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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 A compendium of stable hotspots in the CHO genome(Biotechnology and Bioengineering, 2023-04-04) Hilliard, William; Lee, Kelvin H.The use of targeted integration for industrial CHO cell line development currently requires significant upfront effort to identify genomic loci capable of supporting multigram per liter therapeutic protein production from a limited number of transgene copies. To address this barrier to widespread adoption, we characterized transgene expression from thousands of stable hotspots in the CHO genome using the Thousands of Reporters Integrated in Parallel high-throughput screening method. This genome-scale data set was used to define a limited set of epigenetic properties of hotspot regions with sizes on the order of 10 kb. Cell lines with landing pad integrations at eight retargeted hotspot candidates consistently exhibited higher transgene mRNA expression than a commercially viable hotspot in equivalent culture conditions. Initial benchmarking of NISTmAb and trastuzumab productivity from one of these hotspots yielded mAb productivities of approximately 0.7–2 g/L (qP range: 2.9–8.2 pg/cell/day) in small-scale fed-batches. These findings indicate the list of hotspot candidates identified here will be a valuable resource for targeted integration platform development within the CHO community.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 Adsorption of 2-propanol on ice probed by ambient pressure X-ray photoelectron spectroscopy(Royal Society of Chemistry, 2015-08-18) Newberg, John T.; Bluhm, Hendrik; John T. Newberg and Hendrik Bluhm; Newberg, John T.The interaction of 2-propanol with ice was examined via ambient pressure X-ray photoelectron spectroscopy (APXPS), a surface sensitive technique that probes the adsorbed 2-propanol directly with submonolayer resolution. Isothermal uptake experiments were performed on vapor deposited ice at 227 K in the presence of the equilibrium water vapor pressure of 0.05 Torr and 2-propanol partial pressures ranging from 5 × 10−5 to 2 × 10−3 Torr. The C 1s APXPS spectra of adsorbed 2-propanol showed two characteristic peaks associated with the COH alcohol group and CMe methyl groups in a 1 : 2 ratio, respectively. Coverage increased with 2-propanol partial pressure and followed first order Langmuir kinetics with a Langmuir constant of K = 6.3 × 103 Torr−1. The 1 : 2 ratio of COH : CMe remained constant with increasing coverage, indicating there is no chemical reaction upon adsorption. The observed Langmuir kinetics using APXPS is consistent with previous observations of other small chain alcohols via indirect adsorption methods using, e.g., Knudsen cell and coated wall flow tube reactors. Graphical abstract: Adsorption of 2-propanol on ice probed by ambient pressure X-ray photoelectron spectroscopyItem Anion Binding as a Strategy for the Synthesis of Porous Salts(Chemistry of Materials, 2022-12-27) Antonio, Alexandra M.; Dworzak, Michael R.; Korman, Kyle J.; Yap, Glenn P. A.; Bloch, Eric D.Porous salts have recently emerged as a promising new class of ultratunable permanently microporous solids. These adsorbents, which were first reported as ionic solids based on porous cations and anions, can be isolated from a wide variety of charged, permanently porous coordination cages. A challenge in realizing the full tunability of such systems, however, lies in the fact that the majority of coordination cages for which surface areas have been reported are comprised of charge-balanced inorganic and organic building blocks that result in neutral cages. As such, most reported permanently porous coordination cages cannot be used as reagents in the synthesis of porous salts. Here, we show that the facile reaction of TBAX (TBA+ = tetra-n-butylammonium; X = F– and Cl–) with molybdenum paddlewheel-based coordination cages of the M4L4 and M24L24 lantern and cuboctahedra structure types, respectively, affords charged cages by virtue of coordination of halide anions to the internal and/or external