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At least 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Pu(VI) Oxalate Crystal Structure and Evidence of Photoreduction to Pu(IV) Oxalate

We report the first crystal structure of a Pu(VI)-oxalate compound. This compound, [PuO 2 (C 2 O 4 )(H 2 O)]·2(H 2 O) (1), crystallizes in space group P21/c with a = 5.5993(3) Å, b = 16.8797(12) Å, c = 9.3886(6) Å, and β = 98.713(6)°. It is isostructural with the previously reported U(VI) compound, [UO 2 (C 2 O 4 )(H 2 O)]·2(H 2 O). Each plutonyl ion (PuO 2 2+ ) is coordinated in the equatorial plane by two side-on bidentate oxalates, creating an infinite chain along [001]. A coordinated water molecule and twisting of the oxalates lead to a distorted pentagonal bipyramidal geometry of the Pu. A photochemical degradation was observed for 1, which resulted in the formation of a secondary crystalline phase. The absorption spectrum of this secondary phase confirmed the presence of Pu(IV), but it did not match the spectrum of Pu(C 2 O 4 ) 2 ·6H 2 O, which is considered to be the primary product of Pu-oxalate precipitation. While compound 1 has previously been proposed to exist in solution, this is the first time it has been isolated via crystallization. Although redox interactions between Pu and oxalate have been documented in the literature, the present study is the first observation of a photochemical reduction of Pu(VI)-oxalate. Finally, this study has expanded on the limited understanding of the Pu(VI)-oxalate system, which is important for nuclear fuel cycle applications.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2022

Crystal structure of diclazuril, C 17 H 9 Cl 3 N 4 O 2

The crystal structure of diclazuril has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional theory techniques. Diclazuril crystallizes in space group P2 1 /a (#14) with a = 27.02080(18), b = 11.42308(8), c = 5.36978(5) Å, β = 91.7912(7)°, V = 1656.629(15) Å 3 , and Z = 4. The crystal structure consists of layers of molecules parallel to the ac-plane. A strong N–H∙∙∙O hydrogen bond links the molecules into dimers along the a-axis with a graph set R2,2(8). The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®).

36 MATERIALS SCIENCE↗
DOE OSTI2021

Optical vibrational spectra and proposed crystal structure of ε-UO 3

ε-UO 3 is an exotic polymorph in the uranium trioxide system with an undetermined crystal structure and limited optical vibrational spectroscopic data. To improve understanding of this compound, we synthesize and investigate the crystal structure and optical vibrational spectra of ε-UO 3 . Infrared spectra collected for ε-UO 3 are in good agreement with previously published results, and our studies extend the available data into the low-energy (600–100 cm –1 ) regime. For the first time, Raman spectra are presented for ε-UO 3 using both 785 and 532 nm excitation wavelengths. Previous reports suggest an impurity phase may be present in ε-UO 3 produced by calcination of U 3 O 8 ; however, spectral center-of-mass calculations, principal component analyses, and Raman spectroscopic mapping employed to investigate this possibility indicate that the product of U 3 O 8 calcined in O 3 (g) in this work is likely phase-pure. A possible novel structure solution for ε-UO 3 is determined via Rietveld refinement of powder X-ray diffraction data and is triclinic, P-1, with a = 4.01 Å, b = 3.85 Å, c = 4.18 Å, and α = 98.26°, β = 90.41°, γ = 120.46° (R wp = 8.30%). The asymmetric unit of ε-UO 3 consists of U(VI) in hexagonal bipyramidal coordination with displaced equatorial oxygen. Further analysis reveals that the structure of ε-UO3 is best described by a 2 × 1 × 2 supercell structure in P-1 with a = 8.03 Å, b = 3.86 Å, c = 8.37 Å with α = 98.26°, β = 90.41°, and γ = 120.46°, although a higher-symmetry structure is possible. Optical vibrational spectroscopic and structural measurements of ε-UO 3 presented here furthers our understanding of this complex uranium oxide and clarifies the origin of reported structural similarity to U 3 O 8 .

