Search NASA⌕ Search

SEARCH · Search NASA

Results for “ligand”

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 325 records · Page 18
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Dioctyl ether radiolysis under used nuclear fuel reprocessing conditions: Foundational knowledge for the development of sacrificial ligand grafts

Radiation-induced ligand destruction and concomitant degradation product formation is unavoidable under envisioned used nuclear fuel reprocessing conditions, and ultimately limits the recyclability of a given solvent system formulation. With this in mind, a novel approach to ligand innovation for advanced separations processes is in the design of tailored “protomolecules,” which when exposed to ionizing radiation undergo desired chemical transformations, thereby allowing for a reprocessing solvent system to advantageously evolve with absorbed radiation dose. Here we provide foundational knowledge for the time-resolved (electron pulse) and steady-state (cobalt-60 gamma) radiolytic behavior of dioctyl ether, a protomolecule grafting surrogate. Gamma irradiation of single-phase solutions of dioctyl ether (5–100 vol.%) in n-dodecane resulted in the loss of dioctyl ether (G = -0.72 µmol J –1 ) and the formation of octane (G = 0.11 µmol J –1 ) and octanol (G = 0.15 µmol J –1 ) degradation products, the latter of which is a known reprocessing phase modifier and radioprotectant. Further, these radiation-induced changes were attributed to direct radiation effects, for more concentrated dioctyl ether solutions, and indirect radiation effects, predominantly driven by the reaction of dioctyl ether with the dodecane radical cation, for which we report a second-order rate coefficient of k = (1.53 ± 0.05) × 10 10 L mol –1 s –1 . Under typical biphasic extraction (4.0 mol L –1 HNO 3 ) and strip (0.1 mol L –1 HNO 3 ) reprocessing conditions, gamma irradiation of 5 vol.% dioctyl ether solvent systems afforded negligible change in the rate of parent molecule destruction but promoted significant differences in the radiolytic behavior of its degradation products. These differences are attributed to their respective interactions with [dioctyl ether/HNO 3 /H 2 O] and [octanol/HNO 3 /H 2 O] adducts extracted into the organic phase. Overall, these results support the grafting of ether linkages to advanced separations ligands (e.g., modified diglycolamides).

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2021

The Story of 5d Metallocorroles: From Metal–Ligand Misfits to New Building Blocks for Cancer Phototherapeutics

Porphyrin chemistry is Shakespearean: over a century of study has not withered the field’s apparently infinite variety. Heme proteins continually astonish us with novel molecular mechanisms, while new porphyrin analogues bowl us over with unprecedented optical, electronic, and metal-binding properties. Within the latter domain, corroles occupy a special place, exhibiting a unique and rich coordination chemistry. The 5d metallocorroles are arguably the icing on that cake. New Zealand chemist Penny Brothers has used the word “misfit” to describe the interactions of boron, a small atom with a predilection for tetrahedral coordination, and porphyrins, classic square-planar ligands. Steve Jobs lionized misfits as those who see things differently and push humanity forward. Both perspectives have inspired us. The 5d metallocorroles are misfits in that they encapsulate a large 5d transition metal ion within the tight cavity of a contracted porphyrin ligand. Given the steric mismatch inherent in their structures, the syntheses of some 5d metallocorroles are understandably capricious, proceeding under highly specific conditions and affording poor yields. Three broad approaches may be distinguished. (a) In the metal–alkyl approach, a free-base corrole is exposed to an alkyllithium and the resulting lithio-corrole is treated with an early transition metal chloride; a variant of the method eschews alkyllithium and deploys a transition metal–alkyl instead, resulting in elimination of the alkyl group as an alkane and insertion of the metal into the corrole. This approach is useful for inserting transition metals from groups 4, 5, and, to some extent, 6, as well as lanthanides and actinides. (b) In our laboratory, we have often deployed a low-valent organometallic approach for the middle transition elements (groups 6, 7, 8, and 9). The reagents are low-valent metal–carbonyl or −olefin complexes, which lose one or more carbon ligands at high temperature, affording coordinatively unsaturated, sticky metal fragments that are trapped by the corrole nitrogens. (c) Finally, a metal acetate approach provides the method of choice for gold and platinum insertion (groups 10 and 11). This Account provides a first-hand perspective of the three approaches, focusing on the last two, which were largely developed in our laboratory. In general, the products were characterized with X-ray crystallography, electrochemistry, and a variety of spectroscopic methods. The physicochemical data, supplemented by relativistic DFT calculations, have provided fascinating insights into periodic trends and relativistic effects. An unexpected feature of many 5d metallocorroles, given their misfit character, is their remarkable stability under thermal, chemical, and photochemical stimulation. Many of them also exhibit long triplet lifetimes on the order of 100 μs and effectively sensitize singlet oxygen formation. Many exhibit phosphorescence in the near-infrared under ambient conditions. Furthermore, water-soluble ReO and Au corroles exhibit impressive photocytotoxicity against multiple cancer cell lines, promising potential applications as cancer phototherapeutics. We thus envision a bright future for the compounds as rugged building blocks for new generations of therapeutic and diagnostic (theranostic) agents.

