Scientific Publications 2007
2007. "Cr(VI) removal from aqueous solution by activated carbon coated with quaternized poly(4-vinylpyridine)." Environmental Science & Technology 41(13):4748-4753. doi:10.1021/es061969b Abstract A composite sorbent (GAC-QPVP) was prepared by coating poly(4-vinylpyridine) onto a commercial activated carbon (F400, Calgon), followed by cross-linking and quaternization processes. The sorbent was characterized by scanning electron microscopy, point of zero charge measurement, and BET analysis. Batch experiments with variable pH, ionic strength, and concentrations of Cr(VI), sorbent, and competing anions were conducted to evaluate the selective sorption of Cr(VI) from aqueous solutions. The equilibrium uptake of Cr(VI) increased with decreasing pH, decreasing ionic strength, and increasing sorbent concentration. The estimated maximum equilibrium uptake of chromium was 53.7 mg/g at pH = 2.25, 30.7 mg/g at pH = 3.65, and 18.9 mg/g at pH = 6.03, which were much higher than the maximum capacity of 3.5 mg/g for the PVP-coated silica gel at pH = 5.0 (optimum pH for Cr(VI) sorption) reported in the literature . The effect of phosphate, sulfate, and nitrate was minor on the selective sorption of Cr(VI) and only when above a specific molar ratio. An ion exchange model that was linked with aqueous speciation chemistry reasonably well describe Cr(VI) sorption as a function of pH, ionic strength, and Cr(VI) concentration. Model simulations suggested that sorbed Cr(VI) was partially reduced to Cr(III) on the sorbent when pH < 4. The presence of Cr(III) on the sorbent was confirmed by the X-ray photoelectron spectroscopic analysis of the reacted sorbent. Overall, the results showed that GAC-QPVP can effectively remove Cr(VI) from aqueous solutions under a wide range of experimental conditions.
2007. "An efficient parallelization scheme for molecular dynamics simulations with many-body, flexible, polarizable empirical potentials: Application to water." Theoretical Chemistry Accounts 117(1):73-84. Abstract An efficient parallelization scheme for classical Molecular Dynamics simulations with flexible polarizable empirical potentials is presented. It is based on the standard Ewald summation technique to handle the long-range electrostatic and induction interactions. The algorithm for this parallelization scheme is designed for systems containing several thousands of polarizable sites in the simulation box. Its performance is evaluated during Molecular Dynamics simulations under periodic boundary conditions with unit cell sizes ranging from 128-512 water molecules employing two exible, polarizable water models [POL1(F) and TTM2-F] containing 1 and 3 polarizable sites respectively. The efficiency of the algorithm, is evaluated against a flexible, pairwise-additive water model (TIP4F). The benchmarks were performed on both shared and distributed memory platforms. As a result of the efficient calculations of the induced dipole moments, a superlinear scaling as a function of the number of the processors is observed in several cases. To the best of our knowledge, this is the first attempt for a parallel implementation of a polarizable potential under periodic boundary conditions. Guidelines for adapting the algorithm for larger systems are also discussed. This research was performed in part using the Molecular Science Computing Facility (MSCF) in the William R. Wiley Environmental Molecular Sciences laboratory, a national scientific user facility sponsored by the U.S. Department of Energy’s Office of Biological and Environmental Research located at the Pacific Northwest National Laboratory. The Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy under contract DE-AC05-76RL01830.
2007. "QUANTIFICATION OF ACTINIDE ALPHA-RADIATION DAMAGE IN MINERALS AND CERAMICS." Nature 445:190-193. doi:10.1038/nature05425 Abstract There are large amounts of heavy alpha-emitters in nuclear waste and nuclear materials inventories stored in various sites around the world. These include plutonium and minor actinides such as americium and curium. In preparation for geological disposal there is a consensus that actinides that have been separated from spent nuclear fuel should be immobilised within mineral-based ceramics rather than glass. Over the long-term, the alpha-decay taking place in these ceramics will severely disrupt their crystalline structure and reduce their durability. A fundamental property in predicting cumulative radiation damage is the number of atoms permanently displaced per alpha–decay. Currently, this number is estimated as 1000-2000 atoms/alpha decay event. Here, we report nuclear magnetic resonance, spin-counting experiments that measure close to 5000 atoms/alpha decay event in radiation damaged natural zircons. New radiological NMR measurements on highly radioactive, 239Pu zircon show damage similar to that created by 238U and 232Th in mineral zircons at the same dose, indicating no significant effect of dose rate. Based on these measurements, the initially crystalline structure of a 10 wt% 239Pu zircon would be amorphous after only 1400 years in a geological repository. These measurements establish a basis for assessing the long-term structural durability of actinide-containing ceramics based on an atomistic understanding of the fundamental damage event.
