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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 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Land Use in Computable General Equilibrium Models

Constant Elasticity of Transformation (CET) functions are widely used to allocate land across uses in Computable General Equilibrium (CGE) models. These models fail to maintain area of land in balance. Several ways have been used or offered to fix this problem. This paper first examines the extent to which the CET approach may generate imbalances in area of land and identifies determinants of such imbalances. It then evaluates the merits, properties, and welfare impacts of the available approaches that restore area of land in balance. We show that heterogeneity in land prices (land rents) is the main source of imbalance in area of land, not the curvature of the CET function. Furthermore, we show that the available approaches that restore area of land in balance either introduce ad hoc adjustments in land allocation or undermine the conventional welfare assessments of the CET results and ignore the opportunity costs of land transformation. The CGE models which applied stochastic productivity distribution functions to allocate land among uses maintain area of land in balance, but they suffer from important limitations and ignore costs of land transformation.

Taheripour, Farzad↗
DOE OSTI2023

Crystal structure of dihydrofolate reductase from the filarial nematode W. bancrofti in complex with NADPH and folate

Lymphatic filariasis is a debilitating illness with an estimated 50 million cases as of 2018. The majority of cases are caused by the parasitic worm W. bancrofti and additional cases by the worms B. malayi and B. timori. Dihydrofolate reductase (DHFR) is an established target in the treatment of cancer, bacterial, and protozoal infections and may be a potential target for drugs targeting parasitic worm infections, including filariasis. Recent studies have shown that known antifolate compounds, including methotrexate, inhibit the activity of W. bancrofti DHFR (WbDHFR). However, the absence of structural information for filarial DHFRs has limited the study of more in-depth structure-function relationships. We report the structure of WbDHFR complexed with NADPH and folate using X-ray diffraction data measured to 2.47 Å resolution. The structure of WbDHFR reveals the usual DHFR fold and is currently only the second nematode DHFR structure in the Protein Data Bank. The equilibrium dissociation constants for NADPH (90 ± 29 nM) and folate (23 ± 4 nM) were determined by equilibrium titrations. The interactions of known antifolates with WbDHFR were analyzed using molecular docking programs and molecular dynamics simulations. Antifolates with a hydrophobic core and extended linker formed favorable interactions with WbDHFR. These combined data should now facilitate the rational design of filarial DHFR inhibitors, which in turn can be used to determine whether DHFR is a viable drug target for filariasis and whether existing antifolates may be repurposed for its treatment.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

First Principle Investigation of Electronic, Transport, and Bulk Properties of Zinc-Blende Magnesium Sulfide

We have studied electronic, structural, and transport properties of zinc-blende magnesium sulfide (zb-MgS). We employed a local density approximation (LDA) potential and the linear combination of atomic orbitals (LCAO) method. Our computational method is able to reach the ground state of a material, as dictated by the second theorem of density functional theory (DFT). Consequently, our findings have the physical content of DFT and agree with available, corresponding experimental ones. The calculated band gap of zb-MgS, a direct gap equal to 4.43 eV, obtained at the experimental lattice constant of 5.620 Å, completely agrees with the experimental band gap of 4.45 ± 0.2 eV. We also report total (DOS) and partial (pDOS) densities of states, electron and hole effective masses, the equilibrium lattice constant, and the bulk modulus. The calculated pDOS also agree with the experiment for the description of the states at the top and the bottom of the valence and conduction bands, respectively.

