Department of Chemistry and Biochemistry

Permanent URI for this community

https://udspace.udel.edu/handle/19716/24438

Visit the Department of Chemistry and Biochemistry for more information. The UDSpace community for this department contains open-access research materials created by members of this department.

Browse

Now showing 1 - 20 of 27

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.
Iron Oxidation by a Fused Cytochrome-Porin Common to Diverse Iron-Oxidizing Bacteria
(mBio, 2021-07-27) Keffer, Jessica L.; McAllister, Sean M.; Garber, Arkadiy I.; Hallahan, Beverly J.; Sutherland, Molly C.; Rozovsky, Sharon; Chan, Clara S.
Iron (Fe) oxidation is one of Earth’s major biogeochemical processes, key to weathering, soil formation, water quality, and corrosion. However, our understanding of microbial contribution is limited by incomplete knowledge of microbial iron oxidation mechanisms, particularly in neutrophilic iron oxidizers. The genomes of many diverse iron oxidizers encode a homolog to an outer membrane cytochrome (Cyc2) shown to oxidize iron in two acidophiles. Phylogenetic analyses show Cyc2 sequences from neutrophiles cluster together, suggesting a common function, though this function has not been verified in these organisms. Therefore, we investigated the iron oxidase function of heterologously expressed Cyc2 from a neutrophilic iron oxidizer Mariprofundus ferrooxydans PV-1. Cyc2PV-1 is capable of oxidizing iron, and its redox potential is 208 ± 20 mV, consistent with the ability to accept electrons from Fe2+ at neutral pH. These results support the hypothesis that Cyc2 functions as an iron oxidase in neutrophilic iron-oxidizing organisms. The results of sequence analysis and modeling reveal that the entire Cyc2 family shares a unique fused cytochrome-porin structure, with a defining consensus motif in the cytochrome region. On the basis of results from structural analyses, we predict that the monoheme cytochrome Cyc2 specifically oxidizes dissolved Fe2+, in contrast to multiheme iron oxidases, which may oxidize solid Fe(II). With our results, there is now functional validation for diverse representatives of Cyc2 sequences. We present a comprehensive Cyc2 phylogenetic tree and offer a roadmap for identifying cyc2/Cyc2 homologs and interpreting their function. The occurrence of cyc2 in many genomes beyond known iron oxidizers presents the possibility that microbial iron oxidation may be a widespread metabolism.
Photo-activatable Ub-PCNA probes reveal new structural features of the Saccharomyces cerevisiae Polη/PCNA complex
(Nucleic Acids Research, 2021-08-14) Shen, Siqi; Davidson, Gregory A; Yang, Kun; Zhuang, Zhihao
The Y-family DNA polymerase η (Polη) is critical for the synthesis past damaged DNA nucleotides in yeast through translesion DNA synthesis (TLS). TLS is initiated by monoubiquitination of proliferating cell nuclear antigen (PCNA) and the subsequent recruitment of TLS polymerases. Although individual structures of the Polη catalytic core and PCNA have been solved, a high-resolution structure of the complex of Polη/PCNA or Polη/monoubiquitinated PCNA (Ub-PCNA) still remains elusive, partly due to the disordered Polη C-terminal region and the flexibility of ubiquitin on PCNA. To circumvent these obstacles and obtain structural insights into this important TLS polymerase complex, we developed photo-activatable PCNA and Ub-PCNA probes containing a p-benzoyl-L-phenylalanine (pBpa) crosslinker at selected positions on PCNA. By photo-crosslinking the probes with full-length Polη, specific crosslinking sites were identified following tryptic digestion and tandem mass spectrometry analysis. We discovered direct interactions of the Polη catalytic core and its C-terminal region with both sides of the PCNA ring. Model building using the crosslinking site information as a restraint revealed multiple conformations of Polη in the polymerase complex. Availability of the photo-activatable PCNA and Ub-PCNA probes will also facilitate investigations into other PCNA-containing complexes important for DNA replication, repair and damage tolerance.
