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At least 109 records · Page 6

Geomagnetic response to solar activity.

The relationship between solar activity and geomagnetic variations is discussed in the light of spacecraft data obtained during the last decade. The effects of centers of solar activity responsible for producing geomagnetic activity on earth are believed to be transmitted through the solar wind, and there is usually a delay of two or three days before the onset of magnetic activity. Attempts to make a one-to-one correspondence between specific solar events and specific magnetic storms, however, are usually unsuccessful, because of the complex and indirect processes linking the two phenomena. Normally, only statistical tendencies can be shown.

Mead, G. D.↗

Determining the Three-Dimensional Structures of Silica-Supported Metal Complexes from the Ground Up

The immobilization of molecularly precise metal complexes to substrates, such as silica, provides an attractive platform for the design of active sites in heterogeneous catalysts. Specific steric and electronic variations of the ligand environment enable the development of structure–activity relationships and the knowledge-driven design of catalysts. At present, however, the three-dimensional environment of the precatalyst, much less the active site, is generally not known for heterogeneous single-site catalysts. We explored the degree to which NMR-based surface-to-complex interatomic distances could be used to solve the three-dimensional structures of three silica-supported metal complexes. Furthermore, the structure solution revealed unexpected features related to the environment around the metal that would be difficult to discern otherwise. This approach appears to be highly robust and, due to its simplicity, is readily applied to most single-site catalysts with little extra effort.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Atomic-scale identification of active sites of oxygen reduction nanocatalysts

Heterogeneous nanocatalysts play a crucial role in both the chemical and energy industries. Despite substantial advancements in theoretical, computational and experimental studies, identifying their active sites remains a major challenge. Here we utilize atomic electron tomography to determine the three-dimensional atomic structure of PtNi and Mo-doped PtNi nanocatalysts for the electrochemical oxygen reduction reaction. We then employ the experimental atomic structures as input to first-principles-trained machine learning to identify the active sites of the nanocatalysts. Through the analysis of the structure–activity relationships, we formulate an equation termed the local environment descriptor, which balances the strain and ligand effects to provide physical and chemical insights into active sites in the oxygen reduction reaction. The ability to determine the three-dimensional atomic structure and chemical composition of realistic nanoparticles, combined with machine learning, could transform our fundamental understanding of the active sites of catalysts and guide the rational design of optimal nanocatalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

In Vitro and In Vivo Inhibition of the Mycobacterium tuberculosis Phosphopantetheinyl Transferase PptT by Amidinoureas

A newly validated target for tuberculosis treatment is phosphopantetheinyl transferase, an essential enzyme that plays a critical role in the biosynthesis of cellular lipids and virulence factors in Mycobacterium tuberculosis. The structure–activity relationships of a recently disclosed inhibitor, amidinourea (AU) 8918 (1), were explored, focusing on the biochemical potency, determination of whole-cell on-target activity for active compounds, and profiling of selective active congeners. These studies show that the AU moiety in AU 8918 is largely optimized and that potency enhancements are obtained in analogues containing a para-substituted aromatic ring. Preliminary data reveal that while some analogues, including 1, have demonstrated cardiotoxicity (e.g., changes in cardiomyocyte beat rate, amplitude, and peak width) and inhibit Ca v 1.2 and Na v 1.5 ion channels (although not hERG channels), inhibition of the ion channels is largely diminished for some of the para-substituted analogues, such as 5k (p-benzamide) and 5n (p-phenylsulfonamide).

60 APPLIED LIFE SCIENCES↗

Infrared Spectroscopic Observation of Oxo- and Superoxo-Intermediates in the Water Oxidation Cycle of a Molecular Ir Catalyst