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

Amidinate Supporting Ligands Influence Molecularity in Formation of Uranium Nitrides

Uranium nitride complexes are attractive targets for chemists as molecular models for the bonding, reactivity, and magnetic properties of next-generation nuclear fuels, but these molecules are uncommon and can be difficult to isolate due to their high reactivity. Here, we describe the synthesis of three new multinuclear uranium nitride complexes, [U(BCMA) 2 ] 2 (μ-N)(μ-κ 1 :κ 1 -BCMA) (7), [(U(BIMA) 2 ) 2 (μ-N)(μ-N i Pr)(K 2 (μ-η 3 :η 3 -CH 2 CHN i Pr)] 2 (8), and [U(BIMA) 2 ] 2 (μ-N)(μ-κ 1 :κ 1 -BIMA) (9) (BCMA = N,N-bis(cyclohexyl)methylamidinate, BIMA = N,N-bis(iso-propyl)methylamidinate), from U(III) and U(IV) amidinate precursors. By varying the amidinate ligand substituents and azide source, we were able to influence the composition and size of these nitride complexes. 15 N isotopic labeling experiments confirmed the bridging nitride moieties in 7–9 were formed via two-electron reduction of azide. The tetra-uranium cluster 8 was isolated in 99% yield via reductive cleavage of the amidinate ligands; this unusual molecule contains nitrogen-based ligands with formal 1–, 2–, and 3– charges. Additionally, chemical oxidation of the U(IV) precursor U(N 3 )(BCMA) 3 yielded the cationic U(V) species [U(N 3 )(BCMA) 3 ][OTf]. Magnetic susceptibility measurements confirmed a U(IV) oxidation state for the uranium centers in the three nitride-bridged complexes and provided a comparison of magnetic behavior in the structurally related U(III)-U(IV)-U(V) series U(BCMA) 3 , U(N 3 )(BCMA) 3 , and [U(N 3 )(BCMA) 3 ][OTf]. At 240 K, the magnetic moments in this series decreased with increasing oxidation state, i.e., U(III) > U(IV) > U(V); this trend follows the decreasing number of 5f valence electrons along this series.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2023

Americium Oxalate: An Experimental and Computational Investigation of Metal–Ligand Bonding

A novel actinide-containing coordination polymer, [Am(C 2 O 4 )(H 2 O) 3 Cl] (Am-1), has been synthesized and structurally characterized. The crystallographic analysis reveals that the structure is two-dimensional and comprised of pseudo-dimeric Am 3+ nodes that are bridged by oxalate ligands to form sheets. Each metal center is nine-coordinate, forming a distorted capped square antiprism geometry with a C 1 symmetry, and features bound oxalate, aqua, and chloro ligands. The Am 3+ –ligand bonds were probed computationally using the quantum theory of atoms in molecules nd natural localized molecular orbital approaches to investigate the underlying mechanisms and hybrid atomic orbital contributions therein. The analyses indicate that the bonds within Am-1 are predominantly ionic and the 5f shell of the Am 3+ metal centers does not add a significant covalent contribution to the bonds. Further, our bonding assessment is supported by measurements on the optical properties of Am-1 using diffuse reflectance and photoluminescence spectroscopies. The position of the principal absorption band at 507 nm ( 5 L 6' ← 7 F 0' ) is notable because it is consistent with previously reported americium oxalate complexes in solution, indicating similarities in the electronic structure and ionic bonding. Compound Am-1 is an active phosphor, featuring strong bright-blue oxalate-based luminescence with no evidence of metal-centered emission.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

From +I to +IV, Alkalis to Actinides: Capturing Cations across the Periodic Table with Keggin Polyoxometalate Ligands

