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Open access publications by faculty, postdocs, and graduate students in the Department of Chemistry and Biochemistry.
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Item Glycolysis Can Be Fun: Rediscovering Glycolysis as a Problem-Solving Introduction to Metabolism(CourseSource, 2024-08-19) Genova, Lauren A.; Procko, Kristen; Grimes, Catherine L.; Williams, Caroline; Cornely, Kathleen; Shor, Audrey; Greene, Amy Styer; Bibel, Brianna; Kumar, Sanjana V.; White, Harold B.A thorough understanding of glycolysis forms a foundation for students to analyze subsequent topics in metabolism, a core competency recognized by multiple national societies for biology and biochemistry. However, when confronted with the names of over ten chemicals and enzymes, along with various energy inputs and outputs, students can regard glycolysis as a daunting memorization task. Here we describe a card sorting activity in which small groups of students work out the steps of the glycolysis pathway before any lectures on the topic. They examine the chemical structures of glycolytic intermediates and deduce their logical order. Subsequent analysis of the reactions and the role of cofactors and substrates is reinforced with a POGIL worksheet. In the process, the students engage in productive discussions of topics often introduced didactically in lecture. The activity was implemented at six different institutions in small (~12 students) and large classrooms (100+ students), and can be adapted to hybrid/online formats. This highly engaging exercise has been well-received by students and instructors in various undergraduate course contexts.Item Thermoelectric Zintl phases with ultralow thermal conductivity: synthesis, structural characterization, and transport properties of Ca10AlSb9 and Ca10CdSb9(Journal of Materials Chemistry A, 2024-09-02) Ghosh, Kowsik; Borgsmiller, Leah; Baranets, Sviatoslav; Snyder, G. Jeffrey; Bobev, SvilenTwo new Zintl antimonides, Ca10MSb9 (M = Al and Cd), have been synthesized and characterized for the first time and their thermoelectric performance has been evaluated without additional optimization. The two phases can be readily synthesized either by Sn-flux or direct solid-state reactions. The compounds are isotypic and crystallize in a tetragonal crystal system with the space group P42/mnm (no. 136). The crystal structure is highly complex with significant structural disorder—both occupational and positional. For its careful elucidation, both single-crystal X-ray diffraction methods and Rietveld refinements of powder X-ray diffraction data for polycrystalline bulk samples were required. Despite the significant disorder, the structures retain their charge balance and these new Zintl phases are shown to be intrinsic semiconductors with a bandgap of about 0.5 eV. High-temperature transport measurements reveal remarkably low thermal conductivity (0.6–0.7 W m−1 K−1) in the temperature range 323 K to 573 K, which is even lower than that of the well-known thermoelectric Zintl material Yb14MnSb11. Additionally, Seebeck coefficient measurements showed a very high value for Ca10AlSb9, approaching 350 μV K−1 at 573 K. Therefore, we speculate that with proper systematic work and further optimization, these and potentially other Zintl compounds from this extended family can show excellent thermoelectric performance.Item Helicobacter pylori and Campylobacter jejuni bacterial holocytochrome c synthase structure-function analysis reveals conservation of heme binding(Communications Biology, 2024-08-13) Yeasmin, Tania; Carroll, Susan C.; Hawtof, David J.; Sutherland, Molly C.Heme trafficking is essential for cellular function, yet mechanisms of transport and/or heme interaction are not well defined. The System I and System II bacterial cytochrome c biogenesis pathways are developing into model systems for heme trafficking due to their functions in heme transport, heme stereospecific positioning, and mediation of heme attachment to apocytochrome c. Here we focus on the System II pathway, CcsBA, that is proposed to be a bi-functional heme transporter and holocytochrome c synthase. An extensive structure-function analysis of recombinantly expressed Helicobacter pylori and Campylobacter jejuni CcsBAs revealed key residues required for heme