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SV-JIM, detailed pairwise structural variant calling using long-reads and genome assemblies
(Methods, 0001) Todd, Clarence; Jin, Lingling; McQuillan, Ian
This paper proposes a detailed process for SV calling that permits a data-driven assessment of multiple SV callers that uses both genome assemblies and long-reads. The process is implemented as a software pipeline named Structural Variant − Jaccard Index Measure, or SVJIM, using the Snakemake [20] workflow management system. Like most state-of-the-art SV callers, SV-JIM detects the presence of variations between pairs of genomes, but it streamlines the numerous SV calling stages into a single process for user convenience and evaluates the multiple SV sets produced using the Jaccard index measure to identify those with the highest consistency among the included SV callers. SV-JIM then produces aggregated SV results based on how many callers supported the reported SVs. For validation, SV-JIM was assessed through three case studies on the Homo sapiens genome and two plant genomes – Brassica nigra and Arabidopsis thaliana. Executing SV-JIM identified a significant amount of inter-caller variance which varied by tens of thousands of results on the larger Brassica nigra and Homo sapiens genomes. Further, aggregating the SV sets helped simplify better retention of the less frequently occurring SV types by requiring a level of minimum support rather than from a specific SV caller combination. Finally, these case studies identified a potential for inflated precision reporting that can occur during evaluation. SV-JIM is available publicly under MIT license at https://github.com/USask-BINFO/SV-JIM
Oxazolium Salts as Organocatalysts for the Umpolung of Aldehydes
(ACS Publications, 10/1/2018) Garapati, Venkata Krishna Rao; Gravel, Michel
Oxazolium salts were successfully employed for the first time as organocatalysts for benzoin, Stetter, and redox esterification reactions. An N-mesityl oxazolium salt catalyzed homobenzoin reaction of aromatic, heteroaromatic, and aliphatic aldehydes delivered α-hydroxy ketones in high yields. This new type of catalyst proved remarkably effective for the Stetter reaction of challenging substrates such as β-alkyl-α,β-unsaturated ketones and electron-rich aromatic aldehydes in comparison to common thiazolium and triazolium salts.
Connecting Molecular Conformation to Aggregation in P3HT Using Near Edge X-ray Absorption Fine Structure Spectroscopy
(American Chemical Society, 10/11/2017) Martinson, Mercedes; Urquhart, Stephen; Eger, Shaylin; Murcia, Victor; Ade, Harald; Collins, Brian
Carbon 1s Near Edge X-ray Absorption Fine Structure (NEXAFS) and UV-vis spectroscopy are used to examine differences between highly aggregated and poorly aggregated forms of the polymer poly(3-hexylthiophene) (P3HT), based on as-cast and annealed regio-random and regio-regular P3HT samples. UV-vis spectra show characteristic signatures of unaggregated P3HT in regio-random P3HT, and of H-aggregation in regio-regular P3HT samples. Distinct spectroscopic differences, including energy shifts, are observed in the NEXAFS spectra of aggregated P3HT relative to the unaggregated forms. These differences are reproduced with Transition – Potential Density Functional Theory (TP-DFT) calculations which explore aggregation and molecular confirmation. Differences in the NEXAFS spectra of P3HT are assigned to thiophene backbone twisting in the unaggregated forms of P3HT, and to various degrees of chain planarization in aggregated forms of P3HT that also correlate to the exciton bandwidth. These results open up the prospect of charactering conformation and related difficult to assess structural details through NEXAFS spectroscopy and correlative theory and electronic structure analysis.