Light and microwave driven spin pumping across FeGaB–BiSb interface
(Physical Review Materials, 2021-12-16) Sharma, Vinay; Wu, Weipeng; Bajracharya, Prabesh; To, Duy Quang; Johnson, Anthony; Janotti, Anderson; Bryant, Garnett W.; Gundlach, Lars; Jungfleisch, M. Benjamin; Budhani, Ramesh C.
Three-dimensional (3D) topological insulators (TIs) with large spin Hall conductivity have emerged as potential candidates for spintronic applications. Here, we report spin to charge conversion in bilayers of amorphous ferromagnet (FM) Fe78Ga13B9 (FeGaB) and 3D TI Bi85Sb15 (BiSb) activated by two complementary techniques: spin pumping and ultrafast spin-current injection. DC magnetization measurements establish the soft magnetic character of FeGaB films, which remains unaltered in the heterostructures of FeGaB-BiSb. Broadband ferromagnetic resonance (FMR) studies reveal enhanced damping of precessing magnetization and large value of spin mixing conductance (5.03×1019m–2) as the spin angular momentum leaks into the TI layer. Magnetic field controlled bipolar DC voltage generated across the TI layer by inverse spin Hall effect is analyzed to extract the values of spin Hall angle and spin diffusion length of BiSb. The spin pumping parameters derived from the measurements of the femtosecond light-pulse-induced terahertz emission are consistent with the result of FMR. The Kubo-Bastin formula and tight-binding model calculations shed light on the thickness-dependent spin-Hall conductivity of the TI films, with predictions that are in remarkable agreement with the experimental data. Our results suggest that room temperature deposited amorphous and polycrystalline heterostructures provide a promising platform for creating novel spin orbit torque devices.
Experimental and Theoretical Study on the Substitution Patterns in Lithium Germanides: The Case of Li15Ge4 vs Li14ZnGe4
(European Journal of Inorganic Chemistry, 2021-12-23) Osman, Hussien H.; Bobev, Svilen
A new ternary lithium zinc germanide, Li13.83Zn1.17(2)Ge4, was synthesized by a high-temperature solid state reaction of the respective elements. The crystal structure was determined by single-crystal X-ray diffraction methods. The new phase crystallizes in the body-centered cubic space group /43d 3d (no. 220) with unit cell parameter of 10.695(1) Å. The crystal structure refinements show that the parent Li15Ge4 structure is stabilized as Li15−xZnxGe4 (x≈1) via random substitution of Li atoms by the one-electron-richer atoms of the element Zn, by virtue of which the number of valence electrons increases, leading to a more electronically stable system. The substitution effects in the parent Li15Ge4 structure were investigated through both theory and experiment, which confirm that the Zn atoms in this structure prefer to occupy only one of the two available crystallographic sites for Li. The preferred substitution pattern established from experimental results is supported by DFT electronic structure calculations, which also explore the subtleties of the chemical bonding and the electronic properties of the title compounds.
Mirror-plane disorder in a nickel chloride Schiff base complex: a suitable case study for crystallographic instruction
(Acta Crystallographica Section C: Structural Chemistry, 2022-01-27) Hsuan, Chang; Chen, Wen-Ching; Shen, Jiun-Shian; Ong, Tiow-Gan; Wang, Vincent C.-C.; Yap, Glenn P. A.
The nickel chloride complex of the Schiff base N2,N20-propanediylbis(2,3-butanedione-2-imine-3-oxime), namely, chlorido(3,9-dimethylundeca-3,8-diene-2,10-dione 10-oxime 2-oximato- 4N,N0,N00,N000)nickel(II), [NiCl(C 11 H19 N4 O2 )], at 100 K crystallizes in the orthorhombic space group Cmce. The structure exhibits mirror disorder of the main molecule that is not present in the bromide analogue. The relatively small number of unique reflections in the data set and the disorder imposed by the crystallographic mirror plane present a challenging educational case study.
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, Svilen
An extended series of rare-earth metal calcium germanides have been synthesized and structurally characterized. The compounds have the general formula RE5−xCaxGe4 (1.5
Natural Product Synthesis by Intramolecular Alkylidene Carbene C−H Insertion
(European Journal of Organic Chemistry, 2022-03-15) Taber, Douglass F.