42 ENGINEERING↗
DOE OSTI2020

Modified Isotherm Modeling to Predict Cs Exchange with Crystalline Silicotitanate in Tank Waste Simulants

The U.S. Department of Energy is working to expedite processing of Hanford tank waste supernate at the Hanford Waste Treatment and Immobilization Plant. To support this goal, Washington River Protection Solutions is designing a Tank Side Cesium Removal (TSCR) system for suspended solids and cesium (Cs/ 137 Cs) removal from Hanford tank waste supernate. The ion exchange media selected for Cs removal at TSCR is crystalline silicotitanate (CST) that is manufactured in a nearly spherical form by Honeywell UOP LLC (UOP; Des Plaines, IL) as product IONSIV® R9140-B (Na form). The Zheng Anthony Miller (ZAM) isotherm model (Zheng et al. 1997) is a multicomponent ion exchange model used to predict the exchange of Group I metals onto CST. The ZAM isotherm has historically been used to predict Cs distribution values from Hanford and Savannah River Site (SRS) tank waste simulants. Figure S.1 summarizes model predictions from the ZAM isotherm that indicate poor prediction of Cs distribution values for simple and complex simulants with the engineered form of CST, IONSIV® R9140-B, and IONSIV® R9120-B where the solid line indicates a perfect fit by the model. The dotted lines indicate ±20% error. Batch contact testing with Hanford tank waste complex and simple simulants was used in conjunction with SRS simulants to experimentally determine Cs distribution values using a modification to the original isotherm model. The experimentally determined maximum Cs capacity for IONSIV® R9140-B CST in both the simple and complex matrices was found to be 0.53±0.3 mmoles Cs/g of CST. This value is not drastically different from the maximum Cs capacity of 0.58 mmoles Cs/g TAM-5 reported by Zheng et al. (1997). However, it is important to note that TAM-5 (commercially IONSIV® IE-910) is a powder. Hamm et al. (2002) determined that a dilution factor was needed to account for the Zr(OH)2 binder in the engineered form of CST. Hamm et al. determined that a dilution factor of 0.68 was appropriate to account for binder contribution and correct overprediction of Cs exchange on the engineered form of CST in ZAM calculations. This reduced the total capacity from 0.58 mmol/g with TAM-5 to 0.39 mmol/g for the engineered form of CST (Hamm et al. 2002). Despite substituting the experimentally determined maximum Cs capacity of 0.55 mmoles Cs/g for the literature-reported capacity of 0.39 mmoles Cs/g, it was determined that additional modifications to the model’s equilibrium rate constants were necessary in refining the isotherm model. The modified model overpredicted K+ uptake by the CST when compared to digested CST results described by Campbell et al. (2019). The modified model was further revised to omit three of the five K+ exchange equilibrium reactions described by ZAM to reduce the additional K+ loading seen by the model. Figure S.2 summarizes the revised model isotherm predictions plotted against measured Kd values.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2024

Coupled feldspar dissolution and secondary mineral precipitation in batch systems: 6. Labradorite dissolution, calcite growth, and clay precipitation at 60 °C and pH 8.2–8.4

Here, we conducted experiments on concurrent labradorite dissolution, calcite precipitation, and clay precipitation in batch reactor systems and tracked reaction processes using multiple isotope tracers. Labradorite was chosen for its role as a major and reactive component in basalt; the experiments thus directly impact our understanding of CO 2 storage in basalt aquifers and enhanced rock weathering. We doped initial solutions with 29 Si, 43 Ca, and Ca 13 CO 3 (s). Experiments were conducted at 60 °C and pH ~ 8.3 for up to 840 h, with isotope ratios in the experimental aqueous solutions measured using MC-ICP-MS. Unidirectional rates of labradorite dissolution near equilibrium were approximately two orders of magnitude slower than far-from-equilibrium rates reported in the literature. Calcite growth occurred near equilibrium and the rates were limited by the labradorite dissolution rates. In the steady state phase, the interplay of these three heterogeneous reactions—labradorite dissolution, calcite growth, and clay precipitation—results in a coupled system that approaches a near-equilibrium state. The system does not reach true equilibrium because labradorite continues to dissolve, albeit at a much slower rate near equilibrium. The overall reaction can be approximated as, Na 0.4 Ca 0.6 Al 1.6 Si 2.4 O 8 + 0.6HCO 3 - + 1·.7H 2 O + 0.4H + → 0.4Na + + 0.6CaCO 3(s) + 0.5Al 2 Si 2 O 5 (OH) 4(s) + 0.6Al(OH) 4 - + 1.4SiO 2 o (aq). The experimental results show that using short-term far-from-equilibrium rate constants would lead to an overestimation of feldspar weathering rates at the Earth’s surface (e.g., basalt weathering and enhanced rock weathering) and CO 2 mineralization in basalt aquifers.

