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DOE OSTI2023

Exploring the Role of Neutral 4-Amino-1,2,4-triazole in the Formation of Hexanuclear f-Element Hydrolysis Products

Our recent observations of an unexpected Ce(III) hydrolysis product from the reaction of 4-amino-1,2,4-triazole (4-NH 2 -1,2,4-Triaz) with CeCl 3 ·7H 2 O, [Ce 6 (μ 3 -O) 4 (μ 3 -OH) 2 (μ 3 -Cl) 2 (Cl) 6 (μ 2 -4-NH 2 -1,2,4-Triaz) 12 ]·7H 2 O, the first high-nuclearity lanthanide complex where all Ln atoms are connected pairwise through 12 N-donor ligands or 12 neutral bridging ligands of any type, prompted us to explore the utility of this ligand in trapping additional f-element examples. Reactions of LnCl 3 ·6H 2 O (Ln = Nd, Eu, Ho) with a large excess of 4-NH 2 -1,2,4-Triaz (20 equiv) and with the addition of small amounts of water to help solubilize the metal salts led to the isolation of the unique hydrolysis products [Nd 6 (μ 3 -OH) 8 Cl 6 (μ 2 -4-NH 2 -1,2,4-Triaz) 12 ][Cl 4 ]·2H 2 O, [Eu 6 (μ 6 -Cl) 0.23 (μ 3 -O 0.77 ) 4 (μ 3 -O) 2.6 (μ 3 -Cl) 0.4 Cl 6 (μ 2 -4-NH 2 -1,2,4-Triaz) 12 ], and [Ho 6 (μ 6 -Cl) 0.21 (μ 3 -O 0.79 ) 4 (μ 3 -OH) 2 Cl 6 (μ 2 -4-NH 2 -1,2,4-Triaz) 12 ][Cl] 3.4 . Here, we also report a Ce(III) analogue prepared in glassware contaminated with Pb(OAc) 2 , namely, [Ce 6 (μ 3 -OH) 8 (BrPbBr 5 )(μ 2 -4-NH 2 -1,2,4-Triaz) 11.5 (OH 2 ) 6 ][Pb 0.84 Br 4.2 ][Br] 3.8 ·2(4-NH 2 -1,2,4-Triaz)·3.6H 2 O. The Nd(III) complex is the structurally most ordered with a clear [Nd 6 (μ 3 -OH) 8 ] cluster core, while the Eu(III) and Ho(III) compounds contain partial occupancy of a μ 6 position and thus result in an incomplete Ln 6 O 9 cluster core formation. The crystallographic results suggest that the 4-NH 2 -1,2,4-Triaz ligand brings Ln(III) ions together, followed by the formation of an Ln 6 O 8 or Ln 6 O 9 core with whatever remaining anions or ligands can be incorporated. Given the complexity of the hydrolysis products of nuclear waste, we expect to continue to find a myriad of closely related complex structures of these types for the f-elements.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2020

An Adaptable N‐Heterocyclic Carbene Macrocycle Hosting Copper in Three Oxidation States

Abstract A neutral hybrid macrocycle with two trans ‐positioned N‐heterocyclic carbenes (NHCs) and two pyridine donors hosts copper in three oxidation states (+I–+III) in a series of structurally characterized complexes ( 1 – 3 ). Redox interconversion of [LCu] +/2+/3+ is electrochemically (quasi)reversible and occurs at moderate potentials ( E 1/2 =−0.45 V and +0.82 V (vs. Fc/Fc + )). A linear C NHC ‐Cu‐C NHC arrangement and hemilability of the two pyridine donors allows the ligand to adapt to the different stereoelectronic and coordination requirements of Cu I versus Cu II /Cu III . Analytical methods such as NMR, UV/Vis, IR, electron paramagnetic resonance, and Cu Kβ high‐energy‐resolution fluorescence detection X‐ray absorption spectroscopies, as well as DFT calculations, give insight into the geometric and electronic structures of the complexes. The XAS signatures of 1 – 3 are textbook examples for Cu I , Cu II , and Cu III species. Facile 2‐electron interconversion combined with the exposure of two basic pyridine N sites in the reduced Cu I form suggest that [LCu] +/2+/3+ may operate in catalysis via coupled 2 e − /2 H + transfer.

