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At least 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Improving Bond Dissociations of Reactive Machine Learning Potentials through Physics-Constrained Data Augmentation

In the field of computational chemistry, predicting bond dissociation energies (BDEs) presents well-known challenges, particularly due to the multireference character of reactive systems. Many chemical reactions involve configurations where single-reference methods fall short, as the electronic structure can significantly change during bond breaking. As generating training data for partially broken bonds is a challenging task, even state-of-the-art reactive machine learning interatomic potentials (MLIPs) often fail to predict reliable BDEs and smooth dissociation curves. By contrast, simple and inexpensive physics-based models, such as the well-established Morse potential, do not suffer from any such limitations. This work leverages the Morse potential to improve reactive MLIPs by augmenting the training data set with inexpensive Morse data along the dissociation pathways. Further, this physics-constrained data augmentation (PCDA) approach results in MLIPs with smooth bond dissociation curves as well as near coupled-cluster level BDEs, all without requiring any expensive multireference quantum mechanical calculations. A case study for methane combustion demonstrates how the PCDA approach can improve an existing reactive MLIP, namely, ANI-1xnr. In conclusion, not only are the BDEs and bond dissociation curves for all radicals and molecules significantly improved compared to ANI-1xnr but the PCDA-trained MLIP retains the reliability of ANI-1xnr when performing reactive molecular dynamics simulations.

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

HEPOM: Using Graph Neural Networks for the Accelerated Predictions of Hydrolysis Free Energies in Different pH Conditions

Hydrolysis is a fundamental family of chemical reactions where water facilitates the cleavage of bonds. The process is ubiquitous in biological and chemical systems, owing to water’s remarkable versatility as a solvent. However, accurately predicting the feasibility of hydrolysis through computational techniques is a difficult task, as subtle changes in reactant structure like heteroatom substitutions or neighboring functional groups can influence the reaction outcome. Furthermore, hydrolysis is sensitive to the pH of the aqueous medium, and the same reaction can have different reaction properties at different pH conditions. In this work, we have combined reaction templates and high-throughput ab initio calculations to construct a diverse data set of hydrolysis free energies. The developed framework automatically identifies reaction centers, generates hydrolysis products, and utilizes a trained graph neural network (GNN) model to predict ΔG values for all potential hydrolysis reactions in a given molecule. The long-term goal of the work is to develop a data-driven, computational tool for high-throughput screening of pH-specific hydrolytic stability and the rapid prediction of reaction products, which can then be applied in a wide array of applications including chemical recycling of polymers and ion-conducting membranes for clean energy generation and storage.

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

Including Physics-Informed Atomization Constraints in Neural Networks for Reactive Chemistry

Machine learning interatomic potentials (MLIPs) have emerged as powerful tools for investigating atomistic systems with high accuracy and a relatively low computational cost. However, a common and unaddressed challenge with many current neural network (NN) MLIP models is their limited ability to accurately predict the relative energies of systems containing isolated or nearly isolated atoms, which appear in various reactive processes. To address this limitation, we present a mathematical technique for modifying any existing atom-centered NN architecture to account for the energies of isolated atoms. The result produces a consistent prediction of the atomization energy (AE) of a system using minimal constraints on the model. Using this technique, we build a model architecture that we call hierarchically interacting particle neural network (HIP-NN)-AE, an AE-constrained version of the HIP-NN, as well as ANI-AE, the AE-constrained version of the accurate NN engine for molecular energies (ANI). Our results demonstrate AE consistency of AE-constrained models, which drastically improves the AE predictions for the models. We compare the AE-constrained approach to unconstrained models as well as models from the literature in other scenarios, such as bond dissociation energies, bond dissociation pathways, and extensibility tests. These results show that the constraints improve the model performance in some of these tasks and do not negatively affect the performance on any tasks. The AE constraint approach thus offers a robust solution to the challenges posed by isolated atoms in energy prediction tasks.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2024

