Chemistry Commons^™

Nature Of Oxygen At Rocksalt And Spinel Oxide Surfaces, Marjorie Langell, J.G. Kim, D. L. Pugmire, W. Mccarroll

Marjorie A. Langell Publications

The chemical environment of oxygen in cobalt-containing metal oxides with compositions M _xM′_{( x – 1)} O and M _xM′_{(3x – 1)} O₄ (M,M′ = Mn,Ni,Co) has been studied by Auger, x-ray and ultraviolet photoelectron, and high resolution electron energy loss spectroscopies. While there is a single type of lattice oxygen in the bulk structure of simple rocksalt and spinel oxides, the nature of oxygen at the surface of the spinel oxides is considerably more complex. Photoemission from core oxygen states in these materials often shows multiple peaks and satellite structure which have been …

Molecular Dynamics Simulation Of Supersaturated Vapor Nucleation In Slit Pore. Ii. Thermostatted Atomic-Wall Model, K.T. Kholmurodov, K. Yasuoka, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

Molecular dynamics simulations of nucleation of a supersaturated Lennard-Jones vapor in slit nanopores are carried out. In this study we extend a previous work [K. Yasuoka, G. T. Gao, and X. C. Zeng, J. Chem. Phys. 112, 4279 (2000)] in that the walls of the slit are treated as actual atomic walls serving as both the confining solid surfaces and a thermostat. The walls are fixed in place in a fcc lattice structure and wall atoms are subjected to a stiff biharmonic potential thereby bounded to lattice sites. The two walls of the slit have an identical surface [fcc (100)], …

Nucleation Of Water And Methanol Droplets On Cations And Anions: The Sign Preference, K.J. Oh, G.T. Gao, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

The barrier height to cation- and anion-induced nucleation to produce water and methanol droplets are calculated by means of an umbrella-sampling Monte Carlo method. The computer simulation corroborates the century-old finding of Wilson that the anion is a better nucleator to produce water droplets than the cation having the same magnitude of charge, even without the presence of external electric field. The simulation also shows that the cation is a better nucleator to produce methanol droplets than the anion.

Energy Gaps In “Metallic” Single-Walled Carbon Nanotubes, Min Ouyang, Jin-Lin Huang, Chin Li Cheung, Charles Lieber

Barry Chin Li Cheung Publications

Metallic single-walled carbon nanotubes have been proposed to be good one-dimensional conductors. However, the finite curvature of the graphene sheet that forms the nanotubes and the broken symmetry due to the local environment may modify their electronic properties. We used low-temperature atomically resolved scanning tunneling microscopy to investigate zigzag and armchair nanotubes, both thought to be metallic. “Metallic” zigzag nanotubes were found to have energy gaps with magnitudes that depend inversely on the square of the tube radius, whereas isolated armchair tubes do not have energy gaps. Additionally, armchair nanotubes packed in bundles have pseudogaps, which exhibit an inverse dependence …

A Greek Cross Dodecaphenylene: Sparteine-Mediated Asymmetric Synthesis Of Chiral D2-Symmetric Π-Conjugated Tetra-O-Phenylenes, Andrzej Rajca, Hua Wang, Pavel Bolshov, Suchada Rajca

Andrzej Rajca Publications

The asymmetric synthesis of a chiral, nonracemic π-conjugated system with D₂ point group of symmetry, dodecaphenylene 4 is described. In the key step, (−)-sparteine- and Cu(II)-mediated oxidation of 2,2′-dilithio-1,1′-biaryls in ether gives the corresponding dimers, tetra-o-phenylenes, in 80% isolated yields and 50–60% ee’s. X-Ray crystallography confirms the structure of rac-4 and its molecular shape of a Greek cross. The torsional angles between the benzene rings in the tetra-o-phenylene core of rac-4 are in the 56.5–71.0° range. However, CD and UV spectra of 4 in CH₂Cl₂ are consistent with significant conjugation between the …

