VTechWorks Repository :: Browsing by Author "Slebodnick, Carla"

Browsing by Author "Slebodnick, Carla"

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Crystal structure of di-μ-chlorido-bis-[di-chlorido-bis-(methanol-κO)iridium(III)] dihydrate: a surprisingly simple chlorido-iridium(III) dinuclear complex with methanol ligands.
Merola, Joseph S.; Slebodnick, Carla; Houser, Christopher (2015-05-01)
The reaction between IrCl3·xH2O in methanol led to the formation of small amounts of the title compound, [Ir2Cl6(CH3OH)4]·2H2O, which consists of two IrCl4O2 octa-hedra sharing an edge via chloride bridges. The mol-ecule lies across an inversion center. Each octa-hedron can be envisioned as being comprised of four chloride ligands in the equatorial plane with methanol ligands in the axial positions. A lattice water mol-ecule is strongly hydrogen-bonded to the coordinating methanol ligands and weak inter-actions with coordinating chloride ligands lead to the formation of a three-dimensional network. This is a surprising structure given that, while many reactions of iridium chloride hydrate are carried out in alcoholic solvents, especially methanol and ethanol, this is the first structure of a chloridoiridium compound with only methanol ligands.
Cyclohexyl Ketone Inhibitors of Pin1 Dock in a Trans-Diaxial Cyclohexane Conformation
Xu, Guoyan G.; Slebodnick, Carla; Etzkorn, Felicia A. (PLOS, 2012-09-19)
Cyclohexyl ketone substrate analogue inhibitors (Ac–pSer-Ψ[C = OCH]-Pip–tryptamine) of Pin1, the cell cycle regulatory peptidyl-prolyl isomerase (PPIase), were designed and synthesized as potential electrophilic acceptors for the Pin1 active site Cys113 nucleophile to test a proposed nucleophilic addition-isomerization mechanism. Because they were weak inhibitors, models of all three stereoisomers were docked into the active site of Pin1. Each isomer consistently minimized to a trans-diaxial cyclohexane conformation. From this, we hypothesize that Pin1 stretches substrates into a trans-pyrrolidine conformation to lower the barrier to isomerization. Our reduced amide inhibitor of Pin1 adopted a similar trans-pyrrolidine conformation in the crystal structure. The molecular model of 1, which mimics the l-Ser-l-Pro stereochemistry, in the Pin1 active site showed a distance of 4.4 Å, and an angle of 31° between Cys113-S and the ketone carbon. The computational models suggest that the mechanism of Pin1 PPIase is not likely to proceed through nucleophilic addition.
Dissolution and Diffusion-Based Reactions within YBa2Cu3O7-x Glass Fibers
Heyl, Hanna; Yang, Shuo; Homa, Daniel S.; Slebodnick, Carla; Wang, Anbo; Pickrell, Gary R. (MDPI, 2019-12-20)
This work presents a thorough identification and analysis of the dissolution and diffusion-based reaction processes that occur during the drawing of YBa₂Cu₃O_7-x (YBCO) glass-clad fibers, using the molten-core approach, on a fiber draw tower in vacuum and in oxygen atmospheres. The results identify the dissolution of the fused silica cladding and the subsequent diffusion of silicon and oxygen into the molten YBCO core. This leads to a phase separation due to a miscibility gap which occurs in the YBCO–SiO₂ system. Due to this phase separation, silica-rich precipitations form upon quenching. XRD analyses reveal that the core of the vacuum as-drawn YBCO fiber is amorphous. Heat-treatments of the vacuum as-drawn fibers in the 800–1200 °C range show that cuprite crystallizes out of the amorphous matrix by 800 °C, followed by cristobalite by 900 °C. Heat-treatments at 1100 °C and 1200 °C lead to the formation of barium copper and yttrium barium silicates. These results provide a fundamental understanding of phase relations in the YBCO–SiO₂ glass-clad system as well as indispensable insights covering general glass-clad fibers drawn using the molten-core approach.