Direct functionalization of unactivated C−H bonds is of increasing importance in organic synthesis. Of the many methods that have been developed, intramolecular alkylidene C−H insertion, proceeding with retention of absolute configuration, is among the most versatile. This Review explores all examples of the use of intramolecular alkylidene C−H insertion in natural product synthesis.
A molecular substitutional disorder case study suitable for instruction: L2CrII(THF)/L2[(trimethylsilyl)methyl]CrIII (L is 2,5-bis{[(2,6-diisopropylphenyl)imino]methyl}pyrrol-1-ide)
(Acta Crystallographica Section C: Structural Chemistry, 2022-04-06) Salisbury, Brian A.; Young, John F.; Theopold, Klaus H.; Yap, Glenn P. A.
A solution of CrII and CrIII complexes, bis(2,5-bis{[(2,6-diisopropylphenyl)imino]methyl}pyrrol-1-ido)(tetrahydrofuran)chromium(II)–bis(2,5-bis{[(2,6-diisopropylphenyl)imino]methyl}pyrrol-1-ido)[(trimethylsilyl)methyl]chromium(III) (0.88/0.12), [Cr(C30H38N3)2(C4H8O)]0.88[Cr(C30H38N3)2(C4H11Si)]0.12 or L2CrII(THF)/L2[(trimethylsilyl)methyl]CrIII (L = 2,5-bis{[(2,6-diisopropylphenyl)imino]methyl}pyrrol-1-ide and THF is tetrahydrofuran), in pentane crystallizes in the monoclinic space group P21/c. The structure obtained shows most of the atoms coincident but with THF disordered with the (trimethylsilyl)methyl ligand. Structures with this disorder, involving more than two or three atoms, seem to appear rarely in the literature; however, in this case, the data set is ideal for the crystallographic instruction of molecular substitution disorder.
Electronically Conductive Hydrogels by in Situ Polymerization of a Water-Soluble EDOT-Derived Monomer
(Advanced Engineering Materials, 2022-05-13) Nguyen, Dan My; Wu, Yuhang; Nolin, Abigail; Lo, Chun-Yuan; Guo, Tianzheng; Dhong, Charles; Martin, David C.; Kayser, Laure V.
Electronically conductive hydrogels have gained popularity in bioelectronic interfaces because their mechanical properties are similar to biological tissues, potentially preventing scaring in implanted electronics. Hydrogels have low elastic moduli, due to their high water content, which facilitates their integration with biological tissues. To achieve electronically conductive hydrogels, however, requires the integration of conducting polymers or nanoparticles. These “hard” components increase the elastic modulus of the hydrogel, removing their desirable compatibility with biological tissues, or lead to the heterogeneous distribution of the conductive material in the hydrogel scaffold. A general strategy to transform hydrogels into electronically conductive hydrogels without affecting the mechanical properties of the parent hydrogel is still lacking. Herein, a two-step method is reported for imparting conductivity to a range of different hydrogels by in-situ polymerization of a water-soluble and neutral conducting polymer precursor: 3,4–ethylenedioxythiophene diethylene glycol (EDOT-DEG). The resulting conductive hydrogels are homogenous, have conductivities around 0.3 S m−1, low impedance, and maintain an elastic modulus of 5–15 kPa, which is similar to the preformed hydrogel. The simple preparation and desirable properties of the conductive hydrogels are likely to lead to new materials and applications in tissue engineering, neural interfaces, biosensors, and electrostimulation.