Coordination chemistry trends across the periodic table are often difficult to probe experimentally due to limitations in finding a versatile but consistent chelating platform that can accommodate various elements without changing its coordination mode. Herein, we present new metal/ligand systems covering a wide range of ionic radii, charges, and elements. Five different ligands derived from the Keggin structure (HBW 11 O 39 8– , PW 11 O 39 7– , SiW 11 O 39 8– , GeW 11 O 39 8– , and GaW 11 O 39 9– ) were successfully crystallized with six different cations (Na + , Sr 2+ , Ba 2+ , La 3+ , Ce 4+ , and Th 4+ ) and characterized by single-crystal X-ray diffraction. Twenty-five new compounds were obtained by using Cs + as the counterion, yielding a consistent base formula of Cs x [M(XW 11 O 39 ) 2 ]·nH 2 O. Despite having a similar first-coordination sphere geometry (i.e., 8-coordinated), the nature of the central cation was found to impact the long-range geometry of the complexes. This unique crystallographic data set shows that, despite the traditional consensus, the local geometry of the cation (i.e., metal–oxygen bond distance) is not enough to depict the full impact of the complexed metal ion. The bending and twisting of the complexes, as well as ligand–ligand distances, were all impacted by the nature of the central cation. We also observed that counterions play a critical role by stabilizing the geometry of the M(XW 11 ) 2 complex and directing complex–complex interactions in the lattice. We also define certain structural limits for this type of complex, with the large Ba 2+ ion seemingly approaching those limits. Finally, this study thus lays the foundation for capturing the coordination chemistry of other rarer elements across the periodic table such as Ra 2+ , Ac 3+ , Bk 4+ , Cf 3+ , etc.

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

Ligand Influence on Indium–Sulfide Cluster Formation and Reactivity

An indium–sulfide tetramer ([InMe 2 (SSiMe 3 )] 4 ), which contains reactive silyl and methyl groups, is shown to be an isolable intermediate in cluster synthesis. The reactive groups allow it to act as a synthon in the formation of multinuclear indium–sulfide architectures, evidenced by the crystallization of a coordination polymer ([In 20 S 14 Me 32 (4,4’-bpy) 5 ·5CH 2 Cl 2 ] n ) utilizing In 10 S 7 clusters as nodes. The reaction between trimethylindium (InMe 3 ) and bis­(trimethylsilyl)­sulfide (S­(SiMe 3 ) 2 ) is explored with and without the presence of a ligating bipyridine. In both cases, a sulfide-indium adduct is formed, which slowly converts into a multimetallic complex. Here, the ligand 2,2’-bipyridine (2,2’-bpy) is coordinated to InMe 3 to form the adduct InMe 3 (bpy), which upon addition of sulfide, eliminates tetramethylsilane (TMS) and binds two additional InMe 3 moieties (InMe 2 (bpy)­(μ 3 -SSiMe 3 )­(InMe 3 ) 2 ). When reacted neatly without bipyridine, InMe 3 and S­(SiMe 3 ) 2 form the adduct InMe 3 (S­(SiMe 3 ) 2 ), which subsequently eliminates TMS and intermolecularly associates to yield [InMe 2 (SSiMe 3 )] 4 . Although stable in an inert atmosphere, [InMe 2 (SSiMe 3 )] 4 undergoes facile hydrolysis to yield [InMeS] n when exposed to air. The effect of ligand addition (4,4’-bipyridine (4,4’-bpy)) to [InMe 2 (SSiMe 3 )] 4 is then examined. In every case, it is shown that the presence of the bpy ligand has a profound influence on the resulting structure, as shown by the unexpected formation of a trimer and In 10 S 7 cluster network.

Bell, Colby Seth [Argonne National Laboratory (ANL↗
DOE OSTI2021

Role of a 3D Structure in Energy Transfer in Mixed-Ligand Metal–Organic Frameworks