interaction and holocytochrome c synthase activity. Homologous residues were previously identified to be required for heme interaction in Helicobacter hepaticus CcsBA. This study provides direct, biochemical evidence that mechanisms of heme interaction are conserved, leading to the proposal that the CcsBA WWD heme-handling domain represents a novel target for therapeutics.Item The emergence of a robust lithium gallium oxide surface layer on gallium-doped LiNiO2 cathodes enables extended cycling stability(Materials Advances, 2024-08-01) Mishra, Mritunjay; Yao, Koffi P. C.LiNiO2 is a promising cobalt-free cathode for lithium-ion batteries due to its high theoretical capacity and low cost. Although intensely studied, the occurrence of several phase transformations and particle pulverization causing capacity fading in cobalt-free LiNiO2 have yet to be effectively resolved. Herein, a sol–gel synthesis process is utilized for gallium (Ga) doping of LiNiO2 at 2% (solution-doping) and 5% (excess-doping) molar ratios. Transmission electron microscopy and X-ray diffraction Rietveld refinement reveal the opportune formation of an α-LiGaO2 shell at 5% doping beyond the solubility limit of 2%. Alongside solution-doping at the Ni and Li crystallographic sites, the emergence of this α-LiGaO2, isostructural and lattice-matched to the R[3 with combining macron]m LiNiO2, is shown to improve capacity retention by a factor of 2.45 after 100 cycles at C/3. Particles with the LiGaO2 shell experience significantly less pulverization during extended cycling. In contrast, the solution-doped LiNiO2 with 2% Ga experiences extensive particle fracturing similar to the baseline undoped LiNiO2. In turn, no significant electrochemical performance difference is found between the solution-doped and baseline LiNiO2. The evidence garnered suggests that a surface gallium oxide phase achievable with excess Ga is key to enabling extended cycling using Ga doping.Item Plant extract mediated synthesis of gold nanoparticles and its application to treatment of cancer(World Journal of Advanced Engineering Technology and Sciences, 2024-07-28) Onivefu, Asishana Paul; Adekunle, Adewale Philip; Okebugwu, Joseph Chibuike; Benibo, Paul Gberiye; Aibor, Lucky Ehimen; Raji-Ayoola, Jumoke Ayodele; Latinwo, Opeyemi Olaoluwa; Onyedum, Nwamaka Nneka; Amoo, Ayosunkanmi Damilola; Ukem, David EffiongPlant extract-mediated synthesis of gold nanoparticles is a promising research area with potential applications in various fields including medicine-cancer research, catalysis, and nanoelectronics. Gold nanoparticles have gained serious attention in recent years as a potential cancer treatment due to their unique optical and physical properties. Plant-mediated synthesis of gold nanoparticles is a promising method to produce biocompatible and non-toxic gold nanoparticles (Au-NPs). This study focuses on the current research on the plant-mediated synthesis of gold nanoparticles and their potential treatment for cancer. It also discussed the latest advancement in nanobot technology. The study will also describe the type of plants used for the synthesis of gold nanoparticles, the mechanisms involved in the synthesis, the advantages of using plant-mediated synthesis, and the disadvantages. Additionally, this study will discuss the efficacy of gold nanoparticles as cancer therapeutics and the instrumentation involved in characterizing the gold nanoparticles (Au-NPs), the opportunities for the use of gold nanoparticles (Au-NPs) in cancer treatment and future possible research in the use of nanotechnology in the fight against cancer. Overall, plant-mediated synthesis of gold nanoparticles holds promise as a safe and effective method for cancer treatment.Item Imidazolium-Based Sulfonating Agent to Control the Degree of Sulfonation of Aromatic Polymers and Enable Plastics-to-Electronics Upgrading(JACS Au, 2024-07-03) Lo, Chun-Yuan; Koutsoukos, Kelsey P.; Nguyen, Dan My; Wu, Yuhang; Angel Trujillo, David Alejandro; Miller, Tabitha; Shrestha, Tulaja; Mackey, Ethan; Damani, Vidhika S.; Kanbur, Uddhav; Opila, Robert; Martin, David C.; Kaphan, David; Kayser, Laure V.The accumulation of plastic waste in the environment is a growing environmental, economic, and societal challenge. Plastic upgrading, the conversion of low-value polymers to high-value