Temperature Dependence in the NEXAFS Spectra of n-Alkane
(American Chemical Society, 11/16/2018) Urquhart, Stephen; Perera, Sahan; Sadegh, Shokatian; Wang, Jian
The near edge X-ray absorption fine structure (NEXAFS) spectra of orthorhombic single crystals of n-octacosane (n-C28H58), recorded at room temperature (298 K) and at cryogenic temperatures (93 K), show distinct differences. The characteristic carbon 1s → σ*C–H band in the NEXAFS spectrum of n-C28H58 is broader and has a lower-energy onset in its room temperature spectrum than in its NEXAFS spectrum recorded at cryogenic temperatures. Density functional theory simulations show that nuclear motion and molecular disorder contribute to the observed spectral broadness and are the origin of the low-energy onset of the C–H band in the room temperature spectrum
Part-per-trillion LC-MS/MS determination of neonicotinoids in small volumes of songbird plasma
(Elsevier, 12/10/2018) Hao, Chunyan; Eng, Margaret; Morrissey, Christy; Sun, Fengrong
Neonicotinoids are the most widely used class of insecticides in the world, and there are increasing concerns about their effects on non-target organisms. Analytical methods to diagnose exposure to neonicotinoids in wildlife are still very limited, particularly for small animals such as songbirds. Blood can be used as a non-lethal sampling matrix, but the sample volume is limited by body size. Neonicotinoids have a low bioaccumulation potential and are rapidly metabolized, therefore, sensitive assays are critically needed to reliably detect their residues in blood samples. We developed an efficient LC-MS/MS method at a part-per-trillion (pg/ml) level to measure eight neonicotinoid related insecticides (acetamiprid, clothianidin, dinotefuran, flonicamid, imidacloprid, nitenpyram, thiacloprid and thiamethoxam) plus one metabolite (6-chloronicotinic acid) in small volumes (50 μL) of avian plasma. The average recovery of target compounds ranged from 95.7 to 101.3%, and relative standard deviations were between 0.82 and 2.13%. We applied the method to screen blood samples from 36 seed-eating songbirds (white-crowned sparrows; Zonotrichia leucophrys) at capture, and detected imidacloprid in 78% (28 of 36), thiamethoxam in 22% (8 of 36), thiacloprid in 11% (4 of 36), and acetamiprid in 11% (4 of 36) of wild-caught sparrows. 6 h after capture, birds were orally dosed with 0 (control), 1.2 or 3.9 mg of imidacloprid/kg bw, test results using this method indicated that plasma imidacloprid was significantly elevated (low 26-times, high 316-times) in exposed groups. This is the first study to confirm neonicotinoid exposure in small free-living songbirds through non-lethal blood sampling, and to demonstrate that environmentally realistic doses significantly elevate circulating imidacloprid concentrations. This sensitive method could be applied to characterize exposure to neonicotinoids in free-living wildlife and in toxicological studies.
Enantioselective Stetter Reactions Catalyzed by Bis(amino)cyclopropenylidenes: Important Role for Water as an Additive
(ACS Publications, 12/15/2020) Rezazadeh Khalkhali, Mehran; Wilde, Myron M. D.; Gravel, Michel
The first highly enantioselective intermolecular Stetter reaction using simple enones is reported. A series of novel chiral BAC structures were designed and prepared. They were tested in the Stetter reaction with simple aldehydes and enones. The products were generated in excellent yields and enantioselectivities (up to 92% ee). Surprisingly, a substoichiometric amount of water was crucial to obtain high enantioselectivities. Chiral BACs were also shown to catalyze 1,6-conjugate addition reactions with paraquinone methides enantioselectively.
Chisholm on Psychological Attributes
(Austrian Ludwig Wittgenstein Society, 1993-01-01) Pfeifer, Karl
What is it for an attribute to be psychological? One clever and inventive, albeit somewhat Byzantine answer to this vexing philosophical question has lately been proposed by Roderick M. Chisholm. Chisholm’s approach is to take a small number of technical philosophical notions as given and then employ these in a series of definitions which together yield an account of the psychological. I examine Chisholm’s account and show that it doesn’t work.
Internal thermal boundary layer stability in phase transition modulated convection
(AGU, 1997-02) Butler, S.L.; Peltier, W.R.