Properties of NoO and YbO

Bond dissociation energies (BDEs) and spectroscopic parameters for the ground states of YbO and NoO were calculated at the Brueckner doubles (BD(T)) level and for NoO at the coupled cluster CCSD(T) level based on the closed-shell configurations Yb 2+ (4f 14 )O 2 – (2p 6 ) and No 2+ (5f 14 )O 2 – (2p 6 ). For YbO, the BD(T) BDE (3.93 eV) and vibrational frequency (686.3 cm –1 ) are consistent with the experiment; the BD(T) bond distance was 1.8492 Å, about 0.04 Å longer than the experiment. For NoO, the calculated BDEs are 3.07 eV (BD(T)) and 3.08 eV (CCSD(T)) and are expected to be good to ±3 kcal/mol (±0.13 eV). Potential energy curves (PECs) for the spin–orbit (Ω) states associated with the f 13 s 1 configurations of YbO and NoO were calculated at the SA-CASSCF/SO-CASPT2/aQ-DK level. PECs considering both the f 13 s 1 and f 14 configurations were calculated at this level, as the ground states are expected to contain both configurations. Due to a bias in the SA-CASSCF to the f 13 s 1 configurations, the f 14 configurations could not be properly described simultaneously with the f 13 s 1 ones. Finally, the natural population analysis based on the natural bond orbitals shows that YbO and NoO are quite ionic, with 5d orbitals being more important in YbO than the 6d orbitals in NoO.

basis sets↗
DOE OSTI2025

Energetic and Electronic Properties of UX +/0/– for X = Li and Be and Comparison of the Properties of the Uranium Atom Binding to 2nd Row Elements Li–F

The bonding and spectroscopic properties of ULi +/0/– and UBe +/0/– to complete the series for UX +/0/– for X = Li to F were investigated by high-level ab initio SO-CASPT2 and CCSD(T) electronic structure calculations. The low-lying spin–orbit states were obtained at the SA-CASPT2/aQ-PP level; bond dissociation energies (BDEs), ionization energies (IEs), adiabatic electronic affinities (AEAs), and vertical detachment energies (VDEs) were calculated at the Feller-Peterson-Dixon (FPD) level. A dense manifold of low-lying states was predicted for ULi +/0/– and UBe +/0/– . Here, the calculated BDEs for ULi (37.7 kJ/mol) and UBe (8.0 kJ/mol) show that UBe is weakly bound. For redox processes, the BDEs increased for ULi + (109.3 kJ/mol), ULi – (47.4 kJ/mol), UBe + (35.6 kJ/mol), and UBe – (72.3 kJ/mol). The IE(ULi) = 4.650 eV is lower than IE(Li); the IE(UBe) = 5.901 eV is close to the IE(U) and to the IEs of UB, UC, UN, UO, and UF. The AEAs of ULi (0.708 eV) and UBe (0.989 eV) are lower than those for UB, UC, UN, and UO but higher than that for EA(UF). Natural bond orbital (NBO) calculations show that ULi has the 5f 3 6d 1 7s 2 configuration for U and 2s 1 for Li, with a small partial negative charge slightly delocalized on U. UBe arises from the U(5f 3 6d 1 7s 2 ) and Be(2s 2 ) electron configurations with no charge separation. The same calculations were made for WX (X = Li, Be, C–F) to enable detailed comparisons of the properties for UX with WX (X = Li–F). For WX, BDE(WX) is higher than that for UX for X = Li to N and lower than BDE(UX) for X = O and F, mostly due to the higher IE of W than U as ionic character becomes more important going from Li to F.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2025

The Electronic Structure of Zirconium and Hafnium Monochalcogenides

High-level ab initio CCSD(T) and spin–orbit icMRCI+Q calculations were used to predict potential energy curves (PECs) for the lowest-lying states of ZrO, ZrS, HfO, and HfS. The prediction of the ground state is basis set dependent at the icMRCI+Q level for ZrO and ZrS due to the small singlet–triplet splitting between the lowest 1 Σ + and 3 Δ states. CCSD(T) with a spin orbit correction predicted the 1 Σ + ground state in agreement with experiment. New all-electron basis sets were developed for Hf to improve the results over those predicted by use of effective core potentials (ECPs) that subsume the 4f electrons into the definition of the core. The use of the new DK-4f basis sets rather than ECPs became more important for HfO and HfS where there is a lack of a good core–valence separation. icMRCI+Q, CCSD(T), and DFT calculations for the spectroscopic parameters of ZrO, ZrS, HfO, and HfS were benchmarked with available experimental data. Bond dissociation energies (BDEs) of these four systems were calculated at the Feller–Peterson–Dixon (FPD) level to be 762.1 (ZrO), 543.5 (ZrS), 803.8 (HfO), and 575.1 kJ/mol (HfS), in excellent agreement with experiment. The HfS BDE was remeasured using the R3PI method, providing an updated experimental measurement of D 0 (HfS) = 5.978 ± 0.002 eV = 576.8 ± 0.2 kJ/mol. This experimental value, combined with experimental measurements of the ionization energies of Hf and HfS, gives the cationic BDE of D 0 (Hf + -S) = 5.124 ± 0.002 eV = 494.4 ± 0.2 kJ/mol.