-UO3↗
DOE OSTI2023

Crystal structure of besifloxacin hydrochloride, C 19 H 22 ClFN 3 O 3 Cl

The crystal structure of besifloxacin hydrochloride has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional theory techniques. Besifloxacin hydrochloride crystallizes in space group P1 (#1) with a = 5.36596(8), b = 10.3234(4), c = 17.9673(14) Å, α = 98.122(5), β = 92.9395(9), γ = 96.1135(3)°, V = 977.483(13) Å 3 , and Z = 2. The crystal structure is approximately centrosymmetric. Strong N–H∙∙∙Cl hydrogen bonds form a corrugated ladder-like chain along the a-axis. The carboxylic acid group in each independent cation acts as the donor in a strong intramolecular O–H∙∙∙O hydrogen bond to an adjacent carbonyl group. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®).

36 MATERIALS SCIENCE↗
DOE OSTI2022

Crystal structure of halofuginone hydrobromide, C 16 H 18 BrClN 3 O 3 Br

The crystal structure of one form of halofuginone hydrobromide has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional theory techniques. Halofuginone hydrobromide crystallizes in space group P2 1 (#4) with a = 8.87398(13), b = 14.25711(20), c = 15.0153(3) Å, β = 91.6867(15)°, V = 1898.87(4) Å 3 , and Z = 4. The crystal structure consists of alternating layers (parallel to the ab-plane) of planar and nonplanar portions of the cations. N–H∙∙∙Br and O–H∙∙∙Br hydrogen bonds link the protonated piperidine rings and bromide anions into a two-dimensional network parallel to the ab-plane. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®).

36 MATERIALS SCIENCE↗
DOE OSTI2024

Crystal structure and shape selection in the growth of 3D metallic crystallites on layered materials: Fe on MoS 2

Nucleation and growth of supported 3D metal clusters or crystallites during deposition on MoS 2 , or on other weakly-adhering layered materials, can potentially produce diverse growth shapes, and even crystal structures differing from the bulk metal. For Fe deposition on MoS 2 , SEM and AFM observations reveal three distinct crystallite shapes. By comparison with atomistic structure models incorporating realistic Fe-MoS 2 interface structures, here we conclude that these are: triangular fcc(111) pyramids with sloped {100} side facets; bcc(110) A-frame tents with sloped {100} side facets; and bcc(110) mesas with vertical {100} and {110} side facets. The following picture is proposed for the competitive formation of clusters and crystallites with different structures: (i) small nanoclusters formed at the onset of deposition exhibit facile fluxional dynamics allowing sampling of different crystal structures and shapes; (ii) sufficient fluxionality implies a Boltzmann distribution of sampled structures, and thus coexistence of different structures follows from the demonstrated similar energies for those structures; (iii) growing clusters reach a threshold size above which the characteristic time scale for restructuring exceeds that for cluster growth. Thereafter, clusters are locked-in to a specific crystal structure and shape as revealed by imaging of larger crystallites. Despite a penalty for fcc(111) over bcc(111) pyramids based on bulk energetics, favorable surface and interface energies makes them preferable for smaller sizes.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Crystal structures of multidrug efflux transporters from Burkholderia pseudomallei suggest details of transport mechanism

BpeB and BpeF are multidrug efflux transporters from Burkholderia pseudomallei that enable multidrug resistance. Here, we report the crystal structures of BpeB and BpeF at 2.94 Å and 3.0 Å resolution, respectively. BpeB was found as an asymmetric trimer, consistent with the widely-accepted functional rotation mechanism for this type of transporter. One of the monomers has a distinct structure that we interpret as an intermediate along this functional cycle. Additionally, a detergent molecule bound in a previously undescribed binding site provides insights into substrate translocation through the pathway. BpeF shares structural similarities with the crystal structure of OqxB from Klebsiella pneumoniae, where both are symmetric trimers composed of three “binding”-state monomers. The structures of BpeB and BpeF further our understanding of the functional mechanisms of transporters belonging to the HAE1-RND superfamily.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Crystal structures of multidrug efflux transporters from Burkholderia pseudomallei suggest details of transport mechanism