Dependence Of 13C Nmr Chemical Shifts On Conformations Of Rna Nucleosides And Nucleotides, Mohsen Ebrahimi, Paolo Rossi, Christopher Rogers, Gerard S. Harbison

Gerard S. Harbison Publications

Cross-polarization magic-angle spinning solid-state NMR spectroscopy has been used to investigate the dependence of ¹³C sugar chemical shifts on specific conformational parameters of a variety of ribonucleotides and ribonucleosides. Solid-state NMR is a valuable tool for nucleoside and nucleotide structural studies since it provides the means to acquire spectra that correspond to single conformations, as opposed to ¹³C solutionNMRmethods. The distinct effects of sugar puckering on the C1′, C4′, and C5′ resonances of C2′ endo (S type) and C3′ endo (N type) furanoid conformations allow us to separate them into two groups. Further analysis of each group reveals …

Solution Structure Of B. Subtilis Acyl Carrier Protein, Guang-Yi Xu, Amy Tam, Laura Lin, Jeffrey Hixon, Christian C. Fritz, Robert Powers

Robert Powers Publications

Background: Acyl carrier protein (ACP) is a fundamental component of fatty acid biosynthesis in which the fatty acid chain is elongated by the fatty acid synthetase system while attached to the 4’-phosphopantetheine prosthetic group (4’- PP) of ACP. Activation of ACP is mediated by holo-acyl carrier protein synthase (ACPS) when ACPS transfers the 4’-PP moiety from coenzyme A (CoA) to Ser36 of apo-ACP. Both ACP and ACPS have been identified as essential for E. coli viability and potential targets for development of antibiotics.

Results: The solution structure of B. subtilis ACP (9 kDa) has been determined using two-dimensional and three-dimensional …

Calculation Of 13C Chemical Shifts In Rna Nucleosides: Structure-13C Chemical Shift Relationships, Paolo Rossi, Gerard S. Harbison

Gerard S. Harbison Publications

Isotropic ¹³C chemical shifts of the ribose sugar in model RNA nucleosides are calculated using SCF and DFT-GIAO ab initio methods for different combinations of ribose sugar pucker, exocyclic torsion angle, and glycosidic torsion angle. Idealized conformations were obtained using structures that were fully optimized by ab initio DFT methods starting with averaged parameters from a collection of crystallographic data. Solid-state coordinates of accurate crystal or neutron diffraction structures were also examined directly without optimization. The resulting ¹³C chemical shifts for the two sets of calculations are then compared. The GIAO-DFT method overestimates the shifts by an average …

Effect Of Carrier-Gas Pressure On Barrier To Nucleation: Monte Carlo Simulation Of Water/Nitrogen System, K.J. Oh, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

Carrier gases are used in most nucleation experiments for releasing the latent heat generated during vapor condensation. In the analysis of experimental data it is often assumed that the carrier gas is inert and would not participate in the nucleation process of the target gas. Several recent nucleation experiments show that the influence of carrier gases to nucleation rate is not negligible under certain conditions. To gain more insight into the carrier-gas effect, we carry out Monte Carlo simulation to compute the free energy of formation of water clusters in the presence of a nitrogen carrier gas. At fixed temperature …

Effects Of External Electric Field On The Interfacial Properties Of Weakly Dipolar Fluid, V. B. Warshavsky, T. V. Bykov, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

In the framework of modified mean-field density-functional theory, effects of a uniform electric field on the interfacial properties of a model dipolar fluid are studied. Both density and orientational order-parameter profiles of the planar vapor-liquid interface are obtained as a function of the field strength. For the dipolar fluids with reduced dipole moment μ₀^*0^*E*/T*!1) can shift the surface tension by few percent. We also find that the electric field actually reduces the thermodynamical surface tension but enhances the mechanical surface tension at the equimolar dividing surface. To detect these field effects on …