2007. "Coherent Carbon Cryogel-Ammonia Borane Nanocomposites for Improved Hydrogen Storage." Journal of Physical Chemistry B 111(26):7469-7472. doi:10.1021/jp072448t Abstract Ammonia borane has been adsorbed into mesoporous carbon cryogels in an effort to manipulate the hydrogen release properties. TEM studies showed that ammonia borane was incorporated into the cyrogel structure. Thermochemical analysis of the dehydrogenation indicated that the hydrogen release properties of ammonia borane were enhanced when incorporated into cryogels. Dehydrogenation occured at lower temperatures and the non-hydrogen volatile products were controlled, liimiting borazine formation.
2007. "A solid-state 55Mn NMR spectroscopy and DFT investigation ofmanganese pentacarbonyl compounds." Physical Chemistry Chemical Physics. PCCP 9:1226-1238. doi:10.1039/b616821c Abstract Central transition 55Mn NMR spectra of several solid manganese pentacarbonyls acquired at magnetic field strengths of 11.75, 17.63, and 21.1 T are presented. The variety of distinct powder sample lineshapes obtained demonstrates the sensitivity of solid-state 55Mn NMR to the local bonding environment, including the presence of crystallographically unique Mn sites, and facilitates the extraction of the Mn chemical shift anisotropies, CSAs, and the nuclear quadrupolar parameters. The compounds investigated include molecules with approximate C4v symmetry, LMn(CO)5 (L ¼ Cl, Br, I, HgMn(CO)5, CH3) and several molecules of lower symmetry (L ¼ PhCH2, Ph3*nClnSn (n ¼ 1, 2, 3)). For these compounds, the Mn CSA values range from o100 ppm for Cl3SnMn(CO)5 to 1260 ppm for ClMn(CO)5. At 21.1 T the 55Mn NMR lineshapes are appreciably influenced by the Mn CSA despite the presence of significant 55Mn quadrupolar coupling constants that range from 8.0 MHz for Cl3SnMn(CO)5 to 35.0 MHz for CH3Mn(CO)5. The breadth of the solid-state 55Mn NMR spectra of the pentacarbonyl halides is dominated by the CSA at all three applied magnetic fields. DFT calculations of the Mn magnetic shielding tensors reproduce the experimental trends and the magnitude of the CSA is qualitatively rationalized using a molecular orbital, MO, interpretation based on Ramsey’s theory of magnetic shielding. In addition to the energy differences between symmetry-appropriate occupied and virtual MOs, the d-character of the Mn MOs is important for determining the paramagnetic shielding contribution to the principal components of the magnetic shielding tensor.
2007. "Peptide Conformations for a Microarray Surface-Tethered Epitope of the TumorSuppressor p53." Journal of Physical Chemistry B 111(49):13797-13806. doi:10.1021/jp075051y Abstract The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. Peptides or proteins near surfaces exhibit different structural properties from those present in a homogeneous solution, and these differences give rise to varied biological activity. Therefore, understanding the detailed molecular structure of these molecules tethered to a surface is important for interpreting the performance of the various microarrays based on the activities of the immobilized peptides or proteins. We performed molecular dynamics simulations of a pentapeptide, RHSVV, an epitope of the tumor suppressor protein p53, tethered via a spacer on a functionalized silica surface and free in solution, to study their structural and conformational differences. These calculations allowed analyses of the peptide-surface interactions, the sequence orientations, and the translational motions of the peptide on the surface to be performed. Conformational similarities are found among dominant structures of the tethered and free peptide. In the peptide microarray simulations, the peptide fluctuates between a parallel and tilted orientation driven in part by the hydrophobic interactions between the nonpolar peptide residues and the methyl-terminated silica surface. The perpendicular movement of the peptide relative to the surface is also restricted due to the hydrophobic nature of the microarray surface. With regard to structures available for recognition and binding, we find that similar conformations to those found in solution are available to the peptide tethered to the surface, but with a shifted equilibrium constant. Comparisons with experimental results show important implications of this for peptide microarray design and assays.
2007. "Reactive Ballistic Deposition of Porous TiO2 Films: Growth and Characterization." Journal of Physical Chemistry C 111(12):4765-4773. doi:10.1021/jp067641m Abstract Nanoporous, high-surface area films of TiO2 are synthesized by reactive ballistic deposition of titanium metal in an oxygen ambient. Auger electron spectroscopy (AES) is used to investigate the stoichiometric dependence of the films on growth conditions (surface temperature and partial pressure of oxygen). Scanning and transmission electron microscopy show that the films consist of arrays of separated filaments. The surface area and the distribution of binding site energies of the films are measured as functions of growth temperature, deposition angle, and annealing conditions using temperature programmed desorption (TPD) of N2. TiO2 films deposited at 50 K at 70º from substrate normal display the greatest specific surface area of ~100 m2/g. In addition, the films retain greater than 70% of their original surface area after annealing to 600 K. The combination of high surface area and thermal stability suggest that these films could serve as supports for applications in heterogeneous catalysis.
