The Role of Iron-Bearing Minerals in NO2 to HONO Conversion on Soil Surfaces.

PubMed

Kebede, Mulu A; Bish, David L; Losovyj, Yaroslav; Engelhard, Mark H; Raff, Jonathan D

2016-08-16

Nitrous acid (HONO) accumulates in the nocturnal boundary layer where it is an important source of daytime hydroxyl radicals. Although there is clear evidence for the involvement of heterogeneous reactions of NO2 on surfaces as a source of HONO, mechanisms remain poorly understood. We used coated-wall flow tube measurements of NO2 reactivity on environmentally relevant surfaces (Fe (hydr)oxides, clay minerals, and soil from Arizona and the Saharan Desert) and detailed mineralogical characterization of substrates to show that reduction of NO2 by Fe-bearing minerals in soil can be a more important source of HONO than the putative NO2 hydrolysis mechanism. The magnitude of NO2-to-HONO conversion depends on the amount of Fe(2+) present in substrates and soil surface acidity. Studies examining the dependence of HONO flux on substrate pH revealed that HONO is formed at soil pH < 5 from the reaction between NO2 and Fe(2+)(aq) present in thin films of water coating the surface, whereas in the range of pH 5-8 HONO stems from reaction of NO2 with structural iron or surface complexed Fe(2+) followed by protonation of nitrite via surface Fe-OH2(+) groups. Reduction of NO2 on ubiquitous Fe-bearing minerals in soil may explain HONO accumulation in the nocturnal boundary layer and the enhanced [HONO]/[NO2] ratios observed during dust storms in urban areas.

Surface complexation modeling calculation of Pb(II) adsorption onto the calcined diatomite

NASA Astrophysics Data System (ADS)

Ma, Shu-Cui; Zhang, Ji-Lin; Sun, De-Hui; Liu, Gui-Xia

2015-12-01

Removal of noxious heavy metal ions (e.g. Pb(II)) by surface adsorption of minerals (e.g. diatomite) is an important means in the environmental aqueous pollution control. Thus, it is very essential to understand the surface adsorptive behavior and mechanism. In this work, the Pb(II) apparent surface complexation reaction equilibrium constants on the calcined diatomite and distributions of Pb(II) surface species were investigated through modeling calculations of Pb(II) based on diffuse double layer model (DLM) with three amphoteric sites. Batch experiments were used to study the adsorption of Pb(II) onto the calcined diatomite as a function of pH (3.0-7.0) and different ionic strengths (0.05 and 0.1 mol L-1 NaCl) under ambient atmosphere. Adsorption of Pb(II) can be well described by Freundlich isotherm models. The apparent surface complexation equilibrium constants (log K) were obtained by fitting the batch experimental data using the PEST 13.0 together with PHREEQC 3.1.2 codes and there is good agreement between measured and predicted data. Distribution of Pb(II) surface species on the diatomite calculated by PHREEQC 3.1.2 program indicates that the impurity cations (e.g. Al3+, Fe3+, etc.) in the diatomite play a leading role in the Pb(II) adsorption and dominant formation of complexes and additional electrostatic interaction are the main adsorption mechanism of Pb(II) on the diatomite under weak acidic conditions.

Thermodynamic Analysis of Nickel(II) and Zinc(II) Adsorption to Biochar.

PubMed

Alam, Md Samrat; Gorman-Lewis, Drew; Chen, Ning; Flynn, Shannon L; Ok, Yong Sik; Konhauser, Kurt O; Alessi, Daniel S

2018-05-21

While numerous studies have investigated metal uptake from solution by biochar, few of these have developed a mechanistic understanding of the adsorption reactions that occur at the biochar surface. In this study, we explore a combined modeling and spectroscopic approach for the first time to describe the molecular level adsorption of Ni(II) and Zn(II) to five types of biochar. Following thorough characterization, potentiometric titrations were carried out to measure the proton (H + ) reactivity of each biochar, and the data was used to develop protonation models. Surface complexation modeling (SCM) supported by synchrotron-based extended X-ray absorption fine structure (EXAFS) was then used to gain insights into the molecular scale metal-biochar surface reactions. The SCM approach was combined with isothermal titration calorimetry (ITC) data to determine the thermodynamic driving forces of metal adsorption. Our results show that the reactivity of biochar toward Ni(II) and Zn(II) directly relates to the site densities of biochar. EXAFS along with FT-IR analyses, suggest that Ni(II) and Zn(II) adsorption occurred primarily through proton-active carboxyl (-COOH) and hydroxyl (-OH) functional groups on the biochar surface. SCM-ITC analyses revealed that the enthalpies of protonation are exothermic and Ni(II) and Zn(II) complexes with biochar surface are slightly exothermic to slightly endothermic. The results obtained from these combined approaches contribute to the better understanding of molecular scale metal adsorption onto the biochar surface, and will facilitate the further development of thermodynamics-based, predictive approaches to biochar removal of metals from contaminated water.

Feshbach resonances in the exit channel of the F + CH3OH → HF + CH3O reaction observed using transition-state spectroscopy

NASA Astrophysics Data System (ADS)

Weichman, Marissa L.; Devine, Jessalyn A.; Babin, Mark C.; Li, Jun; Guo, Lifen; Ma, Jianyi; Guo, Hua; Neumark, Daniel M.

2017-10-01

The transition state governs how chemical bonds form and cleave during a chemical reaction and its direct characterization is a long-standing challenge in physical chemistry. Transition state spectroscopy experiments based on negative-ion photodetachment provide a direct probe of the vibrational structure and metastable resonances that are characteristic of the reactive surface. Dynamical resonances are extremely sensitive to the topography of the reactive surface and provide an exceptional point of comparison with theory. Here we study the seven-atom F + CH3OH → HF + CH3O reaction using slow photoelectron velocity-map imaging spectroscopy of cryocooled CH3OHF- anions. These measurements reveal spectral features associated with a manifold of vibrational Feshbach resonances and bound states supported by the post-transition state potential well. Quantum dynamical calculations yield excellent agreement with the experimental results, allow the assignment of spectral structure and demonstrate that the key dynamics of complex bimolecular reactions can be captured with a relatively simple theoretical framework.

Feshbach resonances in the exit channel of the F + CH3OH → HF + CH3O reaction observed using transition-state spectroscopy.

PubMed

Weichman, Marissa L; DeVine, Jessalyn A; Babin, Mark C; Li, Jun; Guo, Lifen; Ma, Jianyi; Guo, Hua; Neumark, Daniel M

2017-10-01

The transition state governs how chemical bonds form and cleave during a chemical reaction and its direct characterization is a long-standing challenge in physical chemistry. Transition state spectroscopy experiments based on negative-ion photodetachment provide a direct probe of the vibrational structure and metastable resonances that are characteristic of the reactive surface. Dynamical resonances are extremely sensitive to the topography of the reactive surface and provide an exceptional point of comparison with theory. Here we study the seven-atom F + CH 3 OH → HF + CH 3 O reaction using slow photoelectron velocity-map imaging spectroscopy of cryocooled CH 3 OHF - anions. These measurements reveal spectral features associated with a manifold of vibrational Feshbach resonances and bound states supported by the post-transition state potential well. Quantum dynamical calculations yield excellent agreement with the experimental results, allow the assignment of spectral structure and demonstrate that the key dynamics of complex bimolecular reactions can be captured with a relatively simple theoretical framework.

Prebiotic molecules formation through the gas-phase reaction between HNO and CH2CHOH2+

NASA Astrophysics Data System (ADS)

Redondo, Pilar; Martínez, Henar; Largo, Antonio; Barrientos, Carmen

2017-07-01

Context. Knowing how the molecules that are present in the ISM can evolve to more complex ones is an interesting topic in interstellar chemistry. The study of possible reactions between detected species can help to understand the evolution in complexity of the interstellar matter and also allows knowing the formation of new molecules which could be candidates to be detected. We focus our attention on two molecules detected in space, vinyl alcohol (CH2CHOH) and azanone (HNO). Aims: We aim to carry out a theoretical study of the ion-molecule reaction between protonated vinyl alcohol and azanone. The viability of formation of complex organic molecules (COMs) from these reactants is expected to provide some insight into the formation of prebiotic species through gas phase reactions. Methods: The reaction of protonated vinyl alcohol with azanone has been theoretically studied by using ab initio methods. Stationary points on the potential energy surface (PES) were characterized at the second-order Moller-Plesset level in conjunction with the aug-cc-pVTZ (correlation-consistent polarized valence triple-zeta) basis set. In addition, the electronic energies were refined by means of single-point calculations at the CCSD(T) level (coupled cluster single and double excitation model augmented with a non-iterative treatment of triple excitations) with the same basis set. Results: From a thermodynamic point of view, twelve products, composed of carbon, oxygen, nitrogen, and hydrogen which could be precursors in the formation of more complex biological molecules, can be obtained from this reaction. Among these, we focus especially on ionized glycine and two of its isomers. The analysis of the PES shows that only formation of cis- and trans-O-protonated imine acetaldehyde, CH2NHCOH+ and, CHNHCHOH+, are viable under interstellar conditions. Conclusions: The reaction of protonated vinyl alcohol with azanone can evolve in the interstellar medium to more complex organic molecules of prebiotic interest. Our results suggest that imine acetaldehyde could be a feasible candidate molecule to be searched for in space.

Quantum chemistry study of dielectric materials deposition

NASA Astrophysics Data System (ADS)

Widjaja, Yuniarto

The drive to continually decrease the device dimensions of integrated circuits in the microelectronics industry requires that deposited films approach subnanometer thicknesses. Hence, a fundamental understanding of the physics and chemistry of film deposition is important to obtain better control of the properties of the deposited film. We use ab initio quantum chemistry calculations to explore chemical reactions at the atomic level. Important thermodynamic and kinetic parameters are then obtained, which can then be used as inputs in constructing first-principles based reactor models. Studies of new systems for which data are not available can be conducted as well. In this dissertation, we use quantum chemistry simulations to study the deposition of gate dielectrics for metal-oxide-semiconductor (MOS) devices. The focus of this study is on heterogeneous reactions between gaseous precursors and solid surfaces. Adsorbate-surface interactions introduce additional degrees of complexity compared to the corresponding gas-phase or solid-state reactions. The applicability and accuracy of cluster approximations to represent solid surfaces are first investigated. The majority of our results are obtained using B3LYP density functional theory (DFT). The structures of reactants, products, and transition states are obtained, followed by calculations of thermochemical and kinetic properties. Whenever experimental data are available, qualitative and/or quantitative comparisons are drawn. Atomistic mechanisms and the energetics of several reactions leading to the deposition of SiO2, Si3N4, and potential new high-kappa materials such as ZrO2, HfO2, and Al 2O3 have been explored in this dissertation. Competing reaction pathways are explored for each of the deposition reactions studied. For example, the potential energy surface (PES) for ZrO2 ALD shows that the reactions proceed through a trapping-mediated mechanism, which results in a competition between desorption and decomposition of the gaseous reactants, i.e. ZrCl4 and H2O, on the ZrO2 surface. This competition results in relatively low saturation coverage, which consequently leads to a slow growth rate and possibly affects the thickness uniformity and conformality. The insights gained are then used to systematically improve deposition reactions. For instance, from the ZrO2 ALD PES, we are able to suggest the use of high temperature and pressure to obtain higher surface coverage.

Spatial and Temporal Scales of Surface Water-Groundwater Interactions

NASA Astrophysics Data System (ADS)

Boano, F.

2016-12-01

The interfaces between surface water and groundwater (i.e., river and lake sediments) represent hotspots for nutrient transformation in watersheds. This intense biochemical activity stems from the peculiar physicochemical properties of these interface areas. Here, the exchange of water and nutrients between surface and subsurface environments creates an ecotone region that can support the presence of different microbial species responsible for nutrient transformation. Previous studies have elucidated that water exchange between rivers and aquifers is organized in a complex system of nested flow cells. Each cell entails a range of residence timescales spanning multiple order of magnitudes, providing opportunities for different biochemical reactions to occur. Physically-bases models represent useful tools to deal with the wide range of spatial and temporal scales that characterize surface-subsurface water exchange. This contribution will present insights about how hydrodynamic processes control scale organization for surface water - groundwater interactions. The specific focus will be the influence of exchange processes on microbial activity and nutrient transformation, discussing how groundwater flow at watershed scale controls flow conditions and hence constrain microbial reactions at much smaller scales.

Comparison of in situ uranium KD values with a laboratory determined surface complexation model

USGS Publications Warehouse

Curtis, G.P.; Fox, P.; Kohler, M.; Davis, J.A.

2004-01-01

Reactive solute transport simulations in groundwater require a large number of parameters to describe hydrologic and chemical reaction processes. Appropriate methods for determining chemical reaction parameters required for reactive solute transport simulations are still under investigation. This work compares U(VI) distribution coefficients (i.e. KD values) measured under field conditions with KD values calculated from a surface complexation model developed in the laboratory. Field studies were conducted in an alluvial aquifer at a former U mill tailings site near the town of Naturita, CO, USA, by suspending approximately 10 g samples of Naturita aquifer background sediments (NABS) in 17-5.1-cm diameter wells for periods of 3 to 15 months. Adsorbed U(VI) on these samples was determined by extraction with a pH 9.45 NaHCO3/Na2CO3 solution. In wells where the chemical conditions in groundwater were nearly constant, adsorbed U concentrations for samples taken after 3 months of exposure to groundwater were indistinguishable from samples taken after 15 months. Measured in situ K D values calculated from the measurements of adsorbed and dissolved U(VI) ranged from 0.50 to 10.6 mL/g and the KD values decreased with increasing groundwater alkalinity, consistent with increased formation of soluble U(VI)-carbonate complexes at higher alkalinities. The in situ K D values were compared with KD values predicted from a surface complexation model (SCM) developed under laboratory conditions in a separate study. A good agreement between the predicted and measured in situ KD values was observed. The demonstration that the laboratory derived SCM can predict U(VI) adsorption in the field provides a critical independent test of a submodel used in a reactive transport model. ?? 2004 Elsevier Ltd. All rights reserved.

Advanced, Non-Toxic, Anti-Corrosion, Anti-Fouling and Foul-Release Coatings Based on Covalently Attached Monolayers, Multilayers and Polymers

DTIC Science & Technology

2007-08-08

McCarthy Polymer Science and Engineering Department, University of Massachusetts, Amherst, Massachusetts 01003 Electrophilic aromatic substitution reactions...with a fluorinated silane reagent. Reduction of the amide groups with borane-THF (BH 3-THF) complex leads to a 69% conversion of surface amides to the

Dramatic Increase in the Signal and Sensitivity of Detection via Self-Assembly of Branched DNA

PubMed Central

Kim, Kyung-Tae; Chae, Chi-Bom

2011-01-01

In molecular testing using PCR, the target DNA is amplified via PCR and the sequence of interest is investigated via hybridization with short oligonucleotide capture probes that are either in a solution or immobilized on solid supports such as beads or glass slides. In this report, we report the discovery of assembly of DNA complex(es) between a capture probe and multiple strands of the PCR product. The DNA complex most likely has branched structure. The assembly of branched DNA was facilitated by the product of asymmetric PCR. The amount of branched DNA assembled was increased five fold when the asymmetric PCR product was denatured and hybridized with a capture probe all in the same PCR reaction mixture. The major branched DNA species appeared to contain three reverse strands (the strand complementary to the capture probe) and two forward strands. The DNA was sensitive to S1 nuclease suggesting that it had single-stranded gaps. Branched DNA also appeared to be assembled with the capture probes immobilized on the surface of solid support when the product of asymmetric PCR was hybridized. Assembly of the branched DNA was also increased when hybridization was performed in complete PCR reaction mixture suggesting the requirement of DNA synthesis. Integration of asymmetric PCR, heat denaturation and hybridization in the same PCR reaction mixture with the capture probes immobilized on the surface of solid support achieved dramatic increase in the signal and sensitivity of detection of DNA. Such a system should be advantageously applied for development of automated process for detection of DNA. PMID:21870112

The Electrode as Organolithium Reagent: Catalyst-Free Covalent Attachment of Electrochemically Active Species to an Azide-Terminated Glassy Carbon Electrode Surface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Das, Atanu K.; Engelhard, Mark H.; Liu, Fei

2013-12-02

Glassy carbon electrodes have been activated for modification with azide groups and subsequent coupling with ferrocenyl reagents by a catalyst-free route using lithium acetylide-ethylenediamine complex, and also by the more common Cu(I)-catalyzed alkyne-azide coupling (CuAAC) route, both affording high surface coverages. Electrodes were preconditioned at ambient temperature under nitrogen, and ferrocenyl surface coverages obtained by CuAAC were comparable to those reported with preconditioning at 1000 °C under hydrogen/nitrogen. The reaction of lithium acetylide-ethylenediamine with the azide-terminated electrode affords a 1,2,3-triazolyllithium-terminated surface that is active toward covalent C-C coupling reactions including displacement at an aliphatic halide and nucleophilic addition at anmore » aldehyde. For example, surface ferrocenyl groups were introduced by reaction with (6-iodohexyl)ferrocene; the voltammetry shows narrow, symmetric peaks indicating uniform attachment. Coverages are competitive with those obtained by the CuAAC route. X-ray photoelectron spectroscopic data, presented for each synthetic step, are consistent with the proposed reactions. This research was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the US Department of Energy, Office of Science, Office of Basic Energy Sciences. Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy. 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.« less

Computational neural networks in chemistry: Model free mapping devices for predicting chemical reactivity from molecular structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Elrod, D.W.

1992-01-01

Computational neural networks (CNNs) are a computational paradigm inspired by the brain's massively parallel network of highly interconnected neurons. The power of computational neural networks derives not so much from their ability to model the brain as from their ability to learn by example and to map highly complex, nonlinear functions, without the need to explicitly specify the functional relationship. Two central questions about CNNs were investigated in the context of predicting chemical reactions: (1) the mapping properties of neural networks and (2) the representation of chemical information for use in CNNs. Chemical reactivity is here considered an example ofmore » a complex, nonlinear function of molecular structure. CNN's were trained using modifications of the back propagation learning rule to map a three dimensional response surface similar to those typically observed in quantitative structure-activity and structure-property relationships. The computational neural network's mapping of the response surface was found to be robust to the effects of training sample size, noisy data and intercorrelated input variables. The investigation of chemical structure representation led to the development of a molecular structure-based connection-table representation suitable for neural network training. An extension of this work led to a BE-matrix structure representation that was found to be general for several classes of reactions. The CNN prediction of chemical reactivity and regiochemistry was investigated for electrophilic aromatic substitution reactions, Markovnikov addition to alkenes, Saytzeff elimination from haloalkanes, Diels-Alder cycloaddition, and retro Diels-Alder ring opening reactions using these connectivity-matrix derived representations. The reaction predictions made by the CNNs were more accurate than those of an expert system and were comparable to predictions made by chemists.« less

A chemical equilibrium model for metal adsorption onto bacterial surfaces

NASA Astrophysics Data System (ADS)

Fein, Jeremy B.; Daughney, Christopher J.; Yee, Nathan; Davis, Thomas A.

1997-08-01

This study quantifies metal adsorption onto cell wall surfaces of Bacillus subtilis by applying equilibrium thermodynamics to the specific chemical reactions that occur at the water-bacteria interface. We use acid/base titrations to determine deprotonation constants for the important surface functional groups, and we perform metal-bacteria adsorption experiments, using Cd, Cu, Pb, and Al, to yield site-specific stability constants for the important metal-bacteria surface complexes. The acid/base properties of the cell wall of B. subtilis can best be characterized by invoking three distinct types of surface organic acid functional groups, with pK a values of 4.82 ± 0.14, 6.9 ± 0.5, and 9.4 ± 0.6. These functional groups likely correspond to carboxyl, phosphate, and hydroxyl sites, respectively, that are displayed on the cell wall surface. The results of the metal adsorption experiments indicate that both the carboxyl sites and the phosphate sites contribute to metal uptake. The values of the log stability constants for metal-carboxyl surface complexes range from 3.4 for Cd, 4.2 for Pb, 4.3 for Cu, to 5.0 for Al. These results suggest that the stabilities of the metal-surface complexes are high enough for metal-bacterial interactions to affect metal mobilities in many aqueous systems, and this approach enables quantitative assessment of the effects of bacteria on metal mobilities.

Infrared Laser Stark Spectroscopy of the OH\\cdot\\cdot\\cdotCH3OH Complex Isolated in Superfluid Helium Droplets

NASA Astrophysics Data System (ADS)

Leavitt, Christopher M.; Brice, Joseph T.; Douberly, Gary E.; Hernandez, Federico J.; Pino, Gustavo A.

2015-06-01

The elimination of volatile organic compounds (VOCs) from the atmosphere is initiated by reactions with OH, NO3 and O3. For oxygenated VOCs, such as alcohols, ketones, ethers, etc., reactions occur nearly exclusively with the hydroxyl radical. Furthermore, the potential energy surfaces associated with reactions between OH and oxygenated VOCs generally feature a pre-reactive complex, stabilized by hydrogen bonding, which results in rate constants that exhibit large negative temperature dependencies. This was explicitly demonstrated recently for the OH + methanol (MeOH) reaction, where the rate constant increased by nearly two orders of magnitude when the temperature decreased from 200 K to below 70 K, highlighting the potential impact of this reaction in the interstellar medium (ISM). In this study, we trap this postulated pre-reactive complex formed between OH and MeOH using He nanodroplet isolation (HENDI) techniques, and probe this species using a combination of mass spectrometry and infrared laser Stark spectroscopy. Atkinson, R.; Arey, J., Chem. Rev. 2003, 103, 4605-4638. Mellouki, A.; Le Bras, G.; Sidebottom, H., Chem. Rev. 2003, 103, 5077-5096. Smith, I. W. M.; Ravishankara, A. R., J. Phys. Chem. A 2002, 106, 4798-4807 Shannon, R. J.; Blitz, M. A.; Goddard, A.; Heard, D. E., Nat. Chem. 2013, 5, 745-749. Martin, J. C. G.; Caravan, R. L.; Blitz, M. A.; Heard, D. E.; Plane, J. M. C., J. Phys. Chem. A 2014, 118, 2693-2701.

CRUNCH_PARALLEL

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shumaker, Dana E.; Steefel, Carl I.

The code CRUNCH_PARALLEL is a parallel version of the CRUNCH code. CRUNCH code version 2.0 was previously released by LLNL, (UCRL-CODE-200063). Crunch is a general purpose reactive transport code developed by Carl Steefel and Yabusake (Steefel Yabsaki 1996). The code handles non-isothermal transport and reaction in one, two, and three dimensions. The reaction algorithm is generic in form, handling an arbitrary number of aqueous and surface complexation as well as mineral dissolution/precipitation. A standardized database is used containing thermodynamic and kinetic data. The code includes advective, dispersive, and diffusive transport.

Thermal stability of bioactive enzymatic papers.

PubMed

Khan, Mohidus Samad; Li, Xu; Shen, Wei; Garnier, Gil

2010-01-01

The thermal stability of two enzymes adsorbed on paper, alkaline phosphatase (ALP) and horseradish peroxidase (HRP), was measured using a colorimetric technique quantifying the intensity of the product complex. The enzymes adsorbed on paper retained their functionality and selectivity. Adsorption on paper increased the enzyme thermal stability by 2-3 orders of magnitude compared to the same enzyme in solution. ALP and HRP enzymatic papers had half-lives of 533 h and 239 h at 23 degrees C, respectively. The thermal degradation of adsorbed enzyme was found to follow two sequential first-order reactions, indication of a reaction system. A complex pattern of enzyme was printed on paper using a thermal inkjet printer. Paper and inkjet printing are ideal material and process to manufacture low-cost-high volume bioactive surfaces.

Detection of sialomucin complex (MUC4) in human ocular surface epithelium and tear fluid.

PubMed

Pflugfelder, S C; Liu, Z; Monroy, D; Li, D Q; Carvajal, M E; Price-Schiavi, S A; Idris, N; Solomon, A; Perez, A; Carraway, K L

2000-05-01

To evaluate human ocular surface epithelium and tear fluid for the presence of sialomucin complex (MUC4), a high-molecular-weight heterodimeric glycoprotein composed of mucin (ASGP-1) and transmembrane (ASGP-2) subunits. Reverse transcription-polymerase chain reaction (RT-PCR) and Northern blot analysis assays were used to identify sialomucin complex RNA in ocular surface epithelia. Immunoprecipitation and immunoblot analysis were used to identify immunoreactive species in human tears and in the corneal and conjunctival epithelia using antibodies specific for carbohydrate and peptide epitopes on the sialomucin complex subunits. Immunofluorescence staining was used to detect sialomucin complex in frozen sections and impression cytology specimens of human cornea and conjunctival epithelia. ASGP-1- and ASGP-2-specific sequences were amplified from RNA extracted from both conjunctival and corneal epithelial biopsies by RT-PCR. Sialomucin complex transcripts were also detected in these tissues by Northern blot analysis, with a greater level of RNA detected in the peripheral than the central corneal epithelium. Sialomucin complex was immunoprecipitated from tear fluid samples and both corneal and conjunctival epithelia and detected by immunoblot analysis with specific anti-ASGP-1 and anti-ASGP-2 antibodies. The ASGP-1 peptide antibody HA-1 stained the full thickness of the corneal and conjunctival epithelia. In contrast, antibody 15H10, which reacts against a carbohydrate epitope on ASGP-1, stained only the superficial epithelial layers of these tissues. No staining was observed in the conjunctival goblet cells. Sialomucin complex was originally identified in rat mammary adenocarcinoma cells and has recently been shown to be produced by the ocular surface epithelia of rats. Furthermore, it has been identified as the rat homologue of human MUC4 mucin. The present studies show that it is expressed in the stratified epithelium covering the surface of the human eye and is present in human tear fluid. Expression of a carbohydrate-dependent epitope on the mucin subunit (ASGP-1) of sialomucin complex occurs in a differentiation-dependent fashion. Sialomucin complex joins MUC1 as another membrane mucin produced by the human ocular surface epithelia but is also found in the tear fluid, presumably in a soluble form, as found on the rat ocular surface.

Reactive Desorption and Radiative Association as Possible Drivers of Complex Molecule Formation in the Cold Interstellar Medium

NASA Astrophysics Data System (ADS)

Vasyunin, A. I.; Herbst, Eric

2013-05-01

The recent discovery of terrestrial-type organic species such as methyl formate and dimethyl ether in the cold interstellar gas has proved that the formation of organic matter in the Galaxy begins at a much earlier stage of star formation than was previously thought. This discovery represents a challenge for astrochemical modelers. The abundances of these molecules cannot be explained by the previously developed "warm-up" scenario, in which organic molecules are formed via diffusive chemistry on surfaces of interstellar grains starting at 30 K, and then released to the gas at higher temperatures during later stages of star formation. In this article, we investigate an alternative scenario in which complex organic species are formed via a sequence of gas-phase reactions between precursor species formed on grain surfaces and then ejected into the gas via efficient reactive desorption, a process in which non-thermal desorption occurs as a result of conversion of the exothermicity of chemical reactions into the ejection of products from the surface. The proposed scenario leads to reasonable if somewhat mixed results at temperatures as low as 10 K and may be considered as a step toward the explanation of abundances of terrestrial-like organic species observed during the earliest stages of star formation.

Pb, Cu, and Zn distributions at humic acid-coated metal-oxide surfaces

DOE PAGES

Wang, Yingge; Michel, F. Marc; Choi, Yongseong; ...

2016-05-09

Here, mineral surfaces are often coated by natural organic matter (NOM), which has a major influence on metal-ion sorption and sequestration because of the abundance of binding sites in such coatings and the changes they cause in local nanoscale environments. The effects of NOM coatings on mineral surfaces are, however, still poorly understood at the molecular level due to the complexity of these systems. In this study, we have applied long-period X-ray standing wave-fluorescence yield (LP-XSW-FY) spectroscopy to measure the partitioning of naturally present Cu(II) (0.0226%), Zn(II) (0.009%), and Pb(II) ( 0.0004%) between Elliott Soil Humic Acid (ESHA) coatings andmore » three model single-crystal metal-oxide substrates: α-Al 2O 3 (0 0 0 1), α-Al 2O 3 (1 1 0 2), and α-Fe 2O 3 (0 0 0 1). The competitive sorption effects among these metal ions for binding sites in the ESHA coatings and on the metal-oxide surfaces were investigated as a function of reaction time, calcium content, and solution pH. Pb(II) ions present in the ESHA coatings were found to redistribute to reactive α-Al 2O 3 (1 1 0 2) and α-Fe 2O 3 (0 0 0 1) surfaces after 3 h of reaction (pH = 6.0, [Ca(II)] = 2 mM). Pb(II) partitioning onto these reactive metal-oxide surfaces increased with increasing reaction time (up to 7 d). In addition, the partitioning of Cu(II) and Zn(II) from the ESHA coating to the α-Fe 2O 3 (0 0 0 1) substrate increased slightly with reaction time (2.4% and 3.7% for Cu(II) and Zn(II), respectively, after 3 h and 6.4% and 7.7% for Cu(II) and Zn(II), respectively, after 72 h of reaction time).« less

Self-organization of multifunctional surfaces--the fingerprints of light on a complex system.

PubMed

Reinhardt, Hendrik; Kim, Hee-Cheol; Pietzonka, Clemens; Kruempelmann, Julia; Harbrecht, Bernd; Roling, Bernhard; Hampp, Norbert

2013-06-25

Nanocomposite patterns and nanotemplates are generated by a single-step bottom-up concept that introduces laser-induced periodic surface structures (LIPSS) as a tool for site-specific reaction control in multicomponent systems. Periodic intensity fluctuations of this photothermal stimulus inflict spatial-selective reorganizations, dewetting scenarios and phase segregations, thus creating regular patterns of anisotropic physicochemical properties that feature attractive optical, electrical, magnetic, and catalytic properties. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Oxidation of dimethylselenide by δMnO2: oxidation product and factors affecting oxidation rate

USGS Publications Warehouse

Wang, Bronwen; Burau, Richard G.

1995-01-01

Volatile dimethylselenide (DMSe) was transformed to a nonvolatile Se compound in a ??-MnO2 suspension. The nonvolatile product was a single compound identified as dimethylselenoxide based on its mass spectra pattern. After 24 h, 100% of the DMSe added to a ??-MnO2 suspension was converted to nonpurgable Se as opposed to 20%, 18%, and 4% conversion for chromate, permanganate, and the filtrate from the suspension, respectively. Manganese was found in solution after reaction. These results imply that the reaction between manganese oxide and DMSe was a heterogeneous redox reaction involving solid phase ??-MnO2 and solution phase DMSe. Oxidation of DMSe to dimethylselenoxide [OSe(CH3)2] by a ??-MnO2 suspension appears to be first order with respect to ??-MnO2, to DMSe, and to hydrogen ion with an overall rate law of d[OSe(CH3)2 ]/dt = 95 M-2 min-1 [MnO2]1[DMSe]1[H+]1 for the MnO2 concentration range of 0.89 ?? 10-3 - 2.46 ?? 10-3 M, the DMSe concentration range of 3.9 ?? 10-7 - 15.5 ?? 10-7 M Se, and a hydrogen ion concentation range of 7.4 ?? 10-6 -9.5 ?? 10-8 M. A general surface site adsorption model is consistent with this rate equation if the uncharged |OMnOH is the surface adsorption site. DMSe acts as a Lewis base, and the manganese oxide surface acts as a Lewis acid. DMSe adsorption to |OMnOH can be viewed as a Lewis acid/ base complex between the largely p orbitals of the DMSe lone pair and the unoccupied eg orbitals on manganese oxide. For such a complex, frontier molecular orbital theory predicts electron transfer to occur via an inner-sphere complex between the DMSe and the manganese oxide. ?? 1995 American Chemical Society.

Mechanism of oxygen reduction reaction on Pt(111) in alkaline solution: Importance of chemisorbed water on surface

DOE PAGES

Liu, Shizhong; White, Michael G.; Liu, Ping

2016-06-30

Here, we report a detailed mechanistic study of the oxygen reduction reaction (ORR) on Pt(111) in alkaline solution, combining density functional theory and kinetic Monte Carlo simulations. A complex reaction network including four possible pathways via either 2e – or 4e – transfer is established and is able to reproduce the experimental measured polarization curve at both low- and high-potential regions. Our results show that it is essential to account for solvation by water and the dynamic coverage of *OH to describe the reaction kinetics well. In addition, a chemisorbed water (*H 2O)-mediated mechanism including 4e – transfers is identified,more » where the reduction steps via *H 2O on the surface are potential-independent and only the final removal of *OH from the surface in the form of OH –(aq) contributes to the current. For the ORR in alkaline solutions, such a mechanism is more competitive than the associative and dissociative mechanisms typically used to describe the ORR in acid solution. Finally, *OH and **O 2 intermediates are found to be critically important for tuning the ORR activity of Pt in alkaline solution. To enhance the activity, the binding of Pt should be tuned in such a way that *OH binding is weak enough to release more surface sites under working conditions, while **O 2 binding is strong enough to enable the ORR via the 4e – transfer mechanism.« less

Reactivity at the Lithium–Metal Anode Surface of Lithium–Sulfur Batteries

DOE PAGES

Camacho-Forero, Luis E.; Smith, Taylor W.; Bertolini, Samuel; ...

2015-11-11

Due to their high energy density and reduced cost, lithium–sulfur batteries are promising alternatives for applications such as electrical vehicles. However, a number of technical challenges need to be overcome in order to make them feasible for commercial uses. These challenges arise from the battery highly interconnected chemistry, which besides the electrochemical reactions includes side reactions at both electrodes and migration of soluble polysulfide (PS) species produced at the cathode to the anode side. The presence of such PS species alters the already complex reactivity of the Li anode. In this paper, interfacial reactions occurring at the surface of Limore » metal anodes due to electrochemical instability of the electrolyte components and PS species are investigated with density functional theory and ab initio molecular dynamics methods. It is found that the bis(trifluoromethane)sulfonimide lithium salt reacts very fast when in contact with the Li surface, and anion decomposition precedes salt dissociation. The anion decomposition mechanisms are fully elucidated. Two of the typical solvents used in Li–S technology, 1,3-dioxolane and 1,2-dimethoxyethane, are found stable during the entire simulation length, in contrast with the case of ethylene carbonate that is rapidly decomposed by sequential 2- or 4-electron mechanisms. Finally, on the other hand, the fast reactivity of the soluble PS species alters the side reactions because the PS totally decomposes before any of the electrolyte components forming Li 2S on the anode surface.« less

Kinetic and mechanisms of methanimine reactions with singlet and triplet molecular oxygen: Substituent and catalyst effects

NASA Astrophysics Data System (ADS)

Asgharzadeh, Somaie; Vahedpour, Morteza

2018-06-01

Methanimine reaction with O2 on singlet and triplet potential energy surfaces are investigated using B3PW91, M06-2X, MP2 and CCSD(T) methods. Thermodynamic and kinetic parameters are calculated at M06-2X method. The most favorable channel involves H-abstraction of CH2NH+O2 to the formation of HCN + H2O2 products via low level energy barrier. The catalytic effect of water molecule on HCN + H2O2 products pathway are investigated. Result shows that contribution of water molecule using complex formation with methanimine can decreases barrier energy of transition state and the reaction rate increases. Also, substituent effect of fluorine atom as deactivating group are investigated on the main reaction pathway.

A polymer supported Cu(I) catalyst for the 'click reaction' in aqueous media.

PubMed

Ul Islam, Rafique; Taher, Abu; Choudhary, Meenakshi; Witcomb, Michael J; Mallick, Kaushik

2015-01-21

Polymer stabilized monovalent copper has been synthesized using an in situ chemical transformation route and was characterized by means of different microscopic, optical and surface characterization techniques, which offered information about the chemical structure of the polymer and the morphology of the complex. The supramolecular material, Cu(i)-poly(2-aminobenzoic acid), denoted Cu(i)-pABA, showed catalytic activity for the cycloaddition reaction between terminal alkynes and azides to synthesize 1,2,3-triazoles with excellent yields. The catalyst was recovered from the reaction mixture and recycled several times without an appreciable loss of catalytic activity. The whole strategy was done under ambient conditions and in the presence of water as a solvent.

Copper-phospholipid interaction at cell membrane model hydrophobic surfaces.

PubMed

Mlakar, Marina; Cuculić, Vlado; Frka, Sanja; Gašparović, Blaženka

2018-04-01

Detailed investigation of Cu (II) binding with natural lipid phosphatidylglycerol (PG) in aqueous solution was carried out by voltammetric measurements at the mercury drop electrode, complemented by monolayer studies in a Langmuir trough and electrophoretic measurements, all used as models for hydrophobic cell membranes. Penetration of copper ions into the PG layer was facilitated by the formation of hydrophilic Cu-Phenanthroline (Phen) complex in the subphase, followed by the mixed ligand Cu-Phen-PG complex formation at the hydrophobic interface. Electrophoretic measurements indicated a comparatively low abundance of the formed mixed ligand complex within the PG vesicles, resulting it the zeta potential change of +0.83mV, while monolayer studies confirmed their co-existence at the interface. The Cu-Phen-PG complex was identified in the pH range from 6 to 9. The stoichiometry of the complex ([PhenCuOHPG]), as well as its stability and kinetics of formation, were determined at the mercury drop electrode. Cu-Phen-PG reduces quasireversibly at about -0.7V vs. Ag/AgCl including reactant adsorption, followed by irreversible mixed complex dissociation, indicating a two-electron transfer - chemical reaction (EC mechanism). Consequently, the surface concentration (γ) of the adsorbed [PhenCuOHPG] complex at the hydrophobic electrode surface was calculated to be (3.35±0.67)×10 -11 molcm -2 . Information on the mechanism of Cu (II) - lipid complex formation is a significant contribution to the understanding of complex processes at natural cell membranes. Copyright © 2017 Elsevier B.V. All rights reserved.

Indirect glyphosate detection based on ninhydrin reaction and surface-enhanced Raman scattering spectroscopy

NASA Astrophysics Data System (ADS)

Xu, Meng-Lei; Gao, Yu; Li, Yali; Li, Xueliang; Zhang, Huanjie; Han, Xiao Xia; Zhao, Bing; Su, Liang

2018-05-01

Glyphosate is one of the most commonly-used and non-selective herbicides in agriculture, which may directly pollute the environment and threaten human health. A simple and effective approach to assessment of its damage to the natural environment is thus quite necessary. However, traditional chromatography-based detection methods usually suffer from complex pretreatment procedures. Herein, we propose a simple and sensitive method for the determination of glyphosate by combining ninhydrin reaction and surface-enhanced Raman scattering (SERS) spectroscopy. The product (purple color dye, PD) of the ninhydrin reaction is found to SERS-active and directly correlate with the glyphosate concentration. The limit of detection of the proposed method for glyphosate is as low as 1.43 × 10- 8 mol·L- 1 with a relatively wider linear concentration range (1.0 × 10- 7-1.0 × 10- 4 mol·L- 1), which demonstrates its great potential in rapid, highly sensitive concentration determination of glyphosate in practical applications for safety assessment of food and environment.

Electrolyte-induced surface transformation and transition-metal dissolution of fully delithiated LiNi 0.8Co 0.15Al 0.05O 2

DOE PAGES

Faenza, Nicholas V.; Lebens-Higgins, Zachary W.; Mukherjee, Pinaki; ...

2017-06-08

Here, enabling practical utilization of layered Rmore » $$\\bar{3}$$ m positive electrodes near full delithiation requires an enhanced understanding of the complex electrode–electrolyte interactions that often induce failure. Using Li[Ni 0.8Co 0.15Al 0.05]O 2 (NCA) as a model layered compound, the chemical and structural stability in a strenuous thermal and electrochemical environment was explored. Operando microcalorimetry and electrochemical impedance spectroscopy identified a fingerprint for a structural decomposition and transition-metal dissolution reaction that occurs on the positive electrode at full delithiation. Surface-sensitive characterization techniques, including X-ray absorption spectroscopy and high-resolution transmission electron microscopy, measured a structural and morphological transformation of the surface and subsurface regions of NCA. Despite the bulk structural integrity being maintained, NCA surface degradation at a high state of charge induces excessive transition-metal dissolution and significant positive electrode impedance development, resulting in a rapid decrease in electrochemical performance. Additionally, the impact of electrolyte salt, positive electrode surface area, and surface Li 2CO 3 content on the magnitude and character of the dissolution reaction was studied.« less

Electrolyte-Induced Surface Transformation and Transition-Metal Dissolution of Fully Delithiated LiNi0.8Co0.15Al0.05O2.

PubMed

Faenza, Nicholas V; Lebens-Higgins, Zachary W; Mukherjee, Pinaki; Sallis, Shawn; Pereira, Nathalie; Badway, Fadwa; Halajko, Anna; Ceder, Gerbrand; Cosandey, Frederic; Piper, Louis F J; Amatucci, Glenn G

2017-09-19

Enabling practical utilization of layered R3̅m positive electrodes near full delithiation requires an enhanced understanding of the complex electrode-electrolyte interactions that often induce failure. Using Li[Ni 0.8 Co 0.15 Al 0.05 ]O 2 (NCA) as a model layered compound, the chemical and structural stability in a strenuous thermal and electrochemical environment was explored. Operando microcalorimetry and electrochemical impedance spectroscopy identified a fingerprint for a structural decomposition and transition-metal dissolution reaction that occurs on the positive electrode at full delithiation. Surface-sensitive characterization techniques, including X-ray absorption spectroscopy and high-resolution transmission electron microscopy, measured a structural and morphological transformation of the surface and subsurface regions of NCA. Despite the bulk structural integrity being maintained, NCA surface degradation at a high state of charge induces excessive transition-metal dissolution and significant positive electrode impedance development, resulting in a rapid decrease in electrochemical performance. Additionally, the impact of electrolyte salt, positive electrode surface area, and surface Li 2 CO 3 content on the magnitude and character of the dissolution reaction was studied.

Oxidovanadium(IV) complexes involving dehydroacetic acid and β-diketones of bioinorganic and medicinal relevance: Their synthesis, characterization, thermal behavior and DFT aspects

NASA Astrophysics Data System (ADS)

Maurya, R. C.; Malik, B. A.; Mir, J. M.; Vishwakarma, P. K.

2015-03-01

Six new mixed-ligand complexes of oxidovanadium(IV) of the general composition [VO(dha)(L)(H2O)], where dhaH = dehydroacetic acid, LH = β-diketones, viz., acetoacetanilide (aaaH), o-acetoacetotoluidide (o-aatdH), o-acetoacetanisidide (o-aansH), acetylacetone (acacH), methyl acetoacetate (macacH) or ethyl acetoacetate (eacacH) have been synthesized by the reaction of VOSO4ṡ5H2O and the ligands given above in aqueous-ethanol medium. The resulting complexes have been characterized on the basis of elemental analyses, vanadium determination, molar conductance and magnetic measurements, mass spectrometry, thermogravimetric analysis, infrared and electron spin resonance spectral studies. The thermal decomposition processes of two representative complexes are discussed and the order of reaction (n) and the activation energy (Ea) for the particular decomposition steps have been calculated from thermogravimetric (TG) curve. Geometry optimizations were performed with the Gaussian 09 software package by using density functional theory (DFT) methods with Becke-3-Lee-Yang-Parr (B3LYP) hybrid exchange-correlation functional and the standard LANL2 MB basis set for dhaH and its complex [VO(dha)(acac)(H2O)]. Molecular surface electrostatic potentials (MSEP), vibrational frequency calculations, bond lengths, bond angles, dihedral angles, natural population analysis and calculations of molecular energies, HOMO and LUMO were made. No imaginary frequency was found in the optimized model compounds and hence ensures that the molecule is in the lowest point of the potential energy surface, that is, a energy minimum. Finally calculated results were applied to simulated Infrared spectra of the title compound which show good agreement with observed spectra. Based on experimental and theoretical data, suitable trans-octahedral structures have been proposed for these complexes.

Oxidative dissolution of pyrite surfaces by hexavalent chromium: Surface site saturation and surface renewal

NASA Astrophysics Data System (ADS)

Graham, Andrew M.; Bouwer, Edward J.

2012-04-01

In-situ reduction of toxic Cr(VI) to nontoxic Cr(III) represents an important natural attenuation process for Cr(VI)-impacted environments. This study investigates the stoichiometry and kinetics of Cr(VI) reduction by pyrite, a reduced iron-sulfur mineral ubiquitous in recent estuarine and marine sediments. Pyrite suspensions at surface loadings of 0.28-2.10 m2/L (typical of estuarine or marine sediments) were capable of completely reducing 7-120 μM Cr(VI) on the timescale of minutes to days, with the time to reaction completion decreasing with increasing pyrite loading, decreasing initial Cr(VI) concentration, and decreasing suspension pH. Analysis of metal species (Cr and Fe) and sulfur species in solution and at the mineral surface indicated that Cr(VI) oxidatively dissolved the pyrite surface, releasing ferrous iron and sulfate into solution as the reaction progressed. Surface disulfide groups were postulated as the Cr(VI)-reactive surface entity. Net production or consumption of aqueous Fe(II) was shown to depend upon the relative rates of proton-promoted Fe(II) release, Fe(II) release due to oxidative dissolution of pyrite in the presence of Cr(VI), and Fe(II) consumption due to homogeneous reaction with Cr(VI). Kinetics of Cr(VI) reduction by pyrite displayed a biphasic pattern, and the time to reaction completion increased dramatically with increasing initial Cr(VI) concentration. Rapid Cr(VI) removal occurred early in the reaction progress, attributable to Cr(VI) loss under an adsorption-limited regime. Slow, approximately zero-order, Cr(VI) removal occurred over the bulk of the time courses, and corresponded to Cr(VI) removal under surface site saturation conditions. Stoichiometric Cr(VI) reduction was able to proceed under surface site limited conditions owing to regeneration of reactive surface sites following desorption/dissolution of oxidized surface products, as demonstrated in repeat Cr(VI)-spiking experiments. The role of surface passivation was evaluated by comparing rates of Cr(VI) reduction in the presence and absence of the Cr(III)-complexing agent citrate. While citrate addition significantly enhanced Cr(III) solubility, rates of Cr(VI) reduction were only marginally accelerated, suggesting that Cr(OH)3(s) coatings did not completely block access of Cr(VI) to reactive surface sites on pyrite. Given the rapid rates of Cr(VI) reduction with pyrite under pH and surface coverage conditions typical of natural environments, we propose that Cr(VI) reduction by pyrite be considered in fate and transport models for Cr in contaminated sediments.

Blood coagulation reactions on nanoscale membrane surfaces

NASA Astrophysics Data System (ADS)

Pureza, Vincent S.

Blood coagulation requires the assembly of several membrane-bound protein complexes composed of regulatory and catalytic subunits. The biomembranes involved in these reactions not only provide a platform for these procoagulant proteins, but can also affect their function. Increased exposure of acidic phospholipids on the outer leaflet of the plasma membrane can dramatically modulate the catalytic efficiencies of such membrane-bound enzymes. Under physiologic conditions, however, these phospholipids spontaneously cluster into a patchwork of membrane microdomains upon which membrane binding proteins may preferentially assemble. As a result, the membrane composition surrounding these proteins is largely unknown. Through the development and use of a nanometer-scale bilayer system that provides rigorous control of the phospholipid membrane environment, I investigated the role of phosphatidylserine, an acidic phospholipid, in the direct vicinity (within nanometers) of two critical membrane-bound procoagulant protein complexes and their respective natural substrates. Here, I present how the assembly and function of the tissue factor˙factor VIIa and factor Va˙factor Xa complexes, the first and final cofactor˙enzyme complexes of the blood clotting cascade, respectively, are mediated by changes in their immediate phospholipid environments.

Surface-Activated Coupling Reactions Confined on a Surface.