Molecular Ir catalysts have emerged as an important class of model catalysts for understanding structure–activity relationships in water oxidation, a reaction that is central to renewable fuel synthesis. Prior efforts have mostly focused on controlling and elucidating the emergence of active species from prepared precursors. However, the development of efficient and stable molecular Ir catalysts also necessitates probing of reaction intermediates. To date, relatively little is known about the key intermediates in the cycles of the molecular Ir catalysts. Herein, we probed the catalytic cycle of a homogeneous Ir catalyst (“blue dimer”) at a Au electrode/aqueous electrolyte interface by combining surface-enhanced infrared absorption spectroscopy (SEIRAS) with phase-sensitive detection (PSD). Cyclic voltammograms (CVs) from 1.4 to 1.7 VRHE (RHE = reversible hydrogen electrode) give rise to a band at ~818 cm –1 , whereas CVs from 1.4 to ≥1.85 VRHE generate an additional band at ~1146 cm –1 . Isotope labeling experiments indicate that the bands at ~818 and ~1146 cm –1 are attributable to oxo (Ir V =O) and superoxo (Ir IV –OO • ) moieties, respectively. Furthermore, this study establishes PSD-SEIRAS as a sensitive tool for probing water oxidation cycles at electrode/electrolyte interfaces and demonstrates that the relative abundance of two key intermediates can be tuned by the thermodynamic driving force of the reaction.

25 ENERGY STORAGE↗

Origins of enhanced oxygen reduction activity of transition metal nitrides

Transition metal nitride (TMN-) based materials have recently emerged as promising non-precious-metal-containing electrocatalysts for the oxygen reduction reaction (ORR) in alkaline media. However, the lack of fundamental understanding of the oxide surface has limited insights into structure–(re)activity relationships and rational catalyst design. Here, in this work, we demonstrate how a well-defined TMN can dictate/control the as-formed oxide surface and the resulting ORR electrocatalytic activity. Structural characterization of MnN nanocuboids revealed that an electrocatalytically active Mn 3 O 4 shell grew epitaxially on the MnN core, with an expansive strain along the [010] direction to the surface Mn 3 O 4 . The strained Mn 3 O 4 shell on the MnN core exhibited an intrinsic activity that was over 300% higher than that of pure Mn 3 O 4 . A combined electrochemical and computational investigation indicated/suggested that the enhancement probably originates from a more hydroxylated oxide surface resulting from the expansive strain. This work establishes a clear and definitive atomistic picture of the nitride/oxide interface and provides a comprehensive mechanistic understanding of the structure–reactivity relationship in TMNs, critical for other catalytic interfaces for different electrochemical processes.

electrocatalysis↗

Discovery and characterization of bromodomain 2–specific inhibitors of BRDT

Bromodomain testis (BRDT), a member of the bromodomain and extraterminal (BET) subfamily that includes the cancer targets BRD2, BRD3, and BRD4, is a validated contraceptive target. All BET subfamily members have two tandem bromodomains (BD1 and BD2). Knockout mice lacking BRDT-BD1 or both bromodomains are infertile. Treatment of mice with JQ1, a BET BD1/BD2 nonselective inhibitor with the highest affinity for BRD4, disrupts spermatogenesis and reduces sperm number and motility. To assess the contribution of each BRDT bromodomain, we screened our collection of DNA-encoded chemical libraries for BRDT-BD1 and BRDT-BD2 binders. High-enrichment hits were identified and resynthesized off-DNA and examined for their ability to compete with JQ1 in BRDT and BRD4 bromodomain AlphaScreen assays. These studies identified CDD-1102 as a selective BRDT-BD2 inhibitor with low nanomolar potency and >1,000-fold selectivity over BRDT-BD1. Structure–activity relationship studies of CDD-1102 produced a series of additional BRDT-BD2/BRD4-BD2 selective inhibitors, including CDD-1302, a truncated analog of CDD-1102 with similar activity, and CDD-1349, an analog with sixfold selectivity for BRDT-BD2 versus BRD4-BD2. BROMOscan bromodomain profiling confirmed the great affinity and selectivity of CDD-1102 and CDD-1302 on all BET BD2 versus BD1 with the highest affinity for BRDT-BD2. Cocrystals of BRDT-BD2 with CDD-1102 and CDD-1302 were determined at 2.27 and 1.90 Å resolution, respectively, and revealed BRDT-BD2 specific contacts that explain the high affinity and selectivity of these compounds. These BD2-specific compounds and their binding to BRDT-BD2 are unique compared with recent reports and enable further evaluation of their nonhormonal contraceptive potential in vitro and in vivo.