The stability of a horizontal thermal boundary layer embedded within a very viscous fluid is investigated using the formalism of linear stability analysis. Thin thermal boundary layers in deep fluid regions and in the absence of phase transition and dynamical effects are thereby shown to be unstable at extremely long wavelengths. The stability of the internal thermal boundary layer which may exist at 660 km depth in the Earth's mantle as a consequence of the dynamical influence of the endothermic phase transition from γ spinel to a mixture of perovskite and magnesiowüstite, recently discussed in some detail by Solheim and Peltier [1994a], is investigated in order to better understand the “avalanche effect” observed in this and similar nonlinear, time dependent simulations of the mantle convection process. It is demonstrated that if the stability problem is treated as purely thermal, then the boundary layer is predicted to be extremely unstable and the presence of the 660‐km endothermic phase transition at middepth within the boundary layer is further destabilizing. When the kinematic effect of flow convergence onto the boundary layer and phase transition region is active, however, it is shown that the layer may be strongly stabilized. In the regime of physically realistic velocity convergence, the critical Rayleigh number is predicted to lie in the range suggested by the numerical simulations of Solheim and Peltier [1994a]. A threshold value of the magnitude of the Clapeyron slope of the endothermic phase transition for a given velocity convergence is also shown to exist, beyond which the fastest‐growing mode of instability changes from avalanche type to layered type.
Morphologically complex plant macrofossils from the Late Silurian of Arctic Canada
(Botanical Society of America, 2002-06) Kotyk, Michele E.; Basinger, James F.; Gensel, Patricia G.; de Freitas, Tim A.
In addition to vegetative remains, fertile remains from ten plants, representing seven distinct taxa whose size and complexity are much greater than most contemporaneous fossils, are reported from late Ludlow (Ludfordian) sediments of Bathurst Island in Nunavut, Canada. Evidence for the age of these beds is gathered from stratigraphic relationships and index fossils including conodonts, graptolites, and brachiopods. Zosterophylls dominate the collection, some of which constitute the earliest record of fertile structures arranged in dense clusters and longitudinal rows along axes. Representatives include a plant that resembles Bathurstia, one species of Zosterophyllum, and two specimens that bear affinity to this genus. Distichophytum is also represented, as is a new zosterophyll named Macivera gracilis. The prevalence of sporangial clustering and reduced sporangial stalks in this flora leads to a discussion of the origins and significance of these morphological features. Following a review of some of the other Silurian floras, particularly the Baragwanathia-bearing Lower Plant Assemblage of Victoria, Australia, which also shows morphological advancement over the rhyniophytoid-dominated floras common to Laurussia, it is concluded that the Bathurst Island flora presents the best evidence to date of substantial morphological diversity, complexity, and stature of vascular land plants in this period.
Recommended nomenclature of epidote-group minerals
(GeoScience World, 2006) Armbruster, Thomas; Bonazzi, Paola; Akasaka, Mashide; Bermanec, Vladimir; Chopin, Christian; Giere, Reto; Heuss-Aßbichler, Soraya; Liebscher, Axel; Menchetti, Silvio; Pan, Yuanming; Pasero, Marco
Epidote-group minerals are monoclinic in symmetry and have topology consistent with space group P21/m and the general formula A2M3[T2O7][TO4](O,F)(OH,O). Zoisite is an orthorhombic polymorph of clinozoisite Ca2Al3[Si2O7][SiO4]O(OH) and is thus not considered a member of the epidote-group. Epidote-group minerals are divided into three subgroups. (1) Members of the clinozoisite subgroup are derived from the mineral clinozoisite Ca2Al3[Si2O7][SiO4]O(OH) by homovalent substitutions only. The key cation- and anion-sites are A1 = M2+, A2 = M2+, M1 = M3+, M2 = M3+, M3 = M3+, O4 = O2-, O10 = (OH)-. In other words, the dominant valence as listed above must be maintained. (2) Members of the