Liu, Yang↗
DOE OSTI2015

Structural variations in terbium(III) complexes with 1,3-adamantanedicarboxylate and diverse co-ligands

Terbium nitrate was reacted with 1,3-adamantanedicarboxylic acid (LH{sub 2}) under solvo-hydrothermal conditions with either N,N-dimethylformamide (DMF) or N,N-dimethylacetamide (DMA) as organic solvents. Hydrolysation of the latter co-solvents resulted in the formation of formate or acetate ions, which are present as co-ligands in the 1D coordination polymer [Tb(L)(HCOO)(H{sub 2}O){sub 2}] (1) and the 2D assembly [Tb(L)(CH{sub 3}COO)(H{sub 2}O)] (2). The increase in dimensionality in the latter arises from the higher connectivity provided by acetate versus formate, the L{sup 2−} ligand being bis-chelating in both cases. The complex [Tb{sub 2}(L){sub 3}(H{sub 2}O){sub 5}][Tb{sub 2}(L){sub 3}(H{sub 2}O){sub 4}]·3H{sub 2}O (3), another 1D species, crystallizes alongside crystals of 2. Further addition of cucurbit[6]uril (CB6), with DMF as co-solvent, gave the two complexes [Tb{sub 2}(L){sub 2}(CB6)(H{sub 2}O){sub 6}](NO{sub 3}){sub 2}·6H{sub 2}O (4) and [H{sub 2}NMe{sub 2}]{sub 2}[Tb(L)(HCOO){sub 2}]{sub 2}·CB6·3H{sub 2}O (5). Complex 4 crystallizes as a 3D framework in which Tb(L){sup +} chains are connected by tetradentate CB6 molecules, while 5 unites a carboxylate-bridged anionic 2D planar assembly and layers of CB6 molecules with counter-cations held at both portals. - Graphical abstract: One- to three-dimensional assemblies are formed in terbium(III) complexes with 1,3-adamantanedicarboxylate obtained under solvo-hydrothermal conditions, these species including formate or acetate co-ligands formed in situ, or additional cucurbit[6]uril molecules. - Highlights: • We report structures of terbium(III) complexes with 1,3-adamantanedicarboxylate. • Solvents able to generate co-ligands or counter-ions in situ have been used. • A 3D species including additional cucurbituril molecules is decribed. • One species displays an alternation of metal–organic and organic sheets.

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

A conformation-selective monoclonal antibody against a small molecule-stabilised signalling-deficient form of TNF

We have recently described the development of a series of small-molecule inhibitors of human tumour necrosis factor (TNF) that stabilise an open, asymmetric, signalling-deficient form of the soluble TNF trimer. Here, we describe the generation, characterisation, and utility of a monoclonal antibody that selectively binds with high affinity to the asymmetric TNF trimer–small molecule complex. The antibody helps to define the molecular dynamics of the apo TNF trimer, reveals the mode of action and specificity of the small molecule inhibitors, acts as a chaperone in solving the human TNF–TNFR1 complex crystal structure, and facilitates the measurement of small molecule target occupancy in complex biological samples. We believe this work defines a role for monoclonal antibodies as tools to facilitate the discovery and development of small-molecule inhibitors of protein–protein interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Feature engineering descriptors, transforms, and machine learning for grain boundaries and variable-sized atom clusters

Abstract Obtaining microscopic structure-property relationships for grain boundaries is challenging due to their complex atomic structures. Recent efforts use machine learning to derive these relationships, but the way the atomic grain boundary structure is represented can have a significant impact on the predictions. Key steps for property prediction common to grain boundaries and other variable-sized atom clustered structures include: (1) describing the atomic structure as a feature matrix, (2) transforming the variable-sized feature matrix to a fixed length common to all structures, and (3) applying a machine learning algorithm to predict properties from the transformed matrices. We examine how these steps and different combinations of engineered features impact the accuracy of grain boundary energy predictions using a database of over 7000 grain boundaries. Additionally, we assess how different engineered features support interpretability, offering insights into the physics of the structure-property relationships.

36 MATERIALS SCIENCE↗
DOE OSTI2014

Literature Review: Silicone Applications in Health Care

Early in the 20 th century, the term ‘silicone’ was coined by Professor Frederic Stanley Kipping, a British chemist and one of the founding fathers of silicon chemistry. The word was given to describe new compounds containing a Si-O linkage (siloxane bond) and basic chemical formula R 2 -Si-O. In industry, silicone usually refers to linear polydimethylsiloxane (PDMS), the most basic silicone polymer containing only methyl groups as substituents in the polymeric structure. However, the term silicone can also be used to describe complex polymer structures that feature a wide range of functional groups, branching or crosslinking. “The properties of basic PDMS materials can be changed by replacing some methyl groups with other organic groups or atoms.” Substitution of this type is useful when specific physical and chemical properties are required of the material, such as adhesion or compatibility with a certain substrate.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Crystal structures of Leishmania mexicana arginase complexed with α,α-disubstituted boronic amino-acid inhibitors