59 BASIC BIOLOGICAL SCIENCES↗

Semantic Property Graph for Scalable Knowledge Graph Analytics

Graphs are a natural and fundamental representation to describe entities, relationships, activities, and evolution of complex systems. Many domains such as communication, citation, procurement, biology, social media, and transportation can be modeled as a set of entities and their relationships. Resource Description Framework (RDF) and Labeled Property Graph (LPG) are two of the most used data models to encode information in a graph. Both models are similar in terms of using basic graph elements such as nodes and edges but differ in terms of the modeling approach, expressibility, serialization, and target applications. RDF is a flexible data exchange model for expressing information about entities but it tends to a have high memory footprint and inefficient storage, which does not make it a natural choice to perform scalable graph analytics. In contrast, LPG has gained traction as a reliable model to perform scalable graph analytic tasks such as sub-graph matching, network alignment, and real-time knowledge graph query. It provides efficient storage, fast traversal, and flexibility to model various real-world domains. At the same time, the LPG lacks the support of a formal knowledge representation such as an ontology to provide automated knowledge inference. We propose Semantic Property Graph (SPG) as a logical projection of reified RDF into the LPG model. SPG continues to use RDF ontology to define the type hierarchy of the projected graph and validate it against a given ontology. We present a framework to convert reified RDF graphs into SPG using two different computing environments. We also present cloud-based graph migration capabilities using Amazon Web Services.

Purohit, Sumit↗

Biomimetic antibiotics based on amphiphilic peptoids and their self-assembly

Bacterial infections pose a serious threat to mankind. Inspired by antimicrobial peptides (AMPs) and their membrane-disruption mechanism, there is immense interest in the design and development of synthetic mimetics for antibacterial applications, overcoming the intrinsic drawbacks of AMPs (e.g. susceptibility to proteolytic degradation). Herein, by exploiting the self-assembly and pore-forming capabilities of sequence-defined peptoids, we discovered a new family of low molecular weight peptoid antibiotics that exhibited excellent broad-spectrum activity and high selectivity toward a panel of clinically significant Gram-positive and Gram-negative bacterial strains. Tuning peptoid sidechain chemistry and structure enabled us to tune the efficacy of antimicrobial activity and study the structure–activity relationship. These findings offer a novel approach to identify new families of antimicrobial peptoids and correlate the pore-forming capability of self-assembling peptoids with their antimicrobial activities. Because peptoids are highly robust and biocompatible, we exhibit these peptoid-based antibiotics will be significant for combating the emerging drug resistance.

59 BASIC BIOLOGICAL SCIENCES↗

Rotationally Driven Ultraviolet Emission of Red Giant Stars

Main-sequence stars exhibit a clear rotation-activity relationship, in which rapidly rotating stars drive strong chromospheric/coronal ultraviolet and X-ray emission. While the vast majority of red giant stars are inactive, a few percent exhibit strong ultraviolet emission. Here we use a sample of 133 red giant stars observed by Sloan Digital Sky Survey APOGEE and Galaxy Evolution Explorer to demonstrate an empirical relationship between near-UV (NUV) excess and rotational velocity (v sin i). Beyond this simple relationship, we find that NUV excess also correlates with rotation period and with Rossby number in a manner that shares broadly similar trends to those found in M dwarfs, including activity saturation among rapid rotators. Our data also suggest that the most extremely rapidly rotating giants may exhibit so-called supersaturation, which could be caused by centrifugal stripping of these stars rotating at a high fraction of breakup speed. As an example application of our empirical rotation-activity relation, we demonstrate that the NUV emission observed from a recently reported system comprising a red giant with a black hole companion is fully consistent with arising from the rapidly rotating red giant in that system. Most fundamentally, our findings suggest a common origin of chromospheric activity in rotation and convection for cool stars from main sequence to red giant stages of evolution.