metal sites on these structures, as confirmed by single-crystal X-ray diffraction, X-ray photoelectron spectroscopy, and nuclear magnetic resonance (NMR) spectroscopy. At a practical level, the TBAX/cage reactions, which are fully reversible upon isolation of the cage with the appropriate solvent, solubilize otherwise rigorously insoluble cages. This method significantly increases the solution processability of these highly porous solids. Toward the formation of new porous salts, halide binding also serves to incorporate charge on neutral cages and make them amenable to simple salt metathesis reactions to afford new porous salts based on anions and cations with intrinsic porosity. A combination of diffraction methods and a suite of spectroscopic tools confirms speciation of the isolated solids, which represent a new class of highly tunable porous salts. Ultimately, this work represents a roadmap for the preparation of new porous solids and showcases the utility and broad applicability of anion binding as a strategy for the synthesis of porous salts.Item Attachment Chemistry of 4-Fluorophenylboronic Acid on TiO2 and Al2O3 Nanoparticles(Chemistry of Materials, 2022-12-13) Byron, Carly; Silva-Quinones, Dhamelyz; Sarkar, Sucharita; Brown, Scott C.; Bai, Shi; Quinn, Caitlin M.; Grzenda, Zachary; Chinn, Mitchell S.; Teplyakov, Andrew V.Surface modification of nanoparticulate TiO2 and Al2O3 materials with 4-fluorophenylboronic acid is investigated in order to both evaluate the novel surface modification schemes and develop spectroscopic labels for surface characterization. The chemistry of the modification is followed on all these surfaces using X-ray photoelectron spectroscopy, multinuclear (11B, 19F, and 13C) solid-state and solution NMR, and infrared spectroscopy to determine the binding modes of this compound using boron and fluorine as probe atoms. Density functional theory model calculations are utilized to visualize predicted surface species and to interpret the results of spectroscopic measurements. A comparison is made among TiO2 rutile, TiO2 anatase, and γ-Al2O3. On all three materials, the modification proceeds via the boronic functional groups, with metal oxide-controlled surface chemistry. The bonding configuration depends on the material and is dominated by a monodentate species for titania and by bidentate species for alumina. The surface structures determined to form on all the oxide semiconductors investigated suggest that sensitization or monolayer doping approaches with a well-defined chemical interaction via a boronic functionality can be developed.Item Authentication of edible oils using an infrared spectral library and digital sample sets: A feasibility study(Journal of Chemometrics, 2023-03-19) Sota-Uba, Isio; White, Collin G.; Booksh, Karl; Lavine, Barry K.A potential method to determine whether two varieties of edible oils can be differentiated by Fourier transform infrared (FTIR) spectroscopy is proposed using digitally generated data of adulterated edible oils from an infrared (IR) spectral library. The first step is the evaluation of digitally blended data sets. Specifically, IR spectra of adulterated edible oils are computed from digitally blending experimental data of the IR spectra of an edible oil and the corresponding adulterant using the appropriate mixing coefficients to achieve the desired level of adulteration. To determine whether two edible oils can be differentiated by FTIR spectroscopy, pure IR spectra of the two edible oils are compared with IR spectra of two edible oils digitally mixed using a genetic algorithm for pattern recognition to solve a ternary classification problem. If the IR spectra of the two edible oils and their binary mixtures are differentiable from principal component plots of the spectral data, then differences between the IR spectra of these two edible oils are of sufficient magnitude to ensure that a reliable classification by FTIR spectroscopy can be obtained. Using this approach, the feasibility of authenticating edible oils such as extra virgin olive oil (EVOO) directly from library