materials, could address this challenge. Among upgrading strategies, the sulfonation of aromatic polymers is a powerful approach to access high-value materials for a range of applications, such as ion-exchange resins and membranes, electronic materials, and pharmaceuticals. While many sulfonation methods have been reported, achieving high degrees of sulfonation while minimizing side reactions that lead to defects in the polymer chains remains challenging. Additionally, sulfonating agents are most often used in large excess, which prevents precise control over the degree of sulfonation of aromatic polymers and their functionality. Herein, we address these challenges using 1,3-disulfonic acid imidazolium chloride ([Dsim]Cl), a sulfonic acid-based ionic liquid, to sulfonate aromatic polymers and upgrade plastic waste to electronic materials. We show that stoichiometric [Dsim]Cl can effectively sulfonate model polystyrene up to 92% in high yields, with minimal defects and high regioselectivity for the para position. Owing to its high reactivity, the use of substoichiometric [Dsim]Cl uniquely allows for precise control over the degree of sulfonation of polystyrene. This approach is also applicable to a wide range of aromatic polymers, including waste plastic. To prove the utility of our approach, samples of poly(styrene sulfonate) (PSS), obtained from either partially sulfonated polystyrene or expanded polystyrene waste, are used as scaffolds for poly(3,4-ethylenedioxythiophene) (PEDOT) to form the ubiquitous conductive material PEDOT:PSS. PEDOT:PSS from plastic waste is subsequently integrated into organic electrochemical transistors (OECTs) or as a hole transport layer (HTL) in a hybrid solar cell and shows the same performance as commercial PEDOT:PSS. This imidazolium-mediated approach to precisely sulfonating aromatic polymers provides a pathway toward upgrading postconsumer plastic waste to high-value electronic materials.Item Applicability of the Zintl Concept to Understanding the Crystal Chemistry of Lithium-Rich Germanides and Stannides(Inorganic Chemistry, 2024-05-29) Ghosh, Kowsik; Rahman, Salina; Ovchinnikov, Alexander; Bobev, SvilenWith this contribution, we take a new, critical look at the structures of the binary phases Li5Ge2 and Li5Sn2. Both are isostructural (centrosymmetric space group R3̅m, no. 166), and in their structures, all germanium (tin) atoms are dimerized. Application of the valence rules will require the allocation of six additional valence electrons per [Ge2] or [Sn2] unit considering single covalent bonds, akin to those in the dihalogen molecules. Alternatively, four additional valence electrons per [Ge2] or [Sn2] anion will be needed if homoatomic double bonds exist, in an analogy with dioxygen. Therefore, five lithium atoms in one formula unit cannot provide the exact number of electrons, leaving open questions as to what is the nature of the chemical bonding within these moieties. Additionally, by means of single-crystal X-ray diffraction, synchrotron powder X-ray diffraction, and neutron powder diffraction, we established that the Li and Sn atoms in Li5Sn2 are partially disordered, i.e., the actual chemical formula of this compound is Li5–xSn2+x (0 < x < 0.1). The convoluted atomic bonding in the case where tin atoms partially displace lithium atoms results in the formation of larger covalently bonded fragments. Our first-principle calculations suggest that such disorder leads to electron doping. Contrary to that, both experimental and computational findings indicate that in the Li5Ge2 structure, the [Ge2] dimers are slightly oxidized, i.e., hole-doped, as a result of approximately 30% vacancies on a Li site, i.e., the actual chemical formula of this compound is Li5–xGe2 (x ≈ 0.3).Item Development of an efficient, effective, and economical technology for proteome analysis(Cell Reports: Methods, 2024-06-11) Martin, Katherine R.; Le, Ha T.; Abdelgawad, Ahmed; Yang, Canyuan; Lu, Guotao; Keffer, Jessica L.; Zhang, Xiaohui; Zhuang, Zhihao; Asare-Okai, Papa Nii; Chan, Clara S.; Batish, Mona; Yu, YanbaoHighlights • Rapid, robust, and cost-effective alternative to proteomics sample preparation • Versatile filter devices can meet a wide range of proteomics analysis needs • On-filter in-cell digestion facilitates low-input proteomics • Ready-to-go E3 