PubMed

Dong, Lei; Liu, Pei Nian; Lin, Nian

2015-10-20

Chemical reactions may take place in a pure phase of gas or liquid or at the interface of two phases (gas-solid or liquid-solid). Recently, the emerging field of "surface-confined coupling reactions" has attracted intensive attention. In this process, reactants, intermediates, and products of a coupling reaction are adsorbed on a solid-vacuum or a solid-liquid interface. The solid surface restricts all reaction steps on the interface, in other words, the reaction takes place within a lower-dimensional, for example, two-dimensional, space. Surface atoms that are fixed in the surface and adatoms that move on the surface often activate the surface-confined coupling reactions. The synergy of surface morphology and activity allow some reactions that are inefficient or prohibited in the gas or liquid phase to proceed efficiently when the reactions are confined on a surface. Over the past decade, dozens of well-known "textbook" coupling reactions have been shown to proceed as surface-confined coupling reactions. In most cases, the surface-confined coupling reactions were discovered by trial and error, and the reaction pathways are largely unknown. It is thus highly desirable to unravel the mechanisms, mechanisms of surface activation in particular, of the surface-confined coupling reactions. Because the reactions take place on surfaces, advanced surface science techniques can be applied to study the surface-confined coupling reactions. Among them, scanning tunneling microscopy (STM) and X-ray photoelectron spectroscopy (XPS) are the two most extensively used experimental tools. The former resolves submolecular structures of individual reactants, intermediates, and products in real space, while the latter monitors the chemical states during the reactions in real time. Combination of the two methods provides unprecedented spatial and temporal information on the reaction pathways. The experimental findings are complemented by theoretical modeling. In particular, density-functional theory (DFT) transition-state calculations have been used to shed light on reaction mechanisms and to unravel the trends of different surface materials. In this Account, we discuss recent progress made in two widely studied surface-confined coupling reactions, aryl-aryl (Ullmann-type) coupling and alkyne-alkyne (Glaser-type) coupling, and focus on surface activation effects. Combined experimental and theoretical studies on the same reactions taking place on different metal surfaces have clearly demonstrated that different surfaces not only reduce the reaction barrier differently and render different reaction pathways but also control the morphology of the reaction products and, to some degree, select the reaction products. We end the Account with a list of questions to be addressed in the future. Satisfactorily answering these questions may lead to using the surface-confined coupling reactions to synthesize predefined products with high yield.

Kinetics of Hydrogen Abstraction and Addition Reactions of 3-Hexene by ȮH Radicals.

PubMed

Yang, Feiyu; Deng, Fuquan; Pan, Youshun; Zhang, Yingjia; Tang, Chenglong; Huang, Zuohua

2017-03-09

Rate coefficients of H atom abstraction and H atom addition reactions of 3-hexene by the hydroxyl radicals were determined using both conventional transition-state theory and canonical variational transition-state theory, with the potential energy surface (PES) evaluated at the CCSD(T)/CBS//BHandHLYP/6-311G(d,p) level and quantum mechanical effect corrected by the compounded methods including one-dimensional Wigner method, multidimensional zero-curvature tunneling method, and small-curvature tunneling method. Results reveal that accounting for approximate 70% of the overall H atom abstractions occur in the allylic site via both direct and indirect channels. The indirect channel containing two van der Waals prereactive complexes exhibits two times larger rate coefficient relative to the direct one. The OH addition reaction also contains two van der Waals complexes, and its submerged barrier results in a negative temperature coefficient behavior at low temperatures. In contrast, The OH addition pathway dominates only at temperatures below 450 K whereas the H atom abstraction reactions dominate overwhelmingly at temperature over 1000 K. All of the rate coefficients calculated with an uncertainty of a factor of 5 were fitted in a quasi-Arrhenius formula. Analyses on the PES, minimum reaction path and activation free Gibbs energy were also performed in this study.

Grain Surface Chemistry and the Composition of Interstellar Ices

NASA Technical Reports Server (NTRS)

Tielens, A. G. G. M.

2006-01-01

Submicron sized dust grains are an important component of the interstellar medium. In particular they provide surface where active chemistry can take place. At the low temperatures (-10 K) of the interstellar medium, colliding gas phase species will stick, diffuse, react, and form an icy mantle on these dust grains. This talk will review the principles of grain surface chemistry and delineate important grain surface routes, focusing on reactions involving H, D, and O among each other and with molecules such as CO. Interstellar ice mantles can be studied through the fundamental vibrations of molecular species in the mid-infrared spectra of sources embedded in or located behind dense molecular clouds. Analysis of this type of data has provided a complex view of the composition of these ices and the processes involved. Specifically, besides grain surface chemistry, the composition of interstellar ices is also affected by thermal processing due to nearby newly formed stars. This leads to segregation between different ice components as well as outgassing. The latter results in the formation of a so-called Hot Core region with a gas phase composition dominated by evaporated mantle species. Studies of such regions provide thus a different view on the ice composition and the chemical processes involved. Interstellar ices can also be processed by FUV photons and high energy cosmic ray ions. Cosmic ray processing likely dominates the return of accreted species to the gas phase where further gas phase reactions can take place. These different chemical routes towards molecular complexity in molecular clouds and particularly regions of star formation will be discussed.

When lithography meets self-assembly: a review of recent advances in the directed assembly of complex metal nanostructures on planar and textured surfaces

NASA Astrophysics Data System (ADS)

Hughes, Robert A.; Menumerov, Eredzhep; Neretina, Svetlana

2017-07-01

One of the foremost challenges in nanofabrication is the establishment of a processing science that integrates wafer-based materials, techniques, and devices with the extraordinary physicochemical properties accessible when materials are reduced to nanoscale dimensions. Such a merger would allow for exacting controls on nanostructure positioning, promote cooperative phenomenon between adjacent nanostructures and/or substrate materials, and allow for electrical contact to individual or groups of nanostructures. With neither self-assembly nor top-down lithographic processes being able to adequately meet this challenge, advancements have often relied on a hybrid strategy that utilizes lithographically-defined features to direct the assembly of nanostructures into organized patterns. While these so-called directed assembly techniques have proven viable, much of this effort has focused on the assembly of periodic arrays of spherical or near-spherical nanostructures comprised of a single element. Work directed toward the fabrication of more complex nanostructures, while still at a nascent stage, has nevertheless demonstrated the possibility of forming arrays of nanocubes, nanorods, nanoprisms, nanoshells, nanocages, nanoframes, core-shell structures, Janus structures, and various alloys on the substrate surface. In this topical review, we describe the progress made in the directed assembly of periodic arrays of these complex metal nanostructures on planar and textured substrates. The review is divided into three broad strategies reliant on: (i) the deterministic positioning of colloidal structures, (ii) the reorganization of deposited metal films at elevated temperatures, and (iii) liquid-phase chemistry practiced directly on the substrate surface. These strategies collectively utilize a broad range of techniques including capillary assembly, microcontact printing, chemical surface modulation, templated dewetting, nanoimprint lithography, and dip-pen nanolithography and employ a wide scope of chemical processes including redox reactions, alloying, dealloying, phase separation, galvanic replacement, preferential etching, template-mediated reactions, and facet-selective capping agents. Taken together, they highlight the diverse toolset available when fabricating organized surfaces of substrate-supported nanostructures.

Effect of surface area and chemisorbed oxygen on the SO2 adsorption capacity of activated char

USGS Publications Warehouse

Lizzio, A.A.; DeBarr, J.A.

1996-01-01

The objective of this study was to determine whether activated char produced from Illinois coal could be used effectively to remove sulfur dioxide from coal combustion flue gas. Chars were prepared from a high-volatile Illinois bituminous coal under a wide range of pyrolysis and activation conditions. A novel char preparation technique was developed to prepare chars with SO2 adsorption capacities significantly greater than that of a commercial activated carbon. In general, there was no correlation between SO2 adsorption capacity and surface area. Temperature-programmed desorption (TPD) was used to determine the nature and extent of carbon-oxygen (C-O) complexes formed on the char surface. TPD data revealed that SO2 adsorption was inversely proportional to the amount of C-O complex. The formation of a stable C-O complex during char preparation may have served only to occupy carbon sites that were otherwise reactive towards SO2 adsorption. A fleeting C(O) complex formed during SO2 adsorption is postulated to be the reaction intermediate necessary for conversion of SO2 to H2SO4. Copyright ?? 1996 Elsevier Science Ltd.

Redox and fungicidal properties of phthalocyanine metal complexes as related to active oxygen.

PubMed

Vol'pin, M E; Novodarova, G N; Krainova NYu; Lapikova, V P; Aver'yanov, A A

2000-10-01

Some chemical and fungicidal effects of 20 phthalocyanines of Co, Fe, Cu, and Al were studied. Under dark conditions, these complexes reduced nitroblue tetrazolium in the presence of KCN, accelerated the autoxidation of ascorbate or hydroquinone and decomposed hydrogen peroxide. In the later reaction, hydroxyl radical was generated as evidenced with the deoxyribose assay. The inhibition by superoxide dismutase and catalase of catalyzed autoxidation of ascorbate suggests the participation of superoxide anion-radical and hydrogen peroxide in the reaction. Most complexes were toxic to the fungus Magnaporthe grisea which causes blast disease of rice. The toxicity was enhanced by light being diminished by antioxidant reagents sequestering active oxygen species. Some complexes (including nontoxic ones), after 1-day contact with a leaf surface of the disease-susceptible rice cultivar, induced the fungitoxicity of leaf diffusate. This toxicity was also light-activated and sensitive to antioxidant reagents. Several complexes, when added to inocula, decreased 2-3 times the frequency of the compatible symptoms of the blast. It is suggested that in planta, the dark redox activity of phthalocyanines along with their photosensitization promote the generation of active oxygen, which damages the parasite and, therefore, favors disease resistance.

Mechanistic investigation of Fe(III) oxide reduction by low molecular weight organic sulfur species

NASA Astrophysics Data System (ADS)

Eitel, Eryn M.; Taillefert, Martial

2017-10-01

Low molecular weight organic sulfur species, often referred to as thiols, are known to be ubiquitous in aquatic environments and represent important chemical reductants of Fe(III) oxides. Thiols are excellent electron shuttles used during dissimilatory iron reduction, and in this capacity could indirectly affect the redox state of sediments, release adsorbed contaminants via reductive dissolution, and influence the carbon cycle through alteration of bacterial respiration processes. Interestingly, the reduction of Fe(III) oxides by thiols has not been previously investigated in environmentally relevant conditions, likely due to analytical limitations associated with the detection of thiols and their oxidized products. In this study, a novel electrochemical method was developed to simultaneously determine thiol/disulfide pair concentrations in situ during the reduction of ferrihydrite in batch reactors. First order rate laws with respect to initial thiol concentration were confirmed for Fe(III) oxyhydroxide reduction by four common thiols: cysteine, homocysteine, cysteamine, and glutathione. Zero order was determined for both Fe(III) oxyhydroxide and proton concentration at circumneutral pH. A kinetic model detailing the molecular mechanism of the reaction was optimized with proposed intermediate surface structures. Although metal oxide overall reduction rate constants were inversely proportional to the complexity of the thiol structure, the extent of metal reduction increased with structure complexity, indicating that surface complexes play a significant role in the ability of these thiols to reduce iron. Taken together, these results demonstrate the importance of considering the molecular reaction mechanism at the iron oxide surface when investigating the potential for thiols to act as electron shuttles during dissimilatory iron reduction in natural environments.

Iron silylamide-grafted periodic mesoporous silica.

PubMed

Deschner, Thomas; Törnroos, Karl W; Anwander, Reiner

2011-08-01

The surface chemistry of a series of well-defined metalorganic ferrous and ferric iron complexes on periodic mesoporous silica (PMS) was investigated. In addition to literature known Fe(II)[N(SiMe(3))(2)](2)(THF), Fe(II)[N(SiPh(2)Me(2))(2)](2), and Fe(III)[N(SiMe(3))(2)](2)Cl(THF), the new complexes [Fe(II){N(SiHMe(2))(2)}(2)](2) and Fe(III)[N(SiHMe(2))(2)](3)(μ-Cl)Li(THF)(3) were employed as grafting precursors. Selection criteria for the molecular precursors were the molecular size (monoiron versus diiron species), the oxidation state of the iron center (II versus III), and the functionality of the silylamido ligand (e.g., built-in spectroscopic probes). Hexagonal channel-like MCM-41 and cubic cage-like SBA-1 were chosen as two distinct PMS materials. The highest iron load (12.8 wt %) was obtained for hybrid material [Fe(II){N(SiHMe(2))(2)}(2)](2)@MCM-41 upon stirring the reaction mixture iron silylamide/PMS/n-hexane for 18 h at ambient temperature. Size-selective grafting and concomitantly extensive surface silylation were found to be prominent for cage-like SBA-1. Here, the surface metalation is governed by the type of iron precursor, the pore size, the reaction time, and the solvent. The formation of surface-attached iron-ligand species is discussed on the basis of diffuse reflectance infrared Fourier transform (DRIFT) and electron paramagnetic resonance (EPR) spectroscopy, nitrogen physisorption, and elemental analysis. © 2011 American Chemical Society

Influence of Marangoni flows on the dynamics of isothermal A + B → C reaction fronts.

PubMed

Tiani, R; Rongy, L

2016-09-28

The nonlinear dynamics of A + B → C fronts is analyzed both numerically and theoretically in the presence of Marangoni flows, i.e., convective motions driven by surface tension gradients. We consider horizontal aqueous solutions where the three species A, B, and C can affect the surface tension of the solution, thereby driving Marangoni flows. The resulting dynamics is studied by numerically integrating the incompressible Navier-Stokes equations coupled to reaction-diffusion-convection (RDC) equations for the three chemical species. We show that the dynamics of the front cannot be predicted solely on the basis of the one-dimensional reaction-diffusion profiles as is the case for buoyancy-driven convection around such fronts. We relate this observation to the structure of Marangoni flows which lead to more complex and exotic dynamics. We find in particular the surprising possibility of a reversal of the front propagation direction in time for some sets of Marangoni numbers, quantifying the influence of each chemical species concentration on the solution surface tension. We explain this reversal analytically and propose a new classification of the convective effects on A + B → C reaction fronts as a function of the Marangoni numbers. The influence of the layer thickness on the RDC dynamics is also presented. Those results emphasize the importance of flow symmetry properties when studying convective front dynamics in a given geometry.

Photophysical studies of newly derivatized mono substituted phthalocyanines grafted onto silica nanoparticles via click chemistry.

PubMed

Fashina, Adedayo; Amuhaya, Edith; Nyokong, Tebello

2015-04-05

This work reports on the synthesis, characterization and photophysical studies of newly derived phthalocyanine complexes and the phthalocyanine-silica nanoparticles conjugates. The derived phthalocyanine complexes have one terminal alkyne group. The derived phthalocyanine complexes showed improved photophysical properties (ФF, ФT, ΦΔ and τT) compared to the respective phthalocyanine complexes from which they were derived. The derived phthalocyanine complexes were conjugated to the surface of an azide functionalized silica nanoparticles via copper (1) catalyzed cyclo-addition reaction. All the conjugates showed lower triplet quantum yields ranging from 0.37 to 0.44 compared to the free phthalocyanine complexes. The triplet lifetimes ranged from 352 to 484 μs for the conjugates and from 341 to 366 μs for the free phthalocyanine complexes. Copyright © 2014 Elsevier B.V. All rights reserved.

Nickel-based anodic electrocatalysts for fuel cells and water splitting

NASA Astrophysics Data System (ADS)

Chen, Dayi

Our world is facing an energy crisis, so people are trying to harvest and utilize energy more efficiently. One of the promising ways to harvest energy is via solar water splitting to convert solar energy to chemical energy stored in hydrogen. Another of the options to utilize energy more efficiently is to use fuel cells as power sources instead of combustion engines. Catalysts are needed to reduce the energy barriers of the reactions happening at the electrode surfaces of the water-splitting cells and fuel cells. Nickel-based catalysts happen to be important nonprecious electrocatalysts for both of the anodic reactions in alkaline media. In alcohol fuel cells, nickel-based catalysts catalyze alcohol oxidation. In water splitting cells, they catalyze water oxidation, i.e., oxygen evolution. The two reactions occur in a similar potential range when catalyzed by nickel-based catalysts. Higher output current density, lower oxidation potential, and complete substrate oxidation are preferred for the anode in the applications. In this dissertation, the catalytic properties of nickel-based electrocatalysts in alkaline medium for fuel oxidation and oxygen evolution are explored. By changing the nickel precursor solubility, nickel complex nanoparticles with tunable sizes on electrode surfaces were synthesized. Higher methanol oxidation current density is achieved with smaller nickel complex nanoparticles. DNA aggregates were used as a polymer scaffold to load nickel ion centers and thus can oxidize methanol completely at a potential about 0.1 V lower than simple nickel electrodes, and the methanol oxidation pathway is changed. Nickel-based catalysts also have electrocatalytic activity towards a wide range of substrates. Experiments show that methanol, ethanol, glycerol and glucose can be deeply oxidized and carbon-carbon bonds can be broken during the oxidation. However, when comparing methanol oxidation reaction to oxygen evolution reaction catalyzed by current nickel-based catalysts, methanol oxidation suffers from high overpotential and catalyst poisoning by high concentration of substrates, so current nickel-based catalysts are more suitable to be used as oxygen evolution catalysts. A photoanode design that applies nickel oxides to a semiconductor that is incorporated with surface-plasmonic metal electrodes to do solar water oxidation with visible light is proposed.

In situ spectroscopic identification of neptunium(V) inner-sphere complexes on the hematite-water interface.

PubMed

Müller, Katharina; Gröschel, Annett; Rossberg, André; Bok, Frank; Franzen, Carola; Brendler, Vinzenz; Foerstendorf, Harald

2015-02-17

Hematite plays a decisive role in regulating the mobility of contaminants in rocks and soils. The Np(V) reactions at the hematite-water interface were comprehensively investigated by a combined approach of in situ vibrational spectroscopy, X-ray absorption spectroscopy and surface complexation modeling. A variety of sorption parameters such as Np(V) concentration, pH, ionic strength, and the presence of bicarbonate was considered. Time-resolved IR spectroscopic sorption experiments at the iron oxide-water interface evidenced the formation of a single monomer Np(V) inner-sphere sorption complex. EXAFS provided complementary information on bidentate edge-sharing coordination. In the presence of atmospherically derived bicarbonate the formation of the bis-carbonato inner-sphere complex was confirmed supporting previous EXAFS findings.1 The obtained molecular structure allows more reliable surface complexation modeling of recent and future macroscopic data. Such confident modeling is mandatory for evaluating water contamination and for predicting the fate and migration of radioactive contaminants in the subsurface environment as it might occur in the vicinity of a radioactive waste repository or a reprocessing plant.

Arsenic behavior in river sediments under redox gradient: a review.

PubMed

Gorny, Josselin; Billon, Gabriel; Lesven, Ludovic; Dumoulin, David; Madé, Benoît; Noiriel, Catherine

2015-02-01

The fate of arsenic - a redox sensitive metalloid - in surface sediments is closely linked to early diagenetic processes. The review presents the main redox mechanisms and final products of As that have been evidenced over the last years. Oxidation of organic matter and concomitant reduction of oxidants by bacterial activity result in redox transformations of As species. The evolution of the sediment reactivity will also induce secondary abiotic reactions like complexation/de-complexation, sorption, precipitation/dissolution and biotic reactions that could, for instance, lead to the detoxification of some As species. Overall, abiotic redox reactions that govern the speciation of As mostly involve manganese (hydr)-oxides and reduced sulfur species produced by the sulfate-reducing bacteria. Bacterial activity is also responsible for the inter-conversion between As(V) and As(III), as well as for the production of methylated arsenic species. In surficial sediments, sorption processes also control the fate of inorganic As(V), through the formation of inner sphere complexes with iron (hydr)-oxides, that are biologically reduced in buried sediment. Arsenic species can also be bound to organic matter, either directly to functional groups or indirectly through metal complexes. Finally, even if the role of reduced sulfur species in the cycling of arsenic in sediments has been evidenced, some of the transformations remain hypothetical and deserve further investigation. Copyright © 2014 Elsevier B.V. All rights reserved.

Cycloaddition Reactions of Cobalt-Complexed Macrocyclic Alkynes: The Transannular Pauson-Khand Reaction.

PubMed

Karabiyikoglu, Sedef; Boon, Byron A; Merlic, Craig A

2017-08-04

The Pauson-Khand reaction is a powerful tool for the synthesis of cyclopentenones through the efficient [2 + 2 + 1] cycloaddition of dicobalt alkyne complexes with alkenes. While intermolecular and intramolecular variants are widely known, transannular versions of this reaction are unknown and the basis of this study. Macrocyclic enyne and dienyne complexes were readily synthesized by palladium(II)-catalyzed oxidative macrocyclizations of bis(vinyl boronate esters) or ring-closing metathesis reactions followed by complexation with dicobalt octacarbonyl. Several reaction modalities of these macrocyclic complexes were uncovered. In addition to the first successful transannular Pauson-Khand reactions, other intermolecular and transannular cycloaddition reactions included intermolecular Pauson-Khand reactions, transannular [4 + 2] cycloaddition reactions, intermolecular [2 + 2 + 2] cycloaddition reactions, and intermolecular [2 + 2 + 1 + 1] cycloaddition reactions. The structural and reaction requirements for each process are presented.

Environmental Processing of Lipids Driven by Aqueous Photochemistry of α-Keto Acids

PubMed Central

2018-01-01

Sunlight can initiate photochemical reactions of organic molecules though direct photolysis, photosensitization, and indirect processes, often leading to complex radical chemistry that can increase molecular complexity in the environment. α-Keto acids act as photoinitiators for organic species that are not themselves photoactive. Here, we demonstrate this capability through the reaction of two α-keto acids, pyruvic acid and 2-oxooctanoic acid, with a series of fatty acids and fatty alcohols. We show for five different cases that a cross-product between the photoinitiated α-keto acid and non-photoactive species is formed during photolysis in aqueous solution. Fatty acids and alcohols are relatively unreactive species, which suggests that α-keto acids are able to act as radical initiators for many atmospherically relevant molecules found in the sea surface microlayer and on atmospheric aerosol particles. PMID:29806009

One-step formation of bifunctionnal aryl/alkyl grafted films on conducting surfaces by the reduction of diazonium salts in the presence of alkyl iodides.

PubMed

Hetemi, Dardan; Hazimeh, Hassan; Decorse, Philippe; Galtayries, Anouk; Combellas, Catherine; Kanoufi, Frédéric; Pinson, Jean; Podvorica, Fetah I

2015-05-19

The formation of partial perfluoroalkyl or alkyl radicals from partial perfluoroalkyl or alkyl iodides (ICH2CH2C6F13 and IC6H13) and their reaction with surfaces takes place at low driving force (∼-0.5 V/SCE) when the electrochemical reaction is performed in acetonitrile in the presence of diazonium salts (ArN2(+)), at a potential where the latter is reduced. By comparison to the direct grafting of ICH2CH2C6F13, this corresponds to a gain of ∼2.1 V in the case of 4-nitrobenzenediazonium. Such electrochemical reaction permits the modification of gold surfaces (and also carbon, iron, and copper) with mixed aryl-alkyl groups (Ar = 3-CH3-C6H4, 4-NO2-C6H4, and 4-Br-C6H4, R = C6H13 or (CH2)2-C6F13). These strongly bonded mixed layers are characterized by IRRAS, XPS, ToF-SIMS, ellipsometry, water contact angles, and cyclic voltammetry. The relative proportions of grafted aryl and alkyl groups can be varied along with the relative concentrations of diazonium and iodide components in the grafting solution. The formation of the films is assigned to the reaction of aryl and alkyl radicals on the surface and on the first grafted layer. The former is obtained from the electrochemical reduction of the diazonium salt; the latter results from the abstraction of an iodine atom by the aryl radical. The mechanism involved in the growth of the film provides an example of complex surface radical chemistry.

Environmental chemistry at vapor/water interfaces: insights from vibrational sum frequency generation spectroscopy.

PubMed

Jubb, Aaron M; Hua, Wei; Allen, Heather C

2012-01-01

The chemistry that occurs at surfaces has been an intense area of study for many years owing to its complexity and importance in describing a wide range of physical phenomena. The vapor/water interface is particularly interesting from an environmental chemistry perspective as this surface plays host to a wide range of chemistries that influence atmospheric and geochemical interactions. The application of vibrational sum frequency generation (VSFG), an inherently surface-specific, even-order nonlinear optical spectroscopy, enables the direct interrogation of various vapor/aqueous interfaces to elucidate the behavior and reaction of chemical species within the surface regime. In this review we discuss the application of VSFG to the study of a variety of atmospherically important systems at the vapor/aqueous interface. Chemical systems presented include inorganic ionic solutions prevalent in aqueous marine aerosols, small molecular solutes, and long-chain fatty acids relevant to fat-coated aerosols. The ability of VSFG to probe both the organization and reactions that may occur for these systems is highlighted. A future perspective toward the application of VSFG to the study of environmental interfaces is also provided.

Potential energy surfaces related to the ion-molecule reaction C/sup +/ + H/sub 2/

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liskow, D.H.; Bender, C.F.; Schaefer, H.F. III

1974-10-01

The C/sup +/ + H/sub 2/ ion-molecule reaction has been studied by several experimental groups and appears likely to become the focal point of much experimental and theoretical activity. Ab initio self-consistent-field and configuration interaction calculations have accordingly been carried out for this system. A double zeta basis set of contracted Gaussian functions was employed and as many as 648 configurations included. For isosceles triangle configurations (C/sub 2V/ point group) the /sup 2/A/sub 1/, /sup 2/B/sub 1/, and /sup 2/B/sub 2/ potential surfaces were considered, while for linear geometries (C/sub infinity V) the /sup 2/..sigma../sup +/ and /sup 2/PI surfacesmore » were studied. For general (C/sub S/) geometry, the lowest /sup 2/A' potential surface was considered. Properties reported include minimum energy paths and energy profiles for the various processes considered. The intuitive correlation diagram of Mahan and Sloane is given qualitative reliability. Pathways to CH/sub 2//sup +/ complex formation are shown to depend crucially on the C/sub S/ potential surface.« less

Arsenic Mobilization Influenced By Iron Reduction And Sulfidogenesis Under Dynamic Flow

NASA Astrophysics Data System (ADS)

Kocar, B. D.; Stewart, B. D.; Herbel, M.; Fendorf, S.

2004-12-01

Sulfidogenesis and iron reduction are ubiquitous processes that occur in a variety of anoxic subsurface and surface environments, which profoundly impact the cycling of arsenic. Of the iron (hydr)oxides, ferrihydrite possesses one of the highest capacities to retain arsenic, and is globally distributed within soils and sediments. Upon dissimilatory iron reduction, ferrihydrite may transform to lower surface area minerals, such as goethite and magnetite, which decreases arsenic retention, thus enhancing its transport. Here we examine how arsenic retained on ferrihydrite is mobilized under dynamic flow in the presence of Sulfurosprillum barnesii strain SES-3, a bacteria capable of reducing both As(V) and Fe(III). Ferrihydrite coated sands, loaded with 150 mg kg-1 As(V), were inoculated with S. barnesii, packed into a column and reacted with a synthetic groundwater solution. Within several days after initiation of flow, the concentration of arsenic in the column effluent increased dramatically coincident with the mineralogical transformation of ferrihydrite and As(V) reduction to As(III). Following the initial pulse of arsenic, effluent concentration then declined to less than 10 μ M. Thus, arsenic release into the aqueous phase is contingent upon the incongruent reduction of As(V) and Fe(III) as mediated by biological activity. Reaction of abiotically or biotically generated dissolved sulfide with iron (hydr)oxides may have a dramatic influence on the fate of arsenic within surface and subsurface environments. Accordingly, we examined the reaction of dissolved bisulfide and iron (hydr)oxide complexed with arsenic in both batch and column systems. Low ratios of sulfide to iron in batch reaction systems result in the formation of elemental sulfur and concomitant arsenic release from the iron (hydr)oxide surface. High sulfide to iron ratios, in contrast, appear to favor the formation of iron and arsenic sulfides. Our findings demonstrate that iron (hydr)oxides may quench reactions between sulfide and constituents sorbed to iron (hydr)oxide surfaces, forming elemental sulfur as opposed to sulfide-arsenic complexes. In addition, reductive transformation of iron (hydr)oxide by dissolved sulfide may release sorbed constituents. Hence, moderate to low concentrations of dissolved sulfide in association with iron (hydr)oxides may inhibit sequestration of important contaminants that are attenuated by Fe(III) and/or S(-II) bearing phases.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Almus, F.E.; Rao, L.V.; Fleck, R.A.

An umbilical vein model was designed in which washed vein segments are filled with a reaction mixture containing factor VIIa, Ca(+)+, and a substrate, either 3H-factor IX or 3H-factor X. The vein wall provides the tissue factor (TF) for factor VIIa/TF complexes that activate the substrates as measured by activation peptide release. The model was developed to study TF induced on venous endothelium in situ. However, unlike previous studies with TF expressed on cultured umbilical vein endothelial cells, factors IX and X were activated without first having to expose the vein wall to a perturbing stimulus. Histologic studies revealed thatmore » washing the vein and mixing the reaction mixture before subsampling had disrupted the endothelium. Immunostaining with anti-TF antibodies revealed no staining of endothelium but intense staining in extensions of Wharton's jelly penetrating fenestrations of the muscularis media of the vein. Thus, the model provided data on factor VIIa/TF formed, not on endothelium, but within the mucoid connective tissue of Wharton's jelly. It is known that factor VIIa/TF formed with TF in suspension or with TF expressed on the surface of cultured cells activates factor X more rapidly than factor IX. In contrast, in the umbilical vein model, when each substrate was present in an 88 nmol/L concentration, factors IX and X were activated at equivalent rates (mean activation rate for factor IX, 18.8 +/- 3.6 nmol/L/h; for factor X, 17.8 +/- 2.9 nmol/L/h; n = 9 paired vein segments). These data strengthen the evidence that factor VIIa/TF activation of factor IX represents a key initial reaction of coagulation in tissues. These results also show that data obtained with factor VIIa/TF complexes formed on the surface of cultured cells need not hold for factor VIIa/TF complexes formed in extracellular matrix.« less

Dynamic processes occurring at the Cr IIIaq-manganite (γ-MnOOH) interface: simultaneous adsorption, microprecipitation, oxidation/reduction, and dissolution

NASA Astrophysics Data System (ADS)

Weaver, Robert M.; Hochella, Michael F.; Ilton, Eugene S.

2002-12-01

The complex interaction between Cr IIIaq and manganite (γ-MnOOH) was systematically studied at room temperature over a pH range of 3 to 6, and within a concentration range of 10 -4 to 10 -2 M CrOH 2+aq. Solution compositional changes during batch reactions were characterized by inductively coupled plasma spectroscopy and ultraviolet-visible spectrophotometry. The manganites were characterized before and after reaction with X-ray photoelectron spectroscopy, scanning electron microscopy (SEM), high-resolution field-emission SEM, and energy-dispersive spectroscopy analysis. Fluid-cell atomic force microscopy was used to follow these metal-mineral interactions in situ. The reactions are characterized by (1) sorption of Cr III and the surface-catalyzed microprecipitation of Cr III-hydroxy hydrate on manganite surfaces, (2) the acidic dissolution of the manganite, and (3) the simultaneous reductive dissolution of manganite coupled with the oxidation of Cr IIIaq to highly toxic Cr VIaq. Cr III-hydroxy hydrate was shown to precipitate on the manganite surface while still undersaturated in bulk solution. The rate of manganite dissolution increased with decreasing pH due both to acid-promoted and Mn-reduction-promoted dissolution. Cr oxidation also increased in the lower pH range, this as a result of its direct redox coupling with Mn reduction. Neither Mn II nor Cr VI were ever detected on manganite surfaces, even at the maximum rate of their generation. At the highest pHs of this study, Cr IIIaq was effectively removed from solution to form Cr III-hydroxy hydrate on manganite surfaces and in the bulk solution, and manganite dissolution and Cr VIaq generation were minimized. All interface reactions described above were heterogeneous across the manganite surfaces. This heterogeneity is a direct result of the heterogeneous semiconducting nature of natural manganite crystals and is also an expression of the proximity effect, whereby redox processes on semiconducting surfaces are not limited to next nearest neighbor sites.

Kinetics of Al + H2O reaction: theoretical study.

PubMed

Sharipov, Alexander; Titova, Nataliya; Starik, Alexander

2011-05-05

Quantum chemical calculations were carried out to study the reaction of Al atom in the ground electronic state with H(2)O molecule. Examination of the potential energy surface revealed that the Al + H(2)O → AlO + H(2) reaction must be treated as a complex process involving two steps: Al + H(2)O → AlOH + H and AlOH + H → AlO + H(2). Activation barriers for these elementary reaction channels were calculated at B3LYP/6-311+G(3df,2p), CBS-QB3, and G3 levels of theory, and appropriate rate constants were estimated by using a canonical variational theory. Theoretical analysis exhibited that the rate constant for the Al + H(2)O → products reaction measured by McClean et al. must be associated with the Al + H(2)O → AlOH + H reaction path only. The process of direct HAlOH formation was found to be negligible at a pressure smaller than 100 atm.

Adsorption of water, sulfates and chloride on arsenopyrite surface

NASA Astrophysics Data System (ADS)

Silva, Juliana C. M.; dos Santos, Egon C.; de Oliveira, Aline; Heine, Thomas; De Abreu, Heitor A.; Duarte, Hélio A.

2018-03-01

Arsenopyrite is one of the sulfide minerals responsible for acid rock drainage (ARD) and is one of the most hazardous in regions affected by mining activities. This phenomenon involves complex reaction mechanism. Although it is intensely investigated, there is a lack of consensus concerning the reaction mechanisms and more information is still necessary. In this work, the adsorption of water, hydrochloric acid, and sulfuric acid on arsenopyrite (001) surface was investigated by means of Density Functional calculations and the results compared to other sulfides aiming to understand the mineral/water interface. The interaction of the chemical species with the (001) FeAsS surface is the first step to understand the intricate oxidation mechanism of arsenopyrite. Molecular water adsorption on (001) FeAsS is more favored than the adsorption of sulfate favoring the dissolution of sulfates and enhancing its oxidation. The estimated adsorption energies of water, sulfates and chloride on other sulfide minerals are compared with the estimated values for arsenopyrite and the chemical reactivity differences discussed in detail.

Carbon dioxide hydrogenation on Ni(110).

PubMed

Vesselli, Erik; De Rogatis, Loredana; Ding, Xunlei; Baraldi, Alessandro; Savio, Letizia; Vattuone, Luca; Rocca, Mario; Fornasiero, Paolo; Peressi, Maria; Baldereschi, Alfonso; Rosei, Renzo; Comelli, Giovanni

2008-08-27

We demonstrate that the key step for the reaction of CO 2 with hydrogen on Ni(110) is a change of the activated molecule coordination to the metal surface. At 90 K, CO 2 is negatively charged and chemically bonded via the carbon atom. When the temperature is increased and H approaches, the H-CO 2 complex flips and binds to the surface through the two oxygen atoms, while H binds to the carbon atom, thus yielding formate. We provide the atomic-level description of this process by means of conventional ultrahigh vacuum surface science techniques combined with density functional theory calculations and corroborated by high pressure reactivity tests. Knowledge about the details of the mechanisms involved in this reaction can yield a deeper comprehension of heterogeneous catalytic organic synthesis processes involving carbon dioxide as a reactant. We show why on Ni the CO 2 hydrogenation barrier is remarkably smaller than that on the common Cu metal-based catalyst. Our results provide a possible interpretation of the observed high catalytic activity of NiCu alloys.

Surface-Accelerated Decomposition of δ-HMX.

PubMed

Sharia, Onise; Tsyshevsky, Roman; Kuklja, Maija M

2013-03-07

Despite extensive efforts to study the explosive decomposition of HMX, a cyclic nitramine widely used as a solid fuel, explosive, and propellant, an understanding of the physicochemical processes, governing the sensitivity of condensed HMX to detonation initiation is not yet achieved. Experimental and theoretical explorations of the initiation of chemistry are equally challenging because of many complex parallel processes, including the β-δ phase transition and the decomposition from both phases. Among four known polymorphs, HMX is produced in the most stable β-phase, which transforms into the most reactive δ-phase under heat or pressure. In this study, the homolytic NO2 loss and HONO elimination precursor reactions of the gas-phase, ideal crystal, and the (100) surface of δ-HMX are explored by first principles modeling. Our calculations revealed that the high sensitivity of δ-HMX is attributed to interactions of surfaces and molecular dipole moments. While both decomposition reactions coexist, the exothermic HONO-isomer formation catalyzes the N-NO2 homolysis, leading to fast violent explosions.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hammond, Glenn Edward; Yang, Xiaofan; Song, Xuehang

The groundwater-surface water interaction zone (GSIZ) plays an important role in riverine and watershed ecosystems as the exchange of waters of variable composition and temperature (hydrologic exchange flows) stimulate microbial activity and associated biogeochemical reactions. Variable temporal and spatial scales of hydrologic exchange flows, heterogeneity of the subsurface environment, and complexity of biogeochemical reaction networks in the GSIZ present challenges to incorporation of fundamental process representations and model parameterization across a range of spatial scales (e.g. from pore-scale to field scale). This paper presents a novel hybrid multiscale simulation approach that couples hydrologic-biogeochemical (HBGC) processes between two distinct length scalesmore » of interest.« less

Ligand Exchange Kinetics of Environmentally Relevant Metals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Panasci, Adele Frances

2014-07-15

The interactions of ground water with minerals and contaminants are of broad interest for geochemists but are not well understood. Experiments on the molecular scale can determine reaction parameters (i.e. rates of ligand exchange, activation entropy, activation entropy, and activation volume) that can be used in computations to gain insight into reactions that occur in natural groundwaters. Experiments to determine the rate of isotopic ligand exchange for three environmentally relevant metals, rhodium (Rh), iron (Fe), and neptunium (Np), are described. Many environmental transformations of metals (e.g. reduction) in soil occur at trivalent centers, Fe(III) in particular. Contaminant ions absorb tomore » mineral surfaces via ligand exchange, and the reversal of this reaction can be dangerous, releasing contaminants into the environment. Ferric iron is difficult to study spectroscopically because most of its complexes are paramagnetic and are generally reactive toward ligand exchange; therefore, Rh(III), which is diamagnetic and less reactive, was used to study substitution reactions that are analogous to those that occur on mineral oxide surfaces. Studies on both Np(V) and Np(VI) are important in their own right, as 237Np is a radioactive transuranic element with a half-life of 2 million years.« less

Tetrel bond-σ-hole bond as a preliminary stage of the SN2 reaction.

PubMed

Grabowski, Sławomir J

2014-02-07

MP2/aug-cc-pVTZ calculations were carried out on complexes of ZH4, ZFH3 and ZF4 (Z = C, Si and Ge) molecules with HCN, LiCN and Cl(-) species acting as Lewis bases through nitrogen centre or chlorine ion. Z-Atoms in these complexes usually act as Lewis acid centres forming σ-hole bonds with Lewis bases. Such noncovalent interactions may adopt a name of tetrel bonds since they concern the elements of the group IV. There are exceptions for complexes of CH4 and CF4, as well as for the F4SiNCH complex where the tetrel bond is not formed. The energetic and geometrical parameters of the complexes were analyzed and numerous correlations between them were found. The Quantum Theory of 'Atoms in Molecules' and Natural Bonds Orbital (NBO) method used here should deepen the understanding of the nature of the tetrel bond. An analysis of the electrostatic potential surfaces of the interacting species is performed. The electron charge redistribution, being the result of the tetrel bond formation, is the same as that of the SN2 reaction. The energetic and geometrical parameters of the complexes analyzed here correspond to different stages of the SN2 process.

Mechanism for chelated sulfate formation from SO2 and bis (triphenylphosphine) platinum

NASA Technical Reports Server (NTRS)

Mehandru, S. P.; Anderson, A. B.

1985-01-01

Structure and energy surface calculations using the atom superposition and electron delocalization molecular orbital theory show that the first step in the reaction between SO2 and the dioxygen complex (PPh3)2PtO2 is the coordination of SO2 with one oxygen atom of the complex, followed by metal-oxygen bond breaking and reorientation, leading to a five-membered cyclic structure. This then rearranges to form the bidentate coordinated sulfate. Alternative pathways are considered and are found to be less favorable.

Lunar and Planetary Science XXXV: Weird Martian Minerals: Complex Mars Surface Processes

NASA Technical Reports Server (NTRS)

2004-01-01

The session "Complex Mars Surface" included the following reports:A Reappraisal of Adsorbed Superoxide Ion as the Cause Behind the Reactivity of the Martian Soils; Sub-Surface Deposits of Hydrous Silicates or Hydrated Magnesium Sulfates as Hydrogen Reservoirs near the Martian Equator: Plausible or Not?; Thermal and Evolved Gas Analysis of Smectites: The Search for Water on Mars; Aqueous Alteration Pathways for K, Th, and U on Mars; Temperature Dependence of the Moessbauer Fraction in Mars-Analog Minerals; Acid-Sulfate Vapor Reactions with Basaltic Tephra: An Analog for Martian Surface Processes; Iron Oxide Weathering in Sulfuric Acid: Implications for Mars; P/Fe as an Aquamarker for Mars; Stable Isotope Composition of Carbonates Formed in Low-Temperature Terrestrial Environments as Martian Analogs; Can the Phosphate Sorption and Occlusion Properties Help to Elucidate the Genesis of Specular Hematite on the Mars Surface?; Sulfate Salts, Regolith Interactions, and Water Storage in Equatorial Martian Regolith; Potential Pathways to Maghemite in Mars Soils: The Key Role of Phosphate; and Mineralogy, Abundance, and Hydration State of Sulfates and Chlorides at the Mars Pathfinder Landing Site.

Copper-catalyzed azide–alkyne cycloaddition (CuAAC) and beyond: new reactivity of copper(i) acetylides†

PubMed Central

Hein, Jason E.

2011-01-01

Copper-catalyzed azide–alkyne cycloaddition (CuAAC) is a widely utilized, reliable, and straightforward way for making covalent connections between building blocks containing various functional groups. It has been used in organic synthesis, medicinal chemistry, surface and polymer chemistry, and bioconjugation applications. Despite the apparent simplicity of the reaction, its mechanism involves multiple reversible steps involving coordination complexes of copper(i) acetylides of varying nuclearity. Understanding and controlling these equilibria is of paramount importance for channeling the reaction into the productive catalytic cycle. This tutorial review examines the history of the development of the CuAAC reaction, its key mechanistic aspects, and highlights the features that make it useful to practitioners in different fields of chemical science. PMID:20309487

Surface-active ionic liquids for palladium-catalysed cross coupling in water: effect of ionic liquid concentration on the catalytically active species† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7ra07757b

PubMed Central

Taskin, Meltem; Cognigni, Alice; Zirbs, Ronald; Reimhult, Erik

2017-01-01

We report the design and synthesis of surface-active ionic liquids for application in palladium-catalyzed cross coupling reactions. A series of dodecylimidazolium-based ionic liquids were applied as additives in the Heck reaction of ethyl acrylate and iodobenzene, and high yields of >90% could be obtained in water without the addition of further ligands. Our results indicate that the ionic liquid concentration in water is the key factor affecting the formation of the catalytically active species and hence the yield. Moreover, imidazolium-based ionic liquids that are able to form a carbene species differ significantly from conventional cationic surfactants, as a concentration dependent formation of the N-heterocyclic carbene complex was observed. PMID:29308189

Spectroscopic studies of organometallic compounds on single crystal metal surfaces: Surface acetylides of silver (110)

NASA Astrophysics Data System (ADS)

Madix, Robert J.

The nature of compounds formed by the reaction of organic molecules with metal surfaces can be studied with a battery of analytical methods based on both physicals and chemical understanding. In this paper the application of UPS, XPS, LEED and EELS as well as temperature programmed reaction spectroscopy (TPRS) and chemical titration methods to the characterization of surface complexes is discussed. Particular emphasis is given to the reaction of acetylene with a single crystal surface of silver, Ag(110). Previous work has shown that this surface, when clean, is unreactive to hydrocarbons, alcohols and carboxylic acids under ultra high vacuum conditions. Preadsorption of oxygen, however, renders the surface reactive, and a wide variety of organometallic surface compounds can be formed. As expected then, no stable adsorption state and no reaction was observed with clean Ag(110) following room temperature exposure to acetylene. Following exposure at 150 K, however, a weekly bound chemisorption state was observed to desorb at 195 K, indicating a binding energy to the surface of approximately 12 kcal/gmole. Reaction with preadsorbed oxygen gave water formulation upon dosing and produced surface intermediates which yeilded two acetylene desorption states at 195 and 175 K. Heating above 300 K to completely desorb the higher temperature state produced new, well-defined LEED Features due to residual surface carbon which disappeared when the surface was heated above 550 K. Clearly, there were distinc changes in the nature of the absorbed layer at 195, 300 and 550 K. These changes were reflected in XPS. For the weakly chemisorbed acetylene a large C(ls) peak at 285.6 eV with a small, broad, indistinc shoulder at higher binding energy (288.2) was observed. The spectrum of the species following acetylene desorption at 275 K, however, showed the formulation of a large C(ls) peak at 283.6 eV in addition to peaks characteristics of the weakly chemisorbed state. This result indicated that the carbon atoms in the surface acetylide became inequivalent. Heating to 300 K produced a single peak at 282.8 eV which reverted to 283.4 when heated above 550 K; the carbon atoms became chemically equivalent. This latter state could be removed completely by O 2 to form CO 2(3). The XPS results showed quantitative conversion of all surface carbon from each state observed. Conclusive evidence regarding the identity of these states was obtained with titration experiments with deuterated acetic acid. CH 3COOD was adsorbed on top of the acetylenic residues at 150 K and heated to note the isotopes of acetylene that desorbed. The 275 K acetylene desorption peak, which showed inequivalent carbon atoms, was titrated by CH 3COOD to form C 2HD, indicating C 2H as the stable surface species. The species formed above 300 K, which showed equivalent carbon atoms in XPS, titrated to form C 2D 2, indicating a C 2 surface species. In each case the formulation of surface acetate was quantitative. The structure of these species was probed further with high resolution electron energy loss spectroscopy. The weakly chemisorbed molecular state exhibited vibrational losses at 300, 700 and 3270 cm -1, characteristics of an acetylene-surface stretching motion, a C-C-H bend and the C-H stretch respectively. No C-C stretch was observed, indicating that the molecule lay parallel to the plane of the surface. For adsorbed C 2H, bands were observed at 300, 690 and 3250cm -1. The high C-H stretching frequency indicated that the C-C bound order was near three. The absence of a C-C stretch in the spectrum was somewhat surprising, but was explained by a σ-π bonded complex in which the -C=CH species was flattened toward the surface by an interaction of an Ag atom with the π system of the acetylide.

Quantitative determination of oxygen defects, surface lewis acidity, and catalytic properties of mesoporous MoO3/SBA-15 catalysts

NASA Astrophysics Data System (ADS)

González, Julio; Wang, Jin An; Chen, Lifang; Manríquez, Maria; Salmones, José; Limas, Roberto; Arellano, Ulises

2018-07-01

A set of MoO3/SBA-15 mesoporous catalysts were characterized with a variety of spectroscopic techniques and their crystalline structures were refined with Rietveld method. Oxygen defect concentration, crystallite size, phase composition, surface acidity, mesoporous regularity, and textural properties were reported. Both α-MoO3 and β-MoO3 phases coexisted but α-MoO3 was predominated. Oxygen defects were created in the orthorhombic structure and its concentration decreased from 3.08% for the 20 wt%MoO3/SBA-15 to 0.55% for the 25 wt%MoO3/SBA-15. All the MoO3/SBA-15 catalysts chiefly contained a big number of Lewis acid sites originating from oxygen defects in MoO3 crystals. In the absence of formic acid, the oxidation of 4,6-dibenzothiophene (4,6-DMDBT) in a model diesel was almost proportional to the number of Lewis acid sites. In the presence of formic acid, 4,6-DMDBT oxidation was significantly affected by the formation of surface peroxometallic complex and Lewis acidity. Formic acid addition could improve the ODS efficiency by promoting peroxometallic complex formation and enhancing oxidant stability. Under the optimal reaction condition using the best 15 and 20 wt%MoO3/SBA-15 catalysts, more than 99% 4,6-DMDBT could be removed at 70 °C within 30 min. This work confirmed that 4,6-DMDBT oxidation is a texture and particle size sensitive and Lewis acidity dependent reaction. This work also shows that crystalline structure refinement combination with experiments can gain new insights in the design of heterogeneous nanocatalysts and help to better understand the catalytic behavior in the oxidative desulfurization reactions.

A Comparison of Blood Factor XII Autoactivation in Buffer, Protein Cocktail, Serum, and Plasma Solutions

PubMed Central

Golas, Avantika; Yeh, Chyi-Huey Josh; Pitakjakpipop, Harit; Siedlecki, Christopher A.; Vogler, Erwin A.