spectra is demonstrated. For this study, both digital and experimental data are combined to generate training and validation data sets to assess detection limits in FTIR spectroscopy for the adulterants.Item Calcium Substitution in Rare-earth Metal Germanides with the Gd5Si4 Type Structure(Journal of Inorganic and General Chemistry, 2022-02-23) Suen, Nian-Tzu; Bobev, SvilenAn extended series of rare-earth metal calcium germanides have been synthesized and structurally characterized. The compounds have the general formula RE5−xCaxGe4 (1.5Item Calculation of chemical-shift tensors of heavy nuclei: a DFT/ZORA investigation of 199Hg chemical-shift tensors in solids, and the effects of cluster size and electronic-state approximations(Royal Society of Chemistry, 2014-06-02) Alkan, Fahri; Dybowski, Cecil; Fahri Alkan and C. Dybowski; Alkan, Fahri; Dybowski, C.Calculations of the nuclear magnetic resonance chemical-shielding tensors of a suite of mercury-containing materials using various cluster models for the structures provide a stringent test of the procedures for forming models and for calculation with various methods. The inclusion of higher co-ordination shells in the molecular clusters permits quantum chemical calculations of 199Hg chemical-shielding tensor elements within 3% of the experimental values. We show that it is possible to reduce the size of computationally expensive molecular-cluster calculations with limited effect on calculated NMR parameters by carefully introducing the frozen core approximation. The importance of the relativistic Hamiltonian for accurate predictions of chemical-shielding values is demonstrated within the molecular cluster approach. The results demonstrate that careful design of a cluster to represent the solid-state structure, inclusion of relativistic components in the Hamiltonian at least at the spin–orbit level, and judicious use of approximations are essential to obtain good agreement with experimental results.Item Chemical-shift tensors of heavy nuclei in network solids: a DFT/ZORA investigation of 207Pb chemical-shift tensors using the bond-valence method(Royal Society of Chemistry, 2015-09-02) Alkan, Fahri; Dybowski, Cecil; Fahri Alkan and C. Dybowski; Alkan, Fahri; Dybowski, CecilCluster models are used in calculation of 207Pb NMR magnetic-shielding parameters of α-PbO, β-PbO, Pb3O4, Pb2SnO4, PbF2, PbCl2, PbBr2, PbClOH, PbBrOH, PbIOH, PbSiO3, and Pb3(PO4)2. We examine the effects of cluster size, method of termination of the cluster, charge on the cluster, introduction of exact exchange, and relativistic effects on calculation of magnetic-shielding tensors with density functional theory. Proper termination of the cluster for a network solid, including approximations such as compensation of charge by the bond-valence (BV) method, is essential to provide results that agree with experiment. The inclusion of relativistic effects at the spin–orbit level for such heavy nuclei is an essential factor in achieving agreement with experiment.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 Chemometric Software supporting NSF Project Variable Selection for Remedying the Effects of Uncontrolled Variation in Data Driven Predictions(Steven D. Brown, 2019-09-15) Poerio, Dominic V.; Kneale, Casey; Brown, Steven D.Item Cholesterol-substituted 3,4-ethylenedioxythiophene (EDOT-MA-cholesterol) and Poly(3,4-ethylenedioxythiophene) (PEDOT-MA-cholesterol)(Giant, 2023-05-23) Wu, Yuhang; Nagane, Samadhan S.; Baugh, Quintin; Lo, Chun-Yuan; Chhatre, Shrirang S.; Lee, Junghyun; Sitarik, Peter; Kayser, Laure V.; Martin, David C.Cholesterol is a rigid, crystalline, non-polar natural substance that exists in animal blood and cell membranes. Some of its derivatives are known to form ordered liquid crystalline mesophases under suitable conditions. In this work, we carefully examined the influence of cholesterol substitution on the characteristics of 3,4-ethylenedioxythiophene (EDOT-MA-cholesterol) and its corresponding polymer poly(3,4-ethylenedioxythiophene) (PEDOT-MA-cholesterol) synthesized by both chemical and electrochemical