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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 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.Item One Pot Photomediated Formation of Electrically Conductive Hydrogels(ACS Polymers Au, 2024-02-14) Nguyen, Dan My; Lo, Chun-Yuan; Guo, Tianzheng; Choi, Taewook; Sundar, Shalini; Swain, Zachary; Wu, Yuhang; Dhong, Charles; Kayser, Laure V.Electrically conductive hydrogels represent an innovative platform for the development of bioelectronic devices. While photolithography technologies have enabled the fabrication of complex architectures with high resolution, photoprinting conductive hydrogels is still a challenging task because the conductive polymer absorbs light which can outcompete photopolymerization of the insulating scaffold. In this study, we introduce an approach to synthesizing conductive hydrogels in one step. Our approach combines the simultaneous photo-cross-linking of a polymeric scaffold and the polymerization of 3,4-ethylene dioxythiophene (EDOT), without additional photocatalysts. This process involves the copolymerization of photo-cross-linkable coumarin-containing monomers with sodium styrenesulfonate to produce a water-soluble poly(styrenesulfonate-co-coumarin acrylate) (P(SS-co-CoumAc)) copolymer. Our findings reveal that optimizing the [SS]:[CoumAc] ratio at 100:5 results in hydrogels with the strain at break up to 16%. This mechanical resilience is coupled with an electronic conductivity of 9.2 S m–1 suitable for wearable electronics. Furthermore, the conductive hydrogels can be photopatterned to achieve micrometer-sized structures with high resolution. The photo-cross-linked hydrogels are used as electrodes to record stable and reliable surface electromyography (sEMG) signals. These novel photo-cross-linkable polymers combined with one-pot PEDOT (poly-EDOT) polymerization open possibilities for rapidly prototyping complex bioelectronic devices and creating custom-designed interfaces between electronics and biological systems.Item Synthesis, Characterization, and Reactivity of Tris(imido)chromium(VI) Complexes(Inorganic Chemistry, 2023-11-27) Wu, Pengcheng; Yap, Glenn P. A.; Theopold, Klaus H.Multiple tris(imido)chromium(VI) complexes, including neutral and ionic compounds, have been synthesized and characterized. (tBuN)2Cr(NHtBu)Cl can be deprotonated by KN(SiMe3)2, yielding K[(tBuN)3CrCl]. This tris(imido) anion undergoes nucleophilic substitution by PPh3 and tBuNH2 to form (tBuN)3Cr(PPh3) and (tBuN)2Cr(NHtBu)2, respectively. (tBuN)2Cr(NHtBu)2 loses one amido proton to form K[(tBuN)3Cr(NHtBu)] upon reaction with KN(SiMe3)2. The imido ligands of K[(tBuN)3CrCl] and (tBuN)3Cr(PPh3) are attacked by the electrophile MeI to produce (tBuN)2Cr(NMetBu)Cl and (tBuN)2Cr(NMetBu)I, respectively. An alternate way to make tris(imido) anions is deprotonation of (tBuN)2Cr(NHtBu)Cl by an alkyl lithium reagent, e.g., Me3SiCH2Li. The resulting Li[(tBuN)3CrCl] was alkylated by a second equivalent of Me3SiCH2Li to form Li[(tBuN)3Cr(CH2SiMe3)]. Reactivity studies of tris(imido) complexes show cycloaddition with PhNCO or CO2 to form metallacycles.Item Exploring Sulfur Sites in Proteins via Triple-Resonance 1H-Detected 77Se NMR(Journal of the American Chemical Society, 2023-11-15) Koscielniak, Janusz; Li, Jess; Sail, Deepak; Swenson, Rolf; Anklin, Clemens; Rozovsky, Sharon; Byrd, R. AndrewNMR spectroscopy has been applied to virtually all sites within proteins and biomolecules; however, the observation of sulfur sites remains very challenging. Recent studies have examined 77Se as a replacement for sulfur and applied 77Se NMR in both the solution and solid states. As a spin-1/2 nuclide, 77Se is attractive as a probe of sulfur sites, and it has a very large chemical shift range (due to a large chemical shift anisotropy), which makes it potentially very sensitive to structural and/or binding interactions as well as dynamics. Despite being a spin-1/2 nuclide, there have been rather limited studies of 77Se, and the ability to use 1H-indirect detection has been sparse. Some examples exist, but in the absence of