NMR Spectrometer: 900-MHz (21.1 Tesla) Varian NMR System (Solids & Liquids) - (Everest) - (subscribed through Sept. 2013) Publications

2013

Arey BW, L Kovarik, O Qafoku, Z Wang, NJ Hess, and AR Felmy. 2013. "Identification of Fragile Microscopic Structures during Mineral Transformations in Wet Supercritical CO2." Microscopy and Microanalysis 19(2):268-275. doi:10.1017/S1431927612014171 Abstract In this study we examine the nature of highly fragile reaction products that form in low water content super critical carbon dioxide (scCO2) using a combination of scanning electron microscopy/focus ion beam (SEM/FIB), confocal Raman spectroscopy, helium ion microscopy (HeIM), and transmission electron microscopy (TEM). HeIM images show these precipitates to be fragile rosettes that can readily decompose even under slight heating from an electron beam. Using the TEM revealed details on the interfacial structure between the newly formed surface precipitates and the underlying initial solid phases. The detailed microscopic analysis revealed that the growth of the precipitates either followed a tip growth mechanism with precipitates forming directly on the forsterite surface if the initial solid was non-porous (natural forsterite) or growth from the surface of the precipitates where fluid was conducted through the porous (nanoforsterite) agglomerates to the growth center. The mechanism of formation of the hydrated/hydroxylated magnesium carbonate compound (HHMC) phases offers insight into the possible mechanisms of carbonate mineral formation from scCO2 solutions which has recently received a great deal of attention as the result of the potential for CO2 to act as an atmospheric greenhouse gas and impact overall global warming. The techniques used here to examine these fragile structures an also be used to examine a wide range of fragile material surfaces. SEM and FIB technologies have now been brought together in a single instrument, which represents a powerful combination for the studies in biological, geological and materials science.
Turcu RVF, DW Hoyt, KM Rosso, JA Sears, Jr, JS Loring, AR Felmy, and JZ Hu. 2013. "Rotor Design for High Pressure Magic Angle Spinning Nuclear Magnetic Resonance." Journal of Magnetic Resonance 226:64-69. doi:10.1016/j.jmr.2012.08.009 Abstract High pressure magic angle spinning (MAS) nuclear magnetic resonance (NMR) with a sample spinning rate exceeding 2.1 kHz and pressure greater than 165 bar has never been realized. In this work, a new sample cell design is reported, suitable for constructing cells of different sizes. Using a 7.5 mm high pressure MAS rotor as an example, internal pressure as high as 200 bar at a sample spinning rate of 6 kHz is achieved. The new high pressure MAS rotor is re-usable and compatible with most commercial NMR set-ups, exhibiting low 1H and 13C NMR background and offering maximal NMR sensitivity. As an example of its many possible applications, this new capability is applied to determine reaction products associated with the carbonation reaction of a natural mineral, antigorite ((Mg,Fe2+)3Si2O5(OH)4), in contact with liquid water in water-saturated supercritical CO2 (scCO2) at 150 bar and 50 C. This mineral is relevant to the deep geologic disposal of CO2, but its iron content results in too many sample spinning sidebands at low spinning rate. Hence, this chemical system is a good case study to demonstrate the utility of the higher sample spinning rates that can be achieved by our new rotor design. We expect this new capability will be useful for exploring solid-state, including interfacial, chemistry at new levels of high-pressure in a wide variety of fields.
Kovarik L, A Genc, CM Wang, A Qiu, CHF Peden, J Szanyi, and JH Kwak. 2013. "Tomography and High-Resolution Electron Microscopy Study of Surfaces and Porosity in a Plate-Like γ-Al2O3." Journal of Physical Chemistry C 117(1):179?186. doi:10.1021/jp306800h Abstract Morphological and surface characteristics of gamma-Al2O3 are topics of high relevance in the field of catalysis. Using tomography and high-resolution S/TEM imaging, we have studied the surface characteristics of a model gamma-Al2O3 synthesized in the shape of platelets and macroscopically defined by (110)Al2O3 and (111)Al2O3 surface facets. We show that the dominant (110)Al2O3 surface of the synthesized gamma-Al2O3 is not atomically flat but undergoes a significant reconstruction, forming nanoscale (111)Al2O3 terraces. In addition to high resolution imaging, tomographic analysis was carried out, enabling an examination of the pores/voids, which were found to be mostly enclosed within the bulk and inaccessible to gasses or metals. Tomographic analysis shows that the surfaces of the pores are defined exclusively by (100)Al2O3 and (111)Al2O3 facets. The importance of these findings is discussed in the context of relative surface energies of low index surfaces and ethanol desorption characteristics.
