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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
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 OSTI2020

Long-range and local crystal structures of the S r 1 - x C a x Ru O 3 perovskites

Here, the crystal structures of the Sr 1–x Ca x RuO 3 (0 ≤ x ≤ 1) perovskites are investigated using both long-range and local structural probes. High-resolution synchrotron powder x-ray-diffraction characterization at ambient temperature shows that the materials have orthorhombic long-range crystal structures to high precision, and we support previous work showing that Ca 2+ substitution for Sr 2+ primarily changes the tilting of rigid corner-sharing RuO 6 octahedra at their shared oxygen vertices. X-ray pair-distribution function analysis for SrRuO 3 , CaRuO 3 , and one intermediate composition show them to display monoclinic symmetry at the local level; when averaged over different domain orientations this yields orthorhombic symmetry in the long range, and no long-range or local phase transitions are observed between 80 and 300 K for materials with intermediate compositions. High-resolution transmission electron microscopy shows that the Sr/Ca distribution is random at the nanoscale. Lastly, we plot magnetic characteristics such as the ferromagnetic T c , Curie-Weiss theta, effective moment, and ambient temperature susceptibility vs the octahedral tilt and unit-cell volume.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
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 OSTI2020

The nitrosoamphetamine metabolite is accommodated in the active site of human hemoglobin: Spectroscopy and crystal structure

Amphetamine-based (Amph) drugs are metabolized in humans to their hydroxylamine (AmphNHOH) and nitroso (AmphNO) derivatives. The latter metabolites are known to bind to the Fe centers of cytochrome P450 and other heme enzymes to inhibit their activities. Although these AmphNHOH/AmphNO metabolites are present in vivo, their interactions with the blood protein hemoglobin (Hb) and the muscle protein (Mb) have been largely discounted due to a perception that the relatively small heme active sites of Hb and Mb will not be able to accommodate the large AmphNO group. Here, we report the 2.15 Å resolution X-ray crystal structure of the AmphNO adduct of adult human hemoglobin as the Hb [ α -Fe III (H 2 O)][ β -Fe II (AmphNO)] derivative. We show that the binding of AmphNO to the β subunit is enabled by an E helix movement and stabilization of ligand binding by H-bonding with the distal His63 residue. We also observe an AmphNHOH group in the Xe2 pocket in close proximity to the α heme site in this derivative. Additionally, UV–vis spectroscopy was used to characterize this and related wt and mutant Mb adducts. Importantly, our X-ray crystal structure of this Hb-nitrosoamphetamine complex represents the first crystal structure of a wild-type heme protein adduct of any amphetamine metabolite. Our results provide a framework for further studies of AmphNHOH/AmphNO interactions with Hb and Mb as viable processes that potentially contribute to the overall biological inorganic chemistry of amphetamine drugs.

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

Psilocybin: crystal structure solutions enable phase analysis of prior art and recently patented examples

Psilocybin {systematic name: 3-[2-(dimethylamino)ethyl]-1 H -indol-4-yl dihydrogen phosphate} is a zwitterionic tryptamine natural product found in numerous species of fungi known for their psychoactive properties. Following its structural elucidation and chemical synthesis in 1959, purified synthetic psilocybin has been evaluated in clinical trials and has shown promise in the treatment of various mental health disorders. In a recent process-scale crystallization investigation, three crystalline forms of psilocybin were repeatedly observed: Hydrate A, Polymorph A, and Polymorph B. The crystal structure for Hydrate A was solved previously by single-crystal X-ray diffraction. This article presents new crystal structure solutions for the two anhydrates, Polymorphs A and B, based on Rietveld refinement using laboratory and synchrotron X-ray diffraction data, and density functional theory (DFT) calculations. Utilizing the three solved structures, an investigation was conducted via Rietveld method (RM) based quantitative phase analysis (QPA) to estimate the contribution of the three different forms in powder X-ray diffraction (PXRD) patterns provided by different sources of bulk psilocybin produced between 1963 and 2021. Over the last 57 years, each of these samples quantitatively reflect one or more of the hydrate and anhydrate polymorphs. In addition to quantitatively evaluating the composition of each sample, this article evaluates correlations between the crystal forms present, corresponding process methods, sample age, and storage conditions. Furthermore, revision is recommended on characterizations in recently granted patents that include descriptions of crystalline psilocybin inappropriately reported as a single-phase `isostructural variant.' Rietveld refinement demonstrated that the claimed material was composed of approximately 81% Polymorph A and 19% Polymorph B, both of which have been identified in historical samples. In this article, we show conclusively that all published data can be explained in terms of three well-defined forms of psilocybin and that no additional forms are needed to explain the diffraction patterns.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1971

Crystal structure of alpha poly-p-xylylene.

A crystal structure of alpha poly-p-xylylene is proposed with the help of data of oriented crystals grown during polymerization. The unit cell is monoclinic with the parameters a = 8.57 A, b = 10.62 A, c = 6.54 A (chain axis), and beta = 101.3 deg. Four repeating units per cell lead to a calculated density of 1.185 g/cu cm and a packing density of 0.71. The probable space group is P2 sub 1/m.