Double helical conformation and extreme rigidity in a rodlike polyelectrolyte
Wang, Ying; He, Yadong; Yu, Zhou; Gao, Jianwei; ten Brinck, Stephanie; Slebodnick, Carla; Fahs, Gregory B.; Zanelotti, Curt J.; Hegde, Maruti; Moore, Robert Bowen; Ensing, Bernd; Dingemans, Theo J.; Qiao, Rui; Madsen, Louis A. (Nature Publishing Group, 2019-02-18)
The ubiquitous biomacromolecule DNA has an axial rigidity persistence length of ~50 nm, driven by its elegant double helical structure. While double and multiple helix structures appear widely in nature, only rarely are these found in synthetic non-chiral macromolecules. Here we report a double helical conformation in the densely charged aromatic polyamide poly(2,2′-disulfonyl-4,4′-benzidine terephthalamide) or PBDT. This double helix macromolecule represents one of the most rigid simple molecular structures known, exhibiting an extremely high axial persistence length (~1 micrometer). We present X-ray diffraction, NMR spectroscopy, and molecular dynamics (MD) simulations that reveal and confirm the double helical conformation. The discovery of this extreme rigidity in combination with high charge density gives insight into the self-assembly of molecular ionic composites with high mechanical modulus (~ 1 GPa) yet with liquid-like ion motions inside, and provides fodder for formation of other 1D-reinforced composites. © 2019, The Author(s).
The Effect of Composition on the High-Pressure Behavior of Rare-Earth Phosphate Minerals
Heffernan, Karina May (Virginia Tech, 2016-08-02)
A comprehensive study on the effect of composition on the structural and elastic properties of MPO4 (M = Ce3+, Gd3+, Tb3+, Y3+, Sc3+) compounds has been completed. CePO4 and GdPO4 are isostructural with monazite (P21/n), and TbPO4, YPO4, and ScPO4, are isostructural with xenotime (I41/amd). Raman spectra are consistent with previous studies and high-pressure spectra showed no phase transitions up to 10 GPa under hydrostatic conditions. The spectra were used to develop Kieffer-type lattice vibrational models to calculate heat capacities of CePO4 and YPO4 and the results lie within 1-3% of experimental values. Equations of state were calculated from high-pressure single-crystal X-ray diffraction data. Bulk moduli (K0) determined from a 3rd-order Birch-Murnaghan equation of state are: 109(3) GPa for CePO4, 128.1(8) GPa for GdPO4, 141(1) GPa for TbPO4 and 166(1) GPa for ScPO4. The inverse relationship observed between K0 and the ionic radius of the RE3+ is shown to be linear. This equation can be used to predict K0 for other rare-earth phosphates. Comparison of these studies, performed under hydrostatic conditions, with previous studies show that MPO4 structures are sensitive to shear stresses created from non-hydrostatic environments. The first structural study of a monazite, GdPO4, is also reported. Compression mechanisms are comprised of "squishing" the GdO9 polyhedra and inter-polyhedral movement. This study and the axial compressibility data for Ce-, Tb-, Gd- and ScPO4 suggest that the compression mechanisms favored by MPO4 compounds are those which remain rigid parallel to polyhedral chains.
Facile Supramolecular Engineering of Porphyrin cis Tautomers: The Case of beta-Octabromo-meso-tetraarylporphyrins
Thomas, Kolle E.; Slebodnick, Carla; Ghosh, Abhik (2020-04-21)
A porphyrin cis tautomer, where the two central NH protons are on adjacent pyrrole rings, has long been invoked as an intermediate in porphyrin tautomerism. Only recently, however, has such a species been isolated and structurally characterized. Thus, single-crystal X-ray structure determinations of two highly saddled free-base porphyrins, beta-heptakis(trifluoromethyl)-mesotetrakis(p-fluorophenyl)porphyrin, H-2[(CF3)(7)TFPP], and beta-octaiodo- 5,10,15,20- tetrakis(4'-trifluoromethylphenyl) porphyrin, H-2[I8TCF3PP], unambiguously revealed cis tautomeric structures, each stabilized as a termolecular complex with a pair of ROH (R = CH3 or H) molecules that form hydrogen-bonded N-H center dot center dot center dot O-H center dot center dot center dot N straps connecting the central NH groups with the antipodal unprotonated nitrogens. The unusual substitution patterns of these two porphyrins, however, have left open the question how readily such supramolecular assemblies might be engineered, which prompted us to examine the much more synthetically accessible beta-octabromo-meso-tetraphenylporphyrins. Herein, single-crystal Xray structures were obtained for two such compounds, 2,3,7,8,12,13,17,18-octabromo-5,10,15,20-tetrakis(4'-trifluoromethylphenyl)porphyrin, H-2[Br8TCF3PP], and 2,3,7,8,12,13,17,18-octabromo-5,10,15,20-tetrakis(4'-fluorophenyl)porphyrin, H-2[Br8TFPP], and although the central hydrogens could not all be located unambiguously, the electron density could be convincingly modeled as porphyrin cis tautomers, existing in each case as a bis-methanol adduct. In addition, a perusal of the Cambridge Structural Database suggests that there may well be additional examples of porphyrin cis tautomers that have not been recognized as such. We are therefore increasingly confident that porphyrin cis tautomers are readily accessible via supramolecular engineering, involving the simple stratagem of crystallizing a strongly saddled porphyrin from a solvent system containing an amphiprotic species such as water or an alcohol.