Chatman SME, PP Zarzycki, T Preocanin, and KM Rosso. 2013. "Effect of Surface Site Interactions on Potentiometric Titration of Hematite (α-Fe2O3) Crystal Faces." Journal of Colloid and Interface Science 391:125-134. doi:10.1016/j.jcis.2012.09.081 Abstract Time dependent potentiometric pH titrations were used to study the effect of atomic scale surface structure on the protonation behavior of the structurally well defined hematite/aqueous electrolyte interfaces. Our recently proposed thermodynamic model [1,23] was applied to measured acidimetric and alkalimetric titration hysteresis loops, collected from highly organized (001), (012), and (113) crystal face terminations using pH equilibration times ranging from 15 to 30 mins. Hysteresis loop areas indicate that (001) faces equilibrate faster than the (012) and (113) faces, consistent with the different expected ensembles of singly, doubly, and triply coordinated surface sites on each face. Strongly non-linear hysteretic pH-potential relationships were found, with slopes exceeding Nernstian, collectively indicating that protonation and deprotonation is much more complex than embodied in present day surface complexation models. The asymmetrical shape of the acidimetric and alkalimetric titration branches were used to illustrate a proposed steric "leaky screen" repulsion/trapping interaction mechanism that stems from high affinity singly-coordinated sites electrostatically and sterically screening lower affinity doubly and triply coordinated sites. Our data indicate that site interaction is the dominant phenomenon defining surface potential accumulation behavior on single crystal faces of metal oxide minerals.
Nielsen TK, AJ Karkamkar, ME Bowden, F Besenbacher, TR Jensen, and T Autrey. 2013. "Methods to Stabilize and Destabilize Ammonium Borohydride." Dalton Transactions 42(3):680-687. doi:10.1039/C2DT31591B Abstract Ammonium borohydride, NH4BH4, has a high hydrogen content of ρm = 24.5 wt% H2 and releases 18 wt% H2 below T = 160 °C. However, the half-life of bulk NH4BH4 at ambient temperatures, ~6 h, is insufficient for practical applications. The decomposition of NH4BH4 (ABH2) was studied at variable hydrogen and argon back pressures to investigate possible pressure mediated stabilization effects. The hydrogen release rate from solid ABH2 at ambient temperatures is reduced by ~16 % upon increasing the hydrogen back pressure from 5 to 54 bar. Similar results were obtained using argon pressure and the observed stabilization may be explained by a positive volume of activation in the transition state leading to hydrogen release. Nanoconfinement in mesoporous silica, MCM-41, was investigated as alternative means to stabilize NH4BH4. However, other factors appear to significantly destabilize NH4BH4 and it rapidly decomposes at ambient temperatures into [(NH3)2BH2][BH4] (DADB) in accordance with the bulk reaction scheme. The hydrogen desorption kinetics from nanoconfined [(NH3)2BH2][BH4] is moderately enhanced as evidenced by a reduction in the DSC decomposition peak temperature of ΔT = -13 °C as compared to the bulk material. Finally, we note a surprising result, storage of DADB at temperature < -30 °C transformed, reversibly, the [(NH3)2BH2][BH4] into a new low temperature polymorph as revealed by both XRD and solid state MAS 11B MAS NMR. TA & AK are thankful for support from the US Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. A portion of the research was performed using EMSL, 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 (PNNL). PNNL is operated by Battelle.
Karkamkar AJ, K Parab, DM Camaioni, D Neiner, HM Cho, TK Nielsen, and T Autrey. 2013. "A Thermodynamic and Kenetic Study of the Heterolytic Activation of Hydrogen by Frustrated Borane-Amine Lewis Pairs." Dalton Transactions 42(3):615-619. doi:10.1039/c2dt31628e Abstract Calorimetry is used to measure the reaction enthalpies of hydrogen activation by 2,6-lutidine (Lut), 2,2,6,6-tetramethylpiperidine (TMP), N-methyl-2,2,6,6-tetramethylpiperidine (MeTMP) and tri-tert-butylphosphine (TBP) with tris(pentafluorophenyl)borane (BCF). At 6.6 bar H2 the conversion of the Lewis acid Lewis base pair to the corresponding ionic pair in bromobenzene at 294 K was quantitative in under 60 minutes. Integration of the heat release from the reaction of the Frustrated Lewis Pair (FLP) with hydrogen as a function of time yields a relative rate of hydrogenation in addition to the enthalpy of hydrogenation. The half-lives of hydrogenation range from 230 seconds with TMP, ΔHH2 = -31.5(0.2) kcal/mol, to 1400 seconds with Lut, ΔHH2 = -23.4(0.4) kcal/mol. The 11B NMR spectrum of B(C6F5)3 in bromobenzene exhibits three distinct traits depending on the sterics of the Lewis base; (i) in the presence of pyridine, only the dative bond adduct pyridine--B(C6F5)3 is observed, (ii) in the presence of TMP and MeTMP only the free B(C6F5)3 is observed, and (iii) in the presence of Lut both the free B(C6F5)3 and the Lut--B(C6F5)3 adduct appear in equilibrium. A measure of the change in Keq of Lut + B(C6F5)3 <->Lut--B(C6F5)3 as a function of temperature provides thermodynamic properties of the Lewis acid Lewis base adduct, ΔH = -17.9(1.0) kcal/mol and a ΔS = -49.2(2.5) cal/mol K, suggesting the Lut--B(C6F5)3 adduct is more stable in bromobenzene than in toluene. This research was supported by the U.S. Department of Energy’s Basic Energy Sciences, Division of Chemical Sciences, Biosciences and Geosciences. D.M.C. and A.K. acknowledges support by the Laboratory Directed Research and Development program at the Pacific Northwest National Laboratory (PNNL) to perform kinetic analyses of the calorimetry data. The work was performed in part at EMSL, a national scientific user facility sponsored by the DOE Office of Biological and Environmental Research. EMSL is located at Pacific Northwest National Laboratory (PNNL), which is operated by Battelle for DOE.