a directly bonded, nonexchangeable 1H, these have been largely limited to smaller molecules. We develop and illustrate approaches using double-labeling of 13C and 77Se in proteins that enable more sensitive triple-resonance schemes via multistep coherence transfers and 1H-detection. These methods require specialized hardware and decoupling schemes, which we developed and will be discussed.Item Surface Functionalization with (3-Glycidyloxypropyl)trimethoxysilane (GOPS) as an Alternative to Blending for Enhancing the Aqueous Stability and Electronic Performance of PEDOT:PSS Thin Films(ACS Applied Materials and Interfaces, 2023-11-29) Osazuwa, Peter O.; Lo, Chun-Yuan; Feng, Xu; Nolin, Abigail; Dhong, Charles; Kayser, Laure V.Organic mixed ionic–electronic conductors, such as poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS), are essential materials for the fabrication of bioelectronic devices due to their unique ability to couple and transport ionic and electronic charges. The growing interest in bioelectronic devices has led to the development of organic electrochemical transistors (OECTs) that can operate in aqueous solutions and transduce ionic signals of biological origin into measurable electronic signals. A common challenge with OECTs is maintaining the stability and performance of the PEDOT:PSS films operating under aqueous conditions. Although the conventional approach of blending the PEDOT:PSS dispersions with a cross-linker such as (3-glycidyloxypropyl)trimethoxysilane (GOPS) helps to ensure strong adhesion of the films to device substrates, it also impacts the morphology and thus electrical properties of the PEDOT:PSS films, which leads to a significant reduction in the performance of OECTs. In this study, we instead functionalize only the surface of the device substrates with GOPS to introduce a silane monolayer before spin-coating the PEDOT:PSS dispersion on the substrate. In all cases, having a GOPS monolayer instead of a blend leads to increased electronic performance metrics, such as three times higher electronic conductivity, volumetric capacitance, and mobility–capacitance product [μC*] value in OECT devices, ultimately leading to a record value of 406 ± 39 F cm–1 V–1 s–1 for amorphous PEDOT:PSS. This increased performance does not come at the expense of operational stability, as both the blend and surface functionalization show similar performance when subjected to pulsed gate bias stress, long-term electrochemical cycling tests, and aging over 150 days. Overall, this study establishes a novel approach to using GOPS as a surface monolayer instead of a blended cross-linker, for achieving high-performance organic mixed ionic–electronic conductors that are stable in water for bioelectronics.Item pKa prediction of per- and polyfluoroalkyl acids in water using in silico gas phase stretching vibrational frequencies and infrared intensities(Physical Chemistry Chemical Physics, 2023-09-01) Murillo-Gelvez, Jimmy; Dmitrenko, Olga; Torralba-Sanchez, Tifany L.; Tratnyek, Paul G.; Di Toro, Dominic M.To successfully understand and model the environmental fate of per- and polyfluoroalkyl substances (PFAS), it is necessary to know key physicochemical properties (PChPs) such as pKa; however, measured PChPs of PFAS are scarce and of uncertain reliability. In this study, quantitative structure–activity relationships (QSARs) were developed by correlating calculated (M062-X/aug-cc-pVDZ) vibrational frequencies (VF) and corresponding infrared intensities (IRInt) to the pKa of carboxylic acids, sulfonic acids, phosphonic acids, sulfonamides, betaines, and alcohols. Antisymmetric stretching VF of the anionic species were used for all subclasses except for alcohols where the OH stretching VF performed better. The individual QSARs predicted the pKa for each subclass mostly within 0.5 pKa units from the experimental values. The inclusion of IRInt as a pKa predictor for carboxylic acids improved the results by decreasing the root-mean-square error from 0.35 to 0.25 (n > 100). Application of the developed QSARs to estimate the pKa of PFAS within each subclass revealed that