polymerization. We found evidence for an ordered lamellar (smectic-like) structure in the EDOT-MA-cholesterol monomer by differential scanning calorimetry (DSC), polarized optical microscopy (POM), and X-ray diffraction techniques. The ordered phase was observed to form on cooling from the isotropic melt at about 80 °C. Due to the insulating and bulky cholesterol side group on the EDOT monomer, we found that there was a maximum charge density for electrodeposition at ∼ 0.155 C.cm−2. A series of electrodepositions were performed from 0 to 0.155 C.cm−2 for probing the change of the charge transport with more charges used for the electrodeposition. We found that the impedance increased in the high-frequency range (above 104 Hz) and decreased in the low-frequency range (below 102 Hz). Three equivalent circuit models were proposed for fitting impedance data at different charge densities for a better understanding of the film growth process. The suppressed cyclic voltammogram (CV) of PEDOT-MA-cholesterol showed that the charge storage capability was essentially eliminated in the thickest films. The limited doping of the films was corroborated by their diminished electrochromic behavior, polaron-dominating absorption in UV-vis, overoxidized S 2p X-ray Photoelectron Spectroscopy (XPS) signal of electrodeposited films, and proton Nuclear Magnetic Resonance (1H NMR) of chemically polymerized samples. Dense film morphologies were confirmed by scanning electron microscopy (SEM). Grazing incident X-ray diffraction (GIWAXS) indicated the disrupted stacking of conjugated chains, which correlated with the decreased conductivity of the PEDOT-MA-cholesterol films. The measurement of the electrical conductivity gave a value of around 3.30 × 10−6 S.cm−1 which is about six orders of magnitude lower than has been seen in PEDOT (∼3 S.cm-1). Graphical abstract available at: https://doi.org/10.1016/j.giant.2023.100163Item Comparing spin injection in Fe75Co25/Bi2Te3 at GHz and optical excitations(Applied Physics Letters, 2023-02-13) Sharma, Vinay; Nepal, Rajeev; Wu, Weipeng; Pogue, E. A.; Kumar, Ravinder; Kolagani, Rajeswari; Gundlach, Lars; Jungfleisch, M. Benjamin; Budhani, Ramesh C.Spin-to-charge conversion (S2CC) processes in thin-film heterostructures have attracted much attention in recent years. Here, we describe the S2CC in a 3D topological insulator Bi2Te3 interfaced with an epitaxial film of Fe75Co25. The quantification of spin-to-charge conversion is made with two complementary techniques: ferromagnetic resonance based inverse spin Hall effect (ISHE) at GHz frequencies and femtosecond light-pulse induced emission of terahertz (THz) radiation. The role of spin rectification due to extrinsic effects like anisotropic magnetoresistance (AMR) and planar Hall effects (PHE) is pronounced at the GHz timescale, whereas the THz measurements do not show any detectible signal, which could be attributed to AMR or PHE. This result may be due to (i) homodyne rectification at GHz, which is absent in THz measurements and (ii) laser-induced thermal spin current generation and magnetic dipole radiation in THz measurements, which is completely absent in GHz range. The converted charge current has been analyzed using the spin diffusion model for the ISHE. We note that regardless of the differences in timescales, the spin diffusion length in the two cases is comparable. Our results aid in understanding the role of spin pumping timescales in the generation of ISHE signals.Item Conformationally Strained trans-Cyclooctene (sTCO) Enables the Rapid Construction of F-18-PET Probes via Tetrazine Ligation(Ivyspring International Publisher, 4/12/16) Wang,Mengzhe; Svatunek,Dennis; Rohlfing,Katarina; Liu,Yu; Wang,Hui; Giglio,Ben; Yuan,Hong; Wu,Zhanghong; Li,Zibo; Fox,Joseph; Mengzhe Wang, Dennis Svatunek, Katarina Rohlfing, Yu Liu, Hui Wang, Ben Giglio, Hong Yuan, Zhanghong Wu, Zibo Li, and Joseph Fox; Liu, Yun; Fox, Joseph MThe bioorthogonal reaction between tetrazines and trans-cyclooctenes is a method for the rapid construction of F-18 probes for PET imaging. Described here is a second