allanite subgroup are REE-rich minerals typified by the eponymous mineral “allanite”. This subgroup may be derived from clinozoisite by homovalent substitutions and one coupled heterovalent substitution of the type A2(REE)3+ + M3M2+ → A2Ca2+ + M3M3+. Thus the valences on the key sites are: A1 = M2+, A2 = M3+, M1 = M3+, M2 = M3+, M3 = M2+, O4 = O2-, O10 = (OH)-. (3) Members of the dollaseite subgroup are REE-rich minerals typified by the eponymous mineral “dollaseite”. This subgroup may be derived from clinozoisite by homovalent substitutions and two coupled heterovalent substitutions of the type A2(REE)3+ + M3M2+ → A2Ca2+ + M3M3+ and M1M2+ + O4F-→ M1M3+ + O4O-2. Thus the valences on the key sites are: A1 = M2+, A2 = M3+, M1 = M2+, M2 = M3+, M3 = M2+, O4 = F-, O10 = (OH)-. The key cation-sites M3 and A1 (and, in principle, M2) determine the root name. In both clinozoisite and allanite subgroups no prefix is added to the root name if M1 = Al. The prefixes ferri, mangani, chromo, and vanado indicate dominant Fe3+, Mn3+, Cr3+, and V3+ on M1, respectively. In the dollaseite subgroup no prefix is added to the root name if M1 = Mg. Otherwise a proper prefix must be attached; the prefixes ferro and mangano indicate dominant Fe2+ and Mn2+ at M1, respectively. The dominant cation on A2 (other than Ca) is treated according to the Extended Levinson suffix designation. This simple nomenclature requires renaming of the following approved species: Niigataite (old) = clinozoisite-(Sr) (new), hancockite (old) = epidote-(Pb) (new), tweddillite (old) = manganipiemontite-(Sr) (new). Minor modifications are necessary for the following species: Strontiopiemontite (old) = piemontite-( Sr) (new), androsite-(La) (old) = manganiandrosite-(La) (new). Before a mineral name can be assigned, the proper subgroup has to be determined. The determination of a proper subgroup is made by the dominating valence at M3, M1, and A2 expressed as M2+ and or M3+, not by a single, dominant ion (i.e., Fe2+, or Mg, or Al). In addition, the dominant valence on O4: X- or X2- must be ascertained. [M2+]A2 > 0.50, [M3+]M3 > 0.50 → clinozoisite subgroup, [M3++ M4+]A2 > 0.50, [M2+]M3 > 0.50 → allanite subgroup, {[M2+]M3+M1 – [M3++ M4+]A2 } > 0.50 and [X-]O4 > 0.5 → dollaseite subgroup. Coupled heterovalent substitutions in epidote-group minerals require a special application of the so-called 50 % rule in solid-solution series. (1) Clinozoisite subgroup: The dominant trivalent cation on M3 determines the name, whereas the A2 cation appearing in the suffix has to be selected from among the divalent cations. (2) Allanite and dollaseite subgroups: For the sites involved in the charge compensation of a heterovalent substitution in A2 and O4 (i.e. M3 in the allanite subgroup; M3 and M1 in the dollaseite subgroup), identification of the relevant end-member formula must take into account the dominant divalent charge-compensating octahedral cation (M2+) and not the dominant cation in these sites. Formal guidelines and examples are provided in order to determine a mineral “working name” from electron-microprobe analytical data.
Widespread Archean basement beneath the Yangtze craton
(GeoScience World, 2006) Zheng, Jianping; Griffin, William L; O’Reilly, Suzanne Y.; Zhang, Ming; Pearson, Norman; Pan, Yuanming
The age distribution of the crust is a fundamental parameter in modeling continental evolution and the rate of crustal accretion through Earth’s history, but this is usually estimated from surface exposures. The exposed Yangtze craton in eastern China consists mainly of Proterozoic rocks with rare Archean outcrops. However, the U-Pb ages and Hf isotope systematics of xenocrystic zircons brought to the surface in lamproite diatremes from three Proterozoic outcrop areas of the craton suggest the widespread presence of unexposed Archean basement, with zircon age populations of 2900–2800 Ma and 2600– 2500 Ma and Hf model ages of 2.6 to ca. 3.5 Ga or older. The zircons also record thermal events reworked on the craton ca. 2020 Ma (remelting of older crust) and 1000–850 Ma (addition of juvenile mantle material). The observation of deep crust significantly older than the upper crust will require revision of models for the rates of crustal generation through time.