the length of the perfluoroalkyl chain has minimal effect on the pKa, consistent with other models but in stark contrast with the limited experimental data available.Item Adsorption and Thermal Decomposition of Triphenyl Bismuth on Silicon (001)(Journal of Physical Chemistry C, 2023-08-24) Lundgren, Eric A. S.; Byron, Carly; Constantinou, Procopios; Stock, Taylor J. Z.; Curson, Neil J.; Thomsen, Lars; Warschkow, Oliver; Teplyakov, Andrew V.; Schofield, Steven R.We investigate the adsorption and thermal decomposition of triphenyl bismuth (TPB) on the silicon (001) surface using atomic-resolution scanning tunneling microscopy, synchrotron-based X-ray photoelectron spectroscopy, and density functional theory calculations. Our results show that the adsorption of TPB at room temperature creates both bismuth–silicon and phenyl–silicon bonds. Annealing above room temperature leads to increased chemical interactions between the phenyl groups and the silicon surface, followed by phenyl detachment and bismuth subsurface migration. The thermal decomposition of the carbon fragments leads to the formation of silicon carbide at the surface. This chemical understanding of the process allows for controlled bismuth introduction into the near surface of silicon and opens pathways for ultra-shallow doping approaches.Item Crystal and electronic structure of the ternary Zintl bismuthide BaLiBi(Zeitschrift für anorganische und allgemeine Chemie | Journal of Inorganic and General Chemistry, 2023-10-02) Ovchinnikov, Alexander; Bobev, SvilenReported is the accurate refinement of the structure of the ternary bismuthide BaLiBi, based on single-crystal X-ray diffraction data. This compound crystallizes with the ZrBeSi structure type with the space group P63/mmc (no. 194), a=4.9917(6) Å, c=9.079(2) Å, V=195.92(7) Å3 with two formula units per unit cell. In addition to being a colored ternary variant of the AlB2 type, the crystal structure of BaLiBi can be also viewed as a “stuffed” variant of the NiAs structure, where the Bi atoms form a hexagonal close packing, the Ba atoms occupy the octahedral voids in this packing, and the Li atoms are located between adjacent tetrahedral voids on their common triangular faces. In the absence of direct Bi–Bi interactions, the BaLiBi crystal structure rationalized according to the notation (Ba2+)(Li+)(Bi3−), suggesting an electron-balanced composition, i. e., a Zintl phase. In line with this notation, scalar-relativistic first-principle calculations with the LMTO code reveal a semiconducting ground state, with a bandgap of about 0.6 eV. Fully relativistic electronic structure calculations predict a semimetallic ground state.Item Modeling the Maturation of the Vocal Fold Lamina Propria Using a Bioorthogonally Tunable Hydrogel Platform(Advanced Healthcare Materials, 2023-08-02) Zou, Xiaoyu; Zhang, He; Benson, Jamie M.; Gao, Hanyuan; Burris, David L.; Fox, Joseph. M.; Jia, XinqiaoToward the goal of establishing an engineered model of the vocal fold lamina propria (LP), mesenchymal stem cells (MSCs) are encapsulated in hyaluronic acid (HA)-based hydrogels employing tetrazine ligation with strained alkenes. To mimic matrix stiffening during LP maturation, diffusion-controlled interfacial bioorthogonal crosslinking is carried out on the soft cellular construct using HA modified with a ferocious dienophile, trans-cyclooctene (TCO). Cultures are maintained in MSC growth media for 14 days to afford a model of a newborn LP that is homogeneously soft (nLP), a homogeneously stiffened construct zero (sLP0) or 7 days (sLP7) post cell encapsulation, and a mature LP model (mLP) with a stiff top layer and a soft bottom layer. Installation of additional HA crosslinks restricts cell spreading. Compared to the nLP controls, sLP7 conditions upregulate the expression of fibrous matrix proteins (Col I, DCN, and FN EDA), classic fibroblastic markers (TNC, FAP, and FSP1), and matrix remodeling enzymes (MMP2, TIMP1, and HAS3). Day 7 stiffening also upregulates the catabolic activities, enhances ECM turnover, and promotes YAP expression. Overall, in situ delayed matrix stiffening