Leishmania arginase is a potential drug target for the treatment of leishmaniasis because this binuclear manganese metalloenzyme initiates de novo polyamine biosynthesis by catalyzing the hydrolysis of L-arginine to generate L-ornithine and urea. The product L-ornithine subsequently undergoes decarboxylation to yield putrescine, which in turn is utilized for spermidine biosynthesis. Polyamines such as spermidine are essential for the growth and survival of the parasite, so inhibition of enzymes in the polyamine-biosynthetic pathway comprises an effective strategy for treating parasitic infections. To this end, two X-ray crystal structures of L. mexicana arginase complexed with α,α-disubstituted boronic amino-acid inhibitors based on the molecular scaffold of 2-( S )-amino-6-boronohexanoic acid are now reported. Structural comparisons with human and parasitic arginase complexes reveal interesting differences in the binding modes of the additional α-substituents, i.e. the D side chains, of these inhibitors. Subtle differences in the three-dimensional contours of the outer active-site rims among arginases from different species lead to different conformations of the D side chains and thus different inhibitor-affinity trends. The structures suggest that it is possible to maintain affinity while fine-tuning intermolecular interactions of the D side chain of α,α-disubstituted boronic amino-acid inhibitors in the search for isozyme-specific and species-specific arginase inhibitors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Accurate structure prediction of peptide–MHC complexes for identifying highly immunogenic antigens

Designing an optimal HIV-1 vaccine faces the challenge of identifying antigens that induce a broad immune capacity. One factor to control the breadth of T cell responses is the surface morphology of a peptide–MHC complex. Here, we present an in silico protocol for predicting peptide–MHC structure. A robust signature of a conformational transition was identified during all-atom molecular dynamics, which results in a model with high accuracy. A large test set was used in constructing our protocol and we went another step further using a blind test with a wild-type peptide and two highly immunogenic mutants, which predicted substantial conformational changes in both mutants. The center residues at position five of the analogs were configured to be accessible to solvent, forming a prominent surface, while the residue of the wild-type peptide was to point laterally toward the side of the binding cleft. We then experimentally determined the structures of the blind test set, using high resolution of X-ray crystallography, which verified predicted conformational changes. Our observation strongly supports a positive association of the surface morphology of a peptide–MHC complex to its immunogenicity. Our study offers the prospect of enhancing immunogenicity of vaccines by identifying MHC binding immunogens.

Park, Min-Sun↗
DOE OSTI2019

Structures of human ENT1 in complex with adenosine reuptake inhibitors

The human equilibrative nucleoside transporter 1 (hENT1), a member of the SLC29 family, plays crucial roles in adenosine signaling, cellular uptake of nucleoside for DNA and RNA synthesis, and nucleoside-derived anticancer and antiviral drug transport in humans. Because of its central role in adenosine signaling, it is the target of adenosine reuptake inhibitors (AdoRI), several of which are used clinically. Despite its importance in human physiology and pharmacology, the molecular basis of hENT1-mediated adenosine transport and its inhibition by AdoRIs are limited, owing to the absence of structural information on hENT1. As such, here, we present crystal structures of hENT1 in complex with two chemically distinct AdoRIs: dilazep and S-(4-nitrobenzyl)-6-thioinosine (NBMPR). Combined with mutagenesis study, our structural analyses elucidate two distinct inhibitory mechanisms exhibited on hENT1 and provide insight into adenosine recognition and transport. Our studies provide a platform for improved pharmacological intervention of adenosine and nucleoside analog drug transport by hENT1.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Cryo-EM Structure of the Mnx Protein Complex Reveals a Tunnel Framework for the Mechanism of Manganese Biomineralization

The global manganese cycle relies on microbes to oxidize soluble Mn(II) to insoluble Mn(IV) oxides. Some microbes require peroxide or superoxide as oxidants, but others can use O 2 directly, via multicopper oxidase (MCO) enzymes. One of these, MnxG from Bacillus sp. strain PL-12, was isolated in tight association with small accessory proteins, MnxE and MnxF. The protein complex, called Mnx, has eluded crystallization efforts, but we now report the 3D structure of a point mutant using cryo-EM single particle analysis, cross-linking mass spectrometry, and AlphaFold Multimer prediction. The ß-sheet–rich complex features MnxG enzyme, capped by a heterohexameric ring of alternating MnxE and MnxF subunits, and a tunnel that runs through MnxG and its MnxE 3 F 3 cap. The tunnel dimensions and charges can accommodate the mechanistically inferred binuclear manganese intermediates. Furthermore, comparison with the Fe(II)-oxidizing MCO, ceruloplasmin, identifies likely coordinating groups for the Mn(II) substrate, at the entrance to the tunnel. Thus, the 3D structure provides a rationale for the established manganese oxidase mechanism, and a platform for further experiments to elucidate mechanistic details of manganese biomineralization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Substrate recognition and catalysis by GH47 α-mannosidases involved in Asn-linked glycan maturation in the mammalian secretory pathway