2012-01-01

Activation of blood plasma coagulation in vitro by contact with material surfaces is demonstrably dependent on plasma-volume-to-activator-surface-area ratio. The only plausible explanation consistent with current understanding of coagulation-cascade biochemistry is that procoagulant stimulus arising from the activation complex of the intrinsic pathway is dependent on activator surface area. And yet, it is herein shown that activation of the blood zymogen factor XII (Hageman factor, FXII) dissolved in buffer, protein cocktail, heat-denatured serum, and FXI deficient plasma does not exhibit activator surface-area dependence. Instead, a highly-variable burst of procoagulant-enzyme yield is measured that exhibits no measurable kinetics, sensitivity to mixing, or solution-temperature dependence. Thus, FXII activation in both buffer and protein-containing solutions does not exhibit characteristics of a biochemical reaction but rather appears to be a “mechanochemical” reaction induced by FXII molecule interactions with hydrophilic activator particles that do not formally adsorb blood proteins from solution. Results of this study strongly suggest that activator surface-area dependence observed in contact activation of plasma coagulation does not solely arise at the FXII activation step of the intrinsic pathway. PMID:23117212

Preparation of the cortical reaction: maturation-dependent migration of SNARE proteins, clathrin, and complexin to the porcine oocyte's surface blocks membrane traffic until fertilization.

PubMed

Tsai, Pei-Shiue; van Haeften, Theo; Gadella, Bart M

2011-02-01

The cortical reaction is a calcium-dependent exocytotic process in which the content of secretory granules is released into the perivitellin space immediately after fertilization, which serves to prevent polyspermic fertilization. In this study, we investigated the involvement and the organization of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins in the docking and fusion of the cortical granule membrane with the oolemma in porcine oocytes. During meiotic maturation, secretory vesicles that were labeled with a granule-specific binding lectin, peanut agglutinin (PNA), migrated toward the oocyte's surface. This surface-orientated redistribution behavior was also observed for the oocyte-specific SNARE proteins SNAP23 and VAMP1 that colocalized with the PNA-labeled structures in the cortex area just under the oolemma and with the exclusive localization area of complexin (a trans-SNARE complex-stabilizing protein). The coming together of these proteins serves to prevent the spontaneous secretion of the docked cortical granules and to prepare the oocyte's surface for the cortical reaction, which should probably be immediately compensated for by a clathrin-mediated endocytosis. In vitro fertilization resulted in the secretion of the cortical granule content and the concomitant release of complexin and clathrin into the oocyte's cytosol, and this is considered to stimulate the observed endocytosis of SNARE-containing membrane vesicles.

Thin film assembly of nanosized cobalt(II) bis(5-phenyl-azo-8-hydroxyquinolate) using static step-by-step soft surface reaction technique: Structural characterization and optical properties.

PubMed

Seleim, S M; Hamdalla, Taymour A; Mahmoud, Mohamed E

2017-09-05

Nanosized (NS) cobalt (II) bis(5-phenyl-azo-8-hydroxyquinolate) (NS Co(II)-(5PA-8HQ) 2 ) thin films have been synthesized using static step-by-step soft surface reaction (SS-b-SSR) technique. Structural and optical characterizations of these thin films have been carried out using thermal gravimetric analysis (TGA), Fourier transform infrared (FT-IR), scanning electron microscopy (SEM), high resolution transmission electron microscopy (HR-TEM) and X-ray diffraction (XRD). The HR-TEM results revealed that the assembled Co(II)-complex exhibited a uniformly NS structure particles in the form of nanorods with width and length up to 16.90nm and 506.38nm, respectively. The linear and nonlinear optical properties have been investigated. The identified energy gap of the designed thin film materials was found 4.01eV. The refractive index of deposited Co(II)-complex thin film was identified by thickness-dependence and found as 1.9 at wavelength 1100nm. In addition, the refractive index was varied by about 0.15 due to an increase in the thickness by 19nm. Copyright © 2017 Elsevier B.V. All rights reserved.

Kaolinite-catalyzed air oxidation of hydrazine: Consideration of several compositional, structural and energetic factors in surface activation

NASA Technical Reports Server (NTRS)

Coyne, L. M.; Mariner, R.; Rice, A.

1991-01-01

Clay minerals have been shown to have numerous, curious, energetic properties by virtue of ultra-violet light release which can be triggered by gentle environmental changes such as wetting and dewetting by a variety of liquids, unique among them water and hydrazine. Since both water and hydrazine play multiple key roles in the air-oxidation of hydrazine on kaolinite surfaces, this reaction would seem to have prime potential for studying interrelationships of energy storage, release and chemical reactivity of clay surfaces, capacities basic to either the Bernal or Cairns-Smith roles of minerals in the origin of life. Establishment of the capacity for stored electronic energy to significantly alter surface chemistry is important, regardless of the reaction chosen to demonstrate it. Hydrazine air oxidation is overawingly complex, given the possibilities for step-wise control and monitoring of parameters. In the light of recently extended characterization of the kaolinite and model sheet catalysts we used to study hydrazine oxidation and gamma-irradiated silica, previous studies of hydrazine air-oxidation on aluminosilicate surfaces have been reevaluated. Our former conclusion remains intact that, whereas trace structural and surface contaminants do play some role in the catalysis of oxidation, they are not the only, nor even the dominant, catalytic centers. Initial intermediates in the oxidation can now be proposed which are consistent with production via O(-)-centers as well as ferric iron centers. The greater than square dependence of the initial reaction rate on the weight of the clay is discussed in the light of these various mechanistic possibilities.

Analysis of carbon-oxygen reactions by use of a square-input response technique and {sup 18}O isotope

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miura, Kouichi; Nakagawa, Hiroyuki

1996-12-31

Carbon gasification reaction has been investigated for decades including the pioneering works of Walker and his co-workers, but its mechanism has not been completely elucidated. The concept of the active surface area (ASA) was proposed by them, and its importance has been recognized. However, since ASA was measured by O{sub 2} chemisorption at below 300{degrees}C where carbon loss through gasification is negligible, it does not reflect the actual gasification situation. To overcome this weak point, measurements of ASA in a batch reactor and the so-called transient kinetic (TK) method were proposed. Ahmed and Back successfully measured the chemisorbed oxygen duringmore » the gasification using a batch reactor, and proposed a new mechanistic sequence for carbon-oxygen reaction which stresses the importance of the reaction between the gaseous oxygen and the chemisorbed oxygen. Radovic et al. proposed the concept of the reactive surface area (RSA), and reported excellent proportionality between the CO{sub 2} gasification rate and the RSA estimated by the TK and the TPD methods. Kapteijn et al. showed that the TK method with labeled molecules is more powerful to examine the mechanism. They found the presence of two types of surface oxygen complexes which desorb at different rates. A Square-input response (SIR) method is applied to the carbon-oxygen reaction. This method allows the observation of transient changes on two step changes. This method has been successfully applied to the analysis of a coal char gasification.« less

A Demonstration of Le Chatelier’s Principle on the Nanoscale

PubMed Central

2017-01-01

Photothermal desorption of molecules from plasmonic nanoparticles is an example of a light-triggered molecular release due to heating of the system. However, this phenomenon ought to work only if the molecule–nanoparticle interaction is exothermic in nature. In this study, we compare protein adsorption behavior onto gold nanoparticles for both endothermic and exothermic complexation reactions, and demonstrate that Le Chatelier’s principle can be applied to predict protein adsorption or desorption on nanomaterial surfaces. Polyelectrolyte-wrapped gold nanorods were used as adsorption platforms for two different proteins, which we were able to adsorb/desorb from the nanorod surface depending on the thermodynamics of their interactions. Furthermore, we show that the behaviors hold up under more complex biological environments such as fetal bovine serum. PMID:29104926

Quantum Chemical Study of CH3 + O2 Combustion Reaction System: Catalytic Effects of Additional CO2 Molecule.

PubMed

Masunov, Artëm E; Wait, Elizabeth; Vasu, Subith S

2017-08-03

The supercritical carbon dioxide diluent is used to control the temperature and to increase the efficiency in oxycombustion fossil fuel energy technology. It may affect the rates of combustion by altering mechanisms of chemical reactions, compared to the ones at low CO 2 concentrations. Here, we investigate potential energy surfaces of the four elementary reactions in the CH 3 + O 2 reactive system in the presence of one CO 2 molecule. In the case of reaction CH 3 + O 2 → CH 2 O + OH (R1 channel), van der Waals (vdW) complex formation stabilizes the transition state and reduces the activation barrier by ∼2.2 kcal/mol. Alternatively, covalently bonded CO 2 may form a six-membered ring transition state and reduce the activation barrier by ∼0.6 kcal/mol. In case of reaction CH 3 + O 2 → CH 3 O + O (R2 channel), covalent participation of CO 2 lowers the barrier for the rate limiting step by 3.9 kcal/mol. This is expected to accelerate the R2 process, important for the branching step of the radical chain reaction mechanism. For the reaction CH 3 + O 2 → CHO + H 2 O (R3 channel) with covalent participation of CO 2 , the activation barrier is lowered by 0.5 kcal/mol. The reaction CH 2 O + OH → CHO + H 2 O (R4 channel) involves hydrogen abstraction from formaldehyde by OH radical. Its barrier is reduced from 7.1 to 0.8 kcal/mol by formation of vdW complex with spectator CO 2 . These new findings are expected to improve the kinetic reaction mechanism describing combustion processes in supercritical CO 2 medium.

Chemical dynamics simulations of X- + CH3Y → XCH3 + Y- gas-phase S(N)2 nucleophilic substitution reactions. Nonstatistical dynamics and nontraditional reaction mechanisms.

PubMed

Manikandan, Paranjothy; Zhang, Jiaxu; Hase, William L

2012-03-29

Extensive classical chemical dynamics simulations of gas-phase X(-) + CH(3)Y → XCH(3) + Y(-) S(N)2 nucleophilic substitution reactions are reviewed and discussed and compared with experimental measurements and predictions of theoretical models. The primary emphasis is on reactions for which X and Y are halogen atoms. Both reactions with the traditional potential energy surface (PES), which include pre- and postreaction potential energy minima and a central barrier, and reactions with nontraditional PESs are considered. These S(N)2 reactions exhibit important nonstatistical atomic-level dynamics. The X(-) + CH(3)Y → X(-)---CH(3)Y association rate constant is less than the capture model as a result of inefficient energy transfer from X(-)+ CH(3)Y relative translation to CH(3)Y rotation and vibration. There is weak coupling between the low-frequency intermolecular modes of the X(-)---CH(3)Y complex and higher frequency CH(3)Y intramolecular modes, resulting in non-RRKM kinetics for X(-)---CH(3)Y unimolecular decomposition. Recrossings of the [X--CH(3)--Y](-) central barrier is important. As a result of the above dynamics, the relative translational energy and temperature dependencies of the S(N)2 rate constants are not accurately given by statistical theory. The nonstatistical dynamics results in nonstatistical partitioning of the available energy to XCH(3) +Y(-) reaction products. Besides the indirect, complex forming atomic-level mechanism for the S(N)2 reaction, direct mechanisms promoted by X(-) + CH(3)Y relative translational or CH(3)Y vibrational excitation are possible, e.g., the roundabout mechanism.

Heat Transfer in Complex Fluids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mehrdad Massoudi

Amongst the most important constitutive relations in Mechanics, when characterizing the behavior of complex materials, one can identify the stress tensor T, the heat flux vector q (related to heat conduction) and the radiant heating (related to the radiation term in the energy equation). Of course, the expression 'complex materials' is not new. In fact, at least since the publication of the paper by Rivlin & Ericksen (1955), who discussed fluids of complexity (Truesdell & Noll, 1992), to the recently published books (Deshpande et al., 2010), the term complex fluids refers in general to fluid-like materials whose response, namely themore » stress tensor, is 'non-linear' in some fashion. This non-linearity can manifest itself in variety of forms such as memory effects, yield stress, creep or relaxation, normal-stress differences, etc. The emphasis in this chapter, while focusing on the constitutive modeling of complex fluids, is on granular materials (such as coal) and non-linear fluids (such as coal-slurries). One of the main areas of interest in energy related processes, such as power plants, atomization, alternative fuels, etc., is the use of slurries, specifically coal-water or coal-oil slurries, as the primary fuel. Some studies indicate that the viscosity of coal-water mixtures depends not only on the volume fraction of solids, and the mean size and the size distribution of the coal, but also on the shear rate, since the slurry behaves as shear-rate dependent fluid. There are also studies which indicate that preheating the fuel results in better performance, and as a result of such heating, the viscosity changes. Constitutive modeling of these non-linear fluids, commonly referred to as non-Newtonian fluids, has received much attention. Most of the naturally occurring and synthetic fluids are non-linear fluids, for example, polymer melts, suspensions, blood, coal-water slurries, drilling fluids, mud, etc. It should be noted that sometimes these fluids show Newtonian (linear) behavior for a given range of parameters or geometries; there are many empirical or semi-empirical constitutive equations suggested for these fluids. There have also been many non-linear constitutive relations which have been derived based on the techniques of continuum mechanics. The non-linearities oftentimes appear due to higher gradient terms or time derivatives. When thermal and or chemical effects are also important, the (coupled) momentum and energy equations can give rise to a variety of interesting problems, such as instability, for example the phenomenon of double-diffusive convection in a fluid layer. In Conclusion, we have studied the flow of a compressible (density gradient type) non-linear fluid down an inclined plane, subject to radiation boundary condition. The heat transfer is also considered where a source term, similar to the Arrhenius type reaction, is included. The non-dimensional forms of the equations are solved numerically and the competing effects of conduction, dissipation, heat generation and radiation are discussed. It is observed that the velocity increases rapidly in the region near the inclined surface and is slower in the region near the free surface. Since R{sub 7} is a measure of the heat generation due to chemical reaction, when the reaction is frozen (R{sub 7}=0.0) the temperature distributions would depend only on R{sub 1}, and R{sub 2}, representing the effects of the pressure force developed in the material due to the distribution, R{sub 3} and R{sub 4} viscous dissipation, R{sub 5} the normal stress coefficient, R{sub 6} the measure of the emissivity of the particles to the thermal conductivity, etc. When the flow is not frozen (RP{sub 7} > 0) the temperature inside the flow domain is much higher than those at the inclined and free surfaces. As a result, heat is transferred away from the flow toward both the inclined surface and the free surface with a rate that increases as R{sub 7} increases. For a given temperature, an increase in {zeta} implies that the activation energy is smaller and thus, the reaction rate is increased leading to an increase in the heat of the reaction. As a result the flow is chemically heated and its temperature increase. The results shown here indicate that for all values of {zeta} used the chemical effects are significant and the temperature is always higher than both the surface temperature and the free surface temperature. The heat transfer is always from the flow toward both the inclined surface and the free stream. It is also noticed that for all values of m chosen in this study, the temperature is higher than the surface and the free stream temperature. The heat transfer at the inclined surface and at the free stream increase slowly for negative values of m to about m=0.5, but it begins to significantly increase for m greater than 0.5.« less

Catalytic asymmetric Michael reactions promoted by a lithium-free lanthanum-BINOL complex

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sasai, Hiroaki; Arai, Takayoshi; Shibasaki, Masakatsu

1994-02-23

In this communication, we report about a new lithium-free BINOL-lanthanum complex, which is quite effective in catalytic asymmetric Michael reaction. We have succeeded in developing effective asymmetric base catalysts, in particular, asymmetric ester enolate catalysts for asymmetric Michael reactions. Two asymmetric lanthanum complexes are now available, namely, BINOL-lanthanum-lithium complex, which is quite effective in catalytic asymmetric nitrosaldol reactions, and a new lithium-free BINOL-lanthanum ester enolate complex, that is very effective in catalytic asymmetric Michael reactions. The two complexes complement each other in their ability to catalyze asymmetric nitroaldol and asymmetric Michael reactions. 14 refs., 1 fig., 2 tabs.

DNA curtains for high-throughput single-molecule optical imaging.

PubMed

Greene, Eric C; Wind, Shalom; Fazio, Teresa; Gorman, Jason; Visnapuu, Mari-Liis

2010-01-01

Single-molecule approaches provide a valuable tool in the arsenal of the modern biologist, and new discoveries continue to be made possible through the use of these state-of-the-art technologies. However, it can be inherently difficult to obtain statistically relevant data from experimental approaches specifically designed to probe individual reactions. This problem is compounded with more complex biochemical reactions, heterogeneous systems, and/or reactions requiring the use of long DNA substrates. Here we give an overview of a technology developed in our laboratory, which relies upon simple micro- or nanofabricated structures in combination with "bio-friendly" lipid bilayers, to align thousands of long DNA molecules into defined patterns on the surface of a microfluidic sample chamber. We call these "DNA curtains," and we have developed several different versions varying in complexity and DNA substrate configuration, which are designed to meet different experimental needs. This novel approach to single-molecule imaging provides a powerful experimental platform that offers the potential for concurrent observation of hundreds or even thousands of protein-DNA interactions in real time. Copyright 2010 Elsevier Inc. All rights reserved.

Molecular complexes in close and far away

PubMed Central

Klemperer, William; Vaida, Veronica

2006-01-01

In this review, gas-phase chemistry of interstellar media and some planetary atmospheres is extended to include molecular complexes. Although the composition, density, and temperature of the environments discussed are very different, molecular complexes have recently been considered as potential contributors to chemistry. The complexes reviewed include strongly bound aggregates of molecules with ions, intermediate-strength hydrogen bonded complexes (primarily hydrates), and weakly bonded van der Waals molecules. In low-density, low-temperature environments characteristic of giant molecular clouds, molecular synthesis, known to involve gas-phase ion-molecule reactions and chemistry at the surface of dust and ice grains is extended here to involve molecular ionic clusters. At the high density and high temperatures found on planetary atmospheres, molecular complexes contribute to both atmospheric chemistry and climate. Using the observational, laboratory, and theoretical database, the role of molecular complexes in close and far away is discussed. PMID:16740667

Global minimum profile error (GMPE) - a least-squares-based approach for extracting macroscopic rate coefficients for complex gas-phase chemical reactions.

PubMed

Duong, Minh V; Nguyen, Hieu T; Mai, Tam V-T; Huynh, Lam K

2018-01-03

Master equation/Rice-Ramsperger-Kassel-Marcus (ME/RRKM) has shown to be a powerful framework for modeling kinetic and dynamic behaviors of a complex gas-phase chemical system on a complicated multiple-species and multiple-channel potential energy surface (PES) for a wide range of temperatures and pressures. Derived from the ME time-resolved species profiles, the macroscopic or phenomenological rate coefficients are essential for many reaction engineering applications including those in combustion and atmospheric chemistry. Therefore, in this study, a least-squares-based approach named Global Minimum Profile Error (GMPE) was proposed and implemented in the MultiSpecies-MultiChannel (MSMC) code (Int. J. Chem. Kinet., 2015, 47, 564) to extract macroscopic rate coefficients for such a complicated system. The capability and limitations of the new approach were discussed in several well-defined test cases.

Oxygen atom transfer reactions of iridium and osmium complexes: theoretical study of characteristic features and significantly large differences between these two complexes.

PubMed

Ishikawa, Atsushi; Nakao, Yoshihide; Sato, Hirofumi; Sakaki, Shigeyoshi

2009-09-07

Oxygen atom transfer reaction between ML(3)=O and ML(3) (L = 2,4,6-trimethylphenyl (Mes) for M = Ir and L = 2,6-diisopropylphenylimide (NAr) for M = Os) was theoretically investigated by DFT method. The optimized geometry of (Mes)(3)Ir-O-Ir(Mes)(3) agrees well with the experimental one, although those of (CH(3))(3)Ir-O-Ir(CH(3))(3) and Ph(3)Ir-O-IrPh(3) are much different from the experimental one of the Mes complex. These results indicate that the bulky ligand plays important roles to determine geometry of the mu-oxo dinuclear Ir complex. Theoretical study of the real systems presents clear pictures of these oxygen atom transfer reactions, as follows: In the Ir reaction system, (i) the mu-oxo bridged dinuclear complex is more stable than the infinite separation system in potential energy surface, indicating this is incomplete oxygen atom transfer reaction which does not occur at very low temperature, (ii) unsymmetrical transition state is newly found, in which one Ir-O distance is longer than the other one, (iii) unsymmetrical local minimum is also newly found between the transition state and the infinite separation system, and (iv) activation barrier (E(a)) is very small. In the Os reaction system, (v) the transition state is symmetrical, while no intermediate is observed unlike the Ir reaction system, and (vi) E(a) is very large. These results are consistent with the experimental results that the reaction rapidly occurs in the Ir system but very slowly in the Os system, and that the mu-oxo bridged dinuclear intermediate is detected in the Ir system but not in the Os system. To elucidate the reasons of these differences between Ir and Os systems, the E(a) value is decomposed into the nuclear and electronic factors. The former is the energy necessary to distort ML(3) and ML(3)=O moieties from their equilibrium geometries to those in the transition state. The latter depends on donor-acceptor interaction between ML(3)=O and ML(3). The nuclear factor is much larger in the Os system than in the Ir system and it contributes to about 70% of the difference in E(a). The energy gap between the donor orbital of ML(3) and the acceptor orbital of ML(3)=O is much larger in the Os system than in the Ir system, which also contributes to the lower E(a) value of the Ir system than that of the Os system.

N-alkyl pyrrolidone ether podands as versatile alkali metal ion chelants.

PubMed

Perrin, Andrea; Myers, Dominic; Fucke, Katharina; Musa, Osama M; Steed, Jonathan W

2014-02-28

This work explores the coordination chemistry of a bis(pyrrolidone) ether ligand. Pyrrolidones are commercially important functional groups because of the high polarity and hence high hydrophilicity and surface affinity. An array of alkali metal ion complexes of a podand bearing two pendant pyrrolidone functionalities, namely 1-{2-[2-(2-oxo-pyrrolid-1-yl)-ethoxy]-ethyl}-pyrrolid-2-one (1) are reported. Reaction of this ligand with sodium hexafluorophosphate gives two discrete species of formulae [Na(1)2]PF6 (3) and [Na3(H2O)2(μ-1)2](PF6)3 (4), and a coordination polymer {[Na3(μ3-1)3(μ2-1)](PF6)3}n (5). The same reaction in methanol gives a 1 : 1 complex, namely [Na2(μ-1)2(MeOH)2](PF6)2 (6). Use of tetraphenyl borate as a less coordinating counter ion gives [Na2(1)2(H2O)4](BPh4)2 (7) and [Na2(1)4](BPh4)2 (8). Two potassium complexes have also been isolated, a monomer [K(1)2]PF6 (9) and a cyclic tetramer [K4(μ4-H2O)2(μ-1)4](PF6)4 (10). The structures illustrate the highly polar nature of the amide carbonyl moiety within bis(pyrrolidone) ethers with longer interactions to the ether oxygen atom. The zinc complex is also reported and {[ZnCl2(μ-1)]}n (11) exhibits bonding only to the carbonyl moieties. The ether oxygen atom is not necessary for Na(+) complexation as exemplified by the structure of the sodium complex of the analogue 1,3-bis(pyrrolid-2-on-1-yl)butane (2). Reaction of compound 1 with lithium salts results in isolation of the protonated ligand.

Quantifying atom addition reactions on amorphous solid water: a review of recent laboratory advances

NASA Astrophysics Data System (ADS)

He, Jiao; Vidali, Gianfranco

2018-06-01

Complex organic molecules found in space are mostly formed on and in the ice mantle covering interstellar dust grains. In clouds where ionizing irradiation is insignificant, chemical reactions on the ice mantle are dominated by thermal processes. Modeling of grain surface chemistry requires detailed information from the laboratory, including sticking coefficients, binding energies, diffusion energy barriers, mechanism of reaction, and chemical desorption rates. In this talk, recent laboratory advances in obtaining these information would be reviewed. Specifically, this talk will focus on the efforts in our group in: 1) Determining the mechanism of atomic hydrogen addition reactions on amorphous solid water (ASW); 2) Measuring the chemical desorption coefficient of H+O3-->O2+OH using the time-resolved scattering technique; and 3) Measuring the diffusion energy barrier of volatile molecules on ASW. Further laboratory studies will be suggested.This research was supported by NSF Astronomy & Astrophysics Research Grant #1615897.

Heterogeneous Electrochemical Immunoassay of Hippuric Acid on the Electrodeposited Organic Films

PubMed Central

Choi, Young-Bong; Kim, Nam-Hyuk; Kim, Seung-Hoi; Tae, Gun-Sik; Kim, Hyug-Han

2014-01-01

By directly coordinating hippuric acid (HA) to the ferrate (Fe) as an electron transfer mediator, we synthesized a Fe-HA complex, which shows a good electrochemical signal and thus enables the electrochemical immunoanalysis for HA. We electrodeposited organic films containing imidazole groups on the electrode surface and then bonded Ni ion (positive charge) to induce immobilization of Fe-HA (negative charge) through the electrostatic interaction. The heterogeneous competitive immunoassay system relies on the interaction between immobilized Fe-HA antigen conjugate and free HA antigen to its antibody (anti-HA). The electric signal becomes weaker due to the hindered electron transfer reaction when a large-sized HA antibody is bound onto the Fe-HA. However, in the presence of HA, the electric signal increases because free HA competitively reacts with the HA antibody prior to actual reaction and thus prevents the HA antibody from interacting with Fe-HA at the electrode surface. This competition reaction enabled an electrochemical quantitative analysis of HA concentration with a detection limit of 0.5 μg mL−1, and thus allowed us to develop a simple and rapid electrochemical immunosensor. PMID:25313491

Arsenic mobilization in shallow aquifers due to CO 2 intrusion from storage reservoirs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xiao, Ting; Dai, Zhenxue; Viswanathan, Hari S.

We developed an integrated framework of combined batch experiments and reactive transport simulations to quantify water-rock-CO 2 interactions and arsenic (As) mobilization responses to CO 2 and/or saline water leakage into USDWs. Experimental and simulation results suggest that when CO 2 is introduced, pH drops immediately that initiates release of As from clay minerals. Calcite dissolution can increase pH slightly and cause As re-adsorption. Thus, the mineralogy of the USDW is ultimately a determining factor of arsenic fate and transport. Salient results suggest that: (1) As desorption/adsorption from/onto clay minerals is the major reaction controlling its mobilization, and clay mineralsmore » could mitigate As mobilization with surface complexation reactions; (2) dissolution of available calcite plays a critical role in buffering pH; (3) high salinity in general hinders As release from minerals; and (4) the magnitude and quantitative uncertainty of As mobilization are predicated on the values of reaction rates and surface area of calcite, adsorption surface areas and equilibrium constants of clay minerals, and cation exchange capacity. Results of this study are intended to improve ability to quantify risks associated with potential leakage of reservoir fluids into shallow aquifers, in particular the possible environmental impacts of As mobilization at carbon sequestration sites.« less

Arsenic mobilization in shallow aquifers due to CO 2 intrusion from storage reservoirs

DOE PAGES

Xiao, Ting; Dai, Zhenxue; Viswanathan, Hari S.; ...

2017-06-05

We developed an integrated framework of combined batch experiments and reactive transport simulations to quantify water-rock-CO 2 interactions and arsenic (As) mobilization responses to CO 2 and/or saline water leakage into USDWs. Experimental and simulation results suggest that when CO 2 is introduced, pH drops immediately that initiates release of As from clay minerals. Calcite dissolution can increase pH slightly and cause As re-adsorption. Thus, the mineralogy of the USDW is ultimately a determining factor of arsenic fate and transport. Salient results suggest that: (1) As desorption/adsorption from/onto clay minerals is the major reaction controlling its mobilization, and clay mineralsmore » could mitigate As mobilization with surface complexation reactions; (2) dissolution of available calcite plays a critical role in buffering pH; (3) high salinity in general hinders As release from minerals; and (4) the magnitude and quantitative uncertainty of As mobilization are predicated on the values of reaction rates and surface area of calcite, adsorption surface areas and equilibrium constants of clay minerals, and cation exchange capacity. Results of this study are intended to improve ability to quantify risks associated with potential leakage of reservoir fluids into shallow aquifers, in particular the possible environmental impacts of As mobilization at carbon sequestration sites.« less

Group 4 transition metal CH2=MF2, CHF=MF2, and HC/MF3 complexes formed by C-F activation and alpha-fluorine transfer.

PubMed

Lyon, Jonathan T; Andrews, Lester

2007-06-11

Group 4 transition metal methylidene difluoride complexes (CH2=MF2) are formed by the reaction of methylene fluoride with laser-ablated metal atoms and are isolated in an argon matrix. Isotopic substitution of the CH2F2 precursor and theoretical computations (B3LYP and CCSD) confirm product identifications and assignments. Our calculations indicate that the CH2=MF2 complexes have near C2v symmetry and are considerably more stable than other possible products (CH2(mu-F)MF and CHF=MHF). The primary reaction exothermicity provides more than enough energy to activate the initial bridge-bonded CH2(mu-F)MF products on the triplet potential energy surface to complete an alpha-F transfer to form the very stable CH2=MF2 products. Analogous experiments with CHF3 produce CHF=TiF2, which is not distorted at the C-H bond, whereas the heavier group 4 metals form lower-energy triplet HC/MF3 complexes, which contain weak degenerate C(p)-M(d) pi-bonding interactions. Comparisons are made with the CH2=MHF methylidene species, which showed considerable agostic distortions.

Nitric oxide reduction in coal combustion: role of char surface complexes in heterogeneous reactions.

PubMed

Arenillas, Ana; Rubiera, Fernando; Pis, José J

2002-12-15

Nitrogen oxides are one of the major environmental problems arising from fossil fuel combustion. Coal char is relatively rich in nitrogen, and so this is an important source of nitrogen oxides during coal combustion. However, due to its carbonaceous nature, char can also reduce NO through heterogeneous reduction. The objectives of this work were on one hand to compare NO emissions from coal combustion in two different types of equipment and on the other hand to study the influence of char surface chemistry on NO reduction. A series of combustion tests were carried out in two different scale devices: a thermogravimetric analyzer coupled to a mass spectrometer and an FTIR (TG-MS-FTIR) and a fluidized bed reactor with an on line battery of analyzers. The TG-MS-FTIR system was also used to perform a specific study on NO heterogeneous reduction reactions using chars with different surface chemistry. According to the results obtained, it can be said that the TG-MS-FTIR system provides valuable information about NO heterogeneous reduction and it can give good trends of the behavior in other combustion equipments (i.e., fluidized bed combustors). It has been also pointed out that NO-char interaction depends to a large extent on temperature. In the low-temperature range (<800 degrees C), NO heterogeneous reduction seems to be controlled by the evolution of surface complexes. In the high-temperature range (>800 degrees C), a different mechanism is involved in NO heterogeneous reduction, the nature of the carbon matrix being a key factor.

Reaction pathways in atomistic models of thin film growth

NASA Astrophysics Data System (ADS)

Lloyd, Adam L.; Zhou, Ying; Yu, Miao; Scott, Chris; Smith, Roger; Kenny, Steven D.

2017-10-01

The atomistic processes that form the basis of thin film growth often involve complex multi-atom movements of atoms or groups of atoms on or close to the surface of a substrate. These transitions and their pathways are often difficult to predict in advance. By using an adaptive kinetic Monte Carlo (AKMC) approach, many complex mechanisms can be identified so that the growth processes can be understood and ultimately controlled. Here the AKMC technique is briefly described along with some special adaptions that can speed up the simulations when, for example, the transition barriers are small. Examples are given of such complex processes that occur in different material systems especially for the growth of metals and metallic oxides.

Arene-chromium tricarbonyl complexes in the Pauson-Khand reaction.

PubMed

Rosillo, Marta; Domínguez, Gema; Casarrubios, Luis; Pérez-Castells, Javier

2005-12-09

[reactions: see text] We show the use of arene-chromium tricarbonyl complexes in intra- and intermolecular Pauson-Khand reactions. Both styrene and ethynylbenzene complexes react with alkynes and olefins. The synthesis of enynes connected through chromium-complexed aromatic rings is developed. The intramolecular Pauson-Khand reaction occurs in a totally diastereoselective manner.

Reactive Landing of Dendrimer Ions onto Activated Self-assembled Monolayer Surfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hu, Qichi; Laskin, Julia

2014-02-06

The reactivity of gaseous, amine-terminated polyamidoamine (PAMAM) dendrimer ions with activated self-assembled monolayer (SAM) surfaces terminated with N-hydroxysuccinimidyl ester groups (NHS-SAM) is examined using mass-selected ion deposition combined with in situ infrared reflection absorption spectroscopy (IRRAS). The reaction extent is determined from depletion of the infrared band at 1753 cm-1, corresponding to the stretching vibration of the NHS carbonyl groups following ion deposition. For reaction yields below 10%, NHS band depletion follows a linear dependence on the ion dose. By comparing the kinetics plots obtained for 1,12-dodecanediamine and different generations of dendrimer ions (G0–G3) containing 4, 8, 16, and 32more » terminal amino group, we demonstrate that the relative reaction efficiency increases linearly with the number of NH2 groups in the molecule. This finding is rationalized assuming the formation of multiple amide bonds upon collision of higher-generation dendrimers with NHS-SAM. Furthermore, by comparing the NHS band depletion following deposition of [M+4H]4+ ions of the G2 dendrimer at 30, 80, and 120 eV, we demonstrate that the ion’s kinetic energy has no measurable effect on reaction efficiency. Similarly, the ion’s charge state only has a minor effect on the reactive landing efficiency of dendrimer ions. Our results indicate that reactive landing is an efficient approach for highly selective covalent immobilization of complex multifunctional molecules onto organic surfaces terminated with labile functional groups.« less

Electronic Structure and Band Gap of Fullerenes on Tungsten Surfaces: Transition from a Semiconductor to a Metal Triggered by Annealing.

PubMed

Monazami, Ehsan; McClimon, John B; Rondinelli, James; Reinke, Petra

2016-12-21

The understanding and control of molecule-metal interfaces is critical to the performance of molecular electronics and photovoltaics devices. We present a study of the interface between C 60 and W, which is a carbide-forming transition metal. The complex solid-state reaction at the interface can be exploited to adjust the electronic properties of the molecule layer. Scanning tunneling microscopy/spectroscopy measurements demonstrate the progression of this reaction from wide band gap (>2.5 eV) to metallic molecular surface during annealing from 300 to 800 K. Differential conduction maps with 10 4 scanning tunneling spectra are used to quantify the transition in the density of states and the reduction of the band gap during annealing with nanometer spatial resolution. The electronic transition is spatially homogeneous, and the surface band gap can therefore be adjusted by a targeted annealing step. The modified molecules, which we call nanospheres, are quite resistant to ripening and coalescence, unlike any other metallic nanoparticle of the same size. Densely packed C 60 and isolated C 60 molecules show the same transition in electronic structure, which confirms that the transformation is controlled by the reaction at the C 60 -W interface. Density functional theory calculations are used to develop possible reaction pathways in agreement with experimentally observed electronic structure modulation. Control of the band gap by the choice of annealing temperature is a unique route to tailoring molecular-layer electronic properties.

Combinatorial pattern discovery approach for the folding trajectory analysis of a beta-hairpin.

PubMed

Parida, Laxmi; Zhou, Ruhong

2005-06-01

The study of protein folding mechanisms continues to be one of the most challenging problems in computational biology. Currently, the protein folding mechanism is often characterized by calculating the free energy landscape versus various reaction coordinates, such as the fraction of native contacts, the radius of gyration, RMSD from the native structure, and so on. In this paper, we present a combinatorial pattern discovery approach toward understanding the global state changes during the folding process. This is a first step toward an unsupervised (and perhaps eventually automated) approach toward identification of global states. The approach is based on computing biclusters (or patterned clusters)-each cluster is a combination of various reaction coordinates, and its signature pattern facilitates the computation of the Z-score for the cluster. For this discovery process, we present an algorithm of time complexity c in RO((N + nm) log n), where N is the size of the output patterns and (n x m) is the size of the input with n time frames and m reaction coordinates. To date, this is the best time complexity for this problem. We next apply this to a beta-hairpin folding trajectory and demonstrate that this approach extracts crucial information about protein folding intermediate states and mechanism. We make three observations about the approach: (1) The method recovers states previously obtained by visually analyzing free energy surfaces. (2) It also succeeds in extracting meaningful patterns and structures that had been overlooked in previous works, which provides a better understanding of the folding mechanism of the beta-hairpin. These new patterns also interconnect various states in existing free energy surfaces versus different reaction coordinates. (3) The approach does not require calculating the free energy values, yet it offers an analysis comparable to, and sometimes better than, the methods that use free energy landscapes, thus validating the choice of reaction coordinates. (An abstract version of this work was presented at the 2005 Asia Pacific Bioinformatics Conference [1].).

Copper(II) sorption onto goethite, hematite and lepidocrocite: a surface complexation model based on ab initio molecular geometries and EXAFS spectroscopy

NASA Astrophysics Data System (ADS)

Peacock, Caroline L.; Sherman, David M.

2004-06-01

We measured the adsorption of Cu(II) onto goethite (α-FeOOH), hematite (α-Fe 2O 3) and lepidocrocite (γ-FeOOH) from pH 2-7. EXAFS spectra show that Cu(II) adsorbs as (CuO 4H n) n-6 and binuclear (Cu 2O 6H n) n-8 complexes. These form inner-sphere complexes with the iron (hydr)oxide surfaces by corner-sharing with two or three edge-sharing Fe(O,OH) 6 polyhedra. Our interpretation of the EXAFS data is supported by ab initio (density functional theory) geometries of analogue Fe 2(OH) 2(H 2O) 8Cu(OH) 4and Fe 3(OH) 4(H 2O) 10Cu 2(OH) 6 clusters. We find no evidence for surface complexes resulting from either monodentate corner-sharing or bidentate edge-sharing between (CuO 4H n) n-6 and Fe(O,OH) 6 polyhedra. Sorption isotherms and EXAFS spectra show that surface precipitates have not formed even though we are supersaturated with respect to CuO and Cu(OH) 2. Having identified the bidentate (FeOH) 2Cu(OH) 20 and tridentate (Fe 3O(OH) 2)Cu 2(OH) 30 surface complexes, we are able to fit the experimental copper(II) adsorption data to the reactions 3( FeOH)+2 Cu2++3 H2O=( Fe3O( OH) 2) Cu2( OH) 30+4 H+ and 2( FeOH)+ Cu2++2 H2O=( FeOH) 2Cu( OH) 20+2 H+. The two stability constants are similar for the three iron (hydr)oxide phases investigated.

Peptide Fragmentation by Corona Discharge Induced Electrochemical Ionization

PubMed Central

Lloyd, John R.; Hess, Sonja

2010-01-01

Fundamental studies have greatly improved our understanding of electrospray, including the underlying electrochemical reactions. Generally regarded as disadvantageous, we have recently shown that corona discharge (CD) can be used as an effective method to create a radical cation species [M]+•, thus optimizing the electrochemical reactions that occur on the surface of the stainless steel (SS) electrospray capillary tip. This technique is known as CD initiated electrochemical ionization (CD-ECI). Here, we report on the fundamental studies using CD-ECI to induce analytically useful in-source fragmentation of a range of molecules that complex transition metals. Compounds that have been selectively fragmented using CD-ECI include enolate forming phenylglycine containing peptides, glycopeptides, nucleosides and phosphopeptides. Collision induced dissociation (CID) or other activation techniques were not necessary for CD-ECI fragmentation. A four step mechanism was proposed: 1. Complexation using either Fe in the SS capillary tip material or Cu(II) as an offline complexation reagent; 2. Electrochemical oxidation of the complexed metal and thus formation of a radical cation (e.g.; Fe - e− → Fe +•); 3. Radical fragmentation of the complexed compound. 4. Electrospray ionization of the fragmented neutrals. Fragmentation patterns resembling b- and y-type ions were observed and allowed the localization of the phosphorylation sites. PMID:20869880

Effects of specific surface area of metallic nickel particles on carbon deposition kinetics

NASA Astrophysics Data System (ADS)

Chen, Zhi-yuan; Bian, Liu-zhen; Yu, Zi-you; Wang, Li-jun; Li, Fu-shen; Chou, Kuo-Chih

2018-02-01

Carbon deposition on nickel powders in methane involves three stages in different reaction temperature ranges. Temperature programing oxidation test and Raman spectrum results indicated the formation of complex and ordered carbon structures at high deposition temperatures. The values of I(D)/ I(G) of the deposited carbon reached 1.86, 1.30, and 1.22 in the first, second, and third stages, respectively. The structure of carbon in the second stage was similar to that in the third stage. Carbon deposited in the first stage rarely contained homogeneous pyrolytic deposit layers. A kinetic model was developed to analyze the carbon deposition behavior in the first stage. The rate-determining step of the first stage is supposed to be interfacial reaction. Based on the investigation of carbon deposition kinetics on nickel powders from different resources, carbon deposition rate is suggested to have a linear relation with the square of specific surface area of nickel particles.

Facile synthesis of three-dimensional diatomite/manganese silicate nanosheet composites for enhanced Fenton-like catalytic degradation of malachite green dye

NASA Astrophysics Data System (ADS)

Jiang, De Bin; Yuan, Yunsong; Zhao, Deqiang; Tao, Kaiming; Xu, Xuan; Zhang, Yu Xin

2018-05-01

In this work, we demonstrate a novel and simple approach for fabrication of the complex three-dimensional (3D) diatomite/manganese silicate nanosheet composite (DMSNs). The manganese silicate nanosheets are uniformly grown on the inner and outer surface of diatomite with controllable morphology using a hydrothermal method. Such structural features enlarged the specific surface area, resulting in more catalytic active sites. In the heterogeneous Fenton-like reaction, the DMSNs exhibited excellent catalytic capability for the degradation of malachite green (MG). Under optimum condition, 500 mg/L MG solution was nearly 93% decolorized at 70 min in the reaction. The presented results show an enhanced catalytic behavior of the DMSNs prepared by the low-cost natural diatomite material and simple controllable process, which indicates their potential for environmental remediation applications. [Figure not available: see fulltext.

Controlled Chemical Patterns with ThermoChemical NanoLithography (TCNL)

NASA Astrophysics Data System (ADS)

Carroll, Keith; Giordano, Anthony; Wang, Debin; Kodali, Vamsi; King, W. P.; Marder, S. R.; Riedo, E.; Curtis, J. E.

2012-02-01

Many research areas, both fundamental and applied, rely upon the ability to organize non-trivial assemblies of molecules on surfaces. In this work, we introduce a significant extension of ThermoChemical NanoLithography (TCNL), a high throughput chemical patterning technique that uses temperature-driven chemical reactions localized near the tip of a thermal cantilever. By combining a chemical kinetics based model with experiments, we have developed a protocol for varying the concentration of surface bound molecules. The result is an unprecedented ability to fabricate extremely complex patterns comprised of varying chemical concentrations, as demonstrated by sinusoidal patterns of amine groups with varying pitches (˜5-15 μm) and the replication of Leonardo da Vinci's Mona Lisa with dimensions of ˜30 x 40 μm^2. Programmed control of the chemical reaction rate should have widespread applications for a technique which has already been shown to nanopattern various substrates including graphene nanowires, piezoelectric crystals, and optoelectronic materials.

Development of a Detailed Surface Chemistry Framework in DSMC

NASA Technical Reports Server (NTRS)

Swaminathan-Gopalan, K.; Borner, A.; Stephani, K. A.

2017-01-01

Many of the current direct simulation Monte Carlo (DSMC) codes still employ only simple surface catalysis models. These include only basic mechanisms such as dissociation, recombination, and exchange reactions, without any provision for adsorption and finite rate kinetics. Incorporating finite rate chemistry at the surface is increasingly becoming a necessity for various applications such as high speed re-entry flows over thermal protection systems (TPS), micro-electro-mechanical systems (MEMS), surface catalysis, etc. In the recent years, relatively few works have examined finite-rate surface reaction modeling using the DSMC method.In this work, a generalized finite-rate surface chemistry framework incorporating a comprehensive list of reaction mechanisms is developed and implemented into the DSMC solver SPARTA. The various mechanisms include adsorption, desorption, Langmuir-Hinshelwood (LH), Eley-Rideal (ER), Collision Induced (CI), condensation, sublimation, etc. The approach is to stochastically model the various competing reactions occurring on a set of active sites. Both gas-surface (e.g., ER, CI) and pure-surface (e.g., LH, desorption) reaction mechanisms are incorporated. The reaction mechanisms could also be catalytic or surface altering based on the participation of the bulk-phase species (e.g., bulk carbon atoms). Marschall and MacLean developed a general formulation in which multiple phases and surface sites are used and we adopt a similar convention in the current work. Microscopic parameters of reaction probabilities (for gas-surface reactions) and frequencies (for pure-surface reactions) that are require for DSMC are computed from the surface properties and macroscopic parameters such as rate constants, sticking coefficients, etc. The energy and angular distributions of the products are decided based on the reaction type and input parameters. Thus, the user has the capability to model various surface reactions via user-specified reaction rate constants, surface properties and parameters.

Location and magnetic relaxation properties of the stable tyrosine radical in photosystem II.

PubMed

Innes, J B; Brudvig, G W

1989-02-07

Dipolar interactions with neighboring metal ions can cause enhanced spin-lattice relaxation of free radicals. We have applied the theory of dipolar relaxation enhancement and shown that the dependence of the enhanced relaxation on the protein structure surrounding the free radical can be used to obtain distances from the free radical to the protein surface. To test the theoretical predictions, we have examined the effect of added Dy3+ complexes on the microwave power saturation of free radicals in two protein complexes of known structure: myoglobin nitroxide and the reaction center from Rhodobacter sphaeroides. Three cases have been considered: (1) metal ions bound to a specific site, (2) metal ions bound randomly over the protein surface, and (3) metal ions distributed randomly in solution. Only case 3, which assumes no specific binding, gave good agreement between the distances obtained by using the two model systems. The effect of added Dy3+ complexes on the microwave power saturation of signal IIslow from photosystem II (PSII) was used to determine the location of the stable tyrosine radical giving rise to signal IIslow. Assuming that the surface of a membrane-bound protein can be approximated as planar, we have obtained distances from the tyrosine radical to the membrane surface in thylakoids, in PSII membranes, and in Tris-washed PSII membranes. The distances we have determined are in good agreement with those predicted on the basis of a structural homology between the D1 and D2 subunits of PSII and the structurally characterized L and M subunits of the reaction center from purple non-sulfur bacteria. We have also examined the temperature dependence of the microwave power at half-saturation (P1/2) of signal IIslow from 4 to 200 K in dark-adapted PSII membranes. Above 70 K, the P1/2 increases as T2.5, which is consistent with a Raman relaxation mechanism.(ABSTRACT TRUNCATED AT 250 WORDS)

DNA surface hybridization regimes

PubMed Central

Gong, Ping; Levicky, Rastislav

2008-01-01

Surface hybridization reactions, in which sequence-specific recognition occurs between immobilized and solution nucleic acids, are routinely carried out to quantify and interpret genomic information. Although hybridization is fairly well understood in bulk solution, the greater complexity of an interfacial environment presents new challenges to a fundamental understanding, and hence application, of these assays. At a surface, molecular interactions are amplified by the two-dimensional nature of the immobilized layer, which focuses the nucleic acid charge and concentration to levels not encountered in solution, and which impacts the hybridization behavior in unique ways. This study finds that, at low ionic strengths, an electrostatic balance between the concentration of immobilized oligonucleotide charge and solution ionic strength governs the onset of hybridization. As ionic strength increases, the importance of electrostatics diminishes and the hybridization behavior becomes more complex. Suppression of hybridization affinity constants relative to solution values, and their weakened dependence on the concentration of DNA counterions, indicate that the immobilized strands form complexes that compete with hybridization to analyte strands. Moreover, an unusual regime is observed in which the surface coverage of immobilized oligonucleotides does not significantly influence the hybridization behavior, despite physical closeness and hence compulsory interactions between sites. These results are interpreted and summarized in a diagram of hybridization regimes that maps specific behaviors to experimental ranges of ionic strength and probe coverage. PMID:18381819

Effects of Dissolved Carbonate on Arsenate Adsorption and Surface Speciation at the Hematite-Water Interface

USGS Publications Warehouse

Arai, Y.; Sparks, D.L.; Davis, J.A.