HDP - A novel heme detoxification protein from the malaria parasite
Dewal, Jani; Nagarkatti, Rana; Beatty, Wandy; Angel, Ross; Slebodnick, Carla; Anderson, John; Kumar, Sanjai; Rathore, Dharmendar (Public Library of Science, 2008-04-25)
When malaria parasites infect host red blood cells (RBC) and proteolyze hemoglobin, a unique, albeit poorly understood parasite-specific mechanism, detoxifies released heme into hemozoin (Hz). Here, we report the identification and characterization of a novel Plasmodium Heme Detoxification Protein (HDP) that is extremely potent in converting heme into Hz. HDP is functionally conserved across Plasmodium genus and its gene locus could not be disrupted. Once expressed, the parasite utilizes a circuitous "Outbound–Inbound’’ trafficking route by initially secreting HDP into the cytosol of infected RBC. A subsequent endocytosis of host cytosol (and hemoglobin) delivers HDP to the food vacuole (FV), the site of Hz formation. As Hz formation is critical for survival, involvement of HDP in this process suggests that it could be a malaria drug target.
Inorganic-Organic Hybrid Networks Constructed from Different Metal Ions and Ligands
Hu, Liangming (Virginia Tech, 2009-04-15)
Hybrid inorganic-organic networks have been studied in both chemistry and materials science due to properties, (e.g. porosity, magnetic and electronic behaviors) that may lead to applications in catalysis, gas absorption and storage. It is important to understand the different structural topologies shown by hybrid networks to help develop practical applications for these materials. The research is focused on the design and synthesis of well-defined hybrid network structures that have potential to contain molecular size cavities that can be used for catalysis and gas storage. In the field of organic-inorganic hybrid networks, the goals are to design and synthesize 1D, 2D and 3D networks with cavities, and to characterize them by X-ray, TGA and surface area measurements. Twenty-six networks have been successfully made with interesting structure topologies. These hybrid network structures are classified into three series based on their ligands. Series I contains ten hybrid networks constructed from the flexible ligand, 4, 4′-trimethylenedipyridine (TMDP), Zn2+ ions, and H3PO3, and with aromatic alcohols as templates to direct the formation of various hybrid network structures. Series II consists of five structures constructed from the relatively rigid ligand, 4, ′-bisimidazolelybipyridine (BIB) with metal ions (Cu2+, Ni2+) and the conjugated bases of H3PO3 and H3PO4. The BIB ligand is not commercially available so is produced and characterized by NMR, mass spectrometry and TGA. Rigid network structures were expected to construct with pores of molecular dimensions with the BIB ligand. To date, the BIB ligand has not yield the desired porous network, however, these 3D hybrid networks have interesting topologies, one of which is an interdigitated network that is the precursor for 3D interpenetrated networks. Series III contains five hybrid structures constructed from various organic ligands, such as tartaric acid, picolinic acid and 1, 2, 4-triazole. In addition to the hybrid networks, six hydrogen bonded networks were prepared. Graph-Analysis is applied to study these hydrogen bonded network structures. The Ï â ¦.Ï interaction is also discussed within the hydrogen bonded networks.
mer-Hydridotris(tri-methyl-phosphane-κP)(d-valinato-κ(2) N,O)iridium hexa-fluorido-phosphate di-chloro-methane 0.675-solvate.