and E4 filter devices are available Motivation Conventional proteomics sample processing methods often have high technical barriers to broad biomedical scientists, leading to difficulties for quick adoption and standardization. Existing protocols are also typically associated with costly reagents and accessories, making them less feasible for resource-limited settings as well as for clinical proteomics and/or core facilities where large numbers of samples are usually processed. Thus, there is a strong unmet need for an easy-to-use, reliable, and low-cost approach for general proteomics sample preparation. Summary We present an efficient, effective, and economical approach, named E3technology, for proteomics sample preparation. By immobilizing silica microparticles into the polytetrafluoroethylene matrix, we develop a robust membrane medium, which could serve as a reliable platform to generate proteomics-friendly samples in a rapid and low-cost fashion. We benchmark its performance using different formats and demonstrate them with a variety of sample types of varied complexity, quantity, and volume. Our data suggest that E3technology provides proteome-wide identification and quantitation performance equivalent or superior to many existing methods. We further propose an enhanced single-vessel approach, named E4technology, which performs on-filter in-cell digestion with minimal sample loss and high sensitivity, enabling low-input and low-cell proteomics. Lastly, we utilized the above technologies to investigate RNA-binding proteins and profile the intact bacterial cell proteome. Graphical abstract available at: https://doi.org/10.1016/j.crmeth.2024.100796Item Fibroblast expression of transmembrane protein smoothened governs microenvironment characteristics after acute kidney injury(The Journal of Clinical Investigation, 2024-07-01) Gui, Yuan; Fu, Haiyan; Palanza, Zachary; Tao, Jianling; Lin, Yi-Han; Min, Wenjian; Qiao, Yi; Bonin, Christopher; Hargis, Geneva; Wang, Yuanyuan; Yang, Peng; Kreutzer, Donald L.; Wang, Yanlin; Liu, Yansheng; Yu, Yanbao; Liu, Youhua; Zhou, DongThe smoothened (Smo) receptor facilitates hedgehog signaling between kidney fibroblasts and tubules during acute kidney injury (AKI). Tubule-derived hedgehog is protective in AKI, but the role of fibroblast-selective Smo is unclear. Here, we report that Smo-specific ablation in fibroblasts reduced tubular cell apoptosis and inflammation, enhanced perivascular mesenchymal cell activities, and preserved kidney function after AKI. Global proteomics of these kidneys identified extracellular matrix proteins, and nidogen-1 glycoprotein in particular, as key response markers to AKI. Intriguingly, Smo was bound to nidogen-1 in cells, suggesting that loss of Smo could affect nidogen-1 accessibility. Phosphoproteomics revealed that the ‘AKI protector’ Wnt signaling pathway was activated in these kidneys. Mechanistically, nidogen-1 interacted with integrin β1 to induce Wnt in tubules to mitigate AKI. Altogether, our results support that fibroblast-selective Smo dictates AKI fate through cell-matrix interactions, including nidogen-1, and offers a robust resource and path to further dissect AKI pathogenesis. Graphical Abstract available at: https://doi.org/10.1172/JCI165836Item Total and Class-Specific Determination of Fluorinated Compounds in Consumer and Food Packaging Samples Using Fluorine-19 Solid-State Nuclear Magnetic Resonance Spectroscopy(Analytical Chemistry, 2024-05-28) Thijs, Mike; Laletas, Ernest; Quinn, Caitlin M.; Raguraman, Subbu V.; Carr, Bryan; Bierganns, PatricHamburger wrapping paper, coated with water-based barrier coatings, used in the food packaging industry was studied by using the total organic fluorine (TOF) method based on combustion ion chromatography and fluorine-19 solid-state nuclear magnetic resonance (19F ss-NMR) spectroscopy. Although the TOF method is a fast and affordable method used to screen for per- and polyfluoroalkyl substances (PFAS), the amount of fluorine it measures is heavily dependent on the extraction step and, therefore could lead to inaccurate results. Fluorine-19 ss-NMR spectroscopy can differentiate between organic and inorganic fluorinated sources, eliminating the need for sample clean up. To illustrate this, the 19F ss-NMR spectra of clean coated paper samples that