Adsorption And Decomposition Of Nickelocene On Ag(100): A High-Resolution Electron Energy Loss Spectroscopy And Temperature Programmed Desorption Study, D. L. Pugmire, C. M. Woodbridge, N. M. Boag, Marjorie Langell

Marjorie A. Langell Publications

Nickelocene adsorption and decomposition on the Ag(100) surface were studied with temperature programmed desorption and high resolution electron energy loss spectroscopy. At monolayer coverages on the relatively inert Ag(100) surface at 175 K, nickelocene physisorbs molecularly, with its molecular axis perpendicular to the surface plane. Nickelocene begins decomposing to adsorbed cyclopentadienyl and nickel at 225 K. Molecular desorption is only observed from multilayer material, at 210 K, or from the first monolayer if adjacent surface sites for decomposition are not available. The cyclopentadienyl decomposes through disproportionation to cyclopentadiene, which desorbs, and adsorbed nickel and carbon fragments on the Ag(100) surface …

Atomically Resolved Single-Walled Carbon Nanotube Intramolecular Junctions, Min Ouyang, Jin-Lin Huang, Chin Li Cheung, Charles M. Lieber

Barry Chin Li Cheung Publications

Intramolecular junctions in single-walled carbon nanotubes are potentially ideal structures for building robust, molecular-scale electronics but have only been studied theoretically at the atomic level. Scanning tunneling microscopy was used to determine the atomic structure and electronic properties of such junctions in single-walled nanotube samples. Metal-semiconductor junctions are found to exhibit an electronically sharp interface without localized junction states, whereas a more diffuse interface and low-energy states are found in metal-metal junctions. Tight-binding calculations for models based on observed atomic structures show good agreement with spectroscopy and provide insight into the topological defects forming intramolecular junctions. These studies have important …

Preliminary X-Ray Diffraction Studies Of The Transcriptional Inhibitory Antibody Fab41.4, Johanna Mazlo, Robyn L. Stanfield, Ian A. Wilson, Steven H. Hinrichs, John J. Stezowski

Department of Chemistry: Faculty Publications

The binding of transcription factor ATF-1 to DNA contributes to gene expression and regulation of cell growth. Antibody Mab41.4, raised against ATF-1, and its derivatives Fab41.4 and scFv41.4 inhibit specific DNA binding in vitro and induce apoptotic death of tumor cells in vivo. Structural studies of Fab41.4 were performed to gain insight into the mechanism of action of this potentially therapeutic antibody. The optimal conditions for crystallization of Fab41.4 were determined. Crystals were needle-like in appearance, displayed C2 space-group symmetry and diffracted to a resolution of 1.6 Å. The unit-cell parameters were determined to be a = 186.64, b = …

Multiple Separations Facilitate Identification Of Protein Variants By Mass Spectrometry, Zhongli Zhang, David L. Smith, Jean B. Smith

Department of Chemistry: Faculty Publications

Identification of variant proteins from complex biological samples promises to contribute much to our understanding of the etiology of pathological states. Characterization of variants, due either to genetic mutations in protein sequences or to post-translational modifications, is considerably more difficult than the simple protein identifications typical of most current proteomic investigations. Identification of a few peptides by database retrieval is not adequate when the goal is to have a complete understanding of the modifications of the protein. Although one advantage of mass spectrometry is its ability to obtain specific responses to several components, the complexity of biological samples is often …

Nonlinear Effects Of Physisorption On Static Friction, G.T. Gao, Xiao Cheng Zeng, Dennis J. Diestler

Xiao Cheng Zeng Publications

The effects of a physisorbed film on the force of static friction in a model contact (monatomic adsorbate confined between plane-parallel walls) were investigated by Monte Carlo simulation. At fixed coverage the friction curve (shear yield stress vs normal stress) exhibits a marked nonlinearity, which results from a competition between adsorbate–wall interactions that predominate at low loads and wall–wall interactions that set in beyond a threshold load, which increases with coverage. Previous proximal-probe and computer experiments, carried out at high coverages, see only the initial (low-load) linear portion of the friction curve.