BpeB and BpeF are multidrug efflux transporters from Burkholderia pseudomallei that enable multidrug resistance. Here, we report the crystal structures of BpeB and BpeF at 2.94 Å and 3.0 Å resolution, respectively. BpeB was found as an asymmetric trimer, consistent with the widely-accepted functional rotation mechanism for this type of transporter. One of the monomers has a distinct structure that we interpret as an intermediate along this functional cycle. Additionally, a detergent molecule bound in a previously undescribed binding site provides insights into substrate translocation through the pathway. BpeF shares structural similarities with the crystal structure of OqxB from Klebsiella pneumoniae, where both are symmetric trimers composed of three “binding”-state monomers. The structures of BpeB and BpeF further our understanding of the functional mechanisms of transporters belonging to the HAE1-RND superfamily.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Cubic Crystal Structure Formation and Optical Properties within the Ag–B II –M IV –X (B II = Sr, Pb; M IV = Si, Ge, Sn; X = S, Se) Family of Semiconductors

Quaternary chalcogenide semiconductors are promising materials for energy conversion and nonlinear optical applications, with properties tunable primarily by varying the elemental composition and crystal structure. Here, we first analyze the connections among several cubic crystal structure types, as well as the orthorhombic Ag 2 PbGeS 4 -type structure, reported for select members within the Ag–B II –M IV –X (B II = Sr, Pb; M IV = Si, Ge, Sn; X = S, Se) compositional space. Focusing on the Ag–Pb–Si–S and Ag–Sr–Sn–S systems, we show that one structure type, with the formulas Ag 2 Pb 3 Si 2 S 8 and Ag 2 Sr 3 Sn 2 S 8 , is favored. We have prepared powder and single-crystal samples of Ag 2 Pb 3 Si 2 S 8 and Ag 2 Sr 3 Sn 2 S 8 , showing that each takes on the noncentrosymmetric cubic space group I$\bar{43}$d and is isostructural to the previously reported compound Ag 2 Sr 3 Ge 2 Se 8 . Through hybrid density functional theory calculations, these cubic compounds are demonstrated to be (quasi-)direct band gap semiconductors with high densities of states at the band maxima. Furthermore, the band-gap energies are measured by reflectance spectroscopy as 1.95(3) and 2.66(4) eV for Ag 2 Pb 3 Si 2 S 8 and Ag 2 Sr 3 Sn 2 S 8 , respectively. We further measure the optical properties and show the electronic band structures of three other isostructural A I –B II –M IV –X-type materials, i.e., Ag 2 Sr 3 Si 2 S 8 , Ag 2 Sr 3 Ge 2 S 8 , and Ag 2 Sr 3 Ge 2 Se 8 , showing that the band gaps can be predictably tuned by element substitution. Detailed visual analyses of the different structures and of their relationships with other members of the Ag–B II –M IV –X compositional family provide a basis for a broader understanding of the structure formation and optoelectronic properties within the quaternary chalcogenide semiconductor family.

14 SOLAR ENERGY↗
DOE OSTI2023

Crystal structure of domain of unknown function 507 (DUF507) reveals a new protein fold

The crystal structure of the domain of unknown function family 507 protein from Aquifex aeolicus is reported (AaDUF507, UniProt O67633, 183 residues). The structure was determined in two space groups (C222 1 and P3 2 21) at 1.9 Å resolution. The phase problem was solved by molecular replacement using an AlphaFold model as the search model. AaDUF507 is a Y-shaped α-helical protein consisting of an anti-parallel 4-helix bundle base and two helical arms that extend 30-Å from the base. The two crystal structures differ by a 25° rigid body rotation of the C-terminal arm. The tertiary structure exhibits pseudo-twofold symmetry. The structural symmetry mirrors internal sequence similarity: residues 11–57 and 102–148 are 30% identical and 53% similar with an E-value of 0.002. In one of the structures, electron density for an unknown ligand, consistent with nicotinamide or similar molecule, may indicate a functional site. Docking calculations suggest potential ligand binding hot spots in the region between the helical arms. Structure-based query of the Protein Data Bank revealed no other protein with a similar tertiary structure, leading us to propose that AaDUF507 represents a new protein fold.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Proposed crystal structure of carbadox, C 11 H 10 N 4 O 4