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

Pd–Methyl Bond Energy─Property Correlations, Noncorrelations, Machine Learning Models, and Application to Polymerization Catalysis

Metal–carbon bonds are a key intermediate in a variety of homogeneous organometallic transformations and often determine the critical thermodynamics and kinetics of catalytic processes. Surprisingly, the influence of different ligands on metal–carbon bond strengths has been largely overlooked. Here, in this study, we evaluated nearly 700 experimental Pd–methyl complexes by calculating their bond dissociation energies using density functional theory (DFT) and compared these bond strengths to several fundamental molecular properties, and this revealed several surprising correlations and noncorrelations. Most surprising was that several fundamental properties, such as the bond length, bond force constant, and bond electron density, have no correlation with bond strength, despite these correlations often holding for main-group compounds. We were indeed able to identify key ligand-dependent chemical features/descriptors that provided a highly accurate machine learning model and provided insight into the general factors that control the Pd–carbon bond strength, such as radical delocalization and nucleophilicity. Insights gained from the Pd–Me bond energy analysis were then applied to CO migratory insertion steps that are part of copolymerization reactions.

binding energy↗
DOE OSTI2025

Toward the Observation of Dimagnesocene

We have examined the electronic structure of C 5 H 5 MgMgC 5 H 5 , or dimagnesocene, using high-level coupled-cluster techniques. This research is suitable in light of the remarkable synthesis of the valence-isoelectronic diberyllocene by Boronski, Crumpton, Wales, and Aldridge. The Mg–Mg bond distance is predicted to be 2.758 Å, and the Mg–Mg bond dissociation energy is predicted to be 51.8 kcal/mol. Unique aspects to the present research is our characterization of the ionization energy and the electron affinity of this molecule, the energy of dissociation into two neutral cyclopentadienyl magnesium radicals, the determination of the neutral structure at the CCSD(T)/cc-pVTZ level, and the computation of the Raman intensities at the MP2/cc-pVDZ level. Apart from mass spectroscopy, the simplest means of experimental detection is gas-phase or matrix-isolated infrared spectroscopy, in which the A 2 ″ peak at 801 cm –1 should be the most prominent, with an intensity of 581 km/mol.

bond cleavage↗
DOE OSTI2024

Chemical Upcycling of Polyolefin Plastics Using Structurally Well-defined Catalysts

Single-use polyolefins are widely used in our daily life and industrial production due to their light weight, low cost, superior stability, and durability. However, the rapid accumulation of plastic waste and low-profit recycling methods resulted in a global plastic crisis. Catalytic hydrogenolysis is regarded as a promising technique, which can effectively and selectively convert polyolefin plastic waste to value-added products. In this perspective, we focus on the design and synthesis of structurally well-defined hydrogenolysis catalysts across mesoscopic, nanoscopic, and atomic scales, accompanied by our insights into future directions in catalyst design for further enhancing catalytic performance. These design principles can also be applied to the depolymerization of other polymers and ultimately realize the chemical upcycling of waste plastics.

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

Production of bio-based lactones as monomers for a circular polymer economy

To create a circular plastics economy, new polymers are being developed that can be chemically recycled. Circular polyesters are of particular interest and to this end, lactones are ideal monomers. Here, this Review examines catalytic routes to convert diols, hydroxy acids, and dicarboxylic acids to lactones, focusing on the development of scalable, atom-economic, and energy-efficient conversions of bio-derived feedstocks. Free energy analysis is used to inform process choices, such as reactor type, reaction phase, and use of solvent. Catalyst design principles are summarized for both direct (bio-substrate to lactone) and indirect (bio-substrate to intermediate to lactone) routes. Finally, we summarize literature that shows that many lactone precursors are readily accessible from various metabolic and chemo-catalytic pathways. Transitioning to bio-based monomers offers an opportunity to reduce reliance on fossil carbon resources, but requires advanced catalytic processes informed by mechanistic insights.

