Chemistry Commons^™

A New Peroxide Fragmentation: Efficient Chemical Generation Of 1O2 In Organic Media, Patrick Dussault, Prasanta Ghorai

Department of Chemistry: Faculty Publications

Monoactivated derivatives of 1,1-dihydroperoxides undergo an unprecedented base-promoted fragmentation to efficiently generate singlet oxygen (¹O₂) in anhydrous organic solvents.

A Multi-Step Nmr Screen For The Identification And Evaluation Of Chemical Leads For Drug Discovery, Kelly A. Mercier, Matthew D. Shortridge, Robert Powers

Department of Chemistry: Faculty Publications

A multi-step NMR based screening assay is described for identifying and evaluating chemical leads for their ability to bind a target protein. The multi-step NMR assay provides structure-related information while being an integral part of a structure based drug discovery and design program. The fundamental principle of the multi-step NMR assay is to combine distinct 1D and 2D NMR techniques, in such a manner, that the inherent strengths and weakness associated with each technique is complementary to each other in the screen. By taking advantage of the combined strengths of 1D and 2D NMR experiments, it is possible to minimize …

Anhydrous Fluoride Salts And Reagents And Methods For Their Production, Stephen G. Dimagno, Haoran Sun

Department of Chemistry: Faculty Publications

Anhydrous organic fluoride salts and reagents prepared by a method comprising the nucleophilic Substitution of a fluorinated aromatic or fluorinated unsaturated organic compound with a salt having the formula: [Q_nM]^x+A_x^- in an inert polar, aprotic solvent; wherein M is an atom capable of supporting a formal positive charge, the n groups Q are independently varied organic moieties, n is an integer such that the [Q_nM] carries at least one formal positive charge, x is an integer defining the number of formal positive charge(s), +, carried by the [Q_nM], A^{- …}

Energy Gradients In Combined Fragment Molecular Orbital And Polarizable Continuum Model (Fmo/Pcm) Calculation, Hui Li, Dmitri G. Federov, Takeshi Nagata, Kazuo Kitaura, Jan H. Jensen, Mark S. Gordon

Hui Li Publications

The analytic energy gradients for the combined fragment molecular orbital and polarizable continuum model (FMO/PCM) method are derived and implemented. Applications of FMO/PCM geometry optimization to polyalanine show that the structures obtained with the FMO/PCM method are very close to those obtained with the corresponding full ab initio PCM methods. FMO/PCM (RHF/6-31G* level) is used to optimize the solution structure of the 304-atom Trp-cage miniprotein and the result is in agreement with NMR experiments. The key factors determining the relative stability of the a-helix, b-turn and the extended form in solution are elucidated for polyalanine.

6:1 Aspect Ratio Silicon Pillar Based Thermal Neutron Detector Filled With 10B, R. J. Nikolic, A. M. Conway, C. E. Reinhart, R. T. Graff, T. F. Wang, N. Deo, Barry Chin Li Cheung

Barry Chin Li Cheung Publications

Current helium-3 tube based thermal neutron detectors have shortcomings in achieving simultaneously high efficiency and low voltage while maintaining adequate fieldability performance. By using a three-dimensional silicon p-i-n diode pillar array filled with boron-10 these constraints can be overcome. The fabricated pillar structured detector reported here is composed of 2 μm diameter silicon pillars with a 4 μm pitch and height of 12 μm. A thermal neutron detection efficiency of 7.3+/−0.6% and a neutron-to-gamma discrimination of 10⁵ at 2 V reverse bias were measured for this detector. When scaled to larger aspect ratio, a high efficiency device is possible.