contained naturally occurring F- ions from the talc raw material and spiked samples containing perfluorooctanoic acid were compared. A range of experimental conditions was explored to improve sensitivity for low PFAS concentrations (in the order of 10–20 mg/kg). Despite the disadvantages of ss-NMR spectroscopy, such as the low limit of detection and resolution, the results demonstrate it can be a viable tool to directly detect PFAS moieties in consumer and food packaging. Therefore, 19F solid-state NMR spectroscopy challenges and complements current methods, which only provide indirect evidence of the presence of PFAS.Item Unraveling the molecular and growth mechanism of colloidal black In2O3−x(Nanoscale, 2024-04-19) Armstrong, Cameron; Otero, Kayla; Hernandez-Pagan, Emil A.Black metal oxides with varying concentrations of O-vacancies display enhanced optical and catalytic properties. However, direct solution syntheses of this class of materials have been limited despite being highly advantageous given the different synthetic handles that can be leveraged towards control of the targeted material. Herein, we present an alternate colloidal synthesis of black In2O3−x nanoparticles from the simple reaction between In(acac)3 and oleyl alcohol. Growth studies by PXRD, TEM, and STEM-EDS coupled to mechanistic insights from 1H, 13C NMR revealed the particles form via two paths, one of which involves In0. We also show that variations in the synthesis atmosphere, ligand environment, and indium precursor can inhibit formation of the black In2O3−x. The optical spectrum for the black nanoparticles displayed a significant redshift when compared to pristine In2O3, consistent with the presence of O-vacancies. Raman spectra and surface analysis also supported the presence of surface oxygen vacancies in the as-synthesized black In2O3−x.Item Interfacial electron transfer of perylenes: Influence of the anchor binding mode(The Journal of Chemical Physics, 2024-01-21) Yan, Han; Harmer, Ryan; Zafar, Binish; Galoppini, Elena; Gundlach, LarsInterfacial electron transfer (IET) through saturated single-linker and dual-linker groups from a perylene chromophore into nanostructured TiO2 films was studied by ultrafast spectroscopy. Perylene chromophores with one and two propanoic acid linker groups in the peri and ortho positions were investigated. In comparison to previously studied perylenes bound via unsaturated acrylic acid linkers, the chromophores with saturated linkers showed bi-exponential IET dynamics. Two distinct transfer times were observed that indicate the presence of two concurrent binding modes. A comparison between ortho- and peri-substituted sensitizers resulted in slower IET dynamics and weaker electronic coupling for ortho substitution. Finally, IET from sensitizers with saturated linker groups is neither promoted nor hindered by a second linker group. This indicates that only one of the two linkers binds covalently to the surface. This study reveals the importance of the anchor-binding mode and design considerations of the linker for regulating IET.Item A Bacillus velezensis strain shows antimicrobial activity against soilborne and foliar fungi and oomycetes(Frontiers in Fungal Biology, 2024-02-23) Wockenfuss, Anna; Chan, Kevin; Cooper, Jessica G.; Chaya, Timothy; Mauriello, Megan A.; Yannarell, Sarah M.; Maresca, Julia A.; Donofrio, Nicole M.Biological control uses naturally occurring antagonists such as bacteria or fungi for environmentally friendly control of plant pathogens. Bacillus spp. have been used for biocontrol of numerous plant and insect pests and are well-known to synthesize a variety of bioactive secondary metabolites. We hypothesized that bacteria isolated from agricultural soil would be effective antagonists of soilborne fungal pathogens. Here, we show that the Delaware soil isolate Bacillus velezensis strain S4 has in vitro activity against soilborne and foliar plant pathogenic fungi, including two with a large host range, and one oomycete. Further, this strain shows putative protease and cellulase activity, consistent with our prior finding that the genome of this organism is highly enriched in antifungal and antimicrobial biosynthetic gene clusters. We demonstrate that this bacterium causes changes to the fungal and oomycete hyphae at the inhibition zone, with some