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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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The Curious Case of Pu + : Insight on 5f Orbital Activity from Inductively Coupled Plasma Tandem Mass Spectrometry (ICP-MS/MS) Reactions
A comprehensive understanding of when and how 5f orbitals participate in complex chemical bonding is important for a variety of applications. The actinides are unique in that they possess 5f orbitals and can access high oxidation states, which make them attractive for use in catalysis. Fundamental studies of actinide–ligand interactions offer a mechanism to examine the activation of the 5f orbitals so that the selectivity of 5f orbitals can be assessed. A previous study examined the reaction of Pu + + CO 2 and determined that the reaction efficiency is restricted by a barrier, namely, promotion from the Pu + ground-state configuration, 5f 6 7s, to a reactive-state configuration, 5f 5 6d 2 . Here, the present study illustrates the benefit of activation of Pu’s 5f orbitals when studying the reaction of Pu + + NO. In this reaction, PuO + forms in an exothermic, barrierless process. The 5f orbitals can and do participate in forming a linear intermediate, [N-Pu-O] + , and this drives the exothermic reaction. Understanding the conditions under which 5f orbitals are active in chemical bonding is the key to exploiting the actinides’ selective catalytic capabilities.
Actinide 5f Occupations: The Case of PuO 2
In actinide chemistry, the formal number of open-shell 5f electrons, n open , is a well-defined quantity with an integer value. The effective 5f occupation, n f , additionally takes donation and back-donation into account, generally has a non-integer value, and has varying numerical definitions. The present study explores the important distinction between n f and n open in actinide chemistry with the example of PuO2, by using electronic structure methods with a relativistic Hamiltonian in combination with experimental Pu M 5 -edge high-energy-resolution X-ray absorption and emission spectroscopic data. The total donation to the metal in PuO 2 is between 3.1 and 2.4 electrons, depending on the type of calculation, most of which is to the Pu 6d and 5f shells. The donation into 5f is sensitive to the approximations in the electronic structure model but likely amounts to 1.6/0.8 electrons when the diffuse regions of the 5f shell are included/excluded. Valence band resonant inelastic X-ray scattering experiments demonstrate that Pu 5f electron density is present in the valence band; thus, there is a clear experimental signature of covalent bonding in PuO 2 . Pu M 5 -edge and M 3 -edge high-energy-resolution X-ray absorption near-edge structures for Pu 3+ and Pu 4+ in an aqueous solution are compared to PuO 2 , showing that Pu in PuO 2 has an nf closer to Pu 4+ (aq).
Understanding Powder X-ray Diffraction Profiles from Layered Minerals: The Case of Kaolinite Nanocrystals
Abstract not provided
CAML: Commutative Algebra Machine Learning─A Case Study on Protein–Ligand Binding Affinity Prediction
Recently, Suwayyid and Wei introduced commutative algebra as an emerging paradigm for machine learning and data science. In this work, we propose commutative algebra machine learning (CAML) for the prediction of protein−ligand binding affinities. Specifically, we apply persistent Stanley−Reisner theory, a key concept in combinatorial commutative algebra, to the affinity predictions of protein−ligand binding and metalloprotein−ligand binding. We present three new algorithms, i.e., element-specific commutative algebra, category-specific commutative algebra, and commutative algebra on bipartite complexes, to tackle the complexity of data involved in (metallo) protein−ligand complexes. We show that the proposed CAML outperforms other state-of-theart methods in (metallo) protein−ligand binding affinity predictions, indicating the great potential of commutative algebra learning.
Commutative Algebra Modeling in Materials Science – A Case Study on Metal–Organic Frameworks (MOFs)
Metal-organic frameworks (MOFs) are a class of important crystalline and highly porous materials whose hierarchical geometry and chemistry hinder interpretable predictions in materials properties. Commutative algebra is a branch of abstract algebra that has been rarely applied in data and material sciences. We introduce the first ever commutative algebra modeling and prediction in materials science. Specifically, category-specific commutative algebra (CSCA) is proposed as a new framework for MOF representation and learning. It integrates element-based categorization with multiscale algebraic invariants to encode both local coordination motifs and global network organization of MOFs. These algebraically consistent, chemically aware representations enable compact, interpretable, and data efficient modeling of MOF properties such as Henry’s constants and uptake capacities for common gases. Compared to traditional geometric and graph-based approaches, CSCA achieves comparable or superior predictive accuracy while substantially improving interpretability and stability across data sets. By aligning commutative algebra with the chemical hierarchy, the CSCA establishes a rigorous and generalizable paradigm for understanding structure and property relationships in porous materials and provides a nonlinear algebra-based framework for data-driven material discovery.