Maturation of Asn-linked oligosaccharides in the eukaryotic secretory pathway requires the trimming of nascent glycan chains to remove all glucose and several mannose residues before extension into complex-type structures on the cell surface and secreted glycoproteins. Multiple glycoside hydrolase family 47 (GH47) α-mannosidases, including endoplasmic reticulum (ER) α-mannosidase I (ERManI) and Golgi α-mannosidase IA (GMIA), are responsible for cleavage of terminal α1,2-linked mannose residues to produce uniquely trimmed oligomannose isomers that are necessary for ER glycoprotein quality control and glycan maturation. ERManI and GMIA have similar catalytic domain structures, but each enzyme cleaves distinct residues from tribranched oligomannose glycan substrates. The structural basis for branch-specific cleavage by ERManI and GMIA was explored by replacing an essential enzyme-bound Ca 2+ ion with a lanthanum (La 3+ ) ion. This ion swap led to enzyme inactivation while retaining high-affinity substrate interactions. Cocrystallization of La 3+ -bound enzymes with Man9GlcNAc 2 substrate analogs revealed enzyme–substrate complexes with distinct modes of glycan branch insertion into the respective enzyme active-site clefts. Both enzymes had glycan interactions that extended across the entire glycan structure, but each enzyme engaged a different glycan branch and used different sets of glycan interactions. Additional mutagenesis and time-course studies of glycan cleavage probed the structural basis of enzyme specificity. Here, the results provide insights into the enzyme catalytic mechanisms and reveal structural snapshots of the sequential glycan cleavage events. The data also indicate that full steric access to glycan substrates determines the efficiency of mannose-trimming reactions that control the conversion to complex-type structures in mammalian cells.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Controlling Molecular Structure and Spin with Multiconfigurational Quantum Chemistry (Final Technical Report)

For many first-row transition metal complexes, structure-property relationships can be obtained from high-level molecular geometry optimizations and subsequent electronic structure studies. The project funded under this award utilized newly implemented fully internally contracted (FIC) nuclear gradients for extended multi-state (XMS) complete active space second-order multireference perturbation theory (CASPT2) to explore geometry changes in first-row transition metal coordination complexes. At the start of the project, only one full geometry optimization using FIC-CASPT2 analytical gradients had been reported (J. Chem. Theory Comput., 2016, 12 (8), 3781), and many open-questions regarding the performance and achievable accuracy in applying such computations to larger complexes persisted. Key deliverables in the report include the implementation of the numerical Hessian and subsequent vibrational analysis in the BAGEL program package. This includes both full Hessian vibrational analysis (FHVA) and a partial Hessian vibrational analysis (PHVA). The latter of which allows us to reduce the significant cost of computing the vibrational frequencies in a large molecule by focusing on the modes of highest interest. The gradient code also proved useful in the development of an approach to improve the Hubbard-U correction by removing bias in predicting spin-splitting in Fe(II) complexes via plane-wave density functional theory (DFT). Finally, we showed for three families of complexes (spin-crossover (SCO) complexes, metallocorroles complexes, and those with metal-metal bonds) that CASPT2 can result in good molecular geometries and established best practices in undertaking this work. We are now using this approach in collaborative projects with experimental groups, which would not have been possible at the start of this project. A common theme also arose through this work that static and dynamic correlation must be recovered in a balanced way to yield quantitative results. By systematically varying how both effects were included, we were able to make key chemical insights. This work supported the training of two postdoctoral scholars, one graduate student, and one undergraduate student in applying high-level wavefunction based methods to challenging systems.