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

Complexation of Lanthanides and Heavy Actinides with Aqueous Sulfur-Donating Ligands

The separation of trivalent lanthanides and actinides is challenging because of their similar sizes and charge densities. S-donating extractants have shown significant selectivity for trivalent actinides over lanthanides, with single-stage americium/ lanthanide separation efficiencies for some thiol-based extractants reported at >99.999%. While such separations could transform the nuclear waste management landscape, these systems are often limited by the hydrolytic and radiolytic stability of the extractant. Progress away from thiol-based systems is limited by the poorly understood and complex interactions of these extractants in organic phases, where molecular aggregation and micelle formation obfuscates assessment of the metal–extractant coordination environment. Because S-donating thioethers are generally more resistant to hydrolysis and oxidation and the aqueous phase coordination chemistry is anticipated to lack complications brought on by micelle formation, we have considered three thioethers, 2,2'-thiodiacetic acid (TDA), (2R,5S)- tetrahydrothiophene-2,5-dicarboxylic acid, and 2,5-thiophenedicarboxylic acid (TPA), as possible trivalent actinide selective reagents. Formation constants, extended X-ray absorption fine structure spectroscopy, and computational studies were completed for thioether complexes with a variety of trivalent lanthanides and actinides including Nd, Eu, Tb, Am, Cm, Bk, and Cf. TPA was found to have moderately higher selectivity for the actinides because of its ability to bind actinides in a different manner than lanthanides, but the utility of TPA is limited by poor water solubility and high rigidity. While significant competition with water for the metal center limits the efficacy of aqueous-based thioethers for separations, the characterization of these solution-phase, S-containing lanthanide and actinide complexes is the most comprehensively available in the literature to date. Here, this is due to the breadth of lanthanides and actinides considered as well as the techniques deployed and serves as a platform for the further development of Scontaining reagents for actinide separations. Additionally, this paper reports on the first bond lengths for Cf and Bk with a neutral S donor.

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

Accurate Prediction of pKb in Amines: Validation of the CAM-B3LYP/6-311+G(d,p)/SMD Model

Amines play several key roles in chemistry and biology and are involved in numerous industrial processes, often with significant economic impacts. Recently, amines are also garnering interest as catalysts for polymer synthesis and for CO 2 fixation, incentivizing the need to rapidly design and screen new amino compounds. Hence, developing reliable methods to predict their physicochemical properties, e.g., the base dissociation constant (pKb), is pivotal. Here, a density functional theory (DFT)-based approach was employed to compute the pKb of substituted amines, exploring the impact of several key parameters, including (i) the number of explicit water molecules at the reaction center, (ii) the van der Waals (vdW) surface, and (iii) solvent polarizability. In previous work, it was determined that including two explicit water molecules at the reaction center resulted in highly accurate pKb estimates for primary amines. Here, we find that including a third water molecule at the reaction center is essential for accurate pKb for secondary and tertiary amines. The revised methodology was then applied to a wider selection of amines, obtaining a minimum average error (MAE) < 0.4. In conclusion, this result represents an extension of our “easy-to-use method,” a simple and direct DFT approach exploiting CAM-B3LYP/SMD/6-311G+(d,p) to compute pKb without post facto modifications.