Use Of Fluorinated Functionality In Enzyme Inhibitor Development: Mechanistic And Analytical Advantages, David B. Berkowitz, Kannan R. Karukurichi, Roberto De La Salud-Bea, David L. Nelson, Christopher D. Mccune

David Berkowitz Publications

On the one hand, owing to its electronegativity, relatively small size, and notable leaving group ability from anionic intermediates, fluorine offers unique opportunities for mechanism-based enzyme inhibitor design. On the other, the “bio-orthogonal” and NMR-active 19-fluorine nucleus allows the bioorganic chemist to follow the mechanistic fate of fluorinated substrate analogues or inhibitors as they are enzymatically processed. This article takes an overview of the field, highlighting key developments along these lines. It begins by highlighting new screening methodologies for drug discovery that involve appropriate tagging of either substrate or the target protein itself with ¹⁹Fmarkers, that then report back …

Half-Metallicity In Hybrid Bcn Nanoribbons, Er-Jun Kan, Xiaojun Wu, Zenyu Li, Xiao Cheng Zeng, Jinlong Yang, J. G. Hou

Xiao Cheng Zeng Publications

The established chemical synthetic strategy toward graphene nanoribbons has greatly prompted and justified the research of theoretical designs of novel materials based on graphene. In this paper, we report the novel half-metallicity in C and BN hybrid zigzag nanoribbons even though stand-alone C or BN nanoribbon possesses a finite band gap. By performing first-principles electronic-structure calculations, we find this unexpected half-metallicity in the hybrid nanostructures stems from a competition between the charge and spin polarizations, as well as from the π orbital hybridization between C and BN. Molecular dynamics simulations indicate that the hybrid nanoribbons are stable. Our results point …

Anisotropy Of Crystal-Melt Interfacial Free Energy Of Silicon By Simulation, Pankaj A. Apte, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

We extend the cleaving wall method to a nonpairwise additive potential. Using this method, we compute the anisotropy of crystal-melt interfacial free energy γ for Stillinger–Weber potential of silicon [F. H. Stillinger and T. A. Weber, Phys. Rev. B 31, 5262 (1985)]. The calculated γ for (100), (111), and (110) orientations are 0.42±0.02, 0.34±0.02, and 0.35±0.03 J &#;m², respectively. The anisotropy in γ we found is consistent with the experimental observation that Si(100)-melt interface develops (111) facets and also helps in explaining a higher undercooling observed for Si(111)-melt interface in Czochralski method.

Medium-Sized Double Magic Metal Clusters: Al@Cu54- And Al@Ag54-, Yi Gao, Nan Shao, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

Medium-sized double magic metal clusters, Al@Ag₅₄^- and Al@₅₄^-, are predicted based on unbiased global search and density functional calculation. Both bimetallic core-shell clusters have icosahedral symmetry, and they are much lower in energies than all other low-lying isomers. In contrast, the icosahedral cluster Al@₅₄^- is a high-energy isomer. Both Al@₅₄^- and Al@Cu₅₄^- exhibit appreciable gaps between the highest occupied molecular orbital and the lowest unoccupied molecular orbital, and strong spherical aromaticity, which provide two additional evidences for the likelihood of their high stability. The simulated anion photoelectron spectra and …

A Set Of Phosphatase-Inert “Molecular Rulers” To Probe For Bivalent Mannose 6-Phosphate Ligand-Receptor Interactions, Xiang Fei, Christopher M. Connelly, Richard G. Macdonald, David B. Berkowitz

David Berkowitz Publications

A set of bivalent mannose 6-phosphonate “molecular rulers” has been synthesized to examine ligand binding to the M6P/IGF2R. The set is estimated to span a P-P distance range of 16–26 Å (MMFF energy minimization on the hydrated phosphonates). Key synthetic transformations include sugar triflate displacement for phosphonate installation and Grubbs I cross-metathesis to achieve bivalency. Relative binding affinities were tested by radioligand displacement assays versus PMP-BSA (pentamannose phosphate-bovine serum albumin). These compounds exhibit slightly higher binding affinities for the receptor (IC_50’s = 3.7–5 μM) than the parent, monomeric mannose 6-phosphonate ligand and M6P itself (IC₅₀ = 11.5 ± …

Identification Of Guanylate Cyclases And Related Signaling Proteins In Sperm Tail From Sea Stars By Mass Spectrometry, Mia Nakachi, Midori Matsumoto, Philip M. Terry, Ronald L. Cerny, Hideaki Moriyama