Merola, Joseph S.; Slebodnick, Carla; Berg, Michael; Ritchie, Melissa K. (2014-03-01)
The title compound, [Ir(C5H10NO2)H(C3H9P)3]PF6·0.675CH2Cl2, an iridium compound with a meridional arrangement of PMe3 groups, O,N-bidentate coordination of d-valine and with a hydride ligand trans to the N atom is compared with the l-valine complex reported previously. As expected, the complexes from the corresponding l and d isomers of valine crystallize in enanti-omorphic space groups (P43 and P41, respectively). In the crystal, N-H⋯O and N-H⋯F hydrogen bonding is observed, the N-H to carbonyl oxygen hydrogen bond producing a helical motif that proceeds along the 41 screw of the c axis.
Nitrogen-Containing Dimeric nor-Multiflorane Triterpene from a Turraea sp.
Rasamison, Vincent E.; Rakotondraibe, L. Harinantenaina; Slebodnick, Carla; Brodie, Peggy J.; Ratsimbason, Michael; TenDyke, Karen; Shen, Yongchun; Randrianjanaka, Lucien M.; Kingston, David G. I. (American Chemical Society, 2014-05-16)
The new triterpene turranoic acid (1) and thenew N-containing nor-triterpene turraenine (2), along with triptocallic acid B (3) and esculentoic acid (4) were isolated from leaves of a Turraea sp. Compounds 1-3 showed weak to moderate in vitro antiplasmodial activity against the chloroquine-resistant Plasmodium falciparum strain FCM29. Compound 1 also displayed weak cytotoxic activity against the non-small lung cancer cell line H522-T1 with an IC50 value of 16.4 μM.
Structural variations of feldspars at high pressure and high temperature
Kolbus, Lindsay Marie (Virginia Tech, 2012-04-24)
Feldspar minerals are framework aluminosilicates that comprise approximately 60 percent of the Earth's crust. The elastic and thermodynamic properties of this important mineral group are needed for the interpretation of seismic wave velocities, for understanding cation partioning patterns and for the determination of phase boundaries and reactions involving feldspars in the Earth's crust. Until recently, no systematic approach has been applied to describe the structural behavior of feldspars as a function of pressure, temperature and composition. In this thesis, high-pressure and high-temperature X-ray diffraction data were collected for feldspars over a range of compositions which has led to the development a structural model that allows one to predict the structural evolution of feldspars at depth in the Earth's crust. Specifically, the equations of state have been determined for two plagioclase feldspars (An20 and An78) with different states of Al/Si ordering using single-crystal X-ray diffraction. This study has shown that the introduction of Al,Si disorder into plagioclase structures at constant composition softens the structure by 4(1)% for An0, 2.5(9)% for An20 and is essentially zero for An78 compositions. The effect of pressure on the structure of an ordered An20 was also determined up to 9.15 GPa using single-crystal X-ray diffraction and it was found that the dominant compression mechanism involves tilting of the AlO4 and SiO4 tetrahedra. Similarly, high-temperature single-crystal X-ray diffraction data collected from an ordered An26 plagioclase and powder X-ray diffraction collected on a suite of Na-rich plagioclases that were refined using the Rietveld method indicate that the major structural response to increased temperature involves tilting of the tetrahedra. Building on ideas originally proposed by Dr. Helen Megaw, the changes in the conformation of the tetrahedral framework of feldspars can be described in terms of four distinct tilt systems of rigid tetrahedra. This model demonstrates that the fundamental reason for the observed anisotropy and volume change of feldspars lies in the topology of the tetrahedral framework with the greatest contribution attributed to tilt systems 2 and 3.
Synthesis of New Molecule-Based Magnets using Bridging Organic Radicals
Houser, Christopher L. (Virginia Tech, 2019-07-12)
Several new families of organic acceptors that are candidates as building blocks of molecule-based ferrimagnets were synthesized and characterized. These families include fluorodicyanostilbenes, a tetrachlorodicyanostilbene, naphthyltricyanoethylenes, bromophenyltricyanoethylenes, and an anthryltricyanoethylene. The magnetic networks were synthesized by reacting each acceptor with V(CO)6. The magnets synthesized in this study were characterized using a SQUID magnetometer, elemental analysis, and infrared spectroscopy. Although some combinations failed to yield magnetically ordered materials, others exhibited ordering temperatures in the range of 95 K – 260 K. The ordering temperatures and saturation magnetizations were compared among families of acceptors and correlated with individual properties of the acceptors such as reduction potential and structure.

Browsing by Author "Slebodnick, Carla"

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