We present a detailed investigation of the photophysical properties of mixed-ligand pyrene- and porphyrin-based metal–organic frameworks (MOFs) as a function of their 3D structure. Solvothermal reactions between metal salts (InCl 3 , Zr(acac) 4 , and ZrCl 4 ) and suitable ratios of 1,3,6,8-tetrakis(p-benzoic acid)pyrene (TBAPy) and meso-tetrakis- (4-carboxyphenyl)porphyrin (TCPP) were performed to prepare a series of mixed-ligand ROD-7, NU-901, and NU-1000 MOFs. Time-resolved and steady-state fluorescence measurements were conducted on the mixed-ligand MOFs to study their photophysics. Based on the results, we concluded that upon excitation of TBAPy linkers in the MOFs, singlet excitation energy migrates across TBAPy linkers until it finds a TCPP unit. TCPP acts as an energy trap and quenches the excitation. The efficiency of TBAPy-to-TBAPy energy transfer was found to be sensitive to the structural parameters of MOFs. Analysis of steady-state and time-resolved fluorescence data revealed that excitation energy transfer (EET) is most efficient in ROD-7, followed by NU-901 and NU-1000. We propose that topology that invokes the shorter interchromophoric distances between TBAPy linkers in ROD-7 is responsible for its higher EET efficiency. The distance dependence of the EET rate constant (kEET) was investigated to gain insight into the mechanistic aspects of energy transfer in MOFs. This study revealed that (a) energy transfer in MOFs deviates from the classical Förster model and (b) the geometrical arrangement of linkers influences the mechanism of EET in MOFs. A theoretical investigation was also performed to determine energy-transfer rate constants along different directions and assess the directionality of energy transfer in these MOFs. The magnitude of rate constants indicated that energy transfer in ROD-7 should be highly anisotropic along the stacking direction. Furthermore, these findings suggest that ROD-7 is a promising candidate to play the role of the light-harvesting and energy-transfer component in solar energy conversion devices, where directional energy transfer is required.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Influence of Surface Ligands on Energetics at FASnI 3 /C 60 Interfaces and Their Impact on Photovoltaic Performance

Interfacial chemistry and energetics significantly impact the performance of photovoltaic devices. In the case of Pb-containing organic metal halide perovskites, photoelectron spectroscopy has been used to determine the energetic alignment of frontier electronic energy levels at various interfaces present in the photovoltaic device. For the Sn-containing analogues, which are less toxic, no such measurements have been made. Through a combination of ultraviolet, inverse, and X-ray photoelectron spectroscopy (UPS, IPES, and XPS, respectively) measurements taken at varying thickness increments during stepwise deposition of C 60 on FASnI 3 , we present the first direct measurements of the frontier electronic energy levels across the FASnI 3 /C 60 interface. The results show band bending in both materials and transport gap widening in FASnI 3 at the interface with C 60 . The XPS results show that iodide diffuses into C 60 and results in n-doping of C 60 . This iodide diffusion out of FASnI 3 impacts the valence and conduction band energies of FASnI 3 more than the core levels, with the core level shifts displaying a different trend than the valence and conduction bands. Surface treatment of FASnI 3 with carboxylic acids and bulky ammonium substituted surface ligands results in slight alterations in the interfacial energetics, and all surface ligands result in similar or improved PV performance relative to the untreated devices. Finally, the greatest PV stability results from treatment with a fluorinated carboxylic acid derivative; however, iodide diffusion is still observed to occur with this surface ligand.

interfacial energetics↗
DOE OSTI2020

Tunable Catalytic Performance of Palladium Nanoparticles for H 2 O 2 Direct Synthesis via Surface-Bound Ligands

There is a critical need for sustainable routes to produce hydrogen peroxide, H 2 O 2 . A promising approach involves direct synthesis from molecular hydrogen and oxygen at (sub)ambient temperatures using unmodified supported Pd catalysts, which are limited by low selectivities. Controlling the environment of Pd active sites via surface ligands is shown to enhance selectivity. Trends among a myriad of surface ligands (i.e., phosphines, thiols, weakly bound molecules) suggest that those containing H-bonding groups lead to the highest H 2 O 2 production, potentially by affecting reaction energetics via H-bonding with key intermediates. These insights lay the groundwork for ligand design to achieve the optimal catalyst performance for H 2 O 2 synthesis.

