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At least 109 records · Page 6

Crystal structure prediction with host-guided inpainting generation and foundation potentials

Unconditional crystal structure generation with diffusion models faces challenges in identifying symmetric crystals as the unit cell size increases. Here, we present the crystal host-guided generation (CHGGen) framework to address this challenge through conditional generation using an inpainting method, which optimizes a fraction of atomic positions within a predefined and symmetrized host structure to improve the success rate for symmetric structure generation. By integrating inpainting structure generation with a foundation potential for structure optimization, we demonstrate the method on the ZnS–P 2 S 5 and Li–Si chemical systems, where the inpainting method generates a higher fraction of symmetric structures than unconditional generation. The practical significance of CHGGen extends to enabling the structural modification of crystal structures, particularly for systems with partial occupancy or intercalation chemistry. The inpainting method also allows for seamless integration with other generative models, providing a versatile framework for accelerating materials discovery.

Zhong, Peichen [University of California, Berkeley↗

Crystal structure of toceranib, C 22 H 25 FN 4 O 2

The crystal structure of toceranib has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional theory techniques. Toceranib crystallizes in space group P2 1 /c (#14) with a = 10.6899(6), b = 24.5134(4), c = 7.8747(4) Å, β = 107.7737(13)°, V = 1965.04(3) Å 3 , and Z = 4. The crystal structure consists of stacks of approximately planar molecules, with N–H∙∙∙O hydrogen bonds between the layers. The commercial reagent sample was a mixture of two or more phases with toceranib being the dominant phase. The difference between the Rietveld-refined and DFT-optimized structures is larger than usual. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®).

36 MATERIALS SCIENCE↗

Crystal structure of oxfendazole, C 15 H 13 N 3 O 3 S

The crystal structure of oxfendazole has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional theory techniques. Oxfendazole crystallizes in space group P2 1 /c (#14) with a = 18.87326(26), b = 10.40333(5), c = 7.25089(5) Å, β = 91.4688(10)° V = 1423.206(10) Å 3 , and Z = 4. The crystal structure consists of stacks of the planar portions of the L-shaped molecules, resulting in layers parallel to the bc-plane. Only weak hydrogen bonds are present. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®).

36 MATERIALS SCIENCE↗

Crystal structure of valbenazine, C 24 H 38 N 2 O 4

The crystal structure of valbenazine has been solved and refined using synchrotron X-ray powder diffraction data and optimized using density functional theory techniques. Valbenazine crystallizes in space groupP2 1 2 1 2 1 (#19) witha= 5.260267(17),b= 17.77028(7),c= 26.16427(9) Å,V= 2445.742(11) Å 3 , andZ= 4 at 295 K. The crystal structure consists of discrete molecules and the mean plane of the molecules is approximately (8,−2,15). There are no obvious strong intermolecular interactions. There is only one weak classical hydrogen bond in the structure, from the amino group to the ether oxygen atom. Two intramolecular and one intermolecular C–H⋯O hydrogen bonds also contribute to the lattice energy. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®)

Materials Science↗

Crystal structure of ractopamine hydrochloride, C 18 H 24 NO 3 Cl

The crystal structure of ractopamine hydrochloride has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional theory techniques. Ractopamine hydrochloride crystallizes in space groupPbca(#61) witha= 38.5871(49),b= 10.7691(3),c= 8.4003(2) Å,V= 3490.75(41) Å 3 , andZ= 8. The ractopamine cation contains two chiral centers, and the sample consists of a mixture of the S,S/R,R/S,R and R,S forms. Models for the two diastereomers S,S and S,R were refined, and yielded equivalent residuals, but the S,R form is significantly lower in energy. The crystal structure consists of layers of molecules parallel to thebc-plane. In each structure one of the H atoms on the protonated N atom acts as a donor in a strong discrete N–H⋯Cl hydrogen bond. Hydroxyl groups act as donors in O–H⋯Cl and O–H⋯O hydrogen bonds. Both the classical and C–H⋯Cl and C–H⋯O hydrogen bonds differ between the forms, helping to explain the large microstrain observed for the sample. The powder pattern has been submitted to ICDD® for inclusion in the Powder Diffraction File™ (PDF®).

Materials Science↗

Crystal structure of elvitegravir Form II, C 23 H 23 ClFNO 5

The crystal structure of elvitegravir Form II has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional theory techniques. Elvitegravir Form II crystallizes in space group P2 1 (#4) with a = 11.54842(7), b = 14.04367(5), c = 13.33333(8) Å, β = 90.0330(6)°, V = 2162.427(14) Å 3 , and Z = 4. The crystal structure consists of alternating layers of parallel molecules perpendicular to the b-axis. The mean planes of the oxoquinoline ring systems in molecules 1 and 2 are 1(22)-1 and -1(22)1. Between the stacks are layers of the halogenated phenyl rings. These exhibit herringbone stacking. In each molecule, the carboxylic acid group forms a strong intramolecular O–H∙∙∙O hydrogen bond to the nearby carbonyl group. The hydroxyl group of each molecule forms a strong hydrogen bond to the carbonyl group of the carboxylic acid of the other molecule. These O–H∙∙∙O hydrogen bonds link the molecules into dimers, with a graph set R2,2(18) > a > c. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®).

36 MATERIALS SCIENCE↗

Crystal structure of danofloxacin mesylate (C 19 H 21 FN 3 O 3 )(CH 3 O 3 S)

The crystal structure of danofloxacin mesylate has been solved and refined using synchrotron X-ray powder diffraction data and optimized using density functional theory techniques. Danofloxacin mesylate crystallizes in space group P1 (#1) with a = 6.77474(8), b = 12.4973(4), c = 12.82826(28) Å, α = 84.8709(29), β = 87.7501(10), γ = 74.9916(4)°, V = 1044.723(11) Å 3 , and Z = 2. The protonation of the danofloxacin cations was established by the analysis of potential intermolecular interactions and differs from that expected from isolated-cation calculations. The crystal structure consists of alternating layers of cations and anions parallel to the ac-plane. There is parallel stacking of the oxoquinoline rings along the a-axis. The expected N–H∙∙∙O hydrogen bonds between the cations and anions are not present. Each cation makes an N–H∙∙∙O hydrogen bond with the other cation, resulting in zig-zag chains along the a-axis. Both cations have strong intramolecular O–H∙∙∙O hydrogen bonds. There are several C–H∙∙∙O hydrogen bonds between the danofloxacin cations and mesylate anions. The powder pattern has been submitted to ICDD® for inclusion in the Powder Diffraction File™ (PDF®).

36 MATERIALS SCIENCE↗

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↗

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↗

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↗

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↗

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↗

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↗

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↗

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↗

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↗