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

Preclinical studies of a PARP targeted, Meitner-Auger emitting, theranostic radiopharmaceutical for metastatic ovarian cancer

Advanced ovarian cancer currently has few therapeutic options. Poly(ADP-ribose) polymerase (PARP) inhibitors bind to nuclear PARP and trap the protein-inhibitor complex to DNA. This work investigates a theranostic PARP inhibitor for targeted radiopharmaceutical therapy of ovarian cancer in vitro and PET imaging of healthy mice in vivo. Methods: [ 77 Br]RD1 was synthesized and assessed for pharmacokinetics and cytotoxicity in human and murine ovarian cancer cell lines. [ 76 Br]RD1 biodistribution and organ uptake in healthy mice were quantified through longitudinal PET/CT imaging and ex vivo radioactivity measurements. Organ-level dosimetry following [ 76/77 Br]RD1 administration was calculated using RAPID, an in-house platform for absorbed dose in mice, and OLINDA for equivalent and effective dose in human. Results: The maximum specific binding (B max ), equilibrium dissociation constant (K d ), and nonspecific binding slope (NS) were calculated for each cell line. These values were used to calculate the cell specific activity uptake for cell viability studies. The half maximal effective concentration (EC 50 ) was measured as 0.17 (95 % CI: 0.13–0.24) nM and 0.46 (0.13–0.24) nM for PARP(+) and PARP(–) expressing cell lines, respectively. The EC 50 was 0.27 (0.21–0.36) nM and 0.30 (0.22–0.41) nM for BRCA1(–) and BRCA1(+) expressing cell lines, respectively. When measuring the EC 50 as a function of cellular activity uptake and nuclear dose, the EC 50 ranges from 0.020 to 0.039 Bq/cell and 3.3–9.2 Gy, respectively. Excretion through the hepatobiliary and renal pathways were observed in mice, with liver uptake of 2.3 ± 0.4 %ID/g after 48 h, contributing to estimated absorbed dose values in mice of 19.3 ± 0.3 mGy/MBq and 290 ± 10 mGy/MBq for [ 77 Br]RD1 and [ 76 Br]RD1, respectively. Conclusion: [ 77 Br]RD1 cytotoxicity was dependent on PARP expression and independent of BRCA1 status. Finally, the in vitro results suggest that [ 77 Br]RD1 cytotoxicity is driven by the targeted Meitner-Auger electron (MAe) radiotherapeutic effect of the agent. Further studies investigating the theranostic potential, organ dose, and tumor uptake of [ 76/77 Br]RD1 are warranted.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2026

Coordination-Induced Weakening of N–H Bonds Driven by Bimetallic Cooperativity in Zr/Co Compounds

The bond dissociation free energy (BDFE) of the element-hydrogen bonds of protic substrates have been found to decrease upon metal coordination. Herein, an early/late heterobimetallic complex is used to examine the impact on the BDFE N−H when the substrate binding site and the redox-active site are two different metals that are spatially separated. A tris- (phosphinoamide) framework is used to link a d 0 ZrIV center with an accessible substrate binding site to a coordinatively saturated redox-active Co center, which serves as an appended electron reservoir. A series of aniline, amido, and imido Zr/Co model compounds were synthesized starting from the Zr IV /Co −I aniline adduct PhH 2 N−Zr(MesNP i Pr 2 ) 3 CoCN t Bu (2). 2,4,6-tristert- butylphenoxyl radical ( t Bu 3 ArO • ) was used to abstract one or two H atoms and produce the amido and imido complexes PhHNZr( MesNP i Pr 2 ) 3 CoCN t Bu (3) and PhN≡Zr(MesNP i Pr 2 ) 3 CoCNtBu (4), respectively. Using open-circuit potential measurements, the BDFE N−H within 2 and 3 were determined to be 37 kcal/mol (2) and 55 kcal/mol (3). Cyclic voltammetry measurements were conducted to determine the Co I/0 and Co 0/−I redox potentials. The pK a s were then estimated using the Bordwell equation to provide further insight into the thermochemical aspects of the observed proton coupled electron transfer (PCET) reactions.