Kubo, S.↗
DOE OSTI2023

BaCu 2 SiS 4 : A New Member of the A II B I 2 M IV Q 4 Chalcogenide Family with a Chiral Crystal Structure

Abstract Noncentrosymmetric ternary and quaternary chalcogenides are studied as promising nonlinear optical (NLO) materials in the mid‐infrared region. Here, we report the synthesis of a new material BaCu 2 SiS 4 in the A II B I 2 M IV Q 4 family ( A =divalent metal; B =monovalent metal; M =tetrel, Q =chalcogen), and discuss its crystal structure, thermal stability, optical behavior, and electronic structure. BaCu 2 SiS 4 crystallizes in the noncentrosymmetric chiral space group P 3 2 21 with lattice parameters a =6.1440(3) Å, c =15.3542(8) Å, V =501.95(6) Å 3 , Z =3. The structure features helical channels formed by corner‐sharing [CuS 4 ] and [SiS 4 ] tetrahedral units. Synthesis was carried out in a molten salt flux, as opposed to a traditional solid‐state route from elements, to minimize the formation of a competing ternary phase, Ba 2 SiS 4 . BaCu 2 SiS 4 is a semiconductor with an experimentally‐determined direct bandgap of ~2.2 eV. The material exhibits second harmonic generation (SHG) activity, confirming the noncentrosymmetric nature of the structure. Analysis of reported A II B I 2 M IV Q 4 crystal structures pointed out a correlation among potential structure types and the radii of the constituent elements. Total energy calculations were carried out to explore the relative stability of several reported crystal structures in this family of compounds.

Sarkar, Arka↗
DOE OSTI2024

Crystal structure of indacaterol hydrogen maleate (C 24 H 29 N 2 O 3 )(HC 4 H 2 O 4 )

The crystal structure of indacaterol hydrogen maleate has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Indacaterol hydrogen maleate crystallizes in space groupP-1 (#24) witha= 8.86616(9),b= 9.75866(21),c= 16.67848(36) Å,α= 102.6301(10), β = 94.1736(6),γ= 113.2644(2)°,V= 1273.095(7) Å 3 , andZ= 2 at 295 K. The crystal structure consists of layers of cations and anions parallel to theab-plane. Traditional N–H⋯O and O–H⋯O hydrogen bonds link the cations and anions into chains along thea-axis. There is a strong intramolecular charge-assisted O–H⋯O hydrogen bond in the non-planar hydrogen maleate anion. There are also two C–H⋯O hydrogen bonds between the anion and cation. The cation makes a strong N–H⋯O hydrogen bond to the anion, but also acts as a hydrogen bond donor to an aromatic C in another cation. The amino group makes bifurcated N–H⋯O hydrogen bonds, one intramolecular and the other intermolecular. The hydroxyl group acts as a donor to another cation. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®).

Materials Science↗
DOE OSTI2020

Li 4 Ru 2 OCl 10 ·10H 2 O: crystal structure, magnetic properties and bonding interactions in ruthenium-oxo complexes

The results of the structural determination, magnetic characterization, and theoretical calculations of a new ruthenium-oxo complex, Li 4 [Ru 2 OCl 10 ]·10H 2 O, are presented. Single crystals were grown using solvent methods and the crystal structure was characterized by single crystal X-ray diffraction. Li 4 [Ru 2 OCl 10 ]·10H 2 O crystallizes into a low-symmetry triclinic structure ($P\bar1$) due to the much smaller Li + cation compared to K + cation in the tetragonal complex K 4 [Ru 2 OCl 10 ]·H 2 O. The X-ray photoelectron spectra confirm only the single valent Ru 4+ in Li 4 [Ru 2 OCl 10 ]·10H 2 O even though two distinct Ru sites exist in the crystal structure. Magnetic measurements reveal the diamagnetic property of Li 4 [Ru 2 OCl 10 ]·10H 2 O with unpaired electrons existing on Ru 4+ . Furthermore, the molecular orbital analysis matches well with the observed UV and magnetic measurements.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Crystal structures of inhibitor complexes of M‐PMV protease with visible flap loops

Abstract Mason‐Pfizer monkey virus protease (PR) was crystallized in complex with two pepstatin‐based inhibitors in P 1 space group. In both crystal structures, the extended flap loops that lock the inhibitor/substrate over the active site, are visible in the electron density either completely or with only small gaps, providing the first observation of the conformation of the flap loops in dimeric complex form of this retropepsin. The H‐bond network in the active site (with D26N mutation) differs from that reported for the P 2 1 crystal structures and is similar to a rarely occurring system in HIV‐1 PR.

Wosicki, Stanislaw↗
DOE OSTI2022

Crystal structure of Campylobacter jejuni lipoprotein Cj1090c

In Gram-negative bacteria, lipopolysaccharide (LPS) is an essential component of the asymmetric outer membrane (OM). LptE is an OM lipoprotein that forms a complex with the β-barrel OM protein, LptD. Incorporation of LPS into the OM outer leaflet is essential for bacterial viability, and mediated by the LptD/E complex. The genome of Campylobacter jejuni, a major foodborne pathogen, contains over 20 putative lipoproteins including Cj1090c. Here, we report the crystal structure of Cj1090c at 2.4 Å resolution, revealing structural evidence for LptE in C. jejuni. The analysis of this crystal structure, along with the genomic context, allows us to propose the C. jejuni LPS transport system for the first time, and also permits for discussion of the features of the LptD/E complex of C. jejuni.

59 BASIC BIOLOGICAL SCIENCES↗