A model for the crystal structure of carbadox has been generated and refined using synchrotron X-ray powder diffraction data and optimized using density functional theory techniques. Carbadox crystallizes in space groupP2 1 (#4) witha= 13.8155(3),b= 21.4662(1),c= 16.3297(3) Å,β= 110.0931(7)°,V= 4548.10(3) Å 3 , andZ= 16. The crystal structure is characterized by approximately parallel stacking of the eight independent carbadox molecules parallel to thebc-plane. There are two different molecular configurations of the eight carbadox molecules; five are in the lower-energy configuration and three are in a ~10% higher-energy configuration. This arrangement likely achieves the lowest-energy crystalline packing via hydrogen bonding. Hydrogen bonds link the molecules both within and between the planes. Each of the amino groups forms a N–H⋯O hydrogen bond to an oxygen atom of the 1,4-dioxidoquinoxaline ring system of another molecule. The result is four pairs of hydrogen-bonded molecules, which form rings with graph setR2,2(14). Variation in specimen preparation can affect the preferred orientation of particles considerably. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®).

Materials Science↗
DOE OSTI2024

X-ray crystal structure of a designed rigidified imaging scaffold in the ligand-free conformation

Imaging scaffolds composed of designed protein cages fused to designed ankyrin repeat proteins (DARPins) have enabled the structure determination of small proteins by cryogenic electron microscopy (cryo-EM). One particularly well characterized scaffold type is a symmetric tetrahedral assembly composed of 24 subunits, 12 A and 12 B, which has three cargo-binding DARPins positioned on each vertex. Here, the X-ray crystal structure of a representative tetrahedral scaffold in the apo state is reported at 3.8 Å resolution. The X-ray crystal structure complements recent cryo-EM findings on a closely related scaffold, while also suggesting potential utility for crystallographic investigations. As observed in this crystal structure, one of the three DARPins, which serve as modular adaptors for binding diverse `cargo' proteins, present on each of the vertices is oriented towards a large solvent channel. The crystal lattice is unusually porous, suggesting that it may be possible to soak crystals of the scaffold with small (≤30 kDa) protein cargo ligands and subsequently determine cage–cargo structures via X-ray crystallography. The results suggest the possibility that cryo-EM scaffolds may be repurposed for structure determination by X-ray crystallography, thus extending the utility of electron-microscopy scaffold designs for alternative structural biology applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Influence of shape on crystal structure and optical properties of heterocyclic conjugated molecules

Organic optoelectronics are increasingly important due to their tunablilty, flexibility, and solution processability. Tuning optical properties of these materials as solids relies on the balance of weak non-covalent interactions that dictate crystal structure, but are difficult to predict. Our research aims to improve our understanding of how electrostatic interactions can direct and facilitate intramolecular interactions that dictate emergent properties of crystalline materials. This paper focuses on exploring how multi-fused thiophene ring systems that are popular in modern organic optoelectronic materials impact intramolecular interactions, while also investigating the role of molecular shape. In these examples, the shape of heterocyclic systems correlate with the crystal structures: while the bent heterocyclics show no discrete and discernable intramolecular interactions, those with bent shapes interact cofacially with one of the electron poor ArF pendants by twisting the arylene ethynylene backbone. Two of the control molecules, which bear non-fluorinated benzyl ester substituents, show intramolecular edge-face interactions, and several of these molecules show clear polymorphic behavior. Furthermore, these findings further our understanding of how discrete interactions can be altered not only by electrostatics, but also by shape, allowing for increasingly nuanced control over the crystal structures and optical properties of optoelectronic materials.

Guzmán, Elisa↗
DOE OSTI2024

Crystal structure of alectinib hydrochloride Type I, C 30 H 35 N 4 O 2 Cl

The crystal structure of alectinib hydrochloride has been solved and refined using synchrotron X-ray powder diffraction data and optimized using density functional theory techniques. Alectinib hydrochloride crystallizes in space groupP2 1 /n(#14) with the following parameters:a= 12.67477(7),b= 10.44076(5),c= 20.38501(12) Å,β= 93.1438(7)°,V= 2693.574(18) Å 3 , andZ= 4 at 295 K. The crystal structure consists of stacks of molecules along theb-axis, and the stacks contain chains of strong N–H⋯Cl hydrogen bonds. One density functional theory calculation moved a proton from an N atom to the Cl, but another calculation yielded a more chemically reasonable result. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®)