of the hyphae forming bubble-like structures and irregular branching. We tested strain S4 against Magnaporthe oryzae spores, which typically form germ tubes and penetration structures called appressoria, on the surface of the leaf. Our results suggest that after 12 hours of incubation with the bacterium, fungal spores form germ tubes, but instead of producing appressoria, they appear to form rounded, bubble-like structures. Future work will investigate whether a single antifungal molecule induces all these effects, or if they are the result of a combination of bacterially produced antimicrobials.Item ChemisTree: A Novel, Interactive Chemistry Game to Teach Students about Electron Configuration(Journal of Chemical Education, 2024-01-12) Goldman, Slade; Coscia, Katie A.; Genova, Lauren A.Electron configuration provides insight into the chemical behaviors of elements and is an important concept for students to master in introductory chemistry. To better strengthen undergraduate students’ mastery of electron configurations of atoms and ions, we designed a novel, interactive chemistry game called ChemisTree that uses active-learning techniques (e.g., physically building electron configurations onto a game board, small group work, and whole class discussion) and incorporates the three rules for electrons filling orbitals (Aufbau principle, Pauli exclusion principle, and Hund’s rule), using LEGO tiles and plates to represent electrons and orbitals. Students watch an introductory video explaining the rules and components of the game prior to applying their knowledge of electron configuration by working in small groups to build the orbital diagrams of atoms and ions using the materials provided in their ChemisTree game kits. Student understanding is assessed using multiple-choice pre/post-test questions, scoring sheets with peer discussion, and self-reported postactivity evaluations. Students who played the game scored significantly higher in the post-test (62.7%) compared to the pre-test (51.2%), representing an 11.5% increase in average score. Here we provide details about the activity and present data suggesting that student understanding of electron configuration is improved.Item Physicochemical and bacteriological assessment of the polyethene packaged sachet water (popularly called “pure water”) as a major source of drinking water in Sagamu, Ogun State, Southwest, Nigeria(World Journal of Advanced Research and Reviews, 2024-03-30) Onivefu, Asishana Paul; Irede, Egwonor Loveth; Edogun, Idemudia Philip; Umanya, Ovie JosephThis study aimed to evaluate the physicochemical and bacteriological characteristics of polyethylene-packaged sachet water, commonly known as "pure water," produced and distributed in the Sagamu local government area of Ogun State, Southwest Nigeria. The research involved analyzing sachet water samples from various producers, sources, and distributors to assess their quality. Samples were collected randomly from six different locations/towns within Sagamu Local Government and subjected to physicochemical and bacteriological analysis. The findings were compared with the permissible limits established by reputable organizations such as WHO, EPA, Canada, and NIS. The results indicated that most parameters fell within the acceptable range set by WHO, EPA, Canada, and NIS. However, the pH levels of the sachet water samples (ranging from 4.73 to 6.10) were found to be acidic, deviating from the expected range of 6.5 to 10.5. Additionally, while the Total Heterotrophic Bacteria count and Enteric Bacteria count were slightly lower than the permissible limits, with Total Enteric Bacteria ranging from 300 to 480 cfu/100ml (permissible limit <500cfu/100ml) and Enteric Bacteria ranging from 280 to 380 cfu/100ml. Recommendations derived from the study include advocating for water-producing industries to establish their raw water sources in contamination-free zones, encouraging the involvement of well-equipped private and government hospitals in monitoring and reporting on the water quality of packaging industries, promoting the provision of safe piped water by credible individuals within communities, and emphasizing the role of regulatory bodies like SON and NAFDAC in continuously assessing the production and packaging standards of drinking water across communities.Item