generation F-18-labeling system based on a conformationally strained trans-cyclooctene (sTCO)-a dienophile that is approximately 2 orders of magnitude more reactive than conventional TCO dienophiles. Starting from a readily prepared tosylate precursor, an F-18 labeled sTCO derivative (F-18-sTCO) could be synthesized in 29.3 +/- 5.1% isolated yield and with high specific activity. Tetrazine ligation was carried out with a cyclic RGD-conjugate of a diphenyl-s-tetrazine analogue (RGD-Tz) chosen from a diene class with an excellent combination of fast reactivity and stability both for the diene as well as the Diels-Alder adduct. For both the tetrazine and the sTCO, mini-PEG spacers were included to enhance solubility and improve the in vivo distribution profile of the resulting probe. Extremely fast reactivity (up to 2.86 x 10(5) M(-1)s(-1) at 25 degrees C in water) has been observed in kinetic studies in the reaction of sTCO with diphenyl-s-tetrazine derivatives. A kinetic study on sTCO diastereomers in 55:45 MeOH:water showed that the syn-diastereomer displayed slightly faster reactivity than the anti-diastereomer. An F-18-sTCO conjugate with RGD-Tz demonstrated prominent and persistent tumor uptake in vivo with good tumor-to-background contrast. Unlike most radiolabeled RGD peptides, the tumor uptake of this PET agent increased from 5.3 +/- 0.2% ID/g at 1 h post injection (p.i.), to 8.9 +/- 0.5% ID/g at 4 h p.i., providing evidence for prolonged blood circulation. These findings suggest that tetrazine ligations employing F-18-sTCO should serve as a powerful and general platform for the rapid construction of peptide or protein derived PET agents.Item Coordination geometry of lead carboxylates – spectroscopic and crystallographic evidence(Royal Society of Chemistry, 2014-12-14) Catalano, Jaclyn; Murphy, Anna; Yao, Yao; Yap, Glenn P. A.; Zumbulyadis, Nicholas; Centeno, Silvia A.; Dybowski, Cecil; Jaclyn Catalano, Anna Murphy, Yao Yao, Glenn P. A. Yap, Nicholas Zumbulyadis, Silvia A. Centeno and Cecil Dybowski; Catalano, Jaclyn; Murphy, Anna; Yao, Yao; Yap, Glenn P. A.; Dybowski, CecilDespite their versatility, only a few single-crystal X-ray structures of lead carboxylates exist, due to difficulties with solubility. In particular, the structures of long-chain metal carboxylates have not been reported. The lone electron pair in Pb(II) can be stereochemically active or inactive, leading to two types of coordination geometries commonly referred to as hemidirected and holodirected structures, respectively. We report 13C and 207Pb solid-state NMR and infrared spectra for a series of lead carboxylates, ranging from lead hexanoate (C6) to lead hexadecanoate (C18). The lead carboxylates based on consistent NMR parameters can be divided in two groups, shorter-chain (C6, C7, and C8) and longer-chain (C9, C10, C11, C12, C14, C16, and C18) carboxylates. This dichotomy suggests two modes of packing in these solids, one for the short-chain lead carboxylates and one for long-chain lead carboxylates. The consistency of the 13C and 207Pb NMR parameters, as well as the IR data, in each group suggests that each motif represents a structure characteristic of each subgroup. We also report the single-crystal X-ray diffraction structure of lead nonanoate (C9), the first single-crystal structure to have been reported for the longer-chain subgroup. Taken together the evidence suggests that the coordination geometry of C6–C8 lead carboxylates is hemidirected, and that of C9–C14, C16 and C18 lead carboxylates is holodirected.Item Coupling Novel Probes with Molecular Localization Microscopy Reveals Cell Wall Homeostatic Mechanisms in Staphylococcus aureus(ACS Chemical Biology, 2022-11-22) Lund, Victoria A.; Gangotra, Haneesh; Zhao, Zhen; Sutton, Joshua A. F.; Wacnik, Katarzyna; DeMeester, Kristen; Liang, Hai; Santiago, Cintia; Grimes, Catherine Leimkuhler; Jones, Simon; Foster, Simon J.Bacterial cell wall peptidoglycan is essential for viability, and its synthesis is targeted by antibiotics, including penicillin. To determine how peptidoglycan homeostasis controls cell