Materials Science↗
DOE OSTI2024

Enhancing Docking Accuracy with PECAN2, a 3D Atomic Neural Network Trained without Co-Complex Crystal Structures

Decades of drug development research have explored a vast chemical space for highly active compounds. The exponential growth of virtual libraries enables easy access to billions of synthesizable molecules. Computational modeling, particularly molecular docking, utilizes physics-based calculations to prioritize molecules for synthesis and testing. Nevertheless, the molecular docking process often yields docking poses with favorable scores that prove to be inaccurate with experimental testing. To address these issues, several approaches using machine learning (ML) have been proposed to filter incorrect poses based on the crystal structures. However, most of the methods are limited by the availability of structure data. Here, we propose a new pose classification approach, PECAN2 (Pose Classification with 3D Atomic Network 2), without the need for crystal structures, based on a 3D atomic neural network with Point Cloud Network (PCN). The new approach uses the correlation between docking scores and experimental data to assign labels, instead of relying on the crystal structures. We validate the proposed classifier on multiple datasets including human mu, delta, and kappa opioid receptors and SARS-CoV-2 Mpro. Our results demonstrate that leveraging the correlation between docking scores and experimental data alone enhances molecular docking performance by filtering out false positives and false negatives.

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

Antiviral Activity and Crystal Structures of HIV-1 gp120 Antagonists

As part of our effort to discover drugs that target HIV-1 entry, we report the antiviral activity and crystal structures of two novel inhibitors in a complex with a gp120 core. NBD-14204 showed similar antiviral activity against all the clinical isolates tested. The IC50 values were in the range of 0.24–0.9 µM with an overall mean of 0.47 ± 0.03 µM, showing slightly better activity against the clinical isolates than against the lab-adapted HIV-1 HXB2 (IC 50 = 0.96 ± 0.1 µM). Moreover, the antiviral activity of NBD-14208 was less consistent, showing a wider range of IC 50 values (0.66–5.7 µM) with an overall mean of 3 ± 0.25 µM and better activity against subtypes B and D (Mean IC 50 2.2–2.5 µM) than the A, C and Rec viruses (Mean IC 50 2.9–3.9 µM). SI of NBD-14204 was about 10-fold higher than NBD-14208, making it a better lead compound for further optimization. In addition, we tested these compounds against S375Y and S375H mutants of gp120, which occurred in some clades and observed these to be sensitive to NBD-14204 and NBD-14208. These inhibitors also showed modest activity against HIV-1 reverse transcriptase. Furthermore, we determined the crystal structures of both inhibitors in complexes with gp120 cores. As expected, both NBD-14204 and NBD-14208 bind primarily within the Phe43 cavity. It is noteworthy that the electron density of the thiazole ring in both structures was poorly defined due to the flexibility of this scaffold, suggesting that these compounds maintain substantial entropy, even when bound to the Phe43 cavity.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Crystal structure of brimonidine hydrogen tartrate, (C 11 H 11 BrN 5 )(HC 4 H 4 O 6 )

The crystal structure of brimonidine hydrogen tartrate has been solved and refined using synchrotron X-ray powder diffraction data and optimized using density functional techniques. Brimonidine hydrogen tartrate crystallizes in space groupP2 1 (#4) witha= 7.56032(2),b= 7.35278(2),c= 30.10149(9) Å,β= 90.1992(2)°,V= 1673.312(10) Å 3 , andZ= 4 at 295 K. The crystal structure consists of alternating layers of cations and anions parallel to theab-plane. Each of the hydrogen tartrate anions is linked to itself by very strong charge-assisted O–H⋯O hydrogen bonds into chains along thea-axis. Each hydroxyl group of each tartrate acts as a donor in an O–H⋯O or O–H⋯N hydrogen bond. One of these is intramolecular, but the other three are intermolecular. These hydrogen bonds link the hydrogen tartrate anions into layers parallel to theab-plane and also link the anion–cation layers. The protonated N atoms act as donors in N–H⋯O or N–H⋯N hydrogen bonds to the carboxyl groups of the tartrates and to a ring nitrogen atom. These link the cations and anions, as well as providing cation–cation links. The amino N atoms of the cations form N–H⋯O hydrogen bonds to hydroxyl groups of the anions. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®)

Materials Science↗