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

Tuning Catalytic Sites on Zr 6 O 8 Metal–Organic Framework Nodes via Ligand and Defect Chemistry Probed with tert -Butyl Alcohol Dehydration to Isobutylene

Metal–organic frameworks (MOFs) have drawn wide attention as candidate catalysts, but some essential questions about their nature and performance have barely been addressed. (1) How do OH groups on MOF nodes act as catalytic sites? (2) What are the relationships among these groups, node defects, and MOF stability, and how do reaction conditions influence them? (3) What are the interplays between catalytic properties and transport limitations? To address these questions, we report an experimental and theoretical investigation of the catalytic dehydration of tert -butyl alcohol (TBA) used to probe the activities of OH groups of Zr 6 O 8 nodes in the MOFs UiO-66 and MOF-808, which have different densities of vacancy sites and different pore sizes. The results show that (1) terminal node OH groups are formed as formate and/or acetate ligands present initially on the nodes react with TBA to form esters, (2) these OH groups act as catalytic sites for TBA dehydration to isobutylene, and (3) TBA also reacts to break node–linker bonds to form esters and thereby unzip the MOFs. The small pores of UiO-66 limit the access of TBA and the reaction with the formate/acetate ligands bound within the pores, whereas the larger pores of MOF-808 facilitate transport and favor reaction in the MOF interior. However, after removal of the formate and acetate ligands by reaction with methanol to form esters, interior active sites in UiO-66 become accessible for the reaction of TBA, with the activity depending on the density of defect sites with terminal OH groups. The number of vacancies on the nodes is important in determining a tradeoff between the catalytic activity of a MOF and its resistance to unzipping. Computations at the level of density functional theory show how the terminal OH groups on node vacancies act as Brønsted bases, facilitating TBA dehydration via a carbocation intermediate in an E1 mechanism; the calculations further illuminate the comparable chemistry of the unzipping.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

An Activity-Based Oxaziridine Platform for Identifying and Developing Covalent Ligands for Functional Allosteric Methionine Sites: Redox-Dependent Inhibition of Cyclin-Dependent Kinase 4

Activity-based protein profiling (ABPP) is a versatile strategy for identifying and characterizing functional protein sites and compounds for therapeutic development. However, the vast majority of ABPP methods for covalent drug discovery target highly nucleophilic amino acids such as cysteine or lysine. Here, we report a methionine-directed ABPP platform using Redox-Activated Chemical Tagging (ReACT), which leverages a biomimetic oxidative ligation strategy for selective methionine modification. Application of ReACT to oncoprotein cyclin-dependent kinase 4 (CDK4) as a representative high-value drug target identified three new ligandable methionine sites. We then synthesized a methionine-targeting covalent ligand library bearing a diverse array of heterocyclic, heteroatom, and stereochemically rich substituents. ABPP screening of this focused library identified 1oxF11 as a covalent modifier of CDK4 at an allosteric M169 site. This compound inhibited kinase activity in a dose-dependent manner on purified protein and in breast cancer cells. Further investigation of 1oxF11 found prominent cation-π and H-bonding interactions stabilizing the binding of this fragment at the M169 site. Quantitative mass-spectrometry studies validated 1oxF11 ligation of CDK4 in breast cancer cell lysates. Further biochemical analyses revealed cross-talk between M169 oxidation and T172 phosphorylation, where M169 oxidation prevented phosphorylation of the activating T172 site on CDK4 and blocked cell cycle progression. Finally, by identifying a new mechanism for allosteric methionine redox regulation on CDK4 and developing a unique modality for its therapeutic intervention, this work showcases a generalizable platform that provides a starting point for engaging in broader chemoproteomics and protein ligand discovery efforts to find and target previously undruggable methionine sites.

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

Molecular Switch Cobalt Redox Shuttle with a Tunable Hexadentate Ligand

Strong-field hexadentate ligands were synthesized and coordinated to cobalt metal centers to result in three new low-spin to low-spin Co(III/II) redox couples. The ligand backbone has been modified with dimethyl amine groups to result in redox potential tuning of the Co(III/II) redox couples from –200 to –430 mV versus Fc +/0 . The redox couples surprisingly undergo a reversible molecular switch rearrangement from five-coordinate Co(II) to six-coordinate Co(III) despite the ligands being hexadentate. The complexes exhibit modestly faster electron self-exchange rate constants of 2.2–4.2 M –1 s –1 compared to the high-spin to low-spin redox couple [Co(bpy) 3 ] 3 + /2 + at 0.27 M –1 s –1 , which is attributed to the change in spin state being somewhat offset by this coordination switching behavior. The complexes were utilized as redox shuttles in dye-sensitized solar cells with the near-IR AP25 + D35 dye system and exhibited improved photocurrents over the [Co(bpy) 3 ] 3 + /2 + redox shuttle (19.8 vs 18.0 mA/cm 2 ). Finally, future directions point toward pairing the low-spin to low-spin Co(II/III) tunable series to dyes with significantly more negative highest occupied molecular orbital potentials that absorb into the near-IR where outer sphere redox shuttles have failed to produce efficient dye regeneration.