Solvation stabilizes intercarbonyl n→π* interactions and polyproline II helix
(Physical Chemistry Chemical Physics, 2022-05-24) Zondlo, Neal J.
n→π* interactions between consecutive carbonyls stabilize the α-helix and polyproline II helix (PPII) conformations in proteins. n→π* interactions have been suggested to provide significant conformational biases to the disordered states of proteins. To understand the roles of solvation on the strength of n→π* interactions, computational investigations were conducted on a model n→π* interaction, the twisted-parallel-offset formaldehyde dimer, as a function of explicit solvation of the donor and acceptor carbonyls, using water and HF. In addition, the effects of urea, thiourea, guanidinium, and monovalent cations on n→π* interaction strength were examined. Solvation of the acceptor carbonyl significantly strengthens the n→π* interaction, while solvation of the donor carbonyl only modestly weakens the n→π* interaction. The n→π* interaction strength was maximized with two solvent molecules on the acceptor carbonyl. Urea stabilized the n→π* interaction via simultaneous engagement of both oxygen lone pairs on the acceptor carbonyl. Solvent effects were further investigated in the model peptides Ac-Pro-NMe2, Ac-Ala-NMe2, and Ac-Pro2-NMe2. Solvent effects in peptides were similar to those in the formaldehyde dimer, with solvation of the acceptor carbonyl increasing n→π* interaction strength and resulting in more compact conformations, in both the proline endo and exo ring puckers, as well as a reduction in the energy difference between these ring puckers. Carbonyl solvation leads to an energetic preference for PPII over both the α-helix and β/extended conformations, consistent with experimental data that protic solvents and protein denaturants both promote PPII. Solvation of the acceptor carbonyl weakens the intraresidue C5 hydrogen bond that stabilizes the β conformation.
Visualization of Confusion Matrices with Network Graphs
(Journal of Chemometrics, 2022-07-05) Gilbraith, William E.; Celani, Caelin P.; Booksh, Karl S.
The use of network analysis as a means of visualizing the off-diagonal (misclassified) elements of a confusion matrix is demonstrated and the potential to use the network graphs as a guide for developing hierarchical classification models is presented. A very brief summary of graph theory is described. This is followed by an explanation and code with examples of how these networks can then be used for visualization of confusion matrices. The use of network graphs to provide insight into differing model performance is also addressed.
A one-shot double-slice selection NMR method for biphasic systems
(Physical Chemistry Chemical Physics, 2022-07-18) Doolittle Catlin, Kaitlyn; Simmons, Julia; Bai, Shi
We propose a new and robust one-shot double-slice selection experiment to detect 1H NMR signals of biphasic systems simultaneously. The resultant spectrum contains opposite-phased peaks representing the chemical species from the two phases, respectively.
Rare-earth Metal Substitution in Calcium Germanides with the Tetragonal Cr5B3 Type Structure
(Journal of Inorganic and General Chemistry, 2022-07-20) Suen, Nian-Tzu; Bobev, Svilen
Calcium germanides with two mid-late rare-earth metals, Ca5−xGdxGe3 and Ca5−xTbxGe3 (x≈0.1−0.2), have been synthesized and structurally characterized. Additionally, a lanthanum-rich germanide with calcium substitutions, La5−xCaxGe3 (x≈0.5) has also been identified. The three structures have been established from single-crystal X-ray diffraction methods and confirmed to crystallize with the Cr5B3-type in the tetragonal space group I4/mcm (no. 140; Z=4; Pearson symbol tI32), where part of the germanium atoms are interconnected into Ge2-dimers, formally [Ge2]6−. Rare-earth metal and calcium atoms are arranged in distorted trigonal prisms, square-antiprisms and cubes, centered by Ge or rare-earth/calcium metal atoms. These studies show that the amount of trivalent rare-earth metal atoms substituting divalent calcium atoms is in direct correlation with the lengths of the Ge−Ge bond within the Ge2-dimers, with distance varying between 2.58 Å in Ca5−xGdxGe3 and 2.75 Å in La5−xCaxGe3. Such an elongation of the Ge−Ge bond is consistent with the notion that the parent Ca5Ge3 Zintl phase (e. g. (Ca2+)5[Ge2]6−[Ge4−]) is being driven out of the ideal valence electron count and further reduced. In this context, this work demonstrates the ability of the germanides with the Cr5B3 structure type to accommodate substitutions and wider valence electron count while maintaining their global structural integrity.