Hideaki Moriyama Publications

Marine invertebrates employ external fertilization to take the advantages of sexual reproduction as one of excellent survival strategies. To prevent mismatching, successful fertilization can be made only after going though strictly defined steps in the fertilization. In sea stars, the fertilization process starts with the chemotaxis of sperm followed by hyperactivation of sperm upon arriving onto the egg coat, and then sperm penetrate to the egg coat before achieving the fusion. To investigate whether the initiation of chemotaxis and the following signaling has species specificity, we conducted comparative studies in the protein level among sea stars, Asterias amurensis, A. forbesi …

Search For Lowest-Energy Structure Of Zintl Dianion Si122-, Ge122-, And Sn122-, Nan Shao, Satya S. Bulusu, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

We perform an unbiased search for the lowest-energy structures of Zintl dianions (Si₁₂^2-, ₁₂^2-, and ₁₂^2-), by using the basin-hopping (BH) global optimization method combined with density functional theory geometric optimization. High-level ab initio calculation at the coupled-cluster level is used to determine relative stabilities and energy ranking among competitive low-lying isomers of the dianions obtained from the BH search. For ₁₂^2-, all BH searches (based on independent initial structures) lead to the same lowest-energy structure _12a^2-, a tricapped trigonal prism (TTP) with C_s group symmetry. Coupled-cluster calculation, …

Structures And Relative Stability Of Medium- And Large-Sized Silicon Clusters. Vi. Fullerene Cage Motifs For Low-Lying Clusters Si39, Si40, Si50, Si60, Si70, And Si80, Soohaeng Yoo, N. Shao, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

We performed a constrained search, combined with density-functional theory optimization, of low-energy geometric structures of silicon clusters Si₃₉, Si₄₀, Si₅₀, Si₆₀, Si₇₀, and Si₈₀. We used fullerene cages as structural motifs to construct initial configurations of endohedral fullerene structures. For Si₃₉, we examined six endohedral fullerene structures using all six homolog C₃₄ fullerene isomers as cage motifs. We found that the Si₃₉ constructed based on the C₃₄(C_s:2) cage motif results in a new leading candidate for the lowest-energy structure …

Ab Initio Calculation Of Carbon Clusters. Ii. Relative Stabilities Of Fullerene And Nonfullerene C24, Wei An, Nan Shao, Satya S. Bulusu, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

Chemical stabilities of six low-energy isomers of C₂₄ derived from global-minimum search are investigated. The six isomers include one classical fullerene (isomer 1) whose cage is composed of only five- and six-membered rings (5/6-MRs), three nonclassical fullerene structures whose cages contain at least one four-membered ring (4-MR), one plate, and one monocyclic ring. Chemical and electronic properties of the six C₂₄ isomers are calculated based on a density-functional theory method (hybrid PBE|PBE functional and cc-pVTZ basis set). The properties include the nucleus-independent chemical shifts (NICS), singlet-triplet splitting, electron affinity, ionization potential, and gap between the highest occupied molecular …

Electronic And Magnetic Properties Of Endohedrally Doped Fullerene Mn@C60: A Total Energy Study, Guangping Li, Renat F. Sabirianov, Jing Lu, Xiao Cheng Zeng, Wai-Ning Mei

Xiao Cheng Zeng Publications

We perform total energy calculations on a manganese atom encapsulated inside a C₆₀ cage using density functional theory with the generalized gradient approximation through three optimization schemes and along four paths inside the cage. We find that when Mn is located in the central region, its electronic and magnetic properties are not exactly the same as those of a free Mn atom due to weak coupling between Mn and the cage. As Mn is shifted toward to the edge, the total energy and spin start to change significantly when Mn is situated about one-third of the way between the …

Cobalt Oxide Surface Chemistry: The Interaction Of Coo(1 0 0), Co3O4 (1 1 0), And Co3O4 (1 1 1) With Oxygen And Water, Sarah C. Petitto, Erin M. Marsh, Gregory A. Carson, Marjorie Langell

Marjorie A. Langell Publications

Cobalt oxides comprise two readily accessible cation oxidation states: Co²⁺ and Co³⁺, which are thermodynamically competitive under common ambient conditions, and redox mechanisms connecting the two states are largely responsible for their success in partial oxidation catalysis. In our studies, CoO(1 0 0), Co₃O₄ (1 1 0), and Co₃O₄ (1 1 1) single crystal substrates have been investigated with X-ray photoelectron spectroscopy (XPS), high-resolution electron energy loss spectroscopy (HREELS), and low energy electron diffraction (LEED) for their surface reactivity toward O₂ and H₂O and for their stability under …