2004-01-01

Effects of dissolved carbonate on arsenate [As(V)] reactivity and surface speciation at the hematite-water interface were studied as a function of pH and two different partial pressures of carbon dioxide gas [PCO2 = 10 -3.5 atm and ???0; CO2-free argon (Ar)] using adsorption kinetics, pseudo-equilibrium adsorption/titration experiments, extended X-ray absorption fine structure spectroscopic (EXAFS) analyses, and surface complexation modeling. Different adsorbed carbonate concentrations, due to the two different atmospheric systems, resulted in an enhanced and/or suppressed extent of As(V) adsorption. As(V) adsorption kinetics [4 g L -1, [As(V)]0 = 1.5 mM and / = 0.01 M NaCl] showed carbonate-enhanced As(V) uptake in the air-equilibrated systems at pH 4 and 6 and at pH 8 after 3 h of reaction. Suppressed As(V) adsorption was observed in the air-equilibrated system in the early stages of the reaction at pH 8. In the pseudo-equilibrium adsorption experiments [1 g L-1, [As(V)] 0 = 0.5 mM and / = 0.01 M NaCl], in which each pH value was held constant by a pH-stat apparatus, effects of dissolved carbonate on As(V) uptake were almost negligible at equilibrium, but titrant (0.1 M HCl) consumption was greater in the air-equilibrated systems (PCO2 = 10-3.5 atm)than in the CO2-free argon system at pH 4-7.75. The EXAFS analyses indicated that As(V) tetrahedral molecules were coordinated on iron octahedral via bidentate mononuclear (???2.8 A??) and bidentate binuclear (???3.3 A??) bonding at pH 4.5-8 and loading levels of 0.46-3.10 ??M m-2. Using the results of the pseudoequilibrium adsorption data and the XAS analyses, the pH-dependent As(V) adsorption under the PCO2 = 10-3.5 atm and the CO2-free argon system was modeled using surface complexation modeling, and the results are consistent with the formation of nonprotonated bidentate surface species at the hematite surfaces. The results also suggest that the acid titrant consumption was strongly affected by changes to electrical double-layer potentials caused by the adsorption of carbonate in the air-equilibrated system. Overall results suggest that the effects of dissolved carbonate on As(V) adsorption were influenced by the reaction conditions [e.g., available surface sites, initial As(V) concentrations, and reaction times]. Quantifying the effects of adsorbed carbonate may be important in predicting As(V) transport processes in groundwater, where iron oxide-coated aquifer materials are exposed to seasonally fluctuating partial pressures of CO2(g).

Role of coordination geometry in dictating the barrier to hydride migration in d6 square-pyramidal iridium and rhodium pincer complexes.

PubMed

Findlater, Michael; Cartwright-Sykes, Alison; White, Peter S; Schauer, Cynthia K; Brookhart, Maurice

2011-08-10

Syntheses of the olefin hydride complexes [(POCOP)M(H)(olefin)][BAr(f)(4)] (6a-M, M = Ir or Rh, olefin = C(2)H(4); 6b-M, M = Ir or Rh, olefin = C(3)H(6); POCOP = 2,6-bis(di-tert-butylphosphinito)benzene; BAr(f) = tetrakis(3,5-trifluoromethylphenyl)borate) are reported. A single-crystal X-ray structure determination of 6b-Ir shows a square-pyramidal coordination geometry for Ir, with the hydride ligand occupying the apical position. Dynamic NMR techniques were used to characterize these complexes. The rates of site exchange between the hydride and the olefinic hydrogens yielded ΔG(++) = 15.6 (6a-Ir), 16.8 (6b-Ir), 12.0 (6a-Rh), and 13.7 (6b-Rh) kcal/mol. The NMR exchange data also established that hydride migration in the propylene complexes yields exclusively the primary alkyl intermediate arising from 1,2-insertion. Unexpectedly, no averaging of the top and bottom faces of the square-pyramidal complexes is observed in the NMR spectra at high temperatures, indicating that the barrier for facial equilibration is >20 kcal/mol for both the Ir and Rh complexes. A DFT computational study was used to characterize the free energy surface for the hydride migration reactions. The classical terminal hydride complexes, [M(POCOP)(olefin)H](+), are calculated to be the global minima for both Rh and Ir, in accord with experimental results. In both the Rh ethylene and propylene complexes, the transition state for hydride migration (TS1) to form the agostic species is higher on the energy surface than the transition state for in-place rotation of the coordinated C-H bond (TS2), while for Ir, TS2 is the high point on the energy surface. Therefore, only for the case of the Rh complexes is the NMR exchange rate a direct measure of the hydride migration barrier. The trends in the experimental barriers as a function of M and olefin are in good agreement with the trends in the calculated exchange barriers. The calculated barriers for the hydride migration reaction in the Rh complexes are ∼2 kcal/mol higher than for the Ir complexes, despite the fact that the energy difference between the olefin hydride ground state and the agostic alkyl structure is ∼4 kcal/mol larger for Ir than for Rh. This feature, together with the high barrier for interchange of the top and bottom faces of the complexes, is proposed to arise from the unique coordination geometry of the agostic complexes and the strong preference for a cis-divacant octahedral geometry in four-coordinate intermediates. © 2011 American Chemical Society

Universality and chaotic dynamics in reactive scattering of ultracold KRb molecules with K atoms

NASA Astrophysics Data System (ADS)

Li, Ming; Makrides, Constantinos; Petrov, Alexander; Kotochigova, Svetlana; Croft, James F. E.; Balakrishnan, Naduvalath; Kendrick, Brian K.

2017-04-01

We study the benchmark reaction between the most-celebrated ultracold polar molecule, KRb, with an ultracold K atom. For the first time we map out an accurate ab initio ground potential energy surface of the K2Rb complex in full dimensionality and performed a numerically exact quantum-mechanical calculation of reaction dynamics based on coupled-channels approach in hyperspherical coordinates. An analysis of the adiabatic hyperspherical potentials reveals a chaotic distribution for the short-range complex that plays a key role in governing the reaction outcome. The equivalent distribution for a lighter collisional system with a smaller density of states (here the Li2Yb trimer) only shows random behavior. We find an extreme sensitivity of our chaotic system to a small perturbation associated with the weak non-additive three-body potential contribution that does not affect the total reaction rate coefficient but leads to a significant change in the rotational distribution in the product molecule. In both cases the distribution of these rates is random or Poissonian. This work was supported in part by NSF Grant PHY-1505557 (N.B.) and PHY-1619788 (S.K.), ARO MURI Grant No. W911NF-12-1-0476 (N.B. & S.K.), and DOE LDRD Grant No. 20170221ER (B.K.).

Formation of mercury sulfide from Hg(II)−thiolate complexes in natural organic matter

USGS Publications Warehouse

Alain Manceau,; Cyprien Lemouchi,; Mironel Enescu,; Anne-Claire Gaillot,; Martine Lanson,; Valerie Magnin,; Pieter Glatzel,; Poulin, Brett; Ryan, Joseph N.; Aiken, George R.; Isabelle Gautier-Lunea,; Kathryn L. Nagy,

2015-01-01

Methylmercury is the environmental form of neurotoxic mercury that is biomagnified in the food chain. Methylation rates are reduced when the metal is sequestered in crystalline mercury sulfides or bound to thiol groups in macromolecular natural organic matter. Mercury sulfide minerals are known to nucleate in anoxic zones, by reaction of the thiol-bound mercury with biogenic sulfide, but not in oxic environments. We present experimental evidence that mercury sulfide forms from thiol-bound mercury alone in aqueous dark systems in contact with air. The maximum amount of nanoparticulate mercury sulfide relative to thiol-bound mercury obtained by reacting dissolved mercury and soil organic matter matches that detected in the organic horizon of a contaminated soil situated downstream from Oak Ridge, TN, in the United States. The nearly identical ratios of the two forms of mercury in field and experimental systems suggest a common reaction mechanism for nucleating the mineral. We identified a chemical reaction mechanism that is thermodynamically favorable in which thiol-bound mercury polymerizes to mercury–sulfur clusters. The clusters form by elimination of sulfur from the thiol complexes via breaking of mercury–sulfur bonds as in an alkylation reaction. Addition of sulfide is not required. This nucleation mechanism provides one explanation for how mercury may be immobilized, and eventually sequestered, in oxygenated surface environments.

From porphyrins to pyrphyrins: adsorption study and metalation of a molecular catalyst on Au(111)

NASA Astrophysics Data System (ADS)

Mette, Gerson; Sutter, Denys; Gurdal, Yeliz; Schnidrig, Stephan; Probst, Benjamin; Iannuzzi, Marcella; Hutter, Jürg; Alberto, Roger; Osterwalder, Jürg

2016-04-01

The molecular ligand pyrphyrin, a tetradentate bipyridine based macrocycle, represents an interesting but widely unexplored class of molecules. It resembles the well-known porphyrin, but consists of pyridyl subunits instead of pyrroles. Metal complexes based on pyrphyrin ligands have recently shown promise as water reduction catalysts in homogeneous photochemical water splitting reactions. In this study, the adsorption and metalation of pyrphyrin on a single crystalline Au(111) surface is investigated in an ultrahigh vacuum by means of scanning tunneling microscopy, low-energy electron diffraction, X-ray photoelectron spectroscopy and density functional theory. Pyrphyrin coverages of approximately one monolayer and less are obtained by sublimation of the molecules on the substrate kept at room temperature. The molecules self-assemble in two distinct phases of long-range molecular ordering depending on the surface coverage. The deposition of cobalt metal and subsequent annealing lead to the formation of Co-ligated pyrphyrin molecules accompanied by a pronounced change of the molecular self-assembly. Electronic structure calculations taking the herringbone reconstruction of Au(111) into account show that the molecules are physisorbed, but preferred adsorption sites are identified where Co and the N atoms of the two terminal cyano groups are optimally coordinated to the surface Au atoms. An intermediate state of the metalation reaction is observed and the reaction steps for the Co metalation of pyrphyrin molecules on Au(111) are established in a joint experimental and computational effort.The molecular ligand pyrphyrin, a tetradentate bipyridine based macrocycle, represents an interesting but widely unexplored class of molecules. It resembles the well-known porphyrin, but consists of pyridyl subunits instead of pyrroles. Metal complexes based on pyrphyrin ligands have recently shown promise as water reduction catalysts in homogeneous photochemical water splitting reactions. In this study, the adsorption and metalation of pyrphyrin on a single crystalline Au(111) surface is investigated in an ultrahigh vacuum by means of scanning tunneling microscopy, low-energy electron diffraction, X-ray photoelectron spectroscopy and density functional theory. Pyrphyrin coverages of approximately one monolayer and less are obtained by sublimation of the molecules on the substrate kept at room temperature. The molecules self-assemble in two distinct phases of long-range molecular ordering depending on the surface coverage. The deposition of cobalt metal and subsequent annealing lead to the formation of Co-ligated pyrphyrin molecules accompanied by a pronounced change of the molecular self-assembly. Electronic structure calculations taking the herringbone reconstruction of Au(111) into account show that the molecules are physisorbed, but preferred adsorption sites are identified where Co and the N atoms of the two terminal cyano groups are optimally coordinated to the surface Au atoms. An intermediate state of the metalation reaction is observed and the reaction steps for the Co metalation of pyrphyrin molecules on Au(111) are established in a joint experimental and computational effort. Electronic supplementary information (ESI) available: More details and results of the XPS experiments and the DFT calculation including also the coordinates of the calculated configurations. See DOI: 10.1039/C5NR08953K

Exploring the synthesis and characterization of nanoenergetic materials from sol-gel chemistry

NASA Astrophysics Data System (ADS)

Walker, Jeremy D.

Nanoenergetic composite materials have been synthesized by a sol-gel chemical process where the addition of a weak base molecule induces the gelation of a hydrated metal salt solution. A proposed 'proton scavenging' mechanism, where a weak base molecule extracts a proton from the coordination sphere of the hydrated iron (III) complex in the gelation process to form iron (III) oxide/hydroxide, FeIIIxOyHz, has been confirmed for the weak base propylene oxide (PO), a 1,2 epoxide, as well as for the weak bases tetrahydrofuran (THF), a 1,4 epoxide, and pyridine, a heterocyclic nitrogen-containing compound. Gelation mechanisms for the formation of FeIIIxOyHz from THF and pyridine have been presented and confirmed through pH, XPS, and IR studies. THF follows a similar mechanism as PO, where the epoxide extracts a proton from the coordination sphere of the hydrated iron complex forming a protonated epoxide, which then undergoes irreversible ring-opening after reaction with a nucleophile in solution. Pyridine also extracts a proton from the hydrated metal complex, however, the stable six-membered molecule has low associated ring strain and does not endure ring-opening. Energetic properties for the Fe2O3/Al and RuO 2/Al sol-gel synthesized systems are also presented. Sol-gel chemistry synthesizes x-ray amorphous oxide matrices which contain substantial quantities of residual water and organic species. The iron (III) matrix, formed from the addition of a weak base epoxide molecule to a hydrated iron (III) nitrate solution, consists of stoichiometric Fe2O3, FeO(OH), and Fe(OH)3 and can only definitely be described as of Fe IIIxOyHz. XPS characterization of the metal oxide matrix synthesized from the addition of the weak base propylene oxide to a hydrated ruthenium (III) chloride solution corresponds to that of hydrous ruthenium (IV) oxide. Fe2O3/Al energetic systems were synthesized from the epoxides PO, trimethylene oxide (TMO) and 3,3 dimethyl oxetane (DMO). Energetic systems formed from each epoxide were each synthesized with different components, including: varying concentrations of nano-scale Al, micron Al, and carbon nanotubes. Surface area analysis of the synthesized matrices shows a direct correlation between the surface area of the iron (III) oxide matrix and the quantified exothermic heat of reaction of the energetic material due to the magnitude of the interfacial surface area contact between the iron (III) oxide matrix and the aluminum particles. The Fe2O3(PO)/Al systems possess the highest heat of reaction values due to the oxide surface area available for contact with the aluminum particles. Also, within systems, 1:1 Fe:nano Al samples possess the highest heat of reaction. Samples with nano-scale Al particles start reaction at 430°C, before the melting point of Al, whereas samples containing micron-Al do not react until ˜800°C, after the melting point of Al. The RuO2/Al energetic systems behave differently dependent on the atmosphere the sample is heated. Heating the RuO2/Al samples in an inert atmosphere results in the complete reduction of the ruthenium oxide matrix to Ru(0) before reaction with the aluminum particles. This results in the exothermic formation of RuxAly intermetallics, with the stoichiometry dependent on the initial Ru:Al concentration. However, heating the samples in an oxygen-rich atmosphere results in an exothermic reaction between RuO2 and Al. Post-reaction analysis of these samples reveals the sole existence of ruthenium (IV) oxide as the exothermic reaction vaporizes the aluminum particles.

Positive Feedback Loops for Factor V and Factor VII Activation Supply Sensitivity to Local Surface Tissue Factor Density During Blood Coagulation

PubMed Central

Balandina, A.N.; Shibeko, A.M.; Kireev, D.A.; Novikova, A.A.; Shmirev, I.I.; Panteleev, M.A.; Ataullakhanov, F.I.

2011-01-01

Blood coagulation is triggered not only by surface tissue factor (TF) density but also by surface TF distribution. We investigated recognition of surface TF distribution patterns during blood coagulation and identified the underlying molecular mechanisms. For these investigations, we employed 1), an in vitro reaction-diffusion experimental model of coagulation; and 2), numerical simulations using a mathematical model of coagulation in a three-dimensional space. When TF was uniformly immobilized over the activating surface, the clotting initiation time in normal plasma increased from 4 min to >120 min, with a decrease in TF density from 100 to 0.7 pmol/m2. In contrast, surface-immobilized fibroblasts initiated clotting within 3–7 min, independently of fibroblast quantity and despite a change in average surface TF density from 0.5 to 130 pmol/m2. Experiments using factor V-, VII-, and VIII-deficient plasma and computer simulations demonstrated that different responses to these two TF distributions are caused by two positive feedback loops in the blood coagulation network: activation of the TF–VII complex by factor Xa, and activation of factor V by thrombin. This finding suggests a new role for these reactions: to supply sensitivity to local TF density during blood coagulation. PMID:22004734

XAFS studies of surface structures of TiO{sub 2} nanoparticles and photocatalytic reduction of metal ions.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, L. X.; Rajh, T.; Wang, Z.

1997-01-01

To probe the origin of the unique functions of titanium dioxide (TiO{sub 2}) nanoparticles observed in photocatalytic reactions, structures of Ti atom sites in titanium dioxide (TiO{sub 2}) nanoparticles with different sizes were studied by Ti K-edge XAFS (X-ray absorption fine structure). Compared to the bulk TiO{sub 2} structure, a shorter Ti-O distance from surface TiO{sub 2} resulting from Ti-OH bonding was observed. The XAFS spectra also revealed an increasing disorder of the lattice with decreasing sizes of the nanoparticles based on a coordination number decrease for the third-shell O atoms as well as changes in relative intensities of pre-edgemore » peaks A1, A2, and A3. However, the Ti sites largely remain octahedral even in the 30 Angstrom diameter particles. These results imply that the increasing number of surface Ti sites as well as possible corner defects in small nanoparticles may be the main cause of the unique surface chemistry exhibited by nanoparticles of TiO{sub 2}. XAFS was also used in monitoring the photoreduction reaction products of Cu{sup 2+} and Hg{sup 2+} on TiO{sub 2} nanoparticle surfaces, with or without surface adsorbers, alanine (Ala) and thiolactic acid (TLA). Ala dramatically enhanced photoreduction of Cu{sup 2+} on TiO{sub 2} nanoparticle surfaces, whereas thiolactic acid did not affect or even hindered Hg{sup 2+} photoreduction. Although both surface adsorbers chelated with the metal ions in the absence of TiO{sub 2} nanoparticles, this chelation was drastically changed in the Cu-Ala complex but was largely retained in the Hg-TLA complex when TiO{sub 2} was present. This may correlate with the different effects of the adsorbers on the photoreduction of the metal. Our experimental results suggest that a proper balance between the affinities of the adsorber to the metal ions and to the surface Ti atoms of TiO{sub 2} may be one of the keys in selecting a surface adsorber for enhanced photoreduction efficiency.« less

Effect of adsorbed films on friction of Al2O3-metal systems

NASA Technical Reports Server (NTRS)

Pepper, S. V.

1976-01-01

The kinetic friction of polycrystalline Al2O3 sliding on Cu, Ni, and Fe in ultrahigh vacuum was studied as a function of the surface chemistry of the metal. Clean metal surfaces were exposed to O2, Cl2, C2H4, and C2H3Cl, and the change in friction due to the adsorbed species was observed. Auger electron spectroscopy assessed the elemental composition of the metal surface. It was found that the systems exposed to Cl2 exhibited low friction, interpreted as the van der Waals force between the Al2O3 and metal chloride. The generation of metal oxide by oxygen exposures resulted in an increase in friction, interpreted as due to strong interfacial bonds established by reaction of metal oxide with Al2O3 to form the complex oxide (spinel). The only effect of C2H4 was to increase the friction of the Fe system, but C2H3Cl exposures decreases friction in both Ni and Fe systems, indicating the dominance of the chlorine over the ethylene complex on the surface

Wave packet and statistical quantum calculations for the He + NeH⁺ → HeH⁺ + Ne reaction on the ground electronic state.

PubMed

Koner, Debasish; Barrios, Lizandra; González-Lezana, Tomás; Panda, Aditya N

2014-09-21

A real wave packet based time-dependent method and a statistical quantum method have been used to study the He + NeH(+) (v, j) reaction with the reactant in various ro-vibrational states, on a recently calculated ab initio ground state potential energy surface. Both the wave packet and statistical quantum calculations were carried out within the centrifugal sudden approximation as well as using the exact Hamiltonian. Quantum reaction probabilities exhibit dense oscillatory pattern for smaller total angular momentum values, which is a signature of resonances in a complex forming mechanism for the title reaction. Significant differences, found between exact and approximate quantum reaction cross sections, highlight the importance of inclusion of Coriolis coupling in the calculations. Statistical results are in fairly good agreement with the exact quantum results, for ground ro-vibrational states of the reactant. Vibrational excitation greatly enhances the reaction cross sections, whereas rotational excitation has relatively small effect on the reaction. The nature of the reaction cross section curves is dependent on the initial vibrational state of the reactant and is typical of a late barrier type potential energy profile.

Improved adhesion of Ni films on X-ray damaged polytetrafluoroethylene

NASA Technical Reports Server (NTRS)

Wheeler, D. R.; Pepper, S. V.

1981-01-01

The considered investigation shows that the adhesion of evaporated Ni on polytetrafluoroethylene (PTFE) is enhanced by irradiating the PTFE surface prior to evaporation. Evidence obtained with the aid of X-ray photoelectron spectroscopy is presented concerning the association of the enhanced adhesion with an interfacial chemical reaction. Evaporated Ni clearly adheres better to the X-ray damaged PTFE surface than to the undamaged surface. There is evidence that the improved adhesion is not related to the Ni-C bond, but rather to the NiF2. A possible mechanism which may be consistent with the data is the formation of a F-Ni-C complex, where C is a member of the polymer chain.

Fast method for reactor and feature scale coupling in ALD and CVD

DOEpatents

Yanguas-Gil, Angel; Elam, Jeffrey W.

2017-08-08

Transport and surface chemistry of certain deposition techniques is modeled. Methods provide a model of the transport inside nanostructures as a single-particle discrete Markov chain process. This approach decouples the complexity of the surface chemistry from the transport model, thus allowing its application under general surface chemistry conditions, including atomic layer deposition (ALD) and chemical vapor deposition (CVD). Methods provide for determination of determine statistical information of the trajectory of individual molecules, such as the average interaction time or the number of wall collisions for molecules entering the nanostructures as well as to track the relative contributions to thin-film growth of different independent reaction pathways at each point of the feature.

On-surface synthesis on a bulk insulator surface

NASA Astrophysics Data System (ADS)

Richter, Antje; Floris, Andrea; Bechstein, Ralf; Kantorovich, Lev; Kühnle, Angelika

2018-04-01

On-surface synthesis has rapidly emerged as a most promising approach to prepare functional molecular structures directly on a support surface. Compared to solution synthesis, performing chemical reactions on a surface offers several exciting new options: due to the absence of a solvent, reactions can be envisioned that are otherwise not feasible due to the insolubility of the reaction product. Perhaps even more important, the confinement to a two-dimensional surface might enable reaction pathways that are not accessible otherwise. Consequently, on-surface synthesis has attracted great attention in the last decade, with an impressive number of classical reactions transferred to a surface as well as new reactions demonstrated that have no classical analogue. So far, the majority of the work has been carried out on conducting surfaces. However, when aiming for electronic decoupling of the resulting structures, e.g. for the use in future molecular electronic devices, non-conducting surfaces are highly desired. Here, we review the current status of on-surface reactions demonstrated on the (10.4) surface of the bulk insulator calcite. Besides thermally induced C-C coupling of halogen-substituted aryls, photochemically induced [2  +  2] cycloaddition has been proven possible on this surface. Moreover, experimental evidence exists for coupling of terminal alkynes as well as diacetylene polymerization. While imaging of the resulting structures with dynamic atomic force microscopy provides a direct means of reaction verification, the detailed reaction pathway often remains unclear. Especially in cases where the presence of metal atoms is known to catalyze the corresponding solution chemistry reaction (e.g. in the case of the Ullmann reaction), disclosing the precise reaction pathway is of importance to understand and generalize on-surface reactivity on a bulk insulator surface. To this end, density-functional theory calculations have proven to provide atomic-scale insights that have greatly contributed to unravelling the details of on-surface synthesis on a bulk insulator surface.

Sorption of trivalent lanthanides and actinides onto montmorillonite: Macroscopic, thermodynamic and structural evidence for ternary hydroxo and carbonato surface complexes on multiple sorption sites.

PubMed

Fernandes, M Marques; Scheinost, A C; Baeyens, B

2016-08-01

The credibility of long-term safety assessments of radioactive waste repositories may be greatly enhanced by a molecular level understanding of the sorption processes onto individual minerals present in the near- and far-fields. In this study we couple macroscopic sorption experiments to surface complexation modelling and spectroscopic investigations, including extended X-ray absorption fine structure (EXAFS) and time-resolved laser fluorescence spectroscopies (TRLFS), to elucidate the uptake mechanism of trivalent lanthanides and actinides (Ln/An(III)) by montmorillonite in the absence and presence of dissolved carbonate. Based on the experimental sorption isotherms for the carbonate-free system, the previously developed 2 site protolysis non electrostatic surface complexation and cation exchange (2SPNE SC/CE) model needed to be complemented with an additional surface complexation reaction onto weak sites. The fitting of sorption isotherms in the presence of carbonate required refinement of the previously published model by reducing the strong site capacity and by adding the formation of Ln/An(III)-carbonato complexes both on strong and weak sites. EXAFS spectra of selected Am samples and TRLFS spectra of selected Cm samples corroborate the model assumptions by showing the existence of different surface complexation sites and evidencing the formation of Ln/An(III) carbonate surface complexes. In the absence of carbonate and at low loadings, Ln/An(III) form strong inner-sphere complexes through binding to three Al(O,OH)6 octahedra, most likely by occupying vacant sites in the octahedral layers of montmorillonite, which are exposed on {010} and {110} edge faces. At higher loadings, Ln/An(III) binds to only one Al octahedron, forming a weaker, edge-sharing surface complex. In the presence of carbonate, we identified a ternary mono- or dicarbonato Ln/An(III) complex binding directly to one Al(O,OH)6 octahedron, revealing that type-A ternary complexes form with the one or two carbonate groups pointing away from the surface into the solution phase. Within the spectroscopically observable concentration range these complexes could only be identified on the weak sites, in line with the small strong site capacity suggested by the refined sorption model. When the solubility of carbonates was exceeded, formation of an Am carbonate hydroxide could be identified. The excellent agreement between the thermodynamic model parameters obtained by fitting the macroscopic data, and the spectroscopically identified mechanisms, demonstrates the mature state of the 2SPNE SC/CE model for predicting and quantifying the retention of Ln/An(III) elements by montmorillonite-rich clay rocks. Copyright © 2016 Elsevier Ltd. All rights reserved.

Novel Visualization Approaches in Environmental Mineralogy

NASA Astrophysics Data System (ADS)

Anderson, C. D.; Lopano, C. L.; Hummer, D. R.; Heaney, P. J.; Post, J. E.; Kubicki, J. D.; Sofo, J. O.

2006-05-01

Communicating the complexities of atomic scale reactions between minerals and fluids is fraught with intrinsic challenges. For example, an increasing number of techniques are now available for the interrogation of dynamical processes at the mineral-fluid interface. However, the time-dependent behavior of atomic interactions between a solid and a liquid is often not adequately captured by two-dimensional line drawings or images. At the same time, the necessity for describing these reactions to general audiences is growing more urgent, as funding agencies are amplifying their encouragement to scientists to reach across disciplines and to justify their studies to public audiences. To overcome the shortcomings of traditional graphical representations, the Center for Environmental Kinetics Analysis is creating three-dimensional visualizations of experimental and simulated mineral reactions. These visualizations are then displayed on a stereo 3D projection system called the GeoWall. Made possible (and affordable) by recent improvements in computer and data projector technology, the GeoWall system uses a combination of computer software and hardware, polarizing filters and polarizing glasses, to present visualizations in true 3D. The three-dimensional views greatly improve comprehension of complex multidimensional data, and animations of time series foster better understanding of the underlying processes. The visualizations also offer an effective means to communicate the complexities of environmental mineralogy to colleagues, students and the public. Here we present three different kinds of datasets that demonstrate the effectiveness of the GeoWall in clarifying complex environmental reactions at the atomic scale. First, a time-resolved series of diffraction patterns obtained during the hydrothermal synthesis of metal oxide phases from precursor solutions can be viewed as a surface with interactive controls for peak scaling and color mapping. Second, the results of Rietveld analysis of cation exchange reactions in Mn oxides has provided three-dimensional difference Fourier maps. When stitched together in a temporal series, these offer an animated view of changes in atomic configurations during the process of exchange. Finally, molecular dynamical simulations are visualized as three-dimensional reactions between vibrating atoms in both the solid and the aqueous phases.

Exploring the nonequilibrium reactivity of molecules with platinum(111)

NASA Astrophysics Data System (ADS)

Dewitt, Kristin Marie

Various aspects of the nonequilibrium reactivity of several, catalytically important, small molecules with Pt(111)were explored. The effect of alkali metal promotion on the thermal chemistry and photochemistry of CH4,N 2, and CO2 was studied. Dissociative sticking coefficients for methane and ethane were measured as a function of gas temperature ( Tg) and surface temperature (Ts) using effusive molecular beam and angle-integrated gas dosing methods. Coupled with physisorbed complex microcanonical unimolecular rate theory these measurements provide a predictive understanding for the kinetics of these C-H bond activation reactions, i.e. allowing us to predict the sticking coefficient of CH 4 and C2H6 for any combination of T s and Tg. Work function thermal programmed desorption was used to examine the correlation between surface structure and surface work function for CH3Br and CO2. Preliminary two-photon photoemission and broad-band infrared-visible sum frequency generation experiments introduce these nonlinear spectroscopy techniques to the arsenal of surface characterization techniques available in our group. All of the disparate components of this work are tied together by one overall theme, developing an improved molecular-level understanding of the reaction dynamics of catalysis.

Molecular Studies of Complex Soil Organic Matter Interactions with Metal Ions and Mineral Surfaces using Classical Molecular Dynamics and Quantum Chemistry Methods

NASA Astrophysics Data System (ADS)

Andersen, A.; Govind, N.; Laskin, A.

2017-12-01

Mineral surfaces have been implicated as potential protectors of soil organic matter (SOM) against decomposition and ultimate mineralization to small molecules which can provide nutrients for plants and soil microbes and can also contribute to the Earth's elemental cycles. SOM is a complex mixture of organic molecules of biological origin at varying degrees of decomposition and can, itself, self-assemble in such a way as to expose some biomolecule types to biotic and abiotic attack while protecting other biomolecule types. The organization of SOM and SOM with mineral surfaces and solvated metal ions is driven by an interplay of van der Waals and electrostatic interactions leading to partitioning of hydrophilic (e.g. sugars) and hydrophobic (e.g., lipids) SOM components that can be bridged with amphiphilic molecules (e.g., proteins). Classical molecular dynamics simulations can shed light on assemblies of organic molecules alone or complexation with mineral surfaces. The role of chemical reactions is also an important consideration in potential chemical changes of the organic species such as oxidation/reduction, degradation, chemisorption to mineral surfaces, and complexation with solvated metal ions to form organometallic systems. For the study of chemical reactivity, quantum chemistry methods can be employed and combined with structural insight provided by classical MD simulations. Moreover, quantum chemistry can also simulate spectroscopic signatures based on chemical structure and is a valuable tool in interpreting spectra from, notably, x-ray absorption spectroscopy (XAS). In this presentation, we will discuss our classical MD and quantum chemistry findings on a model SOM system interacting with mineral surfaces and solvated metal ions.

Acid-base properties of aqueous illite surfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Du, Q.; Sun, Z.; Forsling, W.

In this paper, the acid-base properties of illite/water suspensions are examined using the constant capacitance surface complexation model. On the basis of results of potentiometric titrations and solubility experiments, the authors conclude that the proton reactions in the supernatants of illite suspensions can be successfully represented by proton reactions of Al(H{sub 2}O){sub 6}{sup 3+} and Si(OH){sub 4} in water solutions. For illustrating the acidic characteristics of aqueous illite surfaces, two surface protonation models are proposed: (1) one site-one pK{sub a} model, {triple_bond}SOH {r_reversible} {triple_bond}SO{sup {minus}} + H{sup +}, pK{sub a}{sup int} = 4.12-4.23; (2) two sites-two pK{sub a}s model, {triple_bond}S{submore » 1}OH {r_reversible} {triple_bond}S{sup 1}O{sup {minus}} + H{sup +}, pK{sub a{sub I}} = 4.17-4.44, and {triple_bond}S{sub II}OH {r_reversible} {triple_bond}S{sub II}O{sup {minus}} + H{sup +}, pK{sub a{sub II}}{sup int} = 6.35-7.74. Evaluation of these two models indicates that both of them can give good descriptions of the experimental data of systems with different illite concentrations and ionic strengths and that the one site-one pK{sub a} model can be considered as a simplification of the two sites-two pK{sub a}s model. Since both models assume only deprotonation reactions at the illite surfaces, they suggest that the surface behavior of the illite is similar to that of amorphous SiO{sub 2}. Model assumptions, experimental procedures, and evaluative criteria are detailed in the paper.« less

Spatially resolved observation of crystal-face-dependent catalysis by single turnover counting

NASA Astrophysics Data System (ADS)

Roeffaers, Maarten B. J.; Sels, Bert F.; Uji-I, Hiroshi; de Schryver, Frans C.; Jacobs, Pierre A.; de Vos, Dirk E.; Hofkens, Johan

2006-02-01

Catalytic processes on surfaces have long been studied by probing model reactions on single-crystal metal surfaces under high vacuum conditions. Yet the vast majority of industrial heterogeneous catalysis occurs at ambient or elevated pressures using complex materials with crystal faces, edges and defects differing in their catalytic activity. Clearly, if new or improved catalysts are to be rationally designed, we require quantitative correlations between surface features and catalytic activity-ideally obtained under realistic reaction conditions. Transmission electron microscopy and scanning tunnelling microscopy have allowed in situ characterization of catalyst surfaces with atomic resolution, but are limited by the need for low-pressure conditions and conductive surfaces, respectively. Sum frequency generation spectroscopy can identify vibrations of adsorbed reactants and products in both gaseous and condensed phases, but so far lacks sensitivity down to the single molecule level. Here we adapt real-time monitoring of the chemical transformation of individual organic molecules by fluorescence microscopy to monitor reactions catalysed by crystals of a layered double hydroxide immersed in reagent solution. By using a wide field microscope, we are able to map the spatial distribution of catalytic activity over the entire crystal by counting single turnover events. We find that ester hydrolysis proceeds on the lateral {1010} crystal faces, while transesterification occurs on the entire outer crystal surface. Because the method operates at ambient temperature and pressure and in a condensed phase, it can be applied to the growing number of liquid-phase industrial organic transformations to localize catalytic activity on and in inorganic solids. An exciting opportunity is the use of probe molecules with different size and functionality, which should provide insight into shape-selective or structure-sensitive catalysis and thus help with the rational design of new or more productive heterogeneous catalysts.

Understanding the Reaction Chemistry of 2,2':5',2''-Terthiophene Films with Vapor-Deposited Ag, Al, and Ca

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sang, Lingzi; Matz, Dallas L.; Pemberton, Jeanne E.

The reaction chemistry of vapor-deposited 2,2':5',2''-terthiophene (α-3T) solid-state thin films with postdeposited Ag, Al, and Ca is investigated in ultrahigh vacuum using Raman spectroscopy. Vapor-deposited Ag forms nanoparticles on these films and induces considerable surface enhanced Raman scattering (SERS) along with a change in molecular symmetry of adjacent α-3T and formation of Ag–S bonds; no other reaction chemistry is observed. Vapor-deposited Al and Ca undergo chemical reaction with α-3T initiated by metal-to-α-3T electron transfer. For Al, the resulting product is predominantly amorphous carbon through initial radical formation and subsequent decomposition reactions. For Ca, the spectral evidence suggests two pathways: onemore » leading to α-3T polymerization and the other resulting in thiophene ring opening, both initiated by radical formation through Ca-to-α-3T electron transfer. These interfacial reactions reflect the complex chemistry that can occur between low work function metals and thiophene-based oligomers. This reactivity is strongly correlated with metal work function.« less

Understanding the Reaction Chemistry of 2,2':5',2"-Terthiophene Films with Vapor-Deposited Ag, Al, and Ca

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sang, Lingzi; Matz, Dallas L.; Pemberton, Jeanne E.

The reaction chemistry of vapor-deposited 2,2':5',2''-terthiophene (α-3T) solid-state thin films with postdeposited Ag, Al, and Ca is investigated in ultrahigh vacuum using Raman spectroscopy. Vapor-deposited Ag forms nanoparticles on these films and induces considerable surface enhanced Raman scattering (SERS) along with a change in molecular symmetry of adjacent α-3T and formation of Ag–S bonds; no other reaction chemistry is observed. Vapor-deposited Al and Ca undergo chemical reaction with α-3T initiated by metal-to-α-3T electron transfer. For Al, the resulting product is predominantly amorphous carbon through initial radical formation and subsequent decomposition reactions. For Ca, the spectral evidence suggests two pathways: onemore » leading to α-3T polymerization and the other resulting in thiophene ring opening, both initiated by radical formation through Ca-to-α-3T electron transfer. These interfacial reactions reflect the complex chemistry that can occur between low work function metals and thiophene-based oligomers. This reactivity is strongly correlated with metal work function.« less

A genetically optimized kinetic model for ethanol electro-oxidation on Pt-based binary catalysts used in direct ethanol fuel cells

NASA Astrophysics Data System (ADS)

Sánchez-Monreal, Juan; García-Salaberri, Pablo A.; Vera, Marcos

2017-09-01

A one-dimensional model is proposed for the anode of a liquid-feed direct ethanol fuel cell. The complex kinetics of the ethanol electro-oxidation reaction is described using a multi-step reaction mechanism that considers free and adsorbed intermediate species on Pt-based binary catalysts. The adsorbed species are modeled using coverage factors to account for the blockage of the active reaction sites on the catalyst surface. The reaction rates are described by Butler-Volmer equations that are coupled to a one-dimensional mass transport model, which incorporates the effect of ethanol and acetaldehyde crossover. The proposed kinetic model circumvents the acetaldehyde bottleneck effect observed in previous studies by incorporating CH3CHOHads among the adsorbed intermediates. A multi-objetive genetic algorithm is used to determine the reaction constants using anode polarization and product selectivity data obtained from the literature. By adjusting the reaction constants using the methodology developed here, different catalyst layers could be modeled and their selectivities could be successfully reproduced.

Probing the evolution of palladium species in Pd@MOF catalysts during the Heck coupling reaction: An operando X-ray absorption spectroscopy study.

PubMed

Yuan, Ning; Pascanu, Vlad; Huang, Zhehao; Valiente, Alejandro; Heidenreich, Niclas; Leubner, Sebastian; Inge, A Ken; Gaar, Jakob; Stock, Norbert; Persson, Ingmar; Martin-Matute, Belen; Zou, Xiaodong

2018-06-11

The mechanism of the Heck C-C coupling reaction catalyzed by Pd@MOFs has been investigated using operando X-ray absorption spectroscopy (XAS) and powder X-ray diffraction (PXRD) combined with transmission electron microscopy (TEM) analysis and nuclear magnetic resonance ( 1 H NMR) kinetic studies. A custom-made reaction cell was used allowing operando PXRD and XAS data collection using high-energy synchrotron radiation. By analyzing the XAS data in combination with ex situ studies, the evolution of the palladium species is followed from the as-synthesized to its deactivated form. An adaptive reaction mechanism is pro-posed. Mononuclear Pd(II) complexes are found to be the dominant active species at the beginning of the reaction, which then gradually transform into Pd nanoclusters with 13-20 Pd atoms on average in later catalytic turnovers. Consumption of available reagent and substrate leads to coordination of Cl - ions to their surfaces, which causes the poisoning of the active sites. By understanding the deactivation process, it was possible to tune the reaction conditions and prolong the lifetime of the catalyst.

Partitioning of dissolved organic matter-bound mercury between a hydrophobic surface and polysulfide-rubber polymer.

PubMed

Kim, Eun-Ah; Luthy, Richard G

2011-11-01

This study investigated the role of dissolved organic matter on mercury partitioning between a hydrophobic surface (polyethylene, PE) and a reduced sulfur-rich surface (polysulfide rubber, PSR). Comparative sorption studies employed polyethylene and polyethylene coated with PSR for reactions with DOM-bound mercuric ions. These studies revealed that PSR enhanced the Hg-DOM removal from water when DOM was Suwannee River natural organic matter (NOM), fulvic acid (FA), or humic acid (HA), while the same amount of 1,3-propanedithiol-bound mercuric ion was removed by both PE and PSR-PE. The differences for Hg-DOM removal efficiencies between PE and PSR-PE varied depending on which DOM was bound to mercuric ion as suggested by the PE/water and PSR-PE/water partition coefficients for mercury. The surface concentrations of mercury on PE and PSR-PE with the same DOM measured by x-ray photoelectron spectroscopy were similar, which indicated the comparable amounts of immobilized mercury on PE and PSR-PE being exposed to the aqueous phase. With these observations, two major pathways for the immobilization reactions between PSR-PE and Hg-DOM were examined: 1) adsorption of Hg-DOM on PE by hydrophobic interactions between DOM and PE, and 2) addition reaction of Hg-DOM onto PSR by a complexation reaction between Hg and PSR. The percent contribution of each pathway was derived from a mass balance and the ratios among aqueous mercury, PE-bound Hg-DOM, and PSR-bound Hg-DOM concentrations. The results indicate strong binding of mercuric ion with both dissolved organic matter and PSR polymer. The FT-IR examination of Hg-preloaded-PSR-PEs after the reaction with DOM corroborated a strong interaction between mercuric ion and 1,3-propanedithiol compared to Hg-HA, Hg-FA, or Hg-NOM interactions. Copyright © 2011 Elsevier Ltd. All rights reserved.

Partitioning of dissolved organic matter-bound mercury between a hydrophobic surface and polysulfide-rubber polymer

PubMed Central

Kim, Eun-Ah

2011-01-01

This study investigated the role of dissolved organic matter on mercury partitioning between a hydrophobic surface (polyethylene, PE) and a reduced sulfur-rich surface (polysulfide rubber, PSR). Comparative sorption studies employed polyethylene and polyethylene coated with PSR for reactions with DOM-bound mercuric ions. These studies revealed that PSR enhanced the Hg-DOM removal from water when DOM was Suwannee River natural organic matter (NOM), fulvic acid (FA), or humic acid (HA), while the same amount of 1,3-propanedithiol-bound mercuric ion was removed by both PE and PSR-PE. The differences for Hg-DOM removal efficiencies between PE and PSR-PE varied depending on which DOM was bound to mercuric ion as suggested by the PE/water and PSR-PE/water partition coefficients for mercury. The surface concentrations of mercury on PE and PSR-PE with the same DOM measured by x-ray – photoelectron spectroscopy were similar, which indicated the comparable amounts of immobilized mercury on PE and PSR-PE being exposed to the aqueous phase. With these observations, two major pathways for the immobilization reactions between PSR-PE and Hg- DOM were examined: 1) adsorption of Hg-DOM on PE by hydrophobic interactions between DOM and PE, and 2) addition reaction of Hg-DOM onto PSR by a complexation reaction between Hg and PSR. The percent contribution of each pathway was derived from a mass balance and the ratios among aqueous mercury, PE-bound Hg-DOM, and PSR-bound Hg-DOM concentrations. The results indicate strong binding of mercuric ion with both dissolved organic matter and PSR polymer. The FT-IR examination of Hg-preloaded-PSR-PEs after the reaction with DOM corroborated a strong interaction between mercuric ion and 1,3-propanedithiol compared to Hg-HA, Hg-FA, or Hg-NOM interactions. PMID:21872900

Beam-induced redox transformation of arsenic during As K-edge XAS measurements: availability of reducing or oxidizing agents and As speciation.

PubMed

Han, Young Soo; Jeong, Hoon Young; Hyun, Sung Pil; Hayes, Kim F; Chon, Chul Min

2018-05-01

During X-ray absorption spectroscopy (XAS) measurements of arsenic (As), beam-induced redox transformation is often observed. In this study, the As species immobilized by poorly crystallized mackinawite (FeS) was assessed for the susceptibility to beam-induced redox reactions as a function of sample properties including the redox state of FeS and the solid-phase As speciation. The beam-induced oxidation of reduced As species was found to be mediated by the atmospheric O 2 and the oxidation products of FeS [e.g. Fe(III) (oxyhydr)oxides and intermediate sulfurs]. Regardless of the redox state of FeS, both arsenic sulfide and surface-complexed As(III) readily underwent the photo-oxidation upon exposure to the atmospheric O 2 during XAS measurements. With strict O 2 exclusion, however, both As(0) and arsenic sulfide were less prone to the photo-oxidation by Fe(III) (oxyhydr)oxides than NaAsO 2 and/or surface-complexed As(III). In case of unaerated As(V)-reacted FeS samples, surface-complexed As(V) was photocatalytically reduced during XAS measurements, but arsenic sulfide did not undergo the photo-reduction.

Chirality of weakly bound complexes: The potential energy surfaces for the hydrogen-peroxide−noble-gas interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Roncaratti, L. F., E-mail: lz@fis.unb.br; Leal, L. A.; Silva, G. M. de

2014-10-07

We consider the analytical representation of the potential energy surfaces of relevance for the intermolecular dynamics of weakly bound complexes of chiral molecules. In this paper we study the H{sub 2}O{sub 2}−Ng (Ng=He, Ne, Ar, Kr, and Xe) systems providing the radial and the angular dependence of the potential energy surface on the relative position of the Ng atom. We accomplish this by introducing an analytical representation which is able to fit the ab initio energies of these complexes in a wide range of geometries. Our analysis sheds light on the role that the enantiomeric forms and the symmetry ofmore » the H{sub 2}O{sub 2} molecule play on the resulting barriers and equilibrium geometries. The proposed theoretical framework is useful to study the dynamics of the H{sub 2}O{sub 2} molecule, or other systems involving O–O and S–S bonds, interacting by non-covalent forces with atoms or molecules and to understand how the relative orientation of the O–H bonds changes along collisional events that may lead to a hydrogen bond formation or even to selectivity in chemical reactions.« less

Adsorption of Fe(II) and U(VI) to carboxyl-functionalized microspheres: The influence of speciation on uranyl reduction studied by titration and XAFS

NASA Astrophysics Data System (ADS)

Boyanov, Maxim I.; O'Loughlin, Edward J.; Roden, Eric E.; Fein, Jeremy B.; Kemner, Kenneth M.

2007-04-01

The chemical reduction of U(VI) by Fe(II) is a potentially important pathway for immobilization of uranium in subsurface environments. Although the presence of surfaces has been shown to catalyze the reaction between Fe(II) and U(VI) aqueous species, the mechanism(s) responsible for the enhanced reactivity remain ambiguous. To gain further insight into the U-Fe redox process at a complexing, non-conducting surface that is relevant to common organic phases in the environment, we studied suspensions containing combinations of 0.1 mM U(VI), 1.0 mM Fe(II), and 4.2 g/L carboxyl-functionalized polystyrene microspheres. Acid-base titrations were used to monitor protolytic reactions, and Fe K-edge and U L-edge X-ray absorption fine structure spectroscopy was used to determine the valence and atomic environment of the adsorbed Fe and U species. In the Fe + surface carboxyl system, a transition from monomeric to oligomeric Fe(II) surface species was observed between pH 7.5 and pH 8.4. In the U + surface carboxyl system, the U(VI) cation was adsorbed as a mononuclear uranyl-carboxyl complex at both pH 7.5 and 8.4. In the ternary U + Fe + surface carboxyl system, U(VI) was not reduced by the solvated or adsorbed Fe(II) at pH 7.5 over a 4-month period, whereas complete and rapid reduction to U(IV) nanoparticles occurred at pH 8.4. The U(IV) product reoxidized rapidly upon exposure to air, but it was stable over a 4-month period under anoxic conditions. Fe atoms were found in the local environment of the reduced U(IV) atoms at a distance of 3.56 Å. The U(IV)-Fe coordination is consistent with an inner-sphere electron transfer mechanism between the redox centers and involvement of Fe(II) atoms in both steps of the reduction from U(VI) to U(IV). The inability of Fe(II) to reduce U(VI) in solution and at pH 7.5 in the U + Fe + carboxyl system is explained by the formation of a transient, "dead-end" U(V)-Fe(III) complex that blocks the U(V) disproportionation pathway after the first electron transfer. The increased reactivity at pH 8.4 relative to pH 7.5 is explained by the reaction of U(VI) with an Fe(II) oligomer, whereby the bonds between Fe atoms facilitate the transfer of a second electron to the hypothetical U(V)-Fe(III) intermediate. We discuss how this mechanism may explain the commonly observed higher efficiency of uranyl reduction by adsorbed or structural Fe(II) relative to aqueous Fe(II).

Mineralogical textural and compositional data on the alteration of basaltic glass from Kilauea, Hawaii to 300 degrees C: Insights to the corrosion of a borosilicate glass waste-form. [Yucca Mountain Project

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smith, D.K.

1990-01-01

Mineralogical, textural and compositional data accompanying greenschist facies metamorphism (to 300{degrees}C) of basalts of the East Rift Zone (ERZ), Kilauea, Hawaii may be evaluated relative to published and experimental results for the surface corrosion of borosilicate glass. The ERZ alteration sequence is dominated by intermittent palagonite, interlayered smectite-chlorite, chlorite, and actinolite-epidote-anhydrite. Alteration is best developed in fractures and vesicles where surface reaction layers root on the glass matrix forming rinds in excess of 100 microns thick. Fractures control fluid circulation and the alteration sequence. Proximal to the glass surface, palagonite, Fe-Ti oxides and clays replace fresh glass as the surfacemore » reaction layer migrates inwards; away from the surface, amphibole, anhydrite, quartz and calcite crystallize from hydrothermal fluids in contact with the glass. The texture and composition of basaltic glass surfaces are similar to those of a SRL-165 glass leached statically for sixty days at 150 {degrees}C. While the ERZ reservoir is a complex open system, conservative comparisons between the alteration of ERZ and synthetic borosilicate glass are warranted. 31 refs., 2 figs.« less

Inhibited proton transfer enhances Au-catalyzed CO2-to-fuels selectivity.