Review of On Bullshit by Harry G. Frankfurt
(Princeton University Press, 2006-01-01) Pfeifer, Karl
According to Frankfurt’s analysis, bullshitting and lying necessarily differ in intention. I argue contra Frankfurt that (i) bullshitting can be lying, and that (ii) bullshitting need involve neither misrepresentation nor intention to deceive. My discussion suggests that bullshit is not capturable by a simple formula and that, although illuminating, Frankfurt’s analysis is limited to one paradigm.
The Impacts of Climate Change on Water-, Food-, Vector- and Rodent-Borne Diseases
(Health Canada, 2008) Charron, Dominique; Fleury, Manon; Lindsay, Robbin; Ogden, Nicholas; Schuster Wallace, Corinne
Endorhizal Fungi in Ranunculus from Western and Arctic Canada: Predominance of Fine Endophytes at High Latitudes
(Bentham Open Archives, 2010-01) Walker, X. J.; Basinger, J. F.; Kaminskyj, S. J. W.
Ranunculus roots were sampled across a latitudinal transect encompassing 52 °N and 82 °N, for years spanning 1963-2007. Samples from 2004 and later were preserved in formalin; earlier samples were taken from herbarium accessions. Roots were examined for colonization by arbuscular mycorrhizae, fine endophyte, and septate endophyte fungi using lactofuchsin-stained material imaged with epifluorescence microscopy. Endorhizal quantitation was assessed for each endorhizal morphotype. Roots from High Arctic (79 °N-82 °N) and mid-latitude (52 °N-54 °N) sites both contained all three endorhizal morphotypes; however, overall fungal colonization was almost three-fold higher in midlatitude samples. Most Ranunculus root colonization (29 % of the root length) in High Arctic samples was from fine endophyte fungi, whereas fine endophyte colonization was ∼ 20 % of root length in mid-latitude roots. In contrast, arbuscular mycorrhizal colonization was 2 % of root length in High Arctic samples and 57 % in mid-latitude samples. Septate endophyte colonization was 11 % and 36 % of root length for High Arctic and mid-latitude samples, respectively. These values are consistent with our previous results for other taxa, and suggest that fine endophytes are important contributors to soil microbial diversity as related to plant survival and competitiveness in the high latitudes.
Xeriscape for Urban Water Security: A Preliminary Study from Saskatoon, Saskatchewan
(JSTOR, 2011) Smith, Brittany; Patrick, Robert J.
Xeriscape is a contemporary landscape maintenance term coined from the Greek xeros, meaning dry, and scape, from the Anglo-Saxon term schap, meaning view. The practice of xeriscape encompasses many landscape styles and materials to produce everything from lush gardens to desert-like landscapes. The purpose of xeriscape is to achieve low garden maintenance measured by less watering, less fertilizer and pesticides, less weeding and less mowing. The defining feature of xeriscape is how water is used with the goal of water efficiency through practices such as mulching, appropriate plant selection and landscape design. As urban regions in Canada look to enhance future water security what opportunities might there be in landscape conversions from mono-culture grass lawns to xeriscape? Using case study research in a Canadian prairie-region city, Saskatoon, Saskatchewan, this research explores household motivation for xeriscape gardening. Through identification of household motivation for xeriscape, urban policy makers will be better able to design programs and incentives aimed at enhancing water security. The results of this research show that households with xeriscape landscaping were motivated mainly by factors related to landscape aesthetic and physical activity rather than water conservation.