79 ASTRONOMY AND ASTROPHYSICS↗

Stratigraphy‐Induced Localization of Microseismicity During CO 2 Injection in Illinois Basin

Abstract Subsurface fluid injection stimulates complex hydromechanical interaction, necessitating the integration of geomechanical data across spatial and temporal scales to consider the sophisticated behavior. Induced seismic response is usually associated with the complex reservoir architecture and pre‐existing features that are three‐dimensional, such as local stratigraphy, fractures, faults, and other discontinuities. This study encompasses laboratory characterization of the coupled hydromechanical response of cores extracted from rock formations in Illinois Basin: reservoir ‐ Mt. Simon sandstone, basal seal ‐ Argenta sandstone, and crystalline basement ‐ Precambrian rhyolite. High‐resolution numerical modeling allows considering the three‐dimensional complexity of the Illinois Basin Decatur Project with spatial resolution comparable to one of the active seismic surveys. A detailed reconstruction of the evolving state of stress in formations lacking direct stress measurements is achieved by numerical modeling that integrated laboratory‐derived hydromechanical properties, a porosity‐permeability relationship, active seismic data, and an inverted three‐dimensional porosity distribution. It appears that the microseismic clusters, mainly observed in the crystalline basement during the injection, are linked to zones experiencing more critically stressed conditions prior to injection. These zones have a potential for reactivation during the injection and are attributed to the specific local stratigraphy of the injection site, as well as transfer of triggering perturbations during the injection.

Bondarenko, N. [University of Illinois Urbana‐Cham↗

Chemical screening by time-resolved X-ray scattering to discover allosteric probes

Abstract Drug discovery relies on efficient identification of small-molecule leads and their interactions with macromolecular targets. However, understanding how chemotypes impact mechanistically important conformational states often remains secondary among high-throughput discovery methods. Here, we present a conformational discovery pipeline integrating time-resolved, high-throughput small-angle X-ray scattering (TR-HT-SAXS) and classic fragment screening applied to allosteric states of the mitochondrial import oxidoreductase apoptosis-inducing factor (AIF). By monitoring oxidized and X-ray-reduced AIF states, TR-HT-SAXS leverages structure and kinetics to generate a multidimensional screening dataset that identifies fragment chemotypes allosterically stimulating AIF dimerization. Fragment-induced dimerization rates, quantified with time-resolved SAXS similarity analysis ( k VR ), capture structure–activity relationships (SAR) across the top-ranked 4-aminoquinoline chemotype. Crystallized AIF–aminoquinoline complexes validate TR-SAXS-guided SAR, supporting this conformational chemotype for optimization. AIF–aminoquinoline structures and mutational analysis reveal active site F482 as an underappreciated allosteric stabilizer of AIF dimerization. This conformational discovery pipeline illustrates TR-HT-SAXS as an effective technology for targeting chemical leads to important macromolecular states.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Synthesis, aphicidal activity and conformation of novel insect kinin analogues as potential eco‐friendly insecticides

Abstract BACKGROUND The discovery of ecofriendly insecticides through a new strategy for aphid control is important because of the substantial resistance and unexpected eco‐toxicity to honeybees caused by traditional insecticides. The insect kinins, a class of multifunctional insect neuropeptides, are considered for potential application in pest control. In our previous work we developed several series of insect kinin analogues and found a promising lead II‐1 with good aphicidal activity. To seek further eco‐friendly aphicides, the optimization of II‐1 is carried out in this study. RESULTS Fifteen novel Yaa 3 modified analogues based on the lead II‐1 were synthesized. The aphicidal tests indicated that IV‐3 , IV‐5 and IV‐10 exhibited significant activity against the soybean aphid Aphis glycines with LC 50 values of 0.0029, 0.0072 and 0.0086 mmol L –1 , respectively, higher than that of lead II‐1 and the commercial Pymetrozine. The molecular modeling results showed that analogues II‐1 , IV‐3 , IV‐5 , IV‐7 and IV‐10 formed a β‐turn‐like conformation, while the conformation of analogues IV‐1 , IV‐2 and IV‐9 seemed to be linear. Some structural elements favorable for the activity were proposed based on the conformation‐activity relationship of the analogues. CONCLUSION Insect kinin analogues derived from lead II‐1 by modifying the hydrolysis site Yaa 3 with natural, sterically hindered α‐ and β‐amino acids showed great potential as eco‐friendly insecticides. Inspiringly, the most active analogue IV‐3 can be a candidate for further development. The β‐turn‐like conformation and the orientation of the aromatic rings of the side chain of Phe 2 and Trp 4 may be critical factors beneficial to activity. © 2019 Society of Chemical Industry