Magnetic Clusters On Single-Walled Carbon Nanotubes: The Kondo Effect In A One-Dimensional Host, Teri W. Odom, Jin-Lin Huang, Chin Li Cheung, Charles M. Lieber

Barry Chin Li Cheung Publications

Single-walled carbon nanotubes are ideal systems for investigating fundamental properties and applications of one-dimensional electronic systems. The interaction of magnetic impurities with electrons confined in one dimension has been studied by spatially resolving the local electronic density of states of small cobalt clusters on metallic single-walled nanotubes with a low-temperature scanning tunneling microscope. Spectroscopic measurements performed on and near these clusters exhibit a narrow peak near the Fermi level that has been identified as a Kondo resonance. Using the scanning tunneling microscope to fabricate ultra-small magnetic nanostructures consisting of small cobalt clusters on short nanotube pieces, spectroscopic studies of this …

Structural Biology With Carbon Nanotube Afm Probes, Adam T. Woolley, Chin Li Cheung, Jason H. Hafner, Charles M. Lieber

Barry Chin Li Cheung Publications

Carbon nanotubes represent ideal probes for high-resolution structural and chemical imaging of biomolecules with atomic force microscopy. Recent advances in fabrication of carbon nanotube probes with sub-nanometer radii promise to yield unique insights into the structure, dynamics and function of biological macromolecules and complexes.

Ice Nanotube: What Does The Unit Cell Look Like?, Kenichiro Koga, Ruben D. Parra, Hideki Tanaka, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

It is discovered that for an n-gonal ice nanotube built from stacking a single type of n-gonal rings of water, the unit cell consists of two stacked n-gonal rings. In one ring the O–H bonds of water molecules line up clockwise whereas in the other ring the O-H bonds line up counterclockwise. Among the n-gonal ice nanotubes examined, the pentagonal or hexagonal ice nanotube appears to be the most stable.

Analysis Of The Nico2O4 Spinel Surface With Auger And X-Ray Photoelectron Spectroscopy, J.-G. Kim, D. L. Pugmire, D. Battaglia, Marjorie Langell

Marjorie A. Langell Publications

Nickel cobaltite, NiCo₂O₄, has been synthesized by sol–gel and thermal decomposition techniques and the surface composition studied with Auger (AES) and X-ray photoelectron spectroscopies (XPS). The asintroduced samples are near-stoichiometric, although samples fabricated by thermal decomposition tend to be oxygen-defi cient by approximately 25% of the predicted spinel concentration. Nickel 2p XPS indicates the predominant form of the metal to be Ni²⁺, with the cations located in octahedral sites. The cobalt cations are equally divided between tetrahedral and octahedral sites as Co³⁺. The oxygen XP 1s spectrum is composed of two peaks, …

Structural Relatedness Of Distinct Determinants Recognized By Monoclonal Antibody Tp25.99 On Ss2-Microglobulin-Associated And Ss2-Microglobulin-Free Hla Class I Heavy Chains, Smruti A. Desai, Xinhui Wang, Elvyra J. Noronha, Qinwei Zhou, Vera Rebmann, Hans Grosse-Wilde, Franklin J. Moy, Robert Powers, Soldano Ferrone

Department of Chemistry: Faculty Publications

The association of HLA class I heavy chains with ß₂-microglobulin (ß₂m) changes their antigenic profile. As a result, Abs react with either ß₂m-free or ß₂m-associated HLA class I heavy chains. An exception to this rule is the mAb TP25.99, which reacts with both ß₂m-associated and ß₂m-free HLA class I heavy chains. The reactivity with ß₂m-associated HLA class I heavy chains is mediated by a conformational determinant expressed on all HLA-A, -B, and -C Ags. This determinant has been mapped to amino acid residues 194–198 in the …

Carbon Nanotube-Based Nonvolatile Random Access Memory For Molecular Computing, Thomas Rueckes, Kyoungha Kim, Ernesto Joselevich, Greg Y. Tseng, Chin Li Cheung, Charles M. Lieber