An ecological quantification of the relationships between water, sanitation and infant, child, and maternal mortality
(Environmental Health, 2012) Cheng, June J.; Schuster Wallace, Corinne; Watt, Susan; Newbold, Bruce; Mente, Andrew
Background: Water and sanitation access are known to be related to newborn, child, and maternal health. Our study attempts to quantify these relationships globally using country-level data: How much does improving access to water and sanitation influence infant, child, and maternal mortality? Methods: Data for 193 countries were abstracted from global databases (World Bank, WHO, and UNICEF). Linear regression was used for the outcomes of under-five mortality rate and infant mortality rate (IMR). These results are presented as events per 1000 live births. Ordinal logistic regression was used to compute odds ratios for the outcome of maternal mortality ratio (MMR). Results: Under-five mortality rate decreased by 1.17 (95%CI 1.08-1.26) deaths per 1000,p< 0.001, for every quartile increase in population water access after adjustments for confounders. There was a similar relationship between quartile increase of sanitation access and under-five mortality rate, with a decrease of 1.66 (95%CI 1.11-1.32) deaths per 1000,p<0.001. Improved water access was also related to IMR, with the IMR decreasing by 1.14 (95%CI 1.05-1.23) deaths per 1000,p< 0.001, with increasing quartile of access to improved water source. The significance of this relationship was retained with quartile improvement in sanitation access, where the decrease in IMR was 1.66 (95%CI 1.11-1.32) deaths per 1000,p< 0.001. The estimated odds ratio that increased quartile of water access was significantly associated with increased quartile of MMR was 0.58 (95%CI 0.39-0.86),p= 0.008. The corresponding odds ratio for sanitation was 0.52 (95%CI 0.32-0.85),p= 0.009, both suggesting that better water and sanitation were associated with decreased MMR. Conclusions: Our analyses suggest that access to water and sanitation independently contribute to child and maternal mortality outcomes. If the world is to seriously address the Millennium Development Goals of reducing child and maternal mortality, then improved water and sanitation accesses are key strategies.
in situ X-ray Absorption Spectroscopic Analysis of Gold-Palladium Bimetallic Nanoparticle Catalysts
(American Chemical Society, 2013) MacLennan, Aimee; Banerjee, Abhinandan; Hu, Yongfeng; Miller, Jeffrey T; Scott, Robert WJ
Gold–palladium core–shell nanoparticles have been previously shown to be extremely effective catalysts for a number of oxidation reactions including the aerobic oxidation of alcohols. However, the novel activity and durability of such catalysts are still poorly understood, and there are several putative mechanisms by which oxidation reactions can proceed. Previously we showed that Pd(II) salts in the presence of Au nanoparticles were also effective catalysts for the room temperature oxidation of crotyl alcohol. Herein we show an in situ X-ray absorption spectroscopy (XAS) study at both the Pd–K and Pd-LIII edges of Au nanoparticle/Pd(II) salt solutions in the presence of crotyl alcohol. Liquid cells with X-ray permeable windows were used to obtain quick-scan XAS data during the oxidation of crotyl alcohol, allowing for time-resolved Pd speciation information and information about the reaction mechanism and kinetics. XAS measurements definitively show that the first step of this reaction involves Pd reduction onto the Au nanoparticles; in addition, further studies of the stability of the resulting Au–Pd core–shell nanoparticles toward oxygen gas suggests that the role of Au in such catalysts is to prevent the reoxidation of the catalytically active surface Pd atoms. Catalytic crotyl alcohol oxidation measurements were done which validated that the in situ reduction of Pd(II) in the presence of Au nanoparticles did indeed result in catalytically active AuPd bimetallic catalysts.