PubMed

Wuttig, Anna; Yaguchi, Momo; Motobayashi, Kenta; Osawa, Masatoshi; Surendranath, Yogesh

2016-08-09

CO2 reduction in aqueous electrolytes suffers efficiency losses because of the simultaneous reduction of water to H2 We combine in situ surface-enhanced IR absorption spectroscopy (SEIRAS) and electrochemical kinetic studies to probe the mechanistic basis for kinetic bifurcation between H2 and CO production on polycrystalline Au electrodes. Under the conditions of CO2 reduction catalysis, electrogenerated CO species are irreversibly bound to Au in a bridging mode at a surface coverage of ∼0.2 and act as kinetically inert spectators. Electrokinetic data are consistent with a mechanism of CO production involving rate-limiting, single-electron transfer to CO2 with concomitant adsorption to surface active sites followed by rapid one-electron, two-proton transfer and CO liberation from the surface. In contrast, the data suggest an H2 evolution mechanism involving rate-limiting, single-electron transfer coupled with proton transfer from bicarbonate, hydronium, and/or carbonic acid to form adsorbed H species followed by rapid one-electron, one-proton, or H recombination reactions. The disparate proton coupling requirements for CO and H2 production establish a mechanistic basis for reaction selectivity in electrocatalytic fuel formation, and the high population of spectator CO species highlights the complex heterogeneity of electrode surfaces under conditions of fuel-forming electrocatalysis.

Acid-base behavior of the gaspeite (NiCO3(s)) surface in NaCl solutions.

PubMed

Villegas-Jiménez, Adrián; Mucci, Alfonso; Pokrovsky, Oleg S; Schott, Jacques

2010-08-03

Gaspeite is a low reactivity, rhombohedral carbonate mineral and a suitable surrogate to investigate the surface properties of other more ubiquitous carbonate minerals, such as calcite, in aqueous solutions. In this study, the acid-base properties of the gaspeite surface were investigated over a pH range of 5 to 10 in NaCl solutions (0.001, 0.01, and 0.1 M) at near ambient conditions (25 +/- 3 degrees C and 1 atm) by means of conventional acidimetric and alkalimetric titration techniques and microelectrophoresis. Over the entire experimental pH range, surface protonation and electrokinetic mobility are strongly affected by the background electrolyte, leading to a significant decrease of the pH of zero net proton charge (PZNPC) and the pH of isoelectric point (pH(iep)) at increasing NaCl concentrations. This challenges the conventional idea that carbonate mineral surfaces are chemically inert to background electrolyte ions. Multiple sets of surface complexation reactions (i.e., ionization and ion adsorption) were formulated within the framework of three electrostatic models (CCM, BSM, and TLM) and their ability to simulate proton adsorption and electrokinetic data was evaluated. A one-site, 3-pK, constant capacitance surface complexation model (SCM) reproduces the proton adsorption data at all ionic strengths and qualitatively predicts the electrokinetic behavior of gaspeite suspensions. Nevertheless, the strong ionic strength dependence exhibited by the optimized SCM parameters reveals that the influence of the background electrolyte on the surface reactivity of gaspeite is not fully accounted for by conventional electrostatic and surface complexation models and suggests that future refinements to the underlying theories are warranted.

Structural evidence for the sorption of Ni(II) atoms on the edges of montmorillonite clay minerals: a polarized X-ray absorption fine structure study

NASA Astrophysics Data System (ADS)

Dähn, Rainer; Scheidegger, André M.; Manceau, Alain; Schlegel, Michel L.; Baeyens, Bart; Bradbury, Michael H.; Chateigner, Daniel

The nature of surface complexes formed on Ni uptake onto montmorillonite (a dioctahedral smectite) has been investigated over an extended time period by polarized extended X-ray absorption fine structure (P-EXAFS) spectroscopy. Self-supporting films of Ni-sorbed montmorillonite were prepared by contacting Ni and montmorillonite at pH 7.2, high ionic strength (0.3 M NaClO 4), and low Ni concentration ([Ni] initial = 19.9 μM) for 14- and 360-d reaction time. The resulting Ni concentration on the clay varied from 4 to 7 μmol/g. Quantitative texture analysis indicates that the montmorillonite particles were well orientated with respect to the plane of the film. The full width at half maximum of the orientation distribution of the c* axes of individual clay platelets about the normal to the film plane was 44.3° (14-d reaction time) and 47.1° (360-d reaction time). These values were used to correct the coordination numbers determined by P-EXAFS for texture effects. Ni K-edge P-EXAFS spectra were recorded at angles between the incident beam and the film normal equal to 10, 35, 55, and 80°. Spectral analysis led to the identification of three nearest cationic subshells containing 2.0 ± 0.5 Al at 3.0 Å and 2.0 ± 0.5 Si at 3.12 Å and 4.0 ± 0.5 Si at 3.26 Å. These distances are characteristic of edge-sharing linkages between Al and Ni octahedra and of corner-sharing linkages between Ni octahedra and Si tetrahedra, as in clay structures. The angular dependence of the Ni-Al and Ni-Si contributions indicates that Ni-Al pairs are oriented parallel to the film plane, whereas Ni-Si pairs are not. The study reveals the formation of Ni inner-sphere mononuclear surface complexes located at the edges of montmorillonite platelets and thus that heavy metals binding to edge sites is a possible sorption mechanism for dioctahedral smectites. Data analysis further suggests that either the number of neighboring Al atoms slightly increases from 1.6 to 2 or that the structural order of the observed surface complexes increases from 0.01 Å 2 to 0.005 Å 2 with increasing reaction time. On the basis of the low Ni-Al coordination numbers, it appears that over an extended reaction time period of 1 yr the diffusion of Ni atoms in the octahedral layer is not the major uptake mechanism of Ni onto montmorillonite.

New Cu (II), Co(II) and Ni(II) complexes of chalcone derivatives: Synthesis, X-ray crystal structure, electrochemical properties and DFT computational studies

NASA Astrophysics Data System (ADS)

Tabti, Salima; Djedouani, Amel; Aggoun, Djouhra; Warad, Ismail; Rahmouni, Samra; Romdhane, Samir; Fouzi, Hosni

2018-03-01

The reaction of nickel(II), copper(II) and cobalt(II) with 4-hydroxy-3-[(2E)-3-(1H-indol-3-yl)prop-2-enoyl]-6-methyl-2H-pyran-2-one (HL) leads to a series of new complexes: Ni(L)2(NH3), Cu(L)2(DMF)2 and Co(L)2(H2O). The crystal structure of the Cu(L)2(DMF)2 complex have been determined by X-ray diffraction methods. The Cu(II) lying on an inversion centre is coordinated to six oxygen atoms forming an octahedral elongated. Additionally, the electrochemical behavior of the metal complexes were investigated by cyclic voltammetry at a glassy carbon electrode (GC) in CH3CN solutions, showing the quasi-reversible redox process ascribed to the reduction of the MII/MI couples. The X-ray single crystal structure data of the complex was matched excellently with the optimized monomer structure of the desired compound; Hirschfeld surface analysis supported the packed crystal lattice 3D network intermolecular forces. HOMO/LUMO energy level and the global reactivity descriptors quantum parameters are also calculated. The electrophilic and nucleophilic potions in the complex surface are theoretically evaluated by molecular electrostatic potential and Mulliken atomic charges analysis.

Co-complexes derived from alkene insertion to alkyne-dicobaltpentacarbonyl complexes: insight into the regioselectivity of pauson-khand reactions of cyclopropenes.

PubMed

Pallerla, Mahesh K; Yap, Glenn P A; Fox, Joseph M

2008-08-15

Described are the X-ray crystallographic and spectral properties of Co-complexes that were isolated from two Pauson-Khand reactions of chiral cyclopropenes. These are the first examples of isolated Co-complexes derived from the putative alkene-insertion intermediates of Pauson-Khand reactions. The binuclear Co-complexes are coordinated to mu-bonded, five-carbon "flyover" carbene ligands. It is proposed that the complexes result from cyclopropane fragmentation subsequent to alkene insertion. The observation of these metal complexes provides a rationale for the origin of regioselectivity in Pauson-Khand reactions of cyclopropenes.

Surface interactions on hydrogel contact lenses: scanning electron microscopy (SEM).

PubMed

Hart, D E

1987-12-01

SEM was used to visualize tear-film/hydrogel polymer surface interactions. Lenses were preserved by fixation including a quaternary ammonium complex to aid in mucin preservation. In less than 2 weeks of continuous wear the anterior surface was completely coated, yet the coating was absent from the posterior lens surface. Tear-film break-up over the deposited lens surface, combined with degradation and deformation at the polymer surface boundary, as well as entrapment of moieties within the polymer matrix, all occurred. These are the likely culprits which can contribute to adverse reactions as well as cause light scatter and diminished vision. Lenses removed directly from the eyes of patients suffering with different forms of conjunctivitis were obtained. Bacterial and viral conjunctivitis can induce a microbially contaminated as well as a heavily deformed and deposited lens. Viable and intact microbes were not typically observed in the mucoprotein layer of hydrogel contact lenses.

Surface Immobilization of Molecular Electrocatalysts for Energy Conversion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bullock, R. Morris; Das, Atanu K.; Appel, Aaron M.

2017-03-22

Electrocatalysts are critically important for a secure energy future, as they facilitate the conversion between electrical energy and chemical energy. Molecular catalysts offer precise control of their structure, and the ability to modify the substituents to understand structure-reactivity relationships that are more difficult to achieve with heterogeneous catalysts. Molecular electrocatalysts can be immobilized on surfaces by covalent bonds or through non-covalent interactions. Advantages of surface immobilization include the need for less catalyst, avoidance of bimolecular decomposition pathways, and easier determination of catalyst lifetime. Copper-catalyzed click reactions are often used to form covalent bonds to surfaces, and pi-pi stacking of pyrenemore » substituents appended to the ligand of a molecular complex is a frequently used method to achieve non-covalent surface immobilization. This mini-review highlights surface confinement of molecular electrocatalysts for reduction of O2, oxidation of H2O, production of H2, and reduction of CO2.« less

Reactions of Ground State Nitrogen Atoms N(4S) with Astrochemically-Relevant Molecules on Interstellar Dusts

NASA Astrophysics Data System (ADS)

Krim, Lahouari; Nourry, Sendres

2015-06-01

In the last few years, ambitious programs were launched to probe the interstellar medium always more accurately. One of the major challenges of these missions remains the detection of prebiotic compounds and the understanding of reaction pathways leading to their formation. These complex heterogeneous reactions mainly occur on icy dust grains, and their studies require the coupling of laboratory experiments mimicking the extreme conditions of extreme cold and dilute media. For that purpose, we have developed an original experimental approach that combine the study of heterogeneous reactions (by exposing neutral molecules adsorbed on ice to non-energetic radicals H, OH, N...) and a neon matrix isolation study at very low temperatures, which is of paramount importance to isolate and characterize highly reactive reaction intermediates. Such experimental approach has already provided answers to many questions raised about some astrochemically-relevant reactions occurring in the ground state on the surface of dust grain ices in dense molecular clouds. The aim of this new present work is to show the implication of ground state atomic nitrogen on hydrogen atom abstraction reactions from some astrochemically-relevant species, at very low temperatures (3K-20K), without providing any external energy. Under cryogenic temperatures and with high barrier heights, such reactions involving N(4S) nitrogen atoms should not occur spontaneously and require an initiating energy. However, the detection of some radicals species as byproducts, in our solid samples left in the dark for hours at 10K, proves that hydrogen abstraction reactions involving ground state N(4S) nitrogen atoms may occur in solid phase at cryogenic temperatures. Our results show the efficiency of radical species formation stemming from non-energetic N-atoms and astrochemically-relevant molecules. We will then discuss how such reactions, involving nitrogen atoms in their ground states, might be the first key step towards complex organic molecules production in the interstellar medium.

Research and Development in support of the Surface Chemistry Branch. Volume 1

DTIC Science & Technology

1988-06-01

reactions could occur in the melt and/or gas phase-and (2) formation of HCN from RDX pyrolysis followed by hydrolysis with atmospheric/RDX decomposition ...interest is the development of electrochemically active transition metal complexes for the catalytic conversion/ decomposition of dissolved gases, such...impregnated charcoals for the collection and catalytic decomposition of toxic vapors (2), and the evaluation of Navy shipboard environments (3). For the

Unified Microscopic-Macroscopic Monte Carlo Simulations of Complex Organic Molecule Chemistry in Cold Cores

NASA Astrophysics Data System (ADS)

Chang, Qiang; Herbst, Eric

2016-03-01

The recent discovery of methyl formate and dimethyl ether in the gas phase of cold cores with temperatures as cold as 10 K challenges our previous astrochemical models concerning the formation of complex organic molecules (COMs). The strong correlation between the abundances and distributions of methyl formate and dimethyl ether further shows that current astrochemical models may be missing important chemical processes in cold astronomical sources. We investigate a scenario in which COMs and the methoxy radical can be formed on dust grains via a so-called chain reaction mechanism, in a similar manner to CO2. A unified gas-grain microscopic-macroscopic Monte Carlo approach with both normal and interstitial sites for icy grain mantles is used to perform the chemical simulations. Reactive desorption with varying degrees of efficiency is included to enhance the nonthermal desorption of species formed on cold dust grains. In addition, varying degrees of efficiency for the surface formation of methoxy are also included. The observed abundances of a variety of organic molecules in cold cores can be reproduced in our models. The strong correlation between the abundances of methyl formate and dimethyl ether in cold cores can also be explained. Nondiffusive chemical reactions on dust grain surfaces may play a key role in the formation of some COMs.

Synchrotron speciation of silver and zinc oxide nanoparticles aged in a kaolin suspension.

PubMed

Scheckel, Kirk G; Luxton, Todd P; El Badawy, Amro M; Impellitteri, Christopher A; Tolaymat, Thabet M

2010-02-15

Assessments of the environmental fate and mobility of nanoparticles must consider the behavior of nanoparticles in relevant environmental systems that may result in speciation changes over time. Environmental conditions may act on nanoparticles to change their size, shape, and surface chemistry. Changing these basic characteristics of nanoparticles may result in a final reaction product that is significantly different than the initial nanomaterial. As such, basing long-term risk and toxicity on the initial properties of a nanomaterial may lead to erroneous conclusions if nanoparticles change upon release to the environment. The influence of aging on the speciation and chemical stability of silver and zinc oxide nanoparticles in kaolin suspensions was examined in batch reactors for up to 18 months. Silver nanoparticles remained unchanged in sodium nitrate suspensions; however, silver chloride was identified with the metallic silver nanoparticles in sodium chloride suspensions and may be attributed to an in situ silver chloride surface coating. Zinc oxide nanoparticles were rapidly converted via destabilization/dissolution mechanisms to Zn(2+) inner-sphere sorption complexes within 1 day of reaction and these sorption complexes were maintained through the 12 month aging processes. Chemical and physical alteration of nanomaterials in the environment must be examined to understand fate, mobility, and toxicology.

Rapid electron exchange between surface-exposed bacterial cytochromes and Fe(III) minerals

PubMed Central

White, Gaye F.; Shi, Zhi; Shi, Liang; Wang, Zheming; Dohnalkova, Alice C.; Marshall, Matthew J.; Fredrickson, James K.; Zachara, John M.; Butt, Julea N.; Richardson, David J.; Clarke, Thomas A.

2013-01-01

The mineral-respiring bacterium Shewanella oneidensis uses a protein complex, MtrCAB, composed of two decaheme cytochromes, MtrC and MtrA, brought together inside a transmembrane porin, MtrB, to transport electrons across the outer membrane to a variety of mineral-based electron acceptors. A proteoliposome system containing a pool of internalized electron carriers was used to investigate how the topology of the MtrCAB complex relates to its ability to transport electrons across a lipid bilayer to externally located Fe(III) oxides. With MtrA facing the interior and MtrC exposed on the outer surface of the phospholipid bilayer, the established in vivo orientation, electron transfer from the interior electron carrier pool through MtrCAB to solid-phase Fe(III) oxides was demonstrated. The rates were 103 times higher than those reported for reduction of goethite, hematite, and lepidocrocite by S. oneidensis, and the order of the reaction rates was consistent with those observed in S. oneidensis cultures. In contrast, established rates for single turnover reactions between purified MtrC and Fe(III) oxides were 103 times lower. By providing a continuous flow of electrons, the proteoliposome experiments demonstrate that conduction through MtrCAB directly to Fe(III) oxides is sufficient to support in vivo, anaerobic, solid-phase iron respiration. PMID:23538304

Dissolved Organic Matter Quality in a Shallow Aquifer of Bangladesh: Implications for Arsenic Mobility.

PubMed

Mladenov, Natalie; Zheng, Yan; Simone, Bailey; Bilinski, Theresa M; McKnight, Diane M; Nemergut, Diana; Radloff, Kathleen A; Rahman, M Moshiur; Ahmed, Kazi Matin

2015-09-15

In some high arsenic (As) groundwater systems, correlations are observed between dissolved organic matter (DOM) and As concentrations, but in other systems, such relationships are absent. The role of labile DOM as the main driver of microbial reductive dissolution is not sufficient to explain the variation in DOM-As relationships. Other processes that may also influence As mobility include complexation of As by dissolved humic substances, and competitive sorption and electron shuttling reactions mediated by humics. To evaluate such humic DOM influences, we characterized the optical properties of filtered surface water (n = 10) and groundwater (n = 24) samples spanning an age gradient in Araihazar, Bangladesh. Further, we analyzed large volume fulvic acid (FA) isolates (n = 6) for optical properties, C and N content, and (13)C NMR spectroscopic distribution. Old groundwater (>30 years old) contained primarily sediment-derived DOM and had significantly higher (p < 0.001) dissolved As concentration than groundwater that was younger than 5 years old. Younger groundwater had DOM spectroscopic signatures similar to surface water DOM and characteristic of a sewage pollution influence. Associations between dissolved As, iron (Fe), and FA concentration and fluorescence properties of isolated FA in this field study suggest that aromatic, terrestrially derived FAs promote As-Fe-FA complexation reactions that may enhance As mobility.

Reactions of methyl groups on a non-reducible metal oxide: The reaction of iodomethane on stoichiometric α-Cr 2O 3(0001)

DOE PAGES

Dong, Yujung; Brooks, John D.; Chen, Tsung-Liang; ...

2015-06-10

The reaction of iodomethane on the nearly stoichiometric α-Cr 2O 3(0001) surface produces gas phase ethylene, methane, and surface iodine adatoms. The reaction is first initiated by the dissociation of iodomethane into surface methyl fragments, -CH 3, and iodine adatoms. Methyl fragments bound at surface Cr cation sites undergo a rate-limiting dehydrogenation reaction to methylene, =CH 2. The methylene intermediates formed from methyl dehydrogenation can then undergo coupling reactions to produce ethylene via two principle reaction pathways: (1) direct coupling of methylene and (2) methylene insertion into the methyl surface bond to form surface ethyl groups which undergo β-H eliminationmore » to produce ethylene. The liberated hydrogen also combines with methyl groups to form methane. Iodine adatoms from the dissociation of iodomethane deactivate the surface by simple site blocking of the surface Cr 3+ cations.« less

Minimum reaction network necessary to describe Ar/CF4 plasma etch

NASA Astrophysics Data System (ADS)

Helpert, Sofia; Chopra, Meghali; Bonnecaze, Roger T.

2018-03-01

Predicting the etch and deposition profiles created using plasma processes is challenging due to the complexity of plasma discharges and plasma-surface interactions. Volume-averaged global models allow for efficient prediction of important processing parameters and provide a means to quickly determine the effect of a variety of process inputs on the plasma discharge. However, global models are limited based on simplifying assumptions to describe the chemical reaction network. Here a database of 128 reactions is compiled and their corresponding rate constants collected from 24 sources for an Ar/CF4 plasma using the platform RODEo (Recipe Optimization for Deposition and Etching). Six different reaction sets were tested which employed anywhere from 12 to all 128 reactions to evaluate the impact of the reaction database on particle species densities and electron temperature. Because many the reactions used in our database had conflicting rate constants as reported in literature, we also present a method to deal with those uncertainties when constructing the model which includes weighting each reaction rate and filtering outliers. By analyzing the link between a reaction's rate constant and its impact on the predicted plasma densities and electron temperatures, we determine the conditions at which a reaction is deemed necessary to the plasma model. The results of this study provide a foundation for determining which minimal set of reactions must be included in the reaction set of the plasma model.

Chiral SiO2 and Ag@SiO2 Materials Templated by Complexes Consisting of Comblike Polyethyleneimine and Tartaric Acid.

PubMed

Yao, Dong-Dong; Murata, Hiroki; Tsunega, Seiji; Jin, Ren-Hua

2015-10-26

A facile avenue to fabricate micrometer-sized chiral (L-, D-) and meso-like (dl-) SiO2 materials with unique structures by using crystalline complexes (cPEI/tart), composed of comblike polyethyleneimine (cPEI) and L-, D-, or dl-tartaric acid, respectively, as catalytic templates is reported. Interestingly, both chiral crystalline complexes appeared as regularly left- and right-twisted bundle structures about 10 μm in length and about 5 μm in diameter, whereas the dl-form occurred as circular structures with about 10 μm diameter. Subsequently, SiO2 @cPEI/tart hybrids with high silica content (>55.0 wt %) were prepared by stirring a mixture containing tetramethoxysilane (TMOS) and the aggregates of the crystalline complexes in water. The chiral SiO2 hybrids and calcined chiral SiO2 showed very strong CD signals and a nanofiber-based morphology on their surface, whereas dl-SiO2 showed no CD activity and a nanosheet-packed disklike shape. Furthermore, metallic silver nanoparticles (Ag NPs) were encapsulated in each silica hybrid to obtain chiral (D and L forms) and meso-like (dl form) Ag@SiO2 composites. Also, the reaction between L-cysteine (Lcys) and these Ag@SiO2 composites was preliminarily investigated. Only chiral L- and D-Ag@SiO2 composites promoted the reaction between Lcys and Ag NPs to produce a molecular [Ag-Lcys]n complex with remarkable exciton chirality, whereas the reaction hardly occurred in the case of meso-like (dl-) Ag@SiO2 composite. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Binding and Energetics of Electron Transfer between an Artificial Four-Helix Mn-Protein and Reaction Centers from Rhodobacter sphaeroides.

PubMed

Espiritu, Eduardo; Olson, Tien L; Williams, JoAnn C; Allen, James P

2017-12-12

The ability of an artificial four-helix bundle Mn-protein, P1, to bind and transfer an electron to photosynthetic reaction centers from the purple bacterium Rhodobacter sphaeroides was characterized using optical spectroscopy. Upon illumination of reaction centers, an electron is transferred from P, the bacteriochlorophyll dimer, to Q A , the primary electron acceptor. The P1 Mn-protein can bind to the reaction center and reduce the oxidized bacteriochlorophyll dimer, P + , with a dissociation constant of 1.2 μM at pH 9.4, comparable to the binding constant of c-type cytochromes. Amino acid substitutions of surface residues on the Mn-protein resulted in increases in the dissociation constant to 8.3 μM. The extent of reduction of P + by the P1 Mn-protein was dependent on the P/P + midpoint potential and the pH. Analysis of the free energy difference yielded a midpoint potential of approximately 635 mV at pH 9.4 for the Mn cofactor of the P1 Mn-protein, a value similar to those found for other Mn cofactors in proteins. The linear dependence of -56 mV/pH is consistent with one proton being released upon Mn oxidation, allowing the complex to maintain overall charge neutrality. These outcomes demonstrate the feasibility of designing four-helix bundles and other artificial metalloproteins to bind and transfer electrons to bacterial reaction centers and establish the usefulness of this system as a platform for designing sites to bind novel metal cofactors capable of performing complex oxidation-reduction reactions.

Modeling Non-Steady Isotopologue and Isotopomer Speciation and Fractionation during Denitrification in Soils

NASA Astrophysics Data System (ADS)

Maggi, F.; Riley, W. J.

2009-12-01

The composition and location of 15N atoms on N2O isotopomers and isotopologues during isotope speciation has been used to characterize soil biological N cycling and N2O surface emissions. Although there exist few experimental observations, no attempt has been made to model N2O isotopomer speciation. The mathematical treatment of biological kinetic reactions in isotopic applications normally makes use of first-order and quasi steady-state complexation assumptions without taking into account changes in enzyme concentration, reaction stoichiometry, and isotopologue and isotopomer speciation. When multiatomic isotopically-labeled reactants are used in a multi-molecurar reaction, these assumptions may fail since they always lead to a constant fractionation factor and cannot describe speciation of isotopologues and isotopomers. We have developed a mathematical framework that is capable of describing isotopologue and isotopmer speciation and fractionation under the assumption of non-steady complexation during biological kinetic reactions that overcome the limitations mentioned above. This framework was applied to a case study of non-steady (variable and inverse) isotopic effects observed during N2O production and consumption in soils. Our mathematical treatment has led to generalized kinetic equations which replicate experimental observations with high accuracy and help interpret non-steady isotopic effects and isotopologue and isotopomer speciation. The kinetic equations introduced and applied here have general validity in describing isotopic effects in any biochemical reactions by considering: changing enzyme concentrations, mass and isotope conservation, and reaction stoichiometry. The equations also describe speciation of any isotopologue and isotopomer product from any isotopologue and isotopmer reactant.

Development of Surface Complexation Models of Cr(VI) Adsorption on Soils, Sediments and Model Mixtures of Kaolinite, Montmorillonite, γ-Alumina, Hydrous Manganese and Ferric Oxides and Goethite

DOE Office of Scientific and Technical Information (OSTI.GOV)

Koretsky, Carla

Hexavalent chromium is a highly toxic contaminant that has been introduced into aquifers and shallow sediments and soils via many anthropogenic activities. Hexavalent chromium contamination is a problem or potential problem in the shallow subsurface at several DOE sites, including Hanford, Idaho National Laboratory, Los Alamos National Laboratory and the Oak Ridge Reservation (DOE, 2008). To accurately quantify the fate and transport of hexavalent chromium at DOE and other contaminated sites, robust geochemical models, capable of correctly predicting changes in chromium chemical form resulting from chemical reactions occurring in subsurface environments are needed. One important chemical reaction that may greatlymore » impact the bioavailability and mobility of hexavalent chromium in the subsurface is chemical binding to the surfaces of particulates, termed adsorption or surface complexation. Quantitative thermodynamic surface complexation models have been derived that can correctly calculate hexavalent chromium adsorption on well-characterized materials over ranges in subsurface conditions, such pH and salinity. However, models have not yet been developed for hexavalent chromium adsorption on many important constituents of natural soils and sediments, such as clay minerals. Furthermore, most of the existing thermodynamic models have been developed for relatively simple, single solid systems and have rarely been tested for the complex mixtures of solids present in real sediments and soils. In this study, the adsorption of hexavalent chromium was measured as a function of pH (3-10), salinity (0.001 to 0.1 M NaNO3), and partial pressure of carbon dioxide(0-5%) on a suite of naturally-occurring solids including goethite (FeOOH), hydrous manganese oxide (MnOOH), hydrous ferric oxide (Fe(OH)3), γ-alumina (Al2O3), kaolinite (Al2Si2O5(OH)4), and montmorillonite (Na3(Al, Mg)2Si4O10(OH)2-nH2O). The results show that all of these materials can bind substantial quantities of hexavalent chromium, especially at low pH. Unexpectedly, experiments with the clay minerals kaolinite and montmorillonite suggest that hexavalent chromium may interact with these solids over much longer periods of time than expected. Furthermore, hexavalent chromium may irreversibly bind to these solids, perhaps because of oxidation-reduction reactions occurring on the surfaces of the clay minerals. More work should be done to investigate and quantify these chemical reactions. Experiments conducted with mixtures of goethite, hydrous manganese oxide, hydrous ferric oxide, γ-alumina, montmorillonite and kaolinite demonstrate that it is possible to correctly predict hexavalent chromium binding in the presence of multiple minerals using thermodynamic models derived for the simpler systems. Further, these models suggest that of the six solid considered in this study, goethite is typically the solid to which most of the hexavalent chromium will bind. Experiments completed with organic-rich and organic-poor natural sediments demonstrate that in organic-rich substrates, organic matter is likely to control uptake of the hexavalent chromium. The models derived and tested in this study for hexavalent chromium binding to γ-alumina, hydrous manganese oxide, goethite, hydrous ferric oxide and clay minerals can be used to better predict changes in hexavalent chromium bioavailability and mobility in contaminated sediments and soils.« less

Kinetics studies of the reactions of main fourth-period monocations (Ga+, Ge+, As+, and Se+) with methyl fluoride.

PubMed

Barrientos, Carmen; Rayón, Víctor Manuel; Largo, Antonio; Sordo, José Ángel; Redondo, Pilar

2013-08-22

Thermodynamics and kinetics theoretical studies on the gas-phase reactions of fluoromethane with main fourth-period monocations (Ga(+), Ge(+), As(+), and Se(+)) have been carried out. Density functional theory (in particular mPW1K functional) was employed in the description of the potential energy surfaces, and refinement of the energies were done at the CCSD(T) level. The reaction rate constants were estimated using variational/conventional microcanonical transition state theory. From a thermodynamic viewpoint, the fluorine abstraction product is predicted for Ga(+) and Ge(+), whereas for As(+) and Se(+) the elimination product, MCH2(+) (M = As, Se) + HF, is the preferred one. Nevertheless, the most favorable channel for the reactions of CH3F with Ga(+) and Se(+) cations present a net activation barrier. In the case of Ga(+), the reaction proceeds via an addition channel forming the adduct complex, CH3FGa(+), whereas for Se(+) no reaction is found, in agreement with the experiments. The predicted reaction rate constants are in reasonable good agreement with the experimental values available. Apart from the harpoon-like mechanism, our results suggest that an oxidative addition mechanism seems to play a relevant role.

Effects of synthetic cohesin-containing scaffold protein architecture on binding dockerin-enzyme fusions on the surface of Lactococcus lactis.

PubMed

Wieczorek, Andrew S; Martin, Vincent J J

2012-12-15

The microbial synthesis of fuels, commodity chemicals, and bioactive compounds necessitates the assemblage of multiple enzyme activities to carry out sequential chemical reactions, often via substrate channeling by means of multi-domain or multi-enzyme complexes. Engineering the controlled incorporation of enzymes in recombinant protein complexes is therefore of interest. The cellulosome of Clostridium thermocellum is an extracellular enzyme complex that efficiently hydrolyzes crystalline cellulose. Enzymes interact with protein scaffolds via type 1 dockerin/cohesin interactions, while scaffolds in turn bind surface anchor proteins by means of type 2 dockerin/cohesin interactions, which demonstrate a different binding specificity than their type 1 counterparts. Recombinant chimeric scaffold proteins containing cohesins of different specificity allow binding of multiple enzymes to specific sites within an engineered complex. We report the successful display of engineered chimeric scaffold proteins containing both type 1 and type 2 cohesins on the surface of Lactococcus lactis cells. The chimeric scaffold proteins were able to form complexes with the Escherichia coli β-glucuronidase fused to either type 1 or type 2 dockerin, and differences in binding efficiencies were correlated with scaffold architecture. We used E. coli β-galactosidase, also fused to type 1 or type 2 dockerins, to demonstrate the targeted incorporation of two enzymes into the complexes. The simultaneous binding of enzyme pairs each containing a different dockerin resulted in bi-enzymatic complexes tethered to the cell surface. The sequential binding of the two enzymes yielded insights into parameters affecting assembly of the complex such as protein size and position within the scaffold. The spatial organization of enzymes into complexes is an important strategy for increasing the efficiency of biochemical pathways. In this study, chimeric protein scaffolds consisting of type 1 and type 2 cohesins anchored on the surface of L. lactis allowed for the controlled positioning of dockerin-fused reporter enzymes onto the scaffolds. By binding single enzymes or enzyme pairs to the scaffolds, our data also suggest that the size and relative positions of enzymes can affect the catalytic profiles of the resulting complexes. These insights will be of great value as we engineer more advanced scaffold-guided protein complexes to optimize biochemical pathways.

Potential for iron oxides to control metal releases in CO2 sequestration scenarios

USGS Publications Warehouse

Berger, P.M.; Roy, W.R.

2011-01-01

The potential for the release of metals into groundwater following the injection of carbon dioxide (CO2) into the subsurface during carbon sequestration projects remains an open research question. Changing the chemical composition of even the relatively deep formation brines during CO2 injection and storage may be of concern because of the recognized risks associated with the limited potential for leakage of CO2-impacted brine to the surface. Geochemical modeling allows for proactive evaluation of site geochemistry before CO2 injection takes place to predict whether the release of metals from iron oxides may occur in the reservoir. Geochemical modeling can also help evaluate potential changes in shallow aquifers were CO2 leakage to occur near the surface. In this study, we created three batch-reaction models that simulate chemical changes in groundwater resulting from the introduction of CO2 at two carbon sequestration sites operated by the Midwest Geological Sequestration Consortium (MGSC). In each of these models, we input the chemical composition of groundwater samples into React??, and equilibrated them with selected mineral phases and CO 2 at reservoir pressure and temperature. The model then simulated the kinetic reactions with other mineral phases over a period of up to 100 years. For two of the simulations, the water was also at equilibrium with iron oxide surface complexes. The first model simulated a recently completed enhanced oil recovery (EOR) project in south-central Illinois in which the MGSC injected into, and then produced CO2, from a sandstone oil reservoir. The MGSC afterwards periodically measured the brine chemistry from several wells in the reservoir for approximately two years. The sandstone contains a relatively small amount of iron oxide, and the batch simulation for the injection process showed detectable changes in several aqueous species that were attributable to changes in surface complexation sites. After using the batch reaction configuration to match measured geochemical changes due to CO2 injection, we modeled potential changes in groundwater chemistry at the Illinois Basin - Decatur Project (IBDP) site in Decatur, Illinois, USA. At the IBDP, the MGSC will inject 1 million tonnes of CO2 over the course of three years at a depth of about 2 km below the surface into the Mt. Simon Formation. Sections of the Mt. Simon Formation contain up to 10 percent iron oxide, and therefore surface complexes on iron oxides should play a major role in controlling brine chemistry. The batch simulation of this system showed a significant decrease in pH after the injection of CO2 with corresponding changes in brine chemistry resulting from both mineral precipitation/dissolution reactions and changes in the chemistry on iron oxide surfaces. To ensure the safety of shallow drinking water sources, there are several shallow monitoring wells at the IBDP that the MGSC samples regularly to determine baseline chemical concentrations. Knowing what geochemical parameters are most sensitive to CO2 disturbances allows us to focus monitoring efforts. Modeling a major influx of CO2 into the shallow groundwater allowed us to determine that were an introduction of CO2 to occur, the only immediate effect will be dolomite dissolution and calcite precipitation. ?? 2011 Published by Elsevier Ltd.

Development of sandwich-form biosensor to detect Mycobacterium tuberculosis complex in clinical sputum specimens.

PubMed

Shojaei, Taha Roodbar; Mohd Salleh, Mohamad Amran; Tabatabaei, Meisam; Ekrami, Alireza; Motallebi, Roya; Rahmani-Cherati, Tavoos; Hajalilou, Abdollah; Jorfi, Raheleh

2014-01-01

Mycobacterium tuberculosis, the causing agent of tuberculosis, comes second only after HIV on the list of infectious agents slaughtering many worldwide. Due to the limitations behind the conventional detection methods, it is therefore critical to develop new sensitive sensing systems capable of quick detection of the infectious agent. In the present study, the surface modified cadmium-telluride quantum dots and gold nanoparticles conjunct with two specific oligonucleotides against early secretory antigenic target 6 were used to develop a sandwich-form fluorescence resonance energy transfer-based biosensor to detect M. tuberculosis complex and differentiate M. tuberculosis and M. bovis Bacille Calmette-Guerin simultaneously. The sensitivity and specificity of the newly developed biosensor were 94.2% and 86.6%, respectively, while the sensitivity and specificity of polymerase chain reaction and nested polymerase chain reaction were considerably lower, 74.2%, 73.3% and 82.8%, 80%, respectively. The detection limits of the sandwich-form fluorescence resonance energy transfer-based biosensor were far lower (10 fg) than those of the polymerase chain reaction and nested polymerase chain reaction (100 fg). Although the cost of the developed nanobiosensor was slightly higher than those of the polymerase chain reaction-based techniques, its unique advantages in terms of turnaround time, higher sensitivity and specificity, as well as a 10-fold lower detection limit would clearly recommend this test as a more appropriate and cost-effective tool for large scale operations. Copyright © 2014 Elsevier Editora Ltda. All rights reserved.

Synthesis and luminescence properties of iridium(III) azide- and triazole-bisterpyridine complexes.

PubMed

Goldstein, Daniel C; Peterson, Joshua R; Cheng, Yuen Yap; Clady, Raphael G C; Schmidt, Timothy W; Thordarson, Pall

2013-07-26

We describe here the synthesis of azide-functionalised iridium(III) bisterpyridines using the "chemistry on the complex" strategy. The resulting azide-complexes are then used in the copper(I)-catalysed azide-alkyne Huisgen 1,3-dipolar cycloaddition "click chemistry" reaction to from the corresponding triazole-functionalised iridium(III) bisterpyridines. The photophysical characteristics, including lifetimes, of these compounds were also investigated. Interestingly, oxygen appears to have very little effect on the lifetime of these complexes in aqueous solutions. Unexpectedly, sodium ascorbate acid appears to quench the luminescence of triazole-functionalised iridium(III) bisterpyridines, but this effect can be reversed by the addition of copper(II) sulfate, which is known to oxidize ascorbate under aerobic conditions. The results demonstrate that iridium(III) bisterpyridines can be functionalized for use in "click chemistry" facilitating the use of these photophysically interesting complexes in the modification of polymers or surfaces, to highlight just two possible applications.

Co-complexes Derived from Alkene Insertion to Alkyne-dicobaltpentacarbonyl complexes: Insight into the Regioselectivity of Pauson-Khand Reactions of Cyclopropenes

PubMed Central

Pallerla, Mahesh K.; Yap, Glenn P. A.; Fox, Joseph M.

2009-01-01

Described are the X-ray crystallographic and spectral properties of Co-complexes that were isolated from two Pauson-Khand reactions of chiral cyclopropenes. These are the first examples of isolated Co-complexes derived from the putative alkene-insertion intermediates of Pauson-Khand reactions. The binuclear Co-complexes are coordinated to μ-bonded, five-carbon “flyover” carbene ligands. It is proposed that the complexes result from cyclopropane fragmentation subsequent to alkene insertion. The observation of these metal complexes provides a rationale for the origin of regioselectivity in Pauson-Khand reactions of cyclopropenes. PMID:18637694

Computational Studies of Candida Antarctica Lipase B to Test its Capability as a Starting Point to Redesign New Diels-Alderases

PubMed Central

Świderek, Katarzyna; Moliner, Vicent

2015-01-01

The design of new biocatalysts is a target that is receiving increasing attention. One of the most popular reactions in this regard is the Diels-Alder cycloaddition due to its applications in organic synthesis and the absence of efficient natural enzymes that catalyze it. In this paper, the possibilities of using the highly promiscuous Candida Antarctica lipase B (CALB) as a protein scaffold to re-design a Diels-Alderase has been explored by means of theoretical quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations. Free energy surfaces have been computed for two reactions in the wild-type and in several mutants with hybrid AM1/MM potentials with corrections at M06-2X/MM level. The study of the counterpart reactions in solution has allowed performing comparative analysis that render interesting conclusion. Since the dienophile anchors very well in the oxyanion hole of all tested protein variants, the slight electronic changes from reactant complex to the transition state suggest that mutations should be focused in favoring the formation of reactive conformations of reactant complex that, in turn, would reduce the energy barrier. PMID:26624234

Experiments Developed to Study Microgravity Smoldering Combustion

NASA Technical Reports Server (NTRS)

Vergilii, Franklin

2001-01-01

The overall objective of the Microgravity Smoldering Combustion (MSC) research program is to understand and predict smoldering combustion under normal and microgravity (near-zero-gravity) conditions to help prevent and control smolder-originated fires, in both environments. Smoldering is defined as a nonflaming, self-sustaining, propagating, exothermic surface reaction. If a material is sufficiently permeable, smoldering is not confined to its outer surface, but can propagate as a reaction wave through the interior of the material. The MSC program will accomplish its goals by conducting smolder experiments on the ground and in a space-based laboratory, and developing theoretical models of the process. Space-based experiments are necessary because smoldering is a very slow process and, consequently, its study in a microgravity environment requires extended periods of time that can only be achieved in space. Smoldering can occur in a variety of processes ranging from the smolder of porous insulating materials to underground coal combustion. Many materials can sustain smoldering, including wood, cloth, foams, tobacco, other dry organic materials, and charcoal. The ignition, propagation, transition to flaming, and extinction of the smolder reaction are controlled by complex, thermochemical mechanisms that are not well understood. As with many forms of combustion, gravity affects the availability of the oxidizer and the transport of heat, and therefore, the rate of combustion. The smoldering combustion of porous materials has been studied both experimentally and theoretically, usually in the context of fire safety. Smoldering encompasses a number of fundamental processes, including heat and mass transfer in a porous media; endothermic pyrolysis of combustible material; ignition, propagation, and extinction of heterogeneous exothermic reactions at the solid-gas pore interface; and the onset of gas phase reactions (flaming) from existing surface reactions. Smoldering presents a serious fire risk because the combustion can propagate slowly in a material's interior and go undetected for long periods of time. It typically yields a substantially higher conversion of fuel to toxic compounds than does flaming (though more slowly), and may undergo a sudden transition to flaming.

Realistic multisite lattice-gas modeling and KMC simulation of catalytic surface reactions: Kinetics and multiscale spatial behavior for CO-oxidation on metal (1 0 0) surfaces

NASA Astrophysics Data System (ADS)

Liu, Da-Jiang; Evans, James W.

2013-12-01

A realistic molecular-level description of catalytic reactions on single-crystal metal surfaces can be provided by stochastic multisite lattice-gas (msLG) models. This approach has general applicability, although in this report, we will focus on the example of CO-oxidation on the unreconstructed fcc metal (1 0 0) or M(1 0 0) surfaces of common catalyst metals M = Pd, Rh, Pt and Ir (i.e., avoiding regimes where Pt and Ir reconstruct). These models can capture the thermodynamics and kinetics of adsorbed layers for the individual reactants species, such as CO/M(1 0 0) and O/M(1 0 0), as well as the interaction and reaction between different reactant species in mixed adlayers, such as (CO + O)/M(1 0 0). The msLG models allow population of any of hollow, bridge, and top sites. This enables a more flexible and realistic description of adsorption and adlayer ordering, as well as of reaction configurations and configuration-dependent barriers. Adspecies adsorption and interaction energies, as well as barriers for various processes, constitute key model input. The choice of these energies is guided by experimental observations, as well as by extensive Density Functional Theory analysis. Model behavior is assessed via Kinetic Monte Carlo (KMC) simulation. We also address the simulation challenges and theoretical ramifications associated with very rapid diffusion and local equilibration of reactant adspecies such as CO. These msLG models are applied to describe adsorption, ordering, and temperature programmed desorption (TPD) for individual CO/M(1 0 0) and O/M(1 0 0) reactant adlayers. In addition, they are also applied to predict mixed (CO + O)/M(1 0 0) adlayer structure on the nanoscale, the complete bifurcation diagram for reactive steady-states under continuous flow conditions, temperature programmed reaction (TPR) spectra, and titration reactions for the CO-oxidation reaction. Extensive and reasonably successful comparison of model predictions is made with experimental data. Furthermore, we discuss the possible transition from traditional mean-field-type bistability and reaction kinetics for lower-pressure to multistability and enhanced fluctuation effects for moderate- or higher-pressure. Behavior in the latter regime reflects a stronger influence of adspecies interactions and also lower diffusivity in the higher-coverage mixed adlayer. We also analyze mesoscale spatiotemporal behavior including the propagation of reaction-diffusion fronts between bistable reactive and inactive states, and associated nucleation-mediated transitions between these states. This behavior is controlled by complex surface mass transport processes, specifically chemical diffusion in mixed reactant adlayers for which we provide a precise theoretical formulation. The msLG models together with an appropriate treatment of chemical diffusivity enable equation-free heterogeneous coupled lattice-gas (HCLG) simulations of spatiotemporal behavior. In addition, msLG + HCLG modeling can describe coverage variations across polycrystalline catalysts surfaces, pressure variations across catalyst surfaces in microreactors, and could be incorporated into a multiphysics framework to describe mass and heat transfer limitations for high-pressure catalysis.

Realistic multisite lattice-gas modeling and KMC simulation of catalytic surface reactions: Kinetics and multiscale spatial behavior for CO-oxidation on metal (100) surfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Dajiang; Evans, James W.

2013-12-01

A realistic molecular-level description of catalytic reactions on single-crystal metal surfaces can be provided by stochastic multisite lattice-gas (msLG) models. This approach has general applicability, although in this report, we will focus on the example of CO-oxidation on the unreconstructed fcc metal (100) or M(100) surfaces of common catalyst metals M = Pd, Rh, Pt and Ir (i.e., avoiding regimes where Pt and Ir reconstruct). These models can capture the thermodynamics and kinetics of adsorbed layers for the individual reactants species, such as CO/M(100) and O/M(100), as well as the interaction and reaction between different reactant species in mixed adlayers,more » such as (CO + O)/M(100). The msLG models allow population of any of hollow, bridge, and top sites. This enables a more flexible and realistic description of adsorption and adlayer ordering, as well as of reaction configurations and configuration-dependent barriers. Adspecies adsorption and interaction energies, as well as barriers for various processes, constitute key model input. The choice of these energies is guided by experimental observations, as well as by extensive Density Functional Theory analysis. Model behavior is assessed via Kinetic Monte Carlo (KMC) simulation. We also address the simulation challenges and theoretical ramifications associated with very rapid diffusion and local equilibration of reactant adspecies such as CO. These msLG models are applied to describe adsorption, ordering, and temperature programmed desorption (TPD) for individual CO/M(100) and O/M(100) reactant adlayers. In addition, they are also applied to predict mixed (CO + O)/M(100) adlayer structure on the nanoscale, the complete bifurcation diagram for reactive steady-states under continuous flow conditions, temperature programmed reaction (TPR) spectra, and titration reactions for the CO-oxidation reaction. Extensive and reasonably successful comparison of model predictions is made with experimental data. Furthermore, we discuss the possible transition from traditional mean-field-type bistability and reaction kinetics for lower-pressure to multistability and enhanced fluctuation effects for moderate- or higher-pressure. Behavior in the latter regime reflects a stronger influence of adspecies interactions and also lower diffusivity in the higher-coverage mixed adlayer. We also analyze mesoscale spatiotemporal behavior including the propagation of reaction diffusion fronts between bistable reactive and inactive states, and associated nucleation-mediated transitions between these states. This behavior is controlled by complex surface mass transport processes, specifically chemical diffusion in mixed reactant adlayers for which we provide a precise theoretical formulation. The msLG models together with an appropriate treatment of chemical diffusivity enable equation-free heterogeneous coupled lattice-gas (HCLG) simulations of spatiotemporal behavior. In addition, msLG + HCLG modeling can describe coverage variations across polycrystalline catalysts surfaces, pressure variations across catalyst surfaces in microreactors, and could be incorporated into a multiphysics framework to describe mass and heat transfer limitations for high-pressure catalysis. (C) 2013 Elsevier Ltd. All rights reserved.« less

Ab Initio Metadynamics Study of the VO2+/VO2+ Redox Reaction Mechanism at the Graphite Edge/Water Interface.

PubMed

Jiang, Zhen; Klyukin, Konstantin; Alexandrov, Vitaly

2018-06-20

Redox flow batteries (RFBs) are promising electrochemical energy storage systems, for which development is impeded by a poor understanding of redox reactions occurring at electrode/electrolyte interfaces. Even for the conventional all-vanadium RFB chemistry employing V 2+ /V 3+ and VO 2 + /VO 2+ couples, there is still no consensus about the reaction mechanism, electrode active sites, and rate-determining step. Herein, we perform Car-Parrinello molecular dynamics-based metadynamics simulations to unravel the mechanism of the VO 2 + /VO 2+ redox reaction in water at the oxygen-functionalized graphite (112̅0) edge surface serving as a representative carbon-based electrode. Our results suggest that during the battery discharge aqueous VO 2 + /VO 2+ species adsorb at the surface C-O groups as inner-sphere complexes, exhibiting faster adsorption/desorption kinetics than V 2+ /V 3+ , at least at low vanadium concentrations considered in our study. We find that this is because (i) VO 2 + /VO 2+ conversion does not involve the slow transfer of an oxygen atom, (ii) protonation of VO 2 + is spontaneous and coupled to interfacial electron transfer in acidic conditions to enable VO 2+ formation, and (iii) V 3+ found to be strongly bound to oxygen groups of the graphite surface features unfavorable desorption kinetics. In contrast, the reverse process taking place upon charging is expected to be more sluggish for the VO 2 + /VO 2+ redox couple because of both unfavorable deprotonation of the VO 2+ water ligands and adsorption/desorption kinetics.