Probing The Electronic And Structural Properties Of Doped Aluminum Clusters: Mal12- (M=Li, Cu, And Au), R. Pal, Li-Feng Cui, Satya S. Bulusu, Hua-Jin Zhai, Lai-Sheng Wang, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

Photoelectron spectroscopy (PES) is combined with theoretical calculations to investigate the electronic and atomic structures of three doped aluminum clusters, MAl₁₂^- (M=Li, Cu, and Au). Well-resolved PES spectra have been obtained at two detachment photon energies, 266 nm (4.661 eV) and 193 nm (6.424 eV). Basin-hopping global optimization method in combination with density-functional theory calculations has been used for the structural searches. Good agreement between the measured PES spectra and theoretical simulations helps to identify the global minimum structures. It is found that LiAl₁₂^- (C_5v) can be viewed as replacing a surface Al …

Phosphorylation Of Claudin-5 And Occludin By Rho Kinase In Brain Endothelial Cells, Masaru Yamamoto, Servio H. Ramirez, Shinji Sato, Tomomi Kiyota, Ronald Cerny, Kozo Kaibuchi, Yuri Persidsky, Tsuneya Ikezu

Ronald Cerny Publications

Critical to the proper maintenance of blood-brainbarrier (BBB) integrity are the endothelial tight junctions (TJs). Posttranslational modifications of essential endothelial TJ proteins, occludin and claudin-5, contribute and possibly disrupt BBB integrity. Our previous work has shown that Rho kinase (RhoK) activation mediates occludin and claudin-5 phosphorylation resulting in diminished barrier tightness and enhanced monocyte migration across BBB in the setting of human immunodeficiency virus-1 encephalitis (HIVE). To determine whether RhoK can directly phosphorylate TJ proteins, we examined phosphorylation of cytoplasmic domains of recombinant claudin- 5 and occludin by RhoK. We found that RhoK predominately phosphorylated two sites on occludin (T382 …

Electrolytic Deposition Of Coatings For Prosthetic Metals And Alloys 2008, Jody G. Redepenning

Jody Redepenning Publications

An article coated with an electrolytically deposited biocompatible composite layer useful as an internal prosthetic device is disclosed. The bio-compatible composite coating that is electrolytically deposited onto the article comprises hydroxyapatite and chitosan. The introduction of chitosan into the crystal matrix of brushite/hydroxyapatite significantly improves the adhesive and chemical and mechanical stability properties of the coating.

Tata-Binding Protein Recognition And Bending Of A Consensus Promoter Are Protein Species Dependent, Jodell E. Whittington, Roberto F. Delgadillo, Torrissa J. Attebury, Laura K. Parkhurst, Margaret A. Daugherty, Lawrence J. Parkhurst

Lawrence Parkhurst Publications

The structure and behavior of full-length human TBP binding the adenovirus major late promoter (AdMLP) have been characterized using biophysical methods. The human protein induces a 97° bend in DNA_AdMLP. The high-resolution functional data provide a quantitative energetic and kinetic description of the partial reaction sequence as native human TBP binds rapidly to a consensus promoter with high affinity. The reaction proceeds with successive formation of three bound species, all having strongly bent DNA, with the concurrence of binding and bending demonstrated by both fluorescence and anisotropy stopped flow. These results establish the protein species dependence of the …

A General And Rapid Cell-Free Approach For The Interrogation Of Protein–Protein, Protein–Dna, And Protein–Rna Interactions And Their Antagonists Utilizing Split-Protein Reporters, Jason R. Porter, Cliff I. Stains, Benjamin W. Jester, Indraneel Ghosh

Cliff Stains Publications

Split-protein reporters have emerged as a powerful methodology for imaging biomolecular interactions which are of much interest as targets for chemical intervention. Herein we describe a systematic evaluation of split-proteins, specifically the green fluorescent protein, β-lactamase, and several luciferases, for their ability to function as reporters in completely cell-free systems to allow for the extremely rapid and sensitive determination of a wide range of biomolecular interactions without the requirement for laborious transfection, cell culture, or protein purification (12–48 h). We demonstrate that the cell-free split-luciferase system in particular is amenable for directly interrogating protein–protein, protein–DNA, and protein–RNA interactions in homogeneous …