Increasing the stability of calixarene-capped porous cages through coordination sphere tuning(Dalton Transactions, 2024-01-05) Dey, Avishek; Dworzak, Michael R.; Korathotage, Kaushalya D. P.; Ghosh, Munmun; Hoq, Jahidul; Montone, Christine M.; Yap, Glenn P. A.; Bloch, Eric D.Chemically and thermally stable permanently porous coordination cages are appealing candidates for separations, catalysis, and as the porous component of new porous liquids. However, many of these applications have not turned to microporous cages as a result of their poor solubility and thermal or hydrolytic stability. Here we describe the design and modular synthesis of iron and cobalt cages where the carboxylate groups of the bridging ligands of well-known calixarene capped coordination cages have been replaced with more basic triazole units. The resultingly higher M–L bond strengths afford highly stable cages that are amenable to modular synthetic approaches and potential functionalization or modification. Owing to the robust nature of these cages, they are highly processable and are isolable in various physical states with tunable porosity depending on the solvation methods used. As the structural integrity of the cages is maintained upon high activation temperatures, apparent losses in porosity can be mediated by resolvation and crystallization or precipitation.Item Yet Another Case of Lithium Metal Atoms and Germanium Atoms Sharing Chemistry in the Solid State: Synthesis and Structural Characterization of Ba2LiGe3(Chemistry - A European Journal, 2023-12-06) Ghosh, Kowsik; Bobev, SvilenSeveral Ba−Li−Ge ternary phases are known and structurally characterized, including the title compound Ba2LiGe3. Its structure is reported to contain [Ge6]10− anions that exhibit delocalized bonding with a Hückel-like aromatic character. The Ge atoms are in the same plane with the Li atoms, and if both types of atoms are considered as covalently bonded, [LiGe3]4− honeycomb-like layers will result. The latter are separated by slabs of Ba2+ cations. However, based on the systematic work detailed herein, it is necessary to re-evaluate the phase as Ba2Li1−xGe3+x (x<0.05). Although small, the homogeneity range is clearly demonstrated in the gradual change of the unit cell for four independent samples. Subsequent characterization by single-crystal X-ray diffraction methods shows that the Ba2Li1−xGe3+x structure, responds to the varied number of valence electrons and the changes are most pronounced for the refined lengths of the Li−Ge and Ge−Ge bonds. Indirectly, the changes in the Ge−Li/Ge distances within layers affect the stacking too, and these changes can be correlated to the variation of the c-cell parameter. Chemical bonding analysis based on TB-LMTO-ASA level calculations affirms the notion for covalent character of the Ge−Ge bonds; the Ba−Ge and Li−Ge interactions also show some degree of covalency. Graphical Abstract available at: https://doi.org/10.1002/chem.202302385 The structure of Ba2Li1−xGe3+x, emphasizing the honeycomb-like [Li1−xGe3+x] layers with Li and Ge atoms (denoted in blue and gold) in a partially disordered state.Item The Drug-Induced Interface That Drives HIV-1 Integrase Hypermultimerization and Loss of Function(mBio, 2023-02-06) Singer, Matthew R.; Dinh, Tung; Levintov, Lev; Annamalai, Arun S.; Rey, Juan S.; Briganti, Lorenzo; Cook, Nicola J.; Pye, Valerie E.; Taylor, Ian A.; Kim, Kyungjin; Engelman, Alan N.; Kim, Baek; Perilla, Juan R.; Kvaratskhelia, Mamuka; Cherepanov, PeterAllosteric HIV-1 integrase (IN) inhibitors (ALLINIs) are an emerging class of small molecules that disrupt viral maturation by inducing the aberrant multimerization of IN. Here, we present cocrystal structures of HIV-1 IN with two potent ALLINIs, namely, BI-D and the drug candidate Pirmitegravir. The structures reveal atomistic details of the ALLINI-induced interface between the HIV-1 IN catalytic core and carboxyl-terminal domains (CCD and CTD). Projecting from their principal binding pocket on the IN CCD dimer, the compounds act as molecular glue by engaging a triad of invariant HIV-1 IN CTD residues, namely, Tyr226, Trp235, and Lys266, to nucleate the CTD-CCD interaction. The drug-induced interface involves the CTD SH3-like fold and extends to the beginning of the IN carboxyl-terminal tail region. We show that mutations