Heterogeneous catalysis in complex, condensed reaction media

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cantu, David C.; Wang, Yang-Gang; Yoon, Yeohoon

Many reactions required for the upgrading of biomass into fuels and chemicals—hydrogenation, hydrodeoxygenation, hydrocracking—are ostensibly similar to those practiced in the upgrading of petroleum into fuels. But, repurposing hydroprocessing catalysts from refinery operations to treat bio-oil has proved to be unsatisfactory. New catalysts are needed because the composition of the biogenic reactants differs from that of petroleum-derived feedstocks (e.g. the low concentration of sulfur in cellulose-derived biomass precludes use of metal sulfide catalysts unless sulfur is added to the reaction stream). New processes are needed because bio-oils oligomerize rapidly, forming intractable coke and “gunk”, at temperatures so low that themore » desired upgrading reactions are impractically slow, and so low that the bio-oil upgrading must be handled as a condensed fluid. Ideally, the new catalysts and processes would exploit the properties of the multiple phases present in condensed bio-oil, notably the polarizability and structure of the fluid near a catalyst’s surface in the cybotactic region. The results of preliminary modeling of the cybotactic region of different catalyst surfaces in the hydrogenation of phenol suggest that Pd catalysts supported on hydrophilic surfaces are more active than catalysts based on lipophilic supports because the former serve to enhance the concentration of the phenol in the vicinity of the Pd. The effect stems from thermodynamics, not the rate of mass transport. This work was supported by the US Department of Energy, Office of Energy Efficiency and Renewable Energy, Bioenergy Technologies Office. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Shizhong; White, Michael G.; Liu, Ping

Here, we report a detailed mechanistic study of the oxygen reduction reaction (ORR) on Pt(111) in alkaline solution, combining density functional theory and kinetic Monte Carlo simulations. A complex reaction network including four possible pathways via either 2e – or 4e – transfer is established and is able to reproduce the experimental measured polarization curve at both low- and high-potential regions. Our results show that it is essential to account for solvation by water and the dynamic coverage of *OH to describe the reaction kinetics well. In addition, a chemisorbed water (*H 2O)-mediated mechanism including 4e – transfers is identified,more » where the reduction steps via *H 2O on the surface are potential-independent and only the final removal of *OH from the surface in the form of OH –(aq) contributes to the current. For the ORR in alkaline solutions, such a mechanism is more competitive than the associative and dissociative mechanisms typically used to describe the ORR in acid solution. Finally, *OH and **O 2 intermediates are found to be critically important for tuning the ORR activity of Pt in alkaline solution. To enhance the activity, the binding of Pt should be tuned in such a way that *OH binding is weak enough to release more surface sites under working conditions, while **O 2 binding is strong enough to enable the ORR via the 4e – transfer mechanism.« less

[The structure of the gastric mucosa of the llamas (Lama guanocoe and Lama lamae). I. Forestomach].

PubMed

Luciano, L; Voss-Wermbter, G; Behnke, M; von Engelhardt, W; Reale, E

1979-01-01

The mucous membrane of the first and second compartments (ventral regions) as well as of the third compartment of Lama guanacoe and Lama lamae stomach shows tubular glands opening into pits. Below the surface epithelium blood capillaries of the fenestrated type form a regular network, each mesh of which surrounds a gastric pit. From a morphological point of view (thin section and freeze-fracture replicas) the columnar cells of the surface epithelium and those of the pits closest to the capillaries are largely similar to the epithelial cells of the rabbit gallbladder. This similarity suggests that at the level of the columnar cells sodium-dependent water reabsorption occurs. This reabsorption has already been demonstrated in the abovementioned compartments by physiological methods. The surface and foveolae epithelial cells as well as some cells of the tubular glands have a secretory function. Their secretory granules contain mucosubstances, as indicated by light-(PAS- and Alcian blue reactions) and electron microscopic (PA-TCH-Ag-reaction) histochemistry. The secretory granules originate from the Golgi complex which shows a positive histochemical reaction in its innermost sacculi at the electron microscope level. Endocrine cells (s. second part of this investigation) are rare. The mucosal membrane of each muscular lip separating the glandular sacs in the first compartment shows a stratified, not keratinized, squamous epithelium.

Binuclear cyclometalated organoplatinum complexes containing 1,1'-bis(diphenylphosphino)ferrocene as spacer ligand: kinetics and mechanism of MeI oxidative addition.

PubMed

Jamali, Sirous; Nabavizadeh, S Masoud; Rashidi, Mehdi

2008-06-16

The binuclear complex [Pt2Me2(ppy)2(mu-dppf)], 1, in which ppy = deprotonated 2-phenylpyridyl and dppf = 1,1'-bis(diphenylphosphino)ferrocene, was synthesized by the reaction of [PtMe(SMe2)(ppy)] with 0.5 equiv of dppf at room temperature. In this reaction when 1 equiv of dppf was used, the dppf chelating complex 2, [PtMe(dppf)(ppy-kappa1C)], was obtained. The reaction of Pt(II)-Pt(II) complex 1 with excess MeI gave the Pt(IV)-Pt(IV) complex [Pt2I2Me4(ppy)2(mu-dppf)], 3. When the reaction was performed with 1 equiv of MeI, a mixture containing unreacted complex 1, a mixed-valence Pt(II)-Pt(IV) complex [PtMe(ppy)(mu-dppf)PtIMe2(ppy)], 4, and complex 3 was obtained. In a comparative study, the reaction of [PtMe(SMe2)(ppy)] with 1 equiv of monodentate phosphine PPh3 gave [PtMe(ppy)(PPh3)], A. MeI was reacted with A to give the platinum(IV) complex [PtMe2I(ppy)(PPh3)], C. All the complexes were fully characterized using multinuclear (1H, 31P, 13C, and 195Pt) NMR spectroscopy, and complex 2 was further identified by single crystal X-ray structure determination. The reaction of binuclear Pt(II)-Pt(II) complex 1 with excess MeI was monitored by low temperature 31P NMR spectroscopy and further by 1H NMR spectroscopy, and the kinetics of the reaction was studied by UV-vis spectroscopy. On the basis of the data, a mechanism has been suggested for the reaction which overall involved stepwise oxidative addition of MeI to the two Pt(II) centers. In this suggested mechanism, the reaction proceeded through a number of Pt(II)-Pt(IV) and Pt(IV)-Pt(IV) intermediates. Although MeI in each step was trans oxidatively added to one of the Pt(II) centers, further trans to cis isomerizations of Me and I groups were also identified. A comparative kinetic study of the reaction of monomeric platinum(II) complex A with MeI was also performed. The rate of reaction of MeI with complex 1 was some 3.5 times faster than that with complex A, indicating that dppf in the complex 1, as compared with PPh 3 in the complex A, has significantly enhanced the electron richness of the platinum centers.

Pt-Mechanistic Study of the β-Hydrogen Elimination from Organoplatinum(II) Enolate Complexes

PubMed Central

Alexanian, Erik J.; Hartwig, John F.

2010-01-01

A detailed mechanistic investigation of the thermal reactions of a series of bisphosphine alkylplatinum(II) enolate complexes is reported. The reactions of methylplatinum enolate complexes in the presence of added phosphine form methane and either free or coordinated enone, depending on the steric properties of the enone. Kinetic studies were conducted to determine the relationship between the rates and mechanism of β-hydrogen elimination from enolate complexes and the rates and mechanism of β-hydrogen elimination from alkyl complexes. The rates of reactions of the enolates were inversely dependent on the concentration of added phosphine, indicating that β-hydrogen elimination from the enolate complexes occurs after reversible dissociation of a phosphine. A normal, primary kinetic isotope effect was measured, and this effect was consistent with rate-limiting β-hydrogen elimination or C-H bond-forming reductive elimination to form methane. Reactions of substituted enolate complexes were also studied to determine the effect of the steric and electronic properties of the enolate complexes on the rates of β-hydrogen elimination. These studies showed that reactions of the alkylplatinum enolate complexes were retarded by electron-withdrawing substituents on the enolate and that reactions of enolate complexes possessing alkyl substituents at the β-position occurred at rates that were similar to those of complexes lacking alkyl substituents at this position. Despite the trend in electronic effects on the rates of reactions of enolate complexes and the substantial electronic differences between an enolate and an alkyl ligand, the rates of decomposition of the enolate complexes were similar to those of the analogous alkyl complexes. To the extent that the rates of reaction of the two types of complex are different, those involving β-hydrogen elimination from the enolate ligand were faster. A difference between the identity of the rate-determining step for decomposition of the two classes of complexes and an effect of stereochemistry on the selectivity for β-hydrogen elimination are possible origins of the observed phenomena. PMID:18954048

The Development and Study of Surface Bound Ruthenium Organometallic Complexes

NASA Astrophysics Data System (ADS)

Abbott, Geoffrey Reuben

The focus of this project has been on the use of mono-diimine ruthenium organometallic complexes, of the general structure [H(Ru)(CO)(L)2(L') 2][PF6] (L=PPh3, DPPENE and L'=Bpy, DcBpy, MBpyC, Phen, AminoPhen) bound to surfaces as luminescent probes. Both biological and inorganic/organic hybrid surfaces have been studied. The complexes were characterized both bound and unbound using standard analytical techniques such as NMR, IR and X-ray crystallography, as well as through several photophysical methods as well. Initially the study focused on how the photophyscial properties of the complexes were affected by incorporation into biological membranes. It was found that by conjugating the probes to a more rigid cholesterol moiety that luminescence was conserved, compared to conjugation with a far more flexible lipid moiety, where luminescence was either lost or reduced. Both the cholesterol and lipid conjugates were able to insert into a lipid membrane, and in the more rigid environment some of the lipid conjugates regained some of their luminescence, but often blue shifted and reduced, depending on the conjugation site. Silica Polyamine Composites (SPCs) were a hybrid material developed in the Rosenberg Lab as useful metal separation materials, that could be easily modified, and had several benefits over current commercially available polymers, or inorganic materials. These SPCs also provided an opportunity for the development of a heterogeneous platform for luminescent complexes as either catalysts or sensors. Upon binding of the luminescent Ru complexes to the surface no loss, or major change in luminescence was seen, however, when bound to the rigid surface a significant increase in excited state lifetime was measured. It is likely that through binding and interacting with the surface that the complexes lost non-radiative decay pathways, resulting in the increase in lifetime, however, these interactions do not seem to affect the energy level of the MLCT band in a large way. With a better understanding of the effects of surface binding on the complexes, the study turned to possible applications, as either sensors or catalysts. Recently the bound complexes have been found to be very useful as toxic metal sensors, as the free amines left on the surface could bind toxic metal ions in close proximity leading to either a quenching or enhancement of the luminescence of the complexes, depending on the metal ion. This process was determined to be a static process, requiring the toxic metal to remain bound to the surface in order to affect the luminescence of the Ru complex. The quenching is thought to be due to a metal-centered electron-transfer reaction, in which the excited-state electron is transferred from the Ru to the toxic metal, but relaxes back to the Ru center. The enhancement of luminescence is due to the external heavy-atom effect, in which heavier atoms mixes MLCT singlet state with the triplet state through spin-orbit coupling.

Development of a Self-Consistent Model of Plutonium Sorption: Quantification of Sorption Enthalpy and Ligand-Promoted Dissolution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Powell, Brian; Kaplan, Daniel I; Arai, Yuji

2016-12-29

This university lead SBR project is a collaboration lead by Dr. Brian Powell (Clemson University) with co-principal investigators Dan Kaplan (Savannah River National Laboratory), Yuji Arai (presently at the University of Illinois), Udo Becker (U of Michigan) and Rod Ewing (presently at Stanford University). Hypothesis: The underlying hypothesis of this work is that strong interactions of plutonium with mineral surfaces are due to formation of inner sphere complexes with a limited number of high-energy surface sites, which results in sorption hysteresis where Pu(IV) is the predominant sorbed oxidation state. The energetic favorability of the Pu(IV) surface complex is strongly influencedmore » by positive sorption entropies, which are mechanistically driven by displacement of solvating water molecules from the actinide and mineral surface during sorption. Objectives: The overarching objective of this work is to examine Pu(IV) and Pu(V) sorption to pure metal (oxyhydr)oxide minerals and sediments using variable temperature batch sorption, X-ray absorption spectroscopy, electron microscopy, and quantum-mechanical and empirical-potential calculations. The data will be compiled into a self-consistent surface complexation model. The novelty of this effort lies largely in the manner the information from these measurements and calculations will be combined into a model that will be used to evaluate the thermodynamics of plutonium sorption reactions as well as predict sorption of plutonium to sediments from DOE sites using a component additivity approach.« less

On the atmospheric oxidation of liquid toluene.

PubMed

Pritchard, Huw O

2006-10-21

This communication presents preliminary computational results on the interaction between triplet (3Sigma) and singlet (1Sigma, 1Delta) oxygen molecules with toluene. All three oxygen species form very weak complexes with toluene and all also appear capable of abstracting a benzylic hydrogen atom to form the HO2 radical. Reaction with singlet molecular oxygen does not convincingly explain the formation of benzylhydroperoxide from toluene residues stored over a long time in brown glass bottles, and it is speculated that this may be a surface-catalysed photochemical reaction. The possible involvement of singlet oxygen molecules in the spontaneous ignition of tyre rubber and of soft coal is discussed briefly and the need for new experimental studies is stressed.

Estimation of the reactive mineral surface area during CO2-rich fluid-rock interaction: the influence of neogenic phases

NASA Astrophysics Data System (ADS)

Scislewski, A.; Zuddas, P.

2010-12-01

Mineral dissolution and precipitation reactions actively participate to control fluid chemistry during water-rock interaction. It is however, difficult to estimate and well normalize bulk reaction rates if the mineral surface area exposed to the aqueous solution and effectively participating on the reactions is unknown. We evaluated the changing of the reactive mineral surface area during the interaction between CO2-rich fluids and Albitite/Granitoid rocks (similar mineralogy but different abundances), reacting under flow-through conditions. Our methodology, adopting an inverse modeling approach, is based on the estimation of dissolution rate and reactive surface area of the different minerals participating in the reactions by the reconstruction the chemical evolution of the interacting fluids. The irreversible mass-transfer processes is defined by a fractional degree of advancement, while calculations were carried out for Albite, Microcline, Biotite and Calcite assuming that the ion activity of dissolved silica and aluminium ions was limited by the equilibrium with quartz and kaolinite. Irrespective of the mineral abundance in granite and albitite, we found that mineral dissolution rates did not change significantly in the investigated range of time where output solution’s pH remained in the range between 6 and 8, indicating that the observed variation in fluid composition depends not on pH but rather on the variation of the parent mineral’s reactive surface area. We found that the reactive surface area of Albite varied by more than 2 orders of magnitude, while Microcline, Calcite and Biotite surface areas changed by 1-2 orders of magnitude. We propose that parent mineral chemical heterogeneity and, particularly, the stability of secondary mineral phases may explain the observed variation of the reactive surface area of the minerals. Formation of coatings at the dissolving parent mineral surfaces significantly reduced the amount of surface available to react with CO2-rich fluids, decreasing the effective reactive surface area. Predictive models of CO2 sequestration under geological conditions should take into account the inhibiting role of surface coating formation. The CO2 rich fluid-rock interactions may also have significant consequences on metal mobilization. Our results indicated that the formation of stable carbonate complexes enhances the solubility of uranium minerals of both albitite and granite, facilitating the U(IV) oxidation, and limiting the extent of uranium adsorption onto particles in oxidized waters. This clearly produces an increase of the uranium mobility with significant consequences for the environment.

Nearside-farside, local angular momentum and resummation theories: Useful tools for understanding the dynamics of complex-mode reactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hankel, Marlies, E-mail: m.hankel@uq.edu.au, E-mail: j.n.l.connor@manchester.ac.uk; Connor, J. N. L., E-mail: m.hankel@uq.edu.au, E-mail: j.n.l.connor@manchester.ac.uk

2015-07-15

A valuable tool for understanding the dynamics of direct reactions is Nearside-Farside (NF) scattering theory. It makes a decomposition of the (resummed) partial wave series for the scattering amplitude, both for the differential cross section (DCS) and the Local Angular Momentum (LAM). This paper makes the first combined application of these techniques to complex-mode reactions. We ask if NF theory is a useful tool for their identification, in particular, can it distinguish complex-mode from direct-mode reactions? We also ask whether NF theory can identify NF interference oscillations in the full DCSs of complex-mode reactions. Our investigation exploits the fact thatmore » accurate quantum scattering matrix elements have recently become available for complex-mode reactions. We first apply NF theory to two simple models for the scattering amplitude of a complex-mode reaction: One involves a single Legendre polynomial; the other involves a single Legendre function of the first kind, whose form is suggested by complex angular momentum theory. We then study, at fixed translational energies, four state-to-state complex-mode reactions. They are: S({sup 1}D) + HD → SH + D, S({sup 1}D) + DH → SD + H, N({sup 2}D) +H{sub 2} → NH + H, and H{sup +} + D{sub 2} → HD + D{sup +}. We compare the NF results for the DCSs and LAMs with those for a state-to-state direct reaction, namely, F + H{sub 2} → FH + H. We demonstrate that NF theory is a valuable tool for identifying and analyzing the dynamics of complex-mode reactions.« less

Interrogation of bimetallic particle oxidation in three dimensions at the nanoscale

PubMed Central

Han, Lili; Meng, Qingping; Wang, Deli; Zhu, Yimei; Wang, Jie; Du, Xiwen; Stach, Eric A.; Xin, Huolin L.

2016-01-01

An understanding of bimetallic alloy oxidation is key to the design of hollow-structured binary oxides and the optimization of their catalytic performance. However, one roadblock encountered in studying these binary oxide systems is the difficulty in describing the heterogeneities that occur in both structure and chemistry as a function of reaction coordinate. This is due to the complexity of the three-dimensional mosaic patterns that occur in these heterogeneous binary systems. By combining real-time imaging and chemical-sensitive electron tomography, we show that it is possible to characterize these systems with simultaneous nanoscale and chemical detail. We find that there is oxidation-induced chemical segregation occurring on both external and internal surfaces. Additionally, there is another layer of complexity that occurs during the oxidation, namely that the morphology of the initial oxide surface can change the oxidation modality. This work characterizes the pathways that can control the morphology in binary oxide materials. PMID:27928998

Structure of tropinone reductase-II complexed with NADP+ and pseudotropine at 1.9 A resolution: implication for stereospecific substrate binding and catalysis.

PubMed

Yamashita, A; Kato, H; Wakatsuki, S; Tomizaki, T; Nakatsu, T; Nakajima, K; Hashimoto, T; Yamada, Y; Oda, J

1999-06-15

Tropinone reductase-II (TR-II) catalyzes the NADPH-dependent reduction of the carbonyl group of tropinone to a beta-hydroxyl group. The crystal structure of TR-II complexed with NADP+ and pseudotropine (psi-tropine) has been determined at 1.9 A resolution. A seven-residue peptide near the active site, disordered in the unliganded structure, is fixed in the ternary complex by participation of the cofactor and substrate binding. The psi-tropine molecule is bound in an orientation which satisfies the product configuration and the stereochemical arrangement toward the cofactor. The substrate binding site displays a complementarity to the bound substrate (psi-tropine) in its correct orientation. In addition, electrostatic interactions between the substrate and Glu156 seem to specify the binding position and orientation of the substrate. A comparison between the active sites in TR-II and TR-I shows that they provide different van der Waals surfaces and electrostatic features. These differences likely contribute to the correct binding mode of the substrates, which are in opposite orientations in TR-II and TR-I, and to different reaction stereospecificities. The active site structure in the TR-II ternary complex also suggests that the arrangement of the substrate, cofactor, and catalytic residues is stereoelectronically favorable for the reaction.

Electrifying model catalysts for understanding electrocatalytic reactions in liquid electrolytes.

PubMed

Faisal, Firas; Stumm, Corinna; Bertram, Manon; Waidhas, Fabian; Lykhach, Yaroslava; Cherevko, Serhiy; Xiang, Feifei; Ammon, Maximilian; Vorokhta, Mykhailo; Šmíd, Břetislav; Skála, Tomáš; Tsud, Nataliya; Neitzel, Armin; Beranová, Klára; Prince, Kevin C; Geiger, Simon; Kasian, Olga; Wähler, Tobias; Schuster, Ralf; Schneider, M Alexander; Matolín, Vladimír; Mayrhofer, Karl J J; Brummel, Olaf; Libuda, Jörg

2018-07-01

Electrocatalysis is at the heart of our future transition to a renewable energy system. Most energy storage and conversion technologies for renewables rely on electrocatalytic processes and, with increasing availability of cheap electrical energy from renewables, chemical production will witness electrification in the near future 1-3 . However, our fundamental understanding of electrocatalysis lags behind the field of classical heterogeneous catalysis that has been the dominating chemical technology for a long time. Here, we describe a new strategy to advance fundamental studies on electrocatalytic materials. We propose to 'electrify' complex oxide-based model catalysts made by surface science methods to explore electrocatalytic reactions in liquid electrolytes. We demonstrate the feasibility of this concept by transferring an atomically defined platinum/cobalt oxide model catalyst into the electrochemical environment while preserving its atomic surface structure. Using this approach, we explore particle size effects and identify hitherto unknown metal-support interactions that stabilize oxidized platinum at the nanoparticle interface. The metal-support interactions open a new synergistic reaction pathway that involves both metallic and oxidized platinum. Our results illustrate the potential of the concept, which makes available a systematic approach to build atomically defined model electrodes for fundamental electrocatalytic studies.

Effects of alpha-amylase reaction mechanisms on analysis of resistant-starch contents.

PubMed

Moore, Samuel A; Ai, Yongfeng; Chang, Fengdan; Jane, Jay-lin

2015-01-22

This study aimed to understand differences in the resistant starch (RS) contents of native and modified starches obtained using two standard methods of RS content analysis: AOAC Method 991.43 and 2002.02. The largest differences were observed in native potato starch, cross-linked wheat distarch phosphate, and high-amylose corn starch stearic-acid complex (RS5) between using AOAC Method 991.43 with Bacillus licheniformis α-amylase (BL) and AOAC Method 2002.02 with porcine pancreatic α-amylase (PPA). To determine possible reasons for these differences, we hydrolyzed raw-starch granules with BL and PPA with equal activity at pH 6.9 and 37°C for up to 84 h and observed the starch granules displayed distinct morphological differences after the hydrolysis. Starches hydrolyzed by BL showed erosion on the surface of the granules; those hydrolyzed by PPA showed pitting on granule surfaces. These results suggested that enzyme reaction mechanisms, including the sizes of the binding sites and the reaction patterns of the two enzymes, contributed to the differences in the RS contents obtained using different methods of RS analysis. Copyright © 2014 Elsevier Ltd. All rights reserved.

In situ spectroscopic and solution analyses of the reductive dissolution of Mn02 by Fe(II)

USGS Publications Warehouse

Villinski, John E.; O'Day, Peggy A.; Corley, Timothy L.; Conklin, Martha H.

2001-01-01

The reductive dissolution of MnO2 by Fe(II) under conditions simulating acid mine drainage (pH 3, 100 mM SO42-) was investigated by utilizing a flow-through reaction cell and synchrotron X-ray absorption spectroscopy. This configuration allows collection of in situ, real-time X-ray absorption near-edge structure (XANES) spectra and bulk solution samples. Analysis of the solution chemistry suggests that the reaction mechanism changed (decreased reaction rate) as MnO2 was reduced and Fe(III) precipitated, primarily as ferrihydrite. Simultaneously, we observed an additional phase, with the local structure of jacobsite (MnFe2O4), in the Mn XANES spectra of reactants and products. The X-ray absorbance of this intermediate phase increased during the experiment, implying an increase in concentration. The presence of this phase, which probably formed as a surface coating, helps to explain the reduced rate of dissolution of manganese(IV) oxide. In natural environments affected by acid mine drainage, the formation of complex intermediate solid phases on mineral surfaces undergoing reductive dissolution may likewise influence the rate of release of metals to solution.

Homogeneous Molecular Catalysis of Electrochemical Reactions: Catalyst Benchmarking and Optimization Strategies.

PubMed

Costentin, Cyrille; Savéant, Jean-Michel

2017-06-21

Modern energy challenges currently trigger an intense interest in catalysis of redox reactions-electrochemical and photochemical-particularly those involving small molecules such as water, hydrogen, oxygen, proton, carbon dioxide. A continuously increasing number of molecular catalysts of these reactions, mostly transition metal complexes, have been proposed, rendering necessary procedures for their rational benchmarking and fueling the quest for leading principles that could inspire the design of improved catalysts. The search of "volcano plots" correlating catalysis kinetics to the stability of the key intermediate is a popular approach to the question in catalysis by surface-active sites, with as foremost example the electrochemical reduction of aqueous proton on metal surfaces. We discussed here for the first time, on theoretical and experimental grounds, the pertinence of such an approach in the field of molecular catalysis. This is the occasion to insist on the virtue of careful mechanism assignments. Particular emphasis is put on the interest of expressing the catalysts' intrinsic kinetic properties by means of catalytic Tafel plots, which relate kinetics and overpotential. We also underscore that the principle and strategies put forward for the catalytic activation of the above-mentioned small molecules are general as illustrated by catalytic applications out of this particular field.

Lateral interactions and non-equilibrium in surface kinetics

NASA Astrophysics Data System (ADS)

Menzel, Dietrich

2016-08-01

Work modelling reactions between surface species frequently use Langmuir kinetics, assuming that the layer is in internal equilibrium, and that the chemical potential of adsorbates corresponds to that of an ideal gas. Coverage dependences of reacting species and of site blocking are usually treated with simple power law coverage dependences (linear in the simplest case), neglecting that lateral interactions are strong in adsorbate and co-adsorbate layers which may influence kinetics considerably. My research group has in the past investigated many co-adsorbate systems and simple reactions in them. We have collected a number of examples where strong deviations from simple coverage dependences exist, in blocking, promoting, and selecting reactions. Interactions can range from those between next neighbors to larger distances, and can be quite complex. In addition, internal equilibrium in the layer as well as equilibrium distributions over product degrees of freedom can be violated. The latter effect leads to non-equipartition of energy over molecular degrees of freedom (for products) or non-equal response to those of reactants. While such behavior can usually be described by dynamic or kinetic models, the deeper reasons require detailed theoretical analysis. Here, a selection of such cases is reviewed to exemplify these points.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Laskin, Julia

In this work, resonant ejection coupled with surface-induced dissociation (SID) in a Fourier transform ion cyclotron resonance mass spectrometer is used to examine fragmentation kinetics of two singly protonated hexapeptides, RYGGFL and KYGGFL, containing the basic arginine residue and less basic lysine residue at the N-terminus. The kinetics of individual reaction channels at different collision energies are probed by applying a short ejection pulse (1 ms) in resonance with the cyclotron frequency of a selected fragment ion and varying the delay time between ion-surface collision and resonant ejection while keeping total reaction delay time constant. Rice-Ramsperger-Kassel-Marcus (RRKM) modeling of themore » experimental data provides accurate threshold energies and activation entropies of individual reaction channels. Substitution of arginine with less basic lysine has a pronounced effect on the observed fragmentation kinetics of several pathways, including the b2 ion formation, but has little or no effect on formation of the b5+H2O fragment ion. The combination of resonant ejection SID, time- and collision energy-resolved SID, and RRKM modeling of both types of experimental data provides a detailed mechanistic understanding of the primary dissociation pathways of complex gaseous ions.« less

Phosphate and phytate adsorption and precipitation on ferrihydrite surfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Xiaoming; Hu, Yongfeng; Tang, Yadong

Phosphorous (P) sorption on mineral surfaces largely controls P mobility and bioavailability, hence its pollution potential, but the sorption speciation and mechanism remain poorly understood. In this study, we have identified and quantified the speciation of both phosphate and phytate sorbed on ferrihydrite with various P loadings at pH 3–8 using differential atomic pair distribution function (d-PDF) analysis, synchrotron-based X-ray diffraction (XRD), and P and Fe K-edge X-ray absorption near edge structure (XANES) and attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy. With increasing P sorption loading for both phosphate and phytate, the sorption mechanism transits from bidentate-binuclear surface complexation tomore » unidentified ternary complexation and to precipitation of amorphous FePO 4 and amorphous Fe-phytate. At a given P sorption loading, phosphate precipitates more readily than phytate. Both phosphate and phytate promote ferrihydrite dissolution with phytate more intensively, but the dissolved FeIII concentration in the bulk solution is low because the majority of the released Fe III precipitate with the anions. Results also show that amorphous FePO 4 and amorphous Fe-phytate have similar PO 4 local coordination environment. In conclusion, these new insights into the P surface complexation and precipitation, and the ligand-promoted dissolution behavior improve our understanding of P fate in soils, aquatic environment and water treatment systems as mediated by mineral-water interfacial reactions.« less

Phosphate and phytate adsorption and precipitation on ferrihydrite surfaces

DOE PAGES

Wang, Xiaoming; Hu, Yongfeng; Tang, Yadong; ...

2017-09-26

Phosphorous (P) sorption on mineral surfaces largely controls P mobility and bioavailability, hence its pollution potential, but the sorption speciation and mechanism remain poorly understood. In this study, we have identified and quantified the speciation of both phosphate and phytate sorbed on ferrihydrite with various P loadings at pH 3–8 using differential atomic pair distribution function (d-PDF) analysis, synchrotron-based X-ray diffraction (XRD), and P and Fe K-edge X-ray absorption near edge structure (XANES) and attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy. With increasing P sorption loading for both phosphate and phytate, the sorption mechanism transits from bidentate-binuclear surface complexation tomore » unidentified ternary complexation and to precipitation of amorphous FePO 4 and amorphous Fe-phytate. At a given P sorption loading, phosphate precipitates more readily than phytate. Both phosphate and phytate promote ferrihydrite dissolution with phytate more intensively, but the dissolved FeIII concentration in the bulk solution is low because the majority of the released Fe III precipitate with the anions. Results also show that amorphous FePO 4 and amorphous Fe-phytate have similar PO 4 local coordination environment. In conclusion, these new insights into the P surface complexation and precipitation, and the ligand-promoted dissolution behavior improve our understanding of P fate in soils, aquatic environment and water treatment systems as mediated by mineral-water interfacial reactions.« less

A computer model for one-dimensional mass and energy transport in and around chemically reacting particles, including complex gas-phase chemistry, multicomponent molecular diffusion, surface evaporation, and heterogeneous reaction

NASA Technical Reports Server (NTRS)

Cho, S. Y.; Yetter, R. A.; Dryer, F. L.

1992-01-01

Various chemically reacting flow problems highlighting chemical and physical fundamentals rather than flow geometry are presently investigated by means of a comprehensive mathematical model that incorporates multicomponent molecular diffusion, complex chemistry, and heterogeneous processes, in the interest of obtaining sensitivity-related information. The sensitivity equations were decoupled from those of the model, and then integrated one time-step behind the integration of the model equations, and analytical Jacobian matrices were applied to improve the accuracy of sensitivity coefficients that are calculated together with model solutions.

Self-organizing biochemical cycles

NASA Technical Reports Server (NTRS)

Orgel, L. E.; Bada, J. L. (Principal Investigator)

2000-01-01

I examine the plausibility of theories that postulate the development of complex chemical organization without requiring the replication of genetic polymers such as RNA. One conclusion is that theories that involve the organization of complex, small-molecule metabolic cycles such as the reductive citric acid cycle on mineral surfaces make unreasonable assumptions about the catalytic properties of minerals and the ability of minerals to organize sequences of disparate reactions. Another conclusion is that data in the Beilstein Handbook of Organic Chemistry that have been claimed to support the hypothesis that the reductive citric acid cycle originated as a self-organized cycle can more plausibly be interpreted in a different way.

Magnesium oxide prepared via metal-chitosan complexation method: Application as catalyst for transesterification of soybean oil and catalyst deactivation studies

NASA Astrophysics Data System (ADS)

Almerindo, Gizelle I.; Probst, Luiz F. D.; Campos, Carlos E. M.; de Almeida, Rusiene M.; Meneghetti, Simoni M. P.; Meneghetti, Mario R.; Clacens, Jean-Marc; Fajardo, Humberto V.

2011-10-01

A simple method to prepare magnesium oxide catalysts for biodiesel production by transesterification reaction of soybean oil with ethanol is proposed. The method was developed using a metal-chitosan complex. Compared to the commercial oxide, the proposed catalysts displayed higher surface area and basicity values, leading to higher yield in terms of fatty acid ethyl esters (biodiesel). The deactivation of the catalyst due to contact with CO2 and H2O present in the ambient air was verified. It was confirmed that the active catalytic site is a hydrogenocarbonate adsorption site.

Relationships between Atomic Level Surface Structure and Stability/Activity of Platinum Surface Atoms in Aqueous Environments

DOE PAGES

Lopes, Pietro P.; Strmcnik, Dusan; Tripkovic, Dusan; ...

2016-03-07

The development of alternative energy systems for clean production, storage and conversion of energy is strongly dependent on our ability to understand, at atomic-molecular-levels, functional links between activity and stability of electrochemical interfaces. Whereas structure-activity relationships are rapidly evolving, the corresponding structure-stability relationships are still missing. Primarily, this is because there is no adequate experimental approach capable of monitoring in situ stability of well-defined single crystals. Here, by blending the power of Inductively Coupled Plasma-Mass Spectrometer (ICP-MS) connected to a stationary probe to measure in situ and real time dissolution rates of surface atoms (at above 0.4 pg cm-2s-1 levels)more » and a rotating disk electrode method for monitoring simultaneously the kinetic rates of electrochemical reactions in a single unite, it was possible to establish almost “atom-by-atom” the structure-stability-activity relationships for platinum single crystals in both acidic and alkaline environments. Furthermore, we found that the degree of stability is strongly dependent on the coordination of surface atoms (less coordinated yields less stable), the nature of covalent (adsorption of hydroxyl, oxygen atoms and halides species), and non-covalent interactions (interactions between hydrated Li cations and surface oxide), the thermodynamic driving force for Pt complexation (Pt ion speciation in solution) and the nature of the electrochemical reaction (the oxygen reduction/evolution and CO oxidation reactions). Consequently, these findings are opening new opportunities for elucidating key fundamental descriptors that govern both activity and stability trends, that ultimately, will assist to develop real energy conversion and storage systems.« less

Energy Dissipation and Nonthermal Diffusion on Interstellar Ice Grains

NASA Astrophysics Data System (ADS)

Fredon, A.; Lamberts, T.; Cuppen, H. M.

2017-11-01

Interstellar dust grains are known to facilitate chemical reactions by acting as a meeting place and adsorbing energy. This process strongly depends on the ability of the reactive species to effectively diffuse over the surface. The cold temperatures around 10 K strongly hamper this for species other than H and H2. However, complex organic molecules have been observed in the gas phase at these cold conditions, indicating that their formation, as well as their return to the gas phase, should be effective. Here, we show how the energy released following surface reactions can be employed to solve both problems by inducing desorption or diffusion. To this purpose, we have performed thousands of Molecular Dynamics simulations to quantify the outcome of an energy dissipation process. Admolecules on top of a crystalline water surface have been given translational energy between 0.5 and 5 eV. Three different surface species are considered (CO2, H2O, and CH4), spanning a range in binding energies, number of internal degrees of freedom, and molecular weights. The admolecules are found to be able to travel up to several hundreds of angstroms before coming to a stand still, allowing for follow-up reactions en route. The probability of travel beyond any particular radius, as determined by our simulations, shows the same r dependence for all three admolecule species. Furthermore, we have been able to quantify the desorption probability, which depends on the binding energy of the species and the translational excitation. We provide expressions that can be incorporated in astrochemical models to predict grain surface formation and return into the gas phase of these products.

Surface Complexation Modeling of Fluoride Adsorption by Soil and the Role of Dissolved Aluminum on Adsorption

NASA Astrophysics Data System (ADS)

Padhi, S.; Tokunaga, T.

2017-12-01

Adsorption of fluoride (F) on soil can control the mobility of F and subsequent contamination of groundwater. Hence, accurate evaluation of adsorption equilibrium is a prerequisite for understanding transport and fate of F in the subsurface. While there have been studies for the adsorption behavior of F with respect to single mineral constituents based on surface complexation models (SCM), F adsorption to natural soil in the presence of complexing agents needs much investigation. We evaluated the adsorption processes of F on a natural granitic soil from Tsukuba, Japan, as a function of initial F concentration, ionic strength, and initial pH. A SCM was developed to model F adsorption behavior. Four possible surface complexation reactions were postulated with and without including dissolved aluminum (Al) and Al-F complex sorption. Decrease in F adsorption with the increase in initial pH was observed in between the initial pH range of 4 to 9, and a decrease in the rate of the reduction of adsorbed F with respect to the increase in the initial pH was observed in the initial pH range of 5 to 7. Ionic strength variation in the range of 0 to 100mM had insignificant effect on F removal. Changes in solution pH were observed by comparing the solution before and after F adsorption experiments. At acidic pH, the solution pH increased, whereas at alkaline pH, the solution pH decreased after equilibrium. The SCM including dissolved Al and the adsorption of Al-F complex can simulate the experimental results quite successfully. Also, including dissolved Al and the adsorption of Al-F complex to the model explained the change in solution pH after F adsorption.

Improved Procedure for Direct Coupling of Carbohydrates to Proteins via Reductive Amination

PubMed Central

Gildersleeve, Jeffrey C.; Oyelaran, Oyindasola; Simpson, John T.; Allred, Benjamin

2009-01-01

Carbohydrate-protein conjugates are utilized extensively in basic research and as immunogens in a variety of bacterial vaccines and cancer vaccines. As a result, there have been significant efforts to develop simple and reliable methods for the construction of these conjugates. While direct coupling via reductive amination is an appealing approach, the reaction is typically very inefficient. In this paper, we report improved reaction conditions providing an approximately 500% increase in yield. In addition to optimizing a series of standard reaction parameters, we found that addition of 500 mM sodium sulfate improves the coupling efficiency. To illustrate the utility of these conditions, a series of high mannose BSA conjugates were produced and incorporated into a carbohydrate microarray. Ligand binding to ConA could be observed and apparent affinity constants (Kds) measured using the array were in good agreement with values reported by surface plasmon resonance. The results show that the conditions are suitable for microgram scale reactions, are compatible with complex carbohydrates, and produce biologically active conjugates. PMID:18597509

Simulation and fitting of complex reaction network TPR: The key is the objective function

DOE PAGES

Savara, Aditya Ashi

2016-07-07

In this research, a method has been developed for finding improved fits during simulation and fitting of data from complex reaction network temperature programmed reactions (CRN-TPR). It was found that simulation and fitting of CRN-TPR presents additional challenges relative to simulation and fitting of simpler TPR systems. The method used here can enable checking the plausibility of proposed chemical mechanisms and kinetic models. The most important finding was that when choosing an objective function, use of an objective function that is based on integrated production provides more utility in finding improved fits when compared to an objective function based onmore » the rate of production. The response surface produced by using the integrated production is monotonic, suppresses effects from experimental noise, requires fewer points to capture the response behavior, and can be simulated numerically with smaller errors. For CRN-TPR, there is increased importance (relative to simple reaction network TPR) in resolving of peaks prior to fitting, as well as from weighting of experimental data points. Using an implicit ordinary differential equation solver was found to be inadequate for simulating CRN-TPR. Lastly, the method employed here was capable of attaining improved fits in simulation and fitting of CRN-TPR when starting with a postulated mechanism and physically realistic initial guesses for the kinetic parameters.« less

Benchmark ab Initio Characterization of the Complex Potential Energy Surfaces of the X- + NH2Y [X, Y = F, Cl, Br, I] Reactions.

PubMed

Hajdu, Bálint; Czakó, Gábor

2018-02-22

We report a comprehensive high-level explicitly correlated ab initio study on the X - + NH 2 Y [X,Y = F, Cl, Br, I] reactions characterizing the stationary points of the S N 2 (Y - + NH 2 X) and proton-transfer (HX + NHY - ) pathways as well as the reaction enthalpies of various endothermic additional product channels such as H - + NHXY, XY - + NH 2 , XY + NH 2 - , and XHY - + NH. Benchmark structures and harmonic vibrational frequencies are obtained at the CCSD(T)-F12b/aug-cc-pVTZ(-PP) level of theory, followed by CCSD(T)-F12b/aug-cc-pVnZ(-PP) [n = Q and 5] and core correlation energy computations. In the entrance and exit channels we find two equivalent hydrogen-bonded C 1 minima, X - ···HH'NY and X - ···H'HNY connected by a C s first-order saddle point, X - ···H 2 NY, as well as a halogen-bonded front-side complex, X - ···YNH 2 . S N 2 reactions can proceed via back-side attack Walden inversion and front-side attack retention pathways characterized by first-order saddle points, submerged [X-NH 2 -Y] - and high-energy [H 2 NXY] - , respectively. Product-like stationary points below the HX + NHY - asymptotes are involved in the proton-transfer processes.

Scattering study of the Ne + NeH+(v0 = 0, j0 = 0) → NeH+ + Ne reaction on an ab initio based analytical potential energy surface

NASA Astrophysics Data System (ADS)

Koner, Debasish; Barrios, Lizandra; González-Lezana, Tomás; Panda, Aditya N.

2016-01-01

Initial state selected dynamics of the Ne + NeH+(v0 = 0, j0 = 0) → NeH+ + Ne reaction is investigated by quantum and statistical quantum mechanical (SQM) methods on the ground electronic state. The three-body ab initio energies on a set of suitably chosen grid points have been computed at CCSD(T)/aug-cc-PVQZ level and analytically fitted. The fitting of the diatomic potentials, computed at the same level of theory, is performed by spline interpolation. A collinear [NeHNe]+ structure lying 0.72 eV below the Ne + NeH+ asymptote is found to be the most stable geometry for this system. Energies of low lying vibrational states have been computed for this stable complex. Reaction probabilities obtained from quantum calculations exhibit dense oscillatory structures, particularly in the low energy region and these get partially washed out in the integral cross section results. SQM predictions are devoid of oscillatory structures and remain close to 0.5 after the rise at the threshold thus giving a crude average description of the quantum probabilities. Statistical cross sections and rate constants are nevertheless in sufficiently good agreement with the quantum results to suggest an important role of a complex-forming dynamics for the title reaction.

An experiment on the dynamics of ion implantation and sputtering of surfaces

NASA Astrophysics Data System (ADS)

Wright, G. M.; Barnard, H. A.; Kesler, L. A.; Peterson, E. E.; Stahle, P. W.; Sullivan, R. M.; Whyte, D. G.; Woller, K. B.

2014-02-01

A major impediment towards a better understanding of the complex plasma-surface interaction is the limited diagnostic access to the material surface while it is undergoing plasma exposure. The Dynamics of ION Implantation and Sputtering Of Surfaces (DIONISOS) experiment overcomes this limitation by uniquely combining powerful, non-perturbing ion beam analysis techniques with a steady-state helicon plasma exposure chamber, allowing for real-time, depth-resolved in situ measurements of material compositions during plasma exposure. Design solutions are described that provide compatibility between the ion beam analysis requirements in the presence of a high-intensity helicon plasma. The three primary ion beam analysis techniques, Rutherford backscattering spectroscopy, elastic recoil detection, and nuclear reaction analysis, are successfully implemented on targets during plasma exposure in DIONISOS. These techniques measure parameters of interest for plasma-material interactions such as erosion/deposition rates of materials and the concentration of plasma fuel species in the material surface.

An experiment on the dynamics of ion implantation and sputtering of surfaces.

PubMed

Wright, G M; Barnard, H A; Kesler, L A; Peterson, E E; Stahle, P W; Sullivan, R M; Whyte, D G; Woller, K B

2014-02-01

A major impediment towards a better understanding of the complex plasma-surface interaction is the limited diagnostic access to the material surface while it is undergoing plasma exposure. The Dynamics of ION Implantation and Sputtering Of Surfaces (DIONISOS) experiment overcomes this limitation by uniquely combining powerful, non-perturbing ion beam analysis techniques with a steady-state helicon plasma exposure chamber, allowing for real-time, depth-resolved in situ measurements of material compositions during plasma exposure. Design solutions are described that provide compatibility between the ion beam analysis requirements in the presence of a high-intensity helicon plasma. The three primary ion beam analysis techniques, Rutherford backscattering spectroscopy, elastic recoil detection, and nuclear reaction analysis, are successfully implemented on targets during plasma exposure in DIONISOS. These techniques measure parameters of interest for plasma-material interactions such as erosion/deposition rates of materials and the concentration of plasma fuel species in the material surface.

Selective scanning tunnelling microscope electron-induced reactions of single biphenyl molecules on a Si(100) surface.

PubMed

Riedel, Damien; Bocquet, Marie-Laure; Lesnard, Hervé; Lastapis, Mathieu; Lorente, Nicolas; Sonnet, Philippe; Dujardin, Gérald

2009-06-03

Selective electron-induced reactions of individual biphenyl molecules adsorbed in their weakly chemisorbed configuration on a Si(100) surface are investigated by using the tip of a low-temperature (5 K) scanning tunnelling microscope (STM) as an atomic size source of electrons. Selected types of molecular reactions are produced, depending on the polarity of the surface voltage during STM excitation. At negative surface voltages, the biphenyl molecule diffuses across the surface in its weakly chemisorbed configuration. At positive surface voltages, different types of molecular reactions are activated, which involve the change of adsorption configuration from the weakly chemisorbed to the strongly chemisorbed bistable and quadristable configurations. Calculated reaction pathways of the molecular reactions on the silicon surface, using the nudge elastic band method, provide evidence that the observed selectivity as a function of the surface voltage polarity cannot be ascribed to different activation energies. These results, together with the measured threshold surface voltages and the calculated molecular electronic structures via density functional theory, suggest that the electron-induced molecular reactions are driven by selective electron detachment (oxidation) or attachment (reduction) processes.

Functional copolymer/organo-MMT nanoarchitectures. VI. Synthesis and characterization of novel nanocomposites by interlamellar controlled/living radical copolymerization via preintercalated RAFT-agent/organoclay complexes.

PubMed

Rzayev, Zakir M O; Söylemez, A Ernur

2011-04-01

We have developed a new approach for the synthesis of polymer nanocomposites using a bifunctional reversible addition-fragmentation chain transfer (RAFT) agent, two types of organo-montmorillonites, such as a non-reactive dimethyldodecyl ammonium (DMDA)-MMT and a reactive octadecylamine (ODA)-MMT organoclays, and a radical initiator. The method includes the following stages: (1) synthesis of RAFT intercalated O-MMTs by a physical or chemical interaction of the RAFT agent having two pendant carboxylic groups [S,S-bis(alpha,alpha'-dimethyl-alpha"-acetic acid)trithiocarbonate] with surface alkyl amines of O-MMT containing tertiary ammonium cation or primary amine groups through strong H-bonding and complexing/amidization reactions, respectively, and (2) utilization of these well-dispersed and intercalated RAFT ... O-MMT complexes and their amide derivatives as new modified RAFT agents in radical-initiated interlamellar controlled/living copolymerization of itaconic acid (IA)-n-butylmethacrylate (BMA) monomer pair. The structure and compositions of the synthesized RAFT ... O-MMT complexes and functional copolymer/O-MMT hybrids were confirmed by FTIR, XRD, thermal (DSC-TGA), SEM and TEM morphology analyses. It was demonstrated that the degree of interaction/exfoliation, morphology and thermal behavior of nanocomposites significantly depended on the type of organoclay and in situ interaction, as well as on the content of flexible butyl-ester linkages as a internal plasticizer. The results of the comparative analysis of the nanocomposites structure-composition-property relations show that the functional copolymer-organoclay hybrids prepared with reactive RAFT ... ODA-MMT complex and containing a combination of partially intercalated and predominantly exfoliated nano-structures exhibit relatively higher thermal stability and fine dispersed morphology. These effects were explained by in situ interfacial chemical reactions through amidization of RAFT with surface alkyl amine of MMT clay in interlamellar copolymerization. This simple and versatile method can be applied to a wide range of functional monomer/comonomer systems and mono- and bifunctional RAFT compounds for preparation new generation of nanomaterials.