promotes a fibroblast transition from MSCs and enhances YAP-regulated mechanosensing.Item Synthesis, crystal and electronic structure of the Zintl phase Ba16Sb11. A case study uncovering greater structural complexity via monoclinic distortion of the tetragonal Ca16Sb11 structure type(Zeitschrift für anorganische und allgemeine Chemie | Journal of Inorganic and General Chemistry, 2023-09-14) Baranets, Sviatoslav; Ovchinnikov, Alexander; Samarakoon, S. M. Gayomi K.; Bobev, SvilenThe binary Zintl phase Ba16Sb11 has been synthesized and structurally characterized. Detailed studies via single-crystal X-ray diffraction methods indicate that although Ba16Sb11 appears to crystallize in the tetragonal Ca16Sb11 structure type (space group Purn:x-wiley:00442313:media:zaac202300148:zaac202300148-math-0001 21m with a=13.5647(9) Å, c=12.4124(12) Å, Z=2, R1=3.14 %; wR2=4.77 %), there exists an extensive structural disorder. Some Ba16Sb11 crystals were found to be monoclinic and the structure was solved and refined in space group P21 (a=18.3929(12) Å, b=13.5233(8) Å, c=18.3978(12) Å, β=94.6600(10)°; Z=4, R1=5.84 %; wR2=9.58 %). The latter corresponds to a 2-fold superstructure of the tetragonal one, which provides a disorder-free structural model. In both descriptions, the disordered tetragonal and the ordered monoclinic superstructure, the basic building units that make up the structure of this Ba-rich compound are pairs of face-shared square antiprisms of Ba atoms, which are centered by Sb atoms. The dimerized antiprisms are linked into parallel chains via square prisms of Ba atoms, which are also centered by Sb atoms. The Zintl concept can be applied in a straightforward manner and as result, the structure of Ba32Sb22 (=2×Ba16Sb11) can be rationalized as (Ba2+)32(Sb3−)20[Sb2]4−. The partitioning of the valence electrons is done taking into an account the homoatomic Sb−Sb contacts (d=3.01 Å), which can be clearly distinguished in the lower symmetry space group. Electronic structure calculations of Ba16Sb11 are in good accordance with the Zintl rationalization and predict a semiconductor with a band gap of 0.77 eV.Item HIV-1 mutants that escape the cytotoxic T-lymphocytes are defective in viral DNA integration(PNAS Nexus, 2022-05-20) Balasubramaniam, Muthukumar; Davids, Benem-Orom; Bryer, Alex; Xu, Chaoyi; Thapa, Santosh; Shi, Jiong; Aiken, Christopher; Pandhare, Jui; Perilla, Juan R.; Dash, ChandravanuHIV-1 replication is durably controlled without antiretroviral therapy (ART) in certain infected individuals called elite controllers (ECs). These individuals express specific human leukocyte antigens (HLA) that tag HIV-infected cells for elimination by presenting viral epitopes to CD8+ cytotoxic T-lymphocytes (CTL). In HIV-infected individuals expressing HLA-B27, CTLs primarily target the viral capsid protein (CA)-derived KK10 epitope. While selection of CA mutation R264K helps HIV-1 escape this potent CTL response, the accompanying fitness cost severely diminishes virus infectivity. Interestingly, selection of a compensatory CA mutation S173A restores HIV-1 replication. However, the molecular mechanism(s) underlying HIV-1 escape from this ART-free virus control by CTLs is not fully understood. Here, we report that the R264K mutation-associated infectivity defect arises primarily from impaired HIV-1 DNA integration, which is restored by the S173A mutation. Unexpectedly, the integration defect of the R264K variant was also restored upon depletion of the host cyclophilin A. These findings reveal a nuclear crosstalk between CA and HIV-1 integration as well as identify a previously unknown role of cyclophilin A in viral DNA integration. Finally, our study identifies a novel immune escape mechanism of an HIV-1 variant escaping a CA-directed CTL response.Item Isocorrole-Loaded Polymer Nanoparticles for Photothermal Therapy under 980 nm Light Excitation(ACS Omega, 2022-10-18) Marek, Maximilian R. J.; Pham, Trong-Nhan; Wang, Jianxin; Cai, Qiuqi; Yap, Glenn P. A.; Day, Emily S.; Rosenthal, JoelPhotothermal therapy (PTT) is a promising treatment option for diseases, including cancer, arthritis, and