Barry Chin Li Cheung Publications

A concept for molecular electronics exploiting carbon nanotubes as both molecular device elements and molecular wires for reading and writing information was developed. Each device element is based on a suspended, crossed nanotube geometry that leads to bistable, electrostatically switchable ON/OFF states. The device elements are naturally addressable in large arrays by the carbon nanotube molecular wires making up the devices. These reversible, bistable device elements could be used to construct nonvolatile random access memory and logic function tables at an integration level approaching 1012 elements per square centimeter and an element operation frequency in excess of 100 gigahertz. The …

Growth And Fabrication With Single-Walled Carbon Nanotube Probe Microscopy Tips, Chin Li Cheung, Jason H. Hafner, Teri W. Odom, Kyoungha Kim, Charles M. Lieber

Barry Chin Li Cheung Publications

Single-walled carbon nanotube (SWNT) probe microscopy tips were grown by a surface growth chemical vapor deposition method. Tips consisting of individual SWNTs (1.5–4 nm in diameter) and SWNT bundles (4–12 nm in diameter) have been prepared by design through variations in the catalyst and growth conditions. In addition to high-resolution imaging, these tips have been used to fabricate SWNT nanostructures by spatially controlled deposition of specific length segments of the nanotube tips.

Femtosecond Luminescence Dynamics In A Nonlinear Optical Organic Dendrimer, O. Varnavski, A. Leanov, L. Liu, James M. Takacs, T. Goodson Iii

James M. Takacs Publications

The ultrafast intrinsic dynamics of an organic dendrimer in solution and in a thin film is reported using fluorescence upconversion spectroscopy. Femtosecond decay is detected at higher emission energies, while at lower energies a fluorescence rise time (∼3 ps) was observed that is dependent on the solvent’s polarity. A strong excitation energy dependence of the decay pattern was also observed. Different synthetic functional groups that comprise the macromolecular dendrimer structure were investigated. The mechanism, which describes the complex dynamics in the dendrimer system, was found to be associated with the excitation of the attached chromophore nitroaminostilbene. These results indicate the …

The Melting Temperature Of Proton-Disordered Hexagonal Ice: A Computer Simulation Of 4-Site Transferable Intermolecular Potential Model Of Water, G.T. Gao, Xiao Cheng Zeng, Hideki Tanaka

Xiao Cheng Zeng Publications

We report computer simulation results of free energies of proton-disordered hexagonal ice and liquid water at atmospheric pressure with the 4-site transferable intermolecular potential model of water. A new reference system is used to calculate the free energy of the ice phase. The melting point of proton-disordered hexagonal ice at atmospheric pressure is found to be T_m=238 (±7) K. This result is consistent with a previous estimation, 230K< T_mK, from molecular dynamic simulation of the surface melting of the proton-disordered hexagonal ice [G.-J. Kroes, Surf. Sci. 275, 365 (1992)].

Quantitative Measurement Of Guest–Host Interactions In Supramolecular Systems: A Comparative Brillouin Scattering Study Of The Dianin’S Compound Clathrand And Two Of Its Isostructural Clathrates, C.A. Sandstedt, D. Michalski, Craig J. Eckhardt

Craig J. Eckhardt Publications

Single, isomorphous crystals of the guest-free clathrand of Dianin’s compound and two of its clathrates containing two ethanols and a heptanol, respectively, have been studied by Brillouin scattering to obtain their complete elastic constant tensors. The values found for individual elastic constants are related to microscopic interactions of the guests and host cage using the clathrand as the reference. Direct correlation of the interference of the guest heptanol molecule with the hexamer hydrogen-bonded network of the host cage to reduced stiffness of this clathrate is demonstrated. In contrast, the ethanol-containing clathrate is demonstrated to have negligible interaction of the guests …