Coordination of N,O-donor appended Schiff base ligand (H2L1) towards Zinc(II) in presence of pseudohalides: Syntheses, crystal structures, photoluminescence, antimicrobial activities and Hirshfeld surfaces

NASA Astrophysics Data System (ADS)

Majumdar, Dhrubajyoti; Biswas, Jayanta Kumar; Mondal, Monojit; Surendra Babu, M. S.; Metre, Ramesh K.; Das, Sourav; Bankura, Kalipada; Mishra, Dipankar

2018-03-01

A series of dinuclear Zn(II) complexes [Zn2 (L1) (CH3OH)2(SCN) (OAc)](1), [Zn2 (L1) (CH3OH)2(N3)2](2) and [Zn2 (L1) (Cl)2(CH3OH)]·CH3OH (3) have been synthesized by the reaction of compartmental Schiff base ligand (H2L1) [N,N‧-Bis(3-ethoxysalicylidenimino)-1,3-diaminopropane] with Zn(OAc)2·2H2O in presence of coligand like KSCN, NaN3 and NaCl respectively. X-ray diffraction analysis revealed that all the complexes are neutral and possess a 4-membered Zn2 (μ2-O)2 ring fastened by the unified coordination action of a doubly deprotonated ligand. In addition, solid state structure of the complexes display extensive intermolecular interaction which has been supported theoretically by Hirshfeld surface analysis with 2D Fingerprint plots. The synthesized Zn(II) metal complexes observed enhancement of luminescence emission compared to the parent Schiff base due to emanating ligand based intraligand (π→π∗) fluorescence. Additionally, Zn(II) metal complexes exhibited considerable antimicrobial potency against some important Gram +ve and Gram -ve bacteria.

Noncovalent immobilization of electrocatalysts on carbon electrodes for fuel production.

PubMed

Blakemore, James D; Gupta, Ayush; Warren, Jeffrey J; Brunschwig, Bruce S; Gray, Harry B

2013-12-11

We show that molecular catalysts for fuel-forming reactions can be immobilized on graphitic carbon electrode surfaces via noncovalent interactions. A pyrene-appended bipyridine ligand (P) serves as the linker between each complex and the surface. Immobilization of a rhodium proton-reduction catalyst, [Cp*Rh(P)Cl]Cl (1), and a rhenium CO2-reduction catalyst, Re(P)(CO)3Cl (2), afford electrocatalytically active assemblies. X-ray photoelectron spectroscopy and electrochemistry confirm catalyst immobilization. Reduction of 1 in the presence of p-toluenesulfonic acid results in catalytic H2 production, while reduction of 2 in the presence of CO2 results in catalytic CO production.

Some fundamental properties and reactions of ice surfaces at low temperatures.

PubMed

Park, Seong-Chan; Moon, Eui-Seong; Kang, Heon

2010-10-14

Ice surfaces offer a unique chemical environment in which reactions occur quite differently from those in liquid water or gas phases. In this article, we examine the basic properties of ice surfaces below the surface premelting temperature and discuss some of the recent investigations carried out on reactions at the ice surfaces. The static and dynamic properties of an ice surface as a reaction medium, such as its structure, molecule diffusion and proton transfer dynamics, and the surface preference of hydronium and hydroxide ions, are discussed in relation to the reactivity of the surface.

Sampling free energy surfaces as slices by combining umbrella sampling and metadynamics.

PubMed

Awasthi, Shalini; Kapil, Venkat; Nair, Nisanth N

2016-06-15

Metadynamics (MTD) is a very powerful technique to sample high-dimensional free energy landscapes, and due to its self-guiding property, the method has been successful in studying complex reactions and conformational changes. MTD sampling is based on filling the free energy basins by biasing potentials and thus for cases with flat, broad, and unbound free energy wells, the computational time to sample them becomes very large. To alleviate this problem, we combine the standard Umbrella Sampling (US) technique with MTD to sample orthogonal collective variables (CVs) in a simultaneous way. Within this scheme, we construct the equilibrium distribution of CVs from biased distributions obtained from independent MTD simulations with umbrella potentials. Reweighting is carried out by a procedure that combines US reweighting and Tiwary-Parrinello MTD reweighting within the Weighted Histogram Analysis Method (WHAM). The approach is ideal for a controlled sampling of a CV in a MTD simulation, making it computationally efficient in sampling flat, broad, and unbound free energy surfaces. This technique also allows for a distributed sampling of a high-dimensional free energy surface, further increasing the computational efficiency in sampling. We demonstrate the application of this technique in sampling high-dimensional surface for various chemical reactions using ab initio and QM/MM hybrid molecular dynamics simulations. Further, to carry out MTD bias reweighting for computing forward reaction barriers in ab initio or QM/MM simulations, we propose a computationally affordable approach that does not require recrossing trajectories. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Elucidation of metal-ion accumulation induced by hydrogen bonds on protein surfaces by using porous lysozyme crystals containing Rh(III) ions as the model surfaces.

PubMed

Ueno, Takafumi; Abe, Satoshi; Koshiyama, Tomomi; Ohki, Takahiro; Hikage, Tatsuo; Watanabe, Yoshihito

2010-03-01

Metal-ion accumulation on protein surfaces is a crucial step in the initiation of small-metal clusters and the formation of inorganic materials in nature. This event is expected to control the nucleation, growth, and position of the materials. There remain many unknowns, as to how proteins affect the initial process at the atomic level, although multistep assembly processes of the materials formation by both native and model systems have been clarified at the macroscopic level. Herein the cooperative effects of amino acids and hydrogen bonds promoting metal accumulation reactions are clarified by using porous hen egg white lysozyme (HEWL) crystals containing Rh(III) ions, as model protein surfaces for the reactions. The experimental results reveal noteworthy implications for initiation of metal accumulation, which involve highly cooperative dynamics of amino acids and hydrogen bonds: i) Disruption of hydrogen bonds can induce conformational changes of amino-acid residues to capture Rh(III) ions. ii) Water molecules pre-organized by hydrogen bonds can stabilize Rh(III) coordination as aqua ligands. iii) Water molecules participating in hydrogen bonds with amino-acid residues can be replaced by Rh(III) ions to form polynuclear structures with the residues. iv) Rh(III) aqua complexes are retained on amino-acid residues through stabilizing hydrogen bonds even at low pH (approximately 2). These metal-protein interactions including hydrogen bonds may promote native metal accumulation reactions and also may be useful in the preparation of new inorganic materials that incorporate proteins.

Hierarchical micron-sized mesoporous/macroporous graphene with well-tuned surface oxygen chemistry for high capacity and cycling stability Li-O2 battery.

PubMed

Zhou, Wei; Zhang, Hongzhang; Nie, Hongjiao; Ma, Yiwen; Zhang, Yining; Zhang, Huamin

2015-02-11

Nonaqueous Li-O2 battery is recognized as one of the most promising energy storage devices for electric vehicles due to its super-high energy density. At present, carbon or catalyst-supporting carbon materials are widely used for cathode materials of Li-O2 battery. However, the unique electrode reaction and complex side reactions lead to numerous hurdles that have to be overcome. The pore blocking caused by the solid products and the byproducts generated from the side reactions severely limit the capacity performance and cycling stability. Thus, there is a great need to develop carbon materials with optimized pore structure and tunable surface chemistry to meet the special requirement of Li-O2 battery. Here, we propose a strategy of vacuum-promoted thermal expansion to fabricate one micron-sized graphene matrix with a hierarchical meso-/macroporous structure, combining with a following deoxygenation treatment to adjust the surface chemistry by reducing the amount of oxygen and selectively removing partial unstable groups. The as-made graphene demonstrates dramatically tailored pore characteristics and a well-tuned surface chemical environment. When applied in Li-O2 battery as cathode, it exhibits an outstanding capacity up to 19 800 mA h g(-1) and is capable of enduring over 50 cycles with a curtaining capacity of 1000 mA h g(-1) at a current density of 1000 mA g(-1). This will provide a novel pathway for the design of cathodes for Li-O2 battery.

Sequential Reactions of Surface-Tethered Glycolytic Enzymes

PubMed Central

Mukai, Chinatsu; Bergkvist, Magnus; Nelson, Jacquelyn L.; Travis, Alexander J.

2014-01-01

SUMMARY The development of complex hybrid organic-inorganic devices faces several challenges, including how they can generate energy. Cells face similar challenges regarding local energy production. Mammalian sperm solve this problem by generating ATP down the flagellar principal piece by means of glycolytic enzymes, several of which are tethered to a cytoskeletal support via germ cell-specific targeting domains. Inspired by this design, we have produced recombinant hexokinase type 1 and glucose-6-phosphate isomerase capable of oriented immobilization on a nickel-nitrilotriacetic acid modified surface. Specific activities of enzymes tethered via this strategy were substantially higher than when randomly adsorbed. Furthermore, these enzymes showed sequential activities when tethered onto the same surface. This is the first demonstration of surface-tethered pathway components showing sequential enzymatic activities, and it provides a first step toward reconstitution of glycolysis on engineered hybrid devices. PMID:19778729

Role of surfaces and interfaces in controlling the mechanical properties of metallic alloys.

PubMed

Lee, Won-Jong; Chia, Wen-Jui; Wang, Jinliu; Chen, Yanfeng; Vaynman, Semyon; Fine, Morris E; Chung, Yip-Wah

2010-11-02

This article explores the subtle effects of surfaces and interfaces on the mechanical properties of bulk metallic alloys using three examples: environmental effects on fatigue life, hydrogen embrittlement effects on the ductility of intermetallics, and the role of coherent precipitates in the toughness of steels. It is demonstrated that the marked degradation of the fatigue life of metals is due to the strong chemisorption of adsorbates on exposed slip steps that are formed during fatigue deformation. These adsorbates reduce the reversibility of slip, thus accelerating fatigue damage in a chemically active gas environment. For certain intermetallic alloys such as Ni(3)Al and Ni(3)Fe, the ductility depends on the ambient gas composition and the atomic ordering in these alloys, both of which govern the complex surface chemical reactions taking place in the vicinity of crack tips. Finally, it is shown that local stresses at a coherent precipitate-matrix interface can activate dislocation motion at low temperatures, thus improving the fracture toughness of bulk alloys such as steels at cryogenic temperatures. These examples illustrate the complex interplay between surface chemistry and mechanics, often yielding unexpected results.

Manipulating the Surface Chemistry of Quantum Dots for Sensitive Ratiometric Fluorescence Detection of Sulfur Dioxide.

PubMed

Li, Huihui; Zhu, Houjuan; Sun, Mingtai; Yan, Yehan; Zhang, Kui; Huang, Dejian; Wang, Suhua

2015-08-11

Herein, we report a novel approach to the rapid visual detection of gaseous sulfur dioxide (SO2) by manipulating the surface chemistry of 3-aminopropyltriethoxysilane (APTS)-modified quantum dots (QDs) using fluorescent coumarin-3-carboxylic acid (CCA) for specific reaction with SO2. The CCA molecules are attached to the surface amino groups of the QDs through electrostatic attraction, thus the fluorescence of CCA is greatly suppressed because of the formation of an ion-pair complex between the ATPS-modified QDs and CCA. Such an interaction is vulnerable to SO2 because SO2 can readily react with surface amino groups to form strong charge-transfer complexes and subsequently release the strongly fluorescent CCA molecules. The mechanism has been carefully verified through a series of control experiments. Upon exposure to different amounts of SO2, the fluorescent color of the nanoparticle-based sensor displays continuously changes from red to blue. Most importantly, the approach owns high selectivity for SO2 and a tolerance of interference, which enables the sensor to detect SO2 in a practical application. Using this fluorescence-based sensing method, we have achieved a visual detection limit of 6 ppb for gaseous SO2.

Review-Physicochemical hydrodynamics of gas bubbles in two phase electrochemical systems.

PubMed

Taqieddin, Amir; Nazari, Roya; Rajic, Ljiljana; Alshawabkeh, Akram

2017-01-01

Electrochemical systems suffer from poor management of evolving gas bubbles. Improved understanding of bubbles behavior helps to reduce overpotential, save energy and enhance the mass transfer during chemical reactions. This work investigates and reviews the gas bubbles hydrodynamics, behavior, and management in electrochemical cells. Although the rate of bubble growth over the electrode surface is well understood, there is no reliable prediction of bubbles break-off diameter from the electrode surface because of the complexity of bubbles motion near the electrode surface. Particle Image Velocimetry (PIV) and Laser Doppler Anemometry (LDA) are the most common experimental techniques to measure bubble dynamics. Although the PIV is faster than LDA, both techniques are considered expensive and time-consuming. This encourages adapting Computational Fluid Dynamics (CFD) methods as an alternative to study bubbles behavior. However, further development of CFD methods is required to include coalescence and break-up of bubbles for better understanding and accuracy. The disadvantages of CFD methods can be overcome by using hybrid methods. The behavior of bubbles in electrochemical systems is still a complex challenging topic which requires a better understanding of the gas bubbles hydrodynamics and their interactions with the electrode surface and bulk liquid, as well as between the bubbles itself.

Molybdate transport in a chemically complex aquifer: Field measurements compared with solute-transport model predictions

USGS Publications Warehouse

Stollenwerk, Kenneth G.

1998-01-01

A natural-gradient tracer test was conducted in an unconfined sand and gravel aquifer on Cape Cod, Massachusetts. Molybdate was included in the injectate to study the effects of variable groundwater chemistry on its aqueous distribution and to evaluate the reliability of laboratory experiments for identifying and quantifying reactions that control the transport of reactive solutes in groundwater. Transport of molybdate in this aquifer was controlled by adsorption. The amount adsorbed varied with aqueous chemistry that changed with depth as freshwater recharge mixed with a plume of sewage-contaminated groundwater. Molybdate adsorption was strongest near the water table where pH (5.7) and the concentration of the competing solutes phosphate (2.3 micromolar) and sulfate (86 micromolar) were low. Adsorption of molybdate decreased with depth as pH increased to 6.5, phosphate increased to 40 micromolar, and sulfate increased to 340 micromolar. A one-site diffuse-layer surface-complexation model and a two-site diffuse-layer surface-complexation model were used to simulate adsorption. Reactions and equilibrium constants for both models were determined in laboratory experiments and used in the reactive-transport model PHAST to simulate the two-dimensional transport of molybdate during the tracer test. No geochemical parameters were adjusted in the simulation to improve the fit between model and field data. Both models simulated the travel distance of the molybdate cloud to within 10% during the 2-year tracer test; however, the two-site diffuse-layer model more accurately simulated the molybdate concentration distribution within the cloud.

Low-temperature remote plasma enhanced atomic layer deposition of ZrO2/zircone nanolaminate film for efficient encapsulation of flexible organic light-emitting diodes.

PubMed

Chen, Zheng; Wang, Haoran; Wang, Xiao; Chen, Ping; Liu, Yunfei; Zhao, Hongyu; Zhao, Yi; Duan, Yu

2017-01-06

Encapsulation is essential to protect the air-sensitive components of organic light-emitting diodes (OLEDs) such as active layers and cathode electrodes. In this study, hybrid zirconium inorganic/organic nanolaminates were fabricated using remote plasma enhanced atomic layer deposition (PEALD) and molecular layer deposition at a low temperature. The nanolaminate serves as a thin-film encapsulation layer for OLEDs. The reaction mechanism of PEALD process was investigated using an in-situ quartz crystal microbalance (QCM) and in-situ quadrupole mass spectrometer (QMS). The bonds present in the films were determined by Fourier transform infrared spectroscopy. The primary reaction byproducts in PEALD, such as CO, CO 2 , NO, H 2 O, as well as the related fragments during the O 2 plasma process were characterized using the QMS, indicating a combustion-like reaction process. The self-limiting nature and growth mechanisms of the ZrO 2 during the complex surface chemical reaction of the ligand and O 2 plasma were monitored using the QCM. The remote PEALD ZrO 2 /zircone nanolaminate structure prolonged the transmission path of water vapor and smooth surface morphology. Consequently, the water barrier properties were significantly improved (reaching 3.078 × 10 -5  g/m 2 /day). This study also shows that flexible OLEDs can be successfully encapsulated to achieve a significantly longer lifetime.

Low-temperature remote plasma enhanced atomic layer deposition of ZrO2/zircone nanolaminate film for efficient encapsulation of flexible organic light-emitting diodes

NASA Astrophysics Data System (ADS)

Chen, Zheng; Wang, Haoran; Wang, Xiao; Chen, Ping; Liu, Yunfei; Zhao, Hongyu; Zhao, Yi; Duan, Yu

2017-01-01

Encapsulation is essential to protect the air-sensitive components of organic light-emitting diodes (OLEDs) such as active layers and cathode electrodes. In this study, hybrid zirconium inorganic/organic nanolaminates were fabricated using remote plasma enhanced atomic layer deposition (PEALD) and molecular layer deposition at a low temperature. The nanolaminate serves as a thin-film encapsulation layer for OLEDs. The reaction mechanism of PEALD process was investigated using an in-situ quartz crystal microbalance (QCM) and in-situ quadrupole mass spectrometer (QMS). The bonds present in the films were determined by Fourier transform infrared spectroscopy. The primary reaction byproducts in PEALD, such as CO, CO2, NO, H2O, as well as the related fragments during the O2 plasma process were characterized using the QMS, indicating a combustion-like reaction process. The self-limiting nature and growth mechanisms of the ZrO2 during the complex surface chemical reaction of the ligand and O2 plasma were monitored using the QCM. The remote PEALD ZrO2/zircone nanolaminate structure prolonged the transmission path of water vapor and smooth surface morphology. Consequently, the water barrier properties were significantly improved (reaching 3.078 × 10-5 g/m2/day). This study also shows that flexible OLEDs can be successfully encapsulated to achieve a significantly longer lifetime.

Theoretical investigation of the reaction of Mn+ with ethylene oxide.

PubMed

Li, Yuanyuan; Guo, Wenyue; Zhao, Lianming; Liu, Zhaochun; Lu, Xiaoqing; Shan, Honghong

2012-01-12

The potential energy surfaces of Mn(+) reaction with ethylene oxide in both the septet and quintet states are investigated at the B3LYP/DZVP level of theory. The reaction paths leading to the products of MnO(+), MnO, MnCH(2)(+), MnCH(3), and MnH(+) are described in detail. Two types of encounter complexes of Mn(+) with ethylene oxide are formed because of attachments of the metal at different sites of ethylene oxide, i.e., the O atom and the CC bond. Mn(+) would insert into a C-O bond or the C-C bond of ethylene oxide to form two different intermediates prior to forming various products. MnO(+)/MnO and MnH(+) are formed in the C-O activation mechanism, while both C-O and C-C activations account for the MnCH(2)(+)/MnCH(3) formation. Products MnO(+), MnCH(2)(+), and MnH(+) could be formed adiabatically on the quintet surface, while formation of MnO and MnCH(3) is endothermic on the PESs with both spins. In agreement with the experimental observations, the excited state a(5)D is calculated to be more reactive than the ground state a(7)S. This theoretical work sheds new light on the experimental observations and provides fundamental understanding of the reaction mechanism of ethylene oxide with transition metal cations.

Synthesis, characterization and properties of copper(I) complexes with bis(diphenylphosphino)-ferrocene ancillary ligand

NASA Astrophysics Data System (ADS)

Liu, Xinfang; Zhang, Songlin; Ding, Yuqiang

2012-06-01

Three copper(I) complexes (2-4) containing dppf ancillary ligand (dppf = bis(diphenylphosphino)-ferrocene) were synthesized when chloride-bridged copper(I) complex 1 reacted with acetanilide and characterized by IR, element analysis and NMR spectrum. And the crystal structures of complexes 2 and 4 have been determined by X-ray diffraction method. Complex 2, an acetate-bridged copper(I) complex, was obtained under N2 atmosphere in un-dried solvent; the acetate ion came from the hydrolysis reaction of acetanilide due to residual water in solvent. Acetanilide was deprotonated and coordinated with the copper(I) centre to form a copper(I) amidate complex 3 when reacted in pre-dried solvent. In addition, a known complex 4, the oxidation product of dppf, was isolated from the same reaction system when reacted in air atmosphere. CV and TG experiments were carried out to check the electron transfer properties and thermal stabilities of complexes 2-3. Finally, the arylation reaction of complex 3 with iodobenzene was performed to study the reaction mechanism of copper(I) catalyzed Goldberg reaction.

The importance of the Maillard-metal complexes and their silicates in astrobiology

NASA Astrophysics Data System (ADS)

Liesch, Patrick J.; Kolb, Vera M.

2007-09-01

The Maillard reaction occurs when sugars and amino acids are mixed together in the solid state or in the aqueous solution. Since both amino acids and sugar-like compounds are found on meteorites, we hypothesized that they would also undergo the Maillard reaction. Our recent work supports this idea. We have shown previously that the water-insoluble Maillard products have substantial similarities with the insoluble organic materials from the meteorites. The Maillard organic materials are also part of the desert varnish on Earth, which is a dark, shiny, hard rock coating that contains iron and manganese and is glazed in silicate. Rocks that are similar in appearance to the desert varnish have been observed on the Martian surface. They may also contain the organic materials. We have undertaken study of the interactions between the Maillard products, iron and other metals, and silicates, to elucidate the role of the Maillard products in the chemistry of desert varnish and meteorites. Specifically, we have synthesized a series of the Maillard-metal complexes, and have tested their reactivity towards silicates. We have studied the properties of these Maillard-metal-silicate products by the IR spectroscopy. The astrobiological potential of the Maillard-metal complexes is assessed.

Nanoscale surface modification of Li-rich layered oxides for high-capacity cathodes in Li-ion batteries

NASA Astrophysics Data System (ADS)

Lan, Xiwei; Xin, Yue; Wang, Libin; Hu, Xianluo

2018-03-01

Li-rich layered oxides (LLOs) have been developed as a high-capacity cathode material for Li-ion batteries, but the structural complexity and unique initial charging behavior lead to several problems including large initial capacity loss, capacity and voltage fading, poor cyclability, and inferior rate capability. Since the surface conditions are critical to electrochemical performance and the drawbacks, nanoscale surface modification for improving LLO's properties is a general strategy. This review mainly summarizes the surface modification of LLOs and classifies them into three types of surface pre-treatment, surface gradient doping, and surface coating. Surface pre-treatment usually introduces removal of Li2O for lower irreversible capacity while surface doping is aimed to stabilize the structure during electrochemical cycling. Surface coating layers with different properties, protective layers to suppress the interface side reaction, coating layers related to structural transformation, and electronic/ionic conductive layers for better rate capability, can avoid the shortcomings of LLOs. In addition to surface modification for performance enhancement, other strategies can also be investigated to achieve high-performance LLO-based cathode materials.

A novel phenomenological multi-physics model of Li-ion battery cells

NASA Astrophysics Data System (ADS)

Oh, Ki-Yong; Samad, Nassim A.; Kim, Youngki; Siegel, Jason B.; Stefanopoulou, Anna G.; Epureanu, Bogdan I.

2016-09-01

A novel phenomenological multi-physics model of Lithium-ion battery cells is developed for control and state estimation purposes. The model can capture electrical, thermal, and mechanical behaviors of battery cells under constrained conditions, e.g., battery pack conditions. Specifically, the proposed model predicts the core and surface temperatures and reaction force induced from the volume change of battery cells because of electrochemically- and thermally-induced swelling. Moreover, the model incorporates the influences of changes in preload and ambient temperature on the force considering severe environmental conditions electrified vehicles face. Intensive experimental validation demonstrates that the proposed multi-physics model accurately predicts the surface temperature and reaction force for a wide operational range of preload and ambient temperature. This high fidelity model can be useful for more accurate and robust state of charge estimation considering the complex dynamic behaviors of the battery cell. Furthermore, the inherent simplicity of the mechanical measurements offers distinct advantages to improve the existing power and thermal management strategies for battery management.

Nucleophilic substitution at silicon (SN2@Si) via a central reaction barrier.

PubMed

Bento, A Patrícia; Bickelhaupt, F Matthias

2007-03-16

It is textbook knowledge that nucleophilic substitution at carbon (SN2@C) proceeds via a central reaction barrier which disappears in the corresponding nucleophilic substitution reaction at silicon (SN2@Si). Here, we address the question why the central barrier disappears from SN2@C to SN2@Si despite the fact that these processes are isostructural and isoelectronic. To this end, we have explored and analyzed the potential energy surfaces (PES) of various Cl-+CR3Cl (R=H, CH3) and Cl-+SiR3Cl model reactions (R=H, CH3, C2H5, and OCH3). Our results show that the nature of the SN2 reaction barrier is in essence steric, but that it can be modulated by electronic factors. Thus, simply by increasing the steric demand of the substituents R around the silicon atom, the SN2@Si mechanism changes from its regular single-well PES (with a stable intermediate transition complex, TC), via a triple-well PES (with a pre- and a post-TS before and after the central TC), to a double-well PES (with a TS; R=OCH3), which is normally encountered for SN2@C reactions.

Calorimetric Determination of Thermodynamic Stability of MAX and MXene Phases

DOE PAGES

Sharma, Geetu; Naguib, Michael; Feng, Dawei; ...

2016-11-19

MXenes are layered two dimensional materials with exciting properties useful to a wide range of energy applications. They are derived from ceramics (MAX phases) by leaching and their properties reflect their resulting complex compositions which include intercalating cations and anions and water. Their thermodynamic stability is likely linked to these functional groups but has not yet been addressed by quantitative experimental measurements. We report enthalpies of formation from the elements at 25 °C measured using high temperature oxide melt solution calorimetry for a layered Ti-Al-C MAX phase, and the corresponding Ti-C based MXene. The thermodynamic stability of the Ti 3Cmore » 2T x MXene (Tx stands for anionic surface moieties, and intercalated cations) was assessed by calculating the enthalpy of reaction of the MAX phase (ideal composition Ti 3AlC 2) to form MXene, The very exothermic enthalpy of reaction confirms the stability of MXene in an aqueous environment. The surface terminations (O, OH and F) and cations (Li) chemisorbed on the surface and intercalated in the interlayers play a major role in the thermodynamic stabilization of MXene. These findings help to understand and potentially improve properties and performance by characterizing the energetics of species binding to MXene surfaces during synthesis and in energy storage, water desalination and other applications.« less

A New Bioinspired Perchlorate Reduction Catalyst with Significantly Enhanced Stability via Rational Tuning of Rhenium Coordination Chemistry and Heterogeneous Reaction Pathway.

PubMed

Liu, Jinyong; Han, Mengwei; Wu, Dimao; Chen, Xi; Choe, Jong Kwon; Werth, Charles J; Strathmann, Timothy J

2016-06-07

Rapid reduction of aqueous ClO4(-) to Cl(-) by H2 has been realized by a heterogeneous Re(hoz)2-Pd/C catalyst integrating Re(O)(hoz)2Cl complex (hoz = oxazolinyl-phenolato bidentate ligand) and Pd nanoparticles on carbon support, but ClOx(-) intermediates formed during reactions with concentrated ClO4(-) promote irreversible Re complex decomposition and catalyst deactivation. The original catalyst design mimics the microbial ClO4(-) reductase, which integrates Mo(MGD)2 complex (MGD = molybdopterin guanine dinucleotide) for oxygen atom transfer (OAT). Perchlorate-reducing microorganisms employ a separate enzyme, chlorite dismutase, to prevent accumulation of the destructive ClO2(-) intermediate. The structural intricacy of MGD ligand and the two-enzyme mechanism for microbial ClO4(-) reduction inspired us to improve catalyst stability by rationally tuning Re ligand structure and adding a ClOx(-) scavenger. Two new Re complexes, Re(O)(htz)2Cl and Re(O)(hoz)(htz)Cl (htz = thiazolinyl-phenolato bidentate ligand), significantly mitigate Re complex decomposition by slightly lowering the OAT activity when immobilized in Pd/C. Further stability enhancement is then obtained by switching the nanoparticles from Pd to Rh, which exhibits high reactivity with ClOx(-) intermediates and thus prevents their deactivating reaction with the Re complex. Compared to Re(hoz)2-Pd/C, the new Re(hoz)(htz)-Rh/C catalyst exhibits similar ClO4(-) reduction activity but superior stability, evidenced by a decrease of Re leaching from 37% to 0.25% and stability of surface Re speciation following the treatment of a concentrated "challenge" solution containing 1000 ppm of ClO4(-). This work demonstrates the pivotal roles of coordination chemistry control and tuning of individual catalyst components for achieving both high activity and stability in environmental catalyst applications.

Bioengineering strategies to generate artificial protein complexes.

PubMed

Kim, Heejae; Siu, Ka-Hei; Raeeszadeh-Sarmazdeh, Maryam; Sun, Qing; Chen, Qi; Chen, Wilfred

2015-08-01

For many applications, increasing synergy between distinct proteins through organization is important for the specificity, regulation, and overall reaction efficiency. Although there are many examples of protein complexes in nature, a generalized method to create these complexes remains elusive. Many conventional techniques such as random chemical conjugation, physical adsorption onto surfaces, and encapsulation within matrices are imprecise approaches and can lead to deactivation of protein native functionalities. More "bio-friendly" approaches such as genetically fused proteins and biological scaffolds often can result in low yields and low complex stability. Alternatively, site-specific protein conjugation or ligation can generate artificial protein complexes that preserve the native functionalities of protein domains and maintain stability through covalent bonds. In this review, we describe three distinct methods to synthesize artificial protein complexes (genetic incorPoration of unnatural amino acids to introduce bio-orthogonal azide and alkyne groups to proteins, split-intein based expressed protein ligation, and sortase mediated ligation) and highlight interesting applications for each technique. © 2015 Wiley Periodicals, Inc.

Kinetic and mechanism formation reaction of complex compound Cu with di-n-buthildithiocarbamate (dbdtc) ligand

NASA Astrophysics Data System (ADS)

Haryani, S.; Kurniawan, C.; Kasmui

2018-04-01

Synthesis of complex compound is one field of research which intensively studied. Metal-dithiocarbamate complexes find wide-ranging applications in nanomaterial and metal separation science, and have potential use as chemotherapeutic, pesticides, and as additives to lubricants. However, the information about is reaction kinetic and mechanism are very much lacking. The research and analyzes results show that reaction synthesis ligand DBDTC and complex compounds Cu-DBDTC. Optimum reaction condition of formation of complex compounds Cu with DBDTC at pH=3, [DBDTC] = 4.10-3 M, and the time of reaction 5 minutes. Based the analysis varian reaction of complex compounds at pH 3 and 4, diffrence significance at the other pH: 5; 5,5; 6; 6,5 ; 7; and 8. The various of mole with reactants comosition difference sigbificance, those the time reaction for 5 and 6 minutes diffrence by significance with the other time, it is 3,4,8, and 10 minutes. The great product to at condition pH 6, the time optimum at 5 minutes and molar ratio of logam: ligand = 1:2. The reaction kinetic equation of complex compound Cu with chelathing ligand DBDTC is V=0.917106 [Cu2+]0.87921 [DBDTC]2.03021. Based on the kinetic data, and formed complex compounds estimation, the mechanism explaining by 2 stages. In the first stage formation of [Cu(DBDTC)], and then [Cu(DBDTC)2] with the last structure geomethry planar rectangle. The result of this research will be more useful if an effort is being done in reaction mechanism by chemical computation method for obtain intermediate, and for constant “k” in same stage, k1.k2. and compound complex constanta (β).

2013 Chemical reactions at surfaces. Surfaces in Energy and the Environment. Gordon Research Conference and Gordon Research Seminar (April 28 - May 3, 2013 - Les Diablerets, Switzerland)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stair, Peter C.

presentations on chemistry at solid and liquid surfaces of relevance to catalysis, synthesis, photochemistry, environmental science, and tribology. Topics include: Fundamental Surface Chemistry; Catalysis; Solid Liquid and Aerosol Interfaces; Surface Photochemistry; Synthesis of Surfaces; Environmental Interfaces; Hot Topics in Surface Chemical Reactions; Tribology; Gas-Surface Scattering and Reactions; Novel Materials and Environments.

Activity–stability relationship in the surface electrochemistry of the oxygen evolution reaction

DOE PAGES

Chang, Seo Hyoung; Connell, Justin G.; Danilovic, Nemanja; ...

2014-07-25

Understanding the functional links between the stability and reactivity of oxide materials during the oxygen evolution reaction (OER) is one key to enabling a vibrant hydrogen economy capable of competing with fossil fuel-based technologies. In this work, by focusing on the surface chemistry of monometallic Ru oxide in acidic and alkaline environments, we found that the kinetics of the OER are almost entirely controlled by the stability of the Ru surface atoms. The same activity–stability relationship was found for more complex, polycrystalline and single-crystalline SrRuO 3 thin films in alkaline solutions. We propose that the electrochemical transformation of either watermore » (acidic solutions) or hydroxyl ions (alkaline solutions) to di-oxygen molecules takes place at defect sites that are inherently present on every electrode surface. During the OER, surface defects are also created by the corrosion of the Ru ions. The dissolution is triggered by the potential-dependent change in the valence state ( n) of Ru: from stable but inactive Ru 4+ to unstable but active Ru n>4+. We conclude that if the oxide is stable then it is completely inactive for the OER. As a result, a practical consequence is that the best materials for the OER should balance stability and activity in such a way that the dissolution rate of the oxide is neither too fast nor too slow.« less

First Principle Estimation of Geochemically Important Transition Metal Oxide Properties: Structure and Dynamics of the Bulk, Surface and Mineral/Aqueous Fluid Interface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Ying; Bylaska, Eric J.; Weare, John H.

Reactions in the mineral surface/reservoir fluid interface control many geochemical processes such as the dissolution and growth of minerals (Yanina and Rosso 2008), heterogeneous oxidation/reduction (Hochella 1990, Brown 2001, Hochella, Lower et al. 2008, Navrotsky, Mazeina et al. 2008), and inorganic respiration (Newman 2010). Key minerals involved in these processes are the transition metal oxides and oxyhydroxides (e.g., hematite, Fe2O3, and goethite, FeOOH)(Brown, Henrich et al. 1999, Brown 2001, Hochella, Lower et al. 2008, Navrotsky, Mazeina et al. 2008). To interpret and predict these processes, it is necessary to have a high level of understanding of the interactions between themore » formations containing these minerals and their reservoir fluids. However, these are complicated chemical events occurring under a wide range of T, P, and X conditions and the interpretation is complicated by the highly heterogeneous nature of natural environments (Hochella 1990, Hochella, Lower et al. 2008, Navrotsky, Mazeina et al. 2008) and the electronic and structural complexity of the oxide materials involved(Cox 1992, Kotliar and Vollhardt 2004, Navrotsky, Mazeina et al. 2008). In addition, also because of the complexity of the minerals involved and the heterogeneous nature of natural systems, the direct observation of these reactions at the atomic level is experimentally extremely difficult. Theoretical simulations will provide important support for analysis of the geochemistry of the mineral surface/fluid region as well as provide essential tools to extrapolate laboratory measurements to the field environment.« less

Mechanism of Benzene Tribopolymerization on the RuO2 (110) Surface

NASA Astrophysics Data System (ADS)

Yang, J.; Qi, Y.; Kim, H. D.; Rappe, A. M.

2018-04-01

A tribopolymer formed on the contacts of microelectromechanical and nanoelectromechanical system (MEMS-NEMS) devices is a major concern hampering their practical use in information technology. Conductive metal oxides, such as RuO2 and ReO3 , have been regarded as promising candidate materials for MEMS-NEMS contacts due to their conductivity, hardness, and relatively chemically inert surfaces. However, recent experimental works demonstrate that trace amounts of a polymer could still form on RuO2 surfaces. We demonstrate the mechanism of this class of unexpected tribopolymer formation by conducting density-functional-theory-based computational compression experiments with benzene as the contamination gas. First, mechanical force during compression changes the benzene molecules from slightly physisorbed to strongly chemisorbed. Further compression causes deformation and chemical linkage of the benzene molecules. Finally, the two contacts detach, with one having a complex organic molecule attached and the other a more reactive surface. The complex organic molecule, which has an oxabicyclic segment, can be viewed as the rudiment of a tribopolymer, and the more reactive surface can trigger the next adsorption-reaction-tribopolymer formation cycle. Based on these results, we also predict tribopolymer formation rates by using transition-state theory and the second-order rate law. We promote a deeper understanding of tribopolymer formation (especially on metal oxides) and provide strategies for suppressing tribopolymerization.

Hierarchical and Well-Ordered Porous Copper for Liquid Transport Properties Control.

PubMed

Pham, Quang N; Shao, Bowen; Kim, Yongsung; Won, Yoonjin

2018-05-09

Liquid delivery through interconnected pore network is essential for various interfacial transport applications ranging from energy storage to evaporative cooling. The liquid transport performance in porous media can be significantly improved through the use of hierarchical morphology that leverages transport phenomena at different length scales. Traditional surface engineering techniques using chemical or thermal reactions often show nonuniform surface nanostructuring within three-dimensional pore network due to uncontrollable diffusion and reactivity in geometrically complex porous structures. Here, we demonstrate hierarchical architectures on the basis of crystalline copper inverse opals using an electrochemistry approach, which offers volumetric controllability of structural and surface properties within the complex porous metal. The electrochemical process sequentially combines subtractive and additive steps-electrochemical polishing and electrochemical oxidation-to improve surface wetting properties without sacrificing structural permeability. We report the transport performance of the hierarchical inverse opals by measuring the capillary-driven liquid rise. The capillary performance parameter of hierarchically engineered inverse opal ( K/ R eff = ∼5 × 10 -3 μm) is shown to be higher than that of a typical crystalline inverse opal ( K/ R eff = ∼1 × 10 -3 μm) owing to the enhancement in fluid permeable and hydrophilic pathways. The new surface engineering method presented in this work provides a rational approach in designing hierarchical porous copper for transport performance enhancements.

NO ICE HYDROGENATION: A SOLID PATHWAY TO NH{sub 2}OH FORMATION IN SPACE

DOE Office of Scientific and Technical Information (OSTI.GOV)

Congiu, Emanuele; Dulieu, Francois; Chaabouni, Henda

2012-05-01

Icy dust grains in space act as catalytic surfaces onto which complex molecules form. These molecules are synthesized through exothermic reactions from precursor radicals and, mostly, hydrogen atom additions. Among the resulting products are species of biological relevance, such as hydroxylamine-NH{sub 2}OH-a precursor molecule in the formation of amino acids. In this Letter, laboratory experiments are described that demonstrate NH{sub 2}OH formation in interstellar ice analogs for astronomically relevant temperatures via successive hydrogenation reactions of solid nitric oxide (NO). Inclusion of the experimental results in an astrochemical gas-grain model proves the importance of a solid-state NO+H reaction channel as amore » starting point for prebiotic species in dark interstellar clouds and adds a new perspective to the way molecules of biological importance may form in space.« less

Density function theoretical study on the complex involved in Th atom-activated C-C bond in C2H6

NASA Astrophysics Data System (ADS)

Qing-Qing, Wang; Peng, Li; Tao, Gao; Hong-Yan, Wang; Bing-Yun, Ao

2016-06-01

Density functional theory (DFT) calculations are performed to investigate the reactivity of Th atom toward ethane C-C bond activation. A comprehensive description of the reaction mechanisms leading to two different reaction products is presented. We report a complete exploration of the potential energy surfaces by taking into consideration different spin states. In addition, the intermediate and transition states along the reaction paths are characterized. Total, partial, and overlap population density of state diagrams and analyses are also presented. Furthermore, the natures of the chemical bonding of intermediate and transition states are studied by using topological method combined with electron localization function (ELF) and Mayer bond order. Infrared spectrum (IR) is obtained and further discussed based on the optimized geometries. Project supported by the National Natural Science Foundation of China (Grant Nos. 21371160, 21401173, and 11364023).

Accurate rates of the complex mechanisms for growth and dissolu-tion of minerals using a combination of rare event theories

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stack, Andrew G; Raiten, Paolo; Gale, Julian D.

2012-01-01

Mineral growth and dissolution are often treated as occurring via a single, reversible process that governs the rate of reaction. We show that multiple, distinct intermediate states can occur during both growth and dissolution. Specifically, we have used metadynamics, a method to efficiently explore the free energy landscape of a system, coupled to umbrella sampling and reactive flux calculations, to examine the mechanism and rates of attachment and detachment of a barium ion onto a stepped, barite (BaSO4) surface. The activation energies calculated for the rate limiting reactions, which are different for attachment and detachment, precisely match those measured experimentallymore » during both growth and dissolution. These results can potentially explain anomalous, non-steady state mineral reaction rates observed experimentally, and will enable the design of more efficient growth inhibitors and facilitate an understanding of the effect of impurities.« less

Hemoglobin and Myoglobin as Reducing Agents in Biological Systems. Redox Reactions of Globins with Copper and Iron Salts and Complexes.

PubMed

Postnikova, G B; Shekhovtsova, E A

2016-12-01

In addition to reversible O2 binding, respiratory proteins of the globin family, hemoglobin (Hb) and myoglobin (Mb), participate in redox reactions with various metal complexes, including biologically significant ones, such as those of copper and iron. HbO 2 and MbO 2 are present in cells in large amounts and, as redox agents, can contribute to maintaining cell redox state and resisting oxidative stress. Divalent copper complexes with high redox potentials (E 0 , 200-600 mV) and high stability constants, such as [Cu(phen) 2 ] 2+ , [Cu(dmphen) 2 ] 2+ , and CuDTA oxidize ferrous heme proteins by the simple outer-sphere electron transfer mechanism through overlapping π-orbitals of the heme and the copper complex. Weaker oxidants, such as Cu2+, CuEDTA, CuNTA, CuCit, CuATP, and CuHis (E 0 ≤ 100-150 mV) react with HbO 2 and MbO 2 through preliminary binding to the protein with substitution of the metal ligands with protein groups and subsequent intramolecular electron transfer in the complex (the site-specific outer-sphere electron transfer mechanism). Oxidation of HbO 2 and MbO 2 by potassium ferricyanide and Fe(3) complexes with NTA, EDTA, CDTA, ATP, 2,3-DPG, citrate, and pyrophosphate PP i proceeds mainly through the simple outer-sphere electron transfer mechanism via the exposed heme edge. According to Marcus theory, the rate of this reaction correlates with the difference in redox potentials of the reagents and their self-exchange rates. For charged reagents, the reaction may be preceded by their nonspecific binding to the protein due to electrostatic interactions. The reactions of LbO 2 with carboxylate Fe complexes, unlike its reactions with ferricyanide, occur via the site-specific outer-sphere electron transfer mechanism, even though the same reagents oxidize structurally similar MbO 2 and cytochrome b 5 via the simple outer-sphere electron transfer mechanism. Of particular biological interest is HbO 2 and MbO 2 transformation into met-forms in the presence of small amounts of metal ions or complexes (catalysis), which, until recently, had been demonstrated only for copper compounds with intermediate redox potentials. The main contribution to the reaction rate comes from copper binding to the "inner" histidines, His97 (0.66 nm from the heme) that forms a hydrogen bond with the heme propionate COO - group, and the distal His64. The affinity of both histidines for copper is much lower than that of the surface histidines residues, and they are inaccessible for modification with chemical reagents. However, it was found recently that the high-potential Fe(3) complex, potassium ferricyanide (400 mV), at a 5 to 20% of molar protein concentration can be an efficient catalyst of MbO 2 oxidation into metMb. The catalytic process includes binding of ferrocyanide anion in the region of the His119 residue due to the presence there of a large positive local electrostatic potential and existence of a "pocket" formed by Lys16, Ala19, Asp20, and Arg118 that is sufficient to accommodate [Fe(CN) 6 ] 4- . Fast, proton-assisted reoxidation of the bound ferrocyanide by oxygen (which is required for completion of the catalytic cycle), unlike slow [Fe(CN) 6 ] 4- oxidation in solution, is provided by the optimal location of neighboring protonated His113 and His116, as it occurs in the enzyme active site.

Kinetic multi-layer model of aerosol surface and bulk chemistry (KM-SUB): the influence of interfacial transport and bulk diffusion on the oxidation of oleic acid by ozone

NASA Astrophysics Data System (ADS)

Shiraiwa, Manabu; Pfrang, Christian; Pöschl, Ulrich

2010-05-01

Aerosols are ubiquitous in the atmosphere and have strong effects on climate and public health. Gas-particle interactions can significantly change the physical and chemical properties of aerosols such as toxicity, reactivity, hygroscopicity and radiative properties. Chemical reactions and mass transport lead to continuous transformation and changes in the composition of atmospheric aerosols ("chemical aging"). Resistor model formulations are widely used to describe and investigate heterogeneous reactions and multiphase processes in laboratory, field and model studies of atmospheric chemistry. The traditional resistor models, however, are usually based on simplifying assumptions such as steady state conditions, homogeneous mixing, and limited numbers of non-interacting species and processes. In order to overcome these limitations, Pöschl, Rudich and Ammann have developed a kinetic model framework (PRA framework) with a double-layer surface concept and universally applicable rate equations and parameters for mass transport and chemical reactions at the gas-particle interface of aerosols and clouds [1]. Based on the PRA framework, we present a novel kinetic multi-layer model that explicitly resolves mass transport and chemical reaction at the surface and in the bulk of aerosol particles (KM-SUB) [2]. The model includes reversible adsorption, surface reactions and surface-bulk exchange as well as bulk diffusion and reaction. Unlike earlier models, KM-SUB does not require simplifying assumptions about steady-state conditions and radial mixing. The temporal evolution and concentration profiles of volatile and non-volatile species at the gas-particle interface and in the particle bulk can be modeled along with surface concentrations and gas uptake coefficients. In this study we explore and exemplify the effects of bulk diffusion on the rate of reactive gas uptake for a simple reference system, the ozonolysis of oleic acid particles, in comparison to experimental data and earlier model studies. We demonstrate how KM-SUB can be used to interpret and analyze experimental data from laboratory studies, and how the results can be extrapolated to atmospheric conditions. In particular, we show how interfacial transport and bulk transport, i.e., surface accommodation, bulk accommodation and bulk diffusion, influence the kinetics of the chemical reaction. Sensitivity studies suggest that in fine air particulate matter oleic acid and compounds with similar reactivity against ozone (C=C double bonds) can reach chemical life-times of multiple hours only if they are embedded in a (semi-)solid matrix with very low diffusion coefficients (~10-10 cm2 s-1). Depending on the complexity of the investigated system, unlimited numbers of volatile and non-volatile species and chemical reactions can be flexibly added and treated with KM-SUB. We propose and intend to pursue the application of KM-SUB as a basis for the development of a detailed master mechanism of aerosol chemistry as well as for the derivation of simplified but realistic parameterizations for large-scale atmospheric and climate models. References [1] Pöschl et al., Atmos. Chem. and Phys., 7, 5989-6023 (2007). [2] Shiraiwa et al., Atmos. Chem. Phys. Discuss., 10, 281-326 (2010).

Field ion microscopic studies of the CO oxidation on platinum: Field ion imaging and titration reactions

NASA Astrophysics Data System (ADS)

Gorodetskii, V.; Drachsel, W.; Block, J. H.

1994-05-01

Elementary steps of the CO oxidation—which are important for understanding the oscillatory behavior of this catalytic reaction—are investigated simultaneously on different Pt-single crystal surfaces by field ion microscopy. Due to preferential ionization probabilities of oxygen as imaging gas on those surface sites, which are adsorbed with oxygen, these sites can be imaged in a lateral resolution on the atomic scale. In the titration reaction a COad-precovered field emitter surface reacts with gaseous oxygen adsorbed from the gas phase or, vice versa, the Oad-precovered surface with carbon monoxide adsorbed from the gas phase. The competition of the manifold of single crystal planes exposed to the titration reaction at the field emitter tip is studied. The surface specificity can be documented in the specific reaction delay times of the different planes and in the propagation rates of the reaction-diffusion wave fronts measured on these individual planes during the titration reaction with a time resolution of 40 ms. At 300 K the COad-precovered surfaces display the {011} regions, precisely the {331} planes as the most active, followed by {012}, {122}, {001}, and finally by {111}. Reaction wave fronts move with a velocity of 8 Å/s at {012}, with ≊0.8 Å/s at {111}, and have a very fast ``switch-on'' reaction at the (001) plane with 500 Å/s. At higher temperature, T=350 K, an acceleration of reaction rates is combined with shorter delay times. The titration reaction of a precovered Oad surface with COgas at T=373 K shows the formation of CO islands starting in the {011} regions with a quickly moving reaction front into the other surface areas without showing particular delay times for different surface symmetries. The two reverse titration reactions have a largely different character. The titration of COad with oxygen adsorbed from the gas phase consists of three different steps, (i) the induction times, (ii) the highly surface specific reaction, and (iii) different rates of wave front propagation. The reaction of COgas with a precovered Oad layer on the other hand starts with nucleating islands around the {011} planes from where the whole emitter surface is populated with COad without pronounced surface specifity.