Zhang, Chuanliang↗

Experimental and Computational Evaluation of Nicotinamide Cofactor Biomimetics

Oxidoreductase enzymes are widely used biocatalysts due to their high enantioselectivity and broad substrate compatibility in useful transformations. Many oxidoreductases require nicotinamide cofactors (i.e., NAD(P)H). To replace this costly natural cofactor, synthetic nicotinamide cofactor biomimetics (NCBs) offer different shapes, binding affinities, and reducing potentials that exceed the capabilities of wild-type NAD(P)H. However, the ill-defined structure–activity relationships (SARs) of various NCBs slow rationally guided innovation, such as customized reducing potentials. Here, we dissect two essential elements of NCB design, holding the nicotinamide invariant. First, the linker length between the nicotinamide and an unconjugated aromatic ring uncovered unexpected benefits to redox activity for two or three carbon linkers. Second, substitution on this unconjugated aryl group (Ring 2) might not be expected to affect activity. However, SAR trends demonstrate substantial benefits to reductive potential conferred by electron-donating functionalities on Ring 2. Furthermore, catalysis by two enzymes demonstrates enzyme-dependent tolerance or sensitivity to the NCB structures. Density functional theory (DFT) and computational modeling provide a theoretical framework to understand and build upon these observations. Ring 2 reaches up to the nicotinamide to stabilize its positive charge after oxidation through π–π stacking and charge transfer. Thus, the systematic examination of NCB’s stability, electrochemical redox potentials, and kinetics uncovers trends for the improved design of NCBs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Discovery of highly potent and ALK2/ALK1 selective kinase inhibitors using DNA-encoded chemistry technology

Activin receptor type 1 (ACVR1; ALK2) and activin receptor like type 1 (ACVRL1; ALK1) are transforming growth factor beta family receptors that integrate extracellular signals of bone morphogenic proteins (BMPs) and activins into Mothers Against Decapentaplegic homolog 1/5 (SMAD1/SMAD5) signaling complexes. Several activating mutations in ALK2 are implicated in fibrodysplasia ossificans progressiva (FOP), diffuse intrinsic pontine gliomas, and ependymomas. The ALK2 R206H mutation is also present in a subset of endometrial tumors, melanomas, non-small lung cancers, and colorectal cancers, and ALK2 expression is elevated in pancreatic cancer. Using DNA-encoded chemistry technology, we screened 3.94 billion unique compounds from our diverse DNA-encoded chemical libraries (DECLs) against the kinase domain of ALK2. Off-DNA synthesis of DECL hits and biochemical validation revealed nanomolar potent ALK2 inhibitors. Further structure-activity relationship studies yielded center for drug discovery (CDD)-2789, a potent [NanoBRET (NB) cell IC50: 0.54 μM] and metabolically stable analog with good pharmacological profile. Crystal structures of ALK2 bound with CDD-2281, CDD-2282, or CDD-2789 show that these inhibitors bind the active site through Van der Waals interactions and solvent-mediated hydrogen bonds. CDD-2789 exhibits high selectivity toward ALK2/ALK1 in KINOMEscan analysis and NB K192 assay. In cell-based studies, ALK2 inhibitors effectively attenuated activin A and BMP-induced Phosphorylated SMAD1/5 activation in fibroblasts from individuals with FOP in a dose-dependent manner. Thus, CDD-2789 is a valuable tool compound for further investigation of the biological functions of ALK2 and ALK1 and the therapeutic potential of specific inhibition of ALK2.

Jimmidi, Ravikumar↗

Developing predictive models for µ opioid receptor binding using machine learning and deep learning techniques

Opioids exert their analgesic effect by binding to the µ opioid receptor (MOR), which initiates a downstream signaling pathway, eventually inhibiting pain transmission in the spinal cord. However, current opioids are addictive, often leading to overdose contributing to the opioid crisis in the United States. Therefore, understanding the structure-activity relationship between MOR and its ligands is essential for predicting MOR binding of chemicals, which could assist in the development of non-addictive or less-addictive opioid analgesics. This study aimed to develop machine learning and deep learning models for predicting MOR binding activity of chemicals. Chemicals with MOR binding activity data were first curated from public databases and the literature. Molecular descriptors of the curated chemicals were calculated using software Mold2. The chemicals were then split into training and external validation datasets. Random forest, k-nearest neighbors, support vector machine, multi-layer perceptron, and long short-term memory models were developed and evaluated using 5-fold cross-validations and external validations, resulting in Matthews correlation coefficients of 0.528–0.654 and 0.408, respectively. Furthermore, prediction confidence and applicability domain analyses highlighted their importance to the models’ applicability. Our results suggest that the developed models could be useful for identifying MOR binders, potentially aiding in the development of non-addictive or less-addictive drugs targeting MOR.