Yang Y, CA Mims, D Mei, CHF Peden, and CT Campbell. 2013. "Mechanistic Studies of Methanol Synthesis over Cu from CO/CO2/H2/H2O Mixtures: the Source of C in Methanol and the Role of Water." Journal of Catalysis 298:10-17. doi:10.1016/j.jcat.2012.10.028 Abstract The low temperature (403 – 453K) conversions of CO:hydrogen and CO2:hydrogen mixtures (6 bar total pressure) to methanol over copper catalysts are both assisted by the presence of small amounts of water (mole fraction ~0.04%-0.5%). For CO2:hydrogen reaction mixtures, the water product from both methanol synthesis and reverse water gas shift serves to initiate both reactions in an autocatalytic manner. In the case of CO:D2 mixtures, very little methanol is produced until small amounts of water are added. The effect of water on methanol production is more immediate than in CO2:D2, yet the steady state rates are similar. Tracer experiments in 13CO:12CO2:hydrogen (with or without added water), show that the dominant source of C in the methanol product gradually shifts from CO2 to CO as the temperature is lowered. Cu-bound formate, the major IR visible surface species under CO2:hydrogen, is not visible in CO:moist hydrogen. Though formate is visible in the tracer experiments, the symmetric stretch is absent. These results, in conjunction with recent DFT calculations on Cu(111), point to carboxyl as a common intermediate for both methanol synthesis and reverse water gas shift, with formate playing a spectator co-adsorbate role.
Baugh L, LA Gallagher, R Patrapuvich, MC Clifton, AS Gardberg, TE Edwards, B Armour, DW Begley, SH Dieterich, DM Dranow, J Abendroth, JW Fairman, D Fox III, BL Staker, I Phan, A Gillespie, R Choi, S Nakazawa-Hewitt, MT Nguyen, AJ Napuli, L Barrett, GW Buchko, R Stacy, PJ Myler, LJ Stewart, C Manoil, and WC Van Voorhis. 2013. "Combining Functional and Structural Genomics to Sample the Essential Burkholderia Structome." PLoS One 8(1):e53851. doi:10.1371/journal.pone.0053851 Abstract Background: The genus Burkholderia includes pathogenic gram-negative bacteria that cause melioidosis, glanders, and pulmonary infections of patients with cancer and cystic fibrosis. Drug resistance has made development of new antimicrobials critical. Many approaches to discovering new antimicrobials, such as structure-based drug design and whole cell phenotypic screens followed by lead refinement, require high-resolution structures of proteins essential to the parasite. Methodology/Principal Findings: We experimentally identified 406 putative essential genes in B. thailandensis, a low virulence species phylogenetically similar to B. pseudomallei, the causative agent of melioidosis, using saturation-level transposon mutagenesis and next-generation sequencing (Tn-seq). We selected 315 protein products of these genes based on structure-determination criteria, such as excluding very large and/or integral membrane proteins, and entered them into the Seattle Structural Genomics Center for Infection Disease (SSGCID) structure determination pipeline. To maximize structural coverage of these targets, we applied an ‘‘ortholog rescue’’ strategy for those producing insoluble or difficult to crystallize proteins, resulting in the addition of 387 orthologs (or paralogs) from seven other Burkholderia species into the SSGCID pipeline. This structural genomics approach yielded structures from 31 putative essential targets from B. thailandensis, and 25 orthologs from other Burkholderia species, yielding an overall structural coverage for 49 of the 406 essential gene families, with a total of 88 depositions into the Protein Data Bank. Of these, 25 proteins have properties of a potential antimicrobial drug target i.e., no close human homolog, part of an essential metabolic pathway, and a deep binding pocket. We describe the structures of several potential drug targets in detail. Conclusions/Significance: This collection of structures, solubility and experimental essentiality data provides a resource for development of drugs against infections and diseases caused by Burkholderia. All expression clones and proteins created in this study are freely available by request.