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

Cu‐Catalyzed Aerobic Oxidative C─C Cleavage in Lignin‐Derived Oligomers and Biological Funneling of the Monomeric Products

Existing methods for lignin deconstruction to aromatic monomers primarily cleave carbon–oxygen bonds within the polymer, resulting in sub-optimal monomer yields and formation of oligomers that retain intact carbon–carbon bonds. Here, we demonstrate that copper-catalyzed aerobic oxidation under aqueous alkaline conditions promotes oxidative cleavage of carbon–carbon bonds in lignin oligomers derived from reductive catalytic fractionation (RCF) of pine and poplar biomass. Fundamental insights are gained from reactions of model compounds that resemble subunits present in RCF oligomers. Optimal results are achieved in a flow reactor that provides precise control over O2 delivery, temperature, and reaction residence time. The Cu-catalyzed aerobic oxidation conditions access aromatic monomers in 19 and 34 wt% monomer yields, respectively, from pine- and poplar-derived RCF oligomers. Overall, the sequence consisting of biomass RCF into monomers and oligomers followed by oxidative deconstruction of the RCF oligomers generates substantially higher yields of aromatic monomers from lignin. Engineered strains of Pseudomonas putida support biological funneling of the oligomer-derived oxygenated aromatic compounds into cis,cis-muconic acid from pine or 2-pyrone-4,6-dicarboxylic acid from poplar.

09 BIOMASS FUELS↗
NASA NTRS1992

The Acid Growth Theory of auxin-induced cell elongation is alive and well

Plant cells elongate irreversibly only when load-bearing bonds in the walls are cleaved. Auxin causes the elongation of stem and coleoptile cells by promoting wall loosening via cleavage of these bonds. This process may be coupled with the intercalation of new cell wall polymers. Because the primary site of auxin action appears to be the plasma membrane or some intracellular site, and wall loosening is extracellular, there must be communication between the protoplast and the wall. Some "wall-loosening factor" must be exported from auxin-impacted cells, which sets into motion the wall loosening events. About 20 years ago, it was suggested that the wall-loosening factor is hydrogen ions. This idea and subsequent supporting data gave rise to the Acid Growth Theory, which states that when exposed to auxin, susceptible cells excrete protons into the wall (apoplast) at an enhanced rate, resulting in a decrease in apoplastic pH. The lowered wall pH then activates wall-loosening processes, the precise nature of which is unknown. Because exogenous acid causes a transient (1-4 h) increase in growth rate, auxin must also mediate events in addition to wall acidification for growth to continue for an extended period of time. These events may include osmoregulation, cell wall synthesis, and maintenance of the capacity of walls to undergo acid-induced wall loosening. At present, we do not know if these phenomena are tightly coupled to wall acidification or if they are the products of multiple independent signal transduction pathways.

NASA Discipline Number 40-50↗
NASA NTRS2007

Antibodies Against Three Forms of Urokinase

Antibodies that bind to preselected regions of the urokinase molecule have been developed. These antibodies can be used to measure small quantities of each of three molecular forms of urokinase that could be contained in microsamples or conditioned media harvested from cultures of mammalian cells. Previously available antibodies and assay techniques do not yield both clear distinctions among, and measurements of, all three forms. Urokinase is a zymogen that is synthesized in a single-chain form, called ScuPA, which is composed of 411 amino acid residues (see figure). ScuPA has very little enzyme activity, but it can be activated in two ways: (1) by cleavage of the peptide bond lysine 158/isoleucine 159 and the loss of lysine 158 to obtain the high molecular-weight (HMW) form of the enzyme or (2) by cleavage of the bond lysine 135/lysine 136 to obtain the low-molecular-weight (LMW) form of the enzyme. The antibodies in question were produced in mice and rabbits by use of peptides as immunogens. The peptides were selected to obtain antibodies that bind to regions of ScuPA that include the lysine 158/isoleucine 159 and the lysine 135/lysine 136 bonds. The antibodies include monoclonal and polyclonal ones that yield indications as to whether either of these bonds is intact. The polyclonal antibodies include ones that preferentially bind to the HMW or LMW forms of the urokinase molecule. The monoclonal antibodies include ones that discriminate between the ScuPA and the HMW form. A combination of these molecular-specific antibodies will enable simultaneous assays of the ScuPA, HMW, and LMW forms in the same specimen of culture medium.

Morrison, Dennis R.↗
NASA NTRS1986

Kinetics of the hydrolysis of guanosine 5'-phospho-2-methylimidazolide

The hydrolysis kinetics of guanosine 5'-phospho-2-methylimidazolide (2-MeImpG) in aqueous buffered solutions of various pH's was studied at 75 and 37 C, using spectrophotometric and HPLC techniques. The hydrolysis was found to be very slow even at low pH. At 75 C and pH at or below l.0, two kinetic processes were observed: the more rapid one was attributed to the hydrolysis of the phosphoimidazolide P-N bond; the second, much slower one, was attributed to the cleavage of the glycosidic bond. It is noted that the P-N hydrolysis in phosphoimidazolides is very slow compared to other phosphoramidates, and that this might be one of the reasons why the phosphoimidazolides showed an extraordinary ability to form long oligomers under template-directed conditions.