Following the Thermal Activation of Au25(SR)18 Clusters for Catalysis by X-Ray Absorption Spectroscopy
(American Chemical Society, 2013) Shivhare, Atal; Chevrier, Daniel; Purves, Randy W; Scott, Robert WJ
We show the thermal activation of phenylethanethiolate (L = SC8H9) and hexanethiolate (L = SC6H13) Au25L18 monolayer protected clusters (MPCs) on carbon black supports, followed by characterization with extended X-ray absorption fine structure (EXAFS) spectroscopy and transmission electron microscopy (TEM). EXAFS analysis shows that the thiolate stabilizers can be partially removed from the surface under mild heating conditions without significant changes in the cluster size. The resulting clusters are shown to be catalytically active for the reduction catalysis of 4-nitrophenol. EXAFS and TEM data show that thermal treatment under air at 200 °C leads to nearly complete removal of all of the thiolate stabilizers with little to no growth in cluster size, while cluster sintering was seen at higher calcination temperatures. The maximum catalytic activity for Au25(SC8H9)18 MPCs was seen at 250 °C activation conditions. These results are consistent with results reported earlier for Au25(SR)18 clusters on ceria by Jin et al., who suggested that cluster integrity was maintained during mild activation conditions. Here, EXAFS data unambiguously show that while the cluster size does not grow significantly, such mild heating conditions do lead to nearly complete removal of the thiolate stabilizers.
Watching Iron Nanoparticles Rust: An In Situ X-ray Absorption Spectroscopic Study
(American Chemical Society, 2014) Yao, Yali; Hu, Yongfeng; Scott, Robert WJ
Iron nanoparticles and iron oxide nanoparticles are among the most commonly studied nanomaterials because of their applications in fields ranging from catalysis to ferrofluids. However, many synthetic methods give iron nanoparticles with large size distributions, and it is difficult to follow the kinetics of iron nanoparticle oxidation reactions and the relative speciation of iron oxidation states in real time. Herein, we introduce a simple approach of controlling the sizes of Fe@FexOy nanoparticles and a novel method for following Fe@FexOy nanoparticle oxidation in situ in liquid solutions by Fe K- and L-edge X-ray absorption near-edge structure (XANES) spectroscopy. XANES results show that these Fe@FexOy nanoparticles have similar XANES spectra before exposure to air. In situ XANES measurements allow for quantitative oxidation kinetics of different nanoparticle sizes to be followed; results show that the rate of Fe(0) oxidation increases with a decrease in average nanoparticle size. However, the rate of Fe core size depletion was found to be ca. 0.02 nm/min for all the nanoparticle systems studied. This suggests similar oxidation mechanisms are at work for all the particle sizes studied. This work shows that in situ liquid cell XANES can be used to follow oxidation state and coordination environment changes in Fe NP dispersions.
Design, synthesis, catalytic application, and strategic redispersion of plasmonic silver nanoparticles in ionic liquid media
(Elsevier, 2014) Banerjee, Abhinandan; Theron, Robin; Scott, Robert WJ
Silver nanoparticles synthesized in tetraalkylphosphonium ionic liquids are found to be excellent catalysts for borohydride-induced reductive degeneration of Eosin-Y, a dye that has been classified as a Class 3 carcinogen by the International Agency for Research on Cancer. TEM images indicated that the size of the Ag nanoparticles was significantly influenced by heat-induced sintering. A strategy was devised to redisperse smaller Ag nanoparticles from their aggregated/sintered counterparts via a two-step protocol that involved oxidative etching of Ag nanoparticles, followed by a re-reduction step. This protocol led to a reduction in the sintered Ag nanoparticle size from 15.7 ± 6.1 nm to 3.7 ± 0.8 nm, which was consistent with the size of the as-synthesized nanoparticles. The as-synthesized and the redispersed Ag nanoparticles were found to catalyze the bleaching of Eosin-Y with comparable efficiencies; first order rate constants for Eosin Y reduction were ∼8 times higher for smaller Ag nanoparticles compared to their sintered counterparts. An examination of the kinetics of Ag nanoparticle etching was performed via temperature-controlled UV–vis spectroscopy. Changes in the oxidation state of Ag during this sequence of events were also followed by in situ X-ray absorption spectroscopy of Ag nanoparticles in the ionic liquid.

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