The birth and evolution of surface science: child of the union of science and technology.

PubMed

Duke, C B

2003-04-01

This article is an account of the birth and evolution of surface science as an interdisciplinary research area. Surface science emanated from the confluence of concepts and tools in physics and chemistry with technological innovations that made it possible to determine the structure and properties of surfaces and interfaces and the dynamics of chemical reactions at surfaces. The combination in the 1960s and 1970s of ultra-high-vacuum (i.e., P < 10(-7) Pascal or 10(-9) Torr) technology with the recognition that electrons in the energy range from 50 to 500 eV exhibited inelastic collision mean free paths of the order of a few angstroms fostered an explosion of activity. The results were a reformulation of the theory of electron solid scattering, the nearly universal use of electron spectroscopies for surface characterization, the rise of surface science as an independent interdisciplinary research area, and the emergence of the American Vacuum Society (AVS) as a major international scientific society. The rise of microelectronics in the 1970s and 1980s resulted in huge increases in computational power. These increases enabled more complex experiments and the utilization of density functional theory for the quantitative prediction of surface structure and dynamics. Development of scanning-probe microscopies in the 1990s led to atomic-resolution images of macroscopic surfaces and interfaces as well as videos of atoms moving about on surfaces during growth and diffusion. Scanning probes have since brought solid-liquid interfaces into the realm of atomic-level surface science, expanding its scope to more complex systems, including fragile biological materials and processes.

Formation of Glycerol through Hydrogenation of CO Ice under Prestellar Core Conditions

NASA Astrophysics Data System (ADS)

Fedoseev, G.; Chuang, K.-J.; Ioppolo, S.; Qasim, D.; van Dishoeck, E. F.; Linnartz, H.

2017-06-01

Observational studies reveal that complex organic molecules (COMs) can be found in various objects associated with different star formation stages. The identification of COMs in prestellar cores, I.e., cold environments in which thermally induced chemistry can be excluded and radiolysis is limited by cosmic rays and cosmic-ray-induced UV photons, is particularly important as this stage sets up the initial chemical composition from which ultimately stars and planets evolve. Recent laboratory results demonstrate that molecules as complex as glycolaldehyde and ethylene glycol are efficiently formed on icy dust grains via nonenergetic atom addition reactions between accreting H atoms and CO molecules, a process that dominates surface chemistry during the “CO freeze-out stage” in dense cores. In the present study we demonstrate that a similar mechanism results in the formation of the biologically relevant molecule glycerol—HOCH2CH(OH)CH2OH—a three-carbon-bearing sugar alcohol necessary for the formation of membranes of modern living cells and organelles. Our experimental results are fully consistent with a suggested reaction scheme in which glycerol is formed along a chain of radical-radical and radical-molecule interactions between various reactive intermediates produced upon hydrogenation of CO ice or its hydrogenation products. The tentative identification of the chemically related simple sugar glyceraldehyde—HOCH2CH(OH)CHO—is discussed as well. These new laboratory findings indicate that the proposed reaction mechanism holds much potential to form even more complex sugar alcohols and simple sugars.

Fate and transport of uranium (VI) in weathered saprolite

DOE PAGES

Kim, Young-Jin; Brooks, Scott C.; Zhang, Fan; ...

2014-11-09

We conducted batch and column experiments to investigate sorption and transport of uranium (U) in the presence of saprolite derived from interbedded shale, limestone, and sandstone sequences. Sorption kinetics were measured at two initial concentrations (C0; 1, 10 mM) and three soil:solution ratios (Rs/w; 0.005, 0.25, 2 kg/L) at pH 4.5 (pH of the saprolite). The rate of U loss from solution (mmole/L/h) increased with increasing Rs/w. Uranium sorption exhibited a fast phase with 80% sorption in the first eight hours for all C0 and Rs/w values and a slow phase during which the reaction slowly approached (pseudo) equilibrium overmore » the next seven days. The pH-dependency of U sorption was apparent in pH sorption edges. U(VI) sorption increased over the pH range 4e6, then decreased sharply at pH > 7.5. U(VI) sorption edges were well described by a surface complexation model using calibrated parameters and the reaction network proposed by Waite et al. (1994). Sorption isotherms measured using the same Rs/w and pH values showed a solids concentration effect where U(VI) sorption capacity and affinity decreased with increasing solids concentration. Moreover, this effect may have been due to either particle aggregation or competition between U(VI) and exchangeable cations for sorption sites. The surface complexation model with calibrated parameters was able to predict the general sorption behavior relatively well, but failed to reproduce solid concentration effects, implying the importance of appropriate design if batch experiments are to be utilized for dynamic systems. Transport of U(VI) through the packed column was significantly retarded. We also conducted transport simulations using the reactive transport model HydroGeoChem (HGC) v5.0 that incorporated the surface complexation reaction network used to model the batch data. Model parameters reported by Waite et al. (1994) provided a better prediction of U transport than optimized parameters derived from our sorption edges. The results presented in this study highlight the challenges in defining appropriate conditions for batch-type experiments used to extrapolate parameters for transport models, and also underline a gap in our ability to transfer batch results to transport simulations.« less

Effect of adsorbed metals ions on the transport of Zn- and Ni-EDTA complexes in a sand and gravel aquifer

USGS Publications Warehouse

Kent, D.B.; Davis, J.A.; Anderson, L.C.D.; Rea, B.A.; Coston, J.A.

2002-01-01

Adsorption, complexation, and dissolution reactions strongly influenced the transport of metal ions complexed with ethylenediaminetetraacetic acid (EDTA) in a predominantly quartz-sand aquifer during two tracer tests conducted under mildly reducing conditions at pH 5.8 to 6.1. In tracer test M89, EDTA complexes of zinc (Zn) and nickel (Ni), along with excess free EDTA, were injected such that the lower portion of the tracer cloud traveled through a region with adsorbed manganese (Mn) and the upper portion of the tracer cloud traveled through a region with adsorbed Zn. In tracer test S89, Ni- and Zn-EDTA complexes, along with excess EDTA complexed with calcium (Ca), were injected into a region with adsorbed Mn. The only discernable chemical reaction between Ni-EDTA and the sediments was a small degree of reversible adsorption leading to minor retardation. In the absence of adsorbed Zn, the injected Zn was displaced from EDTA complexes by iron(III) [Fe(III)] dissolved from the sediments. Displacement of Zn by Fe(III) on EDTA became increasingly thermodynamically favorable with decreasing total EDTA concentration. The reaction was slow compared to the time-scale of transport. Free EDTA rapidly dissolved aluminum (Al) from the sediments, which was subsequently displaced slowly by Fe. In the portion of tracer cloud M89 that traveled through the region contaminated with adsorbed Zn, little displacement of Zn complexed with EDTA was observed, and Al was rapidly displaced from EDTA by Zn desorbed from the sediments, in agreement with equilibrium calculations. In tracer test S89, desorption of Mn dominated over the more thermodynamically favorable dissolution of Al oxyhydroxides. Comparison with results from M89 suggests that dissolution of Al oxyhydroxides in coatings on these sediment grains by Ca-EDTA was rate-limited whereas that by free EDTA reached equilibrium on the time-scale of transport. Rates of desorption are much faster than rates of dissolution of Fe oxyhydroxides from sediment-grain surfaces and, therefore, adsorbed metal ions can strongly influence the speciation of ligands like EDTA in soils and sediments, especially over small temporal and spatial scales. Copyright ?? 2002 Elsevier Science Ltd.

Characterising Complex Enzyme Reaction Data

PubMed Central

Rahman, Syed Asad; Thornton, Janet M.

2016-01-01

The relationship between enzyme-catalysed reactions and the Enzyme Commission (EC) number, the widely accepted classification scheme used to characterise enzyme activity, is complex and with the rapid increase in our knowledge of the reactions catalysed by enzymes needs revisiting. We present a manual and computational analysis to investigate this complexity and found that almost one-third of all known EC numbers are linked to more than one reaction in the secondary reaction databases (e.g., KEGG). Although this complexity is often resolved by defining generic, alternative and partial reactions, we have also found individual EC numbers with more than one reaction catalysing different types of bond changes. This analysis adds a new dimension to our understanding of enzyme function and might be useful for the accurate annotation of the function of enzymes and to study the changes in enzyme function during evolution. PMID:26840640

Hydration of AN Acid Anhydride: the Water Complex of Acetic Sulfuric Anhydride

NASA Astrophysics Data System (ADS)

Smith, CJ; Huff, Anna; Mackenzie, Becca; Leopold, Ken

2017-06-01

The water complex of acetic sulfuric anhydride (ASA, CH_{3}COOSO_{2}OH) has been observed by pulsed nozzle Fourier transform microwave spectroscopy. ASA is formed in situ in the supersonic jet via the reaction of SO_{3} and acetic acid and subsequently forms a complex with water during the expansion. Spectra of the parent and fully deuterated form, as well as those of the species derived from CH_{3}^{13}COOH, have been observed. The fitted internal rotation barrier of the methyl group is 219.599(21), \\wn indicating the complexation with water lowers the internal rotation barrier of the methyl group by 9% relative to that of free ASA. The observed species is one of several isomers identified theoretically in which the water inserts into the intramolecular hydrogen bond of the ASA. Aspects of the intermolecular potential energy surface are discussed.

Mechanistic investigations of CO-photoextrusion and oxidative addition reactions of early transition-metal carbonyls: (η(5)-C5H5)M(CO)4 (M = V, Nb, Ta).

PubMed

Su, Shih-Hao; Su, Ming-Der

2016-06-28

The mechanisms for the photochemical Si-H bond activation reaction are studied theoretically using a model system of the group 5 organometallic compounds, η(5)-CpM(CO)4 (M = V, Nb, and Ta), with the M06-2X method and the Def2-SVPD basis set. Three types of reaction pathways that lead to final insertion products are identified. The structures of the intersystem crossings, which play a central role in these photo-activation reactions, are determined. The intermediates and transitional structures in either the singlet or triplet states are also calculated to provide a mechanistic explanation of the reaction pathways. All of the potential energy surfaces for the group 5 η(5)-CpM(CO)4 complexes are quite similar. In particular, the theoretical evidence suggests that after irradiation using light, η(5)-CpM(CO)4 quickly loses one CO ligand to yield two tricarbonyls, in either the singlet or the triplet states. The triplet tricarbonyl 16-electron intermediates, ([η(5)-CpM(CO)3](3)), play a key role in the formation of the final oxidative addition product, η(5)-CpM(CO)3(H)(SiMe3). However, the singlet counterparts, ([η(5)-CpM(CO)3](1)), play no role in the formation of the final product molecule, but their singlet metal centers interact weakly with solvent molecules ((Me3)SiH) to produce alkyl-solvated organometallic complexes, which are observable experimentally. This theoretical evidence is in accordance with the available experimental observations.

Unraveling the Reaction Chemistry of Icy Ocean World Surfaces

NASA Astrophysics Data System (ADS)

Hudson, R.; Loeffler, M. J.; Gerakines, P.

2017-12-01

The diverse endogenic chemistry of ocean worlds can be divided among interior, surface, and above-surface process, with contributions from exogenic agents such as solar, cosmic, and magnetospheric radiation. Bombardment from micrometeorites to comets also can influence chemistry by both delivering new materials and altering pre-existing ones, and providing energy to drive reactions. Geological processes further complicate the chemistry by transporting materials from one environment to another. In this presentation the focus will be on some of the thermally driven and radiation-induced changes expected from icy materials, primarily covalent and ionic compounds. Low-temperature conversions of a few relatively simple molecules into ions possessing distinct infrared (IR) features will be covered, with an emphasis on such features as might be identified through either orbiting spacecraft or landers. The low-temperature degradation of a few bioorganic molecules, such as DNA nucleobases and some common amino acids, will be used as examples of the more complex, and potentially misleading, chemistry expected for icy moons of the outer solar system. This work was supported by NASA's Emerging Worlds and Outer Planets Research programs, as well as the NASA Astrobiology Institute's Goddard Center for Astrobiology.

"Click" on Alkynylated Carbon Quantum Dots: An Efficient Surface Functionalization for Specific Biosensing and Bioimaging.

PubMed

Gao, Ming Xuan; Yang, Lin; Zheng, Yi; Yang, Xiao Xi; Zou, Hong Yan; Han, Jing; Liu, Ze Xi; Li, Yuan Fang; Huang, Cheng Zhi

2017-02-10

Surface functionalization is an essential pre requisite for wide and specific applications of nanoparticles such as photoluminescent (PL) carbon quantum dots (CQDs), but it remains a major challenge. In this report, alkynylated CQDs, prepared from carboxyl-rich CQDs through amidation with propargylamine in the presence of 1,1'-carbonyldiimidazole, were modified efficiently with azido molecular beacon DNA through a copper(I)-catalyzed alkyne-azide cycloaddition reaction (CuAAC). As a proof-of-concept, the DNA-modified CQDs are then bonded with gold nanoparticles (AuNPs, 5 nm) through a gold-sulfur bond. Owing to the emission enhancement, this complex can then be applied to the recognition of a single-base- mismatched target. The same functionalizing strategy applied to click the alkynylated CQDs with a nuclear localization sequence (NLS) peptide showed that the NLS-modified CQDs could target the nuclei specifically. These results indicate that surface functionalization of CQDs through a nonstoichiometric copper chalcogenide nanocrystal- (nsCuCNC-) catalyzed click reaction is efficient, and has significant potential in the fields of biosensing and bioimaging. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Surface catalysis of uranium(VI) reduction by iron(II)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liger, E.; Charlet, L.; Van Cappellen, P.

1999-10-01

Colloidal hematite ({alpha}-Fe{sub 2}O{sub 3}) is used as model solid to investigate the kinetic effect of specific adsorption interactions on the chemical reduction of uranyl (U{sup VI}O{sub 2}{sup 2+}) by ferrous iron. Acid-base titrations and Fe(II) and uranyl adsorption experiments are performed on hematite suspensions, under O{sub 2}- and CO{sub 2}-free conditions. The results are explained in terms of a constant capacitance surface complexation model of the hematite-aqueous solution interface. Two distinct Fe(II) surface complexes are required to reproduce the data: ({equivalent{underscore}to}Fe{sup III}OFe{sup II}){sup +} (or {equivalent{underscore}to}Fe{sup III}OFe{sup II}(OH{sub 2}){sub n}{sup +}) and {equivalent{underscore}to}Fe{sup III}OFe{sup II}OH{sup 0} (or {equivalent{underscore}to}Fe{sup III}OFe{supmore » II}(OH{sub 2}){sub n{minus}1}OH{sup 0}). The latter complex represents a significant fraction of total adsorbed Fe(II) at pH {gt} 6.5. Uranyl binding to the hematite particles is characterized by a sharp adsorption edge between pH 4 and pH 5.5. Because of the absence of competing aqueous carbonate complexes, uranyl remains completely adsorbed at pH {gt} 7. A single mononuclear surface complex accounts for the adsorption of uranyl over the entire range of experimental conditions. Although thermodynamically feasible, no reaction between uranyl and Fe(II) is observed in homogeneous solution at pH 7.5, for periods of up to three days. In hematite suspensions, however, surface-bound uranyl reacts on a time scale of hours. Based on Fourier Transformed Infrared spectra, chemical reduction of U(VI) is inferred to be the mechanism responsible for the disappearance of uranyl. The kinetics of uranyl reduction are quantified by measuring the decrease with time of the concentration of U(VI) extractable from the hematite particles by NaHCO{sub 3}. In the presence of excess Fe(II), the initial rate of U(VI) reduction exhibits a first-order dependence on the concentration of adsorbed uranyl. The pseudo-first-order rate constant varies with pH (range, 6--7.5) and the total (dissolved + adsorbed) concentration of Fe(II) (range, 2--160 {micro}M). When analyzing the rate data in terms of the calculated surface speciation, the variability of the rate constant can be accounted for entirely by changes in the concentration of the Fe(II) monohydroxo surface complex {equivalent{underscore}to}Fe{sup III}OFe{sup II}OH{sup 0}. Therefore, the rate law is derived for the hematite-catalyzed reduction of uranyl by Fe(II), where the bimolecular rate constant {kappa} has a value of 399 {+-} 25 M{sup {minus}1} min{sup {minus}1} at 25 C. The hydroxo surface complex is the rate-controlling reductant species, because it provides the most favorable coordination environment in which electrons are removed from Fe(II). Natural particulate matter collected in the hypolimnion of a seasonally stratified lake also causes the rapid reduction of uranyl by Fe(II), Ferrihydrite, identified in the particulate matter by X-ray diffraction, is one possible mineral phase accelerating the reaction between U(VI) and Fe(II). At near-neutral pH and total Fe(II) levels less than 1 mM, the pseudo-first-order rate constants of chemical U(VI) reduction, measured in the presence of the hematite and lake particles, are of the same order of magnitude as the highest corresponding rate coefficients for enzymatic U(VI) reduction in bacterial cultures. Hence, based on the results of this study, surface-catalyzed U(VI) reduction by Fe(II) is expected to be a major pathway of uranium immobilization in a wide range of redox-stratified environments.« less

A density functional theory study on the carbon chain growth of ethanol formation on Cu-Co (111) and (211) surfaces

NASA Astrophysics Data System (ADS)

Ren, Bohua; Dong, Xiuqin; Yu, Yingzhe; Wen, Guobin; Zhang, Minhua

2017-08-01

Calculations based on the first-principle density functional theory were carried out to study the most controversial reactions in ethanol formation from syngas on Cu-Co surfaces: CO dissociation mechanism and the key reactions of carbon chain growth of ethanol formation (HCO insertion reactions) on four model surfaces (Cu-Co (111) and (211) with Cu-rich or Co-rich surfaces) to investigate the synergy of the Cu and Co components since the complete reaction network of ethanol formation from syngas is a huge computational burden to calculate on four Cu-Co surface models. We investigated adsorption of important species involved in these reactions, activation barrier and reaction energy of H-assisted dissociation mechanism, directly dissociation of CO, and HCO insertion reactions (CHx + HCO → CHxCHO (x = 1-3)) on four Cu-Co surface models. It was found that reactions on Cu-rich (111) and (211) surfaces all have lower activation barrier in H-assisted dissociation and HCO insertion reactions, especially CH + HCO → CHCHO reaction. The PDOS of 4d orbitals of surface Cu and Co atoms of all surfaces were studied. Analysis of d-band center of Cu and Co atoms and the activation barrier data suggested the correlation between electronic property and catalytic performance. Cu-Co bimetallic with Cu-rich surface allows Co to have higher catalytic activity through the interaction of Cu and Co atom. Then it will improve the adsorption of CO and catalytic activity of Co. Thus it is more favorable to the carbon chain growth in ethanol formation. Our study revealed the factors influencing the carbon chain growth in ethanol production and explained the internal mechanism from electronic property aspect.

Reactions and reaction rates in the regional aquifer beneath the Pajarito Plateau, north-central New Mexico, USA

NASA Astrophysics Data System (ADS)

Hereford, Anne G.; Keating, Elizabeth H.; Guthrie, George D.; Zhu, Chen

2007-05-01

Reactions and reaction rates within aquifers are fundamental components of critical hydrological processes. However, reactions simulated in laboratory experiments typically demonstrate rates that are much faster than those observed in the field. Therefore, it is necessary to conduct more reaction rate analyses in natural settings. This study of geochemical reactions in the regional aquifer in the Pajarito Plateau near Los Alamos, New Mexico combines modeling with petrographic assessment to further knowledge and understanding of complex natural hydrologic systems. Groundwater geochemistry shows marked evolution along assumed flow paths. The flow path chosen for this study was evaluated using inverse mass balance modeling to calculate the mass transfer. X-ray diffraction and field emission gun scanning electron microscopy were used to identify possible reactants and products. Considering the mineralogy of the aquifer and saturation indices for the regional water refined initial interpretations. Calculations yielded dissolution rates for plagioclase on the order of 10-15 mol s-1 m-2 and for K-feldspar on the order of 10-17 mol s-1 m-2, orders of magnitude slower than laboratory rates. While these rates agree with other aquifer studies, they must be considered in the light of the uncertainty associated with geometric surface area estimates, 14C ages, and aquifer properties.

Exploring chemical reaction mechanisms through harmonic Fourier beads path optimization.

PubMed

Khavrutskii, Ilja V; Smith, Jason B; Wallqvist, Anders

2013-10-28

Here, we apply the harmonic Fourier beads (HFB) path optimization method to study chemical reactions involving covalent bond breaking and forming on quantum mechanical (QM) and hybrid QM∕molecular mechanical (QM∕MM) potential energy surfaces. To improve efficiency of the path optimization on such computationally demanding potentials, we combined HFB with conjugate gradient (CG) optimization. The combined CG-HFB method was used to study two biologically relevant reactions, namely, L- to D-alanine amino acid inversion and alcohol acylation by amides. The optimized paths revealed several unexpected reaction steps in the gas phase. For example, on the B3LYP∕6-31G(d,p) potential, we found that alanine inversion proceeded via previously unknown intermediates, 2-iminopropane-1,1-diol and 3-amino-3-methyloxiran-2-ol. The CG-HFB method accurately located transition states, aiding in the interpretation of complex reaction mechanisms. Thus, on the B3LYP∕6-31G(d,p) potential, the gas phase activation barriers for the inversion and acylation reactions were 50.5 and 39.9 kcal∕mol, respectively. These barriers determine the spontaneous loss of amino acid chirality and cleavage of peptide bonds in proteins. We conclude that the combined CG-HFB method further advances QM and QM∕MM studies of reaction mechanisms.

User's guide to PHREEQC (Version 2) : a computer program for speciation, batch-reaction, one-dimensional transport, and inverse geochemical calculations

USGS Publications Warehouse

Parkhurst, David L.; Appelo, C.A.J.

1999-01-01

PHREEQC version 2 is a computer program written in the C programming language that is designed to perform a wide variety of low-temperature aqueous geochemical calculations. PHREEQC is based on an ion-association aqueous model and has capabilities for (1) speciation and saturation-index calculations; (2) batch-reaction and one-dimensional (1D) transport calculations involving reversible reactions, which include aqueous, mineral, gas, solid-solution, surface-complexation, and ion-exchange equilibria, and irreversible reactions, which include specified mole transfers of reactants, kinetically controlled reactions, mixing of solutions, and temperature changes; and (3) inverse modeling, which finds sets of mineral and gas mole transfers that account for differences in composition between waters, within specified compositional uncertainty limits.New features in PHREEQC version 2 relative to version 1 include capabilities to simulate dispersion (or diffusion) and stagnant zones in 1D-transport calculations, to model kinetic reactions with user-defined rate expressions, to model the formation or dissolution of ideal, multicomponent or nonideal, binary solid solutions, to model fixed-volume gas phases in addition to fixed-pressure gas phases, to allow the number of surface or exchange sites to vary with the dissolution or precipitation of minerals or kinetic reactants, to include isotope mole balances in inverse modeling calculations, to automatically use multiple sets of convergence parameters, to print user-defined quantities to the primary output file and (or) to a file suitable for importation into a spreadsheet, and to define solution compositions in a format more compatible with spreadsheet programs. This report presents the equations that are the basis for chemical equilibrium, kinetic, transport, and inverse-modeling calculations in PHREEQC; describes the input for the program; and presents examples that demonstrate most of the program's capabilities.

Multifunctional Ultra-High Vacuum Apparatus for Studies of the Interactions of Chemical Warfare Agents on Complex Surfaces

DTIC Science & Technology

2014-01-02

colleagues employed solid state NMR to study the decomposition of CWAs on MgO,36 AgY and NaY zeolites ,37 CaO,38 and Al2O3.39 More recently, the...37G. W. Wagner and P. W. Bartram, “Reactions of VX, HD, and their simu- lants with NaY and AgY zeolites . Desulfurization of VX on AgY,” Lang- muir 15

Insight into association reactions on metal surfaces: Density-functional theory studies of hydrogenation reactions on Rh(111)

NASA Astrophysics Data System (ADS)

Liu, Zhi-Pan; Hu, P.; Lee, Ming-Hsien

2003-09-01

Hydrogenation reaction, as one of the simplest association reactions on surfaces, is of great importance both scientifically and technologically. They are essential steps in many industrial processes in heterogeneous catalysis, such as ammonia synthesis (N2+3H2→2NH3). Many issues in hydrogenation reactions remain largely elusive. In this work, the NHx (x=0,1,2) hydrogenation reactions (N+H→NH, NH+H→NH2 and NH2+H→NH3) on Rh(111) are used as a model system to study the hydrogenation reactions on metal surfaces in general using density-functional theory. In addition, C and O hydrogenation (C+H→CH and O+H→OH) and several oxygenation reactions, i.e., C+O, N+O, O+O reactions, are also calculated in order to provide a further understanding of the barrier of association reactions. The reaction pathways and the barriers of all these reactions are determined and reported. For the C, N, NH, and O hydrogenation reactions, it is found that there is a linear relationship between the barrier and the valency of R (R=C, N, NH, and O). Detailed analyses are carried out to rationalize the barriers of the reactions, which shows that: (i) The interaction energy between two reactants in the transition state plays an important role in determining the trend in the barriers; (ii) there are two major components in the interaction energy: The bonding competition and the direct Pauli repulsion; and (iii) the Pauli repulsion effect is responsible for the linear valency-barrier trend in the C, N, NH, and O hydrogenation reactions. For the NH2+H reaction, which is different from other hydrogenation reactions studied, the energy cost of the NH2 activation from the IS to the TS is the main part of the barrier. The potential energy surface of the NH2 on metal surfaces is thus crucial to the barrier of NH2+H reaction. Three important factors that can affect the barrier of association reactions are generalized: (i) The bonding competition effect; (ii) the local charge densities of the reactants along the reaction direction; and (iii) the potential energy surface of the reactants on the surface. The lowest energy pathway for a surface association reaction should correspond to the one with the best compromise of these three factors.

SCScore: Synthetic Complexity Learned from a Reaction Corpus.

PubMed

Coley, Connor W; Rogers, Luke; Green, William H; Jensen, Klavs F

2018-02-26

Several definitions of molecular complexity exist to facilitate prioritization of lead compounds, to identify diversity-inducing and complexifying reactions, and to guide retrosynthetic searches. In this work, we focus on synthetic complexity and reformalize its definition to correlate with the expected number of reaction steps required to produce a target molecule, with implicit knowledge about what compounds are reasonable starting materials. We train a neural network model on 12 million reactions from the Reaxys database to impose a pairwise inequality constraint enforcing the premise of this definition: that on average, the products of published chemical reactions should be more synthetically complex than their corresponding reactants. The learned metric (SCScore) exhibits highly desirable nonlinear behavior, particularly in recognizing increases in synthetic complexity throughout a number of linear synthetic routes.

Wet-dry cycles impact DOM retention in subsurface soils

NASA Astrophysics Data System (ADS)

Olshansky, Yaniv; Root, Robert A.; Chorover, Jon

2018-02-01

Transport and reactivity of carbon in the critical zone are highly controlled by reactions of dissolved organic matter (DOM) with subsurface soils, including adsorption, transformation and exchange. These reactions are dependent on frequent wet-dry cycles common to the unsaturated zone, particularly in semi-arid regions. To test for an effect of wet-dry cycles on DOM interaction and stabilization in subsoils, samples were collected from subsurface (Bw) horizons of an Entisol and an Alfisol from the Catalina-Jemez Critical Zone Observatory and sequentially reacted (four batch steps) with DOM extracted from the corresponding soil litter layers. Between each reaction step, soils either were allowed to air dry (wet-dry treatment) before introduction of the following DOM solution or were maintained under constant wetness (continually wet treatment). Microbial degradation was the dominant mechanism of DOM loss from solution for the Entisol subsoil, which had higher initial organic C content, whereas sorptive retention predominated in the lower C Alfisol subsoil. For a given soil, bulk dissolved organic C losses from solution were similar across treatments. However, a combination of Fourier transform infrared (FTIR) and near-edge X-ray absorption fine structure (NEXAFS) spectroscopic analyses revealed that wet-dry treatments enhanced the interactions between carboxyl functional groups and soil particle surfaces. Scanning transmission X-ray microscopy (STXM) data suggested that cation bridging by Ca2+ was the primary mechanism for carboxyl association with soil surfaces. STXM data also showed that spatial fractionation of adsorbed OM on soil organo-mineral surfaces was diminished relative to what might be inferred from previously published observations pertaining to DOM fractionation on reaction with specimen mineral phases. This study provides direct evidence of the role of wet-dry cycles in affecting sorption reactions of DOM to a complex soil matrix. In the soil environment, where wet-dry cycles occur at different frequencies from site to site and along the soil profile, different interactions between DOM and soil surfaces are expected and need to be considered for the overall assessment of carbon dynamics.

The effect of Pd ensemble structure on the O2 dissociation and CO oxidation mechanisms on Au—Pd(100) surface alloys

NASA Astrophysics Data System (ADS)

Oǧuz, Ismail-Can; Mineva, Tzonka; Guesmi, Hazar

2018-01-01

The reactivity of various Pd ensembles on the Au—Pd(100) alloy catalyst toward CO oxidation was investigated by using density functional theory (DFT). This study was prompted by the search for efficient catalysts operating at low temperature for the CO oxidation reaction that is of primary environmental importance. To this aim, we considered Pd modified Au(100) surfaces including Pd monomers, Pd dimers, second neighboring Pd atoms, and Pd chains in a comparative study of the minimum energy reaction pathways. The effect of dispersion interactions was included in the calculations of the O2 dissociation reaction pathway by using the DFT-D3 scheme. The addition of the dispersion interaction strongly improves the adsorption ability of O2 on the Au—Pd surface but does not affect the activation energy barriers of the Transitions States (TSs). As for O2 to dissociate, it is imperative that the TS has lower activation energy than the O2 desorption energy. DFT-D3 is found to favor, in some cases, O2 dissociation on configurations being identified from uncorrected DFT calculations as inactive. This is the case of the second neighboring Pd configuration for which uncorrected DFT predicts positive Gibbs free energy (ΔG) of the O2 adsorption, therefore an endergonic reaction. With the addition of D3 correction, ΔG becomes negative that reveals a spontaneous O2 adsorption. Among the investigated Au—Pd (100) ensembles, the Pd chain dissociates most easily O2 and highly stabilizes the dissociated O atoms; however, it has an inferior reactivity toward CO oxidation and CO2 formation. Indeed, CO strongly adsorbs on the palladium bridge sites and therefore poisoning the surface Pd chain. By contrast, the second neighboring Pd configuration that shows somewhat lower ability to dissociate O2 turns out to be more reactive in the CO2 formation step. These results evidence the complex effect of Pd ensembles on the CO oxidation reaction. Associative CO oxidation proceeds with high energy barriers on all the considered Pd ensembles and should be excluded, in agreement with experimental observations.

Kinetics and mechanism of olefin catalytic hydroalumination by organoaluminum compounds

NASA Astrophysics Data System (ADS)

Koledina, K. F.; Gubaidullin, I. M.

2016-05-01

The complex reaction mechanism of α-olefin catalytic hydroalumination by alkylalanes is investigated via mathematical modeling that involves plotting the kinetic models for the individual reactions that make up a complex system and a separate study of their principles. Kinetic parameters of olefin catalytic hydroalumination are estimated. Activation energies of the possible steps of the schemes of complex reaction mechanisms are compared and possible reaction pathways are determined.

Delivery of the high-mobility group box 1 box A peptide using heparin in the acute lung injury animal models.

PubMed

Song, Ji Hyun; Kim, Ji Yeon; Piao, Chunxian; Lee, Seonyeong; Kim, Bora; Song, Su Jeong; Choi, Joon Sig; Lee, Minhyung

2016-07-28

In this study, the efficacy of the high-mobility group box-1 box A (HMGB1A)/heparin complex was evaluated for the treatment of acute lung injury (ALI). HMGB1A is an antagonist against wild-type high-mobility group box-1 (wtHMGB1), a pro-inflammatory cytokine that is involved in ALIs. HMGB1A has positive charges and can be captured in the mucus layer after intratracheal administration. To enhance the delivery and therapeutic efficiency of HMGB1A, the HMGB1A/heparin complex was produced using electrostatic interactions, with the expectation that the nano-sized complex with a negative surface charge could efficiently penetrate the mucus layer. Additionally, heparin itself had an anti-inflammatory effect. Complex formation with HMGB1A and heparin was confirmed by atomic force microscopy. The particle size and surface charge of the HMGB1A/heparin complex at a 1:1 weight ratio were 113nm and -25mV, respectively. Intratracheal administration of the complex was performed into an ALI animal model. The results showed that the HMGB1A/heparin complex reduced pro-inflammatory cytokines, including tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6), and IL-1β, more effectively than HMGB1A or heparin alone. Hematoxylin and eosin staining confirmed the decreased inflammatory reaction in the lungs after delivery of the HMGB1A/heparin complex. In conclusion, the HMGB1A/heparin complex might be useful to treat ALI. Copyright © 2016 Elsevier B.V. All rights reserved.

Abiogenic photochemical synthesis on surface of meteorites and other small space bodies

NASA Astrophysics Data System (ADS)

Simakov, Michael B.; Kuzicheva, Eugenia A.

The abiogenic photochemical synthesis of complex biochemical compounds on the surface of small bodies in our Solar system was examined. Hydrated minerals are found within a chondrite matrix of meteorites together with significant amounts of organic matter. Clays are likely to have formed when water was present on parent meteoritic bodies. In order to verify the existence of a relationship between abiogenic synthesis of nucleotides and inorganic components of the meteorites, we have investigated possible abiogenic reactions associated with different clay (montmorillonite, kaolinite) and a basaltic one (Tyatya's volcanic ash) under action of open space energy sources as a model of different exobiological environments on the surface of small space bodies. The abiogenic synthesis of natural adenine nucleotides from a mixture of adenosine and inorganic phosphate has been observed following irradiation with VUV light in the presence of different mineral samples. The yields of the products (5'AMP, 2'AMP, 3'AMP, 2'3'cAMP and 3'5'cAMP) depended on irradiation time and kinds of minerals used. The discovery that meteoritic organic compounds may be trapped and protected within a clay mineral matrix has implications for our understanding of prebiotic molecular evolution in the early Solar system. Clay minerals may also have concentrated organic compounds thereby promoting polymerization reactions. An adsorption/binding of nucleic acids components by clay crystals could change the electron distribution and/or the conformation of the molecules. The remnant water molecules in the clay sheets also could influence the course of the reaction. Clay immobilization of phosphate could play an important role in this reaction. Chondritic material could have been a common component of the inner Solar system shortly after its formation and the biologically useful products of clay mineral-organic matter interactions could have also widespread, and delivered to planetary surfaces through the accretion of carbonaceous asteroids.

An abiogenic photochemical synthesis on surface of meteorites and other small space bodies

NASA Astrophysics Data System (ADS)

Simakov, M.; Kuzicheva, E.

Abiogenic photochemical synthesis of complex biochemical compounds on the surface of small bodies in our Solar system was examined. The hydrated minerals are found within a chondrite matrix of meteorites together with significant amounts of organic matter. Clays are likely to have formed when water was presented on parent meteoritic bodies. In order to verify the existence of a relationship between abiogenic synthesis of nucleotides and inorganic components of the meteorites we have investigated possible abiogenic reactions at the presence of different clay minerals (montmorillonite, kaolinite) and basaltic sample (Tjatja's volcanic ash) under action of open space energy sources for modeling of different exobiological environments on the surface of small space bodies. The abiogenic synthesis of natural adenine nucleotides from mixture of adenosine plus inorganic phosphate has been observed under an irradiation with VUV radiation at the presence of different mineral samples. The yields of the products (5'AMP, 2'AMP, 3'AMP, 2'3'cAMP and 3'5'cAMP) were depended from irradiation time and kind of used minerals. The discovery that meteoritic organic compounds may be trapped and protected within a clay mineral matrix has implications for our understanding of prebiotic molecular evolution in the early Solar system. Clay minerals may have concentrated organic compounds thereby promoting polymerization reactions also. An adsorption/binding of nucleic acids components by clay crystals could change in the electron distribution and/or the conformation of the molecules. The remnant water molecules in the clay sheets also could influence on the course of the reaction. Besides, an immobilization of phosphate on clay also could play an important role in our reaction. Chondritic material would have been a common component of the inner Solar system shortly after its formation and the biologically useful products of clay mineral-organic matter interactions would have also widespread, and delivered to planetary surfaces through the accretion of carbonaceous asteroids.

Sorption behavior of the Pt(II) complex anion on manganese dioxide (δ-MnO2): a model reaction to elucidate the mechanism by which Pt is concentrated into a marine ferromanganese crust

NASA Astrophysics Data System (ADS)

Maeno, Mamiko Yamashita; Ohashi, Hironori; Yonezu, Kotaro; Miyazaki, Akane; Okaue, Yoshihiro; Watanabe, Koichiro; Ishida, Tamao; Tokunaga, Makoto; Yokoyama, Takushi

2016-02-01

It is difficult to directly investigate the chemical state of Pt in marine ferromanganese crusts (a mixture of hydrous iron(III) oxide and manganese dioxide (δ-MnO2)) because it is present at extremely low concentration levels. This paper attempts to elucidate the mechanism by which Pt is concentrated into marine ferromanganese crust from the Earth's continental crust through ocean water. In this investigation, the sorption behavior of the Pt(II) complex ions on the surface of the δ-MnO2 that is a host of Pt was examined as a model reaction. The δ-MnO2 sorbing Pt was characterized by X-ray photoelectron spectroscopy (XPS) and X-ray absorption fine structure (XAFS) to determine the chemical state of the Pt. Hydrolytic Pt(II) complex ions were specifically sorbed above pH 6 by the formation of a Mn-O-Pt bond. XPS spectra and XANES spectra for δ-MnO2 sorbing Pt showed that the sorbed Pt(II) was oxidized to Pt(IV) on δ-MnO2. The extended X-ray absorption fine structure (EXAFS) analysis showed that the coordination structure of Pt sorbed on δ-MnO2 is almost the same as that of the [Pt(OH)6]2- complex ion used as a standard. Therefore, the mechanism for the concentration of Pt in marine ferromanganese crust may be an oxidative substitution (penetration of Pt(IV) into structure of δ-MnO2) by a reduction-oxidation reaction between Pt(II) in [PtCl4-n(OH)n]2- and Mn(IV) in δ-MnO2 through a Mn-O-Pt bond.

On-Surface Synthesis and Reactivity of Functional Organic and Metal-Organic Adsorbates at Metal Surfaces by Vibrational Spectroscopy

NASA Astrophysics Data System (ADS)

Williams, Christopher Glen

Surface self-assembly is a promising way to introduce functionality to a surface through design at the molecular level. These self-assembled species allow for new on-surface type reactions to be observed and studied. The experiments described in this thesis demonstrate that the molecules used in self-assembly can potentially lead to interesting synthesis pathways and can be used to explore previously under-researched reaction pathways and surface molecular architecture activity or stability. Alkanes are an unreactive species typically used for driving molecular assembly in surface structures. However, with molecular design, alkanes are capable of reacting on surfaces not typically associated with alkane reactivity. Utilizing high-resolution electron energy loss spectroscopy (HREELS) and octaethylporphyrin, we could observe that dehydrogenation is possible on Cu(100) and Ag(111) surfaces at 500 and 610 K respectively. HREELS revealed that after the dehydrogenation, the molecule undergoes an intramolecular C-C bond formation leading to a tetrabenzo-porphyrin structure. Controls with deposited tetrabenzo-porphyrin were performed to verify the structure. This work provides the first example of dehydrocyclization on Cu(100) and Ag(111) to be analyzed by vibrational spectroscopy. Alkyl species in the 1,3,5-tris-(3,5-diethylphenyl)benzene molecule also undergo a dehydrogenation on Cu(100) and Au(111) at 450 and 500 K. The design of this molecule does not let the intramolecular dehydrocyclization reaction take place, but instead the dehydrogenation leads to intermolecular C-C bond formation between molecular species as noted by the formation of extended structure across the surface. Controls with triphenyl-benzene were done to help characterize the peaks in the spectra and observe varying reactivity when the ethyl groups are absent. The fabrication of uniform single-site metal centers at surfaces is important for higher selectivity in next-generation heterogeneous catalysts. We accomplished this by metal coordination to redox non-innocent dipyridyl-tetrazine ligands. We utilize HREELS to observe a surface confined redox process of dipyridyl-tetrazine with V, Fe, Ag, and Pt. With the formation of the V-dipyridyl-tetrazine species, we are able to see that oxygen exposures to the surface results in a more selective vanadyl species formation as opposed to the multiple binding conformations observed with metallic vanadium nanoparticles. This thesis also reveals that the metal substrate used does not play a passive role with the metal-organic complex. Instead, we are the first to characterize a replacement of the coordinating metal species with atoms from the Ag(111) substrate. This replacement results in the redox reaction between the coordinating metal species and the substrate metal.

Consumption and diffusion of dissolved oxygen in sedimentary rocks.

PubMed

Manaka, M; Takeda, M

2016-10-01

Fe(II)-bearing minerals (e.g., biotite, chlorite, and pyrite) are a promising reducing agent for the consumption of atmospheric oxygen in repositories for the geological disposal of high-level radioactive waste. To estimate effective diffusion coefficients (D e , in m 2 s -1 ) for dissolved oxygen (DO) and the reaction rates for the oxidation of Fe(II)-bearing minerals in a repository environment, we conducted diffusion-chemical reaction experiments using intact rock samples of Mizunami sedimentary rock. In addition, we conducted batch experiments on the oxidation of crushed sedimentary rock by DO in a closed system. From the results of the diffusion-chemical reaction experiments, we estimated the values of D e for DO to lie within the range 2.69×10 -11

Chemoselective Reactions for the Synthesis of Glycoconjugates from Unprotected Carbohydrates.

PubMed

Villadsen, Klaus; Martos-Maldonado, Manuel C; Jensen, Knud J; Thygesen, Mikkel B

2017-04-04

Glycobiology is the comprehensive biological investigation of carbohydrates. The study of the role and function of complex carbohydrates often requires the attachment of carbohydrates to surfaces, their tagging with fluorophores, or their conversion into natural or non-natural glycoconjugates, such as glycopeptides or glycolipids. Glycobiology and its "omics", glycomics, require easy and robust chemical methods for the construction of these glycoconjugates. This review gives an overview of the rapidly expanding field of chemical reactions that selectively convert unprotected carbohydrates into glycoconjugates through the anomeric position. The discussion is divided in terms of the anomeric bond type of the newly formed glycoconjugates, including O-, N-, S-, and C-glycosides. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Efficient approach to obtain free energy gradient using QM/MM MD simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Asada, Toshio; Koseki, Shiro; The Research Institute for Molecular Electronic Devices

2015-12-31

The efficient computational approach denoted as charge and atom dipole response kernel (CDRK) model to consider polarization effects of the quantum mechanical (QM) region is described using the charge response and the atom dipole response kernels for free energy gradient (FEG) calculations in the quantum mechanical/molecular mechanical (QM/MM) method. CDRK model can reasonably reproduce energies and also energy gradients of QM and MM atoms obtained by expensive QM/MM calculations in a drastically reduced computational time. This model is applied on the acylation reaction in hydrated trypsin-BPTI complex to optimize the reaction path on the free energy surface by means ofmore » FEG and the nudged elastic band (NEB) method.« less

Spectroscopic study on variations in illite surface properties after acid-base titration.

PubMed

Liu, Wen-xin; Coveney, R M; Tang, Hong-xiao

2003-07-01

FT-IR, Raman microscopy, XRD, 29Si and 27Al MAS NMR, were used to investigate changes in surface properties of a natural illite sample after acid-base potentiometric titration. The characteristic XRD lines indicated the presence of surface Al-Si complexes, preferable to Al(OH)3 precipitates. In the microscopic Raman spectra, the vibration peaks of Si-O and Al-O bonds diminished as a result of treatment with acid, then increased after hydroxide back titration. The varied ratio of signal intensity between (IV)Al and (VI)Al species in 27Al MAS NMR spectra, together with the stable BET surface area after acidimetric titration, suggested that edge faces and basal planes in the layer structure of illite participated in dissolution of structural components. The combined spectroscopic evidence demonstrated that the reactions between illite surfaces and acid-leaching silicic acid and aluminum ions should be considered in the model description of surface acid-base properties of the aqueous illite.

Mechanistic Studies on the Galvanic Replacement Reaction between Multiply Twinned Particles of Ag and HAuCl4 in an Organic Medium

PubMed Central

Lu, Xianmao; Tuan, Hsing-Yu; Chen, Jingyi; Li, Zhi-Yuan; Korgel, Brian A; Xia, Younan

2008-01-01

This article presents a mechanistic study on the galvanic replacement reaction between 11- and 14-nm multiply twinned particles (MTPs) of Ag and HAuCl4 in chloroform. We monitored both morphological and spectral changes as the molar ratio of HAuCl4 to Ag was increased. The details of reaction were different from previous observations on single-crystal Ag nanocubes and cubooctahedrons. Because Au and Ag form alloys rapidly within small MTPs rich in vacancy and grain boundary defects, a complete Au shell did not form on the surface of each individual Ag template. Instead, the replacement reaction resulted in the formation of alloy nanorings and nanocages from Ag MTPs of decahedral or icosahedral shape. For the nanorings and nanocages derived from 11-nm Ag MTPs, the surface plasmon resonance (SPR) peak can be continuously shifted from 400 to 616 nm. When the size of Ag MTPs was increased to 14 nm, the SPR peak can be further shifted to 740 nm, a wavelength sought by biomedical applications. We have also investigated the effects of capping ligands and AgCl precipitate on the replacement reaction. While hollow structures were routinely generated from oleylamine-capped Ag MTPs, we obtained very few hollow structures by using a stronger capping ligand such as oleic acid or tri-n-octylphosphine oxide (TOPO). Addition of extra oleylamine was found to be critical to the formation of well-controlled, uniform hollow structures free of AgCl contamination thanks to the formation of a soluble complex between AgCl and oleylamine. PMID:17243691

Hydration of Concrete: The First Steps.

PubMed

Thissen, Peter; Natzeck, Carsten; Giraudo, Nicolas; Weidler, Peter; Wöll, Christof

2018-04-12

Concrete is the most important construction material used by mankind and, at the same time, one of the most complex substances known in materials science. Since this mineral compound is highly porous, a better understanding of its surface chemistry, and in particular the reaction with water, is urgently required to understand and avoid corrosion of infrastructure like buildings and bridges. We have gained insight into proton transfer from concrete upon contact with water by applying the so-called Surface Science approach to a well-defined mineral, Wollastonite. Data from IR (infrared) spectroscopy reveal that exposure of this calcium-silicate (CS) substrate to H 2 O leads to dissociation and the formation of OH-species. This proton transfer is a chemical reaction of key importance, since on the one hand it triggers the conversion of cement into concrete (a calcium-silicate-hydrate phase), but on the other hand also governs the corrosion of concrete. Interestingly, we find that no proton transfer takes place when the same surface is exposed to methanol. In order to understand this unexpected difference, the analysis of the spectroscopic data obtained was aided by a detailed, first-principles computational study employing density functional theory (DFT). The combined experimental and theoretical effort allows derivation of a consistent picture of proton transfer reactions occurring in CS and CSH phases. Implications for strategies to protect this backbone of urban infrastructure from corrosion in harsh, aqueous environments will be discussed. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Explanation of the Reaction of Monoclonal Antibodies with Candida Albicans Cell Surface in Terms of Compound Poisson Process

NASA Astrophysics Data System (ADS)

Dudek, Mirosław R.; Mleczko, Józef

Surprisingly, still very little is known about the mathematical modeling of peaks in the binding affinities distribution function. In general, it is believed that the peaks represent antibodies directed towards single epitopes. In this paper, we refer to fluorescence flow cytometry experiments and show that even monoclonal antibodies can display multi-modal histograms of affinity distribution. This result take place when some obstacles appear in the paratope-epitope reaction such that the process of reaching the specific epitope ceases to be a point Poisson process. A typical example is the large area of cell surface, which could be unreachable by antibodies leading to the heterogeneity of the cell surface repletion. In this case the affinity of cells to bind the antibodies should be described by a more complex process than the pure-Poisson point process. We suggested to use a doubly stochastic Poisson process, where the points are replaced by a binomial point process resulting in the Neyman distribution. The distribution can have a strongly multinomial character, and with the number of modes depending on the concentration of antibodies and epitopes. All this means that there is a possibility to go beyond the simplified theory, one response towards one epitope. As a consequence, our description provides perspectives for describing antigen-antibody reactions, both qualitatively and quantitavely, even in the case when some peaks result from more than one binding mechanism.