Kanavarioti, Anastassia↗
DOE OSTI2025

Spectroscopy and crystallography define carotenoid oxygenases as a new subclass of mononuclear non-heme Fe II enzymes

Carotenoid cleavage dioxygenases (CCDs) are non-heme Fe II enzymes that catalyze the oxidative cleavage of alkene bonds in carotenoids, stilbenoids, and related compounds. How these enzymes control the reaction of dioxygen (O 2 ) with their alkene substrates is unclear. Here, we apply spectroscopy in conjunction with X-ray crystallography to define the iron coordination geometry of a model CCD, CAO1 (Neurospora crassa carotenoid oxygenase 1), in its resting state and following substrate binding and coordination sphere substitutions. Resting CAO1 exhibits a five-coordinate (5C), square pyramidal Fe II center that undergoes steric distortion toward a trigonal bipyramidal geometry in the presence of piceatannol. Titrations with the O 2 -analog, nitric oxide, show a >100-fold increase in iron–nitric oxide affinity upon substrate binding, defining a crucial role for the substrate in activating the Fe II site for O 2 reactivity. The importance of the 5C Fe II structure for reactivity was probed through mutagenesis of the second-sphere Thr151 residue of CAO1, which occludes ligand binding at the sixth coordination position. A T151G substitution resulted in the conversion of the iron center to a six-coordinate state and a 135-fold reduction in apparent catalytic efficiency toward piceatannol compared with the wildtype enzyme. Substrate complexation resulted in partial six-coordinate to 5C conversion, indicating solvent dissociation from the iron center. Additional substitutions at this site demonstrated a general functional importance of the occluding residue within the CCD superfamily. Taken together, these data suggest an ordered mechanism of CCD catalysis occurring via substrate-promoted solvent replacement by O 2 . CCDs thus represent a new class of mononuclear non-heme Fe II enzymes.

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

Capture of volatile RuO 4 from oxidized simulated used nuclear fuel solutions

Ruthenium is a challenging fission product in used nuclear fuel (UNF) reprocessing due to its complex redox chemistry, variable speciation in nitric acid, partial extractability, and volatility. This work presents a strategy for Ru removal based on the volatilization of RuO 4 using the strong oxidant sodium bismuthate, followed by RuO 2 deposition onto various substrates. Among the materials tested, polymer-based substrates such as polyolefin wax film (Parafilm®), exhibited superior performance, achieving up to near-quantitative Ru removal from solution. After dissolution of the substrate, 99.6% of the Ru was recovered as RuO 2 . The deposition mechanism onto the polyolefin wax film involves both physisorption and chemical reaction through oxidative cleavage of olefinic bonds within the polymer. In contrast, on inorganic substrates such as Al foil, RuO 4 undergoes incomplete surface adsorption and reduction, as confirmed by FTIR and XPS analyses. This approach remains effective under conditions of simulated oxidation of UNF solutions, selectively removing Ru while leaving other fission products in solution. As a result, capture of RuO 4 offers a practical and efficient strategy for ruthenium decontamination and recovery, offering a route for integration into existing UNF reprocessing flowsheets to enhance overall process safety and performance.

Ruthenium↗
DOE OSTI2025

Thiol- and Disulfide-Functionalized Polycyclooctene: Metathesis Polymerization, Degradation, and Reformation

The enormous global production and use of polymers and plastics, combined with slower and less efficient disposal and recycling methods, have led to a worldwide growth in plastic waste. Here, we describe an approach that builds degradability into macromolecular polyolefins through the design of telechelic oligomers with reactive functional groups that enables control over polymer deconstruction and reconstruction. Our work exploits disulfide-containing polymers that have emerged as promising cyclable materials due to their dynamic reversibility (bond formation and cleavage) driven by redox chemistry under mild conditions. Specifically, we describe the synthesis of a telechelic α,ω-dithiopolycyclooctene (PCOE) by ring-opening metathesis polymerization using a dithioacetate chain transfer agent, followed by deprotection to convert the chain-end thioacetates to thiols. This process was studied towards control over the degree of oxidation to yield disulfide-containing PCOE, followed by an evaluation of reductive degradation and oxidative repolymerization. Overall, this approach facilitates the production of disulfide-containing unsaturated polyolefins and the integration of degradable and reformable moieties into soluble, processable, metathesis-derived polymers.

Lee, Kyoungwon↗