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

Bandwidth Control and Symmetry Breaking in a Mott‐Hubbard Correlated Metal

Abstract In Mott materials strong electron correlation yields a spectrum of complex electronic structures. Recent synthesis advancements open realistic opportunities for harnessing Mott physics to design transformative devices. However, a major bottleneck in realizing such devices remains the lack of control over the electron correlation strength. This stems from the complexity of the electronic structure, which often veils the basic mechanisms underlying the correlation strength. This study presents control of the correlation strength by tuning the degree of orbital overlap using picometer‐scale lattice engineering. This study illustrates how bandwidth control and concurrent symmetry breaking can govern the electronic structure of a correlated SrVO 3 model system. This study shows how tensile and compressive biaxial strain oppositely affect the SrVO 3 in‐plane and out‐of‐plane orbital occupancy, resulting in the partial alleviation of the orbital degeneracy. The spectral weight redistribution under strain is derived and explained, which illustrates how high tensile strain drives the system toward a Mott insulating state. Implementation of such concepts can push correlated electron phenomena closer toward new solid‐state devices and circuits. These findings therefore pave the way for understanding and controlling electron correlation in a broad range of functional materials, driving this powerful resource for novel electronics closer toward practical realization.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2017

Numerical Simulations of Saturn's B Ring: Granular Friction as a Mediator between Self-gravity Wakes and Viscous Overstability

We study the B ring’s complex optical depth structure. The source of this structure may be the complex dynamics of the Keplerian shear and the self-gravity of the ring particles. The outcome of these dynamic effects depends sensitively on the collisional and physical properties of the particles. Two mechanisms can emerge that dominate the macroscopic physical structure of the ring: self-gravity wakes and viscous overstability. Here we study the interplay between these two mechanisms by using our recently developed particle collision method that allows us to better model the inter-particle contact physics. We find that for a constant ring surface density and particle internal density, particles with rough surfaces tend to produce axisymmetric ring features associated with the viscous overstability, while particles with smoother surfaces produce self-gravity wakes.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

Syntheses, crystal structures, and properties of four complexes based on polycarboxylate and imidazole ligands

Four metal–organic coordination polymers [Zn(HL)(H{sub 2}O)]·4H{sub 2}O (1), [Zn(HL)(L{sub 1})]·4H{sub 2}O (2), [Cu(HL)(H{sub 2}O)]·3H{sub 2}O (3) and [Cu(HL)(L{sub 1})]·5H{sub 2}O (4) were synthesized by reactions of the corresponding metal(II) salts with semirigid polycarboxylate ligand (5-((4-carboxypiperidin-1-yl)methyl)isophthalic acid hydrochloride, H{sub 3}L·HCl) or auxiliary ligand (1,4-di(1H-imidazol-4-yl)benzene, L{sub 1}). The structures of the compounds were characterized by elemental analysis, FT-IR spectroscopy and single-crystal X-ray diffraction. The use of auxiliary ligand L{sub 1} has great influence on the structures of two pairs of complexes 1, 2 and 3, 4. Complex 1 is a uninodal 3-connected rare 2-fold interpenetrating ZnSc net with a Point (Schlafli) symbol of (10{sup 3}) while 2 is a one-dimensional (1D) ladder structure. Compound 3 features a two-dimensional (2D) honeycomb network with typical 6{sup 3}-hcb topology, while 4 is 2D network with (4, 4) sql topology based on binuclear Cu{sup II} subunits. The non-covalent bonding interactions such as hydrogen bonds, π···π stacking and C–H···π exist in complexes 1–4, which contributes to stabilize crystal structure and extend the low-dimensional entities into high-dimensional frameworks. And the photoluminescent property of 1 and 2 and gas sorption property of 4 have been investigated. - Graphical abstract: Four new coordination polymers have been obtained and their photoluminescent and gas sorption properties have also been investigated. - Highlights: • Two pairs of Zn{sup II}/ Cu{sup II} compounds have been synthesized. • Auxiliary ligand-controlled assembly of the complexes is reported. • The luminescent properties of complexes 1–2 were investigated. • The gas sorption property of 4 has been investigated.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Upper crustal structure beneath East Java from ambient noise tomography: A preliminary result

East Java has a fairly complex geological structure. Physiographically East Java can be divided into three zones, i.e. the Southern Mountains zone in the southern part, the Kendeng zone in the middle part, and the Rembang zone in the northern part. Most of the seismic hazards in this region are due to processes in the upper crust. In this study, the Ambient Noise Tomography (ANT) method is used to image the upper crustal structure beneath East Java. We have used seismic waveform data recorded by 8Meteorological, Climatological and Geophysical Agency (BMKG) stationary seismographic stations and 16 portable seismographs installed for 2 to 8 weeks. The data were processed to obtain waveforms fromnoise cross-correlation between pairs of seismographic stations. Our preliminary results indicate that the Kendeng zone, an area of low gravity anomaly, is associated with a low velocity zone. On the other hand, the southern mountain range, which has a high gravity anomaly, is related to a high velocity anomaly as shown by our tomographic images.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