Raw Data for sp-2022-000499.csv
(2022-07-26) Higgins, Devon N.; Taylor, Michael S. Jr.; Krasnomowitz, Justin M.; Johnston, Murray V.
The effects of composition, size, and phase state on ultrafine seed particle growth by ⍺-pinene ozonolysis were determined from diameter growth measurements after a fixed reaction time in a flow tube reactor. Modeling time-dependent particle growth under a given set of conditions allowed the reaction growth factor (GF) to be determined, which is defined as the fraction of ⍺-pinene molecules that react to give a product that grows the particles. Growth factors were compared for initial seed particle diameters of 40 nm, 60 nm, and 80 nm that were composed of freshly formed ⍺-pinene SOA, effloresced am-monium sulfate, and deliquesced ammonium sulfate. Overall, SOA seed particles gave the lowest growth factors. Efflo-resced ammonium sulfate particles gave somewhat higher growth factors and showed a slight dependence on relative humidi-ty. Deliquesced ammonium sulfate particles gave the highest growth factors. Seed particle size dependencies suggested that both surface- and volume- limited reactions may contribute to growth. Overall, the growth factors were found to vary by more than 4x across the reaction conditions studied. The results highlight the crucial role that seed particle characteristics play in determining particle growth rates in a size range relevant to formation of cloud condensation nuclei.
Dynamic regulation of Zn(II) sequestration by calgranulin C
(Protein Science, 2022-08-13) Wang, Qian; Kuci, Deniz; Bhattacharya, Shibani; Hadden-Perilla, Jodi A.; Gupta, Rupal
Calgranulin C performs antimicrobial activity in the human immune response by sequestering Zn(II). This biological function is afforded with the aid of two structurally distinct Ca(II)-binding EF hand motifs, wherein one of which bears an unusual amino acid sequence. Here, we utilize solution state NMR relaxation measurements to investigate the mechanism of Ca(II)-modulated enhancement of Zn(II) sequestration by calgranulin C. Using C13/N15 CPMG dispersion experiments we have measured pH-dependent major and minor state populations exchanging on micro-to-millisecond timescale. This conformational exchange takes place exclusively in the Ca(II)-bound state and can be mapped to residues located in the EF-I loop and the linker between the tandem EF hands. Molecular dynamics (MD) simulations spanning nano-to-microsecond timescale offer insights into the role of pH-dependent electrostatic interactions in EF-hand dynamics. Our results suggest a pH-regulated dynamic equilibrium of conformations that explore a range of “closed” and partially “open” sidechain configurations within the Zn(II) binding site. We propose a novel mechanism by which Ca(II) binding to a non-canonical EF loop regulates its flexibility and tunes the antimicrobial activity of calgranulin C.
Graphene Absorption Enhanced by Quasi-Bound-State-in-Continuum in Long-Wavelength Plasmonic–Photonic System
(Advanced Optical Materials, 2022-09-07) Kananen, Thomas; Wiggins, Marcie; Wang, Zi; Wang, Feifan; Soman, Anishkumar; Booksh, Karl; Alù, Andrea; Gu, Tingyi
Graphene plasmonic structures can support enhanced and localized light–mater interactions within extremely small mode volumes. However, the external quantum efficiency of the resulting devices is fundamentally limited by material scattering and radiation loss. Here, such radiation loss channels are suppressed by tailoring the structure to support a symmetry-protected bound-state-in-the-continuum (BIC) system. With practical loss rates and doping level in graphene, over 90% absorption near critical coupling is expected from numerical simulation. Experimentally measured peak absorption of 68% is achieved in such a tailored graphene photonic–plasmonic system, with maximum 50% contrast to the control sample without graphene. Significant reduction of the plasmon absorption for a different spacer thickness verifies the sensitivity of the system to the quasi-BIC condition.