Bond dissociation free energy↗
DOE OSTI2020

A Quantum-Based Approach to Predict Primary Radiation Damage in Polymeric Networks

Initial atomistic-level radiation damage in chemically reactive materials is thought to induce reaction cascades that can result in undesirable degradation of macroscale properties. Ensembles of quantum-based molecular dynamics (QMD) simulations can accurately predict these cascades, but extracting chemical insights from the many underlying trajectories is a labor-intensive process that can require substantial a priori intuition. We develop here a general and automated graph-based approach to extract all chemically distinct structures sampled in QMD simulations and apply our approach to predict primary radiation damage of polydimethylsiloxane (PDMS), the main constituent of silicones. A postprocessing protocol is developed to identify underlying polymer backbone structures as connected components in QMD trajectories. Furthermore, these backbones form a repository of radiation-damaged structures. A scheme for extracting and updating a library of isomorphically distinct structures is proposed to identify the spanning set and aid chemical interpretation of the repository. The analyses are applied to ensembles of cascade QMD simulations in which the four element types in PDMS are selectively excited in primary knock-on atom events. Our approach reveals a much higher degree of combinatorial complexity in this system than was inferred through radiolysis experiments. Probabilities are extracted for radiation-induced network changes including formation of branch points, carbon linkages, cycles, bond scissions, and carbon uptake into the Si–O siloxane backbone network. The general analysis framework presented here is readily extendable to modeling chemical degradation of other polymers and molecular materials and provides a basis for future quantum-informed multiscale modeling of radiation damage.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Electric Field Effects on Water and Ion Structure and Diffusion at the Orthoclase (001)–Water Interface

Understanding the electrochemical properties of mineral–water interfaces tends to rely upon electrical double layer (EDL) models, but these models are based on the assumption that electrostatic equilibrium is constantly maintained. In reality, interfacial reactions, ion diffusion, and their electrochemical signatures are based in nonequilibrium conditions of locally or globally imbalanced electrical fields where current EDL models have limited purview. In this work, we performed molecular dynamics (MD) simulations of the orthoclase (001) surface in contact with a 1 M NaCl aqueous solution under various electric fields, to explore the interplay between EDL structure and dynamics when perturbed by electric fields of different direction and strength, by confinement, and by different distributions of structural surface charge. The simulations showed that confinement between two opposing (001) surfaces led to the development of an induced field when the applied field was perpendicular to the surfaces and, as a result, to ionic diffusion coefficients that were independent of electric field strength. In contrast, when the applied field was parallel to the surfaces, confinement resulted in ionic diffusion coefficients that were more strongly dependent on the magnitude of the electric field than in bulk water. Differences in the density and distribution of aluminol groups on the two surfaces had a significant impact on how the interfacial structure and dynamics varied in the presence of an electric field. Notably, these differences resulted in an electro-osmotic flow with opposite directions at the two surfaces under parallel applied electric field. Overall, the MD simulations highlighted the importance of considering atomic-level structure and heterogeneities when developing models of the electrochemical properties of mineral–water interfaces.

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

Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses

To cope with sudden changes in the external environment, the budding yeast Saccharomyces cerevisiae orchestrates a multifaceted response that spans many levels of physiology. Several studies have interrogated the transcriptome response to endoplasmic reticulum (ER) stress and the role of regulators such as the Ire1 kinase and Hac1 transcription factors. However, less is known about responses to ER stress at other levels of physiology. Here, we used quantitative phosphoproteomics and computational network inference to uncover the yeast phosphoproteome response to the reducing agent dithiothreitol (DTT) and the upstream signaling network that controls it. We profiled wild-type cells and mutants lacking IRE1 or MAPK kinases MKK1 and MKK2, before and at various times after DTT treatment. In addition to revealing downstream targets of these kinases, our inference approach predicted new regulators in the DTT response, including cell-cycle regulator Cdc28 and osmotic-response kinase Rck2, which we validated computationally. Our results also revealed similarities and surprising differences in responses to different stress conditions, especially in the response of protein kinase A targets. Furthermore, these results have implications for the breadth of signaling programs that can give rise to common stress response signatures.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Radiation Damage Mechanisms in Oxide-Based Solid Electrolytes