Reconciling Work Functions and Adsorption Enthalpies for Implicit Solvent Models: A Pt (111)/Water Interface Case Study
Implicit solvent models are a computationally efficient method of representing solid/liquid interfaces prevalent in electrocatalysis, energy storage, and materials science. However, electronic structure changes induced at the metallic surface by the dielectric continuum are not fully understood. To address this, we perform DFT calculations for the Pt(111)/water interface, in order to compare Poisson–Boltzmann continuum solvation methods with ab initio molecular dynamics (AIMD) simulations of explicit solvent. We show that the implicit solvent cavity can be parametrized in terms of the electric dipole moment change at the equilibrated explicit Pt/water interface to obtain the potential of zero charge (PZC). We also compare the accuracy of aqueous enthalpies of adsorption of phenol on Pt(111) using geometry and charge density based dielectric cavitation methods. The ability to parametrize the cavity according to individual atoms, as afforded in the geometry based approach, is key to obtaining accurate enthalpy changes of adsorption under aqueous conditions. Additionally, we show that the electronic structure changes induced by explicit solvent and our proposed implicit solvent parametrization scheme yield comparable density difference profiles and d-band projected density of states. We therefore demonstrate the capability of implicit solvent approaches to capture both the energetics of adsorption processes and the main electronic effects of aqueous solvent on the metallic surface. Therefore, this work provides a scheme for computationally efficient simulations of interfacial processes for applications in areas such as heterogeneous catalysis and electrochemistry.
Correction to Reconciling Work Functions and Adsorption Enthalpies for Implicit Solvent Models: A Pt (111)/Water Interface Case Study
This errata is to correct the acknowledgment in the original published article. G.B. (partial support), V.-A.G., M.-T.N., and R.R. were supported by the U.S. Department of Energy, Office of Science, Basic Energy Sciences, Chemical Sciences, Geosciences, and Biosciences Division. Computer resources were provided by Research Computing at Pacific Northwest National Laboratory and the National Energy Research Scientific Computing Center (NERSC), a U.S. Department of Energy Office of Science User Facility operated under Contract No. DE-AC02-05CH11231. PNNL is operated by Battelle for the U.S. Department of Energy under Contract DE-AC05-76RL01830. G.B. acknowledges the EPSRC for partial support in PhD funding. The authors acknowledge the use of the IRIDIS High Performance Computing Facility (IRIDIS 5) and associated support services at the University of Southampton in the completion of this work. We are grateful to the UK Materials and Molecular Modeling Hub (Thomas HPC) for computational resources, which is partially funded by EPSRC (EP/P020194/1).
DMRG on Top of Plane-Wave Kohn–Sham Orbitals: A Case Study of Defected Boron Nitride
In this paper, we analyze the numerical aspects of the inherent multi reference density matrix renormalization group (DMRG) calculations on top of the periodic Kohn-Sham density functional theory using the complete active space approach. The potential of the framework is illustrated by studying hexagonal boron nitride nanoflakes embedding a charged single boron vacancy point defect by revealing a vertical energy spectrum with a prominent multireference character. We investigate the consistency of the DMRG energy spectrum from the perspective of sample size, basis size, and active space selection protocol. Results obtained from standard quantum chemical atom-centered basis calculations and plane-wave based counterparts show excellent agreement. Furthermore, we also discuss the spectrum of the periodic sheet which is in good agreement with extrapolated data of finite clusters. These results pave the way toward applying the DMRG method in extended correlated solid-state systems, such as point defect qubit in wide band gap semiconductors.
In Silico Ultrafast Nonlinear Spectroscopy Meets Experiments: The Case of Perylene Bisimide Dye
Not Available
Dynamics-Based Peptide–MHC Binding Optimization by a Convolutional Variational Autoencoder: A Use-Case Model for CASTELO
An unsolved challenge in the development of antigen-specific immunotherapies is determining the optimal antigens to target. Comprehension of antigen–major histocompatibility complex (MHC) binding is paramount toward achieving this goal. Here, we apply CASTELO, a combined machine learning-molecular dynamics (ML-MD) approach, to identify per-residue antigen binding contributions and then design novel antigens of increased MHC-II binding affinity for a type 1 diabetes-implicated system. We build upon a small-molecule lead optimization algorithm by training a convolutional variational autoencoder (CVAE) on MD trajectories of 48 different systems across four antigens and four HLA serotypes. We develop several new machine learning metrics including a structure-based anchor residue classification model as well as cluster comparison scores. ML-MD predictions agree well with experimental binding results and free energy perturbation-predicted binding affinities. Moreover, ML-MD metrics are independent of traditional MD stability metrics such as contact area and root-mean-square fluctuations (RMSF), which do not reflect binding affinity data. Finally, our work supports the role of structure-based deep learning techniques in antigen-specific immunotherapy design.