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

Mechanistic Insight into Tunable Spin Relaxation in Two-Dimensional Type-II Ligand-Perovskite Heterostructures

Two-dimensional (2D) metal-halide perovskites with spin-dependent optical properties hold great promise for spintronic and quantum applications. However, their spin lifetimes, especially for n = 1 2D perovskites, are typically limited to subpicosecond time scales due to rapid spin relaxation driven by strong spin−orbit coupling (SOC), electron−hole exchange interactions, and phonon-mediated scattering. Here, we demonstrate that type-II ligand-perovskite heterostructures overcome these constraints by reducing electron−hole wave function overlap and exciton binding energy. Compared to the type-I 2D perovskite (PEA) 2 PbI 4 with a spin lifetime of 0.29 ps at room temperature, our engineered type-II systems achieve substantially extended spin lifetimes, ∼6.37 ps for (4Tm) 2 PbI 4 and ∼18.47 ps for (4TCNm) 2 PbI 4 . In both materials, spatial charge separation across the perovskite−ligand interface mitigates the Bir−Aronov− Pikus (BAP) mechanism. Temperature- and fluence-dependent measurements reveal Elliott−Yafet (EY)-dominated spin relaxation in (4Tm) 2 PbI 4 , consistent with the observation of coherent phonon oscillation, whereas (4TCNm) 2 PbI 4 exhibits D’yakonov−Perel (DP)-dominated spin relaxation, with weaker phonon coupling further suppressing the EY relaxation, enabling spin lifetimes up to ∼126.81 ps at 5 K. Our findings establish a structural design framework for tailoring spin dynamics in 2D perovskites, offering a promising strategy to engineering spin and optoelectronic properties via rational ligand engineering.

Excitons↗
DOE OSTI2023

Near Quantitative Removal of Selenate and Sulfate Anions from Wastewaters by Cocrystallization with Chelating Hydrogen-Bonding Guanidinium Ligands

Selenium (Se) has become an environmental contaminant of aquatic ecosystems as a result of human activities, particularly mining, fossil fuel combustion, and agricultural activities. By leveraging the high sulfate concentrations relative to Se oxyanions (i.e., SeO n 2– , n = 3, 4) present in some wastewaters, we have developed an efficient approach to Se-oxyanion removal by cocrystallization with bisiminoguanidinium (BIG) ligands that form crystalline sulfate/selenate solid solutions. The crystallization of the sulfate, selenate and selenite, oxyanions and of sulfate/selenate mixtures with five candidate BIG ligands are reported along with the thermodynamics of crystallization and aqueous solubilities. Oxyanion removal experiments with the top two performing candidate ligands show a near quantitative removal (>99%) of sulfate or selenate from solution. When both sulfate and selenate are present, there is near quantitative removal (>99%) of selenate, down to sub-ppb Se levels, with no discrimination between the two oxyanions during cocrystallization. Reducing the selenate concentrations by 3 orders of magnitude or more relative to sulfate, as found in many wastewaters, led to no measurable loss in Se removal efficiencies. This work offers a simple and effective alternative to selective separation of trace amounts of highly toxic selenate oxyanions from wastewaters, to meet stringent regulatory discharge limits.

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

Structural insights on ligand recognition at the human leukotriene B4 receptor 1

The leukotriene B4 receptor 1 (BLT1) regulates the recruitment and chemotaxis of different cell types and plays a role in the pathophysiology of infectious, allergic, metabolic, and tumorigenic human diseases. Here we present a crystal structure of human BLT1 (hBLT1) in complex with a selective antagonist MK-D-046, developed for the treatment of type 2 diabetes and other inflammatory conditions. Comprehensive analysis of the structure and structure-activity relationship data, reinforced by site-directed mutagenesis and docking studies, reveals molecular determinants of ligand binding and selectivity toward different BLT receptor subtypes and across species. The structure helps to identify a putative membrane-buried ligand access channel as well as potential receptor binding modes of endogenous agonists. These structural insights of hBLT1 enrich our understanding of its ligand recognition and open up future avenues in structure-based drug design.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Ligand-modified nanoparticle surfaces influence CO electroreduction selectivity