Ion implantation is a promising approach to mitigate dendrite formation in metal anode solid-state batteries by modifying the chemical and mechanical properties of oxide-based electrolyte surfaces such as Li 7 La 3 Zr 2 O 12 (LLZO). Yet, the detailed atomistic mechanisms and potentially adverse side effects of ion implantation remain poorly understood. In this study, we used molecular dynamics simulations to elucidate the evolution of radiation-induced damage in LLZO. The results reveal that radiation damage is primarily driven by recoils from heavy ions in the lattice, producing antisite defect clusters whose density decreases as recoil energy increases, a counterintuitive finding that highlights complex cascade fragmentation. Radiation-induced disruption to the crystal sublattice connectivity, especially in the La–O network critical for Li-ion transport, leads to degradation in ionic pathways at low energies, while higher energy cascades can form new conduction pathways via enhanced Zr–O network connectivity. These findings provide a mechanistic foundation for optimizing ion implantation strategies that balance disruption of the lattice for surface modification for dendrite resistance with preservation of essential ionic conductivity.

Defects↗
DOE OSTI2025

Reliable p K a Prediction through Efficient Incorporation of Anharmonicity within the Nuclear–Electronic Orbital Framework

Accurate pK a prediction is critical for understanding chemical reactivity and molecular properties across a wide range of applications. Computational approaches usually invoke a harmonic treatment of the vibrational modes for zero-point energies, as well as thermal and entropic contributions. Herein, we present a general protocol for relative pK a prediction that incorporates the significant anharmonic effects using nuclear–electronic orbital (NEO) theory. This protocol is validated against experimental data for a range of molecules in acetonitrile, including protonated nitrogen bases, nitrophenols, anilines, and diamines, as well as cobalt electrocatalysts. For simple acids, the NEO approach offers only a slight improvement over conventional density functional theory with the standard harmonic vibrational treatment, whereas for hydrogen-bonded acids, the NEO approach offers more significantly improved performance at a comparable computational cost. This accessible methodology provides a practical route for accurate pKa prediction in challenging systems and is extendable to related thermodynamic properties such as hydricities and proton-coupled redox potentials.

Density functional theory↗
DOE OSTI2020

Visualization of Aluminum Ions at the Mica Water Interface Links Hydrolysis State-to-Surface Potential and Particle Adhesion

When hydrolyzable cations such as aluminum interact with solid-water interfaces, macroscopic interfacial properties (e.g., surface charge and potential) and interfacial phenomena (e.g., particle adhesion) become tightly linked with the microscopic details of ion adsorption and speciation. We use in situ atomic force microscopy to directly image individual aluminum ions at a mica-water interface and show how adsorbate populations change with pH and aluminum activity. Complementary streaming potential measurements then allow us to build a triple layer model (TLM) that links surface potentials to adsorbate populations, via equilibrium binding constants. Our model predicts that hydrolyzed species dominate the mica-water interface, even when unhydrolyzed species dominate the solution. Ab initio molecular dynamics (AIMD) simulations confirm that aluminum hydrolysis is strongly promoted at the interface. The TLM indicates that hydrolyzed adsorbates are responsible for surface-potential inversions, and we find strong correlations between hydrolyzed adsorbates and particle-adhesion forces, suggesting that these species mediate adhesion by chemical bridging.

Legg, Benjamin A.↗
DOE OSTI2023

Sterically attenuated electronic communication in cobalt complexes of meridional isoquinoline-derived ligands for applications in electrocatalysis