Wang Z, AR Felmy, CJ Thompson, JS Loring, AG Joly, KM Rosso, HT Schaef, and DA Dixon. 2013. "Near-Infrared Spectroscopic Investigation of Water in Supercritical CO2 and the Effect of CaCl2." Fluid Phase Equilibria 338:155-163. doi:10.1016/j.fluid.2012.11.012 Abstract Near-infrared (NIR) spectroscopy was applied to investigate the dissolution and chemical interaction of water dissolved into supercritical carbon dioxide (scCO2) and the influence of CaCl2 in the co-existing aqueous phase at fo empe e : 40 50 75 nd 100 C at 90 atm. Consistent with the trend of the vapor pressure of water, the solubility of pure water in scCO2 inc e ed f om 40 ˚C (0.32 mole%) o 100 ˚C (1.61 mole%). The presence of CaCl2 negatively affects the solubility of water in scCO2: at a given temperature and pressure the solubility of water decreased as the concentration of CaCl2 in the aqueous phase increased, following the trend of the activity of water. A 40 ˚C, the water concentration in scCO2 in contact with saturated CaCl2 aqueous solution was only 0.16 mole%, a drop of more than 50% as compared to pure water while that a 100 ˚C was 1.12 mole%, a drop of over 30% as compared to pure water, under otherwise the same conditions. Analysis of the spectral profiles suggested that water dissolved into scCO2 exists in the monomeric form under the evaluated temperature and pressure conditions, for both neat water and CaCl2 solutions. However, its rotational degrees of freedom decrease at lower temperatures due to higher fluid densities, leading to formation of weak H2O:CO2 Lewis acid-base complexes. Similarly, the nearly invariant spectral profiles of dissolved water in the presence and absence of saturated CaCl2 under the same experimental conditions was taken as evidence that CaCl2 dissolution in scCO2 was limited as the dissolved Ca2+/CaCl2 would likely be highly hydrated and would alter the overall spectra of waters in the scCO2 phase.
Zhang Y, A Gardberg, TE Edwards, B Sankaran, H Robinson, SM Varnum, and GW Buchko. 2013. "Structural Insights into the Functional Role of the Hcn Sub-domain of the Receptor-Binding Domain of the Botulinum Neurotoxin Mosaic Serotype C/D." Biochimie 95(7):1379-1385. doi:10.1016/j.biochi.2013.03.006 Abstract Botulinum neurotoxin (BoNT), the causative agent of the deadly neuroparalytic disease botulism, is the most poisonous protein known for humans. Produced by different strains of the anaerobic bacterium Clostridium botulinum, BoNT effects cellular intoxication via a multistep mechanism executed by the three modules of the activated protein. Endocytosis, the first step of cellular intoxication, is triggered by the ~50 kDa, heavy-chain receptor-binding module (HCR) that is specific for a ganglioside and a protein receptor on neuronal cell surfaces. This dual receptor recognition mechanism between BoNT and the host cell’s membrane is well documented and occurs via specific intermolecular interactions with the C-terminal sub-domain, Hcc, of BoNT-HCR. The N-terminal sub-domain of BoNT-HCR, Hcn, comprises ~50% of BoNT-HCR and adopts a B-sheet jelly roll fold. While suspected in assisting cell surface recognition, no unambiguous function for the Hcn sub-domain in BoNT has been indentified. To obtain insights into the potential function of the Hcn sub-domain in BoNT, the first crystal structure of a BoNT with an organic ligand bound to the Hcn sub-domain has been obtained. Here, we describe the crystal structure of BoNT/CD-HCR determined at 1.70 Å resolution with a tetraethylene glycol (PG4) molecule bound in an hydrophobic cleft between B-strands in the B-sheet jelly fold roll of the Hcn sub-domain. The molecule is completely engulfed in the cleft, making numerous hydrophobic (Y932, S959, W966, and D1042) and hydrophilic (S935, W977, L979, N1013, and I1066) contacts with the protein’s side chain and backbone that may mimic in vivo interactions with the phospholipid membranes on neuronal cell surfaces. A sulfate ion was also observed bound to residues T1176, D1177, K1196, and R1243 in the Hcc sub-domain of BoNT/CD-HCR. In the crystal structure of a similar protein, BoNT/D-HCR, a sialic acid

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