Conserved Sequences Of Sperm-Activating Peptide And Its Receptor Throughout Evolution, Despite Speciation In The Sea Star Asterias Amurensis And Closely Related Species, Mia Nakachi, Motonori Hoshi, Midori Matsumoto, Hideaki Moriyama

Hideaki Moriyama Publications

The asteroidal sperm-activating peptides (asterosaps) from the egg jelly bind to their sperm receptor, a membrane-bound guanylate cyclase, on the tail to activate sperm in sea stars. Asterosaps are produced as single peptides and then cleaved into shorter peptides. Sperm activation is followed by the acrosome reaction, which is subfamily specific. In order to investigate the molecular details of the asterosap-receptor interaction, corresponding cDNAs have been cloned, sequenced and analysed from the Asteriinae subfamily including Asterias amurensis, A. rubens, A. jorbesi and Aphelasterias japonica, as well as Distolasterias nipon from the Coscinasteriinae subfamily. Averages of 29% and 86% identity …

Staphylococcus Aureus Primase Has Higher Initiation Specificity, Interacts With Single-Stranded Dna Stronger, But Is Less Stimulated By Its Helicase Than Escherichia Coli Primase, Scott A. Koepsell, Marilynn A. Larson, Christopher Frey, Steven H. Hinrichs, Mark A. Griep

Mark A. Griep Publications

The study of primases from model organisms such as Escherichia coli, phage T7 and phage T4 has demonstrated the essential nature of primase function, which is to generate de novo RNA polymers to prime DNA polymerase. However, little is known about the function of primases from other eubacteria. Their overall low primary sequence homology may result in functional differences. To help understand which primase functions were conserved, primase and its replication partner helicase from the pathogenic Gram-positive bacteria Staphylococcus aureus were compared in detail with that of E. coli primase and helicase. The conserved properties were to primer initiation …

Local Structures Surrounding Zr In Nanostructurally Stabilized Cubic Zirconia: Structural Origin Of Phase Stability, Y. L. Soo, P. J. Chen, S. H. Huang, T. J. Shiu, T. Y. Tsai, Y. H. Chow, Y. C. Lin, S. C. Weng, S. L. Chang, G. Wang, Chin Li Cheung, Renat F. Sabirianov, Wai-Ning Mei, F. Namavar, H. Haider, K. L. Garvin, J. F. Lee, H. Y. Lee, P. P. Chu

Department of Chemistry: Faculty Publications

Local environment surrounding Zr atoms in the thin films of nanocrystalline zirconia (ZrO₂) has been investigated by using the extended x-ray absorption fine structure (EXAFS) technique. These films prepared by the ion beam assisted deposition exhibit long-range structural order of cubic phase and high hardness at room temperature without chemical stabilizers. The local structure around Zr probed by EXAFS indicates a cubic Zr sublattice with O atoms located on the nearest tetragonal sites with respect to the Zr central atoms, as well as highly disordered locations. Similar Zr local structure was also found in a ZrO₂ nanocrystal …

Soil Chemistry Northwest New Mexico, Larry V. Benson

United States Geological Survey: Datasets

These data result from soil chemistry samples extracted from several regions in northwest New Mexico and were used in the following publications:

Larry V. Benson, J. Stein, H. Taylor, R. Friedman, and T. C. Windes. 2006. The agricultural productivity of Chaco Canyon and the source(s) of pre-Hispanic maize found in the Pueblo Bonito Great House. In: J. E. Staller, R. H. Tykot, and B. F. Benz, eds. Histories of Maize: Multidisciplinary Approaches to the Prehistory, Linguistics, Biogeography, Domestication, and Evolution of Maize, 289–314. Elsevier/Academic Press.