periodontitis. Typical photothermal agents (PTAs) absorb light in the near-infrared (NIR)-I region of 650–900 nm with a predominant focus around 800 nm, as these wavelengths are minimally absorbed by water and blood in the tissue. Recently, interest has grown in developing nanomaterials that offer more efficient photothermal conversion and that can be excited by light close to or within the NIR-II window of 1000–1700 nm, which offers less absorption by melanin. Herein, we report on the development of 5,5-diphenyl isocorrole (5-DPIC) complexes containing either Zn(II) or Pd(II) (Zn[5-DPIC] and Pd[5-DPIC], respectively) that absorb strongly across the 850–1000 nm window. We also show that poly(lactic-co-glycolic acid) (PLGA) nanoparticles loaded with these designer isocorroles exhibit low toxicity toward triple-negative breast cancer (TNBC) cells in the dark but enable efficient heat production and photothermal cell ablation upon excitation with 980 nm light. These materials represent an exciting new platform for 980 nm activated PTT and demonstrate the potential for designer isocorroles to serve as effective PTAs.Item Selection Criteria for Small-Molecule Inhibitors in Area-Selective Atomic Layer Deposition: Fundamental Surface Chemistry Considerations(Accounts of Chemical Research, 2023-08-01) Mameli, Alfredo; Teplyakov, Andrew V.Conspectus Atomically precise and highly selective surface reactions are required for advancing microelectronics fabrication. Advanced atomic processing approaches make use of small molecule inhibitors (SMI) to enable selectivity between growth and nongrowth surfaces. The selectivity between growth and nongrowth substrates is eventually lost for any known combinations, because of defects, new defect formation, and simply because of a Boltzmann distribution of molecular reactivities on surfaces. The selectivity can then be restored by introducing etch-back correction steps. Most recent developments combine the design of highly selective combinations of growth and nongrowth substrates with atomically precise cycles of deposition and etching methods. At that point, a single additional step is often used to passivate the unwanted defects or selected surface chemical sites with SMI. This step is designed to chemically passivate the reactive groups and defects of the nongrowth substrates both before and/or during the deposition of material onto the growth substrate. This approach requires applications of the fundamental knowledge of surface chemistry and reactivity of small molecules to effectively block deposition on nongrowth substrates and to not substantially affect deposition on the growth surface. Thus, many of the concepts of classical surface chemistry that had been developed over several decades can be applied to design such small molecule inhibitors. This article will outline the approaches for such design. This is especially important now, since the ever-increasing number of applications of this concept still rely on trial-and-error approaches in selecting SMI. At the same time, there is a very substantial breadth of surface chemical reactivity analysis that can be put to use in this process that will relate the effectiveness of a potential SMI on any combination of surfaces with the following: selectivity; chemical stability of a molecule on a specific surface; volatility; steric hindrance, geometry, packing, and precursor of choice for material deposition; strength of adsorption as detailed by interdisplacement to determine the most stable SMI; fast attachment reaction kinetics; and minimal number of various binding modes. The down-selection of the SMI from the list of chemicals that satisfy the preliminary criteria will be decided based on optimal combinations of these requirements. Although the specifics of SMI selection are always affected by the complexity of the overall process and will depend drastically on the materials and devices that are or will be needed, this roadmap will assist in choosing the potential effective SMIs based on quite an exhaustive set of “SMI families” in connection with general types of target surfaces.