Carbon Nanotube Atomic Force Microscopy Tips: Direct Growth By Chemical Vapor Deposition And Application To High-Resolution Imaging, Chin Li Cheung, Jason H. Hafner, Charles M. Lieber

Barry Chin Li Cheung Publications

Carbon nanotubes are potentially ideal atomic force microscopy probes because they can have diameters as small as one nanometer, have robust mechanical properties, and can be specifically functionalized with chemical and biological probes at the tip ends. This communication describes methods for the direct growth of carbon nanotube tips by chemical vapor deposition (CVD) using ethylene and iron catalysts deposited on commercial silicon-cantilever-tip assemblies. Scanning electron microscopy and transmission electron microscopy measurements demonstrate that multiwalled nanotube and single-walled nanotube tips can be grown by predictable variations in the CVD growth conditions. Force-displacement measurements made on the tips show that they …

X-Ray Structure Of The Quinoprotein Ethanol Dehydrogenase From Pseudomonas Aeruginosa: Basis Of Substrate Specificity, Thomas Keitel, Annette Diehl, Tobias Knaute, John J. Stezowski, Wolfgang Hohne, Helmut Görisch

John J. Stezowski Publications

The homodimeric enzyme form of quinoprotein ethanol dehydrogenase from Pseudomonas aeruginosa ATCC 17933 crystallizes readily with the space group R3. The X-ray structure was solved at 2.6 Å resolution by molecular replacement. Aside from differences in some loops, the folding of the enzyme is very similar to the large subunit of the quinoprotein methanol dehydrogenases from Methylobacterium extorquens or Methylophilus W3A1. Eight W-shaped β-sheet motifs are arranged circularly in a propeller-like fashion forming a disk-shaped superbarrel. No electron density for a small subunit like that in methanol dehydrogenase could be found. The prosthetic group is located in the centre …

Freezing Transition Of A Strongly Dipolar Simple Fluid, G.T. Gao, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

The freezing transition of a strongly dipolar Lennard-Jones fluid is investigated using Monte Carlo simulation. It is found that the system undergoes a ferroelectric liquid-to-solid transition when cooled under a constant pressure. Near the triple point the stable solid phase is a body-centered orthorhombic ferroelectric crystal; a metastable ferroelectric solid phase with distorted hexagonal lattice structure is also discovered. To locate the freezing point, Gibbs free energies of the solid and liquid phase are determined using a thermodynamic integration method.

Molecular Dynamics Simulation Of Supersaturated Vapor Nucleation In Slit Pore, K. Yasuoka, G.T. Gao, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

Molecular dynamics simulations of nucleation of Lennard-Jones vapor confined in a slit pore have been performed. The walls of the slit pore are structureless walls; each wall interacts with vapor molecules via Lennard-Jones 9–3 potential. The rate of nucleation in the steady state is determined by analyzing time evolution of the cluster size distribution. At the same vapor density and temperature, the nucleation rate in the slit pore is higher than in the homogeneous vapor [K. Yasuoka and M. Matsumoto, J. Chem. Phys. 109, 8451 (1998)], irrespective of the strength of attraction between the wall and vapor molecules. However, this …

Octafluoro-Meso Tetraarylporphyrins And Methods For Making These Compounds, Stephen G. Dimagno

Department of Chemistry: Faculty Publications

The novel compounds of the present invention are f-octafluoro-meso-tetraarylporphyrins of formula (I) and their metallic complexes of formula (II):

B-octafluoro-meso-tetraaryl porphyrins are Synthesized by reacting 3,4-difluoropyrrole with an aromatic aldehyde in the presence of boron trifluoride etherate, followed by oxidation. The difluoropyrrole used in this reaction is pro duced by reacting 3,3,4,4-tetrafluoropyrroline or its corre sponding Salt, 3,3,4,4-tetrafluoropyrrolidinium Salt, with a base Such as potassium tert-butoxide. The metalloporphyrins of the present invention are Synthesized by deprontonating B-octafluoro-meso-tetraarylporphyrin ligands and treating Said ligands with metal ions.