may be applied to a wide range of systems to meet experimental needs.

computational materials↗
DOE OSTI2026

Ground and excited state gradients with end-to-end differentiable semiempirical quantum chemistry

Accurate and efficient gradients of molecular energy with respect to nuclear degrees of freedom are essential for geometry optimization and molecular dynamics, including simulations that go beyond the Born–Oppenheimer regime. A common approach involves deriving analytical formulas for new electronic structure methods, which is often conceptually difficult and requires tedious coding. Here, we implement analytical, semi-numerical, and automatic differentiation (AD)-based gradient pathways for semiempirical Hamiltonian models in the PYSEQM software package, leveraging both graphics processing unit (GPU) and central processing unit (CPU) architectures. We further extend these capabilities to excited states calculated using the configuration interaction singles and time-dependent Hartree–Fock ansätze. We benchmark wall time, peak memory usage, and accuracy across three molecular families of varying chemical complexity, including systems of up to a thousand atoms. For ground-state simulations, analytical and AD gradients achieve near-identical GPU runtimes, while semi-numerical gradients are slower on GPU but remain competitive on CPU. For excited states, both analytical and custom AD approaches using implicit differentiation show similar performance and low memory requirements, whereas gradients with full AD are memory-limited. AD gradients match analytical ones in accuracy across all tested systems, aided by a quaternion-based diatomic frame rotation for two-center quantities that ensures smooth energy surfaces. Overall, automatic differentiation emerges as a practical alternative to analytical gradients in semiempirical quantum chemistry, offering high accuracy while allowing seamless integration in AI-driven workflows and popular packages, such as PyTorch and JAX. Our results provide actionable guidance for selecting optimal gradient strategies in large-scale ground- and excited-state molecular dynamics simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

A Modified Model Dielectric Function for Analyzing Optical Spectra of InGaN Nanofilms on Sapphire Substrates

Due to a lower InN bandgap energy Eg~0.7 eV, InxGa1−xN/Sapphire epifilms are considered valuable in the development of low-dimensional heterostructure-based photonic devices. Adjusting the composition x and thickness d in epitaxially grown films has offered many possibilities of light emission across a wide spectral range, from ultraviolet through visible into near-infrared regions. Optical properties have played important roles in making semiconductor materials useful in electro-optic applications. Despite the efforts to grow InxGa1−xN/Sapphire samples, no x- and d-dependent optical studies exist for ultrathin films. Many researchers have used computationally intensive methods to study the electronic band structures Ejk→, and subsequently derive optical properties. By including inter-band transitions at critical points from Ejk→, we have developed a semiempirical approach to comprehend the optical characteristics of InN, GaN and InxGa1−xN. Refractive indices of InxGa1−xN and sapphire substrate are meticulously integrated into a transfer matrix method to simulate d- and x-dependent reflectivity RE and transmission TE spectra of nanostructured InxGa1−xN/Sapphire epifilms. Analyses of RE and TE have offered accurate x-dependent shifts of energy gaps for InxGa1−xN (x = 0.5, 0.7) in excellent agreement with the experimental data.

Talwar, Devki N. (ORCID:0000000202723195)↗
DOE OSTI2026

Energy-Screened Many-Body Expansion for Protein–Ligand Interactions: Examining Convergence for Metalloenzymes Through Seven–Body Interactions

Fragment-based quantum chemistry is a powerful strategy for calculating protein−ligand interaction energies using quantum chemistry methods. Rigorous convergence often requires hundreds of atoms in the protein binding-site model, especially if that model is constructed using distance-based criteria to select amino acid residues, while three- and four-body calculations exhibit instability related to combinatorial proliferation in the number of subsystem calculations. Here, we report an energy-based screening protocol for the many-body expansion applied to protein−ligand interactions, implemented in the open-source FRAGME∩T code. Using a combination of aggressive screening based on semiempirical quantum chemistry, with an improved graph-theoretical algorithm to eliminate unimportant subsystems, we are able to perform n-body calculations up to n = 7 using density functional theory in triple-ζ basis sets. Distance cutoffs further reduce the cost without compromising accuracy. Rapid and stable convergence of the many-body expansion is obtained by n = 4, for a pair of metalloenzymes in which a divalent ion coordinates directly to the ligand. As compared to previous results that relied solely on distance cutoffs, oscillations in the n-body corrections are reduced or eliminated, although residual errors remain in one case. This work demonstrates that benchmark-quality protein−ligand interaction energies can be systematically converged using a method with excellent parallel efficiency and scalability.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