architecture, growth, and division, we have developed novel labeling approaches. These are compatible with super-resolution fluorescence microscopy to examine peptidoglycan synthesis, hydrolysis, and the localization of the enzymes required for its biosynthesis (penicillin binding proteins (PBPs)). Synthesis of a cephalosporin-based fluorescent probe revealed a pattern of PBPs at the septum during division, supporting a model of dispersed peptidoglycan synthesis. Metabolic and hydroxylamine-based probes respectively enabled the synthesis of glycan strands and associated reducing termini of the peptidoglycan to be mapped. Foci and arcs of reducing termini appear as a result of both synthesis of glycan strands and glucosaminidase activity of the major peptidoglycan hydrolase, SagB. Our studies provide molecular level details of how essential peptidoglycan dynamics are controlled during growth and division.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 Cr−Cr Quintuple Bonds: Ligand Topology and Interplay Between Metal−Metal and Metal−Ligand Bonding(American Chemical Society, 2015-10-26) Falceto, Andrés; Theopold, Klaus H.; Alvarez, Santiago; Andrés Falceto, Klaus H. Theopold, and Santiago Alvarez; Theopold, Klaus H.Chromium–chromium quintuple bonds seem to be approaching the lower limit for their bond distances, and this computational density functional theory study tries to explore the geometrical and electronic factors that determine that distance and to find ways to fine-tune it via the ligand choice. While for monodentate ligands the Cr–Cr distance is predicted to shorten as the Cr–Cr–L bond angle increases, with bridging bidentate ligands the trend is the opposite, since those ligands with a larger number of spacers between the donor atoms favor larger bond angles and longer bond distances. Compared to Cr–Cr quadruple bonds, the quintuple bonding in Cr2L2 compounds (with L a bridging bidentate N-donor ligand) involves a sophisticated mechanism that comprises a positive pyramidality effect for the σ and one π bond, but a negative effect for one of the δ bonds. Moreover, the shorter Cr–Cr distances produce a mismatch of the bridging ligand lone pairs and the metal acceptor orbitals, which results in a negative correlation of the Cr–Cr and Cr–N bond distances in both experimental and calculated structures.Item Cyclophilin A stabilizes the HIV-1 capsid through a novel non-canonical binding site(Nature Publishing Group, 2016-03-04) Liu, Chuang; Perilla, Juan R.; Ning, Jiying; Lu, Manman; Hou, Guangjin; Ramalho, Ruben; Himes, Benjamin A.; Zhao, Gongpu; Bedwell, Gregory J.; Byeon, In-Ja; Ahn, Jinwoo; Gronenborn, Angela M.; Prevelige, Peter E.; Rousso, Itay; Aiken, Christopher; Polenova, Tatyana; Schulten, Klaus; Zhang, Peijun; Chuang Liu, Juan R. Perilla, Jiying Ning, Manman Lu, Guangjin Hou, Ruben Ramalho, Benjamin A. Himes, Gongpu Zhao, Gregory J. Bedwell, In-Ja Byeon, Jinwoo Ahn, Angela M. Gronenborn, Peter E. Prevelige, Itay Rousso, Christopher Aiken, Tatyana Polenova, Klaus Schulten & Peijun Zhang; Lu, Manman; Hou, Guangjin; Polenova, TatyanaThe host cell factor cyclophilin A (CypA) interacts directly with the HIV-1 capsid and regulates viral infectivity. Although the crystal structure of CypA in complex with the N-terminal domain of the HIV-1 capsid protein (CA) has been known for nearly two decades, how CypA interacts with the viral capsid and modulates HIV-1 infectivity remains unclear. We determined the cryoEM structure of CypA in complex with the assembled HIV-1 capsid at 8-Å resolution. The structure exhibits a distinct CypA-binding pattern in which CypA selectively bridges the two CA hexamers along the direction of highest curvature. EM-guided all-atom molecular dynamics simulations and solid-state NMR further reveal that the CypA-binding pattern is achieved by single-CypA molecules simultaneously interacting with two CA subunits, in different hexamers, through a previously uncharacterized non-canonical interface. These results provide new insights into how CypA stabilizes the HIV-1 capsid and is recruited to facilitate HIV-1 infection.