Proline C–H bonds as loci for proline assembly via C–H/O interactions
(ChemBioChem, 2022-09-21) Daniecki, Noah J.; Bhatt, Megh R.; Yap, Glenn P. A.; Zondlo, Neal Joseph
Proline residues within proteins lack a traditional hydrogen bond donor. However, the hydrogens of proline are all sterically accessible, with polarized C–H bonds that can be sites for molecular recognition. C–H/O interactions, between proline C–H bonds and oxygen lone pairs, have been previously identified as modes of recognition in proteins. A series of proline derivatives was synthesized, including 4R-hydroxyproline nitrobenzoate methyl ester, acylated on the proline nitrogen with bromoacetyl and glycolyl groups, and Boc-4S-(4-iodophenyl)hydroxyproline methyl amide. All three derivatives exhibited multiple close intermolecular C–H/O interactions in the crystallographic state, with H•••O distances as close as 2.3 Å. These observed distances are well below the 2.72 Å sum of the van der Waals radii of H and O. We further analyzed the role of C–H/O interactions in all previously crystallized derivatives of these amino acids, and found that all 26 structures exhibited close intermolecular C–H/O interactions. Finally, we analyzed all proline residues in the Cambridge Structural Database. The majority of these structures exhibited intermolecular C–H/O interactions at proline C–H bonds, suggesting that C–H/O interactions are an inherent and important mode for recognition of and higher-order assembly at proline residues. Due to steric accessibility and multiple polarized C–H bonds, proline residues are uniquely positioned as sites for binding and recognition via C–H/O interactions.
Recent Developments with Icetexane Natural Products
(Chemistry and Biodiversity, 2022-10-10) Naeini, Ali Amiri; Ziegelmeier, Alexandre A.; Chain, William J.
Icetexane diterpenoids are a diverse family of natural products sourced from several species of terrestrial plants. Icetexanes exhibit a broad array of biological activities and together with their complex 6-7-6 tricyclic scaffolds, they have piqued the interest of synthetic organic chemists, natural products chemists, and biological investigators over the past four decades and were reviewed 13 years ago. This review summarizes icetexane natural products isolated since 2009, provides an overview of new synthetic approaches to the icetexane problem, and proposes an additional classification of icetexanes based on novel structures that are unlike previously isolated materials.
Enhanced thermoelectric performance in the zintl antimonides (Ca,RE)9Cd4Sb9 (RE = rare-earth metal). Synergy between increased structural complexity and drive towards optimized chemical bonding
(Materials Today Advances, 2022-10-27) Ogunbunmi, M. O.; Baranets, S.; Bobev, S.
The interplay of structural complexity, high carrier mobility, and high density of states effective mass can play a pivotal role in achieving enhanced thermoelectric (TE) performance in candidate materials. In this regard, the Zintl phases represent a class of compounds that are susceptible to harboring these key ingredients. This, in addition to their amenability to various forms of chemical substitution mechanisms makes them a good choice of systems to explore systematically. Here we demonstrate the role-play of these ingredients in achieving excellent TE properties on single-crystals of Ca9–xREyCd4+δSb9 (RE = Ce, Pr, Nd, Sm, Gd, Tb; x ≈ 0.5–0.8, y ≈ 0.5–0.7, δ ≈ 0.25). These phases represent a new addition to the “9–4–9” family with intricate chemical bonding arising from both a purposely introduced disorder on Ca sites and the inherent presence of interstitial Cd positions. Many of the newly synthesized and characterized phases show moderate values of the Seebeck coefficient, lying in the range of 71–116 μV/K at 600 K and evolving as degenerate semiconductors. Simultaneously, the electrical resistivity ρ(T) of the measured samples can be as low as 0.18 mΩ cm at this temperature. As a result, the observed TE power factors in the Ce-, Nd-, and Sm-samples are in the range 6–46 μW/cm.K2. For Ca9–xCexCd4+δSb9, the estimated thermoelectric quality factor B > 0.4 at 300 K, which corresponds to a figure of merit zT ≥ 1. Calculations based on the single parabolic band (SPB) model show that the optimum region for thermoelectric performance requires carrier concentration n = 2–6 × 1019 cm−3 thus providing for an open window to further tune the TE properties.

Browse

Browsing Department of Chemistry and Biochemistry by Issue Date

Results Per Page

Sort Options