Improving the kinetics and selectivity of CO 2 /CO electroreduction to valuable multi-carbon products is a challenge for science and is a requirement for practical relevance. Here we develop a thiol-modified surface ligand strategy that promotes electrochemical CO-to-acetate. We explore a picture wherein nucleophilic interaction between the lone pairs of sulfur and the empty orbitals of reaction intermediates contributes to making the acetate pathway more energetically accessible. Density functional theory calculations and Raman spectroscopy suggest a mechanism where the nucleophilic interaction increases the sp 2 hybridization of CO (ad) , facilitating the rate-determining step, CO* to (CHO)*. We find that the ligands stabilize the (HOOC–CH 2 )* intermediate, a key intermediate in the acetate pathway. In-situ Raman spectroscopy shows shifts in C–O, Cu–C, and C–S vibrational frequencies that agree with a picture of surface ligand-intermediate interactions. A Faradaic efficiency of 70% is obtained on optimized thiol-capped Cu catalysts, with onset potentials 100 mV lower than in the case of reference Cu catalysts.

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

Ligand efficacy shifts a nuclear receptor conformational ensemble between transcriptionally active and repressive states

Abstract Nuclear receptors (NRs) are thought to dynamically alternate between transcriptionally active and repressive conformations, which are stabilized upon ligand binding. Most NR ligand series exhibit limited bias, primarily consisting of transcriptionally active agonists or neutral antagonists, but not repressive inverse agonists—a limitation that restricts understanding of the functional NR conformational ensemble. Here, we report a NR ligand series for peroxisome proliferator-activated receptor gamma (PPARγ) that spans a pharmacological spectrum from repression (inverse agonism) to activation (agonism) where subtle structural modifications switch compound activity. While crystal structures provide snapshots of the fully repressive state, NMR spectroscopy and conformation-activity relationship analysis reveals that compounds within the series shift the PPARγ conformational ensemble between transcriptionally active and repressive conformations that are natively populated in the apo/ligand-free ensemble. Our findings reveal a molecular framework for minimal chemical modifications that enhance PPARγ inverse agonism and elucidate their influence on the dynamic PPARγ conformational ensemble.

Science & Technology - Other Topics↗
DOE OSTI2022

Decoding the protein–ligand interactions using parallel graph neural networks

Abstract Protein–ligand interactions (PLIs) are essential for biochemical functionality and their identification is crucial for estimating biophysical properties for rational therapeutic design. Currently, experimental characterization of these properties is the most accurate method, however, this is very time-consuming and labor-intensive. A number of computational methods have been developed in this context but most of the existing PLI prediction heavily depends on 2D protein sequence data. Here, we present a novel parallel graph neural network (GNN) to integrate knowledge representation and reasoning for PLI prediction to perform deep learning guided by expert knowledge and informed by 3D structural data. We develop two distinct GNN architectures: $$\hbox {GNN}_{\mathrm{F}}$$ GNN F is the base implementation that employs distinct featurization to enhance domain-awareness, while $$\hbox {GNN}_{\mathrm{P}}$$ GNN P is a novel implementation that can predict with no prior knowledge of the intermolecular interactions. The comprehensive evaluation demonstrated that GNN can successfully capture the binary interactions between ligand and protein’s 3D structure with 0.979 test accuracy for $$\hbox {GNN}_{\mathrm{F}}$$ GNN F and 0.958 for $$\hbox {GNN}_{\mathrm{P}}$$ GNN P for predicting activity of a protein–ligand complex. These models are further adapted for regression tasks to predict experimental binding affinities and $$\hbox {pIC}_{\mathrm{50}}$$ pIC 50 crucial for compound’s potency and efficacy. We achieve a Pearson correlation coefficient of 0.66 and 0.65 on experimental affinity and 0.50 and 0.51 on $$\hbox {pIC}_{\mathrm{50}}$$ pIC 50 with $$\hbox {GNN}_{\mathrm{F}}$$ GNN F and $$\hbox {GNN}_{\mathrm{P}}$$ GNN P , respectively, outperforming similar 2D sequence based models. Our method can serve as an interpretable and explainable artificial intelligence (AI) tool for predicted activity, potency, and biophysical properties of lead candidates. To this end, we show the utility of $$\hbox {GNN}_{\mathrm{P}}$$ GNN P on SARS-Cov-2 protein targets by screening a large compound library and comparing the prediction with the experimentally measured data.

59 BASIC BIOLOGICAL SCIENCES↗