Data-Driven Many-Body Models for Molecular Fluids: CO 2 /H 2 O Mixtures as a Case Study
In this study, we extend the scope of the many-body TTM-nrg and MB-nrg potential energy functions (PEFs), originally introduced for halide ion–water and alkali-metal ion–water interactions, to the modeling of carbon dioxide (CO2) and water (H2O) mixtures as prototypical examples of molecular fluids. Both TTM-nrg and MB-nrg PEFs are derived entirely from electronic structure data obtained at the coupled cluster level of theory and are, by construction, compatible with MB-pol, a many-body PEF that has been shown to accurately reproduce the properties of water. Although both TTM-nrg and MB-nrg PEFs adopt the same functional forms for describing permanent electrostatics, polarization, and dispersion, they differ in the representation of short-range contributions, with the TTM-nrg PEFs relying on conventional Born–Mayer expressions and the MB-nrg PEFs employing multidimensional permutationally invariant polynomials. By providing a physically correct description of many-body effects at both short and long ranges, the MB-nrg PEFs are shown to quantitatively represent the global potential energy surfaces of the CO 2 –CO 2 and CO 2 –H 2 O dimers and the energetics of small clusters, as well as to correctly reproduce various properties in both gas and liquid phases. Furthermore, building upon previous studies of aqueous systems, our analysis provides further evidence for the accuracy and efficiency of the MB-nrg framework in representing molecular interactions in fluid mixtures at different temperature and pressure conditions.
Perspectives on van der Waals Density Functionals: The Case of TiS 2
The van der Waals interaction is of foundational importance for a wide variety of physical systems. In particular, van der Waals forces lie at the heart of potential device technologies that may be realized from the functional organization of layered two-dimensional (2D) nanomaterials. Furthermore, for intermediate to large-scale applications modeling, van der Waals density functionals have become the de facto choice for first-principles calculations. In particular, the vdW-DF family of functionals have provided a systematic approach to this theoretically challenging problem. While much progress has been made, there remains room for improvement in the microscopic description of vdW forces from these density functionals. In this work, we compute benchmark results for the binding energy and the electronic density response to binding in TiS2 via accurate diffusion quantum Monte Carlo calculations. We compare these benchmark data to results obtained from local, semilocal, and van der Waals functionals. In particular, we gauge the quality of the original vdW-DF/vdW-DF2 functionals, as well as updated variants such as vdW-DF-C09, vdW-DF-optB88, vdW-DF-optB86b, and vdW-DF2-B86R. We find a close relationship between the accuracy of predicted interlayer separation distances and binding energies for TiS 2 , with the vdW-DF-optB88 functional performing very well in terms of both quantities. In general, the more recently developed functionals are systematic improvements over older ones. However, when considering the response of the electron density to binding, we find that local-density approximation (LDA) and PBEsol generally outperform the vdW-DF functionals in describing the interlayer charge accumulation with vdW-DF-C09 variants performing the best overall.
From Molecules to Solids: A vdW-DF-C09 Case Study of the Mercury Dihalides
The mercury dihalides show a remarkable diversity in the structural preferences in their minimum energy structure types, spanning molecular to strongly bound ionic solids. A challenge in the development of density functional methods for extended systems is to arrive at strategies that serve equally well such a broad range of bonding modes or structural preferences. The chemical bonding and the stabilities of mercury dihalides and the general utility and reliability of the van der Waals density functional with C09 exchange (vdW-DF-C09) in predicting or describing the energetics and structural preferences in these metal dihalides is examined. Here, we show that, in contrast with the uncorrected generalized gradient approximation of the Perdew-Burke-Erzenhoff (PBE) exchange-correlation functional, qualitative and quantitative patterns in the bonding of the mercury dihalide solids are well reproduced with vdW-DF-C09 for the full series of HgX 2 systems for X = F, Cl, Br, and I. The possible existence of a low-temperature cotunnite polymorph for HgF 2 and PbF 2 is posited.