Research & Experimental Medicine↗

Extragalactic Radio Jets and Intergalactic Medium 2

During the mid 1990s, the ROSAT satellite provided the highest resolution X-ray imaging, with useful X-ray spectroscopy, and excellent sensitivity. ROSAT"s PSPC and HRI instruments gave us our first high-quality data on the AGN phenomenon in nearby galaxies - the central theme of this research project. Initially this project concentrated on separating the AGN-related component of the X-ray emission from thermal radiation from the surrounding atmospheres in radio galaxies. There was ample reason to believe that this separation would be possible, although earlier work had taken the view that the X-ray emission from radio galaxies is either wholly AGN-related (and hence of sub-arcsec scale), or wholly from the galaxy and cluster atmospheres (and hence of scales - 10 arcsec or more in the low-redshift radio galaxies that we chose to study). First with the PSPC, and then with the HRI, we proved that a wide range of AGN core X ray emissivities could be found, and that the generic radio galaxy produces both AGN-related and atmosphere-related X-radiation. We demonstrated that there is a close relationship between the core X-ray power and the core radio power, and found instances in which the hot atmospheres of the galaxies must be participating in cooling flows, and other cases where those atmospheres are relatively stable. In some cases, there is a clear active relationship between the extended radio emission and the X-ray atmospheres: thus in NGC 326, we interpret the distorted radio structure as evidence of buoyancy as the radio plasma rises through the cluster atmosphere. In 3C 449, we can see that the radio plasma is displacing the X-ray emitting gas. In a further case (NGC 1265), we hoped that the motion of a radio galaxy through a cluster atmosphere would be apparent though the wake that it might establish - unfortunately, other structure in the atmosphere of the Perseus cluster tends to dominate our X-ray image, and no useful limits could be placed on the strength of the wake. In the light of so-called "unified" models of AGN, it is expected that the low-power radio galaxies studied under these programmes are the unbeamed counterparts of BL Lac objects. Accordingly, we predicted that BL Lac objects, as a class, should show X-ray halos from atmospheres similar to those associated with radio galaxies. The difficulty with studying this is that BL Lac objects tend to be X-ray bright, and the halos then vanish under the wings of the point response function. We found a BL Lac with less of a dynamic range problem, mapped it with the ROSAT HRI, and duly found an atmosphere (Hardcastle et al. 1999). Unfortunately for unification models, this atmosphere is exceptionally dense, so that it must be participating in an intense cooling flow. The implications of this for unification models are far from clear, and further work is under way.

Birkinshaw, Mark↗

Probing the surface of promoted CuO-Cr 2 O 3 -Fe 2 O 3 catalysts during CO 2 activation

The influence of basic oxide promoters on copper-chromium-iron oxide catalysts was investigated to determine the nature of surface oxygen species and structure-activity relationship for the reverse water-gas shift reaction. The catalysts were characterized with in situ XRD, in situ Raman, in situ XPS, in situ HS-LEIS and H 2 -TPR. Two surface oxygen sites with different reduction characteristics were found to be present. The overall CO 2 activation rate was found to correlate with both the number and reducibility of the more active oxygen species that were likely associated with the Cu-FeO x interfacial regions for enhanced hydrogen spillover. While addition of K 2 O somewhat preserved the interfacial regions and facilitated the reduction kinetics of surface oxygen, both Na 2 O and CaO significantly suppressed the availability of metallic Cu as well as the Cu-FeO x interfaces, leading to decreased reactivity. These findings provide a direction to promote the copper-iron catalysts by creating more metal-metal oxide interfacial sites.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