Larry V. Benson. 2017. The Chuska Slope as an agricultural alternative to Chaco …

Novel Approach For Synthesis Of 2:1 Permethylated Β-Cyclodextrin–C60 Conjugate, Zhu Guan, Yali Wang, Yong Chen, Yongmin Zhang

Department of Chemistry: Dissertations, Theses, and Student Research

Amphiphilic cyclodextrin–fullerene conjugates have potential biological activity, due to their water solubility. In order to study the influence of the linker of these conjugates on solubility and aggregation, a permethylated β-cyclodextrin–C₆₀ conjugate with a short linker –(CH₂)₂NHCO–, which is attached to the secondary face of β-cyclodextrin was synthesized. Its solubility in water and its UV spectrum in CH₂Cl₂ and water were investigated.

Effects, Uptake, And Fate Of 2,4,6-Trinitrotoluene Aged In Soil In Plants And Worms, Elly Ph Best, Henry E. Tatem, Kaaren N. Geter, Melissa L. Wells, Brian K. Lane

United States Army Corps of Engineers, Omaha District

The present study was aimed at providing data to be used at predicting exposure-based effects of 2,4,6-trinitrotoluene (TNT) aged in soil on endpoint organisms representing two trophic levels. These data can be used to define criteria or reference values for environmental management and conducting specific risk assessment. Long-term exposure tests were conducted to evaluate sublethal toxicity and uptake of aged soil-based explosives, with TNT as the main contaminant. In these tests, plants were exposed for 55 d, and biomass and explosives residues were determined. Worms were exposed for 28 and 42 d, and biomass, number, and tissue residues were determined. …

Origin And Paleoclimatic Significance Of Late Quaternary Loess In Nebraska: Evidence From Stratigraphy, Chronology, Sedimentology, And Geochemistry, Daniel R. Muhs, E. Arthur Bettis Iii, John N. Aleinikoff, John P. Mcgeehin, Jossh Beann, Gary Skipp, Brian D. Marshall, Helen M. Roberts, William C. Johnson, Rachel Benton

United States Geological Survey: Staff Publications

Loess is one of the most extensive surficial geologic deposits in mid-continental North America, particularly in the central Great Plains region of Nebraska. Last-glacial-age loess (Peoria Loess) reaches its greatest known thickness in the world in this area. New stratigraphic, geochronologic, mineralogic, and geochemical data yield information about the age and provenance of Peoria Loess, as well as evaluation of recent climate models.

Oligo(Vinylidene Fluoride) Langmuir-Blodgett Films Studied By Spectroscopic, Rafal Korlacki, J. Travis Johnston, Jihee Kim, Stephen Ducharme, Daniel W. Thompson, Vladimir M. Fridkin, Zhongxin Ge, James M. Takacs

Stephen Ducharme Publications

Thin films of amphiphilic vinylidene fluoride oligomers prepared by Langmuir–Blodgett deposition on silicone substrates were investigated by comparing experimental and theoretical mid-infrared (IR) spectra. The experimental spectra were obtained using infrared spectroscopic ellipsometry. Theoretical spectra were calculated using density functional theory. Excellent correspondence of major IR bands in both data sets shows that the molecular backbone is oriented with the long axis normal to the substrate plane. This is in contrast to poly vinylidene fluoride[1] LB films, in which the polymer chains are parallel to the substrate.

Nitrated Alpha-Synuclein-Activated Microglial Profiling For Parkinson’S Disease, Ashley D. Reynolds, Jason G. Glanzer, Irena Kadiu, Mary Ricardo-Dukelow, Anathbandhu Chaudhuri, Pawel Ciborowski, Ronald Cerny, Benjamin Gelman, Mark P. Thomas, R. Lee Mosley, Howard E. Gendelman

Ronald Cerny Publications

(PD). This can occur, in part, by modulation of glial function following activation by soluble or insoluble modified alphasynuclein (α-syn), a chief component of Lewy bodies that is released from affected dopaminergic neurons. α-Syn is nitrated during oxidative stress responses and in its aggregated form, induces inflammatory microglial functions. Elucidation of these microglial function changes in PD could lead to new insights into disease mechanisms. To this end, PD-associated inflammation was modeled by stimulation of microglia with aggregated and nitrated α-syn. These activated microglia were ameboid in morphology and elicited dopaminergic neurotoxicity. A profile of nitrated, aggregated α-syn-stimulated microglia was …