of HIV-1 IN CTD residues that participate in the interface with the CCD greatly reduce the IN-aggregation properties of Pirmitegravir. Our results explain the mechanism of the ALLINI-induced condensation of HIV-1 IN and provide a reliable template for the rational development of this series of antiretrovirals through the optimization of their key contacts with the viral target. IMPORTANCE Despite the remarkable success of combination antiretroviral therapy, HIV-1 remains among the major causes of human suffering and loss of life in poor and developing nations. To prevail in this drawn-out battle with the pandemic, it is essential to continue developing advanced antiviral agents to fight drug resistant HIV-1 variants. Allosteric integrase inhibitors (ALLINIs) are an emerging class of HIV-1 antagonists that are orthogonal to the current antiretroviral drugs. These small molecules act as highly specific molecular glue, which triggers the aggregation of HIV-1 integrase. In this work, we present high-resolution crystal structures that reveal the crucial interactions made by two potent ALLINIs, namely, BI-D and Pirmitegravir, with HIV-1 integrase. Our results explain the mechanism of drug action and will inform the development of this promising class of small molecules for future use in antiretroviral regimens.Item Results from Exploratory Work in Li-Rich Regions of the AE-Li-Ge Systems (AE = Ca, Sr, Ba)(Crystals, 2023-12-31) Zhang, Jiliang; Bobev, SvilenThe compounds AELi2Ge (AE = Ca, Sr and Ba) were synthesized, and their structures were determined as a part of the exploratory work in the Li-rich regions of the respective ternary systems. The three compounds are isostructural, and their crystal structure is analogous with the orthorhombic structure of BaLi2Si and KLi2As (space group Pmmn). The atomic arrangement can be viewed as an intergrowth of corrugated AEGe layers, alternated with slabs of Li atoms, suggestive of the possible application of these phases as electrode materials for lithium-ion batteries. Both experimental electronic density and calculated electronic structure suggest the existence of Li–Li and Li–Ge interactions with largely covalent character. Despite that, the valence electrons can be partitioned as (AE2+)(Li+)2(Ge4–), i.e., the title compounds can be viewed as valence-precise Zintl phases. The band structure calculations for BaLi2Ge show that a bona fide energy gap in the band structure does not exist and that the expected poor metallic behavior is originated from the AEGe sub-lattice and related to hybridization of Ba5d and Ge3p states in the valence band in proximity of the Fermi level. In addition, electrochemical measurements indicate that Li atoms can be intercalated into CaGe with a maximum capacity of 446 mAh/g, close to the theoretical value of 480 mAh/g of CaLi2Ge, which reveals the possibility of this Li-rich compound to be used as an electrode in Li-ion batteries.Item Hydrogen-Bonded Organic Frameworks Based on Endless-Stacked Amides for Iodine Capture and Detection(Advanced Functional Materials, 2023-12-10) Li, Bin; Qiu, Weiguang; Yap, Glenn P. A.; Dory, Yves L.; Claverie, Jerome P.Recently, hydrogen-bonded organic frameworks (HOFs) have emerged as a rapidly advancing class of porous materials with significant potential for applications in the absorption and detection of various chemicals. Here, the unique ability of amide groups to form endless-stacking H-bonds is implemented in the design of HOFs. Starting from benzene-1,3,5-tricarboxamide and amide-containing tribenzocyclynes as foundational building blocks, a diverse range of HOFs featuring 1D, 2D, or 3D hydrogen-bonded frameworks has been synthesized. Among those, all three porous HOFs, HOF_B-Hex, HOF_T-Pr and HOF_T-Hex exhibited permanent porosity, thereby demonstrating the effectiveness of amide-based HOFs strategy. Notably, HOF_T-Hex stands out with a 42% pore volume and an impressive iodine capture efficiency of 6.4 g g−1. The iodine capture capacity is influenced not only by pore volume but also by the presence of accessible π-electrons within the material (i.e., electrons not engaged in a π–π stacking interaction. Furthermore, some of these HOFs exhibited fluorescent responses to iodine positioning them as highly promising materials for both the capture and sensing of iodine.