2007. "The distinct proteome of placental malaria parasites." Molecular and Biochemical Parasitology 155(1):57-65. doi:10.1016/j.molbiopara.2007.05.010 Abstract Malaria proteins expressed on the surface of Plasmodium falciparum infected erythrocytes (IE) mediate adhesion and are targeted by protective immune responses. During pregnancy, IE sequester in the placenta. Placental IE bind to the molecule chondroitin sulfate A (CSA) and preferentially transcribe the gene that encodes VAR2CSA, a member of the PfEMP1 variant surface antigen family. Over successive pregnancies women develop specific immunity to CSA-binding IE and antibodies to VAR2CSA. We used tandem mass spectrometry together with accurate mass and time tag technology to study IE membrane fractions of placental parasites. VAR2CSA peptides were detected in placental IE and in IE from children, but the MC variant of VAR2CSA was specifically associated with placental IE. We identified six conserved hypothetical proteins with putative TM or signal peptides that were exclusively expressed by the placental IE, and 11 such proteins that were significantly more abundant in placental IE. One of these hypothetical proteins, PFI1785w, is a 42kDa molecule detected by Western blot in parasites infecting pregnant women but not those infecting children.
2007. "Design and Synthesis of Self-Assembled Monolayers on Mesoporous Supports (SAMMS): The Importance of Ligand Posture in Functional Nanomaterials." Journal of Materials Chemistry 17:2863-2874. doi:10.1039/b702422c Abstract Water, and water quality, are issues of critical importance to the future of humankind. The Earth’s water supplies have been contaminated by a wide variety of industrial, military and natural sources. The need exists for an efficient separation technology to remove heavy metal and radionuclide contamination from water. Surfactant templated synthesis of mesoporous ceramics provides a versatile foundation upon which to build high efficiency environmental sorbents. These nanoporous ceramics condense a huge amount of surface area into a very small volume. These mesoporous architectures can be subsequently functionalized through molecular self-assembly. These functional mesoporous materials offer significant capabilities in terms of removal of heavy metals and radionuclides from a variety of liquid media, including groundwater, contaminated oils and contaminated chemical weapons. They are highly efficient sorbents, whose rigid, open pore structure allows for rapid, efficient sorption kinetics. Their interfacial chemistry can be fine-tuned to selectively sequester a specific target species, such as heavy metals, tetrahedral oxometallate anions and radionuclides. This manuscript provides a review of the design, synthesis and performance of the sorbent materials. The role that ligand posture plays in the chemistry of these interfacial ligand fields is discussed.
2007. "Electronic Structure and Fragmentation Properties of [Fe4S4(SEt)4-X(SSEt)x]2-." International Journal of Mass Spectrometry 263(2-3):260-266. Abstract A limited exposure of (n-Bu4N)2[Fe4S4(SEt)4] solutions in acetonitrile to air was found to produce a new series of [4Fe-4S] cluster complexes, [Fe4S4(SEt)4-x(SSEt)x]2- (x = 1-4), with the original –SEt ligands substituted by –SSEt di-sulfide ligands, which were formed due to partial decomposition of the [4Fe-4S] core in parent [Fe4S4(SEt)4]2-. The products were first observed in the experiments with an ESI-Ion Trap-TOF mass spectrometer and were further identified using high resolution FTICR (Fourier Transform Ion Cyclotron Resonance) mass spectrometer. Photoelectron spectra of the [Fe4S4(SEt)4-x(SSEt)x]2- dianions revealed that the –SSEt coordination induced little change in the electronic structure of the [4Fe-4S] cluster, but the electron binding energies of [Fe4S4(SEt)4-x(SSEt)x]2- increased from 0.52 to 0.73 eV with increase in x from 0 to 4, suggesting a greater electron withdrawing ability of –SSEt than -SEt. In high resolution MS/MS experiments on [Fe4S4(SEt)3(SSEt)]2-/1-, clusters with both charge states yielded fragment [Fe4S4(SEt)3]-, suggesting that –SSEt could be lost either as a negatively charged ion SSEt- from the doubly charged precursor, or as a radical •SSEt from the singly charged species. The biological implication of the interaction between [Fe4S4(SEt)4]2- and O2 is discussed in comparison to the air exposure of [4Fe-4S] proteins to the air.