The ability to synthetically tune the ligand frameworks of redox-active molecules is of critical importance to the economy of solar fuels because manipulating their redox properties can afford control over the operating potentials of sustained electrocatalytic or photoelectrocatalytic processes. The electronic and steric properties of 2,2′:6′,2″-terpyridine (Terpy) ligand frameworks can be tuned by functional group substitution on ligand backbones, and these correlate strongly to their Hammett parameters. The synthesis of a new series of tridentate meridional ligands of 2,4,6-trisubstituted pyridines that engineers the ability to finely tune the redox potentials of cobalt complexes to more positive potentials than that of their Terpy analogs is achieved by aryl-functionalizing at the four-position and by including isoquinoline at the two- and six-positions of pyridine (Aryl-DiQ). Their cobalt complex syntheses, their electronic properties, and their catalytic activity for carbon dioxide (CO2) reduction are reported and compared to their Terpy analogs. The cobalt derivatives generally experience a positive shift in their redox features relative to the Terpy-based analogs, covering a complementary potential range. Although those evaluated fail to produce any quantifiable products for the reduction of CO2 and suffer from long-term instability, these results suggest possible alternate strategies for stabilizing these compounds during catalysis. We speculate that lower equilibrium association constants to the cobalt center are intrinsic to these ligands, which originate from a steric interaction between protons on the pyridine and isoquinoline moieties. Nevertheless, the new Aryl-DiQ ligand framework has been engineered to selectively tune homoleptic cobalt complexes’ redox potentials.

Chemistry↗
DOE OSTI2025

The impact of curation errors in the PDBBind Database on machine learning predictions of protein–protein binding affinity

The PDBBind database has been widely utilized for the computational prediction of protein–protein binding affinities. While the accuracy of the PDBBind-curated equilibrium dissociation constants (K D ) has been reported for the protein–ligand subset of the PDBBind database, the curation accuracy has not been reported for the protein–protein subset. Here, we present a detailed manual analysis for the subset of PDBBind records with PubMed Central Open Access primary publications and find that ~19% of these records had K D values that were not supported by their primary publications. The impact of these putative curation errors on the machine learning-based prediction of K D from experimental protein–protein 3D structures was evaluated and correcting the curation errors improved the Pearson correlation coefficient between measured and random forest-predicted log 10 (K D ) values by ~8 percentage points. This finding underscores the importance of dataset accuracy for computational modelling and highlights the need for more stringent curation processes when extracting information from the scientific literature.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Different bonding type along each crystallographic axis: Computational study of poly($\textit{p}$-phenylene terephthalamide)

Poly($\textit{p}$-phenylene terephthalamide) (PPTA) exhibits van der Waals (vdW) bonding along its $\textit{a}$ axis, hydrogen bonding along its $\textit{b}$ axis, and covalent bonding along its $\textit{c}$ axis. In this work, we explore the structural and mechanical properties of PPTA using density functional theory with various functionals including LDA, PBE, PBE+rVV10L, SCAN, and SCAN+rVV10, compared with available experiments. The hierarchy of nonempirical semilocal functionals LDA, PBE, and SCAN (not fitted to any multicenter bonded system) includes differing amounts of intermediate-range vdW interaction. rVV10 is the long-range vdW correction. (rVV10L differs from rVV10 only in the value of a range parameter.) Among the tested functionals, SCAN shows the best performance for the lattice parameters of PPTA along the two crystal directions involving vdW or hydrogen-bond interaction. The equilibrium lattice constants obtained by SCAN and PBE+rVV10L are closest to experimental data, while SCAN+rVV10 slightly overbinds the system. We study the mechanical response of PPTA by applying strain along three lattice directions. Due to the inclusion of vdW interaction, SCAN, PBE+rVV10L, and SCAN+rVV10 all exhibit correct bonding strain-energy curves. On the contrary, PBE strongly underestimates the vdW interaction needed to resist uniaxial stretching along the $\textit{a}$ axis. The Young's modulus and yield strength of PPTA are computed and compared with previous results. The experimental values are much smaller than the computed ones, mainly due to the fact that the PPTA fiber samples used for measurements are mechanically weaker than the perfect molecular crystals considered in the simulations. Interestingly, when a compressive uniaxial stress of 25 Kbar is applied along the $\textit{b}$ axis, a structural phase transition, in which the hydrogen bonds reform along one diagonal of the $\textit{ab}$ rectangle, is predicted by SCAN.

36 MATERIALS SCIENCE↗